diff --git a/lib/spack/docs/.gitignore b/lib/spack/docs/.gitignore
index 0b6258af5093edb487d5b30cd55c0362d09731af..1624dfeaeab0fbd15657f1e73506a38f239b6433 100644
--- a/lib/spack/docs/.gitignore
+++ b/lib/spack/docs/.gitignore
@@ -3,3 +3,5 @@ command_index.rst
spack*.rst
llnl*.rst
_build
+.spack-env
+spack.lock
diff --git a/lib/spack/docs/build_systems/intelpackage.rst b/lib/spack/docs/build_systems/intelpackage.rst
index 30c567373e0874a5f6f87809ec4e7ec565326c34..f7d975899e90e041e2005079322b5e9358eea9a9 100644
--- a/lib/spack/docs/build_systems/intelpackage.rst
+++ b/lib/spack/docs/build_systems/intelpackage.rst
@@ -120,7 +120,7 @@ version numbers seen with most other Spack packages. For example, we have:
...
Preferred version:
professional.2018.3 http:...
-
+
Safe versions:
professional.2018.3 http:...
...
@@ -728,7 +728,7 @@ For packages that contain a compiler, follow `the previous section
.. code-block:: console
- $ spack install intel-mpi@2018.3.199
+ $ spack install intel-mpi@2018.3.199
$ spack install intel-mpi@2018.3.199 %intel@18
4. To prepare the new packages for use with client packages,
@@ -802,7 +802,7 @@ by one of the following means:
Configure the order of compilers in the appropriate ``packages.yaml`` file,
under either an ``all:`` or client-package-specific entry, in a
``compiler:`` list. Consult the Spack documentation for
- :ref:`Configuring Package Preferences <configs-tutorial-package-prefs>`
+ `Configuring Package Preferences <https://spack-tutorial.readthedocs.io/en/latest/tutorial_configuration.html#configuring-package-preferences>`_
and
:ref:`Concretization Preferences <concretization-preferences>`.
@@ -851,7 +851,7 @@ client packages, edit the ``packages.yaml`` file. Customize, either in the
the virtual packages and whose values are the Spack specs that satisfy the
virtual package, in order of decreasing preference. To learn more about the
``providers:`` settings, see the Spack tutorial for
-:ref:`Configuring Package Preferences <configs-tutorial-package-prefs>`
+`Configuring Package Preferences <https://spack-tutorial.readthedocs.io/en/latest/tutorial_configuration.html#configuring-package-preferences>`_
and the section
:ref:`Concretization Preferences <concretization-preferences>`.
@@ -972,7 +972,7 @@ a *virtual* ``mkl`` package is declared in Spack.
.. code-block:: python
self.spec['blas'].headers.include_flags
-
+
and to generate linker options (``-L<dir> -llibname ...``), use the same as above,
.. code-block:: python
diff --git a/lib/spack/docs/conf.py b/lib/spack/docs/conf.py
index cacbbb3a4126c3e65db74e9e86f1127854858529..e5305a9317589dfcaee5ca7cc1a03fbc95d846b8 100644
--- a/lib/spack/docs/conf.py
+++ b/lib/spack/docs/conf.py
@@ -159,7 +159,7 @@ def setup(sphinx):
# List of patterns, relative to source directory, that match files and
# directories to ignore when looking for source files.
-exclude_patterns = ['_build', '_spack_root']
+exclude_patterns = ['_build', '_spack_root', '.spack-env']
# The reST default role (used for this markup: `text`) to use for all documents.
#default_role = None
diff --git a/lib/spack/docs/index.rst b/lib/spack/docs/index.rst
index 5c93285cbbf27cb82c361ae9f17765cf635729a0..48af67982aa1eee3fd35fb2ced2d98265fcc4bb6 100644
--- a/lib/spack/docs/index.rst
+++ b/lib/spack/docs/index.rst
@@ -55,7 +55,7 @@ or refer to the full manual below.
getting_started
basic_usage
workflows
- tutorial
+ Tutorial: Spack 101 <https://spack-tutorial.readthedocs.io>
known_issues
.. toctree::
diff --git a/lib/spack/docs/spack.yaml b/lib/spack/docs/spack.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..bade961fce438319a66dc8456c4a5faa95dc4ccd
--- /dev/null
+++ b/lib/spack/docs/spack.yaml
@@ -0,0 +1,19 @@
+# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+#
+# These are requirements for building the documentation. You can run
+# these commands in this directory to install Sphinx and its plugins,
+# then build the docs:
+#
+# spack install
+# spack env activate .
+# make
+#
+spack:
+ specs:
+ - py-sphinx
+ - py-sphinxcontrib-programoutput
+ - py-sphinx-rtd-theme
diff --git a/lib/spack/docs/tutorial.rst b/lib/spack/docs/tutorial.rst
deleted file mode 100644
index 4ece87ade008941bb22949fd0e14bdfd7f0b7898..0000000000000000000000000000000000000000
--- a/lib/spack/docs/tutorial.rst
+++ /dev/null
@@ -1,75 +0,0 @@
-.. Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
- Spack Project Developers. See the top-level COPYRIGHT file for details.
-
- SPDX-License-Identifier: (Apache-2.0 OR MIT)
-
-.. _spack-101:
-
-=============================
-Tutorial: Spack 101
-=============================
-
-This is a full-day introduction to Spack with lectures and live demos.
-It was last presented at the `Practice and Experience in Advanced
-Research Computing Conference (PEARC19)
-<https://www.pearc19.pearc.org/>`_ on July 31, 2019.
-
-You can use these materials to teach a course on Spack at your own site,
-or you can just skip ahead and read the live demo scripts to see how
-Spack is used in practice.
-
-.. _sc16-slides:
-
-.. rubric:: Slides
-
-.. figure:: tutorial/sc16-tutorial-slide-preview.png
- :target: https://spack.io/slides/spack-pearc19-tutorial-slides.pdf
- :height: 72px
- :align: left
- :alt: Slide Preview
-
-`Download Slides <https://spack.io/slides/spack-pearc19-tutorial-slides.pdf>`_.
-
-**Full citation:** Levi Baber, Gregory Becker, Adam J. Stewart, and Todd
-Gamblin. Managing HPC Software Complexity with Spack. Tutorial presented
-at the Practice and Experience in Advanced Research Computing Conference
-(PEARC19). July 31, 2019. Chicago, IL, USA.
-
-.. _sc16-live-demos:
-
-.. rubric:: Live Demos
-
-We provide scripts that take you step-by-step through basic Spack tasks.
-They correspond to sections in the slides above. You can use one of the
-following methods to run through the scripts:
-
- 1. We provide the `spack/tutorial
- <https://hub.docker.com/r/spack/tutorial>`_ container image on
- Docker Hub that you can use to do the tutorial on your local
- machine. You can invoke ``docker run -it spack/tutorial`` to start
- using the container.
-
- 2. When we host the tutorial, we also provision VM instances in `AWS
- <https://aws.amazon.com/>`_, so that users who are unfamiliar with
- Docker can simply log into a VPM to do the demo exercises.
-
-You should now be ready to run through our demo scripts:
-
- 1. :ref:`basics-tutorial`
- 2. :ref:`configs-tutorial`
- 3. :ref:`packaging-tutorial`
- 4. :ref:`environments-tutorial`
- 5. :ref:`modules-tutorial`
- 6. :ref:`build-systems-tutorial`
- 7. :ref:`advanced-packaging-tutorial`
-
-Full contents:
-
-.. toctree::
- tutorial_basics
- tutorial_configuration
- tutorial_packaging
- tutorial_environments
- tutorial_modules
- tutorial_buildsystems
- tutorial_advanced_packaging
diff --git a/lib/spack/docs/tutorial/examples/0.package.py b/lib/spack/docs/tutorial/examples/0.package.py
deleted file mode 100644
index 990ba7d3d872c8aab312390091a5420d3cfbad92..0000000000000000000000000000000000000000
--- a/lib/spack/docs/tutorial/examples/0.package.py
+++ /dev/null
@@ -1,39 +0,0 @@
-# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
-#
-# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-
-#
-# This is a template package file for Spack. We've put "FIXME"
-# next to all the things you'll want to change. Once you've handled
-# them, you can save this file and test your package like this:
-#
-# spack install mpileaks
-#
-# You can edit this file again by typing:
-#
-# spack edit mpileaks
-#
-# See the Spack documentation for more information on packaging.
-# If you submit this package back to Spack as a pull request,
-# please first remove this boilerplate and all FIXME comments.
-#
-from spack import *
-
-
-class Mpileaks(Package):
- """FIXME: Put a proper description of your package here."""
-
- # FIXME: Add a proper url for your package's homepage here.
- homepage = "http://www.example.com"
- url = "https://github.com/LLNL/mpileaks/releases/download/v1.0/mpileaks-1.0.tar.gz"
-
- version('1.0', sha256='2e34cc4505556d1c1f085758e26f2f8eea0972db9382f051b2dcfb1d7d9e1825')
-
- # FIXME: Add dependencies if required.
- # depends_on('foo')
-
- def install(self, spec, prefix):
- # FIXME: Unknown build system
- make()
- make('install')
diff --git a/lib/spack/docs/tutorial/examples/1.package.py b/lib/spack/docs/tutorial/examples/1.package.py
deleted file mode 100644
index f2d515fa4a42dc23c8103e25024e186f374dcbee..0000000000000000000000000000000000000000
--- a/lib/spack/docs/tutorial/examples/1.package.py
+++ /dev/null
@@ -1,24 +0,0 @@
-# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
-#
-# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-
-from spack import *
-
-
-class Mpileaks(Package):
- """Tool to detect and report MPI objects like MPI_Requests and
- MPI_Datatypes."""
-
- homepage = "https://github.com/LLNL/mpileaks"
- url = "https://github.com/LLNL/mpileaks/releases/download/v1.0/mpileaks-1.0.tar.gz"
-
- version('1.0', sha256='2e34cc4505556d1c1f085758e26f2f8eea0972db9382f051b2dcfb1d7d9e1825')
-
- # FIXME: Add dependencies if required.
- # depends_on('foo')
-
- def install(self, spec, prefix):
- # FIXME: Unknown build system
- make()
- make('install')
diff --git a/lib/spack/docs/tutorial/examples/2.package.py b/lib/spack/docs/tutorial/examples/2.package.py
deleted file mode 100644
index d0f1e6d062622712314dd5061e2c0adf4bfe684c..0000000000000000000000000000000000000000
--- a/lib/spack/docs/tutorial/examples/2.package.py
+++ /dev/null
@@ -1,25 +0,0 @@
-# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
-#
-# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-
-from spack import *
-
-
-class Mpileaks(Package):
- """Tool to detect and report MPI objects like MPI_Requests and
- MPI_Datatypes."""
-
- homepage = "https://github.com/LLNL/mpileaks"
- url = "https://github.com/LLNL/mpileaks/releases/download/v1.0/mpileaks-1.0.tar.gz"
-
- version('1.0', sha256='2e34cc4505556d1c1f085758e26f2f8eea0972db9382f051b2dcfb1d7d9e1825')
-
- depends_on('mpi')
- depends_on('adept-utils')
- depends_on('callpath')
-
- def install(self, spec, prefix):
- # FIXME: Unknown build system
- make()
- make('install')
diff --git a/lib/spack/docs/tutorial/examples/3.package.py b/lib/spack/docs/tutorial/examples/3.package.py
deleted file mode 100644
index 05fd7aa00a2f003c3c6eaed893a566c4f46f504b..0000000000000000000000000000000000000000
--- a/lib/spack/docs/tutorial/examples/3.package.py
+++ /dev/null
@@ -1,25 +0,0 @@
-# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
-#
-# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-
-from spack import *
-
-
-class Mpileaks(Package):
- """Tool to detect and report MPI objects like MPI_Requests and
- MPI_Datatypes."""
-
- homepage = "https://github.com/LLNL/mpileaks"
- url = "https://github.com/LLNL/mpileaks/releases/download/v1.0/mpileaks-1.0.tar.gz"
-
- version('1.0', sha256='2e34cc4505556d1c1f085758e26f2f8eea0972db9382f051b2dcfb1d7d9e1825')
-
- depends_on('mpi')
- depends_on('adept-utils')
- depends_on('callpath')
-
- def install(self, spec, prefix):
- configure()
- make()
- make('install')
diff --git a/lib/spack/docs/tutorial/examples/4.package.py b/lib/spack/docs/tutorial/examples/4.package.py
deleted file mode 100644
index 626e7d3fec1c2a2018cb9735cc6072f414f0d52e..0000000000000000000000000000000000000000
--- a/lib/spack/docs/tutorial/examples/4.package.py
+++ /dev/null
@@ -1,27 +0,0 @@
-# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
-#
-# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-
-from spack import *
-
-
-class Mpileaks(Package):
- """Tool to detect and report MPI objects like MPI_Requests and
- MPI_Datatypes."""
-
- homepage = "https://github.com/LLNL/mpileaks"
- url = "https://github.com/LLNL/mpileaks/releases/download/v1.0/mpileaks-1.0.tar.gz"
-
- version('1.0', sha256='2e34cc4505556d1c1f085758e26f2f8eea0972db9382f051b2dcfb1d7d9e1825')
-
- depends_on('mpi')
- depends_on('adept-utils')
- depends_on('callpath')
-
- def install(self, spec, prefix):
- configure('--prefix={0}'.format(prefix),
- '--with-adept-utils={0}'.format(spec['adept-utils'].prefix),
- '--with-callpath={0}'.format(spec['callpath'].prefix))
- make()
- make('install')
diff --git a/lib/spack/docs/tutorial/examples/5.package.py b/lib/spack/docs/tutorial/examples/5.package.py
deleted file mode 100644
index 9a1dec20792b296126923c33ef695d3adf86b1d7..0000000000000000000000000000000000000000
--- a/lib/spack/docs/tutorial/examples/5.package.py
+++ /dev/null
@@ -1,42 +0,0 @@
-# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
-#
-# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-
-from spack import *
-
-
-class Mpileaks(Package):
- """Tool to detect and report MPI objects like MPI_Requests and
- MPI_Datatypes."""
-
- homepage = "https://github.com/LLNL/mpileaks"
- url = "https://github.com/LLNL/mpileaks/releases/download/v1.0/mpileaks-1.0.tar.gz"
-
- version('1.0', sha256='2e34cc4505556d1c1f085758e26f2f8eea0972db9382f051b2dcfb1d7d9e1825')
-
- variant('stackstart', values=int, default=0,
- description='Specify the number of stack frames to truncate')
-
- depends_on('mpi')
- depends_on('adept-utils')
- depends_on('callpath')
-
- def install(self, spec, prefix):
- stackstart = int(spec.variants['stackstart'].value)
-
- args = [
- '--prefix={0}'.format(prefix),
- '--with-adept-utils={0}'.format(spec['adept-utils'].prefix),
- '--with-callpath={0}'.format(spec['callpath'].prefix),
- ]
-
- if stackstart:
- args.extend([
- '--with-stack-start-c={0}'.format(stackstart),
- '--with-stack-start-fortran={0}'.format(stackstart)
- ])
-
- configure(*args)
- make()
- make('install')
diff --git a/lib/spack/docs/tutorial/examples/Autotools/0.package.py b/lib/spack/docs/tutorial/examples/Autotools/0.package.py
deleted file mode 100644
index 213965e5c6336f6292d60f9bd2f97c8752f7562f..0000000000000000000000000000000000000000
--- a/lib/spack/docs/tutorial/examples/Autotools/0.package.py
+++ /dev/null
@@ -1,27 +0,0 @@
-# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
-#
-# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-
-from spack import *
-
-
-class Mpileaks(AutotoolsPackage):
- """Tool to detect and report leaked MPI objects like MPI_Requests and
- MPI_Datatypes."""
-
- homepage = "https://github.com/hpc/mpileaks"
- url = "https://github.com/hpc/mpileaks/releases/download/v1.0/mpileaks-1.0.tar.gz"
-
- version('1.0', '8838c574b39202a57d7c2d68692718aa')
-
- depends_on("mpi")
- depends_on("adept-utils")
- depends_on("callpath")
-
- def install(self, spec, prefix):
- configure("--prefix=" + prefix,
- "--with-adept-utils=" + spec['adept-utils'].prefix,
- "--with-callpath=" + spec['callpath'].prefix)
- make()
- make("install")
diff --git a/lib/spack/docs/tutorial/examples/Autotools/1.package.py b/lib/spack/docs/tutorial/examples/Autotools/1.package.py
deleted file mode 100644
index 639f1305960aa15378d948bc30c3da7a218dbf95..0000000000000000000000000000000000000000
--- a/lib/spack/docs/tutorial/examples/Autotools/1.package.py
+++ /dev/null
@@ -1,32 +0,0 @@
-# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
-#
-# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-
-from spack import *
-
-
-class Mpileaks(AutotoolsPackage):
- """Tool to detect and report leaked MPI objects like MPI_Requests and
- MPI_Datatypes."""
-
- homepage = "https://github.com/hpc/mpileaks"
- url = "https://github.com/hpc/mpileaks/releases/download/v1.0/mpileaks-1.0.tar.gz"
-
- version('1.0', '8838c574b39202a57d7c2d68692718aa')
-
- variant("stackstart", values=int, default=0,
- description="Specify the number of stack frames to truncate")
-
- depends_on("mpi")
- depends_on("adept-utils")
- depends_on("callpath")
-
- def configure_args(self):
- stackstart = int(self.spec.variants['stackstart'].value)
- args = ["--with-adept-utils=" + spec['adept-utils'].prefix,
- "--with-callpath=" + spec['callpath'].prefix]
- if stackstart:
- args.extend(['--with-stack-start-c=%s' % stackstart,
- '--with-stack-start-fortran=%s' % stackstart])
- return args
diff --git a/lib/spack/docs/tutorial/examples/Cmake/0.package.py b/lib/spack/docs/tutorial/examples/Cmake/0.package.py
deleted file mode 100644
index b8c96a19293d869b57238bcd75322b0eae623101..0000000000000000000000000000000000000000
--- a/lib/spack/docs/tutorial/examples/Cmake/0.package.py
+++ /dev/null
@@ -1,41 +0,0 @@
-# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
-#
-# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-
-#
-# This is a template package file for Spack. We've put "FIXME"
-# next to all the things you'll want to change. Once you've handled
-# them, you can save this file and test your package like this:
-#
-# spack install callpath
-#
-# You can edit this file again by typing:
-#
-# spack edit callpath
-#
-# See the Spack documentation for more information on packaging.
-# If you submit this package back to Spack as a pull request,
-# please first remove this boilerplate and all FIXME comments.
-#
-from spack import *
-
-
-class Callpath(CMakePackage):
- """FIXME: Put a proper description of your package here."""
-
- # FIXME: Add a proper url for your package's homepage here.
- homepage = "http://www.example.com"
- url = "https://github.com/llnl/callpath/archive/v1.0.1.tar.gz"
-
- version('1.0.3', 'c89089b3f1c1ba47b09b8508a574294a')
-
- # FIXME: Add dependencies if required.
- # depends_on('foo')
-
- def cmake_args(self):
- # FIXME: Add arguments other than
- # FIXME: CMAKE_INSTALL_PREFIX and CMAKE_BUILD_TYPE
- # FIXME: If not needed delete this function
- args = []
- return args
diff --git a/lib/spack/docs/tutorial/examples/Cmake/1.package.py b/lib/spack/docs/tutorial/examples/Cmake/1.package.py
deleted file mode 100644
index 8a0d9d0e822d6956b05e33a448e60d69954b2b1c..0000000000000000000000000000000000000000
--- a/lib/spack/docs/tutorial/examples/Cmake/1.package.py
+++ /dev/null
@@ -1,23 +0,0 @@
-# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
-#
-# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-
-from spack import *
-
-
-class Callpath(CMakePackage):
- """Library for representing callpaths consistently in
- distributed-memory performance tools."""
-
- homepage = "https://github.com/llnl/callpath"
- url = "https://github.com/llnl/callpath/archive/v1.0.3.tar.gz"
-
- version('1.0.3', 'c89089b3f1c1ba47b09b8508a574294a')
-
- depends_on("elf", type="link")
- depends_on("libdwarf")
- depends_on("dyninst")
- depends_on("adept-utils")
- depends_on("mpi")
- depends_on("cmake@2.8:", type="build")
diff --git a/lib/spack/docs/tutorial/examples/Cmake/2.package.py b/lib/spack/docs/tutorial/examples/Cmake/2.package.py
deleted file mode 100644
index 2b4faca90dd440ccec6e8e9f48adaa1def73ae19..0000000000000000000000000000000000000000
--- a/lib/spack/docs/tutorial/examples/Cmake/2.package.py
+++ /dev/null
@@ -1,33 +0,0 @@
-# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
-#
-# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-
-from spack import *
-
-
-class Callpath(CMakePackage):
- """Library for representing callpaths consistently in
- distributed-memory performance tools."""
-
- homepage = "https://github.com/llnl/callpath"
- url = "https://github.com/llnl/callpath/archive/v1.0.3.tar.gz"
-
- version('1.0.3', 'c89089b3f1c1ba47b09b8508a574294a')
-
- depends_on("elf", type="link")
- depends_on("libdwarf")
- depends_on("dyninst")
- depends_on("adept-utils")
- depends_on("mpi")
- depends_on("cmake@2.8:", type="build")
-
- def cmake_args(self):
- args = ["-DCALLPATH_WALKER=dyninst"]
-
- if self.spec.satisfies("^dyninst@9.3.0:"):
- std.flag = self.compiler.cxx_flag
- args.append("-DCMAKE_CXX_FLAGS='{0}' -fpermissive'".format(
- std_flag))
-
- return args
diff --git a/lib/spack/docs/tutorial/examples/Makefile/0.package.py b/lib/spack/docs/tutorial/examples/Makefile/0.package.py
deleted file mode 100644
index 8ad252f5b396fd29669840a3201db9f12b488edb..0000000000000000000000000000000000000000
--- a/lib/spack/docs/tutorial/examples/Makefile/0.package.py
+++ /dev/null
@@ -1,26 +0,0 @@
-# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
-#
-# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-
-from spack import *
-
-
-class Bowtie(MakefilePackage):
- """FIXME: Put a proper description of your package here."""
-
- # FIXME: Add a proper url for your package's homepage here.
- homepage = "http://www.example.com"
- url = "https://downloads.sourceforge.net/project/bowtie-bio/bowtie/1.2.1.1/bowtie-1.2.1.1-src.zip"
-
- version('1.2.1.1', 'ec06265730c5f587cd58bcfef6697ddf')
-
- # FIXME: Add dependencies if required.
- # depends_on('foo')
-
- def edit(self, spec, prefix):
- # FIXME: Edit the Makefile if necessary
- # FIXME: If not needed delete this function
- # makefile = FileFilter('Makefile')
- # makefile.filter('CC = .*', 'CC = cc')
- return
diff --git a/lib/spack/docs/tutorial/examples/Makefile/1.package.py b/lib/spack/docs/tutorial/examples/Makefile/1.package.py
deleted file mode 100644
index 16988dc1b0450bf01a0ebd1238b7fa684e5cb071..0000000000000000000000000000000000000000
--- a/lib/spack/docs/tutorial/examples/Makefile/1.package.py
+++ /dev/null
@@ -1,27 +0,0 @@
-# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
-#
-# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-
-from spack import *
-
-
-class Bowtie(MakefilePackage):
- """Bowtie is an ultrafast, memory efficient short read aligner
- for short DNA sequences (reads) from next-gen sequencers."""
-
- homepage = "https://sourceforge.net/projects/bowtie-bio/"
- url = "https://downloads.sourceforge.net/project/bowtie-bio/bowtie/1.2.1.1/bowtie-1.2.1.1-src.zip"
-
- version('1.2.1.1', 'ec06265730c5f587cd58bcfef6697ddf')
-
- variant("tbb", default=False, description="Use Intel thread building block")
-
- depends_on("tbb", when="+tbb")
-
- def edit(self, spec, prefix):
- # FIXME: Edit the Makefile if necessary
- # FIXME: If not needed delete this function
- # makefile = FileFilter('Makefile')
- # makefile.filter('CC = .*', 'CC = cc')
- return
diff --git a/lib/spack/docs/tutorial/examples/Makefile/2.package.py b/lib/spack/docs/tutorial/examples/Makefile/2.package.py
deleted file mode 100644
index 0973b2028e7bd8beb20cf5dcbc2eede710a80857..0000000000000000000000000000000000000000
--- a/lib/spack/docs/tutorial/examples/Makefile/2.package.py
+++ /dev/null
@@ -1,25 +0,0 @@
-# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
-#
-# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-
-from spack import *
-
-
-class Bowtie(MakefilePackage):
- """Bowtie is an ultrafast, memory efficient short read aligner
- for short DNA sequences (reads) from next-gen sequencers."""
-
- homepage = "https://sourceforge.net/projects/bowtie-bio/"
- url = "https://downloads.sourceforge.net/project/bowtie-bio/bowtie/1.2.1.1/bowtie-1.2.1.1-src.zip"
-
- version('1.2.1.1', 'ec06265730c5f587cd58bcfef6697ddf')
-
- variant("tbb", default=False, description="Use Intel thread building block")
-
- depends_on("tbb", when="+tbb")
-
- def edit(self, spec, prefix):
- makefile = FileFilter("Makefile")
- makefile.filter('CC= .*', 'CC = ' + env['CC'])
- makefile.filter('CXX = .*', 'CXX = ' + env['CXX'])
diff --git a/lib/spack/docs/tutorial/examples/Makefile/3.package.py b/lib/spack/docs/tutorial/examples/Makefile/3.package.py
deleted file mode 100644
index 6a1942e627f8ef8224708ec3b820537527560482..0000000000000000000000000000000000000000
--- a/lib/spack/docs/tutorial/examples/Makefile/3.package.py
+++ /dev/null
@@ -1,36 +0,0 @@
-# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
-#
-# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-
-from spack import *
-
-
-class Bowtie(MakefilePackage):
- """Bowtie is an ultrafast, memory efficient short read aligner
- for short DNA sequences (reads) from next-gen sequencers."""
-
- homepage = "https://sourceforge.net/projects/bowtie-bio/"
- url = "https://downloads.sourceforge.net/project/bowtie-bio/bowtie/1.2.1.1/bowtie-1.2.1.1-src.zip"
-
- version('1.2.1.1', 'ec06265730c5f587cd58bcfef6697ddf')
-
- variant("tbb", default=False, description="Use Intel thread building block")
-
- depends_on("tbb", when="+tbb")
-
- def edit(self, spec, prefix):
- makefile = FileFilter("Makefile")
- makefile.filter('CC= .*', 'CC = ' + env['CC'])
- makefile.filter('CXX = .*', 'CXX = ' + env['CXX'])
-
- @property
- def build_targets(self):
- if "+tbb" in spec:
- return []
- else:
- return ["NO_TBB=1"]
-
- @property
- def install_targets(self):
- return ['prefix={0}'.format(self.prefix), 'install']
diff --git a/lib/spack/docs/tutorial/examples/PyPackage/0.package.py b/lib/spack/docs/tutorial/examples/PyPackage/0.package.py
deleted file mode 100644
index 9ad94189d92447ad255644071929809f6c823304..0000000000000000000000000000000000000000
--- a/lib/spack/docs/tutorial/examples/PyPackage/0.package.py
+++ /dev/null
@@ -1,41 +0,0 @@
-# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
-#
-# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-
-#
-# This is a template package file for Spack. We've put "FIXME"
-# next to all the things you'll want to change. Once you've handled
-# them, you can save this file and test your package like this:
-#
-# spack install py-pandas
-#
-# You can edit this file again by typing:
-#
-# spack edit py-pandas
-#
-# See the Spack documentation for more information on packaging.
-# If you submit this package back to Spack as a pull request,
-# please first remove this boilerplate and all FIXME comments.
-#
-from spack import *
-
-
-class PyPandas(PythonPackage):
- """FIXME: Put a proper description of your package here."""
-
- # FIXME: Add a proper url for your package's homepage here.
- homepage = "http://www.example.com"
- url = "https://pypi.io/packages/source/p/pandas/pandas-0.19.0.tar.gz"
-
- version('0.19.0', 'bc9bb7188e510b5d44fbdd249698a2c3')
-
- # FIXME: Add dependencies if required.
- # depends_on('py-setuptools', type='build')
- # depends_on('py-foo', type=('build', 'run'))
-
- def build_args(self, spec, prefix):
- # FIXME: Add arguments other than --prefix
- # FIXME: If not needed delete this function
- args = []
- return args
diff --git a/lib/spack/docs/tutorial/examples/PyPackage/1.package.py b/lib/spack/docs/tutorial/examples/PyPackage/1.package.py
deleted file mode 100644
index 8ac335d4a6e0a582a8db594258771b94c9363155..0000000000000000000000000000000000000000
--- a/lib/spack/docs/tutorial/examples/PyPackage/1.package.py
+++ /dev/null
@@ -1,32 +0,0 @@
-# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
-#
-# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-
-from spack import *
-
-
-class PyPandas(PythonPackage):
- """pandas is a Python package providing fast, flexible, and expressive
- data structures designed to make working with relational or
- labeled data both easy and intuitive. It aims to be the
- fundamental high-level building block for doing practical, real
- world data analysis in Python. Additionally, it has the broader
- goal of becoming the most powerful and flexible open source data
- analysis / manipulation tool available in any language.
- """
- homepage = "http://pandas.pydata.org/"
- url = "https://pypi.io/packages/source/p/pandas/pandas-0.19.0.tar.gz"
-
- version('0.19.0', 'bc9bb7188e510b5d44fbdd249698a2c3')
- version('0.18.0', 'f143762cd7a59815e348adf4308d2cf6')
- version('0.16.1', 'fac4f25748f9610a3e00e765474bdea8')
- version('0.16.0', 'bfe311f05dc0c351f8955fbd1e296e73')
-
- depends_on('py-dateutil', type=('build', 'run'))
- depends_on('py-numpy', type=('build', 'run'))
- depends_on('py-setuptools', type='build')
- depends_on('py-cython', type='build')
- depends_on('py-pytz', type=('build', 'run'))
- depends_on('py-numexpr', type=('build', 'run'))
- depends_on('py-bottleneck', type=('build', 'run'))
diff --git a/lib/spack/docs/tutorial/sc16-tutorial-slide-preview.png b/lib/spack/docs/tutorial/sc16-tutorial-slide-preview.png
deleted file mode 100644
index e7f9b2e323065e8cbdc200ce344d4fd99e145dd1..0000000000000000000000000000000000000000
Binary files a/lib/spack/docs/tutorial/sc16-tutorial-slide-preview.png and /dev/null differ
diff --git a/lib/spack/docs/tutorial_advanced_packaging.rst b/lib/spack/docs/tutorial_advanced_packaging.rst
deleted file mode 100644
index 876a6e8f70a74f44743a784fb94ff1981e3aa9b4..0000000000000000000000000000000000000000
--- a/lib/spack/docs/tutorial_advanced_packaging.rst
+++ /dev/null
@@ -1,515 +0,0 @@
-.. Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
- Spack Project Developers. See the top-level COPYRIGHT file for details.
-
- SPDX-License-Identifier: (Apache-2.0 OR MIT)
-
-.. _advanced-packaging-tutorial:
-
-============================
-Advanced Topics in Packaging
-============================
-
-Spack tries to automatically configure packages with information from
-dependencies such that all you need to do is to list the dependencies
-(i.e., with the ``depends_on`` directive) and the build system (for example
-by deriving from :code:`CmakePackage`).
-
-However, there are many special cases. Often you need to retrieve details
-about dependencies to set package-specific configuration options, or to
-define package-specific environment variables used by the package's build
-system. This tutorial covers how to retrieve build information from
-dependencies, and how you can automatically provide important information to
-dependents in your package.
-
-----------------------
-Setup for the tutorial
-----------------------
-
-.. note::
-
- We do not recommend doing this section of the tutorial in a
- production Spack instance.
-
-The tutorial uses custom package definitions with missing sections that
-will be filled in during the tutorial. These package definitions are stored
-in a separate package repository, which can be enabled with:
-
-.. code-block:: console
-
- $ spack repo add --scope=site var/spack/repos/tutorial
-
-This section of the tutorial may also require a newer version of
-gcc. If you have not already installed gcc@7.2.0 and added it to your
-configuration, you can do so with:
-
-.. code-block:: console
-
- $ spack install gcc@7.2.0 %gcc@5.4.0
- $ spack compiler add --scope=site `spack location -i gcc@7.2.0 %gcc@5.4.0`
-
-If you are using the tutorial docker image, all dependency packages
-will have been installed. Otherwise, to install these packages you can use
-the following commands:
-
-.. code-block:: console
-
- $ spack install openblas
- $ spack install netlib-lapack
- $ spack install mpich
-
-Now, you are ready to set your preferred ``EDITOR`` and continue with
-the rest of the tutorial.
-
-.. note::
-
- Several of these packages depend on an MPI implementation. You can use
- OpenMPI if you install it from scratch, but this is slow (>10 min.).
- A binary cache of MPICH may be provided, in which case you can force
- the package to use it and install quickly. All tutorial examples with
- packages that depend on MPICH include the spec syntax for building with it
-
-.. _adv_pkg_tutorial_start:
-
----------------------------------------
-Modifying a package's build environment
----------------------------------------
-
-Spack sets up several environment variables like ``PATH`` by default to aid in
-building a package, but many packages make use of environment variables which
-convey specific information about their dependencies (e.g., ``MPICC``).
-This section covers how to update your Spack packages so that package-specific
-environment variables are defined at build-time.
-
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-Set environment variables in dependent packages at build-time
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-Dependencies can set environment variables that are required when their
-dependents build. For example, when a package depends on a python extension
-like py-numpy, Spack's ``python`` package will add it to ``PYTHONPATH``
-so it is available at build time; this is required because the default setup
-that spack does is not sufficient for python to import modules.
-
-Any package can override the
-:py:func:`setup_dependent_build_environment <spack.package.PackageBase.setup_dependent_build_environment>`
-method to setup the build environment for a dependent.
-This method takes as an argument a :py:class:`EnvironmentModifications <spack.util.environment.EnvironmentModifications>`
-object which includes convenience methods to update the environment. For
-example, an MPI implementation can set ``MPICC`` for packages that depend on it:
-
-.. code-block:: python
-
- def setup_dependent_build_environment(self, env, dependent_spec):
- env.set('MPICC', join_path(self.prefix.bin, 'mpicc'))
-
-In this case packages that depend on ``mpi`` will have ``MPICC`` defined in
-their environment when they build. This section is focused on setting up the
-build-time environment but it's worth noting that a similar method called
-:py:func:`setup_dependent_run_environment <spack.package.PackageBase.setup_dependent_run_environment>`
-can be used to code modifications that will be included in Spack's automatically-generated
-module files.
-
-We can practice by editing the ``mpich`` package to set the ``MPICC``
-environment variable in the build-time environment of dependent packages.
-
-.. code-block:: console
-
- root@advanced-packaging-tutorial:/# spack edit mpich
-
-Once you're finished, the method should look like this:
-
-.. code-block:: python
-
- def setup_dependent_build_environment(self, env, dependent_spec):
- env.set('MPICC', join_path(self.prefix.bin, 'mpicc'))
- env.set('MPICXX', join_path(self.prefix.bin, 'mpic++'))
- env.set('MPIF77', join_path(self.prefix.bin, 'mpif77'))
- env.set('MPIF90', join_path(self.prefix.bin, 'mpif90'))
-
- env.set('MPICH_CC', spack_cc)
- env.set('MPICH_CXX', spack_cxx)
- env.set('MPICH_F77', spack_f77)
- env.set('MPICH_F90', spack_fc)
- env.set('MPICH_FC', spack_fc)
-
-At this point we can, for instance, install ``netlib-scalapack`` with
-``mpich``:
-
-.. code-block:: console
-
- root@advanced-packaging-tutorial:/# spack install netlib-scalapack ^mpich
- ...
- ==> Created stage in /usr/local/var/spack/stage/netlib-scalapack-2.0.2-km7tsbgoyyywonyejkjoojskhc5knz3z
- ==> No patches needed for netlib-scalapack
- ==> Building netlib-scalapack [CMakePackage]
- ==> Executing phase: 'cmake'
- ==> Executing phase: 'build'
- ==> Executing phase: 'install'
- ==> Successfully installed netlib-scalapack
- Fetch: 0.01s. Build: 3m 59.86s. Total: 3m 59.87s.
- [+] /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/netlib-scalapack-2.0.2-km7tsbgoyyywonyejkjoojskhc5knz3z
-
-
-and double check the environment logs to verify that every variable was
-set to the correct value.
-
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-Set environment variables in your own package
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-Packages can override the
-:py:func:`setup_build_environment <spack.package.PackageBase.setup_build_environment>`
-or the
-:py:func:`setup_run_environment <spack.package.PackageBase.setup_run_environment>`
-methods to modify their own build-time or run-time environment respectively.
-An example of a package that overrides both methods is ``qt``:
-
-.. code-block:: python
-
- def setup_build_environment(self, env):
- env.set('MAKEFLAGS', '-j{0}'.format(make_jobs))
-
- def setup_run_environment(self, env):
- env.set('QTDIR', self.prefix)
-
-When ``qt`` builds, ``MAKEFLAGS`` will be defined in the environment. Likewise, when a
-module file is created for ``qt`` it will contain commands to define ``QTDIR`` appropriately.
-
-To contrast with ``qt``'s
-:py:func:`setup_dependent_build_environment <spack.package.PackageBase.setup_dependent_build_environment>`
-function:
-
-.. code-block:: python
-
- def setup_dependent_build_environment(self, env, dependent_spec):
- env.set('QTDIR', self.prefix)
-
-Let's see how it works by completing the ``elpa`` package:
-
-.. code-block:: console
-
- root@advanced-packaging-tutorial:/# spack edit elpa
-
-In the end your method should look like:
-
-.. code-block:: python
-
- def setup_build_environment(self, env):
- spec = self.spec
-
- env.set('CC', spec['mpi'].mpicc)
- env.set('FC', spec['mpi'].mpifc)
- env.set('CXX', spec['mpi'].mpicxx)
- env.set('SCALAPACK_LDFLAGS', spec['scalapack'].libs.joined())
-
- env.append_flags('LDFLAGS', spec['lapack'].libs.search_flags)
- env.append_flags('LIBS', spec['lapack'].libs.link_flags)
-
-At this point it's possible to proceed with the installation of ``elpa ^mpich``
-
-------------------------------
-Retrieving library information
-------------------------------
-
-Although Spack attempts to help packages locate their dependency libraries
-automatically (e.g. by setting ``PKG_CONFIG_PATH`` and ``CMAKE_PREFIX_PATH``),
-a package may have unique configuration options that are required to locate
-libraries. When a package needs information about dependency libraries, the
-general approach in Spack is to query the dependencies for the locations of
-their libraries and set configuration options accordingly. By default most
-Spack packages know how to automatically locate their libraries. This section
-covers how to retrieve library information from dependencies and how to locate
-libraries when the default logic doesn't work.
-
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-Accessing dependency libraries
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-If you need to access the libraries of a dependency, you can do so
-via the ``libs`` property of the spec, for example in the ``arpack-ng``
-package:
-
-.. code-block:: python
-
- def install(self, spec, prefix):
- lapack_libs = spec['lapack'].libs.joined(';')
- blas_libs = spec['blas'].libs.joined(';')
-
- cmake(*[
- '-DLAPACK_LIBRARIES={0}'.format(lapack_libs),
- '-DBLAS_LIBRARIES={0}'.format(blas_libs)
- ], '.')
-
-Note that ``arpack-ng`` is querying virtual dependencies, which Spack
-automatically resolves to the installed implementation (e.g. ``openblas``
-for ``blas``).
-
-We've started work on a package for ``armadillo``. You should open it,
-read through the comment that starts with ``# TUTORIAL:`` and complete
-the ``cmake_args`` section:
-
-.. code-block:: console
-
- root@advanced-packaging-tutorial:/# spack edit armadillo
-
-If you followed the instructions in the package, when you are finished your
-``cmake_args`` method should look like:
-
-.. code-block:: python
-
- def cmake_args(self):
- spec = self.spec
-
- return [
- # ARPACK support
- '-DARPACK_LIBRARY={0}'.format(spec['arpack-ng'].libs.joined(";")),
- # BLAS support
- '-DBLAS_LIBRARY={0}'.format(spec['blas'].libs.joined(";")),
- # LAPACK support
- '-DLAPACK_LIBRARY={0}'.format(spec['lapack'].libs.joined(";")),
- # SuperLU support
- '-DSuperLU_INCLUDE_DIR={0}'.format(spec['superlu'].prefix.include),
- '-DSuperLU_LIBRARY={0}'.format(spec['superlu'].libs.joined(";")),
- # HDF5 support
- '-DDETECT_HDF5={0}'.format('ON' if '+hdf5' in spec else 'OFF')
- ]
-
-As you can see, getting the list of libraries that your dependencies provide
-is as easy as accessing the their ``libs`` attribute. Furthermore, the interface
-remains the same whether you are querying regular or virtual dependencies.
-
-At this point you can complete the installation of ``armadillo`` using ``openblas``
-as a LAPACK provider (``armadillo ^openblas ^mpich``):
-
-.. code-block:: console
-
- root@advanced-packaging-tutorial:/# spack install armadillo ^openblas ^mpich
- ==> pkg-config is already installed in /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/pkg-config-0.29.2-ae2hwm7q57byfbxtymts55xppqwk7ecj
- ...
- ==> superlu is already installed in /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/superlu-5.2.1-q2mbtw2wo4kpzis2e2n227ip2fquxrno
- ==> Installing armadillo
- ==> Using cached archive: /usr/local/var/spack/cache/armadillo/armadillo-8.100.1.tar.xz
- ==> Staging archive: /usr/local/var/spack/stage/armadillo-8.100.1-n2eojtazxbku6g4l5izucwwgnpwz77r4/armadillo-8.100.1.tar.xz
- ==> Created stage in /usr/local/var/spack/stage/armadillo-8.100.1-n2eojtazxbku6g4l5izucwwgnpwz77r4
- ==> Applied patch undef_linux.patch
- ==> Building armadillo [CMakePackage]
- ==> Executing phase: 'cmake'
- ==> Executing phase: 'build'
- ==> Executing phase: 'install'
- ==> Successfully installed armadillo
- Fetch: 0.01s. Build: 3.96s. Total: 3.98s.
- [+] /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/armadillo-8.100.1-n2eojtazxbku6g4l5izucwwgnpwz77r4
-
-Hopefully the installation went fine and the code we added expanded to the right list
-of semicolon separated libraries (you are encouraged to open ``armadillo``'s
-build logs to double check).
-
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-Providing libraries to dependents
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-Spack provides a default implementation for ``libs`` which often works
-out of the box. A user can write a package definition without having to
-implement a ``libs`` property and dependents can retrieve its libraries
-as shown in the above section. However, the default implementation assumes that
-libraries follow the naming scheme ``lib<package name>.so`` (or e.g.
-``lib<package name>.a`` for static libraries). Packages which don't
-follow this naming scheme must implement this function themselves, e.g.
-``opencv``:
-
-.. code-block:: python
-
- @property
- def libs(self):
- shared = "+shared" in self.spec
- return find_libraries(
- "libopencv_*", root=self.prefix, shared=shared, recurse=True
- )
-
-This issue is common for packages which implement an interface (i.e.
-virtual package providers in Spack). If we try to build another version of
-``armadillo`` tied to ``netlib-lapack`` (``armadillo ^netlib-lapack ^mpich``)
-we'll notice that this time the installation won't complete:
-
-.. code-block:: console
-
- root@advanced-packaging-tutorial:/# spack install armadillo ^netlib-lapack ^mpich
- ==> pkg-config is already installed in /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/pkg-config-0.29.2-ae2hwm7q57byfbxtymts55xppqwk7ecj
- ...
- ==> openmpi is already installed in /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/openmpi-3.0.0-yo5qkfvumpmgmvlbalqcadu46j5bd52f
- ==> Installing arpack-ng
- ==> Using cached archive: /usr/local/var/spack/cache/arpack-ng/arpack-ng-3.5.0.tar.gz
- ==> Already staged arpack-ng-3.5.0-bloz7cqirpdxj33pg7uj32zs5likz2un in /usr/local/var/spack/stage/arpack-ng-3.5.0-bloz7cqirpdxj33pg7uj32zs5likz2un
- ==> No patches needed for arpack-ng
- ==> Building arpack-ng [Package]
- ==> Executing phase: 'install'
- ==> Error: RuntimeError: Unable to recursively locate netlib-lapack libraries in /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/netlib-lapack-3.6.1-jjfe23wgt7nkjnp2adeklhseg3ftpx6z
- RuntimeError: RuntimeError: Unable to recursively locate netlib-lapack libraries in /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/netlib-lapack-3.6.1-jjfe23wgt7nkjnp2adeklhseg3ftpx6z
-
- /usr/local/var/spack/repos/builtin/packages/arpack-ng/package.py:105, in install:
- 5 options.append('-DCMAKE_INSTALL_NAME_DIR:PATH=%s/lib' % prefix)
- 6
- 7 # Make sure we use Spack's blas/lapack:
- >> 8 lapack_libs = spec['lapack'].libs.joined(';')
- 9 blas_libs = spec['blas'].libs.joined(';')
- 10
- 11 options.extend([
-
- See build log for details:
- /usr/local/var/spack/stage/arpack-ng-3.5.0-bloz7cqirpdxj33pg7uj32zs5likz2un/arpack-ng-3.5.0/spack-build-out.txt
-
-Unlike ``openblas`` which provides a library named ``libopenblas.so``,
-``netlib-lapack`` provides ``liblapack.so``, so it needs to implement
-customized library search logic. Let's edit it:
-
-.. code-block:: console
-
- root@advanced-packaging-tutorial:/# spack edit netlib-lapack
-
-and follow the instructions in the ``# TUTORIAL:`` comment as before.
-What we need to implement is:
-
-.. code-block:: python
-
- @property
- def lapack_libs(self):
- shared = True if '+shared' in self.spec else False
- return find_libraries(
- 'liblapack', root=self.prefix, shared=shared, recursive=True
- )
-
-i.e., a property that returns the correct list of libraries for the LAPACK interface.
-
-We use the name ``lapack_libs`` rather than ``libs`` because
-``netlib-lapack`` can also provide ``blas``, and when it does it is provided
-as a separate library file. Using this name ensures that when
-dependents ask for ``lapack`` libraries, ``netlib-lapack`` will retrieve only
-the libraries associated with the ``lapack`` interface. Now we can finally
-install ``armadillo ^netlib-lapack ^mpich``:
-
-.. code-block:: console
-
- root@advanced-packaging-tutorial:/# spack install armadillo ^netlib-lapack ^mpich
- ...
-
- ==> Building armadillo [CMakePackage]
- ==> Executing phase: 'cmake'
- ==> Executing phase: 'build'
- ==> Executing phase: 'install'
- ==> Successfully installed armadillo
- Fetch: 0.01s. Build: 3.75s. Total: 3.76s.
- [+] /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/armadillo-8.100.1-sxmpu5an4dshnhickh6ykchyfda7jpyn
-
-Since each implementation of a virtual package is responsible for locating the
-libraries associated with the interfaces it provides, dependents do not need
-to include special-case logic for different implementations and for example
-need only ask for :code:`spec['blas'].libs`.
-
-----------------------
-Other Packaging Topics
-----------------------
-
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-Attach attributes to other packages
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-Build tools usually also provide a set of executables that can be used
-when another package is being installed. Spack gives you the opportunity
-to monkey-patch dependent modules and attach attributes to them. This
-helps make the packager experience as similar as possible to what would
-have been the manual installation of the same package.
-
-An example here is the ``automake`` package, which overrides
-:py:func:`setup_dependent_package <spack.package.PackageBase.setup_dependent_package>`:
-
-.. code-block:: python
-
- def setup_dependent_package(self, module, dependent_spec):
- # Automake is very likely to be a build dependency,
- # so we add the tools it provides to the dependent module
- executables = ['aclocal', 'automake']
- for name in executables:
- setattr(module, name, self._make_executable(name))
-
-so that every other package that depends on it can use directly ``aclocal``
-and ``automake`` with the usual function call syntax of :py:class:`Executable <spack.util.executable.Executable>`:
-
-.. code-block:: python
-
- aclocal('--force')
-
-^^^^^^^^^^^^^^^^^^^^^^^
-Extra query parameters
-^^^^^^^^^^^^^^^^^^^^^^^
-
-An advanced feature of the Spec's build-interface protocol is the support
-for extra parameters after the subscript key. In fact, any of the keys used in the query
-can be followed by a comma-separated list of extra parameters which can be
-inspected by the package receiving the request to fine-tune a response.
-
-Let's look at an example and try to install ``netcdf ^mpich``:
-
-.. code-block:: console
-
- root@advanced-packaging-tutorial:/# spack install netcdf ^mpich
- ==> libsigsegv is already installed in /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/libsigsegv-2.11-fypapcprssrj3nstp6njprskeyynsgaz
- ==> m4 is already installed in /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/m4-1.4.18-r5envx3kqctwwflhd4qax4ahqtt6x43a
- ...
- ==> Error: AttributeError: 'list' object has no attribute 'search_flags'
- AttributeError: AttributeError: 'list' object has no attribute 'search_flags'
-
- /usr/local/var/spack/repos/builtin/packages/netcdf/package.py:207, in configure_args:
- 50 # used instead.
- 51 hdf5_hl = self.spec['hdf5:hl']
- 52 CPPFLAGS.append(hdf5_hl.headers.cpp_flags)
- >> 53 LDFLAGS.append(hdf5_hl.libs.search_flags)
- 54
- 55 if '+parallel-netcdf' in self.spec:
- 56 config_args.append('--enable-pnetcdf')
-
- See build log for details:
- /usr/local/var/spack/stage/netcdf-4.4.1.1-gk2xxhbqijnrdwicawawcll4t3c7dvoj/netcdf-4.4.1.1/spack-build-out.txt
-
-We can see from the error that ``netcdf`` needs to know how to link the *high-level interface*
-of ``hdf5``, and thus passes the extra parameter ``hl`` after the request to retrieve it.
-Clearly the implementation in the ``hdf5`` package is not complete, and we need to fix it:
-
-.. code-block:: console
-
- root@advanced-packaging-tutorial:/# spack edit hdf5
-
-If you followed the instructions correctly, the code added to the
-``lib`` property should be similar to:
-
-.. code-block:: python
- :emphasize-lines: 1
-
- query_parameters = self.spec.last_query.extra_parameters
- key = tuple(sorted(query_parameters))
- libraries = query2libraries[key]
- shared = '+shared' in self.spec
- return find_libraries(
- libraries, root=self.prefix, shared=shared, recurse=True
- )
-
-where we highlighted the line retrieving the extra parameters. Now we can successfully
-complete the installation of ``netcdf ^mpich``:
-
-.. code-block:: console
-
- root@advanced-packaging-tutorial:/# spack install netcdf ^mpich
- ==> libsigsegv is already installed in /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/libsigsegv-2.11-fypapcprssrj3nstp6njprskeyynsgaz
- ==> m4 is already installed in /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/m4-1.4.18-r5envx3kqctwwflhd4qax4ahqtt6x43a
- ...
- ==> Installing netcdf
- ==> Using cached archive: /usr/local/var/spack/cache/netcdf/netcdf-4.4.1.1.tar.gz
- ==> Already staged netcdf-4.4.1.1-gk2xxhbqijnrdwicawawcll4t3c7dvoj in /usr/local/var/spack/stage/netcdf-4.4.1.1-gk2xxhbqijnrdwicawawcll4t3c7dvoj
- ==> Already patched netcdf
- ==> Building netcdf [AutotoolsPackage]
- ==> Executing phase: 'autoreconf'
- ==> Executing phase: 'configure'
- ==> Executing phase: 'build'
- ==> Executing phase: 'install'
- ==> Successfully installed netcdf
- Fetch: 0.01s. Build: 24.61s. Total: 24.62s.
- [+] /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/netcdf-4.4.1.1-gk2xxhbqijnrdwicawawcll4t3c7dvoj
diff --git a/lib/spack/docs/tutorial_basics.rst b/lib/spack/docs/tutorial_basics.rst
deleted file mode 100644
index 9a6a2074b3c805cd49f9c9b19ad1dd46fbe5104c..0000000000000000000000000000000000000000
--- a/lib/spack/docs/tutorial_basics.rst
+++ /dev/null
@@ -1,1736 +0,0 @@
-.. Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
- Spack Project Developers. See the top-level COPYRIGHT file for details.
-
- SPDX-License-Identifier: (Apache-2.0 OR MIT)
-
-.. _basics-tutorial:
-
-=========================================
-Basic Installation Tutorial
-=========================================
-
-This tutorial will guide you through the process of installing
-software using Spack. We will first cover the `spack install` command,
-focusing on the power of the spec syntax and the flexibility it gives
-to users. We will also cover the `spack find` command for viewing
-installed packages and the `spack uninstall` command. Finally, we will
-touch on how Spack manages compilers, especially as it relates to
-using Spack-built compilers within Spack. We will include full output
-from all of the commands demonstrated, although we will frequently
-call attention to only small portions of that output (or merely to the
-fact that it succeeded). The provided output is all from an AWS
-instance running Ubuntu 16.04
-
-.. _basics-tutorial-install:
-
-----------------
-Installing Spack
-----------------
-
-Spack works out of the box. Simply clone spack and get going. We will
-clone Spack and immediately checkout the most recent release, v0.12.
-
-.. code-block:: console
-
- $ git clone https://github.com/spack/spack
- git clone https://github.com/spack/spack
- Cloning into 'spack'...
- remote: Enumerating objects: 68, done.
- remote: Counting objects: 100% (68/68), done.
- remote: Compressing objects: 100% (56/56), done.
- remote: Total 135389 (delta 40), reused 16 (delta 9), pack-reused 135321
- Receiving objects: 100% (135389/135389), 47.31 MiB | 1.01 MiB/s, done.
- Resolving deltas: 100% (64414/64414), done.
- Checking connectivity... done.
- $ cd spack
- $ git checkout releases/v0.12
- Branch releases/v0.12 set up to track remote branch releases/v0.12 from origin.
- Switched to a new branch 'releases/v0.12'
-
-Next add Spack to your path. Spack has some nice command line
-integration tools, so instead of simply appending to your ``PATH``
-variable, source the spack setup script. Then add Spack to your path.
-
-.. code-block:: console
-
- $ . share/spack/setup-env.sh
-
-You're good to go!
-
------------------
-What is in Spack?
------------------
-
-The ``spack list`` command shows available packages.
-
-.. code-block:: console
-
- $ spack list
- ==> 2907 packages.
- abinit libgpuarray py-espresso r-mlrmbo
- abyss libgridxc py-espressopp r-mmwrweek
- accfft libgtextutils py-et-xmlfile r-mnormt
- ...
-
-The ``spack list`` command can also take a query string. Spack
-automatically adds wildcards to both ends of the string. For example,
-we can view all available python packages.
-
-.. code-block:: console
-
- $ spack list py-
- ==> 479 packages.
- lumpy-sv py-funcsigs py-numpydoc py-utililib
- perl-file-copy-recursive py-functools32 py-olefile py-pywavelets
- py-3to2 py-future py-ont-fast5-api py-pyyaml
- ...
-
--------------------
-Installing Packages
--------------------
-
-Installing a package with Spack is very simple. To install a piece of
-software, simply type ``spack install <package_name>``.
-
-.. code-block:: console
-
- $ spack install zlib
- ==> Installing zlib
- ==> Searching for binary cache of zlib
- ==> Warning: No Spack mirrors are currently configured
- ==> No binary for zlib found: installing from source
- ==> Fetching http://zlib.net/fossils/zlib-1.2.11.tar.gz
- ######################################################################## 100.0%
- ==> Staging archive: /home/spack1/spack/var/spack/stage/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb/zlib-1.2.11.tar.gz
- ==> Created stage in /home/spack1/spack/var/spack/stage/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb
- ==> No patches needed for zlib
- ==> Building zlib [Package]
- ==> Executing phase: 'install'
- ==> Successfully installed zlib
- Fetch: 3.27s. Build: 2.18s. Total: 5.44s.
- [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb
-
-Spack can install software either from source or from a binary
-cache. Packages in the binary cache are signed with GPG for
-security. For the tutorial we have prepared a binary cache so you
-don't have to wait on slow compilation from source. To be able to
-install from the binary cache, we will need to configure Spack with
-the location of the binary cache and trust the GPG key that the binary
-cache was signed with.
-
-.. code-block:: console
-
- $ spack mirror add tutorial /mirror
- $ spack gpg trust /mirror/public.key
- gpg: keybox '/home/spack1/spack/opt/spack/gpg/pubring.kbx' created
- gpg: /home/spack1/spack/opt/spack/gpg/trustdb.gpg: trustdb created
- gpg: key 3B7C69B2: public key "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" imported
- gpg: Total number processed: 1
- gpg: imported: 1
-
-You'll learn more about configuring Spack later in the tutorial, but
-for now you will be able to install the rest of the packages in the
-tutorial from a binary cache using the same ``spack install``
-command. By default this will install the binary cached version if it
-exists and fall back on installing from source.
-
-Spack's spec syntax is the interface by which we can request specific
-configurations of the package. The ``%`` sigil is used to specify
-compilers.
-
-.. code-block:: console
-
- $ spack install zlib %clang
- ==> Installing zlib
- ==> Searching for binary cache of zlib
- ==> Finding buildcaches in /mirror/build_cache
- ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64-gcc-7.2.0-texinfo-6.5-cuqnfgfhhmudqp5f7upmld6ax7pratzw.spec.yaml
- ######################################################################## 100.0%
- ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64-gcc-4.7-zlib-1.2.11-bq2wtdxakpjytk2tjr7qu23i4py2fi2r.spec.yaml
- ######################################################################## 100.0%
- ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64-gcc-5.4.0-dyninst-9.3.2-bu6s2jzievsjkwtcnrtimc5b625j5omf.spec.yaml
- ######################################################################## 100.0%
- ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64-gcc-7.2.0-openmpi-3.1.3-do5xfer2whhk7gc26atgs3ozr3ljbvs4.spec.yaml
- ...
- ==> Installing zlib from binary cache
- ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/clang-3.8.0-2ubuntu4/zlib-1.2.11/linux-ubuntu16.04-x86_64-clang-3.8.0-2ubuntu4-zlib-1.2.11-4pt75q7qq6lygf3hgnona4lyc2uwedul.spack
- ######################################################################## 100.0%
- gpg: Signature made Sat Nov 10 05:08:01 2018 UTC using RSA key ID 3B7C69B2
- gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
- gpg: WARNING: This key is not certified with a trusted signature!
- gpg: There is no indication that the signature belongs to the owner.
- Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2
- ==> Successfully installed zlib from binary cache
- [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/clang-3.8.0-2ubuntu4/zlib-1.2.11-4pt75q7qq6lygf3hgnona4lyc2uwedul
-
-Note that this installation is located separately from the previous
-one. We will discuss this in more detail later, but this is part of what
-allows Spack to support arbitrarily versioned software.
-
-You can check for particular versions before requesting them. We will
-use the ``spack versions`` command to see the available versions, and then
-install a different version of ``zlib``.
-
-.. code-block:: console
-
- $ spack versions zlib
- ==> Safe versions (already checksummed):
- 1.2.11 1.2.8 1.2.3
- ==> Remote versions (not yet checksummed):
- 1.2.10 1.2.7 1.2.5.1 1.2.4.2 1.2.3.7
- ...
-
-The ``@`` sigil is used to specify versions, both of packages and of
-compilers.
-
-.. code-block:: console
-
- $ spack install zlib@1.2.8
- ==> Installing zlib
- ==> Searching for binary cache of zlib
- ==> Finding buildcaches in /mirror/build_cache
- ==> Installing zlib from binary cache
- ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.8/linux-ubuntu16.04-x86_64-gcc-5.4.0-zlib-1.2.8-bkyl5bhuep6fmhuxzkmhqy25qefjcvzc.spack
- ######################################################################## 100.0%
- gpg: Signature made Sat Nov 10 05:18:30 2018 UTC using RSA key ID 3B7C69B2
- gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
- gpg: WARNING: This key is not certified with a trusted signature!
- gpg: There is no indication that the signature belongs to the owner.
- Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2
- ==> Successfully installed zlib from binary cache
- [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.8-bkyl5bhuep6fmhuxzkmhqy25qefjcvzc
-
- $ spack install zlib %gcc@4.7
- ==> Installing zlib
- ==> Searching for binary cache of zlib
- ==> Finding buildcaches in /mirror/build_cache
- ==> Installing zlib from binary cache
- ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-4.7/zlib-1.2.11/linux-ubuntu16.04-x86_64-gcc-4.7-zlib-1.2.11-bq2wtdxakpjytk2tjr7qu23i4py2fi2r.spack
- ######################################################################## 100.0%
- gpg: Signature made Sat Nov 10 04:55:30 2018 UTC using RSA key ID 3B7C69B2
- gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
- gpg: WARNING: This key is not certified with a trusted signature!
- gpg: There is no indication that the signature belongs to the owner.
- Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2
- ==> Successfully installed zlib from binary cache
- [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-4.7/zlib-1.2.11-bq2wtdxakpjytk2tjr7qu23i4py2fi2r
-
-The spec syntax also includes compiler flags. Spack accepts
-``cppflags``, ``cflags``, ``cxxflags``, ``fflags``, ``ldflags``, and
-``ldlibs`` parameters. The values of these fields must be quoted on
-the command line if they include spaces. These values are injected
-into the compile line automatically by the Spack compiler wrappers.
-
-.. code-block:: console
-
- $ spack install zlib @1.2.8 cppflags=-O3
- ==> Installing zlib
- ==> Searching for binary cache of zlib
- ==> Finding buildcaches in /mirror/build_cache
- ==> Installing zlib from binary cache
- ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.8/linux-ubuntu16.04-x86_64-gcc-5.4.0-zlib-1.2.8-64mns5mvdacqvlashkf7v6lqrxixhmxu.spack
- ######################################################################## 100.0%
- gpg: Signature made Sat Nov 10 05:31:54 2018 UTC using RSA key ID 3B7C69B2
- gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
- gpg: WARNING: This key is not certified with a trusted signature!
- gpg: There is no indication that the signature belongs to the owner.
- Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2
- ==> Successfully installed zlib from binary cache
- [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.8-64mns5mvdacqvlashkf7v6lqrxixhmxu
-
-The ``spack find`` command is used to query installed packages. Note that
-some packages appear identical with the default output. The ``-l`` flag
-shows the hash of each package, and the ``-f`` flag shows any non-empty
-compiler flags of those packages.
-
-.. code-block:: console
-
- $ spack find
- ==> 5 installed packages.
- -- linux-ubuntu16.04-x86_64 / clang@3.8.0-2ubuntu4 --------------
- zlib@1.2.11
-
- -- linux-ubuntu16.04-x86_64 / gcc@4.7 ---------------------------
- zlib@1.2.11
-
- -- linux-ubuntu16.04-x86_64 / gcc@5.4.0 -------------------------
- zlib@1.2.8 zlib@1.2.8 zlib@1.2.11
-
-
- $ spack find -lf
- ==> 5 installed packages.
- -- linux-ubuntu16.04-x86_64 / clang@3.8.0-2ubuntu4 --------------
- 4pt75q7 zlib@1.2.11%clang
-
-
- -- linux-ubuntu16.04-x86_64 / gcc@4.7 ---------------------------
- bq2wtdx zlib@1.2.11%gcc
-
-
- -- linux-ubuntu16.04-x86_64 / gcc@5.4.0 -------------------------
- bkyl5bh zlib@1.2.8%gcc
-
- 64mns5m zlib@1.2.8%gcc cppflags="-O3"
-
- 5nus6kn zlib@1.2.11%gcc
-
-Spack generates a hash for each spec. This hash is a function of the full
-provenance of the package, so any change to the spec affects the
-hash. Spack uses this value to compare specs and to generate unique
-installation directories for every combinatorial version. As we move into
-more complicated packages with software dependencies, we can see that
-Spack reuses existing packages to satisfy a dependency only when the
-existing package's hash matches the desired spec.
-
-.. code-block:: console
-
- $ spack install tcl
- ==> zlib is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb
- ==> Installing tcl
- ==> Searching for binary cache of tcl
- ==> Finding buildcaches in /mirror/build_cache
- ==> Installing tcl from binary cache
- ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/tcl-8.6.8/linux-ubuntu16.04-x86_64-gcc-5.4.0-tcl-8.6.8-qhwyccywhx2i6s7ob2gvjrjtj3rnfuqt.spack
- ######################################################################## 100.0%
- gpg: Signature made Sat Nov 10 05:07:15 2018 UTC using RSA key ID 3B7C69B2
- gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
- gpg: WARNING: This key is not certified with a trusted signature!
- gpg: There is no indication that the signature belongs to the owner.
- Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2
- ==> Successfully installed tcl from binary cache
- [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/tcl-8.6.8-qhwyccywhx2i6s7ob2gvjrjtj3rnfuqt
-
-Dependencies can be explicitly requested using the ``^`` sigil. Note that
-the spec syntax is recursive. Anything we could specify about the
-top-level package, we can also specify about a dependency using ``^``.
-
-.. code-block:: console
-
- $ spack install tcl ^zlib @1.2.8 %clang
- ==> Installing zlib
- ==> Searching for binary cache of zlib
- ==> Finding buildcaches in /mirror/build_cache
- ==> Installing zlib from binary cache
- ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/clang-3.8.0-2ubuntu4/zlib-1.2.8/linux-ubuntu16.04-x86_64-clang-3.8.0-2ubuntu4-zlib-1.2.8-i426yu3o6lyau5fv5ljwsajfkqxj5rl5.spack
- ######################################################################## 100.0%
- gpg: Signature made Sat Nov 10 05:09:01 2018 UTC using RSA key ID 3B7C69B2
- gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
- gpg: WARNING: This key is not certified with a trusted signature!
- gpg: There is no indication that the signature belongs to the owner.
- Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2
- ==> Successfully installed zlib from binary cache
- [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/clang-3.8.0-2ubuntu4/zlib-1.2.8-i426yu3o6lyau5fv5ljwsajfkqxj5rl5
- ==> Installing tcl
- ==> Searching for binary cache of tcl
- ==> Installing tcl from binary cache
- ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/clang-3.8.0-2ubuntu4/tcl-8.6.8/linux-ubuntu16.04-x86_64-clang-3.8.0-2ubuntu4-tcl-8.6.8-6wc66etr7y6hgibp2derrdkf763exwvc.spack
- ######################################################################## 100.0%
- gpg: Signature made Sat Nov 10 05:10:21 2018 UTC using RSA key ID 3B7C69B2
- gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
- gpg: WARNING: This key is not certified with a trusted signature!
- gpg: There is no indication that the signature belongs to the owner.
- Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2
- ==> Successfully installed tcl from binary cache
- [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/clang-3.8.0-2ubuntu4/tcl-8.6.8-6wc66etr7y6hgibp2derrdkf763exwvc
-
-Packages can also be referred to from the command line by their package
-hash. Using the ``spack find -lf`` command earlier we saw that the hash
-of our optimized installation of zlib (``cppflags="-O3"``) began with
-``64mns5m``. We can now explicitly build with that package without typing
-the entire spec, by using the ``/`` sigil to refer to it by hash. As with
-other tools like git, you do not need to specify an *entire* hash on the
-command line. You can specify just enough digits to identify a hash
-uniquely. If a hash prefix is ambiguous (i.e., two or more installed
-packages share the prefix) then spack will report an error.
-
-.. code-block:: console
-
- $ spack install tcl ^/64mn
- ==> zlib is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.8-64mns5mvdacqvlashkf7v6lqrxixhmxu
- ==> Installing tcl
- ==> Searching for binary cache of tcl
- ==> Finding buildcaches in /mirror/build_cache
- ==> Installing tcl from binary cache
- ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/tcl-8.6.8/linux-ubuntu16.04-x86_64-gcc-5.4.0-tcl-8.6.8-am4pbatrtga3etyusg2akmsvrswwxno2.spack
- ######################################################################## 100.0%
- gpg: Signature made Sat Nov 10 05:11:53 2018 UTC using RSA key ID 3B7C69B2
- gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
- gpg: WARNING: This key is not certified with a trusted signature!
- gpg: There is no indication that the signature belongs to the owner.
- Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2
- ==> Successfully installed tcl from binary cache
- [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/tcl-8.6.8-am4pbatrtga3etyusg2akmsvrswwxno2
-
-The ``spack find`` command can also take a ``-d`` flag, which can show
-dependency information. Note that each package has a top-level entry,
-even if it also appears as a dependency.
-
-.. code-block:: console
-
- $ spack find -ldf
- ==> 9 installed packages
- -- linux-ubuntu16.04-x86_64 / clang@3.8.0-2ubuntu4 --------------
- 6wc66et tcl@8.6.8%clang
- i426yu3 ^zlib@1.2.8%clang
-
- i426yu3 zlib@1.2.8%clang
-
- 4pt75q7 zlib@1.2.11%clang
-
-
- -- linux-ubuntu16.04-x86_64 / gcc@4.7 ---------------------------
- bq2wtdx zlib@1.2.11%gcc
-
-
- -- linux-ubuntu16.04-x86_64 / gcc@5.4.0 -------------------------
- am4pbat tcl@8.6.8%gcc
- 64mns5m ^zlib@1.2.8%gcc cppflags="-O3"
-
- qhwyccy tcl@8.6.8%gcc
- 5nus6kn ^zlib@1.2.11%gcc
-
- bkyl5bh zlib@1.2.8%gcc
-
- 64mns5m zlib@1.2.8%gcc cppflags="-O3"
-
- 5nus6kn zlib@1.2.11%gcc
-
-
-Let's move on to slightly more complicated packages. ``HDF5`` is a
-good example of a more complicated package, with an MPI dependency. If
-we install it "out of the box," it will build with ``openmpi``.
-
-.. code-block:: console
-
- $ spack install hdf5
- ==> Installing libsigsegv
- ==> Searching for binary cache of libsigsegv
- ==> Finding buildcaches in /mirror/build_cache
- ==> Installing libsigsegv from binary cache
- ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/libsigsegv-2.11/linux-ubuntu16.04-x86_64-gcc-5.4.0-libsigsegv-2.11-fypapcprssrj3nstp6njprskeyynsgaz.spack
- ######################################################################## 100.0%
- gpg: Signature made Sat Nov 10 05:08:01 2018 UTC using RSA key ID 3B7C69B2
- gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
- gpg: WARNING: This key is not certified with a trusted signature!
- gpg: There is no indication that the signature belongs to the owner.
- Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2
- ==> Successfully installed libsigsegv from binary cache
- [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/libsigsegv-2.11-fypapcprssrj3nstp6njprskeyynsgaz
- ==> Installing m4
- ==> Searching for binary cache of m4
- ==> Installing m4 from binary cache
- ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/m4-1.4.18/linux-ubuntu16.04-x86_64-gcc-5.4.0-m4-1.4.18-suf5jtcfehivwfesrc5hjy72r4nukyel.spack
- ######################################################################## 100.0%
- gpg: Signature made Sat Nov 10 05:24:11 2018 UTC using RSA key ID 3B7C69B2
- gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
- gpg: WARNING: This key is not certified with a trusted signature!
- gpg: There is no indication that the signature belongs to the owner.
- Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2
- ==> Successfully installed m4 from binary cache
- [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/m4-1.4.18-suf5jtcfehivwfesrc5hjy72r4nukyel
- ==> Installing libtool
- ==> Searching for binary cache of libtool
- ==> Installing libtool from binary cache
- ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/libtool-2.4.6/linux-ubuntu16.04-x86_64-gcc-5.4.0-libtool-2.4.6-o2pfwjf44353ajgr42xqtvzyvqsazkgu.spack
- ######################################################################## 100.0%
- gpg: Signature made Sat Nov 10 05:12:47 2018 UTC using RSA key ID 3B7C69B2
- gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
- gpg: WARNING: This key is not certified with a trusted signature!
- gpg: There is no indication that the signature belongs to the owner.
- Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2
- ==> Successfully installed libtool from binary cache
- [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/libtool-2.4.6-o2pfwjf44353ajgr42xqtvzyvqsazkgu
- ==> Installing pkgconf
- ==> Searching for binary cache of pkgconf
- ==> Installing pkgconf from binary cache
- ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/pkgconf-1.4.2/linux-ubuntu16.04-x86_64-gcc-5.4.0-pkgconf-1.4.2-fovrh7alpft646n6mhis5mml6k6e5f4v.spack
- ######################################################################## 100.0%
- gpg: Signature made Sat Nov 10 05:00:47 2018 UTC using RSA key ID 3B7C69B2
- gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
- gpg: WARNING: This key is not certified with a trusted signature!
- gpg: There is no indication that the signature belongs to the owner.
- Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2
- ==> Successfully installed pkgconf from binary cache
- [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/pkgconf-1.4.2-fovrh7alpft646n6mhis5mml6k6e5f4v
- ==> Installing util-macros
- ==> Searching for binary cache of util-macros
- ==> Installing util-macros from binary cache
- ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/util-macros-1.19.1/linux-ubuntu16.04-x86_64-gcc-5.4.0-util-macros-1.19.1-milz7fmttmptcic2qdk5cnel7ll5sybr.spack
- ######################################################################## 100.0%
- gpg: Signature made Sat Nov 10 05:31:54 2018 UTC using RSA key ID 3B7C69B2
- gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
- gpg: WARNING: This key is not certified with a trusted signature!
- gpg: There is no indication that the signature belongs to the owner.
- Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2
- ==> Successfully installed util-macros from binary cache
- [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/util-macros-1.19.1-milz7fmttmptcic2qdk5cnel7ll5sybr
- ==> Installing libpciaccess
- ==> Searching for binary cache of libpciaccess
- ==> Installing libpciaccess from binary cache
- ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/libpciaccess-0.13.5/linux-ubuntu16.04-x86_64-gcc-5.4.0-libpciaccess-0.13.5-5urc6tcjae26fbbd2wyfohoszhgxtbmc.spack
- ######################################################################## 100.0%
- gpg: Signature made Sat Nov 10 05:09:34 2018 UTC using RSA key ID 3B7C69B2
- gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
- gpg: WARNING: This key is not certified with a trusted signature!
- gpg: There is no indication that the signature belongs to the owner.
- Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2
- ==> Successfully installed libpciaccess from binary cache
- [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/libpciaccess-0.13.5-5urc6tcjae26fbbd2wyfohoszhgxtbmc
- ==> Installing xz
- ==> Searching for binary cache of xz
- ==> Installing xz from binary cache
- ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/xz-5.2.4/linux-ubuntu16.04-x86_64-gcc-5.4.0-xz-5.2.4-teneqii2xv5u6zl5r6qi3pwurc6pmypz.spack
- ######################################################################## 100.0%
- gpg: Signature made Sat Nov 10 05:05:03 2018 UTC using RSA key ID 3B7C69B2
- gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
- gpg: WARNING: This key is not certified with a trusted signature!
- gpg: There is no indication that the signature belongs to the owner.
- Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2
- ==> Successfully installed xz from binary cache
- [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/xz-5.2.4-teneqii2xv5u6zl5r6qi3pwurc6pmypz
- ==> zlib is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb
- ==> Installing libxml2
- ==> Searching for binary cache of libxml2
- ==> Installing libxml2 from binary cache
- ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/libxml2-2.9.8/linux-ubuntu16.04-x86_64-gcc-5.4.0-libxml2-2.9.8-wpexsphdmfayxqxd4up5vgwuqgu5woo7.spack
- ######################################################################## 100.0%
- gpg: Signature made Sat Nov 10 04:56:04 2018 UTC using RSA key ID 3B7C69B2
- gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
- gpg: WARNING: This key is not certified with a trusted signature!
- gpg: There is no indication that the signature belongs to the owner.
- Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2
- ==> Successfully installed libxml2 from binary cache
- [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/libxml2-2.9.8-wpexsphdmfayxqxd4up5vgwuqgu5woo7
- ==> Installing ncurses
- ==> Searching for binary cache of ncurses
- ==> Installing ncurses from binary cache
- ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/ncurses-6.1/linux-ubuntu16.04-x86_64-gcc-5.4.0-ncurses-6.1-3o765ourmesfrji6yeclb4wb5w54aqbh.spack
- ######################################################################## 100.0%
- gpg: Signature made Sat Nov 10 05:04:49 2018 UTC using RSA key ID 3B7C69B2
- gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
- gpg: WARNING: This key is not certified with a trusted signature!
- gpg: There is no indication that the signature belongs to the owner.
- Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2
- ==> Successfully installed ncurses from binary cache
- [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/ncurses-6.1-3o765ourmesfrji6yeclb4wb5w54aqbh
- ==> Installing readline
- ==> Searching for binary cache of readline
- ==> Installing readline from binary cache
- ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/readline-7.0/linux-ubuntu16.04-x86_64-gcc-5.4.0-readline-7.0-nxhwrg7xwc6nbsm2v4ezwe63l6nfidbi.spack
- ######################################################################## 100.0%
- gpg: Signature made Sat Nov 10 05:04:56 2018 UTC using RSA key ID 3B7C69B2
- gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
- gpg: WARNING: This key is not certified with a trusted signature!
- gpg: There is no indication that the signature belongs to the owner.
- Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2
- ==> Successfully installed readline from binary cache
- [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/readline-7.0-nxhwrg7xwc6nbsm2v4ezwe63l6nfidbi
- ==> Installing gdbm
- ==> Searching for binary cache of gdbm
- ==> Installing gdbm from binary cache
- ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/gdbm-1.14.1/linux-ubuntu16.04-x86_64-gcc-5.4.0-gdbm-1.14.1-q4fpyuo7ouhkeq6d3oabtrppctpvxmes.spack
- ######################################################################## 100.0%
- gpg: Signature made Sat Nov 10 05:18:34 2018 UTC using RSA key ID 3B7C69B2
- gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
- gpg: WARNING: This key is not certified with a trusted signature!
- gpg: There is no indication that the signature belongs to the owner.
- Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2
- ==> Successfully installed gdbm from binary cache
- [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gdbm-1.14.1-q4fpyuo7ouhkeq6d3oabtrppctpvxmes
- ==> Installing perl
- ==> Searching for binary cache of perl
- ==> Installing perl from binary cache
- ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/perl-5.26.2/linux-ubuntu16.04-x86_64-gcc-5.4.0-perl-5.26.2-ic2kyoadgp3dxfejcbllyplj2wf524fo.spack
- ######################################################################## 100.0%
- gpg: Signature made Sat Nov 10 05:12:45 2018 UTC using RSA key ID 3B7C69B2
- gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
- gpg: WARNING: This key is not certified with a trusted signature!
- gpg: There is no indication that the signature belongs to the owner.
- Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2
- ==> Successfully installed perl from binary cache
- [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/perl-5.26.2-ic2kyoadgp3dxfejcbllyplj2wf524fo
- ==> Installing autoconf
- ==> Searching for binary cache of autoconf
- ==> Installing autoconf from binary cache
- ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/autoconf-2.69/linux-ubuntu16.04-x86_64-gcc-5.4.0-autoconf-2.69-3sx2gxeibc4oasqd4o5h6lnwpcpsgd2q.spack
- ######################################################################## 100.0%
- gpg: Signature made Sat Nov 10 05:24:03 2018 UTC using RSA key ID 3B7C69B2
- gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
- gpg: WARNING: This key is not certified with a trusted signature!
- gpg: There is no indication that the signature belongs to the owner.
- Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2
- ==> Successfully installed autoconf from binary cache
- [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/autoconf-2.69-3sx2gxeibc4oasqd4o5h6lnwpcpsgd2q
- ==> Installing automake
- ==> Searching for binary cache of automake
- ==> Installing automake from binary cache
- ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/automake-1.16.1/linux-ubuntu16.04-x86_64-gcc-5.4.0-automake-1.16.1-rymw7imfehycqxzj4nuy2oiw3abegooy.spack
- ######################################################################## 100.0%
- gpg: Signature made Sat Nov 10 05:12:03 2018 UTC using RSA key ID 3B7C69B2
- gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
- gpg: WARNING: This key is not certified with a trusted signature!
- gpg: There is no indication that the signature belongs to the owner.
- Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2
- ==> Successfully installed automake from binary cache
- [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/automake-1.16.1-rymw7imfehycqxzj4nuy2oiw3abegooy
- ==> Installing numactl
- ==> Searching for binary cache of numactl
- ==> Installing numactl from binary cache
- ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/numactl-2.0.11/linux-ubuntu16.04-x86_64-gcc-5.4.0-numactl-2.0.11-ft463odrombnxlc3qew4omckhlq7tqgc.spack
- ######################################################################## 100.0%
- gpg: Signature made Sat Nov 10 05:30:34 2018 UTC using RSA key ID 3B7C69B2
- gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
- gpg: WARNING: This key is not certified with a trusted signature!
- gpg: There is no indication that the signature belongs to the owner.
- Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2
- ==> Successfully installed numactl from binary cache
- [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/numactl-2.0.11-ft463odrombnxlc3qew4omckhlq7tqgc
- ==> Installing hwloc
- ==> Searching for binary cache of hwloc
- ==> Installing hwloc from binary cache
- ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/hwloc-1.11.9/linux-ubuntu16.04-x86_64-gcc-5.4.0-hwloc-1.11.9-43tkw5mt6huhv37vqnybqgxtkodbsava.spack
- ######################################################################## 100.0%
- gpg: Signature made Sat Nov 10 05:08:00 2018 UTC using RSA key ID 3B7C69B2
- gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
- gpg: WARNING: This key is not certified with a trusted signature!
- gpg: There is no indication that the signature belongs to the owner.
- Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2
- ==> Successfully installed hwloc from binary cache
- [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/hwloc-1.11.9-43tkw5mt6huhv37vqnybqgxtkodbsava
- ==> Installing openmpi
- ==> Searching for binary cache of openmpi
- ==> Installing openmpi from binary cache
- ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/openmpi-3.1.3/linux-ubuntu16.04-x86_64-gcc-5.4.0-openmpi-3.1.3-3njc4q5pqdpptq6jvqjrezkffwokv2sx.spack
- ######################################################################## 100.0%
- gpg: Signature made Sat Nov 10 05:01:54 2018 UTC using RSA key ID 3B7C69B2
- gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
- gpg: WARNING: This key is not certified with a trusted signature!
- gpg: There is no indication that the signature belongs to the owner.
- Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2
- ==> Successfully installed openmpi from binary cache
- [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/openmpi-3.1.3-3njc4q5pqdpptq6jvqjrezkffwokv2sx
- ==> Installing hdf5
- ==> Searching for binary cache of hdf5
- ==> Installing hdf5 from binary cache
- ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/hdf5-1.10.4/linux-ubuntu16.04-x86_64-gcc-5.4.0-hdf5-1.10.4-ozyvmhzdew66byarohm4p36ep7wtcuiw.spack
- ######################################################################## 100.0%
- gpg: Signature made Sat Nov 10 05:23:04 2018 UTC using RSA key ID 3B7C69B2
- gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
- gpg: WARNING: This key is not certified with a trusted signature!
- gpg: There is no indication that the signature belongs to the owner.
- Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2
- ==> Successfully installed hdf5 from binary cache
- [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/hdf5-1.10.4-ozyvmhzdew66byarohm4p36ep7wtcuiw
-
-Spack packages can also have build options, called variants. Boolean
-variants can be specified using the ``+`` and ``~`` or ``-``
-sigils. There are two sigils for ``False`` to avoid conflicts with
-shell parsing in different situations. Variants (boolean or otherwise)
-can also be specified using the same syntax as compiler flags. Here
-we can install HDF5 without MPI support.
-
-.. code-block:: console
-
- $ spack install hdf5~mpi
- ==> zlib is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb
- ==> Installing hdf5
- ==> Searching for binary cache of hdf5
- ==> Finding buildcaches in /mirror/build_cache
- ==> Installing hdf5 from binary cache
- ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/hdf5-1.10.4/linux-ubuntu16.04-x86_64-gcc-5.4.0-hdf5-1.10.4-5vcv5r67vpjzenq4apyebshclelnzuja.spack
- ######################################################################## 100.0%
- gpg: Signature made Sat Nov 10 05:23:24 2018 UTC using RSA key ID 3B7C69B2
- gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
- gpg: WARNING: This key is not certified with a trusted signature!
- gpg: There is no indication that the signature belongs to the owner.
- Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2
- ==> Successfully installed hdf5 from binary cache
- [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/hdf5-1.10.4-5vcv5r67vpjzenq4apyebshclelnzuja
-
-We might also want to install HDF5 with a different MPI
-implementation. While MPI is not a package itself, packages can depend on
-abstract interfaces like MPI. Spack handles these through "virtual
-dependencies." A package, such as HDF5, can depend on the MPI
-interface. Other packages (``openmpi``, ``mpich``, ``mvapich``, etc.)
-provide the MPI interface. Any of these providers can be requested for
-an MPI dependency. For example, we can build HDF5 with MPI support
-provided by mpich by specifying a dependency on ``mpich``. Spack also
-supports versioning of virtual dependencies. A package can depend on the
-MPI interface at version 3, and provider packages specify what version of
-the interface *they* provide. The partial spec ``^mpi@3`` can be safisfied
-by any of several providers.
-
-.. code-block:: console
-
- $ spack install hdf5+hl+mpi ^mpich
- ==> libsigsegv is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/libsigsegv-2.11-fypapcprssrj3nstp6njprskeyynsgaz
- ==> m4 is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/m4-1.4.18-suf5jtcfehivwfesrc5hjy72r4nukyel
- ==> pkgconf is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/pkgconf-1.4.2-fovrh7alpft646n6mhis5mml6k6e5f4v
- ==> ncurses is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/ncurses-6.1-3o765ourmesfrji6yeclb4wb5w54aqbh
- ==> readline is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/readline-7.0-nxhwrg7xwc6nbsm2v4ezwe63l6nfidbi
- ==> gdbm is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gdbm-1.14.1-q4fpyuo7ouhkeq6d3oabtrppctpvxmes
- ==> perl is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/perl-5.26.2-ic2kyoadgp3dxfejcbllyplj2wf524fo
- ==> autoconf is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/autoconf-2.69-3sx2gxeibc4oasqd4o5h6lnwpcpsgd2q
- ==> automake is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/automake-1.16.1-rymw7imfehycqxzj4nuy2oiw3abegooy
- ==> libtool is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/libtool-2.4.6-o2pfwjf44353ajgr42xqtvzyvqsazkgu
- ==> Installing texinfo
- ==> Searching for binary cache of texinfo
- ==> Finding buildcaches in /mirror/build_cache
- ==> Installing texinfo from binary cache
- ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/texinfo-6.5/linux-ubuntu16.04-x86_64-gcc-5.4.0-texinfo-6.5-zs7a2pcwhq6ho2cj2x26uxfktwkpyucn.spack
- ######################################################################## 100.0%
- gpg: Signature made Sat Nov 10 05:18:29 2018 UTC using RSA key ID 3B7C69B2
- gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
- gpg: WARNING: This key is not certified with a trusted signature!
- gpg: There is no indication that the signature belongs to the owner.
- Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2
- ==> Successfully installed texinfo from binary cache
- [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/texinfo-6.5-zs7a2pcwhq6ho2cj2x26uxfktwkpyucn
- ==> Installing findutils
- ==> Searching for binary cache of findutils
- ==> Installing findutils from binary cache
- ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/findutils-4.6.0/linux-ubuntu16.04-x86_64-gcc-5.4.0-findutils-4.6.0-d4iajxsopzrlcjtasahxqeyjkjv5jx4v.spack
- ######################################################################## 100.0%
- gpg: Signature made Sat Nov 10 05:07:17 2018 UTC using RSA key ID 3B7C69B2
- gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
- gpg: WARNING: This key is not certified with a trusted signature!
- gpg: There is no indication that the signature belongs to the owner.
- Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2
- ==> Successfully installed findutils from binary cache
- [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/findutils-4.6.0-d4iajxsopzrlcjtasahxqeyjkjv5jx4v
- ==> Installing mpich
- ==> Searching for binary cache of mpich
- ==> Installing mpich from binary cache
- ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/mpich-3.2.1/linux-ubuntu16.04-x86_64-gcc-5.4.0-mpich-3.2.1-p3f7p2r5ntrynqibosglxvhwyztiwqs5.spack
- ######################################################################## 100.0%
- gpg: Signature made Sat Nov 10 05:23:57 2018 UTC using RSA key ID 3B7C69B2
- gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
- gpg: WARNING: This key is not certified with a trusted signature!
- gpg: There is no indication that the signature belongs to the owner.
- Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2
- ==> Successfully installed mpich from binary cache
- [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/mpich-3.2.1-p3f7p2r5ntrynqibosglxvhwyztiwqs5
- ==> zlib is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb
- ==> Installing hdf5
- ==> Searching for binary cache of hdf5
- ==> Installing hdf5 from binary cache
- ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/hdf5-1.10.4/linux-ubuntu16.04-x86_64-gcc-5.4.0-hdf5-1.10.4-xxd7syhgej6onpyfyewxqcqe7ltkt7ob.spack
- ######################################################################## 100.0%
- gpg: Signature made Sat Nov 10 05:07:32 2018 UTC using RSA key ID 3B7C69B2
- gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
- gpg: WARNING: This key is not certified with a trusted signature!
- gpg: There is no indication that the signature belongs to the owner.
- Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2
- ==> Successfully installed hdf5 from binary cache
- [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/hdf5-1.10.4-xxd7syhgej6onpyfyewxqcqe7ltkt7ob
-
-We'll do a quick check in on what we have installed so far.
-
-.. code-block:: console
-
- $ spack find -ldf
- ==> 32 installed packages
- -- linux-ubuntu16.04-x86_64 / clang@3.8.0-2ubuntu4 --------------
- 6wc66et tcl@8.6.8%clang
- i426yu3 ^zlib@1.2.8%clang
-
- i426yu3 zlib@1.2.8%clang
-
- 4pt75q7 zlib@1.2.11%clang
-
-
- -- linux-ubuntu16.04-x86_64 / gcc@4.7 ---------------------------
- bq2wtdx zlib@1.2.11%gcc
-
-
- -- linux-ubuntu16.04-x86_64 / gcc@5.4.0 -------------------------
- 3sx2gxe autoconf@2.69%gcc
- suf5jtc ^m4@1.4.18%gcc
- fypapcp ^libsigsegv@2.11%gcc
- ic2kyoa ^perl@5.26.2%gcc
- q4fpyuo ^gdbm@1.14.1%gcc
- nxhwrg7 ^readline@7.0%gcc
- 3o765ou ^ncurses@6.1%gcc
-
- rymw7im automake@1.16.1%gcc
- ic2kyoa ^perl@5.26.2%gcc
- q4fpyuo ^gdbm@1.14.1%gcc
- nxhwrg7 ^readline@7.0%gcc
- 3o765ou ^ncurses@6.1%gcc
-
- d4iajxs findutils@4.6.0%gcc
-
- q4fpyuo gdbm@1.14.1%gcc
- nxhwrg7 ^readline@7.0%gcc
- 3o765ou ^ncurses@6.1%gcc
-
- 5vcv5r6 hdf5@1.10.4%gcc
- 5nus6kn ^zlib@1.2.11%gcc
-
- ozyvmhz hdf5@1.10.4%gcc
- 3njc4q5 ^openmpi@3.1.3%gcc
- 43tkw5m ^hwloc@1.11.9%gcc
- 5urc6tc ^libpciaccess@0.13.5%gcc
- wpexsph ^libxml2@2.9.8%gcc
- teneqii ^xz@5.2.4%gcc
- 5nus6kn ^zlib@1.2.11%gcc
- ft463od ^numactl@2.0.11%gcc
-
- xxd7syh hdf5@1.10.4%gcc
- p3f7p2r ^mpich@3.2.1%gcc
- 5nus6kn ^zlib@1.2.11%gcc
-
- 43tkw5m hwloc@1.11.9%gcc
- 5urc6tc ^libpciaccess@0.13.5%gcc
- wpexsph ^libxml2@2.9.8%gcc
- teneqii ^xz@5.2.4%gcc
- 5nus6kn ^zlib@1.2.11%gcc
- ft463od ^numactl@2.0.11%gcc
-
- 5urc6tc libpciaccess@0.13.5%gcc
-
- fypapcp libsigsegv@2.11%gcc
-
- o2pfwjf libtool@2.4.6%gcc
-
- wpexsph libxml2@2.9.8%gcc
- teneqii ^xz@5.2.4%gcc
- 5nus6kn ^zlib@1.2.11%gcc
-
- suf5jtc m4@1.4.18%gcc
- fypapcp ^libsigsegv@2.11%gcc
-
- p3f7p2r mpich@3.2.1%gcc
-
- 3o765ou ncurses@6.1%gcc
-
- ft463od numactl@2.0.11%gcc
-
- 3njc4q5 openmpi@3.1.3%gcc
- 43tkw5m ^hwloc@1.11.9%gcc
- 5urc6tc ^libpciaccess@0.13.5%gcc
- wpexsph ^libxml2@2.9.8%gcc
- teneqii ^xz@5.2.4%gcc
- 5nus6kn ^zlib@1.2.11%gcc
- ft463od ^numactl@2.0.11%gcc
-
- ic2kyoa perl@5.26.2%gcc
- q4fpyuo ^gdbm@1.14.1%gcc
- nxhwrg7 ^readline@7.0%gcc
- 3o765ou ^ncurses@6.1%gcc
-
- fovrh7a pkgconf@1.4.2%gcc
-
- nxhwrg7 readline@7.0%gcc
- 3o765ou ^ncurses@6.1%gcc
-
- am4pbat tcl@8.6.8%gcc
- 64mns5m ^zlib@1.2.8%gcc cppflags="-O3"
-
- qhwyccy tcl@8.6.8%gcc
- 5nus6kn ^zlib@1.2.11%gcc
-
- zs7a2pc texinfo@6.5%gcc
- ic2kyoa ^perl@5.26.2%gcc
- q4fpyuo ^gdbm@1.14.1%gcc
- nxhwrg7 ^readline@7.0%gcc
- 3o765ou ^ncurses@6.1%gcc
-
- milz7fm util-macros@1.19.1%gcc
-
- teneqii xz@5.2.4%gcc
-
- bkyl5bh zlib@1.2.8%gcc
-
- 64mns5m zlib@1.2.8%gcc cppflags="-O3"
-
- 5nus6kn zlib@1.2.11%gcc
-
-
-Spack models the dependencies of packages as a directed acyclic graph
-(DAG). The ``spack find -d`` command shows the tree representation of
-that graph. We can also use the ``spack graph`` command to view the entire
-DAG as a graph.
-
-.. code-block:: console
-
- $ spack graph hdf5+hl+mpi ^mpich
- o hdf5
- |\
- o | zlib
- /
- o mpich
- o findutils
- |\
- | |\
- | | |\
- | | | |\
- o | | | | texinfo
- | | | o | automake
- | |_|/| |
- |/| | | |
- | | | |/
- | | | o autoconf
- | |_|/|
- |/| |/
- | |/|
- o | | perl
- o | | gdbm
- o | | readline
- o | | ncurses
- o | | pkgconf
- / /
- | o libtool
- |/
- o m4
- o libsigsegv
-
-You may also have noticed that there are some packages shown in the
-``spack find -d`` output that we didn't install explicitly. These are
-dependencies that were installed implicitly. A few packages installed
-implicitly are not shown as dependencies in the ``spack find -d``
-output. These are build dependencies. For example, ``libpciaccess`` is a
-dependency of openmpi and requires ``m4`` to build. Spack will build ``m4`` as
-part of the installation of ``openmpi``, but it does not become a part of
-the DAG because it is not linked in at run time. Spack handles build
-dependencies differently because of their different (less strict)
-consistency requirements. It is entirely possible to have two packages
-using different versions of a dependency to build, which obviously cannot
-be done with linked dependencies.
-
-``HDF5`` is more complicated than our basic example of zlib and
-openssl, but it's still within the realm of software that an experienced
-HPC user could reasonably expect to install given a bit of time. Now
-let's look at an even more complicated package.
-
-.. code-block:: console
-
- $ spack install trilinos
- ==> Installing diffutils
- ==> Searching for binary cache of diffutils
- ==> Finding buildcaches in /mirror/build_cache
- ==> Installing diffutils from binary cache
- ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/diffutils-3.6/linux-ubuntu16.04-x86_64-gcc-5.4.0-diffutils-3.6-2rhuivgjrna2nrxhntyde6md2khcvs34.spack
- ######################################################################## 100.0%
- gpg: Signature made Sat Nov 10 05:30:17 2018 UTC using RSA key ID 3B7C69B2
- gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
- gpg: WARNING: This key is not certified with a trusted signature!
- gpg: There is no indication that the signature belongs to the owner.
- Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2
- ==> Successfully installed diffutils from binary cache
- [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/diffutils-3.6-2rhuivgjrna2nrxhntyde6md2khcvs34
- ==> Installing bzip2
- ==> Searching for binary cache of bzip2
- ==> Installing bzip2 from binary cache
- ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/bzip2-1.0.6/linux-ubuntu16.04-x86_64-gcc-5.4.0-bzip2-1.0.6-ufczdvsqt6edesm36xiucyry7myhj7e7.spack
- ######################################################################## 100.0%
- gpg: Signature made Sat Nov 10 05:34:37 2018 UTC using RSA key ID 3B7C69B2
- gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
- gpg: WARNING: This key is not certified with a trusted signature!
- gpg: There is no indication that the signature belongs to the owner.
- Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2
- ==> Successfully installed bzip2 from binary cache
- [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/bzip2-1.0.6-ufczdvsqt6edesm36xiucyry7myhj7e7
- ==> zlib is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb
- ==> Installing boost
- ==> Searching for binary cache of boost
- ==> Installing boost from binary cache
- ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/boost-1.68.0/linux-ubuntu16.04-x86_64-gcc-5.4.0-boost-1.68.0-zbgfxapchxa4awxdwpleubfuznblxzvt.spack
- ######################################################################## 100.0%
- gpg: Signature made Sat Nov 10 04:58:55 2018 UTC using RSA key ID 3B7C69B2
- gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
- gpg: WARNING: This key is not certified with a trusted signature!
- gpg: There is no indication that the signature belongs to the owner.
- Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2
- ==> Successfully installed boost from binary cache
- [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/boost-1.68.0-zbgfxapchxa4awxdwpleubfuznblxzvt
- ==> pkgconf is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/pkgconf-1.4.2-fovrh7alpft646n6mhis5mml6k6e5f4v
- ==> ncurses is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/ncurses-6.1-3o765ourmesfrji6yeclb4wb5w54aqbh
- ==> readline is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/readline-7.0-nxhwrg7xwc6nbsm2v4ezwe63l6nfidbi
- ==> gdbm is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gdbm-1.14.1-q4fpyuo7ouhkeq6d3oabtrppctpvxmes
- ==> perl is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/perl-5.26.2-ic2kyoadgp3dxfejcbllyplj2wf524fo
- ==> Installing openssl
- ==> Searching for binary cache of openssl
- ==> Installing openssl from binary cache
- ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/openssl-1.0.2o/linux-ubuntu16.04-x86_64-gcc-5.4.0-openssl-1.0.2o-b4y3w3bsyvjla6eesv4vt6aplpfrpsha.spack
- ######################################################################## 100.0%
- gpg: Signature made Sat Nov 10 05:24:10 2018 UTC using RSA key ID 3B7C69B2
- gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
- gpg: WARNING: This key is not certified with a trusted signature!
- gpg: There is no indication that the signature belongs to the owner.
- Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2
- ==> Successfully installed openssl from binary cache
- [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/openssl-1.0.2o-b4y3w3bsyvjla6eesv4vt6aplpfrpsha
- ==> Installing cmake
- ==> Searching for binary cache of cmake
- ==> Installing cmake from binary cache
- ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/cmake-3.12.3/linux-ubuntu16.04-x86_64-gcc-5.4.0-cmake-3.12.3-otafqzhh4xnlq2mpakch7dr3tjfsrjnx.spack
- ######################################################################## 100.0%
- gpg: Signature made Sat Nov 10 05:33:15 2018 UTC using RSA key ID 3B7C69B2
- gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
- gpg: WARNING: This key is not certified with a trusted signature!
- gpg: There is no indication that the signature belongs to the owner.
- Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2
- ==> Successfully installed cmake from binary cache
- [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/cmake-3.12.3-otafqzhh4xnlq2mpakch7dr3tjfsrjnx
- ==> Installing glm
- ==> Searching for binary cache of glm
- ==> Installing glm from binary cache
- ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/glm-0.9.7.1/linux-ubuntu16.04-x86_64-gcc-5.4.0-glm-0.9.7.1-jnw622jwcbsymzj2fsx22omjl7tmvaws.spack
- ######################################################################## 100.0%
- gpg: Signature made Sat Nov 10 05:30:33 2018 UTC using RSA key ID 3B7C69B2
- gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
- gpg: WARNING: This key is not certified with a trusted signature!
- gpg: There is no indication that the signature belongs to the owner.
- Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2
- ==> Successfully installed glm from binary cache
- [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/glm-0.9.7.1-jnw622jwcbsymzj2fsx22omjl7tmvaws
- ==> libsigsegv is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/libsigsegv-2.11-fypapcprssrj3nstp6njprskeyynsgaz
- ==> m4 is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/m4-1.4.18-suf5jtcfehivwfesrc5hjy72r4nukyel
- ==> libtool is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/libtool-2.4.6-o2pfwjf44353ajgr42xqtvzyvqsazkgu
- ==> util-macros is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/util-macros-1.19.1-milz7fmttmptcic2qdk5cnel7ll5sybr
- ==> libpciaccess is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/libpciaccess-0.13.5-5urc6tcjae26fbbd2wyfohoszhgxtbmc
- ==> xz is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/xz-5.2.4-teneqii2xv5u6zl5r6qi3pwurc6pmypz
- ==> libxml2 is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/libxml2-2.9.8-wpexsphdmfayxqxd4up5vgwuqgu5woo7
- ==> autoconf is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/autoconf-2.69-3sx2gxeibc4oasqd4o5h6lnwpcpsgd2q
- ==> automake is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/automake-1.16.1-rymw7imfehycqxzj4nuy2oiw3abegooy
- ==> numactl is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/numactl-2.0.11-ft463odrombnxlc3qew4omckhlq7tqgc
- ==> hwloc is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/hwloc-1.11.9-43tkw5mt6huhv37vqnybqgxtkodbsava
- ==> openmpi is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/openmpi-3.1.3-3njc4q5pqdpptq6jvqjrezkffwokv2sx
- ==> Installing hdf5
- ==> Searching for binary cache of hdf5
- ==> Installing hdf5 from binary cache
- ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/hdf5-1.10.4/linux-ubuntu16.04-x86_64-gcc-5.4.0-hdf5-1.10.4-oqwnui7wtovuf2id4vjwcxfmxlzjus6y.spack
- ######################################################################## 100.0%
- gpg: Signature made Sat Nov 10 05:09:10 2018 UTC using RSA key ID 3B7C69B2
- gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
- gpg: WARNING: This key is not certified with a trusted signature!
- gpg: There is no indication that the signature belongs to the owner.
- Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2
- ==> Successfully installed hdf5 from binary cache
- [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/hdf5-1.10.4-oqwnui7wtovuf2id4vjwcxfmxlzjus6y
- ==> Installing openblas
- ==> Searching for binary cache of openblas
- ==> Installing openblas from binary cache
- ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/openblas-0.3.3/linux-ubuntu16.04-x86_64-gcc-5.4.0-openblas-0.3.3-cyeg2yiitpuqglhvbox5gtbgsim2v5vn.spack
- ######################################################################## 100.0%
- gpg: Signature made Sat Nov 10 05:32:04 2018 UTC using RSA key ID 3B7C69B2
- gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
- gpg: WARNING: This key is not certified with a trusted signature!
- gpg: There is no indication that the signature belongs to the owner.
- Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2
- ==> Successfully installed openblas from binary cache
- [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/openblas-0.3.3-cyeg2yiitpuqglhvbox5gtbgsim2v5vn
- ==> Installing hypre
- ==> Searching for binary cache of hypre
- ==> Installing hypre from binary cache
- ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/hypre-2.15.1/linux-ubuntu16.04-x86_64-gcc-5.4.0-hypre-2.15.1-fshksdpecwiq7r6vawfswpboedhbisju.spack
- ######################################################################## 100.0%
- gpg: Signature made Sat Nov 10 05:07:34 2018 UTC using RSA key ID 3B7C69B2
- gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
- gpg: WARNING: This key is not certified with a trusted signature!
- gpg: There is no indication that the signature belongs to the owner.
- Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2
- ==> Successfully installed hypre from binary cache
- [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/hypre-2.15.1-fshksdpecwiq7r6vawfswpboedhbisju
- ==> Installing matio
- ==> Searching for binary cache of matio
- ==> Installing matio from binary cache
- ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/matio-1.5.9/linux-ubuntu16.04-x86_64-gcc-5.4.0-matio-1.5.9-lmzdgssvobdljw52mtahelu2ju7osh6h.spack
- ######################################################################## 100.0%
- gpg: Signature made Sat Nov 10 05:05:13 2018 UTC using RSA key ID 3B7C69B2
- gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
- gpg: WARNING: This key is not certified with a trusted signature!
- gpg: There is no indication that the signature belongs to the owner.
- Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2
- ==> Successfully installed matio from binary cache
- [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/matio-1.5.9-lmzdgssvobdljw52mtahelu2ju7osh6h
- ==> Installing metis
- ==> Searching for binary cache of metis
- ==> Installing metis from binary cache
- ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/metis-5.1.0/linux-ubuntu16.04-x86_64-gcc-5.4.0-metis-5.1.0-3wnvp4ji3wwu4v4vymszrhx6naehs6jc.spack
- ######################################################################## 100.0%
- gpg: Signature made Sat Nov 10 05:31:42 2018 UTC using RSA key ID 3B7C69B2
- gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
- gpg: WARNING: This key is not certified with a trusted signature!
- gpg: There is no indication that the signature belongs to the owner.
- Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2
- ==> Successfully installed metis from binary cache
- [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/metis-5.1.0-3wnvp4ji3wwu4v4vymszrhx6naehs6jc
- ==> Installing netlib-scalapack
- ==> Searching for binary cache of netlib-scalapack
- ==> Installing netlib-scalapack from binary cache
- ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/netlib-scalapack-2.0.2/linux-ubuntu16.04-x86_64-gcc-5.4.0-netlib-scalapack-2.0.2-wotpfwfctgfkzzn2uescucxvvbg3tm6b.spack
- ######################################################################## 100.0%
- gpg: Signature made Sat Nov 10 05:07:22 2018 UTC using RSA key ID 3B7C69B2
- gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
- gpg: WARNING: This key is not certified with a trusted signature!
- gpg: There is no indication that the signature belongs to the owner.
- Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2
- ==> Successfully installed netlib-scalapack from binary cache
- [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/netlib-scalapack-2.0.2-wotpfwfctgfkzzn2uescucxvvbg3tm6b
- ==> Installing mumps
- ==> Searching for binary cache of mumps
- ==> Installing mumps from binary cache
- ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/mumps-5.1.1/linux-ubuntu16.04-x86_64-gcc-5.4.0-mumps-5.1.1-acsg2dzroox2swssgc5cwgkvdy6jcm5q.spack
- ######################################################################## 100.0%
- gpg: Signature made Sat Nov 10 05:18:32 2018 UTC using RSA key ID 3B7C69B2
- gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
- gpg: WARNING: This key is not certified with a trusted signature!
- gpg: There is no indication that the signature belongs to the owner.
- Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2
- ==> Successfully installed mumps from binary cache
- [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/mumps-5.1.1-acsg2dzroox2swssgc5cwgkvdy6jcm5q
- ==> Installing netcdf
- ==> Searching for binary cache of netcdf
- ==> Installing netcdf from binary cache
- ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/netcdf-4.6.1/linux-ubuntu16.04-x86_64-gcc-5.4.0-netcdf-4.6.1-mhm4izpogf4mrjidyskb6ewtzxdi7t6g.spack
- ######################################################################## 100.0%
- gpg: Signature made Sat Nov 10 05:11:57 2018 UTC using RSA key ID 3B7C69B2
- gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
- gpg: WARNING: This key is not certified with a trusted signature!
- gpg: There is no indication that the signature belongs to the owner.
- Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2
- ==> Successfully installed netcdf from binary cache
- [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/netcdf-4.6.1-mhm4izpogf4mrjidyskb6ewtzxdi7t6g
- ==> Installing parmetis
- ==> Searching for binary cache of parmetis
- ==> Installing parmetis from binary cache
- ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/parmetis-4.0.3/linux-ubuntu16.04-x86_64-gcc-5.4.0-parmetis-4.0.3-uv6h3sqx6quqg22hxesi2mw2un3kw6b7.spack
- ######################################################################## 100.0%
- gpg: Signature made Sat Nov 10 05:12:04 2018 UTC using RSA key ID 3B7C69B2
- gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
- gpg: WARNING: This key is not certified with a trusted signature!
- gpg: There is no indication that the signature belongs to the owner.
- Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2
- ==> Successfully installed parmetis from binary cache
- [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/parmetis-4.0.3-uv6h3sqx6quqg22hxesi2mw2un3kw6b7
- ==> Installing suite-sparse
- ==> Searching for binary cache of suite-sparse
- ==> Installing suite-sparse from binary cache
- ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/suite-sparse-5.3.0/linux-ubuntu16.04-x86_64-gcc-5.4.0-suite-sparse-5.3.0-zaau4kifha2enpdcn3mjlrqym7hm7yon.spack
- ######################################################################## 100.0%
- gpg: Signature made Sat Nov 10 05:22:54 2018 UTC using RSA key ID 3B7C69B2
- gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
- gpg: WARNING: This key is not certified with a trusted signature!
- gpg: There is no indication that the signature belongs to the owner.
- Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2
- ==> Successfully installed suite-sparse from binary cache
- [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/suite-sparse-5.3.0-zaau4kifha2enpdcn3mjlrqym7hm7yon
- ==> Installing trilinos
- ==> Searching for binary cache of trilinos
- ==> Installing trilinos from binary cache
- ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/trilinos-12.12.1/linux-ubuntu16.04-x86_64-gcc-5.4.0-trilinos-12.12.1-rlsruavxqvwk2tgxzxboclbo6ykjf54r.spack
- ######################################################################## 100.0%
- gpg: Signature made Sat Nov 10 05:18:10 2018 UTC using RSA key ID 3B7C69B2
- gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
- gpg: WARNING: This key is not certified with a trusted signature!
- gpg: There is no indication that the signature belongs to the owner.
- Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2
- ==> Successfully installed trilinos from binary cache
-
-Now we're starting to see the power of Spack. Trilinos in its default
-configuration has 23 top level dependecies, many of which have
-dependencies of their own. Installing more complex packages can take
-days or weeks even for an experienced user. Although we've done a
-binary installation for the tutorial, a source installation of
-trilinos using Spack takes about 3 hours (depending on the system),
-but only 20 seconds of programmer time.
-
-Spack manages constistency of the entire DAG. Every MPI dependency will
-be satisfied by the same configuration of MPI, etc. If we install
-``trilinos`` again specifying a dependency on our previous HDF5 built
-with ``mpich``:
-
-.. code-block:: console
-
- $ spack install trilinos +hdf5 ^hdf5+hl+mpi ^mpich
- ==> diffutils is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/diffutils-3.6-2rhuivgjrna2nrxhntyde6md2khcvs34
- ==> bzip2 is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/bzip2-1.0.6-ufczdvsqt6edesm36xiucyry7myhj7e7
- ==> zlib is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb
- ==> boost is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/boost-1.68.0-zbgfxapchxa4awxdwpleubfuznblxzvt
- ==> pkgconf is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/pkgconf-1.4.2-fovrh7alpft646n6mhis5mml6k6e5f4v
- ==> ncurses is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/ncurses-6.1-3o765ourmesfrji6yeclb4wb5w54aqbh
- ==> readline is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/readline-7.0-nxhwrg7xwc6nbsm2v4ezwe63l6nfidbi
- ==> gdbm is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gdbm-1.14.1-q4fpyuo7ouhkeq6d3oabtrppctpvxmes
- ==> perl is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/perl-5.26.2-ic2kyoadgp3dxfejcbllyplj2wf524fo
- ==> openssl is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/openssl-1.0.2o-b4y3w3bsyvjla6eesv4vt6aplpfrpsha
- ==> cmake is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/cmake-3.12.3-otafqzhh4xnlq2mpakch7dr3tjfsrjnx
- ==> glm is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/glm-0.9.7.1-jnw622jwcbsymzj2fsx22omjl7tmvaws
- ==> libsigsegv is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/libsigsegv-2.11-fypapcprssrj3nstp6njprskeyynsgaz
- ==> m4 is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/m4-1.4.18-suf5jtcfehivwfesrc5hjy72r4nukyel
- ==> autoconf is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/autoconf-2.69-3sx2gxeibc4oasqd4o5h6lnwpcpsgd2q
- ==> automake is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/automake-1.16.1-rymw7imfehycqxzj4nuy2oiw3abegooy
- ==> libtool is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/libtool-2.4.6-o2pfwjf44353ajgr42xqtvzyvqsazkgu
- ==> texinfo is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/texinfo-6.5-zs7a2pcwhq6ho2cj2x26uxfktwkpyucn
- ==> findutils is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/findutils-4.6.0-d4iajxsopzrlcjtasahxqeyjkjv5jx4v
- ==> mpich is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/mpich-3.2.1-p3f7p2r5ntrynqibosglxvhwyztiwqs5
- ==> hdf5 is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/hdf5-1.10.4-xxd7syhgej6onpyfyewxqcqe7ltkt7ob
- ==> openblas is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/openblas-0.3.3-cyeg2yiitpuqglhvbox5gtbgsim2v5vn
- ==> Installing hypre
- ==> Searching for binary cache of hypre
- ==> Finding buildcaches in /mirror/build_cache
- ==> Installing hypre from binary cache
- ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/hypre-2.15.1/linux-ubuntu16.04-x86_64-gcc-5.4.0-hypre-2.15.1-obewuozolon7tkdg4cfxc6ae2tzkronb.spack
- ######################################################################## 100.0%
- gpg: Signature made Sat Nov 10 05:34:36 2018 UTC using RSA key ID 3B7C69B2
- gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
- gpg: WARNING: This key is not certified with a trusted signature!
- gpg: There is no indication that the signature belongs to the owner.
- Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2
- ==> Successfully installed hypre from binary cache
- [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/hypre-2.15.1-obewuozolon7tkdg4cfxc6ae2tzkronb
- ==> Installing matio
- ==> Searching for binary cache of matio
- ==> Installing matio from binary cache
- ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/matio-1.5.9/linux-ubuntu16.04-x86_64-gcc-5.4.0-matio-1.5.9-gvyqldhifflmvcrtui3b6s64jcczsxxh.spack
- ######################################################################## 100.0%
- gpg: Signature made Sat Nov 10 05:25:11 2018 UTC using RSA key ID 3B7C69B2
- gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
- gpg: WARNING: This key is not certified with a trusted signature!
- gpg: There is no indication that the signature belongs to the owner.
- Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2
- ==> Successfully installed matio from binary cache
- [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/matio-1.5.9-gvyqldhifflmvcrtui3b6s64jcczsxxh
- ==> metis is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/metis-5.1.0-3wnvp4ji3wwu4v4vymszrhx6naehs6jc
- ==> Installing netlib-scalapack
- ==> Searching for binary cache of netlib-scalapack
- ==> Installing netlib-scalapack from binary cache
- ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/netlib-scalapack-2.0.2/linux-ubuntu16.04-x86_64-gcc-5.4.0-netlib-scalapack-2.0.2-p7iln2pcosw2ipyqoyr7ie6lpva2oj7r.spack
- ######################################################################## 100.0%
- gpg: Signature made Sat Nov 10 05:32:20 2018 UTC using RSA key ID 3B7C69B2
- gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
- gpg: WARNING: This key is not certified with a trusted signature!
- gpg: There is no indication that the signature belongs to the owner.
- Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2
- ==> Successfully installed netlib-scalapack from binary cache
- [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/netlib-scalapack-2.0.2-p7iln2pcosw2ipyqoyr7ie6lpva2oj7r
- ==> Installing mumps
- ==> Searching for binary cache of mumps
- ==> Installing mumps from binary cache
- ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/mumps-5.1.1/linux-ubuntu16.04-x86_64-gcc-5.4.0-mumps-5.1.1-cumcj5a75cagsznpjrgretxdg6okxaur.spack
- ######################################################################## 100.0%
- gpg: Signature made Sat Nov 10 05:33:18 2018 UTC using RSA key ID 3B7C69B2
- gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
- gpg: WARNING: This key is not certified with a trusted signature!
- gpg: There is no indication that the signature belongs to the owner.
- Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2
- ==> Successfully installed mumps from binary cache
- [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/mumps-5.1.1-cumcj5a75cagsznpjrgretxdg6okxaur
- ==> Installing netcdf
- ==> Searching for binary cache of netcdf
- ==> Installing netcdf from binary cache
- ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/netcdf-4.6.1/linux-ubuntu16.04-x86_64-gcc-5.4.0-netcdf-4.6.1-wmmx5sgwfds34v7bkkhiduar5yecrnnd.spack
- ######################################################################## 100.0%
- gpg: Signature made Sat Nov 10 05:24:01 2018 UTC using RSA key ID 3B7C69B2
- gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
- gpg: WARNING: This key is not certified with a trusted signature!
- gpg: There is no indication that the signature belongs to the owner.
- Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2
- ==> Successfully installed netcdf from binary cache
- [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/netcdf-4.6.1-wmmx5sgwfds34v7bkkhiduar5yecrnnd
- ==> Installing parmetis
- ==> Searching for binary cache of parmetis
- ==> Installing parmetis from binary cache
- ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/parmetis-4.0.3/linux-ubuntu16.04-x86_64-gcc-5.4.0-parmetis-4.0.3-jehtatan4y2lcobj6waoqv66jj4libtz.spack
- ######################################################################## 100.0%
- gpg: Signature made Sat Nov 10 05:07:41 2018 UTC using RSA key ID 3B7C69B2
- gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
- gpg: WARNING: This key is not certified with a trusted signature!
- gpg: There is no indication that the signature belongs to the owner.
- Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2
- ==> Successfully installed parmetis from binary cache
- [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/parmetis-4.0.3-jehtatan4y2lcobj6waoqv66jj4libtz
- ==> suite-sparse is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/suite-sparse-5.3.0-zaau4kifha2enpdcn3mjlrqym7hm7yon
- ==> Installing trilinos
- ==> Searching for binary cache of trilinos
- ==> Installing trilinos from binary cache
- ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/trilinos-12.12.1/linux-ubuntu16.04-x86_64-gcc-5.4.0-trilinos-12.12.1-kqc52moweigxqxzwzfqajc6ocxwdwn4w.spack
- ######################################################################## 100.0%
- gpg: Signature made Sat Nov 10 05:30:15 2018 UTC using RSA key ID 3B7C69B2
- gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
- gpg: WARNING: This key is not certified with a trusted signature!
- gpg: There is no indication that the signature belongs to the owner.
- Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2
- ==> Successfully installed trilinos from binary cache
- [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/trilinos-12.12.1-kqc52moweigxqxzwzfqajc6ocxwdwn4w
-
-
-We see that every package in the trilinos DAG that depends on MPI now
-uses ``mpich``.
-
-.. code-block:: console
-
- $ spack find -d trilinos
- ==> 2 installed packages
- -- linux-ubuntu16.04-x86_64 / gcc@5.4.0 -------------------------
- trilinos@12.12.1
- ^boost@1.68.0
- ^bzip2@1.0.6
- ^zlib@1.2.11
- ^glm@0.9.7.1
- ^hdf5@1.10.4
- ^openmpi@3.1.3
- ^hwloc@1.11.9
- ^libpciaccess@0.13.5
- ^libxml2@2.9.8
- ^xz@5.2.4
- ^numactl@2.0.11
- ^hypre@2.15.1
- ^openblas@0.3.3
- ^matio@1.5.9
- ^metis@5.1.0
- ^mumps@5.1.1
- ^netlib-scalapack@2.0.2
- ^netcdf@4.6.1
- ^parmetis@4.0.3
- ^suite-sparse@5.3.0
-
- trilinos@12.12.1
- ^boost@1.68.0
- ^bzip2@1.0.6
- ^zlib@1.2.11
- ^glm@0.9.7.1
- ^hdf5@1.10.4
- ^mpich@3.2.1
- ^hypre@2.15.1
- ^openblas@0.3.3
- ^matio@1.5.9
- ^metis@5.1.0
- ^mumps@5.1.1
- ^netlib-scalapack@2.0.2
- ^netcdf@4.6.1
- ^parmetis@4.0.3
- ^suite-sparse@5.3.0
-
-
-As we discussed before, the ``spack find -d`` command shows the
-dependency information as a tree. While that is often sufficient, many
-complicated packages, including trilinos, have dependencies that
-cannot be fully represented as a tree. Again, the ``spack graph``
-command shows the full DAG of the dependency information.
-
-.. code-block:: console
-
- $ spack graph trilinos
- o trilinos
- |\
- | |\
- | | |\
- | | | |\
- | | | | |\
- | | | | | |\
- | | | | | | |\
- | | | | | | | |\
- | | | | | | | | |\
- | | | | | | | | | |\
- | | | | | | | | | | |\
- | | | | | | | | | | | |\
- | | | | | | | | | | | | |\
- o | | | | | | | | | | | | | suite-sparse
- |\ \ \ \ \ \ \ \ \ \ \ \ \ \
- | |_|_|/ / / / / / / / / / /
- |/| | | | | | | | | | | | |
- | |\ \ \ \ \ \ \ \ \ \ \ \ \
- | | |_|_|_|_|_|/ / / / / / /
- | |/| | | | | | | | | | | |
- | | | |_|_|_|_|_|_|_|/ / /
- | | |/| | | | | | | | | |
- | | | o | | | | | | | | | parmetis
- | | |/| | | | | | | | | |
- | |/|/| | | | | | | | | |
- | | | |/ / / / / / / / /
- | | | | | | o | | | | | mumps
- | |_|_|_|_|/| | | | | |
- |/| | | |_|/| | | | | |
- | | | |/| |/ / / / / /
- | | | | |/| | | | | |
- | | | | o | | | | | | netlib-scalapack
- | |_|_|/| | | | | | |
- |/| | |/| | | | | | |
- | | |/|/ / / / / / /
- | o | | | | | | | | metis
- | |/ / / / / / / /
- | | | | | | | o | glm
- | | |_|_|_|_|/ /
- | |/| | | | | |
- | o | | | | | | cmake
- | |\ \ \ \ \ \ \
- | o | | | | | | | openssl
- | |\ \ \ \ \ \ \ \
- | | | | | o | | | | netcdf
- | | |_|_|/| | | | |
- | |/| | |/| | | | |
- | | | | | |\ \ \ \ \
- | | | | | | | |_|/ /
- | | | | | | |/| | |
- | | | | | | | o | | matio
- | | |_|_|_|_|/| | |
- | |/| | | | |/ / /
- | | | | | | | o | hypre
- | |_|_|_|_|_|/| |
- |/| | | | |_|/ /
- | | | | |/| | |
- | | | | | | o | hdf5
- | | |_|_|_|/| |
- | |/| | | |/ /
- | | | | |/| |
- | | | | o | | openmpi
- | | |_|/| | |
- | |/| | | | |
- | | | | |\ \ \
- | | | | | o | | hwloc
- | | | | |/| | |
- | | | | | |\ \ \
- | | | | | | |\ \ \
- | | | | | | o | | | libxml2
- | | |_|_|_|/| | | |
- | |/| | | |/| | | |
- | | | | | | | | | o boost
- | | |_|_|_|_|_|_|/|
- | |/| | | | | | | |
- | o | | | | | | | | zlib
- | / / / / / / / /
- | | | | | o | | | xz
- | | | | | / / /
- | | | | | o | | libpciaccess
- | | | | |/| | |
- | | | | | |\ \ \
- | | | | | o | | | util-macros
- | | | | | / / /
- | | | o | | | | numactl
- | | | |\ \ \ \ \
- | | | | |_|_|/ /
- | | | |/| | | |
- | | | | |\ \ \ \
- | | | | | |_|/ /
- | | | | |/| | |
- | | | | | |\ \ \
- | | | | | o | | | automake
- | | |_|_|/| | | |
- | |/| | | | | | |
- | | | | | |/ / /
- | | | | | o | | autoconf
- | | |_|_|/| | |
- | |/| | |/ / /
- | | | |/| | |
- | o | | | | | perl
- | o | | | | | gdbm
- | o | | | | | readline
- | |/ / / / /
- | o | | | | ncurses
- | | |_|/ /
- | |/| | |
- | o | | | pkgconf
- | / / /
- o | | | openblas
- / / /
- | o | libtool
- |/ /
- o | m4
- o | libsigsegv
- /
- o bzip2
- o diffutils
-
-You can control how the output is displayed with a number of options.
-
-The ASCII output from ``spack graph`` can be difficult to parse for
-complicated packages. The output can be changed to the ``graphviz``
-``.dot`` format using the ``--dot`` flag.
-
-.. code-block:: console
-
- $ spack graph --dot trilinos | dot -Tpdf trilinos_graph.pdf
-
-.. _basics-tutorial-uninstall:
-
----------------------
-Uninstalling Packages
----------------------
-
-Earlier we installed many configurations each of zlib and tcl. Now we
-will go through and uninstall some of those packages that we didn't
-really need.
-
-.. code-block:: console
-
- $ spack find -d tcl
- ==> 3 installed packages
- -- linux-ubuntu16.04-x86_64 / clang@3.8.0-2ubuntu4 --------------
- tcl@8.6.8
- ^zlib@1.2.8
-
-
- -- linux-ubuntu16.04-x86_64 / gcc@5.4.0 -------------------------
- tcl@8.6.8
- ^zlib@1.2.8
-
- tcl@8.6.8
- ^zlib@1.2.11
-
-
- $ spack find zlib
- ==> 6 installed packages.
- -- linux-ubuntu16.04-x86_64 / clang@3.8.0-2ubuntu4 --------------
- zlib@1.2.8 zlib@1.2.11
-
- -- linux-ubuntu16.04-x86_64 / gcc@4.7 ---------------------------
- zlib@1.2.11
-
- -- linux-ubuntu16.04-x86_64 / gcc@5.4.0 -------------------------
- zlib@1.2.8 zlib@1.2.8 zlib@1.2.11
-
-We can uninstall packages by spec using the same syntax as install.
-
-.. code-block:: console
-
- $ spack uninstall zlib %gcc@4.7
- ==> The following packages will be uninstalled:
-
- -- linux-ubuntu16.04-x86_64 / gcc@4.7 ---------------------------
- bq2wtdx zlib@1.2.11%gcc+optimize+pic+shared
-
- ==> Do you want to proceed? [y/N] y
- ==> Successfully uninstalled zlib@1.2.11%gcc@4.7+optimize+pic+shared arch=linux-ubuntu16.04-x86_64 /bq2wtdx
-
- $ spack find -lf zlib
- ==> 5 installed packages.
- -- linux-ubuntu16.04-x86_64 / clang@3.8.0-2ubuntu4 --------------
- i426yu3 zlib@1.2.8%clang
- 4pt75q7 zlib@1.2.11%clang
-
-
- -- linux-ubuntu16.04-x86_64 / gcc@5.4.0 -------------------------
- bkyl5bh zlib@1.2.8%gcc
- 64mns5m zlib@1.2.8%gcc cppflags="-O3"
- 5nus6kn zlib@1.2.11%gcc
-
-We can also uninstall packages by referring only to their hash.
-
-We can use either ``-f`` (force) or ``-R`` (remove dependents as well) to
-remove packages that are required by another installed package.
-
-.. code-block:: console
-
- $ spack uninstall zlib/i426
- ==> Error: Will not uninstall zlib@1.2.8%clang@3.8.0-2ubuntu4/i426yu3
-
- The following packages depend on it:
- -- linux-ubuntu16.04-x86_64 / clang@3.8.0-2ubuntu4 --------------
- 6wc66et tcl@8.6.8%clang
-
- ==> Error: Use \`spack uninstall --dependents\` to uninstall these dependencies as well.
-
- $ spack uninstall -R zlib/i426
- ==> The following packages will be uninstalled:
-
- -- linux-ubuntu16.04-x86_64 / clang@3.8.0-2ubuntu4 --------------
- 6wc66et tcl@8.6.8%clang
- i426yu3 zlib@1.2.8%clang+optimize+pic+shared
- ==> Do you want to proceed? [y/N] y
- ==> Successfully uninstalled tcl@8.6.8%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64 /6wc66et
- ==> Successfully uninstalled zlib@1.2.8%clang@3.8.0-2ubuntu4+optimize+pic+shared arch=linux-ubuntu16.04-x86_64 /i426yu3
-
-Spack will not uninstall packages that are not sufficiently
-specified. The ``-a`` (all) flag can be used to uninstall multiple
-packages at once.
-
-.. code-block:: console
-
- $ spack uninstall trilinos
- ==> Error: trilinos matches multiple packages:
-
- -- linux-ubuntu16.04-x86_64 / gcc@5.4.0 -------------------------
- rlsruav trilinos@12.12.1%gcc~alloptpkgs+amesos+amesos2+anasazi+aztec+belos+boost build_type=RelWithDebInfo ~cgns~complex~dtk+epetra+epetraext+exodus+explicit_template_instantiation~float+fortran~fortrilinos+gtest+hdf5+hypre+ifpack+ifpack2~intrepid~intrepid2~isorropia+kokkos+metis~minitensor+ml+muelu+mumps~nox~openmp~phalanx~piro~pnetcdf~python~rol~rythmos+sacado~shards+shared~stk+suite-sparse~superlu~superlu-dist~teko~tempus+teuchos+tpetra~x11~xsdkflags~zlib+zoltan+zoltan2
- kqc52mo trilinos@12.12.1%gcc~alloptpkgs+amesos+amesos2+anasazi+aztec+belos+boost build_type=RelWithDebInfo ~cgns~complex~dtk+epetra+epetraext+exodus+explicit_template_instantiation~float+fortran~fortrilinos+gtest+hdf5+hypre+ifpack+ifpack2~intrepid~intrepid2~isorropia+kokkos+metis~minitensor+ml+muelu+mumps~nox~openmp~phalanx~piro~pnetcdf~python~rol~rythmos+sacado~shards+shared~stk+suite-sparse~superlu~superlu-dist~teko~tempus+teuchos+tpetra~x11~xsdkflags~zlib+zoltan+zoltan2
-
- ==> Error: You can either:
- a) use a more specific spec, or
- b) use `spack uninstall --all` to uninstall ALL matching specs.
-
-
- $ spack uninstall /rlsr
- ==> The following packages will be uninstalled:
-
- -- linux-ubuntu16.04-x86_64 / gcc@5.4.0 -------------------------
- rlsruav trilinos@12.12.1%gcc~alloptpkgs+amesos+amesos2+anasazi+aztec+belos+boost build_type=RelWithDebInfo ~cgns~complex~dtk+epetra+epetraext+exodus+explicit_template_instantiation~float+fortran~fortrilinos+gtest+hdf5+hypre+ifpack+ifpack2~intrepid~intrepid2~isorropia+kokkos+metis~minitensor+ml+muelu+mumps~nox~openmp~phalanx~piro~pnetcdf~python~rol~rythmos+sacado~shards+shared~stk+suite-sparse~superlu~superlu-dist~teko~tempus+teuchos+tpetra~x11~xsdkflags~zlib+zoltan+zoltan2
- ==> Do you want to proceed? [y/N] y
- ==> Successfully uninstalled trilinos@12.12.1%gcc@5.4.0~alloptpkgs+amesos+amesos2+anasazi+aztec+belos+boost build_type=RelWithDebInfo ~cgns~complex~dtk+epetra+epetraext+exodus+explicit_template_instantiation~float+fortran~fortrilinos+gtest+hdf5+hypre+ifpack+ifpack2~intrepid~intrepid2~isorropia+kokkos+metis~minitensor+ml+muelu+mumps~nox~openmp~phalanx~piro~pnetcdf~python~rol~rythmos+sacado~shards+shared~stk+suite-sparse~superlu~superlu-dist~teko~tempus+teuchos+tpetra~x11~xsdkflags~zlib+zoltan+zoltan2 arch=linux-ubuntu16.04-x86_64 /rlsruav
-
------------------------------
-Advanced ``spack find`` Usage
------------------------------
-
-We will go over some additional uses for the ``spack find`` command not
-already covered in the :ref:`basics-tutorial-install` and
-:ref:`basics-tutorial-uninstall` sections.
-
-The ``spack find`` command can accept what we call "anonymous specs."
-These are expressions in spec syntax that do not contain a package
-name. For example, ``spack find ^mpich`` will return every installed
-package that depends on mpich, and ``spack find cppflags="-O3"`` will
-return every package which was built with ``cppflags="-O3"``.
-
-.. code-block:: console
-
- $ spack find ^mpich
- ==> 8 installed packages
- -- linux-ubuntu16.04-x86_64 / gcc@5.4.0 -------------------------
- hdf5@1.10.4 matio@1.5.9 netcdf@4.6.1 parmetis@4.0.3
- hypre@2.15.1 mumps@5.1.1 netlib-scalapack@2.0.2 trilinos@12.12.1
-
- $ spack find cppflags=-O3
- ==> 1 installed packages.
- -- linux-ubuntu16.04-x86_64 / gcc@5.4.0 -------------------------
- zlib@1.2.8
-
-The ``find`` command can also show which packages were installed
-explicitly (rather than pulled in as a dependency) using the ``-x``
-flag. The ``-X`` flag shows implicit installs only. The ``find`` command can
-also show the path to which a spack package was installed using the ``-p``
-command.
-
-.. code-block:: console
-
- $ spack find -px
- ==> 10 installed packages
- -- linux-ubuntu16.04-x86_64 / clang@3.8.0-2ubuntu4 --------------
- zlib@1.2.11 /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/clang-3.8.0-2ubuntu4/zlib-1.2.11-4pt75q7qq6lygf3hgnona4lyc2uwedul
-
- -- linux-ubuntu16.04-x86_64 / gcc@5.4.0 -------------------------
- hdf5@1.10.4 /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/hdf5-1.10.4-5vcv5r67vpjzenq4apyebshclelnzuja
- hdf5@1.10.4 /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/hdf5-1.10.4-ozyvmhzdew66byarohm4p36ep7wtcuiw
- hdf5@1.10.4 /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/hdf5-1.10.4-xxd7syhgej6onpyfyewxqcqe7ltkt7ob
- tcl@8.6.8 /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/tcl-8.6.8-am4pbatrtga3etyusg2akmsvrswwxno2
- tcl@8.6.8 /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/tcl-8.6.8-qhwyccywhx2i6s7ob2gvjrjtj3rnfuqt
- trilinos@12.12.1 /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/trilinos-12.12.1-kqc52moweigxqxzwzfqajc6ocxwdwn4w
- zlib@1.2.8 /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.8-bkyl5bhuep6fmhuxzkmhqy25qefjcvzc
- zlib@1.2.8 /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.8-64mns5mvdacqvlashkf7v6lqrxixhmxu
- zlib@1.2.11 /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb
-
----------------------
-Customizing Compilers
----------------------
-
-
-Spack manages a list of available compilers on the system, detected
-automatically from from the user's ``PATH`` variable. The ``spack
-compilers`` command is an alias for the command ``spack compiler list``.
-
-.. code-block:: console
-
- $ spack compilers
- ==> Available compilers
- -- clang ubuntu16.04-x86_64 -------------------------------------
- clang@3.8.0-2ubuntu4 clang@3.7.1-2ubuntu2
-
- -- gcc ubuntu16.04-x86_64 ---------------------------------------
- gcc@5.4.0 gcc@4.7
-
-The compilers are maintained in a YAML file. Later in the tutorial you
-will learn how to configure compilers by hand for special cases. Spack
-also has tools to add compilers, and compilers built with Spack can be
-added to the configuration.
-
-.. code-block:: console
-
- $ spack install gcc @7.2.0
- ==> libsigsegv is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/libsigsegv-2.11-fypapcprssrj3nstp6njprskeyynsgaz
- ==> m4 is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/m4-1.4.18-suf5jtcfehivwfesrc5hjy72r4nukyel
- ==> pkgconf is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/pkgconf-1.4.2-fovrh7alpft646n6mhis5mml6k6e5f4v
- ==> ncurses is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/ncurses-6.1-3o765ourmesfrji6yeclb4wb5w54aqbh
- ==> readline is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/readline-7.0-nxhwrg7xwc6nbsm2v4ezwe63l6nfidbi
- ==> gdbm is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gdbm-1.14.1-q4fpyuo7ouhkeq6d3oabtrppctpvxmes
- ==> perl is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/perl-5.26.2-ic2kyoadgp3dxfejcbllyplj2wf524fo
- ==> autoconf is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/autoconf-2.69-3sx2gxeibc4oasqd4o5h6lnwpcpsgd2q
- ==> automake is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/automake-1.16.1-rymw7imfehycqxzj4nuy2oiw3abegooy
- ==> libtool is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/libtool-2.4.6-o2pfwjf44353ajgr42xqtvzyvqsazkgu
- ==> Installing gmp
- ==> Searching for binary cache of gmp
- ==> Finding buildcaches in /mirror/build_cache
- ==> Installing gmp from binary cache
- ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/gmp-6.1.2/linux-ubuntu16.04-x86_64-gcc-5.4.0-gmp-6.1.2-qc4qcfz4monpllc3nqupdo7vwinf73sw.spack
- ######################################################################## 100.0%
- gpg: Signature made Sat Nov 10 05:18:16 2018 UTC using RSA key ID 3B7C69B2
- gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
- gpg: WARNING: This key is not certified with a trusted signature!
- gpg: There is no indication that the signature belongs to the owner.
- Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2
- ==> Successfully installed gmp from binary cache
- [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gmp-6.1.2-qc4qcfz4monpllc3nqupdo7vwinf73sw
- ==> Installing isl
- ==> Searching for binary cache of isl
- ==> Installing isl from binary cache
- ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/isl-0.18/linux-ubuntu16.04-x86_64-gcc-5.4.0-isl-0.18-vttqoutnsmjpm3ogb52rninksc7hq5ax.spack
- ######################################################################## 100.0%
- gpg: Signature made Sat Nov 10 05:05:19 2018 UTC using RSA key ID 3B7C69B2
- gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
- gpg: WARNING: This key is not certified with a trusted signature!
- gpg: There is no indication that the signature belongs to the owner.
- Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2
- ==> Successfully installed isl from binary cache
- [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/isl-0.18-vttqoutnsmjpm3ogb52rninksc7hq5ax
- ==> Installing mpfr
- ==> Searching for binary cache of mpfr
- ==> Installing mpfr from binary cache
- ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/mpfr-3.1.6/linux-ubuntu16.04-x86_64-gcc-5.4.0-mpfr-3.1.6-jnt2nnp5pmvikbw7opueajlbwbhmjxyv.spack
- ######################################################################## 100.0%
- gpg: Signature made Sat Nov 10 05:32:07 2018 UTC using RSA key ID 3B7C69B2
- gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
- gpg: WARNING: This key is not certified with a trusted signature!
- gpg: There is no indication that the signature belongs to the owner.
- Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2
- ==> Successfully installed mpfr from binary cache
- [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/mpfr-3.1.6-jnt2nnp5pmvikbw7opueajlbwbhmjxyv
- ==> Installing mpc
- ==> Searching for binary cache of mpc
- ==> Installing mpc from binary cache
- ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/mpc-1.1.0/linux-ubuntu16.04-x86_64-gcc-5.4.0-mpc-1.1.0-iuf3gc3zpgr4n4mditnxhff6x3joxi27.spack
- ######################################################################## 100.0%
- gpg: Signature made Sat Nov 10 05:30:35 2018 UTC using RSA key ID 3B7C69B2
- gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
- gpg: WARNING: This key is not certified with a trusted signature!
- gpg: There is no indication that the signature belongs to the owner.
- Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2
- ==> Successfully installed mpc from binary cache
- [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/mpc-1.1.0-iuf3gc3zpgr4n4mditnxhff6x3joxi27
- ==> zlib is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb
- Installing gcc
- ==> Searching for binary cache of gcc
- ==> Finding buildcaches in /mirror/build_cache
- ==> Installing gcc from binary cache
- ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0/linux-ubuntu16.04-x86_64-gcc-5.4.0-gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs.spack
- ######################################################################## 100.0%
- gpg: Signature made Sat Nov 10 05:22:47 2018 UTC using RSA key ID 3B7C69B2
- gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
- gpg: WARNING: This key is not certified with a trusted signature!
- gpg: There is no indication that the signature belongs to the owner.
- Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F D6E9 9CFA 4A45 3B7C 69B2
- ==> Successfully installed gcc from binary cache
- [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs
-
- $ spack find -p gcc
- spack find -p gcc
- ==> 1 installed package
- -- linux-ubuntu16.04-x86_64 / gcc@5.4.0 -------------------------
- gcc@7.2.0 /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs
-
-We can add gcc to Spack as an available compiler using the ``spack
-compiler add`` command. This will allow future packages to build with
-gcc@7.2.0.
-
-.. code-block:: console
-
- $ spack compiler add `spack location -i gcc@7.2.0`
- ==> Added 1 new compiler to /home/ubuntu/.spack/linux/compilers.yaml
- gcc@7.2.0
- ==> Compilers are defined in the following files:
- /home/ubuntu/.spack/linux/compilers.yaml
-
-We can also remove compilers from our configuration using ``spack compiler remove <compiler_spec>``
-
-.. code-block:: console
-
- $ spack compiler remove gcc@7.2.0
- ==> Removed compiler gcc@7.2.0
diff --git a/lib/spack/docs/tutorial_buildsystems.rst b/lib/spack/docs/tutorial_buildsystems.rst
deleted file mode 100644
index 9f3785e7ee76df77767926168de59cbc9588b1e2..0000000000000000000000000000000000000000
--- a/lib/spack/docs/tutorial_buildsystems.rst
+++ /dev/null
@@ -1,807 +0,0 @@
-.. Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
- Spack Project Developers. See the top-level COPYRIGHT file for details.
-
- SPDX-License-Identifier: (Apache-2.0 OR MIT)
-
-.. _build-systems-tutorial:
-
-==============================
-Spack Package Build Systems
-==============================
-
-You may begin to notice after writing a couple of package template files a
-pattern emerge for some packages. For example, you may find yourself writing
-an :code:`install()` method that invokes: :code:`configure`, :code:`cmake`,
-:code:`make`, :code:`make install`. You may also find yourself writing
-:code:`"prefix=" + prefix` as an argument to :code:`configure` or :code:`cmake`.
-Rather than having you repeat these lines for all packages, Spack has
-classes that can take care of these patterns. In addition,
-these package files allow for finer grained control of these build systems.
-In this section, we will describe each build system and give examples on
-how these can be manipulated to install a package.
-
------------------------
-Package Class Hierarchy
------------------------
-
-.. graphviz::
-
- digraph G {
-
- node [
- shape = "record"
- ]
- edge [
- arrowhead = "empty"
- ]
-
- PackageBase -> Package [dir=back]
- PackageBase -> MakefilePackage [dir=back]
- PackageBase -> AutotoolsPackage [dir=back]
- PackageBase -> CMakePackage [dir=back]
- PackageBase -> PythonPackage [dir=back]
- }
-
-The above diagram gives a high level view of the class hierarchy and how each
-package relates. Each subclass inherits from the :code:`PackageBaseClass`
-super class. The bulk of the work is done in this super class which includes
-fetching, extracting to a staging directory and installing. Each subclass
-then adds additional build-system-specific functionality. In the following
-sections, we will go over examples of how to utilize each subclass and to see
-how powerful these abstractions are when packaging.
-
------------------
-Package
------------------
-
-We've already seen examples of a :code:`Package` class in our walkthrough for writing
-package files, so we won't be spending much time with them here. Briefly,
-the Package class allows for abitrary control over the build process, whereas
-subclasses rely on certain patterns (e.g. :code:`configure` :code:`make`
-:code:`make install`) to be useful. :code:`Package` classes are particularly useful
-for packages that have a non-conventional way of being built since the packager
-can utilize some of Spack's helper functions to customize the building and
-installing of a package.
-
--------------------
-Autotools
--------------------
-
-As we have seen earlier, packages using :code:`Autotools` use :code:`configure`,
-:code:`make` and :code:`make install` commands to execute the build and
-install process. In our :code:`Package` class, your typical build incantation will
-consist of the following:
-
-.. code-block:: python
-
- def install(self, spec, prefix):
- configure("--prefix=" + prefix)
- make()
- make("install")
-
-You'll see that this looks similar to what we wrote in our packaging tutorial.
-
-The :code:`Autotools` subclass aims to simplify writing package files and provides
-convenience methods to manipulate each of the different phases for a :code:`Autotools`
-build system.
-
-:code:`Autotools` packages consist of four phases:
-
-1. :code:`autoreconf()`
-2. :code:`configure()`
-3. :code:`build()`
-4. :code:`install()`
-
-
-Each of these phases have sensible defaults. Let's take a quick look at some
-the internals of the :code:`Autotools` class:
-
-.. code-block:: console
-
- $ spack edit --build-system autotools
-
-
-This will open the :code:`AutotoolsPackage` file in your text editor.
-
-.. note::
- The examples showing code for these classes is abridged to avoid having
- long examples. We only show what is relevant to the packager.
-
-
-.. literalinclude:: _spack_root/lib/spack/spack/build_systems/autotools.py
- :language: python
- :emphasize-lines: 33,36,54
- :lines: 30-76,240-248
- :linenos:
-
-
-Important to note are the highlighted lines. These properties allow the
-packager to set what build targets and install targets they want for their
-package. If, for example, we wanted to add as our build target :code:`foo`
-then we can append to our :code:`build_targets` property:
-
-.. code-block:: python
-
- build_targets = ["foo"]
-
-Which is similiar to invoking make in our Package
-
-.. code-block:: python
-
- make("foo")
-
-This is useful if we have packages that ignore environment variables and need
-a command-line argument.
-
-Another thing to take note of is in the :code:`configure()` method.
-Here we see that the :code:`prefix` argument is already included since it is a
-common pattern amongst packages using :code:`Autotools`. We then only have to
-override :code:`configure_args()`, which will then return it's output to
-to :code:`configure()`. Then, :code:`configure()` will append the common
-arguments
-
-Packagers also have the option to run :code:`autoreconf` in case a package
-needs to update the build system and generate a new :code:`configure`. Though,
-for the most part this will be unnecessary.
-
-Let's look at the :code:`mpileaks` package.py file that we worked on earlier:
-
-.. code-block:: console
-
- $ spack edit mpileaks
-
-Notice that mpileaks is a :code:`Package` class but uses the :code:`Autotools`
-build system. Although this package is acceptable let's make this into an
-:code:`AutotoolsPackage` class and simplify it further.
-
-.. literalinclude:: tutorial/examples/Autotools/0.package.py
- :language: python
- :emphasize-lines: 9
- :linenos:
-
-We first inherit from the :code:`AutotoolsPackage` class.
-
-
-Although we could keep the :code:`install()` method, most of it can be handled
-by the :code:`AutotoolsPackage` base class. In fact, the only thing that needs
-to be overridden is :code:`configure_args()`.
-
-.. literalinclude:: tutorial/examples/Autotools/1.package.py
- :language: python
- :emphasize-lines: 25,26,27,28,29,30,31,32
- :linenos:
-
-Since Spack takes care of setting the prefix for us we can exclude that as
-an argument to :code:`configure`. Our packages look simpler, and the packager
-does not need to worry about whether they have properly included :code:`configure`
-and :code:`make`.
-
-This version of the :code:`mpileaks` package installs the same as the previous,
-but the :code:`AutotoolsPackage` class lets us do it with a cleaner looking
-package file.
-
------------------
-Makefile
------------------
-
-Packages that utilize :code:`Make` or a :code:`Makefile` usually require you
-to edit a :code:`Makefile` to set up platform and compiler specific variables.
-These packages are handled by the :code:`Makefile` subclass which provides
-convenience methods to help write these types of packages.
-
-A :code:`MakefilePackage` class has three phases that can be overridden. These include:
-
- 1. :code:`edit()`
- 2. :code:`build()`
- 3. :code:`install()`
-
-Packagers then have the ability to control how a :code:`Makefile` is edited, and
-what targets to include for the build phase or install phase.
-
-Let's also take a look inside the :code:`MakefilePackage` class:
-
-.. code-block:: console
-
- $ spack edit --build-system makefile
-
-Take note of the following:
-
-
-.. literalinclude:: _spack_root/lib/spack/spack/build_systems/makefile.py
- :language: python
- :lines: 14,43-61,70-88
- :emphasize-lines: 21,27,34
- :linenos:
-
-Similar to :code:`Autotools`, :code:`MakefilePackage` class has properties
-that can be set by the packager. We can also override the different
-methods highlighted.
-
-
-Let's try to recreate the Bowtie_ package:
-
-.. _Bowtie: http://bowtie-bio.sourceforge.net/index.shtml
-
-
-.. code-block:: console
-
- $ spack create -f https://downloads.sourceforge.net/project/bowtie-bio/bowtie/1.2.1.1/bowtie-1.2.1.1-src.zip
- ==> This looks like a URL for bowtie
- ==> Found 1 version of bowtie:
-
- 1.2.1.1 https://downloads.sourceforge.net/project/bowtie-bio/bowtie/1.2.1.1/bowtie-1.2.1.1-src.zip
-
- ==> How many would you like to checksum? (default is 1, q to abort) 1
- ==> Downloading...
- ==> Fetching https://downloads.sourceforge.net/project/bowtie-bio/bowtie/1.2.1.1/bowtie-1.2.1.1-src.zip
- ######################################################################## 100.0%
- ==> Checksummed 1 version of bowtie
- ==> This package looks like it uses the makefile build system
- ==> Created template for bowtie package
- ==> Created package file: /Users/mamelara/spack/var/spack/repos/builtin/packages/bowtie/package.py
-
-Once the fetching is completed, Spack will open up your text editor in the
-usual fashion and create a template of a :code:`MakefilePackage` package.py.
-
-.. literalinclude:: tutorial/examples/Makefile/0.package.py
- :language: python
- :linenos:
-
-Spack was successfully able to detect that :code:`Bowtie` uses :code:`Make`.
-Let's add in the rest of our details for our package:
-
-.. literalinclude:: tutorial/examples/Makefile/1.package.py
- :language: python
- :emphasize-lines: 10,11,13,14,18,20
- :linenos:
-
-As we mentioned earlier, most packages using a :code:`Makefile` have hard-coded
-variables that must be edited. These variables are fine if you happen to not
-care about setup or types of compilers used but Spack is designed to work with
-any compiler. The :code:`MakefilePackage` subclass makes it easy to edit
-these :code:`Makefiles` by having an :code:`edit()` method that
-can be overridden.
-
-Let's take a look at the default :code:`Makefile` that :code:`Bowtie` provides.
-If we look inside, we see that :code:`CC` and :code:`CXX` point to our GNU
-compiler:
-
-.. code-block:: console
-
- $ spack stage bowtie
-
-.. note::
- As usual make sure you have shell support activated with spack:
- :code:`source /path/to/spack_root/spack/share/spack/setup-env.sh`
-
-.. code-block:: console
-
- $ spack cd -s bowtie
- $ cd bowtie-1.2
- $ vim Makefile
-
-
-.. code-block:: make
-
- CPP = g++ -w
- CXX = $(CPP)
- CC = gcc
- LIBS = $(LDFLAGS) -lz
- HEADERS = $(wildcard *.h)
-
-To fix this, we need to use the :code:`edit()` method to write our custom
-:code:`Makefile`.
-
-.. literalinclude:: tutorial/examples/Makefile/2.package.py
- :language: python
- :emphasize-lines: 23,24,25
- :linenos:
-
-Here we use a :code:`FileFilter` object to edit our :code:`Makefile`. It takes
-in a regular expression and then replaces :code:`CC` and :code:`CXX` to whatever
-Spack sets :code:`CC` and :code:`CXX` environment variables to. This allows us to
-build :code:`Bowtie` with whatever compiler we specify through Spack's
-:code:`spec` syntax.
-
-Let's change the build and install phases of our package:
-
-.. literalinclude:: tutorial/examples/Makefile/3.package.py
- :language: python
- :emphasize-lines: 28,29,30,31,32,35,36
- :linenos:
-
-Here demonstrate another strategy that we can use to manipulate our package
-We can provide command-line arguments to :code:`make()`. Since :code:`Bowtie`
-can use :code:`tbb` we can either add :code:`NO_TBB=1` as a argument to prevent
-:code:`tbb` support or we can just invoke :code:`make` with no arguments.
-
-:code:`Bowtie` requires our :code:`install_target` to provide a path to
-the install directory. We can do this by providing :code:`prefix=` as a command
-line argument to :code:`make()`.
-
-Let's look at a couple of other examples and go through them:
-
-.. code-block:: console
-
- $ spack edit esmf
-
-Some packages allow environment variables to be set and will honor them.
-Packages that use :code:`?=` for assignment in their :code:`Makefile`
-can be set using environment variables. In our :code:`esmf` example we
-set two environment variables in our :code:`edit()` method:
-
-.. code-block:: python
-
- def edit(self, spec, prefix):
- for var in os.environ:
- if var.startswith('ESMF_'):
- os.environ.pop(var)
-
- # More code ...
-
- if self.compiler.name == 'gcc':
- os.environ['ESMF_COMPILER'] = 'gfortran'
- elif self.compiler.name == 'intel':
- os.environ['ESMF_COMPILER'] = 'intel'
- elif self.compiler.name == 'clang':
- os.environ['ESMF_COMPILER'] = 'gfortranclang'
- elif self.compiler.name == 'nag':
- os.environ['ESMF_COMPILER'] = 'nag'
- elif self.compiler.name == 'pgi':
- os.environ['ESMF_COMPILER'] = 'pgi'
- else:
- msg = "The compiler you are building with, "
- msg += "'{0}', is not supported by ESMF."
- raise InstallError(msg.format(self.compiler.name))
-
-As you may have noticed, we didn't really write anything to the :code:`Makefile`
-but rather we set environment variables that will override variables set in
-the :code:`Makefile`.
-
-Some packages include a configuration file that sets certain compiler variables,
-platform specific variables, and the location of dependencies or libraries.
-If the file is simple and only requires a couple of changes, we can overwrite
-those entries with our :code:`FileFilter` object. If the configuration involves
-complex changes, we can write a new configuration file from scratch.
-
-Let's look at an example of this in the :code:`elk` package:
-
-.. code-block:: console
-
- $ spack edit elk
-
-.. code-block:: python
-
- def edit(self, spec, prefix):
- # Dictionary of configuration options
- config = {
- 'MAKE': 'make',
- 'AR': 'ar'
- }
-
- # Compiler-specific flags
- flags = ''
- if self.compiler.name == 'intel':
- flags = '-O3 -ip -unroll -no-prec-div'
- elif self.compiler.name == 'gcc':
- flags = '-O3 -ffast-math -funroll-loops'
- elif self.compiler.name == 'pgi':
- flags = '-O3 -lpthread'
- elif self.compiler.name == 'g95':
- flags = '-O3 -fno-second-underscore'
- elif self.compiler.name == 'nag':
- flags = '-O4 -kind=byte -dusty -dcfuns'
- elif self.compiler.name == 'xl':
- flags = '-O3'
- config['F90_OPTS'] = flags
- config['F77_OPTS'] = flags
-
- # BLAS/LAPACK support
- # Note: BLAS/LAPACK must be compiled with OpenMP support
- # if the +openmp variant is chosen
- blas = 'blas.a'
- lapack = 'lapack.a'
- if '+blas' in spec:
- blas = spec['blas'].libs.joined()
- if '+lapack' in spec:
- lapack = spec['lapack'].libs.joined()
- # lapack must come before blas
- config['LIB_LPK'] = ' '.join([lapack, blas])
-
- # FFT support
- if '+fft' in spec:
- config['LIB_FFT'] = join_path(spec['fftw'].prefix.lib,
- 'libfftw3.so')
- config['SRC_FFT'] = 'zfftifc_fftw.f90'
- else:
- config['LIB_FFT'] = 'fftlib.a'
- config['SRC_FFT'] = 'zfftifc.f90'
-
- # MPI support
- if '+mpi' in spec:
- config['F90'] = spec['mpi'].mpifc
- config['F77'] = spec['mpi'].mpif77
- else:
- config['F90'] = spack_fc
- config['F77'] = spack_f77
- config['SRC_MPI'] = 'mpi_stub.f90'
-
- # OpenMP support
- if '+openmp' in spec:
- config['F90_OPTS'] += ' ' + self.compiler.openmp_flag
- config['F77_OPTS'] += ' ' + self.compiler.openmp_flag
- else:
- config['SRC_OMP'] = 'omp_stub.f90'
-
- # Libxc support
- if '+libxc' in spec:
- config['LIB_libxc'] = ' '.join([
- join_path(spec['libxc'].prefix.lib, 'libxcf90.so'),
- join_path(spec['libxc'].prefix.lib, 'libxc.so')
- ])
- config['SRC_libxc'] = ' '.join([
- 'libxc_funcs.f90',
- 'libxc.f90',
- 'libxcifc.f90'
- ])
- else:
- config['SRC_libxc'] = 'libxcifc_stub.f90'
-
- # Write configuration options to include file
- with open('make.inc', 'w') as inc:
- for key in config:
- inc.write('{0} = {1}\n'.format(key, config[key]))
-
-:code:`config` is just a dictionary that we can add key-value pairs to. By the
-end of the :code:`edit()` method we write the contents of our dictionary to
-:code:`make.inc`.
-
----------------
-CMake
----------------
-
-CMake_ is another common build system that has been gaining popularity. It works
-in a similar manner to :code:`Autotools` but with differences in variable names,
-the number of configuration options available, and the handling of shared libraries.
-Typical build incantations look like this:
-
-.. _CMake: https://cmake.org
-
-.. code-block:: python
-
- def install(self, spec, prefix):
- cmake("-DCMAKE_INSTALL_PREFIX:PATH=/path/to/install_dir ..")
- make()
- make("install")
-
-As you can see from the example above, it's very similar to invoking
-:code:`configure` and :code:`make` in an :code:`Autotools` build system. However,
-the variable names and options differ. Most options in CMake are prefixed
-with a :code:`'-D'` flag to indicate a configuration setting.
-
-In the :code:`CMakePackage` class we can override the following phases:
-
-1. :code:`cmake()`
-2. :code:`build()`
-3. :code:`install()`
-
-The :code:`CMakePackage` class also provides sensible defaults so we only need to
-override :code:`cmake_args()`.
-
-Let's look at these defaults in the :code:`CMakePackage` class in the :code:`_std_args()` method:
-
-.. code-block:: console
-
- $ spack edit --build-system cmake
-
-.. literalinclude:: _spack_root/lib/spack/spack/build_systems/cmake.py
- :language: python
- :lines: 102-147
- :emphasize-lines: 10,18,24,36,37,38,44
- :linenos:
-
-Some :code:`CMake` packages use different generators. Spack is able to support
-Unix-Makefile_ generators as well as Ninja_ generators.
-
-.. _Unix-Makefile: https://cmake.org/cmake/help/v3.4/generator/Unix%20Makefiles.html
-.. _Ninja: https://cmake.org/cmake/help/v3.4/generator/Ninja.html
-
-If no generator is specified Spack will default to :code:`Unix Makefiles`.
-
-Next we setup the build type. In :code:`CMake` you can specify the build type
-that you want. Options include:
-
-1. :code:`empty`
-2. :code:`Debug`
-3. :code:`Release`
-4. :code:`RelWithDebInfo`
-5. :code:`MinSizeRel`
-
-With these options you can specify whether you want your executable to have
-the debug version only, release version or the release with debug information.
-Release executables tend to be more optimized than Debug. In Spack, we set
-the default as RelWithDebInfo unless otherwise specified through a variant.
-
-Spack then automatically sets up the :code:`-DCMAKE_INSTALL_PREFIX` path,
-appends the build type (:code:`RelWithDebInfo` default), and then specifies a verbose
-:code:`Makefile`.
-
-Next we add the :code:`rpaths` to :code:`-DCMAKE_INSTALL_RPATH:STRING`.
-
-
-Finally we add to :code:`-DCMAKE_PREFIX_PATH:STRING` the locations of all our
-dependencies so that :code:`CMake` can find them.
-
-In the end our :code:`cmake` line will look like this (example is :code:`xrootd`):
-
-.. code-block:: console
-
- $ cmake $HOME/spack/var/spack/stage/xrootd-4.6.0-4ydm74kbrp4xmcgda5upn33co5pwddyk/xrootd-4.6.0 -G Unix Makefiles -DCMAKE_INSTALL_PREFIX:PATH=$HOME/spack/opt/spack/darwin-sierra-x86_64/clang-9.0.0-apple/xrootd-4.6.0-4ydm74kbrp4xmcgda5upn33co5pwddyk -DCMAKE_BUILD_TYPE:STRING=RelWithDebInfo -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON -DCMAKE_FIND_FRAMEWORK:STRING=LAST -DCMAKE_INSTALL_RPATH_USE_LINK_PATH:BOOL=FALSE -DCMAKE_INSTALL_RPATH:STRING=$HOME/spack/opt/spack/darwin-sierra-x86_64/clang-9.0.0-apple/xrootd-4.6.0-4ydm74kbrp4xmcgda5upn33co5pwddyk/lib:$HOME/spack/opt/spack/darwin-sierra-x86_64/clang-9.0.0-apple/xrootd-4.6.0-4ydm74kbrp4xmcgda5upn33co5pwddyk/lib64 -DCMAKE_PREFIX_PATH:STRING=$HOME/spack/opt/spack/darwin-sierra-x86_64/clang-9.0.0-apple/cmake-3.9.4-hally3vnbzydiwl3skxcxcbzsscaasx5
-
-We can see now how :code:`CMake` takes care of a lot of the boilerplate code
-that would have to be otherwise typed in.
-
-Let's try to recreate callpath_:
-
-.. _callpath: https://github.com/LLNL/callpath.git
-
-.. code-block:: console
-
- $ spack create -f https://github.com/llnl/callpath/archive/v1.0.3.tar.gz
- ==> This looks like a URL for callpath
- ==> Found 4 versions of callpath:
-
- 1.0.3 https://github.com/LLNL/callpath/archive/v1.0.3.tar.gz
- 1.0.2 https://github.com/LLNL/callpath/archive/v1.0.2.tar.gz
- 1.0.1 https://github.com/LLNL/callpath/archive/v1.0.1.tar.gz
- 1.0 https://github.com/LLNL/callpath/archive/v1.0.tar.gz
-
- ==> How many would you like to checksum? (default is 1, q to abort) 1
- ==> Downloading...
- ==> Fetching https://github.com/LLNL/callpath/archive/v1.0.3.tar.gz
- ######################################################################## 100.0%
- ==> Checksummed 1 version of callpath
- ==> This package looks like it uses the cmake build system
- ==> Created template for callpath package
- ==> Created package file: /Users/mamelara/spack/var/spack/repos/builtin/packages/callpath/package.py
-
-
-which then produces the following template:
-
-.. literalinclude:: tutorial/examples/Cmake/0.package.py
- :language: python
- :linenos:
-
-Again we fill in the details:
-
-.. literalinclude:: tutorial/examples/Cmake/1.package.py
- :language: python
- :linenos:
- :emphasize-lines: 9,13,14,18,19,20,21,22,23
-
-As mentioned earlier, Spack will use sensible defaults to prevent repeated code
-and to make writing :code:`CMake` package files simpler.
-
-In callpath, we want to add options to :code:`CALLPATH_WALKER` as well as add
-compiler flags. We add the following options like so:
-
-.. literalinclude:: tutorial/examples/Cmake/2.package.py
- :language: python
- :linenos:
- :emphasize-lines: 26,30,31
-
-Now we can control our build options using :code:`cmake_args()`. If defaults are
-sufficient enough for the package, we can leave this method out.
-
-:code:`CMakePackage` classes allow for control of other features in the
-build system. For example, you can specify the path to the "out of source"
-build directory and also point to the root of the :code:`CMakeLists.txt` file if it
-is placed in a non-standard location.
-
-A good example of a package that has its :code:`CMakeLists.txt` file located at a
-different location is found in :code:`spades`.
-
-.. code-block:: console
-
- $ spack edit spades
-
-.. code-block:: python
-
- root_cmakelists_dir = "src"
-
-Here :code:`root_cmakelists_dir` will tell Spack where to find the location
-of :code:`CMakeLists.txt`. In this example, it is located a directory level below in
-the :code:`src` directory.
-
-Some :code:`CMake` packages also require the :code:`install` phase to be
-overridden. For example, let's take a look at :code:`sniffles`.
-
-.. code-block:: console
-
- $ spack edit sniffles
-
-In the :code:`install()` method, we have to manually install our targets
-so we override the :code:`install()` method to do it for us:
-
-.. code-block:: python
-
- # the build process doesn't actually install anything, do it by hand
- def install(self, spec, prefix):
- mkdir(prefix.bin)
- src = "bin/sniffles-core-{0}".format(spec.version.dotted)
- binaries = ['sniffles', 'sniffles-debug']
- for b in binaries:
- install(join_path(src, b), join_path(prefix.bin, b))
-
-
---------------
-PythonPackage
---------------
-
-Python extensions and modules are built differently from source than most
-applications. Python uses a :code:`setup.py` script to install Python modules.
-The script consists of a call to :code:`setup()` which provides the information
-required to build a module to Distutils. If you're familiar with pip or
-easy_install, setup.py does the same thing.
-
-These modules are usually installed using the following line:
-
-.. code-block:: console
-
- $ python setup.py install
-
-There are also a list of commands and phases that you can call. To see the full
-list you can run:
-
-.. code-block:: console
-
- $ python setup.py --help-commands
- Standard commands:
- build build everything needed to install
- build_py "build" pure Python modules (copy to build directory)
- build_ext build C/C++ extensions (compile/link to build directory)
- build_clib build C/C++ libraries used by Python extensions
- build_scripts "build" scripts (copy and fixup #! line)
- clean (no description available)
- install install everything from build directory
- install_lib install all Python modules (extensions and pure Python)
- install_headers install C/C++ header files
- install_scripts install scripts (Python or otherwise)
- install_data install data files
- sdist create a source distribution (tarball, zip file, etc.)
- register register the distribution with the Python package index
- bdist create a built (binary) distribution
- bdist_dumb create a "dumb" built distribution
- bdist_rpm create an RPM distribution
- bdist_wininst create an executable installer for MS Windows
- upload upload binary package to PyPI
- check perform some checks on the package
-
-
-We can write package files for Python packages using the :code:`Package` class,
-but the class brings with it a lot of methods that are useless for Python packages.
-Instead, Spack has a :code:`PythonPackage` subclass that allows packagers
-of Python modules to be able to invoke :code:`setup.py` and use :code:`Distutils`,
-which is much more familiar to a typical python user.
-
-To see the defaults that Spack has for each a methods, we will take a look
-at the :code:`PythonPackage` class:
-
-.. code-block:: console
-
- $ spack edit --build-system python
-
-We see the following:
-
-
-.. literalinclude:: _spack_root/lib/spack/spack/build_systems/python.py
- :language: python
- :lines: 19,146-357
- :linenos:
-
-Each of these methods have sensible defaults or they can be overridden.
-
-We will write a package file for Pandas_:
-
-.. _pandas: https://pandas.pydata.org
-
-.. code-block:: console
-
- $ spack create -f https://pypi.io/packages/source/p/pandas/pandas-0.19.0.tar.gz
- ==> This looks like a URL for pandas
- ==> Warning: Spack was unable to fetch url list due to a certificate verification problem. You can try running spack -k, which will not check SSL certificates. Use this at your own risk.
- ==> Found 1 version of pandas:
-
- 0.19.0 https://pypi.io/packages/source/p/pandas/pandas-0.19.0.tar.gz
-
- ==> How many would you like to checksum? (default is 1, q to abort) 1
- ==> Downloading...
- ==> Fetching https://pypi.io/packages/source/p/pandas/pandas-0.19.0.tar.gz
- ######################################################################## 100.0%
- ==> Checksummed 1 version of pandas
- ==> This package looks like it uses the python build system
- ==> Changing package name from pandas to py-pandas
- ==> Created template for py-pandas package
- ==> Created package file: /Users/mamelara/spack/var/spack/repos/builtin/packages/py-pandas/package.py
-
-And we are left with the following template:
-
-.. literalinclude:: tutorial/examples/PyPackage/0.package.py
- :language: python
- :linenos:
-
-As you can see this is not any different than any package template that we have
-written. We have the choice of providing build options or using the sensible
-defaults
-
-Luckily for us, there is no need to provide build args.
-
-Next we need to find the dependencies of a package. Dependencies are usually
-listed in :code:`setup.py`. You can find the dependencies by searching for
-:code:`install_requires` keyword in that file. Here it is for :code:`Pandas`:
-
-.. code-block:: python
-
- # ... code
- if sys.version_info[0] >= 3:
-
- setuptools_kwargs = {
- 'zip_safe': False,
- 'install_requires': ['python-dateutil >= 2',
- 'pytz >= 2011k',
- 'numpy >= %s' % min_numpy_ver],
- 'setup_requires': ['numpy >= %s' % min_numpy_ver],
- }
- if not _have_setuptools:
- sys.exit("need setuptools/distribute for Py3k"
- "\n$ pip install distribute")
-
- # ... more code
-
-You can find a more comprehensive list at the Pandas documentation_.
-
-.. _documentation: https://pandas.pydata.org/pandas-docs/stable/install.html
-
-
-By reading the documentation and :code:`setup.py` we found that :code:`Pandas`
-depends on :code:`python-dateutil`, :code:`pytz`, and :code:`numpy`, :code:`numexpr`,
-and finally :code:`bottleneck`.
-
-Here is the completed :code:`Pandas` script:
-
-.. literalinclude:: tutorial/examples/PyPackage/1.package.py
- :language: python
- :linenos:
-
-It is quite important to declare all the dependencies of a Python package.
-Spack can "activate" Python packages to prevent the user from having to
-load each dependency module explictly. If a dependency is missed, Spack will
-be unable to properly activate the package and it will cause an issue. To
-learn more about extensions go to :ref:`cmd-spack-extensions`.
-
-From this example, you can see that building Python modules is made easy
-through the :code:`PythonPackage` class.
-
--------------------
-Other Build Systems
--------------------
-
-Although we won't get in depth with any of the other build systems that Spack
-supports, it is worth mentioning that Spack does provide subclasses
-for the following build systems:
-
-1. :code:`IntelPackage`
-2. :code:`SconsPackage`
-3. :code:`WafPackage`
-4. :code:`RPackage`
-5. :code:`PerlPackage`
-6. :code:`QMakePackage`
-
-
-Each of these classes have their own abstractions to help assist in writing
-package files. For whatever doesn't fit nicely into the other build-systems,
-you can use the :code:`Package` class.
-
-Hopefully by now you can see how we aim to make packaging simple and
-robust through these classes. If you want to learn more about these build
-systems, check out :ref:`installation_procedure` in the Packaging Guide.
diff --git a/lib/spack/docs/tutorial_configuration.rst b/lib/spack/docs/tutorial_configuration.rst
deleted file mode 100644
index 879bb949670b713252cc094013851fcb5a97cffa..0000000000000000000000000000000000000000
--- a/lib/spack/docs/tutorial_configuration.rst
+++ /dev/null
@@ -1,951 +0,0 @@
-.. Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
- Spack Project Developers. See the top-level COPYRIGHT file for details.
-
- SPDX-License-Identifier: (Apache-2.0 OR MIT)
-
-.. _configs-tutorial:
-
-======================
-Configuration Tutorial
-======================
-
-This tutorial will guide you through various configuration options
-that allow you to customize Spack's behavior with respect to
-software installation. We will first cover the configuration file
-hierarchy. Then, we will cover configuration options for compilers,
-focusing on how they can be used to extend Spack's compiler auto-detection.
-Next, we will cover the packages configuration file, focusing on
-how it can be used to override default build options as well as
-specify external package installations to use. Finally, we will
-briefly touch on the config configuration file, which manages more
-high-level Spack configuration options.
-
-For all of these features, we will demonstrate how we build up a full
-configuration file. For some, we will then demonstrate how the
-configuration affects the install command, and for others we will use
-the ``spack spec`` command to demonstrate how the configuration
-changes have affected Spack's concretization algorithm. The provided
-output is all from a server running Ubuntu version 16.04.
-
-.. _configs-tutorial-scopes:
-
---------------------
-Configuration Scopes
---------------------
-
-Depending on your use case, you may want to provide configuration
-settings common to everyone on your team, or you may want to set
-default behaviors specific to a single user account. Spack provides
-six configuration *scopes* to handle this customization. These scopes,
-in order of decreasing priority, are:
-
-============ ===================================================
-Scope Directory
-============ ===================================================
-Command-line N/A
-Custom Custom directory, specified with ``--config-scope``
-User ``~/.spack/``
-Site ``$SPACK_ROOT/etc/spack/``
-System ``/etc/spack/``
-Defaults ``$SPACK_ROOT/etc/spack/defaults/``
-============ ===================================================
-
-Spack's default configuration settings reside in
-``$SPACK_ROOT/etc/spack/defaults``. These are useful for reference,
-but should never be directly edited. To override these settings,
-create new configuration files in any of the higher-priority
-configuration scopes.
-
-A particular cluster may have multiple Spack installations associated
-with different projects. To provide settings common to all Spack
-installations, put your configuration files in ``/etc/spack``.
-To provide settings specific to a particular Spack installation,
-you can use the ``$SPACK_ROOT/etc/spack`` directory.
-
-For settings specific to a particular user, you will want to add
-configuration files to the ``~/.spack`` directory. When Spack first
-checked for compilers on your system, you may have noticed that it
-placed your compiler configuration in this directory.
-
-Configuration settings can also be placed in a custom location,
-which is then specified on the command line via ``--config-scope``.
-An example use case is managing two sets of configurations, one for
-development and another for production preferences.
-
-Settings specified on the command line have precedence over all
-other configuration scopes.
-
-You can also use ``spack config blame <config>`` for displaying
-the effective configuration. Spack will show from which scopes
-the configuration has been assembled.
-
-^^^^^^^^^^^^^^^^^^^^^^^^
-Platform-specific Scopes
-^^^^^^^^^^^^^^^^^^^^^^^^
-
-Some facilities manage multiple platforms from a single shared
-file system. In order to handle this, each of the configuration
-scopes listed above has two *sub-scopes*: platform-specific and
-platform-independent. For example, compiler settings can be stored
-in ``compilers.yaml`` configuration files in the following locations:
-
-#. ``~/.spack/<platform>/compilers.yaml``
-#. ``~/.spack/compilers.yaml``
-#. ``$SPACK_ROOT/etc/spack/<platform>/compilers.yaml``
-#. ``$SPACK_ROOT/etc/spack/compilers.yaml``
-#. ``/etc/spack/<platform>/compilers.yaml``
-#. ``/etc/spack/compilers.yaml``
-#. ``$SPACK_ROOT/etc/defaults/<platform>/compilers.yaml``
-#. ``$SPACK_ROOT/etc/defaults/compilers.yaml``
-
-These files are listed in decreasing order of precedence, so files in
-``~/.spack/<platform>`` will override settings in ``~/.spack``.
-
------------
-YAML Format
------------
-
-Spack configurations are YAML dictionaries. Every configuration file
-begins with a top-level dictionary that tells Spack which
-configuration set it modifies. When Spack checks its configuration,
-the configuration scopes are updated as dictionaries in increasing
-order of precedence, allowing higher precedence files to override
-lower. YAML dictionaries use a colon ":" to specify key-value
-pairs. Spack extends YAML syntax slightly to allow a double-colon
-"::" to specify a key-value pair. When a double-colon is used to
-specify a key-value pair, instead of adding that section, Spack
-replaces what was in that section with the new value. For example,
-consider a user's compilers configuration file as follows:
-
-.. code-block:: yaml
-
- compilers::
- - compiler:
- environment: {}
- extra_rpaths: []
- flags: {}
- modules: []
- operating_system: ubuntu16.04
- paths:
- cc: /usr/bin/gcc
- cxx: /usr/bin/g++
- f77: /usr/bin/gfortran
- fc: /usr/bin/gfortran
- spec: gcc@5.4.0
- target: x86_64
-
-
-This ensures that no other compilers are used, as the user configuration
-scope is the last scope searched and the ``compilers::`` line replaces
-all previous configuration files information. If the same
-configuration file had a single colon instead of the double colon, it
-would add the GCC version 5.4.0 compiler to whatever other compilers
-were listed in other configuration files.
-
-.. _configs-tutorial-compilers:
-
-----------------------
-Compiler Configuration
-----------------------
-
-For most tasks, we can use Spack with the compilers auto-detected the
-first time Spack runs on a system. As discussed in the basic
-installation tutorial, we can also tell Spack where compilers are
-located using the ``spack compiler add`` command. However, in some
-circumstances we want even more fine-grained control over the
-compilers available. This section will teach you how to exercise that
-control using the compilers configuration file.
-
-We will start by opening the compilers configuration file:
-
-.. code-block:: console
-
- $ spack config edit compilers
-
-
-.. code-block:: yaml
-
- compilers:
- - compiler:
- environment: {}
- extra_rpaths: []
- flags: {}
- modules: []
- operating_system: ubuntu16.04
- paths:
- cc: /usr/bin/clang-3.7
- cxx: /usr/bin/clang++-3.7
- f77: null
- fc: null
- spec: clang@3.7.1-2ubuntu2
- target: x86_64
- - compiler:
- environment: {}
- extra_rpaths: []
- flags: {}
- modules: []
- operating_system: ubuntu16.04
- paths:
- cc: /usr/bin/clang
- cxx: /usr/bin/clang++
- f77: null
- fc: null
- spec: clang@3.8.0-2ubuntu4
- target: x86_64
- - compiler:
- environment: {}
- extra_rpaths: []
- flags: {}
- modules: []
- operating_system: ubuntu16.04
- paths:
- cc: /usr/bin/gcc-4.7
- cxx: /usr/bin/g++-4.7
- f77: /usr/bin/gfortran-4.7
- fc: /usr/bin/gfortran-4.7
- spec: gcc@4.7
- target: x86_64
- - compiler:
- environment: {}
- extra_rpaths: []
- flags: {}
- modules: []
- operating_system: ubuntu16.04
- paths:
- cc: /usr/bin/gcc
- cxx: /usr/bin/g++
- f77: /usr/bin/gfortran
- fc: /usr/bin/gfortran
- spec: gcc@5.4.0
- target: x86_64
-
-
-This specifies two versions of the GCC compiler and two versions of the
-Clang compiler with no Flang compiler. Now suppose we have a code that
-we want to compile with the Clang compiler for C/C++ code, but with
-gfortran for Fortran components. We can do this by adding another entry
-to the ``compilers.yaml`` file.
-
-.. code-block:: yaml
-
- - compiler:
- environment: {}
- extra_rpaths: []
- flags: {}
- modules: []
- operating_system: ubuntu16.04
- paths:
- cc: /usr/bin/clang
- cxx: /usr/bin/clang++
- f77: /usr/bin/gfortran
- fc: /usr/bin/gfortran
- spec: clang@3.8.0-gfortran
- target: x86_64
-
-
-Let's talk about the sections of this compiler entry that we've changed.
-The biggest change we've made is to the ``paths`` section. This lists
-the paths to the compilers to use for each language/specification.
-In this case, we point to the Clang compiler for C/C++ and the gfortran
-compiler for both specifications of Fortran. We've also changed the
-``spec`` entry for this compiler. The ``spec`` entry is effectively the
-name of the compiler for Spack. It consists of a name and a version
-number, separated by the ``@`` sigil. The name must be one of the supported
-compiler names in Spack (gcc, intel, pgi, xl, xl_r, clang, nag, cce, arm).
-The version number can be an arbitrary string of alphanumeric characters,
-as well as ``-``, ``.``, and ``_``. The ``target`` and ``operating_system``
-sections we leave unchanged. These sections specify when Spack can use
-different compilers, and are primarily useful for configuration files that
-will be used across multiple systems.
-
-We can verify that our new compiler works by invoking it now:
-
-.. code-block:: console
-
- $ spack install --no-cache zlib %clang@3.8.0-gfortran
- ...
-
-
-This new compiler also works on Fortran codes:
-
-.. code-block:: console
-
- $ spack install --no-cache cfitsio~bzip2 %clang@3.8.0-gfortran
- ...
-
-
-^^^^^^^^^^^^^^
-Compiler Flags
-^^^^^^^^^^^^^^
-
-Some compilers may require specific compiler flags to work properly in
-a particular computing environment. Spack provides configuration
-options for setting compiler flags every time a specific compiler is
-invoked. These flags become part of the package spec and therefore of
-the build provenance. As on the command line, the flags are set
-through the implicit build variables ``cflags``, ``cxxflags``, ``cppflags``,
-``fflags``, ``ldflags``, and ``ldlibs``.
-
-Let's open our compilers configuration file again and add a compiler flag:
-
-.. code-block:: yaml
-
- - compiler:
- environment: {}
- extra_rpaths: []
- flags:
- cppflags: -g
- modules: []
- operating_system: ubuntu16.04
- paths:
- cc: /usr/bin/clang
- cxx: /usr/bin/clang++
- f77: /usr/bin/gfortran
- fc: /usr/bin/gfortran
- spec: clang@3.8.0-gfortran
- target: x86_64
-
-
-We can test this out using the ``spack spec`` command to show how the
-spec is concretized:
-
-.. code-block:: console
-
- $ spack spec cfitsio %clang@3.8.0-gfortran
- Input spec
- --------------------------------
- cfitsio%clang@3.8.0-gfortran
-
- Normalized
- --------------------------------
- cfitsio%clang@3.8.0-gfortran
-
- Concretized
- --------------------------------
- cfitsio@3.410%clang@3.8.0-gfortran cppflags="-g" +bzip2+shared arch=linux-ubuntu16.04-x86_64
- ^bzip2@1.0.6%clang@3.8.0-gfortran cppflags="-g" +shared arch=linux-ubuntu16.04-x86_64
-
-
-We can see that ``cppflags="-g"`` has been added to every node in the DAG.
-
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-Advanced Compiler Configuration
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-There are three fields of the compiler configuration entry that we
-have not yet talked about.
-
-The ``modules`` field of the compiler is used primarily on Cray systems,
-but can be useful on any system that has compilers that are only
-useful when a particular module is loaded. Any modules in the
-``modules`` field of the compiler configuration will be loaded as part
-of the build environment for packages using that compiler.
-
-The ``extra_rpaths`` field of the compiler configuration is used for
-compilers that do not rpath all of their dependencies by
-default. Since compilers are often installed externally to Spack,
-Spack is unable to manage compiler dependencies and enforce
-rpath usage. This can lead to packages not finding link dependencies
-imposed by the compiler properly. For compilers that impose link
-dependencies on the resulting executables that are not rpath'ed into
-the executable automatically, the ``extra_rpaths`` field of the compiler
-configuration tells Spack which dependencies to rpath into every
-executable created by that compiler. The executables will then be able
-to find the link dependencies imposed by the compiler. As an example,
-this field can be set by:
-
-.. code-block:: yaml
-
- - compiler:
- ...
- extra_rpaths:
- - /apps/intel/ComposerXE2017/compilers_and_libraries_2017.5.239/linux/compiler/lib/intel64_lin
- ...
-
-
-The ``environment`` field of the compiler configuration is used for
-compilers that require environment variables to be set during build
-time. For example, if your Intel compiler suite requires the
-``INTEL_LICENSE_FILE`` environment variable to point to the proper
-license server, you can set this in ``compilers.yaml`` as follows:
-
-.. code-block:: yaml
-
- - compiler:
- environment:
- set:
- INTEL_LICENSE_FILE: 1713@license4
- ...
-
-
-In addition to ``set``, ``environment`` also supports ``unset``,
-``prepend-path``, and ``append-path``.
-
-.. _configs-tutorial-package-prefs:
-
--------------------------------
-Configuring Package Preferences
--------------------------------
-
-Package preferences in Spack are managed through the ``packages.yaml``
-configuration file. First, we will look at the default
-``packages.yaml`` file.
-
-.. code-block:: console
-
- $ spack config --scope defaults edit packages
-
-
-.. literalinclude:: _spack_root/etc/spack/defaults/packages.yaml
- :language: yaml
-
-
-This sets the default preferences for compilers and for providers of
-virtual packages. To illustrate how this works, suppose we want to
-change the preferences to prefer the Clang compiler and to prefer
-MPICH over OpenMPI. Currently, we prefer GCC and OpenMPI.
-
-.. code-block:: console
-
- $ spack spec hdf5
- Input spec
- --------------------------------
- hdf5
-
- Concretized
- --------------------------------
- hdf5@1.10.4%gcc@5.4.0~cxx~debug~fortran~hl+mpi+pic+shared~szip~threadsafe arch=linux-ubuntu16.04-x86_64
- ^openmpi@3.1.3%gcc@5.4.0~cuda+cxx_exceptions fabrics= ~java~legacylaunchers~memchecker~pmi schedulers= ~sqlite3~thread_multiple+vt arch=linux-ubuntu16.04-x86_64
- ^hwloc@1.11.9%gcc@5.4.0~cairo~cuda+libxml2+pci+shared arch=linux-ubuntu16.04-x86_64
- ^libpciaccess@0.13.5%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
- ^libtool@2.4.6%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
- ^m4@1.4.18%gcc@5.4.0 patches=3877ab548f88597ab2327a2230ee048d2d07ace1062efe81fc92e91b7f39cd00,c0a408fbffb7255fcc75e26bd8edab116fc81d216bfd18b473668b7739a4158e,fc9b61654a3ba1a8d6cd78ce087e7c96366c290bc8d2c299f09828d793b853c8 +sigsegv arch=linux-ubuntu16.04-x86_64
- ^libsigsegv@2.11%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
- ^pkgconf@1.4.2%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
- ^util-macros@1.19.1%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
- ^libxml2@2.9.8%gcc@5.4.0~python arch=linux-ubuntu16.04-x86_64
- ^xz@5.2.4%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
- ^zlib@1.2.11%gcc@5.4.0+optimize+pic+shared arch=linux-ubuntu16.04-x86_64
- ^numactl@2.0.11%gcc@5.4.0 patches=592f30f7f5f757dfc239ad0ffd39a9a048487ad803c26b419e0f96b8cda08c1a arch=linux-ubuntu16.04-x86_64
- ^autoconf@2.69%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
- ^perl@5.26.2%gcc@5.4.0+cpanm patches=0eac10ed90aeb0459ad8851f88081d439a4e41978e586ec743069e8b059370ac +shared+threads arch=linux-ubuntu16.04-x86_64
- ^gdbm@1.14.1%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
- ^readline@7.0%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
- ^ncurses@6.1%gcc@5.4.0~symlinks~termlib arch=linux-ubuntu16.04-x86_64
- ^automake@1.16.1%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
-
-
-Now we will open the packages configuration file and update our
-preferences.
-
-.. code-block:: console
-
- $ spack config edit packages
-
-
-.. code-block:: yaml
-
- packages:
- all:
- compiler: [clang, gcc, intel, pgi, xl, nag]
- providers:
- mpi: [mpich, openmpi]
-
-
-Because of the configuration scoping we discussed earlier, this
-overrides the default settings just for these two items.
-
-.. code-block:: console
-
- $ spack spec hdf5
- Input spec
- --------------------------------
- hdf5
-
- Concretized
- --------------------------------
- hdf5@1.10.4%clang@3.8.0-2ubuntu4~cxx~debug~fortran~hl+mpi+pic+shared~szip~threadsafe arch=linux-ubuntu16.04-x86_64
- ^mpich@3.2.1%clang@3.8.0-2ubuntu4 device=ch3 +hydra netmod=tcp +pmi+romio~verbs arch=linux-ubuntu16.04-x86_64
- ^findutils@4.6.0%clang@3.8.0-2ubuntu4 patches=84b916c0bf8c51b7e7b28417692f0ad3e7030d1f3c248ba77c42ede5c1c5d11e,bd9e4e5cc280f9753ae14956c4e4aa17fe7a210f55dd6c84aa60b12d106d47a2 arch=linux-ubuntu16.04-x86_64
- ^autoconf@2.69%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
- ^m4@1.4.18%clang@3.8.0-2ubuntu4 patches=3877ab548f88597ab2327a2230ee048d2d07ace1062efe81fc92e91b7f39cd00,c0a408fbffb7255fcc75e26bd8edab116fc81d216bfd18b473668b7739a4158e,fc9b61654a3ba1a8d6cd78ce087e7c96366c290bc8d2c299f09828d793b853c8 +sigsegv arch=linux-ubuntu16.04-x86_64
- ^libsigsegv@2.11%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
- ^perl@5.26.2%clang@3.8.0-2ubuntu4+cpanm patches=0eac10ed90aeb0459ad8851f88081d439a4e41978e586ec743069e8b059370ac +shared+threads arch=linux-ubuntu16.04-x86_64
- ^gdbm@1.14.1%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
- ^readline@7.0%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
- ^ncurses@6.1%clang@3.8.0-2ubuntu4~symlinks~termlib arch=linux-ubuntu16.04-x86_64
- ^pkgconf@1.4.2%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
- ^automake@1.16.1%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
- ^libtool@2.4.6%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
- ^texinfo@6.5%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
- ^zlib@1.2.11%clang@3.8.0-2ubuntu4+optimize+pic+shared arch=linux-ubuntu16.04-x86_64
-
-
-^^^^^^^^^^^^^^^^^^^
-Variant Preferences
-^^^^^^^^^^^^^^^^^^^
-
-The packages configuration file can also set variant preferences for
-package variants. For example, let's change our preferences to build all
-packages without shared libraries. We will accomplish this by turning
-off the ``shared`` variant on all packages that have one.
-
-.. code-block:: yaml
-
- packages:
- all:
- compiler: [clang, gcc, intel, pgi, xl, nag]
- providers:
- mpi: [mpich, openmpi]
- variants: ~shared
-
-
-We can check the effect of this command with ``spack spec hdf5`` again.
-
-.. code-block:: console
-
- $ spack spec hdf5
- Input spec
- --------------------------------
- hdf5
-
- Concretized
- --------------------------------
- hdf5@1.10.4%clang@3.8.0-2ubuntu4~cxx~debug~fortran~hl+mpi+pic~shared~szip~threadsafe arch=linux-ubuntu16.04-x86_64
- ^mpich@3.2.1%clang@3.8.0-2ubuntu4 device=ch3 +hydra netmod=tcp +pmi+romio~verbs arch=linux-ubuntu16.04-x86_64
- ^findutils@4.6.0%clang@3.8.0-2ubuntu4 patches=84b916c0bf8c51b7e7b28417692f0ad3e7030d1f3c248ba77c42ede5c1c5d11e,bd9e4e5cc280f9753ae14956c4e4aa17fe7a210f55dd6c84aa60b12d106d47a2 arch=linux-ubuntu16.04-x86_64
- ^autoconf@2.69%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
- ^m4@1.4.18%clang@3.8.0-2ubuntu4 patches=3877ab548f88597ab2327a2230ee048d2d07ace1062efe81fc92e91b7f39cd00,c0a408fbffb7255fcc75e26bd8edab116fc81d216bfd18b473668b7739a4158e,fc9b61654a3ba1a8d6cd78ce087e7c96366c290bc8d2c299f09828d793b853c8 +sigsegv arch=linux-ubuntu16.04-x86_64
- ^libsigsegv@2.11%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
- ^perl@5.26.2%clang@3.8.0-2ubuntu4+cpanm patches=0eac10ed90aeb0459ad8851f88081d439a4e41978e586ec743069e8b059370ac ~shared+threads arch=linux-ubuntu16.04-x86_64
- ^gdbm@1.14.1%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
- ^readline@7.0%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
- ^ncurses@6.1%clang@3.8.0-2ubuntu4~symlinks~termlib arch=linux-ubuntu16.04-x86_64
- ^pkgconf@1.4.2%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
- ^automake@1.16.1%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
- ^libtool@2.4.6%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
- ^texinfo@6.5%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
- ^zlib@1.2.11%clang@3.8.0-2ubuntu4+optimize+pic~shared arch=linux-ubuntu16.04-x86_64
-
-
-So far we have only made global changes to the package preferences. As
-we've seen throughout this tutorial, HDF5 builds with MPI enabled by
-default in Spack. If we were working on a project that would routinely
-need serial HDF5, that might get annoying quickly, having to type
-``hdf5~mpi`` all the time. Instead, we'll update our preferences for
-HDF5.
-
-.. code-block:: yaml
-
- packages:
- all:
- compiler: [clang, gcc, intel, pgi, xl, nag]
- providers:
- mpi: [mpich, openmpi]
- variants: ~shared
- hdf5:
- variants: ~mpi
-
-
-Now hdf5 will concretize without an MPI dependency by default.
-
-.. code-block:: console
-
- $ spack spec hdf5
- Input spec
- --------------------------------
- hdf5
-
- Concretized
- --------------------------------
- hdf5@1.10.4%clang@3.8.0-2ubuntu4~cxx~debug~fortran~hl~mpi+pic+shared~szip~threadsafe arch=linux-ubuntu16.04-x86_64
- ^zlib@1.2.11%clang@3.8.0-2ubuntu4+optimize+pic~shared arch=linux-ubuntu16.04-x86_64
-
-
-In general, every attribute that we can set for all packages we can
-set separately for an individual package.
-
-^^^^^^^^^^^^^^^^^
-External Packages
-^^^^^^^^^^^^^^^^^
-
-The packages configuration file also controls when Spack will build
-against an externally installed package. On these systems we have a
-pre-installed zlib.
-
-.. code-block:: yaml
-
- packages:
- all:
- compiler: [clang, gcc, intel, pgi, xl, nag]
- providers:
- mpi: [mpich, openmpi]
- variants: ~shared
- hdf5:
- variants: ~mpi
- zlib:
- paths:
- zlib@1.2.8%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64: /usr
-
-
-Here, we've told Spack that zlib 1.2.8 is installed on our system.
-We've also told it the installation prefix where zlib can be found.
-We don't know exactly which variants it was built with, but that's
-okay.
-
-.. code-block:: console
-
- $ spack spec hdf5
- Input spec
- --------------------------------
- hdf5
-
- Concretized
- --------------------------------
- hdf5@1.10.4%gcc@5.4.0~cxx~debug~fortran~hl~mpi+pic+shared~szip~threadsafe arch=linux-ubuntu16.04-x86_64
- ^zlib@1.2.8%gcc@5.4.0+optimize+pic~shared arch=linux-ubuntu16.04-x86_64
-
-
-You'll notice that Spack is now using the external zlib installation,
-but the compiler used to build zlib is now overriding our compiler
-preference of clang. If we explicitly specify Clang:
-
-.. code-block:: console
-
- $ spack spec hdf5 %clang
- Input spec
- --------------------------------
- hdf5%clang
-
- Concretized
- --------------------------------
- hdf5@1.10.4%clang@3.8.0-2ubuntu4~cxx~debug~fortran~hl~mpi+pic+shared~szip~threadsafe arch=linux-ubuntu16.04-x86_64
- ^zlib@1.2.11%clang@3.8.0-2ubuntu4+optimize+pic~shared arch=linux-ubuntu16.04-x86_64
-
-
-Spack concretizes to both HDF5 and zlib being built with Clang.
-This has a side-effect of rebuilding zlib. If we want to force
-Spack to use the system zlib, we have two choices. We can either
-specify it on the command line, or we can tell Spack that it's
-not allowed to build its own zlib. We'll go with the latter.
-
-.. code-block:: yaml
-
- packages:
- all:
- compiler: [clang, gcc, intel, pgi, xl, nag]
- providers:
- mpi: [mpich, openmpi]
- variants: ~shared
- hdf5:
- variants: ~mpi
- zlib:
- paths:
- zlib@1.2.8%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64: /usr
- buildable: False
-
-
-Now Spack will be forced to choose the external zlib.
-
-.. code-block:: console
-
- $ spack spec hdf5 %clang
- Input spec
- --------------------------------
- hdf5%clang
-
- Concretized
- --------------------------------
- hdf5@1.10.4%clang@3.8.0-2ubuntu4~cxx~debug~fortran~hl~mpi+pic+shared~szip~threadsafe arch=linux-ubuntu16.04-x86_64
- ^zlib@1.2.8%gcc@5.4.0+optimize+pic~shared arch=linux-ubuntu16.04-x86_64
-
-
-This gets slightly more complicated with virtual dependencies. Suppose
-we don't want to build our own MPI, but we now want a parallel version
-of HDF5? Well, fortunately we have MPICH installed on these systems.
-
-.. code-block:: yaml
-
- packages:
- all:
- compiler: [clang, gcc, intel, pgi, xl, nag]
- providers:
- mpi: [mpich, openmpi]
- variants: ~shared
- hdf5:
- variants: ~mpi
- zlib:
- paths:
- zlib@1.2.8%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64: /usr
- buildable: False
- mpich:
- paths:
- mpich@3.2%gcc@5.4.0 device=ch3 +hydra netmod=tcp +pmi+romio~verbs arch=linux-ubuntu16.04-x86_64: /usr
- buildable: False
-
-
-If we concretize ``hdf5+mpi`` with this configuration file, we will just
-build with an alternate MPI implementation.
-
-.. code-block:: console
-
- $ spack spec hdf5+mpi %clang
- Input spec
- --------------------------------
- hdf5%clang+mpi
-
- Concretized
- --------------------------------
- hdf5@1.10.4%clang@3.8.0-2ubuntu4~cxx~debug~fortran~hl+mpi+pic+shared~szip~threadsafe arch=linux-ubuntu16.04-x86_64
- ^openmpi@3.1.3%clang@3.8.0-2ubuntu4~cuda+cxx_exceptions fabrics= ~java~legacylaunchers~memchecker~pmi schedulers= ~sqlite3~thread_multiple+vt arch=linux-ubuntu16.04-x86_64
- ^hwloc@1.11.9%clang@3.8.0-2ubuntu4~cairo~cuda+libxml2+pci~shared arch=linux-ubuntu16.04-x86_64
- ^libpciaccess@0.13.5%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
- ^libtool@2.4.6%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
- ^m4@1.4.18%clang@3.8.0-2ubuntu4 patches=3877ab548f88597ab2327a2230ee048d2d07ace1062efe81fc92e91b7f39cd00,c0a408fbffb7255fcc75e26bd8edab116fc81d216bfd18b473668b7739a4158e,fc9b61654a3ba1a8d6cd78ce087e7c96366c290bc8d2c299f09828d793b853c8 +sigsegv arch=linux-ubuntu16.04-x86_64
- ^libsigsegv@2.11%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
- ^pkgconf@1.4.2%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
- ^util-macros@1.19.1%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
- ^libxml2@2.9.8%clang@3.8.0-2ubuntu4~python arch=linux-ubuntu16.04-x86_64
- ^xz@5.2.4%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
- ^zlib@1.2.8%gcc@5.4.0+optimize+pic~shared arch=linux-ubuntu16.04-x86_64
- ^numactl@2.0.11%clang@3.8.0-2ubuntu4 patches=592f30f7f5f757dfc239ad0ffd39a9a048487ad803c26b419e0f96b8cda08c1a arch=linux-ubuntu16.04-x86_64
- ^autoconf@2.69%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
- ^perl@5.26.2%clang@3.8.0-2ubuntu4+cpanm patches=0eac10ed90aeb0459ad8851f88081d439a4e41978e586ec743069e8b059370ac ~shared+threads arch=linux-ubuntu16.04-x86_64
- ^gdbm@1.14.1%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
- ^readline@7.0%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
- ^ncurses@6.1%clang@3.8.0-2ubuntu4~symlinks~termlib arch=linux-ubuntu16.04-x86_64
- ^automake@1.16.1%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
-
-
-We have only expressed a preference for MPICH over other MPI
-implementations, and Spack will happily build with one we haven't
-forbid it from building. We could resolve this by requesting
-``hdf5+mpi%clang^mpich`` explicitly, or we can configure Spack not to
-use any other MPI implementation. Since we're focused on
-configurations here and the former can get tedious, we'll need to
-modify our ``packages.yaml`` file again.
-
-While we're at it, we can configure HDF5 to build with MPI by default
-again.
-
-.. code-block:: yaml
-
- packages:
- all:
- compiler: [clang, gcc, intel, pgi, xl, nag]
- providers:
- mpi: [mpich, openmpi]
- variants: ~shared
- zlib:
- paths:
- zlib@1.2.8%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64: /usr
- buildable: False
- mpich:
- paths:
- mpich@3.2%gcc@5.4.0 device=ch3 +hydra netmod=tcp +pmi+romio~verbs arch=linux-ubuntu16.04-x86_64: /usr
- buildable: False
- openmpi:
- buildable: False
- mvapich2:
- buildable: False
- intel-mpi:
- buildable: False
- intel-parallel-studio:
- buildable: False
- spectrum-mpi:
- buildable: False
- mpilander:
- buildable: False
- charm:
- buildable: False
- charmpp:
- buildable: False
-
-
-Now that we have configured Spack not to build any of the possible
-providers for MPI, we can try again.
-
-.. code-block:: console
-
- $ spack spec hdf5 %clang
- Input spec
- --------------------------------
- hdf5%clang
-
- Concretized
- --------------------------------
- hdf5@1.10.4%clang@3.8.0-2ubuntu4~cxx~debug~fortran~hl+mpi+pic~shared~szip~threadsafe arch=linux-ubuntu16.04-x86_64
- ^mpich@3.2%gcc@5.4.0 device=ch3 +hydra netmod=tcp +pmi+romio~verbs arch=linux-ubuntu16.04-x86_64
- ^zlib@1.2.8%gcc@5.4.0+optimize+pic~shared arch=linux-ubuntu16.04-x86_64
-
-
-By configuring most of our package preferences in ``packages.yaml``,
-we can cut down on the amount of work we need to do when specifying
-a spec on the command line. In addition to compiler and variant
-preferences, we can specify version preferences as well. Except for
-selecting providers via `^`, anything that you can specify on the
-command line can be specified in ``packages.yaml`` with the exact
-same spec syntax.
-
-^^^^^^^^^^^^^^^^^^^^^^^^
-Installation Permissions
-^^^^^^^^^^^^^^^^^^^^^^^^
-
-The ``packages.yaml`` file also controls the default permissions
-to use when installing a package. You'll notice that by default,
-the installation prefix will be world readable but only user writable.
-
-Let's say we need to install ``converge``, a licensed software package.
-Since a specific research group, ``fluid_dynamics``, pays for this
-license, we want to ensure that only members of this group can access
-the software. We can do this like so:
-
-.. code-block:: yaml
-
- packages:
- converge:
- permissions:
- read: group
- group: fluid_dynamics
-
-
-Now, only members of the ``fluid_dynamics`` group can use any
-``converge`` installations.
-
-.. warning::
-
- Make sure to delete or move the ``packages.yaml`` you have been
- editing up to this point. Otherwise, it will change the hashes
- of your packages, leading to differences in the output of later
- tutorial sections.
-
-
------------------
-High-level Config
------------------
-
-In addition to compiler and package settings, Spack allows customization
-of several high-level settings. These settings are stored in the generic
-``config.yaml`` configuration file. You can see the default settings by
-running:
-
-.. code-block:: console
-
- $ spack config --scope defaults edit config
-
-
-.. literalinclude:: _spack_root/etc/spack/defaults/config.yaml
- :language: yaml
-
-
-As you can see, many of the directories Spack uses can be customized.
-For example, you can tell Spack to install packages to a prefix
-outside of the ``$SPACK_ROOT`` hierarchy. Module files can be
-written to a central location if you are using multiple Spack
-instances. If you have a fast scratch file system, you can run builds
-from this file system with the following ``config.yaml``:
-
-.. code-block:: yaml
-
- config:
- build_stage:
- - /scratch/$user/spack-stage
-
-
-.. note::
-
- It is important to distinguish the build stage directory from other
- directories in your scratch space to ensure ``spack clean`` does not
- inadvertently remove unrelated files. Spack prepends ``spack-stage-``
- to temporary staging directory names to reduce this risk. Using a
- combination of ``spack`` and or ``stage`` in each specified path, as
- shown in the default settings and documented examples, will add
- another layer of protection. See :ref:`config-yaml` for details.
-
-
-On systems with compilers that absolutely *require* environment variables
-like ``LD_LIBRARY_PATH``, it is possible to prevent Spack from cleaning
-the build environment with the ``dirty`` setting:
-
-.. code-block:: yaml
-
- config:
- dirty: true
-
-
-However, this is strongly discouraged, as it can pull unwanted libraries
-into the build.
-
-One last setting that may be of interest to many users is the ability
-to customize the parallelism of Spack builds. By default, Spack
-installs all packages in parallel with the number of jobs equal to the
-number of cores on the node (up to a maximum of 16). For example, on a
-node with 16 cores, this will look like:
-
-.. code-block:: console
-
- $ spack install --no-cache --verbose --overwrite zlib
- ==> Installing zlib
- ==> Using cached archive: /home/user/spack/var/spack/cache/zlib/zlib-1.2.11.tar.gz
- ==> Staging archive: /home/user/spack/var/spack/stage/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb/zlib-1.2.11.tar.gz
- ==> Created stage in /home/user/spack/var/spack/stage/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb
- ==> No patches needed for zlib
- ==> Building zlib [Package]
- ==> Executing phase: 'install'
- ==> './configure' '--prefix=/home/user/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb'
- ...
- ==> 'make' '-j16'
- ...
- ==> 'make' '-j16' 'install'
- ...
- ==> Successfully installed zlib
- Fetch: 0.00s. Build: 1.03s. Total: 1.03s.
- [+] /home/user/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb
-
-
-As you can see, we are building with all 16 cores on the node. If you are
-on a shared login node, this can slow down the system for other users. If
-you have a strict ulimit or restriction on the number of available licenses,
-you may not be able to build at all with this many cores. On nodes with 64+
-cores, you may not see a significant speedup of the build anyway. To limit
-the number of cores our build uses, set ``build_jobs`` like so:
-
-.. code-block:: yaml
-
- config:
- build_jobs: 2
-
-
-If we uninstall and reinstall zlib, we see that it now uses only 2 cores:
-
-.. code-block:: console
-
- $ spack install --no-cache --verbose --overwrite zlib
- ==> Installing zlib
- ==> Using cached archive: /home/user/spack/var/spack/cache/zlib/zlib-1.2.11.tar.gz
- ==> Staging archive: /home/user/spack/var/spack/stage/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb/zlib-1.2.11.tar.gz
- ==> Created stage in /home/user/spack/var/spack/stage/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb
- ==> No patches needed for zlib
- ==> Building zlib [Package]
- ==> Executing phase: 'install'
- ==> './configure' '--prefix=/home/user/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb'
- ...
- ==> 'make' '-j2'
- ...
- ==> 'make' '-j2' 'install'
- ...
- ==> Successfully installed zlib
- Fetch: 0.00s. Build: 1.03s. Total: 1.03s.
- [+] /home/user/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb
-
-
-Obviously, if you want to build everything in serial for whatever reason,
-you would set ``build_jobs`` to 1.
-
---------
-Examples
---------
-
-For examples of how other sites configure Spack, see
-https://github.com/spack/spack-configs. If you use Spack at your site
-and want to share your config files, feel free to submit a pull request!
diff --git a/lib/spack/docs/tutorial_environments.rst b/lib/spack/docs/tutorial_environments.rst
deleted file mode 100644
index 4b86dbd5acaec8116f59f3d55e02ad5a646adbc2..0000000000000000000000000000000000000000
--- a/lib/spack/docs/tutorial_environments.rst
+++ /dev/null
@@ -1,815 +0,0 @@
-.. Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
- Spack Project Developers. See the top-level COPYRIGHT file for details.
-
- SPDX-License-Identifier: (Apache-2.0 OR MIT)
-
-.. _environments-tutorial:
-
-=====================
-Environments Tutorial
-=====================
-
-We've shown you how to install and remove packages with Spack. You can
-use :ref:`cmd-spack-install` to install packages,
-:ref:`cmd-spack-uninstall` to remove them, and :ref:`cmd-spack-find` to
-look at and query what is installed. We've also shown you how to
-customize Spack's installation with configuration files like
-:ref:`packages.yaml <build-settings>`.
-
-If you build a lot of software, or if you work on multiple projects,
-managing everything in one place can be overwhelming. The default ``spack
-find`` output may contain many packages, but you may want to *just* focus
-on packages for a particular project. Moreover, you may want to include
-special configuration with your package groups, e.g., to build all the
-packages in the same group the same way.
-
-Spack **environments** provide a way to handle these problems.
-
--------------------
-Environment basics
--------------------
-
-Let's look at the output of ``spack find`` at this point in the tutorial.
-
-.. code-block:: console
-
- $ spack find
- ==> 70 installed packages
- -- linux-ubuntu16.04-x86_64 / clang@3.8.0-2ubuntu4 --------------
- tcl@8.6.8 zlib@1.2.8 zlib@1.2.11
-
- -- linux-ubuntu16.04-x86_64 / gcc@4.7 ---------------------------
- zlib@1.2.11
-
- -- linux-ubuntu16.04-x86_64 / gcc@5.4.0 -------------------------
- adept-utils@1.0.1 hdf5@1.10.4 mpc@1.1.0 perl@5.26.2
- autoconf@2.69 hdf5@1.10.4 mpfr@3.1.6 pkgconf@1.4.2
- automake@1.16.1 hdf5@1.10.4 mpich@3.2.1 readline@7.0
- boost@1.68.0 hwloc@1.11.9 mpileaks@1.0 suite-sparse@5.3.0
- bzip2@1.0.6 hypre@2.15.1 mumps@5.1.1 tar@1.30
- callpath@1.0.4 hypre@2.15.1 mumps@5.1.1 tcl@8.6.8
- cmake@3.12.3 isl@0.18 ncurses@6.1 tcl@8.6.8
- diffutils@3.6 libdwarf@20180129 netcdf@4.6.1 texinfo@6.5
- dyninst@9.3.2 libiberty@2.31.1 netcdf@4.6.1 trilinos@12.12.1
- elfutils@0.173 libpciaccess@0.13.5 netlib-scalapack@2.0.2 trilinos@12.12.1
- findutils@4.6.0 libsigsegv@2.11 netlib-scalapack@2.0.2 util-macros@1.19.1
- gcc@7.2.0 libtool@2.4.6 numactl@2.0.11 xz@5.2.4
- gdbm@1.14.1 libxml2@2.9.8 openblas@0.3.3 zlib@1.2.8
- gettext@0.19.8.1 m4@1.4.18 openmpi@3.1.3 zlib@1.2.8
- glm@0.9.7.1 matio@1.5.9 openssl@1.0.2o zlib@1.2.11
- gmp@6.1.2 matio@1.5.9 parmetis@4.0.3
- hdf5@1.10.4 metis@5.1.0 parmetis@4.0.3
-
-
-This is a complete, but cluttered view. There are packages built with
-both ``openmpi`` and ``mpich``, as well as multiple variants of other
-packages, like ``zlib``. The query mechanism we learned about in ``spack
-find`` can help, but it would be nice if we could start from a clean
-slate without losing what we've already done.
-
-
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-Creating and activating environments
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-The ``spack env`` command can help. Let's create a new environment:
-
-.. code-block:: console
-
- $ spack env create myproject
- ==> Created environment 'myproject' in ~/spack/var/spack/environments/myproject
-
-An environment is a virtualized ``spack`` instance that you can use for a
-specific purpose. You can see the environments we've created so far like this:
-
-.. code-block:: console
-
- $ spack env list
- ==> 1 environments
- myproject
-
-And you can **activate** an environment with ``spack env activate``:
-
-.. code-block:: console
-
- $ spack env activate myproject
-
-Once you enter an environment, ``spack find`` shows only what is in the
-current environment. That's nothing, so far:
-
-.. code-block:: console
-
- $ spack find
- ==> In environment myproject
- ==> No root specs
-
- ==> 0 installed packages
-
-The ``spack find`` output is still *slightly* different. It tells you
-that you're in the ``myproject`` environment, so that you don't panic
-when you see that there is nothing installed. It also says that there
-are *no root specs*. We'll get back to what that means later.
-
-If you *only* want to check what environment you are in, you can use
-``spack env status``:
-
-.. code-block:: console
-
- $ spack env status
- ==> In environment myproject
-
-And, if you want to leave this environment and go back to normal Spack,
-you can use ``spack env deactivate``. We like to use the
-``despacktivate`` alias (which Spack sets up automatically) for short:
-
-.. code-block:: console
-
- $ despacktivate # short alias for `spack env deactivate`
- $ spack env status
- ==> No active environment
- $ spack find
- netcdf@4.6.1 readline@7.0 zlib@1.2.11
- diffutils@3.6 hdf5@1.10.4 m4@1.4.18 netcdf@4.6.1 suite-sparse@5.3.0
- dyninst@10.0.0 hwloc@1.11.9 matio@1.5.9 netlib-scalapack@2.0.2 tar@1.30
- elfutils@0.173 hypre@2.15.1 matio@1.5.9 netlib-scalapack@2.0.2 tcl@8.6.8
- findutils@4.6.0 hypre@2.15.1 metis@5.1.0 numactl@2.0.11 tcl@8.6.8
- gcc@7.2.0 intel-tbb@2019 mpc@1.1.0 openblas@0.3.3 texinfo@6.5~
-
-
-^^^^^^^^^^^^^^^^^^^
-Installing packages
-^^^^^^^^^^^^^^^^^^^
-
-Ok, now that we understand how creation and activation work, let's go
-back to ``myproject`` and *install* a few packages:
-
-.. code-block:: console
-
- $ spack env activate myproject
- $ spack install tcl
- ==> tcl is already installed in ~/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/tcl-8.6.8-qhwyccywhx2i6s7ob2gvjrjtj3rnfuqt
- $ spack install trilinos
- ==> trilinos is already installed in ~/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/trilinos-12.12.1-rlsruavxqvwk2tgxzxboclbo6ykjf54r
- $ spack find
- ==> In environment myproject
- ==> Root specs
- tcl trilinos
-
- ==> 22 installed packages
- -- linux-ubuntu16.04-x86_64 / gcc@5.4.0 -------------------------
- boost@1.68.0 hwloc@1.11.9 matio@1.5.9 netlib-scalapack@2.0.2 parmetis@4.0.3 xz@5.2.4
- bzip2@1.0.6 hypre@2.15.1 metis@5.1.0 numactl@2.0.11 suite-sparse@5.3.0 zlib@1.2.11
- glm@0.9.7.1 libpciaccess@0.13.5 mumps@5.1.1 openblas@0.3.3 tcl@8.6.8
- hdf5@1.10.4 libxml2@2.9.8 netcdf@4.6.1 openmpi@3.1.3 trilinos@12.12.1
-
-We've installed ``tcl`` and ``trilinos`` in our environment, along with
-all of their dependencies. We call ``tcl`` and ``trilinos`` the
-**roots** because we asked for them explicitly. The other 20 packages
-listed under "installed packages" are present because they were needed as
-dependencies. So, these are the roots of the packages' dependency graph.
-
-The "<package> is already installed" messages above are generated because
-we already installed these packages in previous steps of the tutorial,
-and we don't have to rebuild them to put them in an environment.
-
-Now let's create *another* project. We'll call this one ``myproject2``:
-
-.. code-block:: console
-
- $ spack env create myproject2
- ==> Created environment 'myproject2' in ~/spack/var/spack/environments/myproject2
- $ spack env activate myproject2
- $ spack install hdf5
- ==> hdf5 is already installed in ~/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/hdf5-1.10.4-ozyvmhzdew66byarohm4p36ep7wtcuiw
- $ spack install trilinos
- ==> trilinos is already installed in ~/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/trilinos-12.12.1-rlsruavxqvwk2tgxzxboclbo6ykjf54r
- $ spack find
- ==> In environment myproject2
- ==> Root specs
- hdf5 trilinos
-
- ==> 22 installed packages
- -- linux-ubuntu16.04-x86_64 / gcc@5.4.0 -------------------------
- boost@1.68.0 hdf5@1.10.4 libxml2@2.9.8 netcdf@4.6.1 openmpi@3.1.3 xz@5.2.4
- bzip2@1.0.6 hwloc@1.11.9 matio@1.5.9 netlib-scalapack@2.0.2 parmetis@4.0.3 zlib@1.2.11
- glm@0.9.7.1 hypre@2.15.1 metis@5.1.0 numactl@2.0.11 suite-sparse@5.3.0
- hdf5@1.10.4 libpciaccess@0.13.5 mumps@5.1.1 openblas@0.3.3 trilinos@12.12.1
-
-Now we have two environments: one with ``tcl`` and ``trilinos``, and
-another with ``hdf5`` and ``trilinos``.
-
-We can uninstall trilinos from ``myproject2`` as you would expect:
-
-.. code-block:: console
-
- $ spack uninstall trilinos
- ==> The following packages will be uninstalled:
-
- -- linux-ubuntu16.04-x86_64 / gcc@5.4.0 -------------------------
- rlsruav trilinos@12.12.1%gcc~alloptpkgs+amesos+amesos2+anasazi+aztec+belos+boost build_type=RelWithDebInfo ~cgns~complex~dtk+epetra+epetraext+exodus+explicit_template_instantiation~float+fortran~fortrilinos+gtest+hdf5+hypre+ifpack+ifpack2~intrepid~intrepid2~isorropia+kokkos+metis~minitensor+ml+muelu+mumps~nox~openmp~phalanx~piro~pnetcdf~python~rol~rythmos+sacado~shards+shared~stk+suite-sparse~superlu~superlu-dist~teko~tempus+teuchos+tpetra~x11~xsdkflags~zlib+zoltan+zoltan2
- ==> Do you want to proceed? [y/N] y
- $ spack find
- ==> In environment myproject2
- ==> Root specs
- hdf5
-
- ==> 8 installed packages
- -- linux-ubuntu16.04-x86_64 / gcc@5.4.0 -------------------------
- hdf5@1.10.4 libpciaccess@0.13.5 numactl@2.0.11 xz@5.2.4
- hwloc@1.11.9 libxml2@2.9.8 openmpi@3.1.3 zlib@1.2.11
-
-Now there is only one root spec, ``hdf5``, which requires fewer
-additional dependencies.
-
-However, we still needed ``trilinos`` for the ``myproject`` environment!
-What happened to it? Let's switch back and see.
-
-.. code-block:: console
-
- $ despacktivate
- $ spack env activate myproject
- $ spack find
- ==> In environment myproject
- ==> Root specs
- tcl trilinos
-
- ==> 22 installed packages
- -- linux-ubuntu16.04-x86_64 / gcc@5.4.0 -------------------------
- boost@1.68.0 hwloc@1.11.9 matio@1.5.9 netlib-scalapack@2.0.2 parmetis@4.0.3 xz@5.2.4
- bzip2@1.0.6 hypre@2.15.1 metis@5.1.0 numactl@2.0.11 suite-sparse@5.3.0 zlib@1.2.11
- glm@0.9.7.1 libpciaccess@0.13.5 mumps@5.1.1 openblas@0.3.3 tcl@8.6.8
- hdf5@1.10.4 libxml2@2.9.8 netcdf@4.6.1 openmpi@3.1.3 trilinos@12.12.1
-
-
-Spack is smart enough to realize that ``trilinos`` is still present in
-the other environment. Trilinos won't *actually* be uninstalled unless
-it is no longer needed by any environments or packages. If it is still
-needed, it is only removed from the environment.
-
--------------------------------
-Dealing with many specs at once
--------------------------------
-
-In the above examples, we just used ``install`` and ``uninstall``. There
-are other ways to deal with groups of packages, as well.
-
-^^^^^^^^^^^^^
-Adding specs
-^^^^^^^^^^^^^
-
-Let's go back to our first ``myproject`` environment and *add* a few specs instead of installing them:
-
-.. code-block:: console
-
- $ spack add hdf5
- ==> Adding hdf5 to environment myproject
- $ spack add gmp
- ==> Adding mumps to environment myproject
- $ spack find
- ==> In environment myproject
- ==> Root specs
- gmp hdf5 tcl trilinos
-
- ==> 22 installed packages
- -- linux-ubuntu16.04-x86_64 / gcc@5.4.0 -------------------------
- boost@1.68.0 hwloc@1.11.9 matio@1.5.9 netlib-scalapack@2.0.2 parmetis@4.0.3 xz@5.2.4
- bzip2@1.0.6 hypre@2.15.1 metis@5.1.0 numactl@2.0.11 suite-sparse@5.3.0 zlib@1.2.11
- glm@0.9.7.1 libpciaccess@0.13.5 mumps@5.1.1 openblas@0.3.3 tcl@8.6.8
- hdf5@1.10.4 libxml2@2.9.8 netcdf@4.6.1 openmpi@3.1.3 trilinos@12.12.1
-
-Let's take a close look at what happened. The two packages we added,
-``hdf5`` and ``gmp``, are present, but they're not installed in the
-environment yet. ``spack add`` just adds *roots* to the environment, but
-it does not automatically install them.
-
-We can install *all* the as-yet uninstalled packages in an environment by
-simply running ``spack install`` with no arguments:
-
-.. code-block:: console
-
- $ spack install
- ==> Concretizing hdf5
- [+] ozyvmhz hdf5@1.10.4%gcc@5.4.0~cxx~debug~fortran~hl+mpi+pic+shared~szip~threadsafe arch=linux-ubuntu16.04-x86_64
- [+] 3njc4q5 ^openmpi@3.1.3%gcc@5.4.0~cuda+cxx_exceptions fabrics= ~java~legacylaunchers~memchecker~pmi schedulers= ~sqlite3~thread_multiple+vt arch=linux-ubuntu16.04-x86_64
- [+] 43tkw5m ^hwloc@1.11.9%gcc@5.4.0~cairo~cuda+libxml2+pci+shared arch=linux-ubuntu16.04-x86_64
- [+] 5urc6tc ^libpciaccess@0.13.5%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
- [+] o2pfwjf ^libtool@2.4.6%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
- [+] suf5jtc ^m4@1.4.18%gcc@5.4.0 patches=3877ab548f88597ab2327a2230ee048d2d07ace1062efe81fc92e91b7f39cd00,c0a408fbffb7255fcc75e26bd8edab116fc81d216bfd18b473668b7739a4158e,fc9b61654a3ba1a8d6cd78ce087e7c96366c290bc8d2c299f09828d793b853c8 +sigsegv arch=linux-ubuntu16.04-x86_64
- [+] fypapcp ^libsigsegv@2.11%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
- [+] fovrh7a ^pkgconf@1.4.2%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
- [+] milz7fm ^util-macros@1.19.1%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
- [+] wpexsph ^libxml2@2.9.8%gcc@5.4.0~python arch=linux-ubuntu16.04-x86_64
- [+] teneqii ^xz@5.2.4%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
- [+] 5nus6kn ^zlib@1.2.11%gcc@5.4.0+optimize+pic+shared arch=linux-ubuntu16.04-x86_64
- [+] ft463od ^numactl@2.0.11%gcc@5.4.0 patches=592f30f7f5f757dfc239ad0ffd39a9a048487ad803c26b419e0f96b8cda08c1a arch=linux-ubuntu16.04-x86_64
- [+] 3sx2gxe ^autoconf@2.69%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
- [+] ic2kyoa ^perl@5.26.2%gcc@5.4.0+cpanm patches=0eac10ed90aeb0459ad8851f88081d439a4e41978e586ec743069e8b059370ac +shared+threads arch=linux-ubuntu16.04-x86_64
- [+] q4fpyuo ^gdbm@1.14.1%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
- [+] nxhwrg7 ^readline@7.0%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
- [+] 3o765ou ^ncurses@6.1%gcc@5.4.0~symlinks~termlib arch=linux-ubuntu16.04-x86_64
- [+] rymw7im ^automake@1.16.1%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
- ==> Concretizing gmp
- [+] qc4qcfz gmp@6.1.2%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
- [+] 3sx2gxe ^autoconf@2.69%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
- [+] suf5jtc ^m4@1.4.18%gcc@5.4.0 patches=3877ab548f88597ab2327a2230ee048d2d07ace1062efe81fc92e91b7f39cd00,c0a408fbffb7255fcc75e26bd8edab116fc81d216bfd18b473668b7739a4158e,fc9b61654a3ba1a8d6cd78ce087e7c96366c290bc8d2c299f09828d793b853c8 +sigsegv arch=linux-ubuntu16.04-x86_64
- [+] fypapcp ^libsigsegv@2.11%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
- [+] ic2kyoa ^perl@5.26.2%gcc@5.4.0+cpanm patches=0eac10ed90aeb0459ad8851f88081d439a4e41978e586ec743069e8b059370ac +shared+threads arch=linux-ubuntu16.04-x86_64
- [+] q4fpyuo ^gdbm@1.14.1%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
- [+] nxhwrg7 ^readline@7.0%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
- [+] 3o765ou ^ncurses@6.1%gcc@5.4.0~symlinks~termlib arch=linux-ubuntu16.04-x86_64
- [+] fovrh7a ^pkgconf@1.4.2%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
- [+] rymw7im ^automake@1.16.1%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
- [+] o2pfwjf ^libtool@2.4.6%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
- ==> Installing environment myproject
- ==> tcl is already installed in ~/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/tcl-8.6.8-qhwyccywhx2i6s7ob2gvjrjtj3rnfuqt
- ==> trilinos is already installed in ~/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/trilinos-12.12.1-rlsruavxqvwk2tgxzxboclbo6ykjf54r
- ==> hdf5 is already installed in ~/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/hdf5-1.10.4-ozyvmhzdew66byarohm4p36ep7wtcuiw
- ==> gmp is already installed in ~/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gmp-6.1.2-qc4qcfz4monpllc3nqupdo7vwinf73sw
-
-Spack will concretize the new roots, and install everything you added to
-the environment. Now we can see the installed roots in the output of
-``spack find``:
-
-.. code-block:: console
-
- $ spack find
- ==> In environment myproject
- ==> Root specs
- gmp hdf5 tcl trilinos
-
- ==> 24 installed packages
- -- linux-ubuntu16.04-x86_64 / gcc@5.4.0 -------------------------
- boost@1.68.0 hdf5@1.10.4 libpciaccess@0.13.5 mumps@5.1.1 openblas@0.3.3 tcl@8.6.8
- bzip2@1.0.6 hdf5@1.10.4 libxml2@2.9.8 netcdf@4.6.1 openmpi@3.1.3 trilinos@12.12.1
- glm@0.9.7.1 hwloc@1.11.9 matio@1.5.9 netlib-scalapack@2.0.2 parmetis@4.0.3 xz@5.2.4
- gmp@6.1.2 hypre@2.15.1 metis@5.1.0 numactl@2.0.11 suite-sparse@5.3.0 zlib@1.2.11
-
-We can build whole environments this way, by adding specs and installing
-all at once, or we can install them with the usual ``install`` and
-``uninstall`` portions. The advantage to doing them all at once is that
-we don't have to write a script outside of Spack to automate this, and we
-can kick off a large build of many packages easily.
-
-^^^^^^^^^^^^^^^^^^^^^
-Configuration
-^^^^^^^^^^^^^^^^^^^^^
-
-So far, ``myproject`` does not have any special configuration associated
-with it. The specs concretize using Spack's defaults:
-
-.. code-block:: console
-
- $ spack spec hypre
- Input spec
- --------------------------------
- hypre
-
- Concretized
- --------------------------------
- hypre@2.15.1%gcc@5.4.0~debug~int64+internal-superlu+mpi+shared arch=linux-ubuntu16.04-x86_64
- ^openblas@0.3.3%gcc@5.4.0 cpu_target= ~ilp64 patches=47cfa7a952ac7b2e4632c73ae199d69fb54490627b66a62c681e21019c4ddc9d,714aea33692304a50bd0ccde42590c176c82ded4a8ac7f06e573dc8071929c33 +pic+shared threads=none ~virtual_machine arch=linux-ubuntu16.04-x86_64
- ^openmpi@3.1.3%gcc@5.4.0~cuda+cxx_exceptions fabrics= ~java~legacylaunchers~memchecker~pmi schedulers= ~sqlite3~thread_multiple+vt arch=linux-ubuntu16.04-x86_64
- ^hwloc@1.11.9%gcc@5.4.0~cairo~cuda+libxml2+pci+shared arch=linux-ubuntu16.04-x86_64
- ^libpciaccess@0.13.5%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
- ^libtool@2.4.6%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
- ^m4@1.4.18%gcc@5.4.0 patches=3877ab548f88597ab2327a2230ee048d2d07ace1062efe81fc92e91b7f39cd00,c0a408fbffb7255fcc75e26bd8edab116fc81d216bfd18b473668b7739a4158e,fc9b61654a3ba1a8d6cd78ce087e7c96366c290bc8d2c299f09828d793b853c8 +sigsegv arch=linux-ubuntu16.04-x86_64
- ^libsigsegv@2.11%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
- ^pkgconf@1.4.2%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
- ^util-macros@1.19.1%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
- ^libxml2@2.9.8%gcc@5.4.0~python arch=linux-ubuntu16.04-x86_64
- ^xz@5.2.4%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
- ^zlib@1.2.11%gcc@5.4.0+optimize+pic+shared arch=linux-ubuntu16.04-x86_64
- ^numactl@2.0.11%gcc@5.4.0 patches=592f30f7f5f757dfc239ad0ffd39a9a048487ad803c26b419e0f96b8cda08c1a arch=linux-ubuntu16.04-x86_64
- ^autoconf@2.69%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
- ^perl@5.26.2%gcc@5.4.0+cpanm patches=0eac10ed90aeb0459ad8851f88081d439a4e41978e586ec743069e8b059370ac +shared+threads arch=linux-ubuntu16.04-x86_64
- ^gdbm@1.14.1%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
- ^readline@7.0%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
- ^ncurses@6.1%gcc@5.4.0~symlinks~termlib arch=linux-ubuntu16.04-x86_64
- ^automake@1.16.1%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
-
-You may want to add extra configuration to your environment. You can see
-how your environment is configured using ``spack config get``:
-
-.. code-block:: console
-
- $ spack config get
- # This is a Spack Environment file.
- #
- # It describes a set of packages to be installed, along with
- # configuration settings.
- spack:
- # add package specs to the `specs` list
- specs: [tcl, trilinos, hdf5, gmp]
-
-It turns out that this is a special configuration format where Spack
-stores the state for the environment. Currently, the file is just a
-``spack:`` header and a list of ``specs``. These are the roots.
-
-You can edit this file to add your own custom configuration. Spack
-provides a shortcut to do that:
-
-.. code-block:: console
-
- spack config edit
-
-You should now see the same file, and edit it to look like this:
-
-.. code-block:: yaml
-
- # This is a Spack Environment file.
- #
- # It describes a set of packages to be installed, along with
- # configuration settings.
- spack:
- packages:
- all:
- providers:
- mpi: [mpich]
-
- # add package specs to the `specs` list
- specs: [tcl, trilinos, hdf5, gmp]
-
-Now if we run ``spack spec`` again in the environment, specs will concretize with ``mpich`` as the MPI implementation:
-
-.. code-block:: console
-
- $ spack spec hypre
- Input spec
- --------------------------------
- hypre
-
- Concretized
- --------------------------------
- hypre@2.15.1%gcc@5.4.0~debug~int64+internal-superlu+mpi+shared arch=linux-ubuntu16.04-x86_64
- ^mpich@3.2.1%gcc@5.4.0 device=ch3 +hydra netmod=tcp +pmi+romio~verbs arch=linux-ubuntu16.04-x86_64
- ^findutils@4.6.0%gcc@5.4.0 patches=84b916c0bf8c51b7e7b28417692f0ad3e7030d1f3c248ba77c42ede5c1c5d11e,bd9e4e5cc280f9753ae14956c4e4aa17fe7a210f55dd6c84aa60b12d106d47a2 arch=linux-ubuntu16.04-x86_64
- ^autoconf@2.69%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
- ^m4@1.4.18%gcc@5.4.0 patches=3877ab548f88597ab2327a2230ee048d2d07ace1062efe81fc92e91b7f39cd00,c0a408fbffb7255fcc75e26bd8edab116fc81d216bfd18b473668b7739a4158e,fc9b61654a3ba1a8d6cd78ce087e7c96366c290bc8d2c299f09828d793b853c8 +sigsegv arch=linux-ubuntu16.04-x86_64
- ^libsigsegv@2.11%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
- ^perl@5.26.2%gcc@5.4.0+cpanm patches=0eac10ed90aeb0459ad8851f88081d439a4e41978e586ec743069e8b059370ac +shared+threads arch=linux-ubuntu16.04-x86_64
- ^gdbm@1.14.1%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
- ^readline@7.0%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
- ^ncurses@6.1%gcc@5.4.0~symlinks~termlib arch=linux-ubuntu16.04-x86_64
- ^pkgconf@1.4.2%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
- ^automake@1.16.1%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
- ^libtool@2.4.6%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
- ^texinfo@6.5%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
- ^openblas@0.3.3%gcc@5.4.0 cpu_target= ~ilp64 patches=47cfa7a952ac7b2e4632c73ae199d69fb54490627b66a62c681e21019c4ddc9d,714aea33692304a50bd0ccde42590c176c82ded4a8ac7f06e573dc8071929c33 +pic+shared threads=none ~virtual_machine arch=linux-ubuntu16.04-x86_64
-
-In addition to the ``specs`` section, an environment's configuration can
-contain any of the configuration options from Spack's various config
-sections. You can add custom repositories, a custom install location,
-custom compilers, or custom external packages, in addition to the ``package``
-preferences we show here.
-
-But now we have a problem. We already installed part of this environment
-with openmpi, but now we want to install it with ``mpich``.
-
-You can run ``spack concretize`` inside of an environment to concretize
-all of its specs. We can run it here:
-
-.. code-block:: console
-
- $ spack concretize -f
- ==> Concretizing tcl
- [+] qhwyccy tcl@8.6.8%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
- [+] 5nus6kn ^zlib@1.2.11%gcc@5.4.0+optimize+pic+shared arch=linux-ubuntu16.04-x86_64
- ==> Concretizing trilinos
- [+] kqc52mo trilinos@12.12.1%gcc@5.4.0~alloptpkgs+amesos+amesos2+anasazi+aztec+belos+boost build_type=RelWithDebInfo ~cgns~complex~dtk+epetra+epetraext+exodus+explicit_template_instantiation~float+fortran~fortrilinos+gtest+hdf5+hypre+ifpack+ifpack2~intrepid~intrepid2~isorropia+kokkos+metis~minitensor+ml+muelu+mumps~nox~openmp~phalanx~piro~pnetcdf~python~rol~rythmos+sacado~shards+shared~stk+suite-sparse~superlu~superlu-dist~teko~tempus+teuchos+tpetra~x11~xsdkflags~zlib+zoltan+zoltan2 arch=linux-ubuntu16.04-x86_64
- [+] zbgfxap ^boost@1.68.0%gcc@5.4.0+atomic+chrono~clanglibcpp cxxstd=default +date_time~debug+exception+filesystem+graph~icu+iostreams+locale+log+math~mpi+multithreaded~numpy patches=2ab6c72d03dec6a4ae20220a9dfd5c8c572c5294252155b85c6874d97c323199 +program_options~python+random+regex+serialization+shared+signals~singlethreaded+system~taggedlayout+test+thread+timer~versionedlayout+wave arch=linux-ubuntu16.04-x86_64
- [+] ufczdvs ^bzip2@1.0.6%gcc@5.4.0+shared arch=linux-ubuntu16.04-x86_64
- [+] 2rhuivg ^diffutils@3.6%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
- [+] 5nus6kn ^zlib@1.2.11%gcc@5.4.0+optimize+pic+shared arch=linux-ubuntu16.04-x86_64
- [+] otafqzh ^cmake@3.12.3%gcc@5.4.0~doc+ncurses+openssl+ownlibs patches=dd3a40d4d92f6b2158b87d6fb354c277947c776424aa03f6dc8096cf3135f5d0 ~qt arch=linux-ubuntu16.04-x86_64
- [+] 3o765ou ^ncurses@6.1%gcc@5.4.0~symlinks~termlib arch=linux-ubuntu16.04-x86_64
- [+] fovrh7a ^pkgconf@1.4.2%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
- [+] b4y3w3b ^openssl@1.0.2o%gcc@5.4.0+systemcerts arch=linux-ubuntu16.04-x86_64
- [+] ic2kyoa ^perl@5.26.2%gcc@5.4.0+cpanm patches=0eac10ed90aeb0459ad8851f88081d439a4e41978e586ec743069e8b059370ac +shared+threads arch=linux-ubuntu16.04-x86_64
- [+] q4fpyuo ^gdbm@1.14.1%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
- [+] nxhwrg7 ^readline@7.0%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
- [+] jnw622j ^glm@0.9.7.1%gcc@5.4.0 build_type=RelWithDebInfo arch=linux-ubuntu16.04-x86_64
- [+] xxd7syh ^hdf5@1.10.4%gcc@5.4.0~cxx~debug~fortran+hl+mpi+pic+shared~szip~threadsafe arch=linux-ubuntu16.04-x86_64
- [+] p3f7p2r ^mpich@3.2.1%gcc@5.4.0 device=ch3 +hydra netmod=tcp +pmi+romio~verbs arch=linux-ubuntu16.04-x86_64
- [+] d4iajxs ^findutils@4.6.0%gcc@5.4.0 patches=84b916c0bf8c51b7e7b28417692f0ad3e7030d1f3c248ba77c42ede5c1c5d11e,bd9e4e5cc280f9753ae14956c4e4aa17fe7a210f55dd6c84aa60b12d106d47a2 arch=linux-ubuntu16.04-x86_64
- [+] 3sx2gxe ^autoconf@2.69%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
- [+] suf5jtc ^m4@1.4.18%gcc@5.4.0 patches=3877ab548f88597ab2327a2230ee048d2d07ace1062efe81fc92e91b7f39cd00,c0a408fbffb7255fcc75e26bd8edab116fc81d216bfd18b473668b7739a4158e,fc9b61654a3ba1a8d6cd78ce087e7c96366c290bc8d2c299f09828d793b853c8 +sigsegv arch=linux-ubuntu16.04-x86_64
- [+] fypapcp ^libsigsegv@2.11%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
- [+] rymw7im ^automake@1.16.1%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
- [+] o2pfwjf ^libtool@2.4.6%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
- [+] zs7a2pc ^texinfo@6.5%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
- [+] obewuoz ^hypre@2.15.1%gcc@5.4.0~debug~int64~internal-superlu+mpi+shared arch=linux-ubuntu16.04-x86_64
- [+] cyeg2yi ^openblas@0.3.3%gcc@5.4.0 cpu_target= ~ilp64 patches=47cfa7a952ac7b2e4632c73ae199d69fb54490627b66a62c681e21019c4ddc9d,714aea33692304a50bd0ccde42590c176c82ded4a8ac7f06e573dc8071929c33 +pic+shared threads=none ~virtual_machine arch=linux-ubuntu16.04-x86_64
- [+] gvyqldh ^matio@1.5.9%gcc@5.4.0+hdf5+shared+zlib arch=linux-ubuntu16.04-x86_64
- [+] 3wnvp4j ^metis@5.1.0%gcc@5.4.0 build_type=Release ~gdb~int64 patches=4991da938c1d3a1d3dea78e49bbebecba00273f98df2a656e38b83d55b281da1 ~real64+shared arch=linux-ubuntu16.04-x86_64
- [+] cumcj5a ^mumps@5.1.1%gcc@5.4.0+complex+double+float~int64~metis+mpi~parmetis~ptscotch~scotch+shared arch=linux-ubuntu16.04-x86_64
- [+] p7iln2p ^netlib-scalapack@2.0.2%gcc@5.4.0 build_type=RelWithDebInfo ~pic+shared arch=linux-ubuntu16.04-x86_64
- [+] wmmx5sg ^netcdf@4.6.1%gcc@5.4.0~dap~hdf4 maxdims=1024 maxvars=8192 +mpi~parallel-netcdf+shared arch=linux-ubuntu16.04-x86_64
- [+] jehtata ^parmetis@4.0.3%gcc@5.4.0 build_type=RelWithDebInfo ~gdb patches=4f892531eb0a807eb1b82e683a416d3e35154a455274cf9b162fb02054d11a5b,50ed2081bc939269689789942067c58b3e522c269269a430d5d34c00edbc5870,704b84f7c7444d4372cb59cca6e1209df4ef3b033bc4ee3cf50f369bce972a9d +shared arch=linux-ubuntu16.04-x86_64
- [+] zaau4ki ^suite-sparse@5.3.0%gcc@5.4.0~cuda~openmp+pic~tbb arch=linux-ubuntu16.04-x86_64
- ==> Concretizing hdf5
- - zjgyn3w hdf5@1.10.4%gcc@5.4.0~cxx~debug~fortran~hl+mpi+pic+shared~szip~threadsafe arch=linux-ubuntu16.04-x86_64
- [+] p3f7p2r ^mpich@3.2.1%gcc@5.4.0 device=ch3 +hydra netmod=tcp +pmi+romio~verbs arch=linux-ubuntu16.04-x86_64
- [+] d4iajxs ^findutils@4.6.0%gcc@5.4.0 patches=84b916c0bf8c51b7e7b28417692f0ad3e7030d1f3c248ba77c42ede5c1c5d11e,bd9e4e5cc280f9753ae14956c4e4aa17fe7a210f55dd6c84aa60b12d106d47a2 arch=linux-ubuntu16.04-x86_64
- [+] 3sx2gxe ^autoconf@2.69%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
- [+] suf5jtc ^m4@1.4.18%gcc@5.4.0 patches=3877ab548f88597ab2327a2230ee048d2d07ace1062efe81fc92e91b7f39cd00,c0a408fbffb7255fcc75e26bd8edab116fc81d216bfd18b473668b7739a4158e,fc9b61654a3ba1a8d6cd78ce087e7c96366c290bc8d2c299f09828d793b853c8 +sigsegv arch=linux-ubuntu16.04-x86_64
- [+] fypapcp ^libsigsegv@2.11%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
- [+] ic2kyoa ^perl@5.26.2%gcc@5.4.0+cpanm patches=0eac10ed90aeb0459ad8851f88081d439a4e41978e586ec743069e8b059370ac +shared+threads arch=linux-ubuntu16.04-x86_64
- [+] q4fpyuo ^gdbm@1.14.1%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
- [+] nxhwrg7 ^readline@7.0%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
- [+] 3o765ou ^ncurses@6.1%gcc@5.4.0~symlinks~termlib arch=linux-ubuntu16.04-x86_64
- [+] fovrh7a ^pkgconf@1.4.2%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
- [+] rymw7im ^automake@1.16.1%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
- [+] o2pfwjf ^libtool@2.4.6%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
- [+] zs7a2pc ^texinfo@6.5%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
- [+] 5nus6kn ^zlib@1.2.11%gcc@5.4.0+optimize+pic+shared arch=linux-ubuntu16.04-x86_64
- ==> Concretizing gmp
- [+] qc4qcfz gmp@6.1.2%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
- [+] 3sx2gxe ^autoconf@2.69%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
- [+] suf5jtc ^m4@1.4.18%gcc@5.4.0 patches=3877ab548f88597ab2327a2230ee048d2d07ace1062efe81fc92e91b7f39cd00,c0a408fbffb7255fcc75e26bd8edab116fc81d216bfd18b473668b7739a4158e,fc9b61654a3ba1a8d6cd78ce087e7c96366c290bc8d2c299f09828d793b853c8 +sigsegv arch=linux-ubuntu16.04-x86_64
- [+] fypapcp ^libsigsegv@2.11%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
- [+] ic2kyoa ^perl@5.26.2%gcc@5.4.0+cpanm patches=0eac10ed90aeb0459ad8851f88081d439a4e41978e586ec743069e8b059370ac +shared+threads arch=linux-ubuntu16.04-x86_64
- [+] q4fpyuo ^gdbm@1.14.1%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
- [+] nxhwrg7 ^readline@7.0%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
- [+] 3o765ou ^ncurses@6.1%gcc@5.4.0~symlinks~termlib arch=linux-ubuntu16.04-x86_64
- [+] fovrh7a ^pkgconf@1.4.2%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
- [+] rymw7im ^automake@1.16.1%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
- [+] o2pfwjf ^libtool@2.4.6%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
-
-Now, all the specs in the environment are concrete and ready to be
-installed with ``mpich`` as the MPI implementation.
-
-Normally, we could just run ``spack config edit``, edit the environment
-configuration, ``spack add`` some specs, and ``spack install``.
-
-But, when we already have installed packages in the environment, we have
-to force everything in the environment to be re-concretized using ``spack
-concretize -f``. *Then* we can re-run ``spack install``.
-
-
------------------------------------
-``spack.yaml`` and ``spack.lock``
------------------------------------
-
-So far we've shown you how to interact with environments from the command
-line, but they also have a file-based interface that can be used by
-developers and admins to manage workflows for projects.
-
-In this section we'll dive a little deeper to see how environments are
-implemented, and how you could use this in your day-to-day development.
-
-^^^^^^^^^^^^^^
-``spack.yaml``
-^^^^^^^^^^^^^^
-
-Earlier, we changed an environment's configuration using ``spack config
-edit``. We were actually editing a special file called ``spack.yaml``.
-Let's take a look.
-
-We can get directly to the current environment's location using ``spack cd``:
-
-.. code-block:: console
-
- $ spack cd -e myproject
- $ pwd
- ~/spack/var/spack/environments/myproject
- $ ls
- spack.lock spack.yaml
-
-We notice two things here. First, the environment is just a directory
-inside of ``var/spack/environments`` within the Spack installation.
-Second, it contains two important files: ``spack.yaml`` and
-``spack.lock``.
-
-``spack.yaml`` is the configuration file for environments that we've
-already seen, but it does not *have* to live inside Spack. If you create
-an environment using ``spack env create``, it is *managed* by
-Spack in the ``var/spack/environments`` directory, and you can refer to
-it by name.
-
-You can actually put a ``spack.yaml`` file *anywhere*, and you can use it
-to bundle an environment, or a list of dependencies to install, with your
-project. Let's make a simple project:
-
-.. code-block:: console
-
- $ cd
- $ mkdir code
- $ cd code
- $ spack env create -d .
- ==> Created environment in ~/code
-
-Here, we made a new directory called *code*, and we used the ``-d``
-option to create an environment in it.
-
-What really happened?
-
-.. code-block:: console
-
- $ ls
- spack.yaml
- $ cat spack.yaml
- # This is a Spack Environment file.
- #
- # It describes a set of packages to be installed, along with
- # configuration settings.
- spack:
- # add package specs to the `specs` list
- specs: []
-
-Spack just created a ``spack.yaml`` file in the code directory, with an
-empty list of root specs. Now we have a Spack environment, *in a
-directory*, that we can use to manage dependencies. Suppose your project
-depends on ``boost``, ``trilinos``, and ``openmpi``. You can add these
-to your spec list:
-
-.. code-block:: yaml
-
- # This is a Spack Environment file.
- #
- # It describes a set of packages to be installed, along with
- # configuration settings.
- spack:
- # add package specs to the `specs` list
- specs:
- - boost
- - trilinos
- - openmpi
-
-And now *anyone* who uses the *code* repository can use this format to
-install the project's dependencies. They need only clone the repository,
-``cd`` into it, and type ``spack install``:
-
-.. code-block:: console
-
- $ spack install
- ==> Concretizing boost
- [+] zbgfxap boost@1.68.0%gcc@5.4.0+atomic+chrono~clanglibcpp cxxstd=default +date_time~debug+exception+filesystem+graph~icu+iostreams+locale+log+math~mpi+multithreaded~numpy patches=2ab6c72d03dec6a4ae20220a9dfd5c8c572c5294252155b85c6874d97c323199 +program_options~python+random+regex+serialization+shared+signals~singlethreaded+system~taggedlayout+test+thread+timer~versionedlayout+wave arch=linux-ubuntu16.04-x86_64
- [+] ufczdvs ^bzip2@1.0.6%gcc@5.4.0+shared arch=linux-ubuntu16.04-x86_64
- [+] 2rhuivg ^diffutils@3.6%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
- [+] 5nus6kn ^zlib@1.2.11%gcc@5.4.0+optimize+pic+shared arch=linux-ubuntu16.04-x86_64
- ==> Concretizing trilinos
- [+] rlsruav trilinos@12.12.1%gcc@5.4.0~alloptpkgs+amesos+amesos2+anasazi+aztec+belos+boost build_type=RelWithDebInfo ~cgns~complex~dtk+epetra+epetraext+exodus+explicit_template_instantiation~float+fortran~fortrilinos+gtest+hdf5+hypre+ifpack+ifpack2~intrepid~intrepid2~isorropia+kokkos+metis~minitensor+ml+muelu+mumps~nox~openmp~phalanx~piro~pnetcdf~python~rol~rythmos+sacado~shards+shared~stk+suite-sparse~superlu~superlu-dist~teko~tempus+teuchos+tpetra~x11~xsdkflags~zlib+zoltan+zoltan2 arch=linux-ubuntu16.04-x86_64
- [+] zbgfxap ^boost@1.68.0%gcc@5.4.0+atomic+chrono~clanglibcpp cxxstd=default +date_time~debug+exception+filesystem+graph~icu+iostreams+locale+log+math~mpi+multithreaded~numpy patches=2ab6c72d03dec6a4ae20220a9dfd5c8c572c5294252155b85c6874d97c323199 +program_options~python+random+regex+serialization+shared+signals~singlethreaded+system~taggedlayout+test+thread+timer~versionedlayout+wave arch=linux-ubuntu16.04-x86_64
- [+] ufczdvs ^bzip2@1.0.6%gcc@5.4.0+shared arch=linux-ubuntu16.04-x86_64
- [+] 2rhuivg ^diffutils@3.6%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
- [+] 5nus6kn ^zlib@1.2.11%gcc@5.4.0+optimize+pic+shared arch=linux-ubuntu16.04-x86_64
- [+] otafqzh ^cmake@3.12.3%gcc@5.4.0~doc+ncurses+openssl+ownlibs patches=dd3a40d4d92f6b2158b87d6fb354c277947c776424aa03f6dc8096cf3135f5d0 ~qt arch=linux-ubuntu16.04-x86_64
- [+] 3o765ou ^ncurses@6.1%gcc@5.4.0~symlinks~termlib arch=linux-ubuntu16.04-x86_64
- [+] fovrh7a ^pkgconf@1.4.2%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
- [+] b4y3w3b ^openssl@1.0.2o%gcc@5.4.0+systemcerts arch=linux-ubuntu16.04-x86_64
- [+] ic2kyoa ^perl@5.26.2%gcc@5.4.0+cpanm patches=0eac10ed90aeb0459ad8851f88081d439a4e41978e586ec743069e8b059370ac +shared+threads arch=linux-ubuntu16.04-x86_64
- [+] q4fpyuo ^gdbm@1.14.1%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
- [+] nxhwrg7 ^readline@7.0%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
- [+] jnw622j ^glm@0.9.7.1%gcc@5.4.0 build_type=RelWithDebInfo arch=linux-ubuntu16.04-x86_64
- [+] oqwnui7 ^hdf5@1.10.4%gcc@5.4.0~cxx~debug~fortran+hl+mpi+pic+shared~szip~threadsafe arch=linux-ubuntu16.04-x86_64
- [+] 3njc4q5 ^openmpi@3.1.3%gcc@5.4.0~cuda+cxx_exceptions fabrics= ~java~legacylaunchers~memchecker~pmi schedulers= ~sqlite3~thread_multiple+vt arch=linux-ubuntu16.04-x86_64
- [+] 43tkw5m ^hwloc@1.11.9%gcc@5.4.0~cairo~cuda+libxml2+pci+shared arch=linux-ubuntu16.04-x86_64
- [+] 5urc6tc ^libpciaccess@0.13.5%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
- [+] o2pfwjf ^libtool@2.4.6%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
- [+] suf5jtc ^m4@1.4.18%gcc@5.4.0 patches=3877ab548f88597ab2327a2230ee048d2d07ace1062efe81fc92e91b7f39cd00,c0a408fbffb7255fcc75e26bd8edab116fc81d216bfd18b473668b7739a4158e,fc9b61654a3ba1a8d6cd78ce087e7c96366c290bc8d2c299f09828d793b853c8 +sigsegv arch=linux-ubuntu16.04-x86_64
- [+] fypapcp ^libsigsegv@2.11%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
- [+] milz7fm ^util-macros@1.19.1%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
- [+] wpexsph ^libxml2@2.9.8%gcc@5.4.0~python arch=linux-ubuntu16.04-x86_64
- [+] teneqii ^xz@5.2.4%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
- [+] ft463od ^numactl@2.0.11%gcc@5.4.0 patches=592f30f7f5f757dfc239ad0ffd39a9a048487ad803c26b419e0f96b8cda08c1a arch=linux-ubuntu16.04-x86_64
- [+] 3sx2gxe ^autoconf@2.69%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
- [+] rymw7im ^automake@1.16.1%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
- [+] fshksdp ^hypre@2.15.1%gcc@5.4.0~debug~int64~internal-superlu+mpi+shared arch=linux-ubuntu16.04-x86_64
- [+] cyeg2yi ^openblas@0.3.3%gcc@5.4.0 cpu_target= ~ilp64 patches=47cfa7a952ac7b2e4632c73ae199d69fb54490627b66a62c681e21019c4ddc9d,714aea33692304a50bd0ccde42590c176c82ded4a8ac7f06e573dc8071929c33 +pic+shared threads=none ~virtual_machine arch=linux-ubuntu16.04-x86_64
- [+] lmzdgss ^matio@1.5.9%gcc@5.4.0+hdf5+shared+zlib arch=linux-ubuntu16.04-x86_64
- [+] 3wnvp4j ^metis@5.1.0%gcc@5.4.0 build_type=Release ~gdb~int64 patches=4991da938c1d3a1d3dea78e49bbebecba00273f98df2a656e38b83d55b281da1 ~real64+shared arch=linux-ubuntu16.04-x86_64
- [+] acsg2dz ^mumps@5.1.1%gcc@5.4.0+complex+double+float~int64~metis+mpi~parmetis~ptscotch~scotch+shared arch=linux-ubuntu16.04-x86_64
- [+] wotpfwf ^netlib-scalapack@2.0.2%gcc@5.4.0 build_type=RelWithDebInfo ~pic+shared arch=linux-ubuntu16.04-x86_64
- [+] mhm4izp ^netcdf@4.6.1%gcc@5.4.0~dap~hdf4 maxdims=1024 maxvars=8192 +mpi~parallel-netcdf+shared arch=linux-ubuntu16.04-x86_64
- [+] uv6h3sq ^parmetis@4.0.3%gcc@5.4.0 build_type=RelWithDebInfo ~gdb patches=4f892531eb0a807eb1b82e683a416d3e35154a455274cf9b162fb02054d11a5b,50ed2081bc939269689789942067c58b3e522c269269a430d5d34c00edbc5870,704b84f7c7444d4372cb59cca6e1209df4ef3b033bc4ee3cf50f369bce972a9d +shared arch=linux-ubuntu16.04-x86_64
- [+] zaau4ki ^suite-sparse@5.3.0%gcc@5.4.0~cuda~openmp+pic~tbb arch=linux-ubuntu16.04-x86_64
- ==> Concretizing openmpi
- [+] 3njc4q5 openmpi@3.1.3%gcc@5.4.0~cuda+cxx_exceptions fabrics= ~java~legacylaunchers~memchecker~pmi schedulers= ~sqlite3~thread_multiple+vt arch=linux-ubuntu16.04-x86_64
- [+] 43tkw5m ^hwloc@1.11.9%gcc@5.4.0~cairo~cuda+libxml2+pci+shared arch=linux-ubuntu16.04-x86_64
- [+] 5urc6tc ^libpciaccess@0.13.5%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
- [+] o2pfwjf ^libtool@2.4.6%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
- [+] suf5jtc ^m4@1.4.18%gcc@5.4.0 patches=3877ab548f88597ab2327a2230ee048d2d07ace1062efe81fc92e91b7f39cd00,c0a408fbffb7255fcc75e26bd8edab116fc81d216bfd18b473668b7739a4158e,fc9b61654a3ba1a8d6cd78ce087e7c96366c290bc8d2c299f09828d793b853c8 +sigsegv arch=linux-ubuntu16.04-x86_64
- [+] fypapcp ^libsigsegv@2.11%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
- [+] fovrh7a ^pkgconf@1.4.2%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
- [+] milz7fm ^util-macros@1.19.1%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
- [+] wpexsph ^libxml2@2.9.8%gcc@5.4.0~python arch=linux-ubuntu16.04-x86_64
- [+] teneqii ^xz@5.2.4%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
- [+] 5nus6kn ^zlib@1.2.11%gcc@5.4.0+optimize+pic+shared arch=linux-ubuntu16.04-x86_64
- [+] ft463od ^numactl@2.0.11%gcc@5.4.0 patches=592f30f7f5f757dfc239ad0ffd39a9a048487ad803c26b419e0f96b8cda08c1a arch=linux-ubuntu16.04-x86_64
- [+] 3sx2gxe ^autoconf@2.69%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
- [+] ic2kyoa ^perl@5.26.2%gcc@5.4.0+cpanm patches=0eac10ed90aeb0459ad8851f88081d439a4e41978e586ec743069e8b059370ac +shared+threads arch=linux-ubuntu16.04-x86_64
- [+] q4fpyuo ^gdbm@1.14.1%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
- [+] nxhwrg7 ^readline@7.0%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
- [+] 3o765ou ^ncurses@6.1%gcc@5.4.0~symlinks~termlib arch=linux-ubuntu16.04-x86_64
- [+] rymw7im ^automake@1.16.1%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
- ==> Installing environment ~/code
- ==> boost is already installed in ~/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/boost-1.68.0-zbgfxapchxa4awxdwpleubfuznblxzvt
- ==> trilinos is already installed in ~/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/trilinos-12.12.1-rlsruavxqvwk2tgxzxboclbo6ykjf54r
- ==> openmpi is already installed in ~/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/openmpi-3.1.3-3njc4q5pqdpptq6jvqjrezkffwokv2sx
-
-
-Spack concretizes the specs in the ``spack.yaml`` file and installs them.
-
-What happened here? If you ``cd`` into a directory that has a
-``spack.yaml`` file in it, Spack considers this directory's environment
-to be activated. The directory does not have to live within Spack; it
-can be anywhere.
-
-So, from ``~/code``, we can actually manipulate ``spack.yaml`` using
-``spack add`` and ``spack remove`` (just like managed environments):
-
-.. code-block:: console
-
- $ spack add hdf5@5.5.1
- ==> Adding hdf5 to environment ~/code
- $ cat spack.yaml
- # This is a Spack Environment file.
- #
- # It describes a set of packages to be installed, along with
- # configuration settings.
- spack:
- # add package specs to the `specs` list
- specs:
- - boost
- - trilinos
- - openmpi
- - hdf5@5.5.1
-
- $ spack remove hdf5
- ==> Removing hdf5 from environment ~/code
- $ cat spack.yaml
- # This is a Spack Environment file.
- #
- # It describes a set of packages to be installed, along with
- # configuration settings.
- spack:
- # add package specs to the `specs` list
- specs:
- - boost
- - trilinos
- - openmpi
-
-
-^^^^^^^^^^^^^^
-``spack.lock``
-^^^^^^^^^^^^^^
-
-Okay, we've covered managed environments, environments in directories, and
-the last thing we'll cover is ``spack.lock``. You may remember that when
-we ran ``spack install``, Spack concretized all the specs in the
-``spack.yaml`` file and installed them.
-
-Whenever we concretize Specs in an environment, all concrete specs in the
-environment are written out to a ``spack.lock`` file *alongside*
-``spack.yaml``. The ``spack.lock`` file is not really human-readable
-like the ``spack.yaml`` file. It is a ``json`` format that contains all
-the information that we need to *reproduce* the build of an
-environment:
-
-.. code-block:: console
-
- $ head spack.lock
- {
- "concrete_specs": {
- "teneqii2xv5u6zl5r6qi3pwurc6pmypz": {
- "xz": {
- "version": "5.2.4",
- "arch": {
- "platform": "linux",
- "platform_os": "ubuntu16.04",
- "target": "x86_64"
- },
- ...
-
-``spack.yaml`` and ``spack.lock`` correspond to two fundamental concepts
-in Spack, but for environments:
-
- * ``spack.yaml`` is the set of *abstract* specs and configuration that
- you want to install.
- * ``spack.lock`` is the set of all fully *concretized* specs generated
- from concretizing ``spack.yaml``
-
-Using either of these, you can recreate an environment that someone else
-built. ``spack env create`` takes an extra optional argument, which can
-be either a ``spack.yaml`` or a ``spack.lock`` file:
-
-.. code-block:: console
-
- $ spack env create my-project spack.yaml
-
- $ spack env create my-project spack.lock
-
-Both of these create a new environment called ``my-project``, but which
-one you choose to use depends on your needs:
-
-#. copying the yaml file allows someone else to build your *requirements*,
- potentially a different way.
-
-#. copying the lock file allows someone else to rebuild your
- *installation* exactly as you built it.
-
-The first use case can *re-concretize* the same specs on new platforms in
-order to build, but it will preserve the abstract requirements. The
-second use case (currently) requires you to be on the same machine, but
-it retains all decisions made during concretization and is faithful to a
-prior install.
diff --git a/lib/spack/docs/tutorial_modules.rst b/lib/spack/docs/tutorial_modules.rst
deleted file mode 100644
index 686da9f26e715e0ba41def620ac8773af5e5b155..0000000000000000000000000000000000000000
--- a/lib/spack/docs/tutorial_modules.rst
+++ /dev/null
@@ -1,1575 +0,0 @@
-.. Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
- Spack Project Developers. See the top-level COPYRIGHT file for details.
-
- SPDX-License-Identifier: (Apache-2.0 OR MIT)
-
-.. _modules-tutorial:
-
-============
-Module Files
-============
-
-In this tutorial, we'll introduce a few concepts that are fundamental
-to the generation of module files with Spack, and we'll guide you through
-the customization of both module files content and their layout on disk. In the end you
-should have a clear understanding of:
-
- * What are module files and how they work
- * How Spack generates them
- * Which commands are available to ease their maintenance
- * How it is possible to customize them in all aspects
-
-.. _module_file_tutorial_overview:
-
--------------------
-Modules at a glance
--------------------
-
-Let's start by summarizing what module files are and how you can use
-them to modify your environment. The idea is to give enough information so that
-people without any previous exposure to them will be able to follow the tutorial
-later on. We'll also give a high-level view of how module files are generated
-in Spack. If you are already familiar with these topics you can quickly skim
-through this section or move directly to :ref:`module_file_tutorial_prerequisites`.
-
-.. _module_file_tutorial_what_are_modules:
-
-^^^^^^^^^^^^^^^^^^^^^^
-What are module files?
-^^^^^^^^^^^^^^^^^^^^^^
-
-Module files are an easy way to modify your environment in a controlled manner
-during a shell session. In general, they contain the information needed to run an
-application or use a library, and they work in conjunction with a tool that
-interprets them.
-Typical module files instruct this tool to modify the environment variables when a
-module file is loaded:
-
- .. code-block:: console
-
- $ module show zlib
- -------------------------------------------------------------------
- /home/mculpo/PycharmProjects/spack/share/spack/modules/linux-ubuntu14.04-x86_64/zlib/1.2.11-gcc-7.2.0-linux-ubuntu14.04-x86_64-co2px3k:
-
- module-whatis A free, general-purpose, legally unencumbered lossless data-compression library.
- prepend-path MANPATH /home/mculpo/PycharmProjects/spack/opt/spack/linux-ubuntu14.04-x86_64/gcc-7.2.0/zlib-1.2.11-co2px3k53m76lm6tofylh2mur2hnicux/share/man
- prepend-path LIBRARY_PATH /home/mculpo/PycharmProjects/spack/opt/spack/linux-ubuntu14.04-x86_64/gcc-7.2.0/zlib-1.2.11-co2px3k53m76lm6tofylh2mur2hnicux/lib
- prepend-path LD_LIBRARY_PATH /home/mculpo/PycharmProjects/spack/opt/spack/linux-ubuntu14.04-x86_64/gcc-7.2.0/zlib-1.2.11-co2px3k53m76lm6tofylh2mur2hnicux/lib
- prepend-path CPATH /home/mculpo/PycharmProjects/spack/opt/spack/linux-ubuntu14.04-x86_64/gcc-7.2.0/zlib-1.2.11-co2px3k53m76lm6tofylh2mur2hnicux/include
- prepend-path PKG_CONFIG_PATH /home/mculpo/PycharmProjects/spack/opt/spack/linux-ubuntu14.04-x86_64/gcc-7.2.0/zlib-1.2.11-co2px3k53m76lm6tofylh2mur2hnicux/lib/pkgconfig
- prepend-path CMAKE_PREFIX_PATH /home/mculpo/PycharmProjects/spack/opt/spack/linux-ubuntu14.04-x86_64/gcc-7.2.0/zlib-1.2.11-co2px3k53m76lm6tofylh2mur2hnicux/
- -------------------------------------------------------------------
-
- $ echo $LD_LIBRARY_PATH
-
- $ module load zlib
- $ echo $LD_LIBRARY_PATH
- /home/mculpo/PycharmProjects/spack/opt/spack/linux-ubuntu14.04-x86_64/gcc-7.2.0/zlib-1.2.11-co2px3k53m76lm6tofylh2mur2hnicux/lib
-
-and to undo the modifications when the same module file is unloaded:
-
- .. code-block:: console
-
- $ module unload zlib
- $ echo $LD_LIBRARY_PATH
-
- $
-
-Different formats exist for module files, and different tools
-provide various levels of support for them. Spack can natively generate:
-
-1. Non-hierarchical module files written in TCL
-2. Hierarchical module files written in Lua
-
-and can build `environment-modules <http://modules.sourceforge.net/>`_
-and `lmod <http://lmod.readthedocs.io/en/latest>`_ as support tools.
-Which of the formats or tools best suits one's needs depends on each particular
-use-case. For the sake of illustration, we'll be working on
-both formats using ``lmod``.
-
-.. seealso::
- Environment modules
- This is the original tool that provided modules support. Its first
- version was coded in C in the early '90s and was later substituted by a version
- completely coded in TCL - the one Spack is distributing. More details on
- its features are given in the `homepage of the project <http://modules.sourceforge.net/>`_
- or in its `github page <https://github.com/cea-hpc/modules>`_. The tool is able to
- interpret the non-hierarchical TCL modulefiles written by Spack.
-
- Lmod
- Lmod is a module system written in Lua, designed to easily handle hierarchies of
- module files. It's a drop-in replacement of Environment Modules and works with
- both of the module file formats generated by Spack.
- Despite being fully compatible with Environment Modules there are many features that
- are unique to Lmod. These features are either
- `targeted towards safety <http://lmod.readthedocs.io/en/latest/010_user.html#safety-features>`_
- or meant to
- `extend the module system functionality <http://lmod.readthedocs.io/en/latest/010_user.html#module-hierarchy>`_.
-
-
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-How do we generate module files?
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-Before we dive into the hands-on sections it's worth spending a couple of words to explain how
-module files are generated by Spack. The following diagram provides a high-level view
-of the process:
-
-
-.. image:: module_file_generation.*
-
-The red dashed line above represents Spack's boundaries, the blue one Spack's dependencies [#f1]_.
-Module files are generated by combining:
-
- * the configuration details in ``config.yaml`` and ``modules.yaml``
- * the information contained in Spack packages (and processed by the module subpackage)
- * a set of template files
-
-with `Jinja2 <http://jinja.pocoo.org/docs/2.9/>`_, an external template engine
-that stamps out each particular module file. As Spack serves very diverse needs
-this process has many points of customization, and we'll explore most of
-them in the next sections.
-
-.. [#f1] Spack vendors its dependencies! This means that Spack comes with a copy of
- each one of its dependencies, including ``Jinja2``, and is already configured to use them.
-
-.. _module_file_tutorial_prerequisites:
-
-----------------------
-Setup for the tutorial
-----------------------
-
-In order to showcase the capabilities of Spack's module file generation, we need
-a representative set of software to work with. This set must include different
-flavors of the same packages installed alongside each other and some
-:ref:`external packages <sec-external-packages>`.
-
-The purpose of this setup is not to make our life harder but to demonstrate
-how Spack can help with similar situations, as they will happen on real HPC clusters.
-For instance, it's often preferable for Spack to use vendor-provided MPI
-implementations than to build one itself.
-
-To keep the set of software we're dealing with manageable, we're going
-to uninstall everything from earlier in the tutorial.
-
-.. code-block: console
-
- $ spack uninstall -ay
-
-^^^^^^^^^^^^^^^^^^^
-Build a module tool
-^^^^^^^^^^^^^^^^^^^
-
-The first thing that we need is the module tool. In this case we
-choose ``lmod`` as it can work with both hierarchical and non-hierarchical
-module file layouts.
-
-.. code-block:: console
-
- $ bin/spack install lmod
-
-Once the module tool is installed we need to have it available in the
-current shell. As the installation directories are definitely not easy
-to remember, we'll employ the command ``spack location`` to retrieve the
-``lmod`` prefix directly from Spack:
-
-.. code-block:: console
-
- $ . $(spack location -i lmod)/lmod/lmod/init/bash
-
-Now we can re-source the setup file and Spack modules will be put in
-our module path.
-
-.. code-block:: console
-
- $ . share/spack/setup-env.sh
-
-.. FIXME: this needs bootstrap support for ``lmod``
-
-.. FIXME: check the docs here, update them if necessary
- If you need to install Lmod or Environment module you can refer
- to the documentation :ref:`here <InstallEnvironmentModules>`.
-
-
-^^^^^^^^^^^^^^^^^^
-Add a new compiler
-^^^^^^^^^^^^^^^^^^
-
-The second step is to build a recent compiler. On first use, Spack
-scans the environment and automatically locates the compiler(s)
-already available on the system. For this tutorial, however, we want
-to use ``gcc@7.2.0``.
-
-
-.. code-block:: console
-
- $ spack install gcc@7.2.0
- ...
- Wait a long time
- ...
-
-Once ``gcc`` is installed we can use shell support to load it and make
-it readily available:
-
-.. code-block:: console
-
- $ spack load gcc@7.2.0
-
-It may not be apparent, but the last command employed the module files
-generated automatically by Spack. What happens under the hood when you use
-the ``spack load`` command is:
-
-1. the spec passed as argument is translated into a module file name
-2. the current module tool is used to load that module file
-
-You can use this command to double check:
-
-.. code-block:: console
-
- $ module list
- Currently Loaded Modules:
- 1) gcc-7.2.0-gcc-5.4.0-b7smjjc
-
-Note that the 7-digit hash at the end of the generated module may vary depending
-on architecture or package version. Now that we have ``gcc@7.2.0`` in ``PATH`` we
-can finally add it to the list of compilers known to Spack:
-
-.. code-block:: console
-
- $ spack compiler add
- ==> Added 1 new compiler to /home/spack1/.spack/linux/compilers.yaml
- gcc@7.2.0
- ==> Compilers are defined in the following files:
- /home/spack1/.spack/linux/compilers.yaml
-
- $ spack compiler list
- ==> Available compilers
- -- clang ubuntu16.04-x86_64 -------------------------------------
- clang@3.8.0-2ubuntu4 clang@3.7.1-2ubuntu2
-
- -- gcc ubuntu16.04-x86_64 ---------------------------------------
- gcc@7.2.0 gcc@5.4.0 gcc@4.7
-
-
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-Build the software that will be used in the tutorial
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-Finally, we should use Spack to install the packages used in the examples:
-
-.. code-block:: console
-
- $ spack install netlib-scalapack ^openmpi ^openblas
- $ spack install netlib-scalapack ^mpich ^openblas
- $ spack install netlib-scalapack ^openmpi ^netlib-lapack
- $ spack install netlib-scalapack ^mpich ^netlib-lapack
- $ spack install py-scipy ^openblas
-
-
-.. _module_file_tutorial_non_hierarchical:
-
------------------------------
-Non-hierarchical module files
------------------------------
-
-If you arrived to this point you should have an environment that looks similar to:
-
-.. code-block:: console
-
- $ module avail
-
- ----------------------------------------------- /home/spack1/spack/share/spack/modules/linux-ubuntu16.04-x86_64 -----------------------------------------------
- autoconf-2.69-gcc-5.4.0-3sx2gxe libsigsegv-2.11-gcc-7.2.0-g67xpfd openssl-1.0.2o-gcc-5.4.0-b4y3w3b
- autoconf-2.69-gcc-7.2.0-yb2makb libtool-2.4.6-gcc-5.4.0-o2pfwjf openssl-1.0.2o-gcc-7.2.0-cvldq3v
- automake-1.16.1-gcc-5.4.0-rymw7im libtool-2.4.6-gcc-7.2.0-kt2udm6 pcre-8.42-gcc-5.4.0-gt5lgzi
- automake-1.16.1-gcc-7.2.0-qoowd5q libxml2-2.9.8-gcc-5.4.0-wpexsph perl-5.26.2-gcc-5.4.0-ic2kyoa
- bzip2-1.0.6-gcc-5.4.0-ufczdvs libxml2-2.9.8-gcc-7.2.0-47gf5kk perl-5.26.2-gcc-7.2.0-fdwz5yu
- bzip2-1.0.6-gcc-7.2.0-mwamumj lmod-7.8-gcc-5.4.0-kmhks3p pkgconf-1.4.2-gcc-5.4.0-fovrh7a
- cmake-3.12.3-gcc-7.2.0-obqgn2v lua-5.3.4-gcc-5.4.0-cpfeo2w pkgconf-1.4.2-gcc-7.2.0-yoxwmgb
- curl-7.60.0-gcc-5.4.0-vzqreb2 lua-luafilesystem-1_6_3-gcc-5.4.0-alakjim py-numpy-1.15.2-gcc-7.2.0-wbwtcxf
- diffutils-3.6-gcc-5.4.0-2rhuivg lua-luaposix-33.4.0-gcc-5.4.0-7wqhwoc py-scipy-1.1.0-gcc-7.2.0-d5n3cph
- diffutils-3.6-gcc-7.2.0-eauxwi7 m4-1.4.18-gcc-5.4.0-suf5jtc py-setuptools-40.4.3-gcc-7.2.0-5dbwfwn
- expat-2.2.5-gcc-5.4.0-emyv67q m4-1.4.18-gcc-7.2.0-wdzvagl python-2.7.15-gcc-7.2.0-ucmr2mn
- findutils-4.6.0-gcc-7.2.0-ca4b7zq mpc-1.1.0-gcc-5.4.0-iuf3gc3 readline-7.0-gcc-5.4.0-nxhwrg7
- gcc-7.2.0-gcc-5.4.0-b7smjjc (L) mpfr-3.1.6-gcc-5.4.0-jnt2nnp readline-7.0-gcc-7.2.0-ccruj2i
- gdbm-1.14.1-gcc-5.4.0-q4fpyuo mpich-3.2.1-gcc-7.2.0-vt5xcat sqlite-3.23.1-gcc-7.2.0-5ltus3a
- gdbm-1.14.1-gcc-7.2.0-zk5lhob ncurses-6.1-gcc-5.4.0-3o765ou tar-1.30-gcc-5.4.0-dk7lrpo
- gettext-0.19.8.1-gcc-5.4.0-tawgous ncurses-6.1-gcc-7.2.0-xcgzqdv tcl-8.6.8-gcc-5.4.0-qhwyccy
- git-2.19.1-gcc-5.4.0-p3gjnfa netlib-lapack-3.8.0-gcc-7.2.0-fj7nayd texinfo-6.5-gcc-7.2.0-cuqnfgf
- gmp-6.1.2-gcc-5.4.0-qc4qcfz netlib-scalapack-2.0.2-gcc-7.2.0-67nmj7g unzip-6.0-gcc-5.4.0-ba23fbg
- hwloc-1.11.9-gcc-7.2.0-gbyc65s netlib-scalapack-2.0.2-gcc-7.2.0-6jgjbyg util-macros-1.19.1-gcc-7.2.0-t62kozq
- isl-0.18-gcc-5.4.0-vttqout netlib-scalapack-2.0.2-gcc-7.2.0-prgo67d xz-5.2.4-gcc-5.4.0-teneqii
- libbsd-0.8.6-gcc-5.4.0-f4qkkwm netlib-scalapack-2.0.2-gcc-7.2.0-zxpt252 xz-5.2.4-gcc-7.2.0-rql5kog
- libiconv-1.15-gcc-5.4.0-u2x3umv numactl-2.0.11-gcc-7.2.0-rifwktk zlib-1.2.11-gcc-5.4.0-5nus6kn
- libpciaccess-0.13.5-gcc-7.2.0-riipwi2 openblas-0.3.3-gcc-7.2.0-xxoxfh4 zlib-1.2.11-gcc-7.2.0-ezuwp4p
- libsigsegv-2.11-gcc-5.4.0-fypapcp openmpi-3.1.3-gcc-7.2.0-do5xfer
-
- Where:
- L: Module is loaded
-
- Use "module spider" to find all possible modules.
- Use "module keyword key1 key2 ..." to search for all possible modules matching any of the "keys".
-
-The non-hierarchical module files that have been generated so far
-follow :ref:`the default rules for module generation <modules-yaml>`.
-Taking a look at the ``gcc`` module you'll see, for example:
-
-.. code-block:: console
-
- $ module show gcc-7.2.0-gcc-5.4.0-b7smjjc
- -------------------------------------------------------------------------------------------------------------------------------------------------------------------
- /home/spack1/spack/share/spack/modules/linux-ubuntu16.04-x86_64/gcc-7.2.0-gcc-5.4.0-b7smjjc:
- -------------------------------------------------------------------------------------------------------------------------------------------------------------------
- whatis("The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Ada, and Go, as well as libraries for these languages. ")
- prepend_path("PATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/bin")
- prepend_path("MANPATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/share/man")
- prepend_path("LD_LIBRARY_PATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/lib")
- prepend_path("LIBRARY_PATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/lib")
- prepend_path("LD_LIBRARY_PATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/lib64")
- prepend_path("LIBRARY_PATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/lib64")
- prepend_path("CPATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/include")
- prepend_path("CMAKE_PREFIX_PATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/")
- setenv("CC","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/bin/gcc")
- setenv("CXX","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/bin/g++")
- setenv("FC","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/bin/gfortran")
- setenv("F77","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/bin/gfortran")
- setenv("F90","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/bin/gfortran")
- help([[The GNU Compiler Collection includes front ends for C, C++, Objective-C,
- Fortran, Ada, and Go, as well as libraries for these languages.
- ]])
-
-As expected, a few environment variables representing paths will be modified
-by the module file according to the default prefix inspection rules.
-
-
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-Filter unwanted modifications to the environment
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-Now consider the case that your site has decided that ``CPATH`` and
-``LIBRARY_PATH`` modifications should not be present in module files. What you can
-do to abide by the rules is to create a configuration file ``~/.spack/modules.yaml``
-with the following content:
-
-.. code-block:: yaml
-
- modules:
- tcl:
- all:
- filter:
- environment_blacklist: ['CPATH', 'LIBRARY_PATH']
-
-Next you should regenerate all the module files:
-
-.. code-block:: console
-
- $ spack module tcl refresh
- ==> You are about to regenerate tcl module files for:
-
- -- linux-ubuntu16.04-x86_64 / gcc@5.4.0 -------------------------
- 3sx2gxe autoconf@2.69 b7smjjc gcc@7.2.0 f4qkkwm libbsd@0.8.6 cpfeo2w lua@5.3.4 3o765ou ncurses@6.1 dk7lrpo tar@1.30
- rymw7im automake@1.16.1 q4fpyuo gdbm@1.14.1 u2x3umv libiconv@1.15 alakjim lua-luafilesystem@1_6_3 b4y3w3b openssl@1.0.2o qhwyccy tcl@8.6.8
- ufczdvs bzip2@1.0.6 tawgous gettext@0.19.8.1 fypapcp libsigsegv@2.11 7wqhwoc lua-luaposix@33.4.0 gt5lgzi pcre@8.42 ba23fbg unzip@6.0
- vzqreb2 curl@7.60.0 p3gjnfa git@2.19.1 o2pfwjf libtool@2.4.6 suf5jtc m4@1.4.18 ic2kyoa perl@5.26.2 teneqii xz@5.2.4
- 2rhuivg diffutils@3.6 qc4qcfz gmp@6.1.2 wpexsph libxml2@2.9.8 iuf3gc3 mpc@1.1.0 fovrh7a pkgconf@1.4.2 5nus6kn zlib@1.2.11
- emyv67q expat@2.2.5 vttqout isl@0.18 kmhks3p lmod@7.8 jnt2nnp mpfr@3.1.6 nxhwrg7 readline@7.0
-
- -- linux-ubuntu16.04-x86_64 / gcc@7.2.0 -------------------------
- yb2makb autoconf@2.69 riipwi2 libpciaccess@0.13.5 6jgjbyg netlib-scalapack@2.0.2 fdwz5yu perl@5.26.2 cuqnfgf texinfo@6.5
- qoowd5q automake@1.16.1 g67xpfd libsigsegv@2.11 zxpt252 netlib-scalapack@2.0.2 yoxwmgb pkgconf@1.4.2 t62kozq util-macros@1.19.1
- mwamumj bzip2@1.0.6 kt2udm6 libtool@2.4.6 67nmj7g netlib-scalapack@2.0.2 wbwtcxf py-numpy@1.15.2 rql5kog xz@5.2.4
- obqgn2v cmake@3.12.3 47gf5kk libxml2@2.9.8 prgo67d netlib-scalapack@2.0.2 d5n3cph py-scipy@1.1.0 ezuwp4p zlib@1.2.11
- eauxwi7 diffutils@3.6 wdzvagl m4@1.4.18 rifwktk numactl@2.0.11 5dbwfwn py-setuptools@40.4.3
- ca4b7zq findutils@4.6.0 vt5xcat mpich@3.2.1 xxoxfh4 openblas@0.3.3 ucmr2mn python@2.7.15
- zk5lhob gdbm@1.14.1 xcgzqdv ncurses@6.1 do5xfer openmpi@3.1.3 ccruj2i readline@7.0
- gbyc65s hwloc@1.11.9 fj7nayd netlib-lapack@3.8.0 cvldq3v openssl@1.0.2o 5ltus3a sqlite@3.23.1
-
- ==> Do you want to proceed? [y/n] y
- ==> Regenerating tcl module files
-
-If you take a look now at the module for ``gcc`` you'll see that the unwanted
-paths have disappeared:
-
-.. code-block:: console
-
- $ module show gcc-7.2.0-gcc-5.4.0-b7smjjc
- -------------------------------------------------------------------------------------------------------------------------------------------------------------------
- /home/spack1/spack/share/spack/modules/linux-ubuntu16.04-x86_64/gcc-7.2.0-gcc-5.4.0-b7smjjc:
- -------------------------------------------------------------------------------------------------------------------------------------------------------------------
- whatis("The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Ada, and Go, as well as libraries for these languages. ")
- prepend_path("PATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/bin")
- prepend_path("MANPATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/share/man")
- prepend_path("LD_LIBRARY_PATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/lib")
- prepend_path("LD_LIBRARY_PATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/lib64")
- prepend_path("CMAKE_PREFIX_PATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/")
- setenv("CC","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/bin/gcc")
- setenv("CXX","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/bin/g++")
- setenv("FC","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/bin/gfortran")
- setenv("F77","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/bin/gfortran")
- setenv("F90","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/bin/gfortran")
- help([[The GNU Compiler Collection includes front ends for C, C++, Objective-C,
- Fortran, Ada, and Go, as well as libraries for these languages.
- ]])
-
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-Prevent some module files from being generated
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-Another common request at many sites is to avoid exposing software that
-is only needed as an intermediate step when building a newer stack.
-Let's try to prevent the generation of
-module files for anything that is compiled with ``gcc@5.4.0`` (the OS provided compiler).
-
-To do this you should add a ``blacklist`` keyword to ``~/.spack/modules.yaml``:
-
-.. code-block:: yaml
- :emphasize-lines: 3,4
-
- modules:
- tcl:
- blacklist:
- - '%gcc@5.4.0'
- all:
- filter:
- environment_blacklist: ['CPATH', 'LIBRARY_PATH']
-
-and regenerate the module files:
-
-This time it is convenient to pass the option ``--delete-tree`` to the command that
-regenerates the module files to instruct it to delete the existing tree and regenerate
-a new one instead of overwriting the files in the existing directory.
-
-.. code-block:: console
-
- $ spack module tcl refresh --delete-tree
- ==> You are about to regenerate tcl module files for:
-
- -- linux-ubuntu16.04-x86_64 / gcc@5.4.0 -------------------------
- 3sx2gxe autoconf@2.69 b7smjjc gcc@7.2.0 f4qkkwm libbsd@0.8.6 cpfeo2w lua@5.3.4 3o765ou ncurses@6.1 dk7lrpo tar@1.30
- rymw7im automake@1.16.1 q4fpyuo gdbm@1.14.1 u2x3umv libiconv@1.15 alakjim lua-luafilesystem@1_6_3 b4y3w3b openssl@1.0.2o qhwyccy tcl@8.6.8
- ufczdvs bzip2@1.0.6 tawgous gettext@0.19.8.1 fypapcp libsigsegv@2.11 7wqhwoc lua-luaposix@33.4.0 gt5lgzi pcre@8.42 ba23fbg unzip@6.0
- vzqreb2 curl@7.60.0 p3gjnfa git@2.19.1 o2pfwjf libtool@2.4.6 suf5jtc m4@1.4.18 ic2kyoa perl@5.26.2 teneqii xz@5.2.4
- 2rhuivg diffutils@3.6 qc4qcfz gmp@6.1.2 wpexsph libxml2@2.9.8 iuf3gc3 mpc@1.1.0 fovrh7a pkgconf@1.4.2 5nus6kn zlib@1.2.11
- emyv67q expat@2.2.5 vttqout isl@0.18 kmhks3p lmod@7.8 jnt2nnp mpfr@3.1.6 nxhwrg7 readline@7.0
-
- -- linux-ubuntu16.04-x86_64 / gcc@7.2.0 -------------------------
- yb2makb autoconf@2.69 riipwi2 libpciaccess@0.13.5 6jgjbyg netlib-scalapack@2.0.2 fdwz5yu perl@5.26.2 cuqnfgf texinfo@6.5
- qoowd5q automake@1.16.1 g67xpfd libsigsegv@2.11 zxpt252 netlib-scalapack@2.0.2 yoxwmgb pkgconf@1.4.2 t62kozq util-macros@1.19.1
- mwamumj bzip2@1.0.6 kt2udm6 libtool@2.4.6 67nmj7g netlib-scalapack@2.0.2 wbwtcxf py-numpy@1.15.2 rql5kog xz@5.2.4
- obqgn2v cmake@3.12.3 47gf5kk libxml2@2.9.8 prgo67d netlib-scalapack@2.0.2 d5n3cph py-scipy@1.1.0 ezuwp4p zlib@1.2.11
- eauxwi7 diffutils@3.6 wdzvagl m4@1.4.18 rifwktk numactl@2.0.11 5dbwfwn py-setuptools@40.4.3
- ca4b7zq findutils@4.6.0 vt5xcat mpich@3.2.1 xxoxfh4 openblas@0.3.3 ucmr2mn python@2.7.15
- zk5lhob gdbm@1.14.1 xcgzqdv ncurses@6.1 do5xfer openmpi@3.1.3 ccruj2i readline@7.0
- gbyc65s hwloc@1.11.9 fj7nayd netlib-lapack@3.8.0 cvldq3v openssl@1.0.2o 5ltus3a sqlite@3.23.1
-
- ==> Do you want to proceed? [y/n] y
- ==> Regenerating tcl module files
-
- $ module avail
-
- ----------------------------------------------- /home/spack1/spack/share/spack/modules/linux-ubuntu16.04-x86_64 -----------------------------------------------
- autoconf-2.69-gcc-7.2.0-yb2makb m4-1.4.18-gcc-7.2.0-wdzvagl perl-5.26.2-gcc-7.2.0-fdwz5yu
- automake-1.16.1-gcc-7.2.0-qoowd5q mpich-3.2.1-gcc-7.2.0-vt5xcat pkgconf-1.4.2-gcc-7.2.0-yoxwmgb
- bzip2-1.0.6-gcc-7.2.0-mwamumj ncurses-6.1-gcc-7.2.0-xcgzqdv py-numpy-1.15.2-gcc-7.2.0-wbwtcxf
- cmake-3.12.3-gcc-7.2.0-obqgn2v netlib-lapack-3.8.0-gcc-7.2.0-fj7nayd py-scipy-1.1.0-gcc-7.2.0-d5n3cph
- diffutils-3.6-gcc-7.2.0-eauxwi7 netlib-scalapack-2.0.2-gcc-7.2.0-67nmj7g py-setuptools-40.4.3-gcc-7.2.0-5dbwfwn
- findutils-4.6.0-gcc-7.2.0-ca4b7zq netlib-scalapack-2.0.2-gcc-7.2.0-6jgjbyg python-2.7.15-gcc-7.2.0-ucmr2mn
- gdbm-1.14.1-gcc-7.2.0-zk5lhob netlib-scalapack-2.0.2-gcc-7.2.0-prgo67d readline-7.0-gcc-7.2.0-ccruj2i
- hwloc-1.11.9-gcc-7.2.0-gbyc65s netlib-scalapack-2.0.2-gcc-7.2.0-zxpt252 sqlite-3.23.1-gcc-7.2.0-5ltus3a
- libpciaccess-0.13.5-gcc-7.2.0-riipwi2 numactl-2.0.11-gcc-7.2.0-rifwktk texinfo-6.5-gcc-7.2.0-cuqnfgf
- libsigsegv-2.11-gcc-7.2.0-g67xpfd openblas-0.3.3-gcc-7.2.0-xxoxfh4 util-macros-1.19.1-gcc-7.2.0-t62kozq
- libtool-2.4.6-gcc-7.2.0-kt2udm6 openmpi-3.1.3-gcc-7.2.0-do5xfer xz-5.2.4-gcc-7.2.0-rql5kog
- libxml2-2.9.8-gcc-7.2.0-47gf5kk openssl-1.0.2o-gcc-7.2.0-cvldq3v zlib-1.2.11-gcc-7.2.0-ezuwp4p
-
- Use "module spider" to find all possible modules.
- Use "module keyword key1 key2 ..." to search for all possible modules matching any of the "keys".
-
-If you look closely you'll see though that we went too far in blacklisting modules:
-the module for ``gcc@7.2.0`` disappeared as it was bootstrapped with ``gcc@5.4.0``. To specify
-exceptions to the blacklist rules you can use ``whitelist``:
-
-.. code-block:: yaml
- :emphasize-lines: 3,4
-
- modules:
- tcl:
- whitelist:
- - gcc
- blacklist:
- - '%gcc@5.4.0'
- all:
- filter:
- environment_blacklist: ['CPATH', 'LIBRARY_PATH']
-
-``whitelist`` rules always have precedence over ``blacklist`` rules. If you regenerate the modules again:
-
-.. code-block:: console
-
- $ spack module tcl refresh -y
- ==> Regenerating tcl module files
-
-
-you'll see that now the module for ``gcc@7.2.0`` has reappeared:
-
-.. code-block:: console
-
- $ module avail gcc-7.2.0-gcc-5.4.0-b7smjjc
-
- -------------------------------------------- /home/spack1/spack/share/spack/modules/linux-ubuntu16.04-x86_64 ---------------------------------------------
- gcc-7.2.0-gcc-5.4.0-b7smjjc
-
- Use "module spider" to find all possible modules.
- Use "module keyword key1 key2 ..." to search for all possible modules matching any of the "keys".
-
-An additional possibility that you can leverage to unclutter the environment
-is that of preventing the generation of module files for implicitly installed
-packages. In this case all one needs to do is to add the following line:
-
-.. code-block:: yaml
- :emphasize-lines: 3
-
- modules:
- tcl:
- blacklist_implicits: true
- whitelist:
- - gcc
- blacklist:
- - '%gcc@5.4.0'
- all:
- filter:
- environment_blacklist: ['CPATH', 'LIBRARY_PATH']
-
-to ``modules.yaml`` and regenerate the module file tree as above.
-
-^^^^^^^^^^^^^^^^^^^^^^^^^
-Change module file naming
-^^^^^^^^^^^^^^^^^^^^^^^^^
-
-The next step in making module files more user-friendly is to
-improve their naming scheme.
-To reduce the length of the hash or remove it altogether you can
-use the ``hash_length`` keyword in the configuration file:
-
-.. code-block:: yaml
- :emphasize-lines: 3
-
- modules:
- tcl:
- hash_length: 0
- whitelist:
- - gcc
- blacklist:
- - '%gcc@5.4.0'
- all:
- filter:
- environment_blacklist: ['CPATH', 'LIBRARY_PATH']
-
-If you try to regenerate the module files now you will get an error:
-
-.. code-block:: console
-
- $ spack module tcl refresh --delete-tree -y
- ==> Error: Name clashes detected in module files:
-
- file: /home/spack1/spack/share/spack/modules/linux-ubuntu16.04-x86_64/netlib-scalapack-2.0.2-gcc-7.2.0
- spec: netlib-scalapack@2.0.2%gcc@7.2.0 build_type=RelWithDebInfo ~pic+shared arch=linux-ubuntu16.04-x86_64
- spec: netlib-scalapack@2.0.2%gcc@7.2.0 build_type=RelWithDebInfo ~pic+shared arch=linux-ubuntu16.04-x86_64
- spec: netlib-scalapack@2.0.2%gcc@7.2.0 build_type=RelWithDebInfo ~pic+shared arch=linux-ubuntu16.04-x86_64
- spec: netlib-scalapack@2.0.2%gcc@7.2.0 build_type=RelWithDebInfo ~pic+shared arch=linux-ubuntu16.04-x86_64
-
- ==> Error: Operation aborted
-
-.. note::
- We try to check for errors upfront!
- In Spack we check for errors upfront whenever possible, so don't worry about your module files:
- as a name clash was detected nothing has been changed on disk.
-
-The problem here is that without
-the hashes the four different flavors of ``netlib-scalapack`` map to the same module file
-name. We can add suffixes to differentiate them:
-
-.. code-block:: yaml
- :emphasize-lines: 9-11,14-17
-
- modules:
- tcl:
- hash_length: 0
- whitelist:
- - gcc
- blacklist:
- - '%gcc@5.4.0'
- all:
- suffixes:
- '^openblas': openblas
- '^netlib-lapack': netlib
- filter:
- environment_blacklist: ['CPATH', 'LIBRARY_PATH']
- netlib-scalapack:
- suffixes:
- '^openmpi': openmpi
- '^mpich': mpich
-
-As you can see it is possible to specify rules that apply only to a
-restricted set of packages using :ref:`anonymous specs <anonymous_specs>`.
-Regenerating module files now we obtain:
-
-.. code-block:: console
-
- $ spack module tcl refresh --delete-tree -y
- ==> Regenerating tcl module files
- $ module avail
-
- ----------------------------------------------- /home/spack1/spack/share/spack/modules/linux-ubuntu16.04-x86_64 -----------------------------------------------
- autoconf-2.69-gcc-7.2.0 m4-1.4.18-gcc-7.2.0 pkgconf-1.4.2-gcc-7.2.0
- automake-1.16.1-gcc-7.2.0 mpich-3.2.1-gcc-7.2.0 py-numpy-1.15.2-gcc-7.2.0-openblas
- bzip2-1.0.6-gcc-7.2.0 ncurses-6.1-gcc-7.2.0 py-scipy-1.1.0-gcc-7.2.0-openblas
- cmake-3.12.3-gcc-7.2.0 netlib-lapack-3.8.0-gcc-7.2.0 py-setuptools-40.4.3-gcc-7.2.0
- diffutils-3.6-gcc-7.2.0 netlib-scalapack-2.0.2-gcc-7.2.0-netlib-mpich python-2.7.15-gcc-7.2.0
- findutils-4.6.0-gcc-7.2.0 netlib-scalapack-2.0.2-gcc-7.2.0-netlib-openmpi readline-7.0-gcc-7.2.0
- gcc-7.2.0-gcc-5.4.0 netlib-scalapack-2.0.2-gcc-7.2.0-openblas-mpich sqlite-3.23.1-gcc-7.2.0
- gdbm-1.14.1-gcc-7.2.0 netlib-scalapack-2.0.2-gcc-7.2.0-openblas-openmpi texinfo-6.5-gcc-7.2.0
- hwloc-1.11.9-gcc-7.2.0 numactl-2.0.11-gcc-7.2.0 util-macros-1.19.1-gcc-7.2.0
- libpciaccess-0.13.5-gcc-7.2.0 openblas-0.3.3-gcc-7.2.0 xz-5.2.4-gcc-7.2.0
- libsigsegv-2.11-gcc-7.2.0 openmpi-3.1.3-gcc-7.2.0 zlib-1.2.11-gcc-7.2.0
- libtool-2.4.6-gcc-7.2.0 openssl-1.0.2o-gcc-7.2.0
- libxml2-2.9.8-gcc-7.2.0 perl-5.26.2-gcc-7.2.0
-
- Use "module spider" to find all possible modules.
- Use "module keyword key1 key2 ..." to search for all possible modules matching any of the "keys".
-
-Finally we can set a ``naming_scheme`` to prevent users from loading
-modules that refer to different flavors of the same library/application:
-
-.. code-block:: yaml
- :emphasize-lines: 4,10,11
-
- modules:
- tcl:
- hash_length: 0
- naming_scheme: '{name}/{version}-{compiler.name}-{compiler.version}'
- whitelist:
- - gcc
- blacklist:
- - '%gcc@5.4.0'
- all:
- conflict:
- - '{name}'
- suffixes:
- '^openblas': openblas
- '^netlib-lapack': netlib
- filter:
- environment_blacklist: ['CPATH', 'LIBRARY_PATH']
- netlib-scalapack:
- suffixes:
- '^openmpi': openmpi
- '^mpich': mpich
-
-The final result should look like:
-
-.. code-block:: console
-
- $ spack module tcl refresh --delete-tree -y
- ==> Regenerating tcl module files
- $ module avail
-
- ----------------------------------------------- /home/spack1/spack/share/spack/modules/linux-ubuntu16.04-x86_64 -----------------------------------------------
- autoconf/2.69-gcc-7.2.0 m4/1.4.18-gcc-7.2.0 pkgconf/1.4.2-gcc-7.2.0
- automake/1.16.1-gcc-7.2.0 mpich/3.2.1-gcc-7.2.0 py-numpy/1.15.2-gcc-7.2.0-openblas
- bzip2/1.0.6-gcc-7.2.0 ncurses/6.1-gcc-7.2.0 py-scipy/1.1.0-gcc-7.2.0-openblas
- cmake/3.12.3-gcc-7.2.0 netlib-lapack/3.8.0-gcc-7.2.0 py-setuptools/40.4.3-gcc-7.2.0
- diffutils/3.6-gcc-7.2.0 netlib-scalapack/2.0.2-gcc-7.2.0-netlib-mpich python/2.7.15-gcc-7.2.0
- findutils/4.6.0-gcc-7.2.0 netlib-scalapack/2.0.2-gcc-7.2.0-netlib-openmpi readline/7.0-gcc-7.2.0
- gcc/7.2.0-gcc-5.4.0 netlib-scalapack/2.0.2-gcc-7.2.0-openblas-mpich sqlite/3.23.1-gcc-7.2.0
- gdbm/1.14.1-gcc-7.2.0 netlib-scalapack/2.0.2-gcc-7.2.0-openblas-openmpi (D) texinfo/6.5-gcc-7.2.0
- hwloc/1.11.9-gcc-7.2.0 numactl/2.0.11-gcc-7.2.0 util-macros/1.19.1-gcc-7.2.0
- libpciaccess/0.13.5-gcc-7.2.0 openblas/0.3.3-gcc-7.2.0 xz/5.2.4-gcc-7.2.0
- libsigsegv/2.11-gcc-7.2.0 openmpi/3.1.3-gcc-7.2.0 zlib/1.2.11-gcc-7.2.0
- libtool/2.4.6-gcc-7.2.0 openssl/1.0.2o-gcc-7.2.0
- libxml2/2.9.8-gcc-7.2.0 perl/5.26.2-gcc-7.2.0
-
- Where:
- D: Default Module
-
- Use "module spider" to find all possible modules.
- Use "module keyword key1 key2 ..." to search for all possible modules matching any of the "keys".
-
-.. note::
- TCL specific directive
- The directives ``naming_scheme`` and ``conflict`` are TCL specific and
- can't be used in the ``lmod`` section of the configuration file.
-
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-Add custom environment modifications
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-At many sites it is customary to set an environment variable in a
-package's module file that points to the folder in which the package
-is installed. You can achieve this with Spack by adding an
-``environment`` directive to the configuration file:
-
-.. code-block:: yaml
- :emphasize-lines: 17-19
-
- modules:
- tcl:
- hash_length: 0
- naming_scheme: '{name}/{version}-{compiler.name}-{compiler.version}'
- whitelist:
- - gcc
- blacklist:
- - '%gcc@5.4.0'
- all:
- conflict:
- - '{name}'
- suffixes:
- '^openblas': openblas
- '^netlib-lapack': netlib
- filter:
- environment_blacklist: ['CPATH', 'LIBRARY_PATH']
- environment:
- set:
- '{name}_ROOT': '{prefix}'
- netlib-scalapack:
- suffixes:
- '^openmpi': openmpi
- '^mpich': mpich
-
-Under the hood Spack uses the :meth:`~spack.spec.Spec.format` API to substitute
-tokens in either environment variable names or values. There are two caveats though:
-
-- The set of allowed tokens in variable names is restricted to
- ``name``, ``version``, ``compiler``, ``compiler.name``,
- ``compiler.version``, ``architecture``
-- Any token expanded in a variable name is made uppercase, but other than that
- case sensitivity is preserved
-
-Regenerating the module files results in something like:
-
-.. code-block:: console
- :emphasize-lines: 15
-
- $ spack module tcl refresh -y
- ==> Regenerating tcl module files
-
- $ module show gcc
- -------------------------------------------------------------------------------------------------------------------------------------------------------------------
- /home/spack1/spack/share/spack/modules/linux-ubuntu16.04-x86_64/gcc/7.2.0-gcc-5.4.0:
- -------------------------------------------------------------------------------------------------------------------------------------------------------------------
- whatis("The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Ada, and Go, as well as libraries for these languages. ")
- conflict("gcc")
- prepend_path("PATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/bin")
- prepend_path("MANPATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/share/man")
- prepend_path("LD_LIBRARY_PATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/lib")
- prepend_path("LD_LIBRARY_PATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/lib64")
- prepend_path("CMAKE_PREFIX_PATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/")
- setenv("CC","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/bin/gcc")
- setenv("CXX","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/bin/g++")
- setenv("FC","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/bin/gfortran")
- setenv("F77","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/bin/gfortran")
- setenv("F90","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/bin/gfortran")
- setenv("GCC_ROOT","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs")
- help([[The GNU Compiler Collection includes front ends for C, C++, Objective-C,
- Fortran, Ada, and Go, as well as libraries for these languages.
- ]])
-
-As you can see, the ``gcc`` module has the environment variable ``GCC_ROOT`` set.
-
-Sometimes it's also useful to apply environment modifications selectively and target
-only certain packages. You can, for instance set the common variables ``CC``, ``CXX``,
-etc. in the ``gcc`` module file and apply other custom modifications to the
-``openmpi`` modules as follows:
-
-.. code-block:: yaml
- :emphasize-lines: 20-32
-
- modules:
- tcl:
- hash_length: 0
- naming_scheme: '{name}/{version}-{compiler.name}-{compiler.version}'
- whitelist:
- - gcc
- blacklist:
- - '%gcc@5.4.0'
- all:
- conflict:
- - '{name}'
- suffixes:
- '^openblas': openblas
- '^netlib-lapack': netlib
- filter:
- environment_blacklist: ['CPATH', 'LIBRARY_PATH']
- environment:
- set:
- '{name}_ROOT': '{prefix}'
- gcc:
- environment:
- set:
- CC: gcc
- CXX: g++
- FC: gfortran
- F90: gfortran
- F77: gfortran
- openmpi:
- environment:
- set:
- SLURM_MPI_TYPE: pmi2
- OMPI_MCA_btl_openib_warn_default_gid_prefix: '0'
- netlib-scalapack:
- suffixes:
- '^openmpi': openmpi
- '^mpich': mpich
-
-This time we will be more selective and regenerate only the ``gcc`` and
-``openmpi`` module files:
-
-.. code-block:: console
-
- $ spack module tcl refresh -y gcc
- ==> Regenerating tcl module files
-
- $ spack module tcl refresh -y openmpi
- ==> Regenerating tcl module files
-
- $ module show gcc
- -------------------------------------------------------------------------------------------------------------------------------------------------------------------
- /home/spack1/spack/share/spack/modules/linux-ubuntu16.04-x86_64/gcc/7.2.0-gcc-5.4.0:
- -------------------------------------------------------------------------------------------------------------------------------------------------------------------
- whatis("The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Ada, and Go, as well as libraries for these languages. ")
- conflict("gcc")
- prepend_path("PATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/bin")
- prepend_path("MANPATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/share/man")
- prepend_path("LD_LIBRARY_PATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/lib")
- prepend_path("LD_LIBRARY_PATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/lib64")
- prepend_path("CMAKE_PREFIX_PATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/")
- setenv("CC","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/bin/gcc")
- setenv("CXX","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/bin/g++")
- setenv("FC","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/bin/gfortran")
- setenv("F77","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/bin/gfortran")
- setenv("F90","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/bin/gfortran")
- setenv("GCC_ROOT","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs")
- setenv("CC","gcc")
- setenv("CXX","g++'")
- setenv("FC","gfortran")
- setenv("F77","gfortran")
- setenv("F90","gfortran")
- help([[The GNU Compiler Collection includes front ends for C, C++, Objective-C,
- Fortran, Ada, and Go, as well as libraries for these languages.
- ]])
-
- $ module show openmpi
- -------------------------------------------------------------------------------------------------------------------------------------------------------------------
- /home/spack1/spack/share/spack/modules/linux-ubuntu16.04-x86_64/openmpi/3.1.3-gcc-7.2.0:
- -------------------------------------------------------------------------------------------------------------------------------------------------------------------
- whatis("An open source Message Passing Interface implementation. ")
- conflict("openmpi")
- prepend_path("PATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-7.2.0/openmpi-3.1.3-do5xfer2whhk7gc26atgs3ozr3ljbvs4/bin")
- prepend_path("MANPATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-7.2.0/openmpi-3.1.3-do5xfer2whhk7gc26atgs3ozr3ljbvs4/share/man")
- prepend_path("LD_LIBRARY_PATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-7.2.0/openmpi-3.1.3-do5xfer2whhk7gc26atgs3ozr3ljbvs4/lib")
- prepend_path("PKG_CONFIG_PATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-7.2.0/openmpi-3.1.3-do5xfer2whhk7gc26atgs3ozr3ljbvs4/lib/pkgconfig")
- prepend_path("CMAKE_PREFIX_PATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-7.2.0/openmpi-3.1.3-do5xfer2whhk7gc26atgs3ozr3ljbvs4/")
- setenv("OPENMPI_ROOT","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-7.2.0/openmpi-3.1.3-do5xfer2whhk7gc26atgs3ozr3ljbvs4")
- setenv("SLURM_MPI_TYPE","pmi2")
- setenv("OMPI_MCA_btl_openib_warn_default_gid_prefix","0")
- help([[An open source Message Passing Interface implementation. The Open MPI
- Project is an open source Message Passing Interface implementation that
- is developed and maintained by a consortium of academic, research, and
- industry partners. Open MPI is therefore able to combine the expertise,
- technologies, and resources from all across the High Performance
- Computing community in order to build the best MPI library available.
- Open MPI offers advantages for system and software vendors, application
- developers and computer science researchers.
- ]])
-
-
-^^^^^^^^^^^^^^^^^^^^^
-Autoload dependencies
-^^^^^^^^^^^^^^^^^^^^^
-
-Spack can also generate module files that contain code to load the
-dependencies automatically. You can, for instance generate python
-modules that load their dependencies by adding the ``autoload``
-directive and assigning it the value ``direct``:
-
-.. code-block:: yaml
- :emphasize-lines: 3,38,39
-
- modules:
- tcl:
- verbose: True
- hash_length: 0
- naming_scheme: '{name}/{version}-{compiler.name}-{compiler.version}'
- whitelist:
- - gcc
- blacklist:
- - '%gcc@5.4.0'
- all:
- conflict:
- - '{name}'
- suffixes:
- '^openblas': openblas
- '^netlib-lapack': netlib
- filter:
- environment_blacklist: ['CPATH', 'LIBRARY_PATH']
- environment:
- set:
- '{name}_ROOT': '{prefix}'
- gcc:
- environment:
- set:
- CC: gcc
- CXX: g++
- FC: gfortran
- F90: gfortran
- F77: gfortran
- openmpi:
- environment:
- set:
- SLURM_MPI_TYPE: pmi2
- OMPI_MCA_btl_openib_warn_default_gid_prefix: '0'
- netlib-scalapack:
- suffixes:
- '^openmpi': openmpi
- '^mpich': mpich
- ^python:
- autoload: 'direct'
-
-and regenerating the module files for every package that depends on ``python``:
-
-.. code-block:: console
-
- root@module-file-tutorial:/# spack module tcl refresh -y ^python
- ==> Regenerating tcl module files
-
-Now the ``py-scipy`` module will be:
-
-.. code-block:: tcl
-
- #%Module1.0
- ## Module file created by spack (https://github.com/spack/spack) on 2018-11-11 22:10:48.834221
- ##
- ## py-scipy@1.1.0%gcc@7.2.0 arch=linux-ubuntu16.04-x86_64 /d5n3cph
- ##
-
-
- module-whatis "SciPy (pronounced 'Sigh Pie') is a Scientific Library for Python. It provides many user-friendly and efficient numerical routines such as routines for numerical integration and optimization."
-
- proc ModulesHelp { } {
- puts stderr "SciPy (pronounced "Sigh Pie") is a Scientific Library for Python. It"
- puts stderr "provides many user-friendly and efficient numerical routines such as"
- puts stderr "routines for numerical integration and optimization."
- }
-
- if { [ module-info mode load ] && ![ is-loaded python/2.7.15-gcc-7.2.0 ] } {
- puts stderr "Autoloading python/2.7.15-gcc-7.2.0"
- module load python/2.7.15-gcc-7.2.0
- }
- if { [ module-info mode load ] && ![ is-loaded openblas/0.3.3-gcc-7.2.0 ] } {
- puts stderr "Autoloading openblas/0.3.3-gcc-7.2.0"
- module load openblas/0.3.3-gcc-7.2.0
- }
- if { [ module-info mode load ] && ![ is-loaded py-numpy/1.15.2-gcc-7.2.0-openblas ] } {
- puts stderr "Autoloading py-numpy/1.15.2-gcc-7.2.0-openblas"
- module load py-numpy/1.15.2-gcc-7.2.0-openblas
- }
- conflict py-scipy
-
- prepend-path LD_LIBRARY_PATH "/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-7.2.0/py-scipy-1.1.0-d5n3cphk2lx2v74ypwb6h7tna7vvgdyn/lib"
- prepend-path CMAKE_PREFIX_PATH "/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-7.2.0/py-scipy-1.1.0-d5n3cphk2lx2v74ypwb6h7tna7vvgdyn/"
- prepend-path PYTHONPATH "/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-7.2.0/py-scipy-1.1.0-d5n3cphk2lx2v74ypwb6h7tna7vvgdyn/lib/python2.7/site-packages"
- setenv PY_SCIPY_ROOT "/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-7.2.0/py-scipy-1.1.0-d5n3cphk2lx2v74ypwb6h7tna7vvgdyn"
-
-and will contain code to autoload all the dependencies:
-
-.. code-block:: console
-
- $ module load py-scipy
- Autoloading python/2.7.15-gcc-7.2.0
- Autoloading openblas/0.3.3-gcc-7.2.0
- Autoloading py-numpy/1.15.2-gcc-7.2.0-openblas
-
-In case messages are unwanted during the autoload procedure, it will be
-sufficient to omit the line setting ``verbose: True`` in the configuration file above.
-
--------------------------
-Hierarchical module files
--------------------------
-
-So far we worked with non-hierarchical module files, i.e. with module files
-that are all generated in the same root directory and don't attempt to
-dynamically modify the ``MODULEPATH``. This results in a flat module structure where
-all the software is visible at the same time:
-
-.. code-block:: console
-
- $ module avail
-
- ----------------------------------------------- /home/spack1/spack/share/spack/modules/linux-ubuntu16.04-x86_64 -----------------------------------------------
- autoconf/2.69-gcc-7.2.0 m4/1.4.18-gcc-7.2.0 pkgconf/1.4.2-gcc-7.2.0
- automake/1.16.1-gcc-7.2.0 mpich/3.2.1-gcc-7.2.0 py-numpy/1.15.2-gcc-7.2.0-openblas (L)
- bzip2/1.0.6-gcc-7.2.0 ncurses/6.1-gcc-7.2.0 py-scipy/1.1.0-gcc-7.2.0-openblas (L)
- cmake/3.12.3-gcc-7.2.0 netlib-lapack/3.8.0-gcc-7.2.0 py-setuptools/40.4.3-gcc-7.2.0
- diffutils/3.6-gcc-7.2.0 netlib-scalapack/2.0.2-gcc-7.2.0-netlib-mpich python/2.7.15-gcc-7.2.0 (L)
- findutils/4.6.0-gcc-7.2.0 netlib-scalapack/2.0.2-gcc-7.2.0-netlib-openmpi readline/7.0-gcc-7.2.0
- gcc/7.2.0-gcc-5.4.0 netlib-scalapack/2.0.2-gcc-7.2.0-openblas-mpich sqlite/3.23.1-gcc-7.2.0
- gdbm/1.14.1-gcc-7.2.0 netlib-scalapack/2.0.2-gcc-7.2.0-openblas-openmpi (D) texinfo/6.5-gcc-7.2.0
- hwloc/1.11.9-gcc-7.2.0 numactl/2.0.11-gcc-7.2.0 util-macros/1.19.1-gcc-7.2.0
- libpciaccess/0.13.5-gcc-7.2.0 openblas/0.3.3-gcc-7.2.0 (L) xz/5.2.4-gcc-7.2.0
- libsigsegv/2.11-gcc-7.2.0 openmpi/3.1.3-gcc-7.2.0 zlib/1.2.11-gcc-7.2.0
- libtool/2.4.6-gcc-7.2.0 openssl/1.0.2o-gcc-7.2.0
- libxml2/2.9.8-gcc-7.2.0 perl/5.26.2-gcc-7.2.0
-
- Where:
- L: Module is loaded
- D: Default Module
-
- Use "module spider" to find all possible modules.
- Use "module keyword key1 key2 ..." to search for all possible modules matching any of the "keys".
-
-This layout is quite simple to deploy, but you can see from the above snippet
-that nothing prevents users from loading incompatible sets of modules:
-
-.. code-block:: console
-
- $ module purge
- $ module load netlib-lapack/3.8.0-gcc-7.2.0 openblas/0.3.3-gcc-7.2.0
- $ module list
-
- Currently Loaded Modules:
- 1) netlib-lapack/3.8.0-gcc-7.2.0 2) openblas/0.3.3-gcc-7.2.0
-
-Even if ``conflicts`` directives are carefully placed in module files, they:
-
- - won't enforce a consistent environment, but will just report an error
- - need constant updates, for instance as soon as a new compiler or MPI library is installed
-
-`Hierarchical module files <http://lmod.readthedocs.io/en/latest/080_hierarchy.html>`_ try to
-overcome these shortcomings by showing at start-up only a restricted view of what is
-available on the system: more specifically only the software that has been installed with
-OS provided compilers. Among this software there will be other - usually more recent - compilers
-that, once loaded, will prepend new directories to ``MODULEPATH`` unlocking all the software
-that was compiled with them. This "unlocking" idea can then be extended arbitrarily to
-virtual dependencies, as we'll see in the following section.
-
-^^^^^^^^^^^^^^^^^
-Core/Compiler/MPI
-^^^^^^^^^^^^^^^^^
-
-The most widely used hierarchy is the so called ``Core/Compiler/MPI`` where, on top
-of the compilers, different MPI libraries also unlock software linked to them.
-There are just a few steps needed to adapt the ``modules.yaml`` file we used previously:
-
- #. enable the ``lmod`` file generator
- #. change the ``tcl`` tag to ``lmod``
- #. remove ``tcl`` specific directives (``naming_scheme`` and ``conflict``)
- #. declare which compilers are considered ``core_compilers``
- #. remove the ``mpi`` related suffixes (as they will be substituted by hierarchies)
-
-After these modifications your configuration file should look like:
-
-.. code-block:: yaml
- :emphasize-lines: 2-8
-
- modules:
- enable::
- - lmod
- lmod:
- core_compilers:
- - 'gcc@5.4.0'
- hierarchy:
- - mpi
- hash_length: 0
- whitelist:
- - gcc
- blacklist:
- - '%gcc@5.4.0'
- all:
- suffixes:
- '^openblas': openblas
- '^netlib-lapack': netlib
- filter:
- environment_blacklist: ['CPATH', 'LIBRARY_PATH']
- environment:
- set:
- '{name}_ROOT': '{prefix}'
- gcc:
- environment:
- set:
- CC: gcc
- CXX: g++
- FC: gfortran
- F90: gfortran
- F77: gfortran
- openmpi:
- environment:
- set:
- SLURM_MPI_TYPE: pmi2
- OMPI_MCA_btl_openib_warn_default_gid_prefix: '0'
-
-
-.. note::
- Double colon in configuration files
- The double colon after ``enable`` is intentional and it serves the
- purpose of overriding the default list of enabled generators so
- that only ``lmod`` will be active (see :ref:`config-overrides` for more
- details).
-
-The directive ``core_compilers`` accepts a list of compilers. Everything built
-using these compilers will create a module in the ``Core`` part of the hierarchy,
-which is the entry point for hierarchical module files. It is
-common practice to put the OS provided compilers in the list and only build common utilities
-and other compilers with them.
-
-If we now regenerate the module files:
-
-.. code-block:: console
-
- $ spack module lmod refresh --delete-tree -y
- ==> Regenerating lmod module files
-
-and update ``MODULEPATH`` to point to the ``Core``:
-
-.. code-block:: console
-
- $ module purge
- $ module unuse $HOME/spack/share/spack/modules/linux-ubuntu16.04-x86_64
- $ module use $HOME/spack/share/spack/lmod/linux-ubuntu16.04-x86_64/Core
-
-asking for the available modules will return:
-
-.. code-block:: console
-
- $ module avail
-
- ----------------------------------------------------------- share/spack/lmod/linux-ubuntu16.04-x86_64/Core ------------------------------------------------------------
- gcc/7.2.0
-
- Use "module spider" to find all possible modules.
- Use "module keyword key1 key2 ..." to search for all possible modules matching any of the "keys".
-
-Unsurprisingly, the only visible module is ``gcc``. Loading that we'll unlock
-the ``Compiler`` part of the hierarchy:
-
-.. code-block:: console
-
- $ module load gcc
- $ module avail
-
- ------------------------------------------- /home/spack1/spack/share/spack/lmod/linux-ubuntu16.04-x86_64/gcc/7.2.0 --------------------------------------------
- autoconf/2.69 findutils/4.6.0 libtool/2.4.6 netlib-lapack/3.8.0 perl/5.26.2 python/2.7.15 xz/5.2.4
- automake/1.16.1 gdbm/1.14.1 libxml2/2.9.8 numactl/2.0.11 pkgconf/1.4.2 readline/7.0 zlib/1.2.11
- bzip2/1.0.6 hwloc/1.11.9 m4/1.4.18 openblas/0.3.3 py-numpy/1.15.2-openblas sqlite/3.23.1
- cmake/3.12.3 libpciaccess/0.13.5 mpich/3.2.1 openmpi/3.1.3 py-scipy/1.1.0-openblas texinfo/6.5
- diffutils/3.6 libsigsegv/2.11 ncurses/6.1 openssl/1.0.2o py-setuptools/40.4.3 util-macros/1.19.1
-
- ----------------------------------------------------------- share/spack/lmod/linux-ubuntu16.04-x86_64/Core ------------------------------------------------------------
- gcc/7.2.0 (L)
-
- Where:
- L: Module is loaded
-
- Use "module spider" to find all possible modules.
- Use "module keyword key1 key2 ..." to search for all possible modules matching any of the "keys".
-
-The same holds true also for the ``MPI`` part, that you can enable by loading
-either ``mpich`` or ``openmpi``. Let's start by loading ``mpich``:
-
-.. code-block:: console
-
- $ module load mpich
- $ module avail
-
- --------------------------------- /home/spack1/spack/share/spack/lmod/linux-ubuntu16.04-x86_64/mpich/3.2.1-vt5xcat/gcc/7.2.0 ----------------------------------
- netlib-scalapack/2.0.2-netlib netlib-scalapack/2.0.2-openblas (D)
-
- ------------------------------------------- /home/spack1/spack/share/spack/lmod/linux-ubuntu16.04-x86_64/gcc/7.2.0 --------------------------------------------
- autoconf/2.69 findutils/4.6.0 libtool/2.4.6 netlib-lapack/3.8.0 perl/5.26.2 python/2.7.15 xz/5.2.4
- automake/1.16.1 gdbm/1.14.1 libxml2/2.9.8 numactl/2.0.11 pkgconf/1.4.2 readline/7.0 zlib/1.2.11
- bzip2/1.0.6 hwloc/1.11.9 m4/1.4.18 openblas/0.3.3 py-numpy/1.15.2-openblas sqlite/3.23.1
- cmake/3.12.3 libpciaccess/0.13.5 mpich/3.2.1 (L) openmpi/3.1.3 py-scipy/1.1.0-openblas texinfo/6.5
- diffutils/3.6 libsigsegv/2.11 ncurses/6.1 openssl/1.0.2o py-setuptools/40.4.3 util-macros/1.19.1
-
- ----------------------------------------------------------- share/spack/lmod/linux-ubuntu16.04-x86_64/Core ------------------------------------------------------------
- gcc/7.2.0 (L)
-
- Where:
- L: Module is loaded
- D: Default Module
-
- Use "module spider" to find all possible modules.
- Use "module keyword key1 key2 ..." to search for all possible modules matching any of the "keys".
-
-
- root@module-file-tutorial:/# module load openblas netlib-scalapack/2.0.2-openblas
- root@module-file-tutorial:/# module list
-
- Currently Loaded Modules:
- 1) gcc/7.2.0 2) mpich/3.2.1 3) openblas/0.3.3 4) netlib-scalapack/2.0.2-openblas
-
-At this point we can showcase the improved consistency that a hierarchical layout provides
-over a non-hierarchical one:
-
-.. code-block:: console
-
- $ module load openmpi
-
- Lmod is automatically replacing "mpich/3.2.1" with "openmpi/3.1.3".
-
-
- Due to MODULEPATH changes, the following have been reloaded:
- 1) netlib-scalapack/2.0.2-openblas
-
-``Lmod`` took care of swapping the MPI provider for us, and it also substituted the
-``netlib-scalapack`` module to conform to the change in the MPI.
-In this way we can't accidentally pull-in two different MPI providers at the
-same time or load a module file for a package linked to ``openmpi`` when ``mpich`` is also loaded.
-Consistency for compilers and MPI is ensured by the tool.
-
-
-^^^^^^^^^^^^^^^^^^^^^^^^^^^
-Add LAPACK to the hierarchy
-^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-The hierarchy just shown is already a great improvement over non-hierarchical layouts,
-but it still has an asymmetry: ``LAPACK`` providers cover the same semantic role
-as ``MPI`` providers, but yet they are not part of the hierarchy.
-
-To be more practical, this means that although we have gained an improved consistency in
-our environment when it comes to ``MPI``, we still have the same problems as we had before
-for ``LAPACK`` implementations:
-
-.. code-block:: console
-
- root@module-file-tutorial:/# module list
-
- Currently Loaded Modules:
- 1) gcc/7.2.0 2) openblas/0.3.3 3) openmpi/3.1.3 4) netlib-scalapack/2.0.2-openblas
-
- root@module-file-tutorial:/# module load netlib-scalapack/2.0.2-netlib
-
- The following have been reloaded with a version change:
- 1) netlib-scalapack/2.0.2-openblas => netlib-scalapack/2.0.2-netlib
-
- root@module-file-tutorial:/# module list
-
- Currently Loaded Modules:
- 1) gcc/7.2.0 2) openblas/0.3.3 3) openmpi/3.1.3 4) netlib-scalapack/2.0.2-netlib
-
-Hierarchies that are deeper than ``Core``/``Compiler``/``MPI`` are
-probably still considered "unusual" or "impractical" at many sites, mainly because
-module files are written manually and keeping track of the combinations
-among multiple providers quickly becomes quite involved.
-
-For instance, having both ``MPI`` and ``LAPACK`` in the hierarchy
-means we must classify software into one of four categories:
-
- #. Software that doesn't depend on ``MPI`` or ``LAPACK``
- #. Software that depends only on ``MPI``
- #. Software that depends only on ``LAPACK``
- #. Software that depends on both
-
-to decide when to show it to the user. The situation becomes more involved as the number of virtual
-dependencies in the hierarchy increases.
-
-We can take advantage of the DAG that Spack maintains for the installed software and solve
-this combinatorial problem in a clean and automated way.
-In some sense Spack's ability to manage this combinatorial complexity makes deeper
-hierarchies feasible.
-
-Coming back to our example, let's add ``lapack`` to the hierarchy and remove any remaining suffix:
-
-.. code-block:: yaml
- :emphasize-lines: 9
-
- modules:
- enable::
- - lmod
- lmod:
- core_compilers:
- - 'gcc@5.4.0'
- hierarchy:
- - mpi
- - lapack
- hash_length: 0
- whitelist:
- - gcc
- blacklist:
- - '%gcc@5.4.0'
- all:
- filter:
- environment_blacklist: ['CPATH', 'LIBRARY_PATH']
- environment:
- set:
- '{name}_ROOT': '{prefix}'
- gcc:
- environment:
- set:
- CC: gcc
- CXX: g++
- FC: gfortran
- F90: gfortran
- F77: gfortran
- openmpi:
- environment:
- set:
- SLURM_MPI_TYPE: pmi2
- OMPI_MCA_btl_openib_warn_default_gid_prefix: '0'
-
-After module files have been regenerated as usual:
-
-.. code-block:: console
-
- root@module-file-tutorial:/# module purge
-
- root@module-file-tutorial:/# spack module lmod refresh --delete-tree -y
- ==> Regenerating lmod module files
-
-we can see that now we have additional components in the hierarchy:
-
-.. code-block:: console
-
- $ module load gcc
- $ module load openblas
- $ module avail
-
- -------------------------------- /home/spack1/spack/share/spack/lmod/linux-ubuntu16.04-x86_64/openblas/0.3.3-xxoxfh4/gcc/7.2.0 --------------------------------
- py-numpy/1.15.2 py-scipy/1.1.0
-
- ------------------------------------------- /home/spack1/spack/share/spack/lmod/linux-ubuntu16.04-x86_64/gcc/7.2.0 --------------------------------------------
- autoconf/2.69 findutils/4.6.0 libtool/2.4.6 netlib-lapack/3.8.0 perl/5.26.2 sqlite/3.23.1
- automake/1.16.1 gdbm/1.14.1 libxml2/2.9.8 numactl/2.0.11 pkgconf/1.4.2 texinfo/6.5
- bzip2/1.0.6 hwloc/1.11.9 m4/1.4.18 openblas/0.3.3 (L) py-setuptools/40.4.3 util-macros/1.19.1
- cmake/3.12.3 libpciaccess/0.13.5 mpich/3.2.1 openmpi/3.1.3 python/2.7.15 xz/5.2.4
- diffutils/3.6 libsigsegv/2.11 ncurses/6.1 openssl/1.0.2o readline/7.0 zlib/1.2.11
-
- ----------------------------------------------------------- share/spack/lmod/linux-ubuntu16.04-x86_64/Core ------------------------------------------------------------
- gcc/7.2.0 (L)
-
- Where:
- L: Module is loaded
-
- Use "module spider" to find all possible modules.
- Use "module keyword key1 key2 ..." to search for all possible modules matching any of the "keys".
-
-
- $ module load openmpi
- $ module avail
-
- --------------------- /home/spack1/spack/share/spack/lmod/linux-ubuntu16.04-x86_64/openmpi/3.1.3-do5xfer/openblas/0.3.3-xxoxfh4/gcc/7.2.0 ---------------------
- netlib-scalapack/2.0.2
-
- -------------------------------- /home/spack1/spack/share/spack/lmod/linux-ubuntu16.04-x86_64/openblas/0.3.3-xxoxfh4/gcc/7.2.0 --------------------------------
- py-numpy/1.15.2 py-scipy/1.1.0
-
- ------------------------------------------- /home/spack1/spack/share/spack/lmod/linux-ubuntu16.04-x86_64/gcc/7.2.0 --------------------------------------------
- autoconf/2.69 findutils/4.6.0 libtool/2.4.6 netlib-lapack/3.8.0 perl/5.26.2 sqlite/3.23.1
- automake/1.16.1 gdbm/1.14.1 libxml2/2.9.8 numactl/2.0.11 pkgconf/1.4.2 texinfo/6.5
- bzip2/1.0.6 hwloc/1.11.9 m4/1.4.18 openblas/0.3.3 (L) py-setuptools/40.4.3 util-macros/1.19.1
- cmake/3.12.3 libpciaccess/0.13.5 mpich/3.2.1 openmpi/3.1.3 (L) python/2.7.15 xz/5.2.4
- diffutils/3.6 libsigsegv/2.11 ncurses/6.1 openssl/1.0.2o readline/7.0 zlib/1.2.11
-
- ---------------------------------------------- /home/spack1/spack/share/spack/lmod/linux-ubuntu16.04-x86_64/Core ----------------------------------------------
- gcc/7.2.0 (L)
-
- Where:
- L: Module is loaded
-
- Use "module spider" to find all possible modules.
- Use "module keyword key1 key2 ..." to search for all possible modules matching any of the "keys".
-
-Both ``MPI`` and ``LAPACK`` providers will now benefit from the same safety features:
-
-.. code-block:: console
-
- $ module load py-numpy netlib-scalapack
- $ module load mpich
-
- Lmod is automatically replacing "openmpi/3.1.3" with "mpich/3.2.1".
-
-
- Due to MODULEPATH changes, the following have been reloaded:
- 1) netlib-scalapack/2.0.2
-
- $ module load netlib-lapack
-
- Lmod is automatically replacing "openblas/0.3.3" with "netlib-lapack/3.8.0".
-
-
- Inactive Modules:
- 1) py-numpy
-
- Due to MODULEPATH changes, the following have been reloaded:
- 1) netlib-scalapack/2.0.2
-
-Because we only compiled ``py-numpy`` with ``openblas`` the module
-is made inactive when we switch the ``LAPACK`` provider. The user
-environment is now consistent by design!
-
-----------------------
-Working with templates
-----------------------
-
-As briefly mentioned in the introduction, Spack uses `Jinja2 <http://jinja.pocoo.org/docs/2.9/>`_
-to generate each individual module file.
-This means that you have all of its flexibility and power when it comes to
-customizing what gets generated!
-
-^^^^^^^^^^^^^^^^^^^^^
-Module file templates
-^^^^^^^^^^^^^^^^^^^^^
-
-The templates that Spack uses to generate module files are stored in the
-``share/spack/templates/module`` directory within the Spack prefix, and
-they all share the same common structure. Usually, they start with a
-header that identifies the type of module being generated. In the case of
-hierarchical module files it's:
-
-.. literalinclude:: _spack_root/share/spack/templates/modules/modulefile.lua
- :language: jinja
- :lines: 1-6
-
-The statements within double curly brackets ``{{ ... }}`` denote
-`expressions <http://jinja.pocoo.org/docs/2.9/templates/#expressions>`_
-that will be evaluated and substituted at module generation time.
-The rest of the file is then divided into
-`blocks <http://jinja.pocoo.org/docs/2.9/templates/#template-inheritance>`_
-that can be overridden or extended by users, if need be.
-`Control structures <http://jinja.pocoo.org/docs/2.9/templates/#list-of-control-structures>`_
-, delimited by ``{% ... %}``,
-are also permitted in the template language:
-
-.. literalinclude:: _spack_root/share/spack/templates/modules/modulefile.lua
- :language: jinja
- :lines: 73-88
-
-The locations where Spack looks for templates are specified
-in ``config.yaml``:
-
-.. literalinclude:: _spack_root/etc/spack/defaults/config.yaml
- :language: yaml
- :lines: 21-24
-
-and can be extended by users to employ custom templates, as we'll see next.
-
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-Extend the default templates
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-Let's assume one of our software is protected by group membership:
-allowed users belong to the same linux group, and access is granted at group level.
-Wouldn't it be nice if people that are not
-yet entitled to use it could receive a helpful message at module load time
-that tells them who to contact in your organization to be inserted in the group?
-
-To automate the generation of module files with such site-specific behavior
-we'll start by extending the list of locations where Spack looks for module
-files. Let's create the file ``~/.spack/config.yaml`` with the content:
-
-.. code-block:: yaml
-
- config:
- template_dirs:
- - $HOME/.spack/templates
-
-This tells Spack to also search another location when looking for template files.
-Next, we need to create our custom template extension in the folder listed above:
-
-.. code-block:: jinja
-
- {% extends "modules/modulefile.lua" %}
- {% block footer %}
- -- Access is granted only to specific groups
- if not isDir("{{ spec.prefix }}") then
- LmodError (
- "You don't have the necessary rights to run \"{{ spec.name }}\".\n\n",
- "\tPlease write an e-mail to 1234@foo.com if you need further information on how to get access to it.\n"
- )
- end
- {% endblock %}
-
-Let's name this file ``group-restricted.lua``. The line:
-
-.. code-block:: jinja
-
- {% extends "modules/modulefile.lua" %}
-
-tells Jinja2 that we are reusing the standard template for hierarchical module files.
-The section:
-
-.. code-block:: jinja
-
- {% block footer %}
- -- Access is granted only to specific groups
- if not isDir("{{ spec.prefix }}") then
- LmodError (
- "You don't have the necessary rights to run \"{{ spec.name }}\".\n\n",
- "\tPlease write an e-mail to 1234@foo.com if you need further information on how to get access to it.\n"
- )
- end
- {% endblock %}
-
-overrides the ``footer`` block.
-Finally, we need to add a couple of lines in ``modules.yaml`` to tell Spack which specs
-need to use the new custom template. For the sake of illustration let's assume
-it's ``netlib-scalapack``:
-
-.. code-block:: yaml
- :emphasize-lines: 35-36
-
- modules:
- enable::
- - lmod
- lmod:
- core_compilers:
- - 'gcc@5.4.0'
- hierarchy:
- - mpi
- - lapack
- hash_length: 0
- whitelist:
- - gcc
- blacklist:
- - '%gcc@5.4.0'
- - readline
- all:
- filter:
- environment_blacklist: ['CPATH', 'LIBRARY_PATH']
- environment:
- set:
- '{name}_ROOT': '{prefix}'
- gcc:
- environment:
- set:
- CC: gcc
- CXX: g++
- FC: gfortran
- F90: gfortran
- F77: gfortran
- openmpi:
- environment:
- set:
- SLURM_MPI_TYPE: pmi2
- OMPI_MCA_btl_openib_warn_default_gid_prefix: '0'
- netlib-scalapack:
- template: 'group-restricted.lua'
-
-If we regenerate the module files one last time:
-
-.. code-block:: console
-
- root@module-file-tutorial:/# spack module lmod refresh -y netlib-scalapack
- ==> Regenerating lmod module files
-
-we'll find the following at the end of each ``netlib-scalapack`` module file:
-
-.. code-block:: lua
-
- -- Access is granted only to specific groups
- if not isDir("/usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-7.2.0/netlib-scalapack-2.0.2-d3lertflood3twaor44eam2kcr4l72ag") then
- LmodError (
- "You don't have the necessary rights to run \"netlib-scalapack\".\n\n",
- "\tPlease write an e-mail to 1234@foo.com if you need further information on how to get access to it.\n"
- )
- end
-
-and every user that doesn't have access to the software will now be redirected to
-the right e-mail address where to ask for it!
diff --git a/lib/spack/docs/tutorial_packaging.rst b/lib/spack/docs/tutorial_packaging.rst
deleted file mode 100644
index ca693ba14f7c21090beaa856110227203d333745..0000000000000000000000000000000000000000
--- a/lib/spack/docs/tutorial_packaging.rst
+++ /dev/null
@@ -1,559 +0,0 @@
-.. Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
- Spack Project Developers. See the top-level COPYRIGHT file for details.
-
- SPDX-License-Identifier: (Apache-2.0 OR MIT)
-
-.. _packaging-tutorial:
-
-=========================
-Package Creation Tutorial
-=========================
-
-This tutorial will walk you through the steps behind building a simple
-package installation script. We'll focus on writing a package for
-mpileaks, an MPI debugging tool. By creating a package file we're
-essentially giving Spack a recipe for how to build a particular piece of
-software. We're describing some of the software's dependencies, where to
-find the package, what commands and options are used to build the package
-from source, and more. Once we've specified a package's recipe, we can
-ask Spack to build that package in many different ways.
-
-This tutorial assumes you have a basic familiarity with some of the Spack
-commands, and that you have a working version of Spack installed. If
-not, we suggest looking at Spack's :ref:`getting_started` guide. This
-tutorial also assumes you have at least a beginner's-level familiarity
-with Python.
-
-Also note that this document is a tutorial. It can help you get started
-with packaging, but is not intended to be complete. See Spack's
-:ref:`packaging-guide` for more complete documentation on this topic.
-
----------------
-Getting Started
----------------
-
-A few things before we get started:
-
-- We'll refer to the Spack installation location via the environment
- variable ``SPACK_ROOT``. You should point ``SPACK_ROOT`` at wherever
- you have Spack installed.
-- Add ``$SPACK_ROOT/bin`` to your ``PATH`` before you start.
-- Make sure your ``EDITOR`` environment variable is set to your
- preferred text editor.
-- We'll be writing Python code as part of this tutorial. You can find
- successive versions of the Python code in
- ``$SPACK_ROOT/lib/spack/docs/tutorial/examples``.
-
--------------------------
-Creating the Package File
--------------------------
-
-We will use a separate package repository for the tutorial. Package
-repositories allow you to separate sets of packages that take
-precedence over one another. We will use the tutorial repo that ships
-with Spack to avoid breaking the builtin Spack packages.
-
-.. code-block:: console
-
- $ spack repo add $SPACK_ROOT/var/spack/repos/tutorial/
- ==> Added repo with namespace 'tutorial'.
-
-Spack comes with a handy command to create a new package: ``spack create``.
-
-This command is given the location of a package's source code, downloads
-the code, and sets up some basic packaging infrastructure for you. The
-mpileaks source code can be found on GitHub, and here's what happens when
-we run ``spack create`` on it:
-
-.. code-block:: console
-
- $ spack create -t generic https://github.com/LLNL/mpileaks/releases/download/v1.0/mpileaks-1.0.tar.gz
- ==> This looks like a URL for mpileaks
- ==> Found 1 version of mpileaks:
-
- 1.0 https://github.com/LLNL/mpileaks/releases/download/v1.0/mpileaks-1.0.tar.gz
-
- ==> How many would you like to checksum? (default is 1, q to abort) 1
- ==> Downloading...
- ==> Fetching https://github.com/LLNL/mpileaks/releases/download/v1.0/mpileaks-1.0.tar.gz
- ############################################################################# 100.0%
- ==> Checksummed 1 version of mpileaks
- ==> Using specified package template: 'generic'
- ==> Created template for mpileaks package
- ==> Created package file: ~/spack/var/spack/repos/tutorial/packages/mpileaks/package.py
-
-Spack should spawn a text editor with this file:
-
-.. literalinclude:: tutorial/examples/0.package.py
- :language: python
-
-Spack has created this file in
-``$SPACK_ROOT/var/spack/repos/tutorial/packages/mpileaks/package.py``. Take a
-moment to look over the file. There's a few placeholders that Spack has
-created, which we'll fill in as part of this tutorial:
-
-- We'll document some information about this package in the comments.
-- We'll fill in the dependency list for this package.
-- We'll fill in some of the configuration arguments needed to build this
- package.
-
-For the moment, exit your editor and let's see what happens when we try
-to build this package:
-
-.. code-block:: console
-
- $ spack install mpileaks
- ==> Installing mpileaks
- ==> Searching for binary cache of mpileaks
- ==> Warning: No Spack mirrors are currently configured
- ==> No binary for mpileaks found: installing from source
- ==> Fetching https://github.com/LLNL/mpileaks/releases/download/v1.0/mpileaks-1.0.tar.gz
- ############################################################################# 100.0%
- ==> Staging archive: ~/spack/var/spack/stage/mpileaks-1.0-sv75n3u5ev6mljwcezisz3slooozbbxu/mpileaks-1.0.tar.gz
- ==> Created stage in ~/spack/var/spack/stage/mpileaks-1.0-sv75n3u5ev6mljwcezisz3slooozbbxu
- ==> No patches needed for mpileaks
- ==> Building mpileaks [Package]
- ==> Executing phase: 'install'
- ==> Error: ProcessError: Command exited with status 2:
- 'make' '-j16'
-
- 1 error found in build log:
- 1 ==> Executing phase: 'install'
- 2 ==> 'make' '-j16'
- >> 3 make: *** No targets specified and no makefile found. Stop.
-
- See build log for details:
- ~/spack/var/spack/stage/mpileaks-1.0-sv75n3u5ev6mljwcezisz3slooozbbxu/spack-build-out.txt
-
-This obviously didn't work; we need to fill in the package-specific
-information. Specifically, Spack didn't try to build any of mpileaks'
-dependencies, nor did it use the proper configure arguments. Let's start
-fixing things.
-
----------------------
-Package Documentation
----------------------
-
-We can bring the ``package.py`` file back into our ``EDITOR`` with the
-``spack edit`` command:
-
-.. code-block:: console
-
- $ spack edit mpileaks
-
-Let's remove some of the ``FIXME`` comments, add links to the mpileaks
-homepage, and document what mpileaks does. I'm also going to cut out the
-Copyright clause at this point to keep this tutorial document shorter,
-but you shouldn't do that normally. The results of these changes can be
-found in ``$SPACK_ROOT/lib/spack/docs/tutorial/examples/1.package.py``
-and are displayed below. Make these changes to your ``package.py``:
-
-.. literalinclude:: tutorial/examples/1.package.py
- :lines: 6-
- :language: python
-
-We've filled in the comment that describes what this package does and
-added a link to its website. That won't help us build yet, but it will
-allow Spack to provide some documentation on this package to other users:
-
-.. code-block:: console
-
- $ spack info mpileaks
- Package: mpileaks
-
- Description:
- Tool to detect and report MPI objects like MPI_Requests and
- MPI_Datatypes.
-
- Homepage: https://github.com/LLNL/mpileaks
-
- Tags:
- None
-
- Preferred version:
- 1.0 https://github.com/LLNL/mpileaks/releases/download/v1.0/mpileaks-1.0.tar.gz
-
- Safe versions:
- 1.0 https://github.com/LLNL/mpileaks/releases/download/v1.0/mpileaks-1.0.tar.gz
-
- Variants:
- None
-
- Installation Phases:
- install
-
- Build Dependencies:
- None
-
- Link Dependencies:
- None
-
- Run Dependencies:
- None
-
- Virtual Packages:
- None
-
-As we fill in more information about this package the ``spack info`` command
-will become more informative. Now let's start making this package build.
-
-------------
-Dependencies
-------------
-
-The mpileaks package depends on three other packages: ``mpi``,
-``adept-utils``, and ``callpath``. Let's add those via the
-``depends_on`` command in our ``package.py`` (this version is in
-``$SPACK_ROOT/lib/spack/docs/tutorial/examples/2.package.py``):
-
-.. literalinclude:: tutorial/examples/2.package.py
- :lines: 6-
- :language: python
-
-Now when we go to build mpileaks, Spack will fetch and build these
-dependencies before building mpileaks. Note that the mpi dependency is a
-different kind of beast than the adept-utils and callpath dependencies;
-there is no mpi package available in Spack. Instead mpi is a *virtual
-dependency*. Spack may satisfy that dependency by installing packages
-such as ``openmpi`` or ``mvapich2``. See the :ref:`packaging-guide` for more
-information on virtual dependencies.
-
-Now when we try to install this package, a lot more happens:
-
-.. code-block:: console
-
- $ spack install mpileaks
- ...
- ==> Successfully installed libdwarf from binary cache
- [+] ~/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/libdwarf-20180129-p4jeflorwlnkoq2vpuyocwrbcht2ayak
- ==> Installing callpath
- ==> Searching for binary cache of callpath
- ==> Installing callpath from binary cache
- ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/callpath-1.0.4/linux-ubuntu16.04-x86_64-gcc-5.4.0-callpath-1.0.4-empvyxdkc4j4pwg7gznwhbiumruey66x.spack
- ######################################################################## 100.0%
- ==> Successfully installed callpath from binary cache
- [+] ~/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/callpath-1.0.4-empvyxdkc4j4pwg7gznwhbiumruey66x
- ==> Installing mpileaks
- ==> Searching for binary cache of mpileaks
- ==> No binary for mpileaks found: installing from source
- ==> Using cached archive: ~/spack/var/spack/cache/mpileaks/mpileaks-1.0.tar.gz
- ==> Staging archive: ~/spack/var/spack/stage/mpileaks-1.0-csoikctsalli4cdkkdk377gprkc472rb/mpileaks-1.0.tar.gz
- ==> Created stage in ~/spack/var/spack/stage/mpileaks-1.0-csoikctsalli4cdkkdk377gprkc472rb
- ==> No patches needed for mpileaks
- ==> Building mpileaks [Package]
- ==> Executing phase: 'install'
- ==> Error: ProcessError: Command exited with status 2:
- 'make' '-j16'
-
- 1 error found in build log:
- 1 ==> Executing phase: 'install'
- 2 ==> 'make' '-j16'
- >> 3 make: *** No targets specified and no makefile found. Stop.
-
- See build log for details:
- ~/spack/var/spack/stage/mpileaks-1.0-csoikctsalli4cdkkdk377gprkc472rb/mpileaks-1.0/spack-build-out.txt
-
-Note that this command may take a while to run and produce more output if
-you don't have an MPI already installed or configured in Spack.
-
-Now Spack has identified and made sure all of our dependencies have been
-built. It found the ``openmpi`` package that will satisfy our ``mpi``
-dependency, and the ``callpath`` and ``adept-utils`` package to satisfy our
-concrete dependencies.
-
-------------------------
-Debugging Package Builds
-------------------------
-
-Our ``mpileaks`` package is still not building. It may be obvious to
-many of you that we never ran the configure script. Let's add a
-call to ``configure()`` to the top of the install routine. The resulting
-``package.py`` is in ``$SPACK_ROOT/lib/spack/docs/tutorial/examples/3.package.py``:
-
-.. literalinclude:: tutorial/examples/3.package.py
- :lines: 6-
- :language: python
-
-If we re-run we still get errors:
-
-.. code-block:: console
-
- $ spack install mpileaks
- ...
- ==> Installing mpileaks
- ==> Searching for binary cache of mpileaks
- ==> Finding buildcaches in /mirror/build_cache
- ==> No binary for mpileaks found: installing from source
- ==> Using cached archive: ~/spack/var/spack/cache/mpileaks/mpileaks-1.0.tar.gz
- ==> Staging archive: ~/spack/var/spack/stage/mpileaks-1.0-csoikctsalli4cdkkdk377gprkc472rb/mpileaks-1.0.tar.gz
- ==> Created stage in ~/spack/var/spack/stage/mpileaks-1.0-csoikctsalli4cdkkdk377gprkc472rb
- ==> No patches needed for mpileaks
- ==> Building mpileaks [Package]
- ==> Executing phase: 'install'
- ==> Error: ProcessError: Command exited with status 1:
- './configure'
-
- 1 error found in build log:
- 25 checking for ~/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/openmpi-3.1.3-3
- njc4q5pqdpptq6jvqjrezkffwokv2sx/bin/mpicc... ~/spack/opt/spack/linux-ubuntu16.04-
- x86_64/gcc-5.4.0/openmpi-3.1.3-3njc4q5pqdpptq6jvqjrezkffwokv2sx/bin/mpicc
- 26 Checking whether ~/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/openmpi-3.1
- .3-3njc4q5pqdpptq6jvqjrezkffwokv2sx/bin/mpicc responds to '-showme:compile'... no
- 27 Checking whether ~/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/openmpi-3.1
- .3-3njc4q5pqdpptq6jvqjrezkffwokv2sx/bin/mpicc responds to '-showme'... no
- 28 Checking whether ~/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/openmpi-3.1
- .3-3njc4q5pqdpptq6jvqjrezkffwokv2sx/bin/mpicc responds to '-compile-info'... no
- 29 Checking whether ~/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/openmpi-3.1
- .3-3njc4q5pqdpptq6jvqjrezkffwokv2sx/bin/mpicc responds to '-show'... no
- 30 ./configure: line 4809: Echo: command not found
- >> 31 configure: error: unable to locate adept-utils installation
-
- See build log for details:
- ~/spack/var/spack/stage/mpileaks-1.0-csoikctsalli4cdkkdk377gprkc472rb/mpileaks-1.0/spack-build-out.txt
-
-Again, the problem may be obvious. But let's pretend we're not
-all experienced Autotools developers and use this opportunity to spend some
-time debugging. We have a few options that can tell us about
-what's going wrong:
-
-As per the error message, Spack has given us a ``spack-build-out.txt`` debug
-log:
-
-.. code-block:: console
-
- ==> Executing phase: 'install'
- ==> './configure'
- checking metadata... no
- checking installation directory variables... yes
- checking for a BSD-compatible install... /usr/bin/install -c
- checking whether build environment is sane... yes
- checking for a thread-safe mkdir -p... /bin/mkdir -p
- checking for gawk... gawk
- checking whether make sets $(MAKE)... yes
- checking for gcc... /home/spack1/spack/lib/spack/env/gcc/gcc
- checking for C compiler default output file name... a.out
- checking whether the C compiler works... yes
- checking whether we are cross compiling... no
- checking for suffix of executables...
- checking for suffix of object files... o
- checking whether we are using the GNU C compiler... yes
- checking whether /home/spack1/spack/lib/spack/env/gcc/gcc accepts -g... yes
- checking for /home/spack1/spack/lib/spack/env/gcc/gcc option to accept ISO C89... none needed
- checking for style of include used by make... GNU
- checking dependency style of /home/spack1/spack/lib/spack/env/gcc/gcc... gcc3
- checking whether /home/spack1/spack/lib/spack/env/gcc/gcc and cc understand -c and -o together... yes
- checking whether we are using the GNU C++ compiler... yes
- checking whether /home/spack1/spack/lib/spack/env/gcc/g++ accepts -g... yes
- checking dependency style of /home/spack1/spack/lib/spack/env/gcc/g++... gcc3
- checking for /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/openmpi-3.0.0-yo5qkfvumpmgmvlbalqcadu46j5bd52f/bin/mpicc... /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/openmpi-3.0.0-yo5qkfvumpmgmvlbalqcadu46j5bd52f/bin/mpicc
- Checking whether /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/openmpi-3.0.0-yo5qkfvumpmgmvlbalqcadu46j5bd52f/bin/mpicc responds to '-showme:compile'... yes
- configure: error: unable to locate adept-utils installation
-
-This gives us the output from the build, and mpileaks isn't
-finding its ``adept-utils`` package. Spack has
-automatically added the include and library directories of
-``adept-utils`` to the compiler's search path, but some packages like
-mpileaks can sometimes be picky and still want things spelled out on
-their command line. But let's continue to pretend we're not experienced
-developers, and explore some other debugging paths:
-
-We can also enter the build area and try to manually run the build:
-
-.. code-block:: console
-
- $ spack build-env mpileaks bash
- $ spack cd mpileaks
-
-The ``spack build-env`` command spawned a new shell that contains the same
-environment that Spack used to build the mpileaks package (you can
-substitute bash for your favorite shell). The ``spack cd`` command
-changed our working dirctory to the last attempted build for mpileaks.
-From here we can manually re-run the build:
-
-.. code-block:: console
-
- $ ./configure
- checking metadata... no
- checking installation directory variables... yes
- checking for a BSD-compatible install... /usr/bin/install -c
- checking whether build environment is sane... yes
- checking for a thread-safe mkdir -p... /bin/mkdir -p
- checking for gawk... gawk
- checking whether make sets $(MAKE)... yes
- checking for gcc... /home/spack1/spack/lib/spack/env/gcc/gcc
- checking for C compiler default output file name... a.out
- checking whether the C compiler works... yes
- checking whether we are cross compiling... no
- checking for suffix of executables...
- checking for suffix of object files... o
- checking whether we are using the GNU C compiler... yes
- checking whether /home/spack1/spack/lib/spack/env/gcc/gcc accepts -g... yes
- checking for /home/spack1/spack/lib/spack/env/gcc/gcc option to accept ISO C89... none needed
- checking for style of include used by make... GNU
- checking dependency style of /home/spack1/spack/lib/spack/env/gcc/gcc... gcc3
- checking whether /home/spack1/spack/lib/spack/env/gcc/gcc and cc understand -c and -o together... yes
- checking whether we are using the GNU C++ compiler... yes
- checking whether /home/spack1/spack/lib/spack/env/gcc/g++ accepts -g... yes
- checking dependency style of /home/spack1/spack/lib/spack/env/gcc/g++... gcc3
- checking for /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/openmpi-3.0.0-yo5qkfvumpmgmvlbalqcadu46j5bd52f/bin/mpicc... /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/openmpi-3.0.0-yo5qkfvumpmgmvlbalqcadu46j5bd52f/bin/mpicc
- Checking whether /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/openmpi-3.0.0-yo5qkfvumpmgmvlbalqcadu46j5bd52f/bin/mpicc responds to '-showme:compile'... yes
- configure: error: unable to locate adept-utils installation
-
-We're seeing the same error, but now we're in a shell where we can run
-the command ourselves and debug as needed. We could, for example, run
-``./configure --help`` to see what options we can use to specify
-dependencies.
-
-We can use the ``exit`` command to leave the shell spawned by ``spack
-build-env``.
-
-------------------------------
-Specifying Configure Arguments
-------------------------------
-
-Let's add the configure arguments to the mpileaks' ``package.py``. This
-version can be found in
-``$SPACK_ROOT/lib/spack/docs/tutorial/examples/4.package.py``:
-
-.. literalinclude:: tutorial/examples/4.package.py
- :lines: 6-
- :language: python
-
-This is all we need for a working mpileaks package! If we install now we'll see:
-
-.. code-block:: console
-
- $ spack install mpileaks
- ...
- ==> Installing mpileaks
- ==> Searching for binary cache of mpileaks
- ==> Finding buildcaches in /mirror/build_cache
- ==> No binary for mpileaks found: installing from source
- ==> Using cached archive: ~/spack/var/spack/cache/mpileaks/mpileaks-1.0.tar.gz
- ==> Staging archive: ~/spack/var/spack/stage/mpileaks-1.0-csoikctsalli4cdkkdk377gprkc472rb/mpileaks-1.0.tar.gz
- ==> Created stage in ~/spack/var/spack/stage/mpileaks-1.0-csoikctsalli4cdkkdk377gprkc472rb
- ==> No patches needed for mpileaks
- ==> Building mpileaks [Package]
- ==> Executing phase: 'install'
- ==> Successfully installed mpileaks
- Fetch: 0.00s. Build: 9.41s. Total: 9.41s.
- [+] ~/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/mpileaks-1.0-csoikctsalli4cdkkdk377gprkc472rb
-
-There are some special circumstances in this package that are worth highlighting.
-Normally, Spack would have automatically detected that mpileaks was an
-Autotools-based package when we ran ``spack create`` and made it an ``AutoToolsPackage``
-class (except we added the ``-t generic`` option to skip this). Instead of
-a full install routine we would have just written:
-
-.. code-block:: python
-
- def configure_args(self):
- return [
- '--with-adept-utils={0}'.format(self.spec['adept-utils'].prefix),
- '--with-callpath={0}'.format(self.spec['callpath'].prefix)
- ]
-
-Similarly, if this had been a CMake-based package we
-would have been filling in a ``cmake_args`` function instead of
-``configure_args``. There are similar default package types for
-many build environments that will be discussed later in the tutorial.
-
---------
-Variants
---------
-
-We have a successful mpileaks build, but let's take some time to improve
-it. ``mpileaks`` has a build-time option to truncate parts of the stack
-that it walks. Let's add a variant to allow users to set this when they
-build mpileaks with Spack.
-
-To do this, we'll add a variant to our package, as per the following (see
-``$SPACK_ROOT/lib/spack/docs/tutorial/examples/5.package.py``):
-
-.. literalinclude:: tutorial/examples/5.package.py
- :lines: 6-
- :language: python
-
-We've added the variant ``stackstart``, and given it a default value of
-``0``. If we install now we can see the stackstart variant added to the
-configure line (output truncated for length):
-
-.. code-block:: console
-
- $ spack install --verbose mpileaks stackstart=4
- ...
- ==> Installing mpileaks
- ==> Searching for binary cache of mpileaks
- ==> Finding buildcaches in /mirror/build_cache
- ==> No binary for mpileaks found: installing from source
- ==> Using cached archive: ~/spack/var/spack/cache/mpileaks/mpileaks-1.0.tar.gz
- ==> Staging archive: ~/spack/var/spack/stage/mpileaks-1.0-meufjojkxve3l7rci2mbud3faidgplto/mpileaks-1.0.tar.gz
- ==> Created stage in ~/spack/var/spack/stage/mpileaks-1.0-meufjojkxve3l7rci2mbud3faidgplto
- ==> No patches needed for mpileaks
- ==> Building mpileaks [Package]
- ==> Executing phase: 'install'
- ==> './configure' '--prefix=~/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/mpileaks-1.0-meufjojkxve3l7rci2mbud3faidgplto' '--with-adept-utils=~/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/adept-utils-1.0.1-7tippnvo5g76wpijk7x5kwfpr3iqiaen' '--with-callpath=~/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/callpath-1.0.4-empvyxdkc4j4pwg7gznwhbiumruey66x' '--with-stack-start-c=4' '--with-stack-start-fortran=4'
-
----------------
-The Spec Object
----------------
-
-This tutorial has glossed over a few important features, which weren't
-too relevant for mpileaks but may be useful for other packages. There
-were several places we reference the ``self.spec`` object. This is a
-powerful class for querying information about what we're building. For
-example, you could use the spec to query information about how a
-package's dependencies were built, or what compiler was being used, or
-what version of a package is being installed. Full documentation can be
-found in the :ref:`packaging-guide`, but here's some quick snippets with
-common queries:
-
-- Am I building ``mpileaks`` version ``1.1`` or greater?
-
-.. code-block:: python
-
- if self.spec.satisfies('@1.1:'):
- # Do things needed for 1.1+
-
-- Is ``openmpi`` the MPI I'm building with?
-
-.. code-block:: python
-
- if self.spec['mpi'].name == 'openmpi':
- # Do openmpi things
-
-- Am I building with ``gcc`` version less than ``5.0.0``:
-
-.. code-block:: python
-
- if self.spec.satisfies('%gcc@:5.0.0'):
- # Add arguments specific to gcc's earlier than 5.0.0
-
-- Am I building with the ``debug`` variant:
-
-.. code-block:: python
-
- if self.spec.satisfies('+debug'):
- # Add -g option to configure flags
-
-- Is my ``dyninst`` dependency greater than version ``8.0``?
-
-.. code-block:: python
-
- if self.spec['dyninst'].satisfies('@8.0:'):
- # Use newest dyninst options
-
-More examples can be found in the thousands of packages already added to
-Spack in ``$SPACK_ROOT/var/spack/repos/builtin/packages``.
-
-Good Luck!
-
-To ensure that future sections of the tutorial run properly, please
-uninstall mpileaks and remove the tutorial repo from your
-configuration.
-
-.. code-block:: console
-
- $ spack uninstall -ay mpileaks
- $ spack repo remove tutorial
- $ rm -rf $SPACK_ROOT/var/spack/repos/tutorial/packages/mpileaks