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Commit 9989f8e2 authored by Massimiliano Culpo's avatar Massimiliano Culpo Committed by Todd Gamblin
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module file support: major rework of docs (#2169) 

* module file support: major rework of docs

* module file support: fixed issues found by @adamjstewart

- list or enumeration should not be indented
- use console instead of bash or csh in things that are not scripts
- other typos

* module file support: fixed other issues found by @adamjstewart

- tables should not be indented
- substitute lines with pyobject to import an entire function
- get help output running commands
- typos

* module file support: fixes according to review comments

- @citibeth moved `spack module loads` after `spack load`
- @glennpj tried to clarify installation table + changes to language
- @tgamblin Removed top level section and moved the whole thing into the reference manual

* module file support: moved directive before spack module loads
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lib/spack/docs/basic_usage.rst
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...@@ -811,572 +811,6 @@ versions are now filtered out. ...@@ -811,572 +811,6 @@ versions are now filtered out.
.. _shell-support: .. _shell-support:
-------------------------------
Integration with module systems
-------------------------------
Spack provides some integration with `Environment Modules
<http://modules.sourceforge.net/>`_ to make it easier to use the
packages it installs. If your system does not already have
Environment Modules, see :ref:`InstallEnvironmentModules`.
.. note::
Spack also supports `Dotkit
<https://computing.llnl.gov/?set=jobs&page=dotkit>`_, which is used
by some systems. If you system does not already have a module
system installed, you should use Environment Modules or LMod.
^^^^^^^^^^^^^^^^^^^^^^^^
Spack and module systems
^^^^^^^^^^^^^^^^^^^^^^^^
You can enable shell support by sourcing some files in the
``/share/spack`` directory.
For ``bash`` or ``ksh``, run:
.. code-block:: sh
export SPACK_ROOT=/path/to/spack
. $SPACK_ROOT/share/spack/setup-env.sh
For ``csh`` and ``tcsh`` run:
.. code-block:: csh
setenv SPACK_ROOT /path/to/spack
source $SPACK_ROOT/share/spack/setup-env.csh
You can put the above code in your ``.bashrc`` or ``.cshrc``, and
Spack's shell support will be available on the command line.
When you install a package with Spack, it automatically generates a module file
that lets you add the package to your environment.
Currently, Spack supports the generation of `Environment Modules
<http://wiki.tcl.tk/12999>`__ and `Dotkit
<https://computing.llnl.gov/?set=jobs&page=dotkit>`_. Generated
module files for each of these systems can be found in these
directories:
.. code-block:: sh
$SPACK_ROOT/share/spack/modules
$SPACK_ROOT/share/spack/dotkit
The directories are automatically added to your ``MODULEPATH`` and
``DK_NODE`` environment variables when you enable Spack's `shell
support <shell-support_>`_.
^^^^^^^^^^^^^^^^^^^^^^^
Using Modules & Dotkits
^^^^^^^^^^^^^^^^^^^^^^^
If you have shell support enabled you should be able to run either
``module avail`` or ``use -l spack`` to see what modules/dotkits have
been installed. Here is sample output of those programs, showing lots
of installed packages.
.. code-block:: console
$ module avail
------- /home/gamblin2/spack/share/spack/modules/linux-debian7-x86_64 --------
adept-utils@1.0%gcc@4.4.7-5adef8da libelf@0.8.13%gcc@4.4.7
automaded@1.0%gcc@4.4.7-d9691bb0 libelf@0.8.13%intel@15.0.0
boost@1.55.0%gcc@4.4.7 mpc@1.0.2%gcc@4.4.7-559607f5
callpath@1.0.1%gcc@4.4.7-5dce4318 mpfr@3.1.2%gcc@4.4.7
dyninst@8.1.2%gcc@4.4.7-b040c20e mpich@3.0.4%gcc@4.4.7
gcc@4.9.1%gcc@4.4.7-93ab98c5 mpich@3.0.4%gcc@4.9.0
gmp@6.0.0a%gcc@4.4.7 mrnet@4.1.0%gcc@4.4.7-72b7881d
graphlib@2.0.0%gcc@4.4.7 netgauge@2.4.6%gcc@4.9.0-27912b7b
launchmon@1.0.1%gcc@4.4.7 stat@2.1.0%gcc@4.4.7-51101207
libNBC@1.1.1%gcc@4.9.0-27912b7b sundials@2.5.0%gcc@4.9.0-27912b7b
libdwarf@20130729%gcc@4.4.7-b52fac98
.. code-block:: console
$ use -l spack
spack ----------
adept-utils@1.0%gcc@4.4.7-5adef8da - adept-utils @1.0
automaded@1.0%gcc@4.4.7-d9691bb0 - automaded @1.0
boost@1.55.0%gcc@4.4.7 - boost @1.55.0
callpath@1.0.1%gcc@4.4.7-5dce4318 - callpath @1.0.1
dyninst@8.1.2%gcc@4.4.7-b040c20e - dyninst @8.1.2
gmp@6.0.0a%gcc@4.4.7 - gmp @6.0.0a
libNBC@1.1.1%gcc@4.9.0-27912b7b - libNBC @1.1.1
libdwarf@20130729%gcc@4.4.7-b52fac98 - libdwarf @20130729
libelf@0.8.13%gcc@4.4.7 - libelf @0.8.13
libelf@0.8.13%intel@15.0.0 - libelf @0.8.13
mpc@1.0.2%gcc@4.4.7-559607f5 - mpc @1.0.2
mpfr@3.1.2%gcc@4.4.7 - mpfr @3.1.2
mpich@3.0.4%gcc@4.4.7 - mpich @3.0.4
mpich@3.0.4%gcc@4.9.0 - mpich @3.0.4
netgauge@2.4.6%gcc@4.9.0-27912b7b - netgauge @2.4.6
sundials@2.5.0%gcc@4.9.0-27912b7b - sundials @2.5.0
The names here should look familiar, they're the same ones from
``spack find``. You *can* use the names here directly. For example,
you could type either of these commands to load the callpath module:
.. code-block:: console
$ use callpath@1.0.1%gcc@4.4.7-5dce4318
.. code-block:: console
$ module load callpath@1.0.1%gcc@4.4.7-5dce4318
Neither of these is particularly pretty, easy to remember, or
easy to type. Luckily, Spack has its own interface for using modules
and dotkits. You can use the same spec syntax you're used to:
========================= ==========================
Environment Modules Dotkit
========================= ==========================
``spack load <spec>`` ``spack use <spec>``
``spack unload <spec>`` ``spack unuse <spec>``
========================= ==========================
And you can use the same shortened names you use everywhere else in
Spack. For example, this will add the ``mpich`` package built with
``gcc`` to your path:
.. code-block:: console
$ spack install mpich %gcc@4.4.7
# ... wait for install ...
$ spack use mpich %gcc@4.4.7
Prepending: mpich@3.0.4%gcc@4.4.7 (ok)
$ which mpicc
~/src/spack/opt/linux-debian7-x86_64/gcc@4.4.7/mpich@3.0.4/bin/mpicc
Or, similarly with modules, you could type:
.. code-block:: console
$ spack load mpich %gcc@4.4.7
These commands will add appropriate directories to your ``PATH``,
``MANPATH``, ``CPATH``, and ``LD_LIBRARY_PATH``. When you no longer
want to use a package, you can type unload or unuse similarly:
.. code-block:: console
$ spack unload mpich %gcc@4.4.7 # modules
$ spack unuse mpich %gcc@4.4.7 # dotkit
.. note::
These ``use``, ``unuse``, ``load``, and ``unload`` subcommands are
only available if you have enabled Spack's shell support *and* you
have dotkit or modules installed on your machine.
^^^^^^^^^^^^^^^^^^^^^^
Ambiguous module names
^^^^^^^^^^^^^^^^^^^^^^
If a spec used with load/unload or use/unuse is ambiguous (i.e. more
than one installed package matches it), then Spack will warn you:
.. code-block:: console
$ spack load libelf
==> Error: Multiple matches for spec libelf. Choose one:
libelf@0.8.13%gcc@4.4.7 arch=linux-debian7-x86_64
libelf@0.8.13%intel@15.0.0 arch=linux-debian7-x86_64
You can either type the ``spack load`` command again with a fully
qualified argument, or you can add just enough extra constraints to
identify one package. For example, above, the key differentiator is
that one ``libelf`` is built with the Intel compiler, while the other
used ``gcc``. You could therefore just type:
.. code-block:: console
$ spack load libelf %intel
To identify just the one built with the Intel compiler.
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Module files generation and customization
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Environment Modules and Dotkit files are generated when packages are installed,
and are placed in the following directories under the Spack root:
.. code-block:: sh
$SPACK_ROOT/share/spack/modules
$SPACK_ROOT/share/spack/dotkit
The content that gets written in each module file can be customized in two ways:
#. overriding part of the ``spack.Package`` API within a ``package.py``
#. writing dedicated configuration files
^^^^^^^^^^^^^^^^^^^^^^^^
Override ``Package`` API
^^^^^^^^^^^^^^^^^^^^^^^^
There are currently two methods in ``spack.Package`` that may affect the content
of module files:
.. code-block:: python
def setup_environment(self, spack_env, run_env):
"""Set up the compile and runtime environments for a package."""
pass
.. code-block:: python
def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
"""Set up the environment of packages that depend on this one"""
pass
As briefly stated in the comments, the first method lets you customize the
module file content for the package you are currently writing, the second
allows for modifications to your dependees module file. In both cases one
needs to fill ``run_env`` with the desired list of environment modifications.
""""""""""""""""""""""""""""""""""""""""""""""""
Example : ``builtin/packages/python/package.py``
""""""""""""""""""""""""""""""""""""""""""""""""
The ``python`` package that comes with the ``builtin`` Spack repository
overrides ``setup_dependent_environment`` in the following way:
.. code-block:: python
def setup_dependent_environment(self, spack_env, run_env, extension_spec):
if extension_spec.package.extends(self.spec):
run_env.prepend_path('PYTHONPATH', os.path.join(extension_spec.prefix, self.site_packages_dir))
to insert the appropriate ``PYTHONPATH`` modifications in the module
files of python packages.
^^^^^^^^^^^^^^^^^
Recursive Modules
^^^^^^^^^^^^^^^^^
In some cases, it is desirable to load not just a module, but also all
the modules it depends on. This is not required for most modules
because Spack builds binaries with RPATH support. However, not all
packages use RPATH to find their dependencies: this can be true in
particular for Python extensions, which are currently *not* built with
RPATH.
Scripts to load modules recursively may be made with the command:
.. code-block:: console
$ spack module loads --dependencies <spec>
An equivalent alternative is:
.. code-block :: console
$ source <( spack module loads --dependencies <spec> )
.. warning::
The ``spack load`` command does not currently accept the
``--dependencies`` flag. Use ``spack module loads`` instead, for
now.
.. See #1662
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Module Commands for Shell Scripts
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Although Spack is flexible, the ``module`` command is much faster.
This could become an issue when emitting a series of ``spack load``
commands inside a shell script. By adding the ``--shell`` flag,
``spack module find`` may also be used to generate code that can be
cut-and-pasted into a shell script. For example:
.. code-block:: console
$ spack module loads --dependencies py-numpy git
# bzip2@1.0.6%gcc@4.9.3=linux-x86_64
module load bzip2-1.0.6-gcc-4.9.3-ktnrhkrmbbtlvnagfatrarzjojmkvzsx
# ncurses@6.0%gcc@4.9.3=linux-x86_64
module load ncurses-6.0-gcc-4.9.3-kaazyneh3bjkfnalunchyqtygoe2mncv
# zlib@1.2.8%gcc@4.9.3=linux-x86_64
module load zlib-1.2.8-gcc-4.9.3-v3ufwaahjnviyvgjcelo36nywx2ufj7z
# sqlite@3.8.5%gcc@4.9.3=linux-x86_64
module load sqlite-3.8.5-gcc-4.9.3-a3eediswgd5f3rmto7g3szoew5nhehbr
# readline@6.3%gcc@4.9.3=linux-x86_64
module load readline-6.3-gcc-4.9.3-se6r3lsycrwxyhreg4lqirp6xixxejh3
# python@3.5.1%gcc@4.9.3=linux-x86_64
module load python-3.5.1-gcc-4.9.3-5q5rsrtjld4u6jiicuvtnx52m7tfhegi
# py-setuptools@20.5%gcc@4.9.3=linux-x86_64
module load py-setuptools-20.5-gcc-4.9.3-4qr2suj6p6glepnedmwhl4f62x64wxw2
# py-nose@1.3.7%gcc@4.9.3=linux-x86_64
module load py-nose-1.3.7-gcc-4.9.3-pwhtjw2dvdvfzjwuuztkzr7b4l6zepli
# openblas@0.2.17%gcc@4.9.3+shared=linux-x86_64
module load openblas-0.2.17-gcc-4.9.3-pw6rmlom7apfsnjtzfttyayzc7nx5e7y
# py-numpy@1.11.0%gcc@4.9.3+blas+lapack=linux-x86_64
module load py-numpy-1.11.0-gcc-4.9.3-mulodttw5pcyjufva4htsktwty4qd52r
# curl@7.47.1%gcc@4.9.3=linux-x86_64
module load curl-7.47.1-gcc-4.9.3-ohz3fwsepm3b462p5lnaquv7op7naqbi
# autoconf@2.69%gcc@4.9.3=linux-x86_64
module load autoconf-2.69-gcc-4.9.3-bkibjqhgqm5e3o423ogfv2y3o6h2uoq4
# cmake@3.5.0%gcc@4.9.3~doc+ncurses+openssl~qt=linux-x86_64
module load cmake-3.5.0-gcc-4.9.3-x7xnsklmgwla3ubfgzppamtbqk5rwn7t
# expat@2.1.0%gcc@4.9.3=linux-x86_64
module load expat-2.1.0-gcc-4.9.3-6pkz2ucnk2e62imwakejjvbv6egncppd
# git@2.8.0-rc2%gcc@4.9.3+curl+expat=linux-x86_64
module load git-2.8.0-rc2-gcc-4.9.3-3bib4hqtnv5xjjoq5ugt3inblt4xrgkd
The script may be further edited by removing unnecessary modules.
^^^^^^^^^^^^^^^
Module Prefixes
^^^^^^^^^^^^^^^
On some systems, modules are automatically prefixed with a certain
string; ``spack module loads`` needs to know about that prefix when it
issues ``module load`` commands. Add the ``--prefix`` option to your
``spack module loads`` commands if this is necessary.
For example, consider the following on one system:
..code-block:: console
$ module avail
linux-SuSE11-x86_64/antlr-2.7.7-gcc-5.3.0-bdpl46y
$ spack module loads antlr # WRONG!
# antlr@2.7.7%gcc@5.3.0~csharp+cxx~java~python arch=linux-SuSE11-x86_64
module load antlr-2.7.7-gcc-5.3.0-bdpl46y
$ spack module loads --prefix linux-SuSE11-x86_64/ antlr
# antlr@2.7.7%gcc@5.3.0~csharp+cxx~java~python arch=linux-SuSE11-x86_64
module load linux-SuSE11-x86_64/antlr-2.7.7-gcc-5.3.0-bdpl46y
^^^^^^^^^^^^^^^^^^^
Configuration files
^^^^^^^^^^^^^^^^^^^
Another way of modifying the content of module files is writing a
``modules.yaml`` configuration file. Following usual Spack conventions, this
file can be placed either at *site* or *user* scope.
The default site configuration reads:
.. literalinclude:: ../../../etc/spack/defaults/modules.yaml
:language: yaml
It basically inspects the installation prefixes for the
existence of a few folders and, if they exist, it prepends a path to a given
list of environment variables.
For each module system that can be enabled a finer configuration is possible:
.. code-block:: yaml
modules:
tcl:
# contains environment modules specific customizations
dotkit:
# contains dotkit specific customizations
The structure under the ``tcl`` and ``dotkit`` keys is almost equal, and will
be showcased in the following by some examples.
"""""""""""""""""""""""""""""""""""""""
Select module files by spec constraints
"""""""""""""""""""""""""""""""""""""""
Using spec syntax it's possible to have different customizations for different
groups of module files.
Considering :
.. code-block:: yaml
modules:
tcl:
all: # Default addition for every package
environment:
set:
BAR: 'bar'
^openmpi:: # A double ':' overrides previous rules
environment:
set:
BAR: 'baz'
zlib:
environment:
prepend_path:
LD_LIBRARY_PATH: 'foo'
zlib%gcc@4.8:
environment:
unset:
- FOOBAR
what will happen is that:
- every module file will set ``BAR=bar``
- unless the associated spec satisfies ``^openmpi`` in which case ``BAR=baz``
- any spec that satisfies ``zlib`` will additionally prepend ``foo`` to ``LD_LIBRARY_PATH``
- any spec that satisfies ``zlib%gcc@4.8`` will additionally unset ``FOOBAR``
.. note::
Order does matter
The modifications associated with the ``all`` keyword are always evaluated
first, no matter where they appear in the configuration file. All the other
spec constraints are instead evaluated top to bottom.
""""""""""""""""""""""""""""""""""""""""
Filter modifications out of module files
""""""""""""""""""""""""""""""""""""""""
Modifications to certain environment variables in module files are generated by
default. Suppose you would like to avoid having ``CPATH`` and ``LIBRARY_PATH``
modified by your dotkit modules. Then :
.. code-block:: yaml
modules:
dotkit:
all:
filter:
# Exclude changes to any of these variables
environment_blacklist: ['CPATH', 'LIBRARY_PATH']
will generate dotkit module files that will not contain modifications to either
``CPATH`` or ``LIBRARY_PATH`` and environment module files that instead will
contain those modifications.
"""""""""""""""""""""
Autoload dependencies
"""""""""""""""""""""
The following lines in ``modules.yaml``:
.. code-block:: yaml
modules:
tcl:
all:
autoload: 'direct'
will produce environment module files that will automatically load their direct
dependencies.
.. note::
Allowed values for ``autoload`` statements
Allowed values for ``autoload`` statements are either ``none``, ``direct``
or ``all``. In ``tcl`` configuration it is possible to use the option
``prerequisites`` that accepts the same values and will add ``prereq``
statements instead of automatically loading other modules.
""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
Blacklist or whitelist the generation of specific module files
""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
Sometimes it is desirable not to generate module files, a common use case being
not providing the users with software built using the system compiler.
A configuration file like:
.. code-block:: yaml
modules:
tcl:
whitelist: ['gcc', 'llvm'] # Whitelist will have precedence over blacklist
blacklist: ['%gcc@4.4.7'] # Assuming gcc@4.4.7 is the system compiler
will skip module file generation for anything that satisfies ``%gcc@4.4.7``,
with the exception of specs that satisfy ``gcc`` or ``llvm``.
""""""""""""""""""""""""""""""""""""""""""""""""
Customize the naming scheme and insert conflicts
""""""""""""""""""""""""""""""""""""""""""""""""
A configuration file like:
.. code-block:: yaml
modules:
tcl:
naming_scheme: '{name}/{version}-{compiler.name}-{compiler.version}'
all:
conflict: ['{name}', 'intel/14.0.1']
will create module files that will conflict with ``intel/14.0.1`` and with the
base directory of the same module, effectively preventing the possibility to
load two or more versions of the same software at the same time.
.. note::
Tokens available for the naming scheme
currently only the tokens shown in the example are available to construct
the naming scheme
.. note::
The ``conflict`` option is ``tcl`` specific
The names of environment modules generated by spack are not always easy to
fully comprehend due to the long hash in the name. There are two module
configuration options to help with that. The first is a global setting to
adjust the hash length. It can be set anywhere from 0 to 32 and has a default
length of 7. This is the representation of the hash in the module file name and
does not affect the size of the package hash. Be aware that the smaller the
hash length the more likely naming conflicts will occur. The following snippet
shows how to set hash length in the module file names:
.. code-block:: yaml
modules:
tcl:
hash_length: 7
To help make module names more readable, and to help alleviate name conflicts
with a short hash, one can use the ``suffixes`` option in the modules
configuration file. This option will add strings to modules that match a spec.
For instance, the following config options,
.. code-block:: yaml
modules:
tcl:
all:
suffixes:
^python@2.7.12: 'python-2.7.12'
^openblas: 'openblas'
will add a ``python-2.7.12`` version string to any packages compiled with
python matching the spec, ``python@2.7.12``. This is useful to know which
version of python a set of python extensions is associated with. Likewise, the
``openblas`` string is attached to any program that has openblas in the spec,
most likely via the ``+blas`` variant specification.
^^^^^^^^^^^^^^^^^^^^^^^^^
Regenerating Module files
^^^^^^^^^^^^^^^^^^^^^^^^^
Module and dotkit files are generated when packages are installed, and
are placed in the directory ``share/spack/modules`` under the Spack
root. The command ``spack refresh`` will regenerate them all without
re-building the packages; for example, if module format or options
have changed:
.. code-block:: console
$ spack module refresh
==> Regenerating tcl module files.
==> Regenerating dotkit module files.
.. _extensions:
--------------------------- ---------------------------
Extensions & Python support Extensions & Python support
--------------------------- ---------------------------
......
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configuration configuration
mirrors mirrors
module_file_support
package_list package_list
command_index command_index
......
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