diff --git a/lib/spack/docs/basic_usage.rst b/lib/spack/docs/basic_usage.rst
index 68f3d07b297c632669b1604d3ac0e1d3429f8599..29791d98c4a63e4a5b08ef3286b03da453e295e4 100644
--- a/lib/spack/docs/basic_usage.rst
+++ b/lib/spack/docs/basic_usage.rst
@@ -372,25 +372,32 @@ how this is done is in :ref:`sec-specs`.
``spack compiler add``
~~~~~~~~~~~~~~~~~~~~~~~
+An alias for ``spack compiler find``.
+
+.. _spack-compiler-find:
+
+``spack compiler find``
+~~~~~~~~~~~~~~~~~~~~~~~
+
If you do not see a compiler in this list, but you want to use it with
-Spack, you can simply run ``spack compiler add`` with the path to
+Spack, you can simply run ``spack compiler find`` with the path to
where the compiler is installed. For example::
- $ spack compiler add /usr/local/tools/ic-13.0.079
+ $ spack compiler find /usr/local/tools/ic-13.0.079
==> Added 1 new compiler to /Users/gamblin2/.spack/compilers.yaml
intel@13.0.079
-Or you can run ``spack compiler add`` with no arguments to force
+Or you can run ``spack compiler find`` with no arguments to force
auto-detection. This is useful if you do not know where compilers are
installed, but you know that new compilers have been added to your
``PATH``. For example, using dotkit, you might do this::
$ module load gcc-4.9.0
- $ spack compiler add
+ $ spack compiler find
==> Added 1 new compiler to /Users/gamblin2/.spack/compilers.yaml
gcc@4.9.0
-This loads the environment module for gcc-4.9.0 to get it into the
+This loads the environment module for gcc-4.9.0 to add it to
``PATH``, and then it adds the compiler to Spack.
.. _spack-compiler-info:
@@ -807,17 +814,22 @@ Environment Modules, you can get it with Spack:
1. Install with::
+.. code-block:: sh
+
spack install environment-modules
2. Activate with::
- MODULES_HOME=`spack location -i environment-modules`
- MODULES_VERSION=`ls -1 $MODULES_HOME/Modules | head -1`
- ${MODULES_HOME}/Modules/${MODULES_VERSION}/bin/add.modules
+Add the following two lines to your ``.bashrc`` profile (or similar):
+
+.. code-block:: sh
+
+ MODULES_HOME=`spack location -i environment-modules`
+ source ${MODULES_HOME}/Modules/init/bash
+
+In case you use a Unix shell other than bash, substitute ``bash`` by
+the appropriate file in ``${MODULES_HOME}/Modules/init/``.
-This adds to your ``.bashrc`` (or similar) files, enabling Environment
-Modules when you log in. It will ask your permission before changing
-any files.
Spack and Environment Modules
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
diff --git a/lib/spack/docs/packaging_guide.rst b/lib/spack/docs/packaging_guide.rst
index 519c0da2329cf85d10db510fca63a8097f5ffca4..34d11308f5e7dc58f4d77f513a4637d04ad02205 100644
--- a/lib/spack/docs/packaging_guide.rst
+++ b/lib/spack/docs/packaging_guide.rst
@@ -1831,6 +1831,23 @@ successfully find ``libdwarf.h`` and ``libdwarf.so``, without the
packager having to provide ``--with-libdwarf=/path/to/libdwarf`` on
the command line.
+Message Parsing Interface (MPI)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+It is common for high performance computing software/packages to use ``MPI``.
+As a result of conretization, a given package can be built using different
+implementations of MPI such as ``Openmpi``, ``MPICH`` or ``IntelMPI``.
+In some scenarios to configure a package one have to provide it with appropriate MPI
+compiler wrappers such as ``mpicc``, ``mpic++``.
+However different implementations of ``MPI`` may have different names for those
+wrappers. In order to make package's ``install()`` method indifferent to the
+choice ``MPI`` implementation, each package which implements ``MPI`` sets up
+``self.spec.mpicc``, ``self.spec.mpicxx``, ``self.spec.mpifc`` and ``self.spec.mpif77``
+to point to ``C``, ``C++``, ``Fortran 90`` and ``Fortran 77`` ``MPI`` wrappers.
+Package developers are advised to use these variables, for example ``self.spec['mpi'].mpicc``
+instead of hard-coding ``join_path(self.spec['mpi'].prefix.bin, 'mpicc')`` for
+the reasons outlined above.
+
+
Forking ``install()``
~~~~~~~~~~~~~~~~~~~~~
diff --git a/lib/spack/env/cc b/lib/spack/env/cc
index 18fd8f7bdb1f28f071f7c52255a3cda624d35c6e..cb07a2ffea6dabbbc2c89ff4bdaf824c1912fe9b 100755
--- a/lib/spack/env/cc
+++ b/lib/spack/env/cc
@@ -162,7 +162,7 @@ fi
# It doesn't work with -rpath.
# This variable controls whether they are added.
add_rpaths=true
-if [[ mode == ld && $OSTYPE == darwin* ]]; then
+if [[ $mode == ld && "$SPACK_SHORT_SPEC" =~ "darwin" ]]; then
for arg in "$@"; do
if [[ $arg == -r ]]; then
add_rpaths=false
diff --git a/lib/spack/spack/__init__.py b/lib/spack/spack/__init__.py
index aee11f061f326b263099a4f13797c916a56c105b..9108e1d0e333d13af55555a4a72416718bbff668 100644
--- a/lib/spack/spack/__init__.py
+++ b/lib/spack/spack/__init__.py
@@ -136,9 +136,7 @@
# don't add a second username if it's already unique by user.
if not _tmp_user in path:
tmp_dirs.append(join_path(path, '%u', 'spack-stage'))
-
-for path in _tmp_candidates:
- if not path in tmp_dirs:
+ else:
tmp_dirs.append(join_path(path, 'spack-stage'))
# Whether spack should allow installation of unsafe versions of
diff --git a/lib/spack/spack/cmd/compiler.py b/lib/spack/spack/cmd/compiler.py
index 3e58e8218474eb0a78c7be286ebad3adfe197f9e..a8e9e2a7a51703d829b949ad5439b6959a06f1b1 100644
--- a/lib/spack/spack/cmd/compiler.py
+++ b/lib/spack/spack/cmd/compiler.py
@@ -44,10 +44,10 @@ def setup_parser(subparser):
scopes = spack.config.config_scopes
- # Add
- add_parser = sp.add_parser('add', help='Add compilers to the Spack configuration.')
- add_parser.add_argument('add_paths', nargs=argparse.REMAINDER)
- add_parser.add_argument('--scope', choices=scopes, default=spack.cmd.default_modify_scope,
+ # Find
+ find_parser = sp.add_parser('find', aliases=['add'], help='Search the system for compilers to add to the Spack configuration.')
+ find_parser.add_argument('add_paths', nargs=argparse.REMAINDER)
+ find_parser.add_argument('--scope', choices=scopes, default=spack.cmd.default_modify_scope,
help="Configuration scope to modify.")
# Remove
@@ -70,7 +70,7 @@ def setup_parser(subparser):
help="Configuration scope to read from.")
-def compiler_add(args):
+def compiler_find(args):
"""Search either $PATH or a list of paths for compilers and add them
to Spack's configuration."""
paths = args.add_paths
@@ -136,7 +136,8 @@ def compiler_list(args):
def compiler(parser, args):
- action = { 'add' : compiler_add,
+ action = { 'add' : compiler_find,
+ 'find' : compiler_find,
'remove' : compiler_remove,
'rm' : compiler_remove,
'info' : compiler_info,
diff --git a/lib/spack/spack/cmd/test-install.py b/lib/spack/spack/cmd/test-install.py
index 656873a2f036f1811a149489ac5a51748ee89e8d..3277e15548dd4acb6dda8d673686108ce5dafef5 100644
--- a/lib/spack/spack/cmd/test-install.py
+++ b/lib/spack/spack/cmd/test-install.py
@@ -23,87 +23,106 @@
# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
import argparse
-import xml.etree.ElementTree as ET
-import itertools
-import re
-import os
import codecs
+import os
+import time
+import xml.dom.minidom
+import xml.etree.ElementTree as ET
import llnl.util.tty as tty
-from llnl.util.filesystem import *
-
import spack
+import spack.cmd
+from llnl.util.filesystem import *
from spack.build_environment import InstallError
from spack.fetch_strategy import FetchError
-import spack.cmd
description = "Run package installation as a unit test, output formatted results."
-def setup_parser(subparser):
- subparser.add_argument(
- '-j', '--jobs', action='store', type=int,
- help="Explicitly set number of make jobs. Default is #cpus.")
-
- subparser.add_argument(
- '-n', '--no-checksum', action='store_true', dest='no_checksum',
- help="Do not check packages against checksum")
- subparser.add_argument(
- '-o', '--output', action='store', help="test output goes in this file")
+def setup_parser(subparser):
+ subparser.add_argument('-j',
+ '--jobs',
+ action='store',
+ type=int,
+ help="Explicitly set number of make jobs. Default is #cpus.")
- subparser.add_argument(
- 'package', nargs=argparse.REMAINDER, help="spec of package to install")
+ subparser.add_argument('-n',
+ '--no-checksum',
+ action='store_true',
+ dest='no_checksum',
+ help="Do not check packages against checksum")
+ subparser.add_argument('-o', '--output', action='store', help="test output goes in this file")
-class JunitResultFormat(object):
- def __init__(self):
- self.root = ET.Element('testsuite')
- self.tests = []
-
- def add_test(self, buildId, testResult, buildInfo=None):
- self.tests.append((buildId, testResult, buildInfo))
-
- def write_to(self, stream):
- self.root.set('tests', '{0}'.format(len(self.tests)))
- for buildId, testResult, buildInfo in self.tests:
- testcase = ET.SubElement(self.root, 'testcase')
- testcase.set('classname', buildId.name)
- testcase.set('name', buildId.stringId())
- if testResult == TestResult.FAILED:
- failure = ET.SubElement(testcase, 'failure')
- failure.set('type', "Build Error")
- failure.text = buildInfo
- elif testResult == TestResult.SKIPPED:
- skipped = ET.SubElement(testcase, 'skipped')
- skipped.set('type', "Skipped Build")
- skipped.text = buildInfo
- ET.ElementTree(self.root).write(stream)
+ subparser.add_argument('package', nargs=argparse.REMAINDER, help="spec of package to install")
class TestResult(object):
PASSED = 0
FAILED = 1
SKIPPED = 2
+ ERRORED = 3
-class BuildId(object):
- def __init__(self, spec):
- self.name = spec.name
- self.version = spec.version
- self.hashId = spec.dag_hash()
-
- def stringId(self):
- return "-".join(str(x) for x in (self.name, self.version, self.hashId))
-
- def __hash__(self):
- return hash((self.name, self.version, self.hashId))
-
- def __eq__(self, other):
- if not isinstance(other, BuildId):
- return False
+class TestSuite(object):
+ def __init__(self, filename):
+ self.filename = filename
+ self.root = ET.Element('testsuite')
+ self.tests = []
- return ((self.name, self.version, self.hashId) ==
- (other.name, other.version, other.hashId))
+ def __enter__(self):
+ return self
+
+ def append(self, item):
+ if not isinstance(item, TestCase):
+ raise TypeError('only TestCase instances may be appended to a TestSuite instance')
+ self.tests.append(item) # Append the item to the list of tests
+
+ def __exit__(self, exc_type, exc_val, exc_tb):
+ # Prepare the header for the entire test suite
+ number_of_errors = sum(x.result_type == TestResult.ERRORED for x in self.tests)
+ self.root.set('errors', str(number_of_errors))
+ number_of_failures = sum(x.result_type == TestResult.FAILED for x in self.tests)
+ self.root.set('failures', str(number_of_failures))
+ self.root.set('tests', str(len(self.tests)))
+
+ for item in self.tests:
+ self.root.append(item.element)
+
+ with open(self.filename, 'wb') as file:
+ xml_string = ET.tostring(self.root)
+ xml_string = xml.dom.minidom.parseString(xml_string).toprettyxml()
+ file.write(xml_string)
+
+
+class TestCase(object):
+
+ results = {
+ TestResult.PASSED: None,
+ TestResult.SKIPPED: 'skipped',
+ TestResult.FAILED: 'failure',
+ TestResult.ERRORED: 'error',
+ }
+
+ def __init__(self, classname, name, time=None):
+ self.element = ET.Element('testcase')
+ self.element.set('classname', str(classname))
+ self.element.set('name', str(name))
+ if time is not None:
+ self.element.set('time', str(time))
+ self.result_type = None
+
+ def set_result(self, result_type, message=None, error_type=None, text=None):
+ self.result_type = result_type
+ result = TestCase.results[self.result_type]
+ if result is not None and result is not TestResult.PASSED:
+ subelement = ET.SubElement(self.element, result)
+ if error_type is not None:
+ subelement.set('type', error_type)
+ if message is not None:
+ subelement.set('message', str(message))
+ if text is not None:
+ subelement.text = text
def fetch_log(path):
@@ -114,46 +133,76 @@ def fetch_log(path):
def failed_dependencies(spec):
- return set(childSpec for childSpec in spec.dependencies.itervalues() if not
- spack.repo.get(childSpec).installed)
-
-
-def create_test_output(topSpec, newInstalls, output, getLogFunc=fetch_log):
- # Post-order traversal is not strictly required but it makes sense to output
- # tests for dependencies first.
- for spec in topSpec.traverse(order='post'):
- if spec not in newInstalls:
- continue
-
- failedDeps = failed_dependencies(spec)
- package = spack.repo.get(spec)
- if failedDeps:
- result = TestResult.SKIPPED
- dep = iter(failedDeps).next()
- depBID = BuildId(dep)
- errOutput = "Skipped due to failed dependency: {0}".format(
- depBID.stringId())
- elif (not package.installed) and (not package.stage.source_path):
- result = TestResult.FAILED
- errOutput = "Failure to fetch package resources."
- elif not package.installed:
- result = TestResult.FAILED
- lines = getLogFunc(package.build_log_path)
- errMessages = list(line for line in lines if
- re.search('error:', line, re.IGNORECASE))
- errOutput = errMessages if errMessages else lines[-10:]
- errOutput = '\n'.join(itertools.chain(
- [spec.to_yaml(), "Errors:"], errOutput,
- ["Build Log:", package.build_log_path]))
- else:
- result = TestResult.PASSED
- errOutput = None
-
- bId = BuildId(spec)
- output.add_test(bId, result, errOutput)
+ return set(item for item in spec.dependencies.itervalues() if not spack.repo.get(item).installed)
+
+
+def get_top_spec_or_die(args):
+ specs = spack.cmd.parse_specs(args.package, concretize=True)
+ if len(specs) > 1:
+ tty.die("Only 1 top-level package can be specified")
+ top_spec = iter(specs).next()
+ return top_spec
+
+
+def install_single_spec(spec, number_of_jobs):
+ package = spack.repo.get(spec)
+
+ # If it is already installed, skip the test
+ if spack.repo.get(spec).installed:
+ testcase = TestCase(package.name, package.spec.short_spec, time=0.0)
+ testcase.set_result(TestResult.SKIPPED, message='Skipped [already installed]', error_type='already_installed')
+ return testcase
+
+ # If it relies on dependencies that did not install, skip
+ if failed_dependencies(spec):
+ testcase = TestCase(package.name, package.spec.short_spec, time=0.0)
+ testcase.set_result(TestResult.SKIPPED, message='Skipped [failed dependencies]', error_type='dep_failed')
+ return testcase
+
+ # Otherwise try to install the spec
+ try:
+ start_time = time.time()
+ package.do_install(keep_prefix=False,
+ keep_stage=True,
+ ignore_deps=False,
+ make_jobs=number_of_jobs,
+ verbose=True,
+ fake=False)
+ duration = time.time() - start_time
+ testcase = TestCase(package.name, package.spec.short_spec, duration)
+ testcase.set_result(TestResult.PASSED)
+ except InstallError:
+ # An InstallError is considered a failure (the recipe didn't work correctly)
+ duration = time.time() - start_time
+ # Try to get the log
+ lines = fetch_log(package.build_log_path)
+ text = '\n'.join(lines)
+ testcase = TestCase(package.name, package.spec.short_spec, duration)
+ testcase.set_result(TestResult.FAILED, message='Installation failure', text=text)
+
+ except FetchError:
+ # A FetchError is considered an error (we didn't even start building)
+ duration = time.time() - start_time
+ testcase = TestCase(package.name, package.spec.short_spec, duration)
+ testcase.set_result(TestResult.ERRORED, message='Unable to fetch package')
+
+ return testcase
+
+
+def get_filename(args, top_spec):
+ if not args.output:
+ fname = 'test-{x.name}-{x.version}-{hash}.xml'.format(x=top_spec, hash=top_spec.dag_hash())
+ output_directory = join_path(os.getcwd(), 'test-output')
+ if not os.path.exists(output_directory):
+ os.mkdir(output_directory)
+ output_filename = join_path(output_directory, fname)
+ else:
+ output_filename = args.output
+ return output_filename
def test_install(parser, args):
+ # Check the input
if not args.package:
tty.die("install requires a package argument")
@@ -162,50 +211,15 @@ def test_install(parser, args):
tty.die("The -j option must be a positive integer!")
if args.no_checksum:
- spack.do_checksum = False # TODO: remove this global.
-
- specs = spack.cmd.parse_specs(args.package, concretize=True)
- if len(specs) > 1:
- tty.die("Only 1 top-level package can be specified")
- topSpec = iter(specs).next()
-
- newInstalls = set()
- for spec in topSpec.traverse():
- package = spack.repo.get(spec)
- if not package.installed:
- newInstalls.add(spec)
-
- if not args.output:
- bId = BuildId(topSpec)
- outputDir = join_path(os.getcwd(), "test-output")
- if not os.path.exists(outputDir):
- os.mkdir(outputDir)
- outputFpath = join_path(outputDir, "test-{0}.xml".format(bId.stringId()))
- else:
- outputFpath = args.output
-
- for spec in topSpec.traverse(order='post'):
- # Calling do_install for the top-level package would be sufficient but
- # this attempts to keep going if any package fails (other packages which
- # are not dependents may succeed)
- package = spack.repo.get(spec)
- if (not failed_dependencies(spec)) and (not package.installed):
- try:
- package.do_install(
- keep_prefix=False,
- keep_stage=True,
- ignore_deps=False,
- make_jobs=args.jobs,
- verbose=True,
- fake=False)
- except InstallError:
- pass
- except FetchError:
- pass
-
- jrf = JunitResultFormat()
- handled = {}
- create_test_output(topSpec, newInstalls, jrf)
-
- with open(outputFpath, 'wb') as F:
- jrf.write_to(F)
+ spack.do_checksum = False # TODO: remove this global.
+
+ # Get the one and only top spec
+ top_spec = get_top_spec_or_die(args)
+ # Get the filename of the test
+ output_filename = get_filename(args, top_spec)
+ # TEST SUITE
+ with TestSuite(output_filename) as test_suite:
+ # Traverse in post order : each spec is a test case
+ for spec in top_spec.traverse(order='post'):
+ test_case = install_single_spec(spec, args.jobs)
+ test_suite.append(test_case)
diff --git a/lib/spack/spack/compiler.py b/lib/spack/spack/compiler.py
index d38c0b00b12d270f283520a2ef2bfa895ff824d1..20896f9eec764e7ada8843aa2033b42f4ee8734c 100644
--- a/lib/spack/spack/compiler.py
+++ b/lib/spack/spack/compiler.py
@@ -97,6 +97,9 @@ class Compiler(object):
# argument used to get C++11 options
cxx11_flag = "-std=c++11"
+ # argument used to get C++14 options
+ cxx14_flag = "-std=c++1y"
+
def __init__(self, cspec, cc, cxx, f77, fc):
def check(exe):
diff --git a/lib/spack/spack/compilers/gcc.py b/lib/spack/spack/compilers/gcc.py
index 64214db32d3a86ec4492b8edeb63cce6d3b1b986..2e57e4485625852344fa83f987918501559abaa3 100644
--- a/lib/spack/spack/compilers/gcc.py
+++ b/lib/spack/spack/compilers/gcc.py
@@ -54,9 +54,16 @@ def cxx11_flag(self):
if self.version < ver('4.3'):
tty.die("Only gcc 4.3 and above support c++11.")
elif self.version < ver('4.7'):
- return "-std=gnu++0x"
+ return "-std=c++0x"
else:
- return "-std=gnu++11"
+ return "-std=c++11"
+
+ @property
+ def cxx14_flag(self):
+ if self.version < ver('4.8'):
+ tty.die("Only gcc 4.8 and above support c++14.")
+ else:
+ return "-std=c++14"
@classmethod
def fc_version(cls, fc):
diff --git a/lib/spack/spack/fetch_strategy.py b/lib/spack/spack/fetch_strategy.py
index 4ea87bea7ea3e71b61b2766b464e1a1acf2b24e3..ce2c4e30c73fee4bb955e61db704b3ae9cc07a24 100644
--- a/lib/spack/spack/fetch_strategy.py
+++ b/lib/spack/spack/fetch_strategy.py
@@ -157,12 +157,26 @@ def fetch(self):
tty.msg("Already downloaded %s" % self.archive_file)
return
+ possible_files = self.stage.expected_archive_files
+ save_file = None
+ partial_file = None
+ if possible_files:
+ save_file = self.stage.expected_archive_files[0]
+ partial_file = self.stage.expected_archive_files[0] + '.part'
+
tty.msg("Trying to fetch from %s" % self.url)
- curl_args = ['-O', # save file to disk
+ if partial_file:
+ save_args = ['-C', '-', # continue partial downloads
+ '-o', partial_file] # use a .part file
+ else:
+ save_args = ['-O']
+
+ curl_args = save_args + [
'-f', # fail on >400 errors
'-D', '-', # print out HTML headers
- '-L', self.url, ]
+ '-L', # resolve 3xx redirects
+ self.url, ]
if sys.stdout.isatty():
curl_args.append('-#') # status bar when using a tty
@@ -178,6 +192,9 @@ def fetch(self):
if self.archive_file:
os.remove(self.archive_file)
+ if partial_file and os.path.exists(partial_file):
+ os.remove(partial_file)
+
if spack.curl.returncode == 22:
# This is a 404. Curl will print the error.
raise FailedDownloadError(
@@ -209,6 +226,9 @@ def fetch(self):
"'spack clean <package>' to remove the bad archive, then fix",
"your internet gateway issue and install again.")
+ if save_file:
+ os.rename(partial_file, save_file)
+
if not self.archive_file:
raise FailedDownloadError(self.url)
diff --git a/lib/spack/spack/stage.py b/lib/spack/spack/stage.py
index d711752c208f936d52a8e10c7799f6771f609c9f..84c47ee66026f8fe1befece987cd1dfaa3c68c3f 100644
--- a/lib/spack/spack/stage.py
+++ b/lib/spack/spack/stage.py
@@ -210,6 +210,18 @@ def _need_to_create_path(self):
return False
+ @property
+ def expected_archive_files(self):
+ """Possible archive file paths."""
+ paths = []
+ if isinstance(self.fetcher, fs.URLFetchStrategy):
+ paths.append(os.path.join(self.path, os.path.basename(self.fetcher.url)))
+
+ if self.mirror_path:
+ paths.append(os.path.join(self.path, os.path.basename(self.mirror_path)))
+
+ return paths
+
@property
def archive_file(self):
"""Path to the source archive within this stage directory."""
diff --git a/lib/spack/spack/test/__init__.py b/lib/spack/spack/test/__init__.py
index 175a49428c4b223f99814b541e71965bd7585dae..3c5edde66b94ca7ff032b964cc3ef2a5b4af8f03 100644
--- a/lib/spack/spack/test/__init__.py
+++ b/lib/spack/spack/test/__init__.py
@@ -61,14 +61,14 @@
'optional_deps',
'make_executable',
'configure_guess',
- 'unit_install',
'lock',
'database',
'namespace_trie',
'yaml',
'sbang',
'environment',
- 'cmd.uninstall']
+ 'cmd.uninstall',
+ 'cmd.test_install']
def list_tests():
diff --git a/lib/spack/spack/test/cc.py b/lib/spack/spack/test/cc.py
index 0b1aeb2a8fe86de5ef05e9e6036079a5c8724c88..594cd6efe9bdc9b21bc6d8c015919271859a1bee 100644
--- a/lib/spack/spack/test/cc.py
+++ b/lib/spack/spack/test/cc.py
@@ -219,3 +219,27 @@ def test_ld_deps(self):
' '.join(test_command))
+ def test_ld_deps_reentrant(self):
+ """Make sure ld -r is handled correctly on OS's where it doesn't
+ support rpaths."""
+ os.environ['SPACK_DEPENDENCIES'] = ':'.join([self.dep1])
+
+ os.environ['SPACK_SHORT_SPEC'] = "foo@1.2=linux-x86_64"
+ reentrant_test_command = ['-r'] + test_command
+ self.check_ld('dump-args', reentrant_test_command,
+ 'ld ' +
+ '-rpath ' + self.prefix + '/lib ' +
+ '-rpath ' + self.prefix + '/lib64 ' +
+
+ '-L' + self.dep1 + '/lib ' +
+ '-rpath ' + self.dep1 + '/lib ' +
+
+ '-r ' +
+ ' '.join(test_command))
+
+ os.environ['SPACK_SHORT_SPEC'] = "foo@1.2=darwin-x86_64"
+ self.check_ld('dump-args', reentrant_test_command,
+ 'ld ' +
+ '-L' + self.dep1 + '/lib ' +
+ '-r ' +
+ ' '.join(test_command))
diff --git a/lib/spack/spack/test/cmd/test_install.py b/lib/spack/spack/test/cmd/test_install.py
new file mode 100644
index 0000000000000000000000000000000000000000..2206c7bea1c9667aece3ae0f4b99dcd8dd050689
--- /dev/null
+++ b/lib/spack/spack/test/cmd/test_install.py
@@ -0,0 +1,190 @@
+##############################################################################
+# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License (as published by
+# the Free Software Foundation) version 2.1 dated February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with this program; if not, write to the Free Software Foundation,
+# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+import collections
+from contextlib import contextmanager
+
+import StringIO
+
+FILE_REGISTRY = collections.defaultdict(StringIO.StringIO)
+
+# Monkey-patch open to write module files to a StringIO instance
+@contextmanager
+def mock_open(filename, mode):
+ if not mode == 'wb':
+ raise RuntimeError('test.test_install : unexpected opening mode for monkey-patched open')
+
+ FILE_REGISTRY[filename] = StringIO.StringIO()
+
+ try:
+ yield FILE_REGISTRY[filename]
+ finally:
+ handle = FILE_REGISTRY[filename]
+ FILE_REGISTRY[filename] = handle.getvalue()
+ handle.close()
+
+import os
+import itertools
+import unittest
+
+import spack
+import spack.cmd
+
+
+# The use of __import__ is necessary to maintain a name with hyphen (which cannot be an identifier in python)
+test_install = __import__("spack.cmd.test-install", fromlist=['test_install'])
+
+
+class MockSpec(object):
+ def __init__(self, name, version, hashStr=None):
+ self.dependencies = {}
+ self.name = name
+ self.version = version
+ self.hash = hashStr if hashStr else hash((name, version))
+
+ def traverse(self, order=None):
+ for _, spec in self.dependencies.items():
+ yield spec
+ yield self
+ #allDeps = itertools.chain.from_iterable(i.traverse() for i in self.dependencies.itervalues())
+ #return set(itertools.chain([self], allDeps))
+
+ def dag_hash(self):
+ return self.hash
+
+ @property
+ def short_spec(self):
+ return '-'.join([self.name, str(self.version), str(self.hash)])
+
+
+class MockPackage(object):
+ def __init__(self, spec, buildLogPath):
+ self.name = spec.name
+ self.spec = spec
+ self.installed = False
+ self.build_log_path = buildLogPath
+
+ def do_install(self, *args, **kwargs):
+ self.installed = True
+
+
+class MockPackageDb(object):
+ def __init__(self, init=None):
+ self.specToPkg = {}
+ if init:
+ self.specToPkg.update(init)
+
+ def get(self, spec):
+ return self.specToPkg[spec]
+
+
+def mock_fetch_log(path):
+ return []
+
+specX = MockSpec('X', "1.2.0")
+specY = MockSpec('Y', "2.3.8")
+specX.dependencies['Y'] = specY
+pkgX = MockPackage(specX, 'logX')
+pkgY = MockPackage(specY, 'logY')
+
+
+class MockArgs(object):
+ def __init__(self, package):
+ self.package = package
+ self.jobs = None
+ self.no_checksum = False
+ self.output = None
+
+
+# TODO: add test(s) where Y fails to install
+class TestInstallTest(unittest.TestCase):
+ """
+ Tests test-install where X->Y
+ """
+
+ def setUp(self):
+ super(TestInstallTest, self).setUp()
+
+ # Monkey patch parse specs
+ def monkey_parse_specs(x, concretize):
+ if x == 'X':
+ return [specX]
+ elif x == 'Y':
+ return [specY]
+ return []
+
+ self.parse_specs = spack.cmd.parse_specs
+ spack.cmd.parse_specs = monkey_parse_specs
+
+ # Monkey patch os.mkdirp
+ self.os_mkdir = os.mkdir
+ os.mkdir = lambda x: True
+
+ # Monkey patch open
+ test_install.open = mock_open
+
+ # Clean FILE_REGISTRY
+ FILE_REGISTRY = collections.defaultdict(StringIO.StringIO)
+
+ pkgX.installed = False
+ pkgY.installed = False
+
+ # Monkey patch pkgDb
+ self.saved_db = spack.repo
+ pkgDb = MockPackageDb({specX: pkgX, specY: pkgY})
+ spack.repo = pkgDb
+
+ def tearDown(self):
+ # Remove the monkey patched test_install.open
+ test_install.open = open
+
+ # Remove the monkey patched os.mkdir
+ os.mkdir = self.os_mkdir
+ del self.os_mkdir
+
+ # Remove the monkey patched parse_specs
+ spack.cmd.parse_specs = self.parse_specs
+ del self.parse_specs
+ super(TestInstallTest, self).tearDown()
+
+ spack.repo = self.saved_db
+
+ def test_installing_both(self):
+ test_install.test_install(None, MockArgs('X') )
+ self.assertEqual(len(FILE_REGISTRY), 1)
+ for _, content in FILE_REGISTRY.items():
+ self.assertTrue('tests="2"' in content)
+ self.assertTrue('failures="0"' in content)
+ self.assertTrue('errors="0"' in content)
+
+ def test_dependency_already_installed(self):
+ pkgX.installed = True
+ pkgY.installed = True
+ test_install.test_install(None, MockArgs('X'))
+ self.assertEqual(len(FILE_REGISTRY), 1)
+ for _, content in FILE_REGISTRY.items():
+ self.assertTrue('tests="2"' in content)
+ self.assertTrue('failures="0"' in content)
+ self.assertTrue('errors="0"' in content)
+ self.assertEqual(sum('skipped' in line for line in content.split('\n')), 2)
diff --git a/lib/spack/spack/test/unit_install.py b/lib/spack/spack/test/unit_install.py
deleted file mode 100644
index 18615b7efe886c5f6e1a0c932442c5109617cbee..0000000000000000000000000000000000000000
--- a/lib/spack/spack/test/unit_install.py
+++ /dev/null
@@ -1,126 +0,0 @@
-##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
-#
-# This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/llnl/spack
-# Please also see the LICENSE file for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
-import itertools
-import unittest
-
-import spack
-
-test_install = __import__("spack.cmd.test-install",
- fromlist=["BuildId", "create_test_output", "TestResult"])
-
-class MockOutput(object):
- def __init__(self):
- self.results = {}
-
- def add_test(self, buildId, passed=True, buildInfo=None):
- self.results[buildId] = passed
-
- def write_to(self, stream):
- pass
-
-class MockSpec(object):
- def __init__(self, name, version, hashStr=None):
- self.dependencies = {}
- self.name = name
- self.version = version
- self.hash = hashStr if hashStr else hash((name, version))
-
- def traverse(self, order=None):
- allDeps = itertools.chain.from_iterable(i.traverse() for i in
- self.dependencies.itervalues())
- return set(itertools.chain([self], allDeps))
-
- def dag_hash(self):
- return self.hash
-
- def to_yaml(self):
- return "<<<MOCK YAML {0}>>>".format(test_install.BuildId(self).stringId())
-
-class MockPackage(object):
- def __init__(self, buildLogPath):
- self.installed = False
- self.build_log_path = buildLogPath
-
-specX = MockSpec("X", "1.2.0")
-specY = MockSpec("Y", "2.3.8")
-specX.dependencies['Y'] = specY
-pkgX = MockPackage('logX')
-pkgY = MockPackage('logY')
-bIdX = test_install.BuildId(specX)
-bIdY = test_install.BuildId(specY)
-
-class UnitInstallTest(unittest.TestCase):
- """Tests test-install where X->Y"""
-
- def setUp(self):
- super(UnitInstallTest, self).setUp()
-
- pkgX.installed = False
- pkgY.installed = False
-
- self.saved_db = spack.repo
- pkgDb = MockPackageDb({specX:pkgX, specY:pkgY})
- spack.repo = pkgDb
-
-
- def tearDown(self):
- super(UnitInstallTest, self).tearDown()
-
- spack.repo = self.saved_db
-
- def test_installing_both(self):
- mo = MockOutput()
-
- pkgX.installed = True
- pkgY.installed = True
- test_install.create_test_output(specX, [specX, specY], mo, getLogFunc=mock_fetch_log)
-
- self.assertEqual(mo.results,
- {bIdX:test_install.TestResult.PASSED,
- bIdY:test_install.TestResult.PASSED})
-
-
- def test_dependency_already_installed(self):
- mo = MockOutput()
-
- pkgX.installed = True
- pkgY.installed = True
- test_install.create_test_output(specX, [specX], mo, getLogFunc=mock_fetch_log)
- self.assertEqual(mo.results, {bIdX:test_install.TestResult.PASSED})
-
- #TODO: add test(s) where Y fails to install
-
-
-class MockPackageDb(object):
- def __init__(self, init=None):
- self.specToPkg = {}
- if init:
- self.specToPkg.update(init)
-
- def get(self, spec):
- return self.specToPkg[spec]
-
-def mock_fetch_log(path):
- return []
diff --git a/share/spack/setup-env.sh b/share/spack/setup-env.sh
index 764af684001706f9240319c6a1b054494aae2762..11a4c0a70c4d79a7586f978cd8844856be86bba5 100755
--- a/share/spack/setup-env.sh
+++ b/share/spack/setup-env.sh
@@ -1,4 +1,4 @@
-##############################################################################
+#####################################################################
# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
@@ -84,7 +84,10 @@ function spack {
if [ "$_sp_arg" = "-h" ]; then
command spack cd -h
else
- cd $(spack location $_sp_arg "$@")
+ LOC="$(spack location $_sp_arg "$@")"
+ if [[ -d "$LOC" ]] ; then
+ cd "$LOC"
+ fi
fi
return
;;
diff --git a/var/spack/repos/builtin/packages/LuaJIT/package.py b/var/spack/repos/builtin/packages/LuaJIT/package.py
new file mode 100644
index 0000000000000000000000000000000000000000..7b2a26921212269d564bcbd3a746d2af100bc658
--- /dev/null
+++ b/var/spack/repos/builtin/packages/LuaJIT/package.py
@@ -0,0 +1,15 @@
+import os
+from spack import *
+
+class Luajit(Package):
+ """Flast flexible JITed lua"""
+ homepage = "http://www.luajit.org"
+ url = "http://luajit.org/download/LuaJIT-2.0.4.tar.gz"
+
+ version('2.0.4', 'dd9c38307f2223a504cbfb96e477eca0')
+
+ def install(self, spec, prefix):
+ # Linking with the C++ compiler is a dirty hack to deal with the fact
+ # that unwinding symbols are not included by libc, this is necessary
+ # on some platforms for the final link stage to work
+ make("install", "PREFIX=" + prefix, "TARGET_LD=" + os.environ['CXX'])
diff --git a/var/spack/repos/builtin/packages/adol-c/openmp_exam.patch b/var/spack/repos/builtin/packages/adol-c/openmp_exam.patch
new file mode 100644
index 0000000000000000000000000000000000000000..8e21c72d921ed231068101620163d68770fc67ab
--- /dev/null
+++ b/var/spack/repos/builtin/packages/adol-c/openmp_exam.patch
@@ -0,0 +1,13 @@
+diff --git a/ADOL-C/examples/additional_examples/openmp_exam/liborpar.cpp b/ADOL-C/examples/additional_examples/openmp_exam/liborpar.cpp
+index fc6fc28..14103d2 100644
+--- a/ADOL-C/examples/additional_examples/openmp_exam/liborpar.cpp
++++ b/ADOL-C/examples/additional_examples/openmp_exam/liborpar.cpp
+@@ -27,7 +27,7 @@ using namespace std;
+ #include <ctime>
+ #include <cmath>
+
+-#include "adolc.h"
++#include <adolc/adolc.h>
+
+ #ifdef _OPENMP
+ #include <omp.h>
diff --git a/var/spack/repos/builtin/packages/adol-c/package.py b/var/spack/repos/builtin/packages/adol-c/package.py
new file mode 100644
index 0000000000000000000000000000000000000000..70933542ca02980a6ced492846b5398aa953a278
--- /dev/null
+++ b/var/spack/repos/builtin/packages/adol-c/package.py
@@ -0,0 +1,80 @@
+from spack import *
+import sys
+
+class AdolC(Package):
+ """A package for the automatic differentiation of first and higher derivatives of vector functions in C and C++ programs by operator overloading."""
+ homepage = "https://projects.coin-or.org/ADOL-C"
+ url = "http://www.coin-or.org/download/source/ADOL-C/ADOL-C-2.6.1.tgz"
+
+ version('head', svn='https://projects.coin-or.org/svn/ADOL-C/trunk/')
+ version('2.6.1', '1032b28427d6e399af4610e78c0f087b')
+
+ variant('doc', default=True, description='Install documentation')
+ variant('openmp', default=False, description='Enable OpenMP support')
+ variant('sparse', default=False, description='Enable sparse drivers')
+ variant('tests', default=True, description='Build all included examples as a test case')
+
+ patch('openmp_exam.patch')
+
+ def install(self, spec, prefix):
+ make_args = ['--prefix=%s' % prefix]
+
+ # --with-cflags=FLAGS use CFLAGS=FLAGS (default: -O3 -Wall -ansi)
+ # --with-cxxflags=FLAGS use CXXFLAGS=FLAGS (default: -O3 -Wall)
+
+ if '+openmp' in spec:
+ if spec.satisfies('%gcc'):
+ make_args.extend([
+ '--with-openmp-flag=-fopenmp' # FIXME: Is this required? -I <path to omp.h> -L <LLVM OpenMP library path>
+ ])
+ else:
+ raise InstallError("OpenMP flags for compilers other than GCC are not implemented.")
+
+ if '+sparse' in spec:
+ make_args.extend([
+ '--enable-sparse'
+ ])
+
+ # We can simply use the bundled examples to check
+ # whether Adol-C works as expected
+ if '+tests' in spec:
+ make_args.extend([
+ '--enable-docexa', # Documeted examples
+ '--enable-addexa' # Additional examples
+ ])
+ if '+openmp' in spec:
+ make_args.extend([
+ '--enable-parexa' # Parallel examples
+ ])
+
+ configure(*make_args)
+ make()
+ make("install")
+
+ # Copy the config.h file, as some packages might require it
+ source_directory = self.stage.source_path
+ config_h = join_path(source_directory,'ADOL-C','src','config.h')
+ install(config_h, join_path(prefix.include,'adolc'))
+
+ # Install documentation to {prefix}/share
+ if '+doc' in spec:
+ install_tree(join_path('ADOL-C','doc'),
+ join_path(prefix.share,'doc'))
+
+ # Install examples to {prefix}/share
+ if '+tests' in spec:
+ install_tree(join_path('ADOL-C','examples'),
+ join_path(prefix.share,'examples'))
+
+ # Run some examples that don't require user input
+ # TODO: Check that bundled examples produce the correct results
+ with working_dir(join_path(source_directory,'ADOL-C','examples')):
+ Executable('./tapeless_scalar')()
+ Executable('./tapeless_vector')()
+
+ with working_dir(join_path(source_directory,'ADOL-C','examples','additional_examples')):
+ Executable('./checkpointing/checkpointing')()
+
+ if '+openmp' in spec:
+ with working_dir(join_path(source_directory,'ADOL-C','examples','additional_examples')):
+ Executable('./checkpointing/checkpointing')()
diff --git a/var/spack/repos/builtin/packages/astyle/package.py b/var/spack/repos/builtin/packages/astyle/package.py
index 7260fd74a1d6f156652263ba8b02f7f32e47c2f9..5274fc018f0b5df8f391204c811d1b6b81a0a43c 100644
--- a/var/spack/repos/builtin/packages/astyle/package.py
+++ b/var/spack/repos/builtin/packages/astyle/package.py
@@ -14,4 +14,5 @@ def install(self, spec, prefix):
make('-f',
join_path(self.stage.source_path,'build','clang','Makefile'),
parallel=False)
+ mkdirp(self.prefix.bin)
install(join_path(self.stage.source_path, 'src','bin','astyle'), self.prefix.bin)
diff --git a/var/spack/repos/builtin/packages/autoconf/package.py b/var/spack/repos/builtin/packages/autoconf/package.py
index 6412e810a6adeaf24648840e9fc7c22416cbc867..b5e29b8a27de23409ab4c5d21b5b8b9c90ca3e1d 100644
--- a/var/spack/repos/builtin/packages/autoconf/package.py
+++ b/var/spack/repos/builtin/packages/autoconf/package.py
@@ -8,6 +8,8 @@ class Autoconf(Package):
version('2.69', '82d05e03b93e45f5a39b828dc9c6c29b')
version('2.62', '6c1f3b3734999035d77da5024aab4fbd')
+ depends_on("m4")
+
def install(self, spec, prefix):
configure("--prefix=%s" % prefix)
diff --git a/var/spack/repos/builtin/packages/bbcp/package.py b/var/spack/repos/builtin/packages/bbcp/package.py
new file mode 100644
index 0000000000000000000000000000000000000000..e9baa5ccf490a031f86a5d63dbd91786770f88cd
--- /dev/null
+++ b/var/spack/repos/builtin/packages/bbcp/package.py
@@ -0,0 +1,17 @@
+from spack import *
+
+class Bbcp(Package):
+ """Securely and quickly copy data from source to target"""
+ homepage = "http://www.slac.stanford.edu/~abh/bbcp/"
+
+ version('git', git='http://www.slac.stanford.edu/~abh/bbcp/bbcp.git', branch="master")
+
+ def install(self, spec, prefix):
+ cd("src")
+ make()
+ # BBCP wants to build the executable in a directory whose name depends on the system type
+ makesname = Executable("../MakeSname")
+ bbcp_executable_path = "../bin/%s/bbcp" % makesname(output=str).rstrip("\n")
+ destination_path = "%s/bin/" % prefix
+ mkdirp(destination_path)
+ install(bbcp_executable_path, destination_path)
diff --git a/var/spack/repos/builtin/packages/binutils/package.py b/var/spack/repos/builtin/packages/binutils/package.py
index 897539a439100a03e63d489de32f6465e372184c..b8064093d27b61c3bb343dd7d1653d83f950650f 100644
--- a/var/spack/repos/builtin/packages/binutils/package.py
+++ b/var/spack/repos/builtin/packages/binutils/package.py
@@ -12,6 +12,10 @@ class Binutils(Package):
version('2.23.2', '4f8fa651e35ef262edc01d60fb45702e')
version('2.20.1', '2b9dc8f2b7dbd5ec5992c6e29de0b764')
+ depends_on('m4')
+ depends_on('flex')
+ depends_on('bison')
+
# Add a patch that creates binutils libiberty_pic.a which is preferred by OpenSpeedShop and cbtf-krell
variant('krellpatch', default=False, description="build with openspeedshop based patch.")
variant('gold', default=True, description="build the gold linker")
diff --git a/var/spack/repos/builtin/packages/cereal/package.py b/var/spack/repos/builtin/packages/cereal/package.py
index a83927456f1dc798e4a459990702f057ec0b4952..6acbf666c8199b3cadc563ffd4f82162dbc13cc6 100644
--- a/var/spack/repos/builtin/packages/cereal/package.py
+++ b/var/spack/repos/builtin/packages/cereal/package.py
@@ -1,4 +1,5 @@
from spack import *
+import os
import shutil
class Cereal(Package):
@@ -30,5 +31,8 @@ def install(self, spec, prefix):
# Install
shutil.rmtree(join_path(prefix, 'doc'), ignore_errors=True)
shutil.rmtree(join_path(prefix, 'include'), ignore_errors=True)
+ shutil.rmtree(join_path(prefix, 'lib'), ignore_errors=True)
shutil.copytree('doc', join_path(prefix, 'doc'), symlinks=True)
shutil.copytree('include', join_path(prefix, 'include'), symlinks=True)
+ # Create empty directory to avoid linker warnings later
+ os.mkdir(join_path(prefix, 'lib'))
diff --git a/var/spack/repos/builtin/packages/cmake/package.py b/var/spack/repos/builtin/packages/cmake/package.py
index 91a4e3b415f75efbc6181cf63e3ca3f5f9835480..2493cf0a130c78a2eb8038a221ea3479e0264bc5 100644
--- a/var/spack/repos/builtin/packages/cmake/package.py
+++ b/var/spack/repos/builtin/packages/cmake/package.py
@@ -30,6 +30,7 @@ class Cmake(Package):
homepage = 'https://www.cmake.org'
url = 'https://cmake.org/files/v3.4/cmake-3.4.3.tar.gz'
+ version('3.5.2', '701386a1b5ec95f8d1075ecf96383e02')
version('3.5.1', 'ca051f4a66375c89d1a524e726da0296')
version('3.5.0', '33c5d09d4c33d4ffcc63578a6ba8777e')
version('3.4.3', '4cb3ff35b2472aae70f542116d616e63')
diff --git a/var/spack/repos/builtin/packages/cnmem/package.py b/var/spack/repos/builtin/packages/cnmem/package.py
new file mode 100644
index 0000000000000000000000000000000000000000..0a83e8fc205948a132fc95d881afbf953ee5654f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/cnmem/package.py
@@ -0,0 +1,12 @@
+from spack import *
+
+class Cnmem(Package):
+ """CNMem mempool for CUDA devices"""
+ homepage = "https://github.com/NVIDIA/cnmem"
+
+ version('git', git='https://github.com/NVIDIA/cnmem.git', branch="master")
+
+ def install(self, spec, prefix):
+ cmake('.',*std_cmake_args)
+ make()
+ make('install')
diff --git a/var/spack/repos/builtin/packages/cryptopp/package.py b/var/spack/repos/builtin/packages/cryptopp/package.py
index bc83cb2b651aaa953160bb7c1ce7b833a4a3a84d..c2778e14da3fdb363c66a6b4ce81fab20615f315 100644
--- a/var/spack/repos/builtin/packages/cryptopp/package.py
+++ b/var/spack/repos/builtin/packages/cryptopp/package.py
@@ -13,6 +13,7 @@ class Cryptopp(Package):
version('5.6.3', '3c5b70e2ec98b7a24988734446242d07')
version('5.6.2', '7ed022585698df48e65ce9218f6c6a67')
+ version('5.6.1', '96cbeba0907562b077e26bcffb483828')
def install(self, spec, prefix):
make()
diff --git a/var/spack/repos/builtin/packages/dealii/package.py b/var/spack/repos/builtin/packages/dealii/package.py
index b251d50ca1df2d2694966d3acc56af5adae7d71d..df8330384d0614268ca87a01fd26031948d64cef 100644
--- a/var/spack/repos/builtin/packages/dealii/package.py
+++ b/var/spack/repos/builtin/packages/dealii/package.py
@@ -12,6 +12,7 @@ class Dealii(Package):
variant('mpi', default=True, description='Compile with MPI')
variant('arpack', default=True, description='Compile with Arpack and PArpack (only with MPI)')
variant('doc', default=False, description='Compile with documentation')
+ variant('gsl' , default=True, description='Compile with GSL')
variant('hdf5', default=True, description='Compile with HDF5 (only with MPI)')
variant('metis', default=True, description='Compile with Metis')
variant('netcdf', default=True, description='Compile with Netcdf (only with MPI)')
@@ -39,6 +40,8 @@ class Dealii(Package):
depends_on ("mpi", when="+mpi")
depends_on ("arpack-ng+mpi", when='+arpack+mpi')
depends_on ("doxygen", when='+doc')
+ depends_on ("gsl", when='@8.5.0:+gsl')
+ depends_on ("gsl", when='@dev+gsl')
depends_on ("hdf5+mpi~cxx", when='+hdf5+mpi') #FIXME NetCDF declares dependency with ~cxx, why?
depends_on ("metis@5:", when='+metis')
depends_on ("netcdf+mpi", when="+netcdf+mpi")
@@ -50,8 +53,8 @@ class Dealii(Package):
depends_on ("trilinos", when='+trilinos+mpi')
# developer dependnecies
- #depends_on ("numdiff") #FIXME
- #depends_on ("astyle") #FIXME
+ depends_on ("numdiff", when='@dev')
+ depends_on ("astyle@2.04", when='@dev')
def install(self, spec, prefix):
options = []
@@ -80,7 +83,6 @@ def install(self, spec, prefix):
(join_path(spec['lapack'].prefix.lib,'liblapack.%s' % dsuf), # FIXME don't hardcode names
join_path(spec['blas'].prefix.lib,'libblas.%s' % dsuf)), # FIXME don't hardcode names
'-DMUPARSER_DIR=%s ' % spec['muparser'].prefix,
- '-DP4EST_DIR=%s' % spec['p4est'].prefix,
'-DUMFPACK_DIR=%s' % spec['suite-sparse'].prefix,
'-DTBB_DIR=%s' % spec['tbb'].prefix,
'-DZLIB_DIR=%s' % spec['zlib'].prefix
@@ -100,7 +102,7 @@ def install(self, spec, prefix):
])
# Optional dependencies for which librariy names are the same as CMake variables
- for library in ('hdf5', 'p4est','petsc', 'slepc','trilinos','metis'):
+ for library in ('gsl','hdf5','p4est','petsc','slepc','trilinos','metis'):
if library in spec:
options.extend([
'-D{library}_DIR={value}'.format(library=library.upper(), value=spec[library].prefix),
@@ -251,3 +253,6 @@ def install(self, spec, prefix):
cmake('.')
make('release')
make('run',parallel=False)
+
+ def setup_environment(self, spack_env, env):
+ env.set('DEAL_II_DIR', self.prefix)
diff --git a/var/spack/repos/builtin/packages/dia/package.py b/var/spack/repos/builtin/packages/dia/package.py
index 1cb5910e46db8d049bb357e2db7447ea80a50abb..25d5f08205e29ffe45d7225394c5970977c47b1f 100644
--- a/var/spack/repos/builtin/packages/dia/package.py
+++ b/var/spack/repos/builtin/packages/dia/package.py
@@ -7,6 +7,7 @@ class Dia(Package):
version('0.97.3', '0e744a0f6a6c4cb6a089e4d955392c3c')
+ depends_on('intltool')
depends_on('gtkplus@2.6.0:')
depends_on('cairo')
#depends_on('libart') # optional dependency, not yet supported by spack.
diff --git a/var/spack/repos/builtin/packages/eigen/package.py b/var/spack/repos/builtin/packages/eigen/package.py
index 1501989812d45ca64512cc1aac386b83bece6e6c..6b38ab0261ad825bf06c407ed86d242a8233b461 100644
--- a/var/spack/repos/builtin/packages/eigen/package.py
+++ b/var/spack/repos/builtin/packages/eigen/package.py
@@ -45,6 +45,7 @@ class Eigen(Package):
# TODO : dependency on googlehash, superlu, adolc missing
+ depends_on('cmake')
depends_on('metis@5:', when='+metis')
depends_on('scotch', when='+scotch')
depends_on('fftw', when='+fftw')
diff --git a/var/spack/repos/builtin/packages/elk/package.py b/var/spack/repos/builtin/packages/elk/package.py
new file mode 100644
index 0000000000000000000000000000000000000000..1d9216fd1a9c182d7ee4864d34e5db3bc8c1d58f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/elk/package.py
@@ -0,0 +1,122 @@
+from spack import *
+import spack
+
+class Elk(Package):
+ '''An all-electron full-potential linearised augmented-plane wave
+ (FP-LAPW) code with many advanced features.'''
+
+ homepage = 'http://elk.sourceforge.net/'
+ url = 'https://sourceforge.net/projects/elk/files/elk-3.3.17.tgz'
+
+ version('3.3.17', 'f57f6230d14f3b3b558e5c71f62f0592')
+
+ # Elk provides these libraries, but allows you to specify your own
+ variant('blas', default=True, description='Build with custom BLAS library')
+ variant('lapack', default=True, description='Build with custom LAPACK library')
+ variant('fft', default=True, description='Build with custom FFT library')
+
+ # Elk does not provide these libraries, but allows you to use them
+ variant('mpi', default=True, description='Enable MPI parallelism')
+ variant('openmp', default=True, description='Enable OpenMP support')
+ variant('libxc', default=True, description='Link to Libxc functional library')
+
+ depends_on('blas', when='+blas')
+ depends_on('lapack', when='+lapack')
+ depends_on('fftw', when='+fft')
+ depends_on('mpi', when='+mpi')
+ depends_on('libxc', when='+libxc')
+
+ # Cannot be built in parallel
+ parallel = False
+
+
+ def configure(self, spec):
+ # Dictionary of configuration options
+ config = {
+ 'MAKE': 'make',
+ 'F90': join_path(spack.build_env_path, 'f90'),
+ 'F77': join_path(spack.build_env_path, 'f77'),
+ 'AR': 'ar',
+ 'LIB_FFT': 'fftlib.a',
+ 'SRC_MPI': 'mpi_stub.f90',
+ 'SRC_OMP': 'omp_stub.f90',
+ 'SRC_libxc': 'libxcifc_stub.f90',
+ 'SRC_FFT': 'zfftifc.f90'
+ }
+
+ # Compiler-specific flags
+ flags = ''
+ if self.compiler.name == 'intel':
+ flags = '-O3 -ip -unroll -no-prec-div -openmp'
+ elif self.compiler.name == 'gcc':
+ flags = '-O3 -ffast-math -funroll-loops -fopenmp'
+ elif self.compiler.name == 'pgi':
+ flags = '-O3 -mp -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 -qsmp=omp'
+ config['F90_OPTS'] = flags
+ config['F77_OPTS'] = flags
+
+ # BLAS/LAPACK support
+ blas = 'blas.a'
+ lapack = 'lapack.a'
+ if '+blas' in spec:
+ blas = join_path(spec['blas'].prefix.lib, 'libblas.so')
+ if '+lapack' in spec:
+ lapack = join_path(spec['lapack'].prefix.lib, 'liblapack.so')
+ config['LIB_LPK'] = ' '.join([lapack, blas]) # lapack must come before blas
+
+ # FFT support
+ if '+fft' in spec:
+ config['LIB_FFT'] = join_path(spec['fftw'].prefix.lib, 'libfftw3.so')
+ config['SRC_FFT'] = 'zfftifc_fftw.f90'
+
+ # MPI support
+ if '+mpi' in spec:
+ config.pop('SRC_MPI')
+ config['F90'] = join_path(spec['mpi'].prefix.bin, 'mpif90')
+ config['F77'] = join_path(spec['mpi'].prefix.bin, 'mpif77')
+
+ # OpenMP support
+ if '+openmp' in spec:
+ config.pop('SRC_OMP')
+
+ # 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'
+ ])
+
+ # 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]))
+
+
+ def install(self, spec, prefix):
+ # Elk only provides an interactive setup script
+ self.configure(spec)
+
+ make()
+ make('test')
+
+ # The Elk Makefile does not provide an install target
+ mkdirp(prefix.bin)
+
+ install('src/elk', prefix.bin)
+ install('src/eos/eos', prefix.bin)
+ install('src/spacegroup/spacegroup', prefix.bin)
+
+ install_tree('examples', join_path(prefix, 'examples'))
+ install_tree('species', join_path(prefix, 'species'))
+
diff --git a/var/spack/repos/builtin/packages/flex/package.py b/var/spack/repos/builtin/packages/flex/package.py
index b065904912ce7dcf44258c02481b2ac2a641a498..e4795893e068b53969aabbb068831ea3d8c6fcc5 100644
--- a/var/spack/repos/builtin/packages/flex/package.py
+++ b/var/spack/repos/builtin/packages/flex/package.py
@@ -6,6 +6,7 @@ class Flex(Package):
homepage = "http://flex.sourceforge.net/"
url = "http://download.sourceforge.net/flex/flex-2.5.39.tar.gz"
+ version('2.6.0', '5724bcffed4ebe39e9b55a9be80859ec')
version('2.5.39', 'e133e9ead8ec0a58d81166b461244fde')
def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/gcc/package.py b/var/spack/repos/builtin/packages/gcc/package.py
index 6043b6227932de76ac64fa3298dc87c9ad132312..8f90757232b3a689187eac300391960cc7dfb73d 100644
--- a/var/spack/repos/builtin/packages/gcc/package.py
+++ b/var/spack/repos/builtin/packages/gcc/package.py
@@ -38,6 +38,7 @@ class Gcc(Package):
list_url = 'http://open-source-box.org/gcc/'
list_depth = 2
+ version('6.1.0', '8fb6cb98b8459f5863328380fbf06bd1')
version('5.3.0', 'c9616fd448f980259c31de613e575719')
version('5.2.0', 'a51bcfeb3da7dd4c623e27207ed43467')
version('4.9.3', '6f831b4d251872736e8e9cc09746f327')
diff --git a/var/spack/repos/builtin/packages/git/package.py b/var/spack/repos/builtin/packages/git/package.py
index 388f84aefdb017e1218977f84fa930ef918bdc6f..77521fd6588eec09b83f49ced1f07bc1485fb061 100644
--- a/var/spack/repos/builtin/packages/git/package.py
+++ b/var/spack/repos/builtin/packages/git/package.py
@@ -7,7 +7,8 @@ class Git(Package):
homepage = "http://git-scm.com"
url = "https://github.com/git/git/tarball/v2.7.1"
- version('2.8.0-rc2', 'c2cf9f2cc70e35f2fafbaf9258f82e4c')
+ version('2.8.1', '1308448d95afa41a4135903f22262fc8')
+ version('2.8.0', 'eca687e46e9750121638f258cff8317b')
version('2.7.3', 'fa1c008b56618c355a32ba4a678305f6')
version('2.7.1', 'bf0706b433a8dedd27a63a72f9a66060')
@@ -23,18 +24,10 @@ class Git(Package):
#version('2.2.1', 'ff41fdb094eed1ec430aed8ee9b9849c')
- # Git compiles with curl support by default on but if your system
- # does not have it you will not be able to clone https repos
- variant("curl", default=False, description="Add the internal support of curl for https clone")
-
- # Git compiles with expat support by default on but if your system
- # does not have it you will not be able to push https repos
- variant("expat", default=False, description="Add the internal support of expat for https push")
-
depends_on("openssl")
depends_on("autoconf")
- depends_on("curl", when="+curl")
- depends_on("expat", when="+expat")
+ depends_on("curl")
+ depends_on("expat")
# Also depends_on gettext: apt-get install gettext (Ubuntu)
@@ -49,23 +42,12 @@ def install(self, spec, prefix):
"--prefix=%s" % prefix,
"--without-pcre",
"--with-openssl=%s" % spec['openssl'].prefix,
- "--with-zlib=%s" % spec['zlib'].prefix
+ "--with-zlib=%s" % spec['zlib'].prefix,
+ "--with-curl=%s" % spec['curl'].prefix,
+ "--with-expat=%s" % spec['expat'].prefix,
]
- if '+curl' in spec:
- configure_args.append("--with-curl=%s" % spec['curl'].prefix)
-
- if '+expat' in spec:
- configure_args.append("--with-expat=%s" % spec['expat'].prefix)
-
which('autoreconf')('-i')
configure(*configure_args)
make()
make("install")
-
-
-
-
-
-
-
diff --git a/var/spack/repos/builtin/packages/glm/package.py b/var/spack/repos/builtin/packages/glm/package.py
index d00c301b4ceb98e7d00eaeb32820d1aba29cfd40..ecae89f1e8b0f08698a4a63874149961351049f2 100644
--- a/var/spack/repos/builtin/packages/glm/package.py
+++ b/var/spack/repos/builtin/packages/glm/package.py
@@ -11,6 +11,8 @@ class Glm(Package):
url = "https://github.com/g-truc/glm/archive/0.9.7.1.tar.gz"
version('0.9.7.1', '61af6639cdf652d1cdd7117190afced8')
+
+ depends_on ("cmake")
def install(self, spec, prefix):
with working_dir('spack-build', create=True):
diff --git a/var/spack/repos/builtin/packages/gmp/package.py b/var/spack/repos/builtin/packages/gmp/package.py
index fe13de3b95e40aadd6d33a0d0f6b500cd7667ee0..85e9c237d6e6cc8e0803eef44fa1d78089847757 100644
--- a/var/spack/repos/builtin/packages/gmp/package.py
+++ b/var/spack/repos/builtin/packages/gmp/package.py
@@ -35,6 +35,8 @@ class Gmp(Package):
version('6.0.0a', 'b7ff2d88cae7f8085bd5006096eed470')
version('6.0.0' , '6ef5869ae735db9995619135bd856b84')
+ depends_on("m4")
+
def install(self, spec, prefix):
configure("--prefix=%s" % prefix)
make()
diff --git a/var/spack/repos/builtin/packages/gmsh/package.py b/var/spack/repos/builtin/packages/gmsh/package.py
index 9d759303cbb0301fe83b04ae97d9c1eec1b7de89..eb2981bba2dc02903bfecedb63de84b65977dd19 100644
--- a/var/spack/repos/builtin/packages/gmsh/package.py
+++ b/var/spack/repos/builtin/packages/gmsh/package.py
@@ -62,6 +62,9 @@ def install(self, spec, prefix):
build_directory = join_path(self.stage.path, 'spack-build')
source_directory = self.stage.source_path
+
+ # Prevent GMsh from using its own strange directory structure on OSX
+ options.append('-DENABLE_OS_SPECIFIC_INSTALL=OFF')
if '+shared' in spec:
options.extend(['-DENABLE_BUILD_SHARED:BOOL=ON',
diff --git a/var/spack/repos/builtin/packages/hdf5/package.py b/var/spack/repos/builtin/packages/hdf5/package.py
index f26e225b83eab20dc8a2b617e23d1c73833106a5..470969832f19fe2f1335d49938aa25843e41f642 100644
--- a/var/spack/repos/builtin/packages/hdf5/package.py
+++ b/var/spack/repos/builtin/packages/hdf5/package.py
@@ -38,7 +38,7 @@ class Hdf5(Package):
list_depth = 3
version('1.10.0', 'bdc935337ee8282579cd6bc4270ad199')
- version('1.8.16', 'b8ed9a36ae142317f88b0c7ef4b9c618')
+ version('1.8.16', 'b8ed9a36ae142317f88b0c7ef4b9c618', preferred=True)
version('1.8.15', '03cccb5b33dbe975fdcd8ae9dc021f24')
version('1.8.13', 'c03426e9e77d7766944654280b467289')
@@ -101,10 +101,10 @@ def install(self, spec, prefix):
extra_args.append('--enable-cxx')
if '+fortran' in spec:
- extra_args.extend([
- '--enable-fortran',
- '--enable-fortran2003'
- ])
+ extra_args.append('--enable-fortran')
+ # '--enable-fortran2003' no longer exists as of version 1.10.0
+ if spec.satisfies('@:1.8.16'):
+ extra_args.append('--enable-fortran2003')
if '+mpi' in spec:
# The HDF5 configure script warns if cxx and mpi are enabled
diff --git a/var/spack/repos/builtin/packages/hwloc/package.py b/var/spack/repos/builtin/packages/hwloc/package.py
index ab7205646ee18e2a99cdd37ed317a009b3c6381f..a461a7482caf1fe29447e447c61f6af25d3c7d5e 100644
--- a/var/spack/repos/builtin/packages/hwloc/package.py
+++ b/var/spack/repos/builtin/packages/hwloc/package.py
@@ -17,6 +17,7 @@ class Hwloc(Package):
list_url = "http://www.open-mpi.org/software/hwloc/"
list_depth = 3
+ version('1.11.3', 'c1d36a9de6028eac1d18ea4782ef958f')
version('1.11.2', 'e4ca55c2a5c5656da4a4e37c8fc51b23')
version('1.11.1', 'feb4e416a1b25963ed565d8b42252fdc')
version('1.9', '1f9f9155682fe8946a97c08896109508')
diff --git a/var/spack/repos/builtin/packages/hydra/package.py b/var/spack/repos/builtin/packages/hydra/package.py
new file mode 100644
index 0000000000000000000000000000000000000000..c1b886827658827e3e05cfef4e4a0e5240740e8b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/hydra/package.py
@@ -0,0 +1,21 @@
+from spack import *
+
+class Hydra(Package):
+ """Hydra is a process management system for starting parallel jobs.
+ Hydra is designed to natively work with existing launcher daemons
+ (such as ssh, rsh, fork), as well as natively integrate with resource
+ management systems (such as slurm, pbs, sge)."""
+
+ homepage = "http://www.mpich.org"
+ url = "http://www.mpich.org/static/downloads/3.2/hydra-3.2.tar.gz"
+ list_url = "http://www.mpich.org/static/downloads/"
+ list_depth = 2
+
+ version('3.2', '4d670916695bf7e3a869cc336a881b39')
+
+
+ def install(self, spec, prefix):
+ configure('--prefix=%s' % prefix)
+
+ make()
+ make("install")
diff --git a/var/spack/repos/builtin/packages/intltool/package.py b/var/spack/repos/builtin/packages/intltool/package.py
new file mode 100644
index 0000000000000000000000000000000000000000..9b3c095378e2beaaef48d68e194bda21c8060859
--- /dev/null
+++ b/var/spack/repos/builtin/packages/intltool/package.py
@@ -0,0 +1,19 @@
+from spack import *
+
+class Intltool(Package):
+ """intltool is a set of tools to centralize translation of many different file formats using GNU gettext-compatible PO files."""
+ homepage = 'https://freedesktop.org/wiki/Software/intltool/'
+
+ version('0.51.0', '12e517cac2b57a0121cda351570f1e63')
+
+ def url_for_version(self, version):
+ """Handle version-based custom URLs."""
+ return 'https://launchpad.net/intltool/trunk/%s/+download/intltool-%s.tar.gz' % (version, version)
+
+ def install(self, spec, prefix):
+
+ # configure, build, install:
+ options = ['--prefix=%s' % prefix ]
+ configure(*options)
+ make()
+ make('install')
diff --git a/var/spack/repos/builtin/packages/ior/package.py b/var/spack/repos/builtin/packages/ior/package.py
new file mode 100644
index 0000000000000000000000000000000000000000..c46650a6749daee29c21a071480ba2632256f7b2
--- /dev/null
+++ b/var/spack/repos/builtin/packages/ior/package.py
@@ -0,0 +1,42 @@
+from spack import *
+import os
+
+class Ior(Package):
+ """The IOR software is used for benchmarking parallel file systems
+ using POSIX, MPI-IO, or HDF5 interfaces."""
+
+ homepage = "https://github.com/LLNL/ior"
+ url = "https://github.com/LLNL/ior/archive/3.0.1.tar.gz"
+
+ version('3.0.1', '71150025e0bb6ea1761150f48b553065')
+
+ variant('hdf5', default=False, description='support IO with HDF5 backend')
+ variant('ncmpi', default=False, description='support IO with NCMPI backend')
+
+ depends_on('mpi')
+ depends_on('hdf5+mpi', when='+hdf5')
+ depends_on('netcdf+mpi', when='+ncmpi')
+
+
+ def install(self, spec, prefix):
+ os.system('./bootstrap')
+
+ config_args = [
+ 'MPICC=%s' % spec['mpi'].prefix.bin + '/mpicc',
+ '--prefix=%s' % prefix,
+ ]
+
+ if '+hdf5' in spec:
+ config_args.append('--with-hdf5')
+ else:
+ config_args.append('--without-hdf5')
+
+ if '+ncmpi' in spec:
+ config_args.append('--with-ncmpi')
+ else:
+ config_args.append('--without-ncmpi')
+
+ configure(*config_args)
+
+ make()
+ make('install')
diff --git a/var/spack/repos/builtin/packages/jemalloc/package.py b/var/spack/repos/builtin/packages/jemalloc/package.py
index 8cec9ea75ba236a81b8d76c113d965f31bf942c9..9cb0fd1f40a699951c5a153d3e4911291c285c66 100644
--- a/var/spack/repos/builtin/packages/jemalloc/package.py
+++ b/var/spack/repos/builtin/packages/jemalloc/package.py
@@ -5,6 +5,7 @@ class Jemalloc(Package):
homepage = "http://www.canonware.com/jemalloc/"
url = "https://github.com/jemalloc/jemalloc/releases/download/4.0.4/jemalloc-4.0.4.tar.bz2"
+ version('4.1.0', 'c4e53c947905a533d5899e5cc3da1f94')
version('4.0.4', '687c5cc53b9a7ab711ccd680351ff988')
variant('stats', default=False, description='Enable heap statistics')
@@ -20,5 +21,8 @@ def install(self, spec, prefix):
configure(*configure_args)
+ # Don't use -Werror
+ filter_file(r'-Werror=\S*', '', 'Makefile')
+
make()
make("install")
diff --git a/var/spack/repos/builtin/packages/jpeg/package.py b/var/spack/repos/builtin/packages/jpeg/package.py
index 87820467dba31a9dd5e9250b92e9704315e5b829..2f15e59ad4e7d1272449e8c3fc2da7e557cf293a 100644
--- a/var/spack/repos/builtin/packages/jpeg/package.py
+++ b/var/spack/repos/builtin/packages/jpeg/package.py
@@ -1,14 +1,19 @@
from spack import *
class Jpeg(Package):
- """jpeg library"""
+ """libjpeg is a widely used free library with functions for handling the
+ JPEG image data format. It implements a JPEG codec (encoding and decoding)
+ alongside various utilities for handling JPEG data."""
+
homepage = "http://www.ijg.org"
- url = "http://www.ijg.org/files/jpegsrc.v9a.tar.gz"
+ url = "http://www.ijg.org/files/jpegsrc.v9b.tar.gz"
+ version('9b', '6a9996ce116ec5c52b4870dbcd6d3ddb')
version('9a', '3353992aecaee1805ef4109aadd433e7')
def install(self, spec, prefix):
configure("--prefix=%s" % prefix)
make()
+ make("test")
make("install")
diff --git a/var/spack/repos/builtin/packages/julia/openblas.patch b/var/spack/repos/builtin/packages/julia/openblas.patch
new file mode 100644
index 0000000000000000000000000000000000000000..f75d7dd04f895cc722a969fadd5cd39a55fd6227
--- /dev/null
+++ b/var/spack/repos/builtin/packages/julia/openblas.patch
@@ -0,0 +1,68 @@
+diff --git a/deps/Makefile b/deps/Makefile
+index 6cb73be..bcd8520 100644
+--- a/deps/Makefile
++++ b/deps/Makefile
+@@ -1049,7 +1049,7 @@ OPENBLAS_BUILD_OPTS += NO_AFFINITY=1
+
+ # Build for all architectures - required for distribution
+ ifeq ($(OPENBLAS_DYNAMIC_ARCH), 1)
+-OPENBLAS_BUILD_OPTS += DYNAMIC_ARCH=1
++OPENBLAS_BUILD_OPTS += DYNAMIC_ARCH=1 MAKE_NO_J=1
+ endif
+
+ # 64-bit BLAS interface
+@@ -1085,6 +1085,7 @@ OPENBLAS_BUILD_OPTS += NO_AVX2=1
+ endif
+
+ $(OPENBLAS_SRC_DIR)/config.status: $(OPENBLAS_SRC_DIR)/Makefile
++ cd $(dir $@) && patch -p1 < ../openblas-make.patch
+ ifeq ($(OS),WINNT)
+ cd $(dir $@) && patch -p1 < ../openblas-win64.patch
+ endif
+diff --git a/deps/openblas.version b/deps/openblas.version
+index 7c97e1b..58b9467 100644
+--- a/deps/openblas.version
++++ b/deps/openblas.version
+@@ -1,2 +1,2 @@
+-OPENBLAS_BRANCH=v0.2.15
+-OPENBLAS_SHA1=53e849f4fcae4363a64576de00e982722c7304f9
++OPENBLAS_BRANCH=v0.2.17
++OPENBLAS_SHA1=a71e8c82f6a9f73093b631e5deab1e8da716b61f
+--- a/deps/openblas-make.patch
++++ b/deps/openblas-make.patch
+@@ -0,0 +1,35 @@
++diff --git a/Makefile.system b/Makefile.system
++index b89f60e..2dbdad0 100644
++--- a/Makefile.system
+++++ b/Makefile.system
++@@ -139,6 +139,10 @@ NO_PARALLEL_MAKE=0
++ endif
++ GETARCH_FLAGS += -DNO_PARALLEL_MAKE=$(NO_PARALLEL_MAKE)
++
+++ifdef MAKE_NO_J
+++GETARCH_FLAGS += -DMAKE_NO_J=$(MAKE_NO_J)
+++endif
+++
++ ifdef MAKE_NB_JOBS
++ GETARCH_FLAGS += -DMAKE_NB_JOBS=$(MAKE_NB_JOBS)
++ endif
++diff --git a/getarch.c b/getarch.c
++index f9c49e6..dffad70 100644
++--- a/getarch.c
+++++ b/getarch.c
++@@ -1012,6 +1012,7 @@ int main(int argc, char *argv[]){
++ #endif
++ #endif
++
+++#ifndef MAKE_NO_J
++ #ifdef MAKE_NB_JOBS
++ printf("MAKE += -j %d\n", MAKE_NB_JOBS);
++ #elif NO_PARALLEL_MAKE==1
++@@ -1021,6 +1022,7 @@ int main(int argc, char *argv[]){
++ printf("MAKE += -j %d\n", get_num_cores());
++ #endif
++ #endif
+++#endif
++
++ break;
++
diff --git a/var/spack/repos/builtin/packages/julia/package.py b/var/spack/repos/builtin/packages/julia/package.py
index 6900af38e4f13941f4fc0d10c51b0766f7632526..25d782266b3502d5face812b265bdacc8e383396 100644
--- a/var/spack/repos/builtin/packages/julia/package.py
+++ b/var/spack/repos/builtin/packages/julia/package.py
@@ -4,43 +4,56 @@
class Julia(Package):
"""The Julia Language: A fresh approach to technical computing"""
homepage = "http://julialang.org"
- url = "http://github.com/JuliaLang/julia/releases/download/v0.4.2/julia-0.4.2.tar.gz"
+ url = "https://github.com/JuliaLang/julia/releases/download/v0.4.3/julia-0.4.3-full.tar.gz"
- version('0.4.3', '7b9f096798fca4bef262a64674bc2b52')
- version('0.4.2', 'ccfeb4f4090c8b31083f5e1ccb03eb06')
+ version('master',
+ git='https://github.com/JuliaLang/julia.git', branch='master')
+ version('0.4.5', '69141ff5aa6cee7c0ec8c85a34aa49a6')
+ version('0.4.3', '8a4a59fd335b05090dd1ebefbbe5aaac')
patch('gc.patch')
+ patch('openblas.patch', when='@0.4:0.4.5')
- # Build-time dependencies
- depends_on("cmake @2.8:")
+ # Build-time dependencies:
# depends_on("awk")
# depends_on("m4")
# depends_on("pkg-config")
- depends_on("python @2.6:2.9")
- # I think that Julia requires the dependencies above, but it builds find (on
- # my system) without these. We should enable them as necessary.
+ # Combined build-time and run-time dependencies:
+ depends_on("binutils")
+ depends_on("cmake @2.8:")
+ depends_on("git")
+ depends_on("openssl")
+ depends_on("python @2.7:2.999")
+
+ # I think that Julia requires the dependencies above, but it
+ # builds fine (on my system) without these. We should enable them
+ # as necessary.
- # Run-time dependencies
+ # Run-time dependencies:
# depends_on("arpack")
# depends_on("fftw +float")
# depends_on("gmp")
+ # depends_on("libgit")
# depends_on("mpfr")
+ # depends_on("openblas")
# depends_on("pcre2")
- # ARPACK: Requires BLAS and LAPACK; needs to use the same version as Julia.
+ # ARPACK: Requires BLAS and LAPACK; needs to use the same version
+ # as Julia.
- # BLAS and LAPACK: Julia prefers 64-bit versions on 64-bit systems. OpenBLAS
- # has an option for this; make it available as variant.
+ # BLAS and LAPACK: Julia prefers 64-bit versions on 64-bit
+ # systems. OpenBLAS has an option for this; make it available as
+ # variant.
- # FFTW: Something doesn't work when using a pre-installed FFTW library; need
- # to investigate.
+ # FFTW: Something doesn't work when using a pre-installed FFTW
+ # library; need to investigate.
- # GMP, MPFR: Something doesn't work when using a pre-installed FFTW library;
- # need to investigate.
+ # GMP, MPFR: Something doesn't work when using a pre-installed
+ # FFTW library; need to investigate.
- # LLVM: Julia works only with specific versions, and might require patches.
- # Thus we let Julia install its own LLVM.
+ # LLVM: Julia works only with specific versions, and might require
+ # patches. Thus we let Julia install its own LLVM.
# Other possible dependencies:
# USE_SYSTEM_OPENLIBM=0
@@ -50,11 +63,21 @@ class Julia(Package):
# USE_SYSTEM_UTF8PROC=0
# USE_SYSTEM_LIBGIT2=0
+ # Run-time dependencies for Julia packages:
+ depends_on("hdf5")
+ depends_on("mpi")
+
def install(self, spec, prefix):
- # Explicitly setting CC, CXX, or FC breaks building libuv, one of
- # Julia's dependencies. This might be a Darwin-specific problem. Given
- # how Spack sets up compilers, Julia should still use Spack's compilers,
- # even if we don't specify them explicitly.
+ if '@master' in spec:
+ # Julia needs to know the offset from a specific commit
+ git = which('git')
+ git('fetch', '--unshallow')
+
+ # Explicitly setting CC, CXX, or FC breaks building libuv, one
+ # of Julia's dependencies. This might be a Darwin-specific
+ # problem. Given how Spack sets up compilers, Julia should
+ # still use Spack's compilers, even if we don't specify them
+ # explicitly.
options = [#"CC=cc",
#"CXX=c++",
#"FC=fc",
diff --git a/var/spack/repos/builtin/packages/libpng/package.py b/var/spack/repos/builtin/packages/libpng/package.py
index 73c8c6234149839b7fc82312698d31aa5a0f6210..9d5782896e9a6c8ea6390dcd7841020e08a1ffed 100644
--- a/var/spack/repos/builtin/packages/libpng/package.py
+++ b/var/spack/repos/builtin/packages/libpng/package.py
@@ -8,6 +8,9 @@ class Libpng(Package):
version('1.6.16', '1a4ad377919ab15b54f6cb6a3ae2622d')
version('1.6.15', '829a256f3de9307731d4f52dc071916d')
version('1.6.14', '2101b3de1d5f348925990f9aa8405660')
+ version('1.5.26', '3ca98347a5541a2dad55cd6d07ee60a9')
+ version('1.4.19', '89bcbc4fc8b31f4a403906cf4f662330')
+ version('1.2.56', '9508fc59d10a1ffadd9aae35116c19ee')
depends_on('zlib')
diff --git a/var/spack/repos/builtin/packages/libtermkey/package.py b/var/spack/repos/builtin/packages/libtermkey/package.py
new file mode 100644
index 0000000000000000000000000000000000000000..7f25edaf76c6c2ccf599cb1b41844f1c288794b0
--- /dev/null
+++ b/var/spack/repos/builtin/packages/libtermkey/package.py
@@ -0,0 +1,17 @@
+from spack import *
+
+class Libtermkey(Package):
+ """Easy keyboard entry processing for terminal programs"""
+ homepage = "http://www.leonerd.org.uk/code/libtermkey/"
+ url = "http://www.leonerd.org.uk/code/libtermkey/libtermkey-0.18.tar.gz"
+
+ version('0.18' , '3be2e3e5a851a49cc5e8567ac108b520')
+ version('0.17' , '20edb99e0d95ec1690fe90e6a555ae6d')
+ version('0.16' , '7a24b675aaeb142d30db28e7554987d4')
+ version('0.15b', '27689756e6c86c56ae454f2ac259bc3d')
+ version('0.14' , 'e08ce30f440f9715c459060e0e048978')
+
+
+ def install(self, spec, prefix):
+ make()
+ make("install", "PREFIX=" + prefix)
diff --git a/var/spack/repos/builtin/packages/libtool/package.py b/var/spack/repos/builtin/packages/libtool/package.py
index 82a54953b23e29f49900e192c32823aa1cd4699c..c804f5ab5d08f7dd9cbf13f3c0af3f3b52af9709 100644
--- a/var/spack/repos/builtin/packages/libtool/package.py
+++ b/var/spack/repos/builtin/packages/libtool/package.py
@@ -8,6 +8,8 @@ class Libtool(Package):
version('2.4.6' , 'addf44b646ddb4e3919805aa88fa7c5e')
version('2.4.2' , 'd2f3b7d4627e69e13514a40e72a24d50')
+ depends_on('m4')
+
def install(self, spec, prefix):
configure("--prefix=%s" % prefix)
diff --git a/var/spack/repos/builtin/packages/libuv/package.py b/var/spack/repos/builtin/packages/libuv/package.py
new file mode 100644
index 0000000000000000000000000000000000000000..eace94d1a68bf81b33d452f4bf04f7fbc80524a1
--- /dev/null
+++ b/var/spack/repos/builtin/packages/libuv/package.py
@@ -0,0 +1,21 @@
+from spack import *
+
+class Libuv(Package):
+ """Multi-platform library with a focus on asynchronous IO"""
+ homepage = "http://libuv.org"
+ url = "https://github.com/libuv/libuv/archive/v1.9.0.tar.gz"
+
+ version('1.9.0', '14737f9c76123a19a290dabb7d1cd04c')
+
+ depends_on('automake')
+ depends_on('autoconf')
+ depends_on('libtool')
+
+ def install(self, spec, prefix):
+ bash = which("bash")
+ bash('autogen.sh')
+ configure('--prefix=%s' % prefix)
+
+ make()
+ make("check")
+ make("install")
diff --git a/var/spack/repos/builtin/packages/libvterm/package.py b/var/spack/repos/builtin/packages/libvterm/package.py
new file mode 100644
index 0000000000000000000000000000000000000000..3212f6550d25289d7c86446c1b4414923ddb3243
--- /dev/null
+++ b/var/spack/repos/builtin/packages/libvterm/package.py
@@ -0,0 +1,12 @@
+from spack import *
+
+class Libvterm(Package):
+ """An abstract library implementation of a terminal emulator"""
+ homepage = "http://www.leonerd.org.uk/code/libvterm/"
+ url = "http://www.leonerd.org.uk/code/libvterm/libvterm-0+bzr681.tar.gz"
+
+ version('681', '7a4325a7350b7092245c04e8ee185ac3')
+
+ def install(self, spec, prefix):
+ make()
+ make("install", "PREFIX=" + prefix)
diff --git a/var/spack/repos/builtin/packages/libxc/package.py b/var/spack/repos/builtin/packages/libxc/package.py
new file mode 100644
index 0000000000000000000000000000000000000000..010a5918c56e6664a4f9942ee0915bd5d7341641
--- /dev/null
+++ b/var/spack/repos/builtin/packages/libxc/package.py
@@ -0,0 +1,18 @@
+from spack import *
+
+class Libxc(Package):
+ """Libxc is a library of exchange-correlation functionals for
+ density-functional theory."""
+
+ homepage = "http://www.tddft.org/programs/octopus/wiki/index.php/Libxc"
+ url = "http://www.tddft.org/programs/octopus/down.php?file=libxc/libxc-2.2.2.tar.gz"
+
+ version('2.2.2', 'd9f90a0d6e36df6c1312b6422280f2ec')
+
+
+ def install(self, spec, prefix):
+ configure('--prefix=%s' % prefix,
+ '--enable-shared')
+
+ make()
+ make("install")
diff --git a/var/spack/repos/builtin/packages/metis/package.py b/var/spack/repos/builtin/packages/metis/package.py
index 41e3ebb429f0b5fdeee5cdd2e2e8288b9bdb240c..b05f23a3dc26f8d38f5d85a19e783f0479ddae67 100644
--- a/var/spack/repos/builtin/packages/metis/package.py
+++ b/var/spack/repos/builtin/packages/metis/package.py
@@ -136,6 +136,7 @@ def install(self, spec, prefix):
source_directory = self.stage.source_path
options.append('-DGKLIB_PATH:PATH={metis_source}/GKlib'.format(metis_source=source_directory))
+ options.append('-DCMAKE_INSTALL_NAME_DIR:PATH=%s/lib' % prefix)
if '+shared' in spec:
options.append('-DSHARED:BOOL=ON')
@@ -184,7 +185,3 @@ def install(self, spec, prefix):
fs = glob.glob(join_path(source_directory,'GKlib',"*.h"))
for f in fs:
install(f, GKlib_dist)
-
- # The shared library is not installed correctly on Darwin; correct this
- if (sys.platform == 'darwin') and ('+shared' in spec):
- fix_darwin_install_name(prefix.lib)
diff --git a/var/spack/repos/builtin/packages/mfem/package.py b/var/spack/repos/builtin/packages/mfem/package.py
new file mode 100644
index 0000000000000000000000000000000000000000..510e09c4e112facc2dbc422c43f11b9b91b1d49f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/mfem/package.py
@@ -0,0 +1,125 @@
+from spack import *
+import glob, string
+
+class Mfem(Package):
+ """Free, lightweight, scalable C++ library for finite element methods."""
+
+ homepage = 'http://www.mfem.org'
+ url = 'https://github.com/mfem/mfem'
+
+# version('3.1', git='https://github.com/mfem/mfem.git',
+# commit='dbae60fe32e071989b52efaaf59d7d0eb2a3b574')
+
+ version('3.1', '841ea5cf58de6fae4de0f553b0e01ebaab9cd9c67fa821e8a715666ecf18fc57',
+ url='http://goo.gl/xrScXn', expand=False)
+
+ variant('metis', default=False, description='Activate support for metis')
+ variant('hypre', default=False, description='Activate support for hypre')
+ variant('suite-sparse', default=False,
+ description='Activate support for SuiteSparse')
+ variant('mpi', default=False, description='Activate support for MPI')
+ variant('lapack', default=False, description='Activate support for LAPACK')
+ variant('debug', default=False, description='Build debug version')
+
+ depends_on('blas', when='+lapack')
+ depends_on('lapack', when='+lapack')
+
+ depends_on('mpi', when='+mpi')
+ depends_on('metis', when='+mpi')
+ depends_on('hypre', when='+mpi')
+
+ depends_on('hypre', when='+hypre')
+
+ depends_on('metis@4:', when='+metis')
+
+ depends_on('suite-sparse', when='+suite-sparse')
+ depends_on('blas', when='+suite-sparse')
+ depends_on('lapack', when='+suite-sparse')
+ depends_on('metis@5:', when='+suite-sparse ^suite-sparse@4.5:')
+ depends_on('cmake', when='^metis@5:')
+
+ def check_variants(self, spec):
+ if '+mpi' in spec and ('+hypre' not in spec or '+metis' not in spec):
+ raise InstallError('mfem+mpi must be built with +hypre ' +
+ 'and +metis!')
+ if '+suite-sparse' in spec and ('+metis' not in spec or
+ '+lapack' not in spec):
+ raise InstallError('mfem+suite-sparse must be built with ' +
+ '+metis and +lapack!')
+ if 'metis@5:' in spec and '%clang' in spec and ('^cmake %gcc' not in spec):
+ raise InstallError('To work around CMake bug with clang, must ' +
+ 'build mfem with mfem[+variants] %clang ' +
+ '^cmake %gcc to force CMake to build with gcc')
+ return
+
+ def install(self, spec, prefix):
+ self.check_variants(spec)
+
+ options = ['PREFIX=%s' % prefix]
+
+ if '+lapack' in spec:
+ lapack_lib = '-L{0} -llapack -L{1} -lblas'.format(
+ spec['lapack'].prefix.lib, spec['blas'].prefix.lib)
+ options.extend(['MFEM_USE_LAPACK=YES',
+ 'LAPACK_OPT=-I%s' % spec['lapack'].prefix.include,
+ 'LAPACK_LIB=%s' % lapack_lib])
+
+ if '+hypre' in spec:
+ options.extend(['HYPRE_DIR=%s' % spec['hypre'].prefix,
+ 'HYPRE_OPT=-I%s' % spec['hypre'].prefix.include,
+ 'HYPRE_LIB=-L%s' % spec['hypre'].prefix.lib +
+ ' -lHYPRE'])
+
+ if '+metis' in spec:
+ metis_lib = '-L%s -lmetis' % spec['metis'].prefix.lib
+ if spec['metis'].satisfies('@5:'):
+ metis_str = 'MFEM_USE_METIS_5=YES'
+ else:
+ metis_str = 'MFEM_USE_METIS_5=NO'
+ options.extend([metis_str,
+ 'METIS_DIR=%s' % spec['metis'].prefix,
+ 'METIS_OPT=-I%s' % spec['metis'].prefix.include,
+ 'METIS_LIB=%s' % metis_lib])
+
+ if '+mpi' in spec: options.extend(['MFEM_USE_MPI=YES'])
+
+ if '+suite-sparse' in spec:
+ ssp = spec['suite-sparse'].prefix
+ ss_lib = '-L%s' % ssp.lib
+ ss_lib += (' -lumfpack -lcholmod -lcolamd -lamd -lcamd' +
+ ' -lccolamd -lsuitesparseconfig')
+
+ no_librt_archs = ['darwin-i686', 'darwin-x86_64']
+ no_rt = any(map(lambda a: spec.satisfies('='+a), no_librt_archs))
+ if not no_rt: ss_lib += ' -lrt'
+ ss_lib += (' ' + metis_lib + ' ' + lapack_lib)
+
+ options.extend(['MFEM_USE_SUITESPARSE=YES',
+ 'SUITESPARSE_DIR=%s' % ssp,
+ 'SUITESPARSE_OPT=-I%s' % ssp.include,
+ 'SUITESPARSE_LIB=%s' % ss_lib])
+
+ if '+debug' in spec: options.extend(['MFEM_DEBUG=YES'])
+
+ # Dirty hack to cope with URL redirect
+ tgz_file = string.split(self.url,'/')[-1]
+ tar = which('tar')
+ tar('xzvf', tgz_file)
+ cd(glob.glob('mfem*')[0])
+ # End dirty hack to cope with URL redirect
+
+ make('config', *options)
+ make('all')
+
+ # Run a small test before installation
+ args = ['-m', join_path('data','star.mesh'), '--no-visualization']
+ if '+mpi' in spec:
+ Executable(join_path(spec['mpi'].prefix.bin,
+ 'mpirun'))('-np',
+ '4',
+ join_path('examples','ex1p'),
+ *args)
+ else:
+ Executable(join_path('examples', 'ex1'))(*args)
+
+ make('install')
diff --git a/var/spack/repos/builtin/packages/mpich/package.py b/var/spack/repos/builtin/packages/mpich/package.py
index b317ec6651dbc5412bf5be18e9ad007f459430eb..2179086fe525edb812905fa285e2e63e03872060 100644
--- a/var/spack/repos/builtin/packages/mpich/package.py
+++ b/var/spack/repos/builtin/packages/mpich/package.py
@@ -43,6 +43,8 @@ class Mpich(Package):
version('3.0.4', '9c5d5d4fe1e17dd12153f40bc5b6dbc0')
variant('verbs', default=False, description='Build support for OpenFabrics verbs.')
+ variant('pmi', default=True, description='Build with PMI support')
+ variant('hydra', default=True, description='Build the hydra process manager')
provides('mpi@:3.0', when='@3:')
provides('mpi@:1.3', when='@1:')
@@ -55,12 +57,15 @@ def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
spack_env.set('MPICH_FC', spack_fc)
def setup_dependent_package(self, module, dep_spec):
- """For dependencies, make mpicc's use spack wrapper."""
- # FIXME : is this necessary ? Shouldn't this be part of a contract with MPI providers?
- module.mpicc = join_path(self.prefix.bin, 'mpicc')
+ self.spec.mpicc = join_path(self.prefix.bin, 'mpicc')
+ self.spec.mpicxx = join_path(self.prefix.bin, 'mpic++')
+ self.spec.mpifc = join_path(self.prefix.bin, 'mpif90')
+ self.spec.mpif77 = join_path(self.prefix.bin, 'mpif77')
def install(self, spec, prefix):
config_args = ["--prefix=" + prefix,
+ "--with-pmi=" + ("yes" if '+pmi' in spec else 'no'),
+ "--with-pm=" + ('hydra' if '+hydra' in spec else 'no'),
"--enable-shared"]
# Variants
diff --git a/var/spack/repos/builtin/packages/mrnet/krell-5.0.1.patch b/var/spack/repos/builtin/packages/mrnet/krell-5.0.1.patch
new file mode 100644
index 0000000000000000000000000000000000000000..53294fbbc63d2e54fc84ead56f833f0476d23b44
--- /dev/null
+++ b/var/spack/repos/builtin/packages/mrnet/krell-5.0.1.patch
@@ -0,0 +1,154 @@
+--- mrnet-3093918/include/mrnet/Types.h 2015-12-10 09:32:24.000000000 -0800
++++ mrnet_top_of_tree/include/mrnet/Types.h 2016-03-16 12:29:33.986132302 -0700
+@@ -23,7 +23,7 @@
+ #ifndef MRNET_VERSION_MAJOR
+ # define MRNET_VERSION_MAJOR 5
+ # define MRNET_VERSION_MINOR 0
+-# define MRNET_VERSION_REV 0
++# define MRNET_VERSION_REV 1
+ #endif
+
+ namespace MRN
+--- mrnet-3093918/include/mrnet_lightweight/Types.h 2015-12-10 09:32:24.000000000 -0800
++++ mrnet_top_of_tree/include/mrnet_lightweight/Types.h 2016-03-16 12:29:33.987132302 -0700
+@@ -30,7 +30,7 @@
+ #ifndef MRNET_VERSION_MAJOR
+ #define MRNET_VERSION_MAJOR 5
+ #define MRNET_VERSION_MINOR 0
+-#define MRNET_VERSION_REV 0
++#define MRNET_VERSION_REV 1
+ #endif
+ void get_Version(int* major,
+ int* minor,
+--- mrnet-3093918/src/lightweight/SerialGraph.c 2015-12-10 09:32:24.000000000 -0800
++++ mrnet_top_of_tree/src/lightweight/SerialGraph.c 2016-03-16 12:29:33.995132302 -0700
+@@ -59,7 +59,7 @@
+
+ mrn_dbg_func_begin();
+
+- sprintf(hoststr, "[%s:%hu:%u:", ihostname, iport, irank);
++ sprintf(hoststr, "[%s:%05hu:%u:", ihostname, iport, irank);
+ mrn_dbg(5, mrn_printf(FLF, stderr, "looking for SubTreeRoot: '%s'\n", hoststr));
+
+ byte_array = sg->byte_array;
+@@ -110,7 +110,7 @@
+
+ mrn_dbg_func_begin();
+
+- len = (size_t) sprintf(hoststr, "[%s:%hu:%u:0]", ihostname, iport, irank);
++ len = (size_t) sprintf(hoststr, "[%s:%05hu:%u:0]", ihostname, iport, irank);
+ mrn_dbg(5, mrn_printf(FLF, stderr, "adding sub tree leaf: %s\n", hoststr));
+
+ len += strlen(sg->byte_array) + 1;
+@@ -139,7 +139,7 @@
+
+ mrn_dbg_func_begin();
+
+- len = (size_t) sprintf(hoststr, "[%s:%hu:%u:1", ihostname, iport, irank);
++ len = (size_t) sprintf(hoststr, "[%s:%05hu:%u:1", ihostname, iport, irank);
+ mrn_dbg(5, mrn_printf(FLF, stderr, "adding sub tree root: %s\n", hoststr));
+
+ len += strlen(sg->byte_array) + 1;
+@@ -360,8 +360,8 @@
+ char old_hoststr[256];
+ char new_hoststr[256];
+
+- sprintf(old_hoststr, "[%s:%hu:%u:", hostname, UnknownPort, irank);
+- sprintf(new_hoststr, "[%s:%hu:%u:", hostname, port, irank);
++ sprintf(old_hoststr, "[%s:%05hu:%u:", hostname, UnknownPort, irank);
++ sprintf(new_hoststr, "[%s:%05hu:%u:", hostname, port, irank);
+
+ old_byte_array = sg->byte_array;
+ new_byte_array = (char*) malloc( strlen(old_byte_array) + 10 );
+--- mrnet-3093918/xplat/src/lightweight/SocketUtils.c 2015-12-10 09:32:24.000000000 -0800
++++ mrnet_top_of_tree/xplat/src/lightweight/SocketUtils.c 2016-03-16 12:29:34.006132303 -0700
+@@ -15,7 +15,7 @@
+ #else
+ const XPlat_Socket InvalidSocket = INVALID_SOCKET;
+ #endif
+-const XPlat_Port InvalidPort = (XPlat_Port)-1;
++const XPlat_Port InvalidPort = (XPlat_Port)0;
+
+ static bool_t SetTcpNoDelay( XPlat_Socket sock )
+ {
+--- mrnet-3093918/conf/configure.in 2015-12-10 09:32:24.000000000 -0800
++++ mrnet_top_of_tree/conf/configure.in 2016-03-16 12:45:54.573196781 -0700
+@@ -107,6 +107,18 @@
+ AC_SUBST(PURIFY)
+
+
++AC_ARG_WITH(expat,
++ [AS_HELP_STRING([--with-expat=PATH],
++ [Absolute path to installation of EXPAT libraries (note: specify the path to the directory containing "include" and "lib" sub-directories)])],
++ [EXPAT_DIR="${withval}"],
++ [EXPAT_DIR=""])
++
++if test "x$EXPAT_DIR" = "x" ; then
++ EXPAT_LIB=""
++else
++ EXPAT_LIB="-L$EXPAT_DIR/lib"
++fi
++
+ dnl === Checks for header files.
+ AC_CHECK_HEADERS([assert.h errno.h fcntl.h limits.h netdb.h signal.h stddef.h stdlib.h stdio.h string.h unistd.h arpa/inet.h netinet/in.h sys/ioctl.h sys/socket.h sys/sockio.h sys/time.h])
+ AC_HEADER_STDBOOL
+@@ -432,7 +444,7 @@
+ CRAYXT_ATH_LIBS_SO="$CRAYXT_ATH_LIBS -lalps"
+ CRAYXT_ATH_LIBS="$CRAYXT_ATH_LIBS -Wl,-Bstatic -lalps -lxmlrpc -Wl,-Bdynamic"
+ CRAYXE_ATH_LIBS_SO="$CRAYXE_ATH_LIBS -lalps"
+- CRAYXE_ATH_LIBS="$CRAYXE_ATH_LIBS -Wl,-Bstatic -lalps -lxmlrpc-epi -lexpat -Wl,-Bdynamic"
++ CRAYXE_ATH_LIBS="$CRAYXE_ATH_LIBS -Wl,-Bstatic -lalps -lxmlrpc-epi $EXPAT_LIB -lexpat -Wl,-Bdynamic"
+
+ AC_CHECK_LIB( [alps], [alps_launch_tool_helper],
+ [HAVE_ATH_LIBS="yes"; EXTRA_LIBS="$CRAYXT_ATH_LIBS $EXTRA_LIBS"; EXTRA_LIBS_SO="$CRAYXT_ATH_LIBS_SO $EXTRA_LIBS_SO"],
+--- mrnet-3093918/configure 2015-12-10 09:32:24.000000000 -0800
++++ mrnet_top_of_tree/configure 2016-03-16 13:47:20.386439143 -0700
+@@ -742,6 +742,7 @@
+ enable_debug
+ enable_ltwt_threadsafe
+ with_purify
++with_expat
+ '
+ ac_precious_vars='build_alias
+ host_alias
+@@ -1399,6 +1400,9 @@
+ containing "include" and "lib" sub-directories)
+ --with-launchmon=PATH Absolute path to installation of LaunchMON
+ --with-purify Use purify for memory debugging
++ --with-expat=PATH Absolute path to installation of EXPAT libraries
++ (note: specify the path to the directory containing
++ "include" and "lib" sub-directories)
+
+ Some influential environment variables:
+ CC C compiler command
+@@ -3541,6 +3545,21 @@
+
+
+
++# Check whether --with-expat was given.
++if test "${with_expat+set}" = set; then :
++ withval=$with_expat; EXPAT_DIR="${withval}"
++else
++ EXPAT_DIR=""
++fi
++
++
++if test "x$EXPAT_DIR" = "x" ; then
++ EXPAT_LIB=""
++else
++ EXPAT_LIB="-L$EXPAT_DIR/lib"
++fi
++
++
+ ac_ext=cpp
+ ac_cpp='$CXXCPP $CPPFLAGS'
+ ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+@@ -5473,7 +5492,7 @@
+ CRAYXT_ATH_LIBS_SO="$CRAYXT_ATH_LIBS -lalps"
+ CRAYXT_ATH_LIBS="$CRAYXT_ATH_LIBS -Wl,-Bstatic -lalps -lxmlrpc -Wl,-Bdynamic"
+ CRAYXE_ATH_LIBS_SO="$CRAYXE_ATH_LIBS -lalps"
+- CRAYXE_ATH_LIBS="$CRAYXE_ATH_LIBS -Wl,-Bstatic -lalps -lxmlrpc-epi -lexpat -Wl,-Bdynamic"
++ CRAYXE_ATH_LIBS="$CRAYXE_ATH_LIBS -Wl,-Bstatic -lalps -lxmlrpc-epi $EXPAT_LIB -lexpat -Wl,-Bdynamic"
+
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for alps_launch_tool_helper in -lalps" >&5
+ $as_echo_n "checking for alps_launch_tool_helper in -lalps... " >&6; }
diff --git a/var/spack/repos/builtin/packages/mrnet/package.py b/var/spack/repos/builtin/packages/mrnet/package.py
index fed944e45f30b5e7c11e5e0d610c489177fe2fdb..b52233be4ae459cd7c0e24e49151f57d4e711ce3 100644
--- a/var/spack/repos/builtin/packages/mrnet/package.py
+++ b/var/spack/repos/builtin/packages/mrnet/package.py
@@ -3,11 +3,18 @@
class Mrnet(Package):
"""The MRNet Multi-Cast Reduction Network."""
homepage = "http://paradyn.org/mrnet"
- url = "ftp://ftp.cs.wisc.edu/paradyn/mrnet/mrnet_4.0.0.tar.gz"
+ url = "ftp://ftp.cs.wisc.edu/paradyn/mrnet/mrnet_5.0.1.tar.gz"
+ list_url = "http://ftp.cs.wisc.edu/paradyn/mrnet"
- version('4.0.0', 'd00301c078cba57ef68613be32ceea2f')
- version('4.1.0', '5a248298b395b329e2371bf25366115c')
+ version('5.0.1-2', git='https://github.com/dyninst/mrnet.git', commit='20b1eacfc6d680d9f6472146d2dfaa0f900cc2e9')
version('5.0.1', '17f65738cf1b9f9b95647ff85f69ecdd')
+ version('4.1.0', '5a248298b395b329e2371bf25366115c')
+ version('4.0.0', 'd00301c078cba57ef68613be32ceea2f')
+
+ # Add a patch that brings mrnet-5.0.1 up to date with the current development tree
+ # The development tree contains fixes needed for the krell based tools
+ variant('krellpatch', default=False, description="Build MRNet with krell openspeedshop based patch.")
+ patch('krell-5.0.1.patch', when='@5.0.1+krellpatch')
variant('lwthreads', default=False, description="Also build the MRNet LW threadsafe libraries")
parallel = False
diff --git a/var/spack/repos/builtin/packages/msgpack-c/package.py b/var/spack/repos/builtin/packages/msgpack-c/package.py
new file mode 100644
index 0000000000000000000000000000000000000000..a363bc89be4dad8cf9c36871167bfeedf4c02b55
--- /dev/null
+++ b/var/spack/repos/builtin/packages/msgpack-c/package.py
@@ -0,0 +1,14 @@
+from spack import *
+
+class MsgpackC(Package):
+ """A small, fast binary interchange format convertible to/from JSON"""
+ homepage = "http://www.msgpack.org"
+ url = "https://github.com/msgpack/msgpack-c/archive/cpp-1.4.1.tar.gz"
+
+ version('1.4.1', 'e2fd3a7419b9bc49e5017fdbefab87e0')
+
+ def install(self, spec, prefix):
+ cmake('.', *std_cmake_args)
+
+ make()
+ make("install")
diff --git a/var/spack/repos/builtin/packages/mvapich2/package.py b/var/spack/repos/builtin/packages/mvapich2/package.py
index 3e60b517dbecab198ce33912e27c33d0e31eb506..c68a04d251dc691ee4ca6da0670a4e3953c66204 100644
--- a/var/spack/repos/builtin/packages/mvapich2/package.py
+++ b/var/spack/repos/builtin/packages/mvapich2/package.py
@@ -147,6 +147,12 @@ def setup_dependent_environment(self, spack_env, run_env, extension_spec):
spack_env.set('MPICH_F90', spack_fc)
spack_env.set('MPICH_FC', spack_fc)
+ def setup_dependent_package(self, module, dep_spec):
+ self.spec.mpicc = join_path(self.prefix.bin, 'mpicc')
+ self.spec.mpicxx = join_path(self.prefix.bin, 'mpicxx')
+ self.spec.mpifc = join_path(self.prefix.bin, 'mpif90')
+ self.spec.mpif77 = join_path(self.prefix.bin, 'mpif77')
+
def install(self, spec, prefix):
# we'll set different configure flags depending on our environment
configure_args = [
diff --git a/var/spack/repos/builtin/packages/ncview/package.py b/var/spack/repos/builtin/packages/ncview/package.py
new file mode 100644
index 0000000000000000000000000000000000000000..1aa13e3f039b8cbabec43fe3be1d4cad1a6567b8
--- /dev/null
+++ b/var/spack/repos/builtin/packages/ncview/package.py
@@ -0,0 +1,20 @@
+from spack import *
+
+class Ncview(Package):
+ """Simple viewer for NetCDF files."""
+ homepage = "http://meteora.ucsd.edu/~pierce/ncview_home_page.html"
+ url = "ftp://cirrus.ucsd.edu/pub/ncview/ncview-2.1.7.tar.gz"
+
+ version('2.1.7', 'debd6ca61410aac3514e53122ab2ba07')
+
+ depends_on("netcdf")
+ depends_on("udunits2")
+
+ # OS Dependencies
+ # Ubuntu: apt-get install libxaw7-dev
+ # CentOS 7: yum install libXaw-devel
+
+ def install(self, spec, prefix):
+ configure('--prefix=%s' % prefix)
+ make()
+ make("install")
diff --git a/var/spack/repos/builtin/packages/netcdf/package.py b/var/spack/repos/builtin/packages/netcdf/package.py
index b60a2c4e9a37cd6f8182f4a763d669c2eaa14c52..4aad0f6f3c81115dde3d66d7e1d6245561f23c4d 100644
--- a/var/spack/repos/builtin/packages/netcdf/package.py
+++ b/var/spack/repos/builtin/packages/netcdf/package.py
@@ -12,15 +12,19 @@ class Netcdf(Package):
version('4.4.0', 'cffda0cbd97fdb3a06e9274f7aef438e')
version('4.3.3', '5fbd0e108a54bd82cb5702a73f56d2ae')
- variant('mpi', default=True, description='Enables MPI parallelism')
- variant('hdf4', default=False, description="Enable HDF4 support")
+ variant('mpi', default=True, description='Enables MPI parallelism')
+ variant('hdf4', default=False, description='Enable HDF4 support')
- # Dependencies:
- depends_on("curl") # required for DAP support
+ depends_on("m4")
depends_on("hdf", when='+hdf4')
- depends_on("hdf5+mpi~cxx", when='+mpi') # required for NetCDF-4 support
- depends_on("hdf5~mpi", when='~mpi') # required for NetCDF-4 support
- depends_on("zlib") # required for NetCDF-4 support
+
+ # Required for DAP support
+ depends_on("curl")
+
+ # Required for NetCDF-4 support
+ depends_on("zlib")
+ depends_on("hdf5+mpi", when='+mpi')
+ depends_on("hdf5~mpi", when='~mpi')
def install(self, spec, prefix):
# Environment variables
@@ -48,7 +52,7 @@ def install(self, spec, prefix):
# /usr/lib/x86_64-linux-gnu/libcurl.so: undefined reference to `SSL_CTX_use_certificate_chain_file@OPENSSL_1.0.0'
LIBS.append("-lcurl")
CPPFLAGS.append("-I%s" % spec['curl'].prefix.include)
- LDFLAGS.append ("-L%s" % spec['curl'].prefix.lib)
+ LDFLAGS.append( "-L%s" % spec['curl'].prefix.lib)
if '+mpi' in spec:
config_args.append('--enable-parallel4')
diff --git a/var/spack/repos/builtin/packages/openblas/make.patch b/var/spack/repos/builtin/packages/openblas/make.patch
new file mode 100644
index 0000000000000000000000000000000000000000..851214211a624669334495353b2149d8350a847a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/openblas/make.patch
@@ -0,0 +1,35 @@
+diff --git a/Makefile.system b/Makefile.system
+index b89f60e..2dbdad0 100644
+--- a/Makefile.system
++++ b/Makefile.system
+@@ -139,6 +139,10 @@ NO_PARALLEL_MAKE=0
+ endif
+ GETARCH_FLAGS += -DNO_PARALLEL_MAKE=$(NO_PARALLEL_MAKE)
+
++ifdef MAKE_NO_J
++GETARCH_FLAGS += -DMAKE_NO_J=$(MAKE_NO_J)
++endif
++
+ ifdef MAKE_NB_JOBS
+ GETARCH_FLAGS += -DMAKE_NB_JOBS=$(MAKE_NB_JOBS)
+ endif
+diff --git a/getarch.c b/getarch.c
+index f9c49e6..dffad70 100644
+--- a/getarch.c
++++ b/getarch.c
+@@ -1012,6 +1012,7 @@ int main(int argc, char *argv[]){
+ #endif
+ #endif
+
++#ifndef MAKE_NO_J
+ #ifdef MAKE_NB_JOBS
+ printf("MAKE += -j %d\n", MAKE_NB_JOBS);
+ #elif NO_PARALLEL_MAKE==1
+@@ -1021,6 +1022,7 @@ int main(int argc, char *argv[]){
+ printf("MAKE += -j %d\n", get_num_cores());
+ #endif
+ #endif
++#endif
+
+ break;
+
diff --git a/var/spack/repos/builtin/packages/openblas/package.py b/var/spack/repos/builtin/packages/openblas/package.py
index 9f13d0690bee8001158423fdc31bbffb6dab9207..99649da9cadb6e8225d7d38bcd5f6464beff158e 100644
--- a/var/spack/repos/builtin/packages/openblas/package.py
+++ b/var/spack/repos/builtin/packages/openblas/package.py
@@ -1,6 +1,7 @@
from spack import *
import sys
import os
+import shutil
class Openblas(Package):
"""OpenBLAS: An optimized BLAS library"""
@@ -12,18 +13,22 @@ class Openblas(Package):
version('0.2.15', 'b1190f3d3471685f17cfd1ec1d252ac9')
variant('shared', default=True, description="Build shared libraries as well as static libs.")
+ variant('openmp', default=True, description="Enable OpenMP support.")
+ variant('fpic', default=True, description="Build position independent code")
# virtual dependency
provides('blas')
provides('lapack')
+ patch('make.patch')
def install(self, spec, prefix):
# Openblas is picky about compilers. Configure fails with
# FC=/abs/path/to/f77, whereas FC=f77 works fine.
# To circumvent this, provide basename only:
make_defs = ['CC=%s' % os.path.basename(spack_cc),
- 'FC=%s' % os.path.basename(spack_f77)]
+ 'FC=%s' % os.path.basename(spack_f77),
+ 'MAKE_NO_J=1']
make_targets = ['libs', 'netlib']
@@ -31,12 +36,19 @@ def install(self, spec, prefix):
if '+shared' in spec:
make_targets += ['shared']
else:
+ if '+fpic' in spec:
+ make_defs.extend(['CFLAGS=-fPIC', 'FFLAGS=-fPIC'])
make_defs += ['NO_SHARED=1']
# fix missing _dggsvd_ and _sggsvd_
if spec.satisfies('@0.2.16'):
make_defs += ['BUILD_LAPACK_DEPRECATED=1']
+ # Add support for OpenMP
+ # Note: Make sure your compiler supports OpenMP
+ if '+openmp' in spec:
+ make_defs += ['USE_OPENMP=1']
+
make_args = make_defs + make_targets
make(*make_args)
@@ -58,6 +70,10 @@ def install(self, spec, prefix):
if '+shared' in spec:
symlink('libopenblas.%s' % dso_suffix, 'liblapack.%s' % dso_suffix)
+ # Openblas may pass its own test but still fail to compile Lapack
+ # symbols. To make sure we get working Blas and Lapack, do a small test.
+ self.check_install(spec)
+
def setup_dependent_package(self, module, dspec):
# This is WIP for a prototype interface for virtual packages.
@@ -70,3 +86,60 @@ def setup_dependent_package(self, module, dspec):
if '+shared' in self.spec:
self.spec.blas_shared_lib = join_path(libdir, 'libopenblas.%s' % dso_suffix)
self.spec.lapack_shared_lib = self.spec.blas_shared_lib
+
+ def check_install(self, spec):
+ "Build and run a small program to test that we have Lapack symbols"
+ print "Checking Openblas installation..."
+ checkdir = "spack-check"
+ with working_dir(checkdir, create=True):
+ source = r"""
+#include <cblas.h>
+#include <stdio.h>
+int main(void) {
+int i=0;
+double A[6] = {1.0, 2.0, 1.0, -3.0, 4.0, -1.0};
+double B[6] = {1.0, 2.0, 1.0, -3.0, 4.0, -1.0};
+double C[9] = {.5, .5, .5, .5, .5, .5, .5, .5, .5};
+cblas_dgemm(CblasColMajor, CblasNoTrans, CblasTrans,
+ 3, 3, 2, 1, A, 3, B, 3, 2, C, 3);
+for (i = 0; i < 9; i++)
+ printf("%f\n", C[i]);
+return 0;
+}
+"""
+ expected = """\
+11.000000
+-9.000000
+5.000000
+-9.000000
+21.000000
+-1.000000
+5.000000
+-1.000000
+3.000000
+"""
+ with open("check.c", 'w') as f:
+ f.write(source)
+ cc = which('cc')
+ # TODO: Automate these path and library settings
+ cc('-c', "-I%s" % join_path(spec.prefix, "include"), "check.c")
+ cc('-o', "check", "check.o",
+ "-L%s" % join_path(spec.prefix, "lib"), "-llapack", "-lblas", "-lpthread")
+ try:
+ check = Executable('./check')
+ output = check(return_output=True)
+ except:
+ output = ""
+ success = output == expected
+ if not success:
+ print "Produced output does not match expected output."
+ print "Expected output:"
+ print '-'*80
+ print expected
+ print '-'*80
+ print "Produced output:"
+ print '-'*80
+ print output
+ print '-'*80
+ raise RuntimeError("Openblas install check failed")
+ shutil.rmtree(checkdir)
diff --git a/var/spack/repos/builtin/packages/openblas/test_cblas_dgemm.c b/var/spack/repos/builtin/packages/openblas/test_cblas_dgemm.c
new file mode 100644
index 0000000000000000000000000000000000000000..634e99d20b5c7bf8c88ae29df8f18e14220debc1
--- /dev/null
+++ b/var/spack/repos/builtin/packages/openblas/test_cblas_dgemm.c
@@ -0,0 +1,13 @@
+#include <cblas.h>
+#include <stdio.h>
+int main(void) {
+int i=0;
+double A[6] = {1.0, 2.0, 1.0, -3.0, 4.0, -1.0};
+double B[6] = {1.0, 2.0, 1.0, -3.0, 4.0, -1.0};
+double C[9] = {.5, .5, .5, .5, .5, .5, .5, .5, .5};
+cblas_dgemm(CblasColMajor, CblasNoTrans, CblasTrans,
+ 3, 3, 2, 1, A, 3, B, 3, 2, C, 3);
+for (i = 0; i < 9; i++)
+ printf("%f\n", C[i]);
+return 0;
+}
diff --git a/var/spack/repos/builtin/packages/openblas/test_cblas_dgemm.output b/var/spack/repos/builtin/packages/openblas/test_cblas_dgemm.output
new file mode 100644
index 0000000000000000000000000000000000000000..b8316d747710758fd25521afe496cb89b6eaf336
--- /dev/null
+++ b/var/spack/repos/builtin/packages/openblas/test_cblas_dgemm.output
@@ -0,0 +1,9 @@
+11.000000
+-9.000000
+5.000000
+-9.000000
+21.000000
+-1.000000
+5.000000
+-1.000000
+3.000000
diff --git a/var/spack/repos/builtin/packages/openmpi/package.py b/var/spack/repos/builtin/packages/openmpi/package.py
index 1b498eb49c6eede9d2328d1869310fdcf3420093..f609dd7863a60134305edf1b3bebbeb72bb53358 100644
--- a/var/spack/repos/builtin/packages/openmpi/package.py
+++ b/var/spack/repos/builtin/packages/openmpi/package.py
@@ -29,6 +29,7 @@ class Openmpi(Package):
variant('psm', default=False, description='Build support for the PSM library.')
variant('psm2', default=False, description='Build support for the Intel PSM2 library.')
+ variant('pmi', default=True, description='Build support for PMI-based launchers')
variant('verbs', default=False, description='Build support for OpenFabrics verbs.')
variant('mxm', default=False, description='Build Mellanox Messaging support')
@@ -38,7 +39,6 @@ class Openmpi(Package):
variant('tm', default=False, description='Build TM (Torque, PBSPro, and compatible) support')
variant('slurm', default=False, description='Build SLURM scheduler component')
- variant('pmi', default=False, description='Build PMI support, optionally adding DIR to the search path')
variant('sqlite3', default=False, description='Build sqlite3 support')
# TODO : support for CUDA is missing
@@ -67,6 +67,13 @@ def verbs(self):
elif self.spec.satisfies('@1.7:'):
return 'verbs'
+ def setup_dependent_package(self, module, dep_spec):
+ self.spec.mpicc = join_path(self.prefix.bin, 'mpicc')
+ self.spec.mpicxx = join_path(self.prefix.bin, 'mpic++')
+ self.spec.mpifc = join_path(self.prefix.bin, 'mpif90')
+ self.spec.mpif77 = join_path(self.prefix.bin, 'mpif77')
+
+
def install(self, spec, prefix):
config_args = ["--prefix=%s" % prefix,
"--with-hwloc=%s" % spec['hwloc'].prefix,
diff --git a/var/spack/repos/builtin/packages/openssl/package.py b/var/spack/repos/builtin/packages/openssl/package.py
index 70afaf4038a19273219d05d17f349b7100094479..d0c95731a2683e53fc4f782e84a5312c87857027 100644
--- a/var/spack/repos/builtin/packages/openssl/package.py
+++ b/var/spack/repos/builtin/packages/openssl/package.py
@@ -3,6 +3,7 @@
from spack import *
+
class Openssl(Package):
"""The OpenSSL Project is a collaborative effort to develop a
robust, commercial-grade, full-featured, and Open Source
@@ -14,10 +15,12 @@ class Openssl(Package):
version('1.0.1h', '8d6d684a9430d5cc98a62a5d8fbda8cf')
version('1.0.1r', '1abd905e079542ccae948af37e393d28')
+ version('1.0.1t', '9837746fcf8a6727d46d22ca35953da1')
version('1.0.2d', '38dd619b2e77cbac69b99f52a053d25a')
version('1.0.2e', '5262bfa25b60ed9de9f28d5d52d77fc5')
version('1.0.2f', 'b3bf73f507172be9292ea2a8c28b659d')
version('1.0.2g', 'f3c710c045cdee5fd114feb69feba7aa')
+ version('1.0.2h', '9392e65072ce4b614c1392eefc1f23d0')
depends_on("zlib")
parallel = False
@@ -30,26 +33,14 @@ def url_for_version(self, version):
# Same idea, but just to avoid issuing the same message multiple times
warnings_given_to_user = getattr(Openssl, '_warnings_given', {})
if openssl_url is None:
- latest = 'http://www.openssl.org/source/openssl-{version}.tar.gz'
- older = 'http://www.openssl.org/source/old/{version_number}/openssl-{version_full}.tar.gz'
- # Try to use the url where the latest tarballs are stored. If the url does not exist (404), then
- # return the url for older format
- version_number = '.'.join([str(x) for x in version[:-1]])
- older_url = older.format(version_number=version_number, version_full=version)
- latest_url = latest.format(version=version)
- response = urllib.urlopen(latest.format(version=version))
- if response.getcode() == 404:
- openssl_url = older_url
- # Checks if we already warned the user for this particular version of OpenSSL.
- # If not we display a warning message and mark this version
+ if self.spec.satisfies('@external'):
+ # The version @external is reserved to system openssl. In that case return a fake url and exit
+ openssl_url = '@external (reserved version for system openssl)'
if not warnings_given_to_user.get(version, False):
- tty.warn('This installation depends on an old version of OpenSSL, which may have known security issues. ')
- tty.warn('Consider updating to the latest version of this package.')
- tty.warn('More details at {homepage}'.format(homepage=Openssl.homepage))
+ tty.msg('Using openssl@external : the version @external is reserved for system openssl')
warnings_given_to_user[version] = True
else:
- openssl_url = latest_url
- # Store the computed URL
+ openssl_url = self.check_for_outdated_release(version, warnings_given_to_user) # Store the computed URL
openssl_urls[version] = openssl_url
# Store the updated dictionary of URLS
Openssl._openssl_url = openssl_urls
@@ -58,6 +49,28 @@ def url_for_version(self, version):
return openssl_url
+ def check_for_outdated_release(self, version, warnings_given_to_user):
+ latest = 'ftp://ftp.openssl.org/source/openssl-{version}.tar.gz'
+ older = 'http://www.openssl.org/source/old/{version_number}/openssl-{version_full}.tar.gz'
+ # Try to use the url where the latest tarballs are stored. If the url does not exist (404), then
+ # return the url for older format
+ version_number = '.'.join([str(x) for x in version[:-1]])
+ try:
+ openssl_url = latest.format(version=version)
+ urllib.urlopen(openssl_url)
+ except IOError:
+ openssl_url = older.format(version_number=version_number, version_full=version)
+ # Checks if we already warned the user for this particular version of OpenSSL.
+ # If not we display a warning message and mark this version
+ if not warnings_given_to_user.get(version, False):
+ tty.warn(
+ 'This installation depends on an old version of OpenSSL, which may have known security issues. ')
+ tty.warn('Consider updating to the latest version of this package.')
+ tty.warn('More details at {homepage}'.format(homepage=Openssl.homepage))
+ warnings_given_to_user[version] = True
+
+ return openssl_url
+
def install(self, spec, prefix):
# OpenSSL uses a variable APPS in its Makefile. If it happens to be set
# in the environment, then this will override what is set in the
diff --git a/var/spack/repos/builtin/packages/osu-micro-benchmarks/package.py b/var/spack/repos/builtin/packages/osu-micro-benchmarks/package.py
new file mode 100644
index 0000000000000000000000000000000000000000..01054471a32d02682a4d85c0aa3ca32da047aa01
--- /dev/null
+++ b/var/spack/repos/builtin/packages/osu-micro-benchmarks/package.py
@@ -0,0 +1,38 @@
+from spack import *
+
+class OsuMicroBenchmarks(Package):
+ """The Ohio MicroBenchmark suite is a collection of independent MPI
+ message passing performance microbenchmarks developed and written at
+ The Ohio State University. It includes traditional benchmarks and
+ performance measures such as latency, bandwidth and host overhead
+ and can be used for both traditional and GPU-enhanced nodes."""
+
+ homepage = "http://mvapich.cse.ohio-state.edu/benchmarks/"
+ url = "http://mvapich.cse.ohio-state.edu/download/mvapich/osu-micro-benchmarks-5.3.tar.gz"
+
+ version('5.3', '42e22b931d451e8bec31a7424e4adfc2')
+
+ variant('cuda', default=False, description="Enable CUDA support")
+
+ depends_on('mpi')
+ depends_on('cuda', when='+cuda')
+
+
+ def install(self, spec, prefix):
+ config_args = [
+ 'CC=%s' % spec['mpi'].prefix.bin + '/mpicc',
+ 'CXX=%s' % spec['mpi'].prefix.bin + '/mpicxx',
+ 'LDFLAGS=-lrt',
+ '--prefix=%s' % prefix
+ ]
+
+ if '+cuda' in spec:
+ config_args.extend([
+ '--enable-cuda',
+ '--with-cuda=%s' % spec['cuda'].prefix,
+ ])
+
+ configure(*config_args)
+
+ make()
+ make('install')
diff --git a/var/spack/repos/builtin/packages/p4est/package.py b/var/spack/repos/builtin/packages/p4est/package.py
index 1e2969fe642c285c3280e90a3e8d54df82a83e79..adf75babb9800b85bc9ea3f6fcbea1a3c3333c9a 100644
--- a/var/spack/repos/builtin/packages/p4est/package.py
+++ b/var/spack/repos/builtin/packages/p4est/package.py
@@ -7,10 +7,17 @@ class P4est(Package):
version('1.1', '37ba7f4410958cfb38a2140339dbf64f')
- # disable by default to make it work on frontend of clusters
- variant('tests', default=False, description='Run small tests')
+ variant('tests', default=True, description='Run small tests')
+ # build dependencies
+ depends_on('automake')
+ depends_on('autoconf')
+ depends_on('libtool@2.4.2:')
+
+ # other dependencies
+ depends_on('lua') # Needed for the submodule sc
depends_on('mpi')
+ depends_on('zlib')
def install(self, spec, prefix):
options = ['--enable-mpi',
@@ -19,16 +26,20 @@ def install(self, spec, prefix):
'--without-blas',
'CPPFLAGS=-DSC_LOG_PRIORITY=SC_LP_ESSENTIAL',
'CFLAGS=-O2',
- 'CC=%s' % join_path(self.spec['mpi'].prefix.bin, 'mpicc'), # TODO: use ENV variables or MPI class wrappers
- 'CXX=%s' % join_path(self.spec['mpi'].prefix.bin, 'mpic++'),
- 'FC=%s' % join_path(self.spec['mpi'].prefix.bin, 'mpif90'),
- 'F77=%s' % join_path(self.spec['mpi'].prefix.bin, 'mpif77'),
+ 'CC=%s' % self.spec['mpi'].mpicc,
+ 'CXX=%s' % self.spec['mpi'].mpicxx,
+ 'FC=%s' % self.spec['mpi'].mpifc,
+ 'F77=%s' % self.spec['mpi'].mpif77
]
configure('--prefix=%s' % prefix, *options)
make()
+ # Make tests optional as sometimes mpiexec can't be run with an error:
+ # mpiexec has detected an attempt to run as root.
+ # Running at root is *strongly* discouraged as any mistake (e.g., in
+ # defining TMPDIR) or bug can result in catastrophic damage to the OS
+ # file system, leaving your system in an unusable state.
if '+tests' in self.spec:
- make("check")
-
+ make("check")
make("install")
diff --git a/var/spack/repos/builtin/packages/papi/package.py b/var/spack/repos/builtin/packages/papi/package.py
index 53d69e28d90897d53f06cb7486391765bb312782..74b3ea9ef9e8f7d355ed236dac2cc34818b956f1 100644
--- a/var/spack/repos/builtin/packages/papi/package.py
+++ b/var/spack/repos/builtin/packages/papi/package.py
@@ -1,5 +1,8 @@
from spack import *
+import glob
import os
+import sys
+from llnl.util.filesystem import fix_darwin_install_name
class Papi(Package):
"""PAPI provides the tool designer and application engineer with a
@@ -18,17 +21,27 @@ class Papi(Package):
version('5.3.0', '367961dd0ab426e5ae367c2713924ffb')
def install(self, spec, prefix):
- os.chdir("src/")
+ with working_dir("src"):
- configure_args=["--prefix=%s" % prefix]
+ configure_args=["--prefix=%s" % prefix]
- # PAPI uses MPI if MPI is present; since we don't require an
- # MPI package, we ensure that all attempts to use MPI fail, so
- # that PAPI does not get confused
- configure_args.append('MPICC=:')
+ # PAPI uses MPI if MPI is present; since we don't require
+ # an MPI package, we ensure that all attempts to use MPI
+ # fail, so that PAPI does not get confused
+ configure_args.append('MPICC=:')
- configure(*configure_args)
+ configure(*configure_args)
- make()
- make("install")
+ # Don't use <malloc.h>
+ for level in [".", "*", "*/*"]:
+ files = glob.iglob(join_path(level, "*.[ch]"))
+ filter_file(r"\<malloc\.h\>", "<stdlib.h>", *files)
+ make()
+ make("install")
+
+ # The shared library is not installed correctly on Darwin
+ if sys.platform == 'darwin':
+ os.rename(join_path(prefix.lib, 'libpapi.so'),
+ join_path(prefix.lib, 'libpapi.dylib'))
+ fix_darwin_install_name(prefix.lib)
diff --git a/var/spack/repos/builtin/packages/paradiseo/enable_eoserial.patch b/var/spack/repos/builtin/packages/paradiseo/enable_eoserial.patch
new file mode 100644
index 0000000000000000000000000000000000000000..8b3ccfeb84d87641a1170fd402931f783c0b0e46
--- /dev/null
+++ b/var/spack/repos/builtin/packages/paradiseo/enable_eoserial.patch
@@ -0,0 +1,14 @@
+diff --git a/eo/src/CMakeLists.txt b/eo/src/CMakeLists.txt
+index b2b445a..d45ddc7 100644
+--- a/eo/src/CMakeLists.txt
++++ b/eo/src/CMakeLists.txt
+@@ -47,7 +47,7 @@ install(DIRECTORY do es ga gp other utils
+ add_subdirectory(es)
+ add_subdirectory(ga)
+ add_subdirectory(utils)
+-#add_subdirectory(serial)
++add_subdirectory(serial) # Required when including <paradiseo/eo/utils/eoTimer.h> , which is need by <paradiseo/eo/mpi/eoMpi.h>
+
+ if(ENABLE_PYEO)
+ add_subdirectory(pyeo)
+
\ No newline at end of file
diff --git a/var/spack/repos/builtin/packages/paradiseo/fix_osx_detection.patch b/var/spack/repos/builtin/packages/paradiseo/fix_osx_detection.patch
new file mode 100644
index 0000000000000000000000000000000000000000..27b240f6736671df83655c2d57e8e733ea76f9bb
--- /dev/null
+++ b/var/spack/repos/builtin/packages/paradiseo/fix_osx_detection.patch
@@ -0,0 +1,13 @@
+diff --git a/cmake/Config.cmake b/cmake/Config.cmake
+index 02593ba..d198ca9 100644
+--- a/cmake/Config.cmake
++++ b/cmake/Config.cmake
+@@ -6,7 +6,7 @@ if(${CMAKE_SYSTEM_NAME} MATCHES "Darwin")
+
+ # detect OS X version. (use '/usr/bin/sw_vers -productVersion' to extract V from '10.V.x'.)
+ execute_process (COMMAND /usr/bin/sw_vers -productVersion OUTPUT_VARIABLE MACOSX_VERSION_RAW)
+- string(REGEX REPLACE "10\\.([0-9]).*" "\\1" MACOSX_VERSION "${MACOSX_VERSION_RAW}")
++ string(REGEX REPLACE "10\\.([0-9]+).*" "\\1" MACOSX_VERSION "${MACOSX_VERSION_RAW}")
+ if(${MACOSX_VERSION} LESS 5)
+ message(FATAL_ERROR "Unsupported version of OS X : ${MACOSX_VERSION_RAW}")
+ return()
diff --git a/var/spack/repos/builtin/packages/paradiseo/fix_tests.patch b/var/spack/repos/builtin/packages/paradiseo/fix_tests.patch
new file mode 100644
index 0000000000000000000000000000000000000000..607c5d52629db0e9dbccfe47efd2c38e99cbd938
--- /dev/null
+++ b/var/spack/repos/builtin/packages/paradiseo/fix_tests.patch
@@ -0,0 +1,13 @@
+diff --git a/moeo/test/t-moeo2DMinHypervolumeArchive.cpp b/moeo/test/t-moeo2DMinHypervolumeArchive.cpp
+index 994a9a4..c4ba77b 100644
+--- a/moeo/test/t-moeo2DMinHypervolumeArchive.cpp
++++ b/moeo/test/t-moeo2DMinHypervolumeArchive.cpp
+@@ -41,7 +41,7 @@
+ #include <moeo>
+ #include <cassert>
+
+-#include<archive/moeo2DMinHyperVolumeArchive.h>
++#include<archive/moeo2DMinHypervolumeArchive.h>
+
+ //-----------------------------------------------------------------------------
+
diff --git a/var/spack/repos/builtin/packages/paradiseo/fix_tutorials.patch b/var/spack/repos/builtin/packages/paradiseo/fix_tutorials.patch
new file mode 100644
index 0000000000000000000000000000000000000000..14cb5fed741fa8c9d6a34e2cd202cce512f2de01
--- /dev/null
+++ b/var/spack/repos/builtin/packages/paradiseo/fix_tutorials.patch
@@ -0,0 +1,13 @@
+diff --git a/eo/tutorial/Lesson3/exercise3.1.cpp b/eo/tutorial/Lesson3/exercise3.1.cpp
+index dc37479..d178941 100644
+--- a/eo/tutorial/Lesson3/exercise3.1.cpp
++++ b/eo/tutorial/Lesson3/exercise3.1.cpp
+@@ -289,7 +289,7 @@ void main_function(int argc, char **argv)
+ checkpoint.add(fdcStat);
+
+ // The Stdout monitor will print parameters to the screen ...
+- eoStdoutMonitor monitor(false);
++ eoStdoutMonitor monitor;
+
+ // when called by the checkpoint (i.e. at every generation)
+ checkpoint.add(monitor);
diff --git a/var/spack/repos/builtin/packages/paradiseo/package.py b/var/spack/repos/builtin/packages/paradiseo/package.py
new file mode 100644
index 0000000000000000000000000000000000000000..34766099da27f46b4f43cd246056eec493d58b11
--- /dev/null
+++ b/var/spack/repos/builtin/packages/paradiseo/package.py
@@ -0,0 +1,66 @@
+from spack import *
+import sys
+
+class Paradiseo(Package):
+ """A C++ white-box object-oriented framework dedicated to the reusable design of metaheuristics."""
+ homepage = "http://paradiseo.gforge.inria.fr/"
+
+ # Installing from the development version is a better option at this
+ # point than using the very old supplied packages
+ version('head', git='https://gforge.inria.fr/git/paradiseo/paradiseo.git')
+ # This is a version that the package formula author has tested successfully.
+ # However, the clone is very large (~1Gb git history). The history in the
+ # head version has been trimmed significantly.
+ version('dev-safe', git='https://gforge.inria.fr/git/paradiseo/paradiseo.git',
+ commit='dbb8fbe9a786efd4d1c26408ac1883442e7643a6')
+
+ variant('mpi', default=True, description='Compile with parallel and distributed metaheuristics module')
+ variant('smp', default=True, description='Compile with symmetric multi-processing module ')
+ variant('edo', default=True, description='Compile with (Experimental) EDO module')
+ #variant('tests', default=False, description='Compile with build tests')
+ #variant('doc', default=False, description='Compile with documentation')
+ variant('debug', default=False, description='Builds a debug version of the libraries')
+ variant('openmp', default=False, description='Enable OpenMP support')
+ variant('gnuplot', default=False, description='Enable GnuPlot support')
+
+ # Required dependencies
+ depends_on ("cmake")
+
+ # Optional dependencies
+ depends_on ("mpi", when="+mpi")
+ depends_on ("doxygen", when='+doc')
+ depends_on ("gnuplot", when='+gnuplot')
+ depends_on ("eigen", when='+edo')
+ depends_on ("boost~mpi", when='+edo~mpi')
+ depends_on ("boost+mpi", when='+edo+mpi')
+
+ # Patches
+ patch('enable_eoserial.patch')
+ patch('fix_osx_detection.patch')
+ patch('fix_tests.patch')
+ patch('fix_tutorials.patch')
+
+ def install(self, spec, prefix):
+ options = []
+ options.extend(std_cmake_args)
+
+ options.extend([
+ '-DCMAKE_BUILD_TYPE:STRING=%s' % ('Debug' if '+debug' in spec else 'Release'),
+ '-DINSTALL_TYPE:STRING=MIN',
+ '-DMPI:BOOL=%s' % ('TRUE' if '+mpi' in spec else 'FALSE'),
+ '-DSMP:BOOL=%s' % ('TRUE' if '+smp' in spec else 'FALSE'), # Note: This requires a C++11 compatible compiler
+ '-DEDO:BOOL=%s' % ('TRUE' if '+edo' in spec else 'FALSE'),
+ '-DENABLE_CMAKE_TESTING:BOOL=%s' % ('TRUE' if '+tests' in spec else 'FALSE'),
+ '-DENABLE_OPENMP:BOOL=%s' % ('TRUE' if '+openmp' in spec else 'FALSE'),
+ '-DENABLE_GNUPLOT:BOOL=%s' % ('TRUE' if '+gnuplot' in spec else 'FALSE')
+ ])
+
+ with working_dir('spack-build', create=True):
+ # Configure
+ cmake('..', *options)
+
+ # Build, test and install
+ make("VERBOSE=1")
+ if '+tests' in spec:
+ make("test")
+ make("install")
diff --git a/var/spack/repos/builtin/packages/parallel-netcdf/package.py b/var/spack/repos/builtin/packages/parallel-netcdf/package.py
index 62a8f7ca0ba9ecf03b5ae7a0da652b22718739ad..e6f8cf026bf2cc41f031dcd6dc0451fa217b7f22 100644
--- a/var/spack/repos/builtin/packages/parallel-netcdf/package.py
+++ b/var/spack/repos/builtin/packages/parallel-netcdf/package.py
@@ -8,6 +8,7 @@ class ParallelNetcdf(Package):
homepage = "https://trac.mcs.anl.gov/projects/parallel-netcdf"
url = "http://cucis.ece.northwestern.edu/projects/PnetCDF/Release/parallel-netcdf-1.6.1.tar.gz"
+ version('1.7.0', '267eab7b6f9dc78c4d0e6def2def3aea4bc7c9f0')
version('1.6.1', '62a094eb952f9d1e15f07d56e535052604f1ac34')
depends_on("m4")
diff --git a/var/spack/repos/builtin/packages/paraview/package.py b/var/spack/repos/builtin/packages/paraview/package.py
index c16054816c18e463ad999047ab205ffad8cb92b1..60f8d3c243da4735c6d85070f2f2dbf9f44344bc 100644
--- a/var/spack/repos/builtin/packages/paraview/package.py
+++ b/var/spack/repos/builtin/packages/paraview/package.py
@@ -27,13 +27,14 @@ class Paraview(Package):
depends_on('bzip2')
depends_on('freetype')
- depends_on('hdf5+mpi', when='+mpi')
- depends_on('hdf5~mpi', when='~mpi')
+ #depends_on('hdf5+mpi', when='+mpi')
+ #depends_on('hdf5~mpi', when='~mpi')
depends_on('jpeg')
depends_on('libpng')
depends_on('libtiff')
depends_on('libxml2')
- depends_on('netcdf')
+ #depends_on('netcdf')
+ #depends_on('netcdf-cxx')
#depends_on('protobuf') # version mismatches?
#depends_on('sqlite') # external version not supported
depends_on('zlib')
@@ -75,13 +76,13 @@ def nfeature_to_bool(feature):
cmake('..',
'-DCMAKE_INSTALL_PREFIX:PATH=%s' % prefix,
'-DBUILD_TESTING:BOOL=OFF',
- '-DVTK_USER_SYSTEM_FREETYPE:BOOL=ON',
- '-DVTK_USER_SYSTEM_HDF5:BOOL=ON',
- '-DVTK_USER_SYSTEM_JPEG:BOOL=ON',
- '-DVTK_USER_SYSTEM_LIBXML2:BOOL=ON',
- '-DVTK_USER_SYSTEM_NETCDF:BOOL=ON',
- '-DVTK_USER_SYSTEM_TIFF:BOOL=ON',
- '-DVTK_USER_SYSTEM_ZLIB:BOOL=ON',
+ '-DVTK_USE_SYSTEM_FREETYPE:BOOL=ON',
+ '-DVTK_USE_SYSTEM_HDF5:BOOL=OFF',
+ '-DVTK_USE_SYSTEM_JPEG:BOOL=ON',
+ '-DVTK_USE_SYSTEM_LIBXML2:BOOL=ON',
+ '-DVTK_USE_SYSTEM_NETCDF:BOOL=OFF',
+ '-DVTK_USE_SYSTEM_TIFF:BOOL=ON',
+ '-DVTK_USE_SYSTEM_ZLIB:BOOL=ON',
*feature_args)
make()
make('install')
diff --git a/var/spack/repos/builtin/packages/pkg-config/package.py b/var/spack/repos/builtin/packages/pkg-config/package.py
index 9964c6ce3463cf48d095abbe4c66f9e037c25421..a803bc3f9b8189210eca1c54b6b4acfb69b186a9 100644
--- a/var/spack/repos/builtin/packages/pkg-config/package.py
+++ b/var/spack/repos/builtin/packages/pkg-config/package.py
@@ -10,7 +10,12 @@ class PkgConfig(Package):
parallel = False
def install(self, spec, prefix):
- configure("--prefix=%s" %prefix, "--enable-shared")
+ configure("--prefix=%s" %prefix,
+ "--enable-shared",
+ "--with-internal-glib") # There's a bootstrapping problem here;
+ # glib uses pkg-config as well, so
+ # break the cycle by using the internal
+ # glib.
make()
make("install")
diff --git a/var/spack/repos/builtin/packages/py-SQLAlchemy/package.py b/var/spack/repos/builtin/packages/py-SQLAlchemy/package.py
new file mode 100644
index 0000000000000000000000000000000000000000..9aecc95c63a85c27bcb1b5c9fb03155e9811573d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-SQLAlchemy/package.py
@@ -0,0 +1,14 @@
+from spack import *
+
+class PySqlalchemy(Package):
+ """The Python SQL Toolkit and Object Relational Mapper"""
+
+ homepage = 'http://www.sqlalchemy.org/'
+ url = "https://pypi.python.org/packages/source/S/SQLAlchemy/SQLAlchemy-1.0.12.tar.gz"
+
+ version('1.0.12', '6d19ef29883bbebdcac6613cf391cac4')
+
+ extends('python')
+
+ def install(self, spec, prefix):
+ python('setup.py', 'install', '--prefix=%s' % prefix)
diff --git a/var/spack/repos/builtin/packages/py-bottleneck/package.py b/var/spack/repos/builtin/packages/py-bottleneck/package.py
index 0aa4208b4de378a6fa4ffaa1a2409bece47ca20a..d43308543bc7fda6b20b96c2474c3ff25e6ac4a5 100644
--- a/var/spack/repos/builtin/packages/py-bottleneck/package.py
+++ b/var/spack/repos/builtin/packages/py-bottleneck/package.py
@@ -7,7 +7,7 @@ class PyBottleneck(Package):
version('1.0.0', '380fa6f275bd24f27e7cf0e0d752f5d2')
- extends('python', ignore=r'bin/f2py$')
+ extends('python')
depends_on('py-numpy')
def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/py-csvkit/package.py b/var/spack/repos/builtin/packages/py-csvkit/package.py
new file mode 100644
index 0000000000000000000000000000000000000000..def30457be4ed5cc0018fe081dd2cc76f9b5a42a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-csvkit/package.py
@@ -0,0 +1,22 @@
+from spack import *
+
+class PyCsvkit(Package):
+ """A library of utilities for working with CSV, the king of tabular file
+ formats"""
+
+ homepage = 'http://csvkit.rtfd.org/'
+ url = "https://pypi.python.org/packages/source/c/csvkit/csvkit-0.9.1.tar.gz"
+
+ version('0.9.1', '48d78920019d18846933ee969502fff6')
+
+ extends('python')
+
+ depends_on('py-dateutil')
+ depends_on('py-dbf')
+ depends_on('py-xlrd')
+ depends_on('py-SQLAlchemy')
+ depends_on('py-six')
+ depends_on('py-openpyxl')
+
+ def install(self, spec, prefix):
+ python('setup.py', 'install', '--prefix=%s' % prefix)
diff --git a/var/spack/repos/builtin/packages/py-dbf/package.py b/var/spack/repos/builtin/packages/py-dbf/package.py
new file mode 100644
index 0000000000000000000000000000000000000000..698b22190301518a17a191b1994574a638515493
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-dbf/package.py
@@ -0,0 +1,15 @@
+from spack import *
+
+class PyDbf(Package):
+ """Pure python package for reading/writing dBase, FoxPro, and Visual FoxPro
+ .dbf files (including memos)"""
+
+ homepage = 'https://pypi.python.org/pypi/dbf'
+ url = "https://pypi.python.org/packages/source/d/dbf/dbf-0.96.005.tar.gz"
+
+ version('0.96.005', 'bce1a1ed8b454a30606e7e18dd2f8277')
+
+ extends('python')
+
+ def install(self, spec, prefix):
+ python('setup.py', 'install', '--prefix=%s' % prefix)
diff --git a/var/spack/repos/builtin/packages/py-jdcal/package.py b/var/spack/repos/builtin/packages/py-jdcal/package.py
new file mode 100644
index 0000000000000000000000000000000000000000..54169b2c217b6f8dbbf587da2db09c57c3d17a98
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-jdcal/package.py
@@ -0,0 +1,14 @@
+from spack import *
+
+class PyJdcal(Package):
+ """Julian dates from proleptic Gregorian and Julian calendars"""
+
+ homepage = 'http://github.com/phn/jdcal'
+ url = "https://pypi.python.org/packages/source/j/jdcal/jdcal-1.2.tar.gz"
+
+ version('1.2', 'ab8d5ba300fd1eb01514f363d19b1eb9')
+
+ extends('python')
+
+ def install(self, spec, prefix):
+ python('setup.py', 'install', '--prefix=%s' % prefix)
diff --git a/var/spack/repos/builtin/packages/py-matplotlib/package.py b/var/spack/repos/builtin/packages/py-matplotlib/package.py
index 45e77dd6313d0fbbc24758c79d17be256a10b8f5..1a190cc5f3103116289d7810ac15462e2b02d7c4 100644
--- a/var/spack/repos/builtin/packages/py-matplotlib/package.py
+++ b/var/spack/repos/builtin/packages/py-matplotlib/package.py
@@ -12,7 +12,7 @@ class PyMatplotlib(Package):
variant('gui', default=False, description='Enable GUI')
variant('ipython', default=False, description='Enable ipython support')
- extends('python', ignore=r'bin/nosetests.*$|bin/pbr$|bin/f2py$')
+ extends('python', ignore=r'bin/nosetests.*$|bin/pbr$')
depends_on('py-pyside', when='+gui')
depends_on('py-ipython', when='+ipython')
@@ -26,6 +26,7 @@ class PyMatplotlib(Package):
depends_on('py-pbr')
depends_on('py-funcsigs')
+ depends_on('pkg-config')
depends_on('freetype')
depends_on('qt', when='+gui')
depends_on('bzip2')
diff --git a/var/spack/repos/builtin/packages/py-numexpr/package.py b/var/spack/repos/builtin/packages/py-numexpr/package.py
index 081a79dec685a115ff2d419eb9c34145bc3d791f..0076aa456b8dff5ad8fb673b5285cfe64aa3141a 100644
--- a/var/spack/repos/builtin/packages/py-numexpr/package.py
+++ b/var/spack/repos/builtin/packages/py-numexpr/package.py
@@ -9,7 +9,7 @@ class PyNumexpr(Package):
version('2.4.6', '17ac6fafc9ea1ce3eb970b9abccb4fbd')
version('2.5', '84f66cced45ba3e30dcf77a937763aaa')
- extends('python', ignore=r'bin/f2py$')
+ extends('python')
depends_on('py-numpy')
def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/py-openpyxl/package.py b/var/spack/repos/builtin/packages/py-openpyxl/package.py
new file mode 100644
index 0000000000000000000000000000000000000000..87ff9f35217f3348fef4d1b717470812122b0cd5
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-openpyxl/package.py
@@ -0,0 +1,17 @@
+from spack import *
+
+class PyOpenpyxl(Package):
+ """A Python library to read/write Excel 2007 xlsx/xlsm files"""
+
+ homepage = 'http://openpyxl.readthedocs.org/'
+ url = "https://pypi.python.org/packages/source/o/openpyxl/openpyxl-2.4.0-a1.tar.gz"
+
+ version('2.4.0-a1', 'e5ca6d23ceccb15115d45cdf26e736fc')
+
+ extends('python')
+
+ depends_on('py-jdcal')
+ depends_on('py-setuptools')
+
+ def install(self, spec, prefix):
+ python('setup.py', 'install', '--prefix=%s' % prefix)
diff --git a/var/spack/repos/builtin/packages/py-pandas/package.py b/var/spack/repos/builtin/packages/py-pandas/package.py
index 2320b1f92f386383f42e965e0469c23d8f27fbd8..59d515eb5e09d4ef94b42ff52daf81525ef3a9fd 100644
--- a/var/spack/repos/builtin/packages/py-pandas/package.py
+++ b/var/spack/repos/builtin/packages/py-pandas/package.py
@@ -10,7 +10,7 @@ class PyPandas(Package):
version('0.16.1', 'fac4f25748f9610a3e00e765474bdea8')
version('0.18.0', 'f143762cd7a59815e348adf4308d2cf6')
- extends('python', ignore=r'bin/f2py$')
+ extends('python')
depends_on('py-dateutil')
depends_on('py-numpy')
depends_on('py-setuptools')
diff --git a/var/spack/repos/builtin/packages/py-scikit-image/package.py b/var/spack/repos/builtin/packages/py-scikit-image/package.py
index 22ce1f837407b52bdad258af0b9ee61991251ca3..d13339060edaa909697de3de8f65ddcb3d3db2b9 100644
--- a/var/spack/repos/builtin/packages/py-scikit-image/package.py
+++ b/var/spack/repos/builtin/packages/py-scikit-image/package.py
@@ -7,7 +7,7 @@ class PyScikitImage(Package):
version('0.12.3', '04ea833383e0b6ad5f65da21292c25e1')
- extends('python', ignore=r'bin/.*\.py$|bin/f2py$')
+ extends('python', ignore=r'bin/.*\.py$')
depends_on('py-dask')
depends_on('py-pillow')
diff --git a/var/spack/repos/builtin/packages/py-setuptools/package.py b/var/spack/repos/builtin/packages/py-setuptools/package.py
index c6d9be1add79dbc9f099a702400320178529e031..1368711978d7b0d61d95044f2fa79bcfda69d9fe 100644
--- a/var/spack/repos/builtin/packages/py-setuptools/package.py
+++ b/var/spack/repos/builtin/packages/py-setuptools/package.py
@@ -5,11 +5,13 @@ class PySetuptools(Package):
homepage = "https://pypi.python.org/pypi/setuptools"
url = "https://pypi.python.org/packages/source/s/setuptools/setuptools-11.3.tar.gz"
- version('11.3.1', '01f69212e019a2420c1693fb43593930')
- version('16.0', '0ace0b96233516fc5f7c857d086aa3ad')
- version('18.1', 'f72e87f34fbf07f299f6cb46256a0b06')
- version('19.2', '78353b1f80375ca5e088f4b4627ffe03')
+ version('20.7.0', '5d12b39bf3e75e80fdce54e44b255615')
+ version('20.6.7', '45d6110f3ec14924e44c33411db64fe6')
version('20.5', 'fadc1e1123ddbe31006e5e43e927362b')
+ version('19.2', '78353b1f80375ca5e088f4b4627ffe03')
+ version('18.1', 'f72e87f34fbf07f299f6cb46256a0b06')
+ version('16.0', '0ace0b96233516fc5f7c857d086aa3ad')
+ version('11.3.1', '01f69212e019a2420c1693fb43593930')
extends('python')
diff --git a/var/spack/repos/builtin/packages/py-xlrd/package.py b/var/spack/repos/builtin/packages/py-xlrd/package.py
new file mode 100644
index 0000000000000000000000000000000000000000..8f25c06aad2602ebc0feccfb9d30a0a44ad65b55
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-xlrd/package.py
@@ -0,0 +1,15 @@
+from spack import *
+
+class PyXlrd(Package):
+ """Library for developers to extract data from Microsoft Excel (tm)
+ spreadsheet files"""
+
+ homepage = 'http://www.python-excel.org/'
+ url = "https://pypi.python.org/packages/source/x/xlrd/xlrd-0.9.4.tar.gz"
+
+ version('0.9.4', '911839f534d29fe04525ef8cd88fe865')
+
+ extends('python')
+
+ def install(self, spec, prefix):
+ python('setup.py', 'install', '--prefix=%s' % prefix)
diff --git a/var/spack/repos/builtin/packages/python/package.py b/var/spack/repos/builtin/packages/python/package.py
index f5237c3b578b9c8900d45d8515428a1e5fe5b344..f7e1d945675d5620aa291aea50bb152a994fe7ec 100644
--- a/var/spack/repos/builtin/packages/python/package.py
+++ b/var/spack/repos/builtin/packages/python/package.py
@@ -151,6 +151,8 @@ def python_ignore(self, ext_pkg, args):
patterns.append(r'setuptools\.pth')
patterns.append(r'bin/easy_install[^/]*$')
patterns.append(r'setuptools.*egg$')
+ if ext_pkg.name != 'py-numpy':
+ patterns.append(r'bin/f2py$')
return match_predicate(ignore_arg, patterns)
diff --git a/var/spack/repos/builtin/packages/qt/package.py b/var/spack/repos/builtin/packages/qt/package.py
index 8cb88e6c854892aa0fda016fac2ec4db7300f8d5..1e1d6302f3709e9c6d17f8f1835e25538d2289f4 100644
--- a/var/spack/repos/builtin/packages/qt/package.py
+++ b/var/spack/repos/builtin/packages/qt/package.py
@@ -29,7 +29,8 @@ class Qt(Package):
depends_on("zlib")
depends_on("dbus", when='@4:')
depends_on("libtiff")
- depends_on("libpng")
+ depends_on("libpng@1.2.56", when='@3')
+ depends_on("libpng", when='@4:')
depends_on("libmng")
depends_on("jpeg")
@@ -100,7 +101,7 @@ def patch(self):
@property
def common_config_args(self):
- return [
+ config_args = [
'-prefix', self.prefix,
'-v',
'-opensource',
@@ -114,19 +115,29 @@ def common_config_args(self):
'-no-openvg',
'-no-pch',
# NIS is deprecated in more recent glibc
- '-no-nis']
+ '-no-nis'
+ ]
+
+ if '+gtk' in self.spec:
+ config_args.append('-gtkstyle')
+ else:
+ config_args.append('-no-gtkstyle')
+
+ return config_args
+
# Don't disable all the database drivers, but should
# really get them into spack at some point.
@when('@3')
def configure(self):
+ # An user report that this was necessary to link Qt3 on ubuntu
+ os.environ['LD_LIBRARY_PATH'] = os.getcwd()+'/lib'
configure('-prefix', self.prefix,
'-v',
'-thread',
'-shared',
'-release',
- '-fast'
- )
+ '-fast')
@when('@4')
def configure(self):
diff --git a/var/spack/repos/builtin/packages/qthreads/ldflags.patch b/var/spack/repos/builtin/packages/qthreads/ldflags.patch
new file mode 100644
index 0000000000000000000000000000000000000000..0c15eab3867cb5db64d12f4b3ebab8bf5e3636f0
--- /dev/null
+++ b/var/spack/repos/builtin/packages/qthreads/ldflags.patch
@@ -0,0 +1,11 @@
+--- a/configure
++++ b/configure
+@@ -40456,7 +40456,7 @@
+ hwloc_saved_LDFLAGS="$LDFLAGS"
+ if test "x$with_hwloc" != x; then
+ CPPFLAGS="-I$with_hwloc/include $CPPFLAGS"
+- LDFLAGS="-L$with_hwloc/lib $CPPFLAGS"
++ LDFLAGS="-L$with_hwloc/lib $LDFLAGS"
+ fi
+
+
diff --git a/var/spack/repos/builtin/packages/qthreads/package.py b/var/spack/repos/builtin/packages/qthreads/package.py
index dacdb7152496bab71bc4f3210adee721eba302ad..5da93409275d3230d103e14da3e506217c8be6d5 100644
--- a/var/spack/repos/builtin/packages/qthreads/package.py
+++ b/var/spack/repos/builtin/packages/qthreads/package.py
@@ -16,7 +16,12 @@ class Qthreads(Package):
version('1.10', '5af8c8bbe88c2a6d45361643780d1671')
+ patch("ldflags.patch")
+ patch("restrict.patch")
+ patch("trap.patch")
+
def install(self, spec, prefix):
- configure("--prefix=%s" % prefix)
+ configure("--prefix=%s" % prefix,
+ "--enable-guard-pages")
make()
make("install")
diff --git a/var/spack/repos/builtin/packages/qthreads/restrict.patch b/var/spack/repos/builtin/packages/qthreads/restrict.patch
new file mode 100644
index 0000000000000000000000000000000000000000..4c95714f6b35c435485527d36d23ee42b9dcdefa
--- /dev/null
+++ b/var/spack/repos/builtin/packages/qthreads/restrict.patch
@@ -0,0 +1,12 @@
+--- a/include/qthread/common.h.in
++++ b/include/qthread/common.h.in
+@@ -84,7 +84,9 @@
+ /* Define to the equivalent of the C99 'restrict' keyword, or to
+ nothing if this is not supported. Do not define if restrict is
+ supported directly. */
++#ifndef restrict
+ #undef restrict
++#endif
+ /* Work around a bug in Sun C++: it does not support _Restrict or
+ __restrict__, even though the corresponding Sun C compiler ends up with
+ "#define restrict _Restrict" or "#define restrict __restrict__" in the
diff --git a/var/spack/repos/builtin/packages/qthreads/trap.patch b/var/spack/repos/builtin/packages/qthreads/trap.patch
new file mode 100644
index 0000000000000000000000000000000000000000..7aa94d82d5bd5d011523f4fc97fcaed646efcc7c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/qthreads/trap.patch
@@ -0,0 +1,11 @@
+--- a/include/qthread/qthread.hpp
++++ b/include/qthread/qthread.hpp
+@@ -236,7 +236,7 @@
+ return qthread_incr64((uint64_t *)operand, incr);
+
+ default:
+- *(int *)(0) = 0;
++ __builtin_trap();
+ }
+ return T(0); // never hit - keep compiler happy
+ }
diff --git a/var/spack/repos/builtin/packages/raja/package.py b/var/spack/repos/builtin/packages/raja/package.py
new file mode 100644
index 0000000000000000000000000000000000000000..f807ab71af517223656afe0778397fa0f8e9c48f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/raja/package.py
@@ -0,0 +1,12 @@
+from spack import *
+
+class Raja(Package):
+ """RAJA Parallel Framework."""
+ homepage = "http://software.llnl.gov/RAJA/"
+
+ version('git', git='https://github.com/LLNL/RAJA.git', branch="master")
+
+ def install(self, spec, prefix):
+ cmake('.',*std_cmake_args)
+ make()
+ make('install')
diff --git a/var/spack/repos/builtin/packages/scons/package.py b/var/spack/repos/builtin/packages/scons/package.py
new file mode 100644
index 0000000000000000000000000000000000000000..594aeced8896535d1893955cdda42dc538443513
--- /dev/null
+++ b/var/spack/repos/builtin/packages/scons/package.py
@@ -0,0 +1,13 @@
+from spack import *
+
+class Scons(Package):
+ """SCons is a software construction tool"""
+ homepage = "http://scons.org"
+ url = "http://downloads.sourceforge.net/project/scons/scons/2.5.0/scons-2.5.0.tar.gz"
+
+ version('2.5.0', '9e00fa0df8f5ca5c5f5975b40e0ed354')
+
+ extends('python')
+
+ def install(self, spec, prefix):
+ python('setup.py', 'install', '--prefix=%s' % prefix)
diff --git a/var/spack/repos/builtin/packages/serf/package.py b/var/spack/repos/builtin/packages/serf/package.py
new file mode 100644
index 0000000000000000000000000000000000000000..a5c9057b99196633e7089c23184aff92e0fca6d2
--- /dev/null
+++ b/var/spack/repos/builtin/packages/serf/package.py
@@ -0,0 +1,51 @@
+##############################################################################
+# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License (as published by
+# the Free Software Foundation) version 2.1 dated February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with this program; if not, write to the Free Software Foundation,
+# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+class Serf(Package):
+ """Apache Serf - a high performance C-based HTTP client library built upon the Apache Portable Runtime (APR) library"""
+ homepage = 'https://serf.apache.org/'
+ url = 'https://archive.apache.org/dist/serf/serf-1.3.8.tar.bz2'
+
+ version('1.3.8', '1d45425ca324336ce2f4ae7d7b4cfbc5567c5446')
+
+ depends_on('apr')
+ depends_on('apr-util')
+ depends_on('scons')
+ depends_on('expat')
+ depends_on('openssl')
+
+ def install(self, spec, prefix):
+ scons = which("scons")
+
+ options = ['PREFIX=%s' % prefix]
+ options.append('APR=%s' % spec['apr'].prefix)
+ options.append('APU=%s' % spec['apr-util'].prefix)
+ options.append('OPENSSL=%s' % spec['openssl'].prefix)
+ options.append('LINKFLAGS=-L%s/lib' % spec['expat'].prefix)
+ options.append('CPPFLAGS=-I%s/include' % spec['expat'].prefix)
+
+ scons(*options)
+ scons('install')
diff --git a/var/spack/repos/builtin/packages/subversion/package.py b/var/spack/repos/builtin/packages/subversion/package.py
index 5db1c3eb92dc9e291d8b5e79ab2f831195f0dcd1..04cde94aad54bdbef8dbc38f905c484b9b342612 100644
--- a/var/spack/repos/builtin/packages/subversion/package.py
+++ b/var/spack/repos/builtin/packages/subversion/package.py
@@ -37,6 +37,7 @@ class Subversion(Package):
depends_on('apr-util')
depends_on('zlib')
depends_on('sqlite')
+ depends_on('serf')
# Optional: We need swig if we want the Perl, Python or Ruby
# bindings.
@@ -54,6 +55,7 @@ def install(self, spec, prefix):
options.append('--with-apr-util=%s' % spec['apr-util'].prefix)
options.append('--with-zlib=%s' % spec['zlib'].prefix)
options.append('--with-sqlite=%s' % spec['sqlite'].prefix)
+ options.append('--with-serf=%s' % spec['serf'].prefix)
#options.append('--with-swig=%s' % spec['swig'].prefix)
configure(*options)
diff --git a/var/spack/repos/builtin/packages/superlu-dist/package.py b/var/spack/repos/builtin/packages/superlu-dist/package.py
index 5cf5e129b41c80725b34b24a58c0efd82a670568..3420d9b90a3003845bd7ac91badc5c48bac53def 100644
--- a/var/spack/repos/builtin/packages/superlu-dist/package.py
+++ b/var/spack/repos/builtin/packages/superlu-dist/package.py
@@ -6,7 +6,9 @@ class SuperluDist(Package):
homepage = "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/"
url = "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/superlu_dist_4.1.tar.gz"
- version('4.3', 'ee66c84e37b4f7cc557771ccc3dc43ae')
+ version('5.0.0', '2b53baf1b0ddbd9fcf724992577f0670')
+ # default to version 4.3 since petsc and trilinos are not tested with 5.0.
+ version('4.3', 'ee66c84e37b4f7cc557771ccc3dc43ae', preferred=True)
version('4.2', 'ae9fafae161f775fbac6eba11e530a65')
version('4.1', '4edee38cc29f687bd0c8eb361096a455')
version('4.0', 'c0b98b611df227ae050bc1635c6940e0')
diff --git a/var/spack/repos/builtin/packages/swig/package.py b/var/spack/repos/builtin/packages/swig/package.py
index 8d46c4fe465854aa1067f2c84507347e5f081872..78a6c6bbae9d7108fde36b45e969b5f390b26d95 100644
--- a/var/spack/repos/builtin/packages/swig/package.py
+++ b/var/spack/repos/builtin/packages/swig/package.py
@@ -22,6 +22,7 @@
# along with this program; if not, write to the Free Software Foundation,
# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
+
from spack import *
class Swig(Package):
@@ -33,14 +34,19 @@ class Swig(Package):
code. In addition, SWIG provides a variety of customization
features that let you tailor the wrapping process to suit your
application."""
+
homepage = "http://www.swig.org"
- url = "http://prdownloads.sourceforge.net/swig/swig-3.0.2.tar.gz"
+ url = "http://prdownloads.sourceforge.net/swig/swig-3.0.8.tar.gz"
+ version('3.0.8', 'c96a1d5ecb13d38604d7e92148c73c97')
version('3.0.2', '62f9b0d010cef36a13a010dc530d0d41')
+ version('2.0.12', 'c3fb0b2d710cc82ed0154b91e43085a4')
+ version('2.0.2', 'eaf619a4169886923e5f828349504a29')
+ version('1.3.40', '2df766c9e03e02811b1ab4bba1c7b9cc')
depends_on('pcre')
def install(self, spec, prefix):
- configure("--prefix=%s" % prefix)
+ configure('--prefix=%s' % prefix)
make()
- make("install")
+ make('install')
diff --git a/var/spack/repos/builtin/packages/the_silver_searcher/package.py b/var/spack/repos/builtin/packages/the_silver_searcher/package.py
index e4020b676609f8d588b56603f7251a8843470640..30f06354bfcc7a808aa453939c2d92d1f2dbc0bb 100644
--- a/var/spack/repos/builtin/packages/the_silver_searcher/package.py
+++ b/var/spack/repos/builtin/packages/the_silver_searcher/package.py
@@ -9,6 +9,7 @@ class TheSilverSearcher(Package):
depends_on('pcre')
depends_on('xz')
+ depends_on('pkg-config')
def install(self, spec, prefix):
configure("--prefix=%s" % prefix)
diff --git a/var/spack/repos/builtin/packages/turbomole/package.py b/var/spack/repos/builtin/packages/turbomole/package.py
new file mode 100644
index 0000000000000000000000000000000000000000..acc95e3b10e6f58c521e3bee01debd7c583df071
--- /dev/null
+++ b/var/spack/repos/builtin/packages/turbomole/package.py
@@ -0,0 +1,124 @@
+from spack import *
+import os
+import subprocess
+
+class Turbomole(Package):
+ """TURBOMOLE: Program Package for ab initio Electronic Structure
+ Calculations. NB: Requires a license to download."""
+
+ # NOTE: Turbomole requires purchase of a license to download. Go to the
+ # NOTE: Turbomole home page, http://www.turbomole-gmbh.com, for details.
+ # NOTE: Spack will search the current directory for this file. It is
+ # NOTE: probably best to add this file to a Spack mirror so that it can be
+ # NOTE: found from anywhere. For information on setting up a Spack mirror
+ # NOTE: see http://software.llnl.gov/spack/mirrors.html
+
+ homepage = "http://www.turbomole-gmbh.com/"
+
+ version('7.0.2', '92b97e1e52e8dcf02a4d9ac0147c09d6',
+ url="file://%s/turbolinux702.tar.gz" % os.getcwd())
+
+ variant('mpi', default=False, description='Set up MPI environment')
+ variant('smp', default=False, description='Set up SMP environment')
+
+ # Turbomole's install is odd. There are three variants
+ # - serial
+ # - parallel, MPI
+ # - parallel, SMP
+ #
+ # Only one of these can be active at a time. MPI and SMP are set as
+ # variants so there could be up to 3 installs per version. Switching
+ # between them would be accomplished with `module swap` commands.
+
+ def do_fetch(self, mirror_only=True):
+ if '+mpi' in self.spec and '+smp' in self.spec:
+ raise InstallError('Can not have both SMP and MPI enabled in the same build.')
+ super(Turbomole, self).do_fetch(mirror_only)
+
+ def get_tm_arch(self):
+ # For python-2.7 we could use `tm_arch = subprocess.check_output()`
+ # Use the following for compatibility with python 2.6
+ if 'TURBOMOLE' in os.getcwd():
+ tm_arch = subprocess.Popen(['sh', 'scripts/sysname'],
+ stdout=subprocess.PIPE).communicate()[0]
+ return tm_arch.rstrip('\n')
+ else:
+ return
+
+ def install(self, spec, prefix):
+ if spec.satisfies('@:7.0.2'):
+ calculate_version = 'calculate_2.4_linux64'
+ molecontrol_version = 'MoleControl_2.5'
+
+ tm_arch=self.get_tm_arch()
+
+ tar = which('tar')
+ dst = join_path(prefix, 'TURBOMOLE')
+
+ tar('-x', '-z', '-f', 'thermocalc.tar.gz')
+ with working_dir('thermocalc'):
+ cmd = 'sh install <<<y'
+ subprocess.call(cmd, shell=True)
+
+ install_tree('basen', join_path(dst, 'basen'))
+ install_tree('cabasen', join_path(dst, 'cabasen'))
+ install_tree(calculate_version, join_path(dst, calculate_version))
+ install_tree('cbasen', join_path(dst, 'cbasen'))
+ install_tree('DOC', join_path(dst, 'DOC'))
+ install_tree('jbasen', join_path(dst, 'jbasen'))
+ install_tree('jkbasen', join_path(dst, 'jkbasen'))
+ install_tree(molecontrol_version, join_path(dst, molecontrol_version))
+ install_tree('parameter', join_path(dst, 'parameter'))
+ install_tree('perlmodules', join_path(dst, 'perlmodules'))
+ install_tree('scripts', join_path(dst, 'scripts'))
+ install_tree('smprun_scripts', join_path(dst, 'smprun_scripts'))
+ install_tree('structures', join_path(dst, 'structures'))
+ install_tree('thermocalc', join_path(dst, 'thermocalc'))
+ install_tree('TURBOTEST', join_path(dst, 'TURBOTEST'))
+ install_tree('xbasen', join_path(dst, 'xbasen'))
+
+ install('Config_turbo_env', dst)
+ install('Config_turbo_env.tcsh', dst)
+ install('README', dst)
+ install('README_LICENSES', dst)
+ install('TURBOMOLE_702_LinuxPC', dst)
+
+ if '+mpi' in spec:
+ install_tree('bin/%s_mpi' % tm_arch, join_path(dst, 'bin', '%s_mpi' % tm_arch))
+ install_tree('libso/%s_mpi' % tm_arch, join_path(dst, 'libso', '%s_mpi' % tm_arch))
+ install_tree('mpirun_scripts/%s_mpi' % tm_arch, join_path(dst, 'mpirun_scripts', '%s_mpi' % tm_arch))
+ elif '+smp' in spec:
+ install_tree('bin/%s_smp' % tm_arch, join_path(dst, 'bin', '%s_smp' % tm_arch))
+ install_tree('libso/%s_smp' % tm_arch, join_path(dst, 'libso', '%s_smp' % tm_arch))
+ install_tree('mpirun_scripts/%s_smp' % tm_arch, join_path(dst, 'mpirun_scripts', '%s_smp' % tm_arch))
+ else:
+ install_tree('bin/%s' % tm_arch, join_path(dst, 'bin', tm_arch))
+ if '+mpi' in spec or '+smp' in spec:
+ install('mpirun_scripts/ccsdf12', join_path(dst, 'mpirun_scripts'))
+ install('mpirun_scripts/dscf', join_path(dst, 'mpirun_scripts'))
+ install('mpirun_scripts/grad', join_path(dst, 'mpirun_scripts'))
+ install('mpirun_scripts/mpgrad', join_path(dst, 'mpirun_scripts'))
+ install('mpirun_scripts/pnoccsd', join_path(dst, 'mpirun_scripts'))
+ install('mpirun_scripts/rdgrad', join_path(dst, 'mpirun_scripts'))
+ install('mpirun_scripts/ricc2', join_path(dst, 'mpirun_scripts'))
+ install('mpirun_scripts/ridft', join_path(dst, 'mpirun_scripts'))
+
+ def setup_environment(self, spack_env, run_env):
+ if self.spec.satisfies('@:7.0.2'):
+ molecontrol_version = 'MoleControl_2.5'
+
+ tm_arch=self.get_tm_arch()
+
+ run_env.set('TURBODIR', join_path(self.prefix, 'TURBOMOLE'))
+ run_env.set('MOLE_CONTROL', join_path(self.prefix, 'TURBOMOLE', molecontrol_version))
+
+ run_env.prepend_path('PATH', join_path(self.prefix, 'TURBOMOLE', 'thermocalc'))
+ run_env.prepend_path('PATH', join_path(self.prefix, 'TURBOMOLE', 'scripts'))
+ if '+mpi' in self.spec:
+ run_env.set('PARA_ARCH', 'MPI')
+ run_env.prepend_path('PATH', join_path(self.prefix, 'TURBOMOLE', 'bin', '%s_mpi' % tm_arch))
+ elif '+smp' in self.spec:
+ run_env.set('PARA_ARCH', 'SMP')
+ run_env.prepend_path('PATH', join_path(self.prefix, 'TURBOMOLE', 'bin', '%s_smp' % tm_arch))
+ else:
+ run_env.prepend_path('PATH', join_path(self.prefix, 'TURBOMOLE', 'bin', tm_arch))
diff --git a/var/spack/repos/builtin/packages/unibilium/package.py b/var/spack/repos/builtin/packages/unibilium/package.py
new file mode 100644
index 0000000000000000000000000000000000000000..ef5de56f791920e1ab83eab8811c37f3245d0635
--- /dev/null
+++ b/var/spack/repos/builtin/packages/unibilium/package.py
@@ -0,0 +1,12 @@
+from spack import *
+
+class Unibilium(Package):
+ """A terminfo parsing library"""
+ homepage = "https://github.com/mauke/unibilium"
+ url = "https://github.com/mauke/unibilium/archive/v1.2.0.tar.gz"
+
+ version('1.2.0', '9b1c97839a880a373da6c097443b43c4')
+
+ def install(self, spec, prefix):
+ make("PREFIX="+prefix)
+ make("install", "PREFIX="+prefix)
diff --git a/var/spack/repos/builtin/packages/wget/package.py b/var/spack/repos/builtin/packages/wget/package.py
index 55728b0515723d2d68702164dccbbdb31885e7f9..4b92659478f19cbbaa85677ee9bed818aafa9dd9 100644
--- a/var/spack/repos/builtin/packages/wget/package.py
+++ b/var/spack/repos/builtin/packages/wget/package.py
@@ -17,6 +17,8 @@ class Wget(Package):
def install(self, spec, prefix):
configure("--prefix=%s" % prefix,
- "--with-ssl=openssl")
+ "--with-ssl=openssl",
+ "OPENSSL_CFLAGS=-I%s" % spec['openssl'].prefix.include,
+ "OPENSSL_LIBS=-L%s -lssl -lcrypto -lz" % spec['openssl'].prefix.lib)
make()
make("install")
diff --git a/var/spack/repos/builtin/packages/xerces-c/package.py b/var/spack/repos/builtin/packages/xerces-c/package.py
index b59ab178aed47925d27e77806caee4d6dfacf540..bd02ddcd4b1eb46fb54a7d09284712b2c32f5f0d 100644
--- a/var/spack/repos/builtin/packages/xerces-c/package.py
+++ b/var/spack/repos/builtin/packages/xerces-c/package.py
@@ -1,19 +1,3 @@
-# FIXME:
-# This is a template package file for Spack. We've conveniently
-# put "FIXME" labels next to all the things you'll want to change.
-#
-# Once you've edited all the FIXME's, delete this whole message,
-# save this file, and test out your package like this:
-#
-# spack install xerces-c
-#
-# You can always get back here to change things with:
-#
-# spack edit xerces-c
-#
-# See the spack documentation for more information on building
-# packages.
-#
from spack import *
class XercesC(Package):
@@ -24,8 +8,8 @@ class XercesC(Package):
"""
homepage = "https://xerces.apache.org/xerces-c"
- url = "https://www.apache.org/dist/xerces/c/3/sources/xerces-c-3.1.2.tar.gz"
- version('3.1.2', '9eb1048939e88d6a7232c67569b23985')
+ url = "https://www.apache.org/dist/xerces/c/3/sources/xerces-c-3.1.3.tar.bz2"
+ version('3.1.3', '5e333b55cb43e6b025ddf0e5d0f0fb0d')
def install(self, spec, prefix):
configure("--prefix=%s" % prefix,
diff --git a/var/spack/repos/builtin/packages/zoltan/package.py b/var/spack/repos/builtin/packages/zoltan/package.py
index e20ae81adbe2f1b74888fddffca1d1ae0411dfdf..738dfb508b0d11681615414de684231223489db8 100644
--- a/var/spack/repos/builtin/packages/zoltan/package.py
+++ b/var/spack/repos/builtin/packages/zoltan/package.py
@@ -1,3 +1,4 @@
+import re, os, glob
from spack import *
class Zoltan(Package):
@@ -12,8 +13,13 @@ class Zoltan(Package):
base_url = "http://www.cs.sandia.gov/~kddevin/Zoltan_Distributions"
version('3.83', '1ff1bc93f91e12f2c533ddb01f2c095f')
+ version('3.8', '9d8fba8a990896881b85351d4327c4a9')
+ version('3.6', '9cce794f7241ecd8dbea36c3d7a880f9')
version('3.3', '5eb8f00bda634b25ceefa0122bd18d65')
+ variant('debug', default=False, description='Builds a debug version of the library')
+ variant('shared', default=True, description='Builds a shared version of the library')
+
variant('fortran', default=True, description='Enable Fortran support')
variant('mpi', default=False, description='Enable MPI support')
@@ -24,28 +30,49 @@ def install(self, spec, prefix):
'--enable-f90interface' if '+fortan' in spec else '--disable-f90interface',
'--enable-mpi' if '+mpi' in spec else '--disable-mpi',
]
+ config_cflags = [
+ '-O0' if '+debug' in spec else '-O3',
+ '-g' if '+debug' in spec else '-g0',
+ ]
+
+ if '+shared' in spec:
+ config_args.append('--with-ar=$(CXX) -shared $(LDFLAGS) -o')
+ config_args.append('RANLIB=echo')
+ config_cflags.append('-fPIC')
if '+mpi' in spec:
- config_args.append('--with-mpi=%s' % spec['mpi'].prefix)
- config_args.append('--with-mpi-compilers=%s' % spec['mpi'].prefix.bin)
config_args.append('CC=%s/mpicc' % spec['mpi'].prefix.bin)
config_args.append('CXX=%s/mpicxx' % spec['mpi'].prefix.bin)
+ config_args.append('--with-mpi=%s' % spec['mpi'].prefix)
+ config_args.append('--with-mpi-compilers=%s' % spec['mpi'].prefix.bin)
# NOTE: Early versions of Zoltan come packaged with a few embedded
# library packages (e.g. ParMETIS, Scotch), which messes with Spack's
# ability to descend directly into the package's source directory.
- if spec.satisfies('@:3.3'):
+ if spec.satisfies('@:3.6'):
cd('Zoltan_v%s' % self.version)
mkdirp('build')
cd('build')
config_zoltan = Executable('../configure')
- config_zoltan('--prefix=%s' % pwd(), *config_args)
+ config_zoltan(
+ '--prefix=%s' % pwd(),
+ '--with-cflags=%s' % ' '.join(config_cflags),
+ '--with-cxxflags=%s' % ' '.join(config_cflags),
+ *config_args)
make()
make('install')
+ # NOTE: Unfortunately, Zoltan doesn't provide any configuration options for
+ # the extension of the output library files, so this script must change these
+ # extensions as a post-processing step.
+ if '+shared' in spec:
+ for libpath in glob.glob('lib/*.a'):
+ libdir, libname = (os.path.dirname(libpath), os.path.basename(libpath))
+ move(libpath, os.path.join(libdir, re.sub(r'\.a$', '.so', libname)))
+
mkdirp(prefix)
move('include', prefix)
move('lib', prefix)