diff options
author | Todd Gamblin <tgamblin@llnl.gov> | 2015-06-07 16:10:32 -0700 |
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committer | Todd Gamblin <tgamblin@llnl.gov> | 2015-06-07 16:10:32 -0700 |
commit | 1857b7736f1c416ebadbe2d49d5297d31e235365 (patch) | |
tree | 24a179c9b44a5f877cc65d6f6f27d6c8fe39b23a | |
parent | ab31f989db4de515aafd900c9235161ce45993b3 (diff) | |
parent | bde9c7eee3fb55258b6c5e0ddb143882ebe0cca3 (diff) | |
download | spack-1857b7736f1c416ebadbe2d49d5297d31e235365.tar.gz spack-1857b7736f1c416ebadbe2d49d5297d31e235365.tar.bz2 spack-1857b7736f1c416ebadbe2d49d5297d31e235365.tar.xz spack-1857b7736f1c416ebadbe2d49d5297d31e235365.zip |
Merge Kevin, Ben, and Saravan's contributions into develop
- includes ATLAS, BLAS, LAPACK, other FastMATH packages.
22 files changed, 580 insertions, 58 deletions
@@ -126,14 +126,7 @@ def main(): try: return_val = command(parser, args) except SpackError, e: - if spack.debug: - # In debug mode, raise with a full stack trace. - raise - elif e.long_message: - tty.die(e.message, e.long_message) - else: - tty.die(e.message) - + e.die() except KeyboardInterrupt: sys.stderr.write('\n') tty.die("Keyboard interrupt.") diff --git a/lib/spack/llnl/util/filesystem.py b/lib/spack/llnl/util/filesystem.py index 3b34e04740..029a7536df 100644 --- a/lib/spack/llnl/util/filesystem.py +++ b/lib/spack/llnl/util/filesystem.py @@ -25,7 +25,7 @@ __all__ = ['set_install_permissions', 'install', 'install_tree', 'traverse_tree', 'expand_user', 'working_dir', 'touch', 'touchp', 'mkdirp', 'force_remove', 'join_path', 'ancestor', 'can_access', 'filter_file', - 'change_sed_delimiter', 'is_exe', 'force_symlink'] + 'FileFilter', 'change_sed_delimiter', 'is_exe', 'force_symlink'] import os import sys @@ -40,7 +40,6 @@ from tempfile import NamedTemporaryFile import llnl.util.tty as tty from spack.util.compression import ALLOWED_ARCHIVE_TYPES - def filter_file(regex, repl, *filenames, **kwargs): """Like sed, but uses python regular expressions. @@ -97,6 +96,15 @@ def filter_file(regex, repl, *filenames, **kwargs): shutil.rmtree(backup, ignore_errors=True) +class FileFilter(object): + """Convenience class for calling filter_file a lot.""" + def __init__(self, *filenames): + self.filenames = filenames + + def filter(self, regex, repl, **kwargs): + return filter_file(regex, repl, *self.filenames, **kwargs) + + def change_sed_delimiter(old_delim, new_delim, *filenames): """Find all sed search/replace commands and change the delimiter. e.g., if the file contains seds that look like 's///', you can diff --git a/lib/spack/spack/build_environment.py b/lib/spack/spack/build_environment.py index f9e795ac42..81fbedc689 100644 --- a/lib/spack/spack/build_environment.py +++ b/lib/spack/spack/build_environment.py @@ -280,6 +280,10 @@ def fork(pkg, function): # Use os._exit here to avoid raising a SystemExit exception, # which interferes with unit tests. os._exit(0) + + except spack.error.SpackError, e: + e.die() + except: # Child doesn't raise or return to main spack code. # Just runs default exception handler and exits. diff --git a/lib/spack/spack/concretize.py b/lib/spack/spack/concretize.py index 15e886ad3c..2e1d5d7f03 100644 --- a/lib/spack/spack/concretize.py +++ b/lib/spack/spack/concretize.py @@ -75,7 +75,23 @@ class DefaultConcretizer(object): if valid_versions: spec.versions = ver([valid_versions[-1]]) else: - raise NoValidVersionError(spec) + # We don't know of any SAFE versions that match the given + # spec. Grab the spec's versions and grab the highest + # *non-open* part of the range of versions it specifies. + # Someone else can raise an error if this happens, + # e.g. when we go to fetch it and don't know how. But it + # *might* work. + if not spec.versions or spec.versions == VersionList([':']): + raise NoValidVersionError(spec) + else: + last = spec.versions[-1] + if isinstance(last, VersionRange): + if last.end: + spec.versions = ver([last.end]) + else: + spec.versions = ver([last.start]) + else: + spec.versions = ver([last]) def concretize_architecture(self, spec): @@ -174,8 +190,8 @@ class UnavailableCompilerVersionError(spack.error.SpackError): class NoValidVersionError(spack.error.SpackError): - """Raised when there is no available version for a package that - satisfies a spec.""" + """Raised when there is no way to have a concrete version for a + particular spec.""" def __init__(self, spec): super(NoValidVersionError, self).__init__( - "No available version of %s matches '%s'" % (spec.name, spec.versions)) + "There are no valid versions for %s that match '%s'" % (spec.name, spec.versions)) diff --git a/lib/spack/spack/error.py b/lib/spack/spack/error.py index e8fa756682..bfa7951a47 100644 --- a/lib/spack/spack/error.py +++ b/lib/spack/spack/error.py @@ -22,6 +22,10 @@ # along with this program; if not, write to the Free Software Foundation, # Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## +import os +import sys +import llnl.util.tty as tty +import spack class SpackError(Exception): """This is the superclass for all Spack errors. @@ -38,6 +42,17 @@ class SpackError(Exception): return self._long_message + def die(self): + if spack.debug: + sys.excepthook(*sys.exc_info()) + os._exit(1) + else: + tty.error(self.message) + if self.long_message: + print self.long_message + os._exit(1) + + def __str__(self): msg = self.message if self.long_message: diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py index 5dd410d0e4..5abf2a6bb3 100644 --- a/lib/spack/spack/package.py +++ b/lib/spack/spack/package.py @@ -471,13 +471,18 @@ class Package(object): """Spec of the extendee of this package, or None if it is not an extension.""" if not self.extendees: return None + + # TODO: allow more than one extendee. name = next(iter(self.extendees)) - if not name in self.spec: - spec, kwargs = self.extendees[name] - return spec - # Need to do this to get the concrete version of the spec - return self.spec[name] + # If the extendee is in the spec's deps already, return that. + for dep in self.spec.traverse(): + if name == dep.name: + return dep + + # Otherwise return the spec from the extends() directive + spec, kwargs = self.extendees[name] + return spec @property @@ -542,7 +547,7 @@ class Package(object): def provides(self, vpkg_name): """True if this package provides a virtual package with the specified name.""" - return vpkg_name in self.provided + return any(s.name == vpkg_name for s in self.provided) def virtual_dependencies(self, visited=None): @@ -561,8 +566,11 @@ class Package(object): on this one.""" dependents = [] for spec in spack.db.installed_package_specs(): - if self.name != spec.name and self.spec in spec: - dependents.append(spec) + if self.name == spec.name: + continue + for dep in spec.traverse(): + if spec == dep: + dependents.append(spec) return dependents @@ -816,17 +824,8 @@ class Package(object): except ProcessError, e: # Annotate with location of build log. e.build_log = log_path - - # One of the processes returned an error code. - # Suppress detailed stack trace here unless in debug mode - if spack.debug: - raise e - else: - tty.error(e) - - # Still need to clean up b/c there was an error. cleanup() - os._exit(1) + raise e except: # other exceptions just clean up and raise. @@ -994,10 +993,13 @@ class Package(object): activated = spack.install_layout.extension_map(self.extendee_spec) for name, aspec in activated.items(): - if aspec != self.spec and self.spec in aspec: - raise ActivationError( - "Cannot deactivate %s beacuse %s is activated and depends on it." - % (self.spec.short_spec, aspec.short_spec)) + if aspec == self.spec: + continue + for dep in aspec.traverse(): + if self.spec == dep: + raise ActivationError( + "Cannot deactivate %s beacuse %s is activated and depends on it." + % (self.spec.short_spec, aspec.short_spec)) self.extendee_spec.package.deactivate(self, **self.extendee_args) diff --git a/lib/spack/spack/spec.py b/lib/spack/spack/spec.py index aa13f0422c..5876fc6cf8 100644 --- a/lib/spack/spack/spec.py +++ b/lib/spack/spack/spec.py @@ -498,7 +498,13 @@ class Spec(object): Possible idea: just use conventin and make virtual deps all caps, e.g., MPI vs mpi. """ - return not spack.db.exists(self.name) + return Spec.is_virtual(self.name) + + + @staticmethod + def is_virtual(name): + """Test if a name is virtual without requiring a Spec.""" + return not spack.db.exists(name) @property @@ -1224,7 +1230,17 @@ class Spec(object): """ other = self._autospec(other) - # First thing we care about is whether the name matches + # A concrete provider can satisfy a virtual dependency. + if not self.virtual and other.virtual: + pkg = spack.db.get(self.name) + if pkg.provides(other.name): + for provided, when_spec in pkg.provided.items(): + if self.satisfies(when_spec, deps=False, strict=strict): + if provided.satisfies(other): + return True + return False + + # Otherwise, first thing we care about is whether the name matches if self.name != other.name: return False @@ -1364,11 +1380,21 @@ class Spec(object): def __getitem__(self, name): - """TODO: reconcile __getitem__, _add_dependency, __contains__""" + """Get a dependency from the spec by its name.""" for spec in self.traverse(): if spec.name == name: return spec + if Spec.is_virtual(name): + # TODO: this is a kind of kludgy way to find providers + # TODO: should we just keep virtual deps in the DAG instead of + # TODO: removing them on concretize? + for spec in self.traverse(): + if spec.virtual: + continue + if spec.package.provides(name): + return spec + raise KeyError("No spec with name %s in %s" % (name, self)) @@ -1380,6 +1406,7 @@ class Spec(object): for s in self.traverse(): if s.satisfies(spec, strict=True): return True + return False diff --git a/lib/spack/spack/test/concretize.py b/lib/spack/spack/test/concretize.py index cc839a2340..b3a77d076a 100644 --- a/lib/spack/spack/test/concretize.py +++ b/lib/spack/spack/test/concretize.py @@ -152,7 +152,10 @@ class ConcretizeTest(MockPackagesTest): spec.concretize() self.assertTrue('zmpi' in spec.dependencies) - self.assertFalse('mpi' in spec) + self.assertTrue(all(not 'mpi' in d.dependencies for d in spec.traverse())) + self.assertTrue('zmpi' in spec) + self.assertTrue('mpi' in spec) + self.assertTrue('fake' in spec.dependencies['zmpi']) @@ -168,7 +171,9 @@ class ConcretizeTest(MockPackagesTest): self.assertTrue('zmpi' in spec.dependencies['callpath'].dependencies) self.assertTrue('fake' in spec.dependencies['callpath'].dependencies['zmpi'].dependencies) - self.assertFalse('mpi' in spec) + self.assertTrue(all(not 'mpi' in d.dependencies for d in spec.traverse())) + self.assertTrue('zmpi' in spec) + self.assertTrue('mpi' in spec) def test_my_dep_depends_on_provider_of_my_virtual_dep(self): diff --git a/lib/spack/spack/test/directory_layout.py b/lib/spack/spack/test/directory_layout.py index beac038410..b3ad8efec4 100644 --- a/lib/spack/spack/test/directory_layout.py +++ b/lib/spack/spack/test/directory_layout.py @@ -167,12 +167,15 @@ class DirectoryLayoutTest(unittest.TestCase): def test_find(self): """Test that finding specs within an install layout works.""" packages = list(spack.db.all_packages())[:max_packages] + + # Create install prefixes for all packages in the list installed_specs = {} for pkg in packages: spec = pkg.spec.concretized() installed_specs[spec.name] = spec self.layout.create_install_directory(spec) + # Make sure all the installed specs appear in DirectoryLayout.all_specs() found_specs = dict((s.name, s) for s in self.layout.all_specs()) for name, spec in found_specs.items(): self.assertTrue(name in found_specs) diff --git a/lib/spack/spack/test/spec_semantics.py b/lib/spack/spack/test/spec_semantics.py index 20df2603f5..6666dbbb52 100644 --- a/lib/spack/spack/test/spec_semantics.py +++ b/lib/spack/spack/test/spec_semantics.py @@ -189,6 +189,67 @@ class SpecSematicsTest(MockPackagesTest): self.check_unsatisfiable('mpich+foo', 'mpich~foo') + def test_satisfies_virtual(self): + self.assertTrue(Spec('mpich').satisfies(Spec('mpi'))) + self.assertTrue(Spec('mpich2').satisfies(Spec('mpi'))) + self.assertTrue(Spec('zmpi').satisfies(Spec('mpi'))) + + + # ================================================================================ + # Indexing specs + # ================================================================================ + def test_self_index(self): + s = Spec('callpath') + self.assertTrue(s['callpath'] == s) + + + def test_dep_index(self): + s = Spec('callpath') + s.normalize() + + self.assertTrue(s['callpath'] == s) + self.assertTrue(type(s['dyninst']) == Spec) + self.assertTrue(type(s['libdwarf']) == Spec) + self.assertTrue(type(s['libelf']) == Spec) + self.assertTrue(type(s['mpi']) == Spec) + + self.assertTrue(s['dyninst'].name == 'dyninst') + self.assertTrue(s['libdwarf'].name == 'libdwarf') + self.assertTrue(s['libelf'].name == 'libelf') + self.assertTrue(s['mpi'].name == 'mpi') + + + def test_spec_contains_deps(self): + s = Spec('callpath') + s.normalize() + self.assertTrue('dyninst' in s) + self.assertTrue('libdwarf' in s) + self.assertTrue('libelf' in s) + self.assertTrue('mpi' in s) + + + def test_virtual_index(self): + s = Spec('callpath') + s.concretize() + + s_mpich = Spec('callpath ^mpich') + s_mpich.concretize() + + s_mpich2 = Spec('callpath ^mpich2') + s_mpich2.concretize() + + s_zmpi = Spec('callpath ^zmpi') + s_zmpi.concretize() + + + self.assertTrue(s['mpi'].name != 'mpi') + self.assertTrue(s_mpich['mpi'].name == 'mpich') + self.assertTrue(s_mpich2['mpi'].name == 'mpich2') + self.assertTrue(s_zmpi['zmpi'].name == 'zmpi') + + for spec in [s, s_mpich, s_mpich2, s_zmpi]: + self.assertTrue('mpi' in spec) + # ================================================================================ # Constraints diff --git a/lib/spack/spack/util/executable.py b/lib/spack/spack/util/executable.py index 6eede0f78e..1dcda0d87f 100644 --- a/lib/spack/spack/util/executable.py +++ b/lib/spack/spack/util/executable.py @@ -124,6 +124,11 @@ class Executable(object): return "<exe: %s>" % self.exe + def __str__(self): + return ' '.join(self.exe) + + + def which(name, **kwargs): """Finds an executable in the path like command-line which.""" path = kwargs.get('path', os.environ.get('PATH', '').split(os.pathsep)) diff --git a/var/spack/packages/arpack/package.py b/var/spack/packages/arpack/package.py new file mode 100644 index 0000000000..8c67c536f3 --- /dev/null +++ b/var/spack/packages/arpack/package.py @@ -0,0 +1,41 @@ +from spack import * +import os +import shutil + +class Arpack(Package): + """A collection of Fortran77 subroutines designed to solve large scale + eigenvalue problems. + """ + homepage = "http://www.caam.rice.edu/software/ARPACK/" + url = "http://www.caam.rice.edu/software/ARPACK/SRC/arpack96.tar.gz" + + version('96', 'fffaa970198b285676f4156cebc8626e') + + depends_on('blas') + depends_on('lapack') + + def patch(self): + # Filter the cray makefile to make a spack one. + shutil.move('ARMAKES/ARmake.CRAY', 'ARmake.inc') + makefile = FileFilter('ARmake.inc') + + # Be sure to use Spack F77 wrapper + makefile.filter('^FC.*', 'FC = f77') + makefile.filter('^FFLAGS.*', 'FFLAGS = -O2 -g') + + # Set up some variables. + makefile.filter('^PLAT.*', 'PLAT = ') + makefile.filter('^home.*', 'home = %s' % os.getcwd()) + makefile.filter('^BLASdir.*', 'BLASdir = %s' % self.spec['blas'].prefix) + makefile.filter('^LAPACKdir.*', 'LAPACKdir = %s' % self.spec['lapack'].prefix) + + # build the library in our own prefix. + makefile.filter('^ARPACKLIB.*', 'ARPACKLIB = %s/libarpack.a' % os.getcwd()) + + + def install(self, spec, prefix): + with working_dir('SRC'): + make('all') + + mkdirp(prefix.lib) + install('libarpack.a', prefix.lib) diff --git a/var/spack/packages/atlas/package.py b/var/spack/packages/atlas/package.py new file mode 100644 index 0000000000..fc683363a7 --- /dev/null +++ b/var/spack/packages/atlas/package.py @@ -0,0 +1,60 @@ +from spack import * +from spack.util.executable import Executable +import os + +class Atlas(Package): + """ + Automatically Tuned Linear Algebra Software, generic shared + ATLAS is an approach for the automatic generation and optimization of + numerical software. Currently ATLAS supplies optimized versions for the + complete set of linear algebra kernels known as the Basic Linear Algebra + Subroutines (BLAS), and a subset of the linear algebra routines in the + LAPACK library. + """ + homepage = "http://math-atlas.sourceforge.net/" + + version('3.11.34', '0b6c5389c095c4c8785fd0f724ec6825', + url='http://sourceforge.net/projects/math-atlas/files/Developer%20%28unstable%29/3.11.34/atlas3.11.34.tar.bz2/download') + version('3.10.2', 'a4e21f343dec8f22e7415e339f09f6da', + url='http://downloads.sourceforge.net/project/math-atlas/Stable/3.10.2/atlas3.10.2.tar.bz2') + + # TODO: make this provide BLAS once it works better. Create a way + # TODO: to mark "beta" packages and require explicit invocation. + + # provides('blas') + + + def patch(self): + # Disable thraed check. LLNL's environment does not allow + # disabling of CPU throttling in a way that ATLAS actually + # understands. + filter_file(r'^\s+if \(thrchk\) exit\(1\);', 'if (0) exit(1);', + 'CONFIG/src/config.c') + # TODO: investigate a better way to add the check back in + # TODO: using, say, MSRs. Or move this to a variant. + + @when('@:3.10') + def install(self, spec, prefix): + with working_dir('ATLAS-Build', create=True): + configure = Executable('../configure') + configure('--prefix=%s' % prefix, '-C', 'ic', 'cc', '-C', 'if', 'f77', "--dylibs") + make() + make('check') + make('ptcheck') + make('time') + make("install") + + + def install(self, spec, prefix): + with working_dir('ATLAS-Build', create=True): + configure = Executable('../configure') + configure('--incdir=%s' % prefix.include, + '--libdir=%s' % prefix.lib, + '--cc=cc', + "--shared") + + make() + make('check') + make('ptcheck') + make('time') + make("install") diff --git a/var/spack/packages/boxlib/package.py b/var/spack/packages/boxlib/package.py new file mode 100644 index 0000000000..4f1b71132f --- /dev/null +++ b/var/spack/packages/boxlib/package.py @@ -0,0 +1,25 @@ +from spack import * + +class Boxlib(Package): + """BoxLib, a software framework for massively parallel + block-structured adaptive mesh refinement (AMR) codes.""" + + homepage = "https://ccse.lbl.gov/BoxLib/" + url = "https://ccse.lbl.gov/pub/Downloads/BoxLib.git"; + + # TODO: figure out how best to version this. No tags in the repo! + version('master', git='https://ccse.lbl.gov/pub/Downloads/BoxLib.git') + + depends_on('mpi') + + def install(self, spec, prefix): + args = std_cmake_args + args += ['-DCCSE_ENABLE_MPI=1', + '-DCMAKE_C_COMPILER=%s' % which('mpicc'), + '-DCMAKE_CXX_COMPILER=%s' % which('mpicxx'), + '-DCMAKE_Fortran_COMPILER=%s' % which('mpif90')] + + cmake('.', *args) + make() + make("install") + diff --git a/var/spack/packages/cblas/package.py b/var/spack/packages/cblas/package.py new file mode 100644 index 0000000000..93cf5fb7b8 --- /dev/null +++ b/var/spack/packages/cblas/package.py @@ -0,0 +1,32 @@ +from spack import * +import os + +class Cblas(Package): + """The BLAS (Basic Linear Algebra Subprograms) are routines that + provide standard building blocks for performing basic vector and + matrix operations.""" + + homepage = "http://www.netlib.org/blas/_cblas/" + + # tarball has no version, but on the date below, this MD5 was correct. + version('2015-06-06', '1e8830f622d2112239a4a8a83b84209a', + url='http://www.netlib.org/blas/blast-forum/cblas.tgz') + + depends_on('blas') + parallel = False + + def patch(self): + mf = FileFilter('Makefile.in') + + mf.filter('^BLLIB =.*', 'BLLIB = %s/libblas.a' % self.spec['blas'].prefix.lib) + mf.filter('^CC =.*', 'CC = cc') + mf.filter('^FC =.*', 'FC = f90') + + + def install(self, spec, prefix): + make('all') + mkdirp(prefix.lib) + + # Rename the generated lib file to libcblas.a + install('./lib/cblas_LINUX.a', '%s/libcblas.a' % prefix.lib) + diff --git a/var/spack/packages/cgm/package.py b/var/spack/packages/cgm/package.py new file mode 100644 index 0000000000..05d6395c5a --- /dev/null +++ b/var/spack/packages/cgm/package.py @@ -0,0 +1,30 @@ +from spack import * + +class Cgm(Package): + """The Common Geometry Module, Argonne (CGMA) is a code library + which provides geometry functionality used for mesh generation and + other applications.""" + homepage = "http://trac.mcs.anl.gov/projects/ITAPS/wiki/CGM" + url = "http://ftp.mcs.anl.gov/pub/fathom/cgm13.1.1.tar.gz" + + version('13.1.1', '4e8dbc4ba8f65767b29f985f7a23b01f') + version('13.1.0', 'a6c7b22660f164ce893fb974f9cb2028') + version('13.1' , '95f724bda04919fc76818a5b7bc0b4ed') + + depends_on("mpi") + + def patch(self): + filter_file('^(#include "CGMParallelConventions.h")', + '//\1', + 'geom/parallel/CGMReadParallel.cpp') + + + def install(self, spec, prefix): + configure("--with-mpi", + "--prefix=%s" % prefix, + "CFLAGS=-static", + "CXXFLAGS=-static", + "FCFLAGS=-static") + + make() + make("install") diff --git a/var/spack/packages/hypre/package.py b/var/spack/packages/hypre/package.py new file mode 100644 index 0000000000..198b3f00dc --- /dev/null +++ b/var/spack/packages/hypre/package.py @@ -0,0 +1,32 @@ +from spack import * + +class Hypre(Package): + """Hypre is a library of high performance preconditioners that + features parallel multigrid methods for both structured and + unstructured grid problems.""" + + homepage = "https://computation.llnl.gov/project/linear_solvers/software.php" + url = "https://computation.llnl.gov/project/linear_solvers/download/hypre-2.10.0b.tar.gz" + + version('2.10.0b', '768be38793a35bb5d055905b271f5b8e') + + depends_on("mpi") + depends_on("blas") + depends_on("lapack") + + def install(self, spec, prefix): + blas_dir = spec['blas'].prefix + lapack_dir = spec['lapack'].prefix + + # Hypre's source is staged under ./src so we'll have to manually + # cd into it. + with working_dir("src"): + configure( + "--prefix=%s" % prefix, + "--with-blas-libs=blas", + "--with-blas-lib-dirs=%s/lib" % blas_dir, + "--with-lapack-libs=\"lapack blas\"", + "--with-lapack-lib-dirs=%s/lib" % lapack_dir, + "--with-MPI") + make() + make("install") diff --git a/var/spack/packages/lapack/package.py b/var/spack/packages/lapack/package.py new file mode 100644 index 0000000000..d9d37e3e4a --- /dev/null +++ b/var/spack/packages/lapack/package.py @@ -0,0 +1,45 @@ +from spack import * + +class Lapack(Package): + """ + LAPACK version 3.X is a comprehensive FORTRAN library that does + linear algebra operations including matrix inversions, least + squared solutions to linear sets of equations, eigenvector + analysis, singular value decomposition, etc. It is a very + comprehensive and reputable package that has found extensive + use in the scientific community. + """ + homepage = "http://www.netlib.org/lapack/" + url = "http://www.netlib.org/lapack/lapack-3.5.0.tgz" + + version('3.5.0', 'b1d3e3e425b2e44a06760ff173104bdf') + version('3.4.2', '61bf1a8a4469d4bdb7604f5897179478') + version('3.4.1', '44c3869c38c8335c2b9c2a8bb276eb55') + version('3.4.0', '02d5706ec03ba885fc246e5fa10d8c70') + version('3.3.1', 'd0d533ec9a5b74933c2a1e84eedc58b4') + + # blas is a virtual dependency. + depends_on('blas') + + # Doesn't always build correctly in parallel + parallel = False + + @when('^netlib-blas') + def get_blas_libs(self): + blas = self.spec['netlib-blas'] + return [join_path(blas.prefix.lib, 'blas.a')] + + + @when('^atlas') + def get_blas_libs(self): + blas = self.spec['atlas'] + return [join_path(blas.prefix.lib, l) + for l in ('libf77blas.a', 'libatlas.a')] + + + def install(self, spec, prefix): + blas_libs = ";".join(self.get_blas_libs()) + cmake(".", '-DBLAS_LIBRARIES=' + blas_libs, *std_cmake_args) + make() + make("install") + diff --git a/var/spack/packages/metis/package.py b/var/spack/packages/metis/package.py index fa13d52127..7ce5ae1925 100644 --- a/var/spack/packages/metis/package.py +++ b/var/spack/packages/metis/package.py @@ -5,28 +5,23 @@ class Metis(Package): partitioning finite element meshes, and producing fill reducing orderings for sparse matrices. The algorithms implemented in METIS are based on the multilevel recursive-bisection, - multilevel k-way, and multi-constraint partitioning schemes - developed in our lab.""" + multilevel k-way, and multi-constraint partitioning schemes.""" homepage = "http://glaros.dtc.umn.edu/gkhome/metis/metis/overview" url = "http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/metis-5.1.0.tar.gz" version('5.1.0', '5465e67079419a69e0116de24fce58fe') - # FIXME: Add dependencies if this package requires them. - # depends_on("foo") - - def patch(self): - filter_file(r'#define IDXTYPEWIDTH 32', '#define IDXTYPEWIDTH 64', 'include/metis.h', - string=True) - + depends_on('mpi') def install(self, spec, prefix): - with working_dir('spack-build', create=True): - cmake('..', - '-DGKLIB_PATH=../GKlib', - '-DBUILD_SHARED_LIBS=TRUE', - *std_cmake_args) - make() - make("install") - + cmake(".", + '-DGKLIB_PATH=%s/GKlib' % pwd(), + '-DSHARED=1', + '-DCMAKE_C_COMPILER=mpicc', + '-DCMAKE_CXX_COMPILER=mpicxx', + '-DSHARED=1', + *std_cmake_args) + + make() + make("install") diff --git a/var/spack/packages/netlib-blas/package.py b/var/spack/packages/netlib-blas/package.py new file mode 100644 index 0000000000..0a6cdb0442 --- /dev/null +++ b/var/spack/packages/netlib-blas/package.py @@ -0,0 +1,40 @@ +from spack import * +import os + + +class NetlibBlas(Package): + """Netlib reference BLAS""" + homepage = "http://www.netlib.org/lapack/" + url = "http://www.netlib.org/lapack/lapack-3.5.0.tgz" + + version('3.5.0', 'b1d3e3e425b2e44a06760ff173104bdf') + + # virtual dependency + provides('blas') + + # Doesn't always build correctly in parallel + parallel = False + + def patch(self): + os.symlink('make.inc.example', 'make.inc') + + mf = FileFilter('make.inc') + mf.filter('^FORTRAN.*', 'FORTRAN = f90') + mf.filter('^LOADER.*', 'LOADER = f90') + mf.filter('^CC =.*', 'CC = cc') + + + def install(self, spec, prefix): + make('blaslib') + + # Tests that blas builds correctly + make('blas_testing') + + # No install provided + mkdirp(prefix.lib) + install('librefblas.a', prefix.lib) + + # Blas virtual package should provide blas.a and libblas.a + with working_dir(prefix.lib): + symlink('librefblas.a', 'blas.a') + symlink('librefblas.a', 'libblas.a') diff --git a/var/spack/packages/parpack/package.py b/var/spack/packages/parpack/package.py new file mode 100644 index 0000000000..622aceca04 --- /dev/null +++ b/var/spack/packages/parpack/package.py @@ -0,0 +1,43 @@ +from spack import * +import os +import shutil + +class Parpack(Package): + """ARPACK is a collection of Fortran77 subroutines designed to solve large + scale eigenvalue problems.""" + + homepage = "http://www.caam.rice.edu/software/ARPACK/download.html" + url = "http://www.caam.rice.edu/software/ARPACK/SRC/parpack96.tar.Z" + + version('96', 'a175f70ff71837a33ff7e4b0b6054f43') + + depends_on('mpi') + depends_on('blas') + depends_on('lapack') + + def patch(self): + # Filter the CJ makefile to make a spack one. + shutil.move('ARMAKES/ARmake.CJ', 'ARmake.inc') + mf = FileFilter('ARmake.inc') + + # Be sure to use Spack F77 wrapper + mf.filter('^FC.*', 'FC = f77') + mf.filter('^FFLAGS.*', 'FFLAGS = -O2 -g') + + # Set up some variables. + mf.filter('^PLAT.*', 'PLAT = ') + mf.filter('^home.*', 'home = %s' % os.getcwd()) + mf.filter('^BLASdir.*', 'BLASdir = %s' % self.spec['blas'].prefix) + mf.filter('^LAPACKdir.*', 'LAPACKdir = %s' % self.spec['lapack'].prefix) + mf.filter('^MAKE.*', 'MAKE = make') + + # build the library in our own prefix. + mf.filter('^ARPACKLIB.*', 'PARPACKLIB = %s/libparpack.a' % os.getcwd()) + + + def install(self, spec, prefix): + with working_dir('PARPACK/SRC/MPI'): + make('all') + + mkdirp(prefix.lib) + install('libparpack.a', prefix.lib) diff --git a/var/spack/packages/petsc/package.py b/var/spack/packages/petsc/package.py new file mode 100644 index 0000000000..4864e39bf1 --- /dev/null +++ b/var/spack/packages/petsc/package.py @@ -0,0 +1,40 @@ +from spack import * + +class Petsc(Package): + """PETSc is a suite of data structures and routines for the + scalable (parallel) solution of scientific applications modeled by + partial differential equations.""" + + homepage = "http://www.mcs.anl.gov/petsc/index.html" + url = "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-3.5.3.tar.gz" + + version('3.5.3', 'd4fd2734661e89f18ac6014b5dd1ef2f') + version('3.5.2', 'ad170802b3b058b5deb9cd1f968e7e13') + version('3.5.1', 'a557e029711ebf425544e117ffa44d8f') + + depends_on("boost") + depends_on("blas") + depends_on("lapack") + depends_on("hypre") + depends_on("parmetis") + depends_on("metis") + depends_on("hdf5") + depends_on("mpi") + + def install(self, spec, prefix): + configure("--prefix=%s" % prefix, + "CC=cc", + "CXX=c++", + "FC=f90", + "--with-blas-lib=%s/libblas.a" % spec['blas'].prefix.lib, + "--with-lapack-lib=%s/liblapack.a" % spec['lapack'].prefix.lib, + "--with-boost-dir=%s" % spec['boost'].prefix, + "--with-hypre-dir=%s" % spec['hypre'].prefix, + "--with-parmetis-dir=%s" % spec['parmetis'].prefix, + "--with-metis-dir=%s" % spec['metis'].prefix, + "--with-hdf5-dir=%s" % spec['hdf5'].prefix, + "--with-shared-libraries=0") + + # PETSc has its own way of doing parallel make. + make('MAKE_NP=%s' % make_jobs, parallel=False) + make("install") |