Merge Kevin, Ben, and Saravan's contributions into develop

- includes ATLAS, BLAS, LAPACK, other FastMATH packages.

11 files changed, 400 insertions, 17 deletions

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")