Add scons support, .zip support, and Cantera package

7 files changed, 505 insertions, 9 deletions

diff --git a/var/spack/repos/builtin/packages/cantera/package.py b/var/spack/repos/builtin/packages/cantera/package.py
new file mode 100644
index 0000000000..a55f883560
--- /dev/null
+++ b/var/spack/repos/builtin/packages/cantera/package.py
@@ -0,0 +1,149 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created 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 Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, 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 Lesser 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 *
+import spack
+import os
+
+
+class Cantera(Package):
+    """Cantera is a suite of object-oriented software tools for problems
+    involving chemical kinetics, thermodynamics, and/or transport processes."""
+
+    homepage = "http://www.cantera.org/docs/sphinx/html/index.html"
+    url      = "https://github.com/Cantera/cantera/archive/v2.2.1.tar.gz"
+
+    version('2.2.1', '9d1919bdef39ddec54485fc8a741a3aa')
+
+    variant('lapack',     default=True,  description='Build with external BLAS/LAPACK libraries')
+    variant('threadsafe', default=True,  description='Build threadsafe, requires Boost')
+    variant('sundials',   default=True,  description='Build with external Sundials')
+    variant('python',     default=False, description='Build the Cantera Python module')
+    variant('matlab',     default=False, description='Build the Cantera Matlab toolbox')
+
+    # Required dependencies
+    depends_on('scons')
+
+    # Recommended dependencies
+    depends_on('blas',      when='+lapack')
+    depends_on('lapack',    when='+lapack')
+    depends_on('boost',     when='+threadsafe')
+    depends_on('sundials',  when='+sundials')  # must be compiled with -fPIC
+
+    # Python module dependencies
+    extends('python', when='+python')
+    depends_on('py-numpy',  when='+python')
+    depends_on('py-scipy',  when='+python')
+    depends_on('py-cython', when='+python')
+    depends_on('py-3to2',   when='+python')
+    # TODO: these "when" specs don't actually work
+    #depends_on('py-unittest2',     when='+python^python@2.6')
+    #depends_on('py-unittest2py3k', when='+python^python@3.1')
+
+    # Matlab toolbox dependencies
+    # TODO: add Matlab package
+    # TODO: allow packages to extend multiple other packages
+    #extends('matlab',   when='+matlab')
+
+    def install(self, spec, prefix):
+        # Required options
+        options = [
+            'prefix={0}'.format(prefix),
+            'CC={0}'.format(os.environ['CC']),
+            'CXX={0}'.format(os.environ['CXX']),
+            'F77={0}'.format(os.environ['F77']),
+            'FORTRAN={0}'.format(os.environ['FC']),
+            'cc_flags=-fPIC',
+            # Allow Spack environment variables to propagate through to SCons
+            'env_vars=all'
+        ]
+
+        # BLAS/LAPACK support
+        if '+lapack' in spec:
+            options.extend([
+                'blas_lapack_libs=lapack,blas',
+                'blas_lapack_dir={0}'.format(spec['lapack'].prefix.lib)
+            ])
+
+        # Threadsafe build, requires Boost
+        if '+threadsafe' in spec:
+            options.extend([
+                'build_thread_safe=yes',
+                'boost_inc_dir={0}'.format(spec['boost'].prefix.include),
+                'boost_lib_dir={0}'.format(spec['boost'].prefix.lib),
+                'boost_thread_lib=boost_thread-mt'
+            ])
+        else:
+            options.append('build_thread_safe=no')
+
+        # Sundials support
+        if '+sundials' in spec:
+            options.extend([
+                'use_sundials=y',
+                'sundials_include={0}'.format(spec['sundials'].prefix.include),
+                'sundials_libdir={0}'.format(spec['sundials'].prefix.lib),
+                'sundials_license={0}'.format(
+                    join_path(spec['sundials'].prefix, 'LICENSE'))
+            ])
+        else:
+            options.append('use_sundials=n')
+
+        # Python module
+        if '+python' in spec:
+            options.extend([
+                'python_package=full',
+                'python_cmd={0}'.format(
+                    join_path(spec['python'].prefix.bin, 'python')),
+                'python_array_home={0}'.format(spec['py-numpy'].prefix)
+            ])
+            if spec['python'].satisfies('@3'):
+                options.extend([
+                    'python3_package=y',
+                    'python3_cmd={0}'.format(
+                        join_path(spec['python'].prefix.bin, 'python')),
+                    'python3_array_home={0}'.format(spec['py-numpy'].prefix)
+                ])
+            else:
+                options.append('python3_package=n')
+        else:
+            options.append('python_package=none')
+            options.append('python3_package=n')
+
+        # Matlab toolbox
+        if '+matlab' in spec:
+            options.extend([
+                'matlab_toolbox=y',
+                'matlab_path={0}'.format(spec['matlab'].prefix)
+            ])
+        else:
+            options.append('matlab_toolbox=n')
+
+        scons('build', *options)
+
+        if '+python' in spec:
+            # Tests will always fail if Python dependencies aren't built
+            #scons('test')  # TODO: 3 expected failures, not sure what's wrong
+            pass
+
+        scons('install')
diff --git a/var/spack/repos/builtin/packages/py-3to2/package.py b/var/spack/repos/builtin/packages/py-3to2/package.py
new file mode 100644
index 0000000000..577662e583
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-3to2/package.py
@@ -0,0 +1,40 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created 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 Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, 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 Lesser 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 Py3to2(Package):
+    """lib3to2 is a set of fixers that are intended to backport code written
+    for Python version 3.x into Python version 2.x."""
+
+    homepage = "https://pypi.python.org/pypi/3to2"
+    url = "https://pypi.python.org/packages/8f/ab/58a363eca982c40e9ee5a7ca439e8ffc5243dde2ae660ba1ffdd4868026b/3to2-1.1.1.zip"
+
+    version('1.1.1', 'cbeed28e350dbdaef86111ace3052824')
+
+    extends('python')
+
+    def install(self, spec, prefix):
+        python('setup.py', 'install', '--prefix=%s' % prefix)
diff --git a/var/spack/repos/builtin/packages/py-unittest2/package.py b/var/spack/repos/builtin/packages/py-unittest2/package.py
new file mode 100644
index 0000000000..c9b0ad5cdf
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-unittest2/package.py
@@ -0,0 +1,41 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created 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 Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, 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 Lesser 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 PyUnittest2(Package):
+    """unittest2 is a backport of the new features added to the unittest
+    testing framework in Python 2.7 and onwards."""
+
+    homepage = "https://pypi.python.org/pypi/unittest2"
+    url      = "https://pypi.python.org/packages/7f/c4/2b0e2d185d9d60772c10350d9853646832609d2f299a8300ab730f199db4/unittest2-1.1.0.tar.gz"
+
+    version('1.1.0', 'f72dae5d44f091df36b6b513305ea000')
+
+    extends('python')
+    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-unittest2py3k/package.py b/var/spack/repos/builtin/packages/py-unittest2py3k/package.py
new file mode 100644
index 0000000000..b2c7510d94
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-unittest2py3k/package.py
@@ -0,0 +1,42 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created 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 Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, 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 Lesser 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 PyUnittest2py3k(Package):
+    """unittest2 is a backport of the new features added to the unittest
+    testing framework in Python 2.7 and 3.2. This is a Python 3 compatible
+    version of unittest2."""
+
+    homepage = "https://pypi.python.org/pypi/unittest2py3k"
+    url      = "https://pypi.python.org/packages/4e/3d/d44421e8d828af1399c1509c196db92e2a58f3764b01a0ee928d7025d1ca/unittest2py3k-0.5.1.tar.gz"
+
+    version('0.5.1', '8824ff92044310d9365f90d892bf0f09')
+
+    extends('python')
+    depends_on('py-setuptools')
+
+    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
index 817db68241..074d3d64b2 100644
--- a/var/spack/repos/builtin/packages/serf/package.py
+++ b/var/spack/repos/builtin/packages/serf/package.py
@@ -41,8 +41,6 @@ class Serf(Package):
     depends_on('zlib')
 
     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)
diff --git a/var/spack/repos/builtin/packages/sundials/package.py b/var/spack/repos/builtin/packages/sundials/package.py
index ba2340f74c..a31cf5fde4 100644
--- a/var/spack/repos/builtin/packages/sundials/package.py
+++ b/var/spack/repos/builtin/packages/sundials/package.py
@@ -24,16 +24,107 @@
 ##############################################################################
 from spack import *
 
+
 class Sundials(Package):
-    """SUNDIALS (SUite of Nonlinear and DIfferential/ALgebraic equation Solvers)"""
+    """SUNDIALS (SUite of Nonlinear and DIfferential/ALgebraic equation
+    Solvers)"""
+
     homepage = "http://computation.llnl.gov/casc/sundials/"
-    url      = "http://computation.llnl.gov/casc/sundials/download/code/sundials-2.5.0.tar.gz"
+    url = "http://computation.llnl.gov/projects/sundials-suite-nonlinear-differential-algebraic-equation-solvers/download/sundials-2.6.2.tar.gz"
+
+    version('2.6.2', '3deeb0ede9f514184c6bd83ecab77d95')
 
-    version('2.5.0', 'aba8b56eec600de3109cfb967aa3ba0f')
+    variant('mpi',     default=True,  description='Enable MPI support')
+    variant('lapack',  default=True,  description='Build with external BLAS/LAPACK libraries')
+    variant('klu',     default=True,  description='Build with SuiteSparse KLU libraries')
+    variant('superlu', default=True,  description='Build with SuperLU_MT libraries')
+    variant('openmp',  default=False, description='Enable OpenMP support')
+    variant('pthread', default=True,  description='Enable POSIX threads support')
 
-    depends_on("mpi")
+    depends_on('mpi',                when='+mpi')
+    depends_on('blas',               when='+lapack')
+    depends_on('lapack',             when='+lapack')
+    depends_on('suite-sparse',       when='+klu')
+    depends_on('superlu-mt+openmp',  when='+superlu+openmp')
+    depends_on('superlu-mt+pthread', when='+superlu+pthread')
 
     def install(self, spec, prefix):
-        configure("--prefix=%s" % prefix)
-        make()
-        make("install")
+        cmake_args = std_cmake_args
+        cmake_args.extend([
+            '-DBUILD_SHARED_LIBS=ON',
+            '-DCMAKE_C_FLAGS=-fPIC'
+        ])
+
+        # MPI support
+        if '+mpi' in spec:
+            cmake_args.extend([
+                '-DMPI_ENABLE=ON',
+                '-DMPI_MPICC={0}'.format(spec['mpi'].mpicc),
+                '-DMPI_MPIF77={0}'.format(spec['mpi'].mpif77)
+            ])
+        else:
+            cmake_args.append('-DMPI_ENABLE=OFF')
+
+        # Building with LAPACK and BLAS
+        if '+lapack' in spec:
+            cmake_args.extend([
+                '-DLAPACK_ENABLE=ON',
+                '-DLAPACK_LIBRARIES={0};{1}'.format(
+                    spec['lapack'].lapack_shared_lib,
+                    spec['blas'].blas_shared_lib
+                )
+            ])
+        else:
+            cmake_args.append('-DLAPACK_ENABLE=OFF')
+
+        # Building with KLU
+        if '+klu' in spec:
+            cmake_args.extend([
+                '-DKLU_ENABLE=ON',
+                '-DKLU_INCLUDE_DIR={0}'.format(
+                    spec['suite-sparse'].prefix.include),
+                '-DKLU_LIBRARY_DIR={0}'.format(
+                    spec['suite-sparse'].prefix.lib)
+            ])
+        else:
+            cmake_args.append('-DKLU_ENABLE=OFF')
+
+        # Building with SuperLU_MT
+        if '+superlu' in spec:
+            cmake_args.extend([
+                '-DSUPERLUMT_ENABLE=ON',
+                '-DSUPERLUMT_INCLUDE_DIR={0}'.format(
+                    spec['superlu-mt'].prefix.include),
+                '-DSUPERLUMT_LIBRARY_DIR={0}'.format(
+                    spec['superlu-mt'].prefix.lib)
+            ])
+            if '+openmp' in spec:
+                cmake_args.append('-DSUPERLUMT_THREAD_TYPE=OpenMP')
+            elif '+pthread' in spec:
+                cmake_args.append('-DSUPERLUMT_THREAD_TYPE=Pthread')
+            else:
+                msg  = 'You must choose either +openmp or +pthread when '
+                msg += 'building with SuperLU_MT'
+                raise RuntimeError(msg)
+        else:
+            cmake_args.append('-DSUPERLUMT_ENABLE=OFF')
+
+        # OpenMP support
+        if '+openmp' in spec:
+            cmake_args.append('-DOPENMP_ENABLE=ON')
+        else:
+            cmake_args.append('-DOPENMP_ENABLE=OFF')
+
+        # POSIX threads support
+        if '+pthread' in spec:
+            cmake_args.append('-DPTHREAD_ENABLE=ON')
+        else:
+            cmake_args.append('-DPTHREAD_ENABLE=OFF')
+
+        with working_dir('build', create=True):
+            cmake('..', *cmake_args)
+
+            make()
+            make('install')
+
+        install('LICENSE', prefix)
diff --git a/var/spack/repos/builtin/packages/superlu-mt/package.py b/var/spack/repos/builtin/packages/superlu-mt/package.py
new file mode 100644
index 0000000000..5eee4bf5d9
--- /dev/null
+++ b/var/spack/repos/builtin/packages/superlu-mt/package.py
@@ -0,0 +1,135 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created 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 Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, 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 Lesser 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 *
+import spack
+import glob
+import os
+
+
+class SuperluMt(Package):
+    """SuperLU is a general purpose library for the direct solution of large,
+    sparse, nonsymmetric systems of linear equations on high performance
+    machines. SuperLU_MT is designed for shared memory parallel machines."""
+
+    homepage = "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/#superlu_mt"
+    url      = "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/superlu_mt_3.1.tar.gz"
+
+    version('3.1', '06ac62f1b4b7d17123fffa0d0c315e91')
+
+    variant('blas',    default=True,  description='Build with external BLAS library')
+
+    # Must choose one or the other
+    variant('openmp',  default=False, description='Build with OpenMP support')
+    variant('pthread', default=True,  description='Build with POSIX threads support')
+
+    # NOTE: must link with a single-threaded BLAS library
+    depends_on('blas', when='+blas')
+
+    # Cannot be built in parallel
+    parallel = False
+
+    def configure(self, spec):
+        # Validate chosen variants
+        if '+openmp' in spec and '+pthread' in spec:
+            msg = 'You cannot choose both +openmp and +pthread'
+            raise RuntimeError(msg)
+        if '~openmp' in spec and '~pthread' in spec:
+            msg = 'You must choose either +openmp or +pthread'
+            raise RuntimeError(msg)
+
+        # List of configuration options
+        config = []
+
+        # The machine (platform) identifier to append to the library names
+        if '+openmp' in spec:
+            # OpenMP
+            config.extend([
+                'PLAT       = _OPENMP',
+                'TMGLIB     = libtmglib.a',
+                'MPLIB      = {0}'.format(self.compiler.openmp_flag),
+                'CFLAGS     = {0}'.format(self.compiler.openmp_flag),
+                'FFLAGS     = {0}'.format(self.compiler.openmp_flag)
+            ])
+        elif '+pthread' in spec:
+            # POSIX threads
+            config.extend([
+                'PLAT       = _PTHREAD',
+                'TMGLIB     = libtmglib$(PLAT).a',
+                'MPLIB      = -lpthread'
+            ])
+
+        # The BLAS library
+        # NOTE: must link with a single-threaded BLAS library
+        if '+blas' in spec:
+            config.extend([
+                'BLASDEF    = -DUSE_VENDOR_BLAS',
+                'BLASLIB    = -L{0} -lblas'.format(spec['blas'].prefix.lib)
+            ])
+        else:
+            config.append('BLASLIB    = ../lib/libblas$(PLAT).a')
+
+        # Generic options
+        config.extend([
+            # The name of the libraries to be created/linked to
+            'SUPERLULIB = libsuperlu_mt$(PLAT).a',
+            'MATHLIB    = -lm',
+            # The archiver and the flag(s) to use when building archives
+            'ARCH       = ar',
+            'ARCHFLAGS  = cr',
+            'RANLIB     = {0}'.format('ranlib' if which('ranlib') else 'echo'),
+            # Definitions used by CPP
+            'PREDEFS    = -D_$(PLAT)',
+            # Compilers and flags
+            'CC         = {0}'.format(os.environ['CC']),
+            'CFLAGS    += $(PREDEFS) -D_LONGINT',
+            'NOOPTS     = -O0',
+            'FORTRAN    = {0}'.format(os.environ['FC']),
+            'LOADER     = {0}'.format(os.environ['CC']),
+            # C preprocessor defs for compilation
+            'CDEFS      = -DAdd_'
+        ])
+
+        # Write configuration options to include file
+        with open('make.inc', 'w') as inc:
+            for option in config:
+                inc.write('{0}\n'.format(option))
+
+    def install(self, spec, prefix):
+        # Set up make include file manually
+        self.configure(spec)
+
+        # BLAS needs to be compiled separately if using internal BLAS library
+        if '+blas' not in spec:
+            make('blaslib')
+
+        make()
+
+        # Install manually
+        install_tree('lib', prefix.lib)
+
+        headers = glob.glob(join_path('SRC', '*.h'))
+        mkdir(prefix.include)
+        for h in headers:
+            install(h, prefix.include)