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-rw-r--r--var/spack/mock_configs/site_spackconfig/compilers.yaml40
-rw-r--r--var/spack/packages/adios/package.py38
-rw-r--r--var/spack/packages/mxml/package.py26
-rw-r--r--var/spack/repos/builtin.mock/packages/externalmodule/package.py37
-rw-r--r--var/spack/repos/builtin.mock/packages/multimethod/package.py42
-rw-r--r--var/spack/repos/builtin/packages/R/package.py63
-rw-r--r--var/spack/repos/builtin/packages/armadillo/package.py67
-rw-r--r--var/spack/repos/builtin/packages/arpack/package.py40
-rw-r--r--var/spack/repos/builtin/packages/bertini/package.py50
-rw-r--r--var/spack/repos/builtin/packages/binutils/package.py3
-rw-r--r--var/spack/repos/builtin/packages/boost/package.py79
-rw-r--r--var/spack/repos/builtin/packages/c-blosc/package.py51
-rw-r--r--var/spack/repos/builtin/packages/caliper/package.py2
-rw-r--r--var/spack/repos/builtin/packages/daal/package.py28
-rw-r--r--var/spack/repos/builtin/packages/dealii/package.py35
-rw-r--r--var/spack/repos/builtin/packages/espresso/package.py26
-rw-r--r--var/spack/repos/builtin/packages/ferret/package.py103
-rw-r--r--var/spack/repos/builtin/packages/hdf5-blosc/package.py206
-rw-r--r--var/spack/repos/builtin/packages/hpl/package.py119
-rw-r--r--var/spack/repos/builtin/packages/intel-parallel-studio/package.py144
-rw-r--r--var/spack/repos/builtin/packages/intel/package.py125
-rw-r--r--var/spack/repos/builtin/packages/ipp/package.py26
-rw-r--r--var/spack/repos/builtin/packages/libpciaccess/package.py2
-rw-r--r--var/spack/repos/builtin/packages/libpthread-stubs/package.py39
-rw-r--r--var/spack/repos/builtin/packages/libxau/package.py44
-rw-r--r--var/spack/repos/builtin/packages/libxcb/package.py7
-rw-r--r--var/spack/repos/builtin/packages/llvm/package.py12
-rw-r--r--var/spack/repos/builtin/packages/lua/package.py2
-rw-r--r--var/spack/repos/builtin/packages/mkl/package.py28
-rw-r--r--var/spack/repos/builtin/packages/openblas/package.py7
-rw-r--r--var/spack/repos/builtin/packages/openmpi/package.py10
-rw-r--r--var/spack/repos/builtin/packages/openssl/package.py2
-rw-r--r--var/spack/repos/builtin/packages/pcre/intel.patch12
-rw-r--r--var/spack/repos/builtin/packages/pcre/package.py14
-rw-r--r--var/spack/repos/builtin/packages/petsc/package.py50
-rw-r--r--var/spack/repos/builtin/packages/py-astropy/package.py35
-rw-r--r--var/spack/repos/builtin/packages/py-beautifulsoup4/package.py41
-rw-r--r--var/spack/repos/builtin/packages/py-emcee/package.py41
-rw-r--r--var/spack/repos/builtin/packages/py-h5py/package.py39
-rw-r--r--var/spack/repos/builtin/packages/py-iminuit/package.py46
-rw-r--r--var/spack/repos/builtin/packages/py-nestle/package.py44
-rw-r--r--var/spack/repos/builtin/packages/py-sncosmo/package.py51
-rw-r--r--var/spack/repos/builtin/packages/py-wcsaxes/package.py43
-rw-r--r--var/spack/repos/builtin/packages/python/package.py193
-rw-r--r--var/spack/repos/builtin/packages/r-BiocGenerics/package.py28
-rw-r--r--var/spack/repos/builtin/packages/r-R6/package.py46
-rw-r--r--var/spack/repos/builtin/packages/r-abind/package.py8
-rw-r--r--var/spack/repos/builtin/packages/r-curl/package.py51
-rw-r--r--var/spack/repos/builtin/packages/r-devtools/package.py50
-rw-r--r--var/spack/repos/builtin/packages/r-digest/package.py56
-rw-r--r--var/spack/repos/builtin/packages/r-filehash/package.py7
-rw-r--r--var/spack/repos/builtin/packages/r-git2r/package.py46
-rw-r--r--var/spack/repos/builtin/packages/r-httr/package.py49
-rw-r--r--var/spack/repos/builtin/packages/r-jsonlite/package.py50
-rw-r--r--var/spack/repos/builtin/packages/r-magic/package.py7
-rw-r--r--var/spack/repos/builtin/packages/r-memoise/package.py44
-rw-r--r--var/spack/repos/builtin/packages/r-mime/package.py42
-rw-r--r--var/spack/repos/builtin/packages/r-openssl/package.py52
-rw-r--r--var/spack/repos/builtin/packages/r-packrat/package.py42
-rw-r--r--var/spack/repos/builtin/packages/r-rstudioapi/package.py42
-rw-r--r--var/spack/repos/builtin/packages/r-whisker/package.py42
-rw-r--r--var/spack/repos/builtin/packages/r-withr/package.py44
-rw-r--r--var/spack/repos/builtin/packages/serf/package.py11
-rw-r--r--var/spack/repos/builtin/packages/slepc/package.py13
-rw-r--r--var/spack/repos/builtin/packages/superlu-dist/package.py47
-rw-r--r--var/spack/repos/builtin/packages/superlu/package.py54
-rw-r--r--var/spack/repos/builtin/packages/tmux/package.py17
-rw-r--r--var/spack/repos/builtin/packages/trilinos/package.py210
-rw-r--r--var/spack/repos/builtin/packages/xorg-util-macros/package.py38
-rw-r--r--var/spack/repos/builtin/packages/xproto/package.py41
70 files changed, 2856 insertions, 393 deletions
diff --git a/var/spack/mock_configs/site_spackconfig/compilers.yaml b/var/spack/mock_configs/site_spackconfig/compilers.yaml
new file mode 100644
index 0000000000..5f8b38007b
--- /dev/null
+++ b/var/spack/mock_configs/site_spackconfig/compilers.yaml
@@ -0,0 +1,40 @@
+compilers:
+ all:
+ clang@3.3:
+ cc: /path/to/clang
+ cxx: /path/to/clang++
+ f77: None
+ fc: None
+ modules: None
+ strategy: PATH
+ gcc@4.5.0:
+ cc: /path/to/gcc
+ cxx: /path/to/g++
+ f77: /path/to/gfortran
+ fc: /path/to/gfortran
+ modules: None
+ strategy: PATH
+ gcc@5.2.0:
+ cc: cc
+ cxx: CC
+ f77: ftn
+ fc: ftn
+ modules:
+ - PrgEnv-gnu
+ - gcc/5.2.0
+ strategy: MODULES
+ intel@15.0.1:
+ cc: cc
+ ccx: CC
+ f77: ftn
+ fc: ftn
+ modules:
+ - PrgEnv-intel
+ - intel/15.0.1
+ strategy: MODULES
+ intel@15.1.2:
+ cc: /path/to/icc
+ cxx: /path/to/ic++
+ f77: /path/to/ifort
+ fc: /path/to/ifort
+ strategy: PATH \ No newline at end of file
diff --git a/var/spack/packages/adios/package.py b/var/spack/packages/adios/package.py
new file mode 100644
index 0000000000..260dcbe851
--- /dev/null
+++ b/var/spack/packages/adios/package.py
@@ -0,0 +1,38 @@
+import os
+
+from spack import *
+class Adios(Package):
+ """The Adaptable IO System (ADIOS) provides a simple,
+ flexible way for scientists to describe the
+ data in their code that may need to be written,
+ read, or processed outside of the running simulation
+ """
+
+ homepage = "http://www.olcf.ornl.gov/center-projects/adios/"
+ url = "http://users.nccs.gov/~pnorbert/adios-1.9.0.tar.gz"
+
+ version('1.9.0', 'dbf5cb10e32add2f04c9b4052b7ffa76')
+
+ # Lots of setting up here for this package
+ # module swap PrgEnv-intel PrgEnv-$COMP
+ # module load cray-netcdf/4.3.3.1
+ # module load cray-hdf5/1.8.14
+ # module load python/2.7.10
+ depends_on('hdf5')
+ depends_on('mxml')
+
+ def install(self, spec, prefix):
+ configure_args = ["--prefix=%s" % prefix,
+ "--with-mxml=%s" % spec['mxml'].prefix,
+ "--with-hdf5=%s" % spec['hdf5'].prefix,
+ "--with-netcdf=%s" % os.environ["NETCDF_DIR"],
+ "--with-infiniband=no",
+ "MPICC=cc","MPICXX=CC","MPIFC=ftn",
+ "CPPFLAGS=-DMPICH_IGNORE_CXX_SEEK"]
+
+ if spec.satisfies('%gcc'):
+ configure_args.extend(["CC=gcc", "CXX=g++", "FC=gfortran"])
+
+ configure(*configure_args)
+ make()
+ make("install")
diff --git a/var/spack/packages/mxml/package.py b/var/spack/packages/mxml/package.py
new file mode 100644
index 0000000000..f79251d312
--- /dev/null
+++ b/var/spack/packages/mxml/package.py
@@ -0,0 +1,26 @@
+import os
+from spack import *
+
+class Mxml(Package):
+ """Mini-XML is a small XML library that you can use to read and write XML
+ and XML-like data files in your application without requiring large
+ non-standard libraries
+ """
+
+ homepage = "http://www.msweet.org"
+ url = "http://www.msweet.org/files/project3/mxml-2.9.tar.gz"
+
+ version('2.9', 'e21cad0f7aacd18f942aa0568a8dee19')
+ version('2.8', 'd85ee6d30de053581242c4a86e79a5d2')
+ version('2.7', '76f2ae49bf0f5745d5cb5d9507774dc9')
+ version('2.6', '68977789ae64985dddbd1a1a1652642e')
+ version('2.5', 'f706377fba630b39fa02fd63642b17e5')
+
+ # module swap PrgEnv-intel PrgEnv-$COMP (Can use whatever compiler you want to use)
+ # Case statement to change CC and CXX flags
+
+ def install(self, spec, prefix):
+ configure('--prefix=%s' % prefix, "--disable-shared", 'CFLAGS=-static')
+ make()
+ make("install")
+
diff --git a/var/spack/repos/builtin.mock/packages/externalmodule/package.py b/var/spack/repos/builtin.mock/packages/externalmodule/package.py
new file mode 100644
index 0000000000..f7b0da3fd9
--- /dev/null
+++ b/var/spack/repos/builtin.mock/packages/externalmodule/package.py
@@ -0,0 +1,37 @@
+
+##############################################################################
+# 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 Externalmodule(Package):
+ homepage = "http://somewhere.com"
+ url = "http://somewhere.com/module-1.0.tar.gz"
+
+ version('1.0', '1234567890abcdef1234567890abcdef')
+
+ depends_on('externalprereq')
+
+ def install(self, spec, prefix):
+ pass
diff --git a/var/spack/repos/builtin.mock/packages/multimethod/package.py b/var/spack/repos/builtin.mock/packages/multimethod/package.py
index def73ad82e..649afa5945 100644
--- a/var/spack/repos/builtin.mock/packages/multimethod/package.py
+++ b/var/spack/repos/builtin.mock/packages/multimethod/package.py
@@ -22,8 +22,11 @@
# 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 imp
+from llnl.util.filesystem import join_path
+from spack.util.naming import mod_to_class
from spack import *
-
+import spack.architecture
class Multimethod(Package):
"""This package is designed for use with Spack's multimethod test.
@@ -101,25 +104,26 @@ class Multimethod(Package):
#
- # Make sure we can switch methods on different architectures
+ # Make sure we can switch methods on different target
#
- @when('arch=x86_64')
- def different_by_architecture(self):
- return 'x86_64'
-
- @when('arch=ppc64')
- def different_by_architecture(self):
- return 'ppc64'
-
- @when('arch=ppc32')
- def different_by_architecture(self):
- return 'ppc32'
-
- @when('arch=arm64')
- def different_by_architecture(self):
- return 'arm64'
-
-
+# for platform_name in ['cray_xc', 'darwin', 'linux']:
+# file_path = join_path(spack.platform_path, platform_name)
+# platform_mod = imp.load_source('spack.platforms', file_path + '.py')
+# cls = getattr(platform_mod, mod_to_class(platform_name))
+
+# platform = cls()
+ platform = spack.architecture.sys_type()
+ targets = platform.targets.values()
+ if len(targets) > 1:
+ targets = targets[:-1]
+
+ for target in targets:
+ @when('target='+target.name)
+ def different_by_target(self):
+ if isinstance(self.spec.architecture.target,basestring):
+ return self.spec.architecture.target
+ else:
+ return self.spec.architecture.target.name
#
# Make sure we can switch methods on different dependencies
#
diff --git a/var/spack/repos/builtin/packages/R/package.py b/var/spack/repos/builtin/packages/R/package.py
index 0177fe1a2b..001dde5329 100644
--- a/var/spack/repos/builtin/packages/R/package.py
+++ b/var/spack/repos/builtin/packages/R/package.py
@@ -22,30 +22,25 @@
# 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 functools
-import glob
-import inspect
import os
-import re
-from contextlib import closing
-import spack
-from llnl.util.lang import match_predicate
from spack import *
from spack.util.environment import *
class R(Package):
- """
- R is 'GNU S', a freely available language and environment for statistical computing and graphics which provides a
- wide variety of statistical and graphical techniques: linear and nonlinear modelling, statistical tests, time series
- analysis, classification, clustering, etc. Please consult the R project homepage for further information.
- """
+ """R is 'GNU S', a freely available language and environment for
+ statistical computing and graphics which provides a wide variety of
+ statistical and graphical techniques: linear and nonlinear modelling,
+ statistical tests, time series analysis, classification, clustering, etc.
+ Please consult the R project homepage for further information."""
+
homepage = "https://www.r-project.org"
url = "http://cran.cnr.berkeley.edu/src/base/R-3/R-3.1.2.tar.gz"
-
+
extendable = True
+ version('3.3.0', '5a7506c8813432d1621c9725e86baf7a')
version('3.2.3', '1ba3dac113efab69e706902810cc2970')
version('3.2.2', '57cef5c2e210a5454da1979562a10e5b')
version('3.2.1', 'c2aac8b40f84e08e7f8c9068de9239a3')
@@ -53,7 +48,8 @@ class R(Package):
version('3.1.3', '53a85b884925aa6b5811dfc361d73fc4')
version('3.1.2', '3af29ec06704cbd08d4ba8d69250ae74')
- variant('external-lapack', default=False, description='Links to externally installed BLAS/LAPACK')
+ variant('external-lapack', default=False,
+ description='Links to externally installed BLAS/LAPACK')
# Virtual dependencies
depends_on('blas', when='+external-lapack')
@@ -65,6 +61,7 @@ class R(Package):
depends_on('icu')
depends_on('glib')
depends_on('zlib')
+ depends_on('bzip2')
depends_on('libtiff')
depends_on('jpeg')
depends_on('cairo')
@@ -72,18 +69,21 @@ class R(Package):
depends_on('freetype')
depends_on('tcl')
depends_on('tk')
+ depends_on('curl')
+ depends_on('pcre')
+ depends_on('jdk')
def install(self, spec, prefix):
rlibdir = join_path(prefix, 'rlib')
- options = ['--prefix=%s' % prefix,
- '--libdir=%s' % rlibdir,
- '--enable-R-shlib',
- '--enable-BLAS-shlib',
- '--enable-R-framework=no']
+ configure_args = ['--prefix=%s' % prefix,
+ '--libdir=%s' % rlibdir,
+ '--enable-R-shlib',
+ '--enable-BLAS-shlib',
+ '--enable-R-framework=no']
if '+external-lapack' in spec:
- options.extend(['--with-blas', '--with-lapack'])
+ configure_args.extend(['--with-blas', '--with-lapack'])
- configure(*options)
+ configure(*configure_args)
make()
make('install')
@@ -106,25 +106,24 @@ class R(Package):
r_libs_path = ':'.join(r_libs_path)
spack_env.set('R_LIBS', r_libs_path)
- # For run time environment set only the path for extension_spec and prepend it to R_LIBS
+ # For run time environment set only the path for extension_spec and
+ # prepend it to R_LIBS
if extension_spec.package.extends(self.spec):
- run_env.prepend_path('R_LIBS', os.path.join(extension_spec.prefix, self.r_lib_dir))
-
+ run_env.prepend_path('R_LIBS', os.path.join(
+ extension_spec.prefix, self.r_lib_dir))
def setup_dependent_package(self, module, ext_spec):
- """
- Called before R modules' install() methods.
-
- In most cases, extensions will only need to have one line::
-
- R('CMD', 'INSTALL', '--library=%s' % self.module.r_lib_dir, '%s' % self.stage.archive_file)
- """
+ """Called before R modules' install() methods. In most cases,
+ extensions will only need to have one line:
+ R('CMD', 'INSTALL', '--library=%s' % self.module.r_lib_dir, '%s' %
+ self.stage.source_path)"""
# R extension builds can have a global R executable function
module.R = Executable(join_path(self.spec.prefix.bin, 'R'))
# Add variable for library directry
module.r_lib_dir = os.path.join(ext_spec.prefix, self.r_lib_dir)
- # Make the site packages directory for extensions, if it does not exist already.
+ # Make the site packages directory for extensions, if it does not exist
+ # already.
if ext_spec.package.is_extension:
mkdirp(module.r_lib_dir)
diff --git a/var/spack/repos/builtin/packages/armadillo/package.py b/var/spack/repos/builtin/packages/armadillo/package.py
new file mode 100644
index 0000000000..b3e5994e30
--- /dev/null
+++ b/var/spack/repos/builtin/packages/armadillo/package.py
@@ -0,0 +1,67 @@
+##############################################################################
+# 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 Armadillo(Package):
+ """Armadillo is a high quality linear algebra library (matrix maths)
+ for the C++ language, aiming towards a good balance between speed and
+ ease of use."""
+
+ homepage = "http://arma.sourceforge.net/"
+ url = "http://sourceforge.net/projects/arma/files/armadillo-7.200.1.tar.xz"
+
+ version('7.200.1', 'ed86d6df0058979e107502e1fe3e469e')
+
+ variant('hdf5', default=False, description='Include HDF5 support')
+
+ depends_on('arpack')
+ depends_on('blas')
+ depends_on('lapack')
+ depends_on('superlu@5.2:')
+ depends_on('hdf5', when='+hdf5')
+
+ def install(self, spec, prefix):
+ cmake_args = [
+ # ARPACK support
+ '-DARPACK_LIBRARY={0}/libarpack.a'.format(
+ spec['arpack'].prefix.lib),
+ # BLAS support
+ '-DBLAS_LIBRARY={0}'.format(spec['blas'].blas_shared_lib),
+ # LAPACK support
+ '-DLAPACK_LIBRARY={0}'.format(spec['lapack'].lapack_shared_lib),
+ # SuperLU support
+ '-DSuperLU_INCLUDE_DIR={0}'.format(spec['superlu'].prefix.include),
+ '-DSuperLU_LIBRARY={0}/libsuperlu.a'.format(
+ spec['superlu'].prefix.lib64),
+ # HDF5 support
+ '-DDETECT_HDF5={0}'.format('ON' if '+hdf5' in spec else 'OFF')
+ ]
+
+ cmake_args.extend(std_cmake_args)
+ cmake('.', *cmake_args)
+
+ make()
+ make('install')
diff --git a/var/spack/repos/builtin/packages/arpack/package.py b/var/spack/repos/builtin/packages/arpack/package.py
index 75158776fe..91b5f06a4a 100644
--- a/var/spack/repos/builtin/packages/arpack/package.py
+++ b/var/spack/repos/builtin/packages/arpack/package.py
@@ -24,12 +24,12 @@
##############################################################################
from spack import *
import os
-import shutil
+
class Arpack(Package):
"""A collection of Fortran77 subroutines designed to solve large scale
- eigenvalue problems.
- """
+ eigenvalue problems."""
+
homepage = "http://www.caam.rice.edu/software/ARPACK/"
url = "http://www.caam.rice.edu/software/ARPACK/SRC/arpack96.tar.gz"
@@ -39,27 +39,35 @@ class Arpack(Package):
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')
+ # Section 1: Paths and Libraries
+
+ # Change the build directory
+ makefile.filter('^home.*', 'home = %s' % os.getcwd())
+
+ # Use external BLAS/LAPACK
+ makefile.filter('^BLASdir.*',
+ 'BLASdir = %s' % self.spec['blas'].prefix)
+ makefile.filter('^LAPACKdir.*',
+ 'LAPACKdir = %s' % self.spec['lapack'].prefix)
+
+ # Do not include the platform in the library name
+ makefile.filter('^PLAT.*', 'PLAT = ')
+ makefile.filter('^ARPACKLIB.*', 'ARPACKLIB = $(home)/libarpack.a')
- # 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)
+ # Section 2: Compilers
- # build the library in our own prefix.
- makefile.filter('^ARPACKLIB.*', 'ARPACKLIB = %s/libarpack.a' % os.getcwd())
+ # Be sure to use the Spack compiler wrapper
+ makefile.filter('^FC.*', 'FC = {0}'.format(os.environ['F77']))
+ makefile.filter('^FFLAGS.*', 'FFLAGS = -O2 -g -fPIC')
+ if not which('ranlib'):
+ makefile.filter('^RANLIB.*', 'RANLIB = touch')
def install(self, spec, prefix):
with working_dir('SRC'):
make('all')
- mkdirp(prefix.lib)
+ mkdir(prefix.lib)
install('libarpack.a', prefix.lib)
diff --git a/var/spack/repos/builtin/packages/bertini/package.py b/var/spack/repos/builtin/packages/bertini/package.py
new file mode 100644
index 0000000000..8d7da705e4
--- /dev/null
+++ b/var/spack/repos/builtin/packages/bertini/package.py
@@ -0,0 +1,50 @@
+##############################################################################
+# 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 Bertini(Package):
+ """Bertini is a general-purpose solver, written in C, that was created
+ for research about polynomial continuation. It solves for the numerical
+ solution of systems of polynomial equations using homotopy continuation."""
+
+ homepage = "https://bertini.nd.edu/"
+ url = "https://bertini.nd.edu/BertiniSource_v1.5.tar.gz"
+
+ version('1.5', 'e3f6cc6e7f9a0cf1d73185e8671af707')
+
+ variant('mpi', default=True, description='Compile in parallel')
+
+ depends_on('flex')
+ depends_on('bison')
+ depends_on('gmp')
+ depends_on('mpfr')
+ depends_on('mpi', when='+mpi')
+
+ def install(self, spec, prefix):
+ configure('--prefix=%s' % prefix)
+
+ make()
+ make("install")
diff --git a/var/spack/repos/builtin/packages/binutils/package.py b/var/spack/repos/builtin/packages/binutils/package.py
index 9e4cc98ae6..5f305abb02 100644
--- a/var/spack/repos/builtin/packages/binutils/package.py
+++ b/var/spack/repos/builtin/packages/binutils/package.py
@@ -30,8 +30,9 @@ class Binutils(Package):
url="https://ftp.gnu.org/gnu/binutils/binutils-2.25.tar.bz2"
+ # 2.26 is incompatible with py-pillow build for some reason.
version('2.26', '64146a0faa3b411ba774f47d41de239f')
- version('2.25', 'd9f3303f802a5b6b0bb73a335ab89d66')
+ version('2.25', 'd9f3303f802a5b6b0bb73a335ab89d66', preferred=True)
version('2.24', 'e0f71a7b2ddab0f8612336ac81d9636b')
version('2.23.2', '4f8fa651e35ef262edc01d60fb45702e')
version('2.20.1', '2b9dc8f2b7dbd5ec5992c6e29de0b764')
diff --git a/var/spack/repos/builtin/packages/boost/package.py b/var/spack/repos/builtin/packages/boost/package.py
index 2f2965eb12..cde76c590a 100644
--- a/var/spack/repos/builtin/packages/boost/package.py
+++ b/var/spack/repos/builtin/packages/boost/package.py
@@ -27,7 +27,7 @@ import spack
import sys
import os
-import sys
+
class Boost(Package):
"""Boost provides free peer-reviewed portable C++ source
@@ -75,23 +75,23 @@ class Boost(Package):
version('1.34.0', 'ed5b9291ffad776f8757a916e1726ad0')
default_install_libs = set(['atomic',
- 'chrono',
- 'date_time',
- 'filesystem',
- 'graph',
- 'iostreams',
- 'locale',
- 'log',
- 'math',
- 'program_options',
- 'random',
- 'regex',
- 'serialization',
- 'signals',
- 'system',
- 'test',
- 'thread',
- 'wave'])
+ 'chrono',
+ 'date_time',
+ 'filesystem',
+ 'graph',
+ 'iostreams',
+ 'locale',
+ 'log',
+ 'math',
+ 'program_options',
+ 'random',
+ 'regex',
+ 'serialization',
+ 'signals',
+ 'system',
+ 'test',
+ 'thread',
+ 'wave'])
# mpi/python are not installed by default because they pull in many
# dependencies and/or because there is a great deal of customization
@@ -109,6 +109,7 @@ class Boost(Package):
variant('multithreaded', default=True, description="Build multi-threaded versions of libraries")
variant('singlethreaded', default=True, description="Build single-threaded versions of libraries")
variant('icu_support', default=False, description="Include ICU support (for regex/locale libraries)")
+ variant('graph', default=False, description="Build the Boost Graph library")
depends_on('icu', when='+icu_support')
depends_on('python', when='+python')
@@ -120,15 +121,18 @@ class Boost(Package):
patch('boost_11856.patch', when='@1.60.0%gcc@4.4.7')
def url_for_version(self, version):
- """Handle Boost's weird URLs, which write the version two different ways."""
+ """
+ Handle Boost's weird URLs,
+ which write the version two different ways.
+ """
parts = [str(p) for p in Version(version)]
dots = ".".join(parts)
underscores = "_".join(parts)
- return "http://downloads.sourceforge.net/project/boost/boost/%s/boost_%s.tar.bz2" % (
- dots, underscores)
+ return "http://downloads.sourceforge.net/project/boost" \
+ "/boost/%s/boost_%s.tar.bz2" % (dots, underscores)
def determine_toolset(self, spec):
- if spec.satisfies("arch=darwin-x86_64"):
+ if spec.satisfies("platform=darwin"):
return 'darwin'
toolsets = {'g++': 'gcc',
@@ -149,20 +153,20 @@ class Boost(Package):
if '+python' in spec:
options.append('--with-python=%s' %
- join_path(spec['python'].prefix.bin, 'python'))
+ join_path(spec['python'].prefix.bin, 'python'))
with open('user-config.jam', 'w') as f:
compiler_wrapper = join_path(spack.build_env_path, 'c++')
f.write("using {0} : : {1} ;\n".format(boostToolsetId,
- compiler_wrapper))
+ compiler_wrapper))
if '+mpi' in spec:
f.write('using mpi : %s ;\n' %
- join_path(spec['mpi'].prefix.bin, 'mpicxx'))
+ join_path(spec['mpi'].prefix.bin, 'mpicxx'))
if '+python' in spec:
f.write('using python : %s : %s ;\n' %
- (spec['python'].version,
- join_path(spec['python'].prefix.bin, 'python')))
+ (spec['python'].version,
+ join_path(spec['python'].prefix.bin, 'python')))
def determine_b2_options(self, spec, options):
if '+debug' in spec:
@@ -178,8 +182,7 @@ class Boost(Package):
'-s', 'BZIP2_INCLUDE=%s' % spec['bzip2'].prefix.include,
'-s', 'BZIP2_LIBPATH=%s' % spec['bzip2'].prefix.lib,
'-s', 'ZLIB_INCLUDE=%s' % spec['zlib'].prefix.include,
- '-s', 'ZLIB_LIBPATH=%s' % spec['zlib'].prefix.lib,
- ])
+ '-s', 'ZLIB_LIBPATH=%s' % spec['zlib'].prefix.lib])
linkTypes = ['static']
if '+shared' in spec:
@@ -191,7 +194,8 @@ class Boost(Package):
if '+singlethreaded' in spec:
threadingOpts.append('single')
if not threadingOpts:
- raise RuntimeError("At least one of {singlethreaded, multithreaded} must be enabled")
+ raise RuntimeError("""At least one of {singlethreaded,
+ multithreaded} must be enabled""")
options.extend([
'toolset=%s' % self.determine_toolset(spec),
@@ -202,9 +206,9 @@ class Boost(Package):
def install(self, spec, prefix):
# On Darwin, Boost expects the Darwin libtool. However, one of the
- # dependencies may have pulled in Spack's GNU libtool, and these two are
- # not compatible. We thus create a symlink to Darwin's libtool and add
- # it at the beginning of PATH.
+ # dependencies may have pulled in Spack's GNU libtool, and these two
+ # are not compatible. We thus create a symlink to Darwin's libtool
+ # and add it at the beginning of PATH.
if sys.platform == 'darwin':
newdir = os.path.abspath('darwin-libtool')
mkdirp(newdir)
@@ -217,7 +221,8 @@ class Boost(Package):
withLibs.append(lib)
if not withLibs:
# if no libraries are specified for compilation, then you dont have
- # to configure/build anything, just copy over to the prefix directory.
+ # to configure/build anything, just copy over to the prefix
+ # directory.
src = join_path(self.stage.source_path, 'boost')
mkdirp(join_path(prefix, 'include'))
dst = join_path(prefix, 'include', 'boost')
@@ -235,6 +240,9 @@ class Boost(Package):
withLibs.remove('chrono')
if not spec.satisfies('@1.43.0:'):
withLibs.remove('random')
+ if '+graph' in spec and '+mpi' in spec:
+ withLibs.remove('graph')
+ withLibs.append('graph_parallel')
# to make Boost find the user-config.jam
env['BOOST_BUILD_PATH'] = './'
@@ -259,6 +267,7 @@ class Boost(Package):
for threadingOpt in threadingOpts:
b2('install', 'threading=%s' % threadingOpt, *b2_options)
- # The shared libraries are not installed correctly on Darwin; correct this
+ # The shared libraries are 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/c-blosc/package.py b/var/spack/repos/builtin/packages/c-blosc/package.py
new file mode 100644
index 0000000000..dee332be14
--- /dev/null
+++ b/var/spack/repos/builtin/packages/c-blosc/package.py
@@ -0,0 +1,51 @@
+##############################################################################
+# 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
+##############################################################################
+
+import sys
+
+from spack import *
+
+class CBlosc(Package):
+ """Blosc, an extremely fast, multi-threaded, meta-compressor library"""
+ homepage = "http://www.blosc.org"
+ url = "https://github.com/Blosc/c-blosc/archive/v1.9.2.tar.gz"
+
+ version('1.9.2', 'dd2d83069d74b36b8093f1c6b49defc5')
+ version('1.9.1', '7d708d3daadfacf984a87b71b1734ce2')
+ version('1.9.0', 'e4c1dc8e2c468e5cfa2bf05eeee5357a')
+ version('1.8.1', 'd73d5be01359cf271e9386c90dcf5b05')
+ version('1.8.0', '5b92ecb287695ba20cc33d30bf221c4f')
+
+ depends_on("cmake")
+ depends_on("snappy")
+ depends_on("zlib")
+
+ def install(self, spec, prefix):
+ cmake('.', *std_cmake_args)
+
+ make()
+ make("install")
+ if sys.platform == 'darwin':
+ fix_darwin_install_name(prefix.lib)
diff --git a/var/spack/repos/builtin/packages/caliper/package.py b/var/spack/repos/builtin/packages/caliper/package.py
index 4b8fe0d8af..a424c73859 100644
--- a/var/spack/repos/builtin/packages/caliper/package.py
+++ b/var/spack/repos/builtin/packages/caliper/package.py
@@ -34,7 +34,7 @@ class Caliper(Package):
homepage = "https://github.com/LLNL/Caliper"
url = ""
- version('master', git='ssh://git@github.com:LLNL/Caliper.git')
+ version('master', git='https://github.com/LLNL/Caliper.git')
variant('mpi', default=False, description='Enable MPI function wrappers.')
diff --git a/var/spack/repos/builtin/packages/daal/package.py b/var/spack/repos/builtin/packages/daal/package.py
new file mode 100644
index 0000000000..e13dd80e19
--- /dev/null
+++ b/var/spack/repos/builtin/packages/daal/package.py
@@ -0,0 +1,28 @@
+from spack import *
+import os
+
+from spack.pkg.builtin.intel import IntelInstaller
+
+
+class Daal(IntelInstaller):
+ """Intel Data Analytics Acceleration Library.
+
+ Note: You will have to add the download file to a
+ mirror so that Spack can find it. For instructions on how to set up a
+ mirror, see http://software.llnl.gov/spack/mirrors.html"""
+
+ homepage = "https://software.intel.com/en-us/daal"
+
+ version('2016.2.181', 'aad2aa70e5599ebfe6f85b29d8719d46',
+ url="file://%s/l_daal_2016.2.181.tgz" % os.getcwd())
+ version('2016.3.210', 'ad747c0dd97dace4cad03cf2266cad28',
+ url="file://%s/l_daal_2016.3.210.tgz" % os.getcwd())
+
+ def install(self, spec, prefix):
+
+ self.intel_prefix = os.path.join(prefix, "pkg")
+ IntelInstaller.install(self, spec, prefix)
+
+ daal_dir = os.path.join(self.intel_prefix, "daal")
+ for f in os.listdir(daal_dir):
+ os.symlink(os.path.join(daal_dir, f), os.path.join(self.prefix, f))
diff --git a/var/spack/repos/builtin/packages/dealii/package.py b/var/spack/repos/builtin/packages/dealii/package.py
index 54b6426d36..23ec74abed 100644
--- a/var/spack/repos/builtin/packages/dealii/package.py
+++ b/var/spack/repos/builtin/packages/dealii/package.py
@@ -80,8 +80,8 @@ class Dealii(Package):
depends_on("netcdf-cxx", when='+netcdf+mpi')
depends_on("oce", when='+oce')
depends_on("p4est", when='+p4est+mpi')
- depends_on("petsc+mpi", when='+petsc+mpi')
- depends_on("slepc", when='+slepc+petsc+mpi')
+ depends_on("petsc@:3.6.4+mpi", when='+petsc+mpi') # FIXME: update after 3.7 is supported upstream. # NOQA: ignore=E501
+ depends_on("slepc@:3.6.3", when='+slepc+petsc+mpi')
depends_on("trilinos", when='+trilinos+mpi')
# developer dependnecies
@@ -108,12 +108,11 @@ class Dealii(Package):
# of Spack's. Be more specific to avoid this.
# Note that both lapack and blas are provided in -DLAPACK_XYZ.
'-DLAPACK_FOUND=true',
- '-DLAPACK_INCLUDE_DIRS=%s;%s' %
- (spec['lapack'].prefix.include,
- spec['blas'].prefix.include),
- '-DLAPACK_LIBRARIES=%s;%s' %
- (spec['lapack'].lapack_shared_lib,
- spec['blas'].blas_shared_lib),
+ '-DLAPACK_INCLUDE_DIRS=%s;%s' % (
+ spec['lapack'].prefix.include, spec['blas'].prefix.include),
+ '-DLAPACK_LIBRARIES=%s;%s' % (
+ spec['lapack'].lapack_shared_lib,
+ spec['blas'].blas_shared_lib),
'-DMUPARSER_DIR=%s' % spec['muparser'].prefix,
'-DUMFPACK_DIR=%s' % spec['suite-sparse'].prefix,
'-DTBB_DIR=%s' % spec['tbb'].prefix,
@@ -168,14 +167,14 @@ class Dealii(Package):
if '+netcdf' in spec:
options.extend([
'-DNETCDF_FOUND=true',
- '-DNETCDF_LIBRARIES=%s;%s' %
- (join_path(spec['netcdf-cxx'].prefix.lib,
- 'libnetcdf_c++.%s' % dsuf),
- join_path(spec['netcdf'].prefix.lib,
- 'libnetcdf.%s' % dsuf)),
- '-DNETCDF_INCLUDE_DIRS=%s;%s' %
- (spec['netcdf-cxx'].prefix.include,
- spec['netcdf'].prefix.include),
+ '-DNETCDF_LIBRARIES=%s;%s' % (
+ join_path(spec['netcdf-cxx'].prefix.lib,
+ 'libnetcdf_c++.%s' % dsuf),
+ join_path(spec['netcdf'].prefix.lib,
+ 'libnetcdf.%s' % dsuf)),
+ '-DNETCDF_INCLUDE_DIRS=%s;%s' % (
+ spec['netcdf-cxx'].prefix.include,
+ spec['netcdf'].prefix.include),
])
else:
options.extend([
@@ -266,9 +265,9 @@ class Dealii(Package):
filter_file(r'(LA::SolverCG solver\(solver_control\);)', ('TrilinosWrappers::SolverDirect::AdditionalData data(false,"Amesos_Superludist"); TrilinosWrappers::SolverDirect solver(solver_control,data);'), 'step-40.cc') # NOQA: ignore=E501
filter_file(r'(LA::MPI::PreconditionAMG preconditioner;)',
(''), 'step-40.cc')
- filter_file(r'(LA::MPI::PreconditionAMG::AdditionalData data;)',
+ filter_file(r'(LA::MPI::PreconditionAMG::AdditionalData data;)', # NOQA: ignore=E501
(''), 'step-40.cc')
- filter_file(r'(preconditioner.initialize\(system_matrix, data\);)',
+ filter_file(r'(preconditioner.initialize\(system_matrix, data\);)', # NOQA: ignore=E501
(''), 'step-40.cc')
filter_file(r'(solver\.solve \(system_matrix, completely_distributed_solution, system_rhs,)', ('solver.solve (system_matrix, completely_distributed_solution, system_rhs);'), 'step-40.cc') # NOQA: ignore=E501
filter_file(r'(preconditioner\);)', (''), 'step-40.cc')
diff --git a/var/spack/repos/builtin/packages/espresso/package.py b/var/spack/repos/builtin/packages/espresso/package.py
index ef6a3ccc7b..447964f286 100644
--- a/var/spack/repos/builtin/packages/espresso/package.py
+++ b/var/spack/repos/builtin/packages/espresso/package.py
@@ -26,20 +26,28 @@ from spack import *
import os
+
class Espresso(Package):
"""
- QE is an integrated suite of Open-Source computer codes for electronic-structure calculations and materials
- modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials.
+ QE is an integrated suite of Open-Source computer codes for
+ electronic-structure calculations and materials modeling at
+ the nanoscale. It is based on density-functional theory, plane
+ waves, and pseudopotentials.
"""
homepage = 'http://quantum-espresso.org'
url = 'http://www.qe-forge.org/gf/download/frsrelease/204/912/espresso-5.3.0.tar.gz'
+ version(
+ '5.4.0',
+ '8bb78181b39bd084ae5cb7a512c1cfe7',
+ url='http://www.qe-forge.org/gf/download/frsrelease/211/968/espresso-5.4.0.tar.gz'
+ )
version('5.3.0', '6848fcfaeb118587d6be36bd10b7f2c3')
- variant('mpi', default=True, description='Build Quantum-ESPRESSO with mpi support')
+ variant('mpi', default=True, description='Builds with mpi support')
variant('openmp', default=False, description='Enables openMP support')
variant('scalapack', default=True, description='Enables scalapack support')
- variant('elpa', default=True, description='Use elpa as an eigenvalue solver')
+ variant('elpa', default=True, description='Uses elpa as an eigenvalue solver')
depends_on('blas')
depends_on('lapack')
@@ -47,7 +55,12 @@ class Espresso(Package):
depends_on('mpi', when='+mpi')
depends_on('fftw~mpi', when='~mpi')
depends_on('fftw+mpi', when='+mpi')
- depends_on('scalapack', when='+scalapack+mpi') # TODO : + mpi needed to avoid false dependencies installation
+ # TODO : + mpi needed to avoid false dependencies installation
+ depends_on('scalapack', when='+scalapack+mpi')
+
+ # Spurious problems running in parallel the Makefile
+ # generated by qe configure
+ parallel = False
def check_variants(self, spec):
error = 'you cannot ask for \'+{variant}\' when \'+mpi\' is not active'
@@ -87,10 +100,9 @@ class Espresso(Package):
configure(*options)
make('all')
- if spec.architecture.startswith('darwin'):
+ if spec.satisfies('platform=darwin'):
mkdirp(prefix.bin)
for filename in glob("bin/*.x"):
install(filename, prefix.bin)
else:
make('install')
-
diff --git a/var/spack/repos/builtin/packages/ferret/package.py b/var/spack/repos/builtin/packages/ferret/package.py
new file mode 100644
index 0000000000..15ddfcee16
--- /dev/null
+++ b/var/spack/repos/builtin/packages/ferret/package.py
@@ -0,0 +1,103 @@
+##############################################################################
+# 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 os
+
+
+class Ferret(Package):
+ """Ferret is an interactive computer visualization and analysis environment
+ designed to meet the needs of oceanographers and meteorologists
+ analyzing large and complex gridded data sets."""
+ homepage = "http://ferret.noaa.gov/Ferret/"
+ url = "ftp://ftp.pmel.noaa.gov/ferret/pub/source/fer_source.tar.gz"
+
+ version('6.96', '51722027c864369f41bab5751dfff8cc',
+ url="ftp://ftp.pmel.noaa.gov/ferret/pub/source/fer_source.tar.gz")
+
+ depends_on("hdf5~mpi~fortran")
+ depends_on("netcdf~mpi")
+ depends_on("netcdf-fortran")
+ depends_on("readline")
+ depends_on("zlib")
+
+ def patch(self):
+ hdf5_prefix = self.spec['hdf5'].prefix
+ netcdff_prefix = self.spec['netcdf-fortran'].prefix
+ readline_prefix = self.spec['readline'].prefix
+ libz_prefix = self.spec['zlib'].prefix
+
+ filter_file(r'^BUILDTYPE.+',
+ 'BUILDTYPE = x86_64-linux',
+ 'FERRET/site_specific.mk')
+ filter_file(r'^INSTALL_FER_DIR.+',
+ 'INSTALL_FER_DIR = %s' % self.spec.prefix,
+ 'FERRET/site_specific.mk')
+ filter_file(r'^HDF5_DIR.+',
+ 'HDF5_DIR = %s' % hdf5_prefix,
+ 'FERRET/site_specific.mk')
+ filter_file(r'^NETCDF4_DIR.+',
+ 'NETCDF4_DIR = %s' % netcdff_prefix,
+ 'FERRET/site_specific.mk')
+ filter_file(r'^READLINE_DIR.+',
+ 'READLINE_DIR = %s' % readline_prefix,
+ 'FERRET/site_specific.mk')
+ filter_file(r'^LIBZ_DIR.+',
+ 'LIBZ_DIR = %s' % libz_prefix,
+ 'FERRET/site_specific.mk')
+ filter_file(r'^JAVA_HOME.+',
+ ' ',
+ 'FERRET/site_specific.mk')
+ filter_file(r'-lm',
+ '-lgfortran -lm',
+ 'FERRET/platform_specific.mk.x86_64-linux')
+
+ def install(self, spec, prefix):
+ hdf5_prefix = spec['hdf5'].prefix
+ netcdff_prefix = spec['netcdf-fortran'].prefix
+ netcdf_prefix = spec['netcdf'].prefix
+ libz_prefix = spec['zlib'].prefix
+ ln = which('ln')
+ ln('-sf',
+ hdf5_prefix + '/lib',
+ hdf5_prefix + '/lib64')
+ ln('-sf',
+ netcdff_prefix + '/lib',
+ netcdff_prefix + '/lib64')
+ ln('-sf',
+ netcdf_prefix + '/lib/libnetcdf.a',
+ netcdff_prefix + '/lib/libnetcdf.a')
+ ln('-sf',
+ netcdf_prefix + '/lib/libnetcdf.la',
+ netcdff_prefix + '/lib/libnetcdf.la')
+ ln('-sf',
+ libz_prefix + '/lib',
+ libz_prefix + '/lib64')
+ os.environ['LDFLAGS'] = '-lquadmath'
+ with working_dir('FERRET', create=False):
+ os.environ['LD_X11'] = '-L/usr/lib/X11 -lX11'
+ os.environ['HOSTTYPE'] = 'x86_64-linux'
+ make(parallel=False)
+ make("install")
diff --git a/var/spack/repos/builtin/packages/hdf5-blosc/package.py b/var/spack/repos/builtin/packages/hdf5-blosc/package.py
new file mode 100644
index 0000000000..50f380083c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/hdf5-blosc/package.py
@@ -0,0 +1,206 @@
+##############################################################################
+# 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
+##############################################################################
+
+import os
+import shutil
+import sys
+
+from spack import *
+
+def _install_shlib(name, src, dst):
+ """Install a shared library from directory src to directory dst"""
+ if sys.platform == "darwin":
+ shlib0 = name + ".0.dylib"
+ shlib = name + ".dylib"
+ shutil.copyfile(join_path(src, shlib0), join_path(dst, shlib0))
+ os.symlink(shlib0, join_path(dst, shlib))
+ else:
+ shlib000 = name + ".so.0.0.0"
+ shlib0 = name + ".so.0"
+ shlib = name + ".dylib"
+ shutil.copyfile(join_path(src, shlib000), join_path(dst, shlib000))
+ os.symlink(shlib000, join_path(dst, shlib0))
+ os.symlink(shlib0, join_path(dst, shlib))
+
+class Hdf5Blosc(Package):
+ """Blosc filter for HDF5"""
+ homepage = "https://github.com/Blosc/hdf5-blosc"
+ url = "https://github.com/Blosc/hdf5-blosc/archive/master.zip"
+
+ version('master', '02c04acbf4bec66ec8a35bf157d1c9de')
+
+ depends_on("c-blosc")
+ depends_on("hdf5")
+ depends_on("libtool")
+
+ parallel = False
+
+ def install(self, spec, prefix):
+ # The included cmake recipe doesn"t work for Darwin
+ # cmake(".", *std_cmake_args)
+ #
+ # make()
+ # make("install")
+ # if sys.platform == "darwin":
+ # fix_darwin_install_name(prefix.lib)
+
+ libtool = Executable(join_path(spec["libtool"].prefix.bin, "libtool"))
+ if "+mpi" in spec["hdf5"]:
+ cc = "mpicc"
+ else:
+ cc = "cc"
+ shlibext = "so" if sys.platform!="darwin" else "dylib"
+ mkdirp(prefix.include)
+ mkdirp(prefix.lib)
+
+ # Build and install filter
+ with working_dir("src"):
+ libtool("--mode=compile", "--tag=CC",
+ "cc", "-g", "-O",
+ "-c", "blosc_filter.c")
+ libtool("--mode=link", "--tag=CC",
+ "cc", "-g", "-O",
+ "-rpath", prefix.lib,
+ "-o", "libblosc_filter.la",
+ "blosc_filter.lo",
+ "-L%s" % spec["c-blosc"].prefix.lib, "-lblosc",
+ "-L%s" % spec["hdf5"].prefix.lib, "-lhdf5")
+ _install_shlib("libblosc_filter", ".libs", prefix.lib)
+
+ # Build and install plugin
+ # The plugin requires at least HDF5 1.8.11:
+ if spec["hdf5"].satisfies("@1.8.11:"):
+ libtool("--mode=compile", "--tag=CC",
+ "cc", "-g", "-O",
+ "-c", "blosc_plugin.c")
+ libtool("--mode=link", "--tag=CC",
+ "cc", "-g", "-O",
+ "-rpath", prefix.lib,
+ "-o", "libblosc_plugin.la",
+ "blosc_plugin.lo",
+ "-L%s" % prefix.lib, "-lblosc_filter",
+ "-L%s" % spec["c-blosc"].prefix.lib, "-lblosc",
+ "-L%s" % spec["hdf5"].prefix.lib, "-lhdf5")
+ _install_shlib("libblosc_plugin", ".libs", prefix.lib)
+
+ self.check_install(spec)
+
+ def check_install(self, spec):
+ "Build and run a small program to test the installed HDF5 Blosc plugin"
+ print "Checking HDF5-Blosc plugin..."
+ checkdir = "spack-check"
+ with working_dir(checkdir, create=True):
+ source = r"""\
+#include <hdf5.h>
+#include <assert.h>
+#include <stdio.h>
+#include <stdlib.h>
+
+#define FILTER_BLOSC 32001 /* Blosc filter ID registered with the HDF group */
+
+int main(int argc, char **argv) {
+ herr_t herr;
+ hid_t file = H5Fcreate("file.h5", H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
+ assert(file >= 0);
+ hsize_t dims[3] = {10, 10, 10};
+ hid_t space = H5Screate_simple(3, dims, NULL);
+ assert(space >= 0);
+ hid_t create_proplist = H5Pcreate(H5P_DATASET_CREATE);
+ assert(create_proplist >= 0);
+ herr = H5Pset_chunk(create_proplist, 3, dims);
+ assert(herr >= 0);
+ herr = H5Pset_filter(create_proplist, FILTER_BLOSC, H5Z_FLAG_OPTIONAL, 0,
+ NULL);
+ assert(herr >= 0);
+ htri_t all_filters_avail = H5Pall_filters_avail(create_proplist);
+ assert(all_filters_avail > 0);
+ hid_t dataset = H5Dcreate(file, "dataset", H5T_NATIVE_DOUBLE, space,
+ H5P_DEFAULT, create_proplist, H5P_DEFAULT);
+ assert(dataset >= 0);
+ double data[10][10][10];
+ for (int k=0; k<10; ++k) {
+ for (int j=0; j<10; ++j) {
+ for (int i=0; i<10; ++i) {
+ data[k][j][i] = 1.0 / (1.0 + i + j + k);
+ }
+ }
+ }
+ herr = H5Dwrite(dataset, H5T_NATIVE_DOUBLE, space, space, H5P_DEFAULT,
+ &data[0][0][0]);
+ assert(herr >= 0);
+ herr = H5Pclose(create_proplist);
+ assert(herr >= 0);
+ herr = H5Dclose(dataset);
+ assert(herr >= 0);
+ herr = H5Sclose(space);
+ assert(herr >= 0);
+ herr = H5Fclose(file);
+ assert(herr >= 0);
+ printf("Done.\n");
+ return 0;
+}
+"""
+ expected = """\
+Done.
+"""
+ with open("check.c", "w") as f:
+ f.write(source)
+ if "+mpi" in spec["hdf5"]:
+ cc = which("mpicc")
+ else:
+ cc = which("cc")
+ # TODO: Automate these path and library settings
+ cc("-c", "-I%s" % spec["hdf5"].prefix.include, "check.c")
+ cc("-o", "check", "check.o",
+ "-L%s" % spec["hdf5"].prefix.lib, "-lhdf5")
+ 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
+ print "Environment:"
+ env = which("env")
+ env()
+ raise RuntimeError("HDF5 Blosc plugin check failed")
+ shutil.rmtree(checkdir)
+
+ def setup_environment(self, spack_env, run_env):
+ spack_env.append_path("HDF5_PLUGIN_PATH", self.spec.prefix.lib)
+ run_env.append_path("HDF5_PLUGIN_PATH", self.spec.prefix.lib)
+
+ def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
+ spack_env.append_path("HDF5_PLUGIN_PATH", self.spec.prefix.lib)
+ run_env.append_path("HDF5_PLUGIN_PATH", self.spec.prefix.lib)
diff --git a/var/spack/repos/builtin/packages/hpl/package.py b/var/spack/repos/builtin/packages/hpl/package.py
new file mode 100644
index 0000000000..efd5c8bb1d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/hpl/package.py
@@ -0,0 +1,119 @@
+##############################################################################
+# 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 os
+import platform
+
+
+class Hpl(Package):
+ """HPL is a software package that solves a (random) dense linear system
+ in double precision (64 bits) arithmetic on distributed-memory computers.
+ It can thus be regarded as a portable as well as freely available
+ implementation of the High Performance Computing Linpack Benchmark."""
+
+ homepage = "http://www.netlib.org/benchmark/hpl/"
+ url = "http://www.netlib.org/benchmark/hpl/hpl-2.2.tar.gz"
+
+ version('2.2', '0eb19e787c3dc8f4058db22c9e0c5320')
+
+ variant('openmp', default=False, description='Enable OpenMP support')
+
+ depends_on('mpi@1.1:')
+ depends_on('blas')
+
+ parallel = False
+
+ def configure(self, spec, arch):
+ # List of configuration options
+ # Order is important
+ config = []
+
+ # OpenMP support
+ if '+openmp' in spec:
+ config.append(
+ 'OMP_DEFS = {0}'.format(self.compiler.openmp_flag)
+ )
+
+ config.extend([
+ # Shell
+ 'SHELL = /bin/sh',
+ 'CD = cd',
+ 'CP = cp',
+ 'LN_S = ln -fs',
+ 'MKDIR = mkdir -p',
+ 'RM = /bin/rm -f',
+ 'TOUCH = touch',
+ # Platform identifier
+ 'ARCH = {0}'.format(arch),
+ # HPL Directory Structure / HPL library
+ 'TOPdir = {0}'.format(os.getcwd()),
+ 'INCdir = $(TOPdir)/include',
+ 'BINdir = $(TOPdir)/bin/$(ARCH)',
+ 'LIBdir = $(TOPdir)/lib/$(ARCH)',
+ 'HPLlib = $(LIBdir)/libhpl.a',
+ # Message Passing library (MPI)
+ 'MPinc = -I{0}'.format(spec['mpi'].prefix.include),
+ 'MPlib = -L{0}'.format(spec['mpi'].prefix.lib),
+ # Linear Algebra library (BLAS or VSIPL)
+ 'LAinc = {0}'.format(spec['blas'].prefix.include),
+ 'LAlib = {0}'.format(spec['blas'].blas_shared_lib),
+ # F77 / C interface
+ 'F2CDEFS = -DAdd_ -DF77_INTEGER=int -DStringSunStyle',
+ # HPL includes / libraries / specifics
+ 'HPL_INCLUDES = -I$(INCdir) -I$(INCdir)/$(ARCH) ' +
+ '-I$(LAinc) -I$(MPinc)',
+ 'HPL_LIBS = $(HPLlib) $(LAlib) $(MPlib)',
+ 'HPL_OPTS = -DHPL_DETAILED_TIMING -DHPL_PROGRESS_REPORT',
+ 'HPL_DEFS = $(F2CDEFS) $(HPL_OPTS) $(HPL_INCLUDES)',
+ # Compilers / linkers - Optimization flags
+ 'CC = {0}'.format(spec['mpi'].mpicc),
+ 'CCNOOPT = $(HPL_DEFS)',
+ 'CCFLAGS = $(HPL_DEFS) -O3',
+ 'LINKER = $(CC)',
+ 'LINKFLAGS = $(CCFLAGS) $(OMP_DEFS)',
+ 'ARCHIVER = ar',
+ 'ARFLAGS = r',
+ 'RANLIB = echo'
+ ])
+
+ # Write configuration options to include file
+ with open('Make.{0}'.format(arch), 'w') as makefile:
+ for var in config:
+ makefile.write('{0}\n'.format(var))
+
+ def install(self, spec, prefix):
+ # Arch used for file naming purposes only
+ arch = '{0}-{1}'.format(platform.system(), platform.processor())
+
+ # Generate Makefile include
+ self.configure(spec, arch)
+
+ make('arch={0}'.format(arch))
+
+ # Manual installation
+ install_tree(join_path('bin', arch), prefix.bin)
+ install_tree(join_path('lib', arch), prefix.lib)
+ install_tree(join_path('include', arch), prefix.include)
+ install_tree('man', prefix.man)
diff --git a/var/spack/repos/builtin/packages/intel-parallel-studio/package.py b/var/spack/repos/builtin/packages/intel-parallel-studio/package.py
new file mode 100644
index 0000000000..493ca16417
--- /dev/null
+++ b/var/spack/repos/builtin/packages/intel-parallel-studio/package.py
@@ -0,0 +1,144 @@
+from spack import *
+import os
+import re
+
+from spack.pkg.builtin.intel import IntelInstaller, filter_pick, \
+ get_all_components
+
+
+class IntelParallelStudio(IntelInstaller):
+ """Intel Parallel Studio.
+
+ Note: You will have to add the download file to a
+ mirror so that Spack can find it. For instructions on how to set up a
+ mirror, see http://software.llnl.gov/spack/mirrors.html"""
+
+ homepage = "https://software.intel.com/en-us/intel-parallel-studio-xe"
+
+ # TODO: can also try the online installer (will download files on demand)
+ version('composer.2016.2', '1133fb831312eb519f7da897fec223fa',
+ url="file://%s/parallel_studio_xe_2016_composer_edition_update2.tgz" # NOQA: ignore=E501
+ % os.getcwd())
+ version('professional.2016.2', '70be832f2d34c9bf596a5e99d5f2d832',
+ url="file://%s/parallel_studio_xe_2016_update2.tgz" % os.getcwd()) # NOQA: ignore=E501
+ version('cluster.2016.2', '70be832f2d34c9bf596a5e99d5f2d832',
+ url="file://%s/parallel_studio_xe_2016_update2.tgz" % os.getcwd()) # NOQA: ignore=E501
+ version('composer.2016.3', '3208eeabee951fc27579177b593cefe9',
+ url="file://%s/parallel_studio_xe_2016_composer_edition_update3.tgz" # NOQA: ignore=E501
+ % os.getcwd())
+ version('professional.2016.3', 'eda19bb0d0d19709197ede58f13443f3',
+ url="file://%s/parallel_studio_xe_2016_update3.tgz" % os.getcwd()) # NOQA: ignore=E501
+ version('cluster.2016.3', 'eda19bb0d0d19709197ede58f13443f3',
+ url="file://%s/parallel_studio_xe_2016_update3.tgz" % os.getcwd()) # NOQA: ignore=E501
+
+ variant('rpath', default=True, description="Add rpath to .cfg files")
+ variant('newdtags', default=False,
+ description="Allow use of --enable-new-dtags in MPI wrappers")
+ variant('all', default=False,
+ description="Install all files with the requested edition")
+ variant('mpi', default=True,
+ description="Install the Intel MPI library and ITAC tool")
+ variant('mkl', default=True, description="Install the Intel MKL library")
+ variant('daal',
+ default=True, description="Install the Intel DAAL libraries")
+ variant('ipp', default=True, description="Install the Intel IPP libraries")
+ variant('tools', default=True, description="""Install the Intel Advisor,\
+VTune Amplifier, and Inspector tools""")
+
+ provides('mpi', when='@cluster:+mpi')
+ provides('mkl', when='+mkl')
+ provides('daal', when='+daal')
+ provides('ipp', when='+ipp')
+
+ def install(self, spec, prefix):
+
+ base_components = "ALL" # when in doubt, install everything
+ mpi_components = ""
+ mkl_components = ""
+ daal_components = ""
+ ipp_components = ""
+
+ if spec.satisfies('+all'):
+ base_components = "ALL"
+ else:
+ all_components = get_all_components()
+ regex = '(comp|openmp|intel-tbb|icc|ifort|psxe|icsxe-pset)'
+ base_components = \
+ filter_pick(all_components, re.compile(regex).search)
+ regex = '(icsxe|imb|mpi|itac|intel-tc|clck)'
+ mpi_components = \
+ filter_pick(all_components, re.compile(regex).search)
+ mkl_components = \
+ filter_pick(all_components, re.compile('(mkl)').search)
+ daal_components = \
+ filter_pick(all_components, re.compile('(daal)').search)
+ ipp_components = \
+ filter_pick(all_components, re.compile('(ipp)').search)
+ regex = '(gdb|vtune|inspector|advisor)'
+ tool_components = \
+ filter_pick(all_components, re.compile(regex).search)
+
+ components = base_components
+ if not spec.satisfies('+all'):
+ if spec.satisfies('+mpi') and 'cluster' in str(spec.version):
+ components += mpi_components
+ if spec.satisfies('+mkl'):
+ components += mkl_components
+ if spec.satisfies('+daal'):
+ components += daal_components
+ if spec.satisfies('+ipp'):
+ components += ipp_components
+ if spec.satisfies('+tools') and (spec.satisfies('@cluster') or
+ spec.satisfies('@professional')):
+ components += tool_components
+
+ self.intel_components = ';'.join(components)
+ IntelInstaller.install(self, spec, prefix)
+
+ absbindir = os.path.dirname(os.path.realpath(os.path.join(
+ self.prefix.bin, "icc")))
+ abslibdir = os.path.dirname(os.path.realpath(os.path.join
+ (self.prefix.lib, "intel64", "libimf.a")))
+
+ os.symlink(self.global_license_file, os.path.join(absbindir,
+ "license.lic"))
+ if spec.satisfies('+tools') and (spec.satisfies('@cluster') or
+ spec.satisfies('@professional')):
+ os.mkdir(os.path.join(self.prefix, "inspector_xe/licenses"))
+ os.symlink(self.global_license_file, os.path.join(
+ self.prefix, "inspector_xe/licenses", "license.lic"))
+ os.mkdir(os.path.join(self.prefix, "advisor_xe/licenses"))
+ os.symlink(self.global_license_file, os.path.join(
+ self.prefix, "advisor_xe/licenses", "license.lic"))
+ os.mkdir(os.path.join(self.prefix, "vtune_amplifier_xe/licenses"))
+ os.symlink(self.global_license_file, os.path.join(
+ self.prefix, "vtune_amplifier_xe/licenses", "license.lic"))
+
+ if (spec.satisfies('+all') or spec.satisfies('+mpi')) and \
+ spec.satisfies('@cluster'):
+ os.symlink(self.global_license_file, os.path.join(
+ self.prefix, "itac_latest", "license.lic"))
+ if spec.satisfies('~newdtags'):
+ wrappers = ["mpif77", "mpif77", "mpif90", "mpif90",
+ "mpigcc", "mpigcc", "mpigxx", "mpigxx",
+ "mpiicc", "mpiicc", "mpiicpc", "mpiicpc",
+ "mpiifort", "mpiifort"]
+ wrapper_paths = []
+ for root, dirs, files in os.walk(spec.prefix):
+ for name in files:
+ if name in wrappers:
+ wrapper_paths.append(os.path.join(spec.prefix,
+ root, name))
+ for wrapper in wrapper_paths:
+ filter_file(r'-Xlinker --enable-new-dtags', r' ',
+ wrapper)
+
+ if spec.satisfies('+rpath'):
+ for compiler_command in ["icc", "icpc", "ifort"]:
+ cfgfilename = os.path.join(absbindir, "%s.cfg" %
+ compiler_command)
+ with open(cfgfilename, "w") as f:
+ f.write('-Xlinker -rpath -Xlinker %s\n' % abslibdir)
+
+ os.symlink(os.path.join(self.prefix.man, "common", "man1"),
+ os.path.join(self.prefix.man, "man1"))
diff --git a/var/spack/repos/builtin/packages/intel/package.py b/var/spack/repos/builtin/packages/intel/package.py
new file mode 100644
index 0000000000..ec3192380a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/intel/package.py
@@ -0,0 +1,125 @@
+from spack import *
+import os
+import re
+
+
+def filter_pick(input_list, regex_filter):
+ """Returns the items in input_list that are found in the regex_filter"""
+ return [l for l in input_list for m in (regex_filter(l),) if m]
+
+
+def unfilter_pick(input_list, regex_filter):
+ """Returns the items in input_list that are not found in the
+ regex_filter"""
+ return [l for l in input_list for m in (regex_filter(l),) if not m]
+
+
+def get_all_components():
+ """Returns a list of all the components associated with the downloaded
+ Intel package"""
+ all_components = []
+ with open("pset/mediaconfig.xml", "r") as f:
+ lines = f.readlines()
+ for line in lines:
+ if line.find('<Abbr>') != -1:
+ component = line[line.find('<Abbr>') + 6:line.find('</Abbr>')]
+ all_components.append(component)
+ return all_components
+
+
+class IntelInstaller(Package):
+ """Base package containing common methods for installing Intel software"""
+
+ homepage = "https://software.intel.com/en-us"
+ intel_components = "ALL"
+ license_required = True
+ license_comment = '#'
+ license_files = ['Licenses/license.lic']
+ license_vars = ['INTEL_LICENSE_FILE']
+ license_url = \
+ 'https://software.intel.com/en-us/articles/intel-license-manager-faq'
+
+ @property
+ def global_license_file(self):
+ """Returns the path where a global license file should be stored."""
+ if not self.license_files:
+ return
+ return join_path(self.global_license_dir, "intel",
+ os.path.basename(self.license_files[0]))
+
+ def install(self, spec, prefix):
+
+ # Remove the installation DB, otherwise it will try to install into
+ # location of other Intel builds
+ if os.path.exists(os.path.join(os.environ["HOME"], "intel",
+ "intel_sdp_products.db")):
+ os.remove(os.path.join(os.environ["HOME"], "intel",
+ "intel_sdp_products.db"))
+
+ if not hasattr(self, "intel_prefix"):
+ self.intel_prefix = self.prefix
+
+ silent_config_filename = 'silent.cfg'
+ with open(silent_config_filename, 'w') as f:
+ f.write("""
+ACCEPT_EULA=accept
+PSET_MODE=install
+CONTINUE_WITH_INSTALLDIR_OVERWRITE=yes
+PSET_INSTALL_DIR=%s
+ACTIVATION_LICENSE_FILE=%s
+ACTIVATION_TYPE=license_file
+PHONEHOME_SEND_USAGE_DATA=no
+CONTINUE_WITH_OPTIONAL_ERROR=yes
+COMPONENTS=%s
+""" % (self.intel_prefix, self.global_license_file, self.intel_components))
+
+ install_script = which("install.sh")
+ install_script('--silent', silent_config_filename)
+
+
+class Intel(IntelInstaller):
+ """Intel Compilers.
+
+ Note: You will have to add the download file to a
+ mirror so that Spack can find it. For instructions on how to set up a
+ mirror, see http://software.llnl.gov/spack/mirrors.html"""
+
+ homepage = "https://software.intel.com/en-us/intel-parallel-studio-xe"
+
+ # TODO: can also try the online installer (will download files on demand)
+ version('16.0.2', '1133fb831312eb519f7da897fec223fa',
+ url="file://%s/parallel_studio_xe_2016_composer_edition_update2.tgz" # NOQA: ignore=E501
+ % os.getcwd())
+ version('16.0.3', '3208eeabee951fc27579177b593cefe9',
+ url="file://%s/parallel_studio_xe_2016_composer_edition_update3.tgz" # NOQA: ignore=E501
+ % os.getcwd())
+
+ variant('rpath', default=True, description="Add rpath to .cfg files")
+
+ def install(self, spec, prefix):
+ components = []
+ all_components = get_all_components()
+ regex = '(comp|openmp|intel-tbb|icc|ifort|psxe|icsxe-pset)'
+ components = filter_pick(all_components, re.compile(regex).search)
+
+ self.intel_components = ';'.join(components)
+ IntelInstaller.install(self, spec, prefix)
+
+ absbindir = os.path.split(os.path.realpath(os.path.join(
+ self.prefix.bin, "icc")))[0]
+ abslibdir = os.path.split(os.path.realpath(os.path.join(
+ self.prefix.lib, "intel64", "libimf.a")))[0]
+
+ # symlink or copy?
+ os.symlink(self.global_license_file, os.path.join(absbindir,
+ "license.lic"))
+
+ if spec.satisfies('+rpath'):
+ for compiler_command in ["icc", "icpc", "ifort"]:
+ cfgfilename = os.path.join(absbindir, "%s.cfg" %
+ compiler_command)
+ with open(cfgfilename, "w") as f:
+ f.write('-Xlinker -rpath -Xlinker %s\n' % abslibdir)
+
+ os.symlink(os.path.join(self.prefix.man, "common", "man1"),
+ os.path.join(self.prefix.man, "man1"))
diff --git a/var/spack/repos/builtin/packages/ipp/package.py b/var/spack/repos/builtin/packages/ipp/package.py
new file mode 100644
index 0000000000..2bd931d5bd
--- /dev/null
+++ b/var/spack/repos/builtin/packages/ipp/package.py
@@ -0,0 +1,26 @@
+from spack import *
+import os
+
+from spack.pkg.builtin.intel import IntelInstaller
+
+
+class Ipp(IntelInstaller):
+ """Intel Integrated Performance Primitives.
+
+ Note: You will have to add the download file to a
+ mirror so that Spack can find it. For instructions on how to set up a
+ mirror, see http://software.llnl.gov/spack/mirrors.html"""
+
+ homepage = "https://software.intel.com/en-us/intel-ipp"
+
+ version('9.0.3.210', '0e1520dd3de7f811a6ef6ebc7aa429a3',
+ url="file://%s/l_ipp_9.0.3.210.tgz" % os.getcwd())
+
+ def install(self, spec, prefix):
+
+ self.intel_prefix = os.path.join(prefix, "pkg")
+ IntelInstaller.install(self, spec, prefix)
+
+ ipp_dir = os.path.join(self.intel_prefix, "ipp")
+ for f in os.listdir(ipp_dir):
+ os.symlink(os.path.join(ipp_dir, f), os.path.join(self.prefix, f))
diff --git a/var/spack/repos/builtin/packages/libpciaccess/package.py b/var/spack/repos/builtin/packages/libpciaccess/package.py
index 42e8711a7d..91cef95cec 100644
--- a/var/spack/repos/builtin/packages/libpciaccess/package.py
+++ b/var/spack/repos/builtin/packages/libpciaccess/package.py
@@ -37,7 +37,7 @@ class Libpciaccess(Package):
def install(self, spec, prefix):
# libpciaccess does not support OS X
- if spec.satisfies('arch=darwin-x86_64'):
+ if spec.satisfies('platform=darwin'):
# create a dummy directory
mkdir(prefix.lib)
return
diff --git a/var/spack/repos/builtin/packages/libpthread-stubs/package.py b/var/spack/repos/builtin/packages/libpthread-stubs/package.py
new file mode 100644
index 0000000000..4bcca43c24
--- /dev/null
+++ b/var/spack/repos/builtin/packages/libpthread-stubs/package.py
@@ -0,0 +1,39 @@
+##############################################################################
+# 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 LibpthreadStubs(Package):
+ """The libpthread-stubs package provides weak aliases for pthread
+ functions not provided in libc or otherwise available by
+ default. """
+ homepage = "http://xcb.freedesktop.org/"
+ url = "http://xcb.freedesktop.org/dist/libpthread-stubs-0.1.tar.bz2"
+
+ version('0.3', 'e8fa31b42e13f87e8f5a7a2b731db7ee')
+
+ def install(self, spec, prefix):
+ configure('--prefix=%s' % prefix)
+ make()
+ make("install")
diff --git a/var/spack/repos/builtin/packages/libxau/package.py b/var/spack/repos/builtin/packages/libxau/package.py
new file mode 100644
index 0000000000..55816ecdbd
--- /dev/null
+++ b/var/spack/repos/builtin/packages/libxau/package.py
@@ -0,0 +1,44 @@
+##############################################################################
+# 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 Libxau(Package):
+ """The libXau package contains a library implementing the X11
+ Authorization Protocol. This is useful for restricting client
+ access to the display."""
+ homepage = "http://xcb.freedesktop.org/"
+ url = "http://ftp.x.org/pub/individual/lib/libXau-1.0.8.tar.bz2"
+
+ version('1.0.8', '685f8abbffa6d145c0f930f00703b21b')
+
+ depends_on('xproto')
+
+ def install(self, spec, prefix):
+ # FIXME: Modify the configure line to suit your build system here.
+ configure('--prefix=%s' % prefix)
+
+ # FIXME: Add logic to build and install here
+ make()
+ make("install")
diff --git a/var/spack/repos/builtin/packages/libxcb/package.py b/var/spack/repos/builtin/packages/libxcb/package.py
index 0f39bb0f1d..746d4567e2 100644
--- a/var/spack/repos/builtin/packages/libxcb/package.py
+++ b/var/spack/repos/builtin/packages/libxcb/package.py
@@ -35,18 +35,19 @@ class Libxcb(Package):
version('1.11', '1698dd837d7e6e94d029dbe8b3a82deb')
version('1.11.1', '118623c15a96b08622603a71d8789bf3')
+
depends_on("python")
depends_on("xcb-proto")
depends_on("pkg-config")
-
- # depends_on('pthread') # Ubuntu: apt-get install libpthread-stubs0-dev
- # depends_on('xau') # Ubuntu: apt-get install libxau-dev
+ depends_on("libpthread-stubs")
+ depends_on('libxau')
def patch(self):
filter_file('typedef struct xcb_auth_info_t {', 'typedef struct {', 'src/xcb.h')
def install(self, spec, prefix):
+ env['PKG_CONFIG_PATH'] = env['PKG_CONFIG_PATH'] + ':/usr/lib64/pkgconfig'
configure("--prefix=%s" % prefix)
make()
diff --git a/var/spack/repos/builtin/packages/llvm/package.py b/var/spack/repos/builtin/packages/llvm/package.py
index c32f66590a..7a6ea7401c 100644
--- a/var/spack/repos/builtin/packages/llvm/package.py
+++ b/var/spack/repos/builtin/packages/llvm/package.py
@@ -267,16 +267,16 @@ class Llvm(Package):
if '+all_targets' not in spec: # all is default on cmake
targets = ['CppBackend', 'NVPTX', 'AMDGPU']
- if 'x86' in spec.architecture.lower():
+ if 'x86' in spec.architecture.target.lower():
targets.append('X86')
- elif 'arm' in spec.architecture.lower():
+ elif 'arm' in spec.architecture.target.lower():
targets.append('ARM')
- elif 'aarch64' in spec.architecture.lower():
+ elif 'aarch64' in spec.architecture.target.lower():
targets.append('AArch64')
- elif 'sparc' in spec.architecture.lower():
+ elif 'sparc' in spec.architecture.target.lower():
targets.append('sparc')
- elif ('ppc' in spec.architecture.lower() or
- 'power' in spec.architecture.lower()):
+ elif ('ppc' in spec.architecture.target.lower() or
+ 'power' in spec.architecture.target.lower()):
targets.append('PowerPC')
cmake_args.append('-DLLVM_TARGETS_TO_BUILD:Bool=' + ';'.join(targets))
diff --git a/var/spack/repos/builtin/packages/lua/package.py b/var/spack/repos/builtin/packages/lua/package.py
index 8ce4a7b94d..761932361b 100644
--- a/var/spack/repos/builtin/packages/lua/package.py
+++ b/var/spack/repos/builtin/packages/lua/package.py
@@ -57,7 +57,7 @@ class Lua(Package):
placement='luarocks')
def install(self, spec, prefix):
- if spec.satisfies("arch=darwin-i686") or spec.satisfies("arch=darwin-x86_64"): # NOQA: ignore=E501
+ if spec.satisfies("platform=darwin"):
target = 'macosx'
else:
target = 'linux'
diff --git a/var/spack/repos/builtin/packages/mkl/package.py b/var/spack/repos/builtin/packages/mkl/package.py
new file mode 100644
index 0000000000..454e78d29c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/mkl/package.py
@@ -0,0 +1,28 @@
+from spack import *
+import os
+
+from spack.pkg.builtin.intel import IntelInstaller
+
+
+class Mkl(IntelInstaller):
+ """Intel Math Kernel Library.
+
+ Note: You will have to add the download file to a
+ mirror so that Spack can find it. For instructions on how to set up a
+ mirror, see http://software.llnl.gov/spack/mirrors.html"""
+
+ homepage = "https://software.intel.com/en-us/intel-mkl"
+
+ version('11.3.2.181', '536dbd82896d6facc16de8f961d17d65',
+ url="file://%s/l_mkl_11.3.2.181.tgz" % os.getcwd())
+ version('11.3.3.210', 'f72546df27f5ebb0941b5d21fd804e34',
+ url="file://%s/l_mkl_11.3.3.210.tgz" % os.getcwd())
+
+ def install(self, spec, prefix):
+
+ self.intel_prefix = os.path.join(prefix, "pkg")
+ IntelInstaller.install(self, spec, prefix)
+
+ mkl_dir = os.path.join(self.intel_prefix, "mkl")
+ for f in os.listdir(mkl_dir):
+ os.symlink(os.path.join(mkl_dir, f), os.path.join(self.prefix, f))
diff --git a/var/spack/repos/builtin/packages/openblas/package.py b/var/spack/repos/builtin/packages/openblas/package.py
index 22e49daaa7..d09ebd6739 100644
--- a/var/spack/repos/builtin/packages/openblas/package.py
+++ b/var/spack/repos/builtin/packages/openblas/package.py
@@ -48,6 +48,13 @@ class Openblas(Package):
patch('make.patch')
def install(self, spec, prefix):
+ # As of 06/2016 there is no mechanism to specify that packages which
+ # depends on Blas/Lapack need C or/and Fortran symbols. For now
+ # require both.
+ if self.compiler.f77 is None:
+ raise InstallError('OpenBLAS requires both C and Fortran ',
+ 'compilers!')
+
# Configure fails to pick up fortran from FC=/abs/path/to/f77, but
# works fine with FC=/abs/path/to/gfortran.
# When mixing compilers make sure that
diff --git a/var/spack/repos/builtin/packages/openmpi/package.py b/var/spack/repos/builtin/packages/openmpi/package.py
index ab71b4b503..695fb82f62 100644
--- a/var/spack/repos/builtin/packages/openmpi/package.py
+++ b/var/spack/repos/builtin/packages/openmpi/package.py
@@ -61,6 +61,7 @@ class Openmpi(Package):
list_url = "http://www.open-mpi.org/software/ompi/"
list_depth = 3
+ version('1.10.3', 'e2fe4513200e2aaa1500b762342c674b')
version('1.10.2', 'b2f43d9635d2d52826e5ef9feb97fd4c')
version('1.10.1', 'f0fcd77ed345b7eafb431968124ba16e')
version('1.10.0', '280cf952de68369cebaca886c5ce0304')
@@ -128,6 +129,13 @@ class Openmpi(Package):
return 'verbs'
def install(self, spec, prefix):
+ # As of 06/2016 there is no mechanism to specify that packages which
+ # depends on MPI need C or/and Fortran implementation. For now
+ # require both.
+ if (self.compiler.f77 is None) or (self.compiler.fc is None):
+ raise InstallError('OpenMPI requires both C and Fortran ',
+ 'compilers!')
+
config_args = ["--prefix=%s" % prefix,
"--with-hwloc=%s" % spec['hwloc'].prefix,
"--enable-shared",
@@ -149,7 +157,7 @@ class Openmpi(Package):
])
if '+verbs' in spec:
path = _verbs_dir()
- if path is not None:
+ if path is not None and path not in ('/usr', '/usr/local'):
config_args.append('--with-%s=%s' % (self.verbs, path))
else:
config_args.append('--with-%s' % self.verbs)
diff --git a/var/spack/repos/builtin/packages/openssl/package.py b/var/spack/repos/builtin/packages/openssl/package.py
index 34ab0703ad..377bffe723 100644
--- a/var/spack/repos/builtin/packages/openssl/package.py
+++ b/var/spack/repos/builtin/packages/openssl/package.py
@@ -100,7 +100,7 @@ class Openssl(Package):
# in the environment, then this will override what is set in the
# Makefile, leading to build errors.
env.pop('APPS', None)
- if spec.satisfies("arch=darwin-x86_64") or spec.satisfies("arch=ppc64"):
+ if spec.satisfies("target=x86_64") or spec.satisfies("target=ppc64"):
# This needs to be done for all 64-bit architectures (except Linux,
# where it happens automatically?)
env['KERNEL_BITS'] = '64'
diff --git a/var/spack/repos/builtin/packages/pcre/intel.patch b/var/spack/repos/builtin/packages/pcre/intel.patch
new file mode 100644
index 0000000000..f160f55e1b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/pcre/intel.patch
@@ -0,0 +1,12 @@
+diff -up pcre-8.38/pcrecpp.cc.intel pcre-8.38/pcrecpp.cc
+--- pcre-8.38/pcrecpp.cc.intel 2014-09-15 07:48:59.000000000 -0600
++++ pcre-8.38/pcrecpp.cc 2016-06-08 16:16:56.702721214 -0600
+@@ -66,7 +66,7 @@ Arg RE::no_arg((void*)NULL);
+ // inclusive test if we ever needed it. (Note that not only the
+ // __attribute__ syntax, but also __USER_LABEL_PREFIX__, are
+ // gnu-specific.)
+-#if defined(__GNUC__) && __GNUC__ >= 3 && defined(__ELF__)
++#if defined(__GNUC__) && __GNUC__ >= 3 && defined(__ELF__) && !defined(__INTEL_COMPILER)
+ # define ULP_AS_STRING(x) ULP_AS_STRING_INTERNAL(x)
+ # define ULP_AS_STRING_INTERNAL(x) #x
+ # define USER_LABEL_PREFIX_STR ULP_AS_STRING(__USER_LABEL_PREFIX__)
diff --git a/var/spack/repos/builtin/packages/pcre/package.py b/var/spack/repos/builtin/packages/pcre/package.py
index 7a9f3b911d..a43729a1ac 100644
--- a/var/spack/repos/builtin/packages/pcre/package.py
+++ b/var/spack/repos/builtin/packages/pcre/package.py
@@ -24,17 +24,29 @@
##############################################################################
from spack import *
+
class Pcre(Package):
"""The PCRE package contains Perl Compatible Regular Expression
libraries. These are useful for implementing regular expression
pattern matching using the same syntax and semantics as Perl 5."""
+
homepage = "http://www.pcre.org"""
url = "ftp://ftp.csx.cam.ac.uk/pub/software/programming/pcre/pcre-8.36.tar.bz2"
version('8.36', 'b767bc9af0c20bc9c1fe403b0d41ad97')
version('8.38', '00aabbfe56d5a48b270f999b508c5ad2')
+ patch("intel.patch")
+
+ variant('utf', default=True,
+ description='Enable support for UTF-8/16/32, '
+ 'incompatible with EBCDIC.')
+
def install(self, spec, prefix):
- configure("--prefix=%s" % prefix)
+ configure_args = ['--prefix=%s' % prefix]
+ if '+utf' in spec:
+ configure_args.append('--enable-utf')
+
+ configure(*configure_args)
make()
make("install")
diff --git a/var/spack/repos/builtin/packages/petsc/package.py b/var/spack/repos/builtin/packages/petsc/package.py
index 6456a1aabf..8dd1d8d2b9 100644
--- a/var/spack/repos/builtin/packages/petsc/package.py
+++ b/var/spack/repos/builtin/packages/petsc/package.py
@@ -28,13 +28,16 @@ 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.
+ 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('3.7.2', '50da49867ce7a49e7a0c1b37f4ec7b34')
+ version('3.6.4', '7632da2375a3df35b8891c9526dbdde7')
version('3.6.3', '91dd3522de5a5ef039ff8f50800db606')
version('3.5.3', 'd4fd2734661e89f18ac6014b5dd1ef2f')
version('3.5.2', 'ad170802b3b058b5deb9cd1f968e7e13')
@@ -69,10 +72,12 @@ class Petsc(Package):
depends_on('hdf5+mpi', when='+hdf5+mpi')
depends_on('parmetis', when='+metis+mpi')
# Hypre does not support complex numbers.
- # Also PETSc prefer to build it without internal superlu, likely due to conflict in headers
- # see https://bitbucket.org/petsc/petsc/src/90564b43f6b05485163c147b464b5d6d28cde3ef/config/BuildSystem/config/packages/hypre.py
+ # Also PETSc prefer to build it without internal superlu, likely due to
+ # conflict in headers see
+ # https://bitbucket.org/petsc/petsc/src/90564b43f6b05485163c147b464b5d6d28cde3ef/config/BuildSystem/config/packages/hypre.py # NOQA: ignore=E501
depends_on('hypre~internal-superlu', when='+hypre+mpi~complex')
- depends_on('superlu-dist', when='+superlu-dist+mpi')
+ depends_on('superlu-dist@:4.3', when='@:3.6.4+superlu-dist+mpi')
+ depends_on('superlu-dist@5.0.0:', when='@3.7:+superlu-dist+mpi')
depends_on('mumps+mpi', when='+mumps+mpi')
depends_on('scalapack', when='+mumps+mpi')
@@ -80,17 +85,17 @@ class Petsc(Package):
if '~mpi' in self.spec:
compiler_opts = [
'--with-cc=%s' % os.environ['CC'],
- '--with-cxx=%s' % (os.environ['CXX'] if self.compiler.cxx is not None else '0'),
- '--with-fc=%s' % (os.environ['FC'] if self.compiler.fc is not None else '0'),
+ '--with-cxx=%s' % (os.environ['CXX'] if self.compiler.cxx is not None else '0'), # NOQA: ignore=E501
+ '--with-fc=%s' % (os.environ['FC'] if self.compiler.fc is not None else '0'), # NOQA: ignore=E501
'--with-mpi=0'
]
- error_message_fmt = '\t{library} support requires "+mpi" to be activated'
+ error_message_fmt = '\t{library} support requires "+mpi" to be activated' # NOQA: ignore=E501
- # If mpi is disabled (~mpi), it's an error to have any of these enabled.
- # This generates a list of any such errors.
+ # If mpi is disabled (~mpi), it's an error to have any of these
+ # enabled. This generates a list of any such errors.
errors = [error_message_fmt.format(library=x)
- for x in ('hdf5', 'hypre', 'parmetis','mumps','superlu-dist')
- if ('+'+x) in self.spec]
+ for x in ('hdf5', 'hypre', 'parmetis', 'mumps', 'superlu-dist') # NOQA: ignore=E501
+ if ('+' + x) in self.spec]
if errors:
errors = ['incompatible variants given'] + errors
raise RuntimeError('\n'.join(errors))
@@ -105,26 +110,31 @@ class Petsc(Package):
options = ['--with-ssl=0']
options.extend(self.mpi_dependent_options())
options.extend([
- '--with-precision=%s' % ('double' if '+double' in spec else 'single'),
- '--with-scalar-type=%s' % ('complex' if '+complex' in spec else 'real'),
+ '--with-precision=%s' % ('double' if '+double' in spec else 'single'), # NOQA: ignore=E501
+ '--with-scalar-type=%s' % ('complex' if '+complex' in spec else 'real'), # NOQA: ignore=E501
'--with-shared-libraries=%s' % ('1' if '+shared' in spec else '0'),
'--with-debugging=%s' % ('1' if '+debug' in spec else '0'),
'--with-blas-lapack-dir=%s' % spec['lapack'].prefix
])
# Activates library support if needed
- for library in ('metis', 'boost', 'hdf5', 'hypre', 'parmetis','mumps','scalapack'):
+ for library in ('metis', 'boost', 'hdf5', 'hypre', 'parmetis',
+ 'mumps', 'scalapack'):
options.append(
- '--with-{library}={value}'.format(library=library, value=('1' if library in spec else '0'))
+ '--with-{library}={value}'.format(library=library, value=('1' if library in spec else '0')) # NOQA: ignore=E501
)
if library in spec:
options.append(
- '--with-{library}-dir={path}'.format(library=library, path=spec[library].prefix)
+ '--with-{library}-dir={path}'.format(library=library, path=spec[library].prefix) # NOQA: ignore=E501
)
- # PETSc does not pick up SuperluDist from the dir as they look for superlu_dist_4.1.a
+ # PETSc does not pick up SuperluDist from the dir as they look for
+ # superlu_dist_4.1.a
if 'superlu-dist' in spec:
options.extend([
- '--with-superlu_dist-include=%s' % spec['superlu-dist'].prefix.include,
- '--with-superlu_dist-lib=%s' % join_path(spec['superlu-dist'].prefix.lib, 'libsuperlu_dist.a'),
+ '--with-superlu_dist-include=%s' %
+ spec['superlu-dist'].prefix.include,
+ '--with-superlu_dist-lib=%s' %
+ join_path(spec['superlu-dist'].prefix.lib,
+ 'libsuperlu_dist.a'),
'--with-superlu_dist=1'
])
else:
diff --git a/var/spack/repos/builtin/packages/py-astropy/package.py b/var/spack/repos/builtin/packages/py-astropy/package.py
index 86875bbcae..a9962777dc 100644
--- a/var/spack/repos/builtin/packages/py-astropy/package.py
+++ b/var/spack/repos/builtin/packages/py-astropy/package.py
@@ -24,29 +24,38 @@
##############################################################################
from spack import *
+
class PyAstropy(Package):
- """
- The Astropy Project is a community effort to develop a single core
+ """The Astropy Project is a community effort to develop a single core
package for Astronomy in Python and foster interoperability between
- Python astronomy packages.
- """
+ Python astronomy packages."""
+
homepage = 'http://www.astropy.org/'
+ url = 'https://pypi.python.org/packages/source/a/astropy/astropy-1.1.2.tar.gz'
+ version('1.1.2', 'cbe32023b5b1177d1e2498a0d00cda51')
version('1.1.post1', 'b52919f657a37d45cc45f5cb0f58c44d')
- def url_for_version(self, version):
- return 'https://pypi.python.org/packages/source/a/astropy/astropy-{0}.tar.gz'.format(version)
-
+ # Required dependencies
extends('python')
+ depends_on('py-numpy')
- depends_on('cfitsio')
- depends_on('expat')
+ # Optional dependencies
depends_on('py-h5py')
- depends_on('py-numpy')
+ depends_on('py-beautifulsoup4')
+ depends_on('py-pyyaml')
depends_on('py-scipy')
+ depends_on('libxml2')
+ depends_on('py-matplotlib')
+ depends_on('py-pytz')
+ depends_on('py-scikit-image')
+ depends_on('py-pandas')
+
+ # System dependencies
+ depends_on('cfitsio')
+ depends_on('expat')
def install(self, spec, prefix):
python('setup.py', 'build', '--use-system-cfitsio',
- '--use-system-expat')
- python('setup.py', 'install', '--prefix=' + prefix)
-
+ '--use-system-expat')
+ python('setup.py', 'install', '--prefix={0}'.format(prefix))
diff --git a/var/spack/repos/builtin/packages/py-beautifulsoup4/package.py b/var/spack/repos/builtin/packages/py-beautifulsoup4/package.py
new file mode 100644
index 0000000000..64368fe70d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-beautifulsoup4/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 PyBeautifulsoup4(Package):
+ """Beautiful Soup is a Python library for pulling data out of HTML and
+ XML files. It works with your favorite parser to provide idiomatic ways
+ of navigating, searching, and modifying the parse tree."""
+
+ homepage = "https://www.crummy.com/software/BeautifulSoup"
+ url = "https://pypi.python.org/packages/source/b/beautifulsoup4/beautifulsoup4-4.4.1.tar.gz"
+
+ version('4.4.1', '8fbd9a7cac0704645fa20d1419036815')
+
+ extends('python')
+
+ def install(self, spec, prefix):
+ python('setup.py', 'install', '--prefix={0}'.format(prefix))
diff --git a/var/spack/repos/builtin/packages/py-emcee/package.py b/var/spack/repos/builtin/packages/py-emcee/package.py
new file mode 100644
index 0000000000..d57ef4bd76
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-emcee/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 PyEmcee(Package):
+ """emcee is an MIT licensed pure-Python implementation of Goodman & Weare's
+ Affine Invariant Markov chain Monte Carlo (MCMC) Ensemble sampler."""
+
+ homepage = "http://dan.iel.fm/emcee/current/"
+ url = "https://pypi.python.org/packages/source/e/emcee/emcee-2.1.0.tar.gz"
+
+ version('2.1.0', 'c6b6fad05c824d40671d4a4fc58dfff7')
+
+ extends('python')
+ depends_on('py-numpy')
+
+ def install(self, spec, prefix):
+ python('setup.py', 'install', '--prefix={0}'.format(prefix))
diff --git a/var/spack/repos/builtin/packages/py-h5py/package.py b/var/spack/repos/builtin/packages/py-h5py/package.py
index de72bac44e..0180b658f5 100644
--- a/var/spack/repos/builtin/packages/py-h5py/package.py
+++ b/var/spack/repos/builtin/packages/py-h5py/package.py
@@ -23,21 +23,42 @@
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
from spack import *
-import re
+
class PyH5py(Package):
- """The h5py package provides both a high- and low-level interface to the HDF5 library from Python."""
+ """The h5py package provides both a high- and low-level interface to the
+ HDF5 library from Python."""
+
homepage = "https://pypi.python.org/pypi/h5py"
url = "https://pypi.python.org/packages/source/h/h5py/h5py-2.4.0.tar.gz"
- version('2.4.0', '80c9a94ae31f84885cc2ebe1323d6758')
+ version('2.6.0', 'ec476211bd1de3f5ac150544189b0bf4')
version('2.5.0', '6e4301b5ad5da0d51b0a1e5ac19e3b74')
+ version('2.4.0', '80c9a94ae31f84885cc2ebe1323d6758')
+
+ variant('mpi', default=False, description='Build with MPI support')
- extends('python', ignore=lambda f: re.match(r'bin/cy*', f))
- depends_on('hdf5')
- depends_on('py-numpy')
- depends_on('py-cython')
+ extends('python')
+
+ # Build dependencies
+ depends_on('py-cython@0.19:')
+ depends_on('pkg-config')
+ depends_on('hdf5@1.8.4:+mpi', when='+mpi')
+ depends_on('hdf5@1.8.4:~mpi', when='~mpi')
+ depends_on('mpi', when='+mpi')
+
+ # Build and runtime dependencies
+ depends_on('py-numpy@1.6.1:')
+
+ # Runtime dependencies
+ depends_on('py-six')
def install(self, spec, prefix):
- python('setup.py', 'configure', '--hdf5=%s' % spec['hdf5'].prefix)
- python('setup.py', 'install', '--prefix=%s' % prefix)
+ python('setup.py', 'configure',
+ '--hdf5={0}'.format(spec['hdf5'].prefix))
+
+ if '+mpi' in spec:
+ env['CC'] = spec['mpi'].mpicc
+ python('setup.py', 'configure', '--mpi')
+
+ python('setup.py', 'install', '--prefix={0}'.format(prefix))
diff --git a/var/spack/repos/builtin/packages/py-iminuit/package.py b/var/spack/repos/builtin/packages/py-iminuit/package.py
new file mode 100644
index 0000000000..47751a702d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-iminuit/package.py
@@ -0,0 +1,46 @@
+##############################################################################
+# 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 PyIminuit(Package):
+ """Interactive IPython-Friendly Minimizer based on SEAL Minuit2."""
+
+ homepage = "https://pypi.python.org/pypi/iminuit"
+ url = "https://pypi.python.org/packages/source/i/iminuit/iminuit-1.2.tar.gz"
+
+ version('1.2', '4701ec472cae42015e26251703e6e984')
+
+ # Required dependencies
+ extends('python')
+ depends_on('py-setuptools')
+
+ # Optional dependencies
+ depends_on('py-numpy')
+ depends_on('py-matplotlib')
+ depends_on('py-cython')
+
+ def install(self, spec, prefix):
+ python('setup.py', 'install', '--prefix={0}'.format(prefix))
diff --git a/var/spack/repos/builtin/packages/py-nestle/package.py b/var/spack/repos/builtin/packages/py-nestle/package.py
new file mode 100644
index 0000000000..16506e3eca
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-nestle/package.py
@@ -0,0 +1,44 @@
+##############################################################################
+# 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 PyNestle(Package):
+ """Nested sampling algorithms for evaluating Bayesian evidence."""
+
+ homepage = "http://kbarbary.github.io/nestle/"
+ url = "https://pypi.python.org/packages/source/n/nestle/nestle-0.1.1.tar.gz"
+
+ version('0.1.1', '4875c0f9a0a8e263c1d7f5fa6ce604c5')
+
+ # Required dependencies
+ extends('python')
+ depends_on('py-numpy')
+
+ # Optional dependencies
+ depends_on('py-scipy')
+
+ def install(self, spec, prefix):
+ python('setup.py', 'install', '--prefix={0}'.format(prefix))
diff --git a/var/spack/repos/builtin/packages/py-sncosmo/package.py b/var/spack/repos/builtin/packages/py-sncosmo/package.py
new file mode 100644
index 0000000000..82ae2a2e69
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-sncosmo/package.py
@@ -0,0 +1,51 @@
+##############################################################################
+# 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 PySncosmo(Package):
+ """SNCosmo is a Python library for high-level supernova cosmology
+ analysis."""
+
+ homepage = "http://sncosmo.readthedocs.io/"
+ url = "https://pypi.python.org/packages/source/s/sncosmo/sncosmo-1.2.0.tar.gz"
+
+ version('1.2.0', '028e6d1dc84ab1c17d2f3b6378b2cb1e')
+
+ # Required dependencies
+ # py-sncosmo binaries are duplicates of those from py-astropy
+ extends('python', ignore=r'bin/.*')
+ depends_on('py-numpy')
+ depends_on('py-scipy')
+ depends_on('py-astropy')
+
+ # Recommended dependencies
+ depends_on('py-matplotlib')
+ depends_on('py-iminuit')
+ depends_on('py-emcee')
+ depends_on('py-nestle')
+
+ def install(self, spec, prefix):
+ python('setup.py', 'install', '--prefix={0}'.format(prefix))
diff --git a/var/spack/repos/builtin/packages/py-wcsaxes/package.py b/var/spack/repos/builtin/packages/py-wcsaxes/package.py
new file mode 100644
index 0000000000..b0adbe3658
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-wcsaxes/package.py
@@ -0,0 +1,43 @@
+##############################################################################
+# 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 PyWcsaxes(Package):
+ """WCSAxes is a framework for making plots of Astronomical data
+ in Matplotlib."""
+
+ homepage = "http://wcsaxes.readthedocs.io/en/latest/index.html"
+ url = "https://github.com/astrofrog/wcsaxes/archive/v0.8.tar.gz"
+
+ version('0.8', 'de1c60fdae4c330bf5ddb9f1ab5ab920')
+
+ extends('python', ignore=r'bin/pbr')
+ depends_on('py-numpy')
+ depends_on('py-matplotlib')
+ depends_on('py-astropy')
+
+ def install(self, spec, prefix):
+ python('setup.py', 'install', '--prefix={0}'.format(prefix))
diff --git a/var/spack/repos/builtin/packages/python/package.py b/var/spack/repos/builtin/packages/python/package.py
index 86c12498e1..b6a62bf742 100644
--- a/var/spack/repos/builtin/packages/python/package.py
+++ b/var/spack/repos/builtin/packages/python/package.py
@@ -22,9 +22,6 @@
# 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 functools
-import glob
-import inspect
import os
import re
from contextlib import closing
@@ -37,11 +34,10 @@ from spack.util.environment import *
class Python(Package):
"""The Python programming language."""
+
homepage = "http://www.python.org"
url = "http://www.python.org/ftp/python/2.7.8/Python-2.7.8.tgz"
- extendable = True
-
version('3.5.1', 'be78e48cdfc1a7ad90efff146dce6cfe')
version('3.5.0', 'a56c0c0b45d75a0ec9c6dee933c41c36')
version('2.7.11', '6b6076ec9e93f05dd63e47eb9c15728b', preferred=True)
@@ -49,6 +45,8 @@ class Python(Package):
version('2.7.9', '5eebcaa0030dc4061156d3429657fb83')
version('2.7.8', 'd4bca0159acb0b44a781292b5231936f')
+ extendable = True
+
depends_on("openssl")
depends_on("bzip2")
depends_on("readline")
@@ -64,39 +62,63 @@ class Python(Package):
# Rest of install is pretty standard except setup.py needs to
# be able to read the CPPFLAGS and LDFLAGS as it scans for the
# library and headers to build
- configure_args= [
- "--prefix=%s" % prefix,
- "--with-threads",
- "--enable-shared",
- "CPPFLAGS=-I%s/include -I%s/include -I%s/include -I%s/include -I%s/include -I%s/include" % (
- spec['openssl'].prefix, spec['bzip2'].prefix,
- spec['readline'].prefix, spec['ncurses'].prefix,
- spec['sqlite'].prefix, spec['zlib'].prefix),
- "LDFLAGS=-L%s/lib -L%s/lib -L%s/lib -L%s/lib -L%s/lib -L%s/lib" % (
- spec['openssl'].prefix, spec['bzip2'].prefix,
- spec['readline'].prefix, spec['ncurses'].prefix,
- spec['sqlite'].prefix, spec['zlib'].prefix)
- ]
+ cppflags = ' -I'.join([
+ spec['openssl'].prefix.include, spec['bzip2'].prefix.include,
+ spec['readline'].prefix.include, spec['ncurses'].prefix.include,
+ spec['sqlite'].prefix.include, spec['zlib'].prefix.include
+ ])
+
+ ldflags = ' -L'.join([
+ spec['openssl'].prefix.lib, spec['bzip2'].prefix.lib,
+ spec['readline'].prefix.lib, spec['ncurses'].prefix.lib,
+ spec['sqlite'].prefix.lib, spec['zlib'].prefix.lib
+ ])
+
+ config_args = [
+ "--prefix={0}".format(prefix),
+ "--with-threads",
+ "--enable-shared",
+ "CPPFLAGS=-I{0}".format(cppflags),
+ "LDFLAGS=-L{0}".format(ldflags)
+ ]
+
if spec.satisfies('@3:'):
- configure_args.append('--without-ensurepip')
- configure(*configure_args)
+ config_args.append('--without-ensurepip')
+
+ configure(*config_args)
+
make()
make("install")
- # Modify compiler paths in configuration files. This is necessary for
- # building site packages outside of spack
- filter_file(r'([/s]=?)([\S=]*)/lib/spack/env(/[^\s/]*)?/(\S*)(\s)',
- (r'\4\5'),
- join_path(prefix.lib, 'python%d.%d' % self.version[:2], '_sysconfigdata.py'))
+ self.filter_compilers(spec, prefix)
+
+ def filter_compilers(self, spec, prefix):
+ """Run after install to tell the configuration files and Makefiles
+ to use the compilers that Spack built the package with.
+
+ If this isn't done, they'll have CC and CXX set to Spack's generic
+ cc and c++. We want them to be bound to whatever compiler
+ they were built with."""
+
+ kwargs = {'ignore_absent': True, 'backup': False, 'string': True}
- python3_version = ''
+ dirname = join_path(prefix.lib,
+ 'python{0}'.format(self.version.up_to(2)))
+
+ config = 'config'
if spec.satisfies('@3:'):
- python3_version = '-%d.%dm' % self.version[:2]
- makefile_filepath = join_path(prefix.lib, 'python%d.%d' % self.version[:2], 'config%s' % python3_version, 'Makefile')
- filter_file(r'([/s]=?)([\S=]*)/lib/spack/env(/[^\s/]*)?/(\S*)(\s)',
- (r'\4\5'),
- makefile_filepath)
+ config = 'config-{0}m'.format(self.version.up_to(2))
+
+ files = [
+ '_sysconfigdata.py',
+ join_path(config, 'Makefile')
+ ]
+ for filename in files:
+ filter_file(env['CC'], self.compiler.cc,
+ join_path(dirname, filename), **kwargs)
+ filter_file(env['CXX'], self.compiler.cxx,
+ join_path(dirname, filename), **kwargs)
# ========================================================================
# Set up environment to make install easy for python extensions.
@@ -104,57 +126,59 @@ class Python(Package):
@property
def python_lib_dir(self):
- return os.path.join('lib', 'python%d.%d' % self.version[:2])
-
+ return join_path('lib', 'python{0}'.format(self.version.up_to(2)))
@property
def python_include_dir(self):
- return os.path.join('include', 'python%d.%d' % self.version[:2])
-
+ return join_path('include', 'python{0}'.format(self.version.up_to(2)))
@property
def site_packages_dir(self):
- return os.path.join(self.python_lib_dir, 'site-packages')
-
+ return join_path(self.python_lib_dir, 'site-packages')
def setup_dependent_environment(self, spack_env, run_env, extension_spec):
- # TODO: do this only for actual extensions.
+ """Set PYTHONPATH to include site-packages dir for the
+ extension and any other python extensions it depends on."""
- # Set PYTHONPATH to include site-packages dir for the
- # extension and any other python extensions it depends on.
python_paths = []
for d in extension_spec.traverse():
if d.package.extends(self.spec):
- python_paths.append(os.path.join(d.prefix, self.site_packages_dir))
+ python_paths.append(join_path(d.prefix,
+ self.site_packages_dir))
pythonpath = ':'.join(python_paths)
spack_env.set('PYTHONPATH', pythonpath)
- # For run time environment set only the path for extension_spec and prepend it to PYTHONPATH
+ # For run time environment set only the path for
+ # extension_spec and prepend it to PYTHONPATH
if extension_spec.package.extends(self.spec):
- run_env.prepend_path('PYTHONPATH', os.path.join(extension_spec.prefix, self.site_packages_dir))
-
+ run_env.prepend_path('PYTHONPATH', join_path(
+ extension_spec.prefix, self.site_packages_dir))
def setup_dependent_package(self, module, ext_spec):
- """
- Called before python modules' install() methods.
+ """Called before python modules' install() methods.
In most cases, extensions will only need to have one line::
- python('setup.py', 'install', '--prefix=%s' % prefix)
- """
+ python('setup.py', 'install', '--prefix={0}'.format(prefix))"""
+
# Python extension builds can have a global python executable function
- if self.version >= Version("3.0.0") and self.version < Version("4.0.0"):
- module.python = Executable(join_path(self.spec.prefix.bin, 'python3'))
+ if Version("3.0.0") <= self.version < Version("4.0.0"):
+ module.python = Executable(join_path(self.spec.prefix.bin,
+ 'python3'))
else:
- module.python = Executable(join_path(self.spec.prefix.bin, 'python'))
+ module.python = Executable(join_path(self.spec.prefix.bin,
+ 'python'))
# Add variables for lib/pythonX.Y and lib/pythonX.Y/site-packages dirs.
- module.python_lib_dir = os.path.join(ext_spec.prefix, self.python_lib_dir)
- module.python_include_dir = os.path.join(ext_spec.prefix, self.python_include_dir)
- module.site_packages_dir = os.path.join(ext_spec.prefix, self.site_packages_dir)
-
- # Make the site packages directory for extensions, if it does not exist already.
+ module.python_lib_dir = join_path(ext_spec.prefix,
+ self.python_lib_dir)
+ module.python_include_dir = join_path(ext_spec.prefix,
+ self.python_include_dir)
+ module.site_packages_dir = join_path(ext_spec.prefix,
+ self.site_packages_dir)
+
+ # Make the site packages directory for extensions
if ext_spec.package.is_extension:
mkdirp(module.site_packages_dir)
@@ -167,25 +191,28 @@ class Python(Package):
ignore_arg = args.get('ignore', lambda f: False)
# Always ignore easy-install.pth, as it needs to be merged.
- patterns = [r'easy-install\.pth$']
+ patterns = [r'site-packages/easy-install\.pth$']
# Ignore pieces of setuptools installed by other packages.
+ # Must include directory name or it will remove all site*.py files.
if ext_pkg.name != 'py-setuptools':
- patterns.append(r'/site[^/]*\.pyc?$')
- patterns.append(r'setuptools\.pth')
- patterns.append(r'bin/easy_install[^/]*$')
- patterns.append(r'setuptools.*egg$')
+ patterns.extend([
+ r'bin/easy_install[^/]*$',
+ r'site-packages/setuptools[^/]*\.egg$',
+ r'site-packages/setuptools\.pth$',
+ r'site-packages/site[^/]*\.pyc?$',
+ r'site-packages/__pycache__/site[^/]*\.pyc?$'
+ ])
if ext_pkg.name != 'py-numpy':
patterns.append(r'bin/f2py$')
return match_predicate(ignore_arg, patterns)
-
def write_easy_install_pth(self, exts):
paths = []
for ext in sorted(exts.values()):
- ext_site_packages = os.path.join(ext.prefix, self.site_packages_dir)
- easy_pth = "%s/easy-install.pth" % ext_site_packages
+ ext_site_packages = join_path(ext.prefix, self.site_packages_dir)
+ easy_pth = join_path(ext_site_packages, "easy-install.pth")
if not os.path.isfile(easy_pth):
continue
@@ -195,15 +222,18 @@ class Python(Package):
line = line.rstrip()
# Skip lines matching these criteria
- if not line: continue
- if re.search(r'^(import|#)', line): continue
- if (ext.name != 'py-setuptools' and
- re.search(r'setuptools.*egg$', line)): continue
+ if not line:
+ continue
+ if re.search(r'^(import|#)', line):
+ continue
+ if ((ext.name != 'py-setuptools' and
+ re.search(r'setuptools.*egg$', line))):
+ continue
paths.append(line)
- site_packages = os.path.join(self.prefix, self.site_packages_dir)
- main_pth = "%s/easy-install.pth" % site_packages
+ site_packages = join_path(self.prefix, self.site_packages_dir)
+ main_pth = join_path(site_packages, "easy-install.pth")
if not paths:
if os.path.isfile(main_pth):
@@ -211,15 +241,22 @@ class Python(Package):
else:
with closing(open(main_pth, 'w')) as f:
- f.write("import sys; sys.__plen = len(sys.path)\n")
+ f.write("""
+import sys
+sys.__plen = len(sys.path)
+""")
for path in paths:
- f.write("%s\n" % path)
- f.write("import sys; new=sys.path[sys.__plen:]; del sys.path[sys.__plen:]; "
- "p=getattr(sys,'__egginsert',0); sys.path[p:p]=new; sys.__egginsert = p+len(new)\n")
-
+ f.write("{0}\n".format(path))
+ f.write("""
+new = sys.path[sys.__plen:]
+del sys.path[sys.__plen:]
+p = getattr(sys, '__egginsert', 0)
+sys.path[p:p] = new
+sys.__egginsert = p + len(new)
+""")
def activate(self, ext_pkg, **args):
- ignore=self.python_ignore(ext_pkg, args)
+ ignore = self.python_ignore(ext_pkg, args)
args.update(ignore=ignore)
super(Python, self).activate(ext_pkg, **args)
@@ -228,12 +265,12 @@ class Python(Package):
exts[ext_pkg.name] = ext_pkg.spec
self.write_easy_install_pth(exts)
-
def deactivate(self, ext_pkg, **args):
args.update(ignore=self.python_ignore(ext_pkg, args))
super(Python, self).deactivate(ext_pkg, **args)
exts = spack.install_layout.extension_map(self.spec)
- if ext_pkg.name in exts: # Make deactivate idempotent.
+ # Make deactivate idempotent
+ if ext_pkg.name in exts:
del exts[ext_pkg.name]
self.write_easy_install_pth(exts)
diff --git a/var/spack/repos/builtin/packages/r-BiocGenerics/package.py b/var/spack/repos/builtin/packages/r-BiocGenerics/package.py
index 0d3b6a3e57..5a6ce72a4b 100644
--- a/var/spack/repos/builtin/packages/r-BiocGenerics/package.py
+++ b/var/spack/repos/builtin/packages/r-BiocGenerics/package.py
@@ -24,15 +24,33 @@
##############################################################################
from spack import *
+
class RBiocgenerics(Package):
"""S4 generic functions needed by many Bioconductor packages."""
- homepage = 'https://www.bioconductor.org/packages/release/bioc/html/BiocGenerics.html'
- url = "https://www.bioconductor.org/packages/release/bioc/src/contrib/BiocGenerics_0.16.1.tar.gz"
-
- version('0.16.1', 'c2148ffd86fc6f1f819c7f68eb2c744f', expand=False)
+ homepage = 'https://bioconductor.org/packages/BiocGenerics/'
+ version('bioc-3.3',
+ git='https://github.com/Bioconductor-mirror/BiocGenerics.git',
+ branch='release-3.3')
+ version('bioc-3.2',
+ git='https://github.com/Bioconductor-mirror/BiocGenerics.git',
+ branch='release-3.2')
extends('R')
+ def validate(self, spec):
+ """
+ Checks that the version of R is appropriate for the Bioconductor
+ version.
+ """
+ if spec.satisfies('@bioc-3.3'):
+ if not spec.satisfies('^R@3.3.0:3.3.9'):
+ raise InstallError('Must use R-3.3 for Bioconductor-3.3')
+ elif spec.satisfies('@bioc-3.2'):
+ if not spec.satisfies('^R@3.2.0:3.2.9'):
+ raise InstallError('Must use R-3.2 for Bioconductor-3.2')
+
def install(self, spec, prefix):
- R('CMD', 'INSTALL', '--library=%s' % self.module.r_lib_dir, '%s' % self.stage.archive_file)
+ self.validate(spec)
+ R('CMD', 'INSTALL', '--library=%s' %
+ self.module.r_lib_dir, '%s' % self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-R6/package.py b/var/spack/repos/builtin/packages/r-R6/package.py
new file mode 100644
index 0000000000..0b75888e79
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-R6/package.py
@@ -0,0 +1,46 @@
+##############################################################################
+# 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 RR6(Package):
+ """The R6 package allows the creation of classes with reference semantics,
+ similar to R's built-in reference classes. Compared to reference classes,
+ R6 classes are simpler and lighter-weight, and they are not built on S4
+ classes so they do not require the methods package. These classes allow
+ public and private members, and they support inheritance, even when the
+ classes are defined in different packages."""
+
+ homepage = "https://github.com/wch/R6/"
+ url = "https://cran.r-project.org/src/contrib/R6_2.1.2.tar.gz"
+ list_url = "https://cran.r-project.org/src/contrib/Archive/R6"
+
+ version('2.1.2', 'b6afb9430e48707be87638675390e457')
+
+ extends('R')
+
+ def install(self, spec, prefix):
+ R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+ self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-abind/package.py b/var/spack/repos/builtin/packages/r-abind/package.py
index 34a1eee79f..96f623a096 100644
--- a/var/spack/repos/builtin/packages/r-abind/package.py
+++ b/var/spack/repos/builtin/packages/r-abind/package.py
@@ -24,6 +24,7 @@
##############################################################################
from spack import *
+
class RAbind(Package):
"""Combine multidimensional arrays into a single array. This is a
generalization of 'cbind' and 'rbind'. Works with vectors, matrices, and
@@ -32,11 +33,12 @@ class RAbind(Package):
homepage = "https://cran.r-project.org/"
url = "https://cran.r-project.org/src/contrib/abind_1.4-3.tar.gz"
+ list_url = "https://cran.r-project.org/src/contrib/Archive/abind"
- version('1.4-3', '10fcf80c677b991bf263d38be35a1fc5', expand=False)
+ version('1.4-3', '10fcf80c677b991bf263d38be35a1fc5')
extends('R')
def install(self, spec, prefix):
-
- R('CMD', 'INSTALL', '--library=%s' % self.module.r_lib_dir, '%s' % self.stage.archive_file)
+ R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+ self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-curl/package.py b/var/spack/repos/builtin/packages/r-curl/package.py
new file mode 100644
index 0000000000..c6e8f22a94
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-curl/package.py
@@ -0,0 +1,51 @@
+##############################################################################
+# 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 RCurl(Package):
+ """The curl() and curl_download() functions provide highly configurable
+ drop-in replacements for base url() and download.file() with better
+ performance, support for encryption (https, ftps), gzip compression,
+ authentication, and other libcurl goodies. The core of the package
+ implements a framework for performing fully customized requests where data
+ can be processed either in memory, on disk, or streaming via the callback
+ or connection interfaces. Some knowledge of libcurl is recommended; for a
+ more-user-friendly web client see the 'httr' package which builds on this
+ package with http specific tools and logic."""
+
+ homepage = "https://github.com/jeroenooms/curl"
+ url = "https://cran.r-project.org/src/contrib/curl_0.9.7.tar.gz"
+ list_url = "https://cran.r-project.org/src/contrib/Archive/RCurl"
+
+ version('0.9.7', 'a101f7de948cb828fef571c730f39217')
+
+ extends('R')
+
+ depends_on('curl')
+
+ def install(self, spec, prefix):
+ R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+ self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-devtools/package.py b/var/spack/repos/builtin/packages/r-devtools/package.py
new file mode 100644
index 0000000000..5f0b7b8779
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-devtools/package.py
@@ -0,0 +1,50 @@
+##############################################################################
+# 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 RDevtools(Package):
+ """Collection of package development tools."""
+
+ homepage = "https://github.com/hadley/devtools"
+ url = "https://cran.r-project.org/src/contrib/devtools_1.11.1.tar.gz"
+ list_url = "https://cran.r-project.org/src/contrib/Archive/devtools"
+
+ version('1.11.1', '242672ee27d24dddcbdaac88c586b6c2')
+
+ extends('R')
+
+ depends_on('r-httr')
+ depends_on('r-memoise')
+ depends_on('r-whisker')
+ depends_on('r-digest')
+ depends_on('r-rstudioapi')
+ depends_on('r-jsonlite')
+ depends_on('r-git2r')
+ depends_on('r-withr')
+
+ def install(self, spec, prefix):
+ R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+ self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-digest/package.py b/var/spack/repos/builtin/packages/r-digest/package.py
new file mode 100644
index 0000000000..1d11afb139
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-digest/package.py
@@ -0,0 +1,56 @@
+##############################################################################
+# 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 RDigest(Package):
+ """Implementation of a function 'digest()' for the creation of hash digests
+ of arbitrary R objects (using the md5, sha-1, sha-256, crc32, xxhash and
+ murmurhash algorithms) permitting easy comparison of R language objects, as
+ well as a function 'hmac()' to create hash-based message authentication
+ code. The md5 algorithm by Ron Rivest is specified in RFC 1321, the sha-1
+ and sha-256 algorithms are specified in FIPS-180-1 and FIPS-180-2, and the
+ crc32 algorithm is described in
+ ftp://ftp.rocksoft.com/cliens/rocksoft/papers/crc_v3.txt. For md5, sha-1,
+ sha-256 and aes, this package uses small standalone implementations that
+ were provided by Christophe Devine. For crc32, code from the zlib library
+ is used. For sha-512, an implementation by Aaron D. Gifford is used. For
+ xxhash, the implementation by Yann Collet is used. For murmurhash, an
+ implementation by Shane Day is used. Please note that this package is not
+ meant to be deployed for cryptographic purposes for which more
+ comprehensive (and widely tested) libraries such as OpenSSL should be
+ used."""
+
+ homepage = "http://dirk.eddelbuettel.com/code/digest.html"
+ url = "https://cran.r-project.org/src/contrib/digest_0.6.9.tar.gz"
+ list_url = "https://cran.r-project.org/src/contrib/Archive/digest"
+
+ version('0.6.9', '48048ce6c466bdb124716e45ba4a0e83')
+
+ extends('R')
+
+ def install(self, spec, prefix):
+ R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+ self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-filehash/package.py b/var/spack/repos/builtin/packages/r-filehash/package.py
index fffae68019..a09b458eaf 100644
--- a/var/spack/repos/builtin/packages/r-filehash/package.py
+++ b/var/spack/repos/builtin/packages/r-filehash/package.py
@@ -24,6 +24,7 @@
##############################################################################
from spack import *
+
class RFilehash(Package):
"""Implements a simple key-value style database where character string keys
are associated with data values that are stored on the disk. A simple
@@ -37,10 +38,12 @@ class RFilehash(Package):
homepage = 'https://cran.r-project.org/'
url = "https://cran.r-project.org/src/contrib/filehash_2.3.tar.gz"
+ list_url = "https://cran.r-project.org/src/contrib/Archive/filehash"
- version('2.3', '01fffafe09b148ccadc9814c103bdc2f', expand=False)
+ version('2.3', '01fffafe09b148ccadc9814c103bdc2f')
extends('R')
def install(self, spec, prefix):
- R('CMD', 'INSTALL', '--library=%s' % self.module.r_lib_dir, '%s' % self.stage.archive_file)
+ R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+ self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-git2r/package.py b/var/spack/repos/builtin/packages/r-git2r/package.py
new file mode 100644
index 0000000000..1f08379d6e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-git2r/package.py
@@ -0,0 +1,46 @@
+##############################################################################
+# 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 RGit2r(Package):
+ """Interface to the 'libgit2' library, which is a pure C implementation of
+ the 'Git' core methods. Provides access to 'Git' repositories to extract
+ data and running some basic 'Git' commands."""
+
+ homepage = "https://github.com/ropensci/git2r"
+ url = "https://cran.r-project.org/src/contrib/git2r_0.15.0.tar.gz"
+ list_url = "https://cran.r-project.org/src/contrib/Archive/git2r"
+
+ version('0.15.0', '57658b3298f9b9aadc0dd77b4ef6a1e1')
+
+ extends('R')
+
+ depends_on('zlib')
+ depends_on('openssl')
+
+ def install(self, spec, prefix):
+ R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+ self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-httr/package.py b/var/spack/repos/builtin/packages/r-httr/package.py
new file mode 100644
index 0000000000..77ec34ab03
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-httr/package.py
@@ -0,0 +1,49 @@
+##############################################################################
+# 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 RHttr(Package):
+ """Useful tools for working with HTTP organised by HTTP verbs (GET(),
+ POST(), etc). Configuration functions make it easy to control additional
+ request components (authenticate(), add_headers() and so on)."""
+
+ homepage = "https://github.com/hadley/httr"
+ url = "https://cran.r-project.org/src/contrib/httr_1.1.0.tar.gz"
+ list_url = "https://cran.r-project.org/src/contrib/Archive/httr"
+
+ version('1.1.0', '5ffbbc5c2529e49f00aaa521a2b35600')
+
+ extends('R')
+
+ depends_on('r-jsonlite')
+ depends_on('r-mime')
+ depends_on('r-curl')
+ depends_on('r-openssl')
+ depends_on('r-R6')
+
+ def install(self, spec, prefix):
+ R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+ self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-jsonlite/package.py b/var/spack/repos/builtin/packages/r-jsonlite/package.py
new file mode 100644
index 0000000000..6e231ed345
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-jsonlite/package.py
@@ -0,0 +1,50 @@
+##############################################################################
+# 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 RJsonlite(Package):
+ """A fast JSON parser and generator optimized for statistical data and the
+ web. Started out as a fork of 'RJSONIO', but has been completely rewritten
+ in recent versions. The package offers flexible, robust, high performance
+ tools for working with JSON in R and is particularly powerful for building
+ pipelines and interacting with a web API. The implementation is based on
+ the mapping described in the vignette (Ooms, 2014). In addition to
+ converting JSON data from/to R objects, 'jsonlite' contains functions to
+ stream, validate, and prettify JSON data. The unit tests included with the
+ package verify that all edge cases are encoded and decoded consistently for
+ use with dynamic data in systems and applications."""
+
+ homepage = "https://github.com/jeroenooms/jsonlite"
+ url = "https://cran.r-project.org/src/contrib/jsonlite_0.9.21.tar.gz"
+ list_url = "https://cran.r-project.org/src/contrib/Archive/jsonlite"
+
+ version('0.9.21', '4fc382747f88a79ff0718a0d06bed45d')
+
+ extends('R')
+
+ def install(self, spec, prefix):
+ R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+ self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-magic/package.py b/var/spack/repos/builtin/packages/r-magic/package.py
index f86917ec0c..f6ba97740b 100644
--- a/var/spack/repos/builtin/packages/r-magic/package.py
+++ b/var/spack/repos/builtin/packages/r-magic/package.py
@@ -24,6 +24,7 @@
##############################################################################
from spack import *
+
class RMagic(Package):
"""A collection of efficient, vectorized algorithms for the creation and
investigation of magic squares and hypercubes, including a variety of
@@ -32,12 +33,14 @@ class RMagic(Package):
homepage = "https://cran.r-project.org/"
url = "https://cran.r-project.org/src/contrib/magic_1.5-6.tar.gz"
+ list_url = "https://cran.r-project.org/src/contrib/Archive/magic"
- version('1.5-6', 'a68e5ced253b2196af842e1fc84fd029', expand=False)
+ version('1.5-6', 'a68e5ced253b2196af842e1fc84fd029')
extends('R')
depends_on('r-abind')
def install(self, spec, prefix):
- R('CMD', 'INSTALL', '--library=%s' % self.module.r_lib_dir, '%s' % self.stage.archive_file)
+ R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+ self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-memoise/package.py b/var/spack/repos/builtin/packages/r-memoise/package.py
new file mode 100644
index 0000000000..6a0fb78650
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-memoise/package.py
@@ -0,0 +1,44 @@
+##############################################################################
+# 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 RMemoise(Package):
+ """Cache the results of a function so that when you call it again with the
+ same arguments it returns the pre-computed value."""
+
+ homepage = "https://github.com/hadley/memoise"
+ url = "https://cran.r-project.org/src/contrib/memoise_1.0.0.tar.gz"
+ list_url = "https://cran.r-project.org/src/contrib/Archive/memoise"
+
+ version('1.0.0', 'd31145292e2a88ae9a504cab1602e4ac')
+
+ extends('R')
+
+ depends_on('r-digest')
+
+ def install(self, spec, prefix):
+ R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+ self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-mime/package.py b/var/spack/repos/builtin/packages/r-mime/package.py
new file mode 100644
index 0000000000..fb079f44c5
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-mime/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 RMime(Package):
+ """Guesses the MIME type from a filename extension using the data derived
+ from /etc/mime.types in UNIX-type systems."""
+
+ homepage = "https://github.com/yihui/mime"
+ url = "https://cran.r-project.org/src/contrib/mime_0.4.tar.gz"
+ list_url = "https://cran.r-project.org/src/contrib/Archive/mime"
+
+ version('0.4', '789cb33e41db2206c6fc7c3e9fbc2c02')
+
+ extends('R')
+
+ def install(self, spec, prefix):
+ R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+ self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-openssl/package.py b/var/spack/repos/builtin/packages/r-openssl/package.py
new file mode 100644
index 0000000000..3e77923d76
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-openssl/package.py
@@ -0,0 +1,52 @@
+##############################################################################
+# 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 ROpenssl(Package):
+ """Bindings to OpenSSL libssl and libcrypto, plus custom SSH pubkey
+ parsers. Supports RSA, DSA and EC curves P-256, P-384 and P-521.
+ Cryptographic signatures can either be created and verified manually or via
+ x509 certificates. AES can be used in cbc, ctr or gcm mode for symmetric
+ encryption; RSA for asymmetric (public key) encryption or EC for Diffie
+ Hellman. High-level envelope functions combine RSA and AES for encrypting
+ arbitrary sized data. Other utilities include key generators, hash
+ functions (md5, sha1, sha256, etc), base64 encoder, a secure random number
+ generator, and 'bignum' math methods for manually performing crypto
+ calculations on large multibyte integers."""
+
+ homepage = "https://github.com/jeroenooms/openssl#readme"
+ url = "https://cran.r-project.org/src/contrib/openssl_0.9.4.tar.gz"
+ list_url = "https://cran.r-project.org/src/contrib/Archive/openssl"
+
+ version('0.9.4', '82a890e71ed0e74499878bedacfb8ccb')
+
+ extends('R')
+
+ depends_on('openssl')
+
+ def install(self, spec, prefix):
+ R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+ self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-packrat/package.py b/var/spack/repos/builtin/packages/r-packrat/package.py
new file mode 100644
index 0000000000..9520952bd7
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-packrat/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 RPackrat(Package):
+ """Manage the R packages your project depends on in an isolated, portable,
+ and reproducible way."""
+
+ homepage = "https://github.com/rstudio/packrat/"
+ url = "https://cran.r-project.org/src/contrib/packrat_0.4.7-1.tar.gz"
+ list_url = "https://cran.r-project.org/src/contrib/Archive/packrat"
+
+ version('0.4.7-1', '80c2413269b292ade163a70ba5053e84')
+
+ extends('R')
+
+ def install(self, spec, prefix):
+ R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+ self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-rstudioapi/package.py b/var/spack/repos/builtin/packages/r-rstudioapi/package.py
new file mode 100644
index 0000000000..0ef2d9b987
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-rstudioapi/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 RRstudioapi(Package):
+ """Access the RStudio API (if available) and provide informative error
+ messages when it's not."""
+
+ homepage = "https://cran.r-project.org/web/packages/rstudioapi/index.html"
+ url = "https://cran.r-project.org/src/contrib/rstudioapi_0.5.tar.gz"
+ list_url = "https://cran.r-project.org/src/contrib/Archive/rstudioapi"
+
+ version('0.5', '6ce1191da74e7bcbf06b61339486b3ba')
+
+ extends('R')
+
+ def install(self, spec, prefix):
+ R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+ self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-whisker/package.py b/var/spack/repos/builtin/packages/r-whisker/package.py
new file mode 100644
index 0000000000..f338d150f1
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-whisker/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 RWhisker(Package):
+ """logicless templating, reuse templates in many programming languages
+ including R"""
+
+ homepage = "http://github.com/edwindj/whisker"
+ url = "https://cran.r-project.org/src/contrib/whisker_0.3-2.tar.gz"
+ list_url = "https://cran.r-project.org/src/contrib/Archive/whisker"
+
+ version('0.3-2', 'c4b9bf9a22e69ce003fe68663ab5e8e6')
+
+ extends('R')
+
+ def install(self, spec, prefix):
+ R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+ self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-withr/package.py b/var/spack/repos/builtin/packages/r-withr/package.py
new file mode 100644
index 0000000000..5ce7437c84
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-withr/package.py
@@ -0,0 +1,44 @@
+##############################################################################
+# 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 RWithr(Package):
+ """A set of functions to run code 'with' safely and temporarily modified
+ global state. Many of these functions were originally a part of the
+ 'devtools' package, this provides a simple package with limited
+ dependencies to provide access to these functions."""
+
+ homepage = "http://github.com/jimhester/withr"
+ url = "https://cran.r-project.org/src/contrib/withr_1.0.1.tar.gz"
+ list_url = "https://cran.r-project.org/src/contrib/Archive/withr"
+
+ version('1.0.1', 'ac38af2c6f74027c9592dd8f0acb7598')
+
+ extends('R')
+
+ def install(self, spec, prefix):
+ R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+ self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/serf/package.py b/var/spack/repos/builtin/packages/serf/package.py
index 3b1d08889c..817db68241 100644
--- a/var/spack/repos/builtin/packages/serf/package.py
+++ b/var/spack/repos/builtin/packages/serf/package.py
@@ -24,8 +24,10 @@
##############################################################################
from spack import *
+
class Serf(Package):
- """Apache Serf - a high performance C-based HTTP client library built upon the Apache Portable Runtime (APR) library"""
+ """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'
@@ -36,6 +38,7 @@ class Serf(Package):
depends_on('scons')
depends_on('expat')
depends_on('openssl')
+ depends_on('zlib')
def install(self, spec, prefix):
scons = which("scons")
@@ -44,8 +47,10 @@ class Serf(Package):
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)
+ options.append('LINKFLAGS=-L%s/lib -L%s/lib' %
+ (spec['expat'].prefix, spec['zlib'].prefix))
+ options.append('CPPFLAGS=-I%s/include -I%s/include' %
+ (spec['expat'].prefix, spec['zlib'].prefix))
scons(*options)
scons('install')
diff --git a/var/spack/repos/builtin/packages/slepc/package.py b/var/spack/repos/builtin/packages/slepc/package.py
index c148a579ec..d3739bf6a6 100644
--- a/var/spack/repos/builtin/packages/slepc/package.py
+++ b/var/spack/repos/builtin/packages/slepc/package.py
@@ -34,13 +34,16 @@ class Slepc(Package):
homepage = "http://www.grycap.upv.es/slepc"
url = "http://slepc.upv.es/download/download.php?filename=slepc-3.6.2.tar.gz"
+ version('3.7.1', '670216f263e3074b21e0623c01bc0f562fdc0bffcd7bd42dd5d8edbe73a532c2')
+ version('3.6.3', '384939d009546db37bc05ed81260c8b5ba451093bf891391d32eb7109ccff876')
version('3.6.2', '2ab4311bed26ccf7771818665991b2ea3a9b15f97e29fd13911ab1293e8e65df')
- variant('arpack', default=False, description='Enables Arpack wrappers')
+ variant('arpack', default=True, description='Enables Arpack wrappers')
- depends_on('petsc')
- depends_on('arpack-ng~mpi',when='+arpack^petsc~mpi')
- depends_on('arpack-ng+mpi',when='+arpack^petsc+mpi')
+ depends_on('petsc@3.7:', when='@3.7.1:')
+ depends_on('petsc@3.6.3:3.6.4', when='@3.6.2:3.6.3')
+ depends_on('arpack-ng~mpi', when='+arpack^petsc~mpi')
+ depends_on('arpack-ng+mpi', when='+arpack^petsc+mpi')
def install(self, spec, prefix):
# set SLEPC_DIR for installation
@@ -64,7 +67,7 @@ class Slepc(Package):
configure('--prefix=%s' % prefix, *options)
make('MAKE_NP=%s' % make_jobs, parallel=False)
- #FIXME:
+ # FIXME:
# make('test')
make('install')
diff --git a/var/spack/repos/builtin/packages/superlu-dist/package.py b/var/spack/repos/builtin/packages/superlu-dist/package.py
index 6c06b5497c..e51d7224d9 100644
--- a/var/spack/repos/builtin/packages/superlu-dist/package.py
+++ b/var/spack/repos/builtin/packages/superlu-dist/package.py
@@ -25,50 +25,54 @@
from spack import *
import glob
+
class SuperluDist(Package):
- """A general purpose library for the direct solution of large, sparse, nonsymmetric systems of linear equations on high performance machines."""
+ """A general purpose library for the direct solution of large, sparse,
+ nonsymmetric systems of linear equations on high performance machines."""
homepage = "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/"
url = "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/superlu_dist_4.1.tar.gz"
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('4.3', 'ee66c84e37b4f7cc557771ccc3dc43ae')
version('4.2', 'ae9fafae161f775fbac6eba11e530a65')
version('4.1', '4edee38cc29f687bd0c8eb361096a455')
version('4.0', 'c0b98b611df227ae050bc1635c6940e0')
- depends_on ('mpi')
- depends_on ('blas')
- depends_on ('lapack')
- depends_on ('parmetis')
- depends_on ('metis@5:')
+ depends_on('mpi')
+ depends_on('blas')
+ depends_on('lapack')
+ depends_on('parmetis')
+ depends_on('metis@5:')
def install(self, spec, prefix):
makefile_inc = []
makefile_inc.extend([
'PLAT = _mac_x',
- 'DSuperLUroot = %s' % self.stage.source_path, #self.stage.path, prefix
+ 'DSuperLUroot = %s' % self.stage.source_path,
'DSUPERLULIB = $(DSuperLUroot)/lib/libsuperlu_dist.a',
'BLASDEF = -DUSE_VENDOR_BLAS',
- 'BLASLIB = -L%s -llapack %s -lblas' % (spec['lapack'].prefix.lib, spec['blas'].prefix.lib), # FIXME: avoid hardcoding blas/lapack lib names
+ 'BLASLIB = %s %s' %
+ (to_link_flags(spec['lapack'].lapack_shared_lib),
+ to_link_flags(spec['blas'].blas_shared_lib)),
'METISLIB = -L%s -lmetis' % spec['metis'].prefix.lib,
'PARMETISLIB = -L%s -lparmetis' % spec['parmetis'].prefix.lib,
'FLIBS =',
- 'LIBS = $(DSUPERLULIB) $(BLASLIB) $(PARMETISLIB) $(METISLIB)',
+ 'LIBS = $(DSUPERLULIB) $(BLASLIB) $(PARMETISLIB) $(METISLIB)', # NOQA: ignore=E501
'ARCH = ar',
'ARCHFLAGS = cr',
'RANLIB = true',
- 'CC = mpicc', # FIXME avoid hardcoding MPI compiler names
- 'CFLAGS = -fPIC -std=c99 -O2 -I%s -I%s' %(spec['parmetis'].prefix.include, spec['metis'].prefix.include),
+ 'CC = %s' % spec['mpi'].mpicc,
+ 'CFLAGS = -fPIC -std=c99 -O2 -I%s -I%s' %
+ (spec['parmetis'].prefix.include,
+ spec['metis'].prefix.include),
'NOOPTS = -fPIC -std=c99',
- 'FORTRAN = mpif77',
+ 'FORTRAN = %s' % spec['mpi'].mpif77,
'F90FLAGS = -O2',
- 'LOADER = mpif77',
+ 'LOADER = %s' % spec['mpi'].mpif77,
'LOADOPTS =',
'CDEFS = -DAdd_'
- ])
+ ])
- #with working_dir('src'):
with open('make.inc', 'w') as fh:
fh.write('\n'.join(makefile_inc))
@@ -83,9 +87,10 @@ class SuperluDist(Package):
mkdirp(headers_location)
mkdirp(prefix.lib)
- headers = glob.glob(join_path(self.stage.source_path, 'SRC','*.h'))
+ headers = glob.glob(join_path(self.stage.source_path, 'SRC', '*.h'))
for h in headers:
- install(h,headers_location)
+ install(h, headers_location)
- superludist_lib = join_path(self.stage.source_path, 'lib/libsuperlu_dist.a')
- install(superludist_lib,self.prefix.lib)
+ superludist_lib = join_path(self.stage.source_path,
+ 'lib/libsuperlu_dist.a')
+ install(superludist_lib, self.prefix.lib)
diff --git a/var/spack/repos/builtin/packages/superlu/package.py b/var/spack/repos/builtin/packages/superlu/package.py
new file mode 100644
index 0000000000..c634c1d1ba
--- /dev/null
+++ b/var/spack/repos/builtin/packages/superlu/package.py
@@ -0,0 +1,54 @@
+##############################################################################
+# 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 Superlu(Package):
+ """SuperLU is a general purpose library for the direct solution of large,
+ sparse, nonsymmetric systems of linear equations on high performance
+ machines. SuperLU is designed for sequential machines."""
+
+ homepage = "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/#superlu"
+ url = "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/superlu_5.2.1.tar.gz"
+
+ version('5.2.1', '3a1a9bff20cb06b7d97c46d337504447')
+
+ depends_on('blas')
+
+ def install(self, spec, prefix):
+ cmake_args = [
+ '-DCMAKE_POSITION_INDEPENDENT_CODE=ON',
+ # BLAS support
+ '-Denable_blaslib=OFF',
+ '-DBLAS_blas_LIBRARY={0}'.format(spec['blas'].blas_shared_lib)
+ ]
+
+ cmake_args.extend(std_cmake_args)
+
+ with working_dir('spack-build', create=True):
+ cmake('..', *cmake_args)
+
+ make()
+ make('install')
diff --git a/var/spack/repos/builtin/packages/tmux/package.py b/var/spack/repos/builtin/packages/tmux/package.py
index c46425c0d3..573ee38a79 100644
--- a/var/spack/repos/builtin/packages/tmux/package.py
+++ b/var/spack/repos/builtin/packages/tmux/package.py
@@ -24,26 +24,33 @@
##############################################################################
from spack import *
+
class Tmux(Package):
"""tmux is a terminal multiplexer. What is a terminal multiplexer? It lets
- you switch easily between several programs in one terminal, detach them (they
- keep running in the background) and reattach them to a different terminal. And
- do a lot more.
+ you switch easily between several programs in one terminal, detach them
+ (they keep running in the background) and reattach them to a different
+ terminal. And do a lot more.
"""
homepage = "http://tmux.github.io"
- url = "https://github.com/tmux/tmux/releases/download/2.1/tmux-2.1.tar.gz"
+ url = "https://github.com/tmux/tmux/releases/download/2.2/tmux-2.2.tar.gz"
version('1.9a', 'b07601711f96f1d260b390513b509a2d')
version('2.1', '74a2855695bccb51b6e301383ad4818c')
+ version('2.2', 'bd95ee7205e489c62c616bb7af040099')
depends_on('libevent')
depends_on('ncurses')
def install(self, spec, prefix):
+ pkg_config_path = ':'.join([
+ spec['libevent'].prefix,
+ spec['ncurses'].prefix
+ ])
+
configure(
"--prefix=%s" % prefix,
- "PKG_CONFIG_PATH=%s:%s" % (spec['libevent'].prefix, spec['ncurses'].prefix))
+ "PKG_CONFIG_PATH=%s" % pkg_config_path)
make()
make("install")
diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py
index 1eaec86405..3a53ac5c01 100644
--- a/var/spack/repos/builtin/packages/trilinos/package.py
+++ b/var/spack/repos/builtin/packages/trilinos/package.py
@@ -23,23 +23,30 @@
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
from spack import *
-import os, sys, glob
+import os
+import sys
-# Trilinos is complicated to build, as an inspiration a couple of links to other repositories which build it:
+# Trilinos is complicated to build, as an inspiration a couple of links to
+# other repositories which build it:
# https://github.com/hpcugent/easybuild-easyblocks/blob/master/easybuild/easyblocks/t/trilinos.py#L111
# https://github.com/koecher/candi/blob/master/deal.II-toolchain/packages/trilinos.package
# https://gitlab.com/configurations/cluster-config/blob/master/trilinos.sh
-# https://github.com/Homebrew/homebrew-science/blob/master/trilinos.rb
-# and some relevant documentation/examples:
+# https://github.com/Homebrew/homebrew-science/blob/master/trilinos.rb and some
+# relevant documentation/examples:
# https://github.com/trilinos/Trilinos/issues/175
+
+
class Trilinos(Package):
- """The Trilinos Project is an effort to develop algorithms and enabling technologies within an object-oriented
- software framework for the solution of large-scale, complex multi-physics engineering and scientific problems.
+ """The Trilinos Project is an effort to develop algorithms and enabling
+ technologies within an object-oriented software framework for the solution
+ of large-scale, complex multi-physics engineering and scientific problems.
A unique design feature of Trilinos is its focus on packages.
"""
homepage = "https://trilinos.org/"
url = "http://trilinos.csbsju.edu/download/files/trilinos-12.2.1-Source.tar.gz"
+ version('12.6.3', '960f5f4d3f7c3da818e5a5fb4684559eff7e0c25f959ef576561b8a52f0e4d1e')
+ version('12.6.2', '0c076090508170ddee5efeed317745027f9418319720dc40a072e478775279f9')
version('12.6.1', 'adcf2d3aab74cdda98f88fee19cd1442604199b0515ee3da4d80cbe8f37d00e4')
version('12.4.2', '7c830f7f0f68b8ad324690603baf404e')
version('12.2.1', '6161926ea247863c690e927687f83be9')
@@ -54,49 +61,52 @@ class Trilinos(Package):
variant('hypre', default=True, description='Compile with Hypre preconditioner')
variant('hdf5', default=True, description='Compile with HDF5')
variant('suite-sparse', default=True, description='Compile with SuiteSparse solvers')
- # not everyone has py-numpy activated, keep it disabled by default to avoid configure errors
+ # not everyone has py-numpy activated, keep it disabled by default to avoid
+ # configure errors
variant('python', default=False, description='Build python wrappers')
variant('shared', default=True, description='Enables the build of shared libraries')
variant('debug', default=False, description='Builds a debug version of the libraries')
+ variant('boost', default=True, description='Compile with Boost')
# Everything should be compiled with -fpic
depends_on('blas')
depends_on('lapack')
- depends_on('boost')
+ depends_on('boost', when='+boost')
depends_on('matio')
depends_on('glm')
depends_on('swig')
- depends_on('metis@5:',when='+metis')
- depends_on('suite-sparse',when='+suite-sparse')
+ depends_on('metis@5:', when='+metis')
+ depends_on('suite-sparse', when='+suite-sparse')
# MPI related dependencies
depends_on('mpi')
depends_on('netcdf+mpi')
- depends_on('parmetis',when='+metis')
- # Trilinos' Tribits config system is limited which makes it
- # very tricky to link Amesos with static MUMPS, see
+ depends_on('parmetis', when='+metis')
+ # Trilinos' Tribits config system is limited which makes it very tricky to
+ # link Amesos with static MUMPS, see
# https://trilinos.org/docs/dev/packages/amesos2/doc/html/classAmesos2_1_1MUMPS.html
- # One could work it out by getting linking flags from mpif90 --showme:link (or alike)
- # and adding results to -DTrilinos_EXTRA_LINK_FLAGS
- # together with Blas and Lapack and ScaLAPACK and Blacs and -lgfortran and
- # it may work at the end. But let's avoid all this by simply using shared libs
- depends_on('mumps@5.0:+mpi+shared',when='+mumps')
- depends_on('scalapack',when='+mumps')
- depends_on('superlu-dist',when='+superlu-dist')
- depends_on('hypre~internal-superlu',when='+hypre')
- depends_on('hdf5+mpi',when='+hdf5')
-
- depends_on('python',when='+python')
+ # One could work it out by getting linking flags from mpif90 --showme:link
+ # (or alike) and adding results to -DTrilinos_EXTRA_LINK_FLAGS together
+ # with Blas and Lapack and ScaLAPACK and Blacs and -lgfortran and it may
+ # work at the end. But let's avoid all this by simply using shared libs
+ depends_on('mumps@5.0:+mpi+shared', when='+mumps')
+ depends_on('scalapack', when='+mumps')
+ depends_on('superlu-dist@:4.3', when='@:12.6.1+superlu-dist')
+ depends_on('superlu-dist', when='@12.6.2:+superlu-dist')
+ depends_on('hypre~internal-superlu', when='+hypre')
+ depends_on('hdf5+mpi', when='+hdf5')
+ depends_on('python', when='+python')
patch('umfpack_from_suitesparse.patch')
# check that the combination of variants makes sense
def variants_check(self):
if '+superlu-dist' in self.spec and self.spec.satisfies('@:11.4.3'):
- # For Trilinos v11 we need to force SuperLUDist=OFF,
- # since only the deprecated SuperLUDist v3.3 together with an Amesos patch
- # is working.
- raise RuntimeError('The superlu-dist variant can only be used with Trilinos @12.0.1:')
+ # For Trilinos v11 we need to force SuperLUDist=OFF, since only the
+ # deprecated SuperLUDist v3.3 together with an Amesos patch is
+ # working.
+ raise RuntimeError('The superlu-dist variant can only be used' +
+ ' with Trilinos @12.0.1:')
def install(self, spec, prefix):
self.variants_check()
@@ -106,54 +116,75 @@ class Trilinos(Package):
options.extend(std_cmake_args)
mpi_bin = spec['mpi'].prefix.bin
- options.extend(['-DTrilinos_ENABLE_ALL_PACKAGES:BOOL=ON',
- '-DTrilinos_ENABLE_ALL_OPTIONAL_PACKAGES:BOOL=ON',
- '-DTrilinos_VERBOSE_CONFIGURE:BOOL=OFF',
- '-DTrilinos_ENABLE_TESTS:BOOL=OFF',
- '-DTrilinos_ENABLE_EXAMPLES:BOOL=OFF',
- '-DCMAKE_BUILD_TYPE:STRING=%s' % ('DEBUG' if '+debug' in spec else 'RELEASE'),
- '-DBUILD_SHARED_LIBS:BOOL=%s' % ('ON' if '+shared' in spec else 'OFF'),
- '-DTPL_ENABLE_MPI:BOOL=ON',
- '-DMPI_BASE_DIR:PATH=%s' % spec['mpi'].prefix,
- '-DTPL_ENABLE_BLAS=ON',
- '-DBLAS_LIBRARY_NAMES=blas', # FIXME: don't hardcode names
- '-DBLAS_LIBRARY_DIRS=%s' % spec['blas'].prefix.lib,
- '-DTPL_ENABLE_LAPACK=ON',
- '-DLAPACK_LIBRARY_NAMES=lapack',
- '-DLAPACK_LIBRARY_DIRS=%s' % spec['lapack'].prefix,
- '-DTPL_ENABLE_Boost:BOOL=ON',
- '-DBoost_INCLUDE_DIRS:PATH=%s' % spec['boost'].prefix.include,
- '-DBoost_LIBRARY_DIRS:PATH=%s' % spec['boost'].prefix.lib,
- '-DTrilinos_ENABLE_EXPLICIT_INSTANTIATION:BOOL=ON',
- '-DTrilinos_ENABLE_CXX11:BOOL=ON',
- '-DTPL_ENABLE_Netcdf:BOOL=ON',
- '-DTPL_ENABLE_HYPRE:BOOL=%s' % ('ON' if '+hypre' in spec else 'OFF'),
- '-DTPL_ENABLE_HDF5:BOOL=%s' % ('ON' if '+hdf5' in spec else 'OFF'),
- ])
+ options.extend([
+ '-DTrilinos_ENABLE_ALL_PACKAGES:BOOL=ON',
+ '-DTrilinos_ENABLE_ALL_OPTIONAL_PACKAGES:BOOL=ON',
+ '-DTrilinos_VERBOSE_CONFIGURE:BOOL=OFF',
+ '-DTrilinos_ENABLE_TESTS:BOOL=OFF',
+ '-DTrilinos_ENABLE_EXAMPLES:BOOL=OFF',
+ '-DCMAKE_BUILD_TYPE:STRING=%s' % (
+ 'DEBUG' if '+debug' in spec else 'RELEASE'),
+ '-DBUILD_SHARED_LIBS:BOOL=%s' % (
+ 'ON' if '+shared' in spec else 'OFF'),
+ '-DTPL_ENABLE_MPI:BOOL=ON',
+ '-DMPI_BASE_DIR:PATH=%s' % spec['mpi'].prefix,
+ '-DTPL_ENABLE_BLAS=ON',
+ '-DBLAS_LIBRARY_NAMES=blas', # FIXME: don't hardcode names
+ '-DBLAS_LIBRARY_DIRS=%s' % spec['blas'].prefix.lib,
+ '-DTPL_ENABLE_LAPACK=ON',
+ '-DLAPACK_LIBRARY_NAMES=lapack',
+ '-DLAPACK_LIBRARY_DIRS=%s' % spec['lapack'].prefix,
+ '-DTrilinos_ENABLE_EXPLICIT_INSTANTIATION:BOOL=ON',
+ '-DTrilinos_ENABLE_CXX11:BOOL=ON',
+ '-DTPL_ENABLE_Netcdf:BOOL=ON',
+ '-DTPL_ENABLE_HYPRE:BOOL=%s' % (
+ 'ON' if '+hypre' in spec else 'OFF'),
+ '-DTPL_ENABLE_HDF5:BOOL=%s' % (
+ 'ON' if '+hdf5' in spec else 'OFF'),
+ ])
+
+ if '+boost' in spec:
+ options.extend([
+ '-DTPL_ENABLE_Boost:BOOL=ON',
+ '-DBoost_INCLUDE_DIRS:PATH=%s' % spec['boost'].prefix.include,
+ '-DBoost_LIBRARY_DIRS:PATH=%s' % spec['boost'].prefix.lib
+ ])
+ else:
+ options.extend(['-DTPL_ENABLE_Boost:BOOL=OFF'])
# Fortran lib
- libgfortran = os.path.dirname (os.popen('%s --print-file-name libgfortran.a' % join_path(mpi_bin,'mpif90') ).read())
+ libgfortran = os.path.dirname(os.popen(
+ '%s --print-file-name libgfortran.a' %
+ join_path(mpi_bin, 'mpif90')).read())
options.extend([
- '-DTrilinos_EXTRA_LINK_FLAGS:STRING=-L%s/ -lgfortran' % libgfortran,
+ '-DTrilinos_EXTRA_LINK_FLAGS:STRING=-L%s/ -lgfortran' % (
+ libgfortran),
'-DTrilinos_ENABLE_Fortran=ON'
])
# for build-debug only:
- #options.extend([
- # '-DCMAKE_VERBOSE_MAKEFILE:BOOL=TRUE'
- #])
+ # options.extend([
+ # '-DCMAKE_VERBOSE_MAKEFILE:BOOL=TRUE'
+ # ])
# suite-sparse related
if '+suite-sparse' in spec:
options.extend([
- '-DTPL_ENABLE_Cholmod:BOOL=OFF', # FIXME: Trilinos seems to be looking for static libs only, patch CMake TPL file?
- #'-DTPL_ENABLE_Cholmod:BOOL=ON',
- #'-DCholmod_LIBRARY_DIRS:PATH=%s' % spec['suite-sparse'].prefix.lib,
- #'-DCholmod_INCLUDE_DIRS:PATH=%s' % spec['suite-sparse'].prefix.include,
+ # FIXME: Trilinos seems to be looking for static libs only,
+ # patch CMake TPL file?
+ '-DTPL_ENABLE_Cholmod:BOOL=OFF',
+ # '-DTPL_ENABLE_Cholmod:BOOL=ON',
+ # '-DCholmod_LIBRARY_DIRS:PATH=%s' % (
+ # spec['suite-sparse'].prefix.lib,
+ # '-DCholmod_INCLUDE_DIRS:PATH=%s' % (
+ # spec['suite-sparse'].prefix.include,
'-DTPL_ENABLE_UMFPACK:BOOL=ON',
- '-DUMFPACK_LIBRARY_DIRS:PATH=%s' % spec['suite-sparse'].prefix.lib,
- '-DUMFPACK_INCLUDE_DIRS:PATH=%s' % spec['suite-sparse'].prefix.include,
- '-DUMFPACK_LIBRARY_NAMES=umfpack;amd;colamd;cholmod;suitesparseconfig'
+ '-DUMFPACK_LIBRARY_DIRS:PATH=%s' % (
+ spec['suite-sparse'].prefix.lib),
+ '-DUMFPACK_INCLUDE_DIRS:PATH=%s' % (
+ spec['suite-sparse'].prefix.include),
+ '-DUMFPACK_LIBRARY_NAMES=umfpack;amd;colamd;cholmod;' +
+ 'suitesparseconfig'
])
else:
options.extend([
@@ -169,9 +200,11 @@ class Trilinos(Package):
'-DMETIS_LIBRARY_NAMES=metis',
'-DTPL_METIS_INCLUDE_DIRS=%s' % spec['metis'].prefix.include,
'-DTPL_ENABLE_ParMETIS:BOOL=ON',
- '-DParMETIS_LIBRARY_DIRS=%s;%s' % (spec['parmetis'].prefix.lib,spec['metis'].prefix.lib),
+ '-DParMETIS_LIBRARY_DIRS=%s;%s' % (
+ spec['parmetis'].prefix.lib, spec['metis'].prefix.lib),
'-DParMETIS_LIBRARY_NAMES=parmetis;metis',
- '-DTPL_ParMETIS_INCLUDE_DIRS=%s' % spec['parmetis'].prefix.include
+ '-DTPL_ParMETIS_INCLUDE_DIRS=%s' % (
+ spec['parmetis'].prefix.include)
])
else:
options.extend([
@@ -184,11 +217,14 @@ class Trilinos(Package):
options.extend([
'-DTPL_ENABLE_MUMPS:BOOL=ON',
'-DMUMPS_LIBRARY_DIRS=%s' % spec['mumps'].prefix.lib,
- '-DMUMPS_LIBRARY_NAMES=dmumps;mumps_common;pord', # order is important!
+ # order is important!
+ '-DMUMPS_LIBRARY_NAMES=dmumps;mumps_common;pord',
'-DTPL_ENABLE_SCALAPACK:BOOL=ON',
- '-DSCALAPACK_LIBRARY_NAMES=scalapack' # FIXME: for MKL it's mkl_scalapack_lp64;mkl_blacs_mpich_lp64
+ # FIXME: for MKL it's mkl_scalapack_lp64;mkl_blacs_mpich_lp64
+ '-DSCALAPACK_LIBRARY_NAMES=scalapack'
])
- # see https://github.com/trilinos/Trilinos/blob/master/packages/amesos/README-MUMPS
+ # see
+ # https://github.com/trilinos/Trilinos/blob/master/packages/amesos/README-MUMPS
cxx_flags.extend([
'-DMUMPS_5_0'
])
@@ -201,16 +237,20 @@ class Trilinos(Package):
# superlu-dist:
if '+superlu-dist' in spec:
# Amesos, conflicting types of double and complex SLU_D
- # see https://trilinos.org/pipermail/trilinos-users/2015-March/004731.html
- # and https://trilinos.org/pipermail/trilinos-users/2015-March/004802.html
+ # see
+ # https://trilinos.org/pipermail/trilinos-users/2015-March/004731.html
+ # and
+ # https://trilinos.org/pipermail/trilinos-users/2015-March/004802.html
options.extend([
'-DTeuchos_ENABLE_COMPLEX:BOOL=OFF',
'-DKokkosTSQR_ENABLE_Complex:BOOL=OFF'
])
options.extend([
'-DTPL_ENABLE_SuperLUDist:BOOL=ON',
- '-DSuperLUDist_LIBRARY_DIRS=%s' % spec['superlu-dist'].prefix.lib,
- '-DSuperLUDist_INCLUDE_DIRS=%s' % spec['superlu-dist'].prefix.include
+ '-DSuperLUDist_LIBRARY_DIRS=%s' %
+ spec['superlu-dist'].prefix.lib,
+ '-DSuperLUDist_INCLUDE_DIRS=%s' %
+ spec['superlu-dist'].prefix.include
])
if spec.satisfies('^superlu-dist@4.0:'):
options.extend([
@@ -221,7 +261,6 @@ class Trilinos(Package):
'-DTPL_ENABLE_SuperLUDist:BOOL=OFF',
])
-
# python
if '+python' in spec:
options.extend([
@@ -248,23 +287,26 @@ class Trilinos(Package):
'-DTrilinos_ENABLE_FEI=OFF'
])
-
with working_dir('spack-build', create=True):
cmake('..', *options)
make()
make('install')
- # When trilinos is built with Python, libpytrilinos is included through
- # cmake configure files. Namely, Trilinos_LIBRARIES in TrilinosConfig.cmake
- # contains pytrilinos. This leads to a run-time error:
- # Symbol not found: _PyBool_Type
- # and prevents Trilinos to be used in any C++ code, which links executable
- # against the libraries listed in Trilinos_LIBRARIES.
- # See https://github.com/Homebrew/homebrew-science/issues/2148#issuecomment-103614509
+ # When trilinos is built with Python, libpytrilinos is included
+ # through cmake configure files. Namely, Trilinos_LIBRARIES in
+ # TrilinosConfig.cmake contains pytrilinos. This leads to a
+ # run-time error: Symbol not found: _PyBool_Type and prevents
+ # Trilinos to be used in any C++ code, which links executable
+ # against the libraries listed in Trilinos_LIBRARIES. See
+ # https://github.com/Homebrew/homebrew-science/issues/2148#issuecomment-103614509
# A workaround it to remove PyTrilinos from the COMPONENTS_LIST :
if '+python' in self.spec:
- filter_file(r'(SET\(COMPONENTS_LIST.*)(PyTrilinos;)(.*)', (r'\1\3'), '%s/cmake/Trilinos/TrilinosConfig.cmake' % prefix.lib)
+ filter_file(r'(SET\(COMPONENTS_LIST.*)(PyTrilinos;)(.*)',
+ (r'\1\3'),
+ '%s/cmake/Trilinos/TrilinosConfig.cmake' %
+ prefix.lib)
- # The shared libraries are not installed correctly on Darwin; correct this
+ # The shared libraries are 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/xorg-util-macros/package.py b/var/spack/repos/builtin/packages/xorg-util-macros/package.py
new file mode 100644
index 0000000000..963d93442f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/xorg-util-macros/package.py
@@ -0,0 +1,38 @@
+##############################################################################
+# 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 XorgUtilMacros(Package):
+ """The util-macros package contains the m4 macros used by all of the Xorg packages."""
+
+ homepage = "http://www.example.com"
+ url = "http://ftp.x.org/pub/individual/util/util-macros-1.19.0.tar.bz2"
+
+ version('1.19.0', '1cf984125e75f8204938d998a8b6c1e1')
+
+ def install(self, spec, prefix):
+ configure("--prefix=%s" % prefix)
+ make()
+ make("install")
diff --git a/var/spack/repos/builtin/packages/xproto/package.py b/var/spack/repos/builtin/packages/xproto/package.py
new file mode 100644
index 0000000000..7be6defb83
--- /dev/null
+++ b/var/spack/repos/builtin/packages/xproto/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 Xproto(Package):
+ """The Xorg protocol headers provide the header files required to
+ build the system, and to allow other applications to build against
+ the installed X Window system."""
+ homepage = "http://www.x.org/"
+ url = "https://www.x.org/archive//individual/proto/xproto-7.0.29.tar.gz"
+
+ version('7.0.29', '16a78dd2c5ad73011105c96235f6a0af')
+
+ depends_on("xorg-util-macros")
+
+ def install(self, spec, prefix):
+ configure('--prefix=%s' % prefix)
+ make()
+ make("install")