diff options
| author | citibeth <rpf2116@columbia.edu> | 2016-03-25 15:36:54 -0400 |
|---|---|---|
| committer | citibeth <rpf2116@columbia.edu> | 2016-03-25 15:36:54 -0400 |
| commit | 8019748396f65feadcdea2854921b6fcc9411e02 (patch) | |
| tree | 9c2dfab3c49c97838b6b54902b5ed830254c441e /var | |
| parent | 6f26c45143e63ee339f9aabc654684056b60654f (diff) | |
| parent | 38ea75e8ca65dd6c896fe7856efdb1d8355ec524 (diff) | |
| download | spack-8019748396f65feadcdea2854921b6fcc9411e02.tar.gz spack-8019748396f65feadcdea2854921b6fcc9411e02.tar.bz2 spack-8019748396f65feadcdea2854921b6fcc9411e02.tar.xz spack-8019748396f65feadcdea2854921b6fcc9411e02.zip | |
Merge remote-tracking branch 'upstream/develop' into efischer/160311-StagedPackage
# Conflicts:
# lib/spack/spack/package.py
Diffstat (limited to 'var')
50 files changed, 1128 insertions, 191 deletions
diff --git a/var/spack/repos/builtin.mock/packages/hypre/package.py b/var/spack/repos/builtin.mock/packages/hypre/package.py new file mode 100644 index 0000000000..f69f16d2cc --- /dev/null +++ b/var/spack/repos/builtin.mock/packages/hypre/package.py @@ -0,0 +1,39 @@ +############################################################################## +# Copyright (c) 2013-2015, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU General Public License (as published by +# the Free Software Foundation) version 2.1 dated February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program; if not, write to the Free Software Foundation, +# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + +class Hypre(Package): + """Hypre is included here as an example of a package that depends on + both LAPACK and BLAS.""" + homepage = "http://www.openblas.net" + url = "http://github.com/xianyi/OpenBLAS/archive/v0.2.15.tar.gz" + + version('0.2.15', 'b1190f3d3471685f17cfd1ec1d252ac9') + + depends_on('lapack') + depends_on('blas') + + def install(self, spec, prefix): + pass diff --git a/var/spack/repos/builtin.mock/packages/openblas-with-lapack/package.py b/var/spack/repos/builtin.mock/packages/openblas-with-lapack/package.py new file mode 100644 index 0000000000..509bfb71e5 --- /dev/null +++ b/var/spack/repos/builtin.mock/packages/openblas-with-lapack/package.py @@ -0,0 +1,38 @@ +############################################################################## +# Copyright (c) 2013-2015, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU General Public License (as published by +# the Free Software Foundation) version 2.1 dated February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program; if not, write to the Free Software Foundation, +# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + +class OpenblasWithLapack(Package): + """Dummy version of OpenBLAS that also provides LAPACK, for testing.""" + homepage = "http://www.openblas.net" + url = "http://github.com/xianyi/OpenBLAS/archive/v0.2.15.tar.gz" + + version('0.2.15', 'b1190f3d3471685f17cfd1ec1d252ac9') + + provides('lapack') + provides('blas') + + def install(self, spec, prefix): + pass diff --git a/var/spack/repos/builtin.mock/packages/python/package.py b/var/spack/repos/builtin.mock/packages/python/package.py new file mode 100644 index 0000000000..c5fed52f53 --- /dev/null +++ b/var/spack/repos/builtin.mock/packages/python/package.py @@ -0,0 +1,43 @@ +############################################################################## +# Copyright (c) 2013-2015, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU General Public License (as published by +# the Free Software Foundation) version 2.1 dated February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program; if not, write to the Free Software Foundation, +# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + +class Python(Package): + """Dummy Python package to demonstrate preferred versions.""" + 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) + version('2.7.10', 'd7547558fd673bd9d38e2108c6b42521') + version('2.7.9', '5eebcaa0030dc4061156d3429657fb83') + version('2.7.8', 'd4bca0159acb0b44a781292b5231936f') + + def install(self, spec, prefix): + pass + diff --git a/var/spack/repos/builtin/packages/arpack-ng/package.py b/var/spack/repos/builtin/packages/arpack-ng/package.py index 0b49d14202..dd86b17a53 100644 --- a/var/spack/repos/builtin/packages/arpack-ng/package.py +++ b/var/spack/repos/builtin/packages/arpack-ng/package.py @@ -35,6 +35,10 @@ class ArpackNg(Package): variant('shared', default=True, description='Enables the build of shared libraries') variant('mpi', default=False, description='Activates MPI support') + # The function pdlamch10 does not set the return variable. This is fixed upstream + # see https://github.com/opencollab/arpack-ng/issues/34 + patch('pdlamch10.patch', when='@3.3:') + depends_on('blas') depends_on('lapack') depends_on('mpi', when='+mpi') @@ -46,7 +50,10 @@ class ArpackNg(Package): options = ['--prefix=%s' % prefix] if '+mpi' in spec: - options.append('--enable-mpi') + options.extend([ + '--enable-mpi', + 'F77=mpif77' #FIXME: avoid hardcoding MPI wrapper names + ]) if '~shared' in spec: options.append('--enable-shared=no') diff --git a/var/spack/repos/builtin/packages/arpack-ng/pdlamch10.patch b/var/spack/repos/builtin/packages/arpack-ng/pdlamch10.patch new file mode 100644 index 0000000000..922828909f --- /dev/null +++ b/var/spack/repos/builtin/packages/arpack-ng/pdlamch10.patch @@ -0,0 +1,15 @@ +diff --git a/PARPACK/SRC/MPI/pdlamch10.f b/PARPACK/SRC/MPI/pdlamch10.f +index 6571da9..2882c2e 100644 +--- a/PARPACK/SRC/MPI/pdlamch10.f ++++ b/PARPACK/SRC/MPI/pdlamch10.f +@@ -86,8 +86,8 @@ + TEMP = TEMP1 + END IF + * +- PDLAMCH = TEMP ++ PDLAMCH10 = TEMP + * +-* End of PDLAMCH ++* End of PDLAMCH10 + * + END diff --git a/var/spack/repos/builtin/packages/atlas/package.py b/var/spack/repos/builtin/packages/atlas/package.py index fc683363a7..b5504122b7 100644 --- a/var/spack/repos/builtin/packages/atlas/package.py +++ b/var/spack/repos/builtin/packages/atlas/package.py @@ -1,31 +1,36 @@ from spack import * from spack.util.executable import Executable -import os +import os.path class Atlas(Package): """ - Automatically Tuned Linear Algebra Software, generic shared - ATLAS is an approach for the automatic generation and optimization of - numerical software. Currently ATLAS supplies optimized versions for the - complete set of linear algebra kernels known as the Basic Linear Algebra - Subroutines (BLAS), and a subset of the linear algebra routines in the - LAPACK library. + Automatically Tuned Linear Algebra Software, generic shared ATLAS is an approach for the automatic generation and + optimization of numerical software. Currently ATLAS supplies optimized versions for the complete set of linear + algebra kernels known as the Basic Linear Algebra Subroutines (BLAS), and a subset of the linear algebra routines + in the LAPACK library. """ homepage = "http://math-atlas.sourceforge.net/" + version('3.10.2', 'a4e21f343dec8f22e7415e339f09f6da', + url='http://downloads.sourceforge.net/project/math-atlas/Stable/3.10.2/atlas3.10.2.tar.bz2', preferred=True) + resource(name='lapack', + url='http://www.netlib.org/lapack/lapack-3.5.0.tgz', + md5='b1d3e3e425b2e44a06760ff173104bdf', + destination='spack-resource-lapack', + when='@3:') + version('3.11.34', '0b6c5389c095c4c8785fd0f724ec6825', url='http://sourceforge.net/projects/math-atlas/files/Developer%20%28unstable%29/3.11.34/atlas3.11.34.tar.bz2/download') - version('3.10.2', 'a4e21f343dec8f22e7415e339f09f6da', - url='http://downloads.sourceforge.net/project/math-atlas/Stable/3.10.2/atlas3.10.2.tar.bz2') - # TODO: make this provide BLAS once it works better. Create a way - # TODO: to mark "beta" packages and require explicit invocation. + variant('shared', default=True, description='Builds shared library') - # provides('blas') + provides('blas') + provides('lapack') + parallel = False def patch(self): - # Disable thraed check. LLNL's environment does not allow + # Disable thread check. LLNL's environment does not allow # disabling of CPU throttling in a way that ATLAS actually # understands. filter_file(r'^\s+if \(thrchk\) exit\(1\);', 'if (0) exit(1);', @@ -33,26 +38,21 @@ class Atlas(Package): # TODO: investigate a better way to add the check back in # TODO: using, say, MSRs. Or move this to a variant. - @when('@:3.10') def install(self, spec, prefix): - with working_dir('ATLAS-Build', create=True): - configure = Executable('../configure') - configure('--prefix=%s' % prefix, '-C', 'ic', 'cc', '-C', 'if', 'f77', "--dylibs") - make() - make('check') - make('ptcheck') - make('time') - make("install") + options = [] + if '+shared' in spec: + options.append('--shared') - def install(self, spec, prefix): - with working_dir('ATLAS-Build', create=True): - configure = Executable('../configure') - configure('--incdir=%s' % prefix.include, - '--libdir=%s' % prefix.lib, - '--cc=cc', - "--shared") + # Lapack resource + lapack_stage = self.stage[1] + lapack_tarfile = os.path.basename(lapack_stage.fetcher.url) + lapack_tarfile_path = join_path(lapack_stage.path, lapack_tarfile) + options.append('--with-netlib-lapack-tarfile=%s' % lapack_tarfile_path) + with working_dir('spack-build', create=True): + configure = Executable('../configure') + configure('--prefix=%s' % prefix, *options) make() make('check') make('ptcheck') diff --git a/var/spack/repos/builtin/packages/binutils/package.py b/var/spack/repos/builtin/packages/binutils/package.py index de04221e33..897539a439 100644 --- a/var/spack/repos/builtin/packages/binutils/package.py +++ b/var/spack/repos/builtin/packages/binutils/package.py @@ -4,10 +4,13 @@ class Binutils(Package): """GNU binutils, which contain the linker, assembler, objdump and others""" homepage = "http://www.gnu.org/software/binutils/" - version('2.25', 'd9f3303f802a5b6b0bb73a335ab89d66',url="ftp://ftp.gnu.org/gnu/binutils/binutils-2.25.tar.bz2") - version('2.24', 'e0f71a7b2ddab0f8612336ac81d9636b',url="ftp://ftp.gnu.org/gnu/binutils/binutils-2.24.tar.bz2") - version('2.23.2', '4f8fa651e35ef262edc01d60fb45702e',url="ftp://ftp.gnu.org/gnu/binutils/binutils-2.23.2.tar.bz2") - version('2.20.1', '2b9dc8f2b7dbd5ec5992c6e29de0b764',url="ftp://ftp.gnu.org/gnu/binutils/binutils-2.20.1.tar.bz2") + url="https://ftp.gnu.org/gnu/binutils/binutils-2.25.tar.bz2" + + version('2.26', '64146a0faa3b411ba774f47d41de239f') + version('2.25', 'd9f3303f802a5b6b0bb73a335ab89d66') + version('2.24', 'e0f71a7b2ddab0f8612336ac81d9636b') + version('2.23.2', '4f8fa651e35ef262edc01d60fb45702e') + version('2.20.1', '2b9dc8f2b7dbd5ec5992c6e29de0b764') # Add a patch that creates binutils libiberty_pic.a which is preferred by OpenSpeedShop and cbtf-krell variant('krellpatch', default=False, description="build with openspeedshop based patch.") diff --git a/var/spack/repos/builtin/packages/cmake/package.py b/var/spack/repos/builtin/packages/cmake/package.py index cc93c7067c..1f93d39769 100644 --- a/var/spack/repos/builtin/packages/cmake/package.py +++ b/var/spack/repos/builtin/packages/cmake/package.py @@ -38,10 +38,12 @@ class Cmake(Package): version('2.8.10.2', '097278785da7182ec0aea8769d06860c') variant('ncurses', default=True, description='Enables the build of the ncurses gui') + variant('openssl', default=True, description="Enables CMake's OpenSSL features") variant('qt', default=False, description='Enables the build of cmake-gui') variant('doc', default=False, description='Enables the generation of html and man page documentation') depends_on('ncurses', when='+ncurses') + depends_on('openssl', when='+openssl') depends_on('qt', when='+qt') depends_on('python@2.7.11:', when='+doc') depends_on('py-sphinx', when='+doc') @@ -77,8 +79,9 @@ class Cmake(Package): options.append('--sphinx-html') options.append('--sphinx-man') - options.append('--') - options.append('-DCMAKE_USE_OPENSSL=ON') + if '+openssl' in spec: + options.append('--') + options.append('-DCMAKE_USE_OPENSSL=ON') configure(*options) make() diff --git a/var/spack/repos/builtin/packages/cryptopp/package.py b/var/spack/repos/builtin/packages/cryptopp/package.py index 1693c4b160..bc83cb2b65 100644 --- a/var/spack/repos/builtin/packages/cryptopp/package.py +++ b/var/spack/repos/builtin/packages/cryptopp/package.py @@ -8,8 +8,8 @@ class Cryptopp(Package): public-key encryption (RSA, DSA), and a few obsolete/historical encryption algorithms (MD5, Panama).""" - homepage = "http://www.cryptopp.com/" - url = "http://www.cryptopp.com/cryptopp563.zip" + homepage = "http://www.cryptopp.com" + base_url = "http://www.cryptopp.com" version('5.6.3', '3c5b70e2ec98b7a24988734446242d07') version('5.6.2', '7ed022585698df48e65ce9218f6c6a67') @@ -25,7 +25,5 @@ class Cryptopp(Package): install('libcryptopp.a', prefix.lib) def url_for_version(self, version): - version_tuple = tuple(v for v in iter(version)) - version_string = reduce(lambda vs, nv: vs + str(nv), version_tuple, "") - - return "%scryptopp%s.zip" % (Cryptopp.homepage, version_string) + version_string = str(version).replace('.', '') + return '%s/cryptopp%s.zip' % (Cryptopp.base_url, version_string) diff --git a/var/spack/repos/builtin/packages/curl/package.py b/var/spack/repos/builtin/packages/curl/package.py index 9e684445c7..ab6305fc08 100644 --- a/var/spack/repos/builtin/packages/curl/package.py +++ b/var/spack/repos/builtin/packages/curl/package.py @@ -7,6 +7,7 @@ class Curl(Package): homepage = "http://curl.haxx.se" url = "http://curl.haxx.se/download/curl-7.46.0.tar.bz2" + version('7.47.1', '9ea3123449439bbd960cd25cf98796fb') version('7.46.0', '9979f989a2a9930d10f1b3deeabc2148') version('7.45.0', '62c1a352b28558f25ba6209214beadc8') version('7.44.0', '6b952ca00e5473b16a11f05f06aa8dae') diff --git a/var/spack/repos/builtin/packages/eigen/package.py b/var/spack/repos/builtin/packages/eigen/package.py index e40046b452..8d6e672f86 100644 --- a/var/spack/repos/builtin/packages/eigen/package.py +++ b/var/spack/repos/builtin/packages/eigen/package.py @@ -48,7 +48,7 @@ class Eigen(Package): depends_on('metis', when='+metis') depends_on('scotch', when='+scotch') depends_on('fftw', when='+fftw') - depends_on('SuiteSparse', when='+suitesparse') + depends_on('suite-sparse', when='+suitesparse') depends_on('mpfr@2.3.0:') # Eigen 3.2.7 requires at least 2.3.0 depends_on('gmp') diff --git a/var/spack/repos/builtin/packages/emacs/package.py b/var/spack/repos/builtin/packages/emacs/package.py index 09eb05d5a7..caa264857e 100644 --- a/var/spack/repos/builtin/packages/emacs/package.py +++ b/var/spack/repos/builtin/packages/emacs/package.py @@ -12,6 +12,8 @@ class Emacs(Package): # GTK or other widget library # libtiff, png, etc. # For now, we assume the system provides all that stuff. + # For Ubuntu 14.04 LTS: + # sudo apt-get install libgtk-3-dev libxpm-dev libtiff5-dev libjpeg8-dev libgif-dev libpng12-dev def install(self, spec, prefix): configure('--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/espresso/package.py b/var/spack/repos/builtin/packages/espresso/package.py index a2bf58f585..59f362ab46 100644 --- a/var/spack/repos/builtin/packages/espresso/package.py +++ b/var/spack/repos/builtin/packages/espresso/package.py @@ -32,6 +32,10 @@ class Espresso(Package): if '+elpa' in spec and ('~mpi' in spec or '~scalapack' in spec): raise RuntimeError(error.format(variant='elpa')) + def setup_environment(self, spack_env, run_env): + # Espresso copies every executable in prefix without creating sub-folders + run_env.prepend_path('PATH', self.prefix) + def install(self, spec, prefix): self.check_variants(spec) diff --git a/var/spack/repos/builtin/packages/gettext/package.py b/var/spack/repos/builtin/packages/gettext/package.py new file mode 100644 index 0000000000..05712d7392 --- /dev/null +++ b/var/spack/repos/builtin/packages/gettext/package.py @@ -0,0 +1,30 @@ +from spack import * + +class Gettext(Package): + """GNU internationalization (i18n) and localization (l10n) library.""" + homepage = "https://www.gnu.org/software/gettext/" + url = "http://ftpmirror.gnu.org/gettext/gettext-0.19.7.tar.xz" + + version('0.19.7', 'f81e50556da41b44c1d59ac93474dca5') + + def install(self, spec, prefix): + options = ['--disable-dependency-tracking', + '--disable-silent-rules', + '--disable-debug', + '--prefix=%s' % prefix, + '--with-included-gettext', + '--with-included-glib', + '--with-included-libcroco', + '--with-included-libunistring', + '--with-emacs', + '--with-lispdir=%s/emacs/site-lisp/gettext' % prefix.share, + '--disable-java', + '--disable-csharp', + '--without-git', # Don't use VCS systems to create these archives + '--without-cvs', + '--without-xz'] + + configure(*options) + + make() + make("install") diff --git a/var/spack/repos/builtin/packages/git/package.py b/var/spack/repos/builtin/packages/git/package.py index ddc5078c4d..586b6ce3c3 100644 --- a/var/spack/repos/builtin/packages/git/package.py +++ b/var/spack/repos/builtin/packages/git/package.py @@ -5,14 +5,22 @@ class Git(Package): system designed to handle everything from small to very large projects with speed and efficiency.""" homepage = "http://git-scm.com" - url = "https://www.kernel.org/pub/software/scm/git/git-2.2.1.tar.gz" + url = "https://github.com/git/git/tarball/v2.7.1" - version('2.6.3', 'b711be7628a4a2c25f38d859ee81b423') - version('2.6.2', 'da293290da69f45a86a311ad3cd43dc8') - version('2.6.1', '4c62ee9c5991fe93d99cf2a6b68397fd') - version('2.6.0', 'eb76a07148d94802a1745d759716a57e') - version('2.5.4', '3eca2390cf1fa698b48e2a233563a76b') - version('2.2.1', 'ff41fdb094eed1ec430aed8ee9b9849c') + version('2.8.0-rc2', 'c2cf9f2cc70e35f2fafbaf9258f82e4c') + version('2.7.3', 'fa1c008b56618c355a32ba4a678305f6') + version('2.7.1', 'bf0706b433a8dedd27a63a72f9a66060') + + + # See here for info on vulnerable Git versions: + # http://www.theregister.co.uk/2016/03/16/git_server_client_patch_now/ + # All the following are vulnerable + #version('2.6.3', 'b711be7628a4a2c25f38d859ee81b423') + #version('2.6.2', 'da293290da69f45a86a311ad3cd43dc8') + #version('2.6.1', '4c62ee9c5991fe93d99cf2a6b68397fd') + #version('2.6.0', 'eb76a07148d94802a1745d759716a57e') + #version('2.5.4', '3eca2390cf1fa698b48e2a233563a76b') + #version('2.2.1', 'ff41fdb094eed1ec430aed8ee9b9849c') # Git compiles with curl support by default on but if your system @@ -24,6 +32,7 @@ class Git(Package): variant("expat", default=False, description="Add the internal support of expat for https push") depends_on("openssl") + depends_on("autoconf") depends_on("curl", when="+curl") depends_on("expat", when="+expat") @@ -47,6 +56,7 @@ class Git(Package): if '+expat' in spec: configure_args.append("--with-expat=%s" % spec['expat'].prefix) + which('autoreconf')('-i') configure(*configure_args) make() make("install") diff --git a/var/spack/repos/builtin/packages/gl2ps/package.py b/var/spack/repos/builtin/packages/gl2ps/package.py new file mode 100644 index 0000000000..cb376b3f03 --- /dev/null +++ b/var/spack/repos/builtin/packages/gl2ps/package.py @@ -0,0 +1,18 @@ +from spack import * + +class Gl2ps(Package): + """GL2PS is a C library providing high quality vector output for any + OpenGL application.""" + + homepage = "http://www.geuz.org/gl2ps/" + url = "http://geuz.org/gl2ps/src/gl2ps-1.3.9.tgz" + + version('1.3.9', '377b2bcad62d528e7096e76358f41140') + + depends_on("libpng") + + def install(self, spec, prefix): + cmake('.', *std_cmake_args) + + make() + make("install") diff --git a/var/spack/repos/builtin/packages/hypre/package.py b/var/spack/repos/builtin/packages/hypre/package.py index 242ee100d7..8d93d48d1f 100644 --- a/var/spack/repos/builtin/packages/hypre/package.py +++ b/var/spack/repos/builtin/packages/hypre/package.py @@ -1,5 +1,5 @@ from spack import * -import os +import os, sys class Hypre(Package): """Hypre is a library of high performance preconditioners that @@ -12,7 +12,8 @@ class Hypre(Package): version('2.10.1', 'dc048c4cabb3cd549af72591474ad674') version('2.10.0b', '768be38793a35bb5d055905b271f5b8e') - variant('shared', default=True, description="Build shared library version (disables static library)") + # hypre does not know how to build shared libraries on Darwin + variant('shared', default=sys.platform!='darwin', description="Build shared library version (disables static library)") depends_on("mpi") depends_on("blas") diff --git a/var/spack/repos/builtin/packages/llvm/package.py b/var/spack/repos/builtin/packages/llvm/package.py index 280e400f69..1d25d59e50 100644 --- a/var/spack/repos/builtin/packages/llvm/package.py +++ b/var/spack/repos/builtin/packages/llvm/package.py @@ -52,7 +52,7 @@ class Llvm(Package): depends_on('cmake @2.8.12.2:') # Universal dependency - depends_on('python@2.7:') + depends_on('python@2.7:2.8') # Seems not to support python 3.X.Y # lldb dependencies depends_on('ncurses', when='+lldb') @@ -133,6 +133,21 @@ class Llvm(Package): } }, { + 'version' : '3.8.0', + 'md5':'07a7a74f3c6bd65de4702bf941b511a0', + 'resources' : { + 'compiler-rt' : 'd6fcbe14352ffb708e4d1ac2e48bb025', + 'openmp' : '8fd7cc35d48051613cf1e750e9f22e40', + 'polly' : '1b3b20f52d34a4024e21a4ea7112caa7', + 'libcxx' : 'd6e0bdbbee39f7907ad74fd56d03b88a', + 'libcxxabi' : 'bbe6b4d72c7c5978550d370af529bcf7', + 'clang' : 'cc99e7019bb74e6459e80863606250c5', + 'clang-tools-extra' : 'c2344f50e0eea0b402f0092a80ddc036', + 'lldb' : 'a5da35ed9cc8c8817ee854e3dbfba00e', + 'llvm-libunwind' : '162ade468607f153cca12be90b5194fa', + } + }, + { 'version' : '3.7.1', 'md5':'bf8b3a2c79e61212c5409041dfdbd319', 'resources' : { diff --git a/var/spack/repos/builtin/packages/mpich/package.py b/var/spack/repos/builtin/packages/mpich/package.py index e2b3654c19..b20dc8dd60 100644 --- a/var/spack/repos/builtin/packages/mpich/package.py +++ b/var/spack/repos/builtin/packages/mpich/package.py @@ -25,6 +25,7 @@ from spack import * import os + class Mpich(Package): """MPICH is a high performance and widely portable implementation of the Message Passing Interface (MPI) standard.""" @@ -46,14 +47,16 @@ class Mpich(Package): provides('mpi@:3.0', when='@3:') provides('mpi@:1.3', when='@1:') - def setup_dependent_environment(self, module, spec, dep_spec): - """For dependencies, make mpicc's use spack wrapper.""" - os.environ['MPICH_CC'] = os.environ['CC'] - os.environ['MPICH_CXX'] = os.environ['CXX'] - os.environ['MPICH_F77'] = os.environ['F77'] - os.environ['MPICH_F90'] = os.environ['FC'] - os.environ['MPICH_FC'] = os.environ['FC'] + def setup_dependent_environment(self, env, dependent_spec): + env.set('MPICH_CC', spack_cc) + env.set('MPICH_CXX', spack_cxx) + env.set('MPICH_F77', spack_f77) + env.set('MPICH_F90', spack_f90) + env.set('MPICH_FC', spack_fc) + def setup_dependent_package(self, module, dep_spec): + """For dependencies, make mpicc's use spack wrapper.""" + # FIXME : is this necessary ? Shouldn't this be part of a contract with MPI providers? module.mpicc = join_path(self.prefix.bin, 'mpicc') def install(self, spec, prefix): diff --git a/var/spack/repos/builtin/packages/mumps/package.py b/var/spack/repos/builtin/packages/mumps/package.py index 44a37903cc..5a254dfd00 100644 --- a/var/spack/repos/builtin/packages/mumps/package.py +++ b/var/spack/repos/builtin/packages/mumps/package.py @@ -20,10 +20,10 @@ class Mumps(Package): variant('complex', default=True, description='Activate the compilation of cmumps and/or zmumps') variant('idx64', default=False, description='Use int64_t/integer*8 as default index type') - + depends_on('scotch + esmumps', when='~ptscotch+scotch') depends_on('scotch + esmumps + mpi', when='+ptscotch') - depends_on('metis', when='~parmetis+metis') + depends_on('metis', when='+metis') depends_on('parmetis', when="+parmetis") depends_on('blas') depends_on('lapack') @@ -38,11 +38,11 @@ class Mumps(Package): def write_makefile_inc(self): if ('+parmetis' in self.spec or '+ptscotch' in self.spec) and '+mpi' not in self.spec: raise RuntimeError('You cannot use the variants parmetis or ptscotch without mpi') - + makefile_conf = ["LIBBLAS = -L%s -lblas" % self.spec['blas'].prefix.lib] orderings = ['-Dpord'] - + if '+ptscotch' in self.spec or '+scotch' in self.spec: join_lib = ' -l%s' % ('pt' if '+ptscotch' in self.spec else '') makefile_conf.extend( @@ -54,15 +54,19 @@ class Mumps(Package): if '+ptscotch' in self.spec: orderings.append('-Dptscotch') - if '+parmetis' in self.spec or '+metis' in self.spec: + if '+parmetis' in self.spec and '+metis' in self.spec: libname = 'parmetis' if '+parmetis' in self.spec else 'metis' makefile_conf.extend( - ["IMETIS = -I%s" % self.spec[libname].prefix.include, - "LMETIS = -L%s -l%s" % (self.spec[libname].prefix.lib, libname)]) + ["IMETIS = -I%s" % self.spec['parmetis'].prefix.include, + "LMETIS = -L%s -l%s -L%s -l%s" % (self.spec['parmetis'].prefix.lib, 'parmetis',self.spec['metis'].prefix.lib, 'metis')]) + + orderings.append('-Dparmetis') + elif '+metis' in self.spec: + makefile_conf.extend( + ["IMETIS = -I%s" % self.spec['metis'].prefix.include, + "LMETIS = -L%s -l%s" % (self.spec['metis'].prefix.lib, 'metis')]) orderings.append('-Dmetis') - if '+parmetis' in self.spec: - orderings.append('-Dparmetis') makefile_conf.append("ORDERINGSF = %s" % (' '.join(orderings))) @@ -101,12 +105,12 @@ class Mumps(Package): # compiler possible values are -DAdd_, -DAdd__ and/or -DUPPER makefile_conf.append("CDEFS = -DAdd_") - + makefile_inc_template = join_path(os.path.dirname(self.module.__file__), 'Makefile.inc') with open(makefile_inc_template, "r") as fh: makefile_conf.extend(fh.read().split('\n')) - + with working_dir('.'): with open("Makefile.inc", "w") as fh: makefile_inc = '\n'.join(makefile_conf) @@ -130,8 +134,9 @@ class Mumps(Package): make_libs.append('zexamples') self.write_makefile_inc() - - make(*make_libs) + + # Build fails in parallel, at least on OS-X + make(*make_libs, parallel=False) install_tree('lib', prefix.lib) install_tree('include', prefix.include) diff --git a/var/spack/repos/builtin/packages/muparser/package.py b/var/spack/repos/builtin/packages/muparser/package.py new file mode 100644 index 0000000000..a1a9ff90e5 --- /dev/null +++ b/var/spack/repos/builtin/packages/muparser/package.py @@ -0,0 +1,18 @@ +from spack import * + +class Muparser(Package): + """C++ math expression parser library.""" + homepage = "http://muparser.beltoforion.de/" + url = "https://github.com/beltoforion/muparser/archive/v2.2.5.tar.gz" + + version('2.2.5', '02dae671aa5ad955fdcbcd3fee313fb7') + + def install(self, spec, prefix): + options = ['--disable-debug', + '--disable-dependency-tracking', + '--prefix=%s' % prefix] + + configure(*options) + + make() + make("install") diff --git a/var/spack/repos/builtin/packages/mvapich2/package.py b/var/spack/repos/builtin/packages/mvapich2/package.py index af5ed1b088..e4e95f92af 100644 --- a/var/spack/repos/builtin/packages/mvapich2/package.py +++ b/var/spack/repos/builtin/packages/mvapich2/package.py @@ -123,7 +123,7 @@ class Mvapich2(Package): count += 1 if count > 1: raise RuntimeError('network variants are mutually exclusive (only one can be selected at a time)') - + network_options = [] # From here on I can suppose that only one variant has been selected if self.enabled(Mvapich2.PSM) in spec: network_options = ["--with-device=ch3:psm"] diff --git a/var/spack/repos/builtin/packages/netlib-lapack/package.py b/var/spack/repos/builtin/packages/netlib-lapack/package.py index fb6b99e27c..78c5a053fe 100644 --- a/var/spack/repos/builtin/packages/netlib-lapack/package.py +++ b/var/spack/repos/builtin/packages/netlib-lapack/package.py @@ -12,6 +12,7 @@ class NetlibLapack(Package): homepage = "http://www.netlib.org/lapack/" url = "http://www.netlib.org/lapack/lapack-3.5.0.tgz" + version('3.6.0', 'f2f6c67134e851fe189bb3ca1fbb5101') version('3.5.0', 'b1d3e3e425b2e44a06760ff173104bdf') version('3.4.2', '61bf1a8a4469d4bdb7604f5897179478') version('3.4.1', '44c3869c38c8335c2b9c2a8bb276eb55') @@ -19,13 +20,13 @@ class NetlibLapack(Package): version('3.3.1', 'd0d533ec9a5b74933c2a1e84eedc58b4') variant('shared', default=False, description="Build shared library version") + variant('fpic', default=False, description="Build with -fpic compiler option") # virtual dependency provides('lapack') # blas is a virtual dependency. depends_on('blas') - depends_on('cmake') # Doesn't always build correctly in parallel @@ -36,24 +37,23 @@ class NetlibLapack(Package): blas = self.spec['netlib-blas'] return [join_path(blas.prefix.lib, 'blas.a')] - @when('^atlas') def get_blas_libs(self): blas = self.spec['atlas'] return [join_path(blas.prefix.lib, l) for l in ('libf77blas.a', 'libatlas.a')] - def install(self, spec, prefix): blas_libs = ";".join(self.get_blas_libs()) cmake_args = [".", '-DBLAS_LIBRARIES=' + blas_libs] if '+shared' in spec: cmake_args.append('-DBUILD_SHARED_LIBS=ON') + if '+fpic' in spec: + cmake_args.append('-DCMAKE_POSITION_INDEPENDENT_CODE=ON') cmake_args += std_cmake_args cmake(*cmake_args) make() make("install") - diff --git a/var/spack/repos/builtin/packages/netlib-scalapack/package.py b/var/spack/repos/builtin/packages/netlib-scalapack/package.py index 22d538560e..c3e6822cdf 100644 --- a/var/spack/repos/builtin/packages/netlib-scalapack/package.py +++ b/var/spack/repos/builtin/packages/netlib-scalapack/package.py @@ -1,8 +1,9 @@ from spack import * +import sys class NetlibScalapack(Package): """ScaLAPACK is a library of high-performance linear algebra routines for parallel distributed memory machines""" - + homepage = "http://www.netlib.org/scalapack/" url = "http://www.netlib.org/scalapack/scalapack-2.0.2.tgz" @@ -11,16 +12,16 @@ class NetlibScalapack(Package): version('2.0.0', '9e76ae7b291be27faaad47cfc256cbfe') # versions before 2.0.0 are not using cmake and requires blacs as # a separated package - + variant('shared', default=True, description='Build the shared library version') variant('fpic', default=False, description="Build with -fpic compiler option") - + provides('scalapack') - + depends_on('mpi') depends_on('lapack') - - def install(self, spec, prefix): + + def install(self, spec, prefix): options = [ "-DBUILD_SHARED_LIBS:BOOL=%s" % ('ON' if '+shared' in spec else 'OFF'), "-DBUILD_STATIC_LIBS:BOOL=%s" % ('OFF' if '+shared' in spec else 'ON'), @@ -32,19 +33,19 @@ class NetlibScalapack(Package): "-DCMAKE_C_FLAGS=-fPIC", "-DCMAKE_Fortran_FLAGS=-fPIC" ]) - + options.extend(std_cmake_args) - + with working_dir('spack-build', create=True): cmake('..', *options) make() make("install") - def setup_dependent_environment(self, module, spec, dependent_spec): - # TODO treat OS that are not Linux... - lib_suffix = '.so' if '+shared' in spec['scalapack'] else '.a' + def setup_dependent_package(self, module, dependent_spec): + spec = self.spec + lib_dsuffix = '.dylib' if sys.platform == 'darwin' else '.so' + lib_suffix = lib_dsuffix if '+shared' in spec else '.a' - spec['scalapack'].fc_link = '-L%s -lscalapack' % spec['scalapack'].prefix.lib - spec['scalapack'].cc_link = spec['scalapack'].fc_link - spec['scalapack'].libraries = [join_path(spec['scalapack'].prefix.lib, - 'libscalapack%s' % lib_suffix)] + spec.fc_link = '-L%s -lscalapack' % spec.prefix.lib + spec.cc_link = spec.fc_link + spec.libraries = [join_path(spec.prefix.lib, 'libscalapack%s' % lib_suffix)] diff --git a/var/spack/repos/builtin/packages/oce/package.py b/var/spack/repos/builtin/packages/oce/package.py new file mode 100644 index 0000000000..06acb96736 --- /dev/null +++ b/var/spack/repos/builtin/packages/oce/package.py @@ -0,0 +1,47 @@ +from spack import * +import platform + +class Oce(Package): + """ + Open CASCADE Community Edition: + patches/improvements/experiments contributed by users over the official Open CASCADE library. + """ + homepage = "https://github.com/tpaviot/oce" + url = "https://github.com/tpaviot/oce/archive/OCE-0.17.tar.gz" + + version('0.17.1', '36c67b87093c675698b483454258af91') + version('0.17' , 'f1a89395c4b0d199bea3db62b85f818d') + version('0.16.1', '4d591b240c9293e879f50d86a0cb2bb3') + version('0.16' , '7a4b4df5a104d75a537e25e7dd387eca') + version('0.15' , '7ec541a1c350ca8a684f74980e48801c') + + depends_on('cmake@2.8:') + + def install(self, spec, prefix): + options = [] + options.extend(std_cmake_args) + options.extend([ + '-DOCE_INSTALL_PREFIX=%s' % prefix, + '-DOCE_BUILD_SHARED_LIB:BOOL=ON', + '-DOCE_BUILD_TYPE:STRING=Release', + '-DOCE_DATAEXCHANGE:BOOL=ON', + '-DOCE_DISABLE_X11:BOOL=ON', + '-DOCE_DRAW:BOOL=OFF', + '-DOCE_MODEL:BOOL=ON', + '-DOCE_MULTITHREAD_LIBRARY:STRING=NONE', # FIXME: add tbb + '-DOCE_OCAF:BOOL=ON', + '-DOCE_USE_TCL_TEST_FRAMEWORK:BOOL=OFF', + '-DOCE_VISUALISATION:BOOL=OFF', + '-DOCE_WITH_FREEIMAGE:BOOL=OFF', + '-DOCE_WITH_GL2PS:BOOL=OFF', + '-DOCE_WITH_OPENCL:BOOL=OFF' + ]) + + if platform.system() == 'Darwin': + options.extend([ + '-DOCE_OSX_USE_COCOA:BOOL=ON', + ]) + + cmake('.', *options) + + make("install/strip") diff --git a/var/spack/repos/builtin/packages/octave/package.py b/var/spack/repos/builtin/packages/octave/package.py new file mode 100644 index 0000000000..6e99c23652 --- /dev/null +++ b/var/spack/repos/builtin/packages/octave/package.py @@ -0,0 +1,183 @@ +from spack import * + +class Octave(Package): + """GNU Octave is a high-level language, primarily intended for numerical + computations. It provides a convenient command line interface for solving + linear and nonlinear problems numerically, and for performing other + numerical experiments using a language that is mostly compatible with + Matlab. It may also be used as a batch-oriented language.""" + + homepage = "https://www.gnu.org/software/octave/" + url = "ftp://ftp.gnu.org/gnu/octave/octave-4.0.0.tar.gz" + + version('4.0.0' , 'a69f8320a4f20a8480c1b278b1adb799') + + # Variants + variant('readline', default=True) + variant('arpack', default=False) + variant('curl', default=False) + variant('fftw', default=False) + variant('fltk', default=False) + variant('fontconfig', default=False) + variant('freetype', default=False) + variant('glpk', default=False) + variant('gl2ps', default=False) + variant('gnuplot', default=False) + variant('magick', default=False) + variant('hdf5', default=False) + variant('jdk', default=False) + variant('llvm', default=False) + variant('opengl', default=False) + variant('qhull', default=False) + variant('qrupdate', default=False) + variant('qscintilla', default=False) + variant('qt', default=False) + variant('suiteparse', default=False) + variant('zlib', default=False) + + # Required dependencies + depends_on('blas') + depends_on('lapack') + depends_on('pcre') + + # Strongly recommended dependencies + depends_on('readline', when='+readline') + + # Optional dependencies + depends_on('arpack', when='+arpack') + depends_on('curl', when='+curl') + depends_on('fftw', when='+fftw') + depends_on('fltk', when='+fltk') + depends_on('fontconfig', when='+fontconfig') + depends_on('freetype', when='+freetype') + depends_on('glpk', when='+glpk') + depends_on('gl2ps', when='+gl2ps') + depends_on('gnuplot', when='+gnuplot') + depends_on('ImageMagick', when='+magick') + depends_on('hdf5', when='+hdf5') + depends_on('jdk', when='+jdk') + depends_on('llvm', when='+llvm') + #depends_on('opengl', when='+opengl') # TODO: add package + depends_on('qhull', when='+qhull') + depends_on('qrupdate', when='+qrupdate') + #depends_on('qscintilla', when='+qscintilla) # TODO: add package + depends_on('qt', when='+qt') + depends_on('suite-sparse',when='+suitesparse') + depends_on('zlib', when='+zlib') + + + def install(self, spec, prefix): + config_args = [ + "--prefix=%s" % prefix + ] + + # Required dependencies + config_args.extend([ + "--with-blas=%s" % spec['blas'].prefix.lib, + "--with-lapack=%s" % spec['lapack'].prefix.lib + ]) + + # Strongly recommended dependencies + if '+readline' in spec: + config_args.append('--enable-readline') + else: + config_args.append('--disable-readline') + + # Optional dependencies + if '+arpack' in spec: + config_args.extend([ + "--with-arpack-includedir=%s" % spec['arpack'].prefix.include, + "--with-arpack-libdir=%s" % spec['arpack'].prefix.lib + ]) + else: + config_args.append("--without-arpack") + + if '+curl' in spec: + config_args.extend([ + "--with-curl-includedir=%s" % spec['curl'].prefix.include, + "--with-curl-libdir=%s" % spec['curl'].prefix.lib + ]) + else: + config_args.append("--without-curl") + + if '+fftw' in spec: + config_args.extend([ + "--with-fftw3-includedir=%s" % spec['fftw'].prefix.include, + "--with-fftw3-libdir=%s" % spec['fftw'].prefix.lib, + "--with-fftw3f-includedir=%s" % spec['fftw'].prefix.include, + "--with-fftw3f-libdir=%s" % spec['fftw'].prefix.lib + ]) + else: + config_args.extend([ + "--without-fftw3", + "--without-fftw3f" + ]) + + if '+fltk' in spec: + config_args.extend([ + "--with-fltk-prefix=%s" % spec['fltk'].prefix, + "--with-fltk-exec-prefix=%s" % spec['fltk'].prefix + ]) + else: + config_args.append("--without-fltk") + + if '+glpk' in spec: + config_args.extend([ + "--with-glpk-includedir=%s" % spec['glpk'].prefix.include, + "--with-glpk-libdir=%s" % spec['glpk'].prefix.lib + ]) + else: + config_args.append("--without-glpk") + + if '+magick' in spec: + config_args.append("--with-magick=%s" % spec['ImageMagick'].prefix.lib) + + if '+hdf5' in spec: + config_args.extend([ + "--with-hdf5-includedir=%s" % spec['hdf5'].prefix.include, + "--with-hdf5-libdir=%s" % spec['hdf5'].prefix.lib + ]) + else: + config_args.append("--without-hdf5") + + if '+jdk' in spec: + config_args.extend([ + "--with-java-homedir=%s" % spec['jdk'].prefix, + "--with-java-includedir=%s" % spec['jdk'].prefix.include, + "--with-java-libdir=%s" % spec['jdk'].prefix.lib + ]) + + if '~opengl' in spec: + config_args.extend([ + "--without-opengl", + "--without-framework-opengl" + ]) + + if '+qhull' in spec: + config_args.extend([ + "--with-qhull-includedir=%s" % spec['qhull'].prefix.include, + "--with-qhull-libdir=%s" % spec['qhull'].prefix.lib + ]) + else: + config_args.append("--without-qhull") + + if '+qrupdate' in spec: + config_args.extend([ + "--with-qrupdate-includedir=%s" % spec['qrupdate'].prefix.include, + "--with-qrupdate-libdir=%s" % spec['qrupdate'].prefix.lib + ]) + else: + config_args.append("--without-qrupdate") + + if '+zlib' in spec: + config_args.extend([ + "--with-z-includedir=%s" % spec['zlib'].prefix.include, + "--with-z-libdir=%s" % spec['zlib'].prefix.lib + ]) + else: + config_args.append("--without-z") + + configure(*config_args) + + make() + make("install") diff --git a/var/spack/repos/builtin/packages/openblas/package.py b/var/spack/repos/builtin/packages/openblas/package.py index 3c909360a4..1d10f217c4 100644 --- a/var/spack/repos/builtin/packages/openblas/package.py +++ b/var/spack/repos/builtin/packages/openblas/package.py @@ -1,10 +1,13 @@ from spack import * +import sys class Openblas(Package): """OpenBLAS: An optimized BLAS library""" homepage = "http://www.openblas.net" url = "http://github.com/xianyi/OpenBLAS/archive/v0.2.15.tar.gz" + version('0.2.17', '664a12807f2a2a7cda4781e3ab2ae0e1') + version('0.2.16', 'fef46ab92463bdbb1479dcec594ef6dc') version('0.2.15', 'b1190f3d3471685f17cfd1ec1d252ac9') # virtual dependency @@ -12,16 +15,24 @@ class Openblas(Package): provides('lapack') def install(self, spec, prefix): - make('libs', 'netlib', 'shared', 'CC=cc', 'FC=f77') + extra=[] + if spec.satisfies('@0.2.16'): + extra.extend([ + 'BUILD_LAPACK_DEPRECATED=1' # fix missing _dggsvd_ and _sggsvd_ + ]) + + make('libs', 'netlib', 'shared', 'CC=cc', 'FC=f77',*extra) + make("tests") make('install', "PREFIX='%s'" % prefix) + lib_dsuffix = 'dylib' if sys.platform == 'darwin' else 'so' # Blas virtual package should provide blas.a and libblas.a with working_dir(prefix.lib): symlink('libopenblas.a', 'blas.a') symlink('libopenblas.a', 'libblas.a') - symlink('libopenblas.so', 'libblas.so') + symlink('libopenblas.%s' % lib_dsuffix, 'libblas.%s' % lib_dsuffix) # Lapack virtual package should provide liblapack.a with working_dir(prefix.lib): symlink('libopenblas.a', 'liblapack.a') - symlink('libopenblas.so', 'liblapack.so') + symlink('libopenblas.%s' % lib_dsuffix, 'liblapack.%s' % lib_dsuffix) diff --git a/var/spack/repos/builtin/packages/openmpi/package.py b/var/spack/repos/builtin/packages/openmpi/package.py index e4484af8c5..9a127f1812 100644 --- a/var/spack/repos/builtin/packages/openmpi/package.py +++ b/var/spack/repos/builtin/packages/openmpi/package.py @@ -41,12 +41,13 @@ class Openmpi(Package): def url_for_version(self, version): return "http://www.open-mpi.org/software/ompi/v%s/downloads/openmpi-%s.tar.bz2" % (version.up_to(2), version) - def setup_dependent_environment(self, module, spec, dep_spec): - """For dependencies, make mpicc's use spack wrapper.""" - os.environ['OMPI_CC'] = 'cc' - os.environ['OMPI_CXX'] = 'c++' - os.environ['OMPI_FC'] = 'f90' - os.environ['OMPI_F77'] = 'f77' + + def setup_dependent_environment(self, spack_env, run_env, dependent_spec): + spack_env.set('OMPI_CC', spack_cc) + spack_env.set('OMPI_CXX', spack_cxx) + spack_env.set('OMPI_FC', spack_fc) + spack_env.set('OMPI_F77', spack_f77) + def install(self, spec, prefix): config_args = ["--prefix=%s" % prefix, diff --git a/var/spack/repos/builtin/packages/p4est/package.py b/var/spack/repos/builtin/packages/p4est/package.py new file mode 100644 index 0000000000..1e2969fe64 --- /dev/null +++ b/var/spack/repos/builtin/packages/p4est/package.py @@ -0,0 +1,34 @@ +from spack import * + +class P4est(Package): + """Dynamic management of a collection (a forest) of adaptive octrees in parallel""" + homepage = "http://www.p4est.org" + url = "http://p4est.github.io/release/p4est-1.1.tar.gz" + + version('1.1', '37ba7f4410958cfb38a2140339dbf64f') + + # disable by default to make it work on frontend of clusters + variant('tests', default=False, description='Run small tests') + + depends_on('mpi') + + def install(self, spec, prefix): + options = ['--enable-mpi', + '--enable-shared', + '--disable-vtk-binary', + '--without-blas', + 'CPPFLAGS=-DSC_LOG_PRIORITY=SC_LP_ESSENTIAL', + 'CFLAGS=-O2', + 'CC=%s' % join_path(self.spec['mpi'].prefix.bin, 'mpicc'), # TODO: use ENV variables or MPI class wrappers + 'CXX=%s' % join_path(self.spec['mpi'].prefix.bin, 'mpic++'), + 'FC=%s' % join_path(self.spec['mpi'].prefix.bin, 'mpif90'), + 'F77=%s' % join_path(self.spec['mpi'].prefix.bin, 'mpif77'), + ] + + configure('--prefix=%s' % prefix, *options) + + make() + if '+tests' in self.spec: + make("check") + + make("install") diff --git a/var/spack/repos/builtin/packages/papi/package.py b/var/spack/repos/builtin/packages/papi/package.py index 910e0aa9f9..53d69e28d9 100644 --- a/var/spack/repos/builtin/packages/papi/package.py +++ b/var/spack/repos/builtin/packages/papi/package.py @@ -13,6 +13,7 @@ class Papi(Package): homepage = "http://icl.cs.utk.edu/papi/index.html" url = "http://icl.cs.utk.edu/projects/papi/downloads/papi-5.4.1.tar.gz" + version('5.4.3', '3211b5a5bb389fe692370f5cf4cc2412') version('5.4.1', '9134a99219c79767a11463a76b0b01a2') version('5.3.0', '367961dd0ab426e5ae367c2713924ffb') diff --git a/var/spack/repos/builtin/packages/paraview/package.py b/var/spack/repos/builtin/packages/paraview/package.py index ccf2d14c06..c16054816c 100644 --- a/var/spack/repos/builtin/packages/paraview/package.py +++ b/var/spack/repos/builtin/packages/paraview/package.py @@ -16,9 +16,9 @@ class Paraview(Package): variant('osmesa', default=False, description='Enable OSMesa support') variant('qt', default=False, description='Enable Qt support') - variant('opengl2', default=False, description='Enable OPengl2 backend') + variant('opengl2', default=False, description='Enable OpenGL2 backend') - depends_on('python', when='+python') + depends_on('python@2:2.7', when='+python') depends_on('py-numpy', when='+python') depends_on('py-matplotlib', when='+python') depends_on('tcl', when='+tcl') @@ -37,11 +37,11 @@ class Paraview(Package): #depends_on('protobuf') # version mismatches? #depends_on('sqlite') # external version not supported depends_on('zlib') - + def url_for_version(self, version): """Handle ParaView version-based custom URLs.""" return self._url_str % (version.up_to(2), version) - + def install(self, spec, prefix): with working_dir('spack-build', create=True): diff --git a/var/spack/repos/builtin/packages/parmetis/enable_external_metis.patch b/var/spack/repos/builtin/packages/parmetis/enable_external_metis.patch new file mode 100644 index 0000000000..514781b8b8 --- /dev/null +++ b/var/spack/repos/builtin/packages/parmetis/enable_external_metis.patch @@ -0,0 +1,13 @@ +diff --git a/CMakeLists.txt b/CMakeLists.txt +index ca945dd..1bf94e9 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -33,7 +33,7 @@ include_directories(${GKLIB_PATH}) + include_directories(${METIS_PATH}/include) + + # List of directories that cmake will look for CMakeLists.txt +-add_subdirectory(${METIS_PATH}/libmetis ${CMAKE_BINARY_DIR}/libmetis) ++#add_subdirectory(${METIS_PATH}/libmetis ${CMAKE_BINARY_DIR}/libmetis) + add_subdirectory(include) + add_subdirectory(libparmetis) + add_subdirectory(programs) diff --git a/var/spack/repos/builtin/packages/parmetis/link-to-lm.patch b/var/spack/repos/builtin/packages/parmetis/link-to-lm.patch new file mode 100644 index 0000000000..faa809231e --- /dev/null +++ b/var/spack/repos/builtin/packages/parmetis/link-to-lm.patch @@ -0,0 +1,14 @@ +diff --git a/libparmetis/CMakeLists.txt b/libparmetis/CMakeLists.txt +index 9cfc8a7..dfc0125 100644 +--- a/libparmetis/CMakeLists.txt ++++ b/libparmetis/CMakeLists.txt +@@ -5,7 +5,7 @@ file(GLOB parmetis_sources *.c) + # Create libparmetis + add_library(parmetis ${ParMETIS_LIBRARY_TYPE} ${parmetis_sources}) + # Link with metis and MPI libraries. +-target_link_libraries(parmetis metis ${MPI_LIBRARIES}) ++target_link_libraries(parmetis metis ${MPI_LIBRARIES} "-lm") + set_target_properties(parmetis PROPERTIES LINK_FLAGS "${MPI_LINK_FLAGS}") + + install(TARGETS parmetis + diff --git a/var/spack/repos/builtin/packages/parmetis/package.py b/var/spack/repos/builtin/packages/parmetis/package.py index c897dec7e4..bc71fb7299 100644 --- a/var/spack/repos/builtin/packages/parmetis/package.py +++ b/var/spack/repos/builtin/packages/parmetis/package.py @@ -25,9 +25,6 @@ from spack import * -# FIXME : lot of code is duplicated from packages/metis/package.py . Inheriting from there may reduce -# FIXME : the installation rules to just a few lines - class Parmetis(Package): """ @@ -43,13 +40,19 @@ class Parmetis(Package): variant('debug', default=False, description='Builds the library in debug mode') variant('gdb', default=False, description='Enables gdb support') - variant('idx64', default=False, description='Use int64_t as default index type') - variant('double', default=False, description='Use double precision floating point types') - depends_on('cmake @2.8:') # build dependency depends_on('mpi') - # FIXME : this should conflict with metis as it builds its own version internally + patch('enable_external_metis.patch') + depends_on('metis') + + # bug fixes from PETSc developers + # https://bitbucket.org/petsc/pkg-parmetis/commits/1c1a9fd0f408dc4d42c57f5c3ee6ace411eb222b/raw/ + patch('pkg-parmetis-1c1a9fd0f408dc4d42c57f5c3ee6ace411eb222b.patch') + # https://bitbucket.org/petsc/pkg-parmetis/commits/82409d68aa1d6cbc70740d0f35024aae17f7d5cb/raw/ + patch('pkg-parmetis-82409d68aa1d6cbc70740d0f35024aae17f7d5cb.patch') + + patch('link-to-lm.patch') depends_on('gdb', when='+gdb') @@ -63,8 +66,8 @@ class Parmetis(Package): # FIXME : Once a contract is defined, MPI compilers should be retrieved indirectly via spec['mpi'] in case # FIXME : they use a non-standard name - options.extend(['-DGKLIB_PATH:PATH={metis_source}/GKlib'.format(metis_source=metis_source), - '-DMETIS_PATH:PATH={metis_source}'.format(metis_source=metis_source), + options.extend(['-DGKLIB_PATH:PATH={metis_source}/GKlib'.format(metis_source=metis_source), # still need headers from METIS source, and they are not installed with METIS. shame... + '-DMETIS_PATH:PATH={metis_source}'.format(metis_source=spec['metis'].prefix), '-DCMAKE_C_COMPILER:STRING=mpicc', '-DCMAKE_CXX_COMPILER:STRING=mpicxx']) @@ -78,18 +81,7 @@ class Parmetis(Package): if '+gdb' in spec: options.append('-DGDB:BOOL=ON') - metis_header = join_path(metis_source, 'include', 'metis.h') - - if '+idx64' in spec: - filter_file('IDXTYPEWIDTH 32', 'IDXTYPEWIDTH 64', metis_header) - - if '+double' in spec: - filter_file('REALTYPEWIDTH 32', 'REALTYPEWIDTH 64', metis_header) - with working_dir(build_directory, create=True): cmake(source_directory, *options) make() make("install") - # Parmetis build system doesn't allow for an external metis to be used, but doesn't copy the required - # metis header either - install(metis_header, self.prefix.include) diff --git a/var/spack/repos/builtin/packages/parmetis/pkg-parmetis-1c1a9fd0f408dc4d42c57f5c3ee6ace411eb222b.patch b/var/spack/repos/builtin/packages/parmetis/pkg-parmetis-1c1a9fd0f408dc4d42c57f5c3ee6ace411eb222b.patch new file mode 100644 index 0000000000..e6b8056c21 --- /dev/null +++ b/var/spack/repos/builtin/packages/parmetis/pkg-parmetis-1c1a9fd0f408dc4d42c57f5c3ee6ace411eb222b.patch @@ -0,0 +1,77 @@ +From 1c1a9fd0f408dc4d42c57f5c3ee6ace411eb222b Mon Sep 17 00:00:00 2001 +From: Jed Brown <jed@59A2.org> +Date: Fri, 12 Oct 2012 15:45:10 -0500 +Subject: [PATCH] ParMetis bug fixes reported by John Fettig [petsc-maint + #133631] + +''' +I have also reported to to Karypis but have received zero +response and he hasn't released any updates to the original release +either. At least he approved my forum posting so that other people +can see the bug and the fix. +http://glaros.dtc.umn.edu/gkhome/node/837 +''' + +Hg-commit: 1c2b9fe39201d404b493885093b5992028b9b8d4 +--- + libparmetis/xyzpart.c | 12 ++++++------ + 1 file changed, 6 insertions(+), 6 deletions(-) + +diff --git a/libparmetis/xyzpart.c b/libparmetis/xyzpart.c +index 3a2c289..63abfcb 100644 +--- a/libparmetis/xyzpart.c ++++ b/libparmetis/xyzpart.c +@@ -104,7 +104,7 @@ void IRBinCoordinates(ctrl_t *ctrl, graph_t *graph, idx_t ndims, real_t *xyz, + + for (i=0; i<nbins; i++) + emarkers[i] = gmin + (gmax-gmin)*i/nbins; +- emarkers[nbins] = gmax*(1.0+2.0*REAL_EPSILON); ++ emarkers[nbins] = gmax*(1.0+copysign(1.0,gmax)*2.0*REAL_EPSILON); + + /* get into a iterative backet boundary refinement */ + for (l=0; l<5; l++) { +@@ -152,7 +152,7 @@ void IRBinCoordinates(ctrl_t *ctrl, graph_t *graph, idx_t ndims, real_t *xyz, + } + } + nemarkers[0] = gmin; +- nemarkers[nbins] = gmax*(1.0+2.0*REAL_EPSILON); ++ nemarkers[nbins] = gmax*(1.0+copysign(1.0,gmax)*2.0*REAL_EPSILON); + rcopy(nbins+1, nemarkers, emarkers); + } + +@@ -218,7 +218,7 @@ void RBBinCoordinates(ctrl_t *ctrl, graph_t *graph, idx_t ndims, real_t *xyz, + + emarkers[0] = gmin; + emarkers[1] = gsum/gnvtxs; +- emarkers[2] = gmax*(1.0+2.0*REAL_EPSILON); ++ emarkers[2] = gmax*(1.0+(gmax < 0 ? -1. : 1.)*2.0*REAL_EPSILON); + cnbins = 2; + + /* get into a iterative backet boundary refinement */ +@@ -227,7 +227,7 @@ void RBBinCoordinates(ctrl_t *ctrl, graph_t *graph, idx_t ndims, real_t *xyz, + iset(cnbins, 0, lcounts); + rset(cnbins, 0, lsums); + for (j=0, i=0; i<nvtxs;) { +- if (cand[i].key < emarkers[j+1]) { ++ if (cand[i].key <= emarkers[j+1]) { + lcounts[j]++; + lsums[j] += cand[i].key; + i++; +@@ -272,12 +272,12 @@ void RBBinCoordinates(ctrl_t *ctrl, graph_t *graph, idx_t ndims, real_t *xyz, + + rsorti(cnbins, nemarkers); + rcopy(cnbins, nemarkers, emarkers); +- emarkers[cnbins] = gmax*(1.0+2.0*REAL_EPSILON); ++ emarkers[cnbins] = gmax*(1.0+(gmax < 0 ? -1. : 1.)*2.0*REAL_EPSILON); + } + + /* assign the coordinate to the appropriate bin */ + for (j=0, i=0; i<nvtxs;) { +- if (cand[i].key < emarkers[j+1]) { ++ if (cand[i].key <= emarkers[j+1]) { + bxyz[cand[i].val*ndims+k] = j; + i++; + } +-- +2.1.1.1.g1fb337f + diff --git a/var/spack/repos/builtin/packages/parmetis/pkg-parmetis-82409d68aa1d6cbc70740d0f35024aae17f7d5cb.patch b/var/spack/repos/builtin/packages/parmetis/pkg-parmetis-82409d68aa1d6cbc70740d0f35024aae17f7d5cb.patch new file mode 100644 index 0000000000..9651d55347 --- /dev/null +++ b/var/spack/repos/builtin/packages/parmetis/pkg-parmetis-82409d68aa1d6cbc70740d0f35024aae17f7d5cb.patch @@ -0,0 +1,35 @@ +From 82409d68aa1d6cbc70740d0f35024aae17f7d5cb Mon Sep 17 00:00:00 2001 +From: Sean Farley <sean@mcs.anl.gov> +Date: Tue, 20 Mar 2012 11:59:44 -0500 +Subject: [PATCH] parmetis: fix bug reported by jfettig; '<' to '<=' in xyzpart + +Hg-commit: 2dd2eae596acaabbc80e0ef875182616f868dbc2 +--- + libparmetis/xyzpart.c | 4 ++-- + 1 file changed, 2 insertions(+), 2 deletions(-) + +diff --git a/libparmetis/xyzpart.c b/libparmetis/xyzpart.c +index 307aed9..3a2c289 100644 +--- a/libparmetis/xyzpart.c ++++ b/libparmetis/xyzpart.c +@@ -111,7 +111,7 @@ void IRBinCoordinates(ctrl_t *ctrl, graph_t *graph, idx_t ndims, real_t *xyz, + /* determine bucket counts */ + iset(nbins, 0, lcounts); + for (j=0, i=0; i<nvtxs;) { +- if (cand[i].key < emarkers[j+1]) { ++ if (cand[i].key <= emarkers[j+1]) { + lcounts[j]++; + i++; + } +@@ -158,7 +158,7 @@ void IRBinCoordinates(ctrl_t *ctrl, graph_t *graph, idx_t ndims, real_t *xyz, + + /* assign the coordinate to the appropriate bin */ + for (j=0, i=0; i<nvtxs;) { +- if (cand[i].key < emarkers[j+1]) { ++ if (cand[i].key <= emarkers[j+1]) { + bxyz[cand[i].val*ndims+k] = j; + i++; + } +-- +2.1.1.1.g1fb337f + diff --git a/var/spack/repos/builtin/packages/petsc/package.py b/var/spack/repos/builtin/packages/petsc/package.py index efe172fc08..3dd117eed1 100644 --- a/var/spack/repos/builtin/packages/petsc/package.py +++ b/var/spack/repos/builtin/packages/petsc/package.py @@ -61,14 +61,24 @@ class Petsc(Package): errors = ['incompatible variants given'] + errors raise RuntimeError('\n'.join(errors)) else: - compiler_opts = [ - '--with-mpi=1', - '--with-mpi-dir=%s' % self.spec['mpi'].prefix, - ] + if self.compiler.name == "clang": + compiler_opts = [ + '--with-mpi=1', + '--with-cc=%s -Qunused-arguments' % join_path(self.spec['mpi'].prefix.bin, 'mpicc'), # Avoid confusing PETSc config by clang: warning: argument unused during compilation + '--with-cxx=%s -Qunused-arguments' % join_path(self.spec['mpi'].prefix.bin, 'mpic++'), + '--with-fc=%s' % join_path(self.spec['mpi'].prefix.bin, 'mpif90'), + '--with-f77=%s' % join_path(self.spec['mpi'].prefix.bin, 'mpif77'), + ] + else: + compiler_opts = [ + '--with-mpi=1', + '--with-mpi-dir=%s' % self.spec['mpi'].prefix, + ] return compiler_opts def install(self, spec, prefix): - options = [] + options = ['--with-debugging=0', + '--with-ssl=0'] options.extend(self.mpi_dependent_options()) options.extend([ '--with-precision=%s' % ('double' if '+double' in spec else 'single'), @@ -90,3 +100,7 @@ class Petsc(Package): # PETSc has its own way of doing parallel make. make('MAKE_NP=%s' % make_jobs, parallel=False) make("install") + + def setup_dependent_environment(self, spack_env, run_env, dependent_spec): + # set up PETSC_DIR for everyone using PETSc package + spack_env.set('PETSC_DIR', self.prefix) diff --git a/var/spack/repos/builtin/packages/py-nose/package.py b/var/spack/repos/builtin/packages/py-nose/package.py index e7c6cf0264..4fee99098e 100644 --- a/var/spack/repos/builtin/packages/py-nose/package.py +++ b/var/spack/repos/builtin/packages/py-nose/package.py @@ -1,11 +1,12 @@ from spack import * + class PyNose(Package): """nose extends the test loading and running features of unittest, making it easier to write, find and run tests.""" homepage = "https://pypi.python.org/pypi/nose" - url = "https://pypi.python.org/packages/source/n/nose/nose-1.3.4.tar.gz" + url = "https://pypi.python.org/packages/source/n/nose/nose-1.3.4.tar.gz" version('1.3.4', '6ed7169887580ddc9a8e16048d38274d') version('1.3.6', '0ca546d81ca8309080fc80cb389e7a16') diff --git a/var/spack/repos/builtin/packages/py-numpy/package.py b/var/spack/repos/builtin/packages/py-numpy/package.py index 0354811186..a08e612df6 100644 --- a/var/spack/repos/builtin/packages/py-numpy/package.py +++ b/var/spack/repos/builtin/packages/py-numpy/package.py @@ -1,24 +1,43 @@ from spack import * class PyNumpy(Package): - """array processing for numbers, strings, records, and objects.""" - homepage = "https://pypi.python.org/pypi/numpy" + """NumPy is the fundamental package for scientific computing with Python. + It contains among other things: a powerful N-dimensional array object, + sophisticated (broadcasting) functions, tools for integrating C/C++ and + Fortran code, and useful linear algebra, Fourier transform, and random + number capabilities""" + homepage = "http://www.numpy.org/" url = "https://pypi.python.org/packages/source/n/numpy/numpy-1.9.1.tar.gz" - version('1.9.1', '78842b73560ec378142665e712ae4ad9') - version('1.9.2', 'a1ed53432dbcd256398898d35bc8e645') + version('1.10.4', 'aed294de0aa1ac7bd3f9745f4f1968ad') + version('1.9.2', 'a1ed53432dbcd256398898d35bc8e645') + version('1.9.1', '78842b73560ec378142665e712ae4ad9') - variant('blas', default=True) + + variant('blas', default=True) + variant('lapack', default=True) extends('python') depends_on('py-nose') - depends_on('netlib-blas+fpic', when='+blas') - depends_on('netlib-lapack+shared', when='+blas') + depends_on('blas', when='+blas') + depends_on('lapack', when='+lapack') def install(self, spec, prefix): + libraries = [] + library_dirs = [] + if '+blas' in spec: + libraries.append('blas') + library_dirs.append(spec['blas'].prefix.lib) + if '+lapack' in spec: + libraries.append('lapack') + library_dirs.append(spec['lapack'].prefix.lib) + + if '+blas' in spec or '+lapack' in spec: with open('site.cfg', 'w') as f: f.write('[DEFAULT]\n') - f.write('libraries=lapack,blas\n') - f.write('library_dirs=%s/lib:%s/lib\n' % (spec['blas'].prefix, spec['lapack'].prefix)) + f.write('libraries=%s\n' % ','.join(libraries)) + f.write('library_dirs=%s\n' % ':'.join(library_dirs)) + python('setup.py', 'install', '--prefix=%s' % prefix) + diff --git a/var/spack/repos/builtin/packages/py-scipy/package.py b/var/spack/repos/builtin/packages/py-scipy/package.py index 3a1124cc15..c2161c90c4 100644 --- a/var/spack/repos/builtin/packages/py-scipy/package.py +++ b/var/spack/repos/builtin/packages/py-scipy/package.py @@ -2,11 +2,12 @@ from spack import * class PyScipy(Package): """Scientific Library for Python.""" - homepage = "https://pypi.python.org/pypi/scipy" + homepage = "http://www.scipy.org/" url = "https://pypi.python.org/packages/source/s/scipy/scipy-0.15.0.tar.gz" - version('0.15.0', '639112f077f0aeb6d80718dc5019dc7a') + version('0.17.0', '5ff2971e1ce90e762c59d2cd84837224') version('0.15.1', 'be56cd8e60591d6332aac792a5880110') + version('0.15.0', '639112f077f0aeb6d80718dc5019dc7a') extends('python') depends_on('py-nose') diff --git a/var/spack/repos/builtin/packages/python/package.py b/var/spack/repos/builtin/packages/python/package.py index dd240d1ea0..f5237c3b57 100644 --- a/var/spack/repos/builtin/packages/python/package.py +++ b/var/spack/repos/builtin/packages/python/package.py @@ -1,11 +1,14 @@ +import functools +import glob +import inspect import os import re from contextlib import closing -from llnl.util.lang import match_predicate -from spack.util.environment import * -from spack import * import spack +from llnl.util.lang import match_predicate +from spack import * +from spack.util.environment import * class Python(Package): @@ -90,35 +93,46 @@ class Python(Package): return os.path.join(self.python_lib_dir, 'site-packages') - def setup_dependent_environment(self, module, spec, ext_spec): - """Called before python modules' install() methods. + 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. + 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)) + + 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 + if extension_spec.package.extends(self.spec): + run_env.prepend_path('PYTHONPATH', os.path.join(extension_spec.prefix, self.site_packages_dir)) + + + def setup_dependent_package(self, module, ext_spec): + """ + 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=%s' % 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(spec.prefix.bin, 'python3')) + module.python = Executable(join_path(self.spec.prefix.bin, 'python3')) else: - module.python = Executable(join_path(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 if it does not exist already. - mkdirp(module.site_packages_dir) - - # Set PYTHONPATH to include site-packages dir for the - # extension and any other python extensions it depends on. - python_paths = [] - for d in ext_spec.traverse(): - if d.package.extends(self.spec): - python_paths.append(os.path.join(d.prefix, self.site_packages_dir)) - os.environ['PYTHONPATH'] = ':'.join(python_paths) - + # Make the site packages directory for extensions, if it does not exist already. + if ext_spec.package.is_extension: + mkdirp(module.site_packages_dir) # ======================================================================== # Handle specifics of activating and deactivating python modules. diff --git a/var/spack/repos/builtin/packages/qrupdate/package.py b/var/spack/repos/builtin/packages/qrupdate/package.py new file mode 100644 index 0000000000..5374d02c97 --- /dev/null +++ b/var/spack/repos/builtin/packages/qrupdate/package.py @@ -0,0 +1,18 @@ +from spack import * + +class Qrupdate(Package): + """qrupdate is a Fortran library for fast updates of QR and + Cholesky decompositions.""" + + homepage = "http://sourceforge.net/projects/qrupdate/" + url = "https://downloads.sourceforge.net/qrupdate/qrupdate-1.1.2.tar.gz" + + version('1.1.2', '6d073887c6e858c24aeda5b54c57a8c4') + + depends_on("blas") + depends_on("lapack") + + def install(self, spec, prefix): + # Build static and dynamic libraries + make("lib", "solib") + make("install", "PREFIX=%s" % prefix) diff --git a/var/spack/repos/builtin/packages/qt/package.py b/var/spack/repos/builtin/packages/qt/package.py index ef5f05601f..d08e8e81e1 100644 --- a/var/spack/repos/builtin/packages/qt/package.py +++ b/var/spack/repos/builtin/packages/qt/package.py @@ -56,9 +56,12 @@ class Qt(Package): depends_on("libxcb") - def setup_dependent_environment(self, module, spec, dep_spec): - """Dependencies of Qt find it using the QTDIR environment variable.""" - os.environ['QTDIR'] = self.prefix + def setup_environment(self, spack_env, env): + env.set('QTDIR', self.prefix) + + + def setup_dependent_environment(self, spack_env, run_env, dspec): + spack_env.set('QTDIR', self.prefix) def patch(self): diff --git a/var/spack/repos/builtin/packages/ruby/package.py b/var/spack/repos/builtin/packages/ruby/package.py index 6b6242362c..e13677e4d2 100644 --- a/var/spack/repos/builtin/packages/ruby/package.py +++ b/var/spack/repos/builtin/packages/ruby/package.py @@ -1,9 +1,8 @@ from spack import * -import spack -import os + class Ruby(Package): - """A dynamic, open source programming language with a focus on + """A dynamic, open source programming language with a focus on simplicity and productivity.""" homepage = "https://www.ruby-lang.org/" @@ -15,11 +14,23 @@ class Ruby(Package): def install(self, spec, prefix): configure("--prefix=%s" % prefix) - make() make("install") - def setup_dependent_environment(self, module, spec, ext_spec): + def setup_dependent_environment(self, spack_env, run_env, extension_spec): + # TODO: do this only for actual extensions. + # Set GEM_PATH to include dependent gem directories + ruby_paths = [] + for d in extension_spec.traverse(): + if d.package.extends(self.spec): + ruby_paths.append(d.prefix) + + spack_env.set_path('GEM_PATH', ruby_paths) + + # The actual installation path for this gem + spack_env.set('GEM_HOME', extension_spec.prefix) + + def setup_dependent_package(self, module, ext_spec): """Called before ruby modules' install() methods. Sets GEM_HOME and GEM_PATH to values appropriate for the package being built. @@ -28,14 +39,5 @@ class Ruby(Package): gem('install', '<gem-name>.gem') """ # Ruby extension builds have global ruby and gem functions - module.ruby = Executable(join_path(spec.prefix.bin, 'ruby')) - module.gem = Executable(join_path(spec.prefix.bin, 'gem')) - - # Set GEM_PATH to include dependent gem directories - ruby_paths = [] - for d in ext_spec.traverse(): - if d.package.extends(self.spec): - ruby_paths.append(d.prefix) - os.environ['GEM_PATH'] = ':'.join(ruby_paths) - # The actual installation path for this gem - os.environ['GEM_HOME'] = ext_spec.prefix + module.ruby = Executable(join_path(self.spec.prefix.bin, 'ruby')) + module.gem = Executable(join_path(self.spec.prefix.bin, 'gem')) diff --git a/var/spack/repos/builtin/packages/silo/package.py b/var/spack/repos/builtin/packages/silo/package.py index d1aed78e0e..b7894e4d2b 100644 --- a/var/spack/repos/builtin/packages/silo/package.py +++ b/var/spack/repos/builtin/packages/silo/package.py @@ -5,24 +5,35 @@ class Silo(Package): data to binary, disk files.""" homepage = "http://wci.llnl.gov/simulation/computer-codes/silo" - url = "https://wci.llnl.gov/content/assets/docs/simulation/computer-codes/silo/silo-4.8/silo-4.8.tar.gz" + base_url = "https://wci.llnl.gov/content/assets/docs/simulation/computer-codes/silo" + version('4.10.2', '9ceac777a2f2469ac8cef40f4fab49c8') + version('4.9', 'a83eda4f06761a86726e918fc55e782a') version('4.8', 'b1cbc0e7ec435eb656dc4b53a23663c9') variant('fortran', default=True, description='Enable Fortran support') + variant('silex', default=False, description='Builds Silex, a GUI for viewing Silo files') - depends_on("hdf5") + depends_on('hdf5') + depends_on('qt', when='+silex') def install(self, spec, prefix): config_args = [ '--enable-fortran' if '+fortran' in spec else '--disable-fortran', + '--enable-silex' if '+silex' in spec else '--disable-silex', ] + if '+silex' in spec: + config_args.append('--with-Qt-dir=%s' % spec['qt'].prefix) + configure( - "--prefix=%s" % prefix, - "--with-hdf5=%s,%s" % (spec['hdf5'].prefix.include, spec['hdf5'].prefix.lib), - "--with-zlib=%s,%s" % (spec['zlib'].prefix.include, spec['zlib'].prefix.lib), + '--prefix=%s' % prefix, + '--with-hdf5=%s,%s' % (spec['hdf5'].prefix.include, spec['hdf5'].prefix.lib), + '--with-zlib=%s,%s' % (spec['zlib'].prefix.include, spec['zlib'].prefix.lib), *config_args) make() - make("install") + make('install') + + def url_for_version(self, version): + return '%s/silo-%s/silo-%s.tar.gz' % (Silo.base_url, version, version) diff --git a/var/spack/repos/builtin/packages/slepc/package.py b/var/spack/repos/builtin/packages/slepc/package.py new file mode 100644 index 0000000000..8b5f24394f --- /dev/null +++ b/var/spack/repos/builtin/packages/slepc/package.py @@ -0,0 +1,49 @@ +import os +from spack import * + + +class Slepc(Package): + """ + Scalable Library for Eigenvalue Computations. + """ + + homepage = "http://www.grycap.upv.es/slepc" + url = "http://slepc.upv.es/download/download.php?filename=slepc-3.6.2.tar.gz" + + version('3.6.2', '2ab4311bed26ccf7771818665991b2ea3a9b15f97e29fd13911ab1293e8e65df') + + variant('arpack', default=False, 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') + + def install(self, spec, prefix): + # set SLEPC_DIR for installation + os.environ['SLEPC_DIR'] = self.stage.source_path + + options = [] + + if '+arpack' in spec: + options.extend([ + '--with-arpack-dir=%s' % spec['arpack-ng'].prefix.lib, + ]) + if 'arpack-ng~mpi' in spec: + options.extend([ + '--with-arpack-flags=-larpack' + ]) + else: + options.extend([ + '--with-arpack-flags=-lparpack,-larpack' + ]) + + configure('--prefix=%s' % prefix, *options) + + make('MAKE_NP=%s' % make_jobs, parallel=False) + #FIXME: + # make('test') + make('install') + + def setup_dependent_environment(self, spack_env, run_env, dependent_spec): + # set up SLEPC_DIR for everyone using SLEPc package + spack_env.set('SLEPC_DIR', self.prefix) diff --git a/var/spack/repos/builtin/packages/SuiteSparse/package.py b/var/spack/repos/builtin/packages/suite-sparse/package.py index 6e130d118f..b57f9967c3 100644 --- a/var/spack/repos/builtin/packages/SuiteSparse/package.py +++ b/var/spack/repos/builtin/packages/suite-sparse/package.py @@ -1,7 +1,7 @@ from spack import * -class Suitesparse(Package): +class SuiteSparse(Package): """ SuiteSparse is a suite of sparse matrix algorithms """ @@ -24,4 +24,3 @@ class Suitesparse(Package): # FIXME : this actually uses the current workaround # FIXME : (blas / lapack always provide libblas and liblapack as aliases) make('install', 'INSTALL=%s' % prefix, 'BLAS=-lblas', 'LAPACK=-llapack') - diff --git a/var/spack/repos/builtin/packages/superlu-dist/package.py b/var/spack/repos/builtin/packages/superlu-dist/package.py new file mode 100644 index 0000000000..9a94de8ba5 --- /dev/null +++ b/var/spack/repos/builtin/packages/superlu-dist/package.py @@ -0,0 +1,64 @@ +from spack import * + +class SuperluDist(Package): + """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('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') + + def install(self, spec, prefix): + makefile_inc = [] + makefile_inc.extend([ + 'PLAT = _mac_x', + 'DSuperLUroot = %s' % self.stage.source_path, #self.stage.path, prefix + '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 + 'METISLIB = -L%s -lmetis' % spec['metis'].prefix.lib, + 'PARMETISLIB = -L%s -lparmetis' % spec['parmetis'].prefix.lib, + 'FLIBS =', + 'LIBS = $(DSUPERLULIB) $(BLASLIB) $(PARMETISLIB) $(METISLIB)', + '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), + 'NOOPTS = -fPIC -std=c99', + 'FORTRAN = mpif77', + 'F90FLAGS = -O2', + 'LOADER = mpif77', + 'LOADOPTS =', + 'CDEFS = -DAdd_' + ]) + + #with working_dir('src'): + with open('make.inc', 'w') as fh: + fh.write('\n'.join(makefile_inc)) + + make("lib", parallel=False) + + # FIXME: + # cd "EXAMPLE" do + # system "make" + + # need to install by hand + headers_location = join_path(self.prefix.include,'superlu_dist') + mkdirp(headers_location) + mkdirp(prefix.lib) + # FIXME: fetch all headers in the folder automatically + for header in ['Cnames.h','cublas_utils.h','dcomplex.h','html_mainpage.h','machines.h','old_colamd.h','psymbfact.h','superlu_ddefs.h','superlu_defs.h','superlu_enum_consts.h','superlu_zdefs.h','supermatrix.h','util_dist.h']: + superludist_header = join_path(self.stage.source_path, 'SRC/',header) + install(superludist_header, headers_location) + + 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/tbb/package.py b/var/spack/repos/builtin/packages/tbb/package.py new file mode 100644 index 0000000000..56ffe4c27c --- /dev/null +++ b/var/spack/repos/builtin/packages/tbb/package.py @@ -0,0 +1,79 @@ +from spack import * +import os +import glob + +class Tbb(Package): + """Widely used C++ template library for task parallelism. + Intel Threading Building Blocks (Intel TBB) lets you easily write parallel + C++ programs that take full advantage of multicore performance, that are + portable and composable, and that have future-proof scalability. + """ + homepage = "http://www.threadingbuildingblocks.org/" + + # Only version-specific URL's work for TBB + version('4.4.3', '80707e277f69d9b20eeebdd7a5f5331137868ce1', url='https://www.threadingbuildingblocks.org/sites/default/files/software_releases/source/tbb44_20160128oss_src_0.tgz') + + def coerce_to_spack(self,tbb_build_subdir): + for compiler in ["icc","gcc","clang"]: + fs = glob.glob(join_path(tbb_build_subdir,"*.%s.inc" % compiler )) + for f in fs: + lines = open(f).readlines() + of = open(f,"w") + for l in lines: + if l.strip().startswith("CPLUS ="): + of.write("# coerced to spack\n") + of.write("CPLUS = $(CXX)\n") + elif l.strip().startswith("CPLUS ="): + of.write("# coerced to spack\n") + of.write("CONLY = $(CC)\n") + else: + of.write(l); + + def install(self, spec, prefix): + # + # we need to follow TBB's compiler selection logic to get the proper build + link flags + # but we still need to use spack's compiler wrappers + # to accomplish this, we do two things: + # + # * Look at the spack spec to determine which compiler we should pass to tbb's Makefile + # + # * patch tbb's build system to use the compiler wrappers (CC, CXX) for + # icc, gcc, clang + # (see coerce_to_spack()) + # + self.coerce_to_spack("build") + + if spec.satisfies('%clang'): + tbb_compiler = "clang" + elif spec.satisfies('%intel'): + tbb_compiler = "icc" + else: + tbb_compiler = "gcc" + + + mkdirp(prefix) + mkdirp(prefix.lib) + + # + # tbb does not have a configure script or make install target + # we simply call make, and try to put the pieces together + # + make("compiler=%s" %(tbb_compiler)) + + # install headers to {prefix}/include + install_tree('include',prefix.include) + + # install libs to {prefix}/lib + tbb_lib_names = ["libtbb", + "libtbbmalloc", + "libtbbmalloc_proxy"] + + for lib_name in tbb_lib_names: + # install release libs + fs = glob.glob(join_path("build","*release",lib_name + ".*")) + for f in fs: + install(f, prefix.lib) + # install debug libs if they exist + fs = glob.glob(join_path("build","*debug",lib_name + "_debug.*")) + for f in fs: + install(f, prefix.lib) diff --git a/var/spack/repos/builtin/packages/tmux/package.py b/var/spack/repos/builtin/packages/tmux/package.py index 23d36db427..f2067d1366 100644 --- a/var/spack/repos/builtin/packages/tmux/package.py +++ b/var/spack/repos/builtin/packages/tmux/package.py @@ -7,10 +7,11 @@ class Tmux(Package): do a lot more. """ - homepage = "http://tmux.sourceforge.net" - url = "http://downloads.sourceforge.net/project/tmux/tmux/tmux-1.9/tmux-1.9a.tar.gz" + homepage = "http://tmux.github.io" + url = "https://github.com/tmux/tmux/releases/download/2.1/tmux-2.1.tar.gz" version('1.9a', 'b07601711f96f1d260b390513b509a2d') + version('2.1', '74a2855695bccb51b6e301383ad4818c') depends_on('libevent') depends_on('ncurses') |