From 310099d88838c8e08d15fb34028263c9294b62e9 Mon Sep 17 00:00:00 2001 From: alalazo Date: Fri, 4 Mar 2016 09:31:03 +0100 Subject: atlas : provides blas and lapack --- var/spack/repos/builtin/packages/atlas/package.py | 58 +++++++++++------------ 1 file changed, 28 insertions(+), 30 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/atlas/package.py b/var/spack/repos/builtin/packages/atlas/package.py index fc683363a7..f9b50417b0 100644 --- a/var/spack/repos/builtin/packages/atlas/package.py +++ b/var/spack/repos/builtin/packages/atlas/package.py @@ -1,31 +1,34 @@ 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('3.11.34', '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') + 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:') - # TODO: make this provide BLAS once it works better. Create a way - # TODO: to mark "beta" packages and require explicit invocation. + 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') - # provides('blas') + variant('shared', default=True, description='Builds shared library') + provides('blas') + provides('lapack') 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 +36,21 @@ 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') -- cgit v1.2.3-70-g09d2 From a2af4940aaf169f3358f19986fc94a02222a8096 Mon Sep 17 00:00:00 2001 From: alalazo Date: Fri, 4 Mar 2016 09:59:16 +0100 Subject: atlas : disabling parallel builds --- var/spack/repos/builtin/packages/atlas/package.py | 2 ++ 1 file changed, 2 insertions(+) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/atlas/package.py b/var/spack/repos/builtin/packages/atlas/package.py index f9b50417b0..b5504122b7 100644 --- a/var/spack/repos/builtin/packages/atlas/package.py +++ b/var/spack/repos/builtin/packages/atlas/package.py @@ -27,6 +27,8 @@ class Atlas(Package): provides('blas') provides('lapack') + parallel = False + def patch(self): # Disable thread check. LLNL's environment does not allow # disabling of CPU throttling in a way that ATLAS actually -- cgit v1.2.3-70-g09d2 From 6ec65cd4ca1e6c2d346c949e21902680f27364c5 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Fri, 11 Mar 2016 15:03:37 -0600 Subject: Add GNU Octave package --- var/spack/repos/builtin/packages/octave/package.py | 182 +++++++++++++++++++++ 1 file changed, 182 insertions(+) create mode 100644 var/spack/repos/builtin/packages/octave/package.py (limited to 'var') 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..6810da6d98 --- /dev/null +++ b/var/spack/repos/builtin/packages/octave/package.py @@ -0,0 +1,182 @@ +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') + + 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@3', 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') + depends_on('qhull', when='+qhull') + #depends_on('qrupdate', when='+qrupdate') + #depends_on('qscintilla', when='+qscintilla) + depends_on('qt', when='+qt') + depends_on('SuiteSparse', 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") -- cgit v1.2.3-70-g09d2 From 145390c7f3a9de6e679f56dc9b275973a459de91 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Fri, 11 Mar 2016 16:57:37 -0600 Subject: Add gl2ps and qrupdate packages --- var/spack/repos/builtin/packages/gl2ps/package.py | 18 ++++++++++++++++ var/spack/repos/builtin/packages/octave/package.py | 24 +++++++++++----------- .../repos/builtin/packages/qrupdate/package.py | 18 ++++++++++++++++ 3 files changed, 48 insertions(+), 12 deletions(-) create mode 100644 var/spack/repos/builtin/packages/gl2ps/package.py create mode 100644 var/spack/repos/builtin/packages/qrupdate/package.py (limited to 'var') 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/octave/package.py b/var/spack/repos/builtin/packages/octave/package.py index 6810da6d98..99847e1dbe 100644 --- a/var/spack/repos/builtin/packages/octave/package.py +++ b/var/spack/repos/builtin/packages/octave/package.py @@ -50,7 +50,7 @@ class Octave(Package): depends_on('fontconfig', when='+fontconfig') depends_on('freetype', when='+freetype') depends_on('glpk', when='+glpk') - #depends_on('gl2ps', when='+gl2ps') + depends_on('gl2ps', when='+gl2ps') depends_on('gnuplot', when='+gnuplot') depends_on('ImageMagick', when='+magick') depends_on('hdf5', when='+hdf5') @@ -58,10 +58,10 @@ class Octave(Package): depends_on('llvm', when='+llvm') #depends_on('opengl', when='+opengl') depends_on('qhull', when='+qhull') - #depends_on('qrupdate', when='+qrupdate') + depends_on('qrupdate', when='+qrupdate') #depends_on('qscintilla', when='+qscintilla) depends_on('qt', when='+qt') - depends_on('SuiteSparse', when='suitesparse') + depends_on('SuiteSparse', when='+suitesparse') depends_on('zlib', when='+zlib') @@ -72,7 +72,7 @@ class Octave(Package): # Required dependencies config_args.extend([ - "--with-blas=%s" % spec['blas'].prefix.lib, + "--with-blas=%s" % spec['blas'].prefix.lib, "--with-lapack=%s" % spec['lapack'].prefix.lib ]) @@ -122,7 +122,7 @@ class Octave(Package): if '+glpk' in spec: config_args.extend([ - "--with-glpk-includedir=%s" % spec['glpk'].prefix.include + "--with-glpk-includedir=%s" % spec['glpk'].prefix.include, "--with-glpk-libdir=%s" % spec['glpk'].prefix.lib ]) else: @@ -160,13 +160,13 @@ class Octave(Package): 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 '+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([ 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..aff44bb2d8 --- /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("openblas") + + def install(self, spec, prefix): + configure('--prefix=%s' % prefix) + + make() + make("install") -- cgit v1.2.3-70-g09d2 From 90f2e40ff92077da1f1b9b4d9aa317b89aa07960 Mon Sep 17 00:00:00 2001 From: Elizabeth F Date: Fri, 11 Mar 2016 23:28:16 -0500 Subject: Added comment to Emacs. --- var/spack/repos/builtin/packages/emacs/package.py | 2 ++ 1 file changed, 2 insertions(+) (limited to 'var') 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) -- cgit v1.2.3-70-g09d2 From 7cd478418d5b8a204a8e6b9a5307ecf71ea83939 Mon Sep 17 00:00:00 2001 From: Elizabeth F Date: Fri, 11 Mar 2016 23:28:36 -0500 Subject: New version of LAPACK --- var/spack/repos/builtin/packages/netlib-lapack/package.py | 1 + 1 file changed, 1 insertion(+) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/netlib-lapack/package.py b/var/spack/repos/builtin/packages/netlib-lapack/package.py index fb6b99e27c..741f4af421 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') -- cgit v1.2.3-70-g09d2 From 8b715d9c3fabdf4658ff4c0c500d01f74e7ed64e Mon Sep 17 00:00:00 2001 From: Erik Schnetter Date: Sun, 13 Mar 2016 21:14:41 -0400 Subject: Update tmux --- var/spack/repos/builtin/packages/tmux/package.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) (limited to 'var') 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') -- cgit v1.2.3-70-g09d2 From f45b8b1083e5f628dd31fa4b7b873b6df7119d0e Mon Sep 17 00:00:00 2001 From: Todd Gamblin Date: Mon, 14 Mar 2016 05:02:50 -0700 Subject: Add some tests for packages with multiple virtual dependencies. - Added mock `hypre` package, depends on `lapack` and `blas`. - test cases where some packages provide both `lapack` and `blas`, but others do not. --- lib/spack/spack/test/concretize.py | 29 +++++++++++++++- .../repos/builtin.mock/packages/hypre/package.py | 39 ++++++++++++++++++++++ .../packages/openblas-with-lapack/package.py | 38 +++++++++++++++++++++ 3 files changed, 105 insertions(+), 1 deletion(-) create mode 100644 var/spack/repos/builtin.mock/packages/hypre/package.py create mode 100644 var/spack/repos/builtin.mock/packages/openblas-with-lapack/package.py (limited to 'var') diff --git a/lib/spack/spack/test/concretize.py b/lib/spack/spack/test/concretize.py index 07828d8ea6..f264faf17a 100644 --- a/lib/spack/spack/test/concretize.py +++ b/lib/spack/spack/test/concretize.py @@ -142,6 +142,34 @@ class ConcretizeTest(MockPackagesTest): for spec in spack.repo.providers_for('mpi@3'))) + def test_concretize_two_virtuals(self): + """Test a package with multiple virtual dependencies.""" + s = Spec('hypre').concretize() + + + def test_concretize_two_virtuals_with_one_bound(self): + """Test a package with multiple virtual dependencies and one preset.""" + s = Spec('hypre ^openblas').concretize() + + + def test_concretize_two_virtuals_with_two_bound(self): + """Test a package with multiple virtual dependencies and two of them preset.""" + s = Spec('hypre ^openblas ^netlib-lapack').concretize() + + + def test_concretize_two_virtuals_with_dual_provider(self): + """Test a package with multiple virtual dependencies and force a provider + that provides both.""" + s = Spec('hypre ^openblas-with-lapack').concretize() + + + def test_concretize_two_virtuals_with_dual_provider_and_a_conflict(self): + """Test a package with multiple virtual dependencies and force a provider + that provides both, and another conflicting package that provides one.""" + s = Spec('hypre ^openblas-with-lapack ^netlib-lapack') + self.assertRaises(spack.spec.MultipleProviderError, s.concretize) + + def test_virtual_is_fully_expanded_for_callpath(self): # force dependence on fake "zmpi" by asking for MPI 10.0 spec = Spec('callpath ^mpi@10.0') @@ -281,4 +309,3 @@ class ConcretizeTest(MockPackagesTest): Spec('d')), Spec('e')) self.assertEqual(None, find_spec(s['b'], lambda s: '+foo' in s)) - 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 -- cgit v1.2.3-70-g09d2 From 0d9a6d3c25de2b8490622c49362b09f706459bc0 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Mon, 14 Mar 2016 14:19:30 -0500 Subject: Updates to qrupdate --- var/spack/repos/builtin/packages/octave/package.py | 17 +++++++++-------- var/spack/repos/builtin/packages/qrupdate/package.py | 10 +++++----- 2 files changed, 14 insertions(+), 13 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/octave/package.py b/var/spack/repos/builtin/packages/octave/package.py index 99847e1dbe..38b355159d 100644 --- a/var/spack/repos/builtin/packages/octave/package.py +++ b/var/spack/repos/builtin/packages/octave/package.py @@ -12,6 +12,7 @@ class Octave(Package): version('4.0.0' , 'a69f8320a4f20a8480c1b278b1adb799') + # Variants variant('readline', default=True) variant('arpack', default=False) variant('curl', default=False) @@ -45,7 +46,7 @@ class Octave(Package): # Optional dependencies depends_on('arpack', when='+arpack') depends_on('curl', when='+curl') - depends_on('fftw@3', when='+fftw') + depends_on('fftw', when='+fftw') depends_on('fltk', when='+fltk') depends_on('fontconfig', when='+fontconfig') depends_on('freetype', when='+freetype') @@ -56,10 +57,10 @@ class Octave(Package): depends_on('hdf5', when='+hdf5') depends_on('jdk', when='+jdk') depends_on('llvm', when='+llvm') - #depends_on('opengl', when='+opengl') + #depends_on('opengl', when='+opengl') # TODO: add package depends_on('qhull', when='+qhull') depends_on('qrupdate', when='+qrupdate') - #depends_on('qscintilla', when='+qscintilla) + #depends_on('qscintilla', when='+qscintilla) # TODO: add package depends_on('qt', when='+qt') depends_on('SuiteSparse', when='+suitesparse') depends_on('zlib', when='+zlib') @@ -146,11 +147,11 @@ class Octave(Package): "--with-java-libdir=%s" % spec['jdk'].prefix.lib ]) - #if '~opengl' in spec: - # config_args.extend([ - # "--without-opengl", - # "--without-framework-opengl" - # ]) + if '~opengl' in spec: + config_args.extend([ + "--without-opengl", + "--without-framework-opengl" + ]) if '+qhull' in spec: config_args.extend([ diff --git a/var/spack/repos/builtin/packages/qrupdate/package.py b/var/spack/repos/builtin/packages/qrupdate/package.py index aff44bb2d8..5374d02c97 100644 --- a/var/spack/repos/builtin/packages/qrupdate/package.py +++ b/var/spack/repos/builtin/packages/qrupdate/package.py @@ -9,10 +9,10 @@ class Qrupdate(Package): version('1.1.2', '6d073887c6e858c24aeda5b54c57a8c4') - depends_on("openblas") + depends_on("blas") + depends_on("lapack") def install(self, spec, prefix): - configure('--prefix=%s' % prefix) - - make() - make("install") + # Build static and dynamic libraries + make("lib", "solib") + make("install", "PREFIX=%s" % prefix) -- cgit v1.2.3-70-g09d2 From bcea1df01ce145aea5e49eaaceb7a063b44ddf80 Mon Sep 17 00:00:00 2001 From: alalazo Date: Tue, 15 Mar 2016 10:49:33 +0100 Subject: environment : refactoreded set_build_environment_variables --- lib/spack/spack/build_environment.py | 56 +++++++++++----------- lib/spack/spack/environment.py | 3 ++ .../repos/builtin/packages/mvapich2/package.py | 2 +- 3 files changed, 33 insertions(+), 28 deletions(-) (limited to 'var') diff --git a/lib/spack/spack/build_environment.py b/lib/spack/spack/build_environment.py index e91a8a1997..770e191ac9 100644 --- a/lib/spack/spack/build_environment.py +++ b/lib/spack/spack/build_environment.py @@ -35,7 +35,7 @@ import sys import spack from llnl.util.filesystem import * -from spack.environment import EnvironmentModifications, apply_environment_modifications +from spack.environment import EnvironmentModifications, apply_environment_modifications, concatenate_paths from spack.util.environment import * from spack.util.executable import Executable, which @@ -127,44 +127,45 @@ def set_build_environment_variables(pkg): # handled by putting one in the /case-insensitive # directory. Add that to the path too. env_paths = [] - def add_env_path(path): - env_paths.append(path) - ci = join_path(path, 'case-insensitive') - if os.path.isdir(ci): env_paths.append(ci) - add_env_path(spack.build_env_path) - add_env_path(join_path(spack.build_env_path, pkg.compiler.name)) - - path_put_first("PATH", env_paths) - path_set(SPACK_ENV_PATH, env_paths) - - # Prefixes of all of the package's dependencies go in - # SPACK_DEPENDENCIES + for item in [spack.build_env_path, join_path(spack.build_env_path, pkg.compiler.name)]: + env_paths.append(item) + ci = join_path(item, 'case-insensitive') + if os.path.isdir(ci): + env_paths.append(ci) + + env = EnvironmentModifications() + for item in reversed(env_paths): + env.prepend_path('PATH', item) + env.set_env(SPACK_ENV_PATH, concatenate_paths(env_paths)) + + # Prefixes of all of the package's dependencies go in SPACK_DEPENDENCIES dep_prefixes = [d.prefix for d in pkg.spec.traverse(root=False)] - path_set(SPACK_DEPENDENCIES, dep_prefixes) + env.set_env(SPACK_DEPENDENCIES, concatenate_paths(dep_prefixes)) + env.set_env('CMAKE_PREFIX_PATH', concatenate_paths(dep_prefixes)) # Add dependencies to CMAKE_PREFIX_PATH # Install prefix - os.environ[SPACK_PREFIX] = pkg.prefix + env.set_env(SPACK_PREFIX, pkg.prefix) # Install root prefix - os.environ[SPACK_INSTALL] = spack.install_path + env.set_env(SPACK_INSTALL, spack.install_path) # Remove these vars from the environment during build because they # can affect how some packages find libraries. We want to make # sure that builds never pull in unintended external dependencies. - pop_keys(os.environ, "LD_LIBRARY_PATH", "LD_RUN_PATH", "DYLD_LIBRARY_PATH") + env.unset_env('LD_LIBRARY_PATH') + env.unset_env('LD_RUN_PATH') + env.unset_env('DYLD_LIBRARY_PATH') # Add bin directories from dependencies to the PATH for the build. - bin_dirs = ['%s/bin' % prefix for prefix in dep_prefixes] - path_put_first('PATH', [bin for bin in bin_dirs if os.path.isdir(bin)]) + bin_dirs = reversed(filter(os.path.isdir, ['%s/bin' % prefix for prefix in dep_prefixes])) + for item in bin_dirs: + env.prepend_path('PATH', item) # Working directory for the spack command itself, for debug logs. if spack.debug: - os.environ[SPACK_DEBUG] = "TRUE" - os.environ[SPACK_SHORT_SPEC] = pkg.spec.short_spec - os.environ[SPACK_DEBUG_LOG_DIR] = spack.spack_working_dir - - # Add dependencies to CMAKE_PREFIX_PATH - path_set("CMAKE_PREFIX_PATH", dep_prefixes) + env.set_env(SPACK_DEBUG, 'TRUE') + env.set_env(SPACK_SHORT_SPEC, pkg.spec.short_spec) + env.set_env(SPACK_DEBUG_LOG_DIR, spack.spack_working_dir) # Add any pkgconfig directories to PKG_CONFIG_PATH pkg_config_dirs = [] @@ -173,8 +174,9 @@ def set_build_environment_variables(pkg): pcdir = join_path(p, libdir, 'pkgconfig') if os.path.isdir(pcdir): pkg_config_dirs.append(pcdir) - path_set("PKG_CONFIG_PATH", pkg_config_dirs) + env.set_env('PKG_CONFIG_PATH', concatenate_paths(pkg_config_dirs)) + return env def set_module_variables_for_package(pkg, m): """Populate the module scope of install() with some useful functions. @@ -269,8 +271,8 @@ def setup_package(pkg): """Execute all environment setup routines.""" env = EnvironmentModifications() env.extend(set_compiler_environment_variables(pkg)) + env.extend(set_build_environment_variables(pkg)) apply_environment_modifications(env) - set_build_environment_variables(pkg) # If a user makes their own package repo, e.g. # spack.repos.mystuff.libelf.Libelf, and they inherit from # an existing class like spack.repos.original.libelf.Libelf, diff --git a/lib/spack/spack/environment.py b/lib/spack/spack/environment.py index 3b73f1c7a2..18fef1ef12 100644 --- a/lib/spack/spack/environment.py +++ b/lib/spack/spack/environment.py @@ -146,6 +146,9 @@ class EnvironmentModifications(object): self.env_modifications.append(item) +def concatenate_paths(paths): + return ':'.join(str(item) for item in paths) + def validate_environment_modifications(env): modifications = collections.defaultdict(list) for item in env: 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"] -- cgit v1.2.3-70-g09d2 From c85888eb5763d453af7b7255b6d8c3461082362f Mon Sep 17 00:00:00 2001 From: alalazo Date: Tue, 15 Mar 2016 13:36:41 +0100 Subject: package : added `environment_modifications` --- lib/spack/spack/build_environment.py | 7 ++++--- lib/spack/spack/package.py | 4 ++++ var/spack/repos/builtin/packages/mpich/package.py | 16 ++++++++++------ .../builtin/packages/netlib-scalapack/package.py | 3 +-- .../repos/builtin/packages/openmpi/package.py | 14 ++++++++------ var/spack/repos/builtin/packages/python/package.py | 20 +++++++++++--------- var/spack/repos/builtin/packages/qt/package.py | 12 +++++++----- var/spack/repos/builtin/packages/ruby/package.py | 22 +++++++++++++--------- 8 files changed, 58 insertions(+), 40 deletions(-) (limited to 'var') diff --git a/lib/spack/spack/build_environment.py b/lib/spack/spack/build_environment.py index 770e191ac9..d321a0e495 100644 --- a/lib/spack/spack/build_environment.py +++ b/lib/spack/spack/build_environment.py @@ -178,6 +178,7 @@ def set_build_environment_variables(pkg): return env + def set_module_variables_for_package(pkg, m): """Populate the module scope of install() with some useful functions. This makes things easier for package writers. @@ -272,7 +273,6 @@ def setup_package(pkg): env = EnvironmentModifications() env.extend(set_compiler_environment_variables(pkg)) env.extend(set_build_environment_variables(pkg)) - apply_environment_modifications(env) # If a user makes their own package repo, e.g. # spack.repos.mystuff.libelf.Libelf, and they inherit from # an existing class like spack.repos.original.libelf.Libelf, @@ -284,8 +284,9 @@ def setup_package(pkg): # Allow dependencies to set up environment as well. for dep_spec in pkg.spec.traverse(root=False): - dep_spec.package.setup_dependent_environment( - pkg.module, dep_spec, pkg.spec) + env.extend(dep_spec.package.environment_modifications(pkg.module, dep_spec, pkg.spec)) + dep_spec.package.setup_dependent_environment(pkg.module, dep_spec, pkg.spec) + apply_environment_modifications(env) def fork(pkg, function): diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py index 696adaf896..224d7f8f4b 100644 --- a/lib/spack/spack/package.py +++ b/lib/spack/spack/package.py @@ -63,6 +63,7 @@ import spack.build_environment import spack.url import spack.util.web import spack.fetch_strategy as fs +from spack.environment import EnvironmentModifications from spack.version import * from spack.stage import Stage, ResourceStage, StageComposite from spack.util.compression import allowed_archive, extension @@ -983,6 +984,9 @@ class Package(object): fromlist=[self.__class__.__name__]) + def environment_modifications(self, module, spec, dependent_spec): + return EnvironmentModifications() + def setup_dependent_environment(self, module, spec, dependent_spec): """Called before the install() method of dependents. diff --git a/var/spack/repos/builtin/packages/mpich/package.py b/var/spack/repos/builtin/packages/mpich/package.py index e2b3654c19..c85e8febf3 100644 --- a/var/spack/repos/builtin/packages/mpich/package.py +++ b/var/spack/repos/builtin/packages/mpich/package.py @@ -46,14 +46,18 @@ class Mpich(Package): provides('mpi@:3.0', when='@3:') provides('mpi@:1.3', when='@1:') + def environment_modifications(self, module, spec, dependent_spec): + env = super(Mpich, self).environment_modifications(module, spec, dependent_spec) + env.set_env('MPICH_CC', os.environ['CC']) + env.set_env('MPICH_CXX', os.environ['CXX']) + env.set_env('MPICH_F77', os.environ['F77']) + env.set_env('MPICH_F90', os.environ['FC']) + env.set_env('MPICH_FC', os.environ['FC']) + return env + 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'] - + # 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/netlib-scalapack/package.py b/var/spack/repos/builtin/packages/netlib-scalapack/package.py index 22d538560e..6dbf367475 100644 --- a/var/spack/repos/builtin/packages/netlib-scalapack/package.py +++ b/var/spack/repos/builtin/packages/netlib-scalapack/package.py @@ -46,5 +46,4 @@ class NetlibScalapack(Package): 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['scalapack'].libraries = [join_path(spec['scalapack'].prefix.lib, 'libscalapack%s' % lib_suffix)] diff --git a/var/spack/repos/builtin/packages/openmpi/package.py b/var/spack/repos/builtin/packages/openmpi/package.py index e4484af8c5..83a3fe7a4f 100644 --- a/var/spack/repos/builtin/packages/openmpi/package.py +++ b/var/spack/repos/builtin/packages/openmpi/package.py @@ -41,12 +41,14 @@ 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 environment_modifications(self, module, spec, dependent_spec): + env = super(Openmpi, self).environment_modifications(module, spec, dependent_spec) + # FIXME : the compilers should point to the current wrappers, not to generic cc etc. + env.set_env('OMPI_CC', 'cc') + env.set_env('OMPI_CXX', 'c++') + env.set_env('OMPI_FC', 'f90') + env.set_env('OMPI_F77', 'f77') + return env def install(self, spec, prefix): config_args = ["--prefix=%s" % prefix, diff --git a/var/spack/repos/builtin/packages/python/package.py b/var/spack/repos/builtin/packages/python/package.py index dd240d1ea0..39ced0a120 100644 --- a/var/spack/repos/builtin/packages/python/package.py +++ b/var/spack/repos/builtin/packages/python/package.py @@ -90,6 +90,17 @@ class Python(Package): return os.path.join(self.python_lib_dir, 'site-packages') + def environment_modifications(self, module, spec, dependent_spec): + env = super(Python, self).environment_modifications(module, spec, dependent_spec) + # 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)) + env.set_env['PYTHONPATH'] = ':'.join(python_paths) + + def setup_dependent_environment(self, module, spec, ext_spec): """Called before python modules' install() methods. @@ -111,15 +122,6 @@ class Python(Package): # 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) - - # ======================================================================== # Handle specifics of activating and deactivating python modules. # ======================================================================== diff --git a/var/spack/repos/builtin/packages/qt/package.py b/var/spack/repos/builtin/packages/qt/package.py index 91afa420c1..373623cd95 100644 --- a/var/spack/repos/builtin/packages/qt/package.py +++ b/var/spack/repos/builtin/packages/qt/package.py @@ -52,11 +52,13 @@ class Qt(Package): depends_on("mesa", when='@4:+mesa') 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 environment_modifications(self, module, spec, dep_spec): + """ + Dependencies of Qt find it using the QTDIR environment variable + """ + env = super(Qt, self).environment_modifications(module, spec, dep_spec) + env.set_env['QTDIR'] = self.prefix + return env def patch(self): if self.spec.satisfies('@4'): diff --git a/var/spack/repos/builtin/packages/ruby/package.py b/var/spack/repos/builtin/packages/ruby/package.py index 6b6242362c..9ec0afa268 100644 --- a/var/spack/repos/builtin/packages/ruby/package.py +++ b/var/spack/repos/builtin/packages/ruby/package.py @@ -15,10 +15,21 @@ class Ruby(Package): def install(self, spec, prefix): configure("--prefix=%s" % prefix) - make() make("install") + def environment_modifications(self, module, spec, ext_spec): + env = super(Ruby, self).environment_modifications(module, spec, ext_spec) + # 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) + env.set_env('GEM_PATH', concatenate_paths(ruby_paths)) + # The actual installation path for this gem + env.set_env('GEM_HOME', ext_spec.prefix) + return env + def setup_dependent_environment(self, module, spec, ext_spec): """Called before ruby modules' install() methods. Sets GEM_HOME and GEM_PATH to values appropriate for the package being built. @@ -31,11 +42,4 @@ class Ruby(Package): 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 + -- cgit v1.2.3-70-g09d2 From 572cb93bf8131d222d2d08bca13fd9de6fded1f4 Mon Sep 17 00:00:00 2001 From: alalazo Date: Tue, 15 Mar 2016 14:05:30 +0100 Subject: package : renamed `setup_dependent_environment` to `module_modifications` --- lib/spack/spack/build_environment.py | 4 ++-- lib/spack/spack/package.py | 4 ++-- var/spack/repos/builtin/packages/mpich/package.py | 6 +++--- .../repos/builtin/packages/netlib-scalapack/package.py | 2 +- var/spack/repos/builtin/packages/openmpi/package.py | 4 ++-- var/spack/repos/builtin/packages/python/package.py | 10 ++++------ var/spack/repos/builtin/packages/qt/package.py | 7 ++----- var/spack/repos/builtin/packages/ruby/package.py | 13 ++++++------- 8 files changed, 22 insertions(+), 28 deletions(-) (limited to 'var') diff --git a/lib/spack/spack/build_environment.py b/lib/spack/spack/build_environment.py index d321a0e495..e86a7c413a 100644 --- a/lib/spack/spack/build_environment.py +++ b/lib/spack/spack/build_environment.py @@ -284,8 +284,8 @@ def setup_package(pkg): # Allow dependencies to set up environment as well. for dep_spec in pkg.spec.traverse(root=False): - env.extend(dep_spec.package.environment_modifications(pkg.module, dep_spec, pkg.spec)) - dep_spec.package.setup_dependent_environment(pkg.module, dep_spec, pkg.spec) + dep_spec.package.module_modifications(pkg.module, dep_spec, pkg.spec) + env.extend(dep_spec.package.environment_modifications(pkg.spec)) apply_environment_modifications(env) diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py index 224d7f8f4b..c1a5c912be 100644 --- a/lib/spack/spack/package.py +++ b/lib/spack/spack/package.py @@ -984,10 +984,10 @@ class Package(object): fromlist=[self.__class__.__name__]) - def environment_modifications(self, module, spec, dependent_spec): + def environment_modifications(self, dependent_spec): return EnvironmentModifications() - def setup_dependent_environment(self, module, spec, dependent_spec): + def module_modifications(self, module, spec, dependent_spec): """Called before the install() method of dependents. Default implementation does nothing, but this can be diff --git a/var/spack/repos/builtin/packages/mpich/package.py b/var/spack/repos/builtin/packages/mpich/package.py index c85e8febf3..d298981c92 100644 --- a/var/spack/repos/builtin/packages/mpich/package.py +++ b/var/spack/repos/builtin/packages/mpich/package.py @@ -46,8 +46,8 @@ class Mpich(Package): provides('mpi@:3.0', when='@3:') provides('mpi@:1.3', when='@1:') - def environment_modifications(self, module, spec, dependent_spec): - env = super(Mpich, self).environment_modifications(module, spec, dependent_spec) + def environment_modifications(self, dependent_spec): + env = super(Mpich, self).environment_modifications(dependent_spec) env.set_env('MPICH_CC', os.environ['CC']) env.set_env('MPICH_CXX', os.environ['CXX']) env.set_env('MPICH_F77', os.environ['F77']) @@ -55,7 +55,7 @@ class Mpich(Package): env.set_env('MPICH_FC', os.environ['FC']) return env - def setup_dependent_environment(self, module, spec, dep_spec): + def module_modifications(self, module, spec, 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') diff --git a/var/spack/repos/builtin/packages/netlib-scalapack/package.py b/var/spack/repos/builtin/packages/netlib-scalapack/package.py index 6dbf367475..ecdea46442 100644 --- a/var/spack/repos/builtin/packages/netlib-scalapack/package.py +++ b/var/spack/repos/builtin/packages/netlib-scalapack/package.py @@ -40,7 +40,7 @@ class NetlibScalapack(Package): make() make("install") - def setup_dependent_environment(self, module, spec, dependent_spec): + def module_modifications(self, module, spec, dependent_spec): # TODO treat OS that are not Linux... lib_suffix = '.so' if '+shared' in spec['scalapack'] else '.a' diff --git a/var/spack/repos/builtin/packages/openmpi/package.py b/var/spack/repos/builtin/packages/openmpi/package.py index 83a3fe7a4f..3a14170457 100644 --- a/var/spack/repos/builtin/packages/openmpi/package.py +++ b/var/spack/repos/builtin/packages/openmpi/package.py @@ -41,8 +41,8 @@ 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 environment_modifications(self, module, spec, dependent_spec): - env = super(Openmpi, self).environment_modifications(module, spec, dependent_spec) + def environment_modifications(self, dependent_spec): + env = super(Openmpi, self).environment_modifications(dependent_spec) # FIXME : the compilers should point to the current wrappers, not to generic cc etc. env.set_env('OMPI_CC', 'cc') env.set_env('OMPI_CXX', 'c++') diff --git a/var/spack/repos/builtin/packages/python/package.py b/var/spack/repos/builtin/packages/python/package.py index 39ced0a120..307cec726b 100644 --- a/var/spack/repos/builtin/packages/python/package.py +++ b/var/spack/repos/builtin/packages/python/package.py @@ -89,19 +89,17 @@ class Python(Package): def site_packages_dir(self): return os.path.join(self.python_lib_dir, 'site-packages') - - def environment_modifications(self, module, spec, dependent_spec): - env = super(Python, self).environment_modifications(module, spec, dependent_spec) + def environment_modifications(self, extension_spec): + env = super(Python, self).environment_modifications(extension_spec) # 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(): + for d in extension_spec.traverse(): if d.package.extends(self.spec): python_paths.append(os.path.join(d.prefix, self.site_packages_dir)) env.set_env['PYTHONPATH'] = ':'.join(python_paths) - - def setup_dependent_environment(self, module, spec, ext_spec): + def module_modifications(self, module, spec, ext_spec): """Called before python modules' install() methods. In most cases, extensions will only need to have one line:: diff --git a/var/spack/repos/builtin/packages/qt/package.py b/var/spack/repos/builtin/packages/qt/package.py index 373623cd95..8391ded3e0 100644 --- a/var/spack/repos/builtin/packages/qt/package.py +++ b/var/spack/repos/builtin/packages/qt/package.py @@ -52,11 +52,8 @@ class Qt(Package): depends_on("mesa", when='@4:+mesa') depends_on("libxcb") - def environment_modifications(self, module, spec, dep_spec): - """ - Dependencies of Qt find it using the QTDIR environment variable - """ - env = super(Qt, self).environment_modifications(module, spec, dep_spec) + def environment_modifications(self, dependent_spec): + env = super(Qt, self).environment_modifications(dependent_spec) env.set_env['QTDIR'] = self.prefix return env diff --git a/var/spack/repos/builtin/packages/ruby/package.py b/var/spack/repos/builtin/packages/ruby/package.py index 9ec0afa268..9caea30ef4 100644 --- a/var/spack/repos/builtin/packages/ruby/package.py +++ b/var/spack/repos/builtin/packages/ruby/package.py @@ -1,6 +1,5 @@ from spack import * -import spack -import os + class Ruby(Package): """A dynamic, open source programming language with a focus on @@ -18,19 +17,19 @@ class Ruby(Package): make() make("install") - def environment_modifications(self, module, spec, ext_spec): - env = super(Ruby, self).environment_modifications(module, spec, ext_spec) + def environment_modifications(self, extension_spec): + env = super(Ruby, self).environment_modifications(extension_spec) # Set GEM_PATH to include dependent gem directories ruby_paths = [] - for d in ext_spec.traverse(): + for d in extension_spec.traverse(): if d.package.extends(self.spec): ruby_paths.append(d.prefix) env.set_env('GEM_PATH', concatenate_paths(ruby_paths)) # The actual installation path for this gem - env.set_env('GEM_HOME', ext_spec.prefix) + env.set_env('GEM_HOME', extension_spec.prefix) return env - def setup_dependent_environment(self, module, spec, ext_spec): + def module_modifications(self, module, spec, ext_spec): """Called before ruby modules' install() methods. Sets GEM_HOME and GEM_PATH to values appropriate for the package being built. -- cgit v1.2.3-70-g09d2 From 68d22253eca40bc4223234d6c26204f292be6a0c Mon Sep 17 00:00:00 2001 From: Todd Gamblin Date: Tue, 15 Mar 2016 17:22:48 -0700 Subject: Add sanity checks to the libelf build. --- var/spack/repos/builtin/packages/libelf/package.py | 3 +++ 1 file changed, 3 insertions(+) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/libelf/package.py b/var/spack/repos/builtin/packages/libelf/package.py index 29bc21b65c..0fcb56c164 100644 --- a/var/spack/repos/builtin/packages/libelf/package.py +++ b/var/spack/repos/builtin/packages/libelf/package.py @@ -38,6 +38,9 @@ class Libelf(Package): provides('elf') + sanity_check_files = ['include/libelf.h'] + sanity_check_dirs = ['lib'] + def install(self, spec, prefix): configure("--prefix=" + prefix, "--enable-shared", -- cgit v1.2.3-70-g09d2 From b45ec3f04e3627dbe3633239560873ae01bf3beb Mon Sep 17 00:00:00 2001 From: alalazo Date: Wed, 16 Mar 2016 10:55:28 +0100 Subject: environment : simplified modification of the environment --- lib/spack/spack/build_environment.py | 12 +++-- lib/spack/spack/cmd/module.py | 2 +- lib/spack/spack/environment.py | 58 +++++++++++----------- lib/spack/spack/test/environment.py | 12 +++-- lib/spack/spack/util/environment.py | 2 +- var/spack/repos/builtin/packages/python/package.py | 1 + 6 files changed, 47 insertions(+), 40 deletions(-) (limited to 'var') diff --git a/lib/spack/spack/build_environment.py b/lib/spack/spack/build_environment.py index e86a7c413a..e5d256a2e0 100644 --- a/lib/spack/spack/build_environment.py +++ b/lib/spack/spack/build_environment.py @@ -35,7 +35,7 @@ import sys import spack from llnl.util.filesystem import * -from spack.environment import EnvironmentModifications, apply_environment_modifications, concatenate_paths +from spack.environment import EnvironmentModifications, concatenate_paths from spack.util.environment import * from spack.util.executable import Executable, which @@ -283,10 +283,12 @@ def setup_package(pkg): set_module_variables_for_package(pkg, mod) # Allow dependencies to set up environment as well. - for dep_spec in pkg.spec.traverse(root=False): - dep_spec.package.module_modifications(pkg.module, dep_spec, pkg.spec) - env.extend(dep_spec.package.environment_modifications(pkg.spec)) - apply_environment_modifications(env) + for dependency_spec in pkg.spec.traverse(root=False): + dependency_spec.package.module_modifications(pkg.module, dependency_spec, pkg.spec) + env.extend(dependency_spec.package.environment_modifications(pkg.spec)) + # TODO : implement validation + #validate(env) + env.apply_modifications() def fork(pkg, function): diff --git a/lib/spack/spack/cmd/module.py b/lib/spack/spack/cmd/module.py index 1d6867c1d9..315d9fc926 100644 --- a/lib/spack/spack/cmd/module.py +++ b/lib/spack/spack/cmd/module.py @@ -80,7 +80,7 @@ def module_find(mtype, spec_array): if not os.path.isfile(mod.file_name): tty.die("No %s module is installed for %s" % (mtype, spec)) - print mod.use_name + print(mod.use_name) def module_refresh(): diff --git a/lib/spack/spack/environment.py b/lib/spack/spack/environment.py index 5a68e10c99..b557bf0bbc 100644 --- a/lib/spack/spack/environment.py +++ b/lib/spack/spack/environment.py @@ -158,41 +158,43 @@ class EnvironmentModifications(object): item = RemovePath(name, path, **kwargs) self.env_modifications.append(item) + def group_by_name(self): + """ + Returns a dict of the modifications grouped by variable name + + Returns: + dict mapping the environment variable name to the modifications to be done on it + """ + modifications = collections.defaultdict(list) + for item in self: + modifications[item.name].append(item) + return modifications + + def clear(self): + """ + Clears the current list of modifications + """ + self.env_modifications.clear() + + def apply_modifications(self): + """ + Applies the modifications and clears the list + """ + modifications = self.group_by_name() + # Apply the modifications to the environment variables one variable at a time + for name, actions in sorted(modifications.items()): + for x in actions: + x.execute() + def concatenate_paths(paths): """ - Concatenates an iterable of paths into a column separated string + Concatenates an iterable of paths into a string of column separated paths Args: paths: iterable of paths Returns: - column separated string + string """ return ':'.join(str(item) for item in paths) - - -def validate_environment_modifications(env): - modifications = collections.defaultdict(list) - for item in env: - modifications[item.name].append(item) - # TODO : once we organized the modifications into a dictionary that maps an environment variable - # TODO : to a list of action to be done on it, we may easily spot inconsistencies and warn the user if - # TODO : something suspicious is happening - return modifications - - -def apply_environment_modifications(env): - """ - Modifies the current environment according to the request in env - - Args: - env: object storing modifications to the environment - """ - modifications = validate_environment_modifications(env) - - # Cycle over the environment variables that will be modified - for variable, actions in modifications.items(): - # Execute all the actions in the order they were issued - for x in actions: - x.execute() diff --git a/lib/spack/spack/test/environment.py b/lib/spack/spack/test/environment.py index f44282d6f3..d0b093b054 100644 --- a/lib/spack/spack/test/environment.py +++ b/lib/spack/spack/test/environment.py @@ -1,6 +1,6 @@ import unittest import os -from spack.environment import EnvironmentModifications, apply_environment_modifications +from spack.environment import EnvironmentModifications class EnvironmentTest(unittest.TestCase): @@ -15,7 +15,7 @@ class EnvironmentTest(unittest.TestCase): env = EnvironmentModifications() env.set_env('A', 'dummy value') env.set_env('B', 3) - apply_environment_modifications(env) + env.apply_modifications() self.assertEqual('dummy value', os.environ['A']) self.assertEqual(str(3), os.environ['B']) @@ -23,7 +23,7 @@ class EnvironmentTest(unittest.TestCase): env = EnvironmentModifications() self.assertEqual('foo', os.environ['UNSET_ME']) env.unset_env('UNSET_ME') - apply_environment_modifications(env) + env.apply_modifications() self.assertRaises(KeyError, os.environ.__getitem__, 'UNSET_ME') def test_path_manipulation(self): @@ -43,7 +43,7 @@ class EnvironmentTest(unittest.TestCase): env.remove_path('REMOVE_PATH_LIST', '/remove/this') env.remove_path('REMOVE_PATH_LIST', '/duplicate/') - apply_environment_modifications(env) + env.apply_modifications() self.assertEqual('/path/first:/path/second:/path/third:/path/last', os.environ['PATH_LIST']) self.assertEqual('/path/first:/path/middle:/path/last', os.environ['EMPTY_PATH_LIST']) self.assertEqual('/path/first:/path/middle:/path/last', os.environ['NEWLY_CREATED_PATH_LIST']) @@ -52,7 +52,9 @@ class EnvironmentTest(unittest.TestCase): def test_extra_arguments(self): env = EnvironmentModifications() env.set_env('A', 'dummy value', who='Pkg1') - apply_environment_modifications(env) + for x in env: + assert hasattr(x, 'who') + env.apply_modifications() self.assertEqual('dummy value', os.environ['A']) def test_extend(self): diff --git a/lib/spack/spack/util/environment.py b/lib/spack/spack/util/environment.py index 00cda8d508..1485992b0f 100644 --- a/lib/spack/spack/util/environment.py +++ b/lib/spack/spack/util/environment.py @@ -64,5 +64,5 @@ def path_put_first(var_name, directories): def dump_environment(path): """Dump the current environment out to a file.""" with open(path, 'w') as env_file: - for key,val in sorted(os.environ.items()): + for key, val in sorted(os.environ.items()): env_file.write("%s=%s\n" % (key, val)) diff --git a/var/spack/repos/builtin/packages/python/package.py b/var/spack/repos/builtin/packages/python/package.py index 307cec726b..2f9948d451 100644 --- a/var/spack/repos/builtin/packages/python/package.py +++ b/var/spack/repos/builtin/packages/python/package.py @@ -98,6 +98,7 @@ class Python(Package): if d.package.extends(self.spec): python_paths.append(os.path.join(d.prefix, self.site_packages_dir)) env.set_env['PYTHONPATH'] = ':'.join(python_paths) + return env def module_modifications(self, module, spec, ext_spec): """Called before python modules' install() methods. -- cgit v1.2.3-70-g09d2 From 9c2996667433e4f69eb25cce2d74a94caeb1646c Mon Sep 17 00:00:00 2001 From: Nicolas Richart Date: Wed, 16 Mar 2016 12:57:17 +0100 Subject: Change urls in binutils to help 'spack checksum/versions' + adding latest version --- var/spack/repos/builtin/packages/binutils/package.py | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) (limited to 'var') 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.") -- cgit v1.2.3-70-g09d2 From 597727f8bedc894330dfd26eab1a82859980f2f1 Mon Sep 17 00:00:00 2001 From: alalazo Date: Wed, 16 Mar 2016 15:19:13 +0100 Subject: tclmodules : added hooks to process EnvironmentModifications objects --- lib/spack/spack/modules.py | 151 +++++++++++++++------ var/spack/repos/builtin/packages/mpich/package.py | 25 +++- var/spack/repos/builtin/packages/python/package.py | 15 +- 3 files changed, 137 insertions(+), 54 deletions(-) (limited to 'var') diff --git a/lib/spack/spack/modules.py b/lib/spack/spack/modules.py index c27043db8c..1a0a0fd4d6 100644 --- a/lib/spack/spack/modules.py +++ b/lib/spack/spack/modules.py @@ -47,18 +47,18 @@ of module file. __all__ = ['EnvModule', 'Dotkit', 'TclModule'] import os +import os.path import re -import textwrap import shutil +import textwrap from glob import glob import llnl.util.tty as tty -from llnl.util.filesystem import join_path, mkdirp - import spack +from spack.environment import * +from llnl.util.filesystem import join_path, mkdirp -"""Registry of all types of modules. Entries created by EnvModule's - metaclass.""" +# Registry of all types of modules. Entries created by EnvModule's metaclass module_types = {} @@ -79,6 +79,32 @@ def print_help(): "") +class PathInspector(object): + dirname2varname = { + 'bin': ('PATH',), + 'man': ('MANPATH',), + 'lib': ('LIBRARY_PATH', 'LD_LIBRARY_PATH'), + 'lib64': ('LIBRARY_PATH', 'LD_LIBRARY_PATH'), + 'include': ('CPATH',), + 'pkgconfig': ('PKG_CONFIG_PATH',) + } + + def __call__(self, env, directory, names): + for name in names: + variables = PathInspector.dirname2varname.get(name, None) + if variables is None: + continue + absolute_path = join_path(os.path.abspath(directory), name) + for variable in variables: + env.prepend_path(variable, absolute_path) + + +def inspect_path(path): + env, inspector = EnvironmentModifications(), PathInspector() + os.path.walk(path, inspector, env) + return env + + class EnvModule(object): name = 'env_module' @@ -88,21 +114,27 @@ class EnvModule(object): if cls.name != 'env_module': module_types[cls.name] = cls - def __init__(self, spec=None): # category in the modules system # TODO: come up with smarter category names. self.category = "spack" - # Descriptions for the module system's UI - self.short_description = "" - self.long_description = "" - # dict pathname -> list of directories to be prepended to in # the module file. self._paths = None self.spec = spec + self.pkg = spec.package # Just stored for convenience + + # short description default is just the package + version + # packages can provide this optional attribute + self.short_description = spec.format("$_ $@") + if hasattr(self.pkg, 'short_description'): + self.short_description = self.pkg.short_description + # long description is the docstring with reduced whitespace. + self.long_description = None + if self.spec.package.__doc__: + self.long_description = re.sub(r'\s+', ' ', self.spec.package.__doc__) @property def paths(self): @@ -130,26 +162,19 @@ class EnvModule(object): add_path(var, directory) # Add python path unless it's an actual python installation - # TODO: is there a better way to do this? + # TODO : is there a better way to do this? + # FIXME : add PYTHONPATH to every python package if self.spec.name != 'python': site_packages = glob(join_path(self.spec.prefix.lib, "python*/site-packages")) if site_packages: add_path('PYTHONPATH', site_packages[0]) + # FIXME : Same for GEM_PATH if self.spec.package.extends(spack.spec.Spec('ruby')): - add_path('GEM_PATH', self.spec.prefix) - - # short description is just the package + version - # TODO: maybe packages can optionally provide it. - self.short_description = self.spec.format("$_ $@") - - # long description is the docstring with reduced whitespace. - if self.spec.package.__doc__: - self.long_description = re.sub(r'\s+', ' ', self.spec.package.__doc__) + add_path('GEM_PATH', self.spec.prefix) return self._paths - def write(self): """Write out a module file for this object.""" module_dir = os.path.dirname(self.file_name) @@ -160,9 +185,18 @@ class EnvModule(object): if not self.paths: return - with open(self.file_name, 'w') as f: - self._write(f) + # Construct the changes that needs to be done on the environment for + env = inspect_path(self.spec.prefix) + # FIXME : move the logic to inspection + env.prepend_path('CMAKE_PREFIX_PATH', self.spec.prefix) + # FIXME : decide how to distinguish between calls done in the installation and elsewhere + env.extend(self.spec.package.environment_modifications(None)) + # site_specific = ...` + if not env: + return + with open(self.file_name, 'w') as f: + self._write(f, env) def _write(self, stream): """To be implemented by subclasses.""" @@ -175,14 +209,12 @@ class EnvModule(object): where this module lives.""" raise NotImplementedError() - @property def use_name(self): """Subclasses should implement this to return the name the module command uses to refer to the package.""" raise NotImplementedError() - def remove(self): mod_file = self.file_name if os.path.exists(mod_file): @@ -205,7 +237,7 @@ class Dotkit(EnvModule): self.spec.compiler.version, self.spec.dag_hash()) - def _write(self, dk_file): + def _write(self, dk_file, env): # Category if self.category: dk_file.write('#c %s\n' % self.category) @@ -231,6 +263,10 @@ class Dotkit(EnvModule): class TclModule(EnvModule): name = 'tcl' path = join_path(spack.share_path, "modules") + formats = { + PrependPath: 'prepend-path {0.name} \"{0.path}\"\n', + SetEnv: 'setenv {0.name} \"{0.value}\"\n' + } @property def file_name(self): @@ -244,25 +280,56 @@ class TclModule(EnvModule): self.spec.compiler.version, self.spec.dag_hash()) - - def _write(self, m_file): - # TODO: cateogry? - m_file.write('#%Module1.0\n') - + def process_environment_command(self, env): + for command in env: + # FIXME : how should we handle errors here? + yield self.formats[type(command)].format(command) + + def _write(self, module_file, env): + """ + Writes a TCL module file for this package + + Args: + module_file: module file stream + env: list of environment modifications to be written in the module file + """ + # TCL Modulefile header + module_file.write('#%Module1.0\n') + # TODO : category ? # Short description if self.short_description: - m_file.write('module-whatis \"%s\"\n\n' % self.short_description) + module_file.write('module-whatis \"%s\"\n\n' % self.short_description) # Long description if self.long_description: - m_file.write('proc ModulesHelp { } {\n') + module_file.write('proc ModulesHelp { } {\n') doc = re.sub(r'"', '\"', self.long_description) - m_file.write("puts stderr \"%s\"\n" % doc) - m_file.write('}\n\n') - - # Path alterations - for var, dirs in self.paths.items(): - for directory in dirs: - m_file.write("prepend-path %s \"%s\"\n" % (var, directory)) - - m_file.write("prepend-path CMAKE_PREFIX_PATH \"%s\"\n" % self.spec.prefix) + module_file.write("puts stderr \"%s\"\n" % doc) + module_file.write('}\n\n') + + # Environment modifications + for line in self.process_environment_command(env): + module_file.write(line) + + # FIXME : REMOVE + # def _write(self, m_file): + # # TODO: cateogry? + # m_file.write('#%Module1.0\n') + # + # # Short description + # if self.short_description: + # m_file.write('module-whatis \"%s\"\n\n' % self.short_description) + # + # # Long description + # if self.long_description: + # m_file.write('proc ModulesHelp { } {\n') + # doc = re.sub(r'"', '\"', self.long_description) + # m_file.write("puts stderr \"%s\"\n" % doc) + # m_file.write('}\n\n') + # + # # Path alterations + # for var, dirs in self.paths.items(): + # for directory in dirs: + # m_file.write("prepend-path %s \"%s\"\n" % (var, directory)) + # + # m_file.write("prepend-path CMAKE_PREFIX_PATH \"%s\"\n" % self.spec.prefix) diff --git a/var/spack/repos/builtin/packages/mpich/package.py b/var/spack/repos/builtin/packages/mpich/package.py index d298981c92..4c34d0308f 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.""" @@ -48,11 +49,25 @@ class Mpich(Package): def environment_modifications(self, dependent_spec): env = super(Mpich, self).environment_modifications(dependent_spec) - env.set_env('MPICH_CC', os.environ['CC']) - env.set_env('MPICH_CXX', os.environ['CXX']) - env.set_env('MPICH_F77', os.environ['F77']) - env.set_env('MPICH_F90', os.environ['FC']) - env.set_env('MPICH_FC', os.environ['FC']) + + if dependent_spec is None: + # We are not using compiler wrappers + cc = self.compiler.cc + cxx = self.compiler.cxx + f77 = self.compiler.f77 + f90 = fc = self.compiler.fc + else: + # Spack compiler wrappers + cc = os.environ['CC'] + cxx = os.environ['CXX'] + f77 = os.environ['F77'] + f90 = fc = os.environ['FC'] + + env.set_env('MPICH_CC', cc) + env.set_env('MPICH_CXX', cxx) + env.set_env('MPICH_F77', f77) + env.set_env('MPICH_F90', f90) + env.set_env('MPICH_FC', fc) return env def module_modifications(self, module, spec, dep_spec): diff --git a/var/spack/repos/builtin/packages/python/package.py b/var/spack/repos/builtin/packages/python/package.py index 2f9948d451..acb3651726 100644 --- a/var/spack/repos/builtin/packages/python/package.py +++ b/var/spack/repos/builtin/packages/python/package.py @@ -91,13 +91,14 @@ class Python(Package): def environment_modifications(self, extension_spec): env = super(Python, self).environment_modifications(extension_spec) - # 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)) - env.set_env['PYTHONPATH'] = ':'.join(python_paths) + if extension_spec is not None: + # 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)) + env.set_env['PYTHONPATH'] = ':'.join(python_paths) return env def module_modifications(self, module, spec, ext_spec): -- cgit v1.2.3-70-g09d2 From fa2a66db6721ef5d7b54b9cede69aa2f1b5b7531 Mon Sep 17 00:00:00 2001 From: citibeth Date: Wed, 16 Mar 2016 15:46:59 -0400 Subject: 1. Disabled git versions known to have vulnerabilities. 2. Added autoconf command to allow building directly from GitHub source. --- var/spack/repos/builtin/packages/git/package.py | 24 +++++++++++++++++------- 1 file changed, 17 insertions(+), 7 deletions(-) (limited to 'var') 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") -- cgit v1.2.3-70-g09d2 From f0f0663d1b9ece1e2b0b0a8f720b1325eec443bb Mon Sep 17 00:00:00 2001 From: alalazo Date: Thu, 17 Mar 2016 15:11:39 +0100 Subject: package : split `environment_modifications` into `setup_environment` and `setup_dependent_environment`. package : renamed `module_modifications` to `modify_module` for consistency --- lib/spack/spack/build_environment.py | 4 +-- lib/spack/spack/modules.py | 5 ++- lib/spack/spack/package.py | 9 +++-- var/spack/repos/builtin/packages/mpich/package.py | 39 +++++++++------------- .../builtin/packages/netlib-scalapack/package.py | 2 +- .../repos/builtin/packages/openmpi/package.py | 19 ++++++----- var/spack/repos/builtin/packages/python/package.py | 27 +++++++-------- var/spack/repos/builtin/packages/qt/package.py | 4 +-- var/spack/repos/builtin/packages/ruby/package.py | 6 ++-- 9 files changed, 52 insertions(+), 63 deletions(-) (limited to 'var') diff --git a/lib/spack/spack/build_environment.py b/lib/spack/spack/build_environment.py index e5d256a2e0..68477145fe 100644 --- a/lib/spack/spack/build_environment.py +++ b/lib/spack/spack/build_environment.py @@ -284,8 +284,8 @@ def setup_package(pkg): # Allow dependencies to set up environment as well. for dependency_spec in pkg.spec.traverse(root=False): - dependency_spec.package.module_modifications(pkg.module, dependency_spec, pkg.spec) - env.extend(dependency_spec.package.environment_modifications(pkg.spec)) + dependency_spec.package.modify_module(pkg.module, dependency_spec, pkg.spec) + dependency_spec.package.setup_dependent_environment(env, pkg.spec) # TODO : implement validation #validate(env) env.apply_modifications() diff --git a/lib/spack/spack/modules.py b/lib/spack/spack/modules.py index 7e395736e4..09895d8c44 100644 --- a/lib/spack/spack/modules.py +++ b/lib/spack/spack/modules.py @@ -162,9 +162,8 @@ class EnvModule(object): # Environment modifications guessed by inspecting the installation prefix env = inspect_path(self.spec.prefix) # Package-specific environment modifications - # FIXME : decide how to distinguish between calls done in the installation and elsewhere - env.extend(self.spec.package.environment_modifications(None)) - # site_specific = ...` + self.spec.package.setup_environment(env) + # TODO : implement site-specific modifications and filters if not env: return diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py index 042833964a..8e56dd1f97 100644 --- a/lib/spack/spack/package.py +++ b/lib/spack/spack/package.py @@ -977,7 +977,7 @@ class Package(object): fromlist=[self.__class__.__name__]) - def environment_modifications(self, dependent_spec): + def setup_environment(self, env): """ Called before the install() method of dependents. @@ -998,9 +998,12 @@ class Package(object): Returns: instance of environment modifications """ - return EnvironmentModifications() + pass + + def setup_dependent_environment(self, env, dependent_spec): + self.setup_environment(env) - def module_modifications(self, module, spec, dependent_spec): + def modify_module(self, module, spec, dependent_spec): """ Called before the install() method of dependents. diff --git a/var/spack/repos/builtin/packages/mpich/package.py b/var/spack/repos/builtin/packages/mpich/package.py index 4c34d0308f..5af9b585ea 100644 --- a/var/spack/repos/builtin/packages/mpich/package.py +++ b/var/spack/repos/builtin/packages/mpich/package.py @@ -47,30 +47,21 @@ class Mpich(Package): provides('mpi@:3.0', when='@3:') provides('mpi@:1.3', when='@1:') - def environment_modifications(self, dependent_spec): - env = super(Mpich, self).environment_modifications(dependent_spec) - - if dependent_spec is None: - # We are not using compiler wrappers - cc = self.compiler.cc - cxx = self.compiler.cxx - f77 = self.compiler.f77 - f90 = fc = self.compiler.fc - else: - # Spack compiler wrappers - cc = os.environ['CC'] - cxx = os.environ['CXX'] - f77 = os.environ['F77'] - f90 = fc = os.environ['FC'] - - env.set_env('MPICH_CC', cc) - env.set_env('MPICH_CXX', cxx) - env.set_env('MPICH_F77', f77) - env.set_env('MPICH_F90', f90) - env.set_env('MPICH_FC', fc) - return env - - def module_modifications(self, module, spec, dep_spec): + def setup_environment(self, env): + env.set_env('MPICH_CC', self.compiler.cc) + env.set_env('MPICH_CXX', self.compiler.cxx) + env.set_env('MPICH_F77', self.compiler.f77) + env.set_env('MPICH_F90', self.compiler.fc) + env.set_env('MPICH_FC', self.compiler.fc) + + def setup_dependent_environment(self, env, dependent_spec): + env.set_env('MPICH_CC', spack_cc) + env.set_env('MPICH_CXX', spack_cxx) + env.set_env('MPICH_F77', spack_f77) + env.set_env('MPICH_F90', spack_f90) + env.set_env('MPICH_FC', spack_fc) + + def modify_module(self, module, spec, 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') diff --git a/var/spack/repos/builtin/packages/netlib-scalapack/package.py b/var/spack/repos/builtin/packages/netlib-scalapack/package.py index ecdea46442..7e7e5b2e2e 100644 --- a/var/spack/repos/builtin/packages/netlib-scalapack/package.py +++ b/var/spack/repos/builtin/packages/netlib-scalapack/package.py @@ -40,7 +40,7 @@ class NetlibScalapack(Package): make() make("install") - def module_modifications(self, module, spec, dependent_spec): + def modify_module(self, module, spec, dependent_spec): # TODO treat OS that are not Linux... lib_suffix = '.so' if '+shared' in spec['scalapack'] else '.a' diff --git a/var/spack/repos/builtin/packages/openmpi/package.py b/var/spack/repos/builtin/packages/openmpi/package.py index 3a14170457..7783ca8766 100644 --- a/var/spack/repos/builtin/packages/openmpi/package.py +++ b/var/spack/repos/builtin/packages/openmpi/package.py @@ -41,14 +41,17 @@ 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 environment_modifications(self, dependent_spec): - env = super(Openmpi, self).environment_modifications(dependent_spec) - # FIXME : the compilers should point to the current wrappers, not to generic cc etc. - env.set_env('OMPI_CC', 'cc') - env.set_env('OMPI_CXX', 'c++') - env.set_env('OMPI_FC', 'f90') - env.set_env('OMPI_F77', 'f77') - return env + def setup_environment(self, env): + env.set_env('OMPI_CC', self.compiler.cc) + env.set_env('OMPI_CXX', self.compiler.cxx) + env.set_env('OMPI_FC', self.compiler.fc) + env.set_env('OMPI_F77', self.compiler.f77) + + def setup_dependent_environment(self, env, dependent_spec): + env.set_env('OMPI_CC', spack_cc) + env.set_env('OMPI_CXX', spack_cxx) + env.set_env('OMPI_FC', spack_fc) + env.set_env('OMPI_F77', spack_f77) def install(self, spec, prefix): config_args = ["--prefix=%s" % prefix, diff --git a/var/spack/repos/builtin/packages/python/package.py b/var/spack/repos/builtin/packages/python/package.py index acb3651726..d47c1d1b2f 100644 --- a/var/spack/repos/builtin/packages/python/package.py +++ b/var/spack/repos/builtin/packages/python/package.py @@ -89,24 +89,21 @@ class Python(Package): def site_packages_dir(self): return os.path.join(self.python_lib_dir, 'site-packages') - def environment_modifications(self, extension_spec): - env = super(Python, self).environment_modifications(extension_spec) - if extension_spec is not None: - # 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)) - env.set_env['PYTHONPATH'] = ':'.join(python_paths) - return env - - def module_modifications(self, module, spec, ext_spec): - """Called before python modules' install() methods. + def setup_dependent_environment(self, env, extension_spec): + # 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)) + env.set_env['PYTHONPATH'] = ':'.join(python_paths) + + def modify_module(self, module, spec, 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"): diff --git a/var/spack/repos/builtin/packages/qt/package.py b/var/spack/repos/builtin/packages/qt/package.py index 0adf352be2..35b9d68462 100644 --- a/var/spack/repos/builtin/packages/qt/package.py +++ b/var/spack/repos/builtin/packages/qt/package.py @@ -55,10 +55,8 @@ class Qt(Package): depends_on("mesa", when='@4:+mesa') depends_on("libxcb") - def environment_modifications(self, dependent_spec): - env = super(Qt, self).environment_modifications(dependent_spec) + def setup_environment(self, env): env.set_env['QTDIR'] = self.prefix - return env def patch(self): if self.spec.satisfies('@4'): diff --git a/var/spack/repos/builtin/packages/ruby/package.py b/var/spack/repos/builtin/packages/ruby/package.py index 9caea30ef4..2d1da8c9af 100644 --- a/var/spack/repos/builtin/packages/ruby/package.py +++ b/var/spack/repos/builtin/packages/ruby/package.py @@ -17,8 +17,7 @@ class Ruby(Package): make() make("install") - def environment_modifications(self, extension_spec): - env = super(Ruby, self).environment_modifications(extension_spec) + def setup_dependent_environment(self, env, extension_spec): # Set GEM_PATH to include dependent gem directories ruby_paths = [] for d in extension_spec.traverse(): @@ -27,9 +26,8 @@ class Ruby(Package): env.set_env('GEM_PATH', concatenate_paths(ruby_paths)) # The actual installation path for this gem env.set_env('GEM_HOME', extension_spec.prefix) - return env - def module_modifications(self, module, spec, ext_spec): + def modify_module(self, module, spec, ext_spec): """Called before ruby modules' install() methods. Sets GEM_HOME and GEM_PATH to values appropriate for the package being built. -- cgit v1.2.3-70-g09d2 From ac394718ec0aa67c468a8529b930eaade0bcbed1 Mon Sep 17 00:00:00 2001 From: alalazo Date: Thu, 17 Mar 2016 18:22:07 +0100 Subject: python : implemented possible solution --- lib/spack/spack/package.py | 11 ++++++++++- var/spack/repos/builtin/packages/py-nose/package.py | 3 ++- 2 files changed, 12 insertions(+), 2 deletions(-) (limited to 'var') diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py index d0b94dbbeb..a7ab20137e 100644 --- a/lib/spack/spack/package.py +++ b/lib/spack/spack/package.py @@ -37,6 +37,7 @@ import os import re import textwrap import time +import glob import llnl.util.tty as tty import spack @@ -55,7 +56,6 @@ from llnl.util.filesystem import * from llnl.util.lang import * from llnl.util.link_tree import LinkTree from llnl.util.tty.log import log_output -from spack.environment import EnvironmentModifications from spack.stage import Stage, ResourceStage, StageComposite from spack.util.compression import allowed_archive from spack.util.environment import dump_environment @@ -1236,6 +1236,15 @@ class Package(object): return " ".join("-Wl,-rpath,%s" % p for p in self.rpath) +class PythonExtension(Package): + def setup_dependent_environment(self, env, dependent_spec): + pass + + def setup_environment(self, env): + site_packages = glob.glob(join_path(self.spec.prefix.lib, "python*/site-packages")) + if site_packages: + env.prepend_path('PYTHONPATH', site_packages[0]) + def validate_package_url(url_string): """Determine whether spack can handle a particular URL or not.""" url = urlparse(url_string) diff --git a/var/spack/repos/builtin/packages/py-nose/package.py b/var/spack/repos/builtin/packages/py-nose/package.py index e7c6cf0264..e817b8eb51 100644 --- a/var/spack/repos/builtin/packages/py-nose/package.py +++ b/var/spack/repos/builtin/packages/py-nose/package.py @@ -1,6 +1,7 @@ from spack import * +from spack.package import PythonExtension -class PyNose(Package): +class PyNose(PythonExtension): """nose extends the test loading and running features of unittest, making it easier to write, find and run tests.""" -- cgit v1.2.3-70-g09d2 From e55880904376847ce767770344059eef1ba7707c Mon Sep 17 00:00:00 2001 From: alalazo Date: Thu, 17 Mar 2016 19:32:31 +0100 Subject: python : fixed typo --- var/spack/repos/builtin/packages/python/package.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/python/package.py b/var/spack/repos/builtin/packages/python/package.py index d47c1d1b2f..d46e1068b6 100644 --- a/var/spack/repos/builtin/packages/python/package.py +++ b/var/spack/repos/builtin/packages/python/package.py @@ -95,7 +95,7 @@ class Python(Package): for d in extension_spec.traverse(): if d.package.extends(self.spec): python_paths.append(os.path.join(d.prefix, self.site_packages_dir)) - env.set_env['PYTHONPATH'] = ':'.join(python_paths) + env.set_env('PYTHONPATH', ':'.join(python_paths)) def modify_module(self, module, spec, ext_spec): """ -- cgit v1.2.3-70-g09d2 From 9e4c757f50ec98e55a74ad13fda70f12ce788891 Mon Sep 17 00:00:00 2001 From: Erik Schnetter Date: Thu, 17 Mar 2016 13:45:57 -0400 Subject: Update curl to 7.47.1 --- var/spack/repos/builtin/packages/curl/package.py | 1 + 1 file changed, 1 insertion(+) (limited to 'var') 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') -- cgit v1.2.3-70-g09d2 From 90268876f7d740e5b7dcfd079168f248a337791a Mon Sep 17 00:00:00 2001 From: Todd Gamblin Date: Thu, 17 Mar 2016 18:49:58 -0700 Subject: Change sanity_check_[file|dir] to sanity_check_is_[file|dir], per #554 - Add documentation as well. --- lib/spack/docs/packaging_guide.rst | 84 ++++++++++++++++++---- lib/spack/spack/package.py | 22 +++--- var/spack/repos/builtin/packages/libelf/package.py | 3 +- 3 files changed, 84 insertions(+), 25 deletions(-) (limited to 'var') diff --git a/lib/spack/docs/packaging_guide.rst b/lib/spack/docs/packaging_guide.rst index 169899212d..c1077e4497 100644 --- a/lib/spack/docs/packaging_guide.rst +++ b/lib/spack/docs/packaging_guide.rst @@ -1559,11 +1559,11 @@ you ask for a particular spec. A user may have certain preferences for how packages should be concretized on their system. For example, one user may prefer packages built with OpenMPI and the Intel compiler. Another user may prefer -packages be built with MVAPICH and GCC. +packages be built with MVAPICH and GCC. Spack can be configured to prefer certain compilers, package versions, depends_on, and variants during concretization. -The preferred configuration can be controlled via the +The preferred configuration can be controlled via the ``~/.spack/packages.yaml`` file for user configuations, or the ``etc/spack/packages.yaml`` site configuration. @@ -1582,32 +1582,32 @@ Here's an example packages.yaml file that sets preferred packages: compiler: [gcc@4.4.7, gcc@4.6:, intel, clang, pgi] providers: mpi: [mvapich, mpich, openmpi] - + At a high level, this example is specifying how packages should be -concretized. The dyninst package should prefer using gcc 4.9 and +concretized. The dyninst package should prefer using gcc 4.9 and be built with debug options. The gperftools package should prefer version 2.2 over 2.4. Every package on the system should prefer mvapich for -its MPI and gcc 4.4.7 (except for Dyninst, which overrides this by preferring gcc 4.9). -These options are used to fill in implicit defaults. Any of them can be overwritten +its MPI and gcc 4.4.7 (except for Dyninst, which overrides this by preferring gcc 4.9). +These options are used to fill in implicit defaults. Any of them can be overwritten on the command line if explicitly requested. -Each packages.yaml file begins with the string ``packages:`` and +Each packages.yaml file begins with the string ``packages:`` and package names are specified on the next level. The special string ``all`` -applies settings to each package. Underneath each package name is -one or more components: ``compiler``, ``variants``, ``version``, -or ``providers``. Each component has an ordered list of spec +applies settings to each package. Underneath each package name is +one or more components: ``compiler``, ``variants``, ``version``, +or ``providers``. Each component has an ordered list of spec ``constraints``, with earlier entries in the list being preferred over later entries. -Sometimes a package installation may have constraints that forbid +Sometimes a package installation may have constraints that forbid the first concretization rule, in which case Spack will use the first legal concretization rule. Going back to the example, if a user -requests gperftools 2.3 or later, then Spack will install version 2.4 +requests gperftools 2.3 or later, then Spack will install version 2.4 as the 2.4 version of gperftools is preferred over 2.3. -An explicit concretization rule in the preferred section will always -take preference over unlisted concretizations. In the above example, +An explicit concretization rule in the preferred section will always +take preference over unlisted concretizations. In the above example, xlc isn't listed in the compiler list. Every listed compiler from gcc to pgi will thus be preferred over the xlc compiler. @@ -2160,6 +2160,62 @@ package, this allows us to avoid race conditions in the library's build system. +.. _sanity-checks: + +Sanity checking an intallation +-------------------------------- + +By default, Spack assumes that a build has failed if nothing is +written to the install prefix, and that it has succeeded if anything +(a file, a directory, etc.) is written to the install prefix after +``install()`` completes. + +Consider a simple autotools build like this: + +.. code-block:: python + + def install(self, spec, prefix): + configure("--prefix=" + prefix) + make() + make("install") + +If you are using using standard autotools or CMake, ``configure`` and +``make`` will not write anything to the install prefix. Only ``make +install`` writes the files, and only once the build is already +complete. Not all builds are like this. Many builds of scientific +software modify the install prefix *before* ``make install``. Builds +like this can falsely report that they were successfully installed if +an error occurs before the install is complete but after files have +been written to the ``prefix``. + + +``sanity_check_is_file`` and ``sanity_check_is_dir`` +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +You can optionally specify *sanity checks* to deal with this problem. +Add properties like this to your package: + +.. code-block:: python + + class MyPackage(Package): + ... + + sanity_check_is_file = ['include/libelf.h'] + sanity_check_is_dir = [lib] + + def install(self, spec, prefix): + configure("--prefix=" + prefix) + make() + make("install") + +Now, after ``install()`` runs, Spack will check whether +``$prefix/include/libelf.h`` exists and is a file, and whether +``$prefix/lib`` exists and is a directory. If the checks fail, then +the build will fail and the install prefix will be removed. If they +succeed, Spack considers the build succeeful and keeps the prefix in +place. + + .. _file-manipulation: File manipulation functions diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py index 02fb3e5834..291056a7b9 100644 --- a/lib/spack/spack/package.py +++ b/lib/spack/spack/package.py @@ -318,16 +318,17 @@ class Package(object): """Most packages are NOT extendable. Set to True if you want extensions.""" extendable = False - """List of prefix-relative file paths. If these do not exist after - install, or if they exist but are not files, sanity checks fail. + """List of prefix-relative file paths (or a single path). If these do + not exist after install, or if they exist but are not files, + sanity checks fail. """ - sanity_check_files = [] + sanity_check_is_file = [] - """List of prefix-relative directory paths. If these do not exist - after install, or if they exist but are not directories, sanity - checks will fail. + """List of prefix-relative directory paths (or a single path). If + these do not exist after install, or if they exist but are not + directories, sanity checks will fail. """ - sanity_check_dirs = [] + sanity_check_is_dir = [] def __init__(self, spec): @@ -966,14 +967,17 @@ class Package(object): def sanity_check_prefix(self): """This function checks whether install succeeded.""" def check_paths(path_list, filetype, predicate): + if isinstance(path_list, basestring): + path_list = [path_list] + for path in path_list: abs_path = os.path.join(self.prefix, path) if not predicate(abs_path): raise InstallError("Install failed for %s. No such %s in prefix: %s" % (self.name, filetype, path)) - check_paths(self.sanity_check_files, 'file', os.path.isfile) - check_paths(self.sanity_check_dirs, 'directory', os.path.isdir) + check_paths(self.sanity_check_is_file, 'file', os.path.isfile) + check_paths(self.sanity_check_is_dir, 'directory', os.path.isdir) installed = set(os.listdir(self.prefix)) installed.difference_update(spack.install_layout.hidden_file_paths) diff --git a/var/spack/repos/builtin/packages/libelf/package.py b/var/spack/repos/builtin/packages/libelf/package.py index 0fcb56c164..9f16708af5 100644 --- a/var/spack/repos/builtin/packages/libelf/package.py +++ b/var/spack/repos/builtin/packages/libelf/package.py @@ -38,8 +38,7 @@ class Libelf(Package): provides('elf') - sanity_check_files = ['include/libelf.h'] - sanity_check_dirs = ['lib'] + sanity_check_is_file = 'include/libelf.h' def install(self, spec, prefix): configure("--prefix=" + prefix, -- cgit v1.2.3-70-g09d2 From 802acb4d166a7ca3ff2db3c0a0c95a3ad8a6a81a Mon Sep 17 00:00:00 2001 From: Erik Schnetter Date: Thu, 17 Mar 2016 13:43:40 -0400 Subject: Update PAPI to 5.4.3 --- var/spack/repos/builtin/packages/papi/package.py | 1 + 1 file changed, 1 insertion(+) (limited to 'var') 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') -- cgit v1.2.3-70-g09d2 From 1b279cd7ff29e09ef9afa1a328b964487b5b2030 Mon Sep 17 00:00:00 2001 From: Erik Schnetter Date: Thu, 17 Mar 2016 13:55:45 -0400 Subject: Update OpenBLAS to 0.2.16 --- var/spack/repos/builtin/packages/openblas/package.py | 1 + 1 file changed, 1 insertion(+) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/openblas/package.py b/var/spack/repos/builtin/packages/openblas/package.py index 3c909360a4..e16d3fe89c 100644 --- a/var/spack/repos/builtin/packages/openblas/package.py +++ b/var/spack/repos/builtin/packages/openblas/package.py @@ -5,6 +5,7 @@ class Openblas(Package): homepage = "http://www.openblas.net" url = "http://github.com/xianyi/OpenBLAS/archive/v0.2.15.tar.gz" + version('0.2.16', 'fef46ab92463bdbb1479dcec594ef6dc') version('0.2.15', 'b1190f3d3471685f17cfd1ec1d252ac9') # virtual dependency -- cgit v1.2.3-70-g09d2 From 4cf4bf3a0343fc93d6f0c14dd89956fa03b8f738 Mon Sep 17 00:00:00 2001 From: alalazo Date: Fri, 18 Mar 2016 11:05:59 +0100 Subject: openssl : solved glitch to prevent spack to freeze when the network is unreachable --- .../repos/builtin/packages/openssl/package.py | 29 +++++++++++++--------- 1 file changed, 17 insertions(+), 12 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/openssl/package.py b/var/spack/repos/builtin/packages/openssl/package.py index 70afaf4038..22d538531a 100644 --- a/var/spack/repos/builtin/packages/openssl/package.py +++ b/var/spack/repos/builtin/packages/openssl/package.py @@ -1,4 +1,4 @@ -import urllib +import urllib2 import llnl.util.tty as tty from spack import * @@ -37,17 +37,22 @@ class Openssl(Package): version_number = '.'.join([str(x) for x in version[:-1]]) older_url = older.format(version_number=version_number, version_full=version) latest_url = latest.format(version=version) - response = urllib.urlopen(latest.format(version=version)) - if response.getcode() == 404: - openssl_url = older_url - # Checks if we already warned the user for this particular version of OpenSSL. - # If not we display a warning message and mark this version - if not warnings_given_to_user.get(version, False): - tty.warn('This installation depends on an old version of OpenSSL, which may have known security issues. ') - tty.warn('Consider updating to the latest version of this package.') - tty.warn('More details at {homepage}'.format(homepage=Openssl.homepage)) - warnings_given_to_user[version] = True - else: + try: + response = urllib2.urlopen(latest.format(version=version), timeout=5) + if response.getcode() == 404: + openssl_url = older_url + # Checks if we already warned the user for this particular version of OpenSSL. + # If not we display a warning message and mark this version + if not warnings_given_to_user.get(version, False): + tty.warn('This installation depends on an old version of OpenSSL, which may have known security issues. ') + tty.warn('Consider updating to the latest version of this package.') + tty.warn('More details at {homepage}'.format(homepage=Openssl.homepage)) + warnings_given_to_user[version] = True + else: + openssl_url = latest_url + except urllib2.URLError: + tty.warn('Cannot connect to network to retrieve OpenSSL version. Using default url.') + warnings_given_to_user[version] = True openssl_url = latest_url # Store the computed URL openssl_urls[version] = openssl_url -- cgit v1.2.3-70-g09d2 From 3b24db92b5ea64814b1294fc6c9c982bbaa9b3c6 Mon Sep 17 00:00:00 2001 From: Erik Schnetter Date: Thu, 17 Mar 2016 13:43:40 -0400 Subject: Update PAPI to 5.4.3 --- var/spack/repos/builtin/packages/papi/package.py | 1 + 1 file changed, 1 insertion(+) (limited to 'var') 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') -- cgit v1.2.3-70-g09d2 From ec8cc2b52839007f0825815c8cfdee8f9a8629a6 Mon Sep 17 00:00:00 2001 From: alalazo Date: Fri, 18 Mar 2016 14:40:53 +0100 Subject: PYTHONPATH : python patches methods for its extensions --- lib/spack/spack/build_environment.py | 4 ++- lib/spack/spack/cmd/uninstall.py | 12 ++++---- lib/spack/spack/directory_layout.py | 2 +- lib/spack/spack/modules.py | 12 ++++++-- lib/spack/spack/package.py | 10 ------- .../repos/builtin/packages/py-nose/package.py | 6 ++-- var/spack/repos/builtin/packages/python/package.py | 34 ++++++++++++++++++++-- 7 files changed, 53 insertions(+), 27 deletions(-) (limited to 'var') diff --git a/lib/spack/spack/build_environment.py b/lib/spack/spack/build_environment.py index 68477145fe..c51fa58477 100644 --- a/lib/spack/spack/build_environment.py +++ b/lib/spack/spack/build_environment.py @@ -282,9 +282,11 @@ def setup_package(pkg): for mod in modules: set_module_variables_for_package(pkg, mod) - # Allow dependencies to set up environment as well. + # Allow dependencies to modify the module for dependency_spec in pkg.spec.traverse(root=False): dependency_spec.package.modify_module(pkg.module, dependency_spec, pkg.spec) + # Allow dependencies to set up environment as well + for dependency_spec in pkg.spec.traverse(root=False): dependency_spec.package.setup_dependent_environment(env, pkg.spec) # TODO : implement validation #validate(env) diff --git a/lib/spack/spack/cmd/uninstall.py b/lib/spack/spack/cmd/uninstall.py index d01aa2136b..2fab8f6f2a 100644 --- a/lib/spack/spack/cmd/uninstall.py +++ b/lib/spack/spack/cmd/uninstall.py @@ -79,7 +79,7 @@ def uninstall(parser, args): try: # should work if package is known to spack pkgs.append(s.package) - except spack.repository.UnknownPackageError, e: + except spack.repository.UnknownPackageError as e: # The package.py file has gone away -- but still # want to uninstall. spack.Package(s).do_uninstall(force=True) @@ -94,11 +94,11 @@ def uninstall(parser, args): for pkg in pkgs: try: pkg.do_uninstall(force=args.force) - except PackageStillNeededError, e: + except PackageStillNeededError as e: tty.error("Will not uninstall %s" % e.spec.format("$_$@$%@$#", color=True)) - print - print "The following packages depend on it:" + print() + print("The following packages depend on it:") display_specs(e.dependents, long=True) - print - print "You can use spack uninstall -f to force this action." + print() + print("You can use spack uninstall -f to force this action.") sys.exit(1) diff --git a/lib/spack/spack/directory_layout.py b/lib/spack/spack/directory_layout.py index 39ee4e203d..da8f1aa1bc 100644 --- a/lib/spack/spack/directory_layout.py +++ b/lib/spack/spack/directory_layout.py @@ -150,7 +150,7 @@ class DirectoryLayout(object): if os.path.exists(path): try: shutil.rmtree(path) - except exceptions.OSError, e: + except exceptions.OSError as e: raise RemoveFailedError(spec, path, e) path = os.path.dirname(path) diff --git a/lib/spack/spack/modules.py b/lib/spack/spack/modules.py index d192bbe004..7303844229 100644 --- a/lib/spack/spack/modules.py +++ b/lib/spack/spack/modules.py @@ -119,13 +119,13 @@ class EnvModule(object): module_types[cls.name] = cls def __init__(self, spec=None): + self.spec = spec + self.pkg = spec.package # Just stored for convenience + # category in the modules system # TODO: come up with smarter category names. self.category = "spack" - self.spec = spec - self.pkg = spec.package # Just stored for convenience - # short description default is just the package + version # packages can provide this optional attribute self.short_description = spec.format("$_ $@") @@ -161,6 +161,12 @@ class EnvModule(object): # Environment modifications guessed by inspecting the installation prefix env = inspect_path(self.spec.prefix) + + # Let the extendee modify their extensions before asking for package-specific modifications + for extendee in self.pkg.extendees: + extendee_spec = self.spec[extendee] + extendee_spec.package.modify_module(self.pkg, extendee_spec, self.spec) + # Package-specific environment modifications self.spec.package.setup_environment(env) # TODO : implement site-specific modifications and filters diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py index 185e3ad2ee..72c84ec624 100644 --- a/lib/spack/spack/package.py +++ b/lib/spack/spack/package.py @@ -1261,16 +1261,6 @@ class Package(object): """Get the rpath args as a string, with -Wl,-rpath, for each element.""" return " ".join("-Wl,-rpath,%s" % p for p in self.rpath) - -class PythonExtension(Package): - def setup_dependent_environment(self, env, dependent_spec): - pass - - def setup_environment(self, env): - site_packages = glob.glob(join_path(self.spec.prefix.lib, "python*/site-packages")) - if site_packages: - env.prepend_path('PYTHONPATH', site_packages[0]) - def validate_package_url(url_string): """Determine whether spack can handle a particular URL or not.""" url = urlparse(url_string) diff --git a/var/spack/repos/builtin/packages/py-nose/package.py b/var/spack/repos/builtin/packages/py-nose/package.py index e817b8eb51..4fee99098e 100644 --- a/var/spack/repos/builtin/packages/py-nose/package.py +++ b/var/spack/repos/builtin/packages/py-nose/package.py @@ -1,12 +1,12 @@ from spack import * -from spack.package import PythonExtension -class PyNose(PythonExtension): + +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/python/package.py b/var/spack/repos/builtin/packages/python/package.py index d46e1068b6..c445d26369 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): @@ -111,6 +114,31 @@ class Python(Package): else: module.python = Executable(join_path(spec.prefix.bin, 'python')) + # The code below patches the any python extension to have good defaults for `setup_dependent_environment` and + # `setup_environment` only if the extension didn't override any of these functions explicitly. + def _setup_env(self, env): + site_packages = glob.glob(join_path(self.spec.prefix.lib, "python*/site-packages")) + if site_packages: + env.prepend_path('PYTHONPATH', site_packages[0]) + + def _setup_denv(self, env, extension_spec): + pass + + pkg_cls = type(ext_spec.package) # Retrieve the type we may want to patch + if 'python' in pkg_cls.extendees: + # List of overrides we are interested in + interesting_overrides = ['setup_environment', 'setup_dependent_environment'] + overrides_found = [ + (name, defining_cls) for name, _, defining_cls, _, in inspect.classify_class_attrs(pkg_cls) + if + name in interesting_overrides and # The attribute has the right name + issubclass(defining_cls, Package) and defining_cls is not Package # and is an actual override + ] + if not overrides_found: + # If no override were found go on patching + pkg_cls.setup_environment = functools.wraps(Package.setup_environment)(_setup_env) + pkg_cls.setup_dependent_environment = functools.wraps(Package.setup_dependent_environment)(_setup_denv) + # 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) -- cgit v1.2.3-70-g09d2 From 5f6f2d5f51fc3700dce13c6aa035943bbc42f6f7 Mon Sep 17 00:00:00 2001 From: alalazo Date: Fri, 18 Mar 2016 14:42:24 +0100 Subject: Revert "openssl : solved glitch to prevent spack to freeze when the network is unreachable" This reverts commit 4cf4bf3a0343fc93d6f0c14dd89956fa03b8f738. --- .../repos/builtin/packages/openssl/package.py | 29 +++++++++------------- 1 file changed, 12 insertions(+), 17 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/openssl/package.py b/var/spack/repos/builtin/packages/openssl/package.py index 22d538531a..70afaf4038 100644 --- a/var/spack/repos/builtin/packages/openssl/package.py +++ b/var/spack/repos/builtin/packages/openssl/package.py @@ -1,4 +1,4 @@ -import urllib2 +import urllib import llnl.util.tty as tty from spack import * @@ -37,22 +37,17 @@ class Openssl(Package): version_number = '.'.join([str(x) for x in version[:-1]]) older_url = older.format(version_number=version_number, version_full=version) latest_url = latest.format(version=version) - try: - response = urllib2.urlopen(latest.format(version=version), timeout=5) - if response.getcode() == 404: - openssl_url = older_url - # Checks if we already warned the user for this particular version of OpenSSL. - # If not we display a warning message and mark this version - if not warnings_given_to_user.get(version, False): - tty.warn('This installation depends on an old version of OpenSSL, which may have known security issues. ') - tty.warn('Consider updating to the latest version of this package.') - tty.warn('More details at {homepage}'.format(homepage=Openssl.homepage)) - warnings_given_to_user[version] = True - else: - openssl_url = latest_url - except urllib2.URLError: - tty.warn('Cannot connect to network to retrieve OpenSSL version. Using default url.') - warnings_given_to_user[version] = True + response = urllib.urlopen(latest.format(version=version)) + if response.getcode() == 404: + openssl_url = older_url + # Checks if we already warned the user for this particular version of OpenSSL. + # If not we display a warning message and mark this version + if not warnings_given_to_user.get(version, False): + tty.warn('This installation depends on an old version of OpenSSL, which may have known security issues. ') + tty.warn('Consider updating to the latest version of this package.') + tty.warn('More details at {homepage}'.format(homepage=Openssl.homepage)) + warnings_given_to_user[version] = True + else: openssl_url = latest_url # Store the computed URL openssl_urls[version] = openssl_url -- cgit v1.2.3-70-g09d2 From ed0b5e649dd6bc480e3faa6ffcca121eb9e264b8 Mon Sep 17 00:00:00 2001 From: "Kelly (KT) Thompson" Date: Fri, 18 Mar 2016 15:54:26 -0600 Subject: + Provide fpic variant for netlib-lapack. --- var/spack/repos/builtin/packages/netlib-lapack/package.py | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/netlib-lapack/package.py b/var/spack/repos/builtin/packages/netlib-lapack/package.py index 741f4af421..78c5a053fe 100644 --- a/var/spack/repos/builtin/packages/netlib-lapack/package.py +++ b/var/spack/repos/builtin/packages/netlib-lapack/package.py @@ -20,13 +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 @@ -37,24 +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") - -- cgit v1.2.3-70-g09d2 From 620c120503c8c23d10feb14e14d37dfc36f4befb Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Sat, 19 Mar 2016 19:32:44 +0100 Subject: fix openblas suffix for OS-X --- var/spack/repos/builtin/packages/openblas/package.py | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/openblas/package.py b/var/spack/repos/builtin/packages/openblas/package.py index e16d3fe89c..781a1e2ec8 100644 --- a/var/spack/repos/builtin/packages/openblas/package.py +++ b/var/spack/repos/builtin/packages/openblas/package.py @@ -1,4 +1,5 @@ from spack import * +import sys class Openblas(Package): """OpenBLAS: An optimized BLAS library""" @@ -16,13 +17,14 @@ class Openblas(Package): make('libs', 'netlib', 'shared', 'CC=cc', 'FC=f77') 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) -- cgit v1.2.3-70-g09d2 From 95ad2875b6bb4dc15eb43b44c1dbdd521c843119 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Sun, 20 Mar 2016 09:25:02 +0100 Subject: fix scalapack suffix for osx --- var/spack/repos/builtin/packages/netlib-scalapack/package.py | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/netlib-scalapack/package.py b/var/spack/repos/builtin/packages/netlib-scalapack/package.py index 22d538560e..a5b6eedafb 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" @@ -32,17 +33,17 @@ 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' + lib_dsuffix = '.dylib' if sys.platform == 'darwin' else '.so' + lib_suffix = lib_dsuffix if '+shared' in spec['scalapack'] else '.a' spec['scalapack'].fc_link = '-L%s -lscalapack' % spec['scalapack'].prefix.lib spec['scalapack'].cc_link = spec['scalapack'].fc_link -- cgit v1.2.3-70-g09d2 From db61a09cf14cc791d7692aac0329e8958b228fb6 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Fri, 18 Mar 2016 16:28:36 +0100 Subject: fix mumps: when installed with parmetis has to be linked with metis --- var/spack/repos/builtin/packages/mumps/package.py | 28 +++++++++++++---------- 1 file changed, 16 insertions(+), 12 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/mumps/package.py b/var/spack/repos/builtin/packages/mumps/package.py index 44a37903cc..5c120c37df 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) @@ -130,7 +134,7 @@ class Mumps(Package): make_libs.append('zexamples') self.write_makefile_inc() - + make(*make_libs) install_tree('lib', prefix.lib) -- cgit v1.2.3-70-g09d2 From d493658a583231eeb778613cf7b6c8c8641c63a0 Mon Sep 17 00:00:00 2001 From: Cyrus Harrison Date: Sun, 20 Mar 2016 15:18:36 -0700 Subject: cmake package: add variant for openssl support The openssl variant defaults to true to preserve spack's current CMake configuration, which is using OpenSSL. Signed-off-by: Cyrus Harrison --- var/spack/repos/builtin/packages/cmake/package.py | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/cmake/package.py b/var/spack/repos/builtin/packages/cmake/package.py index cc93c7067c..be930a90ab 100644 --- a/var/spack/repos/builtin/packages/cmake/package.py +++ b/var/spack/repos/builtin/packages/cmake/package.py @@ -38,6 +38,7 @@ 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') @@ -77,8 +78,9 @@ 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() -- cgit v1.2.3-70-g09d2 From bba66cbe2836e364b58a611a5a5f5ae0d9692df4 Mon Sep 17 00:00:00 2001 From: Cyrus Harrison Date: Sun, 20 Mar 2016 19:27:22 -0700 Subject: cmake: depend on openssl when openssl variant=true --- var/spack/repos/builtin/packages/cmake/package.py | 1 + 1 file changed, 1 insertion(+) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/cmake/package.py b/var/spack/repos/builtin/packages/cmake/package.py index be930a90ab..1f93d39769 100644 --- a/var/spack/repos/builtin/packages/cmake/package.py +++ b/var/spack/repos/builtin/packages/cmake/package.py @@ -43,6 +43,7 @@ class Cmake(Package): 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') -- cgit v1.2.3-70-g09d2 From 7b283bfaffa5509915d91392878203bba8a8d2cb Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Mon, 21 Mar 2016 07:48:17 +0100 Subject: fix petsc on osx --- var/spack/repos/builtin/packages/petsc/package.py | 20 +++++++++++++++----- 1 file changed, 15 insertions(+), 5 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/petsc/package.py b/var/spack/repos/builtin/packages/petsc/package.py index efe172fc08..7239baaf7f 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'), -- cgit v1.2.3-70-g09d2 From b926d8a0cdcf47de029e372cf15e281266930378 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Mon, 21 Mar 2016 14:33:00 +0100 Subject: build parmetis against external metis --- .../packages/parmetis/enable_external_metis.patch | 13 ++++++++++++ .../repos/builtin/packages/parmetis/package.py | 24 ++++------------------ 2 files changed, 17 insertions(+), 20 deletions(-) create mode 100644 var/spack/repos/builtin/packages/parmetis/enable_external_metis.patch (limited to 'var') 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/package.py b/var/spack/repos/builtin/packages/parmetis/package.py index c897dec7e4..3f18dd76b8 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 +40,11 @@ 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') depends_on('gdb', when='+gdb') @@ -63,8 +58,8 @@ 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 +73,7 @@ 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) -- cgit v1.2.3-70-g09d2 From 3fcaf5b9031c3d55b152844b97cd432078340f4b Mon Sep 17 00:00:00 2001 From: alalazo Date: Mon, 21 Mar 2016 14:47:05 +0100 Subject: llvm : update to 3.8.0 --- var/spack/repos/builtin/packages/llvm/package.py | 15 +++++++++++++++ 1 file changed, 15 insertions(+) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/llvm/package.py b/var/spack/repos/builtin/packages/llvm/package.py index 280e400f69..5c38b5b88c 100644 --- a/var/spack/repos/builtin/packages/llvm/package.py +++ b/var/spack/repos/builtin/packages/llvm/package.py @@ -132,6 +132,21 @@ class Llvm(Package): 'llvm-libunwind' : 'http://llvm.org/svn/llvm-project/libunwind/trunk', } }, + { + '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', -- cgit v1.2.3-70-g09d2 From 3a3443dff63167fc0331672871af4c0cc1fe5903 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Mon, 21 Mar 2016 15:14:48 +0100 Subject: parmetis patches by PETSc developers --- .../repos/builtin/packages/parmetis/package.py | 6 ++ ...-1c1a9fd0f408dc4d42c57f5c3ee6ace411eb222b.patch | 77 ++++++++++++++++++++++ ...-82409d68aa1d6cbc70740d0f35024aae17f7d5cb.patch | 35 ++++++++++ 3 files changed, 118 insertions(+) create mode 100644 var/spack/repos/builtin/packages/parmetis/pkg-parmetis-1c1a9fd0f408dc4d42c57f5c3ee6ace411eb222b.patch create mode 100644 var/spack/repos/builtin/packages/parmetis/pkg-parmetis-82409d68aa1d6cbc70740d0f35024aae17f7d5cb.patch (limited to 'var') diff --git a/var/spack/repos/builtin/packages/parmetis/package.py b/var/spack/repos/builtin/packages/parmetis/package.py index 3f18dd76b8..c691cf4191 100644 --- a/var/spack/repos/builtin/packages/parmetis/package.py +++ b/var/spack/repos/builtin/packages/parmetis/package.py @@ -46,6 +46,12 @@ class Parmetis(Package): 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') + depends_on('gdb', when='+gdb') def install(self, spec, prefix): 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 +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 +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 Date: Mon, 21 Mar 2016 16:18:02 +0100 Subject: llvm : does not support python 3 --- var/spack/repos/builtin/packages/llvm/package.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/llvm/package.py b/var/spack/repos/builtin/packages/llvm/package.py index 5c38b5b88c..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') -- cgit v1.2.3-70-g09d2 From c5c92d50eb78673c635a7ed26145bf10a15c20cb Mon Sep 17 00:00:00 2001 From: Ben Boeckel Date: Mon, 21 Mar 2016 11:24:36 -0400 Subject: paraview: remove trailing whitespace --- var/spack/repos/builtin/packages/paraview/package.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/paraview/package.py b/var/spack/repos/builtin/packages/paraview/package.py index ccf2d14c06..b3312736f1 100644 --- a/var/spack/repos/builtin/packages/paraview/package.py +++ b/var/spack/repos/builtin/packages/paraview/package.py @@ -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): -- cgit v1.2.3-70-g09d2 From 8e77f1776020c2a6edf9eb284615d99c905821e9 Mon Sep 17 00:00:00 2001 From: Ben Boeckel Date: Mon, 21 Mar 2016 11:54:58 -0400 Subject: paraview: fix variant description typo --- var/spack/repos/builtin/packages/paraview/package.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/paraview/package.py b/var/spack/repos/builtin/packages/paraview/package.py index b3312736f1..0c3c7c1621 100644 --- a/var/spack/repos/builtin/packages/paraview/package.py +++ b/var/spack/repos/builtin/packages/paraview/package.py @@ -16,7 +16,7 @@ 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('py-numpy', when='+python') -- cgit v1.2.3-70-g09d2 From 553fff270a13d40fb9a41569bebf5075a740d8ac Mon Sep 17 00:00:00 2001 From: Ben Boeckel Date: Mon, 21 Mar 2016 11:24:49 -0400 Subject: paraview: disallow python3 ParaView is not Python3-ready. --- var/spack/repos/builtin/packages/paraview/package.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/paraview/package.py b/var/spack/repos/builtin/packages/paraview/package.py index 0c3c7c1621..c16054816c 100644 --- a/var/spack/repos/builtin/packages/paraview/package.py +++ b/var/spack/repos/builtin/packages/paraview/package.py @@ -18,7 +18,7 @@ class Paraview(Package): variant('qt', default=False, description='Enable Qt support') 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') -- cgit v1.2.3-70-g09d2 From 953fb35f82c099936f833f31dcd292ffa1a3ec06 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Mon, 21 Mar 2016 18:00:32 +0100 Subject: add superlu_dist package --- .../repos/builtin/packages/superlu-dist/package.py | 63 ++++++++++++++++++++++ 1 file changed, 63 insertions(+) create mode 100644 var/spack/repos/builtin/packages/superlu-dist/package.py (limited to 'var') 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..c4c76909b3 --- /dev/null +++ b/var/spack/repos/builtin/packages/superlu-dist/package.py @@ -0,0 +1,63 @@ +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) + # 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) -- cgit v1.2.3-70-g09d2 From 439d47b4e45c674ab9aa4ebd0c2bfaf6911ade60 Mon Sep 17 00:00:00 2001 From: Todd Gamblin Date: Mon, 21 Mar 2016 01:48:18 -0700 Subject: Refactor environment setup. - Gave setup_environment and setup_dependent_environment more similar signatures. They now allows editing the Spack env and the runtime env for *this* package and dependents, respectively. - modify_module renamed to setup_dependent_python_module for symmetry with setup_dependent_environment and to avoid confusion with environment modules. - removed need for patching Package objects at runtime. - adjust packages to reflect these changes. --- lib/spack/spack/build_environment.py | 35 +++--- lib/spack/spack/modules.py | 3 +- lib/spack/spack/package.py | 120 ++++++++++++++++----- var/spack/repos/builtin/packages/mpich/package.py | 9 +- .../builtin/packages/netlib-scalapack/package.py | 2 +- .../repos/builtin/packages/openmpi/package.py | 18 ++-- var/spack/repos/builtin/packages/python/package.py | 39 ++----- var/spack/repos/builtin/packages/qt/package.py | 10 +- var/spack/repos/builtin/packages/ruby/package.py | 12 +-- 9 files changed, 151 insertions(+), 97 deletions(-) (limited to 'var') diff --git a/lib/spack/spack/build_environment.py b/lib/spack/spack/build_environment.py index 59b234624c..5688d47e2d 100644 --- a/lib/spack/spack/build_environment.py +++ b/lib/spack/spack/build_environment.py @@ -84,7 +84,7 @@ class MakeExecutable(Executable): return super(MakeExecutable, self).__call__(*args, **kwargs) -def set_compiler_environment_variables(pkg): +def set_compiler_environment_variables(pkg, env): assert pkg.spec.concrete # Set compiler variables used by CMake and autotools assert all(key in pkg.compiler.link_paths for key in ('cc', 'cxx', 'f77', 'fc')) @@ -92,7 +92,6 @@ def set_compiler_environment_variables(pkg): # Populate an object with the list of environment modifications # and return it # TODO : add additional kwargs for better diagnostics, like requestor, ttyout, ttyerr, etc. - env = EnvironmentModifications() link_dir = spack.build_env_path env.set_env('CC', join_path(link_dir, pkg.compiler.link_paths['cc'])) env.set_env('CXX', join_path(link_dir, pkg.compiler.link_paths['cxx'])) @@ -113,7 +112,7 @@ def set_compiler_environment_variables(pkg): return env -def set_build_environment_variables(pkg): +def set_build_environment_variables(pkg, env): """ This ensures a clean install environment when we build packages """ @@ -134,7 +133,6 @@ def set_build_environment_variables(pkg): if os.path.isdir(ci): env_paths.append(ci) - env = EnvironmentModifications() for item in reversed(env_paths): env.prepend_path('PATH', item) env.set_env(SPACK_ENV_PATH, concatenate_paths(env_paths)) @@ -180,7 +178,7 @@ def set_build_environment_variables(pkg): return env -def set_module_variables_for_package(pkg, m): +def set_module_variables_for_package(pkg, module): """Populate the module scope of install() with some useful functions. This makes things easier for package writers. """ @@ -190,6 +188,8 @@ def set_module_variables_for_package(pkg, m): jobs = 1 elif pkg.make_jobs: jobs = pkg.make_jobs + + m = module m.make_jobs = jobs # TODO: make these build deps that can be installed if not found. @@ -271,9 +271,12 @@ def parent_class_modules(cls): def setup_package(pkg): """Execute all environment setup routines.""" - env = EnvironmentModifications() - env.extend(set_compiler_environment_variables(pkg)) - env.extend(set_build_environment_variables(pkg)) + spack_env = EnvironmentModifications() + run_env = EnvironmentModifications() + + set_compiler_environment_variables(pkg, spack_env) + set_build_environment_variables(pkg, spack_env) + # If a user makes their own package repo, e.g. # spack.repos.mystuff.libelf.Libelf, and they inherit from # an existing class like spack.repos.original.libelf.Libelf, @@ -285,12 +288,20 @@ def setup_package(pkg): # Allow dependencies to modify the module for dependency_spec in pkg.spec.traverse(root=False): - dependency_spec.package.modify_module(pkg.module, dependency_spec, pkg.spec) + dpkg = dependency_spec.package + dpkg.setup_dependent_python_module(pkg.module, pkg.spec) + # Allow dependencies to set up environment as well for dependency_spec in pkg.spec.traverse(root=False): - dependency_spec.package.setup_dependent_environment(env, pkg.spec) - validate(env, tty.warn) - env.apply_modifications() + dpkg = dependency_spec.package + dpkg.setup_dependent_environment(spack_env, run_env, pkg.spec) + + # Allow the package to apply some settings. + pkg.setup_environment(spack_env, run_env) + + # Make sure nothing's strange about the Spack environment. + validate(spack_env, tty.warn) + spack_env.apply_modifications() def fork(pkg, function): diff --git a/lib/spack/spack/modules.py b/lib/spack/spack/modules.py index 4e98d50001..05c93cd3e6 100644 --- a/lib/spack/spack/modules.py +++ b/lib/spack/spack/modules.py @@ -164,7 +164,8 @@ class EnvModule(object): self.pkg.module, extendee_spec, self.spec) # Package-specific environment modifications - self.spec.package.setup_environment(env) + spack_env = EnvironmentModifications() + self.spec.package.setup_environment(spack_env, env) # TODO : implement site-specific modifications and filters if not env: diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py index acad5a28f6..9d8ac87bd7 100644 --- a/lib/spack/spack/package.py +++ b/lib/spack/spack/package.py @@ -1002,56 +1002,120 @@ class Package(object): return __import__(self.__class__.__module__, fromlist=[self.__class__.__name__]) - def setup_environment(self, env): - """ - Appends in `env` the list of environment modifications needed to use this package outside of spack. + def setup_environment(self, spack_env, run_env): + """Set up the compile and runtime environemnts for a package. - Default implementation does nothing, but this can be overridden if the package needs a particular environment. + `spack_env` and `run_env` are `EnvironmentModifications` + objects. Package authors can call methods on them to alter + the environment within Spack and at runtime. - Example : + Both `spack_env` and `run_env` are applied within the build + process, before this package's `install()` method is called. + + Modifications in `run_env` will *also* be added to the + generated environment modules for this package. + + Default implementation does nothing, but this can be + overridden if the package needs a particular environment. - 1. A lot of Qt extensions need `QTDIR` set. This can be used to do that. + Examples: + + 1. Qt extensions need `QTDIR` set. Args: - env: list of environment modifications to be updated + spack_env (EnvironmentModifications): list of + modifications to be applied when this package is built + within Spack. + + run_env (EnvironmentModifications): list of environment + changes to be applied when this package is run outside + of Spack. + """ pass - def setup_dependent_environment(self, env, dependent_spec): - """ - Called before the install() method of dependents. - Appends in `env` the list of environment modifications needed by dependents (or extensions) during the - installation of a package. The default implementation delegates to `setup_environment`, but can be overridden - if the modifications to the environment happen to be different from the one needed to use the package outside - of spack. + def setup_dependent_environment(self, spack_env, run_env, dependent_spec): + """Set up the environment of packages that depend on this one. + + This is similar to `setup_environment`, but it is used to + modify the compile and runtime environments of packages that + *depend* on this one. This gives packages like Python and + others that follow the extension model a way to implement + common environment or compile-time settings for dependencies. - This is useful if there are some common steps to installing all extensions for a certain package. + By default, this delegates to self.setup_environment() Example : - 1. Installing python modules generally requires `PYTHONPATH` to point to the lib/pythonX.Y/site-packages - directory in the module's install prefix. This could set that variable. + 1. Installing python modules generally requires + `PYTHONPATH` to point to the lib/pythonX.Y/site-packages + directory in the module's install prefix. This could + set that variable. Args: - env: list of environment modifications to be updated - dependent_spec: dependent (or extension) of this spec - """ - self.setup_environment(env) - def modify_module(self, module, spec, dependent_spec): + spack_env (EnvironmentModifications): list of + modifications to be applied when the dependent package + is bulit within Spack. + + run_env (EnvironmentModifications): list of environment + changes to be applied when the dependent package is + run outside of Spack. + + dependent_spec (Spec): The spec of the dependent package + about to be built. This allows the extendee (self) to + query the dependent's state. Note that *this* + package's spec is available as `self.spec`. + + This is useful if there are some common steps to installing + all extensions for a certain package. + """ + self.setup_environment(spack_env, run_env) + + + def setup_dependent_python_module(self, module, dependent_spec): + """Set up Python module-scope variables for dependent packages. + Called before the install() method of dependents. - Default implementation does nothing, but this can be overridden by an extendable package to set up the module of - its extensions. This is useful if there are some common steps to installing all extensions for a - certain package. + Default implementation does nothing, but this can be + overridden by an extendable package to set up the module of + its extensions. This is useful if there are some common steps + to installing all extensions for a certain package. Example : - 1. Extensions often need to invoke the 'python' interpreter from the Python installation being extended. - This routine can put a 'python' Executable object in the module scope for the extension package to simplify - extension installs. + 1. Extensions often need to invoke the `python` + interpreter from the Python installation being + extended. This routine can put a 'python' Executable + object in the module scope for the extension package to + simplify extension installs. + + 2. MPI compilers could set some variables in the + dependent's scope that point to `mpicc`, `mpicxx`, + etc., allowing them to be called by common names + regardless of which MPI is used. + + 3. BLAS/LAPACK implementations can set some variables + indicating the path to their libraries, since these + paths differ by BLAS/LAPACK implementation. + + Args: + + module (module): The Python `module` object of the + dependent package. Packages can use this to set + module-scope variables for the dependent to use. + + dependent_spec (Spec): The spec of the dependent package + about to be built. This allows the extendee (self) to + query the dependent's state. Note that *this* + package's spec is available as `self.spec`. + + This is useful if there are some common steps to installing + all extensions for a certain package. + """ pass diff --git a/var/spack/repos/builtin/packages/mpich/package.py b/var/spack/repos/builtin/packages/mpich/package.py index 5af9b585ea..90b5d42eab 100644 --- a/var/spack/repos/builtin/packages/mpich/package.py +++ b/var/spack/repos/builtin/packages/mpich/package.py @@ -47,13 +47,6 @@ class Mpich(Package): provides('mpi@:3.0', when='@3:') provides('mpi@:1.3', when='@1:') - def setup_environment(self, env): - env.set_env('MPICH_CC', self.compiler.cc) - env.set_env('MPICH_CXX', self.compiler.cxx) - env.set_env('MPICH_F77', self.compiler.f77) - env.set_env('MPICH_F90', self.compiler.fc) - env.set_env('MPICH_FC', self.compiler.fc) - def setup_dependent_environment(self, env, dependent_spec): env.set_env('MPICH_CC', spack_cc) env.set_env('MPICH_CXX', spack_cxx) @@ -61,7 +54,7 @@ class Mpich(Package): env.set_env('MPICH_F90', spack_f90) env.set_env('MPICH_FC', spack_fc) - def modify_module(self, module, spec, dep_spec): + def setup_dependent_python_module(self, module, spec, 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') diff --git a/var/spack/repos/builtin/packages/netlib-scalapack/package.py b/var/spack/repos/builtin/packages/netlib-scalapack/package.py index 36f506f7cd..62abfcc48e 100644 --- a/var/spack/repos/builtin/packages/netlib-scalapack/package.py +++ b/var/spack/repos/builtin/packages/netlib-scalapack/package.py @@ -40,7 +40,7 @@ class NetlibScalapack(Package): make() make("install") - def modify_module(self, module, spec, dependent_spec): + def setup_dependent_python_module(self, module, spec, dependent_spec): lib_dsuffix = '.dylib' if sys.platform == 'darwin' else '.so' lib_suffix = lib_dsuffix if '+shared' in spec['scalapack'] else '.a' diff --git a/var/spack/repos/builtin/packages/openmpi/package.py b/var/spack/repos/builtin/packages/openmpi/package.py index 7783ca8766..c91a13e376 100644 --- a/var/spack/repos/builtin/packages/openmpi/package.py +++ b/var/spack/repos/builtin/packages/openmpi/package.py @@ -41,17 +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_environment(self, env): - env.set_env('OMPI_CC', self.compiler.cc) - env.set_env('OMPI_CXX', self.compiler.cxx) - env.set_env('OMPI_FC', self.compiler.fc) - env.set_env('OMPI_F77', self.compiler.f77) - - def setup_dependent_environment(self, env, dependent_spec): - env.set_env('OMPI_CC', spack_cc) - env.set_env('OMPI_CXX', spack_cxx) - env.set_env('OMPI_FC', spack_fc) - env.set_env('OMPI_F77', spack_f77) + + def setup_dependent_environment(self, spack_env, run_env, dependent_spec): + spack_env.set_env('OMPI_CC', spack_cc) + spack_env.set_env('OMPI_CXX', spack_cxx) + spack_env.set_env('OMPI_FC', spack_fc) + spack_env.set_env('OMPI_F77', spack_f77) + def install(self, spec, prefix): config_args = ["--prefix=%s" % prefix, diff --git a/var/spack/repos/builtin/packages/python/package.py b/var/spack/repos/builtin/packages/python/package.py index c445d26369..593a27708c 100644 --- a/var/spack/repos/builtin/packages/python/package.py +++ b/var/spack/repos/builtin/packages/python/package.py @@ -92,13 +92,21 @@ class Python(Package): def site_packages_dir(self): return os.path.join(self.python_lib_dir, 'site-packages') - def setup_dependent_environment(self, env, extension_spec): - # Set PYTHONPATH to include site-packages dir for the extension and any other python extensions it depends on. + + 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)) - env.set_env('PYTHONPATH', ':'.join(python_paths)) + + pythonpath = ':'.join(python_paths) + spack_env.set_env('PYTHONPATH', pythonpath) + run_env.set_env('PYTHONPATH', pythonpath) + def modify_module(self, module, spec, ext_spec): """ @@ -114,31 +122,6 @@ class Python(Package): else: module.python = Executable(join_path(spec.prefix.bin, 'python')) - # The code below patches the any python extension to have good defaults for `setup_dependent_environment` and - # `setup_environment` only if the extension didn't override any of these functions explicitly. - def _setup_env(self, env): - site_packages = glob.glob(join_path(self.spec.prefix.lib, "python*/site-packages")) - if site_packages: - env.prepend_path('PYTHONPATH', site_packages[0]) - - def _setup_denv(self, env, extension_spec): - pass - - pkg_cls = type(ext_spec.package) # Retrieve the type we may want to patch - if 'python' in pkg_cls.extendees: - # List of overrides we are interested in - interesting_overrides = ['setup_environment', 'setup_dependent_environment'] - overrides_found = [ - (name, defining_cls) for name, _, defining_cls, _, in inspect.classify_class_attrs(pkg_cls) - if - name in interesting_overrides and # The attribute has the right name - issubclass(defining_cls, Package) and defining_cls is not Package # and is an actual override - ] - if not overrides_found: - # If no override were found go on patching - pkg_cls.setup_environment = functools.wraps(Package.setup_environment)(_setup_env) - pkg_cls.setup_dependent_environment = functools.wraps(Package.setup_dependent_environment)(_setup_denv) - # 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) diff --git a/var/spack/repos/builtin/packages/qt/package.py b/var/spack/repos/builtin/packages/qt/package.py index 35b9d68462..039aeb3c31 100644 --- a/var/spack/repos/builtin/packages/qt/package.py +++ b/var/spack/repos/builtin/packages/qt/package.py @@ -55,8 +55,14 @@ class Qt(Package): depends_on("mesa", when='@4:+mesa') depends_on("libxcb") - def setup_environment(self, env): - env.set_env['QTDIR'] = self.prefix + + def setup_environment(self, spack_env, env): + env.set_env('QTDIR', self.prefix) + + + def setup_dependent_environment(self, spack_env, run_env, dspec): + spack_env.set_env('QTDIR', self.prefix) + def patch(self): if self.spec.satisfies('@4'): diff --git a/var/spack/repos/builtin/packages/ruby/package.py b/var/spack/repos/builtin/packages/ruby/package.py index 2d1da8c9af..39f65f51d2 100644 --- a/var/spack/repos/builtin/packages/ruby/package.py +++ b/var/spack/repos/builtin/packages/ruby/package.py @@ -2,7 +2,7 @@ from spack import * 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/" @@ -17,15 +17,17 @@ class Ruby(Package): make() make("install") - def setup_dependent_environment(self, env, extension_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) - env.set_env('GEM_PATH', concatenate_paths(ruby_paths)) + + spack_env.set_env('GEM_PATH', concatenate_paths(ruby_paths)) # The actual installation path for this gem - env.set_env('GEM_HOME', extension_spec.prefix) + spack_env.set_env('GEM_HOME', extension_spec.prefix) def modify_module(self, module, spec, ext_spec): """Called before ruby modules' install() methods. Sets GEM_HOME @@ -38,5 +40,3 @@ class Ruby(Package): # 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')) - - -- cgit v1.2.3-70-g09d2 From b1516f64eb75c108eded1e9ee7e0480a4552236a Mon Sep 17 00:00:00 2001 From: Todd Gamblin Date: Mon, 21 Mar 2016 02:21:31 -0700 Subject: Rename some environment methods to be less repetitive, add set_path. --- lib/spack/spack/build_environment.py | 45 +++++++++++----------- lib/spack/spack/environment.py | 22 ++++++++++- lib/spack/spack/test/environment.py | 22 +++++++---- var/spack/repos/builtin/packages/mpich/package.py | 10 ++--- .../repos/builtin/packages/openmpi/package.py | 8 ++-- var/spack/repos/builtin/packages/python/package.py | 4 +- var/spack/repos/builtin/packages/qt/package.py | 4 +- var/spack/repos/builtin/packages/ruby/package.py | 5 ++- 8 files changed, 73 insertions(+), 47 deletions(-) (limited to 'var') diff --git a/lib/spack/spack/build_environment.py b/lib/spack/spack/build_environment.py index 5688d47e2d..fc5b7d6207 100644 --- a/lib/spack/spack/build_environment.py +++ b/lib/spack/spack/build_environment.py @@ -36,7 +36,7 @@ import sys import spack import llnl.util.tty as tty from llnl.util.filesystem import * -from spack.environment import EnvironmentModifications, concatenate_paths, validate +from spack.environment import EnvironmentModifications, validate from spack.util.environment import * from spack.util.executable import Executable, which @@ -93,22 +93,23 @@ def set_compiler_environment_variables(pkg, env): # and return it # TODO : add additional kwargs for better diagnostics, like requestor, ttyout, ttyerr, etc. link_dir = spack.build_env_path - env.set_env('CC', join_path(link_dir, pkg.compiler.link_paths['cc'])) - env.set_env('CXX', join_path(link_dir, pkg.compiler.link_paths['cxx'])) - env.set_env('F77', join_path(link_dir, pkg.compiler.link_paths['f77'])) - env.set_env('FC', join_path(link_dir, pkg.compiler.link_paths['fc'])) + env.set('CC', join_path(link_dir, pkg.compiler.link_paths['cc'])) + env.set('CXX', join_path(link_dir, pkg.compiler.link_paths['cxx'])) + env.set('F77', join_path(link_dir, pkg.compiler.link_paths['f77'])) + env.set('FC', join_path(link_dir, pkg.compiler.link_paths['fc'])) + # Set SPACK compiler variables so that our wrapper knows what to call compiler = pkg.compiler if compiler.cc: - env.set_env('SPACK_CC', compiler.cc) + env.set('SPACK_CC', compiler.cc) if compiler.cxx: - env.set_env('SPACK_CXX', compiler.cxx) + env.set('SPACK_CXX', compiler.cxx) if compiler.f77: - env.set_env('SPACK_F77', compiler.f77) + env.set('SPACK_F77', compiler.f77) if compiler.fc: - env.set_env('SPACK_FC', compiler.fc) + env.set('SPACK_FC', compiler.fc) - env.set_env('SPACK_COMPILER_SPEC', str(pkg.spec.compiler)) + env.set('SPACK_COMPILER_SPEC', str(pkg.spec.compiler)) return env @@ -135,25 +136,25 @@ def set_build_environment_variables(pkg, env): for item in reversed(env_paths): env.prepend_path('PATH', item) - env.set_env(SPACK_ENV_PATH, concatenate_paths(env_paths)) + env.set_path(SPACK_ENV_PATH, env_paths) # Prefixes of all of the package's dependencies go in SPACK_DEPENDENCIES dep_prefixes = [d.prefix for d in pkg.spec.traverse(root=False)] - env.set_env(SPACK_DEPENDENCIES, concatenate_paths(dep_prefixes)) - env.set_env('CMAKE_PREFIX_PATH', concatenate_paths(dep_prefixes)) # Add dependencies to CMAKE_PREFIX_PATH + env.set_path(SPACK_DEPENDENCIES, dep_prefixes) + env.set_path('CMAKE_PREFIX_PATH', dep_prefixes) # Add dependencies to CMAKE_PREFIX_PATH # Install prefix - env.set_env(SPACK_PREFIX, pkg.prefix) + env.set(SPACK_PREFIX, pkg.prefix) # Install root prefix - env.set_env(SPACK_INSTALL, spack.install_path) + env.set(SPACK_INSTALL, spack.install_path) # Remove these vars from the environment during build because they # can affect how some packages find libraries. We want to make # sure that builds never pull in unintended external dependencies. - env.unset_env('LD_LIBRARY_PATH') - env.unset_env('LD_RUN_PATH') - env.unset_env('DYLD_LIBRARY_PATH') + env.unset('LD_LIBRARY_PATH') + env.unset('LD_RUN_PATH') + env.unset('DYLD_LIBRARY_PATH') # Add bin directories from dependencies to the PATH for the build. bin_dirs = reversed(filter(os.path.isdir, ['%s/bin' % prefix for prefix in dep_prefixes])) @@ -162,9 +163,9 @@ def set_build_environment_variables(pkg, env): # Working directory for the spack command itself, for debug logs. if spack.debug: - env.set_env(SPACK_DEBUG, 'TRUE') - env.set_env(SPACK_SHORT_SPEC, pkg.spec.short_spec) - env.set_env(SPACK_DEBUG_LOG_DIR, spack.spack_working_dir) + env.set(SPACK_DEBUG, 'TRUE') + env.set(SPACK_SHORT_SPEC, pkg.spec.short_spec) + env.set(SPACK_DEBUG_LOG_DIR, spack.spack_working_dir) # Add any pkgconfig directories to PKG_CONFIG_PATH pkg_config_dirs = [] @@ -173,7 +174,7 @@ def set_build_environment_variables(pkg, env): pcdir = join_path(p, libdir, 'pkgconfig') if os.path.isdir(pcdir): pkg_config_dirs.append(pcdir) - env.set_env('PKG_CONFIG_PATH', concatenate_paths(pkg_config_dirs)) + env.set_path('PKG_CONFIG_PATH', pkg_config_dirs) return env diff --git a/lib/spack/spack/environment.py b/lib/spack/spack/environment.py index 74aef57fe8..72aafa4e2d 100644 --- a/lib/spack/spack/environment.py +++ b/lib/spack/spack/environment.py @@ -29,6 +29,12 @@ class UnsetEnv(NameModifier): os.environ.pop(self.name, None) # Avoid throwing if the variable was not set +class SetPath(NameValueModifier): + def execute(self): + string_path = concatenate_paths(self.value) + os.environ[self.name] = string_path + + class AppendPath(NameValueModifier): def execute(self): environment_value = os.environ.get(self.name, '') @@ -103,7 +109,7 @@ class EnvironmentModifications(object): } return args - def set_env(self, name, value, **kwargs): + def set(self, name, value, **kwargs): """ Stores in the current object a request to set an environment variable @@ -115,7 +121,7 @@ class EnvironmentModifications(object): item = SetEnv(name, value, **kwargs) self.env_modifications.append(item) - def unset_env(self, name, **kwargs): + def unset(self, name, **kwargs): """ Stores in the current object a request to unset an environment variable @@ -126,6 +132,18 @@ class EnvironmentModifications(object): item = UnsetEnv(name, **kwargs) self.env_modifications.append(item) + def set_path(self, name, elts, **kwargs): + """ + Stores a request to set a path generated from a list. + + Args: + name: name o the environment variable to be set. + elts: elements of the path to set. + """ + kwargs.update(self._get_outside_caller_attributes()) + item = SetPath(name, elts, **kwargs) + self.env_modifications.append(item) + def append_path(self, name, path, **kwargs): """ Stores in the current object a request to append a path to a path list diff --git a/lib/spack/spack/test/environment.py b/lib/spack/spack/test/environment.py index 3e03760c01..6c8f5ea43c 100644 --- a/lib/spack/spack/test/environment.py +++ b/lib/spack/spack/test/environment.py @@ -11,21 +11,27 @@ class EnvironmentTest(unittest.TestCase): os.environ['PATH_LIST'] = '/path/second:/path/third' os.environ['REMOVE_PATH_LIST'] = '/a/b:/duplicate:/a/c:/remove/this:/a/d:/duplicate/:/f/g' - def test_set_env(self): + def test_set(self): env = EnvironmentModifications() - env.set_env('A', 'dummy value') - env.set_env('B', 3) + env.set('A', 'dummy value') + env.set('B', 3) env.apply_modifications() self.assertEqual('dummy value', os.environ['A']) self.assertEqual(str(3), os.environ['B']) - def test_unset_env(self): + def test_unset(self): env = EnvironmentModifications() self.assertEqual('foo', os.environ['UNSET_ME']) - env.unset_env('UNSET_ME') + env.unset('UNSET_ME') env.apply_modifications() self.assertRaises(KeyError, os.environ.__getitem__, 'UNSET_ME') + def test_set_path(self): + env = EnvironmentModifications() + env.set_path('A', ['foo', 'bar', 'baz']) + env.apply_modifications() + self.assertEqual('foo:bar:baz', os.environ['A']) + def test_path_manipulation(self): env = EnvironmentModifications() @@ -51,7 +57,7 @@ class EnvironmentTest(unittest.TestCase): def test_extra_arguments(self): env = EnvironmentModifications() - env.set_env('A', 'dummy value', who='Pkg1') + env.set('A', 'dummy value', who='Pkg1') for x in env: assert 'who' in x.args env.apply_modifications() @@ -59,8 +65,8 @@ class EnvironmentTest(unittest.TestCase): def test_extend(self): env = EnvironmentModifications() - env.set_env('A', 'dummy value') - env.set_env('B', 3) + env.set('A', 'dummy value') + env.set('B', 3) copy_construct = EnvironmentModifications(env) self.assertEqual(len(copy_construct), 2) for x, y in zip(env, copy_construct): diff --git a/var/spack/repos/builtin/packages/mpich/package.py b/var/spack/repos/builtin/packages/mpich/package.py index 90b5d42eab..c4d9940bb7 100644 --- a/var/spack/repos/builtin/packages/mpich/package.py +++ b/var/spack/repos/builtin/packages/mpich/package.py @@ -48,11 +48,11 @@ class Mpich(Package): provides('mpi@:1.3', when='@1:') def setup_dependent_environment(self, env, dependent_spec): - env.set_env('MPICH_CC', spack_cc) - env.set_env('MPICH_CXX', spack_cxx) - env.set_env('MPICH_F77', spack_f77) - env.set_env('MPICH_F90', spack_f90) - env.set_env('MPICH_FC', spack_fc) + 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_python_module(self, module, spec, dep_spec): """For dependencies, make mpicc's use spack wrapper.""" diff --git a/var/spack/repos/builtin/packages/openmpi/package.py b/var/spack/repos/builtin/packages/openmpi/package.py index c91a13e376..9a127f1812 100644 --- a/var/spack/repos/builtin/packages/openmpi/package.py +++ b/var/spack/repos/builtin/packages/openmpi/package.py @@ -43,10 +43,10 @@ class Openmpi(Package): def setup_dependent_environment(self, spack_env, run_env, dependent_spec): - spack_env.set_env('OMPI_CC', spack_cc) - spack_env.set_env('OMPI_CXX', spack_cxx) - spack_env.set_env('OMPI_FC', spack_fc) - spack_env.set_env('OMPI_F77', spack_f77) + 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): diff --git a/var/spack/repos/builtin/packages/python/package.py b/var/spack/repos/builtin/packages/python/package.py index 593a27708c..4f55bc803e 100644 --- a/var/spack/repos/builtin/packages/python/package.py +++ b/var/spack/repos/builtin/packages/python/package.py @@ -104,8 +104,8 @@ class Python(Package): python_paths.append(os.path.join(d.prefix, self.site_packages_dir)) pythonpath = ':'.join(python_paths) - spack_env.set_env('PYTHONPATH', pythonpath) - run_env.set_env('PYTHONPATH', pythonpath) + spack_env.set('PYTHONPATH', pythonpath) + run_env.set('PYTHONPATH', pythonpath) def modify_module(self, module, spec, ext_spec): diff --git a/var/spack/repos/builtin/packages/qt/package.py b/var/spack/repos/builtin/packages/qt/package.py index 039aeb3c31..d08e8e81e1 100644 --- a/var/spack/repos/builtin/packages/qt/package.py +++ b/var/spack/repos/builtin/packages/qt/package.py @@ -57,11 +57,11 @@ class Qt(Package): def setup_environment(self, spack_env, env): - env.set_env('QTDIR', self.prefix) + env.set('QTDIR', self.prefix) def setup_dependent_environment(self, spack_env, run_env, dspec): - spack_env.set_env('QTDIR', self.prefix) + 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 39f65f51d2..7ff1898ce9 100644 --- a/var/spack/repos/builtin/packages/ruby/package.py +++ b/var/spack/repos/builtin/packages/ruby/package.py @@ -25,9 +25,10 @@ class Ruby(Package): if d.package.extends(self.spec): ruby_paths.append(d.prefix) - spack_env.set_env('GEM_PATH', concatenate_paths(ruby_paths)) + spack_env.set_path('GEM_PATH', ruby_paths) + # The actual installation path for this gem - spack_env.set_env('GEM_HOME', extension_spec.prefix) + spack_env.set('GEM_HOME', extension_spec.prefix) def modify_module(self, module, spec, ext_spec): """Called before ruby modules' install() methods. Sets GEM_HOME -- cgit v1.2.3-70-g09d2 From 23bf70296e4a02f49c301b1b744055802b1e8dc1 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Tue, 22 Mar 2016 09:22:42 +0100 Subject: arpack: add a patch for 3.3 --- var/spack/repos/builtin/packages/arpack-ng/package.py | 4 ++++ .../repos/builtin/packages/arpack-ng/pdlamch10.patch | 15 +++++++++++++++ 2 files changed, 19 insertions(+) create mode 100644 var/spack/repos/builtin/packages/arpack-ng/pdlamch10.patch (limited to 'var') diff --git a/var/spack/repos/builtin/packages/arpack-ng/package.py b/var/spack/repos/builtin/packages/arpack-ng/package.py index 0b49d14202..614071cf53 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') 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 -- cgit v1.2.3-70-g09d2 From aca8b5c89de7058ab58f2eb3392e8b023b16fe8a Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Tue, 22 Mar 2016 09:27:00 +0100 Subject: move suite sparse to a proper folder --- .../repos/builtin/packages/SuiteSparse/package.py | 27 ---------------------- .../repos/builtin/packages/suite-sparse/package.py | 27 ++++++++++++++++++++++ 2 files changed, 27 insertions(+), 27 deletions(-) delete mode 100644 var/spack/repos/builtin/packages/SuiteSparse/package.py create mode 100644 var/spack/repos/builtin/packages/suite-sparse/package.py (limited to 'var') diff --git a/var/spack/repos/builtin/packages/SuiteSparse/package.py b/var/spack/repos/builtin/packages/SuiteSparse/package.py deleted file mode 100644 index 6e130d118f..0000000000 --- a/var/spack/repos/builtin/packages/SuiteSparse/package.py +++ /dev/null @@ -1,27 +0,0 @@ -from spack import * - - -class Suitesparse(Package): - """ - SuiteSparse is a suite of sparse matrix algorithms - """ - homepage = 'http://faculty.cse.tamu.edu/davis/suitesparse.html' - url = 'http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-4.5.1.tar.gz' - - version('4.5.1', 'f0ea9aad8d2d1ffec66a5b6bfeff5319') - - depends_on('blas') - depends_on('lapack') - - depends_on('metis@5.1.0', when='@4.5.1') - - def install(self, spec, prefix): - # The build system of SuiteSparse is quite old-fashioned - # It's basically a plain Makefile which include an header (SuiteSparse_config/SuiteSparse_config.mk) - # with a lot of convoluted logic in it. - # Any kind of customization will need to go through filtering of that file - - # 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/suite-sparse/package.py b/var/spack/repos/builtin/packages/suite-sparse/package.py new file mode 100644 index 0000000000..6e130d118f --- /dev/null +++ b/var/spack/repos/builtin/packages/suite-sparse/package.py @@ -0,0 +1,27 @@ +from spack import * + + +class Suitesparse(Package): + """ + SuiteSparse is a suite of sparse matrix algorithms + """ + homepage = 'http://faculty.cse.tamu.edu/davis/suitesparse.html' + url = 'http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-4.5.1.tar.gz' + + version('4.5.1', 'f0ea9aad8d2d1ffec66a5b6bfeff5319') + + depends_on('blas') + depends_on('lapack') + + depends_on('metis@5.1.0', when='@4.5.1') + + def install(self, spec, prefix): + # The build system of SuiteSparse is quite old-fashioned + # It's basically a plain Makefile which include an header (SuiteSparse_config/SuiteSparse_config.mk) + # with a lot of convoluted logic in it. + # Any kind of customization will need to go through filtering of that file + + # 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') + -- cgit v1.2.3-70-g09d2 From 3c5a1605d5e3cba881b743bf561f0966b1a3ad8b Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Tue, 22 Mar 2016 09:27:39 +0100 Subject: adjust the class name for suite sparse --- var/spack/repos/builtin/packages/suite-sparse/package.py | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/suite-sparse/package.py b/var/spack/repos/builtin/packages/suite-sparse/package.py index 6e130d118f..b57f9967c3 100644 --- a/var/spack/repos/builtin/packages/suite-sparse/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') - -- cgit v1.2.3-70-g09d2 From cb97e8dd9301e5bbc6752caed2f4861a2a06f494 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Tue, 22 Mar 2016 09:43:10 +0100 Subject: adjust eigen and octave to use new names of suite sparse --- var/spack/repos/builtin/packages/eigen/package.py | 2 +- var/spack/repos/builtin/packages/octave/package.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) (limited to 'var') 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/octave/package.py b/var/spack/repos/builtin/packages/octave/package.py index 38b355159d..6e99c23652 100644 --- a/var/spack/repos/builtin/packages/octave/package.py +++ b/var/spack/repos/builtin/packages/octave/package.py @@ -62,7 +62,7 @@ class Octave(Package): depends_on('qrupdate', when='+qrupdate') #depends_on('qscintilla', when='+qscintilla) # TODO: add package depends_on('qt', when='+qt') - depends_on('SuiteSparse', when='+suitesparse') + depends_on('suite-sparse',when='+suitesparse') depends_on('zlib', when='+zlib') -- cgit v1.2.3-70-g09d2 From a26992ef55fed958c15b45b989fc0a4d57f02251 Mon Sep 17 00:00:00 2001 From: Todd Gamblin Date: Tue, 22 Mar 2016 01:56:16 -0700 Subject: Change from PR #552: rename setup_dependent_python_module -> setup_dependent_package - Fixed in package.py - Fixed wrong prototypes in packages that use it. - Fixed build_environment to set module variables properly - added hacky fix to ensure spec/package consistency in build processes. - Need to think about defensive spec copy done by `Repo.get`. May be time to think about an immutable spec implementation. --- lib/spack/spack/build_environment.py | 52 ++++++++++++++++------ lib/spack/spack/package.py | 2 +- var/spack/repos/builtin/packages/mpich/package.py | 2 +- .../builtin/packages/netlib-scalapack/package.py | 22 ++++----- 4 files changed, 52 insertions(+), 26 deletions(-) (limited to 'var') diff --git a/lib/spack/spack/build_environment.py b/lib/spack/spack/build_environment.py index fc5b7d6207..119a255a34 100644 --- a/lib/spack/spack/build_environment.py +++ b/lib/spack/spack/build_environment.py @@ -225,7 +225,7 @@ def set_module_variables_for_package(pkg, module): m.spack_cc = join_path(link_dir, pkg.compiler.link_paths['cc']) m.spack_cxx = join_path(link_dir, pkg.compiler.link_paths['cxx']) m.spack_f77 = join_path(link_dir, pkg.compiler.link_paths['f77']) - m.spack_f90 = join_path(link_dir, pkg.compiler.link_paths['fc']) + m.spack_fc = join_path(link_dir, pkg.compiler.link_paths['fc']) # Emulate some shell commands for convenience m.pwd = os.getcwd @@ -270,32 +270,56 @@ def parent_class_modules(cls): return result +def setup_module_variables_for_dag(pkg): + """Set module-scope variables for all packages in the DAG.""" + for spec in pkg.spec.traverse(order='post'): + # If a user makes their own package repo, e.g. + # spack.repos.mystuff.libelf.Libelf, and they inherit from + # an existing class like spack.repos.original.libelf.Libelf, + # then set the module variables for both classes so the + # parent class can still use them if it gets called. + spkg = spec.package + modules = parent_class_modules(spkg.__class__) + for mod in modules: + set_module_variables_for_package(spkg, mod) + set_module_variables_for_package(spkg, spkg.module) + + def setup_package(pkg): """Execute all environment setup routines.""" spack_env = EnvironmentModifications() run_env = EnvironmentModifications() + # Before proceeding, ensure that specs and packages are consistent + # + # This is a confusing behavior due to how packages are + # constructed. `setup_dependent_package` may set attributes on + # specs in the DAG for use by other packages' install + # method. However, spec.package will look up a package via + # spack.repo, which defensively copies specs into packages. This + # code ensures that all packages in the DAG have pieces of the + # same spec object at build time. + # + # This is safe for the build process, b/c the build process is a + # throwaway environment, but it is kind of dirty. + # + # TODO: Think about how to avoid this fix and do something cleaner. + for s in pkg.spec.traverse(): s.package.spec = s + set_compiler_environment_variables(pkg, spack_env) set_build_environment_variables(pkg, spack_env) - - # If a user makes their own package repo, e.g. - # spack.repos.mystuff.libelf.Libelf, and they inherit from - # an existing class like spack.repos.original.libelf.Libelf, - # then set the module variables for both classes so the - # parent class can still use them if it gets called. - modules = parent_class_modules(pkg.__class__) - for mod in modules: - set_module_variables_for_package(pkg, mod) + setup_module_variables_for_dag(pkg) # Allow dependencies to modify the module - for dependency_spec in pkg.spec.traverse(root=False): + spec = pkg.spec + for dependency_spec in spec.traverse(root=False): dpkg = dependency_spec.package - dpkg.setup_dependent_python_module(pkg.module, pkg.spec) + dpkg.setup_dependent_package(pkg.module, spec) # Allow dependencies to set up environment as well - for dependency_spec in pkg.spec.traverse(root=False): + for dependency_spec in spec.traverse(root=False): dpkg = dependency_spec.package - dpkg.setup_dependent_environment(spack_env, run_env, pkg.spec) + dpkg.setup_dependent_environment(spack_env, run_env, spec) # Allow the package to apply some settings. pkg.setup_environment(spack_env, run_env) diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py index 9d8ac87bd7..9af3221837 100644 --- a/lib/spack/spack/package.py +++ b/lib/spack/spack/package.py @@ -1075,7 +1075,7 @@ class Package(object): self.setup_environment(spack_env, run_env) - def setup_dependent_python_module(self, module, dependent_spec): + def setup_dependent_package(self, module, dependent_spec): """Set up Python module-scope variables for dependent packages. Called before the install() method of dependents. diff --git a/var/spack/repos/builtin/packages/mpich/package.py b/var/spack/repos/builtin/packages/mpich/package.py index c4d9940bb7..b20dc8dd60 100644 --- a/var/spack/repos/builtin/packages/mpich/package.py +++ b/var/spack/repos/builtin/packages/mpich/package.py @@ -54,7 +54,7 @@ class Mpich(Package): env.set('MPICH_F90', spack_f90) env.set('MPICH_FC', spack_fc) - def setup_dependent_python_module(self, module, spec, dep_spec): + 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') diff --git a/var/spack/repos/builtin/packages/netlib-scalapack/package.py b/var/spack/repos/builtin/packages/netlib-scalapack/package.py index 62abfcc48e..c3e6822cdf 100644 --- a/var/spack/repos/builtin/packages/netlib-scalapack/package.py +++ b/var/spack/repos/builtin/packages/netlib-scalapack/package.py @@ -1,4 +1,5 @@ from spack import * +import sys class NetlibScalapack(Package): """ScaLAPACK is a library of high-performance linear algebra routines for parallel distributed memory machines""" @@ -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'), @@ -40,10 +41,11 @@ class NetlibScalapack(Package): make() make("install") - def setup_dependent_python_module(self, module, spec, dependent_spec): + 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['scalapack'] else '.a' + 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)] -- cgit v1.2.3-70-g09d2 From 6eb97a30a36f0a0f072826d473a641dd143345ed Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Tue, 22 Mar 2016 14:24:27 +0100 Subject: arpack: fix for +mpi variant --- var/spack/repos/builtin/packages/arpack-ng/package.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/arpack-ng/package.py b/var/spack/repos/builtin/packages/arpack-ng/package.py index 614071cf53..dd86b17a53 100644 --- a/var/spack/repos/builtin/packages/arpack-ng/package.py +++ b/var/spack/repos/builtin/packages/arpack-ng/package.py @@ -50,7 +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') -- cgit v1.2.3-70-g09d2 From d25026b74936f9988cdaf701258c937b3965c106 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Tue, 22 Mar 2016 16:26:16 +0100 Subject: add OCE package --- var/spack/repos/builtin/packages/oce/package.py | 47 +++++++++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 var/spack/repos/builtin/packages/oce/package.py (limited to 'var') 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") -- cgit v1.2.3-70-g09d2 From 7618dc504cb58e115a0a95b130bcfc485cd8341d Mon Sep 17 00:00:00 2001 From: Erik Schnetter Date: Tue, 22 Mar 2016 19:17:39 +0100 Subject: temporary fix Hypre for OSX by building static lib by default --- var/spack/repos/builtin/packages/hypre/package.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) (limited to 'var') 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") -- cgit v1.2.3-70-g09d2 From e56f5c4d6b4626a428b3c209f00eff59cd37b22f Mon Sep 17 00:00:00 2001 From: Cyrus Harrison Date: Tue, 22 Mar 2016 16:59:40 +0100 Subject: add Intel TBB package --- var/spack/repos/builtin/packages/tbb/package.py | 79 +++++++++++++++++++++++++ 1 file changed, 79 insertions(+) create mode 100644 var/spack/repos/builtin/packages/tbb/package.py (limited to 'var') 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) -- cgit v1.2.3-70-g09d2 From 5f68e14d3bd90e4a71f6366a328dcc97fc6e8a92 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Tue, 22 Mar 2016 19:41:31 +0100 Subject: add gettext package --- .../repos/builtin/packages/gettext/package.py | 30 ++++++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 var/spack/repos/builtin/packages/gettext/package.py (limited to 'var') 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") -- cgit v1.2.3-70-g09d2 From fd1784369a20650c3fc6f84d57ed4e6be59afc44 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Tue, 22 Mar 2016 19:50:15 +0100 Subject: add muparser package --- var/spack/repos/builtin/packages/muparser/package.py | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 var/spack/repos/builtin/packages/muparser/package.py (limited to 'var') 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") -- cgit v1.2.3-70-g09d2 From d05e4581c9d249c0736d8d58b394860ca05f8402 Mon Sep 17 00:00:00 2001 From: Joseph Ciurej Date: Tue, 22 Mar 2016 12:31:26 -0700 Subject: Added the '+silex' variant to the Silo package. Added a number of different versions to the Silo package. --- var/spack/repos/builtin/packages/silo/package.py | 23 +++++++++++++++++------ 1 file changed, 17 insertions(+), 6 deletions(-) (limited to 'var') 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) -- cgit v1.2.3-70-g09d2 From 1728a0c3e60d55d1181f14ef5a677b1652a0680b Mon Sep 17 00:00:00 2001 From: Joseph Ciurej Date: Tue, 22 Mar 2016 12:33:11 -0700 Subject: Updated the 'crypto++' package to use an improved URL formation scheme (inspired by changes made to the 'Silo' package). --- var/spack/repos/builtin/packages/cryptopp/package.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/cryptopp/package.py b/var/spack/repos/builtin/packages/cryptopp/package.py index 1693c4b160..743a3ac70f 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') @@ -28,4 +28,4 @@ class Cryptopp(Package): 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) + return '%s/cryptopp%s.zip' % (Cryptopp.base_url, version_string) -- cgit v1.2.3-70-g09d2 From 27f337aa11104a6e625db6e40f8d9414954123ee Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Tue, 22 Mar 2016 11:44:38 +0100 Subject: petsc: set PETSC_DIR in dependent_env --- var/spack/repos/builtin/packages/petsc/package.py | 4 ++++ 1 file changed, 4 insertions(+) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/petsc/package.py b/var/spack/repos/builtin/packages/petsc/package.py index 7239baaf7f..3dd117eed1 100644 --- a/var/spack/repos/builtin/packages/petsc/package.py +++ b/var/spack/repos/builtin/packages/petsc/package.py @@ -100,3 +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) -- cgit v1.2.3-70-g09d2 From 24264eb00e4f4e3661ea1a28e9cbe3a97cd69580 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Tue, 22 Mar 2016 11:45:18 +0100 Subject: add slepc package --- var/spack/repos/builtin/packages/slepc/package.py | 49 +++++++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 var/spack/repos/builtin/packages/slepc/package.py (limited to 'var') 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) -- cgit v1.2.3-70-g09d2 From 6c8d51f403213cf3a49373d4dca03fac565a73b4 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Tue, 22 Mar 2016 22:58:14 +0100 Subject: add p4est package --- var/spack/repos/builtin/packages/p4est/package.py | 34 +++++++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 var/spack/repos/builtin/packages/p4est/package.py (limited to 'var') 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") -- cgit v1.2.3-70-g09d2 From 474db2085e223b8226a6ae799232bb2fede3efde Mon Sep 17 00:00:00 2001 From: Joseph Ciurej Date: Tue, 22 Mar 2016 15:55:54 -0700 Subject: Simplified the 'url_for_version' function for the 'Crypto++' package. --- var/spack/repos/builtin/packages/cryptopp/package.py | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/cryptopp/package.py b/var/spack/repos/builtin/packages/cryptopp/package.py index 743a3ac70f..bc83cb2b65 100644 --- a/var/spack/repos/builtin/packages/cryptopp/package.py +++ b/var/spack/repos/builtin/packages/cryptopp/package.py @@ -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, "") - + version_string = str(version).replace('.', '') return '%s/cryptopp%s.zip' % (Cryptopp.base_url, version_string) -- cgit v1.2.3-70-g09d2 From 5b3c96a9bb0ba6501512c93dcdb26510e796314e Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Wed, 23 Mar 2016 08:07:45 +0100 Subject: fix superlu-dist lib installation --- var/spack/repos/builtin/packages/superlu-dist/package.py | 1 + 1 file changed, 1 insertion(+) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/superlu-dist/package.py b/var/spack/repos/builtin/packages/superlu-dist/package.py index c4c76909b3..9a94de8ba5 100644 --- a/var/spack/repos/builtin/packages/superlu-dist/package.py +++ b/var/spack/repos/builtin/packages/superlu-dist/package.py @@ -54,6 +54,7 @@ class SuperluDist(Package): # 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) -- cgit v1.2.3-70-g09d2 From c4134ee71e43a6a2a38822e25cc72ca73efdcfea Mon Sep 17 00:00:00 2001 From: Todd Gamblin Date: Wed, 23 Mar 2016 00:36:32 -0700 Subject: Fix #608: broken numpy build. - Failed to catch all instances of modify_module when it was renamed to setup_dependent_package. - Refactored remaining modify_module calls. - Also modified Python's setup_dependent_package slightly: only creates empty site-packages directory for Python extensions now, not for all dependents. --- lib/spack/spack/modules.py | 4 ++-- lib/spack/spack/preferred_packages.py | 4 +++- var/spack/repos/builtin/packages/python/package.py | 11 ++++++----- var/spack/repos/builtin/packages/ruby/package.py | 6 +++--- 4 files changed, 14 insertions(+), 11 deletions(-) (limited to 'var') diff --git a/lib/spack/spack/modules.py b/lib/spack/spack/modules.py index 05c93cd3e6..8ed98e5d38 100644 --- a/lib/spack/spack/modules.py +++ b/lib/spack/spack/modules.py @@ -160,8 +160,8 @@ class EnvModule(object): # package-specific modifications for extendee in self.pkg.extendees: extendee_spec = self.spec[extendee] - extendee_spec.package.modify_module( - self.pkg.module, extendee_spec, self.spec) + extendee_spec.package.setup_dependent_package( + self.pkg.module, self.spec) # Package-specific environment modifications spack_env = EnvironmentModifications() diff --git a/lib/spack/spack/preferred_packages.py b/lib/spack/spack/preferred_packages.py index 4d8526c75f..f0a5382dc9 100644 --- a/lib/spack/spack/preferred_packages.py +++ b/lib/spack/spack/preferred_packages.py @@ -150,7 +150,9 @@ class PreferredPackages(object): def version_compare(self, pkgname, a, b): """Return less-than-0, 0, or greater than 0 if version a of pkgname is respecively less-than, equal-to, or greater-than version b of pkgname. - One version is less-than another if it is preferred over the other.""" + Versions marked 'preferred=True' in package.py take precedence over any + versions not marked preferred. + """ return self._spec_compare(pkgname, 'version', a, b, True, None) diff --git a/var/spack/repos/builtin/packages/python/package.py b/var/spack/repos/builtin/packages/python/package.py index 4f55bc803e..6d9030805b 100644 --- a/var/spack/repos/builtin/packages/python/package.py +++ b/var/spack/repos/builtin/packages/python/package.py @@ -108,7 +108,7 @@ class Python(Package): run_env.set('PYTHONPATH', pythonpath) - def modify_module(self, module, spec, ext_spec): + def setup_dependent_package(self, module, ext_spec): """ Called before python modules' install() methods. @@ -118,17 +118,18 @@ class Python(Package): """ # 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) + # 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/ruby/package.py b/var/spack/repos/builtin/packages/ruby/package.py index 7ff1898ce9..e13677e4d2 100644 --- a/var/spack/repos/builtin/packages/ruby/package.py +++ b/var/spack/repos/builtin/packages/ruby/package.py @@ -30,7 +30,7 @@ class Ruby(Package): # The actual installation path for this gem spack_env.set('GEM_HOME', extension_spec.prefix) - def modify_module(self, module, spec, ext_spec): + 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. @@ -39,5 +39,5 @@ class Ruby(Package): gem('install', '.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')) + module.ruby = Executable(join_path(self.spec.prefix.bin, 'ruby')) + module.gem = Executable(join_path(self.spec.prefix.bin, 'gem')) -- cgit v1.2.3-70-g09d2 From 01918a6f4891ab985b8619daaadc1bf484e4db17 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Wed, 23 Mar 2016 05:26:51 +0100 Subject: fix MUMPS build on OSX (set parallel=False) --- var/spack/repos/builtin/packages/mumps/package.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/mumps/package.py b/var/spack/repos/builtin/packages/mumps/package.py index 5c120c37df..5a254dfd00 100644 --- a/var/spack/repos/builtin/packages/mumps/package.py +++ b/var/spack/repos/builtin/packages/mumps/package.py @@ -135,7 +135,8 @@ class Mumps(Package): 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) -- cgit v1.2.3-70-g09d2 From cc582dd4b435ba06dc140b1ca96b688871e36abb Mon Sep 17 00:00:00 2001 From: Todd Gamblin Date: Wed, 23 Mar 2016 02:02:49 -0700 Subject: Add mock python package. --- .../repos/builtin.mock/packages/python/package.py | 43 ++++++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 var/spack/repos/builtin.mock/packages/python/package.py (limited to 'var') 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 + -- cgit v1.2.3-70-g09d2 From 34a8f0c96bc50870f20f094d95b403b2bb19487d Mon Sep 17 00:00:00 2001 From: alalazo Date: Wed, 23 Mar 2016 17:01:52 +0100 Subject: espresso : fixes #454 --- var/spack/repos/builtin/packages/espresso/package.py | 4 ++++ 1 file changed, 4 insertions(+) (limited to 'var') 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) -- cgit v1.2.3-70-g09d2 From 4e5dfc8b18ed30e261fe6b6dd014c8991937934d Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Wed, 23 Mar 2016 19:40:16 +0100 Subject: fix missing (depricated) _dggsvd_ and _sggsvd_ in Openblas 0.2.16 --- var/spack/repos/builtin/packages/openblas/package.py | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/openblas/package.py b/var/spack/repos/builtin/packages/openblas/package.py index 781a1e2ec8..1d10f217c4 100644 --- a/var/spack/repos/builtin/packages/openblas/package.py +++ b/var/spack/repos/builtin/packages/openblas/package.py @@ -6,6 +6,7 @@ class Openblas(Package): 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') @@ -14,7 +15,14 @@ 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' -- cgit v1.2.3-70-g09d2 From 9b8b17b6f1ec22ce4ac2115e5f7687beba21dd19 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Thu, 24 Mar 2016 10:36:02 +0100 Subject: fix parmetis on Ubuntu with GNU compilers by linking to lm --- var/spack/repos/builtin/packages/parmetis/link-to-lm.patch | 14 ++++++++++++++ var/spack/repos/builtin/packages/parmetis/package.py | 2 ++ 2 files changed, 16 insertions(+) create mode 100644 var/spack/repos/builtin/packages/parmetis/link-to-lm.patch (limited to 'var') 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 c691cf4191..bc71fb7299 100644 --- a/var/spack/repos/builtin/packages/parmetis/package.py +++ b/var/spack/repos/builtin/packages/parmetis/package.py @@ -52,6 +52,8 @@ class Parmetis(Package): # https://bitbucket.org/petsc/pkg-parmetis/commits/82409d68aa1d6cbc70740d0f35024aae17f7d5cb/raw/ patch('pkg-parmetis-82409d68aa1d6cbc70740d0f35024aae17f7d5cb.patch') + patch('link-to-lm.patch') + depends_on('gdb', when='+gdb') def install(self, spec, prefix): -- cgit v1.2.3-70-g09d2 From 758a9c9096bd6c306f2dba0e40b46544dcec1992 Mon Sep 17 00:00:00 2001 From: alalazo Date: Wed, 23 Mar 2016 11:18:11 +0100 Subject: python extensions : create PYTHONPATH in module files --- lib/spack/spack/modules.py | 10 +++++----- var/spack/repos/builtin/packages/python/package.py | 5 ++++- 2 files changed, 9 insertions(+), 6 deletions(-) (limited to 'var') diff --git a/lib/spack/spack/modules.py b/lib/spack/spack/modules.py index 6c32937c3c..d45fdde703 100644 --- a/lib/spack/spack/modules.py +++ b/lib/spack/spack/modules.py @@ -161,13 +161,13 @@ class EnvModule(object): # Let the extendee modify their extensions before asking for # package-specific modifications - for extendee in self.pkg.extendees: - extendee_spec = self.spec[extendee] - extendee_spec.package.setup_dependent_package( - self.pkg.module, self.spec) + spack_env = EnvironmentModifications() + for item in self.pkg.extendees: + package = self.spec[item].package + package.setup_dependent_package(self.pkg.module, self.spec) + package.setup_dependent_environment(spack_env, env, self.spec) # Package-specific environment modifications - spack_env = EnvironmentModifications() self.spec.package.setup_environment(spack_env, env) # TODO : implement site-specific modifications and filters diff --git a/var/spack/repos/builtin/packages/python/package.py b/var/spack/repos/builtin/packages/python/package.py index 6d9030805b..f5237c3b57 100644 --- a/var/spack/repos/builtin/packages/python/package.py +++ b/var/spack/repos/builtin/packages/python/package.py @@ -105,7 +105,10 @@ class Python(Package): pythonpath = ':'.join(python_paths) spack_env.set('PYTHONPATH', pythonpath) - run_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): -- cgit v1.2.3-70-g09d2 From 8643e2191357dd6f53bfafdfd51f43b770e2137c Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Thu, 24 Mar 2016 12:34:58 -0500 Subject: Simplified NumPy dependencies --- .../repos/builtin/packages/py-numpy/package.py | 37 ++++++++++++++++------ .../repos/builtin/packages/py-scipy/package.py | 5 +-- 2 files changed, 31 insertions(+), 11 deletions(-) (limited to 'var') 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') -- cgit v1.2.3-70-g09d2 From 254f65f2994de32da8681c24838beb32bbbc5fe1 Mon Sep 17 00:00:00 2001 From: Alfredo Gimenez Date: Thu, 24 Mar 2016 10:48:38 -0700 Subject: Remove incorrect sanity check for libelf --- var/spack/repos/builtin/packages/libelf/package.py | 2 -- 1 file changed, 2 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/libelf/package.py b/var/spack/repos/builtin/packages/libelf/package.py index 9f16708af5..29bc21b65c 100644 --- a/var/spack/repos/builtin/packages/libelf/package.py +++ b/var/spack/repos/builtin/packages/libelf/package.py @@ -38,8 +38,6 @@ class Libelf(Package): provides('elf') - sanity_check_is_file = 'include/libelf.h' - def install(self, spec, prefix): configure("--prefix=" + prefix, "--enable-shared", -- cgit v1.2.3-70-g09d2