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author | Audrey Thoma <las_thoma15@iastate.edu> | 2017-07-18 13:43:42 -0500 |
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committer | Adam J. Stewart <ajstewart426@gmail.com> | 2017-07-18 13:43:42 -0500 |
commit | 0e28afef1e5632419b4516f62c42015b5cac5d6c (patch) | |
tree | d04397a89d828a3be34b54a1eb0ab8a2eb7087e1 | |
parent | 68a8f63569a295a26c9ebc3ddda9a4f1f183e78f (diff) | |
download | spack-0e28afef1e5632419b4516f62c42015b5cac5d6c.tar.gz spack-0e28afef1e5632419b4516f62c42015b5cac5d6c.tar.bz2 spack-0e28afef1e5632419b4516f62c42015b5cac5d6c.tar.xz spack-0e28afef1e5632419b4516f62c42015b5cac5d6c.zip |
raxml: new package (#4777)
* raxml: new package
* changed compiler variable
* removing if statement regarding intel compiler
-rw-r--r-- | var/spack/repos/builtin/packages/raxml/package.py | 107 |
1 files changed, 107 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/raxml/package.py b/var/spack/repos/builtin/packages/raxml/package.py new file mode 100644 index 0000000000..198347b0c1 --- /dev/null +++ b/var/spack/repos/builtin/packages/raxml/package.py @@ -0,0 +1,107 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the NOTICE and LICENSE files for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * +import glob + + +class Raxml(Package): + """RAxML (Randomized Axelerated Maximum Likelihood) is a program for + sequential and parallel Maximum Likelihood based inference of large + phylogenetic trees.""" + + homepage = "https://sco.h-its.org/exelixis/web/software/raxml" + url = "https://github.com/stamatak/standard-RAxML/archive/v8.2.11.tar.gz" + + version('8.2.11', '6bd5c4e1f93003ccf13c9b59a5d080ab') + + variant('mpi', default=True, description='Enable MPI parallel support') + variant('pthreads', default=False, description='Enable pthreads version') + variant('sse', default=True, description='Enable SSE in order to substantially speed up execution') + variant('avx', default=False, description='Enable AVX in order to substantially speed up execution') + + depends_on('mpi', when='+mpi') + + # Compiles with either GCC or ICC. + conflicts('%cce') + conflicts('%clang') + conflicts('%nag') + conflicts('%pgi') + conflicts('%xl') + conflicts('%xl_r') + + def install(self, spec, prefix): + mkdirp(prefix.bin) + files = glob.iglob("Makefile.*") + for file in files: + makefile = FileFilter(file) + makefile.filter('gcc', spack_cc) + + if '+mpi' and '+avx' and '+pthreads' in spec: + make('-f', 'Makefile.AVX.HYBRID.gcc') + install('raxmlHPC-HYBRID-AVX', prefix.bin) + + elif '+mpi' and '+sse' and '+pthreads' in spec: + make('-f', 'Makefile.SSE3.HYBRID.gcc') + install('raxmlHPC-HYBRID-SSE3', prefix.bin) + + elif '+mpi' and '+pthreads' in spec: + make('-f', 'Makefile.HYBRID.gcc') + install('raxmlHPC-HYBRID', prefix.bin) + + elif '+mpi' and '+avx' in spec: + make('-f', 'Makefile.AVX.MPI.gcc') + install('raxmlHPC-MPI-AVX', prefix.bin) + + elif '+mpi' and '+sse' in spec: + make('-f', 'Makefile.SSE3.MPI.gcc') + install('raxmlHPC-MPI-SSE3', prefix.bin) + + elif '+mpi' in spec: + make('-f', 'Makefile.MPI.gcc') + install('raxmlHPC-MPI', prefix.bin) + + elif '+pthreads' and '+avx' in spec: + make('-f', 'Makefile.AVX.PTHREADS.gcc') + install('raxmlHPC-PTHREADS-AVX', prefix.bin) + + elif '+pthreads' and '+sse' in spec: + make('-f', 'Makefile.SSE3.PTHREADS.gcc') + install('raxmlHPC-PTHREADS-SSE3', prefix.bin) + + elif '+pthreads' in spec: + make('-f', 'Makefile.PTHREADS.gcc') + install('raxmlHPC-PTHREADS', prefix.bin) + + elif '+sse' in spec: + make('-f', 'Makefile.SSE3.gcc') + install('raxmlHPC-SSE3', prefix.bin) + + elif '+avx' in spec: + make('-f', 'Makefile.AVX.gcc') + install('raxmlHPC-AVX', prefix.bin) + + else: + make('-f', 'Makefile.gcc') + install('raxmlHPC', prefix.bin) |