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# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
import fnmatch
import os
from spack import *
class Cosmomc(Package):
"""CosmoMC is a Fortran 2008 Markov-Chain Monte-Carlo (MCMC) engine
for exploring cosmological parameter space, together with
Fortran and python code for analysing Monte-Carlo samples and
importance sampling (plus a suite of scripts for building grids
of runs, plotting and presenting results)."""
homepage = "http://cosmologist.info/cosmomc/"
url = "https://github.com/cmbant/CosmoMC/archive/Nov2016.tar.gz"
version('2016.11', sha256='b83edbf043ff83a4dde9bc14c56a09737dbc41ffe247a8e9c9a26892ed8745ba')
version('2016.06', sha256='23fa23eef40846c17d3740be63a7fefde13880cbb81545a44d14034277d9ffc0')
def url_for_version(self, version):
names = {'2016.11': "Nov2016",
'2016.06': "June2016"}
return ("https://github.com/cmbant/CosmoMC/archive/%s.tar.gz" %
names[str(version)])
variant('mpi', default=True, description='Enable MPI support')
variant('planck', default=False,
description='Enable Planck Likelihood code and baseline data')
variant('python', default=True, description='Enable Python bindings')
extends('python', when='+python')
depends_on('mpi', when='+mpi')
depends_on('planck-likelihood', when='+planck')
depends_on('py-matplotlib', type=('build', 'run'), when='+python')
depends_on('py-numpy', type=('build', 'run'), when='+python')
depends_on('py-pandas', type=('build', 'run'), when='+python')
depends_on('py-scipy', type=('build', 'run'), when='+python')
depends_on('py-six', type=('build', 'run'), when='+python')
depends_on('python @2.7:2.999,3.4:', type=('build', 'run'), when='+python')
patch('Makefile.patch')
patch('errorstop.patch')
parallel = False
def install(self, spec, prefix):
# Clean up environment to avoid configure problems
os.environ.pop('LINKMPI', '')
os.environ.pop('NERSC_HOST', '')
os.environ.pop('NONCLIKLIKE', '')
os.environ.pop('PICO', '')
os.environ.pop('PRECISION', '')
os.environ.pop('RECOMBINATION', '')
os.environ.pop('WMAP', '')
# Set up Planck data if requested
clikdir = join_path('data', 'clik')
try:
os.remove(clikdir)
except OSError:
pass
if '+planck' in spec:
os.symlink(join_path(os.environ['CLIK_DATA'], 'plc_2.0'), clikdir)
else:
os.environ.pop('CLIK_DATA', '')
os.environ.pop('CLIK_PATH', '')
os.environ.pop('CLIK_PLUGIN', '')
# Choose compiler
# Note: Instead of checking the compiler vendor, we should
# rewrite the Makefile to use Spack's options all the time
if spec.satisfies('%gcc'):
if not spec.satisfies('%gcc@6:'):
raise InstallError(
"When using GCC, "
"CosmoMC requires version gcc@6: for building")
choosecomp = 'ifortErr=1' # choose gfortran
elif spec.satisfies('%intel'):
if not spec.satifies('%intel@14:'):
raise InstallError(
"When using the Intel compiler, "
"CosmoMC requires version intel@14: for building")
choosecomp = 'ifortErr=0' # choose ifort
else:
raise InstallError("Only GCC and Intel compilers are supported")
# Configure MPI
if '+mpi' in spec:
wantmpi = 'BUILD=MPI'
mpif90 = 'MPIF90C=%s' % spec['mpi'].mpifc
else:
wantmpi = 'BUILD=NOMPI'
mpif90 = 'MPIF90C='
# Choose BLAS and LAPACK
lapack = ("LAPACKL=%s" %
(spec['lapack'].libs + spec['blas'].libs).ld_flags)
# Build
make(choosecomp, wantmpi, mpif90, lapack)
# Install
mkdirp(prefix.bin)
install('cosmomc', prefix.bin)
root = join_path(prefix.share, 'cosmomc')
mkdirp(root)
entries = [
'batch1',
'batch2',
'batch3',
'camb',
'chains',
'clik_latex.paramnames',
'clik_units.paramnames',
'cosmomc.cbp',
'data',
'distgeneric.ini',
'distparams.ini',
'disttest.ini',
'docs',
'job_script',
'job_script_MOAB',
'job_script_SLURM',
'paramnames',
'params_generic.ini',
'planck_covmats',
'scripts',
# don't copy 'source'
'test.ini',
'test_pico.ini',
'test_planck.ini',
'tests',
]
if '+python' in spec:
entries += ['python']
for entry in entries:
if os.path.isfile(entry):
install(entry, root)
else:
install_tree(entry, join_path(root, entry))
for dirpath, dirnames, filenames in os.walk(prefix):
for filename in fnmatch.filter(filenames, '*~'):
os.remove(os.path.join(dirpath, filename))
@run_after('install')
@on_package_attributes(run_tests=True)
def check_install(self):
prefix = self.prefix
spec = self.spec
os.environ.pop('LINKMPI', '')
os.environ.pop('NERSC_HOST', '')
os.environ.pop('NONCLIKLIKE', '')
os.environ.pop('PICO', '')
os.environ.pop('PRECISION', '')
os.environ.pop('RECOMBINATION', '')
os.environ.pop('WMAP', '')
os.environ.pop('COSMOMC_LOCATION', '')
os.environ.pop('PLC_LOCATION', '')
os.environ.pop('CLIKPATH', '')
os.environ.pop('PLANCKLIKE', '')
exe = spec['cosmomc'].command.path
args = []
if '+mpi' in spec:
# Add mpirun prefix
args = ['-np', '1', exe]
exe = join_path(spec['mpi'].prefix.bin, 'mpiexec')
cosmomc = Executable(exe)
with working_dir('spack-check', create=True):
for entry in [
'camb',
'chains',
'data',
'paramnames',
'planck_covmats',
]:
os.symlink(join_path(prefix.share, 'cosmomc', entry), entry)
inifile = join_path(prefix.share, 'cosmomc', 'test.ini')
cosmomc(*(args + [inifile]))
if '+planck' in spec:
inifile = join_path(prefix.share, 'cosmomc', 'test_planck.ini')
cosmomc(*(args + [inifile]))
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