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# Copyright 2013-2023 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.package 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 = "https://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 @2.7:2,3.4:", 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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