cosmomc: New package CosmoMC (#3292)
* cosmomc: New package CosmoMC * cosmomc: Improve version numbering scheme * planck-likelihood: New package * cosmomc: Pacify flake8 * cosmomc: Code cleanup as requested in the review * cosmomc: Various updates suggested during review * cosmomc: Limit compiler versions (as documented in the build instructions) * cosmomc: Correct flake8 error * cosmomc: Use `libs` instead of `lapack_libs` * planck-likelihood: Make makefile output more verbose and readable * planck-likelilhood: Correct order of libraries when calling linker * cosmomc: Clean up check for suitable compiler * planck-likelihood: Use modern mechanism to set environment variables
This commit is contained in:
Erik Schnetter
committed by
Adam J. Stewart
Adam J. Stewart
parent
21e913bac5
commit
2ac343e92e
26
var/spack/repos/builtin/packages/cosmomc/Makefile.patch
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26
var/spack/repos/builtin/packages/cosmomc/Makefile.patch
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@@ -0,0 +1,26 @@
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--- a/Makefile
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+++ b/Makefile
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@@ -7,8 +7,7 @@
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rebuild: clean delete cosmomc
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-cosmomc: BUILD ?= MPI
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-cosmomc_debug: BUILD ?= MPI
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+BUILD ?= MPI
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getdist: ./source/*.*90
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cd ./source && make getdist BUILD=$(BUILD)
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--- a/source/Makefile
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+++ b/source/Makefile
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@@ -57,11 +57,7 @@
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#commented above is (I think) for Mac; this is standard linux (sudo apt-get install liblapack-dev)
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LAPACKL = -lblas -llapack
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-#march native does not work on Mac, otherwise use (comment out if your cluster is inhomogeneous)
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-ifneq ($(shell uname -s),Darwin)
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-#native optimization does not work on Mac
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FFLAGS+=-march=native
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-endif
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endif
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11
var/spack/repos/builtin/packages/cosmomc/errorstop.patch
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11
var/spack/repos/builtin/packages/cosmomc/errorstop.patch
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@@ -0,0 +1,11 @@
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--- a/camb/constants.f90
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+++ b/camb/constants.f90
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@@ -87,7 +87,7 @@
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global_error_message=''
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end if
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if (present(id)) then
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- if (id==0) error stop('Error id must be non-zero')
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+ if (id==0) error stop
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global_error_flag=id
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else
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global_error_flag=-1
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201
var/spack/repos/builtin/packages/cosmomc/package.py
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var/spack/repos/builtin/packages/cosmomc/package.py
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@@ -0,0 +1,201 @@
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##############################################################################
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# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
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# Produced at the Lawrence Livermore National Laboratory.
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#
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# This file is part of Spack.
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# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
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# LLNL-CODE-647188
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#
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# For details, see https://github.com/llnl/spack
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# Please also see the LICENSE file for our notice and the LGPL.
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#
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# This program is free software; you can redistribute it and/or modify
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# it under the terms of the GNU Lesser General Public License (as
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# published by the Free Software Foundation) version 2.1, February 1999.
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#
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# This program is distributed in the hope that it will be useful, but
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# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
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# conditions of the GNU Lesser General Public License for more details.
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#
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# You should have received a copy of the GNU Lesser General Public
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# License along with this program; if not, write to the Free Software
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# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
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##############################################################################
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from spack import *
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import fnmatch
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import os
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class Cosmomc(Package):
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"""CosmoMC is a Fortran 2008 Markov-Chain Monte-Carlo (MCMC) engine
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for exploring cosmological parameter space, together with
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Fortran and python code for analysing Monte-Carlo samples and
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importance sampling (plus a suite of scripts for building grids
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of runs, plotting and presenting results)."""
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homepage = "http://cosmologist.info/cosmomc/"
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url = "https://github.com/cmbant/CosmoMC/archive/Nov2016.tar.gz"
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version('2016.11', '98620cb746352f68fb0c1196e9a070ac')
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version('2016.06', '92dc651d1407cca6ea9228992165f5cb')
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def url_for_version(self, version):
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names = {'2016.11': "Nov2016",
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'2016.06': "June2016"}
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return ("https://github.com/cmbant/CosmoMC/archive/%s.tar.gz" %
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names[str(version)])
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variant('mpi', default=True, description='Enable MPI support')
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variant('planck', default=False,
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description='Enable Planck Likelihood code and baseline data')
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patch('Makefile.patch')
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patch('errorstop.patch')
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depends_on('mpi', when='+mpi')
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depends_on('planck-likelihood', when='+planck')
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depends_on('python @2.7:2.999,3.4:')
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parallel = False
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def install(self, spec, prefix):
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# Clean up environment to avoid configure problems
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os.environ.pop('LINKMPI', '')
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os.environ.pop('NERSC_HOST', '')
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os.environ.pop('NONCLIKLIKE', '')
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os.environ.pop('PICO', '')
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os.environ.pop('PRECISION', '')
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os.environ.pop('RECOMBINATION', '')
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os.environ.pop('WMAP', '')
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# Set up Planck data if requested
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clikdir = join_path('data', 'clik')
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try:
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os.remove(clikdir)
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except OSError:
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pass
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if '+planck' in spec:
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os.symlink(join_path(os.environ['CLIK_DATA'], 'plc_2.0'), clikdir)
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else:
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os.environ.pop('CLIK_DATA', '')
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os.environ.pop('CLIK_PATH', '')
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os.environ.pop('CLIK_PLUGIN', '')
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# Choose compiler
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# Note: Instead of checking the compiler vendor, we should
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# rewrite the Makefile to use Spack's options all the time
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if spec.satisfies('%gcc'):
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if not spec.satisfies('%gcc@6:'):
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raise InstallError(
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"When using GCC, "
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"CosmoMC requires version gcc@6: for building")
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choosecomp = 'ifortErr=1' # choose gfortran
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elif spec.satisfies('%intel'):
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if not spec.satifies('%intel@14:'):
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raise InstallError(
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"When using the Intel compiler, "
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"CosmoMC requires version intel@14: for building")
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choosecomp = 'ifortErr=0' # choose ifort
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else:
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raise InstallError("Only GCC and Intel compilers are supported")
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# Configure MPI
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if '+mpi' in spec:
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wantmpi = 'BUILD=MPI'
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mpif90 = 'MPIF90C=%s' % spec['mpi'].mpifc
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else:
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wantmpi = 'BUILD=NOMPI'
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mpif90 = 'MPIF90C='
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# Choose BLAS and LAPACK
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lapack = ("LAPACKL=%s" %
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(spec['lapack'].libs + spec['blas'].libs).ld_flags)
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# Build
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make(choosecomp, wantmpi, mpif90, lapack)
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# Install
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mkdirp(prefix.bin)
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install('cosmomc', prefix.bin)
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root = join_path(prefix.share, 'cosmomc')
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mkdirp(root)
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entries = [
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'batch1',
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'batch2',
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'batch3',
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'camb',
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'chains',
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'clik_latex.paramnames',
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'clik_units.paramnames',
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'cosmomc.cbp',
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'data',
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'distgeneric.ini',
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'distparams.ini',
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'disttest.ini',
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'docs',
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'job_script',
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'job_script_MOAB',
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'job_script_SLURM',
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'paramnames',
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'params_generic.ini',
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'planck_covmats',
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'python',
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'scripts',
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# don't copy 'source'
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'test.ini',
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'test_pico.ini',
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'test_planck.ini',
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'tests',
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]
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for entry in entries:
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if os.path.isfile(entry):
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install(entry, root)
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else:
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install_tree(entry, join_path(root, entry))
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for dirpath, dirnames, filenames in os.walk(prefix):
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for filename in fnmatch.filter(filenames, '*~'):
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os.remove(os.path.join(dirpath, filename))
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@on_package_attributes(run_tests=True)
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@run_after('install')
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def check_install(self):
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prefix = self.prefix
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spec = self.spec
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os.environ.pop('LINKMPI', '')
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os.environ.pop('NERSC_HOST', '')
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os.environ.pop('NONCLIKLIKE', '')
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os.environ.pop('PICO', '')
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os.environ.pop('PRECISION', '')
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os.environ.pop('RECOMBINATION', '')
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os.environ.pop('WMAP', '')
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os.environ.pop('COSMOMC_LOCATION', '')
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os.environ.pop('PLC_LOCATION', '')
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os.environ.pop('CLIKPATH', '')
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os.environ.pop('PLANCKLIKE', '')
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exe = join_path(prefix.bin, 'cosmomc')
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args = []
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if '+mpi' in spec:
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# Add mpirun prefix
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args = ['-np', '1', exe]
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exe = join_path(spec['mpi'].prefix.bin, 'mpiexec')
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cosmomc = Executable(exe)
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with working_dir('spack-check', create=True):
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for entry in [
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'camb',
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'chains',
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'data',
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'paramnames',
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'planck_covmats',
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]:
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os.symlink(join_path(prefix.share, 'cosmomc', entry), entry)
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inifile = join_path(prefix.share, 'cosmomc', 'test.ini')
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cosmomc(*(args + [inifile]))
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if '+planck' in spec:
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inifile = join_path(prefix.share, 'cosmomc', 'test_planck.ini')
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cosmomc(*(args + [inifile]))
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