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cosmomc: New package CosmoMC (#3292)

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* 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 2017-03-09 09:14:13 -05:00 committed by Adam J. Stewart
parent 21e913bac5
commit 2ac343e92e
6 changed files with 418 additions and 0 deletions
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26
var/spack/repos/builtin/packages/cosmomc/Makefile.patch Normal file
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--- a/Makefile
+++ b/Makefile
@@ -7,8 +7,7 @@
rebuild: clean delete cosmomc
-cosmomc: BUILD ?= MPI
-cosmomc_debug: BUILD ?= MPI
+BUILD ?= MPI
getdist: ./source/*.*90
cd ./source && make getdist BUILD=$(BUILD)
--- a/source/Makefile
+++ b/source/Makefile
@@ -57,11 +57,7 @@
#commented above is (I think) for Mac; this is standard linux (sudo apt-get install liblapack-dev)
LAPACKL = -lblas -llapack
-#march native does not work on Mac, otherwise use (comment out if your cluster is inhomogeneous)
-ifneq ($(shell uname -s),Darwin)
-#native optimization does not work on Mac
FFLAGS+=-march=native
-endif
endif

11
var/spack/repos/builtin/packages/cosmomc/errorstop.patch Normal file
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@ -0,0 +1,11 @@
--- a/camb/constants.f90
+++ b/camb/constants.f90
@@ -87,7 +87,7 @@
global_error_message=''
end if
if (present(id)) then
- if (id==0) error stop('Error id must be non-zero')
+ if (id==0) error stop
global_error_flag=id
else
global_error_flag=-1

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var/spack/repos/builtin/packages/cosmomc/package.py Normal file
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##############################################################################
# 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 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 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 fnmatch
import os
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', '98620cb746352f68fb0c1196e9a070ac')
version('2016.06', '92dc651d1407cca6ea9228992165f5cb')
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')
patch('Makefile.patch')
patch('errorstop.patch')
depends_on('mpi', when='+mpi')
depends_on('planck-likelihood', when='+planck')
depends_on('python @2.7:2.999,3.4:')
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',
'python',
'scripts',
# don't copy 'source'
'test.ini',
'test_pico.ini',
'test_planck.ini',
'tests',
]
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))
@on_package_attributes(run_tests=True)
@run_after('install')
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 = join_path(prefix.bin, 'cosmomc')
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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--- a/src/bflike/bflike_smw.f90
+++ b/src/bflike/bflike_smw.f90
@@ -1600,6 +1600,8 @@
ok = .false.
call fid%init()
+
+ unit = 3001
open(unit = unit,file=trim(filein),status='old',action='read',&
iostat=istat)

21
var/spack/repos/builtin/packages/planck-likelihood/make.patch Normal file
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--- a/Makefile
+++ b/Makefile
@@ -336,15 +336,15 @@
$(BDIR)/libclik_f90.$(SO): $(BDIR)/libclik.$(SO) $(addprefix $(ODIR)/,clik_fortran.o clik.f90.o)
@$(ECHO) "build $(BLUE_COLOR)$(@) $(NO_COLOR)"
- @$(LD) $(SHARED) $(LDFLAG) $(LAPACK) -L$(BDIR) -lclik $^ -o $@
+ @$(LD) -o $@ $(addprefix $(ODIR)/,clik_fortran.o clik.f90.o) -L$(BDIR) -lclik $(SHARED) $(LAPACK) $(LDFLAG)
$(BDIR)/clik_example_C: $(ODIR)/clik_example_c.o $(BDIR)/libclik.$(SO)
@$(ECHO) "build $(BLUE_COLOR)$(@) $(NO_COLOR)"
- @$(CC) $(LDFLAG) $(LAPACK) -L$(BDIR) -lclik $< -o $@
+ @$(CC) -o $@ $(ODIR)/clik_example_c.o -L$(BDIR) -lclik $(LAPACK) $(LDFLAG)
$(BDIR)/clik_example_f90: $(ODIR)/clik_example_f90.f90.o $(BDIR)/libclik_f90.$(SO)
@$(ECHO) "build $(BLUE_COLOR)$(@) $(NO_COLOR)"
- @$(FC) $(LDFLAG) $(LAPACK) -L$(BDIR) -lclik_f90 -lclik $< -o $@
+ @$(FC) -o $@ $(ODIR)/clik_example_f90.f90.o -L$(BDIR) -lclik_f90 -lclik $(LAPACK) $(LDFLAG)
$(BDIR)/liblapack_clik.$(SO): |$(BDIR)
ifndef MKL_LIB_FULLPATH

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var/spack/repos/builtin/packages/planck-likelihood/package.py Normal file
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##############################################################################
# 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 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 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 *
class PlanckLikelihood(Package):
"""2015 Cosmic Microwave Background (CMB) spectra and likelihood code"""
homepage = "https://wiki.cosmos.esa.int/planckpla2015/index.php/CMB_spectrum_%26_Likelihood_Code"
url = "http://irsa.ipac.caltech.edu/data/Planck/release_2/software/COM_Likelihood_Code-v2.0.R2.00.tar.bz2"
version('2.00', '7a081679ff249dc4f94fb7177e16e818',
url="http://irsa.ipac.caltech.edu/data/Planck/release_2/software/COM_Likelihood_Code-v2.0.R2.00.tar.bz2")
variant('lensing-ext', default=False,
description="Provide lensing-ext data")
variant('plik-DS', default=False,
description="Provide plik-DS data")
variant('plik-HM-ext', default=False,
description="Provide plik-HM-ext data")
variant('plik-unbinned', default=False,
description="Provide plik-unbinned data")
patch('fortran.patch')
patch('make.patch')
resource(
name='baseline',
url="http://irsa.ipac.caltech.edu/data/Planck/release_2/software/COM_Likelihood_Data-baseline_R2.00.tar.gz",
md5='7e784819cea65dbc290ea3619420295a',
destination='.')
resource(
name='lensing-ext',
url="http://irsa.ipac.caltech.edu/data/Planck/release_2/software/COM_Likelihood_Data-extra-lensing-ext.R2.00.tar.gz",
md5='091736f73b47a09162050bee27d68399',
destination='.',
when='+lensing-ext')
resource(
name='plik-DS',
url="http://irsa.ipac.caltech.edu/data/Planck/release_2/software/COM_Likelihood_Data-extra-plik-DS.R2.00.tar.gz",
md5='76ac04f989025eecab3825aba7e41f36',
destination='.',
when='+plik-DS')
resource(
name='plik-HM-ext',
url="http://irsa.ipac.caltech.edu/data/Planck/release_2/software/COM_Likelihood_Data-extra-plik-HM-ext.R2.00.tar.gz",
md5='1c3bd8221f973b7bf7e76647451fd6e5',
destination='.',
when='+plik-HM-ext')
resource(
name='plik-unbinned',
url="http://irsa.ipac.caltech.edu/data/Planck/release_2/software/COM_Likelihood_Data-extra-plik-unbinned.R2.00.tar.gz",
md5='c5869aa6b6581b6863d2a6e0ffd3826c',
destination='.',
when='+plik-unbinned')
depends_on('blas')
depends_on('cfitsio +shared')
depends_on('lapack')
# Note: Could also install Python bindings
parallel = False
def install(self, spec, prefix):
# Configure
# Don't hide build commands
filter_file("^\t@", "\t", "Makefile")
makeflags = [
'PREFIX=%s' % prefix,
'COLORS=0',
'CFITSIOPATH=%s' % spec['cfitsio'].prefix,
'CC=cc',
'FC=fc',
'IFORTLIBPATH=',
'IFORTRUNTIME=-lintlc -limf -lsvml -liomp5 -lifportmt -lifcoremt',
'GFORTRANLIBPATH=',
'GFORTRANRUNTIME=-lgfortran -lgomp',
'LAPACKLIBPATH=',
'LAPACK=%s' % (spec['lapack'].libs + spec['blas'].libs).ld_flags,
'COPENMP=%s' % self.compiler.openmp_flag,
'FOPENMP=%s' % self.compiler.openmp_flag,
]
# Build
make(*makeflags)
# Install
make('install', *makeflags)
fix_darwin_install_name(prefix.lib)
dirs = ['plc_2.0']
if '+lensing-ext' in spec:
dirs.append('lensing_ext')
if '+plik-DS' in spec:
dirs.append('plik_DS')
if '+plik-HM-ext' in spec:
dirs.append('plik_HM_ext')
if '+plik-unbinned' in spec:
dirs.append('plik_unbinned')
for dir in dirs:
install_tree(dir, join_path(prefix, 'share', 'clik', dir))
def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
prefix = self.prefix
spack_env.set('CLIK_PATH', prefix)
spack_env.set('CLIK_DATA', join_path(prefix, 'share', 'clik'))
spack_env.set('CLIK_PLUGIN', 'rel2015')
def setup_environment(self, spack_env, run_env):
prefix = self.prefix
run_env.set('CLIK_PATH', prefix)
run_env.set('CLIK_DATA', join_path(prefix, 'share', 'clik'))
run_env.set('CLIK_PLUGIN', 'rel2015')
@on_package_attributes(run_tests=True)
@run_after('install')
def check_install(self):
prefix = self.prefix
clik_example_C = Executable(join_path(prefix.bin, 'clik_example_C'))
with working_dir('spack-check', create=True):
clik_example_C(join_path(prefix, 'share', 'clik',
'plc_2.0', 'hi_l', 'plik',
'plik_dx11dr2_HM_v18_TT.clik'))