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

6 files changed, 418 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/cosmomc/Makefile.patch b/var/spack/repos/builtin/packages/cosmomc/Makefile.patch
new file mode 100644
index 0000000000..f7241af3d0
--- /dev/null
+++ b/var/spack/repos/builtin/packages/cosmomc/Makefile.patch
@@ -0,0 +1,26 @@
+--- 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
+ 
diff --git a/var/spack/repos/builtin/packages/cosmomc/errorstop.patch b/var/spack/repos/builtin/packages/cosmomc/errorstop.patch
new file mode 100644
index 0000000000..b23e925daf
--- /dev/null
+++ b/var/spack/repos/builtin/packages/cosmomc/errorstop.patch
@@ -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
diff --git a/var/spack/repos/builtin/packages/cosmomc/package.py b/var/spack/repos/builtin/packages/cosmomc/package.py
new file mode 100644
index 0000000000..a6a4409b25
--- /dev/null
+++ b/var/spack/repos/builtin/packages/cosmomc/package.py
@@ -0,0 +1,201 @@
+##############################################################################
+# 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]))
diff --git a/var/spack/repos/builtin/packages/planck-likelihood/fortran.patch b/var/spack/repos/builtin/packages/planck-likelihood/fortran.patch
new file mode 100644
index 0000000000..b63d268eca
--- /dev/null
+++ b/var/spack/repos/builtin/packages/planck-likelihood/fortran.patch
@@ -0,0 +1,11 @@
+--- 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)
diff --git a/var/spack/repos/builtin/packages/planck-likelihood/make.patch b/var/spack/repos/builtin/packages/planck-likelihood/make.patch
new file mode 100644
index 0000000000..6f3ce81b80
--- /dev/null
+++ b/var/spack/repos/builtin/packages/planck-likelihood/make.patch
@@ -0,0 +1,21 @@
+--- 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
diff --git a/var/spack/repos/builtin/packages/planck-likelihood/package.py b/var/spack/repos/builtin/packages/planck-likelihood/package.py
new file mode 100644
index 0000000000..c5c5cac6cf
--- /dev/null
+++ b/var/spack/repos/builtin/packages/planck-likelihood/package.py
@@ -0,0 +1,148 @@
+##############################################################################
+# 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'))