Revert "cosmo: Remove package"

This reverts commit 2a7a337.

repos/c2sm/packages/cosmo/package.py

@@ -0,0 +1,329 @@
+# Copyright 2013-2018 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 subprocess, itertools, os
+from spack import *
+
+
+class Cosmo(MakefilePackage):
+    """COSMO: Numerical Weather Prediction Model. Needs access to private GitHub."""
+
+    homepage = "http://www.cosmo-model.org"
+    url = "https://github.com/COSMO-ORG/cosmo/archive/6.0.tar.gz"
+    git = '[email protected]:COSMO-ORG/cosmo.git'
+    apn_git = '[email protected]:MeteoSwiss-APN/cosmo.git'
+    c2sm_git = '[email protected]:C2SM-RCM/cosmo.git'
+    empa_git = '[email protected]:C2SM-RCM/cosmo-ghg.git'
+    maintainers = ['mjaehn', 'juckerj']
+
+    version('org-master', branch='master')
+    version('6.0', tag='6.0')
+
+    version('apn-mch', git=apn_git, branch='mch')
+    version('5.09a.mch1.2.p2', git=apn_git, tag='5.09a.mch1.2.p2')
+
+    version('6.1_2023.11', git=c2sm_git, tag='6.1_2023.11')
+    version('c2sm-master', git=c2sm_git, branch='master')
+    version('c2sm-features', git=c2sm_git, branch='c2sm-features')
+    version('empa-ghg', git=empa_git, branch='c2sm')
+
+    # pass spec from spec to test_cosmo.py in yaml-format
+    # There are three different types of test_cosmo.py around:
+
+    # COSMO-ORG
+    patch('patches/org-master/spec_as_yaml/patch.test_cosmo',
+          when='@org-master')
+    patch('patches/org-master/spec_as_yaml/patch.test_cosmo', when='@6.0')
+    # APN-MCH
+    patch('patches/apn-mch/spec_as_yaml/patch.test_cosmo', when='@apn-mch')
+    patch('patches/5.09a.mch1.2.p2/spec_as_yaml/patch.test_cosmo',
+          when='@5.09a.mch1.2.p2')
+
+    # pass spec from spec to serialize_cosmo.py in yaml-format
+
+    # There are two different types of serialize_cosmo.py around:
+
+    # COSMO-ORG
+    patch('patches/org-master/spec_as_yaml/patch.serialize_cosmo',
+          when='@org-master +serialize')
+    patch('patches/org-master/spec_as_yaml/patch.serialize_cosmo',
+          when='@6.0 +serialize')
+    patch('patches/c2sm-features/spec_as_yaml/patch.serialize_cosmo',
+          when='@c2sm-features +serialize')
+    patch('patches/empa-ghg/spec_as_yaml/patch.serialize_cosmo',
+          when='@empa-ghg +serialize')
+
+    # APN-MCH
+    patch('patches/apn-mch/spec_as_yaml/patch.serialize_cosmo',
+          when='@apn-mch +serialize')
+    patch('patches/5.09a.mch1.2.p2/spec_as_yaml/patch.serialize_cosmo',
+          when='@5.09a.mch1.2.p2 +serialize')
+
+    # build dependency
+    depends_on('[email protected]:', type='build')
+    depends_on('libgrib1', type='build')
+
+    # build and link dependency
+    depends_on('mpi +fortran')
+    depends_on('netcdf-fortran')
+    depends_on('netcdf-c +mpi')
+    depends_on('[email protected]')
+    depends_on('eccodes +fortran')
+    # WORKAROUND: A build and link dependency should imply that the same compiler is used. This enforces it.
+    depends_on('eccodes %nvhpc', when='%nvhpc')
+    depends_on('eccodes %gcc', when='%gcc')
+
+    # run dependency
+    depends_on('slurm', type='run')
+
+    depends_on('cosmo-eccodes-definitions', type=('build', 'run'))
+    depends_on('serialbox +fortran ^python@2:2.9',
+               when='+serialize',
+               type=('build', 'link', 'run'))
+    depends_on('oasis', when='+oasis', type=('build', 'link', 'run'))
+
+    variant('serialize',
+            default=False,
+            description='Build with serialization enabled')
+    variant('parallel', default=True, description='Build parallel COSMO')
+    variant('debug', default=False, description='Build debug mode')
+    variant('real_type',
+            default='double',
+            description='Build with double or single precision enabled',
+            values=('double', 'float'),
+            multi=False)
+    variant('slave', default='none', description='Build on slave')
+    variant('pollen', default=False, description='Build with pollen enabled')
+    variant('verbose',
+            default=False,
+            description='Build cosmo with verbose enabled')
+    variant('set_version',
+            default=False,
+            description='Pass cosmo tag version to Makefile')
+    variant('gt1',
+            default=False,
+            description='Build dycore with gridtools 1.1.3')
+    variant('cuda_arch',
+            default='none',
+            description='Build with cuda_arch',
+            values=('80', '70', '60', '37'),
+            multi=False)
+    variant('oasis',
+            default=False,
+            description='Build with the unified oasis interface')
+
+    conflicts(
+        '@dev-build',
+        msg=
+        "Please use only official versions listed with 'spack info cosmo'. Even when using 'devbuildcosmo'. C2SM introduced 'dev-build' to avoid name conflicts with the upstream instance. Since spack-c2sm v0.18.1.0 this is not relevant anymore."
+    )
+    conflicts('+pollen', when='@org-master,master')
+    # - ML - A conflict should be added there if the oasis variant is
+    # chosen and the version is neither c2sm-features nor
+    # dev-build. The problem is that this doesn't seem possible in a
+    # native spack way. Hence the dirty check at the beginning of
+    # setup_build_environment method
+
+    build_directory = 'cosmo/ACC'
+
+    # v0.20.1 does not fully support builds of COSMO
+    # users should continue using v0.18.1.x on Daint
+    # once support on Alps has been clarified finalize
+    # recipe and remove line below.
+    manual_download = True
+
+    def setup_build_environment(self, env):
+
+        # - ML - Dirty conflict check (see above)
+        if self.spec.variants['oasis'].value and self.spec.version not in (
+                Version('c2sm-features')):
+            raise InstallError(
+                '+oasis variant only compatible with the @c2sm-features versions'
+            )
+
+        self.setup_run_environment(env)
+
+        # Check mpi provider
+        self.mpi_spec = self.spec['mpi']
+
+        grib_prefix = self.spec['eccodes'].prefix
+        env.set(
+            'GRIBAPIL',
+            str(self.spec['eccodes:fortran'].libs.ld_flags) + ' ' +
+            str(self.spec['jasper'].libs.ld_flags))
+        grib_inc_dir_path = os.path.join(grib_prefix, 'include')
+        if os.path.exists(grib_inc_dir_path):
+            env.set('GRIBAPII', '-I' + grib_inc_dir_path)
+        else:
+            env.set('GRIBAPII', '')
+
+        # libaec
+        if 'libaec' in self.spec:
+            env.set('AECL', '-L' + self.spec['libaec'].prefix + '/lib64 -laec')
+            env.set('AECI', '-I' + self.spec['libaec'].prefix + '/include')
+
+        # Netcdf library
+        env.set(
+            'NETCDFL',
+            '-L' + self.spec['netcdf-fortran'].prefix + '/lib -lnetcdff -L' +
+            self.spec['netcdf-c'].prefix + '/lib -lnetcdf')
+        env.set('NETCDFI',
+                '-I' + self.spec['netcdf-fortran'].prefix + '/include')
+
+        # Grib1 library
+        if self.compiler.name == 'gcc':
+            env.set('GRIBDWDL',
+                    '-L' + self.spec['libgrib1'].prefix + '/lib -lgrib1_gnu')
+        elif self.compiler.name == 'cce':
+            env.set('GRIBDWDL',
+                    '-L' + self.spec['libgrib1'].prefix + '/lib -lgrib1_cray')
+        elif self.compiler.name == 'nvhpc':
+            env.set('GRIBDWDL',
+                    '-L' + self.spec['libgrib1'].prefix + '/lib -lgrib1_pgi')
+        else:
+            env.set(
+                'GRIBDWDL', '-L' + self.spec['libgrib1'].prefix +
+                '/lib -lgrib1_' + self.compiler.name)
+        env.set('GRIBDWDI', '-I' + self.spec['libgrib1'].prefix + '/include')
+
+        # MPI library
+        if self.mpi_spec.name == 'openmpi':
+            env.set('MPIL', '-L' + self.mpi_spec.prefix + ' -lmpi')
+
+        else:
+            env.set('MPIL', '-L' + self.spec['mpi'].prefix + ' -lmpich')
+
+        env.set('MPII', '-I' + self.mpi_spec.prefix + '/include')
+
+        # Serialbox library
+        if '+serialize' in self.spec:
+            env.set('SERIALBOX', self.spec['serialbox'].prefix)
+            env.set('SERIALBOXL',
+                    self.spec['serialbox:fortran,c'].libs.ld_flags)
+            env.set('SERIALBOXI',
+                    '-I' + self.spec['serialbox'].prefix + '/include')
+
+        # OASIS library
+        if '+oasis' in self.spec:
+            oasis_prefix = self.spec['oasis'].prefix
+            env.set(
+                'PSMILEL',
+                '-L{:s}/lib -lpsmile.MPI1 -lscrip -lmct -lmpeu'.format(
+                    oasis_prefix))
+            env.set(
+                'PSMILEI',
+                '-I{0:s}/build/lib/psmile.MPI1 -I{0:s}/build/lib/mct'.format(
+                    oasis_prefix))
+            env.set('MPPIOI', '-I{:s}/build/lib/mct'.format(oasis_prefix))
+
+        # Linker flags
+        if self.compiler.name in ('pgi',
+                                  'nvhpc') and '~cppdycore' in self.spec:
+            env.set('LFLAGS', '-lstdc++')
+
+        # Compiler & linker variables
+        if self.compiler.name in ('pgi', 'nvhpc'):
+            env.set('F90', self.mpi_spec.mpifc + ' -D__PGI_FORTRAN__')
+            env.set('LD', self.mpi_spec.mpifc + ' -D__PGI_FORTRAN__')
+        else:
+            env.set('F90', self.mpi_spec.mpifc)
+            env.set('LD', self.mpi_spec.mpifc)
+
+    @property
+    def build_targets(self):
+        build = []
+        if self.spec.variants['pollen'].value:
+            build.append('POLLEN=1')
+        if self.spec.variants['oasis'].value:
+            build.append('COUP_OAS=1')
+        if self.spec.variants['real_type'].value == 'float':
+            build.append('SINGLEPRECISION=1')
+        if '+serialize' in self.spec:
+            build.append('SERIALIZE=1')
+        if self.spec.variants['verbose'].value:
+            build.append('VERBOSE=1')
+        if '+set_version' in self.spec:
+            build.append('COSMO_VERSION=' + self.spec.format('{version}'))
+        MakeFileTarget = ''
+        if '+parallel' in self.spec:
+            MakeFileTarget += 'par'
+        else:
+            MakeFileTarget += 'seq'
+        if '+debug' in self.spec:
+            MakeFileTarget += 'debug'
+        else:
+            MakeFileTarget += 'opt'
+        build.append(MakeFileTarget)
+
+        return build
+
+    def edit(self, spec, prefix):
+        with working_dir(self.build_directory):
+            OptionsFileName = 'Options'
+            if self.compiler.name == 'gcc':
+                OptionsFileName += '.gnu'
+            elif self.compiler.name in ('pgi', 'nvhpc'):
+                OptionsFileName += '.pgi'
+            elif self.compiler.name == 'cce':
+                OptionsFileName += '.cray'
+            OptionsFileName += '.cpu'
+            OptionsFile = FileFilter(OptionsFileName)
+
+            makefile = FileFilter('Makefile')
+            makefile.filter('/Options.*', '/' + OptionsFileName)
+            if self.spec.version == Version('empa-ghg'):
+                if '~serialize' in spec:
+                    makefile.filter(
+                        'TARGET     :=.*',
+                        'TARGET     := {0}'.format('cosmo-ghg_cpu'))
+                else:
+                    makefile.filter('TARGET     :=.*',
+                                    'TARGET     := {0}'.format('cosmo-ghg'))
+            else:
+                if '~serialize' in spec:
+                    makefile.filter('TARGET     :=.*',
+                                    'TARGET     := {0}'.format('cosmo_cpu'))
+                else:
+                    makefile.filter('TARGET     :=.*',
+                                    'TARGET     := {0}'.format('cosmo'))
+
+            # Pre-processor flags
+            if self.mpi_spec.name == 'mpich':
+                OptionsFile.filter(
+                    'PFLAGS   = -Mpreprocess.*',
+                    'PFLAGS   = -Mpreprocess -DNO_MPI_HOST_DATA')
+
+    def install(self, spec, prefix):
+
+        with working_dir(self.build_directory):
+            mkdir(prefix.bin)
+            if self.spec.version == Version('empa-ghg'):
+                if '+serialize' in spec:
+                    install('cosmo-ghg_serialize', prefix.bin)
+                else:
+                    install('cosmo-ghg_cpu', prefix.bin)
+                    install('cosmo-ghg_cpu', 'test/testsuite')
+            else:
+                if '+serialize' in spec:
+                    install('cosmo_serialize', prefix.bin)
+                else:
+                    install('cosmo_cpu', prefix.bin)
+                    install('cosmo_cpu', 'test/testsuite')
+
+    @run_after('install')
+    @on_package_attributes(run_tests=True)
+    def test(self):
+        with open('spec.yaml', mode='w') as f:
+            f.write(self.spec.to_yaml())
+        try:
+            subprocess.run([
+                self.build_directory + '/test/tools/test_cosmo.py', '-s',
+                'spec.yaml', '-b',
+                str('.')
+            ],
+                           stderr=subprocess.STDOUT,
+                           check=True)
+        except:
+            raise InstallError('Testsuite failed')

repos/c2sm/packages/cosmo/patches/5.09a.mch1.2.p2

@@ -0,0 +1 @@
+apn-mch/

repos/c2sm/packages/cosmo/patches/apn-mch/spec_as_yaml/patch.serialize_cosmo

@@ -0,0 +1,20 @@
+diff --git a/cosmo/ACC/test/tools/serialize_cosmo.py b/cosmo/ACC/test/tools/serialize_cosmo.py
+index 624fd295..fc15c712 100755
+--- a/cosmo/ACC/test/tools/serialize_cosmo.py
++++ b/cosmo/ACC/test/tools/serialize_cosmo.py
+@@ -15,7 +15,14 @@ def main():
+     parser.add_argument('-b', '--base_directory', type=str, help='Cosmo base directory', required=True)
+     args=parser.parse_args()
+
+-    cosmo_spec = spack.cmd.parse_specs(args.spec)[0]
++    try:
++        # assume spec is passed as a yaml-file
++        with open(args.spec,"r") as f:
++          cosmo_spec = Spec.from_yaml(f)
++    except:
++        # assume spec is passed as a string
++        cosmo_spec = Spec(args.spec)
++
+     cosmo_spec.concretize()
+
+     serialize_cosmo(cosmo_spec, args.base_directory)

repos/c2sm/packages/cosmo/patches/apn-mch/spec_as_yaml/patch.test_cosmo

@@ -0,0 +1,21 @@
+diff --git a/cosmo/ACC/test/tools/test_cosmo.py b/cosmo/ACC/test/tools/test_cosmo.py
+index 733bde4a..2a166bbd 100755
+--- a/cosmo/ACC/test/tools/test_cosmo.py
++++ b/cosmo/ACC/test/tools/test_cosmo.py
+@@ -16,7 +16,15 @@ def main():
+     parser.add_argument('-b', '--base_directory', type=str, help='Cosmo base directory')
+     args=parser.parse_args()
+
+-    test_cosmo(Spec(args.spec), args.base_directory)
++    try:
++        # assume spec is passed as a yaml-file
++        with open(args.spec,"r") as f:
++          cosmo_spec = Spec.from_yaml(f)
++    except:
++        # assume spec is passed as a string
++        cosmo_spec = Spec(args.spec)
++
++    test_cosmo(cosmo_spec, args.base_directory)
+
+ def test_cosmo(cosmo_spec, base_directory):
+

repos/c2sm/packages/cosmo/patches/c2sm-features/spec_as_yaml/patch.serialize_cosmo

@@ -0,0 +1 @@
+../../org-master/spec_as_yaml/patch.serialize_cosmo

repos/c2sm/packages/cosmo/patches/c2sm-master

@@ -0,0 +1 @@
+org-master/

repos/c2sm/packages/cosmo/patches/empa-ghg/spec_as_yaml/patch.serialize_cosmo

@@ -0,0 +1 @@
+../../org-master/spec_as_yaml/patch.serialize_cosmo