Merge pull request #908 from xylar/update-to-1.8.0-alpha.1

Update to v1.8.0-alpha.1

Author: xylar

E3SM-Project

@@ -222,7 +222,8 @@ def _partition_scrip_file(self, in_filename):
             in_filename,
             h5m_filename,
         ]
-        check_call(args, logger)
+        # run in "parallel" with one task and one thread for Intel-MPI support
+        run_command(args, 1, 1, 1, self.config, logger)
 
         # Partition source SCRIP
         args = [
@@ -231,7 +232,8 @@ def _partition_scrip_file(self, in_filename):
             h5m_filename,
             part_filename,
         ]
-        check_call(args, logger)
+        # run in "parallel" with one task and one thread for Intel-MPI support
+        run_command(args, 1, 1, 1, self.config, logger)
 
         logger.info('  Done.')
 

compass/ocean/mesh/remap_topography.py

@@ -159,7 +159,8 @@ def _partition_scrip_file(self, in_filename):
             in_filename,
             h5m_filename,
         ]
-        check_call(args, logger)
+        # run in "parallel" with one task and one thread for Intel-MPI support
+        run_command(args, 1, 1, 1, self.config, logger)
 
         # Partition source SCRIP
         args = [
@@ -168,7 +169,8 @@ def _partition_scrip_file(self, in_filename):
             h5m_filename,
             part_filename,
         ]
-        check_call(args, logger)
+        # run in "parallel" with one task and one thread for Intel-MPI support
+        run_command(args, 1, 1, 1, self.config, logger)
 
         logger.info('  Done.')
         return part_filename

compass/ocean/tests/global_ocean/files_for_e3sm/remap_sea_surface_salinity_restoring.py

@@ -1 +1 @@
-__version__ = '1.7.0-alpha.3'
+__version__ = '1.8.0-alpha.1'

compass/version.py

@@ -495,7 +495,7 @@ def build_spack_env(config, update_spack, machine, compiler, mpi,  # noqa: C901
     specs = list()
 
     if cmake != 'None':
-        specs.append(f'"cmake@{cmake}"')
+        specs.append(f'cmake@{cmake}')
 
     e3sm_hdf5_netcdf = config.getboolean('deploy', 'use_e3sm_hdf5_netcdf')
     if not e3sm_hdf5_netcdf:
@@ -504,50 +504,53 @@ def build_spack_env(config, update_spack, machine, compiler, mpi,  # noqa: C901
         netcdf_fortran = config.get('deploy', 'netcdf_fortran')
         pnetcdf = config.get('deploy', 'pnetcdf')
         specs.extend([
-            f'"hdf5@{hdf5}+cxx+fortran+hl+mpi+shared"',
-            f'"netcdf-c@{netcdf_c}+mpi~parallel-netcdf"',
-            f'"netcdf-fortran@{netcdf_fortran}"',
-            f'"parallel-netcdf@{pnetcdf}+cxx+fortran"'])
+            f'hdf5@{hdf5}+cxx+fortran+hl+mpi+shared',
+            f'netcdf-c@{netcdf_c}+mpi~parallel-netcdf',
+            f'netcdf-fortran@{netcdf_fortran}',
+            f'parallel-netcdf@{pnetcdf}+cxx+fortran'])
 
     if esmf != 'None':
-        specs.append(f'"esmf@{esmf}+mpi+netcdf~pnetcdf~external-parallelio"')
+        specs.append(f'esmf@{esmf}+mpi+netcdf~pnetcdf~external-parallelio')
     if lapack != 'None':
-        specs.append(f'"netlib-lapack@{lapack}"')
+        specs.append(f'netlib-lapack@{lapack}')
         include_e3sm_lapack = False
     else:
         include_e3sm_lapack = True
     if metis != 'None':
         specs.append(
-            f'"metis@{metis}+int64+real64"')
+            f'metis@{metis}+int64+real64')
     if moab != 'None':
         specs.append(
-            f'"moab@{moab}+mpi+hdf5+netcdf+pnetcdf+metis+parmetis+tempest"')
+            f'moab@{moab}+mpi+hdf5+netcdf+pnetcdf+metis+parmetis+tempest')
     if petsc != 'None':
-        specs.append(f'"petsc@{petsc}+mpi+batch"')
+        specs.append(f'petsc@{petsc}+mpi+batch')
 
     custom_spack = ''
     if scorpio != 'None':
         specs.append(
-            f'"scorpio'
-            f'@{scorpio}+pnetcdf~timing+internal-timing~tools+malloc"')
+            f'e3sm-scorpio'
+            f'@{scorpio}+mpi~timing~internal-timing~tools+malloc')
         # make sure scorpio, not esmf, libraries are linked
         lib_path = \
             f'{spack_branch_base}/var/spack/environments/' \
             f'{spack_env}/.spack-env/view/lib'
-        scorpio_lib_path = '$(spack find --format "{prefix}" scorpio)'
+        scorpio_lib_path = '$(spack find --format "{prefix}" e3sm-scorpio)'
+        if scorpio_lib_path == '':
+            raise ValueError('Could not find e3sm-scorpio in Spack. '
+                             'Did something go wrong with the build?')
         custom_spack = \
             f'{custom_spack}' \
             f'ln -sfn {scorpio_lib_path}/lib/libpioc.a {lib_path}\n' \
             f'ln -sfn {scorpio_lib_path}/lib/libpiof.a {lib_path}\n'
 
     if parallelio != 'None':
         specs.append(
-            f'"parallelio'
-            f'@{parallelio}+pnetcdf~timing"')
+            f'parallelio'
+            f'@{parallelio}+pnetcdf~timing')
 
     if albany != 'None':
-        specs.append(f'"trilinos-for-albany@{albany}{trilinos_variants}"')
-        specs.append(f'"albany@{albany}{albany_variants}"')
+        specs.append(f'trilinos-for-albany@{albany}{trilinos_variants}')
+        specs.append(f'albany@{albany}{albany_variants}')
 
     yaml_template = f'{spack_template_path}/{machine}_{compiler}_{mpi}.yaml'
     if not os.path.exists(yaml_template):

conda/bootstrap.py

@@ -16,7 +16,7 @@ ipython
 jupyter
 lxml
 {% if include_mache %}
-mache=1.27.0
+mache=1.31.0
 {% endif %}
 matplotlib-base >=3.9.1
 metis

conda/compass_env/spec-file.template

@@ -102,7 +102,7 @@ def main():
     if local_mache:
         mache = ''
     else:
-        mache = '"mache=1.27.0"'
+        mache = '"mache=1.31.0"'
 
     setup_install_env(env_name, activate_base, args.use_local, logger,
                       args.recreate, conda_base, mache)

conda/configure_compass_env.py

@@ -26,15 +26,15 @@ albany_variants = +mpas~py+unit_tests
 trilinos_variants =
 # cmake newer than 3.23.0 needed for Trilinos
 cmake = 3.23.0:
-esmf = 8.7.0
-hdf5 = 1.14.3
+esmf = 8.8.1
+hdf5 = 1.14.6
 lapack = 3.9.1
 metis = 5.1.0
 moab = master
 netcdf_c = 4.9.2
-netcdf_fortran = 4.6.1
+netcdf_fortran = 4.6.2
 petsc = 3.19.1
-pnetcdf = 1.13.0
-scorpio = 1.6.5
+pnetcdf = 1.14.0
+scorpio = 1.8.1
 # parallelio = 2.6.3
 parallelio = None