Merge pull request #555 from xylar/update_to_1.2.0-alpha.5

Update to v1.2.0-alpha.5

.pre-commit-config.yaml

@@ -8,8 +8,6 @@ repos:
     hooks:
       - id: trailing-whitespace
       - id: end-of-file-fixer
-      - id: check-yaml
-        exclude: conda/recipe
 
   # Can run individually with `pre-commit run isort --all-files`
   - repo: https://github.com/PyCQA/isort

compass/machines/chicoma-cpu.cfg

@@ -4,11 +4,11 @@
 [paths]
 
 # A shared root directory where MPAS standalone data can be found
-database_root = /usr/projects/regionalclimate/COMMON_MPAS/mpas_standalonedata/
+database_root = /usr/projects/e3sm/mpas_standalonedata/
 
 # the path to the base conda environment where compass environments have
 # been created
-compass_envs = /usr/projects/climate/SHARED_CLIMATE/compass/chicoma-cpu/base
+compass_envs = /usr/projects/e3sm/compass/chicoma-cpu/base
 
 
 # Options related to deploying a compass conda environment on supported
@@ -22,7 +22,7 @@ compiler = gnu
 mpi_gnu = mpich
 
 # the base path for spack environments used by compass
-spack = /usr/projects/climate/SHARED_CLIMATE/compass/chicoma-cpu/spack
+spack = /usr/projects/e3sm/compass/chicoma-cpu/spack
 
 # whether to use the same modules for hdf5, netcdf-c, netcdf-fortran and
 # pnetcdf as E3SM (spack modules are used otherwise)
@@ -51,4 +51,3 @@ partition = standard
 
 # The job quality of service (QOS) to use
 qos = standard
-

compass/version.py

@@ -1 +1 @@
-__version__ = '1.2.0-alpha.4'
+__version__ = '1.2.0-alpha.5'

conda/albany_supported.txt

@@ -1,8 +1,5 @@
 # a list of supported machine, compiler and mpi combinations for Albany
 
-anvil, gnu, openmpi
 chicoma-cpu, gnu, mpich
 chrysalis, gnu, openmpi
-compy, gnu, openmpi
-cori-haswell, gnu, mpt
 pm-cpu, gnu, mpich

conda/bootstrap.py

@@ -21,6 +21,7 @@
     get_logger,
     get_spack_base,
     install_miniconda,
+    log_message,
     parse_args,
 )
 
@@ -190,11 +191,9 @@ def get_env_setup(args, config, machine, compiler, mpi, env_type, source_path,
 
     if args.with_petsc:
         lib_suffix = f'{lib_suffix}_petsc'
-        message = 'Turning off OpenMP because it doesn\'t work well with PETSc'
-        if logger is None:
-            print(message)
-        else:
-            logger.info(message)
+        log_message(
+            logger,
+            'Turning off OpenMP because it doesn\'t work well with PETSc')
         args.without_openmp = True
     else:
         config.set('deploy', 'petsc', 'None')
@@ -389,6 +388,7 @@ def build_spack_env(config, update_spack, machine, compiler, mpi, spack_env,
                     spack_base, spack_template_path, env_vars, tmpdir, logger):
 
     albany = config.get('deploy', 'albany')
+    cmake = config.get('deploy', 'cmake')
     esmf = config.get('deploy', 'esmf')
     lapack = config.get('deploy', 'lapack')
     petsc = config.get('deploy', 'petsc')
@@ -398,39 +398,46 @@ def build_spack_env(config, update_spack, machine, compiler, mpi, spack_env,
 
     specs = list()
 
+    if cmake != 'None':
+        specs.append(f'cmake "@{cmake}"')
+
     e3sm_hdf5_netcdf = config.getboolean('deploy', 'use_e3sm_hdf5_netcdf')
     if not e3sm_hdf5_netcdf:
         hdf5 = config.get('deploy', 'hdf5')
         netcdf_c = config.get('deploy', 'netcdf_c')
         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~pio+pnetcdf')
+        specs.append(f'esmf "@{esmf}+mpi+netcdf~pio+pnetcdf"')
     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 petsc != 'None':
-        specs.append(f'petsc@{petsc}+mpi+batch')
+        specs.append(f'petsc "@{petsc}+mpi+batch"')
 
     if scorpio != 'None':
         specs.append(
-            f'scorpio@{scorpio}+pnetcdf~timing+internal-timing~tools+malloc')
+            f'scorpio '
+            f'"@{scorpio}+pnetcdf~timing+internal-timing~tools+malloc"')
 
     if albany != 'None':
-        specs.append(f'albany@{albany}+mpas')
+        specs.append(f'albany "@{albany}+mpas"')
 
     yaml_template = f'{spack_template_path}/{machine}_{compiler}_{mpi}.yaml'
     if not os.path.exists(yaml_template):
         yaml_template = None
     if update_spack:
+        home_dir = os.path.expanduser('~')
+        log_message(logger, 'Removing ~/.spack for safety')
+        safe_rmtree(os.path.join(home_dir, '.spack'))
         make_spack_env(spack_path=spack_branch_base, env_name=spack_env,
                        spack_specs=specs, compiler=compiler, mpi=mpi,
                        machine=machine,
@@ -792,6 +799,13 @@ def check_supported(library, machine, compiler, mpi, source_path):
                      f'on {machine}')
 
 
+def safe_rmtree(path):
+    try:
+        shutil.rmtree(path)
+    except OSError:
+        pass
+
+
 def main():  # noqa: C901
     args = parse_args(bootstrap=True)
 
@@ -871,10 +885,7 @@ def main():  # noqa: C901
 
         build_dir = f'conda/build{activ_suffix}'
 
-        try:
-            shutil.rmtree(build_dir)
-        except OSError:
-            pass
+        safe_rmtree(build_dir)
         try:
             os.makedirs(build_dir)
         except FileExistsError:

conda/compass_env/spec-file.template

@@ -16,7 +16,7 @@ jigsawpy=0.3.3
 jupyter
 lxml
 {% if include_mache %}
-mache=1.10.0
+mache=1.14.0
 {% endif %}
 matplotlib-base
 metis

conda/configure_compass_env.py

@@ -101,7 +101,7 @@ def main():
     if local_mache:
         mache = ''
     else:
-        mache = '"mache=1.10.0"'
+        mache = '"mache=1.14.0"'
 
     setup_install_env(env_name, activate_base, args.use_local, logger,
                       args.recreate, conda_base, mache)

conda/default.cfg

@@ -21,6 +21,8 @@ mpi = nompi
 
 # the version of various packages to include if using spack
 albany = develop
+# cmake newer than 3.23.0 needed for Trilinos
+cmake = 3.23.0:
 esmf = 8.2.0
 hdf5 = 1.12.1
 lapack = 3.9.1

conda/petsc_supported.txt

@@ -7,7 +7,4 @@ chicoma-cpu, gnu, mpich
 chrysalis, intel, openmpi
 chrysalis, gnu, openmpi
 compy, intel, impi
-compy, gnu, openmpi
-cori-haswell, intel, mpt
-cori-haswell, gnu, mpt
 pm-cpu, gnu, mpich

conda/recipe/meta.yaml

@@ -1,5 +1,5 @@
 {% set name = "compass" %}
-{% set version = "1.2.0alpha.4" %}
+{% set version = "1.2.0alpha.5" %}
 {% set build = 0 %}
 
 {% if mpi == "nompi" %}
@@ -52,7 +52,7 @@ requirements:
     - jigsawpy 0.3.3
     - jupyter
     - lxml
-    - mache 1.10.0
+    - mache 1.14.0
     - matplotlib-base
     - metis
     - mpas_tools 0.19.0

conda/shared.py

@@ -220,6 +220,13 @@ def restore_bashrc():
             shutil.move(src, dst)
 
 
+def log_message(logger, message):
+    if logger is None:
+        print(message)
+    else:
+        logger.info(message)
+
+
 def get_logger(name, log_filename):
     print(f'Logging to: {log_filename}\n')
     try:

conda/unsupported.txt

@@ -9,6 +9,7 @@ chrysalis, gnu, impi
 chrysalis, oneapi-ifx, openmpi
 chrysalis, oneapi-ifx, impi
 compy, intel, mvapich2
+compy, gnu, openmpi
 compy, pgi, impi
 compy, pgi, mvapich2
 pm-cpu, nvidia, mpich

docs/design_docs/compass_package.rst

@@ -2208,7 +2208,6 @@ The available machines are listed with:
     Machines:
        anvil
        default
-       cori-haswell
        chrysalis
        compy
 

docs/developers_guide/machines/index.rst

@@ -63,10 +63,6 @@ the MPAS model.
 |              +------------+-----------+-------------------+
 |              | gnu        | openmpi   | gfortran          |
 +--------------+------------+-----------+-------------------+
-| cori-haswell | intel      | mpt       | intel-cray        |
-|              +------------+-----------+-------------------+
-|              | gnu        | mpt       | gnu-cray          |
-+--------------+------------+-----------+-------------------+
 | pm-cpu       | gnu        | mpich     | gnu-cray          |
 +--------------+------------+-----------+-------------------+
 
@@ -79,7 +75,6 @@ Below are specifics for each supported machine
    chicoma
    chrysalis
    compy
-   cori
    perlmutter