Update to 0.10.0-alpha.1

.github/workflows/build_workflow.yml

@@ -118,6 +118,9 @@ jobs:
             source load_polaris_test_mpich.sh
           fi
           python -c "import polaris; import polaris.version; print(polaris.version.__version__)"
+          polaris --help
+          polaris list --help
+          polaris list
 
       - if: ${{ steps.skip_check.outputs.should_skip != 'true' }}
         name: Build Sphinx Docs

configure_polaris_envs.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python3
 import os
 import sys
-from configparser import ConfigParser
+from configparser import ConfigParser, ExtendedInterpolation
 
 from deploy.shared import (
     check_call,
@@ -105,7 +105,7 @@ def _get_config(config_file):
     # we can't load polaris so we find the config files
     here = os.path.abspath(os.path.dirname(__file__))
     default_config = os.path.join(here, 'deploy/default.cfg')
-    config = ConfigParser()
+    config = ConfigParser(interpolation=ExtendedInterpolation())
     config.read(default_config)
 
     if config_file is not None:

deploy/albany_supported.txt

@@ -1,9 +1,6 @@
 # a list of supported machine, compiler and mpi combinations for Albany
 
-anvil, gnu, openmpi
-chicoma-cpu, gnu, mpich
 chrysalis, gnu, openmpi
-compy, gnu, openmpi
 frontier, craygnu, mpich
 frontier, craygnu-mphipcc, mpich
 frontier, craycray, mpich

deploy/bootstrap.py

@@ -10,7 +10,7 @@
 import stat
 import subprocess
 import time
-from configparser import ConfigParser
+from configparser import ConfigParser, ExtendedInterpolation
 from typing import Dict
 
 import progressbar
@@ -269,7 +269,7 @@ def _get_config(config_file, machine):
     # we can't load polaris so we find the config files
     here = os.path.abspath(os.path.dirname(__file__))
     default_config = os.path.join(here, 'default.cfg')
-    config = ConfigParser()
+    config = ConfigParser(interpolation=ExtendedInterpolation())
     config.read(default_config)
 
     if machine is not None:
@@ -554,7 +554,7 @@ def _build_conda_env(options, activate_base):
     else:
         mpi_prefix = f'mpi_{conda_mpi}'
 
-    channel_list = ['-c conda-forge', '-c defaults']
+    channel_list = ['-c conda-forge']
     if use_local:
         channel_list = ['--use-local'] + channel_list
     if local_conda_build is not None:
@@ -772,15 +772,6 @@ def _get_env_vars(machine, compiler, mpi):
 
     env_vars = f'{env_vars}export MPAS_EXTERNAL_LIBS=""\n'
 
-    if 'intel' in compiler and machine == 'anvil':
-        env_vars = (
-            f'{env_vars}'
-            f'export I_MPI_CC=icc\n'
-            f'export I_MPI_CXX=icpc\n'
-            f'export I_MPI_F77=ifort\n'
-            f'export I_MPI_F90=ifort\n'
-        )
-
     if machine.startswith('conda'):
         # we're using parallelio so we don't have ADIOS support
         env_vars = f'{env_vars}export HAVE_ADIOS=false\n'
@@ -869,6 +860,7 @@ def _build_spack_soft_env(options):  # noqa: C901
     os.chdir(build_dir)
 
     esmf = config.get('deploy', 'esmf')
+    moab = config.get('deploy', 'spack_moab')
 
     if config.has_option('deploy', 'spack_mirror'):
         spack_mirror = config.get('deploy', 'spack_mirror')
@@ -895,6 +887,11 @@ def _build_spack_soft_env(options):  # noqa: C901
     if esmf != 'None':
         specs.append(f'esmf@{esmf}+mpi+netcdf~pnetcdf~external-parallelio')
 
+    if moab != 'None':
+        specs.append(
+            f'moab@{moab}+eigen+fortran+hdf5+mpi+netcdf+pnetcdf+zoltan+tempest'
+        )
+
     yaml_template: str | None = None
     template_path = f'{spack_template_path}/{machine}_{compiler}_{mpi}.yaml'
     if os.path.exists(template_path):
@@ -950,7 +947,6 @@ def _build_spack_libs_env(options, compiler, mpi, env_vars):  # noqa: C901
     cmake = config.get('deploy', 'cmake')
     lapack = config.get('deploy', 'lapack')
     metis = config.get('deploy', 'metis')
-    moab = config.get('deploy', 'spack_moab')
     parmetis = config.get('deploy', 'parmetis')
     petsc = config.get('deploy', 'petsc')
     scorpio = config.get('deploy', 'scorpio')
@@ -984,10 +980,6 @@ def _build_spack_libs_env(options, compiler, mpi, env_vars):  # noqa: C901
         include_e3sm_lapack = True
     if metis != 'None':
         specs.append(f'metis@{metis}+int64+real64~shared')
-    if moab != 'None':
-        specs.append(
-            f'moab@{moab}+mpi+hdf5+netcdf+pnetcdf+metis+parmetis+tempest'
-        )
     if parmetis != 'None':
         specs.append(f'parmetis@{parmetis}+int64~shared')
     if petsc != 'None':
@@ -1038,10 +1030,8 @@ def _build_spack_libs_env(options, compiler, mpi, env_vars):  # noqa: C901
         mpi=mpi,
         shell='sh',
         machine=machine,
-        config_file=machine_config,
         include_e3sm_lapack=include_e3sm_lapack,
         include_e3sm_hdf5_netcdf=e3sm_hdf5_netcdf,
-        yaml_template=yaml_template,
     )
 
     spack_view = (
@@ -1064,7 +1054,7 @@ def _build_spack_libs_env(options, compiler, mpi, env_vars):  # noqa: C901
             stdcxx = '-lc++'
         else:
             stdcxx = '-lstdc++'
-        if mpi == 'openmpi' and machine in ['anvil', 'chrysalis']:
+        if mpi == 'openmpi' and machine in ['chrysalis']:
             mpicxx = '-lmpi_cxx'
         else:
             mpicxx = ''
@@ -1517,7 +1507,7 @@ def _get_possible_hosts():
     possible_hosts = dict()
     for filename in files:
         machine = os.path.splitext(os.path.split(filename)[1])[0]
-        config = ConfigParser()
+        config = ConfigParser(interpolation=ExtendedInterpolation())
         config.read(filename)
         if config.has_section('discovery') and config.has_option(
             'discovery', 'hostname_contains'

deploy/conda-dev-spec.template

@@ -11,9 +11,9 @@ importlib_resources
 ipython
 jupyter
 lxml
-{% if include_mache %}
+{%- if include_mache %}
 mache={{ mache }}
-{% endif %}
+{%- endif %}
 matplotlib-base>=3.9.0
 metis={{ metis }}
 moab={{ moab }}=*_tempest_*
@@ -22,9 +22,9 @@ mpas_tools={{ mpas_tools }}
 nco
 netcdf4=*=nompi_*
 numpy>=2.0,<3.0
-{% if supports_otps %}
+{%- if supports_otps %}
 otps={{ otps }}
-{% endif %}
+{%- endif %}
 progressbar2
 pyamg>=4.2.2
 pyproj
@@ -49,7 +49,7 @@ pre-commit
 ruff
 
 # Development
-{% if mpi != "nompi" %}
+{%- if mpi != "nompi" %}
 c-compiler
 cmake
 cxx-compiler
@@ -62,7 +62,7 @@ m4
 make
 {{ mpi }}
 {{ openmp }}
-{% endif %}
+{%- endif %}
 
 # CF-compliance
 cfchecker

deploy/default.cfg

@@ -21,26 +21,26 @@ mpi = nompi
 
 # versions of conda packages
 geometric_features = 1.6.1
-mache = 1.32.0
-conda_moab = 5.5.1
-mpas_tools = 1.3.2
+mache = 2.1.0
+conda_moab = 5.6.0
+mpas_tools = 1.4.0
 otps = 2021.10
 parallelio = 2.6.6
 
 # versions of conda or spack packages (depending on machine type)
 esmf = 8.9.0
 metis = 5.1.0
-netcdf_c = 4.9.2
+netcdf_c = 4.9.3
 netcdf_fortran = 4.6.2
-pnetcdf = 1.14.0
+pnetcdf = 1.14.1
 
 # versions of spack packages
 albany = developcompass-2024-03-13
 # cmake newer than 3.23.0 needed for Trilinos
 cmake = 3.23.0:
 hdf5 = 1.14.6
 lapack = 3.9.1
-spack_moab = master
+spack_moab = ${conda_moab}
 parmetis = 4.0.3
 petsc = 3.19.1
 scorpio = 1.8.2

deploy/petsc_supported.txt

@@ -1,11 +1,7 @@
 # a list of supported machine, compiler and mpi combinations for Netlib LAPACK
 # and PETSc
 
-anvil, intel, impi
-anvil, gnu, openmpi
-chicoma-cpu, gnu, mpich
 chrysalis, intel, openmpi
 chrysalis, gnu, openmpi
-compy, intel, impi
 frontier, craygnu, mpich
 pm-cpu, gnu, mpich

deploy/unsupported.txt

@@ -1,23 +1,9 @@
 # a list of unsupported machine, compiler and mpi combinations
 
 # no spack available
-anvil, gnu, impi
-chicoma-cpu, aocc, mpich
-chicoma-cpu, amdclang, mpich
 chrysalis, intel, impi
 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, aocc, mpich
 pm-cpu, amdclang, mpich
-
-# cannot build MOAB in spack
-anvil, gnu, mvapich
-
-# compiles but tests unreliable (errors or hanging),
-# see https://github.com/MPAS-Dev/compass/issues/336
-anvil, intel, mvapich

docs/developers_guide/command_line.md

@@ -334,9 +334,9 @@ so that new revisions can be added without removing older ones (supported by
 older polaris versions).  See {ref}`dev-step-cached-output` for more details.
 
 The command `polaris cache` is used to update the file `cached_files.json`
-within a component.  This command is only available on Anvil and Chrysalis,
+within a component.  This command is only available on Chrysalis,
 since developers can only copy files from a Polaris work directory onto the
-LCRC server from these two machines.
+LCRC server from Chrysalis.
 ```none
 $ polaris cache --help
 usage: polaris cache [-h] [-i STEP [STEP ...]] [-d DATE] [-r]

docs/developers_guide/framework/build.md

@@ -34,7 +34,7 @@ Common:
   submodules and templates)
 
 MPAS-Ocean:
-- `POLARIS_MACHINE` — machine ID used by the template (e.g., chrysalis, anvil)
+- `POLARIS_MACHINE` — machine ID used by the template (e.g., chrysalis, frontier)
 - `POLARIS_COMPILER` — compiler toolchain ID (e.g., intel, gnu)
 - `POLARIS_MPI` — MPI library ID (e.g., openmpi, mpich)
 - `LOAD_POLARIS_ENV` — path to the shell snippet used to load the Polaris build

docs/developers_guide/machines/aurora.md

@@ -0,0 +1,14 @@
+(dev-machine-aurora)=
+
+# Aurora
+
+## oneapi-ifx
+
+This is the default polaris compiler on Aurora.  If the environment has
+been set up properly (see {ref}`dev-conda-env`), you should be able to source:
+
+```bash
+source load_dev_polaris_0.10.0-alpha.1_aurora_oneapi-ifx_mpich.sh
+```
+
+MPAS components do not yet support Aurora, but Omega does.