From eb32d82ac17f2ac0d2dfe49cea5227367cf75424 Mon Sep 17 00:00:00 2001 From: Xylar Asay-Davis Date: Thu, 7 Nov 2024 20:56:05 -0600 Subject: [PATCH 01/11] Update to v0.5.0-alpha.1 --- polaris/version.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/polaris/version.py b/polaris/version.py index 339472a8c..7a35f4197 100644 --- a/polaris/version.py +++ b/polaris/version.py @@ -1 +1 @@ -__version__ = '0.4.0-alpha.2' +__version__ = '0.5.0-alpha.1' From d461d335194b28447bdc3008c5898d8b4171b844 Mon Sep 17 00:00:00 2001 From: Xylar Asay-Davis Date: Thu, 7 Nov 2024 21:06:08 -0600 Subject: [PATCH 02/11] Update dependency versions --- deploy/conda-dev-spec.template | 5 +---- deploy/default.cfg | 18 +++++++++--------- 2 files changed, 10 insertions(+), 13 deletions(-) diff --git a/deploy/conda-dev-spec.template b/deploy/conda-dev-spec.template index 718240d6c..084b772d4 100644 --- a/deploy/conda-dev-spec.template +++ b/deploy/conda-dev-spec.template @@ -1,8 +1,5 @@ -# This file may be used to create an environment using: -# $ conda create --name --file - # Base -python>=3.9,<=3.12 +python>=3.9,<3.13 antimeridian cartopy cartopy_offlinedata diff --git a/deploy/default.cfg b/deploy/default.cfg index 9ac940c4f..3adc5646b 100644 --- a/deploy/default.cfg +++ b/deploy/default.cfg @@ -20,26 +20,26 @@ python = 3.12 mpi = nompi # versions of conda packages -geometric_features = 1.2.0 -mache = 1.24.0 -mpas_tools = 0.34.1 +geometric_features = 1.5.0 +mache = 1.26.0 +mpas_tools = 0.35.0 otps = 2021.10 -parallelio = 2.6.2 +parallelio = 2.6.3 # versions of conda or spack packages (depending on machine type) -esmf = 8.6.1 +esmf = 8.7.0 metis = 5.1.0 -moab = 5.5.1 +moab = master netcdf_c = 4.9.2 netcdf_fortran = 4.6.1 pnetcdf = 1.13.0 # versions of spack packages -albany = develop +albany = developcompass-2024-03-13 # cmake newer than 3.23.0 needed for Trilinos cmake = 3.23.0: -hdf5 = 1.14.1 +hdf5 = 1.14.3 lapack = 3.9.1 parmetis = 4.0.3 petsc = 3.19.1 -scorpio = 1.4.2 +scorpio = 1.6.5 From b27d7d19e3cb4ccfa021c61a6a7c94bd93996968 Mon Sep 17 00:00:00 2001 From: Xylar Asay-Davis Date: Thu, 7 Nov 2024 21:10:24 -0600 Subject: [PATCH 03/11] Update E3SM-Project submodule to latest master --- e3sm_submodules/E3SM-Project | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/e3sm_submodules/E3SM-Project b/e3sm_submodules/E3SM-Project index ae514946f..67ae4d5d7 160000 --- a/e3sm_submodules/E3SM-Project +++ b/e3sm_submodules/E3SM-Project @@ -1 +1 @@ -Subproject commit ae514946f348917eaa3c23405447642a843f8436 +Subproject commit 67ae4d5d770e97ecf689aae239500de428d7153b From d50394ce782f06ee8f0f4a2152832ebd7dbc7373 Mon Sep 17 00:00:00 2001 From: Xylar Asay-Davis Date: Thu, 7 Nov 2024 21:10:38 -0600 Subject: [PATCH 04/11] Update MALI-Dev submodule to latest develop --- e3sm_submodules/MALI-Dev | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/e3sm_submodules/MALI-Dev b/e3sm_submodules/MALI-Dev index e23c40196..114c37340 160000 --- a/e3sm_submodules/MALI-Dev +++ b/e3sm_submodules/MALI-Dev @@ -1 +1 @@ -Subproject commit e23c401962f26fa2a9aee62eff3f54004aa759b0 +Subproject commit 114c37340c75a4c86e8d53e8bd042ffe37faf6c0 From c04f18d1730d53f3ab8f04fd258d545707bf50be Mon Sep 17 00:00:00 2001 From: Xylar Asay-Davis Date: Thu, 7 Nov 2024 21:11:04 -0600 Subject: [PATCH 05/11] Update Omega submodule to latest develop --- e3sm_submodules/Omega | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/e3sm_submodules/Omega b/e3sm_submodules/Omega index c80c46dd2..801ceaaf0 160000 --- a/e3sm_submodules/Omega +++ b/e3sm_submodules/Omega @@ -1 +1 @@ -Subproject commit c80c46dd200c6deb643d50354093b60b92374c83 +Subproject commit 801ceaaf0960b2ca4484227bbc63f5131c0735d1 From 623784166eac123d9a8d7ae3a1098324203eca72 Mon Sep 17 00:00:00 2001 From: Xylar Asay-Davis Date: Thu, 7 Nov 2024 21:54:06 -0600 Subject: [PATCH 06/11] Use separate versions of moab for conda and spack --- deploy/bootstrap.py | 6 ++++-- deploy/default.cfg | 3 ++- 2 files changed, 6 insertions(+), 3 deletions(-) diff --git a/deploy/bootstrap.py b/deploy/bootstrap.py index 61d0c837a..f52473c2a 100755 --- a/deploy/bootstrap.py +++ b/deploy/bootstrap.py @@ -563,11 +563,13 @@ def _build_conda_env(options, activate_base): mpi_prefix=mpi_prefix, include_mache=not local_mache) - for package in ['esmf', 'geometric_features', 'mache', 'metis', 'moab', + for package in ['esmf', 'geometric_features', 'mache', 'metis', 'mpas_tools', 'netcdf_c', 'netcdf_fortran', 'otps', 'parallelio', 'pnetcdf']: replacements[package] = config.get('deploy', package) + replacements['moab'] = config.get('deploy', 'conda_moab') + spec_file = template.render(**replacements) spec_filename = f'spec-file-{conda_mpi}.txt' @@ -868,7 +870,7 @@ 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', 'moab') + moab = config.get('deploy', 'spack_moab') parmetis = config.get('deploy', 'parmetis') petsc = config.get('deploy', 'petsc') scorpio = config.get('deploy', 'scorpio') diff --git a/deploy/default.cfg b/deploy/default.cfg index 3adc5646b..7a6f474dc 100644 --- a/deploy/default.cfg +++ b/deploy/default.cfg @@ -22,6 +22,7 @@ mpi = nompi # versions of conda packages geometric_features = 1.5.0 mache = 1.26.0 +conda_moab = 5.5.1 mpas_tools = 0.35.0 otps = 2021.10 parallelio = 2.6.3 @@ -29,7 +30,6 @@ parallelio = 2.6.3 # versions of conda or spack packages (depending on machine type) esmf = 8.7.0 metis = 5.1.0 -moab = master netcdf_c = 4.9.2 netcdf_fortran = 4.6.1 pnetcdf = 1.13.0 @@ -40,6 +40,7 @@ albany = developcompass-2024-03-13 cmake = 3.23.0: hdf5 = 1.14.3 lapack = 3.9.1 +spack_moab = master parmetis = 4.0.3 petsc = 3.19.1 scorpio = 1.6.5 From 4a30ebf8520f07c8d317ee7b3e7382c8df6b3ae3 Mon Sep 17 00:00:00 2001 From: Xylar Asay-Davis Date: Thu, 7 Nov 2024 22:25:13 -0600 Subject: [PATCH 07/11] fix _safe_stat() It needs to return the stat, and we need to continue if it returns None. --- deploy/bootstrap.py | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/deploy/bootstrap.py b/deploy/bootstrap.py index f52473c2a..6781d108b 100755 --- a/deploy/bootstrap.py +++ b/deploy/bootstrap.py @@ -1181,6 +1181,8 @@ def _update_permissions(options, directories): # noqa: C901 # os.walk() for directory in directories: dir_stat = _safe_stat(directory) + if dir_stat is None: + continue perm = dir_stat.st_mode & mask @@ -1220,6 +1222,8 @@ def _update_permissions(options, directories): # noqa: C901 directory = os.path.join(root, directory) dir_stat = _safe_stat(directory) + if dir_stat is None: + continue if dir_stat.st_uid != new_uid: # current user doesn't own this dir so let's move on @@ -1244,6 +1248,8 @@ def _update_permissions(options, directories): # noqa: C901 pass file_name = os.path.join(root, file_name) file_stat = _safe_stat(file_name) + if file_stat is None: + continue if file_stat.st_uid != new_uid: # current user doesn't own this file so let's move on @@ -1341,7 +1347,7 @@ def _safe_rmtree(path): @_ignore_file_errors def _safe_stat(path): - os.stat(path) + return os.stat(path) def _discover_machine(quiet=False): From 15ad6bb50da19850cfa7d8471de38d6846ccef0f Mon Sep 17 00:00:00 2001 From: Xylar Asay-Davis Date: Tue, 12 Nov 2024 20:13:22 -0600 Subject: [PATCH 08/11] Update to mpas_tools 0.36.0 --- deploy/default.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/deploy/default.cfg b/deploy/default.cfg index 7a6f474dc..8348cbdfc 100644 --- a/deploy/default.cfg +++ b/deploy/default.cfg @@ -23,7 +23,7 @@ mpi = nompi geometric_features = 1.5.0 mache = 1.26.0 conda_moab = 5.5.1 -mpas_tools = 0.35.0 +mpas_tools = 0.36.0 otps = 2021.10 parallelio = 2.6.3 From 2492cc71a8ca307d6bd63d1d63e70edfe5efecae Mon Sep 17 00:00:00 2001 From: Xylar Asay-Davis Date: Mon, 18 Nov 2024 09:46:00 -0600 Subject: [PATCH 09/11] Update Omega submodule This brings in newer modules needed for Chicoma --- e3sm_submodules/Omega | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/e3sm_submodules/Omega b/e3sm_submodules/Omega index 801ceaaf0..8247b3712 160000 --- a/e3sm_submodules/Omega +++ b/e3sm_submodules/Omega @@ -1 +1 @@ -Subproject commit 801ceaaf0960b2ca4484227bbc63f5131c0735d1 +Subproject commit 8247b3712c50d90da5e7ce68dbc7284ce3445b76 From 5a93c6b7f90bd6363c8d5009d590094e5e62579f Mon Sep 17 00:00:00 2001 From: Xylar Asay-Davis Date: Tue, 19 Nov 2024 15:07:36 -0600 Subject: [PATCH 10/11] Update to mache 1.27.0 --- deploy/default.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/deploy/default.cfg b/deploy/default.cfg index 8348cbdfc..90cc5cad5 100644 --- a/deploy/default.cfg +++ b/deploy/default.cfg @@ -21,7 +21,7 @@ mpi = nompi # versions of conda packages geometric_features = 1.5.0 -mache = 1.26.0 +mache = 1.27.0 conda_moab = 5.5.1 mpas_tools = 0.36.0 otps = 2021.10 From ee0da5aa89d691bb76ab6eef796b1ed637bf72d0 Mon Sep 17 00:00:00 2001 From: Xylar Asay-Davis Date: Wed, 20 Nov 2024 05:13:06 -0600 Subject: [PATCH 11/11] Fix exclude for setuptools We want to exclude deploy and utils because they aren't really part of the package. We definitely want to exlude e3sm_submodules because otherwise installation takes forever when submodules are checked out. --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index bef85afa2..c6cd82e41 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -62,7 +62,7 @@ requires = ["setuptools>=60"] build-backend = "setuptools.build_meta" [tool.setuptools.packages.find] -exclude = ["docs*", "conda*"] +exclude = ["deploy*", "docs*", "e3sm_submodules*", "licenses*", "utils*"] [tool.setuptools.dynamic] version = { attr = "polaris.version.__version__" }