Merge pull request #793 from xylar/update-to-1.3.0-alpha.1

Update to compass v1.3.0-alpha.1

compass/landice/tests/circular_shelf/albany_input.yaml

@@ -1,8 +1,6 @@
 %YAML 1.1
 ---
 ANONYMOUS:
-  Build Type: Tpetra
-
   Problem:
     LandIce Viscosity:
       Type: 'Glen''s Law'

compass/landice/tests/dome/albany_input.yaml

@@ -1,8 +1,6 @@
 %YAML 1.1
 ---
 ANONYMOUS:
-  Build Type: Tpetra
-
   Problem:
     LandIce Viscosity:
       Type: 'Glen''s Law'

compass/landice/tests/ensemble_generator/albany_input.yaml

@@ -1,8 +1,6 @@
 %YAML 1.1
 ---
 ANONYMOUS:
-  Build Type: Tpetra
-
   Problem:
     LandIce Field Norm:
       sliding_velocity_basalside:

compass/landice/tests/greenland/albany_input.yaml

@@ -1,8 +1,6 @@
 %YAML 1.1
 ---
 ANONYMOUS:
-  Build Type: Tpetra
-
 # Discretization Description
   Discretization:
     Exodus Output File Name: albany_output.exo

compass/landice/tests/humboldt/albany_input.yaml

@@ -1,8 +1,6 @@
 %YAML 1.1
 ---
 ANONYMOUS:
-  Build Type: Tpetra
-
   Problem:
     LandIce Field Norm:
       sliding_velocity_basalside:

compass/landice/tests/humboldt/albany_input_depthInt.yaml

@@ -1,8 +1,6 @@
 %YAML 1.1
 ---
 ANONYMOUS:
-  Build Type: Tpetra
-
   Problem:
     LandIce Field Norm:
       sliding_velocity_basalside:

compass/landice/tests/ismip6_run/ismip6_ais_proj2300/albany_input.yaml

@@ -1,10 +1,6 @@
 %YAML 1.1
 ---
 ANONYMOUS:
-# In order to use ML, change Tpetra to Epetra in the following line,
-# and "Preconditioner Type: MueLu" to " Preconditioner Type: ML" several lines below
-  Build Type: Tpetra
-
   Problem:
     LandIce Field Norm:
       sliding_velocity_basalside:

compass/landice/tests/mismipplus/albany_input.yaml

@@ -1,8 +1,6 @@
 %YAML 1.1
 ---
 ANONYMOUS:
-  Build Type: Tpetra
-
   Problem:
     Dirichlet BCs:
       SDBC on NS dirichlet for DOF U1 prescribe Field: dirichlet_field

compass/landice/tests/thwaites/albany_input.yaml

@@ -1,8 +1,6 @@
 %YAML 1.1
 ---
 ANONYMOUS:
-  Build Type: Tpetra
-
 # Problem Description
   Problem:
     Cubature Degree: 4

compass/landice/tests/thwaites/albany_input_depthInt.yaml

@@ -1,8 +1,6 @@
 %YAML 1.1
 ---
 ANONYMOUS:
-  Build Type: Tpetra
-
   Problem:
     Depth Integrated Model: true
 

compass/machines/chicoma-cpu.cfg

@@ -28,6 +28,8 @@ spack = /usr/projects/e3sm/compass/chicoma-cpu/spack
 # pnetcdf as E3SM (spack modules are used otherwise)
 use_e3sm_hdf5_netcdf = True
 
+# location of a spack mirror for compass to use
+spack_mirror = /usr/projects/e3sm/compass/chicoma-cpu/spack/spack_mirror
 
 # The parallel section describes options related to running jobs in parallel
 [parallel]

compass/ocean/suites/nonhydro.txt

@@ -0,0 +1,2 @@
+ocean/nonhydro/solitary_wave
+ocean/nonhydro/stratified_seiche

compass/version.py

@@ -1 +1 @@
-__version__ = '1.2.0-alpha.9'
+__version__ = '1.3.0-alpha.1'

conda/bootstrap.py

@@ -340,50 +340,15 @@ def build_conda_env(env_type, recreate, mpi, conda_mpi, version,
             check_call(commands, logger=logger)
 
         if recreate or update_jigsaw:
-            # remove conda jigsaw and jigsaw-python
-            t0 = time.time()
-            commands = \
-                f'{activate_env} && ' \
-                f'conda remove -y --force-remove jigsaw jigsawpy'
-            check_call(commands, logger=logger)
-
-            commands = \
-                f'{activate_env} && ' \
-                f'cd {source_path} && ' \
-                f'git submodule update --init jigsaw-python'
-            check_call(commands, logger=logger)
-
-            print('Building JIGSAW\n')
-            # add build tools to deployment env, not compass env
-            commands = \
-                f'conda install -y cmake cxx-compiler && ' \
-                f'cd {source_path}/jigsaw-python && ' \
-                f'python setup.py build_external'
-            check_call(commands, logger=logger)
-
-            print('Installing JIGSAW and JIGSAW-Python\n')
-            commands = \
-                f'{activate_env} && ' \
-                f'cd {source_path}/jigsaw-python && ' \
-                f'python -m pip install --no-deps -e . && ' \
-                f'cp jigsawpy/_bin/* ${{CONDA_PREFIX}}/bin'
-            check_call(commands, logger=logger)
-
-            t1 = time.time()
-            total = t1 - t0
-            message = f'JIGSAW install took {total:.1f} s.'
-            if logger is None:
-                print(message)
-            else:
-                logger.info(message)
+            build_jigsaw(activate_env, source_path, env_path, logger)
 
         # install (or reinstall) compass in edit mode
         print('Installing compass\n')
         commands = \
             f'{activate_env} && ' \
             f'cd {source_path} && ' \
             f'rm -rf compass.egg-info && ' \
-            f'python -m pip install -e .'
+            f'python -m pip install --no-deps -e .'
         check_call(commands, logger=logger)
 
         print('Installing pre-commit\n')
@@ -394,6 +359,57 @@ def build_conda_env(env_type, recreate, mpi, conda_mpi, version,
         check_call(commands, logger=logger)
 
 
+def build_jigsaw(activate_env, source_path, env_path, logger):
+    # remove conda jigsaw and jigsaw-python
+    t0 = time.time()
+    commands = \
+        f'{activate_env} && ' \
+        f'conda remove -y --force-remove jigsaw jigsawpy'
+    check_call(commands, logger=logger)
+
+    commands = \
+        f'{activate_env} && ' \
+        f'cd {source_path} && ' \
+        f'git submodule update --init jigsaw-python'
+    check_call(commands, logger=logger)
+
+    print('Building JIGSAW\n')
+    # add build tools to deployment env, not compass env
+    jigsaw_build_deps = 'cxx-compiler cmake'
+    netcdf_lib = f'{env_path}/lib/libnetcdf.so'
+    cmake_args = f'-DCMAKE_BUILD_TYPE=Release -DNETCDF_LIBRARY={netcdf_lib}'
+
+    commands = \
+        f'conda install -y {jigsaw_build_deps} && ' \
+        f'cd {source_path}/jigsaw-python/external/jigsaw && ' \
+        f'rm -rf tmp && ' \
+        f'mkdir tmp && ' \
+        f'cd tmp && ' \
+        f'cmake .. {cmake_args} && ' \
+        f'cmake --build . --config Release --target install --parallel 4 && ' \
+        f'cd {source_path}/jigsaw-python && ' \
+        f'rm -rf jigsawpy/_bin jigsawpy/_lib && ' \
+        f'cp -r external/jigsaw/bin/ jigsawpy/_bin && ' \
+        f'cp -r external/jigsaw/lib/ jigsawpy/_lib'
+    check_call(commands, logger=logger)
+
+    print('Installing JIGSAW and JIGSAW-Python\n')
+    commands = \
+        f'{activate_env} && ' \
+        f'cd {source_path}/jigsaw-python && ' \
+        f'python -m pip install --no-deps -e . && ' \
+        f'cp jigsawpy/_bin/* ${{CONDA_PREFIX}}/bin'
+    check_call(commands, logger=logger)
+
+    t1 = time.time()
+    total = int(t1 - t0 + 0.5)
+    message = f'JIGSAW install took {total:.1f} s.'
+    if logger is None:
+        print(message)
+    else:
+        logger.info(message)
+
+
 def get_env_vars(machine, compiler, mpilib):
 
     if machine is None:
@@ -449,10 +465,16 @@ def build_spack_env(config, update_spack, machine, compiler, mpi,  # noqa: C901
     cmake = config.get('deploy', 'cmake')
     esmf = config.get('deploy', 'esmf')
     lapack = config.get('deploy', 'lapack')
+    moab = config.get('deploy', 'moab')
     petsc = config.get('deploy', 'petsc')
     scorpio = config.get('deploy', 'scorpio')
     parallelio = config.get('deploy', 'parallelio')
 
+    if config.has_option('deploy', 'spack_mirror'):
+        spack_mirror = config.get('deploy', 'spack_mirror')
+    else:
+        spack_mirror = None
+
     spack_branch_base = f'{spack_base}/{spack_env}'
 
     specs = list()
@@ -479,6 +501,9 @@ def build_spack_env(config, update_spack, machine, compiler, mpi,  # noqa: C901
         include_e3sm_lapack = False
     else:
         include_e3sm_lapack = True
+    if moab != 'None':
+        specs.append(
+            f'"moab@{moab}+mpi+hdf5+netcdf+pnetcdf+metis+parmetis+tempest"')
     if petsc != 'None':
         specs.append(f'"petsc@{petsc}+mpi+batch"')
 
@@ -503,7 +528,7 @@ def build_spack_env(config, update_spack, machine, compiler, mpi,  # noqa: C901
 
     if albany != 'None':
         specs.append(f'"trilinos-for-albany@{albany}"')
-        specs.append(f'"albany@{albany}+mpas"')
+        specs.append(f'"albany@{albany}+mpas~py+unit_tests"')
 
     yaml_template = f'{spack_template_path}/{machine}_{compiler}_{mpi}.yaml'
     if not os.path.exists(yaml_template):
@@ -526,7 +551,7 @@ def build_spack_env(config, update_spack, machine, compiler, mpi,  # noqa: C901
                        include_e3sm_lapack=include_e3sm_lapack,
                        include_e3sm_hdf5_netcdf=e3sm_hdf5_netcdf,
                        yaml_template=yaml_template, tmpdir=tmpdir,
-                       custom_spack=custom_spack)
+                       custom_spack=custom_spack, spack_mirror=spack_mirror)
 
         # remove ESMC/ESMF include files that interfere with MPAS time keeping
         include_path = f'{spack_branch_base}/var/spack/environments/' \
@@ -645,11 +670,11 @@ def write_load_compass(template_path, activ_path, conda_base, env_type,
                mkdir -p conda/logs
                echo Reinstalling compass package in edit mode...
                rm -rf compass.egg-info
-               python -m pip install -e . &> conda/logs/install_compass.log
+               python -m pip install --no-deps -e . &> conda/logs/install_compass.log
                echo Done.
                echo
             fi
-            """
+            """  # noqa: E501
     else:
         update_compass = ''
 
@@ -1049,7 +1074,7 @@ def main():  # noqa: C901
                 commands = f'source {conda_base}/etc/profile.d/conda.sh && ' \
                            f'conda activate {conda_env_name} && ' \
                            'cd ../build_mache/mache && ' \
-                           'python -m pip install .'
+                           'python -m pip install --no-deps .'
                 check_call(commands, logger=logger)
 
             previous_conda_env = conda_env_name

conda/compass_env/spec-file.template

@@ -6,7 +6,7 @@ python>=3.8
 cartopy
 cartopy_offlinedata
 cmocean
-esmf=*={{ mpi_prefix }}_*
+esmf=8.6.0={{ mpi_prefix }}_*
 ffmpeg
 geometric_features=1.3.0
 git
@@ -16,11 +16,13 @@ ipython
 jupyter
 lxml
 {% if include_mache %}
-mache=1.17.0
+mache=1.20.0
 {% endif %}
 matplotlib-base
 metis
-mpas_tools=0.29.0
+moab >=5.5.1
+moab=*={{ mpi_prefix }}_tempest_*
+mpas_tools=0.32.0
 nco
 netcdf4=*=nompi_*
 numpy
@@ -30,7 +32,7 @@ otps=2021.10
 progressbar2
 pyamg >=4.2.2
 pyproj
-pyremap>=1.1.0,<2.0.0
+pyremap>=1.3.0,<2.0.0
 requests
 ruamel.yaml
 # having pip check problems with this version

conda/configure_compass_env.py

@@ -100,7 +100,7 @@ def main():
     if local_mache:
         mache = ''
     else:
-        mache = '"mache=1.17.0"'
+        mache = '"mache=1.20.0"'
 
     setup_install_env(env_name, activate_base, args.use_local, logger,
                       args.recreate, conda_base, mache)
@@ -114,7 +114,7 @@ def main():
                    f'git clone -b {args.mache_branch} ' \
                    f'[email protected]:{args.mache_fork}.git mache && ' \
                    f'cd mache && ' \
-                   f'python -m pip install .'
+                   f'python -m pip install --no-deps .'
 
         check_call(commands, logger=logger)
 

conda/default.cfg

@@ -14,22 +14,23 @@ recreate = False
 suffix =
 
 # the python version
-python = 3.10
+python = 3.11
 
 # the MPI version (nompi, mpich or openmpi)
 mpi = nompi
 
 # the version of various packages to include if using spack
-albany = compass-2023-08-03
+albany = compass-2024-03-13
 # cmake newer than 3.23.0 needed for Trilinos
 cmake = 3.23.0:
-esmf = 8.4.2
-hdf5 = 1.14.1
+esmf = 8.6.0
+hdf5 = 1.14.3
 lapack = 3.9.1
+moab = 5.5.1
 netcdf_c = 4.9.2
 netcdf_fortran = 4.6.0
 petsc = 3.19.1
 pnetcdf = 1.12.3
-scorpio = 1.4.1
-# parallelio = 2.5.10
+scorpio = 1.6.0
+# parallelio = 2.6.2
 parallelio = None