Merge pull request #857 from xylar/update-to-1.5.0-alpha.1

Update to 1.5.0-alpha.1

compass/job/__init__.py

@@ -93,6 +93,12 @@ def write_job_script(config, machine, target_cores, min_cores, work_dir,
             job_name = 'compass'
         else:
             job_name = f'compass_{suite}'
+
+    if config.has_option('parallel', 'gpus_per_node'):
+        gpus_per_node = config.get('parallel', 'gpus_per_node')
+    else:
+        gpus_per_node = ''
+
     wall_time = config.get('job', 'wall_time')
 
     template = Template(resources.read_text(
@@ -101,7 +107,8 @@ def write_job_script(config, machine, target_cores, min_cores, work_dir,
     text = template.render(job_name=job_name, account=account,
                            nodes=f'{nodes}', wall_time=wall_time, qos=qos,
                            partition=partition, constraint=constraint,
-                           reservation=reservation, suite=suite,
+                           reservation=reservation,
+                           gpus_per_node=gpus_per_node, suite=suite,
                            pre_run_commands=pre_run_commands,
                            post_run_commands=post_run_commands)
     text = _clean_up_whitespace(text)

compass/job/job_script.template

@@ -19,6 +19,9 @@
 {% if constraint != '' -%}
 #SBATCH  --constraint={{ constraint }}
 {%- endif %}
+{% if gpus_per_node != '' -%}
+#SBATCH  --gpus-per-node={{ gpus_per_node }}
+{%- endif %}
 
 source load_compass_env.sh
 {{ pre_run_commands }}

compass/machines/pm-gpu.cfg

@@ -0,0 +1,44 @@
+
+# The paths section describes paths that are used within the ocean core test
+# cases.
+[paths]
+
+# A shared root directory where MPAS standalone data can be found
+database_root = /global/cfs/cdirs/e3sm/mpas_standalonedata
+
+# the path to the base conda environment where compass environments have
+# been created
+compass_envs = /global/common/software/e3sm/compass/pm-gpu/base
+
+
+# Options related to deploying a compass conda environment on supported
+# machines
+[deploy]
+
+# the compiler set to use for system libraries and MPAS builds
+compiler = gnugpu
+
+# the system MPI library to use for gnugpu compiler
+mpi_gnugpu = mpich
+
+# the system MPI library to use for nvidiagpu compiler
+mpi_nvidiagpu = mpich
+
+# the base path for spack environments used by compass
+spack = /global/cfs/cdirs/e3sm/software/compass/pm-gpu/spack
+
+# whether to use the same modules for hdf5, netcdf-c, netcdf-fortran and
+# pnetcdf as E3SM (spack modules are used otherwise)
+use_e3sm_hdf5_netcdf = True
+
+# The parallel section describes options related to running jobs in parallel.
+# Most options in this section come from mache so here we just add or override
+# some defaults
+[parallel]
+
+# cores per node on the machine
+cores_per_node = 64
+
+# threads per core (set to 1 because trying to hyperthread seems to be causing
+# hanging on perlmutter)
+threads_per_core = 1

compass/parallel.py

@@ -66,6 +66,11 @@ def get_available_parallel_resources(config):
         cores_per_node=cores_per_node,
         mpi_allowed=mpi_allowed
     )
+
+    if config.has_option('parallel', 'gpus_per_node'):
+        available_resources['gpus_per_node'] = \
+            config.getint('parallel', 'gpus_per_node')
+
     return available_resources
 
 

compass/version.py

@@ -1 +1 @@
-__version__ = '1.4.0-alpha.7'
+__version__ = '1.5.0-alpha.1'

conda/albany_supported.txt

@@ -3,4 +3,5 @@
 chicoma-cpu, gnu, mpich
 chrysalis, gnu, openmpi
 pm-cpu, gnu, mpich
+pm-gpu, gnugpu, mpich
 morpheus, gnu, openmpi

conda/bootstrap.py

@@ -476,6 +476,9 @@ def build_spack_env(config, update_spack, machine, compiler, mpi,  # noqa: C901
     scorpio = config.get('deploy', 'scorpio')
     parallelio = config.get('deploy', 'parallelio')
 
+    # for now, we'll assume Cuda is needed anytime GPUs are present
+    with_cuda = config.has_option('parallel', 'gpus_per_node')
+
     if config.has_option('deploy', 'spack_mirror'):
         spack_mirror = config.get('deploy', 'spack_mirror')
     else:
@@ -536,8 +539,14 @@ def build_spack_env(config, update_spack, machine, compiler, mpi,  # noqa: C901
             f'@{parallelio}+pnetcdf~timing"')
 
     if albany != 'None':
-        specs.append(f'"trilinos-for-albany@{albany}"')
-        specs.append(f'"albany@{albany}+mpas~py+unit_tests"')
+        if with_cuda:
+            albany_cuda = '+cuda+uvm+sfad sfadsize=12'
+            trilinos_cuda = '+cuda+uvm'
+        else:
+            albany_cuda = ''
+            trilinos_cuda = ''
+        specs.append(f'"trilinos-for-albany@{albany}{trilinos_cuda}"')
+        specs.append(f'"albany@{albany}+mpas~py+unit_tests{albany_cuda}"')
 
     yaml_template = f'{spack_template_path}/{machine}_{compiler}_{mpi}.yaml'
     if not os.path.exists(yaml_template):
@@ -1082,8 +1091,9 @@ def main():  # noqa: C901
                 print('Install local mache\n')
                 commands = f'source {conda_base}/etc/profile.d/conda.sh && ' \
                            f'conda activate {conda_env_name} && ' \
-                           'cd ../build_mache/mache && ' \
-                           'python -m pip install --no-deps .'
+                           f'cd ../build_mache/mache && ' \
+                           f'conda install -y --file spec-file.txt && ' \
+                           f'python -m pip install --no-deps .'
                 check_call(commands, logger=logger)
 
             previous_conda_env = conda_env_name

conda/compass_env/spec-file.template

@@ -16,7 +16,7 @@ ipython
 jupyter
 lxml
 {% if include_mache %}
-mache=1.23.0
+mache=1.25.0
 {% endif %}
 matplotlib-base >=3.9.1
 metis
@@ -49,8 +49,8 @@ cmake
 cxx-compiler
 fortran-compiler
 libnetcdf=4.9.2={{ mpi_prefix }}_*
-libpnetcdf=1.12.3={{ mpi_prefix }}_*
-parallelio=2.6.2={{ mpi_prefix }}_*
+libpnetcdf=1.13.0={{ mpi_prefix }}_*
+parallelio=2.6.3={{ mpi_prefix }}_*
 m4
 make
 {{ mpi }}

conda/configure_compass_env.py

@@ -100,7 +100,7 @@ def main():
     if local_mache:
         mache = ''
     else:
-        mache = '"mache=1.23.0"'
+        mache = '"mache=1.25.0"'
 
     setup_install_env(env_name, activate_base, args.use_local, logger,
                       args.recreate, conda_base, mache)
@@ -114,6 +114,7 @@ def main():
                    f'git clone -b {args.mache_branch} ' \
                    f'[email protected]:{args.mache_fork}.git mache && ' \
                    f'cd mache && ' \
+                   f'conda install -y --file spec-file.txt && ' \
                    f'python -m pip install --no-deps .'
 
         check_call(commands, logger=logger)

conda/default.cfg

@@ -29,9 +29,9 @@ lapack = 3.9.1
 metis = 5.1.0
 moab = 5.5.1
 netcdf_c = 4.9.2
-netcdf_fortran = 4.6.0
+netcdf_fortran = 4.6.1
 petsc = 3.19.1
-pnetcdf = 1.12.3
-scorpio = 1.6.3
-# parallelio = 2.6.2
+pnetcdf = 1.13.0
+scorpio = 1.6.5
+# parallelio = 2.6.3
 parallelio = None

conda/unsupported.txt

@@ -15,7 +15,8 @@ compy, pgi, mvapich2
 pm-cpu, nvidia, mpich
 pm-cpu, aocc, mpich
 pm-cpu, amdclang, mpich
-
+pm-gpu, gnu, mpich
+pm-gpu, nvidia, mpich
 
 # compiles but tests unreliable (errors or hanging),
 # see https://github.com/MPAS-Dev/compass/issues/336