Merge pull request #641 from xylar/update-to-1.2.0-alpha.6

Update to 1.2.0-alpha.6

compass/machines/__init__.py

@@ -0,0 +1,54 @@
+import os
+import socket
+
+try:
+    from importlib.resources import contents as imp_res_contents
+except ImportError:
+    # python<=3.8
+    from importlib_resources import contents as imp_res_contents
+
+from mache import discover_machine as mache_discover_machine
+
+from compass.config import CompassConfigParser
+
+
+def discover_machine(quiet=False):
+    """
+    Figure out the machine from the host name
+
+    Parameters
+    ----------
+    quiet : bool, optional
+        Whether to print warnings if the machine name is ambiguous
+
+    Returns
+    -------
+    machine : str
+        The name of the current machine
+    """
+    machine = mache_discover_machine(quiet=quiet)
+    if machine is None:
+        possible_hosts = _get_possible_hosts()
+        hostname = socket.gethostname()
+        for possible_machine, hostname_contains in possible_hosts.items():
+            if hostname_contains in hostname:
+                machine = possible_machine
+                break
+    return machine
+
+
+def _get_possible_hosts():
+    machine_contents = imp_res_contents('compass.machines')
+    possible_hosts = dict()
+    for filename in machine_contents:
+        if filename.endswith('.cfg'):
+            machine = os.path.split(filename)[0]
+            config = CompassConfigParser()
+            config.add_from_package('compass.machines', filename)
+            if config.has_section('discovery') and \
+                    config.has_option('discovery', 'hostname_contains'):
+                hostname_contains = config.get('discovery',
+                                               'hostname_contains')
+                possible_hosts[machine] = hostname_contains
+
+    return possible_hosts

compass/machines/eligos.cfg

@@ -0,0 +1,60 @@
+# The parallel section describes options related to running jobs in parallel
+[parallel]
+
+# parallel system of execution: slurm, cobalt or single_node
+system = single_node
+
+# whether to use mpirun or srun to run a task
+parallel_executable = mpirun
+
+# cores per node on the machine
+cores_per_node = 4
+
+
+# Config options related to spack environments
+[spack]
+
+# whether to load modules from the spack yaml file before loading the spack
+# environment
+modules_before = False
+
+# whether to load modules from the spack yaml file after loading the spack
+# environment
+modules_after = False
+
+
+# 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 = /home/xylar/data/mpas/mpas_standalonedata
+
+# the path to the base conda environment where compass environments have
+# been created
+compass_envs = /home/xylar/data/mpas/compass_envs
+
+
+# Options related to deploying a compass conda environment on supported
+# machines
+[deploy]
+
+# the compiler set to use for system libraries and MPAS builds
+compiler = gnu
+
+# the system MPI library to use for gnu compiler
+mpi_gnu = openmpi
+
+# the base path for spack environments used by compass
+spack = /home/xylar/data/mpas/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 = False
+
+
+# Options related to machine discovery
+[discovery]
+
+# a substring used to identify this machine from its hostname
+hostname_contains = eligos

compass/machines/morpheus.cfg

@@ -0,0 +1,60 @@
+# The parallel section describes options related to running jobs in parallel
+[parallel]
+
+# parallel system of execution: slurm, cobalt or single_node
+system = single_node
+
+# whether to use mpirun or srun to run a task
+parallel_executable = mpirun
+
+# cores per node on the machine
+cores_per_node = 8
+
+
+# Config options related to spack environments
+[spack]
+
+# whether to load modules from the spack yaml file before loading the spack
+# environment
+modules_before = False
+
+# whether to load modules from the spack yaml file after loading the spack
+# environment
+modules_after = False
+
+
+# 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 = /home/xylar/data/mpas/mpas_standalonedata
+
+# the path to the base conda environment where compass environments have
+# been created
+compass_envs = /home/xylar/data/mpas/compass_envs
+
+
+# Options related to deploying a compass conda environment on supported
+# machines
+[deploy]
+
+# the compiler set to use for system libraries and MPAS builds
+compiler = gnu
+
+# the system MPI library to use for gnu compiler
+mpi_gnu = openmpi
+
+# the base path for spack environments used by compass
+spack = /home/xylar/data/mpas/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 = False
+
+
+# Options related to machine discovery
+[discovery]
+
+# a substring used to identify this machine from its hostname
+hostname_contains = morpheus

compass/setup.py

@@ -4,12 +4,11 @@
 import sys
 import warnings
 
-from mache import discover_machine
-
 from compass import provenance
 from compass.config import CompassConfigParser
 from compass.io import symlink
 from compass.job import write_job_script
+from compass.machines import discover_machine
 from compass.mpas_cores import get_mpas_cores
 
 
@@ -432,7 +431,8 @@ def _get_basic_config(config_file, machine, mpas_model_path, mpas_core):
 
     # add the E3SM config options from mache
     if machine is not None:
-        config.add_from_package('mache.machines', f'{machine}.cfg')
+        config.add_from_package('mache.machines', f'{machine}.cfg',
+                                exception=False)
 
     # add the compass machine config file
     if machine is None:

compass/version.py

@@ -1 +1 @@
-__version__ = '1.2.0-alpha.5'
+__version__ = '1.2.0-alpha.6'

conda/albany_supported.txt

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