Merge pull request #204 from xylar/update-to-0.4.0-alpha.1

Update to 0.4.0-alpha.1

deploy/bootstrap.py

@@ -511,6 +511,11 @@ def build_spack_soft_env(config, update_spack, machine, env_type,  # noqa: C901
 
     esmf = config.get('deploy', 'esmf')
 
+    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()
@@ -545,7 +550,8 @@ def build_spack_soft_env(config, update_spack, machine, env_type,  # noqa: C901
                        spack_specs=specs, compiler=compiler, mpi=mpi,
                        machine=machine, config_file=machine_config,
                        include_e3sm_hdf5_netcdf=e3sm_hdf5_netcdf,
-                       yaml_template=yaml_template, tmpdir=tmpdir)
+                       yaml_template=yaml_template, tmpdir=tmpdir,
+                       spack_mirror=spack_mirror)
 
     spack_view = f'{spack_branch_base}/var/spack/environments/' \
                  f'{spack_env}/.spack-env/view'
@@ -593,12 +599,12 @@ def build_spack_libs_env(config, update_spack, machine, compiler,  # noqa: C901
     else:
         include_e3sm_lapack = True
     if metis != 'None':
-        specs.append(f'"metis@{metis}~shared"')
+        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}~shared"')
+        specs.append(f'"parmetis@{parmetis}+int64~shared"')
     if petsc != 'None':
         specs.append(f'"petsc@{petsc}+mpi+batch"')
 

deploy/default.cfg

@@ -21,7 +21,7 @@ mpi = nompi
 
 # versions of conda packages
 geometric_features = 1.2.0
-mache = 1.19.0
+mache = 1.24.0
 mpas_tools = 0.34.1
 otps = 2021.10
 parallelio = 2.6.0

polaris/machines/chicoma-cpu.cfg

@@ -28,6 +28,9 @@ spack = /usr/projects/e3sm/polaris/chicoma-cpu/spack
 # pnetcdf as E3SM (spack modules are used otherwise)
 use_e3sm_hdf5_netcdf = True
 
+# location of a spack mirror for polaris to use
+spack_mirror = /usr/projects/e3sm/polaris/chicoma-cpu/spack/spack_mirror
+
 
 # The parallel section describes options related to running jobs in parallel
 [parallel]
@@ -42,6 +45,11 @@ cores_per_node = 128
 # hanging on perlmutter)
 threads_per_core = 1
 
+# quality of service
+# overriding mache because the debug qos also requires --reservaiton debug,
+# which polaris doesn't currently support
+qos = standard
+
 
 # Config options related to creating a job script
 [job]

polaris/version.py

@@ -1 +1 @@
-__version__ = '0.3.0-alpha.2'
+__version__ = '0.4.0-alpha.1'

utils/omega/ctest/omega_ctest.py

@@ -13,7 +13,7 @@
 
 def make_build_script(machine, compiler, branch, build_only, mesh_filename,
                       planar_mesh_filename, sphere_mesh_filename,
-                      debug, clean, cmake_flags):
+                      debug, clean, cmake_flags, account):
     """
     Make a shell script for checking out Omega and its submodules, building
     Omega and its ctests, linking to testing data files, and running ctests.
@@ -45,6 +45,9 @@ def make_build_script(machine, compiler, branch, build_only, mesh_filename,
     if cmake_flags is None:
         cmake_flags = ''
 
+    if account is not None:
+        cmake_flags = f'{cmake_flags} -DOMEGA_CIME_PROJECT={account}'
+
     script = template.render(update_omega_submodule=update_omega_submodule,
                              polaris_source_dir=polaris_source_dir,
                              omega_base_dir=branch,
@@ -108,15 +111,16 @@ def download_meshes(config):
     return download_targets
 
 
-def write_job_script(config, machine, compiler, submit):
+def write_job_script(config, machine, compiler, account, submit):
     """
     Write a job script for running the build script
     """
 
-    if config.has_option('parallel', 'account'):
-        account = config.get('parallel', 'account')
-    else:
-        account = ''
+    if account is None:
+        if config.has_option('parallel', 'account'):
+            account = config.get('parallel', 'account')
+        else:
+            account = ''
 
     nodes = 1
 
@@ -190,6 +194,8 @@ def main():
                         help='Whether to only build Omega in debug mode')
     parser.add_argument('--cmake_flags', dest='cmake_flags',
                         help='Quoted string with additional cmake flags')
+    parser.add_argument('--account', dest='account',
+                        help='slurm account to submit the job to')
 
     args = parser.parse_args()
 
@@ -206,6 +212,7 @@ def main():
     debug = args.debug
     clean = args.clean
     cmake_flags = args.cmake_flags
+    account = args.account
 
     if 'SLURM_JOB_ID' in os.environ:
         # already on a comptue node so we will just run ctests directly
@@ -221,15 +228,16 @@ def main():
         build_only=build_only, mesh_filename=mesh_filename,
         planar_mesh_filename=planar_mesh_filename,
         sphere_mesh_filename=sphere_mesh_filename,
-        debug=debug, clean=clean, cmake_flags=cmake_flags)
+        debug=debug, clean=clean, cmake_flags=cmake_flags,
+        account=account)
 
     # clear environment variables and start fresh with those from login
     # so spack doesn't get confused by conda
     subprocess.check_call(f'env -i HOME="$HOME" bash -l {script_filename}',
                           shell=True)
 
     write_job_script(config=config, machine=machine, compiler=compiler,
-                     submit=submit)
+                     account=account, submit=submit)
 
 
 if __name__ == '__main__':