MPAS-Dev · xylar · Jan 12, 2023 · Jan 12, 2023 · Jan 12, 2023 · Jan 12, 2023
diff --git a/azure-pipelines.yml b/azure-pipelines.yml
@@ -37,7 +37,11 @@ jobs:
       eval "$(conda shell.bash hook)"
       conda config --add channels conda-forge
       conda config --set channel_priority strict
-      conda install --yes "conda!=22.11.0" conda-build mamba boa
+      conda update --yes --all
+      conda install --yes mamba
+      # workaround based on recent failures
+      rm /usr/share/miniconda/pkgs/cache/*.json
+      mamba install --yes conda-build boa
     displayName: Update conda base environment
 
   - bash: |
@@ -158,7 +162,11 @@ jobs:
       eval "$(conda shell.bash hook)"
       conda config --add channels conda-forge
       conda config --set channel_priority strict
-      conda install --yes python=$PYTHON_VERSION "conda!=22.11.0" conda-build mamba boa
+      conda update --yes --all
+      conda install --yes mamba
+      # workaround based on recent failures
+      rm /usr/share/miniconda/pkgs/cache/*.json
+      mamba install --yes conda-build boa
     displayName: Update conda base environment
 
   - bash: |
@@ -213,7 +221,9 @@ jobs:
       eval "$(conda shell.bash hook)"
       conda config --add channels conda-forge
       conda config --set channel_priority strict
-      conda install --yes "conda!=22.11.0" conda-build mamba boa
+      conda update --yes --all
+      conda install --yes mamba
+      mamba install --yes conda-build boa
     displayName: Update conda base environment
 
   - bash: |

diff --git a/ci/recipe/meta.yaml b/ci/recipe/meta.yaml
@@ -33,7 +33,7 @@ requirements:
     - geometric_features >=0.5.0
     - gsw
     - lxml
-    - mache >=1.1.2
+    - mache >=1.11.0
     - matplotlib-base >=3.0.2
     - mpas_tools >=0.14.0
     - nco >=4.8.1

diff --git a/dev-spec.txt b/dev-spec.txt
@@ -14,7 +14,7 @@ f90nml
 geometric_features>=0.5.0
 gsw
 lxml
-mache >=1.1.2
+mache >=1.11.0
 matplotlib-base>=3.0.2
 mpas_tools>=0.14.0
 nco>=4.8.1

diff --git a/docs/tutorials/dev_getting_started.rst b/docs/tutorials/dev_getting_started.rst
@@ -480,7 +480,7 @@ Anvil or Chrysalis:
     /lcrc/group/e3sm/ac.xylar/acme_scratch/anvil/20200305.A_WCYCL1850.ne4_oQU480.anvil
     /lcrc/group/e3sm/ac.xylar/acme_scratch/anvil/20201025.GMPAS-IAF.T62_oQU240wLI.anvil
 
-Cori:
+Cori and Perlmutter:
 
 .. code-block::
 
@@ -597,7 +597,7 @@ match your own preferred workflow.
 
 .. note::
 
-    On some E3SM supported machines like Badger and Chicoma, there is no
+    On some E3SM supported machines like Chicoma, there is no
     web portal so you will want to just manually replace the part of the
     ``basePath`` given by ``/lcrc/group/e3sm/${web_portal:username}`` in the
     example above.
@@ -700,9 +700,10 @@ Then, running MPAS-Analysis is as simple as:
 
     $ mpas_analysis -m <machine> myrun.cfg
 
-where ``<machine>`` is the name of the machine (all lowercase).  We treat
-``cori-haswell`` and ``cori-knl`` as separate machines (and we strongly
-recommend that you use only ``cori-haswell``).
+where ``<machine>`` is the name of the machine (all lowercase).  On Cori, we
+only support the Haswell nodes (so the machine name is ``cori-haswell``).  For
+now, we only support CPU nodes on Perlmutter (``pm-cpu``) and Chicoma
+(``chicoma-cpu``).
 
 Typical output is the analysis is running correctly looks something like:
 
@@ -777,14 +778,14 @@ e.g.:
 
 .. note::
 
-    On Cori, you will need to change the permissions so you can see the
-    webpage online:
+    On Cori and Perlmutter, you will need to change the permissions so you can
+    see the webpage online:
 
     .. code-block:: bash
 
         $ chmod -R ugo+rX /global/cfs/cdirs/e3sm/www/<username>
 
-    where ``<username>`` is your Cori username.
+    where ``<username>`` is your NERSC username.
 
 If the web page is incomplete, it presumably means there was an error during
 the analysis run, since the web page is generated as the final step.  Check

diff --git a/docs/users_guide/config/execute.rst b/docs/users_guide/config/execute.rst
@@ -110,26 +110,22 @@ for calls to ``ncremap`` from E3SM-Unified on compute nodes:
 
     ncremapParallelExec = srun
 
-E3SM supported machines with system MPI support in E3SM-Unified 1.5.0:
+E3SM supported machines with system MPI support in E3SM-Unified 1.8.1:
 
 * Anvil
 
-* Badger
+* Chicoma
 
 * Chrysalis
 
 * Compy
 
 * Cori-Haswell
 
-* Grizzly
+* Perlmutter
 
 These machines do **not** have MPI support in E3SM-Unified:
 
-* Cori-KNL
-
-* Cooley
-
 * Andes
 
 * Acme1
@@ -143,7 +139,7 @@ Parallel Mask Creation
 
 Tasks that involve :ref:`config_region_groups` can generate the masks for each
 region in the group on the fly.  This is done with the mask generation
-command-line tools form MPAS-Tools (see 
+command-line tools form MPAS-Tools (see
 `Mask Creation with Python Multiprocessing <http://mpas-dev.github.io/MPAS-Tools/stable/mesh_conversion.html#mask-creation-with-pthon-multiprocessing>`_),
 which support 3 modes of parallelism: "spawn", "fork" and "forkserver". For
 technical details on these modes, see

diff --git a/mpas_analysis/configuration/badger.cfg → mpas_analysis/configuration/chicoma-cpu.cfg b/mpas_analysis/configuration/badger.cfg → mpas_analysis/configuration/chicoma-cpu.cfg
@@ -2,7 +2,7 @@
 ## options related to executing parallel tasks
 
 # the number of parallel tasks (1 means tasks run in serial, the default)
-parallelTaskCount = 12
+parallelTaskCount = 24
 
 # the parallelism mode in ncclimo ("serial", "bck" or "mpi")
 # Set this to "bck" (background parallelism) in most cases.  The default number
@@ -18,7 +18,7 @@ ncclimoThreads = 12
 
 # the number of MPI tasks to use in creating mapping files (1 means tasks run in
 # serial, the default)
-mapMpiTasks = 12
+mapMpiTasks = 24
 
 # "None" if ESMF should perform mapping file generation in serial without a
 # command, or one of "srun" or "mpirun" if it should be run in parallel (or ins

diff --git a/mpas_analysis/configuration/pm-cpu.cfg b/mpas_analysis/configuration/pm-cpu.cfg
@@ -0,0 +1,30 @@
+[execute]
+## options related to executing parallel tasks
+
+# the number of parallel tasks (1 means tasks run in serial, the default)
+parallelTaskCount = 24
+
+# the parallelism mode in ncclimo ("serial", "bck" or "mpi")
+# Set this to "bck" (background parallelism) in most cases.  The default number
+# of threads (see below) is 12, one for each monthly climatology. Set to "mpi"
+# to run one MPI task on each node and however many threads per node to reach
+# 12 total threads.
+ncclimoParallelMode = bck
+
+# the number of total threads to use when ncclimo runs in "bck" or "mpi" mode.
+# Reduce this number if ncclimo is crashing (maybe because it is out of memory).
+# The number of threads must be a factor of 12 (1, 2, 3, 4, 6 or 12).
+ncclimoThreads = 12
+
+# the number of MPI tasks to use in creating mapping files (1 means tasks run in
+# serial, the default)
+mapMpiTasks = 24
+
+# "None" if ESMF should perform mapping file generation in serial without a
+# command, or one of "srun" or "mpirun" if it should be run in parallel (or ins
+# serial but with a command)
+mapParallelExec = srun
+
+# "None" if ncremap should perform remapping without a command, or "srun"
+# possibly with some flags if it should be run with that command
+ncremapParallelExec = srun
diff --git a/mpas_analysis/ocean/time_series_antarctic_melt.py b/mpas_analysis/ocean/time_series_antarctic_melt.py
@@ -557,7 +557,7 @@ def run_task(self):
             obsFileName = '{}/{}'.format(observationsDirectory,
                                          obsFileNameDict[obsName])
             obsDict[obsName] = {}
-            obsFile = csv.reader(open(obsFileName, 'rU'))
+            obsFile = csv.reader(open(obsFileName, 'r'))
             next(obsFile, None)  # skip the header line
             for line in obsFile:  # some later useful values commented out
                 shelfName = line[0]

diff --git a/suite/run_suite.bash b/suite/run_suite.bash
@@ -21,7 +21,7 @@ do
     env=test_mpas_analysis_py${py}
     mamba create -y -n ${env} --use-local python=${py} mpas-analysis sphinx \
         mock sphinx_rtd_theme "tabulate>=0.8.2" m2r2 "mistune<2" pytest \
-	      "mache>=1.1.2" jinja2
+	      "esmf=*=nompi_*" jinja2
     conda activate ${env}
     pytest
     conda deactivate

diff --git a/suite/setup.py b/suite/setup.py
@@ -65,6 +65,12 @@ def main():
         output_base = f'{scratch}/analysis_testing'
         simulation = '20200305.A_WCYCL1850.ne4_oQU480.anvil'
         mesh = 'QU480'
+    elif machine == 'pm-cpu':
+        input_base = '/global/cfs/cdirs/e3sm/xylar'
+        scratch = os.environ['SCRATCH']
+        output_base = f'{scratch}/analysis_testing'
+        simulation = '20200305.A_WCYCL1850.ne4_oQU480.anvil'
+        mesh = 'QU480'
     elif machine == 'compy':
         input_base = '/compyfs/asay932/analysis_testing/test_output'
         output_base = f'/compyfs/{username}/analysis_testing'