Merge tag 'dev/ncar_240311' into mnlevy1981/add_MARBL

NCAR · Mar 15, 2024 · ddd5d46 · ddd5d46
2 parents 7bb68c5 + 13fbeb7
commit ddd5d46
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diff --git a/.github/actions/macos-setup/action.yml b/.github/actions/macos-setup/action.yml
@@ -16,3 +16,18 @@ runs:
         brew install netcdf-fortran
         brew install mpich
         echo "::endgroup::"
+
+    # NOTE: Floating point exceptions are currently disabled due to an error in
+    # HDF5 1.4.3.  They will be re-enabled when the default brew version has
+    # been updated to a working version.
+
+    - name: Set compiler flags
+      shell: bash
+      run: |
+        cd .testing
+        echo "FCFLAGS_DEBUG = -g -O0 -Wextra -Wno-compare-reals -fbacktrace -fcheck=bounds" >> config.mk
+        echo "FCFLAGS_REPRO = -g -O2 -fbacktrace" >> config.mk
+        echo "FCFLAGS_INIT = -finit-real=snan -finit-integer=2147483647 -finit-derived" >> config.mk
+        echo "FCFLAGS_FMS = -g -fbacktrace -O0" >> config.mk
+        cat config.mk
+        echo "::endgroup::"
diff --git a/.github/actions/testing-setup/action.yml b/.github/actions/testing-setup/action.yml
@@ -31,17 +31,6 @@ runs:
         REPORT_ERROR_LOGS=true make deps/lib/libFMS.a -s -j
         echo "::endgroup::"
 
-    - name: Store compiler flags used in Makefile
-      shell: bash
-      run: |
-        echo "::group::config.mk"
-        cd .testing
-        echo "FCFLAGS_DEBUG=-g -O0 -Wextra -Wno-compare-reals -fbacktrace -ffpe-trap=invalid,zero,overflow -fcheck=bounds" >> config.mk
-        echo "FCFLAGS_REPRO=-g -O2 -fbacktrace" >> config.mk
-        echo "FCFLAGS_INIT=-finit-real=snan -finit-integer=2147483647 -finit-derived" >> config.mk
-        cat config.mk
-        echo "::endgroup::"
-
     - name: Compile MOM6 in symmetric memory mode
       shell: bash
       run: |

diff --git a/.github/actions/ubuntu-setup/action.yml b/.github/actions/ubuntu-setup/action.yml
@@ -17,3 +17,15 @@ runs:
         sudo apt-get install libopenmpi-dev
         sudo apt-get install linux-tools-common
         echo "::endgroup::"
+
+    - name: Store compiler flags used in Makefile
+      shell: bash
+      run: |
+        echo "::group::config.mk"
+        cd .testing
+        echo "FCFLAGS_DEBUG = -g -O0 -Wextra -Wno-compare-reals -fbacktrace -ffpe-trap=invalid,zero,overflow -fcheck=bounds" >> config.mk
+        echo "FCFLAGS_REPRO = -g -O2 -fbacktrace" >> config.mk
+        echo "FCFLAGS_INIT = -finit-real=snan -finit-integer=2147483647 -finit-derived" >> config.mk
+        echo "FCFLAGS_FMS = -g -fbacktrace -O0" >> config.mk
+        cat config.mk
+        echo "::endgroup::"
diff --git a/.github/workflows/coverage.yml b/.github/workflows/coverage.yml
@@ -19,19 +19,29 @@ jobs:
 
     - uses: ./.github/actions/testing-setup
 
-    - name: Compile unit testing
-      run: make -j build/unit/MOM_unit_tests
+    - name: Compile file parser unit tests
+      run: make -j build/unit/test_MOM_file_parser
 
-    - name: Run unit tests
+    - name: Run file parser unit tests
       run: make run.cov.unit
 
+    - name: Compile unit testing
+      run: make -j build.unit
+
+    - name: Run (single processor) unit tests
+      run: make run.unit
+
     - name: Report unit test coverage to CI (PR)
       if: github.event_name == 'pull_request'
       run: make report.cov.unit REQUIRE_COVERAGE_UPLOAD=true
+      env:
+        CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
 
     - name: Report unit test coverage to CI (Push)
       if: github.event_name != 'pull_request'
       run: make report.cov.unit
+      env:
+        CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
 
     - name: Compile ocean-only MOM6 with code coverage
       run: make -j build/cov/MOM6
@@ -42,7 +52,11 @@ jobs:
     - name: Report coverage to CI (PR)
       if: github.event_name == 'pull_request'
       run: make report.cov REQUIRE_COVERAGE_UPLOAD=true
+      env:
+        CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
 
     - name: Report coverage to CI (Push)
       if: github.event_name != 'pull_request'
       run: make report.cov
+      env:
+        CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
diff --git a/.github/workflows/perfmon.yml b/.github/workflows/perfmon.yml
@@ -1,6 +1,6 @@
 name: Performance Monitor
 
-on: [pull_request]
+on: [push, pull_request]
 
 jobs:
   build-test-perfmon:
@@ -20,19 +20,34 @@ jobs:
     - uses: ./.github/actions/testing-setup
 
     - name: Compile optimized models
+      if: ${{ github.event_name == 'pull_request' }}
       run: >-
         make -j build.prof
         MOM_TARGET_SLUG=$GITHUB_REPOSITORY
         MOM_TARGET_LOCAL_BRANCH=$GITHUB_BASE_REF
         DO_REGRESSION_TESTS=true
 
     - name: Generate profile data
+      if: ${{ github.event_name == 'pull_request' }}
       run: >-
         pip install f90nml &&
         make profile
         DO_REGRESSION_TESTS=true
 
     - name: Generate perf data
+      if: ${{ github.event_name == 'pull_request' }}
       run: |
         sudo sysctl -w kernel.perf_event_paranoid=2
         make perf DO_REGRESSION_TESTS=true
+
+    - name: Compile timing tests
+      run: |
+        make -j build.timing
+
+    - name: Run timing tests
+      run: |
+        make -j run.timing
+
+    - name: Display timing results
+      run: |
+        make -j show.timing
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
@@ -10,7 +10,6 @@ stages:
 # We use the "fetch" strategy to speed up the startup of stages
 variables:
   JOB_DIR: "/lustre/f2/scratch/oar.gfdl.ogrp-account/runner/builds/$CI_PIPELINE_ID"
-  WORKSPACE: "/lustre/f2/scratch/oar.gfdl.ogrp-account/runner/$CI_RUNNER_ID"
   GIT_STRATEGY: fetch
 
 # Always eport value of $JOB_DIR
@@ -185,9 +184,9 @@ actions:gnu:
     - make -s -j
     - MPIRUN= make preproc -s -j
     - echo -e "\e[0Ksection_end:`date +%s`:compile\r\e[0K"
-    - (echo '#!/bin/bash';echo 'make MPIRUN="srun -mblock --exclusive" WORKSPACE=$WORKSPACE test -s -j') > job.sh
-    - sbatch --clusters=c5 --nodes=2 --time=0:10:00 --account=gfdl_o --qos=debug --job-name=MOM6.gnu.testing --output=log.$CI_JOB_ID --wait job.sh || ( cat log.$CI_JOB_ID ; exit 911 ) && make WORKSPACE=$WORKSPACE test -s
-    - make WORKSPACE=$WORKSPACE test.summary
+    - (echo '#!/bin/bash';echo 'make MPIRUN="srun -mblock --exclusive" test -s -j') > job.sh
+    - sbatch --clusters=c5 --nodes=2 --time=0:10:00 --account=gfdl_o --qos=debug --job-name=MOM6.gnu.testing --output=log.$CI_JOB_ID --wait job.sh || ( cat log.$CI_JOB_ID ; exit 911 ) && make test -s
+    - make test.summary
 
 actions:intel:
   stage: tests
@@ -205,9 +204,9 @@ actions:intel:
     - make -s -j
     - MPIRUN= make preproc -s -j
     - echo -e "\e[0Ksection_end:`date +%s`:compile\r\e[0K"
-    - (echo '#!/bin/bash';echo 'make MPIRUN="srun -mblock --exclusive" WORKSPACE=$WORKSPACE test -s -j') > job.sh
-    - sbatch --clusters=c5 --nodes=2 --time=0:10:00 --account=gfdl_o --qos=debug --job-name=MOM6.intel.testing --output=log.$CI_JOB_ID --wait job.sh || ( cat log.$CI_JOB_ID ; exit 911 ) && make WORKSPACE=$WORKSPACE test -s
-    - make WORKSPACE=$WORKSPACE test.summary
+    - (echo '#!/bin/bash';echo 'make MPIRUN="srun -mblock --exclusive" test -s -j') > job.sh
+    - sbatch --clusters=c5 --nodes=2 --time=0:10:00 --account=gfdl_o --qos=debug --job-name=MOM6.intel.testing --output=log.$CI_JOB_ID --wait job.sh || ( cat log.$CI_JOB_ID ; exit 911 ) && make test -s
+    - make test.summary
 
 # Tests
 #

diff --git a/.readthedocs.yml b/.readthedocs.yml
@@ -1,5 +1,14 @@
+# Read the Docs configuration file for Sphinx projects
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
 version: 2
 
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.11"
+
 # Extra formats
 # PDF generation is failing for now; disabled on 2020-12-02
 #formats:
@@ -10,7 +19,5 @@ sphinx:
   configuration: docs/conf.py
 
 python:
-  # make sure we're using Python 3
-  version: 3
   install:
     - requirements: docs/requirements.txt