Update gsd/develop-chem from gsl/develop, add NASA GOCART repository

.github/pull_request_template.md

@@ -1,29 +1,46 @@
+# PR Checklist
+
+- [ ] Ths PR is up-to-date with the top of all sub-component repositories except for those sub-components which are the subject of this PR. Please consult the ufs-weather-model [wiki](https://github.com/ufs-community/ufs-weather-model/wiki/Making-code-changes-in-the-UFS-weather-model-and-its-subcomponents) if you are unsure how to do this.
+
+- [ ] This PR has been tested using a branch which is up-to-date with the top of all sub-component repositories except for those sub-components which are the subject of this PR
+
+- [ ] An Issue describing the work contained in this PR has been created either in the subcomponent(s) or in the ufs-weather-model. The Issue should be created in the repository that is most relevant to the changes in contained in the PR. The Issue and the dependent sub-component PR 
+are specified below.
+
+- [ ] If new or updated input data is required by this PR, it is clearly stated in the text of the PR.
+
+## Instructions: All subsequent sections of text should be filled in as appropriate.
+
+The information provided below allows the code managers to understand the changes relevant to this PR, whether those changes are in the ufs-weather-model repository or in a subcomponent repository. Ufs-weather-model code managers will use the information provided to add any applicable labels, assign reviewers and place it in the Commit Queue. Once the PR is in the Commit Queue, it is the PR owner's responsiblity to keep the PR up-to-date with the develop branch of ufs-weather-model. 
+
 ## Description
 
-(Instructions: this, and all subsequent sections of text should be removed and filled in as appropriate.)
-Provide a detailed description of what this PR does.
-What bug does it fix, or what feature does it add?
-Is a change of answers expected from this PR?
-Are any library updates included in this PR (modulefiles etc.)?
+Provide a detailed description of what this PR does. What bug does it fix, or what feature does it add? Is a change of answers expected from this PR? Are any library updates included in this PR (modulefiles etc.)?
 
 ### Issue(s) addressed
 
 Link the issues to be closed with this PR, whether in this repository, or in another repository.
-(Remember, issues should always be created before starting work on a PR branch!)
+(Remember, issues must always be created before starting work on a PR branch!) 
 - fixes #<issue_number>
 - fixes noaa-emc/fv3atm/issues/<issue_number>
 
 ## Testing
 
-How were these changes tested?
-What compilers / HPCs was it tested with?
-Are the changes covered by regression tests? (If not, why? Do new tests need to be added?)
-Have regression tests and unit tests (utests) been run? On which platforms and with which compilers? (Note that unit tests can only be run on tier-1 platforms)
+How were these changes tested? What compilers / HPCs was it tested with? Are the changes covered by regression tests? (If not, why? Do new tests need to be added?) Have regression tests and unit tests (utests) been run? On which platforms and with which compilers? (Note that unit tests can only be run on tier-1 platforms)
+
+- [ ] hera.intel
+- [ ] hera.gnu
+- [ ] orion.intel
+- [ ] cheyenne.intel 
+- [ ] cheyenne.gnu
+- [ ] gaea.intel 
+- [ ] jet.intel
+- [ ] wcoss_cray
+- [ ] wcoss_dell_p3
 
 ## Dependencies
 
-If testing this branch requires non-default branches in other repositories, list them.
-Those branches should have matching names (ideally)
+If testing this branch requires non-default branches in other repositories, list them. Those branches should have matching names (ideally).
 
 Do PRs in upstream repositories need to be merged first?
 If so add the "waiting for other repos" label and list the upstream PRs

.github/workflows/main.yml → .github/workflows/build_test.yml

@@ -1,17 +1,15 @@
-name: Pull Request Tests
+name: Pull request tests
 
 on:
   push:
-    branches:
-    - develop
+    branches: ['develop']
   pull_request:
-    branches:
-    - develop
+    branches: ['develop']
 
 jobs:
   setup:
     name: Set up
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-20.04
 
     outputs:
       tn: ${{ steps.parse.outputs.tn }}
@@ -46,7 +44,7 @@ jobs:
   build:
     name: Build (${{ matrix.bld_set }})
     needs: setup
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-20.04
 
     strategy:
       fail-fast: false
@@ -68,7 +66,7 @@ jobs:
     - name: Free up disk space
       run: |
         sudo docker rmi $(sudo docker image ls | grep -E -m1 '<none>' | awk '{ print $3 }')
-        sudo docker rmi $(sudo docker image ls | awk '/ci-test-base/ { print $3 }')
+        sudo docker rmi $(sudo docker image ls | awk '/ubuntu-hpc/ { print $3 }')
 
     - name: Prepare artifacts
       run: |
@@ -85,8 +83,7 @@ jobs:
   utest:
     name: Unit test (${{ needs.setup.outputs.tn }}, ${{ matrix.test_set }})
     needs: [setup,build]
-    runs-on: ubuntu-latest
-    #runs-on: self-hosted
+    runs-on: self-hosted
 
     strategy:
       fail-fast: false
@@ -101,7 +98,7 @@ jobs:
     - name: Prepare artifacts
       run: |
         tar xvjf artifact.tar.bz2 && rm -f artifact.tar.bz2
-        sudo docker load --input ${{ needs.setup.outputs.img }}.tar.gz && rm -f ${{ needs.setup.outputs.img }}.tar.gz
+        docker load --input ${{ needs.setup.outputs.img }}.tar.gz && rm -f ${{ needs.setup.outputs.img }}.tar.gz
 
     - name: Run utest
       run: ./ci.sh -n ${{ needs.setup.outputs.tn }} -r ${{ matrix.test_set }}
@@ -117,5 +114,7 @@ jobs:
       if: ${{ always() }}
       run: |
         rm -f ci.sh ci.test
-        sudo docker rm  my-container && sudo docker rmi ${{ needs.setup.outputs.img }}:latest
-        sudo docker volume rm DataVolume
+        docker stop my-container && docker rm  my-container && docker rmi ${{ needs.setup.outputs.img }}:latest
+        docker volume rm DataVolume
+        #docker rmi minsukjinoaa/fv3-input-data:input-data-20210115
+        rm -f memory_stat

.github/workflows/manage.yml → .github/workflows/manage_workflows.yml

@@ -2,35 +2,37 @@ name: Manage workflows
 
 on:
   workflow_run:
-    workflows: ["Pull Request Tests"]
+    workflows: ["Pull request tests"]
     types:
       - requested
 
 jobs:
   job1:
-    name: Job 1
-    runs-on: ubuntu-latest
+    name: Cancel workflows
+    runs-on: ubuntu-20.04
 
     steps:
       - name: Checkout codes
         uses: actions/checkout@v2
 
-      - name: Check if skip-ci is requested
+      - name: Check if run-ci is requested
         run: |
+          sleep 40
           cd ${GITHUB_WORKSPACE}/tests/ci
           repo="${GITHUB_API_URL}/repos/${GITHUB_REPOSITORY}/actions/runs"
           tr_id=$(cat ${GITHUB_EVENT_PATH} | ./json_helper.py get_trigger_id)
           tr_br=$(cat ${GITHUB_EVENT_PATH} | ./json_helper.py get_trigger_br)
-          check=$(cat ${GITHUB_EVENT_PATH} | ./json_helper.py check_skip)
-          echo "::set-env name=TRIGGER_ID::${tr_id}"
-          echo "::set-env name=TRIGGER_BR::${tr_br}"
-          echo "skip-ci: ${check}"
-          if [[ $check == yes ]]; then
-            echo "skip-ci is requested"
-            echo '::set-env name=CURR_JOB::cancelled'
+          check=$(cat ${GITHUB_EVENT_PATH} | ./json_helper.py check_run)
+          echo "TRIGGER_ID=${tr_id}" >> $GITHUB_ENV
+          echo "TRIGGER_BR=${tr_br}" >> $GITHUB_ENV
+          echo "run-ci: ${check}"
+          if [[ $check == no ]]; then
+            echo "run-ci is not requested"
+            echo "CURR_JOB=cancelled" >> $GITHUB_ENV
             curl -X POST -H "Authorization: token ${{ secrets.GITHUB_TOKEN }}" -H "Accept: application/vnd.github.v3+json" ${repo}/$tr_id/cancel
           else
-            echo '::set-env name=CURR_JOB::running'
+            echo "run-ci is requested"
+            echo "CURR_JOB=running" >> $GITHUB_ENV
           fi
 
       - name: Cancel redundant jobs

.github/workflows/start_runners.yml

@@ -0,0 +1,33 @@
+name: Start runners
+
+on:
+  workflow_run:
+    workflows: ["Pull request tests"]
+    types:
+      - requested
+
+jobs:
+  job1:
+    name: Start AWS runners
+    runs-on: ubuntu-20.04
+
+    steps:
+    - name: Check out codes
+      uses: actions/checkout@v2
+
+    - name: Configure AWS
+      uses: aws-actions/configure-aws-credentials@v1
+      with:
+        aws-access-key-id: ${{ secrets.AWS_ACCESS_KEY_ID }}
+        aws-secret-access-key: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
+        aws-region: us-east-1
+
+    - name: Check the status of build and start self-hosted runners
+      env:
+        aws_instance_id: ${{ secrets.AWS_INSTANCE_ID }}
+      run: |
+        cd ${GITHUB_WORKSPACE}/tests/ci
+        conclusion=$(cat ${GITHUB_EVENT_PATH} | ./build_status_check.py)
+        if [[ $conclusion == "success" ]]; then
+          aws ec2 start-instances --instance-ids $aws_instance_id
+        fi

.github/workflows/stop_runners.yml

@@ -0,0 +1,25 @@
+name: Stop runners
+
+on:
+  workflow_run:
+    workflows: ["Pull request tests"]
+    types:
+      - completed
+
+jobs:
+  job1:
+    name: Stop AWS runners
+    runs-on: ubuntu-20.04
+
+    steps:
+    - name: Configure AWS
+      uses: aws-actions/configure-aws-credentials@v1
+      with:
+        aws-access-key-id: ${{ secrets.AWS_ACCESS_KEY_ID }}
+        aws-secret-access-key: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
+        aws-region: us-east-1
+
+    - name: Stop self-hosted runners
+      env:
+        aws_instance_id: ${{ secrets.AWS_INSTANCE_ID }}
+      run: aws ec2 stop-instances --instance-ids $aws_instance_id

.gitignore

@@ -1,2 +1,70 @@
+# Prerequisites
+*.d
+
+# Compiled Object files
+*.slo
+*.lo
+*.o
+*.obj
+
+# Precompiled Headers
+*.gch
+*.pch
+
+# Compiled Dynamic libraries
+*.so
+*.dylib
+*.dll
+
+# Fortran module files
+*.mod
+*.smod
+
+# Compiled Static libraries
+*.lai
+*.la
+*.a
+*.lib
+
+# Executables
+*.exe
+*.out
+*.app
+*.x
+
+# system files
+*.swp
+*~
+.DS_Store
+
+# python files
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# CMake files and directories
+build*/
+install*/
+CMakeLists.txt.user
+CMakeCache.txt
+CMakeFiles
+CMakeScripts
+cmake_install.cmake
+install_manifest.txt
+compile_commands.json
+CTestTestfile.cmake
+_deps
+
+# repo-specific ignorables
 coupled*.mk
 rt.conf.single
+ufs_model
+tests/modules.fv3_*
+tests/ecflow_run/
+tests/log_*/
+tests/lock/
+tests/Compile_*.log
+tests/fail_test
+log*
+build*.log*

.gitmodules

@@ -1,20 +1,44 @@
 [submodule "FV3"]
-	path = FV3
-	url = https://github.com/NOAA-GSL/fv3atm
-	branch = gsd/develop-chem
+  path = FV3
+  url = https://github.com/NOAA-GSL/fv3atm
+  branch = gsl/develop-chem
 [submodule "NEMS"]
-	path = NEMS
-	url = https://github.com/NOAA-EMC/NEMS
-	branch = develop
+  path = NEMS
+  url = https://github.com/NOAA-EMC/NEMS
+  branch = develop
 [submodule "FMS"]
-	path = FMS
-	url = https://github.com/NOAA-GFDL/FMS
-	branch = master
+  path = FMS
+  url = https://github.com/NOAA-GFDL/FMS
+  branch = release/2020.04
 [submodule "WW3"]
-	path = WW3
-	url = https://github.com/NOAA-EMC/WW3
-	branch = develop
+  path = WW3
+  url = https://github.com/NOAA-EMC/WW3
+  branch = develop
 [submodule "stochastic_physics"]
-	path = stochastic_physics
-	url = https://github.com/noaa-psd/stochastic_physics
-	branch = master
+  path = stochastic_physics
+  url = https://github.com/noaa-gsl/stochastic_physics
+  branch = gsl/develop
+[submodule "gocart"]
+  path = gocart
+  url = https://github.com/NOAA-GSL/GOCART
+  branch = gsl/develop-chem
+[submodule "CMakeModules"]
+  path = CMakeModules
+  url = https://github.com/NOAA-EMC/CMakeModules
+  branch = develop
+[submodule "CMEPS"]
+  path = CMEPS-interface/CMEPS
+  url = https://github.com/NOAA-EMC/CMEPS.git
+  branch = emc/develop
+[submodule "MOM6"]
+  path = MOM6-interface/MOM6
+  url = https://github.com/NOAA-EMC/MOM6
+  branch = dev/emc
+[submodule "CICE"]
+  path = CICE-interface/CICE
+  url = https://github.com/NOAA-EMC/CICE
+  branch = emc/develop
+[submodule "DATM"]
+  path = DATM
+  url = https://github.com/NOAA-EMC/NEMSdatm
+  branch = develop