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Merge pull request #4 from E3SM-Project/develop_e3sm_update
This PR updates the WW3 source code to include the CMake build system and CPP directives for switch options.
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‎.github/ISSUE_TEMPLATE/add-development-request.md‎

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‎.github/ISSUE_TEMPLATE/bug_report.md‎

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---
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name: Bug report
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about: Create a report to help us improve WW3
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about: Create a bug report to help us improve WW3
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title: ''
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labels: 'bug'
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assignees: ''
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A clear and concise description of what the bug is.
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**To Reproduce**
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Steps to reproduce the behavior:
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Steps to reproduce the behavior.
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**Expected behavior**
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A clear and concise description of what you expected to happen.

‎.github/ISSUE_TEMPLATE/config.yml‎

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blank_issues_enabled: true
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contact_links:
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- name: Q&A about using WW3
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url: https://github.com/NOAA-EMC/WW3/discussions/new?category=q-a
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about: Ask the community for help
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- name: General
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url: https://github.com/NOAA-EMC/WW3/discussions/new?category=general
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about: Chat about anything and everything here

‎.github/ISSUE_TEMPLATE/documentation.md‎

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---
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name: Documentation request/update
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about: Add new section in the documentation or report a type/mistake in the documentation
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name: Documentation
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about: Any issues in documentation including reporting a typo/mistake in the documentation or a missing section.
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title: ''
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labels: 'documentation'
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assignees: ''
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---
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**Describe the section in the documentation that is missing or requires an update?**
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<!-- Describe the section in the documentation that is missing or requires an update? -->
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**Report a bug/typo in the documentation**
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**Link the issue(s) associated with this documentation update**
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‎.github/pull_request_template.md‎

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# Pull Request Summary
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(Instructions: this, and all subsequent sections of text should be removed and filled in as appropriate.)
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Please describe the PR summary
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<!-- A short overview of the PR -->
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## Description
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<!--
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Provide a detailed description of what this PR does.
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What bug does it fix, or what feature does it add?
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Is a change of answers expected from this PR?
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### Issue(s) addressed
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* Is there an issue associated with this development (bug fix, enhancement, new feature)?
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Please add a reference to a related issue(s) in WW3 repository (Follow [link](https://docs.github.com/en/github/managing-your-work-on-github/linking-a-pull-request-to-an-issue)).
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Link the issues to be closed with this PR, whether in this repository, or in another repository.
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(Remember, issues should always be created before starting work on a PR branch!).
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Note that properly "linked issues" (either automatic links, or manual ones using the correct keywords) will be automatically closed when the PR is merged.
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Please also include the following information:
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* Add any suggestions for a reviewer
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* Mention any labels that should be added: _bug_, _documentation_, _enhancement_, _new feature_
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* Are answer changes expected from this PR? Please describe the changes and the reason why in addition to which of the following labels would apply: _mod_def change_, _out_grd change_, _out_pnt change_, _restart file change_, _Regression test_
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-->
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### Issue(s) addressed
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<!--
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* Please list any issues associated with this PR, including those the PR will fix/close. For example:
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- fixes #<issue_number>
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- fixes noaa-emc/ww3/issues/<issue_number>
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-->
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### Commit Message
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<!--
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Please provide a short summary of this PR, which will be used during _Squash and Merge_ and will be shown as a git log message. Be sure to add any co-authors here.
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-->
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### Check list
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* Is your feature branch up to date with the authoritative repository (NOAA/develop)?
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* Make sure you have checked the [checklist for a developer submitting to develop](https://github.com/NOAA-EMC/WW3/wiki/Code-Management#checklist-for-a-developer-submitting-to-develop), [checklist for a developer submitting to develop](https://github.com/NOAA-EMC/WW3/wiki/Code-Management#checklist-for-a-developer-submitting-to-develop) and [updating version number](https://github.com/NOAA-EMC/WW3/wiki/Code-Management#checklist-for-updating-version-number)
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* Reviewers: @mentions of suggested reviewers of the proposed changes.
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<!-- After creating the PR you can check each of the items below that have been completed -->
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- [ ] Branch is up to date with the authoritative repository (NOAA-EMC) develop branch.
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- [ ] Checked the [checklist for a developer submitting to develop](https://github.com/NOAA-EMC/WW3/wiki/Code-Management#checklist-for-a-developer-submitting-to-develop).
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- [ ] If a version number update is required, checked the [updating version number](https://github.com/NOAA-EMC/WW3/wiki/Code-Management#checklist-for-updating-version-number) checklist.
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- [ ] If a new feature was added, a regression test for testing the new feature is added.
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### Testing
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* How were these changes tested?
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* Are the changes covered by regression tests? (If not, why? Do new tests need to be added?)
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* If a new feature was added, was a new regression test added?
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* Have regression tests been run?
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* Which compiler / HPC you used to run the regression tests in the PR?
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* Please provide the summary output of matrix.comp (_matrix.Diff.out_, _matrixCompFull.out_ and _matrixCompSummary.out_):
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Please indicate the expected changes in the outputs ([excluding the known list of non-identical tests](https://github.com/NOAA-EMC/WW3/wiki/How-to-use-matrix.comp-to-compare-regtests-with-master#4-look-at-results)).
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* Have the matrix regression tests been run (if yes, please note HPC and compiler)?
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* Please provide the summary output of matrix.comp (_matrix.Diff.txt_, _matrixCompFull.txt_ and _matrixCompSummary.txt_):
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* Please indicate the expected changes in the regression test output ([Note the known list of non-identical tests](https://github.com/NOAA-EMC/WW3/wiki/How-to-use-matrix.comp-to-compare-regtests-with-master#4-look-at-results)).
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* Please provide the summary output of matrix.comp (_matrix.Diff.txt_, _matrixCompFull.txt_ and _matrixCompSummary.txt_):
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‎.github/workflows/gnu.yml‎

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name: GNU Linux Build
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on: [push, pull_request]
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env:
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cache_key: gnu4
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CC: gcc-10
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FC: gfortran-10
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CXX: g++-10
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# Split into a steup step, and a WW3 build step which
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# builds multiple switches in a matrix. The setup is run once and
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# the environment is cached so each build of WW3 can share the dependencies.
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jobs:
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setup:
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runs-on: ubuntu-20.04
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steps:
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# Cache spack, OASIS, and compiler
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# No way to flush Action cache, so key may have # appended
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- name: cache-env
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id: cache-env
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uses: actions/cache@v2
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with:
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path: |
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spack
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~/.spack
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work_oasis3-mct
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key: spack-${{ runner.os }}-${{ env.cache_key }}
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- name: checkout-ww3
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if: steps.cache-env.outputs.cache-hit != 'true'
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uses: actions/checkout@v2
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with:
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path: ww3
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# Build WW3 spack environment
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- name: install-dependencies-with-spack
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if: steps.cache-env.outputs.cache-hit != 'true'
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run: |
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# Install NetCDF, ESMF, g2, etc using Spack
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git clone -c feature.manyFiles=true https://github.com/spack/spack.git
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source spack/share/spack/setup-env.sh
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spack env create ww3-gnu ww3/model/ci/spack.yaml
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spack env activate ww3-gnu
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spack compiler find
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spack external find
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spack add [email protected]
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spack concretize
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spack install --dirty -v
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- name: build-oasis
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if: steps.cache-env.outputs.cache-hit != 'true'
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run: |
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source spack/share/spack/setup-env.sh
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spack env activate ww3-gnu
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export WWATCH3_DIR=${GITHUB_WORKSPACE}/ww3/model
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export OASIS_INPUT_PATH=${GITHUB_WORKSPACE}/ww3/regtests/ww3_tp2.14/input/oasis3-mct
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export OASIS_WORK_PATH=${GITHUB_WORKSPACE}/ww3/regtests/ww3_tp2.14/input/work_oasis3-mct
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cd ww3/regtests/ww3_tp2.14/input/oasis3-mct/util/make_dir
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cmake .
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make VERBOSE=1
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cp -r ${GITHUB_WORKSPACE}/ww3/regtests/ww3_tp2.14/input/work_oasis3-mct ${GITHUB_WORKSPACE}
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build:
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needs: setup
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strategy:
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matrix:
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switch: [Ifremer1, NCEP_st2, NCEP_st4, ite_pdlib, NCEP_st4sbs, NCEP_glwu, OASACM, UKMO, MULTI_ESMF]
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runs-on: ubuntu-20.04
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steps:
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- name: checkout-ww3
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uses: actions/checkout@v2
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with:
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path: ww3
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- name: cache-env
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id: cache-env
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uses: actions/cache@v2
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with:
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path: |
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spack
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~/.spack
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work_oasis3-mct
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key: spack-${{ runner.os }}-${{ env.cache_key }}
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- name: build-ww3
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run: |
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source spack/share/spack/setup-env.sh
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spack env activate ww3-gnu
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cd ww3
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export CC=mpicc
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export FC=mpif90
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export OASISDIR=${GITHUB_WORKSPACE}/work_oasis3-mct
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mkdir build && cd build
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if [[ ${{ matrix.switch }} == "MULTI_ESMF" ]]; then
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cmake .. -DMULTI_ESMF=ON -DSWITCH=multi_esmf
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else
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cmake .. -DSWITCH=${{ matrix.switch }}
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fi
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make -j2 VERBOSE=1
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‎.github/workflows/intel.yml‎

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name: Intel Linux Build
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on: [push, pull_request]
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# Use custom shell with -l so .bash_profile is sourced which loads intel/oneapi/setvars.sh
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# without having to do it in manually every step
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defaults:
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run:
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shell: bash -leo pipefail {0}
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# Set I_MPI_CC/F90 so Intel MPI wrapper uses icc/ifort instead of gcc/gfortran
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env:
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cache_key: intel5
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CC: icc
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FC: ifort
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CXX: icpc
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I_MPI_CC: icc
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I_MPI_F90: ifort
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# Split into a dependency build step, and a WW3 build step which
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# builds multiple switches in a matrix. The setup is run once and
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# the environment is cached so each build of WW3 can share the dependencies.
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jobs:
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setup:
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runs-on: ubuntu-latest
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steps:
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# Cache spack, OASIS, and compiler
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# No way to flush Action cache, so key may have # appended
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- name: cache-env
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id: cache-env
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uses: actions/cache@v2
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with:
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path: |
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spack
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~/.spack
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work_oasis3-mct
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/opt/intel
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key: spack-${{ runner.os }}-${{ env.cache_key }}
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- name: install-intel-compilers
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if: steps.cache-env.outputs.cache-hit != 'true'
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run: |
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wget https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB
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sudo apt-key add GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB
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echo "deb https://apt.repos.intel.com/oneapi all main" | sudo tee /etc/apt/sources.list.d/oneAPI.list
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sudo apt-get update
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sudo apt-get install intel-oneapi-dev-utilities intel-oneapi-mpi-devel intel-oneapi-openmp intel-oneapi-compiler-fortran intel-oneapi-compiler-dpcpp-cpp-and-cpp-classic
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echo "source /opt/intel/oneapi/setvars.sh" >> ~/.bash_profile
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- name: checkout-ww3
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if: steps.cache-env.outputs.cache-hit != 'true'
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uses: actions/checkout@v2
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with:
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path: ww3
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# Build WW3 spack environment
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- name: install-dependencies-with-spack
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if: steps.cache-env.outputs.cache-hit != 'true'
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run: |
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# Install NetCDF, ESMF, g2, etc using Spack
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git clone -c feature.manyFiles=true https://github.com/spack/spack.git
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source spack/share/spack/setup-env.sh
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spack env create ww3-intel ww3/model/ci/spack.yaml
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spack env activate ww3-intel
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spack compiler find
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spack external find
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spack add intel-oneapi-mpi
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spack concretize
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spack install --dirty -v
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- name: build-oasis
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if: steps.cache-env.outputs.cache-hit != 'true'
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run: |
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source spack/share/spack/setup-env.sh
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spack env activate ww3-intel
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export WWATCH3_DIR=${GITHUB_WORKSPACE}/ww3/model
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export OASIS_INPUT_PATH=${GITHUB_WORKSPACE}/ww3/regtests/ww3_tp2.14/input/oasis3-mct
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export OASIS_WORK_PATH=${GITHUB_WORKSPACE}/ww3/regtests/ww3_tp2.14/input/work_oasis3-mct
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cd ww3/regtests/ww3_tp2.14/input/oasis3-mct/util/make_dir
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cmake .
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make
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cp -r ${GITHUB_WORKSPACE}/ww3/regtests/ww3_tp2.14/input/work_oasis3-mct ${GITHUB_WORKSPACE}
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build:
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needs: setup
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strategy:
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matrix:
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switch: [Ifremer1, NCEP_st2, NCEP_st4, ite_pdlib, NCEP_st4sbs, NCEP_glwu, OASACM, UKMO, MULTI_ESMF]
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runs-on: ubuntu-latest
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steps:
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- name: checkout-ww3
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uses: actions/checkout@v2
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with:
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path: ww3
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- name: install-intel
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run: |
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echo "source /opt/intel/oneapi/setvars.sh" >> ~/.bash_profile
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- name: cache-env
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id: cache-env
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uses: actions/cache@v2
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with:
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path: |
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spack
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~/.spack
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work_oasis3-mct
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/opt/intel
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key: spack-${{ runner.os }}-${{ env.cache_key }}
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- name: build-ww3
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run: |
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source spack/share/spack/setup-env.sh
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spack env activate ww3-intel
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cd ww3
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export CC=mpicc
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export FC=mpif90
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export OASISDIR=${GITHUB_WORKSPACE}/work_oasis3-mct
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mkdir build && cd build
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if [[ ${{ matrix.switch }} == "MULTI_ESMF" ]]; then
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cmake .. -DMULTI_ESMF=ON -DSWITCH=multi_esmf
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else
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cmake .. -DSWITCH=${{ matrix.switch }}
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fi
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make -j2
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