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Merge branch 'thorntonpe:master' into rfiorella/IM3-topunit-rad
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rfiorella authored Aug 5, 2024
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2 changes: 1 addition & 1 deletion .circleci/config.yml
Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@ version: 2.1
jobs:
build:
machine:
image: ubuntu-2004:202010-01
image: ubuntu-2004:2024.01.1
steps:
- checkout
- run: bash .circleci/setup.sh
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4 changes: 4 additions & 0 deletions .circleci/setup.sh
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Expand Up @@ -11,6 +11,10 @@ function download
return $?
}

# Install Singularity deps:

sudo apt-get update && sudo apt-get -y install uuid-dev

# Install Singularity
download && \
tar -xzf singularity-${VERSION}.tar.gz && \
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2 changes: 2 additions & 0 deletions .github/dependabot.yml
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Expand Up @@ -11,3 +11,5 @@ updates:
reviewers:
- "mahf708"
- "bartgol"
labels:
- "AT: Integrate Without Testing"
14 changes: 14 additions & 0 deletions .github/workflows/e3sm-gh-ci-cime-tests.yml
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Expand Up @@ -3,12 +3,25 @@ name: gh
on:
pull_request:
branches: [ master ]
paths:
# first, yes to these
- 'cime_config/**'
- 'components/eam/**'
- 'components/elm/**'
- 'driver-moab/**'
- 'driver-mct/**'
# second, no to these
- '!components/eam/docs/**'
- '!components/eam/mkdocs.yml'
- '!components/elm/docs/**'
- '!components/elm/mkdocs.yml'

workflow_dispatch:

jobs:

ci:
if: ${{ github.event.repository.name == 'e3sm' }}
runs-on: ubuntu-latest
strategy:
fail-fast: false
Expand All @@ -18,6 +31,7 @@ jobs:
- SMS_P4.ne4pg2_oQU480.F2010.singularity_gnu
- REP_P4.ne4pg2_oQU480.F2010.singularity_gnu
- ERS_P4.ne4pg2_oQU480.F2010.singularity_gnu
- ERS_P4.ne4pg2_oQU480.F2010.singularity_gnu.eam-wcprod_F2010
- ERP_P4.ne4pg2_oQU480.F2010.singularity_gnu
- PET_P4.ne4pg2_oQU480.F2010.singularity_gnu
- PEM_P4.ne4pg2_oQU480.F2010.singularity_gnu
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59 changes: 59 additions & 0 deletions .github/workflows/e3sm-gh-ci-w-cime-tests.yml
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@@ -0,0 +1,59 @@
name: gh

on:
pull_request:
branches: [ master ]
paths-ignore:
- 'mkdocs.yaml'
- 'docs/**'
- 'components/*/docs/**'
- 'components/*/mkdocs.yml'

workflow_dispatch:

jobs:

ci-w:
runs-on: ubuntu-latest
strategy:
fail-fast: false
matrix:
test:
- SMS_D_P8.ne4pg2_oQU480.WCYCL2010NS.singularity_gnu
- SMS_P8.ne4pg2_oQU480.WCYCL2010NS.singularity_gnu
- REP_P8.ne4pg2_oQU480.WCYCL2010NS.singularity_gnu
- ERS_P8.ne4pg2_oQU480.WCYCL2010NS.singularity_gnu
- ERS_P8.ne4pg2_oQU480.WCYCL2010NS.singularity_gnu.allactive-wcprod_1850
- ERP_P8.ne4pg2_oQU480.WCYCL2010NS.singularity_gnu
- PET_P8.ne4pg2_oQU480.WCYCL2010NS.singularity_gnu
- PEM_P8.ne4pg2_oQU480.WCYCL2010NS.singularity_gnu
container:
image: ghcr.io/mahf708/e3sm-imgs:v0.0.6

steps:
-
name: Checkout
uses: actions/checkout@v4
with:
show-progress: false
submodules: recursive
-
name: CIME
working-directory: cime/scripts
run: |
mkdir -p $HOME/projects/e3sm/cesm-inputdata/atm/cam/physprops/
wget https://web.lcrc.anl.gov/public/e3sm/inputdata/atm/cam/physprops/p3_lookup_table_1.dat-v4.1.2
mv p3_lookup_table_1.dat-v4.1.2 $HOME/projects/e3sm/cesm-inputdata/atm/cam/physprops/
export USER=test
./create_test ${{ matrix.test }} --wait --debug
-
name: Artifacts
uses: actions/upload-artifact@v4
if: ${{ always() }}
with:
name: ${{ matrix.test }}
path: |
~/projects/e3sm/scratch/${{ matrix.test }}*/TestStatus.log
~/projects/e3sm/scratch/${{ matrix.test }}*/bld/*.bldlog.*
~/projects/e3sm/scratch/${{ matrix.test }}*/run/*.log.*
~/projects/e3sm/scratch/${{ matrix.test }}*/run/*.cprnc.out
28 changes: 28 additions & 0 deletions .github/workflows/e3sm-gh-md-linter.yml
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@@ -0,0 +1,28 @@
name: markdown

# if .md files are touched in a PR, lint them!

on:
pull_request:
branches: ["master"]
paths:
- '**/*.md'

jobs:
linter:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
with:
fetch-depth: 0
- uses: tj-actions/changed-files@v44
id: changed-files
with:
files: '**/*.md'
separator: ","
- uses: DavidAnson/markdownlint-cli2-action@v16
if: steps.changed-files.outputs.any_changed == 'true'
with:
config: 'docs/.markdownlint.json'
globs: ${{ steps.changed-files.outputs.all_changed_files }}
separator: ","
6 changes: 3 additions & 3 deletions .github/workflows/e3sm-gh-pages.yml
Original file line number Diff line number Diff line change
Expand Up @@ -15,7 +15,7 @@ concurrency:

jobs:
Build-and-Deploy-docs:
if: ${{ github.event.repository.name != 'scream' }}
if: ${{ github.event.repository.name == 'e3sm' }}
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
Expand All @@ -31,7 +31,7 @@ jobs:
- name: Show action trigger
run: echo "= The job was automatically triggered by a ${{github.event_name}} event on repo ${{github.event.repository.name}}."
- name: Set up Python 3.10
uses: actions/setup-python@v5.0.0
uses: actions/setup-python@v5.1.0
with:
python-version: "3.10"
- name: Install python deps
Expand All @@ -53,7 +53,7 @@ jobs:
folder: ./site/
# If it's a PR from within the same repo, deploy to a preview page
# For security reasons, PRs from forks cannot write into gh-pages for now
- if: ${{ github.event_name == 'pull_request' && github.event.pull_request.head.repo.full_name == github.repository }}
- if: ${{ github.event_name == 'pull_request' && github.event.pull_request.head.repo.full_name == github.repository && github.actor != 'dependabot[bot]' }}
name: Preview docs
uses: rossjrw/pr-preview-action@v1
with:
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2 changes: 1 addition & 1 deletion .github/workflows/eamxx-gh-pages.yml
Original file line number Diff line number Diff line change
Expand Up @@ -54,7 +54,7 @@ jobs:
echo "= The job was automatically triggered by a ${{github.event_name}} event."
- name: Set up Python 3.10
uses: actions/setup-python@v5.0.0
uses: actions/setup-python@v5.1.0
with:
python-version: "3.10"

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62 changes: 62 additions & 0 deletions .github/workflows/eamxx_default_files.yml
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@@ -0,0 +1,62 @@
name: inputdata

on:
push:
branches: [ master ]
pull_request:
branches: [ master ]
schedule:
- cron: '00 00 * * *'
workflow_dispatch:

jobs:
scream-defaults:
runs-on: ubuntu-latest
outputs:
event_name: ${{ github.event_name }}
steps:
- name: Check out the repository
uses: actions/checkout@v4
with:
show-progress: false
submodules: false
- name: Set up Python 3.11
uses: actions/[email protected]
with:
python-version: "3.11"
- name: Run unit tests
working-directory: components/eamxx/cime_config/
run: |
python -m unittest tests/eamxx_default_files.py -v
notify-scream-defaults:
needs: scream-defaults
if: ${{ failure() && needs.scream-defaults.outputs.event_name != 'pull_request' }}
runs-on: ubuntu-latest
steps:
- name: Create issue
run: |
previous_issue_number=$(gh issue list \
--label "$LABELS" \
--json number \
--jq '.[0].number')
if [[ -n $previous_issue_number ]]; then
gh issue comment "$previous_issue_number" \
--body "$BODY"
else
gh issue create \
--title "$TITLE" \
--assignee "$ASSIGNEES" \
--label "$LABELS" \
--body "$BODY"
fi
env:
GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
GH_REPO: ${{ github.repository }}
TITLE: Inputdata server file missing
ASSIGNEES: mahf708,bartgol
LABELS: bug,input file,notify-file-gh-action
BODY: |
Workflow failed! There's likely a missing file specified in the configs! For more information, please see:
- Workflow URL: https://github.com/${{ github.repository }}/actions/runs/${{ github.run_id }} (number ${{ github.run_number }}, attempt ${{ github.run_attempt }})
- Workflow SHA: ${{ github.sha }}
7 changes: 7 additions & 0 deletions .gitignore
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Expand Up @@ -30,6 +30,13 @@ site
# Ignore emacs backup files
*~

#Ignore Mac folder files
.DS_Store

#Ignore vscode dir
.vscode


# Ignore mkdocs site-generated files in eamxx
components/eamxx/site/*
# Ignore auto-generated eamxx_params.md file
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4 changes: 2 additions & 2 deletions CITATION.cff
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Expand Up @@ -8,8 +8,8 @@ type: software
authors:
- given-names: E3SM
family-names: Project
version: 2.1.0
doi: 10.11578/E3SM/dc.20230110.5
version: 3.0.0
doi: 10.11578/E3SM/dc.20240301.3
repository-code: 'https://github.com/E3SM-Project/E3SM'
url: 'https://e3sm.org'
license: BSD-3-Clause
20 changes: 11 additions & 9 deletions README.md
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Expand Up @@ -9,12 +9,14 @@ the most challenging and demanding climate-change research problems and
Department of Energy mission needs while efficiently using DOE Leadership
Computing Facilities.

DOI: [10.11578/E3SM/dc.20230110.5](http://dx.doi.org/10.11578/E3SM/dc.20230110.5)
DOI: [10.11578/E3SM/dc.20240301.3](http://dx.doi.org/10.11578/E3SM/dc.20240301.3)

Please visit the [project website](https://e3sm.org) or our [Confluence site](https://acme-climate.atlassian.net/wiki/spaces/DOC/overview)
for further details.

For questions about the model, use [Github Discussions](https://github.com/E3SM-Project/E3SM/discussions)
For questions about the model, use [Github Discussions](https://github.com/E3SM-Project/E3SM/discussions).

See our Github-hosted documentation at [https://e3sm-project.github.io/E3SM/](https://e3sm-project.github.io/E3SM/).

Table of Contents
--------------------------------------------------------------------------------
Expand All @@ -27,7 +29,7 @@ Table of Contents

Quick Start
--------------------------------------------------------------------------------
The [Quick Start](https://e3sm.org/model/running-e3sm/e3sm-quick-start/) page
The [Quick Start](https://e3sm.org/model/running-e3sm/e3sm-quick-start/) page
includes instructions on obtaining the necessary code and input data for model
setup and execution on a supported machine.

Expand All @@ -42,7 +44,7 @@ To run E3SM, it is recommended that you obtain time on a

Running
--------------------------------------------------------------------------------
Please refer to [Running E3SM](https://e3sm.org/model/running-e3sm/)
Please refer to [Running E3SM](https://e3sm.org/model/running-e3sm/)
for instructions on running the model.

Contributing
Expand All @@ -64,11 +66,11 @@ the following BibTeX entry is provided.
author = {{E3SM Project}},
abstractNote = {{E3SM} is a state-of-the-art fully coupled model of the {E}arth's
climate including important biogeochemical and cryospheric processes.},
howpublished = {[Computer Software] \url{https://dx.doi.org/10.11578/E3SM/dc.20230110.5}},
url = {https://dx.doi.org/10.11578/E3SM/dc.20230110.5},
doi = {10.11578/E3SM/dc.20230110.5},
year = 2023,
month = jan,
howpublished = {[Computer Software] \url{https://dx.doi.org/10.11578/E3SM/dc.20240301.3}},
url = {https://dx.doi.org/10.11578/E3SM/dc.20240301.3},
doi = {10.11578/E3SM/dc.20240301.3},
year = 2024,
month = mar,
}
```

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20 changes: 16 additions & 4 deletions cime_config/allactive/config_compsets.xml
Original file line number Diff line number Diff line change
Expand Up @@ -70,9 +70,15 @@
<lname>1850_EAM%CMIP6_ELM%CNPRDCTCBCTOP_MPASSI_MPASO_MOSART_SGLC_SWAV</lname>
</compset>

<!-- Same as WCYCL1850NS but for 2010 (to avoid needing transient files). Mainly for testing. -->
<compset>
<alias>WCYCL2010NS</alias>
<lname>2010_EAM%CMIP6_ELM%CNPRDCTCBCTOP_MPASSI_MPASO_MOSART_SGLC_SWAV</lname>
</compset>

<compset>
<alias>WCYCL1950</alias>
<lname>1950SOI_EAM%CMIP6_ELM%SPBC_MPASSI_MPASO_MOSART_SGLC_SWAV</lname>
<lname>1950SOI_EAM%CMIP6_ELM%CNPRDCTCBCTOP_MPASSI_MPASO_MOSART_SGLC_SWAV</lname>
</compset>

<compset>
Expand Down Expand Up @@ -113,12 +119,17 @@

<compset>
<alias>WCYCLSSP585</alias>
<lname>SSP585SOI_EAM%CMIP6_ELM%SPBC_MPASSI_MPASO_MOSART_SGLC_SWAV</lname>
<lname>SSP585SOI_EAM%CMIP6_ELM%CNPRDCTCBCTOP_MPASSI_MPASO_MOSART_SGLC_SWAV</lname>
</compset>

<compset>
<alias>WCYCLSSP370</alias>
<lname>SSP370SOI_EAM%CMIP6_ELM%SPBC_MPASSI_MPASO_MOSART_SGLC_SWAV</lname>
<lname>SSP370SOI_EAM%CMIP6_ELM%CNPRDCTCBCTOP_MPASSI_MPASO_MOSART_SGLC_SWAV</lname>
</compset>

<compset>
<alias>WCYCLSSP245</alias>
<lname>SSP245SOI_EAM%CMIP6_ELM%CNPRDCTCBCTOP_MPASSI_MPASO_MOSART_SGLC_SWAV</lname>
</compset>

<!-- E3SM v1 science compsets -->
Expand Down Expand Up @@ -393,7 +404,7 @@

<compset>
<alias>BGWCYCL1850</alias>
<lname>1850_EAM%CMIP6_ELM%SPBC_MPASSI_MPASO_MOSART_MALI%STATIC_SWAV</lname>
<lname>1850_EAM%CMIP6_ELM%SPBC_MPASSI_MPASO_MOSART_MALI_SWAV</lname>
</compset>

<!-- EAMXX fully coupled compset -->
Expand Down Expand Up @@ -443,6 +454,7 @@
<value compset="20TR_EAM">1850-01-01</value>
<value compset="SSP585.*_EAM">2015-01-01</value>
<value compset="SSP370.*_EAM">2015-01-01</value>
<value compset="SSP245.*_EAM">2015-01-01</value>
</values>
</entry>

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