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…merge_2023_10_02

* upstream/master: (746 commits)
  Make "column_package" the default column_physics_type for BGC
  Ascent needs to use static hdf5 libs
  Don't change submodule
  Reorg csm_share Depends
  Clean up csm_share depends files a bit
  Update bld files to match Registry changes, using automated scripts
  Move some description changes from bld files to Registry
  Homme: Fix config.h comment style.
  Homme: Distinguish between F90 and C++ in HOMMEXX_ENABLE_GPU symbol use.
  Add missing variable to omp directive
  Add missing variable to omp directive
  Update CIME submodule
  Fix a few things I missed
  Homme: Comment out two builds that aren't used in ctests.
  Hommexx: Fix issues related to qsize=0.
  Hommexx: Remove redundant HOMMEXX_ENABLE_GPU definition.
  Homme: Fix potential bad access to an array.
  Homme: Add USE_MPI_RUN_SCRIPT to standalone system.
  Homme(xx)/SL: Add SL-transport feature to doubly periodic mode.
  Get rid of last Makefile Depends
  ...
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jgfouca committed Nov 2, 2023
2 parents b1e68f6 + 3872f4c commit 86f738e
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Showing 425 changed files with 29,361 additions and 79,965 deletions.
1 change: 0 additions & 1 deletion .circleci/checkout.sh
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Expand Up @@ -2,5 +2,4 @@

# Replace all ssh URLs to submodules with HTTP URLs
sed -i 's/git@github.com:/https:\/\/github.com\//' .gitmodules
sed -i 's/git@github.com:/https:\/\/github.com\//' cime/.gitmodules
git submodule update --init --recursive
5 changes: 3 additions & 2 deletions .circleci/container.sh
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@@ -1,7 +1,8 @@
#!/bin/bash

wget -t 3 -O e3sm.sif http://portal.nersc.gov/project/e3sm/lukasz/e3sm.sif || \
wget -t 3 -O e3sm.sif https://dabdceba-6d04-11e5-ba46-22000b92c6ec.e.globus.org/containers/public/e3sm.sif
singularity pull e3sm.sif \
docker://ghcr.io/mahf708/e3sm-imgs@sha256:d1030a6f4e3a53f682859436a26b30a9477d69423829ae1d9c1b5ab4e255430d

if [ $? -ne 0 ]; then
exit -1
fi
2 changes: 1 addition & 1 deletion .circleci/run.sh
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Expand Up @@ -57,7 +57,7 @@ rc=$?
if [ $rc -ne 0 ]; then
print_bldlog "e3sm"
print_bldlog "csm_share"
print_bldlog "pio"
print_bldlog "spio"
print_bldlog "mct"
print_bldlog "gptl"
exit $rc
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50 changes: 50 additions & 0 deletions .github/workflows/e3sm-gh-pages.yml
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@@ -0,0 +1,50 @@
name: Build and deploy gh-pages branch with Mkdocs

on:
# Runs every time master branch is updated
push:
branches: ["master"]
# Runs every time a PR is open against master
pull_request:
branches: ["master"]
workflow_dispatch:

concurrency:
# Prevent 2+ copies of this workflow from running concurrently
group: e3sm-docs-action

jobs:
Build-and-Deploy-docs:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
with:
show-progress: false
fetch-depth: 0 # Needed, or else gh-pages won't be fetched, and push rejected
submodules: false # speeds up clone and not building anything in submodules
- name: Show action trigger
run: echo "= The job was automatically triggered by a ${{github.event_name}} event."
- name: Set up Python 3.10
uses: actions/setup-python@v4.7.0
with:
python-version: "3.10"
- name: Install python deps
run: python3 -m pip install mkdocs-material pymdown-extensions mkdocs-monorepo-plugin mdutils
# build every time (PR or push to master)
- name: Build
run: mkdocs build --strict --verbose
# Only deploy to the main github page when there is a push to master
- if: ${{ github.event_name == 'push' }}
name: GitHub Pages action
uses: JamesIves/github-pages-deploy-action@v4
with:
# Do not remove existing pr-preview pages
clean-exclude: pr-preview
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 }}
name: Preview docs
uses: rossjrw/pr-preview-action@v1
with:
source-dir: ./site/
3 changes: 3 additions & 0 deletions .gitignore
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Expand Up @@ -24,6 +24,9 @@ buildnmlc
buildlibc
buildlib_cmakec

#the site directory
site

# Ignore emacs backup files
*~

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7 changes: 7 additions & 0 deletions .gitmodules
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Expand Up @@ -70,9 +70,16 @@
path = components/ww3/src/WW3
url = git@github.com:E3SM-Project/WW3.git
branch = e3sm
[submodule "components/eam/src/physics/crm/pam/external"]
path = components/eam/src/physics/crm/pam/external
url = git@github.com:E3SM-Project/PAM.git
[submodule "components/mpas-seaice/src/icepack"]
path = components/mpas-seaice/src/icepack
url = git@github.com:E3SM-Project/Icepack.git
[submodule "externals/haero"]
path = externals/haero
url = git@github.com:eagles-project/haero.git
[submodule "externals/mam4xx"]
path = externals/mam4xx
url = git@github.com:eagles-project/mam4xx.git

58 changes: 20 additions & 38 deletions cime_config/allactive/config_pesall.xml
Original file line number Diff line number Diff line change
Expand Up @@ -265,7 +265,7 @@
<grid name="a%ne30np4">
<mach name="pm-cpu|alvarez">
<pes compset="JRA_ELM.+MPASSI.+MPASO.+MOSART.+SGLC.+SWAV" pesize="any">
<comment>"pm-cpu 4 nodes, 256 partition, 128x1, c8"</comment>
<comment>"pm-cpu 4 nodes, 256 partition, 128x1"</comment>
<ntasks>
<ntasks_atm>-4</ntasks_atm>
<ntasks_lnd>-4</ntasks_lnd>
Expand All @@ -274,11 +274,8 @@
<ntasks_ocn>-4</ntasks_ocn>
<ntasks_glc>-1</ntasks_glc>
<ntasks_wav>-1</ntasks_wav>
<ntasks_cpl>64</ntasks_cpl>
<ntasks_cpl>-4</ntasks_cpl>
</ntasks>
<pstrid>
<pstrid_cpl>8</pstrid_cpl>
</pstrid>
</pes>
</mach>
<mach name="gcp12">
Expand Down Expand Up @@ -552,11 +549,11 @@
<grid name="a%ne120np4">
<mach name="pm-cpu|alvarez">
<pes compset=".*EAM.+ELM.+MPASSI.+MPASO.+MOSART.+SWAV.*" pesize="any">
<comment>ne120-wcycl on 42 nodes 128x1c8 ~0.7 sypd</comment>
<comment>ne120-wcycl on 42 nodes 128x1 ~0.7 sypd</comment>
<MAX_MPITASKS_PER_NODE>128</MAX_MPITASKS_PER_NODE>
<ntasks>
<ntasks_atm>3072</ntasks_atm>
<ntasks_cpl>384</ntasks_cpl>
<ntasks_cpl>3072</ntasks_cpl>
<ntasks_ice>3072</ntasks_ice>
<ntasks_lnd>2560</ntasks_lnd>
<ntasks_rof>512</ntasks_rof>
Expand Down Expand Up @@ -584,9 +581,6 @@
<rootpe_glc>0</rootpe_glc>
<rootpe_wav>0</rootpe_wav>
</rootpe>
<pstrid>
<pstrid_cpl>8</pstrid_cpl>
</pstrid>
</pes>
</mach>
<mach name="theta">
Expand Down Expand Up @@ -1252,15 +1246,15 @@
</mach>
<mach name="pm-cpu|alvarez">
<pes compset=".*EAM.+ELM.+MPASSI.+MPASO.+MOSART.+" pesize="any">
<comment> -compset A_WCYCL* -res ne30pg2_oECv3 with MPASO on 7 nodes, 128x1 c8 </comment>
<comment> -compset A_WCYCL* -res ne30pg2_oECv3 with MPASO on 7 nodes, 128x1 </comment>
<MAX_MPITASKS_PER_NODE>128</MAX_MPITASKS_PER_NODE>
<ntasks>
<ntasks_atm>640</ntasks_atm>
<ntasks_lnd>640</ntasks_lnd>
<ntasks_rof>640</ntasks_rof>
<ntasks_ice>640</ntasks_ice>
<ntasks_ocn>256</ntasks_ocn>
<ntasks_cpl>80</ntasks_cpl>
<ntasks_cpl>640</ntasks_cpl>
</ntasks>
<nthrds>
<nthrds_atm>1</nthrds_atm>
Expand All @@ -1278,20 +1272,17 @@
<rootpe_ocn>640</rootpe_ocn>
<rootpe_cpl>0</rootpe_cpl>
</rootpe>
<pstrid>
<pstrid_cpl>8</pstrid_cpl>
</pstrid>
</pes>
<pes compset=".*EAM.+ELM.+MPASSI.+MPASO.+MOSART.+" pesize="L">
<comment> -compset A_WCYCL* -res ne30pg2_oECv3 with MPASO on 58 nodes, ~20 sypd</comment>
<comment> -compset A_WCYCL* -res ne30pg2_oECv3 with MPASO on 58 nodes, 128x1, ~20 sypd</comment>
<MAX_MPITASKS_PER_NODE>128</MAX_MPITASKS_PER_NODE>
<ntasks>
<ntasks_atm>5504</ntasks_atm>
<ntasks_lnd>5248</ntasks_lnd>
<ntasks_rof>256</ntasks_rof>
<ntasks_ice>5248</ntasks_ice>
<ntasks_ocn>1920</ntasks_ocn>
<ntasks_cpl>688</ntasks_cpl>
<ntasks_cpl>5504</ntasks_cpl>
</ntasks>
<nthrds>
<nthrds_atm>1</nthrds_atm>
Expand All @@ -1309,9 +1300,6 @@
<rootpe_ocn>5504</rootpe_ocn>
<rootpe_cpl>0</rootpe_cpl>
</rootpe>
<pstrid>
<pstrid_cpl>8</pstrid_cpl>
</pstrid>
</pes>
</mach>
</grid>
Expand Down Expand Up @@ -1757,7 +1745,7 @@
</mach>
<mach name="pm-cpu|alvarez">
<pes compset="any" pesize="any">
<comment>"pm-cpu ne30np4 and ne30np4.pg2 2 nodes 1 thread, 128x1 c8"</comment>
<comment>"pm-cpu ne30np4 and ne30np4.pg2 2 nodes 1 thread, 128x1"</comment>
<ntasks>
<ntasks_atm>-2</ntasks_atm>
<ntasks_lnd>-2</ntasks_lnd>
Expand All @@ -1766,11 +1754,8 @@
<ntasks_ocn>-2</ntasks_ocn>
<ntasks_glc>-2</ntasks_glc>
<ntasks_wav>-2</ntasks_wav>
<ntasks_cpl>32</ntasks_cpl>
<ntasks_cpl>-2</ntasks_cpl>
</ntasks>
<pstrid>
<pstrid_cpl>8</pstrid_cpl>
</pstrid>
</pes>
</mach>
<mach name="crusher-scream-gpu">
Expand Down Expand Up @@ -1967,21 +1952,21 @@
</mach>
<mach name="anvil">
<pes compset=".*EAM.+ELM.+MPASSI.+MPASO.+MOSART.+SWAV.+" pesize="S">
<comment> for testing only, scaled from compy </comment>
<comment> RRM-WCYCL: 64 nodes 2.133 sypd </comment>
<ntasks>
<ntasks_atm>720</ntasks_atm>
<ntasks_lnd>720</ntasks_lnd>
<ntasks_rof>720</ntasks_rof>
<ntasks_ice>720</ntasks_ice>
<ntasks_ocn>324</ntasks_ocn>
<ntasks_cpl>720</ntasks_cpl>
<ntasks_atm>1800</ntasks_atm>
<ntasks_lnd>1800</ntasks_lnd>
<ntasks_rof>1800</ntasks_rof>
<ntasks_ice>1800</ntasks_ice>
<ntasks_ocn>504</ntasks_ocn>
<ntasks_cpl>1800</ntasks_cpl>
</ntasks>
<rootpe>
<rootpe_atm>0</rootpe_atm>
<rootpe_lnd>0</rootpe_lnd>
<rootpe_rof>0</rootpe_rof>
<rootpe_ice>0</rootpe_ice>
<rootpe_ocn>720</rootpe_ocn>
<rootpe_ocn>1800</rootpe_ocn>
<rootpe_cpl>0</rootpe_cpl>
</rootpe>
</pes>
Expand Down Expand Up @@ -2095,14 +2080,14 @@
</mach>
<mach name="pm-cpu|alvarez">
<pes compset=".*EAM.+ELM.+MPASSI.+MPASO.+MOSART.+" pesize="any">
<comment> 8 nodes, 128x1 c8</comment>
<comment> 8 nodes, 128x1</comment>
<ntasks>
<ntasks_atm>640</ntasks_atm>
<ntasks_lnd>640</ntasks_lnd>
<ntasks_rof>640</ntasks_rof>
<ntasks_ice>640</ntasks_ice>
<ntasks_ocn>384</ntasks_ocn>
<ntasks_cpl>80</ntasks_cpl>
<ntasks_cpl>640</ntasks_cpl>
</ntasks>
<rootpe>
<rootpe_atm>0</rootpe_atm>
Expand All @@ -2120,9 +2105,6 @@
<nthrds_ocn>1</nthrds_ocn>
<nthrds_cpl>1</nthrds_cpl>
</nthrds>
<pstrid>
<pstrid_cpl>1</pstrid_cpl>
</pstrid>
</pes>
</mach>
</grid>
Expand Down
5 changes: 3 additions & 2 deletions cime_config/config_files.xml
Original file line number Diff line number Diff line change
Expand Up @@ -348,6 +348,7 @@
<value component="scream" >$COMP_ROOT_DIR_ATM/cime_config/testdefs/testmods_dirs</value>
<value component="mpaso" >$COMP_ROOT_DIR_OCN/cime_config/testdefs/testmods_dirs</value>
<value component="mpassi" >$COMP_ROOT_DIR_ICE/cime_config/testdefs/testmods_dirs</value>
<value component="ww3" >$COMP_ROOT_DIR_WAV/cime_config/testdefs/testmods_dirs</value>
</values>
<group>case_last</group>
<file>env_case.xml</file>
Expand Down Expand Up @@ -540,9 +541,9 @@
<value lib="gptl">$SRCROOT/share/build/buildlib.gptl</value>
<value lib="pio">$CIMEROOT/CIME/build_scripts/buildlib.pio</value>
<value lib="spio">$SRCROOT/share/build/buildlib.spio</value>
<value lib="mct">$CIMEROOT/CIME/build_scripts/buildlib.mct</value>
<value lib="mct">$SRCROOT/share/build/buildlib.mct</value>
<value lib="csm_share">$SRCROOT/share/build/buildlib.csm_share</value>
<value lib="mpi-serial">$CIMEROOT/CIME/build_scripts/buildlib.mpi-serial</value>
<value lib="mpi-serial">$SRCROOT/share/build/buildlib.mpi-serial</value>
<value lib="cprnc">$CIMEROOT/CIME/build_scripts/buildlib.cprnc</value>
</values>
<group>case_last</group>
Expand Down
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