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Merge maint-3.0 to master #6777

Merged
merged 23 commits into from
Nov 26, 2024
Merged

Merge maint-3.0 to master #6777

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8a6317e
Add moab_dev test suite
rljacob Oct 4, 2024
5ce020b
restart case ERS_Vmoab_Ld3.T62_oQU120.CMPASO-NYF fix
iulian787 Oct 4, 2024
5667b49
Merge branch 'iulian787/restart_moab_oQU120' into rljacob/mbcpl/add-t…
iulian787 Oct 7, 2024
bcf8e7d
get ice domain for data from SDICE structure
iulian787 Oct 8, 2024
bd78709
Merge branch 'iulian787/restart_moab_oQU120' into rljacob/mbcpl/add-t…
iulian787 Oct 8, 2024
99165ed
activate gh/ci on maint-3.0
mahf708 Oct 24, 2024
019bc13
Merge branch 'mahf708/ig/maint-3.0-gh-ci' in to maint-3.0 (PR #6707)
rljacob Oct 27, 2024
daae468
Chemistry output bug fix
jinboxie Oct 29, 2024
5bec775
Add e3sm_prod PEs for maint-3.0 on Improv
amametjanov Oct 31, 2024
43ba2f5
Modify pe layouts for anvil
rljacob Nov 1, 2024
24f19fb
Merge branch 'rljacob/test/anvil-pes' into maint-3.0 (PR #6728)
rljacob Nov 1, 2024
0a1fa17
Update anvil pelayout for v3 RRM
rljacob Nov 2, 2024
c8d45d6
Merge branch 'rljacob/test/anvil-rrm' into maint-3.0 (PR #6731)
rljacob Nov 2, 2024
b17bb0f
Merge branch 'rljacob/mbcpl/add-tests' into maint-3.0 (PR #6712)
rljacob Nov 6, 2024
580c366
remove tri grid land mesh on component side
iulian787 Oct 18, 2024
cf99325
forgot about this one
iulian787 Oct 18, 2024
4165e3e
ocean import/export alignment
iulian787 Oct 22, 2024
04b66a0
compare before importing
iulian787 Oct 22, 2024
3742c43
set aream for rof when it is not computed by us
iulian787 Oct 23, 2024
28f8501
index for aream
iulian787 Oct 23, 2024
fa1c317
Merge branch 'azamat/improv-maint30/fix-oom-prod-tests' into maint-3.0
amametjanov Nov 8, 2024
3f899ce
Merge branch 'jinboxie/atm/chemistry_output_maint-3.0' into maint-3.0…
wlin7 Nov 21, 2024
0e747dc
Merge branch 'iulian787/land_grid_simple' (PR #6754) into maint-3.0
rljacob Nov 25, 2024
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12 changes: 9 additions & 3 deletions .github/workflows/e3sm-gh-ci-cime-tests.yml
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Expand Up @@ -2,7 +2,9 @@ name: gh

on:
pull_request:
branches: [ master ]
branches:
- master
- maint-3.0
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@mahf708 I did a test merge and this diff is real. Do we want this change?

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Yeah, it's fine to include it. It just means when PRs are open against maint-3.0, the actions will run. So, this won't impact regular PRs to master. It's better to include so that we don't have to see this diff again (in other syncs)

paths:
# first, yes to these
- '.github/workflows/e3sm-gh-ci-cime-tests.yml'
Expand All @@ -22,10 +24,14 @@ on:

workflow_dispatch:

concurrency:
group: ${{ github.workflow }}-${{ github.event_name }}-${{ github.event.pull_request.number || github.run_id }}
cancel-in-progress: true

jobs:

ci:
if: ${{ github.event.repository.name == 'e3sm' }}
if: ${{ github.repository == 'E3SM-Project/E3SM' }}
runs-on: ubuntu-latest
strategy:
fail-fast: false
Expand All @@ -36,7 +42,7 @@ jobs:
- SMS_D_Ln5_P4.ne4pg2_oQU480.F2010-SCREAMv1-MPASSI.ghci-oci_gnu
- ERS_Ld5_P4.ne4pg2_oQU480.F2010-SCREAMv1-MPASSI.ghci-oci_gnu.eamxx-prod
container:
image: ghcr.io/e3sm-project/containers-ghci:ghci-0.1.0
image: ghcr.io/e3sm-project/containers-ghci:ghci-0.2.0

steps:
-
Expand Down
16 changes: 11 additions & 5 deletions .github/workflows/e3sm-gh-ci-w-cime-tests.yml
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@@ -1,8 +1,10 @@
name: gh
name: gh-w

on:
pull_request:
branches: [ master ]
branches:
- master
- maint-3.0
paths-ignore:
- 'mkdocs.yaml'
- 'docs/**'
Expand All @@ -11,10 +13,14 @@ on:

workflow_dispatch:

concurrency:
group: ${{ github.workflow }}-${{ github.event_name }}-${{ github.event.pull_request.number || github.run_id }}
cancel-in-progress: true

jobs:

ci-w:
if: ${{ github.event.repository.name == 'e3sm' }}
ci:
if: ${{ github.repository == 'E3SM-Project/E3SM' }}
runs-on: ubuntu-latest
strategy:
fail-fast: false
Expand All @@ -23,7 +29,7 @@ jobs:
- SMS_D_Ld1_P8.ne4pg2_oQU480.WCYCL2010NS.ghci-oci_gnu
- ERS_Ld3_P8.ne4pg2_oQU480.WCYCL2010NS.ghci-oci_gnu.allactive-wcprod_1850
container:
image: ghcr.io/e3sm-project/containers-ghci:ghci-0.1.0
image: ghcr.io/e3sm-project/containers-ghci:ghci-0.2.0

steps:
-
Expand Down
5 changes: 5 additions & 0 deletions .github/workflows/e3sm-gh-md-linter.yml
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Expand Up @@ -10,8 +10,13 @@ on:
# for now let's not lint files in eamxx
- '!components/eamxx/**/*.md'

concurrency:
group: ${{ github.workflow }}-${{ github.event_name }}-${{ github.event.pull_request.number || github.run_id }}
cancel-in-progress: true

jobs:
linter:
if: ${{ github.repository == 'E3SM-Project/E3SM' }}
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
Expand Down
2 changes: 1 addition & 1 deletion .github/workflows/e3sm-gh-pages.yml
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Expand Up @@ -15,7 +15,7 @@ concurrency:

jobs:
Build-and-Deploy-docs:
if: ${{ github.event.repository.name == 'e3sm' }}
if: ${{ github.repository == 'E3SM-Project/E3SM' }}
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
Expand Down
10 changes: 6 additions & 4 deletions .github/workflows/e3sm-gh-tools-mkatmsrffile-test.yml
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Expand Up @@ -11,8 +11,13 @@ on:
- cron: '00 15 * * 2'
workflow_dispatch:

concurrency:
group: ${{ github.workflow }}-${{ github.event_name }}-${{ github.event.pull_request.number || github.run_id }}
cancel-in-progress: true

jobs:
mkatmsrffile-test:
if: ${{ github.repository == 'E3SM-Project/E3SM' }}
runs-on: ubuntu-latest
defaults:
run:
Expand All @@ -31,18 +36,15 @@ jobs:
uses: conda-incubator/setup-miniconda@v3
with:
activate-environment: "envmkatmsrffile"
miniforge-variant: Mambaforge
miniforge-version: latest
use-mamba: true
mamba-version: "*"
channel-priority: strict
auto-update-conda: true
python-version: 3.11
-
name: Install dependencies
run: |
echo $CONDA_PREFIX
mamba install -y nco xarray numba numpy netcdf4
conda install -y nco xarray numba numpy netcdf4 -c conda-forge
-
name: Run tests
working-directory: components/eam/tools/mkatmsrffile
Expand Down
5 changes: 5 additions & 0 deletions .github/workflows/eamxx-gh-ci-standalone.yml
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Expand Up @@ -15,9 +15,14 @@ on:

workflow_dispatch:

concurrency:
group: ${{ github.workflow }}-${{ github.event_name }}-${{ github.event.pull_request.number || github.run_id }}
cancel-in-progress: true

jobs:

ci:
if: ${{ github.repository == 'E3SM-Project/E3SM' }}
runs-on: ubuntu-latest
strategy:
fail-fast: false
Expand Down
2 changes: 1 addition & 1 deletion .github/workflows/eamxx-gh-pages.yml
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Expand Up @@ -34,7 +34,7 @@ concurrency:
jobs:

eamxx-docs:
if: ${{ github.event.repository.name == 'scream' }}
if: ${{ github.repository == 'E3SM-Project/scream' }}
runs-on: ubuntu-latest

steps:
Expand Down
6 changes: 5 additions & 1 deletion .github/workflows/eamxx_default_files.yml
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Expand Up @@ -11,9 +11,13 @@ on:
- cron: '00 00 * * *'
workflow_dispatch:

concurrency:
group: ${{ github.workflow }}-${{ github.event_name }}-${{ github.event.pull_request.number || github.run_id }}
cancel-in-progress: true

jobs:
scream-defaults:
if: ${{ github.event.repository.name == 'e3sm' }}
if: ${{ github.repository == 'E3SM-Project/E3SM' }}
runs-on: ubuntu-latest
outputs:
event_name: ${{ github.event_name }}
Expand Down
31 changes: 23 additions & 8 deletions cime_config/allactive/config_pesall.xml
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Expand Up @@ -1169,14 +1169,14 @@
<pes compset="any" pesize="any">
<comment>improv: any compset on ne30np4 grid</comment>
<ntasks>
<ntasks_atm>-4</ntasks_atm>
<ntasks_lnd>-4</ntasks_lnd>
<ntasks_rof>-4</ntasks_rof>
<ntasks_ice>-4</ntasks_ice>
<ntasks_ocn>-4</ntasks_ocn>
<ntasks_cpl>-4</ntasks_cpl>
<ntasks_glc>-4</ntasks_glc>
<ntasks_wav>-4</ntasks_wav>
<ntasks_atm>-6</ntasks_atm>
<ntasks_lnd>-6</ntasks_lnd>
<ntasks_rof>-6</ntasks_rof>
<ntasks_ice>-6</ntasks_ice>
<ntasks_ocn>-6</ntasks_ocn>
<ntasks_cpl>-6</ntasks_cpl>
<ntasks_glc>-6</ntasks_glc>
<ntasks_wav>-6</ntasks_wav>
</ntasks>
</pes>
<pes compset=".*EAM.+ELM.+MPASSI.+SGLC.+SWAV.+BGC.*" pesize="any">
Expand Down Expand Up @@ -2065,6 +2065,21 @@
</rootpe>
</pes>
</mach>
<mach name="improv">
<pes compset=".*EAM.+ELM.+MPASSI.+MPASO.+MOSART.+SGLC.+SWAV.+" pesize="S">
<comment>improv+allactive: RRM-WCYCL on 6 nodes</comment>
<ntasks>
<ntasks_atm>-6</ntasks_atm>
<ntasks_lnd>-6</ntasks_lnd>
<ntasks_rof>-6</ntasks_rof>
<ntasks_ice>-6</ntasks_ice>
<ntasks_ocn>-6</ntasks_ocn>
<ntasks_cpl>-6</ntasks_cpl>
<ntasks_glc>-6</ntasks_glc>
<ntasks_wav>-6</ntasks_wav>
</ntasks>
</pes>
</mach>
<mach name="chrysalis">
<pes compset=".*EAM.+ELM.+MPASSI.+MPASO.+MOSART.+SGLC.+SWAV.+" pesize="T">
<comment> cmod016b64x1 s=2.4 </comment>
Expand Down
2 changes: 1 addition & 1 deletion cime_config/machines/config_machines.xml
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Expand Up @@ -2775,7 +2775,7 @@ commented out until "*** No rule to make target '.../libadios2pio-nm-lib.a'" iss
<env name="PATH">/lcrc/group/e3sm/soft/improv/pnetcdf/1.12.3/gcc-12.3.0/openmpi-4.1.6/bin:/lcrc/group/e3sm/soft/improv/netcdf-fortran/4.6.1b/gcc-12.3.0/openmpi-4.1.6/bin:/lcrc/group/e3sm/soft/improv/netcdf-c/4.9.2b/gcc-12.3.0/openmpi-4.1.6/bin:/lcrc/group/e3sm/soft/improv/openmpi/4.1.6/gcc-12.3.0/bin:/lcrc/group/e3sm/soft/perl/improv/bin:$ENV{PATH}</env>
<env name="LD_LIBRARY_PATH">$SHELL{lp=/lcrc/group/e3sm/soft/improv/netlib-lapack/3.12.0/gcc-12.3.0:/lcrc/group/e3sm/soft/improv/pnetcdf/1.12.3/gcc-12.3.0/openmpi-4.1.6/lib:/lcrc/group/e3sm/soft/improv/netcdf-fortran/4.6.1b/gcc-12.3.0/openmpi-4.1.6/lib:/lcrc/group/e3sm/soft/improv/netcdf-c/4.9.2b/gcc-12.3.0/openmpi-4.1.6/lib:/opt/pbs/lib:/lcrc/group/e3sm/soft/improv/openmpi/4.1.6/gcc-12.3.0/lib; if [ -z "$LD_LIBRARY_PATH" ]; then echo $lp; else echo "$lp:$LD_LIBRARY_PATH"; fi}</env>
<env name="MOAB_ROOT">$SHELL{if [ -z "$MOAB_ROOT" ]; then echo /lcrc/soft/climate/moab/improv/gnu; else echo "$MOAB_ROOT"; fi}</env>
<env name="OMPI_MCA_sharedfp">^lockedfile</env>
<env name="OMPI_MCA_sharedfp">^lockedfile,individual</env>
</environment_variables>
<environment_variables BUILD_THREADED="TRUE">
<env name="OMP_STACKSIZE">128M</env>
Expand Down
59 changes: 40 additions & 19 deletions cime_config/testmods_dirs/config_pes_tests.xml
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Expand Up @@ -161,31 +161,41 @@
</ntasks>
</pes>
<pes compset=".*EAM.+ELM.+MPASSI.+MPASO.+MOSART.+SGLC.+SWAV.+_SESP$" pesize="any">
<comment>tests+anvil: --compset WCYCL* --res ne30pg2_IcoswISC30E3r5 on 16 nodes pure-MPI </comment>
<comment>tests+anvil: --compset WCYCL* --res ne30pg2_IcoswISC30E3r5 on 25 nodes pure-MPI </comment>
<ntasks>
<ntasks_atm>396</ntasks_atm>
<ntasks_lnd>396</ntasks_lnd>
<ntasks_rof>396</ntasks_rof>
<ntasks_ice>396</ntasks_ice>
<ntasks_ocn>180</ntasks_ocn>
<ntasks_cpl>396</ntasks_cpl>
<ntasks_atm>675</ntasks_atm>
<ntasks_lnd>324</ntasks_lnd>
<ntasks_rof>324</ntasks_rof>
<ntasks_ice>360</ntasks_ice>
<ntasks_ocn>216</ntasks_ocn>
<ntasks_cpl>684</ntasks_cpl>
</ntasks>
<rootpe>
<rootpe_ocn>396</rootpe_ocn>
<rootpe_atm>0</rootpe_atm>
<rootpe_lnd>360</rootpe_lnd>
<rootpe_rof>360</rootpe_rof>
<rootpe_ice>0</rootpe_ice>
<rootpe_ocn>684</rootpe_ocn>
<rootpe_cpl>0</rootpe_cpl>
</rootpe>
</pes>
<pes compset=".*EAM.+ELM.+MPASSI.+MPASO.+SGLC_SWAV_SIAC_SESP_BGC.*" pesize="any">
<comment>tests+anvil: --compset BGC* --res ne30pg2_r05_IcoswISC30E3r5 on 30 nodes pure-MPI </comment>
<ntasks>
<ntasks_atm>675</ntasks_atm>
<ntasks_lnd>684</ntasks_lnd>
<ntasks_rof>684</ntasks_rof>
<ntasks_ice>684</ntasks_ice>
<ntasks_ocn>396</ntasks_ocn>
<ntasks_lnd>324</ntasks_lnd>
<ntasks_rof>324</ntasks_rof>
<ntasks_ice>360</ntasks_ice>
<ntasks_ocn>216</ntasks_ocn>
<ntasks_cpl>684</ntasks_cpl>
</ntasks>
<rootpe>
<rootpe_atm>0</rootpe_atm>
<rootpe_lnd>360</rootpe_lnd>
<rootpe_rof>360</rootpe_rof>
<rootpe_ice>0</rootpe_ice>
<rootpe_ocn>684</rootpe_ocn>
<rootpe_cpl>0</rootpe_cpl>
</rootpe>
</pes>
</mach>
Expand All @@ -203,6 +213,17 @@
<ntasks_cpl>-6</ntasks_cpl>
</ntasks>
</pes>
<pes compset="EAM.+ELM.+DOCN." pesize="any">
<comment>"tests+anvil, F compset, 6 nodes"</comment>
<ntasks>
<ntasks_atm>-16</ntasks_atm>
<ntasks_lnd>-16</ntasks_lnd>
<ntasks_rof>-16</ntasks_rof>
<ntasks_ice>-16</ntasks_ice>
<ntasks_ocn>-16</ntasks_ocn>
<ntasks_cpl>-16</ntasks_cpl>
</ntasks>
</pes>
</mach>
</grid>
<grid name="oi%IcoswISC30.*">
Expand Down Expand Up @@ -241,17 +262,17 @@
</mach>
<mach name="anvil">
<pes compset=".*EAM.+ELM.+MPASSI.+MPASO.+MOSART.+SWAV.+" pesize="any">
<comment>tests+anvil: --compset WCYCL1850 --res northamericax4v1pg2_WC14to60E2r3 on 64 nodes pure-MPI, 2.133 sypd </comment>
<comment>tests+anvil: --compset WCYCL1850 --res northamericax4v1pg2_WC14to60E2r3 on 69 nodes pure-MPI, 2.046 sypd </comment>
<ntasks>
<ntasks_atm>1800</ntasks_atm>
<ntasks_lnd>1800</ntasks_lnd>
<ntasks_rof>1800</ntasks_rof>
<ntasks_ice>1800</ntasks_ice>
<ntasks_atm>1980</ntasks_atm>
<ntasks_lnd>1980</ntasks_lnd>
<ntasks_rof>1980</ntasks_rof>
<ntasks_ice>1944</ntasks_ice>
<ntasks_ocn>504</ntasks_ocn>
<ntasks_cpl>1800</ntasks_cpl>
<ntasks_cpl>1980</ntasks_cpl>
</ntasks>
<rootpe>
<rootpe_ocn>1800</rootpe_ocn>
<rootpe_ocn>1980</rootpe_ocn>
</rootpe>
</pes>
</mach>
Expand Down
13 changes: 13 additions & 0 deletions cime_config/tests.py
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Expand Up @@ -761,6 +761,19 @@
)
},

"e3sm_moab_dev" : {
"time" : "01:00:00",
"tests" : (
"ERS_Vmoab_Ld3.ne4pg2_oQU480.WCYCL1850NS",
"ERS_Vmoab_Ld3.ne4pg2_oQU480.F1850",
"ERS_Vmoab_Ld3.ne4pg2_ne4pg2.I1850CNPRDCTCBCTOP",
"ERS_Vmoab_Ld3.T62_oQU240wLI.GMPAS-IAF",
"ERS_Vmoab_Ld3.T62_oQU120.CMPASO-NYF",
"ERS_Vmoab_Ld3.r05_r05.RMOSGPCC",
)
},



"e3sm_gpuacc" : {
"tests" : (
Expand Down
17 changes: 2 additions & 15 deletions components/data_comps/dice/src/ice_comp_mct.F90
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Expand Up @@ -79,16 +79,6 @@ subroutine ice_init_mct( EClock, cdata, x2i, i2x, NLFilename )
logical :: scmMode = .false. ! single column mode
real(R8) :: scmLat = shr_const_SPVAL ! single column lat
real(R8) :: scmLon = shr_const_SPVAL ! single column lon
#ifdef HAVE_MOAB
character(CL) :: filePath ! generic file path
character(CL) :: fileName ! generic file name
character(CS) :: timeName ! domain file: time variable name
character(CS) :: lonName ! domain file: lon variable name
character(CS) :: latName ! domain file: lat variable name
character(CS) :: hgtName ! domain file: hgt variable name
character(CS) :: maskName ! domain file: mask variable name
character(CS) :: areaName ! domain file: area variable name
#endif
character(*), parameter :: subName = "(ice_init_mct) "
!-------------------------------------------------------------------------------

Expand Down Expand Up @@ -171,12 +161,9 @@ subroutine ice_init_mct( EClock, cdata, x2i, i2x, NLFilename )

#ifdef HAVE_MOAB
if (my_task == master_task) then
call shr_stream_getDomainInfo(SDICE%stream(1), filePath,fileName,timeName,lonName, &
latName,hgtName,maskName,areaName)
call shr_stream_getFile(filePath,fileName)
! send path of ice domain to MOAB coupler.
call seq_infodata_PutData( infodata, ice_domain=fileName)
write(logunit,*), ' filename: ', filename
write(logunit,*), ' file used for ice domain ', SDICE%domainFile
call seq_infodata_PutData( infodata, ice_domain=SDICE%domainFile)
endif
#endif
!----------------------------------------------------------------------------
Expand Down
4 changes: 3 additions & 1 deletion components/eam/src/chemistry/mozart/rate_diags.F90
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Expand Up @@ -126,7 +126,7 @@ subroutine rate_diags_calc( rxt_rates, vmr, m, ncol, lchnk, pver, pdeldry, mbar
rxt_rates(:ncol,:,rxt_tag_map(i)) = rxt_rates(:ncol,:,rxt_tag_map(i)) * m(:,:)
call outfld( rate_names(i), rxt_rates(:ncol,:,rxt_tag_map(i)), ncol, lchnk )

if ( .not. history_UCIgaschmbudget_2D .and. .not. history_UCIgaschmbudget_2D_levels) return
if (history_UCIgaschmbudget_2D .or. history_UCIgaschmbudget_2D_levels) then

if (rate_names(i) .eq. 'r_lch4') then
!kg/m2/sec
Expand Down Expand Up @@ -166,6 +166,8 @@ subroutine rate_diags_calc( rxt_rates, vmr, m, ncol, lchnk, pver, pdeldry, mbar
endif

endif

endif
enddo

end subroutine rate_diags_calc
Expand Down
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