+ source /etc/profile.d/larson-group.sh
++ export GIT_EDITOR=vi
++ GIT_EDITOR=vi
++ export SVN_EDITOR=vi
++ SVN_EDITOR=vi
++ export OMP_STACKSIZE=1048579
++ OMP_STACKSIZE=1048579
++ export LMOD_ROOT=/opt/lmod/
++ LMOD_ROOT=/opt/lmod/
++ source /opt/lmod//lmod/lmod/init/bash
+++ '[' -z '' ']'
+++ case "$-" in
+++ __lmod_vx=x
+++ '[' -n x ']'
+++ set +x
Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for this output (/usr/local/spack/opt/spack/linux-pop22-skylake_avx512/gcc-12.2.0/lmod-8.7.37-fq24mybyn2li6got2bxzk62ejh5d3p4z/lmod/lmod/init/bash)
Shell debugging restarted
+++ unset __lmod_vx
+++ find /usr/local/spack/share/spack/lmod/linux-pop22-x86_64/Core -print -quit
++ export MODULEPATH=/usr/local/spack/share/spack/lmod/linux-pop22-x86_64/Core
++ MODULEPATH=/usr/local/spack/share/spack/lmod/linux-pop22-x86_64/Core
+ ulimit -s 8388608
+ python3 /home/pub/jenkins_BFB_test_configs/sys_admin/python_nightly_test_suite/run_test.py -c /home/pub/jenkins_BFB_test_configs/cam_BFB_coarse_res_gfortran_test_config
Installing nightly test requirements into /home/jenkins/.cache/sys_admin/python_nightly_test_suite/overlie/venv
Using Python 3.12.3 environment at: /home/jenkins/.cache/sys_admin/python_nightly_test_suite/overlie/venv
Resolved 9 packages in 247ms
Downloading cftime (1.6MiB)
Downloading numpy (16.0MiB)
Downloading netcdf4 (10.1MiB)
Downloaded cftime
Downloaded netcdf4
Downloaded numpy
Prepared 5 packages in 845ms
Installed 5 packages in 15ms
+ certifi==2026.10.19
+ cftime==1.6.6.1
+ netcdf4==1.7.5
+ numpy==2.5.4
+ packaging==26.3
Checking out externals...
Sparse checkout cam-sima fxsparse ../.sima_phys_utils_sparse_checkout
Successfully checked out cam-sima at sima0_07_000
cam-sima up to date.
Sparse checkout mpas fxsparse ../.mpas_sparse_checkout
Successfully checked out mpas at v8.4.0
mpas up to date.
Sparse checkout cosp2 fxsparse ../.cosp_sparse_checkout
Successfully checked out cosp2 at v2.2.1
cosp2 up to date.
Sparse checkout ext_co2_cooling fxsparse ../.ext_co2_cooling_sparse_checkout
Successfully checked out ext_co2_cooling at v1.1
ext_co2_cooling up to date.
chem_proc up to date.
carma up to date.
pumas-frozen up to date.
ali_arms up to date.
atmos_phys up to date.
Recursively checking out submodules of atmos_phys
fv3 up to date.
Recursively checking out submodules of fv3
geoschem up to date.
Recursively checking out submodules of geoschem
cloud_j up to date.
hetp up to date.
hemco up to date.
Recursively checking out submodules of hemco
rrtmgp-data up to date.
rtm up to date.
mosart up to date.
ccs_config up to date.
fms up to date.
Recursively checking out submodules of fms
share up to date.
cdeps up to date.
Recursively checking out submodules of cdeps
cmeps up to date.
tools/CUPiD up to date.
Recursively checking out submodules of tools/CUPiD
tuv-x up to date.
mizuRoute up to date.
Recursively checking out submodules of mizuRoute
parallelio up to date.
Recursively checking out submodules of HEMCO
cice up to date.
Recursively checking out submodules of cice
clm up to date.
Recursively checking out submodules of clm
cime up to date.
Recursively checking out submodules of cime
Recursively checking out submodules of src
Recursively checking out submodules of fates
Copying ccs_config files
Restricting NVHPC OpenACC rules to CLUBB
Applying CAM-SIMA Filepath workaround
Removing old code directory /home/jenkins/cam_output/caseroot/UWM_debug_FHISTC_MTso_cam7_ne3pg3_ne3pg3_mg37_larson-group_gnu in 10 seconds.
To abort, press ctrl-c
----- Case Setup -----
Compset longname is HIST_CAM70%MT_CLM60%SP_CICE%PRES_DOCN%DOM_MOSART_SGLC_SWAV
Compset specification file is /home/jenkins/workspace/cam_BFB_coarse_res_gfortran_test/cime_config/config_compsets.xml
Automatically adding SESP to compset
Compset forcing is Historic transient
ATM component is CAM cam7 physics:CAM mid top model
LND component is clm6.0:Satellite phenology:
ICE component is Sea ICE (cice) model version 6 :prescribed cice
OCN component is DOCN prescribed ocean mode
ROF component is MOSART: MOdel for Scale Adaptive River Transport
GLC component is Stub glacier (land ice) component
WAV component is Stub wave component
ESP component is Stub external system processing (ESP) component
Pes specification file is /home/jenkins/workspace/cam_BFB_coarse_res_gfortran_test/cime_config/config_pes.xml
Compset specific settings: name is RUN_STARTDATE and value is 1979-01-01
Compset specific settings: name is LND_SETS_DUST_EMIS_DRV_FLDS and value is FALSE
Machine is larson-group
Pes setting: grid match is a%ne3np4
Pes setting: grid is a%ne3np4.pg3_l%ne3np4.pg3_oi%ne3np4.pg3_r%r05_g%null_w%null_z%null_m%gx3v7
Pes setting: compset is HIST_CAM70%MT_CLM60%SP_CICE%PRES_DOCN%DOM_MOSART_SGLC_SWAV_SESP
Pes setting: tasks is {'NTASKS_ATM': 24, 'NTASKS_LND': 24, 'NTASKS_ROF': 24, 'NTASKS_ICE': 24, 'NTASKS_OCN': 24, 'NTASKS_GLC': 24, 'NTASKS_WAV': 24, 'NTASKS_CPL': 24}
Pes setting: threads is {'NTHRDS_ATM': 1, 'NTHRDS_LND': 1, 'NTHRDS_ROF': 1, 'NTHRDS_ICE': 1, 'NTHRDS_OCN': 1, 'NTHRDS_GLC': 1, 'NTHRDS_WAV': 1, 'NTHRDS_CPL': 1}
Pes setting: rootpe is {'ROOTPE_ATM': 0, 'ROOTPE_LND': 0, 'ROOTPE_ROF': 0, 'ROOTPE_ICE': 0, 'ROOTPE_OCN': 0, 'ROOTPE_GLC': 0, 'ROOTPE_WAV': 0, 'ROOTPE_CPL': 0}
Pes setting: pstrid is {}
Pes setting: excl_stride is {}
Pes other settings: {}
Pes other settings append: {}
Pes comments: none
setting additional fields from config_pes: {}, append {}
Compset is: HIST_CAM70%MT_CLM60%SP_CICE%PRES_DOCN%DOM_MOSART_SGLC_SWAV_SESP
Grid is: a%ne3np4.pg3_l%ne3np4.pg3_oi%ne3np4.pg3_r%r05_g%null_w%null_z%null_m%gx3v7
Components in compset are: ['cam', 'clm', 'cice', 'docn', 'mosart', 'sglc', 'swav', 'sesp']
Using project from config_machines.xml: none
No charge_account info available, using value from PROJECT
cesm model version found: cam_4ncar_20240605_2f3c896-3213-g2f580e8d1
Batch_system_type is none
Creating Case directory /home/jenkins/cam_output/caseroot/UWM_debug_FHISTC_MTso_cam7_ne3pg3_ne3pg3_mg37_larson-group_gnu
Creating batch scripts
Writing case.run script from input template /home/jenkins/workspace/cam_BFB_coarse_res_gfortran_test/ccs_config/machines/template.case.run
Creating file .case.run
Writing case.st_archive script from input template /home/jenkins/workspace/cam_BFB_coarse_res_gfortran_test/ccs_config/machines/template.st_archive
Creating file case.st_archive
Writing case.cupid script from input template /home/jenkins/workspace/cam_BFB_coarse_res_gfortran_test/ccs_config/machines/template.cupid
Creating file case.cupid
Creating user_nl_xxx files for components and cpl
Running cam.case_setup.py
If an old case build already exists, might want to run 'case.build --clean' before building
You can now run './preview_run' to get more info on how your case will be run
----- Compile Configuration -----
----- Compile -----
Building case in directory /home/jenkins/cam_output/caseroot/UWM_debug_FHISTC_MTso_cam7_ne3pg3_ne3pg3_mg37_larson-group_gnu
sharedlib_only is False
model_only is False
Generating component namelists as part of build
2026-10-21 16:45:55 atm
Create namelist for component cam
Calling /home/jenkins/workspace/cam_BFB_coarse_res_gfortran_test/cime_config/buildnml
...calling cam buildcpp to set build time options
CAM namelist copy: file1 /home/jenkins/cam_output/caseroot/UWM_debug_FHISTC_MTso_cam7_ne3pg3_ne3pg3_mg37_larson-group_gnu/Buildconf/camconf/atm_in file2 /home/jenkins/cam_output/scratch/UWM_debug_FHISTC_MTso_cam7_ne3pg3_ne3pg3_mg37_larson-group_gnu/run/atm_in
2026-10-21 16:45:56 lnd
Create namelist for component clm
Calling /home/jenkins/workspace/cam_BFB_coarse_res_gfortran_test/components/clm//cime_config/buildnml
2026-10-21 16:45:56 ice
Create namelist for component cice
Calling /home/jenkins/workspace/cam_BFB_coarse_res_gfortran_test/components/cice//cime_config/buildnml
RUN: /home/jenkins/workspace/cam_BFB_coarse_res_gfortran_test/components/cice/bld/generate_cice_decomp.pl -ccsmroot /home/jenkins/workspace/cam_BFB_coarse_res_gfortran_test -res ne3np4.pg3 -nx 486 -ny 1 -nproc 4 -thrds 1 -output all
FROM: /home/jenkins/cam_output/caseroot/UWM_debug_FHISTC_MTso_cam7_ne3pg3_ne3pg3_mg37_larson-group_gnu
output: 486 1 81 1 2 roundrobin square-ice
2026-10-21 16:45:56 ocn
Create namelist for component docn
Calling /home/jenkins/workspace/cam_BFB_coarse_res_gfortran_test/components/cdeps/docn/cime_config/buildnml
docn_mode is prescribed
2026-10-21 16:45:56 rof
Create namelist for component mosart
Calling /home/jenkins/workspace/cam_BFB_coarse_res_gfortran_test/components/mosart//cime_config/buildnml
2026-10-21 16:45:56 glc
Create namelist for component sglc
Calling /home/jenkins/workspace/cam_BFB_coarse_res_gfortran_test/cime/CIME/non_py/src/components/stub_comps_nuopc/sglc/cime_config/buildnml
2026-10-21 16:45:56 wav
Create namelist for component swav
Calling /home/jenkins/workspace/cam_BFB_coarse_res_gfortran_test/cime/CIME/non_py/src/components/stub_comps_nuopc/swav/cime_config/buildnml
2026-10-21 16:45:56 esp
Create namelist for component sesp
Calling /home/jenkins/workspace/cam_BFB_coarse_res_gfortran_test/cime/CIME/non_py/src/components/stub_comps_nuopc/sesp/cime_config/buildnml
2026-10-21 16:45:56 cpl
Create namelist for component drv
Calling /home/jenkins/workspace/cam_BFB_coarse_res_gfortran_test/components/cmeps/cime_config/buildnml
Writing nuopc_runconfig for components ['CPL', 'ATM', 'LND', 'ICE', 'OCN', 'ROF']
libs from case_support_libraries ['gptl', 'pio', 'csm_share', 'FTorch', 'CDEPS']
Building gptl with output to file /home/jenkins/cam_output/scratch/UWM_debug_FHISTC_MTso_cam7_ne3pg3_ne3pg3_mg37_larson-group_gnu/bld/gptl.bldlog.261021-164555
Calling /home/jenkins/workspace/cam_BFB_coarse_res_gfortran_test/cime/CIME/build_scripts/buildlib.gptl
Component gptl build complete with 21 warnings
Building pio with output to file /home/jenkins/cam_output/scratch/UWM_debug_FHISTC_MTso_cam7_ne3pg3_ne3pg3_mg37_larson-group_gnu/bld/pio.bldlog.261021-164555
Calling /home/jenkins/workspace/cam_BFB_coarse_res_gfortran_test/cime/CIME/build_scripts/buildlib.pio
Building csm_share with output to file /home/jenkins/cam_output/scratch/UWM_debug_FHISTC_MTso_cam7_ne3pg3_ne3pg3_mg37_larson-group_gnu/bld/csm_share.bldlog.261021-164555
Calling /home/jenkins/workspace/cam_BFB_coarse_res_gfortran_test/share/buildlib.csm_share
Component csm_share build complete with 214 warnings
Build script /home/jenkins/workspace/cam_BFB_coarse_res_gfortran_test/libraries/FTorch/buildlib for component FTorch not found.
Building CDEPS with output to file /home/jenkins/cam_output/scratch/UWM_debug_FHISTC_MTso_cam7_ne3pg3_ne3pg3_mg37_larson-group_gnu/bld/CDEPS.bldlog.261021-164555
Calling /home/jenkins/workspace/cam_BFB_coarse_res_gfortran_test/components/cdeps/cime_config/buildlib
Sending interrupt signal to process
Terminated
=============================== Configuring Test ===============================
Working directory set to: /home/jenkins/workspace/cam_BFB_coarse_res_gfortran_test
Checking specified repo: /home/jenkins/workspace/cam_BFB_coarse_res_gfortran_test
Using /home/jenkins/workspace/cam_BFB_coarse_res_gfortran_test with origin https://github.com/larson-group/cam.git
Output Save Mode: none
Using branch: clubb_silhs_devel
Making list from 'UnresolvedCommits':
CheckRange = False: only comparing baseline to final commit.
Run Output Path: /home/jenkins/cam_output/scratch/UWM_debug_FHISTC_MTso_cam7_ne3pg3_ne3pg3_mg37_larson-group_gnu/run/UWM_debug_FHISTC_MTso_cam7_ne3pg3_ne3pg3_mg37_larson-group_gnu.cam.rh0.1979-01-02-00000.nc
Run commands: ['rm -f /home/jenkins/cam_output/scratch/UWM_debug_FHISTC_MTso_cam7_ne3pg3_ne3pg3_mg37_larson-group_gnu/run/UWM_debug_FHISTC_MTso_cam7_ne3pg3_ne3pg3_mg37_larson-group_gnu.cam.rh0.1979-01-02-00000.nc &&\nrun_scripts/set_up_repo.py --caseroot /home/$USER/cam_output/caseroot/UWM_debug_FHISTC_MTso_cam7_ne3pg3_ne3pg3_mg37_larson-group_gnu --reuse_build . &&\nsed -i -e \'s/^CASE=.*/CASE="UWM_debug_FHISTC_MTso_cam7_ne3pg3_ne3pg3_mg37"/\' -e \'s/^COMPSET=.*/COMPSET="FHISTC_MTso"/\' -e \'s/ -silhs / /g\' -e \'s/ -psubcols \\$NUMSC//g\' -e \'s/ -DSILHS//g\' -e "s/^subcol_scheme = .*/subcol_scheme = \'off\'/" -e \'s/^use_subcol_microp = .*/use_subcol_microp = .false./\' -e \'s/^microp_uniform = .*/microp_uniform = .false./\' -e "s/, \'SILHS_CLUBB_PRECIP_FRAC\',//" -e "/^\'SILHS_CLUBB_ICE_SS_FRAC\'/d" run_scripts/run_cesm_uwm_coarse_res.sh &&\nrun_scripts/run_cesm_uwm_coarse_res.sh']
Diffing command: python3 run_scripts/netcdf_3D_vars_diff.py
=============================== Running Test ===============================
Parsing message from commit: 2f580e8d1cd40a359888fef12607a0787034b814
Checking Commit: 2f580e8d1cd40a359888fef12607a0787034b814
Running: final commit to check, not labelled BIT_CHANGING
Checking out 2f580e8d1cd40a359888fef12607a0787034b814
Running: 'rm -f /home/jenkins/cam_output/scratch/UWM_debug_FHISTC_MTso_cam7_ne3pg3_ne3pg3_mg37_larson-group_gnu/run/UWM_debug_FHISTC_MTso_cam7_ne3pg3_ne3pg3_mg37_larson-group_gnu.cam.rh0.1979-01-02-00000.nc &&
run_scripts/set_up_repo.py --caseroot /home/$USER/cam_output/caseroot/UWM_debug_FHISTC_MTso_cam7_ne3pg3_ne3pg3_mg37_larson-group_gnu --reuse_build . &&
sed -i -e 's/^CASE=.*/CASE="UWM_debug_FHISTC_MTso_cam7_ne3pg3_ne3pg3_mg37"/' -e 's/^COMPSET=.*/COMPSET="FHISTC_MTso"/' -e 's/ -silhs / /g' -e 's/ -psubcols \$NUMSC//g' -e 's/ -DSILHS//g' -e "s/^subcol_scheme = .*/subcol_scheme = 'off'/" -e 's/^use_subcol_microp = .*/use_subcol_microp = .false./' -e 's/^microp_uniform = .*/microp_uniform = .false./' -e "s/, 'SILHS_CLUBB_PRECIP_FRAC',//" -e "/^'SILHS_CLUBB_ICE_SS_FRAC'/d" run_scripts/run_cesm_uwm_coarse_res.sh &&
run_scripts/run_cesm_uwm_coarse_res.sh'
================== ERROR ==================
Commit: 2f580e8d1cd40a359888fef12607a0787034b814
Unexpected error: Command 'rm -f /home/jenkins/cam_output/scratch/UWM_debug_FHISTC_MTso_cam7_ne3pg3_ne3pg3_mg37_larson-group_gnu/run/UWM_debug_FHISTC_MTso_cam7_ne3pg3_ne3pg3_mg37_larson-group_gnu.cam.rh0.1979-01-02-00000.nc &&
run_scripts/set_up_repo.py --caseroot /home/$USER/cam_output/caseroot/UWM_debug_FHISTC_MTso_cam7_ne3pg3_ne3pg3_mg37_larson-group_gnu --reuse_build . &&
sed -i -e 's/^CASE=.*/CASE="UWM_debug_FHISTC_MTso_cam7_ne3pg3_ne3pg3_mg37"/' -e 's/^COMPSET=.*/COMPSET="FHISTC_MTso"/' -e 's/ -silhs / /g' -e 's/ -psubcols \$NUMSC//g' -e 's/ -DSILHS//g' -e "s/^subcol_scheme = .*/subcol_scheme = 'off'/" -e 's/^use_subcol_microp = .*/use_subcol_microp = .false./' -e 's/^microp_uniform = .*/microp_uniform = .false./' -e "s/, 'SILHS_CLUBB_PRECIP_FRAC',//" -e "/^'SILHS_CLUBB_ICE_SS_FRAC'/d" run_scripts/run_cesm_uwm_coarse_res.sh &&
run_scripts/run_cesm_uwm_coarse_res.sh' returned non-zero exit status 1.
There was a problem with a run command.
===========================================
System Exit detected. Calling test.cleanup()
=============================== Cleanup ===============================
Removing all generated output
Exiting with code: 1
Terminated
