Started by user <a href='/jenkins/user/sdomke' class='jenkins-table__link model-link model-link--float'>Steffen Domke</a>
Checking out git <a href='https://github.com/larson-group/cam.git'>https://github.com/larson-group/cam.git</a> into /home/jenkins/workspace/branch_cam_test@script/800691b231d95c534d49060ef200db30805e761447d5de1a9dcea602b1366aec to read jenkins_tests/cam_scam_gfortran_debug_test/Jenkinsfile
The recommended git tool is: git
 &gt; git rev-parse --resolve-git-dir /home/jenkins/workspace/branch_cam_test@script/800691b231d95c534d49060ef200db30805e761447d5de1a9dcea602b1366aec/.git # timeout=10
Fetching changes from the remote Git repository
 &gt; git config remote.origin.url <a href='https://github.com/larson-group/cam.git'>https://github.com/larson-group/cam.git</a> # timeout=10
Cleaning workspace
 &gt; git rev-parse --verify HEAD # timeout=10
Resetting working tree
 &gt; git reset --hard # timeout=10
 &gt; git clean -ffdx # timeout=10
Fetching upstream changes from <a href='https://github.com/larson-group/cam.git'>https://github.com/larson-group/cam.git</a>
 &gt; git --version # timeout=10
 &gt; git --version # 'git version 2.34.1'
 &gt; git fetch --tags --force --progress -- <a href='https://github.com/larson-group/cam.git'>https://github.com/larson-group/cam.git</a> +refs/heads/*:refs/remotes/origin/* # timeout=10
 &gt; git rev-parse refs/remotes/origin/checking_clubb_err_handling^{commit} # timeout=10
Checking out Revision 148d79df2c2d900f3ed2b9c52dab7ef47ecdde91 (refs/remotes/origin/checking_clubb_err_handling)
 &gt; git config core.sparsecheckout # timeout=10
 &gt; git checkout -f 148d79df2c2d900f3ed2b9c52dab7ef47ecdde91 # timeout=10
Commit message: "Update clubb_intr.F90"
 &gt; git rev-list --no-walk f14f13ae7f2edfbf4159baf853343121960fbf44 # timeout=10
<span class="pipeline-new-node" nodeId="2" startId="2">[Pipeline] Start of Pipeline
</span><span class="pipeline-new-node" nodeId="3" startId="3" enclosingId="2">[Pipeline] node
</span><span class="pipeline-node-3">Running on <a href='/jenkins/computer/mitch/' class='jenkins-table__link model-link model-link--float'>mitch</a> in /home/jenkins/workspace/branch_cam_test
</span><span class="pipeline-new-node" nodeId="4" startId="4" enclosingId="3">[Pipeline] {
</span><span class="pipeline-new-node" nodeId="5" startId="5" enclosingId="4">[Pipeline] stage
</span><span class="pipeline-new-node" nodeId="6" startId="6" enclosingId="5" label="Declarative: Checkout SCM">[Pipeline] { (Declarative: Checkout SCM)
</span><span class="pipeline-new-node" nodeId="7" enclosingId="6">[Pipeline] checkout
</span><span class="pipeline-node-7">The recommended git tool is: git
Cloning the remote Git repository
Cloning repository <a href='https://github.com/larson-group/cam.git'>https://github.com/larson-group/cam.git</a>
 &gt; git init /home/jenkins/workspace/branch_cam_test # timeout=10
Fetching upstream changes from <a href='https://github.com/larson-group/cam.git'>https://github.com/larson-group/cam.git</a>
 &gt; git --version # timeout=10
 &gt; git --version # 'git version 2.34.1'
 &gt; git fetch --tags --force --progress -- <a href='https://github.com/larson-group/cam.git'>https://github.com/larson-group/cam.git</a> +refs/heads/*:refs/remotes/origin/* # timeout=10
Avoid second fetch
 &gt; git config remote.origin.url <a href='https://github.com/larson-group/cam.git'>https://github.com/larson-group/cam.git</a> # timeout=10
 &gt; git config --add remote.origin.fetch +refs/heads/*:refs/remotes/origin/* # timeout=10
 &gt; git rev-parse refs/remotes/origin/checking_clubb_err_handling^{commit} # timeout=10
Checking out Revision 148d79df2c2d900f3ed2b9c52dab7ef47ecdde91 (refs/remotes/origin/checking_clubb_err_handling)
Commit message: "Update clubb_intr.F90"
</span><span class="pipeline-new-node" nodeId="8" startId="6">[Pipeline] }
</span><span class="pipeline-new-node" nodeId="9" startId="5">[Pipeline] // stage
</span><span class="pipeline-new-node" nodeId="10" startId="10" enclosingId="4">[Pipeline] withEnv
</span><span class="pipeline-new-node" nodeId="11" startId="11" enclosingId="10">[Pipeline] {
</span><span class="pipeline-new-node" nodeId="12" startId="12" enclosingId="11">[Pipeline] stage
</span><span class="pipeline-new-node" nodeId="13" startId="13" enclosingId="12" label="Checkout Externals and Copy Custom Files">[Pipeline] { (Checkout Externals and Copy Custom Files)
</span><span class="pipeline-new-node" nodeId="14" enclosingId="13">[Pipeline] sh
</span><span class="pipeline-node-14">+ python run_scripts/set_up_repo.py .
</span><span class="pipeline-node-7"> &gt; git config core.sparsecheckout # timeout=10
 &gt; git checkout -f 148d79df2c2d900f3ed2b9c52dab7ef47ecdde91 # timeout=10
</span><span class="pipeline-node-14">Checking out externals...
Copying ccs_config files
</span><span class="pipeline-new-node" nodeId="15" startId="13">[Pipeline] }
</span><span class="pipeline-new-node" nodeId="16" startId="12">[Pipeline] // stage
</span><span class="pipeline-new-node" nodeId="17" startId="17" enclosingId="11">[Pipeline] stage
</span><span class="pipeline-new-node" nodeId="18" startId="18" enclosingId="17" label="Remove Old Output">[Pipeline] { (Remove Old Output)
</span><span class="pipeline-new-node" nodeId="19" enclosingId="18">[Pipeline] sh
</span><span class="pipeline-node-19">+ rm -rf /home/jenkins/cam_output/scratch/test_scam_ATEX /home/jenkins/cam_output/scratch/test_scam_ARM97
</span><span class="pipeline-new-node" nodeId="20" startId="20" enclosingId="18">[Pipeline] script
</span><span class="pipeline-new-node" nodeId="21" startId="21" enclosingId="20">[Pipeline] {
</span><span class="pipeline-new-node" nodeId="22" enclosingId="21">[Pipeline] sh
</span><span class="pipeline-node-22">+ rm -rf /home/jenkins/workspace/branch_cam_test/cime/scripts/test_scam_ATEX /home/jenkins/workspace/branch_cam_test/cime/scripts/test_scam_ARM97
</span><span class="pipeline-new-node" nodeId="23" startId="21">[Pipeline] }
</span><span class="pipeline-new-node" nodeId="24" startId="20">[Pipeline] // script
</span><span class="pipeline-new-node" nodeId="25" startId="18">[Pipeline] }
</span><span class="pipeline-new-node" nodeId="26" startId="17">[Pipeline] // stage
</span><span class="pipeline-new-node" nodeId="27" startId="27" enclosingId="11">[Pipeline] stage
</span><span class="pipeline-new-node" nodeId="28" startId="28" enclosingId="27" label="Run atex">[Pipeline] { (Run atex)
</span><span class="pipeline-new-node" nodeId="29" enclosingId="28">[Pipeline] sh
</span><span class="pipeline-node-29">+ 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
+ run_scripts/run_scam.bash ATEX
----- Case Setup -----
Compset longname is 2000_CAM60%SCAMATEX_CLM50%SP_CICE%PRES_DOCN%DOM_SROF_SGLC_SWAV
Compset specification file is /home/jenkins/workspace/branch_cam_test/cime_config/config_compsets.xml
Automatically adding SESP to compset
Compset forcing is 1972-2004
ATM component is CAM cam6 physics:
LND component is clm5.0:Satellite phenology:
ICE component is Sea ICE (cice) model version 6 :prescribed cice
OCN component is DOCN   prescribed ocean mode
ROF component is Stub river component
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/branch_cam_test/cime_config/config_pes.xml
Compset specific settings: name is RUN_STARTDATE and value is 1969-02-15
Compset specific settings: name is STOP_N and value is 47
Compset specific settings: name is STOP_OPTION and value is nhours
Compset specific settings: name is START_TOD and value is 0
Compset specific settings: name is PTS_MODE and value is TRUE
Compset specific settings: name is PTS_LAT and value is 15.0
Compset specific settings: name is PTS_LON and value is 345.0
Machine is larson-group
vid is comment
vid is ntasks
vid is nthrds
vid is rootpe
Pes setting: grid          is a%T42_l%T42_oi%T42_r%null_g%null_w%null_z%null_m%gx1v7 
Pes setting: compset       is 2000_CAM60%SCAMATEX_CLM50%SP_CICE%PRES_DOCN%DOM_SROF_SGLC_SWAV_SESP 
Pes setting: tasks       is {'NTASKS_ATM': 1, 'NTASKS_LND': 1, 'NTASKS_ROF': 1, 'NTASKS_ICE': 1, 'NTASKS_OCN': 1, 'NTASKS_GLC': 1, 'NTASKS_WAV': 1, 'NTASKS_CPL': 1} 
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 other settings: {}
Pes comments: none
setting additional fields from config_pes: {}
 Compset is: 2000_CAM60%SCAMATEX_CLM50%SP_CICE%PRES_DOCN%DOM_SROF_SGLC_SWAV_SESP 
 Grid is: a%T42_l%T42_oi%T42_r%null_g%null_w%null_z%null_m%gx1v7 
 Components in compset are: ['cam', 'clm', 'cice', 'docn', 'srof', 'sglc', 'swav', 'sesp'] 

This is a CESM scientifically supported compset at this resolution.

No project info available
No charge_account info available, using value from PROJECT
cesm model version found: cam_4ncar_20240605_2f3c896-791-g148d79df
Batch_system_type is none
 Creating Case directory /home/jenkins/workspace/branch_cam_test/cime/scripts/test_scam_ATEX
This component includes user_mods /home/jenkins/workspace/branch_cam_test/cime_config/usermods_dirs/scam_mandatory
Adding user mods directory /home/jenkins/workspace/branch_cam_test/cime_config/usermods_dirs/scam_mandatory
RUN: /home/jenkins/workspace/branch_cam_test/cime/scripts/test_scam_ATEX/shell_commands
FROM: /home/jenkins/workspace/branch_cam_test/cime/scripts/test_scam_ATEX
Creating batch scripts
Writing case.run script from input template /home/jenkins/workspace/branch_cam_test/ccs_config/machines/template.case.run
Creating file .case.run
Writing case.st_archive script from input template /home/jenkins/workspace/branch_cam_test/ccs_config/machines/template.st_archive
Creating file case.st_archive
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 -----
----- Run configuration -----
----- Compile -----
Building case in directory /home/jenkins/workspace/branch_cam_test/cime/scripts/test_scam_ATEX
sharedlib_only is False
model_only is False
Generating component namelists as part of build
  2025-03-25 15:50:55 atm 
Create namelist for component cam
   Calling /home/jenkins/workspace/branch_cam_test/cime_config/buildnml
     ...calling cam buildcpp to set build time options
CAM namelist copy: file1 /home/jenkins/workspace/branch_cam_test/cime/scripts/test_scam_ATEX/Buildconf/camconf/atm_in file2 /home/jenkins/cam_output/scratch/test_scam_ATEX/run/atm_in 
  2025-03-25 15:50:55 lnd 
Create namelist for component clm
   Calling /home/jenkins/workspace/branch_cam_test/components/clm//cime_config/buildnml
WARNING: CLM is starting up from a cold state
  2025-03-25 15:50:56 ice 
Create namelist for component cice
   Calling /home/jenkins/workspace/branch_cam_test/components/cice//cime_config/buildnml
  2025-03-25 15:50:56 ocn 
Create namelist for component docn
   Calling /home/jenkins/workspace/branch_cam_test/components/cdeps/docn/cime_config/buildnml
docn_mode is prescribed
  2025-03-25 15:50:56 rof 
Create namelist for component srof
   Calling /home/jenkins/workspace/branch_cam_test/cime/CIME/non_py/src/components/stub_comps_nuopc/srof/cime_config/buildnml
  2025-03-25 15:50:56 glc 
Create namelist for component sglc
   Calling /home/jenkins/workspace/branch_cam_test/cime/CIME/non_py/src/components/stub_comps_nuopc/sglc/cime_config/buildnml
  2025-03-25 15:50:56 wav 
Create namelist for component swav
   Calling /home/jenkins/workspace/branch_cam_test/cime/CIME/non_py/src/components/stub_comps_nuopc/swav/cime_config/buildnml
  2025-03-25 15:50:56 esp 
Create namelist for component sesp
   Calling /home/jenkins/workspace/branch_cam_test/cime/CIME/non_py/src/components/stub_comps_nuopc/sesp/cime_config/buildnml
  2025-03-25 15:50:56 cpl 
Create namelist for component drv
   Calling /home/jenkins/workspace/branch_cam_test/components/cmeps/cime_config/buildnml
Writing nuopc_runconfig for components ['CPL', 'ATM', 'LND', 'ICE', 'OCN']
Building gptl with output to file /home/jenkins/cam_output/scratch/test_scam_ATEX/bld/gptl.bldlog.250325-155055
   Calling /home/jenkins/workspace/branch_cam_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/test_scam_ATEX/bld/pio.bldlog.250325-155055
   Calling /home/jenkins/workspace/branch_cam_test/cime/CIME/build_scripts/buildlib.pio
Building csm_share with output to file /home/jenkins/cam_output/scratch/test_scam_ATEX/bld/csm_share.bldlog.250325-155055
   Calling /home/jenkins/workspace/branch_cam_test/share/buildlib.csm_share
Component csm_share build complete with 254 warnings
Building CDEPS with output to file /home/jenkins/cam_output/scratch/test_scam_ATEX/bld/CDEPS.bldlog.250325-155055
   Calling /home/jenkins/workspace/branch_cam_test/components/cdeps/cime_config/buildlib
Component CDEPS build complete with 200 warnings
         - Building clm library 
Building lnd with output to /home/jenkins/cam_output/scratch/test_scam_ATEX/bld/lnd.bldlog.250325-155055
Component lnd build complete with 2623 warnings
clm built in 99.739108 seconds
         - Building atm Library 
Building atm with output to /home/jenkins/cam_output/scratch/test_scam_ATEX/bld/atm.bldlog.250325-155055
         - Building ice Library 
Building ice with output to /home/jenkins/cam_output/scratch/test_scam_ATEX/bld/ice.bldlog.250325-155055
         - Building ocn Library 
Building ocn with output to /home/jenkins/cam_output/scratch/test_scam_ATEX/bld/ocn.bldlog.250325-155055
docn built in 0.499938 seconds
Error: Arithmetic NaN converting REAL(4) to REAL(8) at (1). This check can be disabled with the option '-fno-range-check'

Component atm build complete with 5448 warnings
cam built in 119.558451 seconds
Component ice build complete with 467 warnings
cice built in 203.174204 seconds
ERROR: BUILD FAIL: cam.buildlib failed, cat /home/jenkins/cam_output/scratch/test_scam_ATEX/bld/atm.bldlog.250325-155055
Error building CAM
</span><span class="pipeline-new-node" nodeId="30" startId="28">[Pipeline] }
</span><span class="pipeline-new-node" nodeId="31" startId="27">[Pipeline] // stage
</span><span class="pipeline-new-node" nodeId="32" startId="32" enclosingId="11">[Pipeline] stage
</span><span class="pipeline-new-node" nodeId="33" startId="33" enclosingId="32" label="Run ARM97 with SILHS">[Pipeline] { (Run ARM97 with SILHS)
</span>Stage "Run ARM97 with SILHS" skipped due to earlier failure(s)
<span class="pipeline-new-node" nodeId="34" enclosingId="33">[Pipeline] getContext
</span><span class="pipeline-new-node" nodeId="35" startId="33">[Pipeline] }
</span><span class="pipeline-new-node" nodeId="36" startId="32">[Pipeline] // stage
</span><span class="pipeline-new-node" nodeId="37" startId="37" enclosingId="11">[Pipeline] stage
</span><span class="pipeline-new-node" nodeId="38" startId="38" enclosingId="37" label="Declarative: Post Actions">[Pipeline] { (Declarative: Post Actions)
</span><span class="pipeline-new-node" nodeId="39" startId="39" enclosingId="38">[Pipeline] script
</span><span class="pipeline-new-node" nodeId="40" startId="40" enclosingId="39">[Pipeline] {
</span><span class="pipeline-new-node" nodeId="41" enclosingId="40">[Pipeline] sh
</span><span class="pipeline-node-41">+ chmod -R 755 /home/jenkins/cam_output/
</span><span class="pipeline-new-node" nodeId="42" enclosingId="40">[Pipeline] sh
</span><span class="pipeline-node-42">+ gzip -d '/home/jenkins/cam_output/scratch/test_scam_ATEX/bld/cesm.bldlog.*.gz'
gzip: /home/jenkins/cam_output/scratch/test_scam_ATEX/bld/cesm.bldlog.*.gz: No such file or directory
</span><span class="pipeline-new-node" nodeId="43" enclosingId="40">[Pipeline] echo
</span><span class="pipeline-node-43">ATEX WARNING: One or more of the build logs were not zipped, this means compilation did not finish
</span><span class="pipeline-new-node" nodeId="44" enclosingId="40">[Pipeline] sh
</span><span class="pipeline-node-44">+ gzip -d '/home/jenkins/cam_output/scratch/test_scam_ATEX/run/cesm.log.*.gz'
gzip: /home/jenkins/cam_output/scratch/test_scam_ATEX/run/cesm.log.*.gz: No such file or directory
</span><span class="pipeline-new-node" nodeId="45" enclosingId="40">[Pipeline] echo
</span><span class="pipeline-node-45">ATEX WARNING: One or more of the run logs were not zipped, this means the code did not run to completion
</span><span class="pipeline-new-node" nodeId="46" enclosingId="40">[Pipeline] sh
</span><span class="pipeline-node-46">+ cat '/home/jenkins/cam_output/scratch/test_scam_ATEX/bld/cesm.bldlog.*'
cat: '/home/jenkins/cam_output/scratch/test_scam_ATEX/bld/cesm.bldlog.*': No such file or directory
</span><span class="pipeline-new-node" nodeId="47" enclosingId="40">[Pipeline] echo
</span><span class="pipeline-node-47">ATEX WARNING: One of the log files (build or run) were not found - the failure must have occured before their creation
</span><span class="pipeline-new-node" nodeId="48" enclosingId="40">[Pipeline] sh
</span><span class="pipeline-node-48">+ gzip -d '/home/jenkins/cam_output/scratch/test_scam_ARM97/bld/cesm.bldlog.*.gz'
gzip: /home/jenkins/cam_output/scratch/test_scam_ARM97/bld/cesm.bldlog.*.gz: No such file or directory
</span><span class="pipeline-new-node" nodeId="49" enclosingId="40">[Pipeline] echo
</span><span class="pipeline-node-49">ARM97 WARNING: One or more of the build logs were not zipped, this means compilation did not finish
</span><span class="pipeline-new-node" nodeId="50" enclosingId="40">[Pipeline] sh
</span><span class="pipeline-node-50">+ gzip -d '/home/jenkins/cam_output/scratch/test_scam_ARM97/run/cesm.log.*.gz'
gzip: /home/jenkins/cam_output/scratch/test_scam_ARM97/run/cesm.log.*.gz: No such file or directory
</span><span class="pipeline-new-node" nodeId="51" enclosingId="40">[Pipeline] echo
</span><span class="pipeline-node-51">ARM97 WARNING: One or more of the run logs were not zipped, this means the code did not run to completion
</span><span class="pipeline-new-node" nodeId="52" enclosingId="40">[Pipeline] sh
</span><span class="pipeline-node-52">+ cat '/home/jenkins/cam_output/scratch/test_scam_ARM97/bld/cesm.bldlog.*'
cat: '/home/jenkins/cam_output/scratch/test_scam_ARM97/bld/cesm.bldlog.*': No such file or directory
</span><span class="pipeline-new-node" nodeId="53" enclosingId="40">[Pipeline] echo
</span><span class="pipeline-node-53">ARM97 WARNING: One of the log files (build or run) were not found - the failure must have occured before their creation
</span><span class="pipeline-new-node" nodeId="54" startId="40">[Pipeline] }
</span><span class="pipeline-new-node" nodeId="55" startId="39">[Pipeline] // script
</span><span class="pipeline-new-node" nodeId="56" startId="56" enclosingId="38">[Pipeline] script
</span><span class="pipeline-new-node" nodeId="57" startId="57" enclosingId="56">[Pipeline] {
</span><span class="pipeline-new-node" nodeId="58" startId="57">[Pipeline] }
</span><span class="pipeline-new-node" nodeId="59" startId="56">[Pipeline] // script
</span><span class="pipeline-new-node" nodeId="60" startId="38">[Pipeline] }
</span><span class="pipeline-new-node" nodeId="61" startId="37">[Pipeline] // stage
</span><span class="pipeline-new-node" nodeId="62" startId="11">[Pipeline] }
</span><span class="pipeline-new-node" nodeId="63" startId="10">[Pipeline] // withEnv
</span><span class="pipeline-new-node" nodeId="64" startId="4">[Pipeline] }
</span><span class="pipeline-new-node" nodeId="65" startId="3">[Pipeline] // node
</span><span class="pipeline-new-node" nodeId="66" startId="2">[Pipeline] End of Pipeline
</span>ERROR: script returned exit code 1
Finished: FAILURE