Started by an SCM change Obtained jenkins_tests/cam_scam_gfortran_debug_test/Jenkinsfile from git https://github.com/larson-group/cam.git [Pipeline] Start of Pipeline [Pipeline] node Still waiting to schedule task Waiting for next available executor Running on nelson in /home/jenkins/workspace/cam_scam_gfortran_debug_test [Pipeline] { [Pipeline] stage [Pipeline] { (Declarative: Checkout SCM) [Pipeline] checkout The recommended git tool is: git Wiping out workspace first. Cloning the remote Git repository Cloning repository https://github.com/larson-group/cam.git > git init /home/jenkins/workspace/cam_scam_gfortran_debug_test # timeout=10 Fetching upstream changes from https://github.com/larson-group/cam.git > git --version # timeout=10 > git --version # 'git version 2.43.0' using GIT_ASKPASS to set credentials larsongroupsysadmin github token > git fetch --tags --force --progress -- https://github.com/larson-group/cam.git +refs/heads/*:refs/remotes/origin/* # timeout=10 Avoid second fetch Checking out Revision a05d60b6d7939a7f17776262bf8634a6f2702773 (refs/remotes/origin/clubb_silhs_devel) Commit message: "Autoupdated CLUBB_core Commit a4826465aeec11af80e51e711d1cc0b8287e96c0 Author: Daniel Ebel Date: Mon Sep 28 10:32:53 2026 -0500 Remove upsilon 0 and 1 if branches (#1365) * Removed unnecessary upsilon_precip_frac_rat == 0 or 1 checks" > git config remote.origin.url https://github.com/larson-group/cam.git # timeout=10 > git config --add remote.origin.fetch +refs/heads/*:refs/remotes/origin/* # timeout=10 > git rev-parse refs/remotes/origin/clubb_silhs_devel^{commit} # timeout=10 > git config core.sparsecheckout # timeout=10 > git checkout -f a05d60b6d7939a7f17776262bf8634a6f2702773 # timeout=10 > git rev-list --no-walk d2c3ca746f856a0b75184e9c4ebc4627213f4866 # timeout=10 [Pipeline] } [Pipeline] // stage [Pipeline] withEnv [Pipeline] { [Pipeline] withEnv [Pipeline] { [Pipeline] stage [Pipeline] { (Checkout Externals and Copy Custom Files) [Pipeline] sh + python run_scripts/set_up_repo.py . 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 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. fms up to date. Recursively checking out submodules of fms ccs_config up to date. cdeps up to date. Recursively checking out submodules of cdeps share up to date. tuv-x up to date. cmeps up to date. mizuRoute up to date. Recursively checking out submodules of mizuRoute parallelio up to date. tools/CUPiD up to date. Recursively checking out submodules of tools/CUPiD cice up to date. Recursively checking out submodules of cice Recursively checking out submodules of HEMCO geoschem up to date. Recursively checking out submodules of geoschem Recursively checking out submodules of src 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 fates Copying ccs_config files Restricting NVHPC OpenACC rules to CLUBB Applying CAM-SIMA Filepath workaround [Pipeline] } [Pipeline] // stage [Pipeline] stage [Pipeline] { (Remove Old Output) [Pipeline] sh + rm -rf /home/jenkins/cam_output/scratch/test_scam_ATEX_cam_scam_gfortran_debug_test /home/jenkins/cam_output/scratch/test_scam_ARM97_cam_scam_gfortran_debug_test [Pipeline] script [Pipeline] { [Pipeline] } [Pipeline] // script [Pipeline] } [Pipeline] // stage [Pipeline] stage [Pipeline] { (Run atex) [Pipeline] sh + 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/ ++ . /opt/lmod//lmod/lmod/init/profile +++ '[' -z '' ']' +++ LMOD_ALLOW_ROOT_USE=yes +++ '[' -n '' ']' +++ '[' yes '!=' yes ']' +++ '[' -z '' ']' +++ export MODULEPATH_ROOT=/usr/local/spack/opt/spack/linux-pop22-skylake_avx512/gcc-12.2.0/lmod-8.7.37-qorv6nkkjzyzntx6wbjupmoxrot26t6r/modulefiles +++ MODULEPATH_ROOT=/usr/local/spack/opt/spack/linux-pop22-skylake_avx512/gcc-12.2.0/lmod-8.7.37-qorv6nkkjzyzntx6wbjupmoxrot26t6r/modulefiles +++ export USER=jenkins +++ USER=jenkins ++++ uname +++ export LMOD_sys=Linux +++ LMOD_sys=Linux +++ '[' -z '' ']' +++ '[' -f /etc/lmod/.modulespath ']' +++ LMOD_MODULEPATH_INIT=/usr/local/spack/opt/spack/linux-pop22-skylake_avx512/gcc-12.2.0/lmod-8.7.37-qorv6nkkjzyzntx6wbjupmoxrot26t6r/lmod/lmod/init/.modulespath +++ '[' -f /usr/local/spack/opt/spack/linux-pop22-skylake_avx512/gcc-12.2.0/lmod-8.7.37-qorv6nkkjzyzntx6wbjupmoxrot26t6r/lmod/lmod/init/.modulespath ']' ++++ /usr/local/spack/opt/spack/linux-pop22-skylake_avx512/gcc-12.2.0/lmod-8.7.37-qorv6nkkjzyzntx6wbjupmoxrot26t6r/lmod/lmod/libexec/addto --append MODULEPATH /usr/local/spack/opt/spack/linux-pop22-skylake_avx512/gcc-12.2.0/lmod-8.7.37-qorv6nkkjzyzntx6wbjupmoxrot26t6r/modulefiles/Linux /usr/local/spack/opt/spack/linux-pop22-skylake_avx512/gcc-12.2.0/lmod-8.7.37-qorv6nkkjzyzntx6wbjupmoxrot26t6r/modulefiles/Core +++ export MODULEPATH=/usr/local/spack/opt/spack/linux-pop22-skylake_avx512/gcc-12.2.0/lmod-8.7.37-qorv6nkkjzyzntx6wbjupmoxrot26t6r/modulefiles/Linux:/usr/local/spack/opt/spack/linux-pop22-skylake_avx512/gcc-12.2.0/lmod-8.7.37-qorv6nkkjzyzntx6wbjupmoxrot26t6r/modulefiles/Core +++ MODULEPATH=/usr/local/spack/opt/spack/linux-pop22-skylake_avx512/gcc-12.2.0/lmod-8.7.37-qorv6nkkjzyzntx6wbjupmoxrot26t6r/modulefiles/Linux:/usr/local/spack/opt/spack/linux-pop22-skylake_avx512/gcc-12.2.0/lmod-8.7.37-qorv6nkkjzyzntx6wbjupmoxrot26t6r/modulefiles/Core ++++ /usr/local/spack/opt/spack/linux-pop22-skylake_avx512/gcc-12.2.0/lmod-8.7.37-qorv6nkkjzyzntx6wbjupmoxrot26t6r/lmod/lmod/libexec/addto --append MODULEPATH /usr/local/spack/opt/spack/linux-pop22-skylake_avx512/gcc-12.2.0/lmod-8.7.37-qorv6nkkjzyzntx6wbjupmoxrot26t6r/lmod/lmod/modulefiles/Core +++ export MODULEPATH=/usr/local/spack/opt/spack/linux-pop22-skylake_avx512/gcc-12.2.0/lmod-8.7.37-qorv6nkkjzyzntx6wbjupmoxrot26t6r/modulefiles/Linux:/usr/local/spack/opt/spack/linux-pop22-skylake_avx512/gcc-12.2.0/lmod-8.7.37-qorv6nkkjzyzntx6wbjupmoxrot26t6r/modulefiles/Core:/usr/local/spack/opt/spack/linux-pop22-skylake_avx512/gcc-12.2.0/lmod-8.7.37-qorv6nkkjzyzntx6wbjupmoxrot26t6r/lmod/lmod/modulefiles/Core +++ MODULEPATH=/usr/local/spack/opt/spack/linux-pop22-skylake_avx512/gcc-12.2.0/lmod-8.7.37-qorv6nkkjzyzntx6wbjupmoxrot26t6r/modulefiles/Linux:/usr/local/spack/opt/spack/linux-pop22-skylake_avx512/gcc-12.2.0/lmod-8.7.37-qorv6nkkjzyzntx6wbjupmoxrot26t6r/modulefiles/Core:/usr/local/spack/opt/spack/linux-pop22-skylake_avx512/gcc-12.2.0/lmod-8.7.37-qorv6nkkjzyzntx6wbjupmoxrot26t6r/lmod/lmod/modulefiles/Core +++ '[' -n '' ']' +++ export BASH_ENV=/usr/local/spack/opt/spack/linux-pop22-skylake_avx512/gcc-12.2.0/lmod-8.7.37-qorv6nkkjzyzntx6wbjupmoxrot26t6r/lmod/lmod/init/bash +++ BASH_ENV=/usr/local/spack/opt/spack/linux-pop22-skylake_avx512/gcc-12.2.0/lmod-8.7.37-qorv6nkkjzyzntx6wbjupmoxrot26t6r/lmod/lmod/init/bash +++ '[' -z '' ']' +++ export MANPATH=: +++ MANPATH=: ++++ /usr/local/spack/opt/spack/linux-pop22-skylake_avx512/gcc-12.2.0/lmod-8.7.37-qorv6nkkjzyzntx6wbjupmoxrot26t6r/lmod/lmod/libexec/addto MANPATH /usr/local/spack/opt/spack/linux-pop22-skylake_avx512/gcc-12.2.0/lmod-8.7.37-qorv6nkkjzyzntx6wbjupmoxrot26t6r/lmod/lmod/share/man +++ export MANPATH=/usr/local/spack/opt/spack/linux-pop22-skylake_avx512/gcc-12.2.0/lmod-8.7.37-qorv6nkkjzyzntx6wbjupmoxrot26t6r/lmod/lmod/share/man: +++ MANPATH=/usr/local/spack/opt/spack/linux-pop22-skylake_avx512/gcc-12.2.0/lmod-8.7.37-qorv6nkkjzyzntx6wbjupmoxrot26t6r/lmod/lmod/share/man: +++ findExec READLINK_CMD /usr/bin/readlink readlink +++ Nm=READLINK_CMD +++ confPath=/usr/bin/readlink +++ execNm=readlink +++ eval READLINK_CMD=/usr/bin/readlink ++++ READLINK_CMD=/usr/bin/readlink +++ '[' '!' -x /usr/bin/readlink ']' +++ unset Nm confPath execNm +++ findExec PS_CMD /usr/bin/ps ps +++ Nm=PS_CMD +++ confPath=/usr/bin/ps +++ execNm=ps +++ eval PS_CMD=/usr/bin/ps ++++ PS_CMD=/usr/bin/ps +++ '[' '!' -x /usr/bin/ps ']' +++ unset Nm confPath execNm +++ findExec EXPR_CMD /usr/bin/expr expr +++ Nm=EXPR_CMD +++ confPath=/usr/bin/expr +++ execNm=expr +++ eval EXPR_CMD=/usr/bin/expr ++++ EXPR_CMD=/usr/bin/expr +++ '[' '!' -x /usr/bin/expr ']' +++ unset Nm confPath execNm +++ findExec BASENAME_CMD /usr/bin/basename basename +++ Nm=BASENAME_CMD +++ confPath=/usr/bin/basename +++ execNm=basename +++ eval BASENAME_CMD=/usr/bin/basename ++++ BASENAME_CMD=/usr/bin/basename +++ '[' '!' -x /usr/bin/basename ']' +++ unset Nm confPath execNm +++ unset -f findExec +++ '[' -f /proc/111281/exe ']' ++++ /usr/bin/readlink /proc/111281/exe +++ my_shell=/usr/bin/bash ++++ /usr/bin/expr /usr/bin/bash : '-*\(.*\)' +++ my_shell=/usr/bin/bash ++++ /usr/bin/basename /usr/bin/bash +++ my_shell=bash +++ case ${my_shell} in +++ '[' -f /usr/local/spack/opt/spack/linux-pop22-skylake_avx512/gcc-12.2.0/lmod-8.7.37-qorv6nkkjzyzntx6wbjupmoxrot26t6r/lmod/lmod/init/bash ']' +++ . /usr/local/spack/opt/spack/linux-pop22-skylake_avx512/gcc-12.2.0/lmod-8.7.37-qorv6nkkjzyzntx6wbjupmoxrot26t6r/lmod/lmod/init/bash ++++ '[' -z '' ']' ++++ case "$-" 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-qorv6nkkjzyzntx6wbjupmoxrot26t6r/lmod/lmod/init/bash) Shell debugging restarted ++++ unset __lmod_vx +++ unset my_shell PS_CMD EXPR_CMD BASENAME_CMD MODULEPATH_INIT LMOD_ALLOW_ROOT_USE READLINK_CMD +++ 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 + run_scripts/run_scam.bash --case-suffix cam_scam_gfortran_debug_test ATEX ----- Case Setup ----- Did not find an alias or longname compset match for 2000_CAM60%SCAMATEX_SLND_SICE_DOCN%AQP3_SROF_SGLC_SWAV Automatically adding SESP to compset Compset forcing is 1972-2004 ATM component is CAM cam6 physics: LND component is Stub land component ICE component is Stub ice component OCN component is DOCN analytic aquaplanet sst - option 3 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/cam_scam_gfortran_debug_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%ne16np4_l%null_oi%ne16np4_r%null_g%null_w%null_z%null_m%gx1v7 Pes setting: compset is 2000_CAM60%SCAMATEX_SLND_SICE_DOCN%AQP3_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 setting: excl_stride is {} Pes other settings: {} Pes other settings append: {} Pes comments: none setting additional fields from config_pes: {}, append {} Compset is: 2000_CAM60%SCAMATEX_SLND_SICE_DOCN%AQP3_SROF_SGLC_SWAV_SESP Grid is: a%ne16np4_l%null_oi%ne16np4_r%null_g%null_w%null_z%null_m%gx1v7 Components in compset are: ['cam', 'slnd', 'sice', 'docn', 'srof', '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_2f3c896-3189-ga05d60b6d Batch_system_type is none Creating Case directory /home/jenkins/workspace/cam_scam_gfortran_debug_test/cime/scripts/test_scam_ATEX_cam_scam_gfortran_debug_test This component includes user_mods /home/jenkins/workspace/cam_scam_gfortran_debug_test/cime_config/usermods_dirs/scam_mandatory Adding user mods directory /home/jenkins/workspace/cam_scam_gfortran_debug_test/cime_config/usermods_dirs/scam_mandatory RUN: /home/jenkins/workspace/cam_scam_gfortran_debug_test/cime/scripts/test_scam_ATEX_cam_scam_gfortran_debug_test/shell_commands FROM: /home/jenkins/workspace/cam_scam_gfortran_debug_test/cime/scripts/test_scam_ATEX_cam_scam_gfortran_debug_test Invalid permissions to create /home/pub/cam_inputdata ERROR: inputdata root is not a directory or is not readable: /home/pub/cam_inputdata [Pipeline] } [Pipeline] // stage [Pipeline] stage [Pipeline] { (Run ARM97 with SILHS) Stage "Run ARM97 with SILHS" skipped due to earlier failure(s) [Pipeline] getContext [Pipeline] } [Pipeline] // stage [Pipeline] stage [Pipeline] { (Declarative: Post Actions) [Pipeline] script [Pipeline] { [Pipeline] sh + chmod -R 755 /home/jenkins/cam_output/ [Pipeline] sh + gzip -d '/home/jenkins/cam_output/scratch/test_scam_ATEX_cam_scam_gfortran_debug_test/bld/cesm.bldlog.*.gz' gzip: /home/jenkins/cam_output/scratch/test_scam_ATEX_cam_scam_gfortran_debug_test/bld/cesm.bldlog.*.gz: No such file or directory [Pipeline] echo ATEX WARNING: One or more of the build logs were not zipped, this means compilation did not finish [Pipeline] sh + gzip -d '/home/jenkins/cam_output/scratch/test_scam_ATEX_cam_scam_gfortran_debug_test/run/cesm.log.*.gz' gzip: /home/jenkins/cam_output/scratch/test_scam_ATEX_cam_scam_gfortran_debug_test/run/cesm.log.*.gz: No such file or directory [Pipeline] echo ATEX WARNING: One or more of the run logs were not zipped, this means the code did not run to completion [Pipeline] sh + cat '/home/jenkins/cam_output/scratch/test_scam_ATEX_cam_scam_gfortran_debug_test/bld/cesm.bldlog.*' cat: '/home/jenkins/cam_output/scratch/test_scam_ATEX_cam_scam_gfortran_debug_test/bld/cesm.bldlog.*': No such file or directory [Pipeline] echo ATEX WARNING: One of the log files (build or run) were not found - the failure must have occured before their creation [Pipeline] sh + gzip -d '/home/jenkins/cam_output/scratch/test_scam_ARM97_cam_scam_gfortran_debug_test/bld/cesm.bldlog.*.gz' gzip: /home/jenkins/cam_output/scratch/test_scam_ARM97_cam_scam_gfortran_debug_test/bld/cesm.bldlog.*.gz: No such file or directory [Pipeline] echo ARM97 WARNING: One or more of the build logs were not zipped, this means compilation did not finish [Pipeline] sh + gzip -d '/home/jenkins/cam_output/scratch/test_scam_ARM97_cam_scam_gfortran_debug_test/run/cesm.log.*.gz' gzip: /home/jenkins/cam_output/scratch/test_scam_ARM97_cam_scam_gfortran_debug_test/run/cesm.log.*.gz: No such file or directory [Pipeline] echo ARM97 WARNING: One or more of the run logs were not zipped, this means the code did not run to completion [Pipeline] sh + cat '/home/jenkins/cam_output/scratch/test_scam_ARM97_cam_scam_gfortran_debug_test/bld/cesm.bldlog.*' cat: '/home/jenkins/cam_output/scratch/test_scam_ARM97_cam_scam_gfortran_debug_test/bld/cesm.bldlog.*': No such file or directory [Pipeline] echo ARM97 WARNING: One of the log files (build or run) were not found - the failure must have occured before their creation [Pipeline] } [Pipeline] // script [Pipeline] script [Pipeline] { [Pipeline] emailext Sending email to: messnermet@uwm.edu [Pipeline] } [Pipeline] // script [Pipeline] } [Pipeline] // stage [Pipeline] } [Pipeline] // withEnv [Pipeline] } [Pipeline] // withEnv [Pipeline] } [Pipeline] // node [Pipeline] End of Pipeline ERROR: script returned exit code 1 Finished: FAILURE