Started by user Gunther Huebler Obtained jenkins_tests/cam_BFB_coarse_res_gfortran_test/Jenkinsfile from git https://github.com/larson-group/cam.git [Pipeline] Start of Pipeline [Pipeline] node Running on Jenkins in /home/jenkins/workspace/cam_BFB_coarse_res_gfortran_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_BFB_coarse_res_gfortran_test # timeout=10 Fetching upstream changes from https://github.com/larson-group/cam.git > git --version # timeout=10 > git --version # 'git version 2.34.1' 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 > 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 Avoid second fetch > git rev-parse refs/remotes/origin/clubb_silhs_devel^{commit} # timeout=10 Checking out Revision 07b885f24884d7b8f04fa69ce3e2d14da0da8c35 (refs/remotes/origin/clubb_silhs_devel) > git config core.sparsecheckout # timeout=10 > git checkout -f 07b885f24884d7b8f04fa69ce3e2d14da0da8c35 # timeout=10 Commit message: "Add a space to create a test commit" > git rev-list --no-walk 07b885f24884d7b8f04fa69ce3e2d14da0da8c35 # timeout=10 [Pipeline] } [Pipeline] // stage [Pipeline] withEnv [Pipeline] { [Pipeline] stage [Pipeline] { (Update sys_admin Repo) [Pipeline] sh + git -C /home/pub/jenkins_BFB_test_configs/sys_admin pull Already up to date. [Pipeline] } [Pipeline] // stage [Pipeline] stage [Pipeline] { (MTso BFB Check) [Pipeline] catchError [Pipeline] { [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/ ++ 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-cascadelake/gcc-12.2.0/lmod-8.7.37-bi3kyxcdrfgw3y7vv2k7c5rjxg75qzju/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 Build script /home/jenkins/workspace/cam_BFB_coarse_res_gfortran_test/libraries/FTorch/buildlib for component FTorch not found. submit_jobs case.run Submit job case.run check for resubmit dout_s False mach larson-group resubmit_num 0 Build script /home/jenkins/workspace/cam_BFB_coarse_res_gfortran_test/libraries/FTorch/buildlib for component FTorch not found. submit_jobs case.run Submit job case.run check for resubmit dout_s False mach larson-group resubmit_num 0 -------- Variable Diff Summary -------- File 1: 07b885f24884d7b8f04fa69ce3e2d14da0da8c35 File 2: 7add1e3967b3f136dc120143d43e5e84d701092d Variables discovered (union): 1720 Variables present in both files: 1720 Variables only in file 1: 0 Variables only in file 2: 0 Variables with differences (all dimensions): 2 Variables identical (all dimensions): 1718 Variables all-zero in file 1 (actual data): 138 Variables all-zero in file 2 (actual data): 138 Variables all-zero in both files (actual data): 138 Variables with >=2 dimensions tested (PASS/FAIL basis): 627 Variables with >=2 dimensions with differences: 2 Variables with >=2 dimensions identical: 625 Variables with >=2 dimensions all-zero in both files (actual data): 105 Variables skipped for PASS/FAIL (fewer than 2 dimensions in both files): 1093 Variables with differences: - FDL | reason=data mismatch | file1: ndim=2, dims=('ilev', 'ncol') | file2: ndim=2, dims=('ilev', 'ncol') - time_written | reason=data mismatch | file1: ndim=2, dims=('time', 'chars') | file2: ndim=2, dims=('time', 'chars') FAIL: Found differences in one or more variables with >=2 dimensions. =============================== 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: 07b885f24884d7b8f04fa69ce3e2d14da0da8c35 Checking Commit: 07b885f24884d7b8f04fa69ce3e2d14da0da8c35 Running: final commit to check, not labelled BIT_CHANGING Checking out 07b885f24884d7b8f04fa69ce3e2d14da0da8c35 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/$USER/cam_output/caseroot/UWM_debug_FHISTC_MTso_cam7_ne3pg3_ne3pg3_mg37_larson-group_gnu --reuse_build . && sed -i -e 's/^CASE=.*/CASE="UWM_debug_FHISTC_MTso_cam7_ne3pg3_ne3pg3_mg37"/' -e 's/^COMPSET=.*/COMPSET="FHISTC_MTso"/' -e 's/ -silhs / /g' -e 's/ -psubcols \$NUMSC//g' -e 's/ -DSILHS//g' -e "s/^subcol_scheme = .*/subcol_scheme = 'off'/" -e 's/^use_subcol_microp = .*/use_subcol_microp = .false./' -e 's/^microp_uniform = .*/microp_uniform = .false./' -e "s/, 'SILHS_CLUBB_PRECIP_FRAC',//" -e "/^'SILHS_CLUBB_ICE_SS_FRAC'/d" run_scripts/run_cesm_uwm_coarse_res.sh && run_scripts/run_cesm_uwm_coarse_res.sh' Checking out 7add1e3967b3f136dc120143d43e5e84d701092d Running: 'rm -f /home/jenkins/cam_output/scratch/UWM_debug_FHISTC_MTso_cam7_ne3pg3_ne3pg3_mg37_larson-group_gnu/run/UWM_debug_FHISTC_MTso_cam7_ne3pg3_ne3pg3_mg37_larson-group_gnu.cam.rh0.1979-01-02-00000.nc && run_scripts/set_up_repo.py --caseroot /home/$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' Diffing: 'python3 run_scripts/netcdf_3D_vars_diff.py 07b885f24884d7b8f04fa69ce3e2d14da0da8c35 7add1e3967b3f136dc120143d43e5e84d701092d' ISSUE WITH COMMIT DETECTED: 07b885f24884d7b8f04fa69ce3e2d14da0da8c35 differs from 7add1e3967b3f136dc120143d43e5e84d701092d =============================== Test Results =============================== Commit Range Checked = 7add1e3967b3f136dc120143d43e5e84d701092d...07b885f24884d7b8f04fa69ce3e2d14da0da8c35 -- CheckRange was set to False, no intermediate commits checked New Unresolved Commits: 07b885f24884d7b8f04fa69ce3e2d14da0da8c35 No fake BIT_CHANGING commits found. Remaining Unresolved Commits (oldest commit is listed first): 07b885f24884d7b8f04fa69ce3e2d14da0da8c35 =============================== Updating Config File =============================== Saving into UnresolvedCommits: 07b885f24884d7b8f04fa69ce3e2d14da0da8c35 Saving into BaselineCommit: 07b885f24884d7b8f04fa69ce3e2d14da0da8c35 =============================== Cleanup =============================== Removing all generated output REMOVING: 7add1e3967b3f136dc120143d43e5e84d701092d REMOVING: 07b885f24884d7b8f04fa69ce3e2d14da0da8c35 ================== Unresolved Commit Status ================== Remaining Unresolved Commits (oldest commit is listed first): 07b885f24884d7b8f04fa69ce3e2d14da0da8c35 Exiting with code: 1 [Pipeline] } ERROR: script returned exit code 1 Setting overall build result to FAILURE [Pipeline] // catchError [Pipeline] } [Pipeline] // stage [Pipeline] stage [Pipeline] { (LTso + SILHS BFB Check) [Pipeline] catchError [Pipeline] { [Pipeline] deleteDir [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_BFB_coarse_res_gfortran_test # timeout=10 Fetching upstream changes from https://github.com/larson-group/cam.git > git --version # timeout=10 > git --version # 'git version 2.34.1' 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 > 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 Avoid second fetch > git rev-parse refs/remotes/origin/clubb_silhs_devel^{commit} # timeout=10 Checking out Revision 07b885f24884d7b8f04fa69ce3e2d14da0da8c35 (refs/remotes/origin/clubb_silhs_devel) > git config core.sparsecheckout # timeout=10 > git checkout -f 07b885f24884d7b8f04fa69ce3e2d14da0da8c35 # timeout=10 Commit message: "Add a space to create a test commit" [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/ ++ 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-cascadelake/gcc-12.2.0/lmod-8.7.37-bi3kyxcdrfgw3y7vv2k7c5rjxg75qzju/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_LTso_SILHS_test_config Build script /home/jenkins/workspace/cam_BFB_coarse_res_gfortran_test/libraries/FTorch/buildlib for component FTorch not found. submit_jobs case.run Submit job case.run check for resubmit dout_s False mach larson-group resubmit_num 0 Build script /home/jenkins/workspace/cam_BFB_coarse_res_gfortran_test/libraries/FTorch/buildlib for component FTorch not found. submit_jobs case.run Submit job case.run check for resubmit dout_s False mach larson-group resubmit_num 0 -------- Variable Diff Summary -------- File 1: 07b885f24884d7b8f04fa69ce3e2d14da0da8c35 File 2: 7add1e3967b3f136dc120143d43e5e84d701092d Variables discovered (union): 1724 Variables present in both files: 1724 Variables only in file 1: 0 Variables only in file 2: 0 Variables with differences (all dimensions): 1 Variables identical (all dimensions): 1723 Variables all-zero in file 1 (actual data): 131 Variables all-zero in file 2 (actual data): 131 Variables all-zero in both files (actual data): 131 Variables with >=2 dimensions tested (PASS/FAIL basis): 629 Variables with >=2 dimensions with differences: 1 Variables with >=2 dimensions identical: 628 Variables with >=2 dimensions all-zero in both files (actual data): 96 Variables skipped for PASS/FAIL (fewer than 2 dimensions in both files): 1095 Variables with differences: - time_written | reason=data mismatch | file1: ndim=2, dims=('time', 'chars') | file2: ndim=2, dims=('time', 'chars') FAIL: Found differences in one or more variables with >=2 dimensions. =============================== 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/subcol_SILHS_UWM_debug_FHISTC_LTso_cam7_ne3pg3_ne3pg3_mg37_larson-group_gnu/run/subcol_SILHS_UWM_debug_FHISTC_LTso_cam7_ne3pg3_ne3pg3_mg37_larson-group_gnu.cam.rh0.1979-01-02-00000.nc Run commands: ['rm -f /home/jenkins/cam_output/scratch/subcol_SILHS_UWM_debug_FHISTC_LTso_cam7_ne3pg3_ne3pg3_mg37_larson-group_gnu/run/subcol_SILHS_UWM_debug_FHISTC_LTso_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/subcol_SILHS_UWM_debug_FHISTC_LTso_cam7_ne3pg3_ne3pg3_mg37_larson-group_gnu --reuse_build --silhs 4 . &&\nsed -i -e \'s/^CASE=.*/CASE="subcol_SILHS_UWM_debug_FHISTC_LTso_cam7_ne3pg3_ne3pg3_mg37"/\' -e \'s/^COMPSET=.*/COMPSET="FHISTC_LTso"/\' 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: 07b885f24884d7b8f04fa69ce3e2d14da0da8c35 Checking Commit: 07b885f24884d7b8f04fa69ce3e2d14da0da8c35 Running: final commit to check, not labelled BIT_CHANGING Checking out 07b885f24884d7b8f04fa69ce3e2d14da0da8c35 Running: 'rm -f /home/jenkins/cam_output/scratch/subcol_SILHS_UWM_debug_FHISTC_LTso_cam7_ne3pg3_ne3pg3_mg37_larson-group_gnu/run/subcol_SILHS_UWM_debug_FHISTC_LTso_cam7_ne3pg3_ne3pg3_mg37_larson-group_gnu.cam.rh0.1979-01-02-00000.nc && run_scripts/set_up_repo.py --caseroot /home/$USER/cam_output/caseroot/subcol_SILHS_UWM_debug_FHISTC_LTso_cam7_ne3pg3_ne3pg3_mg37_larson-group_gnu --reuse_build --silhs 4 . && sed -i -e 's/^CASE=.*/CASE="subcol_SILHS_UWM_debug_FHISTC_LTso_cam7_ne3pg3_ne3pg3_mg37"/' -e 's/^COMPSET=.*/COMPSET="FHISTC_LTso"/' run_scripts/run_cesm_uwm_coarse_res.sh && run_scripts/run_cesm_uwm_coarse_res.sh' Checking out 7add1e3967b3f136dc120143d43e5e84d701092d Running: 'rm -f /home/jenkins/cam_output/scratch/subcol_SILHS_UWM_debug_FHISTC_LTso_cam7_ne3pg3_ne3pg3_mg37_larson-group_gnu/run/subcol_SILHS_UWM_debug_FHISTC_LTso_cam7_ne3pg3_ne3pg3_mg37_larson-group_gnu.cam.rh0.1979-01-02-00000.nc && run_scripts/set_up_repo.py --caseroot /home/$USER/cam_output/caseroot/subcol_SILHS_UWM_debug_FHISTC_LTso_cam7_ne3pg3_ne3pg3_mg37_larson-group_gnu --reuse_build --silhs 4 . && sed -i -e 's/^CASE=.*/CASE="subcol_SILHS_UWM_debug_FHISTC_LTso_cam7_ne3pg3_ne3pg3_mg37"/' -e 's/^COMPSET=.*/COMPSET="FHISTC_LTso"/' run_scripts/run_cesm_uwm_coarse_res.sh && run_scripts/run_cesm_uwm_coarse_res.sh' Diffing: 'python3 run_scripts/netcdf_3D_vars_diff.py 07b885f24884d7b8f04fa69ce3e2d14da0da8c35 7add1e3967b3f136dc120143d43e5e84d701092d' ISSUE WITH COMMIT DETECTED: 07b885f24884d7b8f04fa69ce3e2d14da0da8c35 differs from 7add1e3967b3f136dc120143d43e5e84d701092d =============================== Test Results =============================== Commit Range Checked = 7add1e3967b3f136dc120143d43e5e84d701092d...07b885f24884d7b8f04fa69ce3e2d14da0da8c35 -- CheckRange was set to False, no intermediate commits checked New Unresolved Commits: 07b885f24884d7b8f04fa69ce3e2d14da0da8c35 No fake BIT_CHANGING commits found. Remaining Unresolved Commits (oldest commit is listed first): 07b885f24884d7b8f04fa69ce3e2d14da0da8c35 =============================== Updating Config File =============================== Saving into UnresolvedCommits: 07b885f24884d7b8f04fa69ce3e2d14da0da8c35 Saving into BaselineCommit: 07b885f24884d7b8f04fa69ce3e2d14da0da8c35 Traceback (most recent call last): File "/home/pub/jenkins_BFB_test_configs/sys_admin/python_nightly_test_suite/run_test.py", line 56, in <module> main() File "/home/pub/jenkins_BFB_test_configs/sys_admin/python_nightly_test_suite/run_test.py", line 44, in main test.update_config_file() File "/home/pub/jenkins_BFB_test_configs/sys_admin/python_nightly_test_suite/tests/bit_diff_test.py", line 828, in update_config_file config_file = open(self.test_config_file,'w') PermissionError: [Errno 13] Permission denied: '/home/pub/jenkins_BFB_test_configs/cam_BFB_coarse_res_gfortran_LTso_SILHS_test_config' [Pipeline] } ERROR: script returned exit code 1 [Pipeline] // catchError [Pipeline] } [Pipeline] // stage [Pipeline] stage [Pipeline] { (Declarative: Post Actions) [Pipeline] script [Pipeline] { [Pipeline] sh + chmod -R 755 /home/jenkins/cam_output [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] // node [Pipeline] End of Pipeline Finished: FAILURE