Started by an SCM change Obtained jenkins_tests/clubb_BFB_varying_flags_gfortran_test/Jenkinsfile from git https://github.com/larson-group/clubb.git [Pipeline] Start of Pipeline [Pipeline] node Still waiting to schedule task Waiting for next available executor Running on nelson in /home/jenkins/workspace/clubb_BFB_varying_flags_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/clubb.git > git init /home/jenkins/workspace/clubb_BFB_varying_flags_gfortran_test # timeout=10 Fetching upstream changes from https://github.com/larson-group/clubb.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/clubb.git +refs/heads/*:refs/remotes/origin/* # timeout=10 Avoid second fetch Checking out Revision be5e217cd91196f514fb60f9668106e072c14c1b (refs/remotes/origin/master) Commit message: "Tiny dash updates (#1327)" > git config remote.origin.url https://github.com/larson-group/clubb.git # timeout=10 > git config --add remote.origin.fetch +refs/heads/*:refs/remotes/origin/* # timeout=10 > git rev-parse refs/remotes/origin/master^{commit} # timeout=10 > git config core.sparsecheckout # timeout=10 > git checkout -f be5e217cd91196f514fb60f9668106e072c14c1b # timeout=10 > git rev-list --no-walk 95d5d12aef49035170773f0714a97f4109bcccdd # 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] { (Run Python Test) [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 "$-" in +++ __lmod_vx=x +++ '[' -n x ']' +++ set +x Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for this output (/usr/local/spack/opt/spack/linux-pop22-skylake_avx512/gcc-12.2.0/lmod-8.7.37-qorv6nkkjzyzntx6wbjupmoxrot26t6r/lmod/lmod/init/bash) Shell debugging restarted +++ unset __lmod_vx +++ find /usr/local/spack/share/spack/lmod/linux-pop22-x86_64/Core -print -quit ++ export MODULEPATH=/usr/local/spack/share/spack/lmod/linux-pop22-x86_64/Core ++ MODULEPATH=/usr/local/spack/share/spack/lmod/linux-pop22-x86_64/Core + module load gcc netcdf-fortran + '[' -z '' ']' + case "$-" in + __lmod_sh_dbg=x + '[' -n x ']' + set +x Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output Lmod Warning: ------------------------------------------------------------------------------- The following dependent module(s) are not currently loaded: gcc-runtime/13.1.0-wiuv7wc (required by: mpich/4.2.1, hdf5/1.14.3-cb5lzz7, netcdf-c/4.9.2, netcdf-fortran/4.5.3), glibc/2.35-tdr5czg (required by: mpich/4.2.1, hdf5/1.14.3-cb5lzz7, netcdf-c/4.9.2, netcdf-fortran/4.5.3) ------------------------------------------------------------------------------- Shell debugging restarted + unset __lmod_sh_dbg + return 0 + python3 /home/pub/jenkins_BFB_test_configs/sys_admin/python_nightly_test_suite/run_test.py -c /home/pub/jenkins_BFB_test_configs/clubb_BFB_varying_flags_gfortran_test_config =============================== Configuring Test =============================== Working directory set to: /home/jenkins/workspace/clubb_BFB_varying_flags_gfortran_test Checking specified repo: /home/jenkins/workspace/clubb_BFB_varying_flags_gfortran_test Using /home/jenkins/workspace/clubb_BFB_varying_flags_gfortran_test with origin https://github.com/larson-group/clubb.git Output Save Mode: none Using branch: master Making list from 'UnresolvedCommits': CheckRange = True: Getting commit range Run Output Path: output Run commands: ['python compile.py -debug', '\nrm -rf output', '\nmkdir output', '\npython run_scripts/run_clubb_w_varying_flags.py --min-cases -max_iters=360 -f input/flag_sets/run_bindiff_w_flags_config_core_flags.json'] Diffing command: run_scripts/run_bindiff_all.py --flag-sets =============================== Running Test =============================== Parsing message from commit: be5e217cd91196f514fb60f9668106e072c14c1b Checking Commit: be5e217cd91196f514fb60f9668106e072c14c1b Running: final commit to check, not labelled BIT_CHANGING Checking out be5e217cd91196f514fb60f9668106e072c14c1b Running: 'python compile.py -debug' Running: 'rm -rf output' Running: 'mkdir output' Running: 'python run_scripts/run_clubb_w_varying_flags.py --min-cases -max_iters=360 -f input/flag_sets/run_bindiff_w_flags_config_core_flags.json' 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 43, in main exit_code = test.run_test() File "/home/pub/jenkins_BFB_test_configs/sys_admin/python_nightly_test_suite/tests/bit_diff_test.py", line 351, in run_test problem_commits, fake_bc_commits = self.find_problem_commits(bit_changing_commits) File "/home/pub/jenkins_BFB_test_configs/sys_admin/python_nightly_test_suite/tests/bit_diff_test.py", line 477, in find_problem_commits if self.diff(commit, last_bc_commit): File "/home/pub/jenkins_BFB_test_configs/sys_admin/python_nightly_test_suite/tests/bit_diff_test.py", line 700, in diff save_path_1 = self.run_and_save_output(commit1) File "/home/pub/jenkins_BFB_test_configs/sys_admin/python_nightly_test_suite/tests/bit_diff_test.py", line 657, in run_and_save_outwrapper script does not seem to be touching the log file in /home/jenkins/workspace/clubb_BFB_varying_flags_gfortran_test@tmp/durable-82adc035 (JENKINS-48300: if on an extremely laggy filesystem, consider -Dorg.jenkinsci.plugins.durabletask.BourneShellScript.HEARTBEAT_CHECK_INTERVAL=86400) [Pipeline] } [Pipeline] // stage [Pipeline] stage [Pipeline] { (Declarative: Post Actions) [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 ERROR: script returned exit code -1 Finished: FAILURE