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+ 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)