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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 "$-" in
+++ __lmod_vx=x
+++ '[' -n x ']'
+++ set +x
Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for this output (/usr/local/spack/opt/spack/linux-pop22-cascadelake/gcc-12.2.0/lmod-8.7.37-bi3kyxcdrfgw3y7vv2k7c5rjxg75qzju/lmod/lmod/init/bash)
Shell debugging restarted
+++ unset __lmod_vx
+++ find /usr/local/spack/share/spack/lmod/linux-pop22-x86_64/Core -print -quit
++ export MODULEPATH=/usr/local/spack/share/spack/lmod/linux-pop22-x86_64/Core
++ MODULEPATH=/usr/local/spack/share/spack/lmod/linux-pop22-x86_64/Core
+ module load nvhpc netcdf-fortran
+ '[' -z '' ']'
+ case "$-" in
+ __lmod_sh_dbg=x
+ '[' -n x ']'
+ set +x
Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output
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_multi_col_gpu_nvhpc_test_config
sed: -e expression #1, char 1: unknown command: `"'
sed: -e expression #1, char 1: unknown command: `"'
sed: -e expression #1, char 1: unknown command: `"'
mkdir: cannot create directory ‘/CLUBB_current’: Permission denied
mkdir: cannot create directory ‘/CLUBB_previous’: Permission denied
mv: cannot stat '/CLUBB_current/*.ctl': No such file or directory
mv: cannot stat '/CLUBB_current/*.dat': No such file or directory
mv: cannot stat '/CLUBB_current/*.nc': No such file or directory
mv: cannot stat '/CLUBB_current/*.txt': No such file or directory
Sending interrupt signal to process
Terminated
sed: -e expression #1, char 1: unknown command: `"'
sed: -e expression #1, char 1: unknown command: `"'
sed: -e expression #1, char 1: unknown command: `"'
mkdir: cannot create directory ‘/CLUBB_current’: Permission denied
mkdir: cannot create directory ‘/CLUBB_previous’: Permission denied
mv: cannot stat '/CLUBB_current/*.ctl': No such file or directory
mv: cannot stat '/CLUBB_current/*.dat': No such file or directory
mv: cannot stat '/CLUBB_current/*.nc': No such file or directory
mv: cannot stat '/CLUBB_current/*.txt': No such file or directory

=============================== Configuring Test ===============================


Working directory set to: /home/jenkins/workspace/clubb_BFB_multi_col_gpu_nvhpc_test
Checking specified repo: /home/jenkins/workspace/clubb_BFB_multi_col_gpu_nvhpc_test

Using /home/jenkins/workspace/clubb_BFB_multi_col_gpu_nvhpc_test with origin https://github.com/larson-group/clubb.git

Output Save Mode: all

Using branch: master

Making list from 'UnresolvedCommits':

CheckRange = True: Getting commit range

Run Output Path: output

Run commands: ['python compile.py -gpu openacc', '\nrm -rf output', '\nmkdir output', '\nsed -i "s:lh_straight_mc.*:lh_straight_mc = true:g" input/tunable_parameters/configurable_model_flags.in', '\nsed -i "s:penta_solve_method.*:penta_solve_method = 2:g" input/tunable_parameters/configurable_model_flags.in', '\nsed -i "s:tridiag_solve_method.*:tridiag_solve_method = 2:g" input/tunable_parameters/configurable_model_flags.in', '\nrun_scripts/create_multi_col_params.py -n 4 -out_file run_scripts/clubb_params_multi_col.in', '\nrun_scripts/run_scm_all.bash -min_cases -params clubb_params_multi_col.in']

Diffing command: run_scripts/run_bindiff_all.py

=============================== Running Test ===============================

Parsing message from commit: 665f3896481654acdb49de9afae25d7a9b24a81c
Parsing message from commit: f3de007e9528afc6cc2d71090bce5c6c53337152
Parsing message from commit: 50a5528a55591d69e8b704dccebe1e7d6baa2669

Checking Commit: 665f3896481654acdb49de9afae25d7a9b24a81c
	Skipping: not final commit and not labelled BIT_CHANGING

Checking Commit: f3de007e9528afc6cc2d71090bce5c6c53337152
	Skipping: not final commit and not labelled BIT_CHANGING

Checking Commit: 50a5528a55591d69e8b704dccebe1e7d6baa2669
	Running: final commit to check, not labelled BIT_CHANGING
	Checking out 50a5528a55591d69e8b704dccebe1e7d6baa2669
	Running: 'python compile.py -gpu openacc'
	Running: 'rm -rf output'
	Running: 'mkdir output'
	Running: 'sed -i "s:lh_straight_mc.*:lh_straight_mc = true:g" input/tunable_parameters/configurable_model_flags.in'
	Running: 'sed -i "s:penta_solve_method.*:penta_solve_method = 2:g" input/tunable_parameters/configurable_model_flags.in'
	Running: 'sed -i "s:tridiag_solve_method.*:tridiag_solve_method = 2:g" input/tunable_parameters/configurable_model_flags.in'
	Running: 'run_scripts/create_multi_col_params.py -n 4 -out_file run_scripts/clubb_params_multi_col.in'
	Running: 'run_scripts/run_scm_all.bash -min_cases -params clubb_params_multi_col.in'

================== WARNING ==================
Commit:  50a5528a55591d69e8b704dccebe1e7d6baa2669

There was a problem copying the output.
Did the run complete?
Is the output path correct? output

The run will continue, and this commit will be
considered unresolved.
===========================================
	Checking out ea0b892fd2c25049cb5d1429994dc80e4ab6ed9f
	Running: 'python compile.py -gpu openacc'
	Running: 'rm -rf output'
	Running: 'mkdir output'
	Running: 'sed -i "s:lh_straight_mc.*:lh_straight_mc = true:g" input/tunable_parameters/configurable_model_flags.in'
	Running: 'sed -i "s:penta_solve_method.*:penta_solve_method = 2:g" input/tunable_parameters/configurable_model_flags.in'
	Running: 'sed -i "s:tridiag_solve_method.*:tridiag_solve_method = 2:g" input/tunable_parameters/configurable_model_flags.in'
	Running: 'run_scripts/create_multi_col_params.py -n 4 -out_file run_scripts/clubb_params_multi_col.in'
	Running: 'run_scripts/run_scm_all.bash -min_cases -params clubb_params_multi_col.in'

================== WARNING ==================
Commit:  ea0b892fd2c25049cb5d1429994dc80e4ab6ed9f

There was a problem copying the output.
Did the run complete?
Is the output path correct? output

The run will continue, and this commit will be
considered unresolved.
===========================================
	ISSUE WITH COMMIT DETECTED: 50a5528a55591d69e8b704dccebe1e7d6baa2669 differs from ea0b892fd2c25049cb5d1429994dc80e4ab6ed9f
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 492, in find_problem_commits
    problem_commits = problem_commits + self.find_all_bc_commits_in_range(commit_range)
  File "/home/pub/jenkins_BFB_test_configs/sys_admin/python_nightly_test_suite/tests/bit_diff_test.py", line 759, in find_all_bc_commits_in_range
    commits_to_check = self.commits_in_range(commit_range[0], commit_range[1])
  File "/home/pub/jenkins_BFB_test_configs/sys_admin/python_nightly_test_suite/tests/bit_diff_test.py", line 830, in commits_in_range
    commits_to_check.append(self.repo.commit(hash))
  File "/usr/local/lib/python3.10/dist-packages/git/repo/base.py", line 660, in commit
    return self.rev_parse(str(rev) + "^0")
  File "/usr/local/lib/python3.10/dist-packages/git/repo/fun.py", line 255, in rev_parse
    obj = cast(Commit_ish, name_to_object(repo, rev[:start]))
  File "/usr/local/lib/python3.10/dist-packages/git/repo/fun.py", line 192, in name_to_object
    return Object.new_from_sha(repo, hex_to_bin(hexsha))
  File "/usr/local/lib/python3.10/dist-packages/git/objects/base.py", line 98, in new_from_sha
    oinfo = repo.odb.info(sha1)
  File "/usr/local/lib/python3.10/dist-packages/git/db.py", line 44, in info
    hexsha, typename, size = self._git.get_object_header(bin_to_hex(binsha))
  File "/usr/local/lib/python3.10/dist-packages/git/cmd.py", line 1461, in get_object_header
    return self.__get_object_header(cmd, ref)
  File "/usr/local/lib/python3.10/dist-packages/git/cmd.py", line 1446, in __get_object_header
    cmd.stdin.flush()
BrokenPipeError: [Errno 32] Broken pipe
script returned exit code 1