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Started by user Gunther Huebler Obtained jenkins_tests/clubb_BFB_multi_col_gpu_nvhpc_test/Jenkinsfile from git https://github.com/larson-group/clubb.git [Pipeline] Start of Pipeline [Pipeline] node Running on Jenkins in /home/jenkins/workspace/clubb_BFB_multi_col_gpu_nvhpc_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_multi_col_gpu_nvhpc_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' > git fetch --tags --force --progress -- https://github.com/larson-group/clubb.git +refs/heads/*:refs/remotes/origin/* # timeout=10 > 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 Avoid second fetch > git rev-parse refs/remotes/origin/master^{commit} # timeout=10 Checking out Revision 50a5528a55591d69e8b704dccebe1e7d6baa2669 (refs/remotes/origin/master) > git config core.sparsecheckout # timeout=10 > git checkout -f 50a5528a55591d69e8b704dccebe1e7d6baa2669 # timeout=10 Commit message: "Small bug fix in fill_holes_parallel on GPU" > git rev-list --no-walk 50a5528a55591d69e8b704dccebe1e7d6baa2669 # 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 "$-" in +++ __lmod_vx=x +++ '[' -n x ']' +++ set +x Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for this output (/usr/local/spack/opt/spack/linux-pop22-cascadelake/gcc-12.2.0/lmod-8.7.37-bi3kyxcdrfgw3y7vv2k7c5rjxg75qzju/lmod/lmod/init/bash) Shell debugging restarted +++ unset __lmod_vx +++ find /usr/local/spack/share/spack/lmod/linux-pop22-x86_64/Core -print -quit ++ export MODULEPATH=/usr/local/spack/share/spack/lmod/linux-pop22-x86_64/Core ++ MODULEPATH=/usr/local/spack/share/spack/lmod/linux-pop22-x86_64/Core + module load nvhpc netcdf-fortran + '[' -z '' ']' + case "$-" 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 Aborted by Gunther Huebler 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 [Pipeline] } [Pipeline] // stage [Pipeline] } [Pipeline] // withEnv [Pipeline] } [Pipeline] // node [Pipeline] End of Pipeline org.jenkinsci.plugins.workflow.actions.ErrorAction$ErrorId: 4097e0ba-3dbe-48c1-8731-d92ceb9cc59c Finished: ABORTED