un called with config file /mnt/odd/rs/v1/output/log/pipeline_APP0Base/107925100_1/cpac_pipeline_config_195db324_2024-09-11T03-18-11Z.yml
raise exception
File "/code/run.py", line 827, in
run_main()
File "/code/run.py", line 796, in run_main
exitcode = CPAC.pipeline.cpac_runner.run(
File "/code/CPAC/pipeline/cpac_runner.py", line 397, in run
run_cpac_on_cluster(config_file, subject_list_file, cluster_files_dir)
File "/code/CPAC/pipeline/cpac_runner.py", line 185, in run_cpac_on_cluster
raise Exception(err_msg)
Exception: Error submitting C-PAC pipeline run to sge queue
I suspect:
SGE batch files have empty -S parameter
causing it to crash (I think)
Describe the bug
un called with config file /mnt/odd/rs/v1/output/log/pipeline_APP0Base/107925100_1/cpac_pipeline_config_195db324_2024-09-11T03-18-11Z.yml raise exception File "/code/run.py", line 827, in
run_main()
File "/code/run.py", line 796, in run_main
exitcode = CPAC.pipeline.cpac_runner.run(
File "/code/CPAC/pipeline/cpac_runner.py", line 397, in run
run_cpac_on_cluster(config_file, subject_list_file, cluster_files_dir)
File "/code/CPAC/pipeline/cpac_runner.py", line 185, in run_cpac_on_cluster
raise Exception(err_msg)
Exception: Error submitting C-PAC pipeline run to sge queue
I suspect: SGE batch files have empty -S parameter causing it to crash (I think)
!
SGE batch file - 2024_09_11_03_18_15
$ -S
$ -N CPAC_APP0Base
$ -t 1-138
$ -q all.q@treehouse.ucdmc.ucdavis
$ -pe mpi_smp 8
$ -A c-pac_user
$ -V
$ -wd /mnt/odd/rs/v1/output/log/cluster_files
echo "Start - TASKID " $SGE_TASK_ID " : " $(date) python -c "from CPAC.pipeline.cpac_pipeline import run; run('/mnt/odd/rs/v1/output/log/pipeline_APP0Base/107925100_1/cpac_pipeline_config_195db324_2024-09-11T03-18-11Z.yml', '/mnt/odd/rs/v1/output/log/pipeline_APP0Base/107925100_1/cpac_data_config_195db324_2024-09-11T03-18-11Z.yml', $SGE_TASK_ID, 'APP0Base', plugin='MultiProc', plugin_args={'n_procs': 8, 'memory_gb': 40.0, 'raise_insufficient': False, 'status_callback': <function log_nodes_cb at 0x7fb0ea661c60>})" echo "End - TASKID " $SGE_TASK_ID " : " $(date)
To reproduce
No response
Preconfig
Custom pipeline configuration
No response
Run command
No response
Expected behavior
run sge
Acceptance criteria
run sge
Screenshots
No response
C-PAC version
1.87 docker
Container platform
No response
Docker and/or Singularity version(s)
No response
Additional context
No response