🐛 SGE fails to start. Unset -S parameter?

[nimzodisaster]

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 [email protected]
#$ -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

• default
• abcd-options
• anat-only
• blank
• ccs-options
• fmriprep-options
• fx-options
• monkey
• monkey-ABCD
• ndmg
• nhp-macaque
• preproc
• rbc-options
• rodent

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

[tamsinrogers]

Hi @nimzodisaster , could you attach your pipeline config file so I can see what might be going on? Thanks!