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Update job_template_v3.txt #30

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@duettwe duettwe commented Jun 9, 2025

I think that covers it?

@duettwe duettwe requested a review from baxpr June 9, 2025 13:54
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baxpr commented Jun 9, 2025

  • Needs to be a separate/new file, not an edit to the existing. Then can specify the different template in the yaml
  • Will need to be copied to the rcq directory to work with production account rcq - we still haven't sorted Out-of-repo dax templates #28
  • Then can you test on that PRL that failed?

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duettwe commented Jun 9, 2025

Ok, removed failures and set this up as CUSTOM (in the same processor tab in REDCap) to only run on the session we've been testing with 258675.

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duettwe commented Jun 10, 2025

Launches failed

2025-06-09 12:05:42,040 - INFO - tasklauncher - writing batch file:/nobackup/vuiis_daily_singularity/Spider_Upload_Dir/BUDR-x-258675-x-258675-x-prl-cmfeo-new_v2-x-123957e9/PBS/BUDR-x-258675-x-258675-x-prl-cmfeo-new_v2-x-123957e9.slurm
sbatch: error: This does not look like a batch script.  The first
sbatch: error: line must start with #! followed by the path to an interpreter.
sbatch: error: For instance: #!/bin/sh
 
2025-06-09 12:05:42,130 - INFO - tasklauncher - job submit results::False
2025-06-09 12:05:44,431 - INFO - tasklauncher - Cluster:0/120 total, 0/100 pending, 55/500 uploads
2025-06-09 12:05:44,944 - INFO - tasklauncher - writing batch file:/nobackup/vuiis_daily_singularity/Spider_Upload_Dir/BUDR-x-258675-x-258675-x-prl-cmfeo-new-notopup_v2-x-325d3f52/PBS/BUDR-x-258675-x-258675-x-prl-cmfeo-new-notopup_v2-x-325d3f52.slurm
sbatch: error: This does not look like a batch script.  The first
sbatch: error: line must start with #! followed by the path to an interpreter.
sbatch: error: For instance: #!/bin/sh

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duettwe commented Jun 10, 2025

I'm not sure why this wouldn't work though. I copied the existing v3 and just added the few lines that fix the container stuff.

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duettwe commented Jun 10, 2025

These have failed this time. Looks like trying to make the PDF?

Making PDF
Running finalize.sh
cp: error writing '/nobackup/vuiis_daily_singularity/Spider_Upload_Dir/BUDR-x-258675-x-258675-x-prl-cmfeo-new-notopup_v2-x-2a77ddb7/spm_cue_mu3_feedback_epsi3_orth1/beta_0001.nii.gz': Input/output error
cp: error writing '/nobackup/vuiis_daily_singularity/Spider_Upload_Dir/BUDR-x-258675-x-258675-x-prl-cmfeo-new-notopup_v2-x-2a77ddb7/spm_cue_mu3_feedback_epsi3_orth1/beta_0006.nii.gz': Input/output error
cp: error writing '/nobackup/vuiis_daily_singularity/Spider_Upload_Dir/BUDR-x-258675-x-258675-x-prl-cmfeo-new-notopup_v2-x-2a77ddb7/spm_cue_mu3_feedback_epsi3_orth1/beta_0011.nii.gz': Input/output error
cp: error writing '/nobackup/vuiis_daily_singularity/Spider_Upload_Dir/BUDR-x-258675-x-258675-x-prl-cmfeo-new-notopup_v2-x-2a77ddb7/spm_cue_mu3_feedback_epsi3_orth1/beta_0016.nii.gz': Input/output error
cp: error writing '/nobackup/vuiis_daily_singularity/Spider_Upload_Dir/BUDR-x-258675-x-258675-x-prl-cmfeo-new-notopup_v2-x-2a77ddb7/spm_cue_mu3_feedback_epsi3_orth1/beta_0021.nii.gz': Input/output error
cp: error writing '/nobackup/vuiis_daily_singularity/Spider_Upload_Dir/BUDR-x-258675-x-258675-x-prl-cmfeo-new-notopup_v2-x-2a77ddb7/spm_cue_mu3_feedback_epsi3_orth1/beta_0026.nii.gz': Input/output error
cp: error writing '/nobackup/vuiis_daily_singularity/Spider_Upload_Dir/BUDR-x-258675-x-258675-x-prl-cmfeo-new-notopup_v2-x-2a77ddb7/spm_cue_mu3_feedback_epsi3_orth1/beta_0031.nii.gz': Input/output error
cp: error writing '/nobackup/vuiis_daily_singularity/Spider_Upload_Dir/BUDR-x-258675-x-258675-x-prl-cmfeo-new-notopup_v2-x-2a77ddb7/spm_cue_mu3_feedback_epsi3_orth1/beta_0036.nii.gz': Input/output error
cp: error writing '/nobackup/vuiis_daily_singularity/Spider_Upload_Dir/BUDR-x-258675-x-258675-x-prl-cmfeo-new-notopup_v2-x-2a77ddb7/spm_cue_mu3_feedback_epsi3_orth1/beta_0041.nii.gz': Input/output error
cp: error writing '/nobackup/vuiis_daily_singularity/Spider_Upload_Dir/BUDR-x-258675-x-258675-x-prl-cmfeo-new-notopup_v2-x-2a77ddb7/spm_cue_mu3_feedback_epsi3_orth1/con_0002.nii.gz': Input/output error
cp: : Input/output error
cp: : Input/output error
cp: : Input/output error
cp: : Input/output error
cp: : Input/output error
cp: error writing '/nobackup/vuiis_daily_singularity/Spider_Upload_Dir/BUDR-x-258675-x-258675-x-prl-cmfeo-new-notopup_v2-x-2a77ddb7/MEANFMRI_MNI/wctrrfmri_mean_all.nii.gz': Input/output error
JOB_FAILED
DONE!

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baxpr commented Jun 10, 2025

Likely https://bug.xnat.vanderbilt.edu/bugzilla/show_bug.cgi?id=3386 - let's try these again once that's resolved

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