Update job_template_v3.txt

[duettwe]

I think that covers it?

[baxpr]

• 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?

[duettwe]

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.

[duettwe]

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

[duettwe]

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.

[duettwe]

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!

[baxpr]

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