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SMART-Lab / smartdispatch

An easy to use job launcher for supercomputers with PBS compatible job manager.
Do What The F*ck You Want To Public License
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Option "launch commands from a file" generates empty commands in PBS. #54

Closed MarcCote closed 9 years ago

MarcCote commented 9 years ago

I saw this when @gabknight tried to use smart_dispatch.py on the mammouth.

gabknight commented 9 years ago

The empty cmd is:

#!/bin/bash
#PBS -V
#PBS -q qwork@mp2
#PBS -l nodes=1:ppn=1
#PBS -l walltime=01:00:00

# Modules #

# Commands #
cd "/home/girardga";  1>> "/home/girardga/SMART_DISPATCH_LOGS/cmd1.sh/logs/.o" 2>> "/home/girardga/SMART_DISPATCH_LOGS/cmd1.sh/logs/.e" &

wait
MarcCote commented 9 years ago

@gabknight I thought it had two commands?

gabknight commented 9 years ago

using the following cmd file (2 jobs), 3 jobs are started, the third one is the one I posted above.

compute_local_tracking_pft.py $SCRATCH/test-retest/V2/Acq1/Seq1/no-nlm/V2-11_fod2mm.nii.gz $SCRATCH/test-retest/V2/Acq1/Seq1/no-nlm/V2-11_interface.nii.gz $SCRATCH/test-retest/V2/Acq1/Seq1/no-nlm/V2-11_map_include.nii.gz $SCRATCH/test-retest/V2//Acq1/Seq1/no-nlm/V2-11_map_exclude.nii.gz $SCRATCH/test-retest/tracking/V2/Acq1/no-nlm/prob.trk --basis mrtrix --algo prob --nt 252930
compute_local_tracking_pft.py $SCRATCH/test-retest/V2/Acq1/Seq1/no-nlm/V2-11_fod2mm.nii.gz $SCRATCH/test-retest/V2/Acq1/Seq1/no-nlm/V2-11_interface.nii.gz $SCRATCH/test-retest/V2/Acq1/Seq1/no-nlm/V2-11_map_include.nii.gz $SCRATCH/test-retest/V2//Acq1/Seq1/no-nlm/V2-11_map_exclude.nii.gz $SCRATCH/test-retest/tracking/V2/Acq1/no-nlm/prob.trk --basis mrtrix --algo prob --nt 252930

You can find everything here: https://www.dropbox.com/s/l50n2vj47e8jl2s/empty_job.zip?dl=0