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Questions tagged [qsub]

Qsub is a job submission command for high performance computing jobs.

Qsub is a job submission command for high performance computing jobs. It is used by some resource managers and some schedulers, a few of which are TORQUE, PBSPro, OpenPBS, and SGE. It has many different options and is the way that a job (work request) gets queued for consideration in the cluster.

Questions with the "qsub" tag should clearly indicate which resource manager or scheduler is being used.

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Is there a way to use qsub and source together?

I wrote a shell script to process a bunch of files separately, like this #!/bin/bash #set parameters (I have many) ... #find the files and do iteratively for File in $FileList; do source MyProcessing.sh done MyProcessing.sh is the calling…
f. c.
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How to run script in remote terminal from text editor?

My question is a bit specific to the scenario I'm facing. I wasn't really sure what to search for to find and answer to it here. I'm working on developing some CUDA-based programs as part of my research. I have access to a supercomputing cluster…
Thomas Antony
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pbs job no output when busy

I am experiencing a problem with PBS where, of all the jobs I submit, there tends to be a fraction that do not produce any output as they should. I have to resubmit them several times until they have all produced the output. I have also noticed…
qAp
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Starting many unrelated jobs in parallel on Grid Engine?

I often want to start a set of entirely unrelated ("embarrassingly" parallel) jobs on a Grid Engine cluster, for load-balancing purposes. What I do at the moment, I generate one Bash script for each job and then submit each of them separately, all…
user438602
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how to use awk and a conditional pipe to submit qsub jobs?

I have a file (fasta) that I am using awk to extract the needed fields from (sequences with their headers). I then pipe it to a BLAST program and finally I pipe it to qsub in order to submit a job. the…
Schrodinger's Cat
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How do I suppress error and output log files in SGE

I'm running code in a Sun Grid Engine batch system that generates large log files. I can choose the output locations using the -o and -e options, but would like to know if I can tell it not to record the output at all.
invisiblerhino
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Error while using -N option with qsub

I tried to use qsub -N "compile-$*" in Makefile and it gives the following error because $* equals to "compile-obj/linux/flow" in this case. qsub: ERROR! argument to -N option must not contain / The whole command which I am using is:- qsub -P…
crazy_prog
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What does -pe mean with respect to scripts?

I was reading a script to submit a job to a cluster. I saw this line: -pe threaded 8 -R y what does this mean?
HSB
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Specifying a non-sequential array for the SGE task ID

I would like to submit a job array with a list of non-sequential numbers for the SGE_TASK_ID and I also get an error that says, "The initial portion of the string 'file.sh' doesn't contain decimal numbers". Any suggestions? I have a file containing…
Barb
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Why does this command for qsub to submit multiple pbs scripts work in the bash shell but not fish?

I have a bunch of .pbs files in one directory. I can qsub the files no problem with this command in the bash shell but for the fish shell, I continuously hit enter and it just creates a new input line. Any ideas why it doesn't work in fish? for…
Kevin
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