Questions tagged [qsub]

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Export commands works in interactive mode, but produces error message in script [duplicate]

I need to export an environmental variable to run a program. I am able to successfully do that in interactive mode. However, when I try to export an environmental variable as part of a bash shell ...
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1answer
81 views

How to run the same command to execute a file in multiple directories?

I want to do the following, I have a set of directories: e.g) 400K 500K 600K and so on In each directory I have a "run.pbs" file, that I want to submit through batch with "qsub run.pbs". I was ...
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1answer
26 views

Submitting HPC jobs within an HPC job

I have a large script which relies on input arguments (with getopts). One of these arguments is a directory containing files (all named *bam) This script has 2 parts: Part1: based on input *bam ...
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2answers
359 views

different results on terminal vs qsub submission

I'm trying to run a command on the terminal and also submit it to the cluster but I am getting different results. When I type on the terminal this : $ for i in *_1.fastq.gz; do echo $i >> t....
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1answer
131 views

using top to identify cpu core number with qsub pbspro

I have a shared memory server with PBSpro installed as the job manager. There are 320 cores total, and pbs is configured so there is 1 job queue having 30 of the 32 cpu's so 300 physical cores to be ...
0
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1answer
248 views

awk not behaving with qsub

I am trying to run a command which is something like this intersectBed -a yeast.v2.bed -b cov.txt -wa -wb | awk -v OFS="\t" '{print $7,$8,$9,$6,$11,$10}' > out.txt out.txt looks like this chrI ...
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votes
3answers
1k views

Are there any disadvantages against using qsub to run tasks all the time?

When I'm running a task on a computer network? I've just started to realize that if I qsub any task, then the task won't hog up my terminal, and I can do other things on the same terminal (which is ...