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Questions tagged [qsub]

The tag has no usage guidance.

0
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1answer
53 views

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 ...
0
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1answer
43 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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0answers
32 views

How to find Bash script location from within, when it's being launched as PBS job?

Is there any way to get the location of the Bash script from within, when it's being launched in a PBS job? I tried $BASH_SOURCE, but it contains another path to the job folder, instead of the one, ...
0
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1answer
19 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 ...
1
vote
2answers
241 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....
0
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1answer
84 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
212 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 ...
3
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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 ...