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Questions tagged [qsub]

19 questions
3
votes
3 answers

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 quite useful even if the task only takes a single…
InquilineKea
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1 answer

Shell Variable Expansion in qsub command through drmaa

I am running a bulk job submission to SGE (Sun Grid Engine) using python drmaa bindings. For the bulk job submission I am submitting a python script that takes in one argument and is command line executable, through a shebang. To properly…
Melendowski
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1 answer

Will `qsub` run my jobs sequentially?

Assume a script including the following content is passed to qsub as qsub myscript.sh #PBS -N Job_name #PBS -l walltime=10:30,mem=320kb #PBS -m be # step1 arg1 arg2 step2 arg3 arg4 Will step1 and step2 run in parallel over different nodes or…
zzkr
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1 answer

How can I submit multiple R job at once?

I have a R-script which runs multiple files say file=1 to 50. I usually submit repeated jobs say 5 times with 10 files each time by changing the number in R-script. So, how can I submit the 5-job at once without submitting the job 5 times? In…
b_takhel
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2 answers

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.txt; zcat $i | \ grep "GCTGGCAAAAAGAAGGTAACATGTTTT" >>…
user3138373
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0 answers

Make a job depend on another but only if timeout

When submitting jobs with qsub, we can make sure that a job only starts after another. More so, we can only execute it depending on the status of that other job. Perhaps only run the new job if the other one fails, or only if exits OK. But in my…
Bram Vanroy
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2 answers

Pass a variable that contains a comma as a -v option to qsub

After seeing the reactions on Stack Overflow on this question and an unfamiliarity with qsub, I believe thqt U&L is better suited for this question. In qsub, we can pass environment variables (a comma-separated list of envar=value pairs) like…
Bram Vanroy
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2 answers

Bash script for reading multiple files

I have multiple R scripts to read (up to 3 i.e. tr1.R, tr2.R, tr3.R). The bash script for reading a single script is given below #!/bin/bash #PBS -l nodes=1:ppn=10,walltime=00:05:00 #PBS -M #PBS -m e module load R/4.0 Rscript ~/tr1.R I tried the…
b_takhel
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0
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2 answers

How to use "qstat" and "grep" to list lines containing a range of numbers?

To monitor the job status in clusters, qstat is used to output lines like this job-ID prior name user state submit/start at queue slots…
lanselibai
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How can I cancel all waiting jobs with qsub?

I am running a lot of jobs with qsub: some are running, some are waiting. Is there a way to cancel all the jobs for a given user which are queued/waiting without giving the individual job IDs?
user443699
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1 answer

How can I run a script from an scpecific node and activating a conda environment?

I have a python program that runs inside a conda environment installed in a specific node of a cluster. I would like to submit it into qsub but just need help. My script is: #!/bin/bash source conda activate myenv pyhton3.6 myprogram.py I have…
TYSH
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2 answers

Syntax for number of cores in a Sun Grid Engine job file

I want to use the HPC of my university to qsub an array job of 3 tasks. Each task runs a Matlab code which uses a solver (MOSEK) that exploits multiple threads to solve an optimization problem. A parameter can control the number of threads we want…
user3285148
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1 answer

Syntax for memory request in a Sun Grid Engine job file

I'm submitting a Matlab job in the cluster of my university using qsub after having logged in a node using ssh. The job runs out of memory. This is the advice I received to fix my issue: "Possible solutions are run on a bigger machine or buy more…
user3285148
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1 answer

Name is nonexistent or not a directory

I'm running an array job (400 Matlab R2018b tasks) in the HPC of my university. After having qsub the .sh file in the terminal, the 400 tasks start by they are immediately killed. In the .o file of each task no errors are reported but only the…
user3285148
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Export commands works in interactive mode, but produces error message in script

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 script, I get this error message: export: Command…
SD23Nov18
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