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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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bash script PBS_ARRAYID variable argument does not qsub to job

I want to pass the PBS_ARRAYID to the main argument vector (argv) through qsub but after reading every return in pages of google results - I cannot get this to work. A constant argument qsubs fine. # #$ -cwd #$ -S /bin/bash #$ -j y #$ -t 1-3 #$ -pe…
forest.peterson
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pass variable script argument to another script then qsub to program

After reading through numerous bash script threads and help sites, I cannot find a solution that works. I want to pass a variable argument 'i' from a script to another script $i, then qsub this to a program "$1". In the program I read the variable…
forest.peterson
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Parallel Processing using subprocess in python2.4

I want to calculate a statistic over all pairwise combinations of the columns of a very large matrix. I have a python script, called jaccard.py that accepts a pair of columns and computes this statistic over the matrix. On my work machine, each…
wflynny
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Torque nested/successive qsub call

I have a jobscript compile.pbs which runs on a single CPU and compiles source code to create an executable. I then have a 2nd job script jobscript.pbs which I call using 32 CPU's to run that newly created executable with MPI. They both work…
MasterHD
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how to qsub job iteratively

how to qsub job iteratively? Let a variable i=2:10, for each i, I would like to run "tmp.r" and to pause 10 seconds before going to the next i. And my script name is test.pbs. I tried this: for i in `seq 1 10`;do;qsub job$i.sub;sleep…
user2458189
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Run a qsub command from a parent folder to all directories below with a file *.dat

I am using Redhat and a pbs queuing system to submit jobs to finite element analysis code. I typically have a folder that contains a .dat file, which is what I want to run, and a .pbs file that will submit the .dat file. To submit the .dat file I…
Benner145
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How to have console output for Intel ManyCore Lab batch jobs?

I'm currently testing an OpenMP parallel program on Intel's ManyCore Testing Lab computers, and have been using qsub -l select=1:ncpus=30 $HOME/myjob to add the job and run it. It puts the output from the program into a file called myjob.o123456…
stealthysnacks
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Submitting jobs using qsub in matlab r2012a

I am running a code which includes a loop where I am splitting my task and sending it using qsub as different jobs. For eg I am calling: function searchweights() startup distrJobs('UseMAR',false); distrJobs('UseMAR',true); end; …
diggy
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Silently submit a job with qsub to SGE

I have a bash script which submits hundreds of jobs using qsub to a slowly responding SGE queue (it takes a good second for each job ID to show up). In order to bypass this time consuming process and not kill my script when I quit my shell, I run…
champost
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qsub path shell script

I have 2 questions about path. first question is related to 'qsub' this is my current folder /home/mtrnn/rnn_class_EE837/src/rnn-learn/result/lissa_1_rec/ in this folder I use qsub -q public_~~~ ./start.sh It works well. The problem is whenever I…
user2268721
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Pass parameter to a perl script executed trough qsub

Hi would like to pass a parameter to my perl script that should be executed trough qsub. So I run: qsub -l nodes=node01 -v "i=500" Test.pl While in Test.pl I try to call i parameter in several way: use Getopt::Long; $result = GetOptions ("i" =>…
desmo
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how to use ssh to run local script in a qsub script between two clusters?

I'm programming script for the operations on 2 clusters. My aim is to focus only one cluster, it means every script source code is only on one of the cluster. For example in Cluster A I have all scripts installed, now I want to ssh to Cluster B to…
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how to pass value into boost option parameter of code from qsub

I have a program that takes some value from user (parameter is passed using boost option). ./prog --my-value 32 Its fine till here, but now I am running the program in multi nodes and multi cores using qsub script(and I am allowed to use pbs script…
solti
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Missing Java library when submitting Grid Engine job

When I qsub a script that runs a java program I get this error: Exception in thread "main" java.lang.UnsatisfiedLinkError: /usr/java/jdk1.6.0_16/jre/lib/amd64/xawt/libmawt.so: libXtst.so.6: cannot open shared object file: No such file or directory …
Tyler F
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how to run a packet capturing programme in torque cluster with 2 compute node and 1 head node?

I configured a cluster using torque pbs with 2 compute node and 1 head node. I submitted job using qsub command like qsub myscript.sh myscript.sh contains some shell code . This script is executed successfully in any compute node and result i got in…
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