Stack Overflow
Stack Overflow

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.

385 questions
5
votes
2 answers

SGE - QSUB fails to submit jobs in -sync mode

I have a perl script that prepares files for input to a binary program and submits the execution of the binary program to the SGE queueing system version 6.2u2. The jobs are submitted with the -sync yoption to permit the parent perl script the…
EMiller
  • 2,792
  • 4
  • 34
  • 55
5
votes
2 answers

Check real time output after qsub a job on cluster

Here is my pbs file: #!/bin/bash #PBS -N myJob #PBS -j oe #PBS -k o #PBS -V #PBS -l nodes=hpg6-15:ppn=12 cd ${PBS_O_WORKDIR} ./mycommand On qsub documentation page, it seems like if I put the line PBS -k o, I should be able to check the real…
Congzheng Song
  • 51
  • 1
  • 2
5
votes
3 answers

Bash script that allows qsub in TORQUE to wait until the job get finished, pretty much like -sync y in SGE system

I'm using a cluster with Torque/Maui system. I have a bash script that submit one job, using qsub command, and afterwards does several things, like move files, write ASCII files, and check the output from the job I submitted. Concerning this output,…
Quim
  • 161
  • 2
  • 7
5
votes
1 answer

Wait for all jobs of a user to finish before submitting subsequent jobs to a PBS cluster

I am trying to adjust some bash scripts to make them run on a (pbs) cluster. The individual tasks are performed by several script thats are started by a main script. So far this main scripts starts multiple scripts in background (by appending &)…
mschilli
  • 1,884
  • 1
  • 26
  • 56
5
votes
1 answer

How to run several commands in one PBS job submission

I have written a code that takes only 1-4 cpus. But when I submit a job on the cluster, I have to take at least one node with 16 cores per job. So I want to run several simulations on each node with each job I submit. I was wondering if there is a…
solora
  • 93
  • 1
  • 6
4
votes
3 answers

using qsub (sge) with multi-threaded applications

i wanted to submit a multi-threaded job to the cluster network i'm working with - but the man page about qsub is not clear how this is done - By default i guess it just sends it as a normal job regardless of the multi-threading - but this might…
dan12345
  • 1,594
  • 4
  • 20
  • 30
4
votes
3 answers

Submit a job to Oracle Grid Engine in Jenkins continuous integration test system

I know how to run a bash script on Jenkins. However, if I use qsub to submit the bash script to OGE system, how does Jenkins know that my job terminates or not?
Leo5188
  • 1,967
  • 2
  • 17
  • 21
4
votes
2 answers

Why doesn't my awk one-liner work when I call it from Perl?

I have no problem using the following command of AWK as a stand alone command, without any error: $ awk '$9 != "NTM" && $9 != ""' myfile.txt | less -Sn But when I apply them inside Perl's script for qsub (i.e. running job in linux cluster)…
neversaint
  • 60,904
  • 137
  • 310
  • 477
4
votes
1 answer

Unexpected value counts using awk

I have a text file called "test.txt" containing multiple lines with the fields separated by a semicolon. I'm trying to take the value of field3 > strip out everything but the numbers in the field > compare it to the value of field 3 in the previous…
villaman
  • 65
  • 3
4
votes
1 answer

run a python script in qsub

I have a python script main_script.py that looks like this: import os Files = os.listdir(os.path.join(path, ".")) FilesNumber = len(Files) for fileID in range (0,FilesNumber): filename = Files[fileID] # load file specified in filename and…
gabboshow
  • 5,359
  • 12
  • 48
  • 98
4
votes
1 answer

qsub: get last job id submitted

I use Sun Grid Engine, how I can get the id of the last job submitted with qsub? currently I use this bash alias alias lastjob="qstat -u $(whoami) |tail -n1| sed '/LOGIN/d'|cut -d' ' -f1"
JuanPablo
  • 23,792
  • 39
  • 118
  • 164
4
votes
1 answer

SGE Cluster qsub email notifications not working

I'm working on an SGE cluster and having some problems with the qsub email notification system. All of my jobs work perfectly, but I seem unable to modify the default behaviour to only notify at an aborted job. The -M flag works correctly, and I…
Chris C
  • 1,625
  • 1
  • 19
  • 22
4
votes
3 answers

Ensuring one Job Per Node on StarCluster / SunGridEngine (SGE)

When qsubing jobs on a StarCluster / SGE cluster, is there an easy way to ensure that each node receives at most one job at a time? I am having issues where multiple jobs end up on the same node leading to out of memory (OOM) issues. I tried using…
Alex Rothberg
  • 10,243
  • 13
  • 60
  • 120
4
votes
2 answers

Determine total CPU count after qsub within PBS script

For a PBS script called with qsub, I want to know how many total CPU's have actually been allocated in case the number defined in the PBS file is overwritten by inputs from the command line. For example with the following pbs script…
MasterHD
  • 2,264
  • 1
  • 32
  • 41
4
votes
1 answer

How fast can one submit consecutive and independent jobs with qsub?

This question is related to pbs job no output when busy. i.e Some of the jobs I submit produce no output when PBS/Torque is 'busy'. I imagine that it is busier when many jobs are being submitted one after another, and as it so happens, of the jobs…
qAp
  • 1,139
  • 2
  • 12
  • 26
1 2
3
…
25 26