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Questions tagged [pbs]

PBS stands for portable batch system, and describes a family of software products for high performance computing.

PBS stands for portable batch system, and describes a family of software products for high performance computing. The software is a resource manager that is used to manage jobs, including their submission, running, and basic managing. They are often used in UNIX cluster environments and can often be used with schedulers.

Modern PBS daemons are descendants from OpenPBS; two notable descendants are TORQUE and PBSPro. TORQUE is an open source product and is maintained by Adaptive Computing. More information can be found on its wikipedia page. Documentation for TORQUE can be found on Adaptive's website. PBSPro is a commercial product that is developed by Altair Engineering. PBSPro's user guide can be found here.

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Can I use PBS environment variables inside the PBS directives of my script?

Something like: #PBS -t 0-99 #PBS -d "~/$PBS_ARRAYID.output" What I want to do here is to redefine the working directory of each individual job in the job array, using the job's array id. Is this valid code? I need to know before I send to the…
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How to know when PBS batch jobs are complete

I have a BASH script that submits multiple serial jobs to the PBS queueing system. Once the jobs are submitted the script ends. The jobs then run on a cluster and when they are all finished I can move on to the next step. A typical workflow might…
Jack Walpole
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Find maximum memory used by a PBS job

After a job is finished, how can I know the maximum resident size it required at any given point while running? (tried /usr/bin/time, but not installed on the server) Thank you!
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Requesting all processors for a node

I need to run a Java application on a PBS cluster and I'm a bit unclear on how it should be behaving. The application starts a few threads, the number of which is decided by looking at the number of cores on the node it's running on. It then starts…
StFS
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Running multiple serially dependent jobs in parallel

I am running some CFD-simulations on a PBS based cluster. I will run a large number of cases, and therefore want to do the pre-processing on the cluster nodes. I need to do two steps, first meshing, and when the meshing is finished, I want to run…
user3423627
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Why does pbs(dsh) schedule my task onto one node?

I want to execute foo.sh on 2 different nodes. Therefore, I wrote the following script: #!/home/farago/bin/dash qsub -N dist -o P -e P-err -V -v "EXECSCRIPT=foo.sh" -l walltime=12:00:00,nodes=2:ppn=1 Cluster_ExecExp_pbsdsh.sh with…
DaveFar
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Syntax for submitting a qsub job without an actual job file?

I would like to submit qsub jobs on the fly without creating discrete job files. So, let's say I have a python script called "get_time.py" that simply reports the time. Instead of making a submission script like this: cat>job.sub<
jake9115
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Running R script through qsub

I am trying to run an R script called test.r through qsub. My R script is as follows: #!/usr/bin/Rscript x <- 1 write.csv(x,"test.csv") If in Ubuntu terminal I type R CMD BATCH test.r, then the script behaves as planned; test.csv gets exported in…
user2763361
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creating new queue using torque/PBS "access from host not allowed"

I have carried out the following commands. qmgr -c "create queue fastq queue_type=execution" qmgr -c "set queue fastq started=true" qmgr -c "set queue fastq enabled=true" qmgr -c "set queue fastq acl_hosts=compute-0-30" qmgr -c "set queue fastq…
Griff
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Bash script error to run MATLAB

I'm trying to run a matlab script (ga_opt_main.m) in a cluster. I have to write a job submission file, which is essentially just a shell script. But I have never written a shell script and this is what I wrote #!/bin/bash #PBS -q *queuename* …
Nithya Subramanian
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Getting "Access from host not allowed, or unknown host" from Torque PBS Server using qstat command

I'm trying to run command qstat but instead of getting the queue status I'm seeing this error: Cannot resolve default server host 'torqueserver' - check server_name file. qstat: cannot connect to server torqueserver (errno=15010) Access from…
Bagata
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Time taken for completion of PBS jobs

On a PBS system I have access to, I'm running some jobs using the -W x=NACCESSPOLICY:SINGLEJOB flag and, anecdotally, it seems that the same jobs take about 10% longer when adding this flag as without. Is this correct behaviour? If so, it surprises…
ChrisW
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setting two queues in torque?

I have one queue called "batch" in a torque setup. I want to create a new queue called "db" for debugging jobs. "db" queue will have several restrictions such as maximum CPU time of 10 min, etc. Both queues would use the same nodes in principle. I…
armando
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How does GNU parallel detect available memories?

GNU parallel has some options to limit the memory usage, preventing memory leakage. Like --memsuspend and --memfree but it seems that the tool has not told how it detects the total amount of available memory? I wonder if I enter a working…
Xscrapert
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running programs with torque

I have a code in fortran which I compiled and then sent to run as a pbs job in a supercomputer. I want to modify the source code and compile it again while keeping the already running program. My question is what happens if I modify the source…
armando
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