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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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is there a way to change the walltime for currently running PBS job

I underestimated the amount of time a job would take. Would it be possible to change the time limit for a job while it is running?
Farhat
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How to submit a job to a specific node in PBS

How do I send a job to a specific node in PBS/TORQUE? I think you must specify the node name after nodes. #PBS -l nodes=abc However, this doesn't seem to work and I'm not sure why. This question was asked here on PBS and specify nodes to use Here…
Ashwin
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how do i find a complete list of available torque pbs queues?

Q: How do I find the available PBS queues on the "typical" Torque MPI system? (asking our admin takes 24+ hours, and the system changes with constant migration) (for example, "Std8" is one possible queue) #PBS -q Std8
russian_spy
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shared memory, MPI and queuing systems

My unix/windows C++ app is already parallelized using MPI: the job is splitted in N cpus and each chunk is executed in parallel, quite efficient, very good speed scaling, the job is done right. But some of the data is repeated in each process, and…
Blklight
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Does qsub pass command line arguments to my script?

When I submit a job using qsub script.sh is $@ setted to some value inside script.sh? That is, are there any command line arguments passed to script.sh?
a06e
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How to return to bash prompt after printing output from backgrounded function?

How can I return to my bash prompt automatically after printing output from a function that was put in the background? For example, when I run the following script in a bash shell: fn(){ sleep 10 echo "Done" exit } fn…
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PBS, refresh stdout

I have a long running Torque/PBS job and I'd like to monitor output. But log file only gets copied after the job is finished. Is there a way to convince PBS to refresh it?
Anycorn
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Running a binary without a top level script in SLURM

In SGE/PBS, I can submit binary executables to the cluster just like I would locally. For example: qsub -b y -cwd echo hello would submit a job named echo, which writes the word "hello" to its output file. How can I submit a similar job to SLURM.…
highBandWidth
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Directly pass parameters to pbs script

Is there a way to directly pass parameters to a .pbs script before submitting a job? I need to loop over a list of files indicated by different numbers and apply a script to analyze each file. The best I've been able to come up with is the…
Sevenless
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delete jobs by grepping qstat output and sending jobid to qdel?

I am using PBS job scheduler on my cluster, and I would like to delete jobs older than a certain date using qdel; alternatively it would be sufficient to be able to sort the results of qstat by date. qstat gives this output: job-ID prior name …
David LeBauer
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How to use the qsub -v command in PBS torque?

I would like to pass variables to a csh script by using "qsub -v" command. I understand we can list the parameters-value pairs as below, qsub -v par1=value1 par2=value2 myScript.csh Does anyone know if the values of these parameters can be a…
Cassie
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Python: PBS submission, what happens if I change script?

I have a script job.bin for executing a code in python (pythoncode.py) on a cluster, submitting jobs via qsub. In job.bin: cd /path/to/my/python/code python pythoncode.py What happens if: a) while pythoncode.py is running, I change its content b)…
johnhenry
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"embarrassingly parallel" programming using python and PBS on a cluster

I have a function (neural network model) which produces figures. I wish to test several parameters, methods and different inputs (meaning hundreds of runs of the function) from python using PBS on a standard cluster with Torque. Note: I tried…
meduz
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R programming - submitting jobs on a multiple node linux cluster using PBS

I am running R on a multiple node Linux cluster. I would like to run my analysis on R using scripts or batch mode without using parallel computing software such as MPI or snow. I know this can be done by dividing the input data such that each node…
CCA
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how to limit number of concurrently running PBS jobs

I have a 64-node cluster, running PBS Pro. If I submit many hundreds of jobs, I can get 64 running at once. This is great, except when all 64 jobs happen to be nearly I/O bound, and are reading/writing to the same disk. In such cases, I'd like to…
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