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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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PBS/Torque - Couldn't delete completed job status information

The command 'qstat -a' outputs lots of lines of information for completed jobs all with status 'C'. It seems that they will stay forever. How to cleanup these unneeded job information since those jobs are already 'completed'? Thanks!
user2884311
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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
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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
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See amount of memory a pbs job is currently using

I know I can see how much memory a pbs job has requested using qstat but is there a way to view how much memory the job is currently using? Thanks!
helicase
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Run Julia codes on a HPC server

I aim to run some Julia codes on a server (no complicated parallel processing involved) using a .pbs file (and qsub). It seems that I should first load module gcc and julia. But I can not find it module avail command load gcc error So should I…
Xu Fe
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Set environment variables all over processes in Julia

I'm currently working with Julia (1.0) to run some parallel code on clusters of an HPC. The HPC is managed with PBS. I'm trying to find a way for broadcasting environment variables over all processes, i.e. a way to broadcast a specific list of…
moudbis
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Connecting laptop(s)/desktop(s) to form a MATLAB computing cluster?

I have experience running parallel jobs on a remote cluster, and parallel (parfor) jobs on a single local machine, but never tried making a cluster of my own. I have access couple of laptops/desktops/servers (root access on all except one server),…
user564376
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Jobs switching from Running state into Queued and back

We observe this strange behavior with some jobs on the cluster running torque pbs and maui: some jobs are switching between (R)unning and (Q)ueued state. Tried google'ing around and didn't find any hints. What could be the reason? Of note, that jobs…
MadH
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matlab batch parallelization in bash

I'm trying to run a piece of code on a large computer cluster in order to analyze different parts of the data. I created 2 loops to assign the jobs to different nodes and the cpu's that the nodes contain. The analysis function I wrote, 'chnJob()',…
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Is there a DRMAA Java library that works with Torque/PBS?

Does anybody know a Java implementation of the DRMAA-API that is known to work with PBS/Torque cluster software? The background behind this: I would like to submit jobs to a newly set-up linux cluster from Java using a DRMAA compliant API. The…
Michael
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Using the script variable OMP_NUM_THREADS in the program source files

If I'm running C++ code on a cluster, is it possible to use the value of OMP_NUM_THREADS in my program? For example, suppose I have two .cpp files main.cpp and func.cpp, where func.cpp is written in parallel using OpenMP. I want to be able to define…
krylov
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What does a file with name ! mean?

My computer (RedHat 6 Linux) has recently created some empty files with the following name: ! Yes, a single exclamation mark. I am wondering what, in anything, in Linux will create files of this name? Perhaps more likely though it is associated…
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Test MPI on a cluster

I am learning OpenMPI on a cluster. Here is my first example. I expect the output would show response from different nodes, but they all respond from the same node node062. I just wonder why and how I can actually get report from different nodes to…
Tim
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PBS non-uniform process request and qstat output

I'm working on a 18 node cluster, running TORQUE/PBS Pro/Open MPI. Setup - 2 CPUs/node, 12 cores/CPU (so 24 allowable process per node). If I submit PBS jobs that need an uneven split across the nodes, e.g. a job that requires say 58 process, I can…
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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…
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