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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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Multiple mpiruns from one file vs multiple file runs

I am working on an older cluster that I am not the administrator of and is in locked configuration which is causing me some issues. The system uses the original mpich and the cluster script is written in Perl using parallel::mpi for the runs. This…
Carole
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Command substitution as a variable in one-liner

I get the following error: > echo "${$(qstat -a | grep kig):0:7}" -bash: ${$(qstat -a | grep kig):0:7}: bad substitution I'm trying to take the number before. of > qstat -a | grep kig 1192530.perceus- kigumen lr_regul pbs.sh …
kirill_igum
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Why does qdel comman return 'Unknown Job Id'

OS Version CentOS release 4.6 (Final) Kernel \r on an \m 2.6.9-100.ELsmp Problem When I run qdel i get the following error: qdel: Unknown Job Id 20432.scyld.localdomain Information Output of qstat -n head0.localdomain: Req'd Req'd Elap Job ID…
Isopycnal Oscillation
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Unable to link ./oceanG to netcdff5.so

I am working on ROMS modeling. I just installed Openmpi on out linux cluster. I also adjusted LD_LIBRARY_PATH accordingly. I am now facing a unique probelm. when I give mpirun -np 4 ./oceanG ocean.in from bash shell, it runs the model fine.…
vihang bhatt
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sh.py not executing xvfb-run

I'm trying to execute xvfb-run via py.sh but I'm getting sh.ErrorReturnCode_1 and no resulting pdf being created. I created a small html file: $ echo '

Hello, World.

' > test.html And I then ran xvfb_run via sh.py in Python: $ python Python…
Mark L
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How to send parallel jobs in pbs_torque and add the output?

I'm using pov-ray (Rendering tool) in Linux. I've to parallelize my code so I can use 10 computers at the same time for rendering, I've to use torque_pbs to accomplish this task. I have an idea how to divide the pixels with the number of processes…
Muhammad Humza Shakeel
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redirecting error messages in a bash script

I'm using a server with PBS. I'm testing it with echo sleep 10 | qsub At the moment there is a problem with the server and an error message is returned. By redirecting this error message echo sleep 10 | qsub 2>&1 nothing will be printed. Now I…
pawel_winzig
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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 get information about a cluster?

I'm using a Infiniband/Gigabit cluster and submit jobs using PBS. Being logged in on a new cluster, how do I get information using the bash about the number of nods and cpus/node one can use there?
pawel_winzig
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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…
user2122920
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PBS running multiple instances of the same program with different arguments

How do you go about running the same program multiple times but with different arguments each instance on a cluster, submitted through a PBS. Also, is it possible to designate each of these programs to a separate node? Currently, if I have a PBS…
abovezero
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OpenMP- no output

I have a C code that requires parallising with openMP. the code itself runs fine serially but not when parallised. the code is being run with PBS and i have included the batch script. The code has two paralised regions, both within a time loop,…
user2054764
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PBS Script: Multiple Jobs, Node Counts, Variables

Between unique jobs in the PBS job array, is it possible to manipulate the number of nods used and/or the value of variables used by the program itself? For example, one script might run my program as different job submissions on 1 node, then 2…
t. fochtman
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pbs job no output when busy

I am experiencing a problem with PBS where, of all the jobs I submit, there tends to be a fraction that do not produce any output as they should. I have to resubmit them several times until they have all produced the output. I have also noticed…
qAp
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Tools for running and monitoring jobs in cluster

We got these two clusters with eight nodes each, and we are looking for a good cluster framework that would allow us to launch jobs, has an inbuilt scheduler with different scheduling policies and a monitoring system with web frontend. Each of the…
excray
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