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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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Calculating IDs for model runs

I'm running some array jobs on a PBS system (although hopefully no knowledge of PBS systems is needed to answer my question!). I've got 24 runs, but I want to split them up into 5 sub-jobs each, so I need to run my script 120 times. After giving…
ChrisW
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How to set number of threads as a downstream variable in PBS job queue

Is there any way to determine how many threads are available to a program when I run it from a PBS job script? In the header of my PBS job script I set #PBS -l nodes=1:ppn=8 Is there a command I can use that will detect the number of threads - so…
Adi
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Is it possible to change a job ID to something human-readable?

I'd like to send myself a text when a job is finished. I understand how to change the job name so that the .o and .e files have the appropriate name. But I'm not sure if there's a way to change the job ID from a string of numbers to a specified key…
Zack Vacanti-Mitchell
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Using Portable Batch System (PBS) Arrays To Work On Different Files Concurrently

I am trying to use PBS Arrays to submit in parallel 5 jobs using the same program on different files. PBS will start five different copies of the script, each with a different integer in the PBS_ARRAYID variable. The script would be run with: qsub…
gdeniz
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How to detect which HPC scheduler (Torque, Sun Grid Engine etc) am I using?

I need to run a different script depending on the type of scheduler, which necessitates a reliable way to detect if the scheduler is Torque, SGE or something else. Something like $SHELL telling which shell I am using. or something like name. I am…
Pradeep Reddy Raamana
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Run a python program whithin a PBS script that generates multiple output files

I am totally new to this. I have to submit a job with TORQUE, and I want to run a python program that generates multiple files (millions). The program has already been written and it works fine. I also wrote a test script that prints 'Hello World'…
dc2
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How to run binary executables in multi-thread HPC cluster?

I have this tool called cgatools from complete genomics (http://cgatools.sourceforge.net/docs/1.8.0/). I need to run some genome analyses in High-Performance Computing Cluster. I tried to run the job allocating more than 50 cores and 250gb memory,…
MAPK
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Why does this command for qsub to submit multiple pbs scripts work in the bash shell but not fish?

I have a bunch of .pbs files in one directory. I can qsub the files no problem with this command in the bash shell but for the fish shell, I continuously hit enter and it just creates a new input line. Any ideas why it doesn't work in fish? for…
Kevin
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