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Search found 12 results on 1 pages for 'qsub'.

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• script unable to find directories/files when running from qsub cluster script

  - by user248237

  I'm calling several unix commands and python on a python script from a qsub shell script, meant to run on a cluster. The trouble is that when the script executes, something seems to go awry in the shell, so that directories and files that exist are not found. For example, in the .out output files of qsub I see the following errors: cd:…

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• using qsub (sge) with multi-threaded applications

  - by dan12345

  i wanted to submit a multi-threaded job to the cluster network i'm working with - but the man page about qsub is not clear how this is done - By default i guess it just sends it as a normal job regardless of the multi-threading - but this might cause problems, i.e. sending many multi-threaded jobs to the same computer, slowing things…

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• qsub: How can I find out what DRM middleware exactly is installed on a cluster?

  - by gojira

  I have a user account on a very big cluster. I have previous experience with Grid Engine and want to use the cluster for array jobs. The documentation tells me to use "qsub" for load balancing / submission of many jobs. Therefore I assumed this means the cluster has Grid Engine. However all my Grid Engine scripts failed to run. I…

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• PBS programming

  - by Werner

  Hi, some short and probably stupid questions about PBS: 1- I submit jobs using qsub job_file is it possible to submit a (sub)job inside a job file? 2- I have the following script: qsub job_a qsub job_b For launching job_b, it would be great to have before the results of job_a finished. Is it possible to put some kind of…

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• How to make bash script run with a latency (i.e. wait 1 sec at each iterations)?

  - by user2413

  I have this bash script; for (( i = 1 ; i <= 160 ; i++ )); do qsub myccomputations"${i}".pbs done Basically, I would prefer if there was a 1 second delay between each iteration. The reason is that at each iterations, it sends the program file mycomputation"${i}$.pbs to a core node for solving. Solving in this instance…

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• Sun Grid Engine : jobs are not well balanced

  - by GlinesMome

  I use Open Grid Scheduler (a fork/copy of Sun Grid Engine). I have tried this configuration from master: # qconf -mattr exechost complex_values slots=8 slave2 # qconf -mq all.q | grep slots slots 100,[slave1=1],[slave2=8] slave1 is down, then I run 10 qsub with a sleep example (so no CPU consumption) but…

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• Running a lot of jobs with sun grid engine

  - by R S

  I want to run a very large number (~30000) of jobs with Sun Grid Engine. I can theoretically, perform 30000 times the "qsub" command to submit jobs. However, I am afraid that will be too much. Is there a better way to do it? (i.e. from a file) Or otherwise, do you think it will work nonetheless? Thank you

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• Sun Grid Engine: Automatically Terminating Idle Interactive Jobs

  - by dmcer

  We're considering using Sun Grid Engine on a small compute cluster. Right now, the current set up is pretty crude and just involves having people ssh to an open machine to run their jobs. We'd like to allow interactive jobs, since that should ease the transition from manually starting jobs to starting them using qsub.…

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• how to check if something is in the queue of torque?

  - by kloop

  I want to re-run some jobs that completed prematurely under torque. These jobs are run through .job scripts (using qsub). However, I don't want to re-run a job which is already in the queue. Given a script filename, how can I know whether it is already in torque's queue (using qstat?) or not? I prefer to do it…

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• Embarrassingly parallel workflow creates too many output files

  - by Hooked

  On a Linux cluster I run many (N > 10^6) independent computations. Each computation takes only a few minutes and the output is a handful of lines. When N was small I was able to store each result in a separate file to be parsed later. With large N however, I find that I am wasting storage space (for the file…

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• Parallel Environment (PE) on Sun Grid Engine (6.2u5) won't run jobs: "only offers 0 slots"

  - by Peter Van Heusden

  I have Sun Grid Engine set up (version 6.2u5) on a Ubuntu 10.10 server with 8 cores. In order to be able to reserve multiple slots, I have a parallel environment (PE) set up like this: pe_name serial slots 999 user_lists NONE xuser_lists NONE start_proc_args /bin/true…

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• Submitting R jobs using PBS

  - by Tony

  I am submitting a job using qsub that runs parallelized R. My intention is to have R programme running on 4 different cores rather than 8 cores. Here are some of my settings in PBS file: #PBS -l nodes=1:ppn=4 .... time R --no-save < program1.R > program1.log I am issuing the command "ta job_id"…

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