qsub

问题 This question is related to pbs job no output when busy. i.e Some of the jobs I submit produce no output when PBS/Torque is 'busy'. I imagine that it is busier when many jobs are being submitted one after another, and as it so happens, of the jobs submitted in this fashion, I often get some that do not produce any output. Here're some codes. Suppose I have a python script called "x_analyse.py" that takes as its input a file containing some data, and analyses the data stored in the file: ./x

问题 I would like to run a script when all of the jobs that I have sent to a server are done. for example, I send ssh server "for i in config*; do qsub ./run 1 $i; done" And I get back a list of the jobs that were started. I would like to automatically start another script on the server to process the output from these jobs once all are completed. I would appreciate any advice that would help me avoid the following inelegant solution: If I save each of the 1000 job id's from the above call in a

问题 how can I parametrize a shell script that is executed on a grid (started with qsub) ? I have a shell script, where I use getopts to read the parameters. When I start (qsub script.sh -r firstparam -s secondparam ..) this working script with qsub I receive error messages, qsub: invalid option -- s qsub: illegal -r value as qsub thinks the parameter are for itself. Yet I have not found any solution. Thanks 回答1: Using the qsub -v option is the proper way: qsub -v par_name=par_value[,par_name=par

问题 I have a script that I am trying to submit to a SGE cluster (on Redhat Linux). The very first part of the script defines the current folder from the full CWD path, as a variable to use downstream: #!/usr/bin/bash # #$ -cwd #$ -A username #$ -M user@server #$ -j y #$ -m aes #$ -N test #$ -o test.log.txt echo 'This is a test.' result="${PWD##*/}" echo $result In bash, this works as expected: CWD: -bash-4.1$ pwd /home/user/test Run script: -bash-4.1$ bash test.sh This is a test. test When I

问题 I am using Redhat and a pbs queuing system to submit jobs to finite element analysis code. I typically have a folder that contains a .dat file, which is what I want to run, and a .pbs file that will submit the .dat file. To submit the .dat file I would run the command "qsub *.pbs" in the directory containing both files. How could I submit or just run "qsub *.pbs" from outside of the directories containing the .dat files. I would typically be two directories up from the .dat files. Thanks 回答1:

问题 I have been given a c shell script that launches 800 individual qsubs for a sample. I need to run this script on more than 500 samples (listed in samples.txt ). To automate the process, I thought about running the script (named SrchDriver ) using the following bash shell script: #!/bin/sh for item in $(cat samples.txt) do (cd dir_"$item"/MAPGAPS && SrchDriver "$item"_Out 3) done This script would launch the SrchDriver script for all samples one right after another which would result in too

问题 I'm using Sun Grid Engine on my ubuntu 14.04 to queue my jobs to be run on my multicore CPU. I've installed and set up SGE on my system but I have problem when testing it. I've created a "hello_world" dir which contains two shell scripts named "hello_world.sh" & "hello_world_qsub.sh" first including a simple command and second including qsub command to submit the first script file as a job to be run. Here's what "hello_world.sh" includes: #!/bin/bash echo "Hello world" > /home/theodore/tmp

问题 Is it possible to do parallelize across a for loop in a PBS file? Below is an my attempt.pbs file. I would like to allocate 4 nodes and simultaneously allocate 16 processes per node. I have successfully done this but now I have 4 jobs and I would like to send one job to each node. (I need to do this because queuing algo will make me wait a few days for submitting 4 separate job on the cluster I'm using) #!/bin/bash #PBS -q normal #PBS -l nodes=4:ppn=16:native #PBS -l walltime=10:00:00 #PBS -N

问题 I have this script which works fine when I call it with sh but it fails when I use qsub. Could someone please help me debug this? I can't seem to find an answer online #!/bin/bash #$ -S /bin/bash #$ -V #$ -cwd #$ -l h_vmem=6G #$ -N MHCIp if [ $# -lt 2 ] then echo need 2 arguments echo "USAGE : qsub run_MHCIprediction.sh <input_peptide_file> <MHCI_allele_file>" exit 0 fi input_file=$1 allele_file=$2 output_prefix=`echo ${input_file} | awk -F"." '{print $1}'` while read -u 10 allele strip

问题 I am currently running multiple Java executable program using qsub. I wrote two scripts: 1) qsub.sh, 2) run.sh qsub.sh #! /bin/bash echo cd `pwd` \; "$@" | qsub run.sh #! /bin/bash for param in 1 2 3 do ./qsub.sh java -jar myProgram.jar -param ${param} done Given the two scripts above, I submit jobs by sh run.sh I want to redirect the messages generated by myProgram.jar -param ${param} So in run.sh , I replaced the 4th line with the following ./qsub.sh java -jar myProgram.jar -param ${param}