PrepareJob

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Revision as of 14:14, 30 April 2015 by 195.37.167.32 (Talk)

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To run your job on the cluster, prepare it on your local machine, then copy it to the cluster. Beside the datafiles you will need a jobfile containing all you setting.

Name your job file and your data files in a consistent way:

  • Job file: myjobfile.sh
  • User: Mustermann
  • Email: max@mustermann.de

These jobfiles are written in a sort of "shell" command syntax of Linux systems.

Lines starting with "##" or "# " are comment lines to document some stuff for better reading afterwards.

Lines starting with "#$" are commands for the job scheduler "qsub".

Lines starting not with "#" are commands to execute programs in this job.

Contents

Examples

You may use one of the following examples as template for you job. Make sure to change your username, mailadress, filenames and eventually program option in the coloured lines. The last line always contains calling the software you want to run, including all the parameters you wish. Instead of giving the number of processors give the varibale $NSLOTS, you will give him the number of CPUs when starting the job.

Beast

#!/bin/csh
#
## Username (Which account to be charged cpu time)
#$ -A Mustermann
#
## Send mail to these users
#$ -M max@mustermann.de
#
## Mail at beginning/end/on suspension
#$ -m bes
#
## Export these environmental variables
#$ -v PVM_ROOT,LD_LIBRARY_PATH=/share/apps/beaglenew
#
## The job is located in the current working directory.
#$ -cwd
## This are the filenames, where to write outputs and error-logs too
#$ -o myjobfile.out
#$ -e myjobfile.err
#
env >./xenv
/share/apps/beast210/bin/beast -beagle -beagle_CPU -beagle_instances $NSLOTS -overwrite ./myjobfile.xml > ./myjobfile.out

Mr Bayes

#!/bin/csh
#
## Username (Which account to be charged cpu time)
#$ -A Mustermann
#
## Send mail to these users
#$ -M max@mustermann.de
#
## Mail at beginning/end/on suspension
#$ -m bes
#
## Export these environmental variables
#$ -v PVM_ROOT,LD_LIBRARY_PATH=/share/apps/beaglenew
#
## The job is located in the current working directory.
#$ -cwd
## This are the filenames, where to write outputs and error-logs too
#$ -o myjobfile.out
#$ -e myjobfile.err
#
env >./xenv
mpirun -np $NSLOTS /share/apps/mrbayes/mb322 ./beispiel.nex </dev/null

Raxml

#!/bin/csh
#
## Username (Which account to be charged cpu time)
#$ -A Mustermann
#
## Send mail to these users
#$ -M max@mustermann.de
#
## Mail at beginning/end/on suspension
#$ -m bes
#
## Export these environmental variables
#$ -v PVM_ROOT
#
## The job is located in the current working directory.
#$ -cwd
## This are the filenames, where to write outputs and error-logs too
#$ -o myjobfile.out
#$ -e myjobfile.err
#
env >./xenv
mpirun -np $NSLOTS /share/apps/raxml/raxmlHPC-MPI-SSE3.icc -s sequencefile.phy -n outputfile.phy -m PROTGAMMAWAG



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