PrepareJob

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(Examples)
(Raxml)
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=== Raxml ===
 
=== Raxml ===
<source lang="bash" line start="1" highlight="4,13,24,25,28" enclose="div">
+
<source lang="bash" start="1" highlight="4,13,24,25,28" enclose="div">
 
#!/bin/csh
 
#!/bin/csh
 
#
 
#

Revision as of 14:10, 30 April 2015

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

  1. #!/bin/csh
  2. #
  3. ## Username (Which account to be charged cpu time)
  4. #$ -A Mustermann
  5. #
  6. #
  7. ## If you want to make it queue now, get rid of the -a option by adding ## before $
  8. ## If you want to make it queue later, use this format [[CC]yy]MMDDhhmm[.SS]
  9. ##$ -a 201407300600
  10. #
  11. #
  12. ## Send mail to these users
  13. #$ -M max@mustermann.de
  14. #
  15. ## Mail at beginning/end/on suspension
  16. #$ -m bes
  17. #
  18. ## Export these environmental variables
  19. #$ -v PVM_ROOT,LD_LIBRARY_PATH=/share/apps/beaglenew
  20. #
  21. ## The job is located in the current working directory.
  22. #$ -cwd
  23. ## This are the filenames, where to write outputs and error-logs too
  24. #$ -o myjobfile.out
  25. #$ -e myjobfile.err
  26. #
  27. env >./xenv
  28. /share/apps/beast210/bin/beast -beagle -beagle_CPU -beagle_instances $NSLOTS -overwrite ./myjobfile.xml > ./myjobfile.out

Mr Bayes

  1. #!/bin/csh
  2. #
  3. ## Username (Which account to be charged cpu time)
  4. #$ -A Mustermann
  5. #
  6. #
  7. ## If you want to make it queue now, get rid of the -a option by adding ## before $
  8. ## If you want to make it queue later, use this format [[CC]yy]MMDDhhmm[.SS]
  9. ##$ -a 201407300600
  10. #
  11. #
  12. ## Send mail to these users
  13. #$ -M max@mustermann.de
  14. #
  15. ## Mail at beginning/end/on suspension
  16. #$ -m bes
  17. #
  18. ## Export these environmental variables
  19. #$ -v PVM_ROOT,LD_LIBRARY_PATH=/share/apps/beaglenew
  20. #
  21. ## The job is located in the current working directory.
  22. #$ -cwd
  23. ## This are the filenames, where to write outputs and error-logs too
  24. #$ -o myjobfile.out
  25. #$ -e myjobfile.err
  26. #
  27. env >./xenv
  28. mpirun -np $NSLOTS /share/apps/mrbayes/mb322 ./beispiel.nex </dev/null

Raxml

#!/bin/csh
#
## Username (Which account to be charged cpu time)
#$ -A Mustermann
#
#
## If you want to make it queue now, get rid of the -a option by adding ## before $
## If you want to make it queue later, use this format [[CC]yy]MMDDhhmm[.SS]
##$ -a 201407300600
#
#
## 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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