PrepareJob

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.

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.

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/beast180/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

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
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/raxml/raxmlHPC-MPI-SSE3.icc -s sequencefile.phy -n outputfile.phy -m PROTGAMMAWAG

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• Step 1: Get an Account
• Step 2: Prepare you Job
• Step 3: Copy your Job to the cluster
• Step 4: Login on the cluster
• Step 5: Start the Job
• Step 6: Wait for the job to be finished
• Step 7: Get your results