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Compiling and Job Submission

Compiling and Job Submission Turning your source code into an executable code, then running it in batch mode. C compiler -g option for debugging -X option to hardcode # of Pes -l to link with a library -O[0-3] for optimization Fortran compiler -g option for debugging

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Compiling and Job Submission

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  1. Compiling and Job Submission Turning your source code into an executable code, then running it in batch mode.

  2. C compiler • -g option for debugging • -X option to hardcode # of Pes • -l to link with a library • -O[0-3] for optimization

  3. Fortran compiler • -g option for debugging • -X option to hardcode # of Pes • -l to link with a library • -O[0-3] for optimization

  4. MPI library • Link with –lmpi • Link with –lelan

  5. Running your program • To run your program in parallel you need to issue the prun command • Use –N to indicate number of nodes • Use –n to indicate number of processors • prun -N ${RMS_NODES} –n ${RMS_PROCS} ./a.out

  6. Interactive • Interactive Mode • Used for compiling and debugging • Done with qsub –I • qsub -I -q debug -l rmsnodes=2:8 -l walltime=30:00

  7. Batch • Batch Mode • Create a script • Submit to the queueing system • Available 24 hours • Should be used for production runs

  8. Sample batch file #!/bin/csh #PBS -l walltime=5:00:00 #PBS -l rmsnodes=4:16 #PBS -j oe set echo # execute program prun -N ${RMS_NODES} -n ${RMS_PROCS} ./a.out

  9. Submit the job • While logged into lemieux, use the qsub command qsub jobfile

  10. Monitor the job • The qstat command displays the status of the job

  11. Delete a job • The qdel command will delete a job • qdel jobid

  12. Output and Error files • Upon completion of your batch job, you should receive an output and an error file

  13. Typical Errors • cpu limit exceeded • Ask for more time in your batch job • Warning: no access to tty; thus no job control in this shell • Simply indicating that it is a batch request, ignore this message

  14. Exercises • Login to lemieux and cd to your scratch directory • cd $SCRATCH

  15. Exercises Cont. • Copy shuf.c from /tmp/training to your scratch directory • cp /tmp/training/shuf.c . • Compile • cc shuf.c –lmpi –lelan –o shuf • Run interactively on 4 processors • prun –N1 –n4 shuf

  16. C Sample Code • shuf.c • Compile, link with the mpi library. • Run on 2-8 processors. • Passes numbers via mpi.

  17. Exercises – Job Submission • Create a job that will • Request 50 seconds of execution time and 2 Pes • Change directory to $SCRATCH • Copy the shuf executable from your home directory to $SCRATCH • Run shuf • Redirect the output to a file called output.shuf • Copy output.shuf to $HOME

  18. Exercises – Job Submission 2 • Submit the job • Check the status • Check the error and output files • Store output.shuf to far

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