Compiling and Job Submission

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
• -O0-3 for optimization

3
Fortran compiler

• -g option for debugging
• -X option to hardcode of Pes
• -l to link with a library
• -O0-3 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 rmsnodes28
• -l walltime3000

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 walltime50000
• PBS -l rmsnodes416
• 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