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isis:mpi

Parallel Error Calculation with MPI and SLmpi

  • For interactive error calculation in isis you can use conf or conf_loop (using Isis_Slaves.num_slaves+1 cores on the host machine).
  • Fast possibility: mpi_fit_pars. It's a routine in the isisscripts, which uses MPI to calculate the confidence intervals in parallel on different machines.
  • Create an isisscript to be submitted via PBS:
    1. load and group data, load best fit model
    2. call result = mpi_fit_pars([pars]);
    3. if you have the isisscripts you can store everything in a fits-file via fits_save_fit(filename,result)
  • How to start the Job on the Remeis Cluster?
    • Create a job-file with mpi-Option (e.g. by qsub_array -p --mpi file.com)
    • the Command File file.com contains the list of scripts to be executed.
    • Set nodes to the number of free parameters. (See below for an example).
        #!/bin/bash 
        #PBS -S /bin/bash -V 
        #PBS -t 0-0\%10000 
        #PBS -l nodes=11 
        #PBS -l walltime=03:00:00 
        #PBS -N file.com 
        #PBS -o example_script.out  
        #PBS -e example_script.err 
        cd /home/user/datadir 
        COMMAND[0]="mpiexec isis-script example_script.sl" 
        /usr/bin/nice -n +15 ${COMMAND[$PBS_ARRAYID]}
isis/mpi.txt · Last modified: 2016-05-11 09:19 by Victoria Grinberg