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:
- load and group data, load best fit model
- call
result = mpi_fit_pars([pars]);
- 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]}