Even though Open Science Grid is a high throughput computing system, sometimes there is a need to run small OpenMPI based jobs. OSG has limited support for this, as long as the core count is small (4 is known to work well, 8 and 16 becomes more difficult due to the limited number of resources).

To get started, first compile your code using the OpenMPI in the modules system. For example:

$ module load openmpi
$ mpicc -o hello hello.c

You can test the executable locally using mpiexec:

$ mpiexec -n 4 hello
Hello world from process 1 of 4
Hello world from process 3 of 4
Hello world from process 0 of 4
Hello world from process 2 of 4

To run your code as a job on OSG, first create a wrapper.sh. Example:

#!/bin/bash

set -e

module load openmpi

mpiexec -n 4 hello

Then, a job submit file:

Requirements = OSGVO_OS_STRING == "RHEL 7" && TARGET.Arch == "X86_64" && HAS_MODULES == True 
request_cpus = 4
request_memory = 4 GB

executable = wrapper.sh

transfer_input_files = hello

output = job.out.$(Cluster).$(Process)
error = job.error.$(Cluster).$(Process)
log = job.log.$(Cluster).$(Process)

on_exit_hold = (ExitBySignal == True) || (ExitCode != 0)
PeriodicRelease = ( (CurrentTime - EnteredCurrentStatus) > 300 ) && (NumJobStarts < 5)

queue 1

Note how the executable is the wrapper.sh script, and that the real executable hello is transferred using the transfer_input_files mechanism.

Please make sure that the number of cores specified in the submit file via request_cpus match the -n argument in the wrapper.sh file.

This page was updated on Nov 12, 2019 at 09:45 from start/resources/openmpi-jobs.md.