Parallel Computing Support User Guide

Summary

This page discusses support for generic parallel computing jobs on the EGI infrastructure. We consider using the MPI-START framework as a means for launching multiple jobs on a cluster. The are several clearly apparent application areas:

* Hadoop-On-Demand/myHadoop
* Charm++
* Parallel R

This is a work in progress.

JDL requirements

As we are using the MPI-START framework, the format of the JDL is the same as for an MPI job. However, the executable hello_bin may launch any process

JobType       = "Normal";
CPUNumber     = 4;
Executable    = "starter.sh";
Arguments     = "OPENMPI hello_bin hello";
InputSandbox  = {"starter.sh", "hello_bin"};
OutputSandbox = {"std.out", "std.err"};
StdOutput     = "std.out";
StdError      = "std.err";
Requirements  = member("MPI-START", other.GlueHostApplicationSoftwareRunTimeEnvironment) && member("OPENMPI", other.GlueHostApplicationSoftwareRunTimeEnvironment);

The starter.sh is based on the code from http://grid.ifca.es/wiki/Middleware/MpiStart/UserDocumentation

hello_bin

This is a very simple code that shows how we detect and execute specific code on the master process only.

Using MPI-START and mpiexec to perform non mpi workloads

Both OpenMPI and MPICH2 define a number of environment variables that are available to every MPI process. In particular, they export variables which relate to the number of process slots allocated to the job and to the MPI Rank of the processes. Using this information one can nominate a "master" or coordinator process in the set of processes. This allows us to accommodate some master/slave use-cases.

MPI Distribution	Rank Variable	Communicator Size variable
OpenMPI	OMPI_COMM_WORLD_RANK	OMPI_COMM_WORLD_SIZE
MPICH2	MPIRUN_RANK	MPIRUN_NPROCS

#!/bin/bash
if test x"$OMPI_COMM_WORLD_RANK" = x"0" ; then
### Code for coordinating master process
else
### Code for slave processes
fi