USF Home
Administrators
Hardware Status



Home
Getting Started
Support and Contacts
Software Portal
Documentation
Tutorial / Links
C Programming Linux MPI Programming
Get Account
Request Licensed Software
 

Rmpi

  1. Rmpi
    1. Description
    2. Version
    3. Authorized Users
    4. Platforms
    5. Local Documentation
      1. Modules
      2. Submitting a Job

Last Modified: 07/14 17:47

Description

Rmpi is a package that provides MPI bindings for the R programming language. In much the same way parallel code is written in other languages such as C or Fortran, R codes can run in parallel across multiple processors or nodes.

Version

  • 2.3.1

Authorized Users

  • circe account holders

Platforms

  • circe cluster

Local Documentation

Modules

Rmpi requires the following module file and some prerequisites to run:

  • apps/R/2.6.1
  • Prerequisites: compilers/pgi/7.0-7.x86_64 openmpi/1.2.6-x86_64-pgi-7.0-7

To run Rmpi on the cluster, ensure that you use module initadd to make the changes persistent. See Modules for more information.

Submitting a Job

The submit script for running Rmpi jobs on the cluster is fairly simple. An example script is provided below: 

#!/bin/bash
#$ -N rmpi-test
#$ -cwd
#$ -pe ompi* 4
#$ -j y
#$ -o output.$JOB_ID

sge_mpirun /opt/apps/R-2.6.0/bin/Rmpi TestRmpi.R

You can submit this job in exactly the same way as you would any other application.