R mpi SNOW for MIP

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Contents

[edit] Introduction

This article will describe how a xml file ought to be configured to describe R using MIP with the Rmpi and snow packages so that parallel R is available in a standard form for BeSTGRID users.

This article is intended only to cover the configuration of R in a parallel environment (e.g. OpenMPI). For configuring R for serial environments see the equivalent article on R.

[edit] Configuration

[edit] Make RMPISNOW script available on the path

On the head node of a rocks cluster the following command will link RMPISNOW to /usr/bin which should be in the PATH for all Linux systems: 

ln -s /usr/lib64/R/library/snow/RMPISNOW /usr/bin/RMPISNOW

Adding this command into the <post></post> section of /export/rocks/install/site-profile/<version>/nodes/extend-compute.xml and rebuild your rocks distribution. This should automatically create the link when the compute nodes are reinstalled.

[edit] Modify RMPISNOW for the Rocks/SGE environment

Some variables passed to RMPISNOW from the Sun Grid Engine and OpenMPI don't match. Run the following command on the head node to correct RMPISNOW: 

sed -i 's/OMPI_MCA_ns_nds_vpid/OMPI_COMM_WORLD_RANK"/g' /usr/lib64/R/library/snow/RMPISNOW

Add this command into the <post></post> section of /export/rocks/install/site-profile/<version>/nodes/extend-compute.xml and rebuild your rocks distribution. This should automatically modify RMPISNOW when the compute nodes are reinstalled.

[edit] Example xml file for R_mpi_SNOW

This should be saved as /usr/local/mip/modules/apac_py/SubCluster/softwareInfoData/R_mpi_SNOW.xml. 

<SoftwarePackages xmlns:glue="http://forge.cnaf.infn.it/glueschema/Spec/V12/R2" xmlns:apac="http://grid.apac.edu.au/glueschema/Spec/V12/R2" xmlns="http://www.ivec.org/softwareSubSchema/Spec/V12/R2" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.ivec.org/softwareSubSchema/Spec/V12/R2 APACSoftwareSubSchemaR2.xsd">
  <SoftwarePackage LocalID="RMPISNOW/2.10.1-Linux" xmlns="http://grid.apac.edu.au/glueschema/Spec/V12/R2">
    <Name>R_mpi_SNOW</Name>
    <Version>2.10.1</Version>
    <Module>RMPISNOW/2.10.1-Linux</Module>
    <SoftwareExecutable LocalID="RMPISNOW/2.10.1-Linux-RMPISNOW">
      <Name>RMPISNOW</Name>
      <Path>/usr/bin</Path>
      <SerialAvail>false</SerialAvail>
      <ParallelAvail>true</ParallelAvail>
    </SoftwareExecutable>
  </SoftwarePackage>
</SoftwarePackages>

This file can the be referenced as source in /usr/local/mip/config/<cluster>_<subcluster>_SIP.ini with: 

[source1]
uri: file:softwareInfoData/localSoftware.xml
format: APACGLUE1.2

[source2]
uri: file:softwareInfoData/R_mpi_SNOW.xml
format: APACGLUE1.2

[edit] Testing RMPISNOW

  • Submit this Image:R-test-snow.txt via Grisu, which should list the hostnames of all the nodes in the Rmpi cluster.
  • This second test script Image:Rmpisnow-test.txt should perform some actual computation on all the nodes in the Rmpi cluster.
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