From BeSTGRID

Contents 1 Introduction 2 Configuration 2.1 Example xml file for MrBayes 3 Testing MrBayes

[edit] Introduction

This article will describe how a xml file ought to be configured to describe MrBayes with MIP so that MrBayes is available in a standard form for BeSTGRID users.

This article covers configuration of MrBayes for both serial and parallel environments.

[edit] Configuration

[edit] Example xml file for MrBayes

This should be saved as /usr/local/mip/modules/apac_py/SubCluster/softwareInfoData/mrbayes.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="MrBayes/3.1.2" xmlns="http://grid.apac.edu.au/glueschema/Spec/V12/R2">
    <Name>MrBayes</Name>
    <Version>3.1.2</Version>
    <Module>mrbayes/3.1.2</Module>
    <SoftwareExecutable LocalID="mrbayes-parallel">
      <Name>mb</Name>
      <Path>/opt/shared/bin</Path>
      <SerialAvail>false</SerialAvail>
      <ParallelAvail>true</ParallelAvail>
    </SoftwareExecutable>
    <SoftwareExecutable LocalID="mrbayes-sequential">
      <Name>mb-serial</Name>
      <Path>/opt/shared/bin/</Path>
      <SerialAvail>true</SerialAvail>
      <ParallelAvail>false</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/mrbayes.xml
format: APACGLUE1.2

[edit] Testing MrBayes

• This test file Image:Primates.nex.txt will test that MrBayes works in parallel, requires a minimum of 25 processors. Modify the Nchains value for different cluster sizes.