Timed MrBayes Analysis 1.3.0

pts/mrbayes-1.3.0 - 09 September 2017 - Fix for higher core count CPUs

downloads.xml

<?xml version="1.0"?>
<!--Phoronix Test Suite v7.4.0m3-->
<PhoronixTestSuite>
  <Downloads>
    <Package>
      <URL>http://managedway.dl.sourceforge.net/sourceforge/mrbayes/mrbayes-3.1.2.tar.gz, http://kent.dl.sourceforge.net/sourceforge/mrbayes/mrbayes-3.1.2.tar.gz</URL>
      <MD5>942e4e0a90fa23481bb1f2e0fa0e0d66</MD5>
      <FileSize>545968</FileSize>
    </Package>
    <Package>
      <URL>http://www.mcs.anl.gov/research/projects/mpich2/downloads/tarballs/1.0.8p1/mpich2-1.0.8p1.tar.gz</URL>
      <MD5>8ff91187e264e75b5f9307018983ba2b</MD5>
      <FileSize>16883298</FileSize>
    </Package>
  </Downloads>
</PhoronixTestSuite>

install.sh

#!/bin/sh

mkdir $HOME/mpich2_

tar -zxvf mpich2-1.0.8p1.tar.gz
cd mpich2-1.0.8p1/
./configure --prefix=$HOME/mpich2_ --enable-fast=all --with-pm=gforker --disable-option-checking
make 
make install
cd ..
rm -rf mpich2-1.0.8p1/

tar -zxvf mrbayes-3.1.2.tar.gz
cd mrbayes-3.1.2/
sed -i -e "s/MPI ?= no/MPI ?= yes/g" Makefile

SSE=$(grep sse /proc/cpuinfo)
if [ ! "$SSE" = "" ]
 then
	sed -i -e "s/OPTFLAGS ?= -O3/OPTFLAGS ?= -O3 -msse -mfpmath=sse -march=native/g" Makefile
fi
#kludge to remove readline dependency. I don't think it affects the speed, so it can probably stay.
sed -i -e "s/USEREADLINE ?= yes/USEREADLINE ?= no/g" Makefile
make -j $NUM_CPU_JOBS PATH=$HOME/mpich2_/bin/:$PATH

cat>job.nex<<EOT
begin mrbayes;
   set autoclose=yes nowarn=yes;
   execute primates.nex;
   lset nst=6 rates=invgamma;
   mcmc ngen=30000 samplefreq=10 nchains=128;
   sump burnin=250;
   sumt burnin=250;
end;
EOT

cd ..

cat>mb<<EOT
#!/bin/sh
cd mrbayes-3.1.2/
../mpich2_/bin/mpiexec -np \$NUM_CPU_CORES ./mb job.nex 2>&1
EOT
chmod +x mb

cat>mrbayes<<EOT
#!/bin/sh
./mb 2>&1
EOT
chmod +x mrbayes

results-definition.xml

<?xml version="1.0"?>
<!--Phoronix Test Suite v7.4.0m3-->
<PhoronixTestSuite>
  <SystemMonitor>
    <Sensor>sys.time</Sensor>
  </SystemMonitor>
</PhoronixTestSuite>

test-definition.xml

<?xml version="1.0"?>
<!--Phoronix Test Suite v7.4.0m3-->
<PhoronixTestSuite>
  <TestInformation>
    <Title>Timed MrBayes Analysis</Title>
    <AppVersion>3.1.2</AppVersion>
    <Description>This test performs a bayesian analysis of a set of primate genome sequences in order to estimate their phylogeny.</Description>
    <ResultScale>Seconds</ResultScale>
    <Proportion>LIB</Proportion>
    <SubTitle>Primate Phylogeny Analysis</SubTitle>
    <TimesToRun>3</TimesToRun>
  </TestInformation>
  <TestProfile>
    <Version>1.3.0</Version>
    <SupportedPlatforms>Linux, Solaris, MacOSX</SupportedPlatforms>
    <SoftwareType>Scientific</SoftwareType>
    <TestType>Processor</TestType>
    <License>Free</License>
    <Status>Verified</Status>
    <ExternalDependencies>build-essential</ExternalDependencies>
    <EnvironmentSize>22</EnvironmentSize>
    <ProjectURL>http://mrbayes.csit.fsu.edu/</ProjectURL>
    <Maintainer>Andrew Schofield</Maintainer>
  </TestProfile>
</PhoronixTestSuite>