Timed MrBayes Analysis 1.4.0

pts/mrbayes-1.4.0 - 11 October 2019 - Update against upstream, add Windows support.

downloads.xml

<?xml version="1.0"?>
<!--Phoronix Test Suite v9.0.1-->
<PhoronixTestSuite>
  <Downloads>
    <Package>
      <URL>https://github.com/NBISweden/MrBayes/archive/v3.2.7a.tar.gz</URL>
      <MD5>504236626ce9a2de1066a8520672f0cc</MD5>
      <SHA256>3eed2e3b1d9e46f265b6067a502a89732b6f430585d258b886e008e846ecc5c6</SHA256>
      <FileName>MrBayes-3.2.7a.tar.gz</FileName>
      <FileSize>545968</FileSize>
      <PlatformSpecific>Linux, Solaris, BSD, MacOSX</PlatformSpecific>
    </Package>
    <Package>
      <URL>https://github.com/NBISweden/MrBayes/releases/download/v3.2.7/MrBayes-3.2.7-WIN.zip</URL>
      <MD5>1c785876594fb64ca3d5d75d2877306a</MD5>
      <SHA256>d9dcf4190f11a9489875d0b9c7ff9caea720b6f17df0b5f8cd0fce428e60cebe</SHA256>
      <FileName>MrBayes-3.2.7-WIN.zip</FileName>
      <FileSize>6514059</FileSize>
      <PlatformSpecific>Windows</PlatformSpecific>
    </Package>
  </Downloads>
</PhoronixTestSuite>

install.sh

#!/bin/sh

tar -zxvf MrBayes-3.2.7a.tar.gz
cd MrBayes-3.2.7a
./configure
make -j $NUM_CPU_CORES
echo $? > ~/install-exit-status

cat>job.nex<<EOT
begin mrbayes;
   set autoclose=yes nowarn=yes;
   execute examples/primates.nex;
   lset nst=2;
   mcmc nruns=1 ngen=1000000 samplefreq=10000;
   sump burnin=250;
   sumt burnin=250;
end;
EOT

cd ~
cat>mrbayes<<EOT
#!/bin/sh
cd MrBayes-3.2.7a/
mpiexec --allow-run-as-root -np \$NUM_CPU_PHYSICAL_CORES ./src/mb job.nex 2>&1
echo \$? > ~/test-exit-status
EOT
chmod +x mrbayes

install_windows.sh

#!/bin/sh

unzip -o MrBayes-3.2.7-WIN.zip

cd MrBayes-3.2.7-WIN/
cat>job.nex<<EOT
begin mrbayes;
   set autoclose=yes nowarn=yes;
   execute examples/primates.nex;
   lset nst=2;
   mcmc nruns=1 ngen=1000000 samplefreq=10000;
   sump burnin=250;
   sumt burnin=250;
end;
EOT

cd ~
cat>mrbayes<<EOT
#!/bin/sh
cd MrBayes-3.2.7-WIN/
./bin/mb.3.2.7-win64.exe job.nex 2>&1
echo \$? > ~/test-exit-status
EOT
chmod +x mrbayes

results-definition.xml

<?xml version="1.0"?>
<!--Phoronix Test Suite v9.0.1-->
<PhoronixTestSuite>
  <SystemMonitor>
    <Sensor>sys.time</Sensor>
  </SystemMonitor>
</PhoronixTestSuite>

test-definition.xml

<?xml version="1.0"?>
<!--Phoronix Test Suite v9.0.1-->
<PhoronixTestSuite>
  <TestInformation>
    <Title>Timed MrBayes Analysis</Title>
    <AppVersion>3.2.7</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>1.4.0</Version>
    <SupportedPlatforms>Linux, Solaris, BSD, MacOSX, Windows</SupportedPlatforms>
    <SoftwareType>Scientific</SoftwareType>
    <TestType>Processor</TestType>
    <License>Free</License>
    <Status>Verified</Status>
    <ExternalDependencies>build-utilities, openmpi-development</ExternalDependencies>
    <EnvironmentSize>22</EnvironmentSize>
    <ProjectURL>https://github.com/NBISweden/MrBayes</ProjectURL>
    <InternalTags>SMP, MPI</InternalTags>
    <Maintainer>Andrew Schofield</Maintainer>
  </TestProfile>
</PhoronixTestSuite>