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Timed MrBayes Analysis 1.3.1
pts/mrbayes-1.3.1
- 07 February 2018 -
Use built-in mpich/mpi, add SHA256 for download file.
downloads.xml
<?xml version="1.0"?> <!--Phoronix Test Suite v7.8.0m3--> <PhoronixTestSuite> <Downloads> <Package> <URL>ftp://ftp.mirrorservice.org/sites/downloads.sourceforge.net/m/mr/mrbayes/mrbayes/3.1.2/mrbayes-3.1.2.tar.gz, http://kent.dl.sourceforge.net/sourceforge/mrbayes/mrbayes-3.1.2.tar.gz</URL> <MD5>942e4e0a90fa23481bb1f2e0fa0e0d66</MD5> <SHA256>c60253de1980c9f0a0eb684fffe7ba428fda7c39a3edcb6acf384b5e1443f2f4</SHA256> <FileSize>545968</FileSize> </Package> </Downloads> </PhoronixTestSuite>
install.sh
#!/bin/sh 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 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/ 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 v7.8.0m3--> <PhoronixTestSuite> <SystemMonitor> <Sensor>sys.time</Sensor> </SystemMonitor> </PhoronixTestSuite>
test-definition.xml
<?xml version="1.0"?> <!--Phoronix Test Suite v7.8.0m3--> <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>1.3.1</Version> <SupportedPlatforms>Linux, Solaris, BSD, MacOSX</SupportedPlatforms> <SoftwareType>Scientific</SoftwareType> <TestType>Processor</TestType> <License>Free</License> <Status>Verified</Status> <ExternalDependencies>build-utilities, openmpi-development</ExternalDependencies> <EnvironmentSize>22</EnvironmentSize> <ProjectURL>http://mrbayes.csit.fsu.edu/</ProjectURL> <Maintainer>Andrew Schofield</Maintainer> </TestProfile> </PhoronixTestSuite>