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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>