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Timed wrapped fastStructure runs for 16 Ks 0.2.1
stunts/structure_threader-faststructure-0.2.1
- 16 September 2015 -
Minor fix in option names.
downloads.xml
<?xml version="1.0"?> <!--Phoronix Test Suite v5.8.0 (Belev)--> <PhoronixTestSuite> <Downloads> <Package> <URL>https://github.com/StuntsPT/Structure_threader/archive/v0.1-rc3.tar.gz</URL> <MD5>ca5c134d8fc24760fd47d730adfde892</MD5> <FileSize>235897</FileSize> </Package> <Package> <URL>https://raw.githubusercontent.com/StuntsPT/Structure_threader/master/PTS/data/BigTestData.str.tar.xz</URL> <MD5>1115759c154152b264a4ff5f87c34c1d</MD5> <FileSize>71044</FileSize> </Package> <Package> <URL>https://github.com/rajanil/fastStructure/archive/v1.0.tar.gz</URL> <MD5>5cbb76e7d49e27a57046ab641b666f97</MD5> <FileSize>100627</FileSize> </Package> <Package> <URL>http://pypi.python.org/packages/source/n/nose/nose-1.3.6.tar.gz</URL> <MD5>0ca546d81ca8309080fc80cb389e7a16</MD5> <FileSize>276273</FileSize> </Package> <Package> <URL>https://github.com/numpy/numpy/archive/v1.9.2.tar.gz</URL> <MD5>90f7434759088acccfddf5ba61b1f908</MD5> <FileSize>4230459</FileSize> </Package> <Package> <URL>https://github.com/scipy/scipy/archive/v0.16.0b2.tar.gz</URL> <MD5>c2e7cf084b0242275ee54df1cf2e9c92</MD5> <FileSize>11608327</FileSize> </Package> <Package> <URL>http://cython.org/release/Cython-0.22.zip</URL> <MD5>b22af7b964903ceff57167dc7d5b9b51</MD5> <FileSize>2095055</FileSize> </Package> <Package> <URL>http://gnu.mirror.vexxhost.com/gsl/gsl-latest.tar.gz</URL> <MD5>e49a664db13d81c968415cd53f62bc8b</MD5> <FileSize>3534080</FileSize> </Package> <Package> <URL>http://www.netlib.org/lapack/lapack-3.5.0.tgz</URL> <MD5>b1d3e3e425b2e44a06760ff173104bdf</MD5> <FileSize>6313139</FileSize> </Package> </Downloads> </PhoronixTestSuite>
install.sh
#!/bin/bash set -e # Define test dir testdir=`pwd` # Get LDFAGS _OLD_LDFLAGS=$LDFLAGS # Create env dir for dependent libraries mkdir -p ${testdir}/env envdir=${testdir}/env # Install dependencies # LAPACK tar xvfz lapack-3.5.0.tgz mkdir -p build-lapack cd build-lapack cmake ../lapack-3.5.0 make #mkdir -p ${envdir}/{bin,lib} mv bin ${envdir} mv lib ${envdir} # cython cd ${testdir} unzip Cython-0.22.zip cd Cython-0.22 export PYTHONPATH=$PYTHONPATH:${envdir}/lib/python2.7/site-packages/ mkdir -p ${envdir}/lib/python2.7/site-packages/ python2 setup.py install --prefix=${envdir} # python-nose cd ${testdir} tar xvfz nose-1.3.6.tar.gz cd nose-1.3.6 python2 setup.py install --prefix=${envdir} # numpy cd ${testdir} tar xvfz v1.9.2.tar.gz cd numpy-1.9.2 sed -e "s|#![ ]*/usr/bin/python$|#!/usr/bin/python2|" \ -e "s|#![ ]*/usr/bin/env python$|#!/usr/bin/env python2|" \ -e "s|#![ ]*/bin/env python$|#!/usr/bin/env python2|" \ -i $(find . -name '*.py') export ATLAS=None export LDFLAGS="$LDFLAGS -shared" python2 setup.py install --prefix=${envdir} # scipy export PATH=$PATH:${envdir}/bin cd ${testdir} tar xvfz v0.16.0b2.tar.gz cd scipy-0.16.0b2 python2 setup.py install --prefix=${envdir} # GNU scientific library cd ${testdir} tar xvzf gsl-latest.tar.gz cd gsl-1.16 export LDFLAGS=${_OLD_LDFLAGS} ./configure --prefix=${envdir} make make install # fastStructure # Extract tarball, enter src dir, build binary and place it in the env dir export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:${envdir}/lib export CFLAGS="-I${envdir}/include" export LDFLAGS="-L${envdir}/lib" cd ${testdir} tar xvfz v1.0.tar.gz cd fastStructure-1.0 cd vars python2 setup.py build_ext --inplace cd .. python2 setup.py build_ext --inplace # Dataset cd ${testdir} tar xvfJ BigTestData.str.tar.xz # Structure_threader cd ${testdir} tar xfvz v0.1-rc3.tar.gz # Create launcher script echo "#!/bin/bash workdir=`pwd` cd Structure_threader-0.1-rc3/ python3 structure_threader.py \$@ -fs \${workdir}/fastStructure-1.0/structure.py > \$LOG_FILE 2>&1 " > structure_threader-faststructure chmod +x structure_threader-faststructure
results-definition.xml
<?xml version="1.0"?> <!--Phoronix Test Suite v5.8.0 (Belev)--> <PhoronixTestSuite> <SystemMonitor> <Sensor>sys.time</Sensor> </SystemMonitor> </PhoronixTestSuite>
test-definition.xml
<?xml version="1.0"?> <!--Phoronix Test Suite v5.8.0 (Belev)--> <PhoronixTestSuite> <TestInformation> <Title>Timed wrapped fastStructure runs for 16 Ks</Title> <AppVersion>0.1-rc3</AppVersion> <Description>Multi threaded bayesian calculation of population attribution, using the "fastStructure" algorithm. Will calculate clusterings for 16 values of "K".</Description> <ResultScale>Seconds</ResultScale> <Proportion>LIB</Proportion> <SubTitle>Cork Oak clustering</SubTitle> <TimesToRun>3</TimesToRun> </TestInformation> <TestProfile> <Version>0.2.1</Version> <SupportedPlatforms>Linux, Solaris, MacOSX, BSD</SupportedPlatforms> <SoftwareType>Scientific</SoftwareType> <TestType>Processor</TestType> <License>Free</License> <Status>Verified</Status> <ExternalDependencies>build-utils, python</ExternalDependencies> <EnvironmentSize>341</EnvironmentSize> <ProjectURL>http://github.com/StuntsPT/Structure_threader</ProjectURL> <Maintainer>Francisco Pina-Martins</Maintainer> </TestProfile> <TestSettings> <Default> <Arguments>-i ../BigTestData -o ../ -K 16 --no-plots 1 --no-tests 1</Arguments> </Default> <Option> <DisplayName>Number of threads to use</DisplayName> <Identifier>Number_of_threads</Identifier> <ArgumentPrefix>-t </ArgumentPrefix> <DefaultEntry>0</DefaultEntry> <Menu> <Entry> <Name>1 thread</Name> <Value>1</Value> </Entry> <Entry> <Name>2 threads</Name> <Value>2</Value> </Entry> <Entry> <Name>4 threads</Name> <Value>4</Value> </Entry> <Entry> <Name>6 threads</Name> <Value>6</Value> </Entry> <Entry> <Name>8 threads</Name> <Value>8</Value> </Entry> <Entry> <Name>10 threads</Name> <Value>10</Value> </Entry> <Entry> <Name>12 threads</Name> <Value>12</Value> </Entry> <Entry> <Name>14 threads</Name> <Value>14</Value> </Entry> <Entry> <Name>16 threads</Name> <Value>16</Value> </Entry> </Menu> </Option> </TestSettings> </PhoronixTestSuite>