Timed wrapped fastStructure runs for 16 Ks 0.2.0

stunts/structure_threader-faststructure-0.2.0 - 16 September 2015 - Added options to choose the number of threads.

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>
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    <Package>
      <URL>https://github.com/numpy/numpy/archive/v1.9.2.tar.gz</URL>
      <MD5>90f7434759088acccfddf5ba61b1f908</MD5>
      <FileSize>4230459</FileSize>
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    <Package>
      <URL>https://github.com/scipy/scipy/archive/v0.16.0b2.tar.gz</URL>
      <MD5>c2e7cf084b0242275ee54df1cf2e9c92</MD5>
      <FileSize>11608327</FileSize>
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    <Package>
      <URL>http://cython.org/release/Cython-0.22.zip</URL>
      <MD5>b22af7b964903ceff57167dc7d5b9b51</MD5>
      <FileSize>2095055</FileSize>
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    <Package>
      <URL>http://gnu.mirror.vexxhost.com/gsl/gsl-latest.tar.gz</URL>
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      <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>
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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>0.2.0</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>Single 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>