Timed 16 wrapped Structure runs 1.0.0

stunts/structure_threader-structure-1.0.0 - 16 September 2015 - Initial commit.

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>http://pritchardlab.stanford.edu/structure_software/release_versions/v2.3.4/structure_kernel_source.tar.gz</URL>
      <MD5>4e0591678cdbfe79347d272b5dceeda1</MD5>
      <FileSize>66375</FileSize>
    </Package>
    <Package>
      <URL>https://raw.githubusercontent.com/StuntsPT/Structure_threader/master/PTS/data/Reduced_dataset.structure</URL>
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    <Package>
      <URL>https://raw.githubusercontent.com/StuntsPT/Structure_threader/master/PTS/data/mainparams</URL>
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    <Package>
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      <FileSize>6257</FileSize>
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  </Downloads>
</PhoronixTestSuite>

install.sh

#!/bin/sh

# Define test dir
testdir=`pwd`

# Create env dir for dependent libraries
mkdir -p ${testdir}/env

# Install dependencies
# Structure
cd ${testdir}
tar -zxvf structure_kernel_source.tar.gz
cd structure_kernel_src
make

# Install Structure_threder
# 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 \$@ -st \${workdir}/structure_kernel_src/structure > \$LOG_FILE 2>&1
" > structure_threader-structure
chmod +x structure_threader-structure

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 16 wrapped Structure runs</Title>
    <AppVersion>0.1-rc3</AppVersion>
    <Description>Bayesian calculation of population attribution, using the "Structure" algorithm. Calculates clusterings for 4 different values of "K" with 4 replciates for each "K".</Description>
    <ResultScale>Seconds</ResultScale>
    <Proportion>LIB</Proportion>
    <SubTitle>Cork Oak clustering</SubTitle>
    <TimesToRun>3</TimesToRun>
  </TestInformation>
  <TestProfile>
    <Version>1.0.0</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>2</EnvironmentSize>
    <ProjectURL>http://github.com/StuntsPT/Structure_threader</ProjectURL>
    <Maintainer>Francisco Pina-Martins</Maintainer>
  </TestProfile>
  <TestSettings>
    <Default>
      <Arguments>-i ../Reduced_dataset.structure -o ../ -K 4 -R 4 --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>