NAMD 1.0.0

pts/namd-1.0.0 - 19 September 2018 - Initial commit finally of NAMD benchmark...

downloads.xml

<?xml version="1.0"?>
<!--Phoronix Test Suite v8.2.0-->
<PhoronixTestSuite>
  <Downloads>
    <Package>
      <URL>https://www.ks.uiuc.edu/Research/namd/2.13b1/download/873189/NAMD_2.13b1_Linux-x86_64-multicore.tar.gz</URL>
      <MD5>42bb5dd33b01fcd40a1f36e4115af8d9</MD5>
      <SHA256>137f1694ff93efa5b9c988a80c3b1c462f0e138c0d5102c1ef038bd13d022040</SHA256>
      <FileName>NAMD_2.13b1_Linux-x86_64-multicore.tar.gz</FileName>
      <FileSize>15103931</FileSize>
      <PlatformSpecific>Linux</PlatformSpecific>
    </Package>
    <Package>
      <URL>https://www.ks.uiuc.edu/Research/namd/utilities/f1atpase.zip</URL>
      <MD5>bec570545a4297dc89ac402b8a59753a</MD5>
      <SHA256>26b37eb20ad532238a85724c43cbaedd58a507ec71ad8a40aff20b98da949fa8</SHA256>
      <FileName>f1atpase.zip</FileName>
      <FileSize>28241682</FileSize>
    </Package>
  </Downloads>
</PhoronixTestSuite>

install.sh

#!/bin/sh

tar -zxvf NAMD_2.13b1_Linux-x86_64-multicore.tar.gz
unzip -o f1atpase.zip
sed -i 's/\/usr\/tmp/\/tmp/g' f1atpase/f1atpase.namd

cd ~
echo "#!/bin/sh
cd NAMD_2.13b1_Linux-x86_64-multicore
./namd2 +p\$NUM_CPU_CORES +setcpuaffinity ../f1atpase/f1atpase.namd > \$LOG_FILE 2>&1" > namd
chmod +x namd

results-definition.xml

<?xml version="1.0"?>
<!--Phoronix Test Suite v8.2.0-->
<PhoronixTestSuite>
  <ResultsParser>
    <OutputTemplate>Info: Benchmark time: 64 CPUs 0.0232228 s/step #_RESULT_# days/ns 4678.59 MB memory</OutputTemplate>
    <LineHint>Benchmark time</LineHint>
    <ResultPrecision>5</ResultPrecision>
  </ResultsParser>
</PhoronixTestSuite>

test-definition.xml

<?xml version="1.0"?>
<!--Phoronix Test Suite v8.2.0-->
<PhoronixTestSuite>
  <TestInformation>
    <Title>NAMD</Title>
    <AppVersion>2.13b1</AppVersion>
    <Description>NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD was developed by the Theoretical and Computational Biophysics Group in the Beckman Institute for Advanced Science and Technology at the University of Illinois at Urbana-Champaign.</Description>
    <ResultScale>days/ns</ResultScale>
    <Proportion>LIB</Proportion>
    <SubTitle>ATPase Simulation - 327,506 Atoms</SubTitle>
    <TimesToRun>3</TimesToRun>
  </TestInformation>
  <TestProfile>
    <Version>1.0.0</Version>
    <SupportedPlatforms>Linux</SupportedPlatforms>
    <SoftwareType>Benchmark</SoftwareType>
    <TestType>Processor</TestType>
    <License>Free</License>
    <Status>Verified</Status>
    <SupportedArchitectures>x86_64</SupportedArchitectures>
    <EnvironmentSize>76</EnvironmentSize>
    <ProjectURL>http://www.ks.uiuc.edu/Research/namd/</ProjectURL>
    <InternalTags>SMP</InternalTags>
    <Maintainer>Michael Larabel</Maintainer>
  </TestProfile>
</PhoronixTestSuite>