NAMD CUDA 1.0.0

pts/namd-cuda-1.0.0 - 22 December 2018 - Initial commit of CUDA version of NAMD benchmark.

downloads.xml

<?xml version="1.0"?>
<!--Phoronix Test Suite v8.6.0m0-->
<PhoronixTestSuite>
  <Downloads>
    <Package>
      <URL>https://www.ks.uiuc.edu/Research/namd/2.13b1/download/873189/NAMD_2.13b1_Linux-x86_64-multicore-CUDA.tar.gz</URL>
      <MD5>ca85c614f615b0eb8305a0445313a97d</MD5>
      <SHA256>4a874845391cdb14c47cf260424b0547707e73b94917e630fd9c8099721bef54</SHA256>
      <FileName>NAMD_2.13b1_Linux-x86_64-multicore-CUDA.tar.gz</FileName>
      <FileSize>250156757</FileSize>
    </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-CUDA.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-CUDA
./namd2 +idlepoll +p\$NUM_CPU_CORES +setcpuaffinity ../f1atpase/f1atpase.namd > \$LOG_FILE 2>&1" > namd-cuda
chmod +x namd-cuda

results-definition.xml

<?xml version="1.0"?>
<!--Phoronix Test Suite v8.6.0m0-->
<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 v8.6.0m0-->
<PhoronixTestSuite>
  <TestInformation>
    <Title>NAMD CUDA</Title>
    <AppVersion>2.13</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. This version of the NAMD test profile uses CUDA GPU acceleration.</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>