NAMD CUDA 1.1.0

pts/namd-cuda-1.1.0 - 27 August 2020 - Update against upstream NAMD 2.14.

downloads.xml

<?xml version="1.0"?>
<!--Phoronix Test Suite v10.0.0m1-->
<PhoronixTestSuite>
  <Downloads>
    <Package>
      <URL>https://www.ks.uiuc.edu/Research/namd/2.14/download/946183/NAMD_2.14_Linux-x86_64-multicore-CUDA.tar.gz</URL>
      <MD5>d267b77d4c1d40ba43862a4673675c31</MD5>
      <SHA256>f1516c79b8d6ba72f34f1a2c0b1d09b4eafd4e2f7bb1fc585fd9fe418d141976</SHA256>
      <FileName>NAMD_2.14_Linux-x86_64-multicore-CUDA.tar.gz</FileName>
      <FileSize>169669114</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_2.14_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_2.14_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 v10.0.0m1-->
<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 v10.0.0m1-->
<PhoronixTestSuite>
  <TestInformation>
    <Title>NAMD CUDA</Title>
    <AppVersion>2.14</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>1.1.0</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>