NAMD CUDA 1.2.0

pts/namd-cuda-1.2.0 - 25 January 2025 - Update against NAMD 3.0.1 upstream.

downloads.xml

<?xml version="1.0"?>
<!--Phoronix Test Suite v10.8.5-->
<PhoronixTestSuite>
  <Downloads>
    <Package>
      <URL>https://www.ks.uiuc.edu/Research/namd/3.0.1/download/453167/NAMD_3.0.1_Linux-x86_64-multicore-CUDA.tar.gz</URL>
      <MD5>c47d7aab89361f2fd6cf9328d2af9c81</MD5>
      <SHA256>ff712dc8e2ceda8f5b76cf059edfce147886e7a082590ac0dd6638c25b0299b0</SHA256>
      <FileName>NAMD_3.0.1_Linux-x86_64-multicore-CUDA.tar.gz</FileName>
      <FileSize>257278276</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>
    <Package>
      <URL>https://www.ks.uiuc.edu/Research/namd/benchmarks/systems/stmv_gpu.tar.gz</URL>
      <MD5>8dcb949aa02b98bb0c4890fd63f09ae8</MD5>
      <SHA256>45b441035aaef4794fe8c37f6fdb0c9f28eed73828039fb3298f775489fec950</SHA256>
      <FileName>stmv_gpu.tar.gz</FileName>
      <FileSize>57126365</FileSize>
    </Package>
  </Downloads>
</PhoronixTestSuite>

install.sh

#!/bin/sh

tar -zxvf NAMD_3.0.1_Linux-x86_64-multicore-CUDA.tar.gz
unzip -o f1atpase.zip
tar -xf stmv_gpu.tar.gz
sed -i 's/\/usr\/tmp/\/tmp/g' f1atpase/f1atpase.namd
cd ~
echo "#!/bin/sh
cd NAMD_3.0.1_Linux-x86_64-multicore-CUDA
./namd3 +idlepoll +p\$NUM_CPU_CORES +setcpuaffinity \$@ > \$LOG_FILE 2>&1" > namd-cuda
chmod +x namd-cuda

results-definition.xml

<?xml version="1.0"?>
<!--Phoronix Test Suite v10.8.5-->
<PhoronixTestSuite>
  <ResultsParser>
    <OutputTemplate>Info: Benchmark time: 64 CPUs 0.0232228 s/step #_RESULT_# days/ns 4678.59 MB memory</OutputTemplate>
    <LineHint>Benchmark time</LineHint>
    <DivideResultDivisor>1</DivideResultDivisor>
    <ResultPrecision>5</ResultPrecision>
  </ResultsParser>
</PhoronixTestSuite>

test-definition.xml

<?xml version="1.0"?>
<!--Phoronix Test Suite v10.8.5-->
<PhoronixTestSuite>
  <TestInformation>
    <Title>NAMD CUDA</Title>
    <AppVersion>3.0.1</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; the non-CUDA version of this test profile is pts/namd.</Description>
    <ResultScale>ns/day</ResultScale>
    <Proportion>HIB</Proportion>
    <SubTitle>ATPase Simulation - 327,506 Atoms</SubTitle>
    <TimesToRun>3</TimesToRun>
  </TestInformation>
  <TestProfile>
    <Version>1.2.0</Version>
    <SupportedPlatforms>Linux</SupportedPlatforms>
    <SoftwareType>Benchmark</SoftwareType>
    <TestType>Graphics</TestType>
    <License>Free</License>
    <Status>Verified</Status>
    <SupportedArchitectures>x86_64</SupportedArchitectures>
    <RequiresDisplay>TRUE</RequiresDisplay>
    <EnvironmentSize>527</EnvironmentSize>
    <ProjectURL>http://www.ks.uiuc.edu/Research/namd/</ProjectURL>
    <InternalTags>SMP</InternalTags>
    <Maintainer>Michael Larabel</Maintainer>
  </TestProfile>
  <TestSettings>
    <Option>
      <DisplayName>Input</DisplayName>
      <Identifier>input</Identifier>
      <Menu>
        <Entry>
          <Name>ATPase with 327,506 Atoms</Name>
          <Value>../f1atpase/f1atpase.namd</Value>
        </Entry>
        <Entry>
          <Name>STMV with 1,066,628 Atoms</Name>
          <Value>../stmv_gpu/stmv.namd</Value>
        </Entry>
      </Menu>
    </Option>
  </TestSettings>
</PhoronixTestSuite>