NAMD 1.4.0

pts/namd-1.4.0 - 22 September 2024 - Update against NAMD 3.0 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/download/342056/NAMD_3.0_Linux-x86_64-multicore.tar.gz</URL>
      <MD5>0db23e33b7d0d8d9f0ffc6cf560e8bf8</MD5>
      <SHA256>c56937319a440911334db222a7076f9fc26058d1b1d0d8dde920d90b11c88619</SHA256>
      <FileName>NAMD_3.0_Linux-x86_64-multicore.tar.gz</FileName>
      <FileSize>11110280</FileSize>
      <PlatformSpecific>Linux</PlatformSpecific>
    </Package>
    <Package>
      <URL>https://www.ks.uiuc.edu/Research/namd/3.0/download/342056/NAMD_3.0_Linux-x86_64-multicore-AVX512.tar.gz</URL>
      <MD5>a3841941d1c73a8fd03de263c7e4444b</MD5>
      <SHA256>3d9430555d663a17d261789e9c0228283431c0b298e3d063338b21bfdb656158</SHA256>
      <FileName>NAMD_3.0_Linux-x86_64-multicore-AVX512.tar.gz</FileName>
      <FileSize>11957642</FileSize>
      <PlatformSpecific>Linux</PlatformSpecific>
    </Package>
    <Package>
      <URL>https://www.ks.uiuc.edu/Research/namd/3.0/download/342056/NAMD_3.0_MacOS-universal-multicore.tar.gz</URL>
      <MD5>c9f8fdd4e3d7024c636464315b40d451</MD5>
      <SHA256>24340e427c45afe33fc6ea7900100904c6b4e020dd741df97e47759dbe6243ec</SHA256>
      <FileName>NAMD_3.0_MacOS-universal-multicore.tar.gz</FileName>
      <FileSize>15550737</FileSize>
      <PlatformSpecific>MacOSX</PlatformSpecific>
    </Package>
    <Package>
      <URL>http://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>http://www.ks.uiuc.edu/Research/namd/utilities/stmv.zip</URL>
      <MD5>f360f4e1eec9ce0a0108d18656e03681</MD5>
      <SHA256>eefdc1909c1c7e1cc2af70286000856387e59e7ad0c7f267460fea2d681e5a49</SHA256>
      <FileName>stmv.zip</FileName>
      <FileSize>28789057</FileSize>
    </Package>
  </Downloads>
</PhoronixTestSuite>

install.sh

#!/bin/sh
tar -zxf NAMD_3.0_Linux-x86_64-multicore.tar.gz
tar -zxf NAMD_3.0_Linux-x86_64-multicore-AVX512.tar.gz
unzip -o f1atpase.zip
unzip -o stmv.zip
sed -i 's/\/usr\/tmp/\/tmp/g' f1atpase/f1atpase.namd
cd ~
echo "#!/bin/bash
if grep avx512 /proc/cpuinfo > /dev/null
then
	cd NAMD_3.0_Linux-x86_64-multicore-AVX512
else
	cd NAMD_3.0_Linux-x86_64-multicore
fi
./namd3 +p\$NUM_CPU_CORES +setcpuaffinity +maffinity +CmiSleepOnIdle \$@ > \$LOG_FILE 2>&1" > namd
chmod +x namd

install_macosx.sh

#!/bin/sh
tar -zxf NAMD_3.0_MacOS-universal-multicore.tar.gz
unzip -o f1atpase.zip
unzip -o stmv.zip
sed -i 's/\/usr\/tmp/\/tmp/g' f1atpase/f1atpase.namd
cd ~
echo "#!/bin/sh
cd NAMD_3.0_MacOS-universal-multicore/
./namd3 +p\$NUM_CPU_CORES +setcpuaffinity +maffinity +CmiSleepOnIdle \$@ > \$LOG_FILE 2>&1" > namd
chmod +x namd

install_windows.sh

#!/bin/sh
unzip -o NAMD_2.14_Win64-multicore.zip
unzip -o f1atpase.zip
unzip -o stmv.zip
sed -i 's/\/usr\/tmp/\/g' f1atpase/f1atpase.namd
echo "You may need to manually install Microsoft Visual C++ 2010 Service Pack 1 Redistributable Package if not already done so for this test to run: https://www.microsoft.com/en-us/download/confirmation.aspx?id=26999" > ~/install-message
cd ~
echo "#!/bin/sh
cd NAMD_2.14_Win64-multicore
./namd2.exe +p\$NUM_CPU_CORES +setcpuaffinity +maffinity +CmiSleepOnIdle \$@ > \$LOG_FILE 2>&1" > namd
chmod +x namd

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</Title>
    <AppVersion>3.0</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>ns/day</ResultScale>
    <Proportion>HIB</Proportion>
    <TimesToRun>3</TimesToRun>
  </TestInformation>
  <TestProfile>
    <Version>1.4.0</Version>
    <SupportedPlatforms>Linux, MacOSX</SupportedPlatforms>
    <SoftwareType>Benchmark</SoftwareType>
    <TestType>Processor</TestType>
    <License>Free</License>
    <Status>Verified</Status>
    <SupportedArchitectures>x86_64</SupportedArchitectures>
    <EnvironmentSize>360</EnvironmentSize>
    <ProjectURL>https://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/stmv.namd</Value>
        </Entry>
      </Menu>
    </Option>
  </TestSettings>
</PhoronixTestSuite>