NAMD 1.2.0

pts/namd-1.2.0 - 20 August 2020 - Update against new upstream NAMD 2.14 release.

downloads.xml

<?xml version="1.0"?>
<!--Phoronix Test Suite v10.0.0m1-->
<PhoronixTestSuite>
  <Downloads>
    <Package>
      <URL>http://www.ks.uiuc.edu/Research/namd/2.14/download/946183/NAMD_2.14_Linux-x86_64-multicore.tar.gz</URL>
      <MD5>dffa2ab4a5f0cd4f5f1cfef12abb09fa</MD5>
      <SHA256>3c4384541b0cbcb84cf9ea9b7b9320ee7cb1747af0e66d3426cc72ccfabaf0a2</SHA256>
      <FileName>NAMD_2.14_Linux-x86_64-multicore.tar.gz</FileName>
      <FileSize>13843974</FileSize>
      <PlatformSpecific>Linux</PlatformSpecific>
    </Package>
    <Package>
      <URL>http://www.ks.uiuc.edu/Research/namd/2.14/download/946183/NAMD_2.14_Win64-multicore.zip</URL>
      <MD5>157f2a167d5b5ea3f1cf4526723c86ab</MD5>
      <SHA256>f059189e90f627bfb22af2c7f3b5d89214ad2208311b688396a4b976ed5cffd6</SHA256>
      <FileName>NAMD_2.14_Win64-multicore.zip</FileName>
      <FileSize>6824629</FileSize>
      <PlatformSpecific>Windows</PlatformSpecific>
    </Package>
    <Package>
      <URL>http://www.ks.uiuc.edu/Research/namd/2.14/download/946183/NAMD_2.14_MacOSX-x86_64-multicore.tar.gz</URL>
      <MD5>a06a3f8ab12bfcc55021a81fd8f9f039</MD5>
      <SHA256>12c0c0a854c5a22a7a896c609b61f2329e84c4f285a0a57e5e5b6da2086034e3</SHA256>
      <FileName>NAMD_2.14_MacOSX-x86_64-multicore.tar.gz</FileName>
      <FileSize>8947149</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>
  </Downloads>
</PhoronixTestSuite>

install.sh

#!/bin/sh

tar -zxvf NAMD_2.14_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_2.14_Linux-x86_64-multicore
./namd2 +p\$NUM_CPU_CORES +setcpuaffinity ../f1atpase/f1atpase.namd > \$LOG_FILE 2>&1" > namd
chmod +x namd

install_macosx.sh

#!/bin/sh

tar -zxvf NAMD_2.14_MacOSX-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_2.14_MacOSX-x86_64-multicore
./namd2 +p\$NUM_CPU_CORES +setcpuaffinity ../f1atpase/f1atpase.namd > \$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
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 ../f1atpase/f1atpase.namd > \$LOG_FILE 2>&1" > namd
chmod +x namd

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</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.</Description>
    <ResultScale>days/ns</ResultScale>
    <Proportion>LIB</Proportion>
    <SubTitle>ATPase Simulation - 327,506 Atoms</SubTitle>
    <TimesToRun>3</TimesToRun>
  </TestInformation>
  <TestProfile>
    <Version>1.2.0</Version>
    <SupportedPlatforms>Linux, Windows, MacOSX</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>