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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>