LAMMPS Molecular Dynamics Simulator 1.2.1

pts/lammps-1.2.1 - 18 September 2020 - Add back Rhodopsin Protein for those wanting the easier model.

downloads.xml

<?xml version="1.0"?>
<!--Phoronix Test Suite v10.0.0m2-->
<PhoronixTestSuite>
  <Downloads>
    <Package>
      <URL>https://github.com/lammps/lammps/archive/patch_24Aug2020.tar.gz</URL>
      <MD5>d73fb5398dcc37b2fcfe652258fad5ce</MD5>
      <SHA256>a2ea34f93ed2cd1c789dad1f5b37b6ab7c9090703bc480ad1a4697fd564c0338</SHA256>
      <FileName>lammps-patch_24Aug2020.tar.gz</FileName>
      <FileSize>126148385</FileSize>
    </Package>
    <Package>
      <URL>http://www.hecbiosim.ac.uk/lammps-benchmarks/send/2-software/10-lammps-bench</URL>
      <MD5>65c3b50b77688611e92fcff330e27e48</MD5>
      <SHA256>485e0615a5422f7c0f48860bfc606485348f92fd1ffe4ad05a23d6e8850ad84b</SHA256>
      <FileName>lammps-hecbiosim-1.tar.gz</FileName>
      <FileSize>428900129</FileSize>
    </Package>
  </Downloads>
</PhoronixTestSuite>

install.sh

#!/bin/sh

tar -xf lammps-patch_24Aug2020.tar.gz
cd lammps-patch_24Aug2020/
mkdir b
cd b
cmake ../cmake/ -DCMAKE_BUILD_TYPE=Release -DPKG_MOLECULE=1 -DPKG_KSPACE=1 -DPKG_RIGID=1 -DPKG_GRANULAR=1 -DPKG_MANYBODY=1 -DBUILD_OMP=OFF
make -j $NUM_CPU_CORES
echo $? > ~/install-exit-status

cd ~/

tar -xf lammps-hecbiosim-1.tar.gz
mv lammps/20k-atoms/benchmark.data lammps-patch_24Aug2020/bench/benchmark.data
mv lammps/20k-atoms/benchmark.in lammps-patch_24Aug2020/bench/benchmark_20k_atoms.in
rm -rf lammps

cat>lammps<<EOT
#!/bin/sh
cd lammps-patch_24Aug2020/bench/
mpirun --allow-run-as-root -np \$NUM_CPU_PHYSICAL_CORES ../b/lmp < \$@ > \$LOG_FILE 2>&1
echo \$? > ~/test-exit-status
EOT
chmod +x lammps

results-definition.xml

<?xml version="1.0"?>
<!--Phoronix Test Suite v10.0.0m2-->
<PhoronixTestSuite>
  <ResultsParser>
    <OutputTemplate>Performance: #_RESULT_# ns/day, 3.475 hours/ns, 39.968 timesteps/s</OutputTemplate>
  </ResultsParser>
</PhoronixTestSuite>

test-definition.xml

<?xml version="1.0"?>
<!--Phoronix Test Suite v10.0.0m2-->
<PhoronixTestSuite>
  <TestInformation>
    <Title>LAMMPS Molecular Dynamics Simulator</Title>
    <AppVersion>24Aug2020</AppVersion>
    <Description>LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator.</Description>
    <ResultScale>ns/day</ResultScale>
    <Proportion>HIB</Proportion>
    <TimesToRun>3</TimesToRun>
  </TestInformation>
  <TestProfile>
    <Version>1.2.1</Version>
    <SupportedPlatforms>Linux, Solaris, BSD</SupportedPlatforms>
    <SoftwareType>Scientific</SoftwareType>
    <TestType>Processor</TestType>
    <License>Free</License>
    <Status>Verified</Status>
    <ExternalDependencies>fortran-compiler, openmpi-development, fftw3-development, cmake, build-utilities</ExternalDependencies>
    <EnvironmentSize>555</EnvironmentSize>
    <ProjectURL>http://lammps.sandia.gov/</ProjectURL>
    <Maintainer>Michael Larabel</Maintainer>
  </TestProfile>
  <TestSettings>
    <Option>
      <DisplayName>Model</DisplayName>
      <Identifier>run-model</Identifier>
      <Menu>
        <Entry>
          <Name>Rhodopsin Protein</Name>
          <Value>in.rhodo</Value>
          <Message>Small input, runs very quickly on modern hardware.</Message>
        </Entry>
        <Entry>
          <Name>20k Atoms</Name>
          <Value>benchmark_20k_atoms.in</Value>
          <Message>A larger input for large core-count systems.</Message>
        </Entry>
      </Menu>
    </Option>
  </TestSettings>
</PhoronixTestSuite>