GROMACS 1.2.0

pts/gromacs-1.2.0 - 26 February 2020 - Update against new GROMACS 2020 upstream, add allow run as root for mpirun.

downloads.xml

<?xml version="1.0"?>
<!--Phoronix Test Suite v9.4.0-->
<PhoronixTestSuite>
  <Downloads>
    <Package>
      <URL>http://ftp.gromacs.org/pub/gromacs/gromacs-2020.tar.gz</URL>
      <MD5>de80ea146f33e76a655e346966a43346</MD5>
      <SHA256>477e56142b3dcd9cb61b8f67b24a55760b04d1655e8684f979a75a5eec40ba01</SHA256>
      <FileName>gromacs-2020.tar.gz</FileName>
      <FileSize>28928068</FileSize>
    </Package>
    <Package>
      <URL>ftp://ftp.gromacs.org/pub/benchmarks/water_GMX50_bare.tar.gz</URL>
      <MD5>d843376d598299d6a209dae063157dc5</MD5>
      <SHA256>2219c10acb97787f80f6638132bad3ff2ca1e68600eef1bc8b89d9560e74c66a</SHA256>
      <FileName>water_GMX50_bare.tar.gz</FileName>
      <FileSize>138438061</FileSize>
    </Package>
  </Downloads>
</PhoronixTestSuite>

install.sh

#!/bin/sh

tar -xf gromacs-2020.tar.gz
tar -xf water_GMX50_bare.tar.gz
mkdir build
cd build
cmake ../gromacs-2020 -DGMX_OPENMP=OFF -DGMX_MPI=ON -DGMX_GPU=OFF -DGMX_BUILD_OWN_FFTW=ON -DGMX_PREFER_STATIC_LIBS=ON -DCMAKE_BUILD_TYPE=Release
make -j $NUM_CPU_CORES
echo $? > ~/install-exit-status
cd ~

echo "#!/bin/sh
unset OMP_NUM_THREADS
cd water-cut1.0_GMX50_bare/1536
rm -f *bench.tpr*
mpirun --allow-run-as-root -np \$NUM_CPU_PHYSICAL_CORES \$HOME/build/bin/gmx_mpi grompp -f pme.mdp  -o bench.tpr
mpirun --allow-run-as-root -np \$NUM_CPU_PHYSICAL_CORES \$HOME/build/bin/gmx_mpi mdrun -resethway -npme 0 -notunepme -noconfout -nsteps 1000 -v -s  bench.tpr > \$LOG_FILE 2>&1
echo \$? > ~/test-exit-status" > gromacs
chmod +x gromacs

results-definition.xml

<?xml version="1.0"?>
<!--Phoronix Test Suite v9.4.0-->
<PhoronixTestSuite>
  <ResultsParser>
    <OutputTemplate>Performance:        #_RESULT_#        3.682</OutputTemplate>
    <LineHint>Performance:</LineHint>
  </ResultsParser>
</PhoronixTestSuite>

test-definition.xml

<?xml version="1.0"?>
<!--Phoronix Test Suite v9.4.0-->
<PhoronixTestSuite>
  <TestInformation>
    <Title>GROMACS</Title>
    <AppVersion>2020</AppVersion>
    <Description>The GROMACS (GROningen MAchine for Chemical Simulations) molecular dynamics package testing on the CPU with the water_GMX50 data.</Description>
    <ResultScale>Ns Per Day</ResultScale>
    <Proportion>HIB</Proportion>
    <SubTitle>Water Benchmark</SubTitle>
    <TimesToRun>3</TimesToRun>
  </TestInformation>
  <TestProfile>
    <Version>1.2.0</Version>
    <SupportedPlatforms>Linux, BSD</SupportedPlatforms>
    <SoftwareType>Benchmark</SoftwareType>
    <TestType>System</TestType>
    <License>Free</License>
    <Status>Verified</Status>
    <ExternalDependencies>build-utilities</ExternalDependencies>
    <EnvironmentSize>1100</EnvironmentSize>
    <ProjectURL>http://www.gromacs.org/</ProjectURL>
    <InternalTags>SMP, MPI</InternalTags>
    <Maintainer>Michael Larabel</Maintainer>
  </TestProfile>
</PhoronixTestSuite>