GROMACS 1.6.0

pts/gromacs-1.6.0 - 13 May 2021 - Update GROMACS against GROMACS 2021.2 upstream, add GPU CUDA build as part of this test profile rather than prior separate gromacs-gpu.

downloads.xml

<?xml version="1.0"?>
<!--Phoronix Test Suite v10.4.0m1-->
<PhoronixTestSuite>
  <Downloads>
    <Package>
      <URL>http://ftp.gromacs.org/gromacs/gromacs-2021.2.tar.gz</URL>
      <MD5>a58ff0662eae5818bddfa740a6c35b2e</MD5>
      <SHA256>d940d865ea91e78318043e71f229ce80d32b0dc578d64ee5aa2b1a4be801aadb</SHA256>
      <FileName>gromacs-2021.2.tar.gz</FileName>
      <FileSize>37976386</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-2021.2.tar.gz
tar -xf water_GMX50_bare.tar.gz
mkdir mpi-build
cd mpi-build
cmake ../gromacs-2021.2 -DGMX_OPENMP=OFF -DGMX_MPI=ON -DGMX_GPU=OFF -DGMX_BUILD_OWN_FFTW=ON -DCMAKE_BUILD_TYPE=Release -DBUILD_SHARED_LIBS=ON
make -j $NUM_CPU_CORES
echo $? > ~/install-exit-status
echo "#!/bin/sh
mpirun --allow-run-as-root -np \$NUM_CPU_PHYSICAL_CORES \$HOME/mpi-build/bin/gmx_mpi grompp -f pme.mdp  -o bench.tpr
mpirun --allow-run-as-root -np \$NUM_CPU_PHYSICAL_CORES \$HOME/mpi-build/bin/gmx_mpi mdrun -resethway -npme 0 -notunepme -noconfout -nsteps 1000 -v -s  bench.tpr
" >  run-gromacs
chmod +x run-gromacs
cd ~

mkdir cuda-build
if ! which nvcc >/dev/null 2>&1 ;
then
	if [ -d /usr/local/cuda ]
	then
		export LD_LIBRARY_PATH=/usr/local/cuda/lib64/:$LD_LIBRARY_PATH
		export PATH=/usr/local/cuda/bin/:$PATH
	fi
fi

if which nvcc >/dev/null 2>&1 ;
then
	cd cuda-build
	cmake ../gromacs-2021.2 -DGMX_MPI=OFF -DGMX_OPENMP=ON -DGMX_GPU=CUDA -DGMX_BUILD_OWN_FFTW=ON -DCMAKE_BUILD_TYPE=Release -DBUILD_SHARED_LIBS=ON
	make -j $NUM_CPU_CORES
	
	echo "#!/bin/sh
	\$HOME/cuda-build/bin/gmx grompp -f pme.mdp 
	\$HOME/cuda-build/bin/gmx mdrun -resethway -noconfout -nsteps 4000 -v -pin on -nb gpu
	" >  run-gromacs
	chmod +x run-gromacs
	cd ~
fi

echo "#!/bin/sh
unset OMP_NUM_THREADS
cd \$2
rm -f *bench.tpr*
\$HOME/\$1/run-gromacs > \$LOG_FILE 2>&1
echo \$? > ~/test-exit-status" > gromacs
chmod +x gromacs

results-definition.xml

<?xml version="1.0"?>
<!--Phoronix Test Suite v10.4.0m1-->
<PhoronixTestSuite>
  <ResultsParser>
    <OutputTemplate>Performance:        #_RESULT_#        3.682</OutputTemplate>
    <LineHint>Performance:</LineHint>
  </ResultsParser>
</PhoronixTestSuite>

test-definition.xml

<?xml version="1.0"?>
<!--Phoronix Test Suite v10.4.0m1-->
<PhoronixTestSuite>
  <TestInformation>
    <Title>GROMACS</Title>
    <AppVersion>2021.2</AppVersion>
    <Description>The GROMACS (GROningen MAchine for Chemical Simulations) molecular dynamics package testing with the water_GMX50 data. This test profile allows selecting between CPU and GPU-based GROMACS builds.</Description>
    <ResultScale>Ns Per Day</ResultScale>
    <Proportion>HIB</Proportion>
    <SubTitle>Water Benchmark</SubTitle>
    <TimesToRun>3</TimesToRun>
  </TestInformation>
  <TestProfile>
    <Version>1.6.0</Version>
    <SupportedPlatforms>Linux, BSD, MacOSX</SupportedPlatforms>
    <SoftwareType>Benchmark</SoftwareType>
    <TestType>System</TestType>
    <License>Free</License>
    <Status>Verified</Status>
    <ExternalDependencies>build-utilities, cmake, openmpi-development</ExternalDependencies>
    <EnvironmentSize>1100</EnvironmentSize>
    <ProjectURL>http://www.gromacs.org/</ProjectURL>
    <InternalTags>SMP, MPI</InternalTags>
    <Maintainer>Michael Larabel</Maintainer>
  </TestProfile>
  <TestSettings>
    <Option>
      <DisplayName>Implementation</DisplayName>
      <Identifier>implementation</Identifier>
      <Menu>
        <Entry>
          <Name>MPI CPU</Name>
          <Value>mpi-build</Value>
        </Entry>
        <Entry>
          <Name>NVIDIA CUDA GPU</Name>
          <Value>cuda-build</Value>
        </Entry>
      </Menu>
    </Option>
    <Option>
      <DisplayName>Input</DisplayName>
      <Identifier>input</Identifier>
      <Menu>
        <Entry>
          <Name>water_GMX50_bare</Name>
          <Value>water-cut1.0_GMX50_bare/1536</Value>
        </Entry>
      </Menu>
    </Option>
  </TestSettings>
</PhoronixTestSuite>