Open Porous Media Git 1.1.2

pts/opm-git-1.1.2 - 15 March 2016 - Updates for MPI, running as root.

downloads.xml

<?xml version="1.0"?>
<!--Phoronix Test Suite v6.2.2-->
<PhoronixTestSuite>
  <Downloads>
    <Package>
      <URL>http://gforge.inria.fr/frs/download.php/file/34618/scotch_6.0.4.tar.gz, http://pkgs.fedoraproject.org/repo/pkgs/scotch/scotch_6.0.4.tar.gz/d58b825eb95e1db77efe8c6ff42d329f/scotch_6.0.4.tar.gz</URL>
      <MD5>d58b825eb95e1db77efe8c6ff42d329f</MD5>
      <SHA256>f53f4d71a8345ba15e2dd4e102a35fd83915abf50ea73e1bf6efe1bc2b4220c7</SHA256>
      <FileSize>4804966</FileSize>
    </Package>
    <Package>
      <URL>http://www.cs.sandia.gov/~kddevin/Zoltan_Distributions/zoltan_distrib_v3.8.tar.gz, http://ftp.mcs.anl.gov/pub/petsc/externalpackages/zoltan_distrib_v3.8.tar.gz</URL>
      <MD5>9d8fba8a990896881b85351d4327c4a9</MD5>
      <SHA256>5bdd46548fb9c73b225bbcf3d206c558c318cb292f0b19645e536315d14aafb7</SHA256>
      <FileSize>5407789</FileSize>
    </Package>
  </Downloads>
</PhoronixTestSuite>

install.sh

#!/bin/sh

# Clean up in case of any Git issues
rm -rf opm-data
rm -rf opm-parser
rm -rf opm-output
rm -rf opm-common
rm -rf opm-core
rm -rf opm-material
rm -rf opm-porsol
rm -rf opm-upscaling
rm -rf dune-cornerpoint
rm -rf opm-autodiff
rm -rf opm-polymer
rm -rf ert

# Download source from github
git clone git://github.com/OPM/opm-data.git
git clone git://github.com/OPM/opm-parser.git
git clone git://github.com/OPM/opm-output.git
git clone git://github.com/OPM/opm-common.git
git clone git://github.com/OPM/opm-core.git
git clone git://github.com/OPM/opm-material.git
git clone git://github.com/OPM/opm-porsol.git
git clone git://github.com/OPM/opm-upscaling.git
git clone git://github.com/OPM/dune-cornerpoint.git
git clone git://github.com/OPM/opm-autodiff.git
git clone git://github.com/OPM/opm-polymer.git
git clone git://github.com/Ensembles/ert.git

# Build Scotch
tar -xvf scotch_6.0.4.tar.gz
cd scotch_6.0.4/src
ln -s Make.inc/Makefile.inc.x86-64_pc_linux2 Makefile.inc
make scotch
make CCD=mpicc ptscotch
mkdir ~/opt
make prefix=$HOME/opt install
cp -f ../include/*.h ~/opt/include/

cd ~

# Build Zoltan
tar -xvf zoltan_distrib_v3.8.tar.gz
mkdir zoltan-build
cd zoltan-build
../Zoltan_v3.8/configure --prefix=$HOME/opt --with-scotch --with-scotch-incdir=$HOME/opt/include --with-scotch-libdir=$HOME/opt/lib
make LIBS="-lscotch -lptscotcherrexit"

# Delete lines having bad perl code no longer supported
sed -i.bak -e '12,16d' ../Zoltan_v3.8/config/generate-makeoptions.pl 

make install
cd ~

# Build ERT
mkdir ert/build
cd ert/build
cmake ../devel
make -j $NUM_CPU_CORES
cd $HOME

# Set cmake variables to file opts.cmake
if [ -x /usr/bin/cmake ]
then
	CMAKE=cmake
elif [ -x /usr/bin/cmake28 ]
then
	# On some RHEL 6 systems they seem to have cmake28 but not cmake
	CMAKE=cmake28
else
	# Fallback
	CMAKE=cmake
fi

CMAKE_EXTRAS="-DERT_ROOT=$HOME/ert -DPTSCOTCH_ROOT=$HOME/opt -DZOLTAN_ROOT=$HOME/opt -DPARMETIS_ROOT=$HOME/opt -DUSE_MPI=ON"

# Build all modules
mkdir opm-common/build
cd opm-common/build
$CMAKE $CMAKE_EXTRAS ..
nice make -j $NUM_CPU_CORES
cd $HOME


mkdir opm-parser/build
cd opm-parser/build
$CMAKE $CMAKE_EXTRAS ..
nice make -j $NUM_CPU_CORES
cd $HOME

mkdir opm-material/build
cd opm-material/build
$CMAKE $CMAKE_EXTRAS ..
nice make -j $NUM_CPU_CORES
cd $HOME

mkdir opm-core/build
cd opm-core/build
$CMAKE $CMAKE_EXTRAS ..
nice make -j $NUM_CPU_CORES
cd $HOME
 
mkdir dune-cornerpoint/build
cd dune-cornerpoint/build
$CMAKE $CMAKE_EXTRAS ..
nice make -j $NUM_CPU_CORES
cd $HOME
 
mkdir opm-porsol/build
cd opm-porsol/build
$CMAKE $CMAKE_EXTRAS ..
nice make -j $NUM_CPU_CORES
cd $HOME
 
mkdir opm-upscaling/build
cd opm-upscaling/build
$CMAKE $CMAKE_EXTRAS ..
nice make -j $NUM_CPU_CORES
cd $HOME

mkdir opm-output/build
cd opm-output/build
$CMAKE $CMAKE_EXTRAS ..
nice make -j $NUM_CPU_CORES
cd $HOME

mkdir opm-autodiff/build
cd opm-autodiff/build
$CMAKE $CMAKE_EXTRAS ..
nice make -j $NUM_CPU_CORES
echo $? > $HOME/install-exit-status
cd $HOME

cd opm-upscaling/build
make upscale_relperm_benchmark
cd $HOME

######################################################
# Run benchmark
######################################################

echo "#!/bin/sh

if [ \"X\$OMP_NUM_THREADS\" = \"X\" ]
then
	OMP_NUM_THREADS=\$NUM_CPU_CORES
fi

if [ ! \"X\$HOSTFILE\" = \"X\" ] && [ -f \$HOSTFILE ]
then
	HOSTFILE=\"--hostfile \$HOSTFILE\"
elif [ -f /etc/hostfile ]
then
	HOSTFILE=\"--hostfile /etc/hostfile\"
else
	HOSTFILE=\"\"
fi

MPIRUN_AS_ROOT_ARG=\"--allow-run-as-root\"
if [ `whoami` != \"root\" ]
then
  MPIRUN_AS_ROOT_ARG=\"\"
fi

if [ \$@ = \"upscale_relperm_benchmark\" ]
then
	mpirun \$MPIRUN_AS_ROOT_ARG -np \$OMP_NUM_THREADS \$HOSTFILE ./opm-upscaling/build/bin/upscale_relperm_benchmark > \$LOG_FILE 2>&1
elif [ \$@ = \"flow_mpi_norne\" ]
then
	cd opm-data/norne
	mpirun \$MPIRUN_AS_ROOT_ARG -np \$OMP_NUM_THREADS \$HOSTFILE ../../opm-autodiff/build/bin/flow_mpi NORNE_ATW2013.DATA > \$LOG_FILE 2>&1
fi

# echo \$? > ~/test-exit-status" > opm-git
chmod +x opm-git

results-definition.xml

<?xml version="1.0"?>
<!--Phoronix Test Suite v6.2.2-->
<PhoronixTestSuite>
  <ResultsParser>
    <OutputTemplate>Total wallclock time:       #_RESULT_# sec  (52 min 59.02 sec)</OutputTemplate>
    <MatchToTestArguments>upscale_relperm_benchmark</MatchToTestArguments>
    <LineHint>Total wallclock time</LineHint>
  </ResultsParser>
  <ResultsParser>
    <OutputTemplate>Total time taken (seconds):  #_RESULT_#</OutputTemplate>
    <LineHint>Total time</LineHint>
  </ResultsParser>
</PhoronixTestSuite>

test-definition.xml

<?xml version="1.0"?>
<!--Phoronix Test Suite v6.2.2-->
<PhoronixTestSuite>
  <TestInformation>
    <Title>Open Porous Media Git</Title>
    <Description>This is a test of a DUNE (Distributed and Unified Numerics Environment) module called OPM Benchmarks from the Open Porous Media project. Open Porous Media is a set of open-source tools concerning simulation of flow and transport of fluids in porous media. This test profile builds OPM and its dependencies from upstream Git.</Description>
    <ResultScale>Seconds</ResultScale>
    <Proportion>LIB</Proportion>
    <TimesToRun>3</TimesToRun>
  </TestInformation>
  <TestProfile>
    <Version>1.1.2</Version>
    <SupportedPlatforms>Linux</SupportedPlatforms>
    <SoftwareType>Utility</SoftwareType>
    <TestType>Processor</TestType>
    <License>Free</License>
    <Status>Verified</Status>
    <ExternalDependencies>build-utilities, fortran-compiler, cmake, boost-development, superlu, suitesparse, tinyxml, openmpi-development, blas-development, dune, lapack-development</ExternalDependencies>
    <EnvironmentSize>2000</EnvironmentSize>
    <ProjectURL>http://www.opm-project.org/</ProjectURL>
    <InternalTags>SMP</InternalTags>
    <Maintainer>Michael Larabel</Maintainer>
  </TestProfile>
  <TestSettings>
    <Option>
      <DisplayName>OPM Benchmark</DisplayName>
      <Identifier>opm-benchmark</Identifier>
      <ArgumentPrefix></ArgumentPrefix>
      <ArgumentPostfix></ArgumentPostfix>
      <DefaultEntry>0</DefaultEntry>
      <Menu>
        <Entry>
          <Name>Upscale-Relperm</Name>
          <Value>upscale_relperm_benchmark</Value>
          <Message></Message>
        </Entry>
        <Entry>
          <Name>Flow MPI Norne</Name>
          <Value>flow_mpi_norne</Value>
          <Message></Message>
        </Entry>
      </Menu>
    </Option>
  </TestSettings>
</PhoronixTestSuite>