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rm -rf $HOME/ibamr
cp -r $HOME/.IBAMR.BAK $HOME/ibamr
cd ~/ibamr
tar xfz boost_1_64_0.tar.gz
mv boost_1_64_0 boost
export BOOST_ROOT=$HOME/ibamr/boost
mkdir -p $BOOST_ROOT/include
ln -s $BOOST_ROOT/boost $BOOST_ROOT/include
rm boost_1_64_0.tar.gz
cd ~/ibamr
mkdir -p hdf5
tar xfz hdf5-1.8.12.tar.gz
cd hdf5-1.8.12
./configure \
CC=gcc \
CXX=g++ \
FC=gfortran \
F77=gfortran \
--enable-production \
--disable-debug \
--prefix=$HOME/ibamr/hdf5
make -j36
make install
cd $HOME/ibamr
rm hdf5-1.8.12.tar.gz
rm -r hdf5-1.8.12
cd $HOME/ibamr
tar xfz silo-4.10.tar.gz
cd silo-4.10
./configure \
CC=gcc \
CXX=g++ \
FC=gfortran \
F77=gfortran \
--prefix=$HOME/ibamr/silo \
--disable-silex
make -j72
make install
cd $HOME/ibamr
rm -r silo-4.10
rm silo-4.10.tar.gz
cd ~/ibamr
export PETSC_DIR=$HOME/ibamr/petsc
export PETSC_ARCH=linux-opt
tar xfz petsc-v3.10.5.tar.gz
mv petsc-v3.10.5 petsc
tar -xf externalpackages.tar
mkdir -p $PETSC_DIR/$PETSC_ARCH
mv externalpackages $PETSC_DIR/$PETSC_ARCH
cd $PETSC_DIR
./configure \
--CC=mpicc \
--CXX=mpicxx \
--FC=mpif90 \
--COPTFLAGS="-O3" \
--CXXOPTFLAGS="-O3" \
--FOPTFLAGS="-O3" \
--PETSC_ARCH=$PETSC_ARCH \
--with-debugging=0 \
--download-hypre=1 \
--download-fblaslapack=1 \
--with-x=0
make -j36
make test
cd ~/ibamr
tar xfz SAMRAI-v2.4.4.tar.gz
mv SAMRAI samrai
cd samrai
cp ../ibamr-samrai-fixes.patch ibamr-samrai-fixes.patch
patch -p1 < ibamr-samrai-fixes.patch
./configure \
CFLAGS="-O3" \
CXXFLAGS="-O3" \
FFLAGS="-O3" \
--prefix=$HOME/ibamr/samrai/linux-g++-opt \
--with-CC=mpicc \
--with-CXX=mpicxx \
--with-F77=mpifort \
--with-hdf5=$HOME/ibamr/hdf5 \
--without-hypre \
--without-silo \
--without-blaslapack \
--without-cubes \
--without-eleven \
--without-kinsol \
--without-petsc \
--without-sundials \
--without-x \
--with-doxygen \
--with-dot \
--disable-debug \
--enable-opt \
--enable-implicit-template-instantiation \
--disable-deprecated
make -j36
make install
cd ~/ibamr
rm SAMRAI-v2.4.4.tar.gz
cd $HOME/ibamr/
tar xfz libmesh-1.2.1.tar.gz
mv libmesh-1.2.1 libmesh
cd ~/ibamr/libmesh
mkdir -p objs-opt
cd objs-opt
../configure \
--prefix=$HOME/ibamr/libmesh/1.2.1-opt \
--with-methods=opt \
PETSC_DIR=$HOME/ibamr/petsc \
PETSC_ARCH=linux-opt \
CC=mpicc \
CXX=mpicxx \
FC=mpif90 \
F77=mpif90 \
--enable-exodus \
--enable-triangle \
--disable-boost \
--disable-openmp \
--disable-perflog \
--disable-pthreads \
--disable-strict-lgpl \
--disable-glibcxx-debugging
make -j36
make install
cd $HOME/ibamr/
rm libmesh-1.2.1.tar.gz
cd ~/ibamr
tar xfz IBAMR-0.5.1.tar.gz
mv IBAMR-0.5.1 IBAMR
cd IBAMR
mkdir -p ibamr-objs-opt
cd ibamr-objs-opt
../configure \
CC=mpicc \
CXX=mpicxx \
F77=mpif90 \
FC=mpif90 \
MPICC=mpicc \
MPICXX=mpicxx \
CFLAGS="-O3 -Wall" \
CXXFLAGS="-O3 -Wall -std=c++11" \
FFLAGS="-O3 -Wall" \
FCFLAGS="-O3 -Wall" \
CPPFLAGS="-DOMPI_SKIP_MPICXX" \
--with-hypre=$PETSC_DIR/$PETSC_ARCH \
--with-samrai=$HOME/ibamr/samrai \
--with-hdf5=$HOME/ibamr/hdf5 \
--with-silo=$HOME/ibamr/silo \
--with-boost=$HOME/ibamr/boost \
--enable-libmesh \
--with-libmesh=$HOME/ibamr/libmesh/1.2.1-opt \
--with-libmesh-method=opt
make lib -j36
echo 'export PETSC_DIR=$HOME/ibamr/petsc' >> $HOME/.bashrc
echo 'export PETSC_ARCH=linux-opt' >> $HOME/.bashrc
echo 'export IBAMR_DIR=$HOME/ibamr/IBAMR/ibamr-objs-opt' >> $HOME/.bashrc
echo 'export BOOST_ROOT=$HOME/ibamr/boost' >> $HOME/.bashrc
source $HOME/.bashrc
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