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INSTALL_OPTIONS_EXT.txt
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INSTALL_OPTIONS_EXT.txt
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Install and compile options for the packages mentioned in the article: "ATUS-PRO: A FEM-based solver for the time-dependent and stationary Gross-Pitaevskii equation".
## MPI ##
cd $HOME # start from top level of your home folder
mkdir temp # create temporary folder
cd temp
wget http://www.open-mpi.org/software/ompi/v1.8/downloads/openmpi-1.8.5.tar.gz
tar xfvz openmpi-2.0.1.tar.gz
cd openmpi-2.0.1
./configure --prefix=/opt/openmpi-2.0.1 --enable-mpi-fortran
make -j
sudo make install
export PATH=$PATH:/opt/openmpi-2.0.1/bin
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/openmpi-2.0.1/lib64
# alternativly: export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/openmpi-2.0.1/lib
check the path with: which mpicc
check the lib folder naming
## HDF5 ##
wget https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.0-patch1/src/hdf5-1.10.0-patch1.tar.gz
tar xfvz hdf5-1.10.0-patch1.tar.gz
cd hdf5-1.10.0-patch1
mdkir build
cd build
cmake -DHDF5_BUILD_CPP_LIB=OFF -DHDF5_ENABLE_PARALLEL=ON -DCMAKE_INSTALL_PREFIX=/opt/hdf5-1.10 ..
or cmake -DHDF5_BUILD_TOOLS=ON -DHDF5_BUILD_CPP_LIB=OFF -DHDF5_ENABLE_PARALLEL=ON -DCMAKE_INSTALL_PREFIX=/opt/hdf5-1.10 ..
make
make install
go into /opt/hdf5-1.10/lib folder and
ln -s libhdf5-shared.so libhdf5.so
ln -s libhdf5_hl-shared.so.100.0.1 libhdf5_hl.so
## GSL ##
cd $HOME/temp
wget ftp://ftp.gnu.org/gnu/gsl/gsl-2.2.1.tar.gz
tar xfvz gsl-2.2.1.tar.gz
cd gsl-2.2.1
./configure --prefix=/opt/gsl-2.2.1
make CFLAGS="-march=native -O3"
sudo make install
## LAPACK ##
cd $HOME/temp
wget http://www.netlib.org/lapack/lapack-3.6.1.tgz
tar xfvz lapack-3.6.1.tgz
cd lapack-3.6.1
mkdir build
cd build
cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_Fortran_FLAGS_RELEASE="-march=native -fpic -O3" -DCMAKE_INSTALL_PREFIX=/opt/lapack-3.6.1 ..
make -j4
sudo make install
## ARPACK-NG ##
git clone https://github.com/opencollab/arpack-ng.git
mkdir build
cd build
cmake -DEXAMPLES=OFF -DMPI=ON -DBUILD_SHARED_LIBS=ON -DBLAS_LIBRARIES=/opt/lapack-3.6.1/lib64/libblas.a -DLAPACK_LIBRARIES=/opt/lapack-3.6.1/lib64/liblapack.a -DCMAKE_INSTALL_PREFIX=/opt/arpack-ng ..
make -j4
sudo make install
my git hash b16d8700a86ad58f29693ae31f73e47ee5b7954c
## PETSc ##
cd $HOME/temp
wget http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-3.6.3.tar.gz
tar xfvz petsc-3.6.3.tar.gz
cd petsc-3.6.3
export PETSC_ARCH=x86_64
./configure --prefix=/opt/petsc-3.6.3 --with-shared-libraries --with-x=0 --with-debugging=0 --with-mpi=1 --download-hypre=yes --download-fblaslapack=1 --download-scalapack --download-mumps --download-ptscotch
make PETSC_DIR=$HOME/temp/petsc-3.6.3 PETSC_ARCH=x86_64 all
sudo make PETSC_DIR=$HOME/temp/petsc-3.6.3 PETSC_ARCH=x86_64 install
## SLEPc ##
cd $HOME/temp
wget http://slepc.upv.es/download/download.php?filename=slepc-3.6.2.tar.gz
tar xfvz slepc-3.6.2.tar.gz
cd slepc-3.6.2
unset PETSC_ARCH
export LD_LIBRARY_PATH=/opt/petsc-3.6.3/lib64:$LD_LIBRARY_PATH
./configure --prefix=/opt/petsc-3.6.3 --with-arpack-dir=/opt/arpack-ng/lib --with-arpack-flags=-lparpack,-larpack
make SLEPC_DIR=$PWD PETSC_DIR=/opt/petsc-3.6.3
sudo make SLEPC_DIR=/home/zeli/tmp/slepc-3.6.2 PETSC_DIR=/opt/petsc-3.6.3 install
## p4est ##
cd $HOME/temp
wget http://p4est.github.io/release/p4est-1.1.tar.gz
tar xfvz p4est-1.1.tar.gz
cd p4est-1.1
./configure --prefix=/opt/p4est-1.1 --enable-mpi --enable-shared --disable-vtk-binary --without-blas
make CFLAGS="-O3 -march=native"
sudo make install
## deal.II ##
cd $HOME/temp
wget https://github.com/dealii/dealii/releases/download/v8.4.1/dealii-8.4.1.tar.gz
tar xfvz dealii-8.4.1.tar.gz
cd dealii-8.4.1
mkdir build
cd build
(without slepc)
cmake -DDEAL_II_WITH_UMFPACK=ON -DDEAL_II_WITH_LAPACK=ON -DLAPACK_DIR=/opt/lapack-3.6.1 -DPETSC_ARCH=x86_64 -DPETSC_DIR=/opt/petsc-3.6.3 -DP4EST_DIR=/opt/p4est-1.1 -DDEAL_II_WITH_THREADS=OFF -DDEAL_II_WITH_MPI=ON -DDEAL_II_WITH_HDF5=OFF -DCMAKE_INSTALL_PREFIX=/opt/deal.II-8.4.1 ..
(with slepc)
cmake -DDEAL_II_WITH_UMFPACK=ON -DDEAL_II_WITH_LAPACK=ON -DLAPACK_DIR=/opt/lapack-3.6.1 -DPETSC_ARCH=x86_64 -DARPACK_DIR=/opt/arpack-ng -DPETSC_DIR=/opt/petsc-3.6.3 -DP4EST_DIR=/opt/p4est-1.1 -DDEAL_II_WITH_THREADS=OFF -DDEAL_II_WITH_MPI=ON -DDEAL_II_WITH_HDF5=OFF -DDEAL_II_WITH_SLEPC=/opt/petsc-3.6.3 -DCMAKE_INSTALL_PREFIX=/opt/deal.II-8.4.1 -DDEAL_II_WITH_HDF5=ON -DHDF5_DIR=/opt/hdf5-1.10 ..
make
sudo make install
## .my_bashrc ##
create a file in your home folder via the command: touch .my_bashrc
copy the following content
export PATH=$PATH:$HOME/bin:/opt/openmpi-2.0.1/bin
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/openmpi-2.0.1/lib64:/opt/gsl-2.2.1/lib64:/opt/p4est-1.1/lib64:/opt/petsc-3.6.3/lib:/opt/deal.II-8.4.1/lib
# alternatively
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/openmpi-2.0.1/lib:/opt/gsl-2.2.1/lib:/opt/p4est-1.1/lib:/opt/petsc-3.6.3/lib:/opt/deal.II-8.4.1/lib
into this file.
You can setup the path then via the command source $HOME/.my_bashrc
## atus-pro ##
source $HOME/.my_bashrc
cd $HOME/temp
tar xfvz atus-pro_v1.0.tar.gz
cd atus-pro_v1.0
mkdir build
cd build
cmake ..
make -j
make doc
#######################################################################################################
## metis and parmetis ##
wget http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/parmetis-4.0.3.tar.gz
vi metis/include/metis.h
go into the metis subfolder
make config prefix=/opt/parmetis-4.0.3
make
sudo make install
go back and repeat
make config prefix=/opt/parmetis-4.0.3
make
sudo make install
## SuperLU ##
wget http://crd-legacy.lbl.gov/~xiaoye/SuperLU/superlu_5.2.1.tar.gz
cmake .. -DCMAKE_INSTALL_PREFIX=/opt/SuperLU_5.2.1 -Denable_blaslib=OFF
## SuperLU_dist ##
wget http://crd-legacy.lbl.gov/~xiaoye/SuperLU/superlu_dist_5.1.3.tar.gz
cmake .. \
-DTPL_PARMETIS_INCLUDE_DIRS="/opt/parmetis-4.0.3/include" \
-DTPL_PARMETIS_LIBRARIES="/opt/parmetis-4.0.3/lib/libparmetis.a;/opt/parmetis-4.0.3/lib/libmetis.a" \
-DCMAKE_C_FLAGS="-std=c99 -march=native -O3" \
-Denable_blaslib=OFF \
-Denable_examples=OFF \
-DBUILD_SHARED_LIBS=ON \
-DCMAKE_C_COMPILER=mpicc \
-DCMAKE_INSTALL_PREFIX=/opt/SuperLU_DIST_5.1.3
## Trilinos ##
git clone https://github.com/trilinos/Trilinos.git
git checkout -b develop origin/develop
git sha c7c2f8fd58b342f24a8857b6416a6f653e83683f
mkdir build
cd build
cmake .. \
-DTrilinos_ENABLE_Sacado=ON \
-DTrilinos_ENABLE_MueLu:BOOL=ON \
-DTrilinos_ENABLE_Stratimikos=ON \
-DCMAKE_BUILD_TYPE=RELEASE \
-DCMAKE_CXX_FLAGS="-g -O3" \
-DCMAKE_C_FLAGS="-g -O3" \
-DCMAKE_FORTRAN_FLAGS="-g -O5" \
-DTrilinos_EXTRA_LINK_FLAGS="-lgfortran" \
-DCMAKE_VERBOSE_MAKEFILE=FALSE \
-DTrilinos_VERBOSE_CONFIGURE=FALSE \
-DTPL_ENABLE_ParMETIS=ON \
-DParMETIS_INCLUDE_DIRS=/opt/parmetis-4.0.3/include \
-DParMETIS_LIBRARY_DIRS=/opt/parmetis-4.0.3/lib \
-DTPL_ENABLE_MPI=ON \
-DBUILD_SHARED_LIBS=ON \
-DTPL_ENABLE_SuperLU:BOOL=ON \
-DTPL_ENABLE_SuperLUDist:BOOL=ON \
-DSuperLUDist_INCLUDE_DIRS:FILEPATH="/opt/SuperLU_DIST_5.1.3/include" \
-DTPL_SuperLUDist_LIBRARIES:FILEPATH="/opt/SuperLU_DIST_5.1.3/lib/libsuperlu_dist.a" \
-DSuperLU_INCLUDE_DIRS:FILEPATH="/opt/SuperLU_5.2.1/include" \
-DTPL_SuperLU_LIBRARIES:FILEPATH="/opt/SuperLU_5.2.1/lib64/libsuperlu.a" \
-DLAPACK_LIBRARY_DIRS=/opt/lapack-3.6.1/lib64 \
-DCMAKE_INSTALL_PREFIX=/opt/trilinos
cmake .. \
-DTrilinos_ENABLE_Sacado=ON \
-DTrilinos_ENABLE_MueLu:BOOL=ON \
-DTrilinos_ENABLE_Stratimikos=ON \
-DCMAKE_BUILD_TYPE=RELEASE \
-DCMAKE_CXX_FLAGS="-g -O3" \
-DCMAKE_C_FLAGS="-g -O3" \
-DCMAKE_FORTRAN_FLAGS="-g -O5" \
-DTrilinos_EXTRA_LINK_FLAGS="-lgfortran" \
-DCMAKE_VERBOSE_MAKEFILE=FALSE \
-DTrilinos_VERBOSE_CONFIGURE=FALSE \
-DTPL_ENABLE_ParMETIS=ON \
-DParMETIS_INCLUDE_DIRS=/opt/parmetis-4.0.3/include \
-DParMETIS_LIBRARY_DIRS=/opt/parmetis-4.0.3/lib \
-DTPL_ENABLE_MPI=ON \
-DBUILD_SHARED_LIBS=ON \
-DTPL_ENABLE_SuperLUDist:BOOL=ON \
-DSuperLUDist_INCLUDE_DIRS:FILEPATH="/opt/SuperLU_DIST_5.1.3/include" \
-DTPL_SuperLUDist_LIBRARIES:FILEPATH="/opt/SuperLU_DIST_5.1.3/lib/libsuperlu_dist.so" \
-DBLAS_LIBRARY_DIRS=/opt/lapack-3.6.1/lib64 \
-DLAPACK_LIBRARY_DIRS=/opt/lapack-3.6.1/lib64 \
-DCMAKE_INSTALL_PREFIX=/opt/trilinos