pyclaw intstall generic linux

pyclaw_install_linux.sh

# This is version 2.0 of the script to install Pyclaw and dependencies on linux PC
# Authors: Aron Ahmadia, Damian San Roman
# Collaborators: David Ketcheson, Lisandro Dalcin
# ------------------------------------------------------------------------------ #
# This version uses github and bitbucket sources, alternatively you may select
# non-git sources, supported via wget
# ------------------------------------------------------------------------------ #
# ------------------------------------------------------------------------------ #

echo "\PETSc + PETSc4py Setup"
echo "~~~~~~~~~~"

echo "pyclaw_prep               - set up build environment"

custom_riemann_prep() {
  pyclaw_prep
  customriemanndir=~/devel/sandbox/emclaw/maxwell_vc_3d
  echo "custom riemann = ${customriemanndir}"
}

pyclaw_prep() {
  echo "pyclaw prerp"
  projdir=/simdesk
  echo "projdir=${projdir}"
  sandbox=${projdir}/sandbox
  echo "sandbox=${sandbox}"
  builddir=${projdir}/opt/share
  echo "builddir=${builddir}"
  logdir=${builddir}/logs
  echo "logdir=${logdir}"
  srcdir=${builddir}/sources
  echo "srcdir=${srcdir}"

  profile=$HOME/.bashrc
  anaconda_ver=2.0.1
  psutil_ver=2.1.1
  mprofiler_ver=0.31
  cython_ver=master
  mpi4py_ver=master
  petsc_ver=3.5.1
  petsc_branch=maint
  petsc_subdir=maint
  petsc4py_branch=maint
  git_source=1

# for visualization
  paraview_ver=4.1.0
  cmake_ver=2.8.12.2
  mkdir -p ${sandbox} ${builddir} ${logdir} ${srcdir}

  #disable_threads="yes"

  #if [ disable_threads == "yes" ] ; then
  #threads_flag="--without-threads"
  #  echo "Python and extension modules will be built without thread support"
  #else
  threads_flag="--with-threads"
  #  echo "Python and extension modules will be built with thread support"
  #fi
  pic_flag="-fpic"

  source ${profile}
}

echo "pyclaw_build_anaconda                 - install anaconda ${anaconda_ver}"
pyclaw_build_anaconda() {
  echo "pyclaw_build_anaconda"
  pyclaw_prep
  cd ${srcdir}
  echo "downloading and unpacking sources"
  if [ ! -f $srcdir/Anaconda-${anaconda_ver}-Linux-x86_64.sh ]; then 
      wget -P ${srcdir} http://09c8d0b2229f813c1b93-c95ac804525aac4b6dba79b00b39d1d3.r79.cf1.rackcdn.com/Anaconda-${anaconda_ver}-Linux-x86_64.sh
  fi

  echo "running installation script, you  might need to interact here"


  bash ${srcdir}/Anaconda-${anaconda_ver}-Linux-x86_64.sh \
    2>&1 | tee ${logdir}/Anaconda-${anaconda_ver}_ppc64_install.log
}


echo "pyclaw_build_psutil                   - install psutils ${psutil_ver}"
pyclaw_build_psutil() {
  echo "pyclaw_build_psutil"
  pyclaw_prep
  cd ${sandbox}
  if [ -d $sandbox/psutil-${psutil_ver} ]; then
      rm -rf psutil-${psutil_ver}
  fi

  echo "downloading and unpacking sources"
  if [ ! -f $srcdir/psutil-${psutil_ver} ]; then
    wget --no-check-certificate -P ${srcdir} https://pypi.python.org/packages/source/p/psutil/psutil-${psutil_ver}.tar.gz
  fi

  tar -zxvf ${srcdir}/psutil-${psutil_ver}.tar.gz
  cd psutil-${psutil_ver}

  python setup.py -v build \
    2>&1 | tee ${logdir}/psutil-${psutil_ver}_build.log  

  python setup.py -v install \
    2>&1 | tee ${logdir}/psutil-${psutil_ver}_install.log  

}

echo "pyclaw_build_profiler                 - install memory profiler ${mprofiler_ver}"
pyclaw_build_profiler() {
  echo "pyclaw_build_profiler"
  pyclaw_prep
  cd ${sandbox}

  if [ -d $sandbox/memory_profiler-${mprofiler_ver} ]; then
      rm -rf memory_profiler-${mprofiler_ver}
  fi

  echo "downloading and unpacking sources"
  if [ ! -f $srcdir/memory_profiler-${mprofiler_ver}.tar.gz ]; then
      wget --no-check-certificate -P ${srcdir} https://pypi.python.org/packages/source/m/memory_profiler/memory_profiler-${mprofiler_ver}.tar.gz
  fi

  tar -zxvf ${srcdir}/memory_profiler-${mprofiler_ver}.tar.gz
  cd memory_profiler-${mprofiler_ver}

  python setup.py -v build \
    2>&1 | tee ${logdir}/memory_profiler-${mprofiler_ver}_build.log  

  python setup.py -v install \
    2>&1 | tee ${logdir}/memory_profiler-${mprofiler_ver}_install.log  

}

echo "pyclaw_build_cython                   - install cython"
pyclaw_build_cython() {
  echo "pyclaw_build_cython"
  pyclaw_prep
  cd ${srcdir}
  if [ ! -d $srcdir/cython ]; then 
    git clone git@github.com:cython/cython.git
  fi
  cd cython
  git checkout ${cython_ver}
  git pull
  
  python setup.py -v build_ext install \
    2>&1 | tee ${logdir}/cython_install.log 
}

echo "pyclaw_build_mpi4py                   - install mpi4py ${mpi4py_ver}"
pyclaw_build_mpi4py() {
  echo "pyclaw_build_mpi4py"
  pyclaw_prep
  cd ${srcdir}
  if [ ! -d $srcdir/mpi4py ]; then 
    git clone git@bitbucket.org:mpi4py/mpi4py.git
  fi
  cd mpi4py
  git pull
  git checkout ${mpi4py_ver}
  git pull

  python setup.py -v build_src build_ext install \
    2>&1 | tee ${logdir}/mpi4py-${mpi4py_ver}_install.log

  python setup.py test \
    2>&1 | tee ${logdir}/mpi4py-${mpi4py_ver}_test.log
}

echo "pyclaw_build_petsc                    - install petsc-${petsc_ver}"
pyclaw_build_petsc() {
  echo "pyclaw_build_petsc"
  pyclaw_prep
  cd ${srcdir}

  if [ ${git_source} -eq 0 ]; then

    if [ ! -f ${srcdir}/petsc-lite-${petsc_ver}.tar.gz ]; then
      wget -P ${srcdir} http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-lite-${petsc_ver}.tar.gz
    fi
  
    tar -zxvf ${srcdir}/petsc-lite-${petsc_ver}.tar.gz
  
    cd petsc-${petsc_ver}
    petsc_src=${srcdir}/petsc-${petsc_ver}
    petsc_subdir=${petsc_ver}
  else
    cd ${srcdir}
    if [ ! -d $srcdir/petsc ]; then 
      git clone -b ${petsc_branch} git@bitbucket.org:petsc/petsc.git petsc
    fi
    cd petsc
    git pull
    petsc_src=${srcdir}/petsc
    petsc_subdir=${petsc_branch}
  fi
  
  echo "configuration"
  conda remove hdf5
  unset PETSC_DIR
  
  ./configure                                                       \
      --known-mpi-shared-libraries=1                                \
      --download-fblaslapack=1                                      \
      --with-shared-libraries=1                                     \
      --download-hdf5=1                                             \
      -CFLAGS=-g -CXXFLAGS=-g                                       \
      -FFLAGS=-g --with-debugging=1                                 \
      -COPTFLAGS=-g                                                 \
      -FOPTFLAGS=-g                                                 \
      --download-make                                               \
      --download-cmake                                              \
      LIBS=-dynamic                                                 \
      PETSC_ARCH=arch-linux-so                                      \
      --prefix=${builddir}/petsc/${petsc_subdir}/linux                \
      2>&1 | tee ${logdir}/petsc-${petsc_subdir}_configure.log

  make PETSC_DIR=${petsc_src} PETSC_ARCH=arch-linux-so  all \
      2>&1 | tee ${logdir}/petsc-${petsc_subdir}_make.log

  make PETSC_DIR=${petsc_src} PETSC_ARCH=arch-linux-so  install \
      2>&1 | tee ${logdir}/petsc-${petsc_subdir}_make_install.log

  echo "export PETSC_DIR"
  echo -e "# added by PETSc install, version ${petsc_branch}"
  echo -e "export PETSC_DIR=${builddir}/petsc/${petsc_subdir}/linux \n" >> ${profile} 
  echo -e "export PETSC_ARCH=arch-linux-so \n" >> ${profile}

  export PETSC_DIR=${builddir}/petsc/${petsc_subdir}/linux
}

echo "pyclaw_build_petsc_git                - install petsc via git"
pyclaw_build_petsc_git() {
  echo "pyclaw_build_petsc_git"
  pyclaw_prep
  cd ${srcdir}
  if [ ! -d $srcdir/petsc ]; then 
    git clone -b ${petsc_branch} git@bitbucket.org:petsc/petsc.git petsc
  fi

  cd petsc
  git checkout ${petsc_branch}
  git pull
  echo "configuration"
  conda remove hdf5
  unset PETSC_DIR
  
  ./configure                                                       \
      --known-mpi-shared-libraries=1                                \
      --download-fblaslapack=1                                      \
      --with-shared-libraries=1                                     \
      --download-hdf5=1                                             \
      -CFLAGS=-g -CXXFLAGS=-g                                       \
      -FFLAGS=-g --with-debugging=1                                 \
      -COPTFLAGS=-g                                                 \
      -FOPTFLAGS=-g                                                 \
      --download-make                                               \
      --download-cmake                                              \
      LIBS=-dynamic                                                 \
      PETSC_ARCH=arch-linux-so                                      \
      --prefix=${builddir}/petsc/${petsc_branch}/linux                \
      2>&1 | tee ${logdir}/petsc-${petsc_branch}_configure.log

  make PETSC_DIR=${srcdir}/petsc PETSC_ARCH=arch-linux-so all \
      2>&1 | tee ${logdir}/petsc-${petsc_branch}_make.log

  make PETSC_DIR=${srcdir}/petsc PETSC_ARCH=arch-linux-so install \
      2>&1 | tee ${logdir}/petsc-${petsc_branch}_make_install.log

  echo "export PETSC_DIR"
  echo -e "# added by PETSc install, version ${petsc_branch}"
  echo -e "export PETSC_DIR=${builddir}/petsc/${petsc_branch}/linux \n" >> ${profile} 
  echo -e "export PETSC_ARCH=arch-linux-so \n" >> ${profile}

  export PETSC_DIR=${builddir}/petsc/${petsc_branch}/linux
}

echo "pyclaw_build_petsc4py_git             - install petsc4py via git"
pyclaw_build_petsc4py_git() {
  echo "pyclaw_build_petsc4py_git"
  pyclaw_prep
  cd ${srcdir}
  if [ ! -d $srcdir/petsc4py ]; then 
    git clone -b ${petsc4py_branch} git@bitbucket.org:petsc/petsc4py.git petsc4py
  fi
  cd petsc4py
  git pull

  export PETSC_DIR=${builddir}/petsc/${petsc_subdir}/linux

  python setup.py -v build_src build_ext install \
    2>&1 | tee ${logdir}/petsc4py-${petsc_branch}_install.log
}

echo "pyclaw_build_petsc4py                 - install petsc4py ${petsc4py_ver}"
pyclaw_build_petsc4py() {
  echo "pyclaw_build_petsc4py"
  pyclaw_prep
  cd ${srcdir}

  if [ ${git_source} -eq 0 ]; then
    echo "downloading and unpacking sources"
    if [ ! -f $srcdir/petsc4py-${petsc4py_ver}.tar.gz ]; then
      wget --no-check-certificate -P ${srcdir} https://petsc4py.googlecode.com/files/petsc4py-${petsc4py_ver}.tar.gz
    fi

    echo "unpacking sources"
    tar -zxvf ${srcdir}/petsc4py-${petsc4py_ver}.tar.gz
    cd ${srcdir}/petsc4py-${petsc4py_ver}

    petsc4py_subdir=${petsc4py_ver}
  else
    if [ ! -d $srcdir/petsc4py ]; then 
      git clone -b ${petsc4py_branch} git@bitbucket.org:petsc/petsc4py.git petsc4py
    fi

    cd ${srcdir}/petsc4py
    git pull

    petsc4py_subdir=${petsc4py_branch}
  fi

  export PETSC_DIR=${builddir}/petsc/${petsc_subdir}/linux

  python setup.py -v build build_ext install \
    2>&1 | tee ${logdir}/petsc4py-${petsc4py_subdir}_install.log

  python setup.py test \
    2>&1 | tee ${logdir}/petsc4py-${petsc4py_subdir}_test.log
}

echo "pyclaw_build_clawpack                 - install clawpack"
pyclaw_build_clawpack() {
  echo "pyclaw_build_clawpack"
  pyclaw_prep

  cd ${sandbox}
  git clone git://github.com/clawpack/clawpack.git
  cd clawpack/
  git submodule init
  git submodule update
  
  pip install -e . \
    2>&1 | tee ${logdir}/clawpack_make_install.log

}

pyclaw_build_cmake(){
  echo "pyclaw_build_cmake"
  pyclaw_prep
  cd ${srcdir}
  if [ ! -f ${srcdir}/cmake-${cmake_ver}.tar.gz ]; then
  wget --no-check-certificate -P ${srcdir} http://www.cmake.org/files/v2.8/cmake-${cmake_ver}.tar.gz
  fi
   
  if [ -d ${srcdir}/cmake-${cmake_ver} ]; then
  rm -rf cmake-${cmake_ver}
  fi
   
  tar -zxvf ${srcdir}/cmake-${cmake_ver}.tar.gz
   
  cd ${srcdir}/cmake-${cmake_ver}
   
  ./bootstrap \
  --prefix=${builddir}/cmake/${cmake_ver} \
  --qt-qmake=qmake \
    2>&1 | tee ${logdir}/cmake_bootstrap.log
   
  make 2>&1 | tee ${logdir}/cmake_make.log
   
  make install 2>&1 | tee ${logdir}/cmake_install.log
   
  cmake_dir=${builddir}/cmake/${cmake_ver}/bin
  export PATH=${cmake_dir}:$PATH
  echo "adding to path"
  line_to_add="export PATH=\"${cmake_dir}"
  printf "\n # added by cmake ${cmake_ver} \n" >> "${profile}"
  printf "%s:$" "${line_to_add}" >> "${profile}"
  printf "PATH\" \n" >> "${profile}"
  unset line_to_add
}
 
pyclaw_build_paraview(){
  echo "pyclaw_build_paraview"
  pyclaw_prep
  cd ${srcdir}
  if [ ! -f $srcdir/ParaView-v4.1.0-source.tar ]; then
  wget --no-check-certificate -P ${srcdir} \
  http://www.paraview.org/paraview-downloads/download.php?submit=Download\&version=v4.1\&type=source\&os=all\&downloadFile=ParaView-v4.1.0-source.tar.gz
  fi
  if [ -d ${srcdir}/ParaView-v4.1.0-source ]; then
  rm -rf ParaView-v4.1.0-source
  fi
   
  tar -zxvf ${srcdir}/paraview-v4.1.0-source.tar
  cd ${builddir}
  mkdir ${builddir}/paraview
  mkdir ${builddir}/paraview/4.1.0/
   
  cd ${builddir}/paraview/4.1.0/
  ccmake ${srcdir}/ParaView-v4.1.0-source
}

pyclaw_build_paraview_git(){
  echo "pyclaw_build_paraview_git"
  pyclaw_prep
  cd ${srcdir}
  if [ ! -d ${srcdir}/ParaView ]; then
    git clone git://paraview.org/ParaView.git ParaView
  fi

  cd ParaView
}
echo "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
echo "pyclaw_build_all - run all install scripts"
pyclaw_build_all() {
  pyclaw_prep
  pyclaw_build_psutil
  pyclaw_build_profiler
  pyclaw_build_cython
  pyclaw_build_mpi4py
  pyclaw_build_petsc_git
  pyclaw_build_petsc4py_git
  pyclaw_build_clawpack
###
}