pyclaw_install_macos.sh

# This is script version 3.0 - HPC & PyClaw in Mac OSX
# ------------------------------------------------------------------------------ #
# This version uses github and bitbucket sources
# ------------------------------------------------------------------------------ #
# ------------------------------------------------------------------------------ #

#!/bin/bash -x
echo -e "\n**************************************************************"
echo "Build a HPC system in MacOSX"
echo "**************************************************************"

echo "hpc_prep                            - set up build environment"
hpc_prep() {
# set working directories
  echo "hpc_preparation"
  echo "setting up directories"
  projdir=/sandbox
  echo "projdir=${projdir}"
  sandbox=${projdir}
  echo "sandbox=${sandbox}"
  builddir=${sandbox}/opt/share
  echo "builddir=${builddir}"
  srcdir=${builddir}/sources
  echo "srcdir=${srcdir}"
  logdir=${builddir}/logs
  echo "logdir=${logdir}"
  appsdir=${sandbox}/apps
  echo "appsdir=${appsdir}"
  simdir=${sandbox}/simdesk
  echo "simdir=${simdir}"
  devdir=${sandbox}/dev
  echo "devdir=${devdir}"

# build directories
  mkdir -p ${builddir} ${srcdir} ${logdir} ${appsdir} ${simdir} ${devdir}

# identify user profiles
  profileb=$HOME/.bash_profile

# packages versions
  mpich_branch=master
  anaconda_ver=2.5.0
  psutil_ver=4.1.0
  mprofiler_ver=0.41
  cython_branch=master
  mpi4py_branch=master
  petsc_branch=maint
  petsc_subdir=maint
  fftw_ver=3.3.4
  fftw_branch=master
  sowing_ver=1.1.18-p1
  petsc4py_branch=maint
  clawpack_branch=master
  ofoam_branch=master
  ofoam_version=2.4.x
  ofoam_third_party=2.4.0
  paraview_branch=release
  cmake_branch=master
  qt_ver=4.8
  qt_release=4.8.6
  glibc_release=master
  sublime_version=2.0.2
  r_release=3
  r_version=3.2.4
  n_cores=8

  # fblaslapack_ver=3.4.2
  # f2cblaslapack_ver=3.4.2.q
  # scalapack_ver=2.0.2
  # hdf5_ver=1.8.13

  has_submodules=("clawpack paraview")

  files=( "${mpich_branch}" \
          "Anaconda2-${anaconda_ver}-MacOSX-x86_64.sh" \
          "psutil-${psutil_ver}.tar.gz" \
          "memory_profiler-${mprofiler_ver}.tar.gz" \
          "${cython_branch}" \
          "${mpi4py_branch}" \
          "fftw-${fftw_ver}.tar.gz" \
          "${fftw_branch}" \
          "${petsc_branch}" \
          "${petsc4py_branch}" \
          "${clawpack_branch}" \
          "${ofoam_branch}" \
          "ofoam_third_party_${ofoam_third_party}" \
          "${paraview_branch}" \
          "${cmake_branch}" \
          "qt-everywhere-opensource-src-${qt_release}.tar.gz" \
          "${glibc_release}" \
          "R_${r_version}.tar.gz" \
          )

  urls=(  "http://git.mpich.org/mpich.git mpich" \
          "http://repo.continuum.io/archive/Anaconda2-${anaconda_ver}-MacOSX-x86_64.sh" \
          "https://pypi.python.org/packages/source/p/psutil/psutil-${psutil_ver}.tar.gz" \
          "https://pypi.python.org/packages/source/m/memory_profiler/memory_profiler-${mprofiler_ver}.tar.gz" \
          "git@github.com:cython/cython.git cython" \
          "git@bitbucket.org:mpi4py/mpi4py.git mpi4py" \
          "http://www.fftw.org/fftw-${fftw_ver}.tar.gz" \
          "git@github.com:FFTW/fftw3.git fftw" \
          "git@bitbucket.org:petsc/petsc.git petsc" \
          "git@bitbucket.org:petsc/petsc4py.git petsc4py" \
          "git@github.com:clawpack/clawpack.git ${simdir}/clawpack" \
          "git@github.com:OpenFOAM/OpenFOAM-${ofoam_version}.git ofoam" \
          "http://downloads.sourceforge.net/foam/ThirdParty-${ofoam_third_party}.tgz" \
          "https://gitlab.kitware.com/paraview/paraview.git paraview" \
          "https://cmake.org/cmake.git cmake" \
          "http://download.qt.io/archive/qt/${qt_ver}/${qt_release}/qt-everywhere-opensource-src-${qt_release}.tar.gz" \
          "git://sourceware.org/git/glibc.git glibc" \
          "https://cran.r-project.org/src/base/R-${r_release}/R-${r_version}.tar.gz" \
          )

  #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 ${profileb}
}


_listcontains() {
  for word in $1; do
    
    if [[ ${2} == *${word}* ]]; then
      echo "${2} and word ${word}"
      return 0
    fi
  done
  return 1
}

_git_init_submodule(){
  branch_name=$1
  echo -e "initializing submodules"
  git submodule init
  git submodule update
  git submodule foreach git checkout ${branch_name}
  git submodule foreach git pull
}

_git_post(){
  repo_dir=$1
  branch_name=$2

  cd ${repo_dir}
  git fetch --tags
  latest_tag=$(git describe --tags `git rev-list --tags --max-count=1`)

  echo "updating repo ${repo_dir}"
  if _listcontains "${has_submodules}" ${repo_dir}; then 
    #   echo Y; else echo N; fi
    # if [[ ${has_submodules} =~ ${repo_dir} ]]; then
    echo " going into submodules for ${repo_dir}"
    _git_init_submodule ${branch_name}
  elif [[ ${repo_dir} == *"glibc"* ]]; then
    git checkout --track -b release `git branch --remotes --list origin/release* | tail -1`
    git pull
  else
    git checkout ${branch_name}
    git pull
  fi
}

_get_src(){
  src_file=$1
  src_url=$2

  cd ${srcdir}

  if [[ ${src_url} == *".git"* ]]; then
    repo_dir=$3
    if [ ! -d ${repo_dir} ]; then
      echo "#### cloning repo ${src_url} into ${repo_dir} #####"
      echo -e ">> git clone ${src_url} ${repo_dir}"
      git clone ${src_url} ${repo_dir}
    fi
      echo "pull and update repo ${repo_dir}"
      _git_post ${repo_dir} ${src_file}
  else
    echo -e "#### downloading ${src_file} to ${srcdir} #####"
    if [ ! -f ${srcdir}/${src_file} ]; then 
      echo -e ">> wget -P ${srcdir} -O ${src_file} ${src_url}"
      wget -P ${srcdir} -O ${src_file} ${src_url}
    else
      echo -e 'src file is present, skipping\n'
    fi
  fi
}

_extract_src() {
  src_file=$1

  cd ${srcdir}

  tar -zxvf ${srcdir}/${src_file}
}

_add_to_profile() {
  echo "adding to profile"
  who_added=$1
  line=$2
  profile=$3
  echo -e "\n# added by ${who_added}\n${line}\n" >> ${profile}
}

echo "hpc_get_sources                     - get all sources"
hpc_get_sources() {
  hpc_prep

  echo "getting sources"
  cd ${srcdir}

  nfiles=${#files[@]}
  nfiles=$((nfiles-1))
  echo " There are $nfiles repositories/files to clone"

  for (( i=0; i<${nfiles}+1; i++ ));
  do
    echo $i "/" ${nfiles} "getting: " ${files[$i]} " from " ${urls[$i]}
    _get_src ${files[$i]} ${urls[$i]}
  done

  cd ${projdir}
}

echo "hpc_build_mpich                     - install mpich2 "
hpc_build_mpich(){
  hpc_prep
  cd ${srcdir}/mpich

  echo "installing mpich to the system"

  if [ ! -f configure ]; then
    echo "first running autogen.sh to compile installation files"
    ./autogen.sh \
    2>&1 | tee ${logdir}/mpich-${mpich_branch}_autogen.log
  fi

  echo "configure"
  ./configure \
    CFLAGS=-fPIC FFLAGS=-fPIC \
    --with-threads \
    --enable-shared --enable-sharedlibs=gcc \
    --enable-fast=all,03 \
    -prefix=${builddir}/mpich/${mpich_branch} \
    --disable-multi-aliases \
    2>&1 | tee ${logdir}/mpich-${mpich_branch}_configure.log

  echo "make build"
  make \
    2>&1 | tee ${logdir}/mpich-${mpich_branch}_make.log

  echo "make install"
  make install \
    2>&1 | tee ${logdir}/mpich-${mpich_branch}_install.log

  mpich_dir=${builddir}/mpich/${mpich_branch}/bin
  export PATH=${mpich_dir}:$PATH

  _add_to_profile "mpich-${mpich_branch}" "export PATH=\"${mpich_dir}:\$PATH\" \n" ${profileb}
}

echo "hpc_build_anaconda                  - install anaconda ${anaconda_ver}"
hpc_build_anaconda() {
  echo "hpc_build_anaconda"
  hpc_prep
  cd ${srcdir}

  bash ${srcdir}/Anaconda2-${anaconda_ver}-MacOSX-x86_64.sh \
    2>&1 | tee ${logdir}/Anaconda-${anaconda_ver}_install.log
}

echo "hpc_build_psutil                    - install psutils ${psutil_ver}"
hpc_build_psutil() {
  echo "hpc_build_psutil"
  hpc_prep

  cd ${srcdir}

  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 "hpc_build_profiler                  - install memory profiler ${mprofiler_ver}"
hpc_build_profiler() {
  echo "hpc_build_profiler"
  hpc_prep
  cd ${srcdir}

  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 "hpc_build_cython                    - install cython"
hpc_build_cython() {
  echo "hpc_build_cython"
  hpc_prep
  cd ${srcdir}/cython
  
  python setup.py -v build_ext install \
    2>&1 | tee ${logdir}/cython_install.log 
}

echo "hpc_build_mpi4py                    - install mpi4py ${mpi4py_branch}"
hpc_build_mpi4py() {
  echo "hpc_build_mpi4py"
  hpc_prep
  cd ${srcdir}/mpi4py

  python setup.py -v build_src build_ext install \
    2>&1 | tee ${logdir}/mpi4py-${mpi4py_branch}_install.log

  python setup.py test \
    2>&1 | tee ${logdir}/mpi4py-${mpi4py_branch}_test.log
}

echo "hpc_build_petsc                     - install petsc"
hpc_build_petsc() {
  echo "hpc_build_petsc"
  hpc_prep
  cd ${srcdir}/petsc

  echo "configuration"
  unset PETSC_DIR
  
  ./configure                                                                   \
      --known-mpi-shared-libraries=1                                            \
      --with-shared-libraries=1                                                 \
      --with-64-bit-indices=1                                                   \
      --download-fblaslapack                                                    \
      --download-scalapack                                                      \
      --download-sowing                                                         \
      --download-hdf5                                                           \
      -CFLAGS=-g -CXXFLAGS=-g                                                   \
      -FFLAGS=-g --with-debugging=1                                             \
      -COPTFLAGS=-g                                                             \
      -FOPTFLAGS=-g                                                             \
      LIBS=-dynamic                                                             \
      PETSC_ARCH=arch-osx-so                                                    \
      --prefix=${builddir}/petsc/${petsc_branch}/osx                            \
      2>&1 | tee ${logdir}/petsc-${petsc_branch}_configure.log

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

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

  make PETSC_DIR=${builddir}/petsc/${petsc_branch}/osx PETSC_ARCH="" test       \
      2>&1 | tee ${logdir}/petsc-${petsc_branch}_make_test.log

  make PETSC_DIR=${builddir}/petsc/${petsc_branch}/osx PETSC_ARCH= streams NPMAX=${n_cores} \
      2>&1 | tee ${logdir}/petsc-${petsc_branch}_make_profile.log

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

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

echo "hpc_build_petsc4py                  - install petsc4py"
hpc_build_petsc4py() {
  echo "hpc_build_petsc4py"
  hpc_prep
  cd ${srcdir}/petsc4py

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

  python setup.py -v build_src build_ext install \
    2>&1 | tee ${logdir}/petsc4py-${petsc4py_branch}_install.log

  python setup.py test \
    2>&1 | tee ${logdir}/petsc4py-${petsc4py_branch}_test.log
}

echo "hpc_build_clawpack                  - install clawpack"
hpc_build_clawpack() {
  echo "hpc_build_clawpack"
  hpc_prep

  cd ${simdir}/clawpack
 
  pip install -e . \
    2>&1 | tee ${logdir}/clawpack_make_install.log
}

echo "hpc_build_paraview                  - install paraview"
hpc_build_paraview() {
  cd ${srcdir}
}
echo "**************************************************************"
echo -e "----  hpc_build_all - run all install scripts ----"
echo -e "    ##### YOU SHOULD RUN hpc_get_sources first! #####"

hpc_build_all() {
  hpc_prep
  hpc_get_sources
  hpc_build_anaconda
  hpc_build_mpich
  hpc_build_psutil
  hpc_build_profiler
  hpc_build_cython
  hpc_build_mpi4py
  hpc_build_petsc
  hpc_build_petsc4py
  hpc_build_clawpack
}