Difference between revisions of "Building on CentOS6"

Revision as of 16:08, 15 June 2018

This build was done on a VirtualBox virtual machine with a clean install of CentOS 6.9. The compiler and library packages available for CentOS 6.9 are quite old, so it is necessary to build GridPACK prerequisites from source and newer versions need to be avoided. This build was done with the a stock compiler (GNU 4.4), but, it in at least one other case, GridPACK was built using Devtoolset-4 (GNU 5.3).

In this description, prerequisite software is installed in an arbitrary path stored in the shell variable `$prefix`.

Requisite System Software

Some needed software can be installed with system packages:

sudo yum install environment-modules openmpi openmpi-devel gcc-c++ cmake bzip2-devel git

Before continuing, it will be necessary to either open another terminal and proceed there, or log out and log in. This makes the module command available for use.

OpenMPI is installed as a "module". In order to use the compiler wrappers the OpenMPI "module" needs to be "loaded":

module load openmpi-x86_64

If this does not work, then OpenMPI can be built by hand. To do this download an OpenMPI tarfile from the download site and unzip it into a directory in your home file area. Some additional information on how to do this can be found here.

After cd'ing into the OpenMPI directory, configure MPI using the script

  ./configure --enable-shared=no --enable-static=yes \
      --prefix="/home/admin/Desktop/software/openmpi-2.1.2/install" CC=gcc CXX=g++ FC=gfortran
  make -j 4
  make install

You will then need to add the MPI compiler wrappers, libraries and man pages to your environment. This can be done in the c-shell using the commands

  setenv PATH /home/admin/Desktop/software/openmpi-2.1.2/install/bin:${PATH}
  setenv MANPATH /home/admin/Desktop/software/openmpi-2.1.2/install/share/man:${MANPATH}
  setenv LD_LIBRARY_PATH /home/admin/Desktop/software/openmpi-2.1.2/install/lib:${LD_LIBRARY_PATH}

Alternatively, if you are using the Bourne shell, the corresponding commands are

  export PATH=/home/admin/Desktop/software/openmpi-2.1.2/install/bin:${PATH}
  export MANPATH=/home/admin/Desktop/software/openmpi-2.1.2/install/share/man:${MANPATH}
  export LD_LIBRARY_PATH=/home/admin/Desktop/software/openmpi-2.1.2/install/lib:${LD_LIBRARY_PATH}

Boost, version 1.54.0

Modern versions of Boost will probably not work here (especially Serialization and MPI). So, an old version is needed.

prefix="$HOME/gridpack"
module load openmpi-1.10-x86_64
rm -f ~/user-config.jam
rm -f ./tools/build/v2/user-config.jam
echo "using mpi : mpicxx ;" >> ./tools/build/v2/user-config.jam
sh ./bootstrap.sh \
    --prefix="$prefix" \
    --without-icu \
    --with-toolset=gcc \
    --without-libraries=python,log
./b2 -a -d+2 link=static stage
./b2 -a -d+2 link=static install

Global Arrays, version 5.6.5

Modern versions of Global Arrays work fine.

prefix="$HOME/gridpack"
module load openmpi-1.10-x86_64
sh autogen.sh
./configure \
    --enable-cxx \
    --disable-f77 \
    --enable-i4 \
    --with-mpi \
    --with-mpi-ts \
    --enable-autodetect=yes \
    --prefix=$prefix \
    --without-blas \
    --without-lapack \
    --without-scalapack \
    --enable-shared=no \
    --enable-static=yes \
    MPICC=mpicc MPICXX=mpicxx MPIF77=mpif90 \
    MPIEXEC=mpiexec MPIRUN=mpirun NPROCS=4
make
make -k check
make install

PETSc, version 3.6.4

For some reason, more recent PETSc versions were not recognized by the GridPACK CMake configuration, possibly because of the old compiler. This version appears to work.

prefix="$HOME/gridpack"
module load openmpi-1.10-x86_64
PETSC_DIR="$prefix/petsc-3.6.4"
export PETSC_DIR
python ./config/configure.py \
python ./config/configure.py \
    PETSC_ARCH=linux-gnu44-real-opt \
    --with-prefix="$prefix/" \
    --with-mpi=1 \
    --with-cc="mpicc" \
    --with-fc="mpif90" \
    --with-cxx="mpicxx" \
    --with-c++-support=1 \
    --with-c-support=0 \
    --with-fortran=1 \
    --with-scalar-type=real \
    --with-precision=double \
    --with-clanguage=c++ \
    --with-fortran-kernels=generic \
    --with-valgrind=0 \
    --download-superlu_dist \
    --download-parmetis \
    --download-metis \
    --download-f2cblaslapack=1 \
    --download-mumps=0 \
    --download-scalapack=0 \
    --with-shared-libraries=0 \
    --with-x=0 \
    --with-mpirun=mpiexec \
    --with-mpiexec=mpiexec \
    --with-debugging=0
make PETSC_DIR=/files0/perksoft/petsc-3.6.4 PETSC_ARCH=linux-gnu48-real-opt all
make PETSC_DIR=/files0/perksoft/petsc-3.6.4 PETSC_ARCH=linux-gnu48-real-opt test

GridPACK

prefix="$HOME/gridpack"
module load openmpi-1.10-x86_64
cmake -Wdev --debug-trycompile \
      -D GA_DIR:PATH="${prefix}" \
      -D BOOST_ROOT:PATH="${prefix}" \
      -D USE_PROGRESS_RANKS:BOOL=OFF \
      -D PETSC_DIR:PATH="${prefix}/petsc-3.6.4" \
      -D PETSC_ARCH:STRING="linux-gnu44-real-opt" \
      -D MPI_CXX_COMPILER:STRING="mpicxx" \
      -D MPI_C_COMPILER:STRING="mpicc" \
      -D MPIEXEC:STRING="mpiexec" \
      -D USE_GLPK:BOOL=OFF \
      -D MPIEXEC_MAX_NUMPROCS:STRING="4" \
      -D GRIDPACK_TEST_TIMEOUT:STRING=10 \
      -D BUILD_SHARED_LIBS:BOOL=OFF \
      -D CMAKE_BUILD_TYPE:STRING=Debug \
      -D CMAKE_VERBOSE_MAKEFILE:BOOL=TRUE \
      -D CMAKE_INSTALL_PREFIX:PATH="${prefix}" \
      ..
make 
make test