Difference between revisions of "Building on CentOS7"

Latest revision as of 15:12, 9 May 2019

This documents a GridPACK build on CentOS 7.5.1804 installed on a VirtualBox virtual machine (VM). Virtual Box is not required and these instructions should work for a Linux system using the CentOS operating sytem. They also work for Red Hat Enterprise Linux (RHEL) 7.

Requisite System Software

In this build, some Prequisite Software was installed as system software packages. Super user priviledges are required to install system software. If you do not have such priviledges, you will need a system administrator perform some of these steps. Super user priviledges are not required to build and use GridPACK, only to install system software.

Most required system software is available in the default CentOS/RHEL repostitories. However, at least one package from the Extra Packages for Enterprise Linux (EPEL) repository is needed. Add access to the EPEL repository with

   sudo yum install epel-release

Install a C++ compiler, CMake, and Git with

   sudo yum install git cmake cmake3 gcc-c++

cmake is required to build. cmake3 is required for GridPACK.

OpenMPI

Install OpenMPI (version 1.10) using

   sudo yum install openmpi openmpi-devel

This will install the module command. 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 mpiexec and compiler wrappers, the correct module must be loaded using

   module load mpi/openmpi-x86_64

This makes the MPI compiler wrappers and mpiexec available to the command line. The OpenMPI module must be loaded each time a terminal session is started.

Boost

Install Boost (version 1.53) with

   sudo yum install boost boost-devel boost-openmpi boost-openmpi-devel

This will install the needed Boost libraries and headers.

Build Packages from Source

Directories or architecture variables that should be set to reflect local user environments are colored red.

In this build, all packages built from source (and GridPACK) were installed in a common directory, $HOME/gridpack. For convenience, a shell variable was set to this directory using, for the C-shell

   set PREFIX = $HOME/gridpack

or in the Bourne shell

   export PREFIX=$HOME/gridpack

The common directory appears as $PREFIX below.

Building GridPACK on CentOS/RHEL 7 requires code be built with pthreads throughout. Before continuing, it will be necessary to set environment variables to make sure proper compilers and their pthread options are used. If using the C-shell:

   setenv CC gcc
   setenv CFLAGS "-pthread"
   setenv CXX g++
   setenv CXXFLAGS "-pthread"
   setenv FC gfortran
   setenv FFLAGS "-pthread"

or in a Bourne shell

   export CC=gcc
   export CFLAGS="-pthread"
   export CXX=g++
   export CXXFLAGS="-pthread"
   export FC=gfortran
   export FFLAGS="-pthread"

PETSc, version 3.7.7

A PETSc package is available through yum (EPEL), but its headers and libraries are installed in locations that the GridPACK configuration does not understand. It's best to just build PETSc from source.

Get the PETSc 3.7.7 source from the | PETSc download page] and unpack it. In this case, it was unpacked in $HOME/gridpack/src/petsc-3.7.7. In the unpacked directory, configure PETSc as follows:

   ./configure \
      PETSC_ARCH=arch-linux2-complex-opt \
      --with-fortran-kernels=1 \
      --download-superlu_dist \
      --download-superlu \
      --download-parmetis \
      --download-metis \
      --download-suitesparse \
      --download-fblaslapack \
      --with-clanguage=c++ \
      --with-shared-libraries=0 \
      --with-scalar-type=complex \
      --with-x=0 \
      --with-mpiexec=mpiexec \
      --prefix="$PREFIX/petsc-3.7.7" \
      --with-debugging=0 CFLAGS=-pthread CXXFLAGS=-pthread FFLAGS=-pthread

This will build some required packages and configure PETSc for compilation. It will complain about how the CC, etc. environment variables were set, but it ignores those and does the right thing. Build the PETSc libraries using

   make PETSC_DIR=$HOME/gridpack/src/petsc-3.7.7 PETSC_ARCH=arch-linux2-complex-opt all

Install PETSc using

   make PETSC_DIR=$HOME/gridpack/src/petsc-3.7.7 PETSC_ARCH=arch-linux2-complex-opt install

The installation can be tested with

   make PETSC_DIR=$PREFIX/petsc-3.7.7 PETSC_ARCH="" test

Global Arrays, 5.6.5

The EPEL repository also has a Global Arrays package that can be installed with yum. However, at the time of writing, this package was not compatible with the GridPACK configuration. So, building GA from soure is necessary.

Get the Global Arrays source from the release page. Unpack in a convenient location. In the unpacked directory, configure, build, and install using

   ./configure --with-mpi-ts --disable-f77 --without-blas \
       --enable-cxx --enable-i4 --prefix="$PREFIX"
   make
   make install

GridPACK

Obtain the GridPACK release or development code and put it in a convenient directory, like $HOME/gridpack/src.

Then, change into the top-most GridPACK source directory, make a build directory e.g.:

   cd $HOME/gridpack/src/GridPACK
   mkdir src/build
   cd src/build

Configure and build GridPACK with

   cmake3 -Wdev --debug-trycompile \
       -D GA_DIR:STRING="$PREFIX" \
       -D USE_PROGRESS_RANKS:BOOL=OFF \
       -D BOOST_ROOT:STRING="/usr" \
       -D PETSC_DIR:STRING="$PREFIX/petsc-3.7.7" \
       -D MPI_CXX_COMPILER:STRING="/usr/lib64/openmpi/bin/mpicxx" \
       -D MPI_C_COMPILER:STRING="/usr/lib64/openmpi/bin/mpicc" \
       -D MPIEXEC:STRING="/usr/lib64/openmpi/bin/mpiexec" \
       -D MPIEXEC_MAX_NUMPROCS:STRING="2" \
       -D GRIDPACK_TEST_TIMEOUT:STRING=400 \
       -D CMAKE_INSTALL_PREFIX:PATH="$PREFIX" \
       -D BUILD_SHARED_LIBS:BOOL=NO \
       ..
   make

If compilation is successful, the unit tests and/or example applications can be run.