Difference between revisions of "Building on RHEL"

Revision as of 19:33, 1 June 2018

THIS PAGE IS UNDER CONSTRUCTION

Preliminaries

The Red Hat Enterprise Linux (RHEL) operating system is found on many Linux workstations. The instructions and scripts on this page have been tested on a workstation using RHEL 7.5 with GNU 4.8.5 compilers. These scripts will probably work with other versions of RHEL and other versions of GNU with minor modifications, but they have been explicitly verified for this operating system. We also include some notes on building GridPACK using Intel compilers.

The build described below assumes that all library and include files are located in a directory /home/palmer/software/linux64. This directory name reflects a particular system and users should select a directory that reflects their own system when building external libraries. The build below assumes that an environment variable PREFIX has been set. If you are using the C-shell environment, then this variable can be set using

 setenv PREFIX /home/palmer/software/linux64

If you are using the Bourne-shell, then this variable can be set using

 export PREFIX=/home/palmer/software/linux64

Using either shell, you can verify that this variable is present and has been set correctly by typing

 env | grep PREFIX

You should see the line

 PREFIX=/home/palmer/software/linux64

in the output. The PREFIX variable can be used to direct the output of the different builds to the same place.

Before starting any builds, the following variables need to be defined in the environment

Since the software on RHEL5 is old, most things have to be built from scratch and installed somewhere outside of the system directories. However, the documentation below is a good starting point for building on later versions of RHEL and other Linux systems. On this system, packages that were built were installed in a single directory, which will be denoted as $prefix here. We discuss how to build the libraries for both GNU and Intel compilers. The GNU 4.1.2 compilers are available by default. If you use Intel compilers, you should set the environment variables

 setenv CC icc
 setenv CXX icpc
 setenv FC ifort
 setenv F77 ifort
 setenv CFLAGS "-pthread"
 setenv CXXFLAGS "-pthread"
 setenv FCFLAGS "-pthread"
 setenv F77FLAGS "-pthread"

These are the c-shell directives. Modify accordingly if you are using some other shell.

Building CMake

CMake version 2.8.12 was built for RHEL5 as follows

 tar xvzf cmake-2.8.12.tar.gz
 cd cmake-2.8.12
 ./bootstrap --prefix=$prefix
 make
 make test
 make install

Two tests failed:

 The following tests FAILED:
          25 - FindPackageTest (Failed)
         230 - CMakeOnly.AllFindModules (Failed)
 Errors while running CTest

This does not seem to affect configuration of GridPACK.

Building MPI

These are the commands for building OpenMPI using the GNU 4.4 compilers

   setenv CC gcc4
   setenv CXX g++4
   setenv F77 gfortran
   setenv FC gfortran
   configure --enable-shared=no --enable-static=yes \
       --prefix="$prefix"
   make -j 4
   make check
   make install

This works for the 1.8.2 release. You can configure using the Intel compilers with the command

   ./configure --enable-shared=no\
               --enable-static=yes\
               --prefix="$prefix" \
               CC=icc CXX=icpc F77=ifort FC=ifort

Note that the environment variables are declared as part of the configure command in this example, but the could also be set using the setenv command.

Building Boost

In Boost 1.54, Boost.Log was added. This uses some compiler capabilities not supported by the ancient RHEL5 compiler, so Boost.Log is disabled. Boost seems to work fine this way on RHEL5.

   echo "using mpi ;" > ~/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
   rm ~/user-config.jam

To build using the Intel compilers, substitute --with-toolset=intel-linux for --with-toolset=gcc. You may also run into problems with the name of the MPI wrapper for the C++ compiler. If it looks like configure is not finding mpic++ then replace the first line in the above script with

   echo "using mpi : /absolute/path/to/mpi/C++/wrapper ;" > ~/user-config.jam

Make sure you include the spaces around ":" and before ";".

This script appears to work with later versions of Boost. Boost has a tendency to use cutting-edge features of the C++ compiler so it is a good idea to use a compiler version that was released at the same time as the Boost version you are working with. If you are having problems, you may better luck moving to an earlier version of Boost. If the Boost build fails, you should delete the entire boost directory and start from scratch. Restarting a failed Boost build does not appear to work in most instances.

Building PETSc

It is a good idea to include SuperLU in PETSc. GridPACK also requires ParMETIS and METIS, so you should include them as part of PETSc instead of building them separately (see below). GridPACK works with several recent versions of PETSc, including versions 3.4-3.7. This example uses PETSc version 3.4.2 and was built with SuperLU:

   set path = ("$prefix/bin" $path )
   setenv PETSC_DIR $prefix/../petsc-3.4.2
   unsetenv PETSC_ARCH
   python ./config/configure.py \
       PETSC_ARCH=arch-linux2-complex-opt \
       --with-prefix="$prefix" \
       --with-mpi=1 \
       --with-cc=mpicc \
       --with-fc=mpif90 \
       --with-cxx=mpicxx \
       --with-c++-support=1 \
       --with-c-support=0 \
       --with-fortran=0 \
       --with-scalar-type=complex \
       --with-fortran-kernels=generic \
       --download-superlu_dist \
       --download-parmetis \
       --download-metis \
       --with-clanguage=c++ \
       --with-shared-libraries=0 \
       --with-dynamic-loading=0 \
       --with-x=0 \
       --with-mpirun=mpirun \
       --with-mpiexec=mpiexec \
       --with-debugging=0
   make PETSC_DIR=$prefix/../petsc-3.4.2 PETSC_ARCH=arch-linux2-complex-opt all
   make PETSC_DIR=$prefix/../petsc-3.4.2 PETSC_ARCH=arch-linux2-complex-opt test

Building ParMETIS

It's easiest to include ParMETIS in the PETSc build. The GridPACK configuration will recognize and use ParMETIS from the PETSc installation. However, if you want to build ParMETIS separately, instructions are below.

In order to get ParMETIS 4.0 to compile with older GNU compilers, a warning option needs to be removed from one of the build system files. In the top ParMETIS source directory, execute the following command:

   sed -i.org -e 's/-Wno-unused-but-set-variable//g' metis/GKlib/GKlibSystem.cmake

Starting in the ParMETIS source directory, build and install METIS first:

   cd metis
   make config prefix="$prefix"
   make
   make install

then build and install ParMETIS:

   cd ..
   make config cc=mpicc cxx=mpicxx prefix="$prefix"
   make 
   make install

Do some tests to make sure it works:

   cd Graphs
   mpirun -np 4 ptest rotor.graph rotor.graph.xyz
   mpirun -np 4 ptest rotor.graph
   mpirun -np 8 ptest bricks.hex3d

The last one seemed to hang.

Building Global Arrays

Download GA into a directory GA_HOME. This configuration command should work for both GNU and Intel compilers if you have the CC, CXX, FC, F77 environment variables set.

   cd $(GA_HOME)
   ./configure --with-mpi-ts --disable-f77 --without-blas --enable-cxx --enable-i4 --prefix=$(GA_HOME)
   make
   make install

Building GridPACK

It is a good idea to build GridPACK in a separate directory. The example below assumes that a build directory has been created under $GRIDPACK/src and that you have cd'd into this directory.

   $prefix/bin/cmake -Wno-dev \
       -D BOOST_ROOT:STRING='/net/flophouse/files0/perksoft/boost-1.53.0' \
       -D PETSC_DIR:STRING='/net/flophouse/files0/perksoft/petsc-3.3-p3' \
       -D PETSC_ARCH:STRING='arch-linux2-cxx-opt' \
       -D PARMETIS_DIR:STRING='/net/flophouse/files0/perksoft/parmetis-4.0' \
       -D GA_DIR:STRING='/net/flophouse/files0/perksoft/ga-5-2' \
       -D MPI_CXX_COMPILER:STRING="$prefix/bin/mpicxx" \
       -D MPI_C_COMPILER:STRING="$prefix/bin/mpicc" \
       -D MPIEXEC:STRING="$prefix/bin/mpiexec" \
       -D CMAKE_BUILD_TYPE:STRING="Debug" \
       -D CMAKE_VERBOSE_MAKEFILE:BOOL=TRUE \
       ..