Difference between revisions of "Building on a Linux Cluster"

Revision as of 19:03, 13 September 2018

This page describes a GridPACK build on a Linux cluster using an Infiniband network for communication. This build is similar to the one described for building GridPACK on a Red Hat Enterprise Linux (RHEL) workstation, so many of the options will be similar. The scripts described below should work for a variety of RHEL systems, but we can verify that they worked on a Linux cluster running RHEL 6.6 with OpenMPI 1.8.3 and using the GNU 4.9.2 compilers. The specific versions of the libraries used to build GridPACK are Boost 1.65.0, Global Arrays 5.6.3 and PETSc 3.7.6. Other versions will likely work with little or no modification, but these versions have actually been built using the scripts below. We have also used these scripts to build GridPACK using Intel compilers and intelmpi. A separate Boost configuration script is needed, but apart from modifying directory locations and the name of the PETSC_ARCH variable, the same configuration scripts can be used for PETSc, Global Arrays and GridPACK. We have verified that the Intel build works on the same versions of all libraries used in the GNU build with the Intel 17.0.4 compilers and 2018.0.128 version of intelmpi.

This build is very similar to the build for a workstation using the RHEL operating system. The main difference is that this build puts all libraries in separate directories after building, while the workstation build puts all files in a single common directory. If you prefer to do you builds so that all libraries and include files end up in a single directory, you should review the workstation build for details on how to do this.

A brief note: Any parameters that need to be modified by the user to reflect directory names or architecture variables on a specific platform have been highlighted in red.

Modules

If your system supports modules, then you can use these to configure your environment so that the software needed to build GridPACK is in your path. For building GridPACK using GNU compilers and the OpenMPI version of MPI, use the modules

   module purge
   module load gcc/4.9.2
   module load openmpi/1.8.3
   module load python/2.7.3
   module load cmake/3.8.2

The details of these modules may vary on your system. In addition, set the environment variables

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

The PETSc build will complain about these environment variables being set, but it will just override them and use its own settings.

If you are interested in an Intel build, then try loading

   module purge
   module intel
   module intelmpi
   module python/2.7.3
   module cmake

and set the environment variables

   setenv CC icc
   setenv CFLAGS "-pthread"
   setenv CXX icpc
   setenv CXXFLAGS "-pthread"
   setenv FC ifort
   setenv FFLAGS "-pthread"

After setting modules, the output of the module list command for the GNU environment should be

   Currently Loaded Modulefiles:
     1) gcc/4.9.2                3) python/2.7.3
     2) openmpi/1.8.3(default)   4) cmake/3.8.2

You will get something similar for Intel. Modules should guarantee that the compilers and MPI libraries are all consistent. If you are not using modules, then you will need to work with your system administrator to make sure that your environment has a consistent set of compilers and MPI libraries.

Boost

A Boost tar file can be obtained from the download page. Information on downloading files can be obtained here. Boost can configured and built using the GNU environment as follows:

   echo "using mpi ;" > ~/user-config.jam
   sh ./bootstrap.sh \
       --prefix="/pic/projects/gridpack/software_new/boost_1_65_0" \
       --without-icu \
       --with-toolset=gcc \
       --without-libraries=python
   ./b2 -a -d+2 link=static stage
   ./b2 -a -d+2 link=static install
   rm ~/user-config.jam

The argument to --prefix will need to be modified to reflect the true location of the Boost libraries on your system. Make sure you include all spaces in the above script exactly as written.

For Intel compilers and intelmpi, the script needs to be modified to

   echo "using mpi : mpicxx ;" > ~/user-config.jam
   sh ./bootstrap.sh \
       --prefix="/pic/projects/gridpack/software_intel/boost_1_65_0" \
       --without-icu \
       --with-toolset=intel-linux \
       --without-libraries=python
   ./b2 -a -d+2 link=static stage
   ./b2 -a -d+2 link=static install
   rm ~/user-config.jam

Note that the argument to --with-toolset is changed and the mpicxx wrapper has been added to the first line (this needs to be done because intelmpi does not supply a compiler wrapper call mpic++). Again, make sure you include all spaces in the above script exactly as written.

PETSc

Tar files containing the complete PETSc library can be obtained from the PETSc download page. Information on downloading tar files can be found here.

In this example, PETSc was configured to include SuperLU. This requires that ParMETIS and METIS be included also, so these libraries do not have to built separately. The configuration script should be run in the top-level PETSc directory. Once you have configure PETSc, there will be a directory linux-openmpi-gnu-cxx-complex-opt that will contain all the PETSc include and library files. Note that the value of the PETSC_ARCH variable used to configure GridPACK (below) must match the value of PETSC_ARCH used to configure PETSc.

   python ./config/configure.py \
     PETSC_ARCH=linux-openmpi-gnu-cxx-complex-opt \
     --with-scalar-type=complex \
     --with-fortran-kernels=generic \
     --download-superlu_dist \
     --download-superlu \
     --download-parmetis \
     --download-metis \
     --download-suitesparse \
     --download-fblaslapack \
     --with-clanguage=c++ \
     --with-shared-libraries=0 \
     --with-x=0 \
     --with-mpiexec=mpiexec \
     --with-debugging=0

When you run this script, the PETSc build process will prompt you on what to do next. Just copy and paste these instructions into the Linux command prompt. The first instruction after configuring is

   xxx=========================================================================xxx
    Configure stage complete. Now build PETSc libraries with (gnumake build):
      make PETSC_DIR=/pic/projects/gridpack/software_new/petsc-3.7.6 PETSC_ARCH=linux-openmpi-gnu-cxx-complex-opt all
   xxx=========================================================================xxx

Follow the instructions and copy

   make PETSC_DIR=/pic/projects/gridpack/software_new/petsc-3.7.6 PETSC_ARCH=linux-openmpi-gnu-cxx-complex-opt all

into the command prompt. Additional instructions will appear at the end of the make. If the make command succeeds, you can stop but you may want to run some of the tests to insure that the build is correct.

If you are using Intel compilers and intelmpi, you should modify the value of PETSC_ARCH variable to reflect this.

If you run into problems configuring or building PETSc, some additional tips can be found here.

Global Arrays

Download GA into a directory from the GA download page. Information on downloading tar files can be found here. Since it is possible to configure GA in different ways, it is often a good idea to create a build directory below the top level GA directory to configure an build GA. In this example, this directory is build_pr. After creating the directory, cd into it and configure with

   cd $(GA_HOME)/build_pr
   ../configure --enable-i4 --enable-cxx --with-mpi-pr --without-blas --disable-f77 --prefix=/pic/projects/gridpack/software_new/ga-5-6/build_pr
   make
   make install

This script assumes that there is a build directory called build_pr that is beneath GA home directory. Be sure and include the --without-blas directive, otherwise the configure will pick up the BLAS library from the environment and this will conflict with BLAS that is downloaded and built by PETSc. This script is configuring GA to use the progress ranks runtime, which is recommended for large scale simulations. The USE_PROGRESS_RANKS variable must be set to TRUE when configuring GridPACK (see below). Also, because the progress ranks runtime requisitions 1 MPI process per SMP node to manage computations, the actual number of processes available to the calculation is less than the number requested when calling mpirun. Because of this you must use at least 2 processes to run GridPACK applications with this configuration. However, for large calculations, this runtime is the most robust and reliable available.

If the communication network is Infiniband, you can configure GA to use the Infiniband runtime instead by replacing --with-mpi-pr with --with-mpi --with-openib. This runtime may be a little faster than progress ranks. In this case the number of processors available to the GridPACK application is the same as the number requested with mpirun. Also, remember to set the USE_PROGRESS_RANKS variable to FALSE if using this runtime.

GridPACK

The following commands can be used to configure and build GridPACK. More information on GridPACK configuration options can be found here.

Make a directory in which to configure and build GridPACK (do not try to build GridPACK in the src directory):

   cd path/to/gridpack/src
   mkdir build
   cd build

Use cmake to configure

   rm -rf CMake*

   cmake -Wdev \
       -D PETSC_DIR:STRING='/pic/projects/gridpack/software_new/petsc-3.7.6' \
       -D PETSC_ARCH:STRING='linux-openmpi-gnu-cxx-complex-opt' \
       -D GA_DIR:STRING='/pic/projects/gridpack/software_new/ga-5-6/build_pr' \
       -D USE_PROGRESS_RANKS:BOOL=TRUE \
       -D GA_EXTRA_LIBS='-lrt' \
       -D MPI_CXX_COMPILER:STRING='mpicxx' \
       -D MPI_C_COMPILER:STRING='mpicc' \
       -D MPIEXEC:STRING='mpiexec' \
       -D MPIEXEC_MAX_NUMPROCS:STRING="3" \
       -D BOOST_ROOT:STRING='/pic/projects/gridpack/software_new/boost_1_65_0' \
       -D CMAKE_INSTALL_PREFIX:PATH='/people/d3g293/gridpack/src/build_const/install' \
       -D CMAKE_BUILD_TYPE:STRING='RELWITHDEBINFO' \
       -D CMAKE_VERBOSE_MAKEFILE:BOOL=TRUE \
       ..    

Alternatively, use the example configuration script (usually most up to date):

   sh ../example_configuration.sh constance

The argument to PETS_ARCH should be the same as the corresponding string in the script to configure PETSc. This script assumes that ParMETIS is part of the PETSc build. If ParMETIS was built separately, then you can include the location of the ParMETIS libraries in the configuration script by adding the line

   -D PARMETIS_DIR:STRING= '/path/to/parmetis/libraries' \

to the GridPACK configuration script.

This script assumes the GA libraries were built using the Infiniband runtime for GA. The directories in this script need to be modified to reflect your system. If the Infiniband runtime for GA is used, then USE_PROGRESS_RANKS should be set to FALSE. The MPIEXEC_MAX_NUMPROCS, which controls the maximum number of processors that are used when running the GridPACK tests, should also be changed to 2.

After configuring GridPACK, build and test:

   make
   make test

Issues

This build has been tested on the PNNL institutional cluster using the software versions list at the top of this page. There are potential improvements that could be made to this build:

• The GNU compilers can take advantage of the cluster hardware if certain options are used. They were not.
• The PETSc build should use the AMCL libraries for BLAS/LAPACK support rather than downloading CBlas.