Installation

Sample scripts to configure and build LBPM are included in the sample_scripts directory. To build this package, MPI and cmake are required, along with a compiler that supports the C++-14 standard. Building in source is not supported.

The essential dependencies needed to build LBPM are:

  1. cmake (version 3.9 or higher)

  2. MPI

  3. HDF5

  4. silo

Building Dependencies

(skip if they are already installed on your system)

  1. Download third-party library source files

zlib-1.2.11.tar.gz
hdf5-1.8.12.tar.gz
silo-4.10.2.tar.gz

  1. Set up path where you want to install

export MPI_DIR=/path/to/mpi
export LBPM_ZLIB_DIR=/path/to/zlib
export LBPM_HDF5_DIR=/path/to/hdf5
export LBPM_SILO_DIR=/path/to/silo

  1. Build third-party library dependencies

tar -xzvf zlib-1.2.11.tar.gz
tar -xzvf hdf5-1.8.12.tar.gz
tar -xzvf silo-4.10.2.tar.gz
cd zlib-1.2.11

./configure --prefix=$LBPM_ZLIB_DIR && make && make install

cd ../hdf5-1.8.12

CC=$MPI_DIR/bin/mpicc  CXX=$MPI_DIR/bin/mpicxx CXXFLAGS="-fPIC -O3 -std=c++14" \
./configure --prefix=$LBPM_HDF5_DIR --enable-parallel --enable-shared --with-zlib=$LBPM_ZLIB_DIR
 make && make install


cd ../silo-4.10.2

CC=$MPI_DIR/bin/mpicc  CXX=$MPI_DIR/bin/mpicxx CXXFLAGS="-fPIC -O3 -std=c++14" \
./configure --prefix=$LBPM_SILO_DIR -with-hdf5=$LBPM_HDF5_DIR/include,$LBPM_HDF5_DIR/lib --enable-static
 make && make install

Building LBPM

Many HPC systems will include all of these dependencies, and LBPM can be built simply by setting the paths to the associated libraries in the cmake configure line.

The steps typically used to build LBPM are as follows:

  1. Set environment variables for the source directory $LBPM_WIA_SOURCE and build directory $LBPM_WIA_DIR

export LBPM_SOURCE=/path/to/source/LBPM
export LBPM_DIR=/path/to/build/LBPM

  1. Set environment variables for the path to HDF5 and SILO (required), and optionally for TimerUtility and NetCDF (optional)

export LBPM_HDF5_DIR=/path/to/hdf5
export LBPM_SILO_DIR=/path/to/silo
export LBPM_TIMER_DIR=/path/to/timer
export LBPM_NETCDF_DIR=/path/to/netcdf

  1. Create the build directory and navigate to it

mkdir $LBPM_WIA_DIR
cd $LBPM_WIA_DIR

  1. Configure the project. Numerous scripts exist to build LBPM on different HPC clusters, which are available in the $LBPM_SOURCE/sample_scripts/ directory. It is often possible to run these scripts directly if one exists for a system similar to the one you are building on. For a standard CPU build:

cmake                                           \
    -D CMAKE_BUILD_TYPE:STRING=Release          \
    -D CMAKE_C_COMPILER:PATH=mpicc              \
    -D CMAKE_CXX_COMPILER:PATH=mpicxx           \
    -D CMAKE_C_FLAGS="-fPIC"                    \
    -D CMAKE_CXX_FLAGS="-fPIC"                  \
    -D CMAKE_CXX_STD=14                         \
    -D USE_TIMER=0                              \
        -D TIMER_DIRECTORY=$LBPM_TIMER_DIR     \
    -D USE_NETCDF=0                             \
        -D NETCDF_DIRECTORY=$LBPM_NETCDF_DIR   \
    -D USE_SILO=1                               \
       -D HDF5_DIRECTORY=$LBPM_HDF5_DIR         \
       -D SILO_DIRECTORY=$LBPM_SILO_DIR         \
    -D USE_CUDA=0                               \
    $LBPM_SOURCE

For GPU support, it is necessary to have CUDA along with a GPU-aware MPI implementation. Otherwise, the LBPM routines should behave identically irrespective of the underlying hardware.

cmake                                           \
    -D CMAKE_BUILD_TYPE:STRING=Release          \
    -D CMAKE_C_COMPILER:PATH=mpicc              \
    -D CMAKE_CXX_COMPILER:PATH=mpicxx           \
    -D CMAKE_C_FLAGS="-fPIC"                    \
    -D CMAKE_CXX_FLAGS="-fPIC"                  \
    -D CMAKE_CXX_STD=14                         \
    -D USE_TIMER=0                              \
        -D TIMER_DIRECTORY=$LBPM_TIMER_DIR     \
    -D USE_NETCDF=0                             \
        -D NETCDF_DIRECTORY=$LBPM_NETCDF_DIR   \
    -D USE_SILO=1                               \
       -D HDF5_DIRECTORY=$LBPM_HDF5_DIR         \
       -D SILO_DIRECTORY=$LBPM_SILO_DIR         \
    -D USE_CUDA=1                               \
    -D CMAKE_CUDA_FLAGS="-arch sm_70"           \
    $LBPM_SOURCE

  1. Build the project (using four cores to build)

make -j4

  1. Install the project

make install

  1. Run the tests to make sure they execute correctly (on a cluster, it is recommended to run these using the batch system rather than on the head node)

ctest

Sample Scripts

The LBPM repository contains sample scripts showing successful CMake configuration, build and install steps for a range of systems. Refer to the project sub-directory below for these examples.

ls $LBPM_SOURCE/sample_scripts