Prerequisites/Dependencies

library	licence	usage	link
GNU	GPLv3+	compiler	gnu.org
OpenMPI	BSD 3-Clause	compiler, MPI Implementation	open-mpi.org
CUDA	CUDA Toolkit End User License Agreement	compiler, CUDA Toolkit and API	developer.nvidia.com
CUDA cub	BSD 3-Clause "New" or "Revised" License	device wide parallel primitives	github.com/NVIDIA/cub
HDF5	HDF5 License (BSD-Style)	parallel HDF5 for I/O operations	hdf5group.org
HighFive	Boost Software License 1.0	C++ wrapper for parallel HDF5	github.com/BlueBrain/HighFive
Boost	Boost Software License 1.0	config file parsing, C++ wrapper for MPI	boost.org
cxxopts	MIT license	command line argument parsing	github.com/jarro2783/cxxopts
libconfig	LGPL-2.1	material config parsing	github.io/libconfig

• in general there is no need for the usage of the GNU compiler and OpenMPI as MPI implementation, as long as a proper C++ compiler as well as MPI implementation (CUDA-aware) are available and corresponding changes in the Makefile are done

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Installing/Building the dependencies

MPI implementation

‍Multiple MPI implementations exist and can be used to execute milupHPC. However, the code was primarily tested with OpenMPI >= 4.0.

OpenMPI

library	licence	usage	link
OpenMPI	BSD 3-Clause	compiler, MPI Implementation	open-mpi.org

see also MPI_Versions.md

• if either MPI is not available or MPI is not CUDA-aware
  • e.g. via ompi_info -a | grep "\-with\-cuda"
• build, see e.g.
  • Building Open MPI
  • Building CUDA-aware Open MPI
  • UCX OpenMPI installation

Boost

library	licence	usage	link
Boost	Boost Software License 1.0	config file parsing, C++ wrapper for MPI	boost.org

• <boost version> e.g. 1_78_0

$ wget https://boostorg.jfrog.io/artifactory/main/release/1.78.0/source/boost_<boost version>.tar.gz
$ tar zxvf boost_<boost version>.tar.gz
$ cd boost_<boost version>
$ ./bootstrap.sh --with-libraries=all
$ vim project-config.jam
$ >> using mpi ;
$ ./b2
$ ./b2 install --prefix=/usr

HighFive

library	licence	usage	link
HighFive	Boost Software License 1.0	C++ wrapper for parallel HDF5	github.com/BlueBrain/HighFive

• git clone https://github.com/BlueBrain/HighFive.git

CUDA cub

• included in the CUDA Toolkit since CUDA 11.0

library	licence	usage	link
CUDA cub	BSD 3-Clause "New" or "Revised" License	device wide parallel primitives	github.com/NVIDIA/cub

• git clone https://github.com/NVIDIA/cub.git
  • in dependence of used CUDA Toolkit e.g. git checkout 1.8.0

Cxxopts

library	licence	usage	link
cxxopts	MIT license	command line argument parsing	github.com/jarro2783/cxxopts

• git clone https://github.com/jarro2783/cxxopts.git

libconfig

library	licence	usage	link
libconfig	LGPL-2.1	material config parsing	github.io/libconfig

• <libconfig version> e.g. 1.7.3

$ wget http://hyperrealm.github.io/libconfig/dist/libconfig-<libconfig version>.tar.gz
$ tar zxvf libconfig-<libconfig version>.tar.gz
$ ./configure --prefix=/usr
$ make
$ make install

HDF5

library	licence	usage	link
HDF5	HDF5 License (BSD-Style)	parallel HDF5 for I/O operations	hdf5group.org

• refer to realease_docs and build parallel

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Postprocessing

For postprocessing purposes several scripts are available. Some of those scripts require the following.

Python

• Python: realpython.com/installing-python
  • and packages: numpy, matplotlib, ...

ffmpeg

$ sudo wget https://johnvansickle.com/ffmpeg/releases/ffmpeg-release-amd64-static.tar.xz
$ sudo wget https://johnvansickle.com/ffmpeg/releases/ffmpeg-release-amd64-static.tar.xz.md5
$ md5sum -c ffmpeg-release-amd64-static.tar.xz.md5
$ sudo tar xvf ffmpeg*.xz
$ cd ffmpeg-*-static
$ sudo ln -s "${PWD}/ffmpeg" /usr/local/bin/
$ sudo ln -s "${PWD}/ffprobe" /usr/local/bin/