See also

You will need to understand how to use the terminal, what are environment variables and please read our compiling introduction.

Note

If you are a scientific user at a supercomputing facility we might have already prepared a software setup for you. See the following chapter if you can skip this step fully or in part by loading existing modules on those systems.

Dependencies

Section author: Axel Huebl

Overview

overview of PIConGPU library dependencies

Overview of inter-library dependencies for parallel execution of PIConGPU on a typical HPC system. Due to common binary incompatibilities between compilers, MPI and boost versions, we recommend to organize software with a version-aware package manager such as spack and to deploy a hierarchical module system such as lmod. A Lmod example setup can be found here.

Requirements

Mandatory

gcc

  • 4.9 to 5.X (depends on your current CUDA version)
  • note: be sure to build all libraries/dependencies with the same gcc version
  • Debian/Ubuntu:
    • sudo apt-get install gcc-4.9 g++-4.9 build-essential
    • sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-4.9 60 --slave /usr/bin/g++ g++ /usr/bin/g++-4.9
  • Arch Linux:
  • Spack:
    • spack install gcc@4.9.4
    • make it the default in your packages.yaml or suffix all following spack install commands with a space and %gcc@4.9.4

CMake

  • 3.7.0 or higher
  • Debian/Ubuntu: sudo apt-get install cmake file cmake-curses-gui
  • Arch Linux: sudo pacman --sync cmake
  • Spack: spack install cmake

MPI 2.3+

  • OpenMPI 1.7+ / MVAPICH2 1.8+ or similar
  • for running on Nvidia GPUs, perform a GPU aware MPI install after installing CUDA
  • Debian/Ubuntu: sudo apt-get install libopenmpi-dev
  • Arch Linux: sudo pacman --sync openmpi
  • Spack:
    • GPU support: spack install openmpi+cuda
    • CPU only: spack install openmpi
  • environment:
    • export MPI_ROOT=<MPI_INSTALL>
    • as long as CUDA awareness (openmpi+cuda) is missing: export OMPI_MCA_mpi_leave_pinned=0

zlib

  • Debian/Ubuntu: sudo apt-get install zlib1g-dev
  • Arch Linux: sudo pacman --sync zlib
  • Spack: spack install zlib

boost

  • 1.62.0-1.64.0 (program_options, regex , filesystem, system, math, serialization and header-only libs, optional: fiber with context, thread, chrono, atomic, date_time)
  • download from http://www.boost.org
  • Debian/Ubuntu: sudo apt-get install libboost-program-options-dev libboost-regex-dev libboost-filesystem-dev libboost-system-dev libboost-thread-dev libboost-chrono-dev libboost-atomic-dev libboost-date-time-dev libboost-math-dev libboost-serialization-dev libboost-fiber-dev libboost-context-dev
  • Arch Linux: sudo pacman --sync boost
  • Spack: spack install boost
  • from source:
    • ./bootstrap.sh --with-libraries=atomic,chrono,context,date_time,fiber,filesystem,math,program_options,regex,serialization,system,thread --prefix=$HOME/lib/boost
    • ./b2 cxxflags="-std=c++11" -j4 && ./b2 install
  • environment: (assumes install from source in $HOME/lib/boost)
    • export BOOST_ROOT=$HOME/lib/boost
    • export LD_LIBRARY_PATH=$BOOST_ROOT/lib:$LD_LIBRARY_PATH

git

  • 1.7.9.5 or higher
  • Debian/Ubuntu: sudo apt-get install git
  • Arch Linux: sudo pacman --sync git
  • Spack: spack install git

rsync

  • Debian/Ubuntu: sudo apt-get install rsync
  • Arch Linux: sudo pacman --sync rsync
  • Spack: spack install rsync

PIConGPU Source Code

  • git clone https://github.com/ComputationalRadiationPhysics/picongpu.git $HOME/src/picongpu
    • optional: update the source code with cd $HOME/src/picongpu && git fetch && git pull
    • optional: change to a different branch with git branch (show) and git checkout <BranchName> (switch)
  • environment:
    • export PICSRC=$PICHOME/src/picongpu
    • export PATH=$PICSRC:$PATH
    • export PATH=$PICSRC/src/tools/bin:$PATH
    • export PYTHONPATH=$PICSRC/lib/python:$PYTHONPATH

Optional Libraries

CUDA

  • 7.5+
  • required if you want to run on Nvidia GPUs
  • Debian/Ubuntu: sudo apt-get install nvidia-cuda-toolkit
  • Arch Linux: sudo pacman --sync cuda
  • Spack: spack install cuda
  • at least one CUDA capable GPU
  • compute capability: sm_20 or higher (for CUDA 9+: sm_30 or higher)
  • full list of CUDA GPUs and their compute capability
  • More is always better. Especially, if we are talking GPUs :-)
  • environment:
    • export CUDA_ROOT=<CUDA_INSTALL>

If you do not install the following libraries, you will not have the full amount of PIConGPU plugins. We recommend to install at least pngwriter and either libSplash (+ HDF5) or ADIOS.

pngwriter

  • 0.5.6+
  • Spack: spack install pngwriter
  • from source:
    • download our modified version from github.com/pngwriter/pngwriter
    • Requires [libpng](http://www.libpng.org/)
      • Debian/Ubuntu: sudo apt-get install libpng-dev
      • Arch Linux: sudo pacman --sync libpng
    • example:
      • mkdir -p ~/src ~/build ~/lib
      • git clone https://github.com/pngwriter/pngwriter.git ~/src/pngwriter/
      • cd ~/build
      • cmake -DCMAKE_INSTALL_PREFIX=$HOME/lib/pngwriter ~/src/pngwriter
      • make install
    • environment: (assumes install from source in $HOME/lib/pngwriter)
      • export PNGWRITER_ROOT=$HOME/lib/pngwriter
      • export LD_LIBRARY_PATH=$PNGWRITER_ROOT/lib:$LD_LIBRARY_PATH

libSplash

  • 1.6.0+ (requires HDF5, boost program-options)
  • Debian/Ubuntu dependencies: sudo apt-get install libhdf5-openmpi-dev libboost-program-options-dev
  • Arch Linux dependencies: sudo pacman --sync hdf5-openmpi boost
  • Spack: spack install libsplash ^hdf5~fortran
  • from source:
    • mkdir -p ~/src ~/build ~/lib
    • git clone https://github.com/ComputationalRadiationPhysics/libSplash.git ~/src/splash/
    • cd ~/build
    • cmake -DCMAKE_INSTALL_PREFIX=$HOME/lib/splash ~/src/splash
    • make install
  • environment: (assumes install from source in $HOME/lib/splash)
    • export SPLASH_ROOT=$HOME/lib/splash
    • export LD_LIBRARY_PATH=$SPLASH_ROOT/lib:$LD_LIBRARY_PATH

HDF5

  • 1.8.6+
  • standard shared version (no c++, enable parallel), e.g. hdf5/1.8.5-threadsafe
  • Debian/Ubuntu: sudo apt-get install libhdf5-openmpi-dev
  • Arch Linux: sudo pacman --sync hdf5-openmpi
  • Spack: spack install hdf5~fortran
  • from source:
    • mkdir -p ~/src ~/build ~/lib
    • cd ~/src
    • download hdf5 source code from release list of the HDF5 group, for example:
    • wget https://www.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8.14/src/hdf5-1.8.14.tar.gz
    • tar -xvzf hdf5-1.8.14.tar.gz
    • cd hdf5-1.8.14
    • ./configure --enable-parallel --enable-shared --prefix $HOME/lib/hdf5/
    • make
    • optional: make test
    • make install
  • environment: (assumes install from source in $HOME/lib/hdf5)
    • export HDF5_ROOT=$HOME/lib/hdf5
    • export LD_LIBRARY_PATH=$HDF5_ROOT/lib:$LD_LIBRARY_PATH

splash2txt

  • requires libSplash and boost program_options, regex
  • converts slices in dumped hdf5 files to plain txt matrices
  • assume you [downloaded](#requirements) PIConGPU to PICSRC=$HOME/src/picongpu
  • mkdir -p ~/build && cd ~/build
  • cmake -DCMAKE_INSTALL_PREFIX=$PICSRC/src/tools/bin $PICSRC/src/tools/splash2txt
  • make
  • make install
  • environment:
    • export PATH=$PATH:$PICSRC/src/splash2txt/build
  • options:
    • splash2txt --help
    • list all available datasets: splash2txt --list <FILE_PREFIX>

png2gas

  • requires libSplash, pngwriter and boost program_options)
  • converts png files to hdf5 files that can be used as an input for a species initial density profiles
  • compile and install exactly as splash2txt above

ADIOS

  • 1.10.0+ (requires MPI and zlib)
  • Debian/Ubuntu: sudo apt-get install libadios-dev libadios-bin
  • Arch Linux using an AUR helper: pacaur --sync libadios
  • Arch Linux using the AUR manually:
    • sudo pacman --sync --needed base-devel
    • git clone https://aur.archlinux.org/libadios.git
    • cd libadios
    • makepkg -sri
  • Spack: spack install adios
  • from source:
    • mkdir -p ~/src ~/build ~/lib
    • cd ~/src
    • wget http://users.nccs.gov/~pnorbert/adios-1.10.0.tar.gz
    • tar -xvzf adios-1.10.0.tar.gz
    • cd adios-1.10.0
    • CFLAGS="-fPIC" ./configure --enable-static --enable-shared --prefix=$HOME/lib/adios --with-mpi=$MPI_ROOT --with-zlib=/usr
    • make
    • make install
  • environment: (assumes install from source in $HOME/lib/adios)
    • export ADIOS_ROOT=$HOME/lib/adios
    • export LD_LIBRARY_PATH=$ADIOS_ROOT/lib:$LD_LIBRARY_PATH

ISAAC

  • 1.3.0+
  • requires boost (header only), IceT, Jansson, libjpeg (preferably libjpeg-turbo), libwebsockets (only for the ISAAC server, but not the plugin itself)
  • enables live in situ visualization, see more here Plugin description
  • Spack: spack install isaac
  • from source: build the in situ library and its dependencies as described in ISAAC’s INSTALL.md
  • environment: set environment variable CMAKE_PREFIX_PATH for each dependency and the ISAAC in situ library

VampirTrace

  • for developers: performance tracing support
  • download 5.14.4 or higher, e.g. from www.tu-dresden.de
  • from source:
    • mkdir -p ~/src ~/build ~/lib
    • cd ~/src
    • wget -O VampirTrace-5.14.4.tar.gz "http://wwwpub.zih.tu-dresden.de/~mlieber/dcount/dcount.php?package=vampirtrace&get=VampirTrace-5.14.4.tar.gz"
    • tar -xvzf VampirTrace-5.14.4.tar.gz
    • cd VampirTrace-5.14.4
    • ./configure --prefix=$HOME/lib/vampirtrace --with-cuda-dir=<CUDA_ROOT>
    • make all -j
    • make install
  • environment: (assumes install from source in $HOME/lib/vampirtrace)
    • export VT_ROOT=$HOME/lib/vampirtrace
    • export PATH=$VT_ROOT/bin:$PATH