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.. seealso::

   You will need to understand how to use `the terminal <http://www.ks.uiuc.edu/Training/Tutorials/Reference/unixprimer.html>`_, what are `environment variables <https://unix.stackexchange.com/questions/44990/what-is-the-difference-between-path-and-ld-library-path/45106#45106>`_ and please read our :ref:`compiling introduction <install-source>`.

Note

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

Dependencies

.. sectionauthor:: 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. An Lmod example setup can be found here.

Requirements

Mandatory

gcc
  • 4.9 - 7 (if you want to build for Nvidia GPUs, supported compilers depend on your current CUDA version)
    • CUDA 9.2 - 10.0: Use gcc 4.9 - 7
    • CUDA 10.1: Use gcc 4.9 - 8
  • note: be sure to build all libraries/dependencies with the same gcc version; GCC 5 or newer is recommended
  • Debian/Ubuntu:
    • sudo apt-get install gcc-5.3 g++-5.3 build-essential
    • sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-5.3 60 --slave /usr/bin/g++ g++ /usr/bin/g++-5.3
  • Arch Linux:
  • Spack:
    • spack install gcc@5.3.0
    • make it the default in your packages.yaml or suffix all following spack install commands with a space and %gcc@5.3.0
CMake
  • 3.11.0 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
  • from source:
    • ./configure --prefix=$HOME/lib/zlib
    • make && make install
  • environent: (assumes install from source in $HOME/lib/zlib)
    • export ZLIB_ROOT=$HOME/lib/zlib
    • export LD_LIBRARY_PATH=$ZLIB_ROOT/lib:$LD_LIBRARY_PATH
    • export CMAKE_PREFIX_PATH=$ZLIB_ROOT:$CMAKE_PREFIX_PATH
boost
  • 1.65.1 - 1.70.0 (program_options, filesystem, system, math, serialization and header-only libs, optional: fiber with context, thread, chrono, atomic, date_time)
  • Debian/Ubuntu: sudo apt-get install libboost-program-options-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:
    • curl -Lo boost_1_65_1.tar.gz https://dl.bintray.com/boostorg/release/1.65.1/source/boost_1_65_1.tar.gz
    • tar -xzf boost_1_65_1.tar.gz
    • cd boost_1_65_1
    • ./bootstrap.sh --with-libraries=atomic,chrono,context,date_time,fiber,filesystem,math,program_options,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
alpaka 0.3.4
  • alpaka is included in the PIConGPU source code
cupla 0.1.0
  • cupla is included in the PIConGPU source code
mallocMC 2.3.0crp
  • only required for CUDA backend
  • mallocMC is included in the PIConGPU source code

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 PIC_EXAMPLES=$PICSRC/share/picongpu/examples
    • export PATH=$PICSRC:$PATH
    • export PATH=$PICSRC/bin:$PATH
    • export PATH=$PICSRC/src/tools/bin:$PATH
    • export PYTHONPATH=$PICSRC/lib/python:$PYTHONPATH

Optional Libraries

CUDA
  • 9.2 - 10.1
  • 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_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.

libpng
  • 1.2.9+ (requires zlib)
  • Debian/Ubuntu dependencies: sudo apt-get install libpng-dev
  • Arch Linux dependencies: sudo pacman --sync libpng
  • Spack: spack install libpng
  • from source:
    • mkdir -p ~/src ~/lib
    • cd ~/src
    • curl -Lo libpng-1.6.34.tar.gz ftp://ftp-osl.osuosl.org/pub/libpng/src/libpng16/libpng-1.6.34.tar.gz
    • tar -xf libpng-1.6.34.tar.gz
    • cd libpng-1.6.34
    • CPPFLAGS=-I$HOME/lib/zlib/include LDFLAGS=-L$HOME/lib/zlib/lib ./configure --enable-static --enable-shared --prefix=$HOME/lib/libpng
    • make
    • make install
  • environment: (assumes install from source in $HOME/lib/libpng)
    • export PNG_ROOT=$HOME/lib/libpng
    • export CMAKE_PREFIX_PATH=$PNG_ROOT:$CMAKE_PREFIX_PATH
    • export LD_LIBRARY_PATH=$PNG_ROOT/lib:$LD_LIBRARY_PATH
pngwriter
  • 0.7.0+ (requires libpng, zlib, and optional freetype)
  • Spack: spack install pngwriter
  • from source:
    • 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 $HOME/lib/pngwriter)
    • export CMAKE_PREFIX_PATH=$HOME/lib/pngwriter:$CMAKE_PREFIX_PATH
    • export LD_LIBRARY_PATH=$HOME/lib/pngwriter/lib:$LD_LIBRARY_PATH
libSplash
  • 1.7.0+ (requires HDF5, boost program-options)
  • Debian/Ubuntu dependencies: sudo apt-get install libhdf5-openmpi-dev libboost-program-options-dev
  • Arch Linux dependencies: sudo pacman --sync hdf5-openmpi boost
  • Spack: spack install libsplash ^hdf5~fortran
  • from source:
    • mkdir -p ~/src ~/build ~/lib
    • git clone https://github.com/ComputationalRadiationPhysics/libSplash.git ~/src/splash/
    • cd ~/build && rm -rf ../build/*
    • cmake -DCMAKE_INSTALL_PREFIX=$HOME/lib/splash -DSplash_USE_MPI=ON -DSplash_USE_PARALLEL=ON ~/src/splash
    • make install
  • environment: (assumes install from source in $HOME/lib/splash)
    • export CMAKE_PREFIX_PATH=$HOME/lib/splash:$CMAKE_PREFIX_PATH
    • export LD_LIBRARY_PATH=$HOME/lib/splash/lib:$LD_LIBRARY_PATH
HDF5
  • 1.8.13+
  • standard shared version (no C++, enable parallel)
  • 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 ~/lib
    • cd ~/src
    • download hdf5 source code from release list of the HDF5 group, for example:
    • curl -Lo hdf5-1.8.20.tar.gz https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8/hdf5-1.8.20/src/hdf5-1.8.20.tar.gz
    • tar -xzf hdf5-1.8.20.tar.gz
    • cd hdf5-1.8.20
    • ./configure --enable-parallel --enable-shared --prefix $HOME/lib/hdf5/
    • make
    • optional: make test
    • make install
    • If you encounter errors related to linking MPI during ./configure, you might try setting the compiler manually via ./configure --enable-parallel --enable-shared --prefix $HOME/lib/hdf5/ CC=mpicc CXX=mpic++.
  • 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
  • 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:$PICSRC/src/splash2txt/build
  • options:
    • splash2txt --help
    • list all available datasets: splash2txt --list <FILE_PREFIX>
png2gas
  • requires libSplash, pngwriter and boost program_options)
  • converts png files to hdf5 files that can be used as an input for species initial density profiles
  • compile and install exactly as splash2txt above
c-blosc
  • general purpose compressor, used in ADIOS for in situ data reduction
  • Debian/Ubuntu: sudo apt-get install libblosc-dev
  • Arch Linux: sudo pacman --sync blosc
  • Spack: spack install c-blosc
  • from source:
    • mkdir -p ~/src ~/build ~/lib
    • cd ~/src
    • curl -Lo c-blosc-1.15.0.tar.gz https://github.com/Blosc/c-blosc/archive/v1.15.0.tar.gz
    • tar -xzf c-blosc-1.15.0.tar.gz
    • cd ~/build && rm -rf ../build/*
    • cmake -DCMAKE_INSTALL_PREFIX=$HOME/lib/c-blosc -DPREFER_EXTERNAL_ZLIB=ON ~/src/c-blosc-1.15.0/
    • make
    • make install
  • environment: (assumes install from source in $HOME/lib/c-blosc)
    • export BLOSC_ROOT=$HOME/lib/c-blosc
    • export CMAKE_PREFIX_PATH=$BLOSC_ROOT:$CMAKE_PREFIX_PATH
    • export LD_LIBRARY_PATH=$BLOSC_ROOT/lib:$LD_LIBRARY_PATH
ADIOS
  • 1.13.1+ (requires MPI, zlib and c-blosc)
  • 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 ~/lib
    • cd ~/src
    • curl -Lo adios-1.13.1.tar.gz http://users.nccs.gov/~pnorbert/adios-1.13.1.tar.gz
    • tar -xzf adios-1.13.1.tar.gz
    • cd adios-1.13.1
    • CFLAGS="-fPIC" ./configure --enable-static --enable-shared --prefix=$HOME/lib/adios --with-mpi=$MPI_ROOT --with-zlib=$HOME/lib/zlib --with-blosc=$HOME/lib/c-blosc
    • 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
  • 1.4.0+
  • 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
    • curl -Lo 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 -xzf 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