Dependencies¶

Section author: Axel Huebl

Overview¶

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 10.1/10.2: 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:
- sudo pacman --sync base-devel
- if the installed version of gcc is too new, compile an older gcc
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¶

3.11.4 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 0.4.0¶

alpaka is included in the PIConGPU source code

cupla 0.2.0¶

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 - 10.2
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