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¶
Requirements¶
Mandatory¶
gcc¶
5.5 - 10.0 (if you want to build for Nvidia GPUs, supported compilers depend on your current CUDA version)
CUDA 9.2 - 10.0: Use gcc 5.5 - 7
CUDA 10.1/10.2: Use gcc 5.5 - 8
CUDA 11.x: Used gcc 5.5 - 10.0
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 g++-5 build-essential
sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-5 60 --slave /usr/bin/g++ g++ /usr/bin/g++-5
Arch Linux:
sudo pacman --sync base-devel
if the installed version of gcc is too new, compile an older gcc
Spack:
spack install gcc@5.5.0
make it the default in your packages.yaml or suffix all following
spack install
commands with a space and%gcc@5.5.0
CMake¶
3.15.0 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 - 1.74.0 (
program_options
,filesystem
,system
,math
,serialization
and header-only libs, optional:fiber
withcontext
,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
PIConGPU Source Code¶
git clone https://github.com/ComputationalRadiationPhysics/picongpu.git $HOME/src/picongpu
optional: update the source code with
cd $HOME/src/picongpu && git fetch && git pull
optional: change to a different branch with
git branch
(show) andgit checkout <BranchName>
(switch)
environment:
export PICSRC=$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:$PYTHONPATH
Optional Libraries¶
CUDA¶
required if you want to run on Nvidia GPUs
Debian/Ubuntu:
sudo apt-get install nvidia-cuda-toolkit
Arch Linux:
sudo pacman --sync cuda
Spack:
spack install cuda
at least one CUDA capable GPU
compute capability:
sm_30
or higherfull list of CUDA GPUs and their compute capability
More is always better. Especially, if we are talking GPUs :-)
environment:
export CUDA_ROOT=<CUDA_INSTALL>
If you do not install the following libraries, you will not have the full amount of PIConGPU plugins. We recommend to install at least pngwriter and openPMD.
libpng¶
1.2.9+ (requires zlib)
Debian/Ubuntu dependencies:
sudo apt-get install libpng-dev
Arch Linux dependencies:
sudo pacman --sync libpng
Spack:
spack install libpng
from source:
mkdir -p ~/src ~/lib
cd ~/src
curl -Lo libpng-1.6.34.tar.gz ftp://ftp-osl.osuosl.org/pub/libpng/src/libpng16/libpng-1.6.34.tar.gz
tar -xf libpng-1.6.34.tar.gz
cd libpng-1.6.34
CPPFLAGS=-I$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
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
c-blosc¶
general purpose compressor, used in ADIOS2 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
openPMD API¶
0.12.0+ (bare minimum) / 0.13.0+ (for streaming IO)
Spack:
spack install openpmd-api
For usage in PIConGPU, the openPMD API must have been built either with support for ADIOS2 or HDF5 (or both). When building the openPMD API from source (described below), these dependencies must be built and installed first.
For ADIOS2, CMake build instructions can be found in the official documentation. The default configuration should generally be sufficient, the
CMAKE_INSTALL_PREFIX
should be set to a fitting location.For HDF5, CMake build instructions can be found in the official documentation. The parameters
-DHDF5_BUILD_CPP_LIB=OFF -DHDF5_ENABLE_PARALLEL=ON
are required, theCMAKE_INSTALL_PREFIX
should be set to a fitting location.
from source:
mkdir -p ~/src ~/lib
cd ~/src
git clone https://github.com/openPMD/openPMD-api.git
cd openPMD-api
mkdir build && cd build
cmake .. -DopenPMD_USE_MPI=ON -DCMAKE_INSTALL_PREFIX=~/lib/openPMD-api
Optionally, specify the parameters-DopenPMD_USE_ADIOS2=ON -DopenPMD_USE_HDF5=ON
. Otherwise, these parameters are set toON
automatically if CMake detects the dependencies on your system.make -j $(nproc) install
environment:* (assumes install from source in
$HOME/lib/openPMD-api
)export CMAKE_PREFIX_PATH="$HOME/lib/openPMD-api:$CMAKE_PREFIX_PATH"
export LD_LIBRARY_PATH="$HOME/lib/openPMD-api/lib:$LD_LIBRARY_PATH"
If PIConGPU is built with openPMD output enabled, the JSON library nlohmann_json will automatically be used, found in the
thirdParty/
directory. By setting the CMake parameterPIC_nlohmann_json_PROVIDER=extern
, CMake can be instructed to search for an installation of nlohmann_json externally. Refer to LICENSE.md for further information.
ISAAC¶
1.4.0+
requires boost (header only), IceT, Jansson, libjpeg (preferably libjpeg-turbo), libwebsockets (only for the ISAAC server, but not the plugin itself)
enables live in situ visualization, see more here Plugin description
Spack:
spack install isaac
from source: build the in situ library and its dependencies as described in ISAAC’s INSTALL.md
environment: set environment variable
CMAKE_PREFIX_PATH
for each dependency and the ISAAC in situ library
VampirTrace¶
for developers: performance tracing support
download 5.14.4 or higher, e.g. from www.tu-dresden.de
from source:
mkdir -p ~/src ~/build ~/lib
cd ~/src
curl -Lo VampirTrace-5.14.4.tar.gz "http://wwwpub.zih.tu-dresden.de/~mlieber/dcount/dcount.php?package=vampirtrace&get=VampirTrace-5.14.4.tar.gz"
tar -xzf VampirTrace-5.14.4.tar.gz
cd VampirTrace-5.14.4
./configure --prefix=$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