openPMD-api 0.9.0a1

C++ & Python API for Scientific I/O with openPMD

C++ & Python API for Scientific I/O with openPMD

This library provides a high-level API for writing and reading scientific data according to openPMD. It allows to build logical file structures which drive scientific I/O libraries such as HDF5 and ADIOS through a common, intuitive interface. Where supported, openPMD-api implements both serial and MPI parallel I/O capabilities.

Usage

C++

#include <openPMD/openPMD.hpp>
#include <iostream>

// ...

auto s = openPMD::Series("samples/git-sample/data%T.h5", openPMD::AccessType::READ_ONLY);

for( auto const& i : s.iterations ) {
    std::cout << "Iteration: " << i.first << "\n";

    for( auto const& m : i.second.meshes ) {
        std::cout << "  Mesh '" << m.first << "' attributes:\n";
        for( auto const& val : m.second.attributes() )
            std::cout << "    " << val << '\n';
    }

    for( auto const& p : i.second.particles ) {
        std::cout << "  Particle species '" << p.first << "' attributes:\n";
        for( auto const& val : p.second.attributes() )
            std::cout << "    " << val << '\n';
    }
}

Python

import openpmd_api

# ...

series = openpmd_api.Series("samples/git-sample/data%T.h5", openPMD.Access_Type.read_only)

for k_i, i in series.iterations.items():
    print("Iteration: {0}".format(k_i))

    for k_m, m in i.meshes.items():
        print("  Mesh '{0}' attributes:".format(k_m))
        for a in m.attributes:
            print("    {0}".format(a))

    for k_p, p in i.particles.items():
        print("  Particle species '{0}' attributes:".format(k_p))
        for a in p.attributes:
            print("    {0}".format(a))

More!

Curious? Our manual shows full read & write examples, both serial and MPI-parallel!

Dependencies

Required:

• CMake 3.11.0+
• C++11 capable compiler, e.g. g++ 4.8+, clang 3.9+, VS 2015+

Shipped internally in share/openPMD/thirdParty/:

• MPark.Variant 1.4.0+ (BSL-1.0)
• Catch2 2.6.1+ (BSL-1.0)
• pybind11 2.3.0+ (new BSD)
• NLohmann-JSON 3.5.0+ (MIT)

Optional I/O backends:

• JSON
• HDF5 1.8.13+
• ADIOS1 1.13.1+
• ADIOS2 2.4.0+ (not yet implemented)

while those can be built either with or without:

• MPI 2.1+, e.g. OpenMPI 1.6.5+ or MPICH2

Optional language bindings:

• Python:
  • Python 3.5 - 3.7
  • pybind 2.3.0+
  • numpy 1.15+
  • mpi4py 2.1+

Installation

Choose one of the install methods below to get started:

Spack

# optional:               +python +adios1 -mpi
spack install openpmd-api
spack load -r openpmd-api

Conda

# optional:            OpenMPI support  =*=mpi_openmpi*
# optional:              MPICH support  =*=mpi_mpich*
conda install -c conda-forge openpmd-api

PyPI

Behind the scenes, this install method compiles from source against the found installations of HDF5, ADIOS and/or MPI (in system paths, from other package managers, or loaded via a module system, ...). The current status for this install method is experimental. Please feel free to report how this works for you.

# optional:             --user
pip install openpmd-api

or with MPI support:

# optional:                                                  --user
openPMD_USE_MPI=ON pip install openpmd-api --no-binary :all:

From Source

openPMD can then be installed using CMake:

git clone https://github.com/openPMD/openPMD-api.git

mkdir openPMD-api-build
cd openPMD-api-build

# optional: for full tests, with unzip
../openPMD-api/.travis/download_samples.sh

# for own install prefix append:
#   -DCMAKE_INSTALL_PREFIX=$HOME/somepath
# for options append:
#   -DopenPMD_USE_...=...
# e.g. for python support add:
#   -DopenPMD_USE_PYTHON=ON -DPYTHON_EXECUTABLE=$(which python)
cmake ../openPMD-api

cmake --build .

# optional
ctest

# sudo might be required for system paths
cmake --build . --target install

The following options can be added to the cmake call to control features. CMake controls options with prefixed -D, e.g. -DopenPMD_USE_MPI=OFF:

CMake Option	Values	Description
openPMD_USE_MPI	AUTO/ON/OFF	Parallel, Multi-Node I/O for clusters
openPMD_USE_JSON	AUTO/ON/OFF	JSON backend (.json files)
openPMD_USE_HDF5	AUTO/ON/OFF	HDF5 backend (.h5 files)
openPMD_USE_ADIOS1	AUTO/ON/OFF	ADIOS1 backend (.bp files)
openPMD_USE_ADIOS2	AUTO/ON/OFF	ADIOS2 backend (.bp files) 1
openPMD_USE_PYTHON	AUTO/ON/OFF	Enable Python bindings
openPMD_USE_INVASIVE_TESTS	ON/OFF	Enable unit tests that modify source code 2
openPMD_USE_VERIFY	ON/OFF	Enable internal VERIFY (assert) macro independent of build type 3
PYTHON_EXECUTABLE	(first found)	Path to Python executable

¹ not yet implemented ² e.g. changes C++ visibility keywords, breaks MSVC ³ this includes most pre-/post-condition checks, disabling without specific cause is highly discouraged

Additionally, the following libraries are shipped internally. The following options allow to switch to external installs:

CMake Option	Values	Library	Version
openPMD_USE_INTERNAL_VARIANT	ON/OFF	MPark.Variant	1.4.0+
openPMD_USE_INTERNAL_CATCH	ON/OFF	Catch2	2.6.1+
openPMD_USE_INTERNAL_PYBIND11	ON/OFF	pybind11	2.3.0+
openPMD_USE_INTERNAL_JSON	ON/OFF	NLohmann-JSON	3.5.0+

By default, this will build as a shared library (libopenPMD.[so|dylib|dll]) and installs also its headers. In order to build a static library, append -DBUILD_SHARED_LIBS=OFF to the cmake command. You can only build a static or a shared library at a time.

By default, the Release version is built. In order to build with debug symbols, pass -DCMAKE_BUILD_TYPE=Debug to your cmake command.

By default, tests and examples are built. In order to skip building those, pass -DBUILD_TESTING=OFF or -DBUILD_EXAMPLES to your cmake command.

Linking to your project

The install will contain header files and libraries in the path set with -DCMAKE_INSTALL_PREFIX.

CMake

If your project is using CMake for its build, one can conveniently use our provided openPMDConfig.cmake package which is installed alongside the library.

First set the following environment hint if openPMD-api was not installed in a system path:

# optional: only needed if installed outside of system paths
export CMAKE_PREFIX_PATH=$HOME/somepath:$CMAKE_PREFIX_PATH

Use the following lines in your project's CMakeLists.txt:

# supports:                       COMPONENTS MPI NOMPI JSON HDF5 ADIOS1 ADIOS2
find_package(openPMD 0.1.0 CONFIG)

if(openPMD_FOUND)
    target_link_libraries(YourTarget PRIVATE openPMD::openPMD)
endif()

Alternatively, add the openPMD-api repository source directly to your project and use it via:

add_subdirectory("path/to/source/of/openPMD-api")

target_link_libraries(YourTarget PRIVATE openPMD::openPMD)

Manually

If your (Linux/OSX) project is build by calling the compiler directly or uses a manually written Makefile, consider using our openPMD.pc helper file for pkg-config which are installed alongside the library.

First set the following environment hint if openPMD-api was not installed in a system path:

# optional: only needed if installed outside of system paths
export PKG_CONFIG_PATH=$HOME/somepath/lib/pkgconfig:$PKG_CONFIG_PATH

Additional linker and compiler flags for your project are available via:

pkg-config --libs openPMD
# -L${HOME}/somepath/lib -lopenPMD

# if you build openPMD-api as static library with `-DBUILD_SHARED_LIBS=OFF`
pkg-config --libs --static openPMD
# -L/usr/local/lib -L/usr/lib/x86_64-linux-gnu/openmpi/lib -lopenPMD -pthread /usr/lib/libmpi.so -pthread /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/libmpi.so /usr/lib/x86_64-linux-gnu/hdf5/openmpi/libhdf5.so /usr/lib/x86_64-linux-gnu/libsz.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libdl.so /usr/lib/x86_64-linux-gnu/libm.so -pthread /usr/lib/libmpi.so -pthread /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/libmpi.so

pkg-config --cflags openPMD
# -I${HOME}/somepath/include