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

Project description

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

Supported openPMD Standard Documentation Status Doxygen Gitter chat Supported Platforms License DOI

Linux/OSX Build Status dev Windows Build Status dev Coverage Status CodeFactor

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++

C++11 C++11 API: Alpha

#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

Python3 Python3 API: Alpha

import openPMD

# ...

series = openPMD.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 3.10.0+
  • C++11 capable compiler, e.g. g++ 4.8+, clang 3.9+, VS 2015+

Shipped internally in share/openPMD/thirdParty/:

Optional I/O backends:

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.X+
    • pybind 2.2.3+
    • numpy

Installation

Spack Package Conda Package

Choose one of the install methods below to get started:

Spack

# optional:               +python ^python@3:
spack install openpmd-api
spack load -r openpmd-api

Conda

Conda Version Conda Downloads

# serial version only
conda install -c conda-forge openpmd-api

From Source

openPMD can then be installed using CMake:

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

mkdir -p 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 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 Enable MPI support
openPMD_USE_HDF5 AUTO/ON/OFF Enable support for HDF5
openPMD_USE_ADIOS1 AUTO/ON/OFF Enable support for ADIOS1
openPMD_USE_ADIOS2 AUTO/ON/OFF Enable support for ADIOS2 1
openPMD_USE_PYTHON AUTO/ON/OFF Enable Python bindings
openPMD_USE_INVASIVE_TESTS AUTO/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. C++ keywords, currently disabled only for 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 1.3.0+
openPMD_USE_INTERNAL_CATCH ON/OFF Catch2 2.2.1+
openPMD_USE_INTERNAL_PYBIND11 ON/OFF pybind11 2.2.3+

By default, this will build as a static library (libopenPMD.a) and installs also its headers. In order to build a static library, append -DBUILD_SHARED_LIBS=ON 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 Config.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 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)

Project details


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