{ "info": { "author": "Fabian Koller, Franz Poeschel, Axel Huebl", "author_email": "f.koller@hzdr.de, f.poeschel@hzdr.de, a.huebl@hzdr.de", "bugtrack_url": null, "classifiers": [ "Development Status :: 3 - Alpha", "Environment :: Console", "Intended Audience :: Science/Research", "License :: OSI Approved :: GNU Lesser General Public License v3 or later (LGPLv3+)", "Natural Language :: English", "Operating System :: OS Independent", "Programming Language :: C++", "Programming Language :: Python :: 3", "Programming Language :: Python :: 3.5", "Programming Language :: Python :: 3.6", "Programming Language :: Python :: 3.7", "Topic :: Database :: Front-Ends", "Topic :: Scientific/Engineering" ], "description": "C++ & Python API for Scientific I/O with openPMD\n================================================\n\n[![Supported openPMD Standard](https://img.shields.io/badge/openPMD-1.0.0--1.1.0-blue.svg)](https://github.com/openPMD/openPMD-standard/releases)\n[![Documentation Status](https://readthedocs.org/projects/openpmd-api/badge/?version=latest)](https://openpmd-api.readthedocs.io/en/latest/?badge=latest)\n[![Doxygen](https://img.shields.io/badge/API-Doxygen-blue.svg)](https://www.openpmd.org/openPMD-api)\n[![Gitter chat](https://img.shields.io/gitter/room/openPMD/API.svg)](https://gitter.im/openPMD/API)\n![Supported Platforms][api-platforms]\n[![License](https://img.shields.io/badge/license-LGPLv3-blue.svg)](https://www.gnu.org/licenses/lgpl-3.0.html)\n[![DOI](https://rodare.hzdr.de/badge/DOI/10.14278/rodare.27.svg)](https://doi.org/10.14278/rodare.27)\n\n[![Linux/OSX Build Status dev](https://img.shields.io/travis/openPMD/openPMD-api/dev.svg?label=dev)](https://travis-ci.org/openPMD/openPMD-api/branches)\n[![Windows Build Status dev](https://ci.appveyor.com/api/projects/status/x95q4n620pqk0e0t/branch/dev?svg=true)](https://ci.appveyor.com/project/ax3l/openpmd-api/branch/dev)\n[![Coverity Scan Build Status](https://scan.coverity.com/projects/17602/badge.svg)](https://scan.coverity.com/projects/openpmd-openpmd-api)\n[![Coverage Status](https://coveralls.io/repos/github/openPMD/openPMD-api/badge.svg)](https://coveralls.io/github/openPMD/openPMD-api)\n[![CodeFactor](https://www.codefactor.io/repository/github/openpmd/openpmd-api/badge)](https://www.codefactor.io/repository/github/openpmd/openpmd-api)\n\n[api-platforms]: https://img.shields.io/badge/platforms-linux%20|%20osx%20|%20win-blue.svg \"Supported Platforms\"\n\nThis library provides a high-level API for writing and reading scientific data according to [openPMD](https://www.openpmd.org/).\nIt allows to build logical file structures which drive scientific I/O libraries such as HDF5 and ADIOS through a common, intuitive interface.\nWhere supported, openPMD-api implements both serial and MPI parallel I/O capabilities.\n\n## Usage\n\n### C++\n\n[![C++11][api-cpp]](https://isocpp.org/) ![C++11 API: Alpha][dev-alpha]\n\n[api-cpp]: https://img.shields.io/badge/language-C%2B%2B11-yellowgreen.svg \"C++11 API\"\n[dev-alpha]: https://img.shields.io/badge/phase-alpha-yellowgreen.svg \"Status: Alpha\"\n\n```cpp\n#include \n#include \n\n// ...\n\nauto s = openPMD::Series(\"samples/git-sample/data%T.h5\", openPMD::AccessType::READ_ONLY);\n\nfor( auto const& i : s.iterations ) {\n std::cout << \"Iteration: \" << i.first << \"\\n\";\n\n for( auto const& m : i.second.meshes ) {\n std::cout << \" Mesh '\" << m.first << \"' attributes:\\n\";\n for( auto const& val : m.second.attributes() )\n std::cout << \" \" << val << '\\n';\n }\n\n for( auto const& p : i.second.particles ) {\n std::cout << \" Particle species '\" << p.first << \"' attributes:\\n\";\n for( auto const& val : p.second.attributes() )\n std::cout << \" \" << val << '\\n';\n }\n}\n```\n\n### Python\n\n[![Python3][api-py3]](https://www.python.org/) ![Python3 API: Alpha][dev-alpha]\n\n[api-py3]: https://img.shields.io/badge/language-Python3-yellowgreen.svg \"Python3 API\"\n\n\n```py\nimport openpmd_api\n\n# ...\n\nseries = openpmd_api.Series(\"samples/git-sample/data%T.h5\", openPMD.Access_Type.read_only)\n\nfor k_i, i in series.iterations.items():\n print(\"Iteration: {0}\".format(k_i))\n\n for k_m, m in i.meshes.items():\n print(\" Mesh '{0}' attributes:\".format(k_m))\n for a in m.attributes:\n print(\" {0}\".format(a))\n\n for k_p, p in i.particles.items():\n print(\" Particle species '{0}' attributes:\".format(k_p))\n for a in p.attributes:\n print(\" {0}\".format(a))\n```\n\n### More!\n\nCurious?\nOur manual shows full [read & write examples](https://openpmd-api.readthedocs.io/en/latest/usage/firstwrite.html), both serial and MPI-parallel!\n\n## Dependencies\n\nRequired:\n* CMake 3.11.0+\n* C++11 capable compiler, e.g. g++ 4.8+, clang 3.9+, VS 2015+\n\nShipped internally in `share/openPMD/thirdParty/`:\n* [MPark.Variant](https://github.com/mpark/variant) 1.4.0+ ([BSL-1.0](https://github.com/mpark/variant/blob/master/LICENSE.md))\n* [Catch2](https://github.com/catchorg/Catch2) 2.6.1+ ([BSL-1.0](https://github.com/catchorg/Catch2/blob/master/LICENSE.txt))\n* [pybind11](https://github.com/pybind/pybind11) 2.3.0+ ([new BSD](https://github.com/pybind/pybind11/blob/master/LICENSE))\n* [NLohmann-JSON](https://github.com/nlohmann/json) 3.5.0+ ([MIT](https://github.com/nlohmann/json/blob/develop/LICENSE.MIT))\n\nOptional I/O backends:\n* [JSON](https://en.wikipedia.org/wiki/JSON)\n* [HDF5](https://support.hdfgroup.org/HDF5) 1.8.13+\n* [ADIOS1](https://www.olcf.ornl.gov/center-projects/adios) 1.13.1+\n* [ADIOS2](https://github.com/ornladios/ADIOS2) 2.4.0+ (*not yet implemented*)\n\nwhile those can be built either with or without:\n* MPI 2.1+, e.g. OpenMPI 1.6.5+ or MPICH2\n\nOptional language bindings:\n* Python:\n * Python 3.5 - 3.7\n * pybind 2.3.0+\n * numpy 1.15+\n * mpi4py 2.1+\n\n## Installation\n\n[![Spack Package](https://img.shields.io/badge/spack.io-openpmd--api-brightgreen.svg)](https://spack.readthedocs.io/en/latest/package_list.html#openpmd-api)\n[![Conda Package](https://img.shields.io/badge/conda.io-openpmd--api-brightgreen.svg)](https://anaconda.org/conda-forge/openpmd-api)\n[![PyPI Package](https://img.shields.io/badge/pypi.org-openpmd--api-yellow.svg)](https://pypi.org/project/openPMD-api)\n[![From Source](https://img.shields.io/badge/from_source-CMake-brightgreen.svg)](https://cmake.org)\n\nChoose *one* of the install methods below to get started:\n\n### [Spack](https://spack.io)\n\n[![Spack Version](https://img.shields.io/spack/v/openpmd-api.svg)](https://spack.readthedocs.io/en/latest/package_list.html#openpmd-api)\n[![Spack Status](https://img.shields.io/badge/method-recommended-brightgreen.svg)](https://spack.readthedocs.io/en/latest/package_list.html#openpmd-api)\n\n```bash\n# optional: +python +adios1 -mpi\nspack install openpmd-api\nspack load -r openpmd-api\n```\n\n### [Conda](https://conda.io)\n\n[![Conda Version](https://img.shields.io/conda/vn/conda-forge/openpmd-api.svg)](https://anaconda.org/conda-forge/openpmd-api)\n[![Conda Status](https://img.shields.io/badge/method-recommended-brightgreen.svg)](https://anaconda.org/conda-forge/openpmd-api)\n[![Conda Downloads](https://img.shields.io/conda/dn/conda-forge/openpmd-api.svg)](https://anaconda.org/conda-forge/openpmd-api)\n\n```bash\n# optional: OpenMPI support =*=mpi_openmpi*\n# optional: MPICH support =*=mpi_mpich*\nconda install -c conda-forge openpmd-api\n```\n\n### [PyPI](https://pypi.org)\n\n[![PyPI Version](https://img.shields.io/pypi/v/openPMD-api.svg)](https://pypi.org/project/openPMD-api)\n[![PyPI Format](https://img.shields.io/pypi/format/openPMD-api.svg)](https://pypi.org/project/openPMD-api)\n[![PyPI Status](https://img.shields.io/badge/method-experimental-yellow.svg)](https://pypi.org/project/openPMD-api)\n[![PyPI Downloads](https://img.shields.io/pypi/dm/openPMD-api.svg)](https://pypi.org/project/openPMD-api)\n\nBehind 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, ...).\nThe current status for this install method is *experimental*.\nPlease feel free to [report](https://github.com/openPMD/openPMD-api/issues/new/choose) how this works for you.\n\n```bash\n# optional: --user\npip install openpmd-api\n```\n\nor with MPI support:\n```bash\n# optional: --user\nopenPMD_USE_MPI=ON pip install openpmd-api --no-binary :all:\n```\n\n### From Source\n\n[![Source Status](https://img.shields.io/badge/method-advanced-brightgreen.svg)](https://cmake.org)\n\nopenPMD can then be installed using [CMake](https://cmake.org/):\n\n```bash\ngit clone https://github.com/openPMD/openPMD-api.git\n\nmkdir openPMD-api-build\ncd openPMD-api-build\n\n# optional: for full tests, with unzip\n../openPMD-api/.travis/download_samples.sh\n\n# for own install prefix append:\n# -DCMAKE_INSTALL_PREFIX=$HOME/somepath\n# for options append:\n# -DopenPMD_USE_...=...\n# e.g. for python support add:\n# -DopenPMD_USE_PYTHON=ON -DPYTHON_EXECUTABLE=$(which python)\ncmake ../openPMD-api\n\ncmake --build .\n\n# optional\nctest\n\n# sudo might be required for system paths\ncmake --build . --target install\n```\n\nThe following options can be added to the `cmake` call to control features.\nCMake controls options with prefixed `-D`, e.g. `-DopenPMD_USE_MPI=OFF`:\n\n| CMake Option | Values | Description |\n|------------------------------|------------------|------------------------------------------------------------------------------|\n| `openPMD_USE_MPI` | **AUTO**/ON/OFF | Parallel, Multi-Node I/O for clusters |\n| `openPMD_USE_JSON` | **AUTO**/ON/OFF | JSON backend (`.json` files) |\n| `openPMD_USE_HDF5` | **AUTO**/ON/OFF | HDF5 backend (`.h5` files) |\n| `openPMD_USE_ADIOS1` | **AUTO**/ON/OFF | ADIOS1 backend (`.bp` files) |\n| `openPMD_USE_ADIOS2` | AUTO/ON/**OFF** | ADIOS2 backend (`.bp` files) 1 |\n| `openPMD_USE_PYTHON` | **AUTO**/ON/OFF | Enable Python bindings |\n| `openPMD_USE_INVASIVE_TESTS` | ON/**OFF** | Enable unit tests that modify source code 2 |\n| `openPMD_USE_VERIFY` | **ON**/OFF | Enable internal VERIFY (assert) macro independent of build type 3 |\n| `PYTHON_EXECUTABLE` | (first found) | Path to Python executable |\n\n1 *not yet implemented*\n2 *e.g. changes C++ visibility keywords, breaks MSVC*\n3 *this includes most pre-/post-condition checks, disabling without specific cause is highly discouraged*\n\nAdditionally, the following libraries are shipped internally.\nThe following options allow to switch to external installs:\n\n| CMake Option | Values | Library | Version |\n|---------------------------------|------------|---------------|---------|\n| `openPMD_USE_INTERNAL_VARIANT` | **ON**/OFF | MPark.Variant | 1.4.0+ |\n| `openPMD_USE_INTERNAL_CATCH` | **ON**/OFF | Catch2 | 2.6.1+ |\n| `openPMD_USE_INTERNAL_PYBIND11` | **ON**/OFF | pybind11 | 2.3.0+ |\n| `openPMD_USE_INTERNAL_JSON` | **ON**/OFF | NLohmann-JSON | 3.5.0+ |\n\nBy default, this will build as a shared library (`libopenPMD.[so|dylib|dll]`) and installs also its headers.\nIn order to build a static library, append `-DBUILD_SHARED_LIBS=OFF` to the `cmake` command.\nYou can only build a static or a shared library at a time.\n\nBy default, the `Release` version is built.\nIn order to build with debug symbols, pass `-DCMAKE_BUILD_TYPE=Debug` to your `cmake` command.\n\nBy default, tests and examples are built.\nIn order to skip building those, pass `-DBUILD_TESTING=OFF` or `-DBUILD_EXAMPLES` to your `cmake` command.\n\n## Linking to your project\n\nThe install will contain header files and libraries in the path set with `-DCMAKE_INSTALL_PREFIX`.\n\n### CMake\n\nIf your project is using CMake for its build, one can conveniently use our provided `openPMDConfig.cmake` package which is installed alongside the library.\n\nFirst set the following environment hint if openPMD-api was *not* installed in a system path:\n\n```bash\n# optional: only needed if installed outside of system paths\nexport CMAKE_PREFIX_PATH=$HOME/somepath:$CMAKE_PREFIX_PATH\n```\n\nUse the following lines in your project's `CMakeLists.txt`:\n```cmake\n# supports: COMPONENTS MPI NOMPI JSON HDF5 ADIOS1 ADIOS2\nfind_package(openPMD 0.1.0 CONFIG)\n\nif(openPMD_FOUND)\n target_link_libraries(YourTarget PRIVATE openPMD::openPMD)\nendif()\n```\n\n*Alternatively*, add the openPMD-api repository source directly to your project and use it via:\n```cmake\nadd_subdirectory(\"path/to/source/of/openPMD-api\")\n\ntarget_link_libraries(YourTarget PRIVATE openPMD::openPMD)\n```\n\n### Manually\n\nIf 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.\n\nFirst set the following environment hint if openPMD-api was *not* installed in a system path:\n\n```bash\n# optional: only needed if installed outside of system paths\nexport PKG_CONFIG_PATH=$HOME/somepath/lib/pkgconfig:$PKG_CONFIG_PATH\n```\n\nAdditional linker and compiler flags for your project are available via:\n```bash\npkg-config --libs openPMD\n# -L${HOME}/somepath/lib -lopenPMD\n\n# if you build openPMD-api as static library with `-DBUILD_SHARED_LIBS=OFF`\npkg-config --libs --static openPMD\n# -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 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