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Release 0.14.3 backports (#1135)
* Read: time/dt also in long double (#1096) * Python: time/dt round-trip Test writing and reading time and dt on an iteration via properties. * Fix: Iteration read of long double time Support reading of `dt` and `time` attributes if they are of type `long double`. (openPMD standard: all `floatX` supported) * Executables: CXX_STANDARD/EXTENSIONS (#1102) Set `CXX_EXTENSIONS OFF` and `CXX_STANDARD_REQUIRED ON` for created executables. This mitigates issues with NVCC 11.0 and C++17 builds seen as added `-std=gnu++17` flags that lead to ``` nvcc fatal : Value 'gnu++17' is not defined for option 'std' ``` when using `nvcc` as CXX compiler directly. * Doc: More Locations -DPython_EXECUTABLE (#1104) Mention the `-DPython_EXECUTABLE` twice more in build examples. * NVCC + C++17 (#1103) * NVCC + C++17 Work-around a build issue with NVCC in C++17 builds. ``` include/openPMD/backend/Attributable.hpp(437): error #289: no instance of constructor "openPMD::Attribute::Attribute" matches the argument list argument types are: (std::__cxx11::string) detected during instantiation of "__nv_bool openPMD::AttributableInterface::setAttribute(const std::__cxx11::string &, T) [with T=std::__cxx11::string]" ``` from ``` inline bool AttributableInterface::setAttribute( std::string const & key, char const value[] ) { return this->setAttribute(key, std::string(value)); } ``` Seen with: - NVCC 11.0.2 + GCC 8.3.0 - NVCC 11.0.2 + GCC 7.5.0 * NVCC 11.0.2 C++17 work-around: Add Comment * Lazy parsing: Make findable in docs and use in openpmd-ls (#1111) * Use deferred iteration parsing in openpmd-ls * Make lazy/deferred parsing searchable * Add a way to search for usesteps key * HDF5: Document HDF5_USE_FILE_LOCKING (#1106) Document a HDF5 read work-around that we currently need on OLCF Jupyter (https://jupyter.olcf.ornl.gov), due to a mounting issue of GPFS in the Jupyter serice (OLCFHELP-3685). From the HDF5 1.10.1 Release Notes: ``` Other New Features and Enhancements =================================== Library ------- - Added a mechanism for disabling the SWMR file locking scheme. The file locking calls used in HDF5 1.10.0 (including patch1) will fail when the underlying file system does not support file locking or where locks have been disabled. To disable all file locking operations, an environment variable named HDF5_USE_FILE_LOCKING can be set to the five-character string 'FALSE'. This does not fundamentally change HDF5 library operation (aside from initial file open/create, SWMR is lock-free), but users will have to be more careful about opening files to avoid problematic access patterns (i.e.: multiple writers) that the file locking was designed to prevent. Additionally, the error message that is emitted when file lock operations set errno to ENOSYS (typical when file locking has been disabled) has been updated to describe the problem and potential resolution better. (DER, 2016/10/26, HDFFV-9918) ``` This also exists as a compilation option for HDF5 in CMake, where it defaults to ``TRUE`` by default, which is also what distributions/ package managers ship. Disabling from Bash: ```bash export HDF5_USE_FILE_LOCKING=FALSE ``` Disabling from Python: ```py import os os.environ['HDF5_USE_FILE_LOCKING'] = "FALSE" ``` * Avoid object slicing when deriving from Series class (#1107) * Make Series class final * Use private constructor to avoid object slicing * Doc: OMPI_MCA_io Control (#1114) Document OpenMPI MPI-I/O backend control. We have documented this long in #446. * openPMD.hpp: Include auxiliary StringManip (#1124) Include this, handy functions. * CXX Std: Remember <variant> Impl. (#1128) We use `<variant>` or `<mpark/variant.hpp>` in our public API interface for datatypes, depending on the C++ standard. This pull request makes sure that the same implementation is used in downstream code, even if the C++ standard is switched. This avoids ABI issues when, e.g., using a C++14 built openPMD-api in a C++17 downstream code. * Spack: No More `load -r` (#1125) The `-r` argument was removed from `spack load` and is now implied. * Fix AppVeyor: Python Executable (#1127) * GH Action: Add MSVC & ClangCL on Win * Fix AppVeyor: Python Executable * Avoid mismatching system Python and Conda Python * Conda: Fix Numpy * CMake: Skip Pipe Test Written in a too special way, we cannot assume SH is always present * Test 8b (Bench Read Parallel): Support Variable encoding, Fix Bugs (#1131) * added support to read variable encoding, plus fixed some bugs * fixed style * Update examples/8b_benchmark_read_parallel.cpp remove commented out code Co-authored-by: Axel Huebl <[email protected]> * Update examples/8b_benchmark_read_parallel.cpp Co-authored-by: Axel Huebl <[email protected]> * Update examples/8b_benchmark_read_parallel.cpp Co-authored-by: Axel Huebl <[email protected]> * Update examples/8b_benchmark_read_parallel.cpp Co-authored-by: Axel Huebl <[email protected]> * Update examples/8b_benchmark_read_parallel.cpp Co-authored-by: Axel Huebl <[email protected]> * Update examples/8b_benchmark_read_parallel.cpp Co-authored-by: Axel Huebl <[email protected]> * Update examples/8b_benchmark_read_parallel.cpp Co-authored-by: Axel Huebl <[email protected]> * Update examples/8b_benchmark_read_parallel.cpp Co-authored-by: Axel Huebl <[email protected]> * Update examples/8b_benchmark_read_parallel.cpp Co-authored-by: Axel Huebl <[email protected]> * Update examples/8b_benchmark_read_parallel.cpp Co-authored-by: Axel Huebl <[email protected]> * Update examples/8b_benchmark_read_parallel.cpp Co-authored-by: Axel Huebl <[email protected]> * removed commented line * updated 8b env option Co-authored-by: Axel Huebl <[email protected]> * HDF5 I/O optimizations (#1129) * Include HDF5 optimization options * Fix code style check * Fix validations and include checks * Fix style check * Remove unecessary strict check * Update documentation with HDF5 tuning options * Update contributions * Fix Guards for H5Pset_all_coll_metadata* * MPI Guard: H5Pset_all_coll_metadata* * Remove duplicated variable Co-authored-by: Axel Huebl <[email protected]> * Include known issues section for HDF5 (#1132) * Update known issues with HDF5 and collective metadata operations * Fix rst link and tiny typo * Add targeted bugfix releases. Co-authored-by: Axel Huebl <[email protected]> * Include check for paged allocation (#1133) * Include check for paged allocation * Update ParallelHDF5IOHandler.cpp * libfabric 1.6+: Document SST Work-Arounds (#1134) * libfabric 1.6+: Document SST Work-Arounds Document work-arounds for libfabric 1.6+ on Cray systems when using data staging / streaming with ADIOS2 SST. Co-authored-by: Franz Pöschel <[email protected]> * Fix: Read Inconsistent Zero Pads (#1118) * [Draft] Fix: Read Inconsistent Zero Pads Some codes mess up the zero-padding in `fileBased` encoding, e.g., when specifying padding to 5 digits but creating >100'000 output steps. Files like those cannot yet be parsed and fell back to no padding, which fails to open the file: ``` openpmd_00000.h5 openpmd_02000.h5 openpmd_101000.h5 openpmd_01000.h5 openpmd_100000.h5 openpmd_104000.h5 ``` Error: ``` RuntimeError: [HDF5] Failed to open HDF5 file diags/diag1/openpmd_0.h5 ``` * Revert previous changes except for test Parse iteration numbers that are longer than their padding Read inconsistent zero padding * Overflow Padding: Read Test * Warn if the prefix does end in a digit * Fix: Don't let oversize numbers accidentally bump the padding * Update test * Issue warnings on misleading patterns also when writing * Minor Style Update Co-authored-by: Franz Pöschel <[email protected]> * Release: 0.14.3 Co-authored-by: Franz Pöschel <[email protected]> Co-authored-by: guj <[email protected]> Co-authored-by: Jean Luca Bez <[email protected]> Co-authored-by: Jean Luca Bez <[email protected]>
1 parent e00bede commit 00532a7

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‎.appveyor.yml‎

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environment:
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matrix:
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- TARGET_ARCH: x86
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CONDA_PY: 36
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CONDA_INSTALL_LOCN: C:\\Miniconda36
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APPVEYOR_BUILD_WORKER_IMAGE: Visual Studio 2017
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platform: x86
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SHARED: ON
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- TARGET_ARCH: x64
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CONDA_PY: 37
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CONDA_PY: 3.7
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CONDA_INSTALL_LOCN: C:\\Miniconda37-x64
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APPVEYOR_BUILD_WORKER_IMAGE: Visual Studio 2017
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platform: x64
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SHARED: ON
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SHARED: OFF
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- TARGET_ARCH: x86
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CONDA_PY: 37
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CONDA_PY: 3.7
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CONDA_INSTALL_LOCN: C:\\Miniconda37
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APPVEYOR_BUILD_WORKER_IMAGE: Visual Studio 2017
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platform: x86
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SHARED: ON
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- TARGET_ARCH: x64
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CONDA_PY: 36
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CONDA_INSTALL_LOCN: C:\\Miniconda36-x64
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APPVEYOR_BUILD_WORKER_IMAGE: Visual Studio 2017
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platform: x64
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SHARED: OFF
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configuration:
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# - Debug
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- Release
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# Add path, activate `conda` and update conda.
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- cmd: call %CONDA_INSTALL_LOCN%\Scripts\activate.bat
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- cmd: conda update --yes --quiet conda
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- cmd: set PYTHONUNBUFFERED=1
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- cmd: conda config --append channels conda-forge
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# Configure the VM.
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- cmd: conda install -n root --quiet --yes numpy>=1.15 cmake hdf5
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# ADIOS2 build only for 64bit Windows and Python 3.6+
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- cmd: if "%TARGET_ARCH%"=="x64" if %CONDA_PY% GEQ 36 conda install -n root --quiet --yes adios2
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- cmd: conda install -n root --quiet --yes numpy cmake hdf5 python=%CONDA_PY%
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# ADIOS2 build only for 64bit Windows
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- cmd: if "%TARGET_ARCH%"=="x64" conda install -n root --quiet --yes adios2 python=%CONDA_PY%
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before_build:
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- cmd: cd C:\projects\openpmd-api
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# - cmd: if "%TARGET_ARCH%"=="x64" "C:\Program Files (x86)\Microsoft Visual Studio 15.9\VC\vcvarsall.bat" amd64
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# CMake configure
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- cmd: cmake -G "%OPENPMD_CMAKE_GENERATOR%" -DCMAKE_BUILD_TYPE=%CONFIGURATION% -DBUILD_SHARED_LIBS=%SHARED% -DBUILD_TESTING=ON -DCMAKE_INSTALL_PREFIX="%CONDA_INSTALL_LOCN%" -DCMAKE_INSTALL_BINDIR="Library\bin" ".."
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- cmd: cmake -G "%OPENPMD_CMAKE_GENERATOR%" -DCMAKE_BUILD_TYPE=%CONFIGURATION% -DBUILD_SHARED_LIBS=%SHARED% -DBUILD_TESTING=ON -DopenPMD_USE_PYTHON=ON -DPython_EXECUTABLE="%CONDA_INSTALL_LOCN%\python.exe" -DCMAKE_INSTALL_PREFIX="%CONDA_INSTALL_LOCN%" -DCMAKE_INSTALL_BINDIR="Library\bin" ".."
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build_script:
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- cmd: cmake --build . --config %CONFIGURATION%
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- cmd: cmake --build . --config %CONFIGURATION% -j 2
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- cmd: cmake --build . --config %CONFIGURATION% --target install
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test_script:
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- cmd: ctest -V -C %CONFIGURATION%
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- cmd: python -c "import openpmd_api; print(openpmd_api.__version__); print(openpmd_api.variants)"
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- cmd: call %CONDA_INSTALL_LOCN%\python.exe -c "import openpmd_api; print(openpmd_api.__version__); print(openpmd_api.variants)"

‎.github/workflows/windows.yml‎

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name: 🪟 Windows
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on: [push, pull_request]
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concurrency:
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group: ${{ github.ref }}-${{ github.head_ref }}-windows
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cancel-in-progress: true
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jobs:
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build_win_msvc:
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name: MSVC w/o MPI
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runs-on: windows-latest
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if: github.event.pull_request.draft == false
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steps:
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- uses: actions/checkout@v2
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- name: Build & Install
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run: |
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python3.exe -m pip install --upgrade pip
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python3.exe -m pip install --upgrade numpy
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pwsh "share\openPMD\download_samples.ps1" build
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cmake -S . -B build `
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-DCMAKE_BUILD_TYPE=Debug `
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-DopenPMD_USE_MPI=OFF
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cmake --build build --config Debug --parallel 2
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cmake --build build --config Debug --target install
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# add before install, and fix Python path:
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# ctest --test-dir build -C Debug --output-on-failure
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build_win_clang:
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name: Clang w/o MPI
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runs-on: windows-2019
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if: github.event.pull_request.draft == false
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steps:
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- uses: actions/checkout@v2
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- uses: seanmiddleditch/gha-setup-ninja@master
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- name: Build & Install
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shell: cmd
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run: |
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python3.exe -m pip install --upgrade pip
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python3.exe -m pip install --upgrade numpy
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call "C:\Program Files (x86)\Microsoft Visual Studio\2019\Enterprise\vc\Auxiliary\build\vcvarsall.bat" x64
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pwsh "share\openPMD\download_samples.ps1" build
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cmake -S . -B build ^
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-G "Ninja" ^
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-DCMAKE_C_COMPILER=clang-cl ^
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-DCMAKE_CXX_COMPILER=clang-cl ^
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-DCMAKE_BUILD_TYPE=Release ^
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-DopenPMD_USE_MPI=OFF
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cmake --build build --config Release --parallel 2
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cmake --build build --config Debug --target install
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# add before install, and fix Python path:
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# ctest --test-dir build -C Debug --output-on-failure

‎.rodare.json‎

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"name": "Schnetter, Erik",
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"orcid": "0000-0002-4518-9017",
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"type": "Other"
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},
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{
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"affiliation": "Lawrence Berkeley National Laboratory",
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"name": "Bez, Jean Luca",
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"orcid": "0000-0002-3915-1135",
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"type": "Other"
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}
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],
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"title": "C++ & Python API for Scientific I/O with openPMD",

‎CHANGELOG.rst‎

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Changelog
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=========
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0.14.2
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------
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**Date:** 2021-11-03
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Read Bugs, C++17 Mixing and HDF5 Performance
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This release makes reads more robust by fixing small API, file-based parsing and test bugs.
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Building the library in C++14 and using it in C++17 will not result in incompatible ABIs anymore.
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HDF5 1.10.1+ performance was improved significantly.
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Changes to "0.14.2"
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^^^^^^^^^^^^^^^^^^^
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Bug Fixes
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"""""""""
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- read:
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- allow inconsistent zero pads #1118
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- time/dt also in long double #1096
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- test 8b - bench read parallel:
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- support variable encoding #1131
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- block located at top left corner was mistaken to read a block in the center #1131
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- CI (AppVeyor): Python executable #1127
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- C++17 mixing: remember ``<variant>`` implementation #1128
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- support NVCC + C++17 #1103
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- avoid object slicing when deriving from ``Series`` class #1107
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- executables: ``CXX_STANDARD``/``EXTENSIONS`` #1102
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Other
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"""""
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- HDF5 I/O optimizations #1129 #1132 #1133
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- libfabric 1.6+: Document SST Work-Arounds #1134
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- OpenMPI: Document ``OMPI_MCA_io`` Control #1114
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- HDF5: Document ``HDF5_USE_FILE_LOCKING`` #1106
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- Lazy parsing: Make findable in docs and use in ``openpmd-ls`` #1111
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- Docs: More Locations ``-DPython_EXECUTABLE`` #1104
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- Spack: No More ``load -r`` #1125
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- ``openPMD.hpp``: include auxiliary ``StringManip`` #1124
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0.14.2
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------
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**Date:** 2021-08-17

‎CITATION.cff‎

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orcid: https://orcid.org/0000-0003-1943-7141
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email: [email protected]
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title: "openPMD-api: C++ & Python API for Scientific I/O with openPMD"
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version: 0.14.2
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version: 0.14.3
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repository-code: https://github.com/openPMD/openPMD-api
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doi: 10.14278/rodare.27
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license: LGPL-3.0-or-later

‎CMakeLists.txt‎

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#
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cmake_minimum_required(VERSION 3.15.0)
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project(openPMD VERSION 0.14.2) # LANGUAGES CXX
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project(openPMD VERSION 0.14.3) # LANGUAGES CXX
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# the openPMD "markup"/"schema" standard version
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set(openPMD_STANDARD_VERSION 1.1.0)
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$<INSTALL_INTERFACE:include>
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# is this a C++17 compile? If yes, skip MPark.Variant
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try_compile(openPMD_HAS_CXX17
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${openPMD_BINARY_DIR}/try_variant
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${openPMD_SOURCE_DIR}/cmake/try_variant.cpp
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CXX_STANDARD_REQUIRED ON
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CXX_EXTENSIONS OFF
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)
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message(STATUS "<variant> supported (C++17 or newer): ${openPMD_HAS_CXX17}")
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# C++11 std::variant (C++17 stdlib preview)
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# TODO not needed with C++17 compiler
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add_library(openPMD::thirdparty::mpark_variant INTERFACE IMPORTED)
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set(openPMD_PC_EXTRA_INCLUDE "")
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if(openPMD_USE_INTERNAL_VARIANT)
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target_include_directories(openPMD::thirdparty::mpark_variant SYSTEM INTERFACE
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$<BUILD_INTERFACE:${openPMD_SOURCE_DIR}/share/openPMD/thirdParty/variant/include>
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)
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message(STATUS "MPark.Variant: Using INTERNAL version '1.4.0'")
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else()
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find_package(mpark_variant 1.3.0 REQUIRED) # TODO: we want 1.4.1+
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target_link_libraries(openPMD::thirdparty::mpark_variant
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INTERFACE mpark_variant)
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get_target_property(EXTERNAL_MPARK_INCLUDE mpark_variant INTERFACE_INCLUDE_DIRECTORIES)
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if(openPMD_HAVE_PKGCONFIG AND EXTERNAL_MPARK_INCLUDE)
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set(openPMD_PC_EXTRA_INCLUDE "-I${EXTERNAL_MPARK_INCLUDE}")
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if(NOT openPMD_HAS_CXX17)
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add_library(openPMD::thirdparty::mpark_variant INTERFACE IMPORTED)
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set(openPMD_PC_EXTRA_INCLUDE "")
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if(openPMD_USE_INTERNAL_VARIANT)
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target_include_directories(openPMD::thirdparty::mpark_variant SYSTEM INTERFACE
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$<BUILD_INTERFACE:${openPMD_SOURCE_DIR}/share/openPMD/thirdParty/variant/include>
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)
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message(STATUS "MPark.Variant: Using INTERNAL version '1.4.0'")
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else()
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find_package(mpark_variant 1.3.0 REQUIRED) # TODO: we want 1.4.1+
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target_link_libraries(openPMD::thirdparty::mpark_variant
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INTERFACE mpark_variant)
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get_target_property(EXTERNAL_MPARK_INCLUDE mpark_variant INTERFACE_INCLUDE_DIRECTORIES)
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if(openPMD_HAVE_PKGCONFIG AND EXTERNAL_MPARK_INCLUDE)
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set(openPMD_PC_EXTRA_INCLUDE "-I${EXTERNAL_MPARK_INCLUDE}")
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endif()
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message(STATUS "MPark.Variant: Found version '${mpark_variant_VERSION}'")
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endif()
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message(STATUS "MPark.Variant: Found version '${mpark_variant_VERSION}'")
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target_link_libraries(openPMD PUBLIC openPMD::thirdparty::mpark_variant)
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target_link_libraries(openPMD PUBLIC openPMD::thirdparty::mpark_variant)
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# Catch2 for unit tests
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if(openPMD_BUILD_TESTING)
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target_compile_options(openPMD.ADIOS1.Serial PUBLIC ${_msvc_options})
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target_link_libraries(openPMD.ADIOS1.Serial PUBLIC openPMD::thirdparty::mpark_variant)
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target_link_libraries(openPMD.ADIOS1.Parallel PUBLIC openPMD::thirdparty::mpark_variant)
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if(NOT openPMD_HAS_CXX17)
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target_link_libraries(openPMD.ADIOS1.Serial PUBLIC openPMD::thirdparty::mpark_variant)
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target_link_libraries(openPMD.ADIOS1.Parallel PUBLIC openPMD::thirdparty::mpark_variant)
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endif()
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target_include_directories(openPMD.ADIOS1.Serial PRIVATE
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${openPMD_SOURCE_DIR}/include ${openPMD_BINARY_DIR}/include)
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set_target_properties(${testname}Tests PROPERTIES
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CXX_EXTENSIONS OFF
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CXX_STANDARD_REQUIRED ON
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)
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endforeach()
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endif()
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if(openPMD_BUILD_CLI_TOOLS)
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foreach(toolname ${openPMD_CLI_TOOL_NAMES})
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add_executable(openpmd-${toolname} src/cli/${toolname}.cpp)
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target_link_libraries(openpmd-${toolname} PRIVATE openPMD)
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set_target_properties(openpmd-${toolname} PROPERTIES
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CXX_EXTENSIONS OFF
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)
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endforeach()
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endif()
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target_link_libraries(${examplename} PRIVATE openPMD)
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set_target_properties(${examplename} PROPERTIES
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CXX_EXTENSIONS OFF
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CXX_STANDARD_REQUIRED ON
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)
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endif()
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else()
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add_executable(${examplename} examples/${examplename}.cpp)
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target_link_libraries(${examplename} PRIVATE openPMD)
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set_target_properties(${examplename} PROPERTIES
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CXX_EXTENSIONS OFF
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CXX_STANDARD_REQUIRED ON
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)
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endif()
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endforeach()
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endif()
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# install third-party libraries
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# TODO not needed with C++17 compiler
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if(openPMD_USE_INTERNAL_VARIANT)
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if(NOT openPMD_HAS_CXX17 AND openPMD_USE_INTERNAL_VARIANT)
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install(DIRECTORY "${openPMD_SOURCE_DIR}/share/openPMD/thirdParty/variant/include/mpark"
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DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}
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endforeach()
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# openpmd-pipe (python) test
1219-
if( openPMD_HAVE_HDF5
1248+
if( NOT WIN32
1249+
AND openPMD_HAVE_HDF5
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AND (openPMD_HAVE_ADIOS2 OR openPMD_HAVE_ADIOS1)
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AND EXAMPLE_DATA_FOUND
12221252
)
@@ -1345,7 +1375,11 @@ if(openPMD_INSTALL)
13451375
endif()
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message("")
13471377
message(" Additionally, install following third party libraries:")
1348-
message(" MPark.Variant: ${openPMD_USE_INTERNAL_VARIANT}")
1378+
if(openPMD_HAS_CXX17)
1379+
message(" MPark.Variant: OFF")
1380+
else()
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message(" MPark.Variant: ${openPMD_USE_INTERNAL_VARIANT}")
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endif()
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else()
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message(" Installation: OFF")
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endif()

‎README.md‎

Lines changed: 4 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -148,7 +148,7 @@ Choose *one* of the install methods below to get started:
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```bash
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# optional: +python +adios1 -adios2 -hdf5 -mpi
150150
spack install openpmd-api
151-
spack load -r openpmd-api
151+
spack load openpmd-api
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```
153153

154154
### [Conda](https://conda.io)
@@ -232,7 +232,7 @@ cd openPMD-api-build
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# for options append:
233233
# -DopenPMD_USE_...=...
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# e.g. for python support add:
235-
# -DopenPMD_USE_PYTHON=ON
235+
# -DopenPMD_USE_PYTHON=ON -DPython_EXECUTABLE=$(which python3)
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cmake ../openPMD-api
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cmake --build .
@@ -412,6 +412,8 @@ Further thanks go to improvements and contributions from:
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Dask guidance & reviews
413413
* [Erik Schnetter (PITP)](https://github.com/eschnett):
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C++ API bug fixes
415+
* [Jean Luca Bez (LBNL)](https://github.com/jeanbez):
416+
HDF5 performance tuning
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### Grants
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