Damaris plugin#693
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…se or on other configs options.
…ide other plugins (trace, mpi, Decl'HDF5, etc.)
…s in the YML file!
…ch element requiring any metadata value uses depends_on YAML attribute to ensure an update of its attributes value to Damaris lib once the metadata are exposed (using Damaris Parameters in the background)!
…ding auto initialize without on_init event, and adding some cmake instruction in enforce finding of Damaris when Damaris_ROOT is provided.
The condition to do that is to always have this sequence at the end of the simulation: PDI_finalize(); MPI_Finalize(); Or provide in the yml conf the code following PDI_finalize(); Code like the following could not be handled: PDI_finalize(); PC_tree_destroy(&conf); free(cur); free(next); MPI_Finalize();
This reverts commit db29c2c.
Fix-local-install-1
* Hide is_client from user, and ending damaris server in background: - The condition to do that is to always have this sequence at the end of the simulation: PDI_finalize(); MPI_Finalize(); - Or provide in the yml conf the code following PDI_finalize(); - Code like the following could not be handled for the moment. But in the future by providing the instructions to execute...: PDI_finalize(); PC_tree_destroy(&conf); free(cur); free(next); MPI_Finalize(); * update copyright * Removing on_init and on_finalize
* Example with only Damaris API (resolves #10)
* fix destruction of conf --------- Co-authored-by: yushan wang <yushan.wang@cea.fr>
* Datasets as regex (pdidev#583) * First version with regex * fix pdidev#582, update authors README and indent * update changelog * adding class for test * fix indent * fix indent * fix spdlog * adding test in parallel * fix error on file * Update plugins/decl_hdf5/README.md Co-authored-by: Benoit Martin <benoitmartin88.pro@gmail.com> * Update plugins/decl_hdf5/README.md Co-authored-by: Benoit Martin <benoitmartin88.pro@gmail.com> * fix pdidev#582, fix request change --------- Co-authored-by: Benoit Martin <benoitmartin88.pro@gmail.com> * Add macOS CI (pdidev#576) * Add macOS CI * Remove chunking check on a non-chunked dataset * Use MPI oversubscription * Disable unqualified std cast call * Use float type instead of integer * Use storage instead of computation * Disable zsh test * use `H5Pget_layout` to check if dataset is chunked * remove warning : cast hsize_t to int before `printf` * Re-enable zsh test with a new env.bash path * add call to `build_and_run_all_tests` and add workaround for macos * add netcdf * initialize CMAKE_FLAGS * disable PYTHON for macos * install hdf5-mpi on macos 14 and 15 * build hdf5 from source + add -j4 * Update copyright headers * Update AUTHORS * Update CHANGELOG.md fixes pdidev#556, fixes pdidev#565, fixes pdidev#587, fixes pdidev#588 --------- Co-authored-by: Julien Bigot <jbigot@users.noreply.github.com> Co-authored-by: yushan wang <yushan.wang@cea.fr> Co-authored-by: Benoit Martin <bmartin@cea.fr> Co-authored-by: Julien Bigot <julien.bigot@cea.fr> * Fix libyaml cmake policy version (pdidev#594) * add CMAKE_POLICY_VERSION_MINIMUM to 3.5 when building libyaml * fix pdidev#593 * update changelog and add comment * Fix github action (CI) access issue of tests.xml (pdidev#584) * Fix github action (CI) access issue of tests.xml * Fix pdidev#585 github action (CI) access issue of tests.xml, and go through PR checklist * Fix pdidev#585 github action (CI) access issue of tests.xml, using an other folder 'tmp_dir_test' containing the tests output, rather than docker's tmpfs * Update AUTHORS --------- Co-authored-by: Benoit Martin <bmartin@cea.fr> * Add CODEOWNERS (pdidev#591) * Add CODEOWNERS --------- Co-authored-by: Benoit Martin <bmartin@cea.fr> Co-authored-by: yushan wang <yushan.wang@cea.fr> * Check of the HDF5 API version to use in error handler (pdidev#600) * Ensuring the use of a compatible HDF5 API versions during errors handling Fix pdidev#567 --------- Co-authored-by: Anida Khizar <anida.khizar@cea.fr> Co-authored-by: Julien Bigot <julien.bigot@cea.fr> Co-authored-by: yushan wang <yushan.wang@cea.fr> * 592 improvement hdf5 dataset as regex (pdidev#597) * fix#592, comment about dataset as regex * Fix pdidev#592, reduce the interior loop * fix copyright * add fmt/range * fix indent * sort name of dataset in case of multiple regex found * fix indent * Fix pdidev#592, dsets as vector, introduce struct for explicit dataset * change Dataset_explicit_type to class * Apply suggestion from @jbigot * Update plugins/decl_hdf5/dataset_explicit_type.h * Update plugins/decl_hdf5/dataset_explicit_type.h * Update plugins/decl_hdf5/dataset_explicit_type.h * Update plugins/decl_hdf5/dataset_explicit_type.h * add std:optional and remove unnecessary comment --------- Co-authored-by: Julien Bigot <jbigot@users.noreply.github.com> * Add workflow_dispatch in pages * Fix pdidev#598, add workflow_dispatch in pages * fix in PC parser * fix in PC parser * add test for catching possible error * catch config error in google test * Use GTest's 'ASSERT_NO_FATAL_FAILURE' to catch a write failure Co-authored-by: Julien Bigot <jbigot@users.noreply.github.com> * code cleaning * Using PDI_NULL_Handler for error catching. Co-authored-by: Benoit Martin <bmartin@cea.fr> * add rwx right to tmp_dir_test --------- Co-authored-by: Julien Bigot <jbigot@users.noreply.github.com> Co-authored-by: Benoit Martin <benoitmartin88.pro@gmail.com> * PDI Release 1.9.3 Update the embedded versions of paraconf, pybind11 & zpp to fix a build issue with recent cmake. (pdidev#632) Sort Doxyfile for easier update Update to be compatible with latest Doxygen (pdidev#629) * Make all pages subpages of the About page * Remove the hand-crafted module page and use the generated topics page instead * Update the layout file * Add missing options in the Doxyfile * Set MARKDOWN_STRICT=NO to prevent backquote errors * Set PAGE_OUTLINE_PANEL=NO to prevent generation of a useless index * Minor CSS update to handle the additional level in the generated HTML * Fix two minor doc bugs Fix pdidev#631 Fix pdidev#629 * Cleanup changelogs before release * Fix HDF5 compression test for MacOS 26 Fix pdidev#627 Co-authored-by: Julian Auriac <julian.auriac@cea.fr> * Indent * Remove Deisa plugin (pdidev#639) * Update the version of dependencies Update the version of dependencies according to our policy: oldest supported Debian, Fedora & Ubuntu, as well as spack 0.19. The new requirements are: CMake 3.22, Doxygen 1.9.1, HDF5 1.10.7, mpi4py 3.1.3, NetCDF 4.8.1, numpy 1.21.5, pyyaml 5.4.1 pybind11 2.9.1, Python 3.10.6, spdlog 1.9.2 * Rely on standard Find* from cmake as much as possible * Add policy(PUSH) in cmake to prevent leaks * Include FindHDF5 from CMake 4.1 and backport it to 3.22 to use its fix for HL Fix pdidev#613 * Fix default CMAKE_BUILD_TYPE value (pdidev#619) * Fix default CMAKE_BUILD_TYPE value * Mock PDI Fix pdidev#438 Co-authored-by: Julian Auriac <julian.auriac@cea.fr> Co-authored-by: Benoit Martin <benoit.martin2@cea.fr> * Update dependencies on googletest & benchmark * PDI Release 1.10.0 * Changelog minor fix * Adding missing LICENSE files and fix some minor indent * Support multiple consecutive calls to `find_package(PDI)` Fix pdidev#526 Co-authored-by: Benoit Martin <benoit.martin2@cea.fr> * add-compression-in-decl_netcdf (pdidev#604) Add deflate and chunking to Decl'NetCDF * Enable hdf5 subfiling2 (pdidev#650) enable HDF5 subfiling support, add test. note: to set the subfiling stripe size (64Mo for example), use `export H5FD_SUBFILING_STRIPE_SIZE= 67108864`. * add type check for reading data from netCDF file (pdidev#646) * add type and sign check for integer read * add size check for float and double variable read * Disable unit tests for JSON dependency (pdidev#651) * Update versions of the langagues standard we use (pdidev#659) Update the versions of the languages standard we use * We require versions of compilers that support more recent versions of the standard already. This is not a user facing change. * Fix for C++ 20 - some incorrect use of fmt:: are only detected now with the use of C++ 20 - C++ 20 introduced mirror operator == that lead to some abiguous calls - Bump embedded spdlog to 1.15 because 1.14 had issues with C++ 20 Fix pdidev#660 * fix pybind11 on macos (pdidev#655) * fix pybind11 linking error on macos and enable Python based plugins for macOS CI * enable netcdf in macos CI (pdidev#667) * enable netcdf in macos CI * Update clang-format to version 18 (pdidev#673) Match the version in test_env:v4 * Renamed some error codes and deprecated the old ones (pdidev#671) Fix pdidev#670 * Finish moving to clang-format 18 * Fully qualify `std::move` calls (pdidev#676) Prevent a compilation warning and incorrect usages Fix pdidev#675 Co-authored-by: yushan wang <yushan.wang@cea.fr> * Enhance subfiling environment checking and update usage notes (pdidev#654) * Enhance README with subfiling usage notes Added important notes for using subfiling correctly. * add MPI thread level check * update readme * fix * fix * update test for subfiling counting * add subfiling stripe size in test * make subfiling_stripe_size configurable in yaml * update readme * make subfiling a new class and add stripe size configuration * update readme * indent * Add subfiling.cxx to decl_hdf5 plugin sources * update upon review notes * enable subfiling check test only if supported * remove subfiling check count test * pass subfiling test from c to cxx * indent * update readme [skip ci] * remove unnecessary headers fropm test * add header in test * throw an error if stripe_size is negative * fix indent [skip ci] * use warning when stripe_size is 0 * Replace Config_error with Spectree_error * Move Spectree_error usage to a consistent location * Improved testing framework (pdidev#669) * Added `pdi/testing.h` that should be used t test plugins. * Ported `plugins/decl_hdf5/tests/decl_hdf5_tests.cxx` as an example. * Fixed a minor bug discovered along the way in Decl'HDF5 Fix pdidev#668 * Do some tests in sequential to not use all CI if everything fails (pdidev#674) * Do some tests in sequential to not use all CI if everything fails * Do not run benchmarks by default Fix pdidev#679 * Fix a bug that was introduced in mock PDI with the (unreleased) move to C++ 20 mock PDI now relies on C++ 20 features when compiling in C++ but did not advertize it * Fix target_compile_features syntax for PDI_C --------- Co-authored-by: jmorice91 <jacques.morice@cea.fr> Co-authored-by: Benoit Martin <benoitmartin88.pro@gmail.com> Co-authored-by: Thomas Padioleau <thomas.padioleau@cea.fr> Co-authored-by: Julien Bigot <jbigot@users.noreply.github.com> Co-authored-by: Benoit Martin <bmartin@cea.fr> Co-authored-by: Julien Bigot <julien.bigot@cea.fr> Co-authored-by: JAuriac <56091659+JAuriac@users.noreply.github.com> Co-authored-by: AnidaKhizar <anida-khizar@hotmail.fr> Co-authored-by: Anida Khizar <anida.khizar@cea.fr> Co-authored-by: Julian Auriac <julian.auriac@cea.fr> Co-authored-by: Benoit Martin <benoit.martin2@cea.fr>
* fix missing change in new error of pdi * fix indent
…o damaris_plugin
rename the example
* Cleaning the code, removing meshes, paraview and python
… file paths for storage
Clarified the description of 'sim_name' and 'name' fields in the README.
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.clang-format;Fix #issuekeyword to autoclose the issue when merged.