Vectorized functions for unpacking the 64-bit amrex particle ids #165
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As implemented in pyAMReX with AMReX-Codes/pyamrex#165
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As implemented in pyAMReX with AMReX-Codes/pyamrex#165
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As implemented in pyAMReX with AMReX-Codes/pyamrex#165
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* pyAMReX: Build System * CI Updates (Changed Options) * Callback modernization (#4) * refactor callbacks.py * added binding code in `pyWarpX.cpp` to add or remove keys from the callback dictionary * minor PR cleanups Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * Added Python level reference to fetch the multifabs (#3) * pyAMReX: Build System * Added Python level reference to Ex_aux * Now uses the multifab map * Fix typo Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * Add initialization and finalize routines (#5) A basic PICMI input file will now run to completion. * Regression Tests: WarpX_PYTHON=ON * Update Imports to nD pyAMReX * IPO/LTO Control Although pybind11 relies heavily on IPO/LTO to create low-latency, small-binary bindings, some compilers will have troubles with that. Thus, we add a compile-time option to optionally disable it when needed. * Fix: Link Legacy WarpXWrappers.cpp * Wrap WarpX instance and start multi particle container * Fix test Python_pass_mpi_comm * Start wrapper for multiparticle container * Add return policy Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * Update fields to use MultiFabs directly Remove EOL white space Removed old routines accessing MultiFabs Update to use "node_centered" * Fix compilation with Python * Update fields.py to use modified MultiFab tag names * Remove incorrect, unused code * Add function to extract the WarpX MultiParticleContainer * Complete class WarpXParticleContainer * Wrap functions getNprocs / getMyProc * restore `install___` callback API - could remove later if we want but should maintain backward compatibility for now * add `gett_new` and `getistep` functions wrappers; fix typos in `callbacks.py`; avoid error in getting `rho` from `fields.py` * Update callback call and `getNproc`/`getMyProc` function * Replace function add_n_particles * Fix setitem in fields.py for 1d and 2d * also update `gett_new()` in `_libwarpx.py` in case we want to keep that API * added binding for `WarpXParIter` - needed to port `libwarpx.depositChargeDensity()` which is an ongoing effort * Wrap function num_real_comp * added binding for `TotalNumberOfParticles` and continue progress on enabling 1d MCC test to run * add `SyncRho()` binding and create helper function in `libwarpx.depositChargeDensity` to manage scope of the particle iter * Clean up issues in fields.py * update bindings for `get_particle_structs` * Fix setitem in fields.py * switch order of initialization for particle container and particle iterator * switch deposit_charge loop to C++ code; bind `ApplyInverseVolumeScalingToChargeDensity` * move `WarpXParticleContainer.cpp` and `MultiParticleContainer.cpp` to new Particles folder * added binding for `ParticleBoundaryBuffer` * More fixes for fields.py * Fix: Backtraces from Python Add the Python executable name with an absolute path, so backtraces in AMReX work. See linked AMReX issue for details. * Cleaning * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Fix: Backtraces from Python Part II Do not add Python script name - it confuses the AMReX ParmParser to build its table. * Fix: CMake Dependencies for Wheel This fixes a racecondition during `pip_install`: it was possible that not all dimensions where yet build from pybind before we start packing them in the wheel for pip install. * MCC Test: Install Callbacks before Run Otherwise hangs in aquiring the gil during shutdown. * addition of `Python/pywarpx/particle_containers.py` and various associated bindings * Fix: CMake Superbuild w/ Shared AMReX We MUST build AMReX as a shared (so/dll/dylib) library, otherwise all the global state in it will cause split-brain situations, where our Python modules operate on different stacks. * add `clear_all()` to callbacks in order to remove all callbacks at finalize * add `-DWarpX_PYTHON=ON` to CI tests that failed to build * add `get_comp_index` and continue to port particle data bindings * Add AMReX Module as `libwarpx_so.amr` Attribute to pass through the already loaded AMReX module with the matching dimensionality to the simulation. * Fix for fields accounting for guard cells * Fix handling of ghost cells in fields * Update & Test: Particle Boundary Scraping * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * CI: Python Updates - modernize Python setups - drop CUDA 11.0 for good and go 11.3+ as documented already ``` Error #3246: Internal Compiler Error (codegen): "there was an error in verifying the lgenfe output!" ``` * CI: Python Updates (chmod) * Add support for cupy in fields.py * Add MultiFab reduction routines * CI: CUDA 11.3 is <= Ubuntu 20.04 * changed `AddNParticles` to take `amrex::Vector` arguments * setup.py: WarpX_PYTHON=ON * update various 2d and rz tests with new APIs * add `-DWarpX_PYTHON_IPO=OFF` to compile string for 2d and 3d Python CI tests to speed up linking * CI: -DpyAMReX_IPO=OFF * CI: -DpyAMReX_IPO=OFF actually adding `=OFF` * CI: Intel Python * CI: macOS Python Executable Ensure we always use the same `python3` executable, as specified by the `PATH` priority. * CMake: Python Multi-Config Build Add support for multi-config generators, especially on Windows. * __init__.py: Windows DLL Support Python 3.8+ on Windows: DLL search paths for dependent shared libraries Refs.: - python/cpython#80266 - https://docs.python.org/3.8/library/os.html#os.add_dll_directory * CI: pywarpx Update our setup.py cannot install pyamrex yet as a dependency. * ABLASTR: `ablastr/export.H` Add a new header to export public globals that are not covered by `WINDOWS_EXPORT_ALL_SYMBOLS`. https://stackoverflow.com/questions/54560832/cmake-windows-export-all-symbols-does-not-cover-global-variables/54568678#54568678 * WarpX: EXPORT Globals in `.dll` files WarpX still uses a lot of globals: - `static` member variables - `extern` global variables These globals cannot be auto-exported with CMake's `WINDOWS_EXPORT_ALL_SYMBOLS` helper and thus we need to mark them manually for DLL export (and import) via the new ABLASTR `ablastr/export.H` helper macros. This starts to export symbols in the: - WarpX and particle container classes - callback hook database map - ES solver * CI: pywarpx Clang CXXFLAGS Down Move CXXFLAGS (`-Werror ...`) down until deps are installed. * GNUmake: Generate `ablastr/export.H` * CMake: More Symbol Exports for Windows * `WarpX-tests.ini`: Simplify Python no-IPO Also avoids subtle differences in compilation that increase compile time. * Update PICMI_inputs_EB_API.py for embedded_boundary_python_API CI test * Fix Python_magnetostatic_eb_3d * Update: Python_restart_runtime_components New Python APIs * Windows: no dllimport for now * CI: Skip `PYINSTALLOPTIONS` For Now * CMake: Dependency Bump Min-Versions for external packages picked up by `find_package`. * Fix F and G_fp names in fields.py * Tests: Disable `Python_pass_mpi_comm` * Wrappers: Cleanup * pyWarpX: Include Cleaning * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fields.py: Fix F and G Wrappers Correct MultiFab names (w/o components). * Remove unused in fields.py * Windows: New Export Headers - ABLASTR: `ablastr/export.H` - WarpX: `Utils/export.H` * removed `WarpInterface.py` since that functionality is now in `particle_containers.py`; removed parts of `WarpXWrappers.cpp` that have been ported to pyamrex * CMake: Link OBJECT Target PRIVATE * CMake: Remove OBJECT Target Simplify and make `app` link `lib` (default: static). Remove OBJECT target. * Fix in fields.py for the components index * Update get_particle_id/cpu As implemented in pyAMReX with AMReX-Codes/pyamrex#165 * WarpX: Update for Private Constructor * Import AMReX Before pyd DLL Call Importing AMReX will add the `add_dll_directory` to a potentially shared amrex DLL on Windows. * Windows CI: Set PATH to amrex_Nd.dll * CMake: AMReX_INSTALL After Python In superbuild, Python can modify `AMReX_BUILD_SHARED_LIBS`. * Clang Win CI: Manually Install requirements Sporadic error is: ``` ... Installing collected packages: pyparsing, numpy, scipy, periodictable, picmistandard ERROR: Could not install packages due to an OSError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\hostedtoolcache\\windows\\Python\\3.11.4\\x64\\Lib\\site-packages\\numpy\\polynomial\\__init__.py' Consider using the `--user` option or check the permissions. ``` * Hopefully final fixes to fields.py * Update getProbLo/getProbHi * Set plasma length strength Co-authored-by: Remi Lehe <remi.lehe@normalesup.org> * Fix fields method to remove CodeQL notice * Update Comments & Some Finalize * Move: set_plasma_lens_strength to MPC --------- Co-authored-by: Roelof Groenewald <40245517+roelof-groenewald@users.noreply.github.com> Co-authored-by: David Grote <dpgrote@lbl.gov> Co-authored-by: Remi Lehe <remi.lehe@normalesup.org> Co-authored-by: Dave Grote <grote1@llnl.gov> Co-authored-by: Roelof Groenewald <regroenewald@gmail.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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