From 6c93d9fc13830d574c69ac7b166f5fbdb0809731 Mon Sep 17 00:00:00 2001 From: Axel Huebl Date: Sat, 12 Aug 2023 11:17:38 -0700 Subject: Transition to pyAMReX (#3474) * 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 * 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 * 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 * 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.: - https://github.com/python/cpython/issues/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 https://github.com/AMReX-Codes/pyamrex/pull/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 * 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 Co-authored-by: Remi Lehe Co-authored-by: Dave Grote Co-authored-by: Roelof Groenewald Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- Source/Python/WarpX.cpp | 201 ++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 201 insertions(+) create mode 100644 Source/Python/WarpX.cpp (limited to 'Source/Python/WarpX.cpp') diff --git a/Source/Python/WarpX.cpp b/Source/Python/WarpX.cpp new file mode 100644 index 000000000..9ef5281b3 --- /dev/null +++ b/Source/Python/WarpX.cpp @@ -0,0 +1,201 @@ +/* Copyright 2021-2022 The WarpX Community + * + * Authors: Axel Huebl + * License: BSD-3-Clause-LBNL + */ +#include "pyWarpX.H" + +#include +// see WarpX.cpp - full includes for _fwd.H headers +#include +#include +#include +#include +#include +#include +#include +#ifdef WARPX_USE_PSATD +# include +# ifdef WARPX_DIM_RZ +# include +# include +# else +# include +# endif // RZ ifdef +#endif // use PSATD ifdef +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include + +#include +#include +#include + +#if defined(AMREX_DEBUG) || defined(DEBUG) +# include +#endif +#include + + +//using namespace warpx; + +namespace warpx { + struct Config {}; +} + +void init_WarpX (py::module& m) +{ + // Expose the WarpX instance + m.def("get_instance", + [] () { return &WarpX::GetInstance(); }, + "Return a reference to the WarpX object."); + + m.def("finalize", &WarpX::Finalize, + "Close out the WarpX related data"); + + py::class_ warpx(m, "WarpX"); + warpx + // WarpX is a Singleton Class with a private constructor + // https://github.com/ECP-WarpX/WarpX/pull/4104 + // https://pybind11.readthedocs.io/en/stable/advanced/classes.html?highlight=singleton#custom-constructors + .def(py::init([]() { + return &WarpX::GetInstance(); + })) + .def_static("get_instance", + [] () { return &WarpX::GetInstance(); }, + "Return a reference to the WarpX object." + ) + .def_static("finalize", &WarpX::Finalize, + "Close out the WarpX related data" + ) + + .def("initialize_data", &WarpX::InitData, + "Initializes the WarpX simulation" + ) + .def("evolve", &WarpX::Evolve, + "Evolve the simulation the specified number of steps" + ) + + // from AmrCore->AmrMesh + .def("Geom", + //[](WarpX const & wx, int const lev) { return wx.Geom(lev); }, + py::overload_cast< int >(&WarpX::Geom, py::const_), + py::arg("lev") + ) + .def("DistributionMap", + [](WarpX const & wx, int const lev) { return wx.DistributionMap(lev); }, + //py::overload_cast< int >(&WarpX::DistributionMap, py::const_), + py::arg("lev") + ) + .def("boxArray", + [](WarpX const & wx, int const lev) { return wx.boxArray(lev); }, + //py::overload_cast< int >(&WarpX::boxArray, py::const_), + py::arg("lev") + ) + .def("multifab", + [](WarpX const & wx, std::string const multifab_name) { + if (wx.multifab_map.count(multifab_name) > 0) { + return wx.multifab_map.at(multifab_name); + } else { + throw std::runtime_error("The MultiFab '" + multifab_name + "' is unknown or is not allocated!"); + } + }, + py::arg("multifab_name"), + py::return_value_policy::reference_internal, + "Return MultiFabs by name, e.g., 'Efield_aux[x][l=0]', 'Efield_cp[x][l=0]', ..." + ) + .def("multi_particle_container", + [](WarpX& wx){ return &wx.GetPartContainer(); }, + py::return_value_policy::reference_internal + ) + .def("get_particle_boundary_buffer", + [](WarpX& wx){ return &wx.GetParticleBoundaryBuffer(); }, + py::return_value_policy::reference_internal + ) + + // Expose functions used to sync the charge density multifab + // accross tiles and apply appropriate boundary conditions + .def("sync_rho", + [](WarpX& wx){ wx.SyncRho(); } + ) +#ifdef WARPX_DIM_RZ + .def("apply_inverse_volume_scaling_to_charge_density", + [](WarpX& wx, amrex::MultiFab* rho, int const lev) { + wx.ApplyInverseVolumeScalingToChargeDensity(rho, lev); + }, + py::arg("rho"), py::arg("lev") + ) +#endif + + // Expose functions to get the current simulation step and time + .def("getistep", + [](WarpX const & wx, int lev){ return wx.getistep(lev); }, + py::arg("lev") + ) + .def("gett_new", + [](WarpX const & wx, int lev){ return wx.gett_new(lev); }, + py::arg("lev") + ) + + .def("set_potential_on_eb", + [](WarpX& wx, std::string potential) { + wx.m_poisson_boundary_handler.setPotentialEB(potential); + }, + py::arg("potential") + ) + ; + + py::class_(m, "Config") +// .def_property_readonly_static( +// "warpx_version", +// [](py::object) { return Version(); }, +// "WarpX version") + .def_property_readonly_static( + "have_mpi", + [](py::object){ +#ifdef AMREX_USE_MPI + return true; +#else + return false; +#endif + }) + .def_property_readonly_static( + "have_gpu", + [](py::object){ +#ifdef AMREX_USE_GPU + return true; +#else + return false; +#endif + }) + .def_property_readonly_static( + "have_omp", + [](py::object){ +#ifdef AMREX_USE_OMP + return true; +#else + return false; +#endif + }) + .def_property_readonly_static( + "gpu_backend", + [](py::object){ +#ifdef AMREX_USE_CUDA + return "CUDA"; +#elif defined(AMREX_USE_HIP) + return "HIP"; +#elif defined(AMREX_USE_DPCPP) + return "SYCL"; +#else + return py::none(); +#endif + }) + ; +} -- cgit v1.2.3