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> --- Python/pywarpx/WarpInterface.py | 190 ---------------------------------------- 1 file changed, 190 deletions(-) delete mode 100644 Python/pywarpx/WarpInterface.py (limited to 'Python/pywarpx/WarpInterface.py') diff --git a/Python/pywarpx/WarpInterface.py b/Python/pywarpx/WarpInterface.py deleted file mode 100644 index dc80e4bc9..000000000 --- a/Python/pywarpx/WarpInterface.py +++ /dev/null @@ -1,190 +0,0 @@ -# Copyright 2019 David Grote -# -# This file is part of WarpX. -# -# License: BSD-3-Clause-LBNL - -# This sets up an interface between Warp and WarpX, allowing access to WarpX data using -# classes from Warp. - -# The routine warp_species will return an instance of the Species class from Warp, -# giving nearly all of the capability of that class, including accessing the data -# using down selection and all of the plots. - -# The class WarpX_EM3D inherits from Warp's EM3D class. It primarily provides -# access to the field plotting routines. - -import warp - -from pywarpx import PGroup - -from . import fields - -# The particle weight is always the first pid -warp.top.wpid = 1 - -def warp_species(warp_type, picmi_species, level=0): - """Returns a Warp species that has a reference to the WarpX particles. - """ - pgroups = PGroup.PGroups(ispecie=picmi_species.species_number, level=level) - return warp.Species(type=warp_type, pgroups=pgroups) - - -class _WarpX_FIELDtype(object): - """Mirrors part of the EM3D_FIELDtype type from Warp - yf - """ - def __init__(self, yf): - self.yf = yf - - -class _WarpX_BLOCKtype(object): - """Mirrors part of the EM3D_BLOCKtype type from Warp - core - xmin, ymin, zmin - xmax, ymax, zmax - dx, dy, dz - xrbnd, yrbnd, zrbnd - """ - def __init__(self, fields, picmi_grid): - self.core = _WarpX_FIELDtype(fields) - self.picmi_grid = picmi_grid - - self.xmin = self.picmi_grid.lower_bound[0] - if self.picmi_grid.number_of_dimensions == 3: - self.ymin = self.picmi_grid.lower_bound[1] - else: - self.ymin = 0. - self.zmin = self.picmi_grid.lower_bound[-1] - - self.xmax = self.picmi_grid.upper_bound[0] - if self.picmi_grid.number_of_dimensions == 3: - self.ymax = self.picmi_grid.upper_bound[1] - else: - self.ymax = 0. - self.zmax = self.picmi_grid.upper_bound[-1] - - self.dx = (self.xmax - self.xmin)/self.picmi_grid.number_of_cells[0] - if self.picmi_grid.number_of_dimensions == 3: - self.dy = (self.ymax - self.ymin)/self.picmi_grid.number_of_cells[1] - else: - self.dy = 1. - self.dz = (self.zmax - self.zmin)/self.picmi_grid.number_of_cells[-1] - - self.xrbnd = 0 - self.yrbnd = 0 - self.zrbnd = 0 - - -class _WarpX_YEEFIELDtype(object): - """Mirrors part of the EM3D_YEEFIELDtype type from Warp - Exp, Eyp, Ezp - Bxp, Byp, Bzp - Ex, Ey, Ez - Bx, By, Bz - Jx, Jy, Jz - """ - def __init__(self, level=0): - self.level = level - self._Ex_wrap = fields.ExWrapper(level, include_ghosts=True) - self._Ey_wrap = fields.EyWrapper(level, include_ghosts=True) - self._Ez_wrap = fields.EzWrapper(level, include_ghosts=True) - self._Bx_wrap = fields.BxWrapper(level, include_ghosts=True) - self._By_wrap = fields.ByWrapper(level, include_ghosts=True) - self._Bz_wrap = fields.BzWrapper(level, include_ghosts=True) - self._Jx_wrap = fields.JxWrapper(level, include_ghosts=True) - self._Jy_wrap = fields.JyWrapper(level, include_ghosts=True) - self._Jz_wrap = fields.JzWrapper(level, include_ghosts=True) - - self._Ex_wrap._getlovects() # --- Calculated nghosts - self.nxguard = self._Ex_wrap.nghosts - self.nyguard = self._Ex_wrap.nghosts - self.nzguard = self._Ex_wrap.nghosts - - def _get_wrapped_array(self, wrapper): - result = wrapper[...] - if len(result.shape) == 2: - # --- Add the middle dimension that Warp is expecting - result.shape = [result.shape[0], 1, result.shape[1]] - return result - - @property - def Exp(self): - return self._get_wrapped_array(self._Ex_wrap) - @property - def Eyp(self): - return self._get_wrapped_array(self._Ey_wrap) - @property - def Ezp(self): - return self._get_wrapped_array(self._Ez_wrap) - @property - def Bxp(self): - return self._get_wrapped_array(self._Bx_wrap) - @property - def Byp(self): - return self._get_wrapped_array(self._By_wrap) - @property - def Bzp(self): - return self._get_wrapped_array(self._Bz_wrap) - @property - def Ex(self): - return self._get_wrapped_array(self._Ex_wrap) - @property - def Ey(self): - return self._get_wrapped_array(self._Ey_wrap) - @property - def Ez(self): - return self._get_wrapped_array(self._Ez_wrap) - @property - def Bx(self): - return self._get_wrapped_array(self._Bx_wrap) - @property - def By(self): - return self._get_wrapped_array(self._By_wrap) - @property - def Bz(self): - return self._get_wrapped_array(self._Bz_wrap) - @property - def Jx(self): - return self._get_wrapped_array(self._Jx_wrap) - @property - def Jy(self): - return self._get_wrapped_array(self._Jy_wrap) - @property - def Jz(self): - return self._get_wrapped_array(self._Jz_wrap) - - -class WarpX_EM3D(warp.EM3D): - """Mirrors part of the Warp EM3D class, mostly diagnostics. - """ - def __init__(self, picmi_grid, level=0): - self.picmi_grid = picmi_grid - self.level = level - - # --- Only define what is necessary for the diagnostics - self.fields = _WarpX_YEEFIELDtype(level) - self.block = _WarpX_BLOCKtype(self.fields, picmi_grid) - - self.isactive = True - - self.l_1dz = (picmi_grid.number_of_dimensions == 1) - self.l_2dxz = (picmi_grid.number_of_dimensions == 2) - try: - picmi_grid.nr - except AttributeError: - self.l_2drz = False - else: - self.l_2drz = True - - self.l4symtry = False - self.l2symtry = False - - self.nx = picmi_grid.number_of_cells[0] - if not self.l_2dxz: - self.ny = picmi_grid.number_of_cells[1] - else: - self.ny = 0 - self.nz = picmi_grid.number_of_cells[-1] - - self.zgrid = 0. # --- This should be obtained from WarpX -- cgit v1.2.3