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 <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.:
- 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 <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>

1 files changed, 0 insertions, 182 deletions

diff --git a/Python/pywarpx/PGroup.py b/Python/pywarpx/PGroup.py
deleted file mode 100644
index 0dcb664e5..000000000
--- a/Python/pywarpx/PGroup.py
+++ /dev/null
@@ -1,182 +0,0 @@
-# Copyright 2017-2019 David Grote
-#
-# This file is part of WarpX.
-#
-# License: BSD-3-Clause-LBNL
-
-import numpy as np
-
-from ._libwarpx import libwarpx
-from ._picmi import constants
-
-
-class PGroup(object):
-    """Implements a class that has the same API as a warp ParticleGroup instance.
-    """
-
-    def __init__(self, igroup, ispecie, level=0):
-        self.igroup = igroup
-        self.ispecie = ispecie
-        self.level = level
-        self.ns = 1 # Number of species
-
-        self.gallot()
-
-    def name(self):
-        return 'WarpXParticleGroup'
-
-    def gallot(self):
-        self.lebcancel_pusher = 0 # turns on/off cancellation of E+VxB within V push (logical type)
-        self.lebcancel = 0 # turns on/off cancellation of E+VxB before V push (logical type)
-
-        self.sm = np.zeros(self.ns) # Species mass [kg]
-        self.sq = np.zeros(self.ns) # Species charge [C]
-        self.sw = np.ones(self.ns) # Species weight, (real particles per simulation particles)
-
-        self.sid = np.arange(self.ns, dtype=int) # Global species index for each species
-        self.ndts = np.ones(self.ns, dtype=int) # Stride for time step advance for each species
-        self.ldts = np.ones(self.ns, dtype=int) # (logical type)
-        self.lvdts = np.ones(self.ns, dtype=int) # (logical type)
-        self.iselfb = np.zeros(self.ns, dtype=int) # Group number for particles that are affected by
-                                                   # their own magnetic field, using the 1/gamma**2
-                                                   # approximation. The correction is not applied to
-                                                   # group number -1.
-        self.fselfb = np.zeros(self.ns) # The scaling factor, vz.
-        self.l_maps = np.zeros(self.ns)
-        self.dtscale = np.ones(self.ns) # Scale factor applied to time step size for each
-                                        # species. Only makes sense in steaday and and
-                                        # transverse slice modes.
-
-        self.limplicit = np.zeros(self.ns, dtype=int) # Flags implicit particle species (logical type)
-        self.iimplicit = np.full(self.ns, -1, dtype=int) # Group number for implicit particles
-        self.ldoadvance = np.ones(self.ns, dtype=int) # Flags whether particles are time advanced (logical type)
-        self.lboundaries = np.ones(self.ns, dtype=int) # Flags whether boundary conditions need to be applied (logical type)
-        self.lparaxial = np.zeros(self.ns, dtype=int) # Flags to turn on/off paraxial approximation (logical type)
-
-        self.zshift = np.zeros(self.ns)
-        self.gamma_ebcancel_max = np.ones(self.ns) # maximum value allowed for ExB cancellation
-
-    # --- Temporary fix
-    gchange = gallot
-
-    def allocated(self, name):
-        return True
-
-    def addspecies(self):
-        pass
-
-    def getnpid(self):
-        return libwarpx.get_nattr()
-    npid = property(getnpid)
-
-    def getnps(self):
-        return np.array([len(self.xp)], dtype='l')
-    nps = property(getnps)
-
-    def getins(self):
-        return np.ones(self.ns, dtype='l')
-    ins = property(getins)
-
-    def getipmax(self):
-        return np.array([0, len(self.xp)], dtype='l')
-    ipmax = property(getipmax)
-
-    def getnpmax(self):
-        return self.nps.sum()
-    npmax = property(getnpmax)
-
-    def getxp(self):
-        return libwarpx.get_particle_x(self.ispecie, self.level)[self.igroup]
-    xp = property(getxp)
-
-    def getyp(self):
-        return libwarpx.get_particle_y(self.ispecie, self.level)[self.igroup]
-    yp = property(getyp)
-
-    def getrp(self):
-        return libwarpx.get_particle_r(self.ispecie, self.level)[self.igroup]
-    rp = property(getrp)
-
-    def getzp(self):
-        return libwarpx.get_particle_z(self.ispecie, self.level)[self.igroup]
-    zp = property(getzp)
-
-    def getuxp(self):
-        return libwarpx.get_particle_ux(self.ispecie, self.level)[self.igroup]
-    uxp = property(getuxp)
-
-    def getuyp(self):
-        return libwarpx.get_particle_uy(self.ispecie, self.level)[self.igroup]
-    uyp = property(getuyp)
-
-    def getuzp(self):
-        return libwarpx.get_particle_uz(self.ispecie, self.level)[self.igroup]
-    uzp = property(getuzp)
-
-    def getw(self):
-        return libwarpx.get_particle_weight(self.ispecie, self.level)[self.igroup]
-
-    def getpid(self, id):
-        pid = libwarpx.get_particle_arrays(self.ispecie, id, self.level)[self.igroup]
-        return np.array([pid]).T
-
-    def getgaminv(self):
-        uxp = self.getuxp()
-        uyp = self.getuyp()
-        uzp = self.getuzp()
-        return np.sqrt(1. - (uxp**2 + uyp**2 + uzp**2)/constants.c**2)
-    gaminv = property(getgaminv)
-
-    def getex(self):
-        raise Exception('Particle E fields not supported')
-    ex = property(getex)
-
-    def getey(self):
-        raise Exception('Particle E fields not supported')
-    ey = property(getey)
-
-    def getez(self):
-        raise Exception('Particle E fields not supported')
-    ez = property(getez)
-
-    def getbx(self):
-        raise Exception('Particle B fields not supported')
-    bx = property(getbx)
-
-    def getby(self):
-        raise Exception('Particle B fields not supported')
-    by = property(getby)
-
-    def getbz(self):
-        raise Exception('Particle B fields not supported')
-    bz = property(getbz)
-
-    def gettheta(self):
-        return libwarpx.get_particle_theta(self.ispecie, self.level)[self.igroup]
-    theta = property(gettheta)
-
-class PGroups(object):
-    def __init__(self, ispecie=0, level=0):
-        self.ispecie = ispecie
-        self.level = level
-
-    def setuppgroups(self):
-        xall = libwarpx.get_particle_x(self.ispecie, self.level)
-        self.ngroups = len(xall)
-
-        self._pgroups = []
-        for igroup in range(self.ngroups):
-            self._pgroups.append(PGroup(igroup, self.ispecie, self.level))
-
-    def __iter__(self):
-        self.setuppgroups()
-        for igroup in range(self.ngroups):
-            yield self._pgroups[igroup]
-
-    def __getitem__(self, key):
-        self.setuppgroups()
-        return self._pgroups[key]
-
-    def __len__(self):
-        self.setuppgroups()
-        return len(self._pgroups)