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, 190 deletions

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