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, 201 insertions, 0 deletions

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 <WarpX.H>
+// see WarpX.cpp - full includes for _fwd.H headers
+#include <BoundaryConditions/PML.H>
+#include <Diagnostics/MultiDiagnostics.H>
+#include <Diagnostics/ReducedDiags/MultiReducedDiags.H>
+#include <EmbeddedBoundary/WarpXFaceInfoBox.H>
+#include <FieldSolver/FiniteDifferenceSolver/FiniteDifferenceSolver.H>
+#include <FieldSolver/FiniteDifferenceSolver/MacroscopicProperties/MacroscopicProperties.H>
+#include <FieldSolver/FiniteDifferenceSolver/HybridPICModel/HybridPICModel.H>
+#ifdef WARPX_USE_PSATD
+#   include <FieldSolver/SpectralSolver/SpectralKSpace.H>
+#   ifdef WARPX_DIM_RZ
+#       include <FieldSolver/SpectralSolver/SpectralSolverRZ.H>
+#       include <BoundaryConditions/PML_RZ.H>
+#   else
+#       include <FieldSolver/SpectralSolver/SpectralSolver.H>
+#   endif // RZ ifdef
+#endif // use PSATD ifdef
+#include <FieldSolver/WarpX_FDTD.H>
+#include <Filter/NCIGodfreyFilter.H>
+#include <Particles/MultiParticleContainer.H>
+#include <Particles/ParticleBoundaryBuffer.H>
+#include <AcceleratorLattice/AcceleratorLattice.H>
+#include <Utils/TextMsg.H>
+#include <Utils/WarpXAlgorithmSelection.H>
+#include <Utils/WarpXConst.H>
+#include <Utils/WarpXProfilerWrapper.H>
+#include <Utils/WarpXUtil.H>
+
+#include <AMReX.H>
+#include <AMReX_ParmParse.H>
+#include <AMReX_ParallelDescriptor.H>
+
+#if defined(AMREX_DEBUG) || defined(DEBUG)
+#   include <cstdio>
+#endif
+#include <string>
+
+
+//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> 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_<warpx::Config>(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
+            })
+        ;
+}