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, 136 insertions, 0 deletions

diff --git a/Source/Python/pyWarpX.cpp b/Source/Python/pyWarpX.cpp
new file mode 100644
index 000000000..37d910f03
--- /dev/null
+++ b/Source/Python/pyWarpX.cpp
@@ -0,0 +1,136 @@
+/* Copyright 2021-2022 The ImpactX Community
+ *
+ * Authors: Axel Huebl
+ * License: BSD-3-Clause-LBNL
+ */
+#include "pyWarpX.H"
+#include "WarpX_py.H"
+
+#include <WarpX.H>  // todo: move this out to Python/WarpX.cpp
+#include <Utils/WarpXUtil.H>  // todo: move to its own Python/Utils.cpp
+#include <Initialization/WarpXAMReXInit.H>
+
+#define STRINGIFY(x) #x
+#define MACRO_STRINGIFY(x) STRINGIFY(x)
+#define CONCAT_NAME(PRE, SUF) PRE ## SUF
+
+// see: CMakeLists.txt, setup.py and __init__.py
+#if defined(WARPX_DIM_1D_Z)
+#  define PYWARPX_MODULE_NAME CONCAT_NAME(warpx_pybind_, 1d)
+#elif defined(WARPX_DIM_XZ)
+#  define PYWARPX_MODULE_NAME CONCAT_NAME(warpx_pybind_, 2d)
+#elif defined(WARPX_DIM_RZ)
+#  define PYWARPX_MODULE_NAME CONCAT_NAME(warpx_pybind_, rz)
+#elif defined(WARPX_DIM_3D)
+#  define PYWARPX_MODULE_NAME CONCAT_NAME(warpx_pybind_, 3d)
+#endif
+
+//using namespace warpx;
+
+
+// forward declarations of exposed classes
+void init_BoundaryBufferParIter (py::module&);
+void init_MultiParticleContainer (py::module&);
+void init_ParticleBoundaryBuffer (py::module&);
+void init_PinnedMemoryParticleContainer (py::module&);
+void init_WarpXParIter (py::module&);
+void init_WarpXParticleContainer (py::module&);
+void init_WarpX(py::module&);
+
+PYBIND11_MODULE(PYWARPX_MODULE_NAME, m) {
+    // make sure AMReX types are known
+#if defined(WARPX_DIM_3D)
+    auto amr = py::module::import("amrex.space3d");
+#elif defined(WARPX_DIM_1D_Z)
+    auto amr = py::module::import("amrex.space1d");
+#else
+    auto amr = py::module::import("amrex.space2d");
+#endif
+
+    m.doc() = R"pbdoc(
+            warpx_pybind
+            --------------
+            .. currentmodule:: warpx_pybind_(1d|2d|3d|rz)
+
+            .. autosummary::
+               :toctree: _generate
+               WarpX
+    )pbdoc";
+
+    // note: order from parent to child classes
+    init_PinnedMemoryParticleContainer(m);
+    init_WarpXParticleContainer(m);
+    init_WarpXParIter(m);
+    init_BoundaryBufferParIter(m);
+    init_ParticleBoundaryBuffer(m);
+    init_MultiParticleContainer(m);
+    init_WarpX(m);
+
+    // expose our amrex module
+    m.attr("amr") = amr;
+
+    // API runtime version
+    //   note PEP-440 syntax: x.y.zaN but x.y.z.devN
+#ifdef PYIMPACTX_VERSION_INFO
+    m.attr("__version__") = MACRO_STRINGIFY(PYIMPACTX_VERSION_INFO);
+#else
+    m.attr("__version__") = "dev";
+#endif
+
+    // authors
+    m.attr("__author__") =
+        "Jean-Luc Vay, David P. Grote, Maxence Thevenet, Remi Lehe, Andrew Myers, Weiqun Zhang, Axel Huebl, et al.";
+
+    // API runtime build-time feature variants
+    // m.attr("variants") = warpx::getVariants();
+    // TODO allow to query runtime versions of all dependencies
+
+    // license SPDX identifier
+    m.attr("__license__") = "BSD-3-Clause-LBNL";
+
+    // TODO broken numpy if not at least v1.15.0: raise warning
+    // auto numpy = py::module::import("numpy");
+    // auto npversion = numpy.attr("__version__");
+    // std::cout << "numpy version: " << py::str(npversion) << std::endl;
+
+    m.def("amrex_init",
+        [](const py::list args) {
+            amrex::Vector<std::string> cargs;
+            amrex::Vector<char*> argv;
+
+            // Populate the "command line"
+            for (const auto& v: args)
+                cargs.push_back(v.cast<std::string>());
+            for (auto& v: cargs)
+                argv.push_back(&v[0]);
+            int argc = argv.size();
+
+            // note: +1 since there is an extra char-string array element,
+            //       that ANSII C requires to be a simple NULL entry
+            //       https://stackoverflow.com/a/39096006/2719194
+            argv.push_back(NULL);
+            char** tmp = argv.data();
+
+            const bool build_parm_parse = (cargs.size() > 1);
+            // TODO: handle version with MPI
+            return warpx::initialization::amrex_init(argc, tmp, build_parm_parse);
+        }, py::return_value_policy::reference,
+        "Initialize AMReX library");
+    m.def("amrex_finalize", [] () { amrex::Finalize(); },
+        "Close out the amrex related data");
+    m.def("convert_lab_params_to_boost",  &ConvertLabParamsToBoost,
+        "Convert input parameters from the lab frame to the boosted frame");
+    m.def("read_BC_params", &ReadBCParams,
+        "Read the boundary condition parametes and check for consistency");
+    m.def("check_gridding_for_RZ_spectral", &CheckGriddingForRZSpectral,
+        "Ensure that the grid is setup appropriately with using the RZ spectral solver");
+
+    // Expose functions to get the processor number
+    m.def("getNProcs", [](){return amrex::ParallelDescriptor::NProcs();} );
+    m.def("getMyProc", [](){return amrex::ParallelDescriptor::MyProc();} );
+
+    // Expose the python callback function installation and removal functions
+    m.def("add_python_callback", &InstallPythonCallback);
+    m.def("remove_python_callback", &ClearPythonCallback);
+    m.def("execute_python_callback", &ExecutePythonCallback, py::arg("name"));
+}