idefix/src/pydefix.cpp at master · idefix-code/idefix · GitHub

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// ***********************************************************************************

// Idefix MHD astrophysical code

// Source file src/pydefix.cpp

// Last modified : 08/2026

// Copyright(C) by :

// - Geoffroy Lesur <geoffroy.lesur@univ-grenoble-alpes.fr> (IPAG/UGA/CNRS - 2023 - 2026)

// - Sébastien Valat <sebastien.valat@univ-grenoble-alpes.fr> (IPAG/UGA/CNRS - 2026)

// and other code contributors

// Licensed under CeCILL 2.1 License, see COPYING for more information

// ***********************************************************************************

#define PYBIND11_DETAILED_ERROR_MESSAGES

#include "pydefix.hpp"

#include <pybind11/embed.h> // everything needed for embedding

#include <pybind11/numpy.h> // for numpy arrays

#include <pybind11/stl.h> // For STL vectors and containers

#include <string>

#include <vector>

#include <csignal>

#include "idefix.hpp"

#include "dataBlock.hpp"

#include "dataBlockHost.hpp"

namespace py = pybind11;

int Pydefix::ninstance = 0;

namespace PydefixTools {

// Functions provided by Idefix in Pydefix for user convenience

py::array_t<real, py::array::c_style> GatherIdefixArray(IdefixHostArray3D<real> in,

DataBlockHost dataHost,

bool keepBoundaries = true,

bool broadcast = true) {

idfx::pushRegion("PydefixTools::GatherIdefixArray");

Grid *grid = dataHost.data->mygrid;

IdefixHostArray3D<real> out;

py::array_t<real, py::array::c_style> pyOut;

if(broadcast || idfx::prank==0) {

if(keepBoundaries) {

// Create a python-managed array, with memory accessible from Kokkos

pyOut = py::array_t<real, py::array::c_style>({grid->np_tot[KDIR],

grid->np_tot[JDIR],

grid->np_tot[IDIR]});

out = Kokkos::View<real***,

Kokkos::LayoutRight,

Kokkos::HostSpace,

Kokkos::MemoryTraits<Kokkos::Unmanaged>>

(reinterpret_cast<real*>(pyOut.request().ptr),

grid->np_tot[KDIR],

grid->np_tot[JDIR],

grid->np_tot[IDIR]);

} else {

pyOut = py::array_t<real, py::array::c_style>({grid->np_int[KDIR],

grid->np_int[JDIR],

grid->np_int[IDIR]});

out = Kokkos::View<real***,

Kokkos::LayoutRight,

Kokkos::HostSpace,

Kokkos::MemoryTraits<Kokkos::Unmanaged>>

(reinterpret_cast<real*>(pyOut.request().ptr),

grid->np_int[KDIR],

grid->np_int[JDIR],

grid->np_int[IDIR]);

}

if(idfx::prank == 0) {

for(int rank = 0 ; rank < idfx::psize ; rank++) {

// np_tot: total size of the incoming array

// np_int: size that should be copied into global

// beg: offset in the incoming array where copy should begin

// gbeg: offset in the global array where copy should be begin

[[maybe_unused]] std::array<int,3> np_int,np_tot, beg, gbeg;

IdefixHostArray3D<real> buf;

if(rank==0) {

np_int = dataHost.np_int;

np_tot = dataHost.np_tot;

gbeg = dataHost.gbeg;

beg = dataHost.beg;

// Add back boundaries

if(keepBoundaries) {

for(int dir = 0 ; dir < DIMENSIONS ; dir++) {

if(dataHost.lbound[dir] != internal) {

np_int[dir] += dataHost.nghost[dir];

gbeg[dir] -= dataHost.nghost[dir];

beg[dir] -= dataHost.nghost[dir];

}

if(dataHost.rbound[dir] != internal) {

np_int[dir] += dataHost.nghost[dir];

}

buf = in;

} else { // target rank >0

#ifdef WITH_MPI

MPI_Status status;

// Fetch the local array size

idfx::MPI_Recv(np_int, 3, MPI_INT, rank, 010, MPI_COMM_WORLD, &status);

idfx::MPI_Recv(np_tot, 3, MPI_INT, rank, 011, MPI_COMM_WORLD, &status);

idfx::MPI_Recv(beg, 3, MPI_INT, rank, 012, MPI_COMM_WORLD, &status);

idfx::MPI_Recv(gbeg, 3, MPI_INT, rank, 013, MPI_COMM_WORLD, &status);

buf = IdefixHostArray3D<real>("pydefix::tempArray",

np_tot[KDIR],np_tot[JDIR],np_tot[IDIR]);

// Fetch data

idfx::MPI_Recv(buf, np_tot[IDIR]*np_tot[JDIR]*np_tot[KDIR],

realMPI, rank, 014, MPI_COMM_WORLD,&status);

#else

IDEFIX_ERROR("Can't deal with psize>1 without MPI.");

#endif

} // target rank

// Copy data from the buffer

for(int k = 0 ; k < np_int[KDIR] ; k++) {

int kt = k+gbeg[KDIR];

if(!keepBoundaries) kt -= dataHost.nghost[KDIR];

for(int j = 0 ; j < np_int[JDIR] ; j++) {

int jt = j+gbeg[JDIR];

if(!keepBoundaries) jt -= dataHost.nghost[JDIR];

for(int i = 0 ; i < np_int[IDIR] ; i++) {

int it = i+gbeg[IDIR];

if(!keepBoundaries) it -= dataHost.nghost[IDIR];

out(kt,jt,it) = buf(k+beg[KDIR],j+beg[JDIR],i+beg[IDIR]);

}

}// End for

}// End loop on target rank for root process

} else { // MPI prank >0

std::array<int,3> np_int = dataHost.np_int;

[[maybe_unused]] std::array<int,3> np_tot = dataHost.np_tot;

std::array<int,3> gbeg = dataHost.gbeg;

std::array<int,3> beg = dataHost.beg;

// Add back boundaries

if(keepBoundaries) {

for(int dir = 0 ; dir < DIMENSIONS ; dir++) {

if(dataHost.lbound[dir] != internal) {

np_int[dir] += dataHost.nghost[dir];

gbeg[dir] -= dataHost.nghost[dir];

beg[dir] -= dataHost.nghost[dir];

}

if(dataHost.rbound[dir] != internal) {

np_int[dir] += dataHost.nghost[dir];

}

#ifdef WITH_MPI

// send the local array size

idfx::MPI_Send(np_int, 3, MPI_INT, 0, 010, MPI_COMM_WORLD);

idfx::MPI_Send(np_tot, 3, MPI_INT, 0, 011, MPI_COMM_WORLD);

idfx::MPI_Send(beg, 3, MPI_INT, 0, 012, MPI_COMM_WORLD);

idfx::MPI_Send(gbeg, 3, MPI_INT, 0, 013, MPI_COMM_WORLD);

idfx::MPI_Send(in, np_tot[IDIR]*np_tot[JDIR]*np_tot[KDIR], realMPI, 0, 014, MPI_COMM_WORLD);

#else

IDEFIX_ERROR("Can't deal with psize>1 without MPI.");

#endif

}

// All is transfered

#ifdef WITH_MPI

if(broadcast) {

idfx::MPI_Bcast(out, out.extent(0)*out.extent(1)*out.extent(2), realMPI, 0, MPI_COMM_WORLD);

}

#endif

idfx::popRegion();

return pyOut;

}

}// namespace PydefixTools

/************************************

* DataBlockHost Python binding

* **********************************/

PYBIND11_EMBEDDED_MODULE(pydefix, m) {

py::class_<DataBlockHost>(m, "DataBlockHost")

.def(py::init<>())

.def_readwrite("x", &DataBlockHost::x)

.def_readwrite("xr", &DataBlockHost::xr)

.def_readwrite("xl", &DataBlockHost::xl)

.def_readwrite("dx", &DataBlockHost::dx)

.def_readwrite("dV", &DataBlockHost::dV)

.def_readwrite("A", &DataBlockHost::A)

.def_readwrite("Vc", &DataBlockHost::Vc)

.def_readwrite("dustVc", &DataBlockHost::dustVc)

#if MHD == YES

.def_readwrite("Vs", &DataBlockHost::Vs)

.def_readwrite("Ve", &DataBlockHost::Ve)

.def_readwrite("J", &DataBlockHost::J)

.def_readwrite("Ex1", &DataBlockHost::Ex1)

.def_readwrite("Ex2", &DataBlockHost::Ex2)

.def_readwrite("Ex3", &DataBlockHost::Ex3)

#endif

.def_readwrite("xbeg", &DataBlockHost::xbeg)

.def_readwrite("xend", &DataBlockHost::xend)

.def_readwrite("gbeg", &DataBlockHost::gbeg)

.def_readwrite("gend", &DataBlockHost::gend)

.def_readwrite("beg", &DataBlockHost::beg)

.def_readwrite("end", &DataBlockHost::end)

.def_readwrite("np_tot", &DataBlockHost::np_tot)

.def_readwrite("np_int", &DataBlockHost::np_int)

.def_readwrite("nghost", &DataBlockHost::nghost)

.def_readwrite("InvDt", &DataBlockHost::InvDt)

.def_readwrite("t",&DataBlockHost::t)

.def_readwrite("dt",&DataBlockHost::dt);

py::class_<GridHost>(m, "GridHost")

.def(py::init<>())

.def_readwrite("x", &GridHost::x)

.def_readwrite("xr", &GridHost::xr)

.def_readwrite("xl", &GridHost::xl)

.def_readwrite("dx", &GridHost::dx)

.def_readwrite("xbeg", &GridHost::xbeg)

.def_readwrite("xend", &GridHost::xend)

.def_readwrite("np_tot", &GridHost::np_tot)

.def_readwrite("np_int", &GridHost::np_int)

.def_readwrite("nghost", &GridHost::nghost);

m.attr("RHO") = RHO;

m.attr("VX1") = VX1;

m.attr("VX2") = VX2;

m.attr("VX3") = VX3;

m.attr("PRS") = PRS;

#if MHD == YES

m.attr("BX1") = BX1;

m.attr("BX2") = BX2;

m.attr("BX3") = BX3;

D_EXPAND(

m.attr("BX1s") = BX1s; ,

m.attr("BX2s") = BX2s; ,

m.attr("BX3s") = BX3s; )

#ifdef EVOLVE_VECTOR_POTENTIAL

m.attr("AX1e") = AX1e;

m.attr("AX2e") = AX2e;

m.attr("AX3e") = AX3e;

#endif

m.attr("IDIR") = IDIR;

m.attr("JDIR") = JDIR;

m.attr("KDIR") = KDIR;

m.attr("prank") = idfx::prank;

m.attr("psize") = idfx::psize;

m.def("GatherIdefixArray",&PydefixTools::GatherIdefixArray,

py::arg("in"),

py::arg("data"),

py::arg("keepBoundaries") = true,

py::arg("broadcast") = true,

"Gather arrays from MPI domain decomposition");

}

template<typename... Ts>

void Pydefix::CallScript(std::string scriptName, std::string funcName, Ts... args) {

idfx::pushRegion("Pydefix::CallScript");

try {

py::module_ script = py::module_::import(scriptName.c_str());

py::object result = script.attr(funcName.c_str())(&args...);

} catch(std::exception &e) {

std::stringstream message;

message << "An exception occured while calling the Python interpreter" << std::endl

<< "in file \"" << scriptName << ".py\" function \"" << funcName << "\":"

<< std::endl

<< e.what() << std::endl;

IDEFIX_ERROR(message);

}

idfx::popRegion();

}

Pydefix::Pydefix(Input &input) {

// Check that the input has a [python] block

if(input.CheckBlock("Python")) {

this->isActive = true;

ninstance++;

// Check whether we need to start an interpreter

if(ninstance==1) {

idfx::cout << "Pydefix: start Python interpreter." << std::endl;

py::initialize_interpreter();

std::signal(SIGINT, SIG_DFL); // restore "terminate on Ctrl-C" signal handler

py::exec("import sys; print(f'Pydefix: Python Version: {sys.version}')");

py::exec("print(f'Pydefix: Executable Path: {sys.executable}')");

py::exec("print(f'Pydefix: Sys Path: {sys.path}')");

}

this->scriptFilename = input.Get<std::string>("Python","script",0);

if(scriptFilename.substr(scriptFilename.length() - 3, 3).compare(".py")==0) {

IDEFIX_ERROR("You should not include the python script .py extension in your input file");

}

if(input.CheckEntry("Python","output_function")>0) {

this->haveOutput = true;

this->outputFunctionName = input.Get<std::string>("Python","output_function",0);

}

if(input.CheckEntry("Python","initflow_function")>0) {

this->haveInitflow = true;

this->initflowFunctionName = input.Get<std::string>("Python","initflow_function",0);

}

void Pydefix::Output(DataBlock &data, int n) {

idfx::pushRegion("Pydefix::Output");

if(!this->isActive) {

IDEFIX_ERROR("Python Outputs requires the [python] block to be defined in your input file.");

}

if(!this->haveOutput) {

IDEFIX_ERROR("No python output function has been defined "

"in your input file [python]:output_function");

}

DataBlockHost dataHost(data);

GridHost gridHost(*data.mygrid);

gridHost.SyncFromDevice();

dataHost.SyncFromDevice();

this->CallScript(this->scriptFilename,this->outputFunctionName,dataHost, gridHost, n);

idfx::popRegion();

}

void Pydefix::InitFlow(DataBlock &data) {

idfx::pushRegion("Pydefix::InitFlow");

if(!this->isActive) {

IDEFIX_ERROR("Python Initflow requires the [python] block to be defined in your input file.");

}

if(!this->haveInitflow) {

IDEFIX_ERROR("No python initflow function has been defined "

"in your input file [python]:initflow_function");

}

DataBlockHost dataHost(data);

dataHost.SyncFromDevice();

this->CallScript(this->scriptFilename,this->initflowFunctionName,dataHost);

dataHost.SyncToDevice();

idfx::popRegion();

}

void Pydefix::ShowConfig() {

if(isActive == false) {

idfx::cout << "Pydefix: DISABLED." << std::endl;

} else {

idfx::cout << "Pydefix: ENABLED." << std::endl;

if(haveOutput) {

idfx::cout << "Pydefix: output function ENABLED." << std::endl;

} else {

idfx::cout << "Pydefix: output function DISABLED." << std::endl;

}

if(haveInitflow) {

idfx::cout << "Pydefix: initflow function ENABLED." << std::endl;

} else {

idfx::cout << "Pydefix: initflow function DISABLED." << std::endl;

}

Pydefix::~Pydefix() {

if(isActive) {

if(ninstance == 1) {

py::finalize_interpreter();

idfx::cout << "Pydefix: shutdown Python interpreter." << std::endl;

}

ninstance--;

isActive = false;

}

py::array_t<real> Pydefix::toNumpyArray(const IdefixHostArray3D<real>& in) {

py::array_t<real, py::array::c_style> array({in.extent(0),in.extent(1),in.extent(2)},in.data());

return array;

}

py::array_t<real> Pydefix::toNumpyArray(const IdefixHostArray4D<real>& in) {

py::array_t<real, py::array::c_style> array({in.extent(0),in.extent(1),in.extent(2),in.extent(3)},in.data());

return array;

}

idefix/src/pydefix.cpp at master · idefix-code/idefix · GitHub

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