Maj terminée. Pour consulter la release notes associée voici le lien :
https://about.gitlab.com/releases/2021/07/07/critical-security-release-gitlab-14-0-4-released/

MPIInterpolationFMM.hpp 13 KB
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// See LICENCE file at project root

// ==== CMAKE =====
// @FUSE_MPI
// @FUSE_BLAS
// ================

#include <iostream>
#include <stdexcept>
#include <cstdio>
#include <cstdlib>


#include "ScalFmmConfig.h"
#include "Containers/FOctree.hpp"
#include "Utils/FMpi.hpp"
#include "Core/FFmmAlgorithmThreadProc.hpp"
#include "Core/FFmmAlgorithmThreadProcPeriodic.hpp"

#include "Files/FFmaGenericLoader.hpp"
#include "Files/FMpiFmaGenericLoader.hpp"
#include "Files/FMpiTreeBuilder.hpp"

#include "Utils/FLeafBalance.hpp"

#include "Kernels/Interpolation/FInterpMatrixKernel.hpp"
#include "Kernels/Chebyshev/FChebSymKernel.hpp"
#include "Kernels/Chebyshev/FChebCell.hpp"

#include "Components/FSimpleLeaf.hpp"
#include "Kernels/P2P/FP2PParticleContainerIndexed.hpp"

#include "Utils/FParameters.hpp"
#include "Utils/FParameterNames.hpp"

//
// Order of the Interpolation approximation
static constexpr unsigned ORDER = 6 ;
using FReal                 = double;
//   1/r kernel
//
using MatrixKernelClass     = FInterpMatrixKernelR<FReal> ;
//
// Typedefs
using ContainerClass = FP2PParticleContainerIndexed<FReal>;
using LeafClass      = FSimpleLeaf<FReal, ContainerClass>;

using CellClass      = FInterpolationCell<FReal, ORDER>;


using OctreeClass    = FOctree<FReal,CellClass,ContainerClass,LeafClass>;

using MatrixKernelClass = FInterpMatrixKernelR<FReal>;
const MatrixKernelClass MatrixKernel;

using KernelClass    = FInterpolationKernel<FReal,CellClass,ContainerClass,MatrixKernelClass,ORDER> ;

using FmmClassProc     = FFmmAlgorithmThreadProc<OctreeClass,CellClass,ContainerClass,KernelClass,LeafClass>;
using FmmClassProcPER  = FFmmAlgorithmThreadProcPeriodic<FReal,OctreeClass,CellClass,ContainerClass,KernelClass,LeafClass>;

/// \file
//!
//! \brief This program runs the MPI FMM with Chebyshev/Lagrange interpolation of 1/r kernel
//!  \authors B. Bramas, O. Coulaud
//!
//!  This code is a short example to use the FMM Algorithm Proc with Chebyshev or equispaced grid points Interpolation for the 1/r kernel


// Simply create particles and try the kernels
int main(int argc, char* argv[])
{
  ///////// PARAMETERS HANDLING //////////////////////////////////////
  //  const FParameterNames LocalOptionPeriodicDeep { {"-periodic","-per"}, "Perdiodic boundary condition (-per 5) the box grow by a facor (3L)^5"};
  FHelpDescribeAndExit(argc, argv,
                       "Driver for Chebyshev Interpolation kernel using MPI  (1/r kernel). "
                       "Usully run using : mpirun -np nb_proc_needed ./ChebyshevInterpolationAlgorithm [params].",
                       FParameterDefinitions::OctreeHeight,
                       FParameterDefinitions::OctreeSubHeight,
                       FParameterDefinitions::InputFile,
                       FParameterDefinitions::OutputFile,
                       FParameterDefinitions::NbThreads,
                       FParameterDefinitions::PeriodicityNbLevels);

  const std::string defaultFile("../Data/test20k.fma");
  const std::string  filename      = FParameters::getStr(argc,argv,    FParameterDefinitions::InputFile.options, defaultFile.c_str());
  const unsigned int TreeHeight    = FParameters::getValue(argc, argv, FParameterDefinitions::OctreeHeight.options, 5);
  const unsigned int SubTreeHeight = FParameters::getValue(argc, argv, FParameterDefinitions::OctreeSubHeight.options, 2);
  const unsigned int NbThreads     = FParameters::getValue(argc, argv, FParameterDefinitions::NbThreads.options, 1);
  bool periodicCondition = false ;
  if(FParameters::existParameter(argc, argv, FParameterDefinitions::PeriodicityNbLevels.options)){
      periodicCondition = true;
    }
  const unsigned int aboveTree = FParameters::getValue(argc, argv, FParameterDefinitions::PeriodicityNbLevels.options, 5);

  omp_set_num_threads(NbThreads);
  std::cout << "\n>> Using " << omp_get_max_threads() << " threads.\n" << std::endl;

  //
  std::cout << "Parameters"<< std::endl
            << "      Octree Depth      " << TreeHeight    << std::endl
            << "      SubOctree depth   " << SubTreeHeight << std::endl;
  if(periodicCondition){
      std::cout << "      AboveTree    "<< aboveTree <<std::endl;

    }
  std::cout    << "      Input file  name: " << filename      << std::endl
               << "      Thread count :    " << NbThreads     << std::endl
               << std::endl;


  ///////// VAR INIT /////////////////////////////////////////////////

  // Initialize values for MPI
  FMpi app(argc,argv);
  //
  // Initialize timer
  FTic time;

  // Creation of the particle loader
  FMpiFmaGenericLoader<FReal> loader(filename,app.global());
  if(!loader.isOpen()) {
      throw std::runtime_error("Particle file couldn't be opened!") ;
    }

  // Initialize empty oct-tree
  OctreeClass tree(TreeHeight, SubTreeHeight, loader.getBoxWidth(), loader.getCenterOfBox());

  FSize localParticlesNumber = 0 ;

  { // -----------------------------------------------------
    if(app.global().processId() == 0){
        std::cout << "Loading & Inserting " << loader.getNumberOfParticles()
                  << " particles ..." << std::endl;
        std::cout << "\tHeight : " << TreeHeight << " \t sub-height : " << SubTreeHeight << std::endl;
      }
    time.tic();

    /* Mock particle structure to balance the tree over the processes. */
    struct TestParticle{
      FSize index;             // Index of the particle in the original file.
      FPoint<FReal> position;  // Spatial position of the particle.
      FReal physicalValue;     // Physical value of the particle.
      /* Returns the particle position. */
      const FPoint<FReal>& getPosition(){
        return position;
      }
    };

    // Temporary array of particles read by this process.
    TestParticle* particles = new TestParticle[loader.getMyNumberOfParticles()];
    memset(particles, 0, (sizeof(TestParticle) * loader.getMyNumberOfParticles()));

    // Index (in file) of the first particle that will be read by this process.
    FSize idxStart = loader.getStart();
    std::cout << "Proc:" << app.global().processId() << " start-index: " << idxStart << std::endl;

    // Read particles from parts.
    for(FSize idxPart = 0 ; idxPart < loader.getMyNumberOfParticles() ; ++idxPart){
        // Store the index (in the original file) the particle.
        particles[idxPart].index = idxPart + idxStart;
        // Read particle from file
        loader.fillParticle(&particles[idxPart].position,
                            &particles[idxPart].physicalValue);
      }

    // Final vector of particles
    FVector<TestParticle> finalParticles;
    FLeafBalance balancer;
    // Redistribute particules between processes
    FMpiTreeBuilder< FReal, TestParticle >::
        DistributeArrayToContainer(app.global(),
                                   particles,
                                   loader.getMyNumberOfParticles(),
                                   tree.getBoxCenter(),
                                   tree.getBoxWidth(),
                                   tree.getHeight(),
                                   &finalParticles,
                                   &balancer);

    // Free temporary array memory.
    delete[] particles;

    // Insert final particles into tree.

    for(FSize idx = 0 ; idx < finalParticles.getSize(); ++idx){
        tree.insert(finalParticles[idx].position,
                    finalParticles[idx].index,
                    finalParticles[idx].physicalValue);
      }

    time.tac();

    localParticlesNumber = finalParticles.getSize() ;

    double timeUsed = time.elapsed();
    double minTime,maxTime;
    std::cout << "Proc:" << app.global().processId()
              << " "     << finalParticles.getSize()
              << " particles have been inserted in the tree. (@Reading and Inserting Particles = "
              << time.elapsed() << " s)."
              << std::endl;

    MPI_Reduce(&timeUsed,&minTime,1,MPI_DOUBLE,MPI_MIN,0,app.global().getComm());
    MPI_Reduce(&timeUsed,&maxTime,1,MPI_DOUBLE,MPI_MAX,0,app.global().getComm());
    if(app.global().processId() == 0){
        std::cout << "readinsert-time-min:" << minTime
                  << " readinsert-time-max:" << maxTime
                  << std::endl;
      }
  } // -----------------------------------------------------
  std::vector<MortonIndex> mortonLeafDistribution(2*app.global().processCount());
  { // -----------------------------------------------------
    std::cout << "\n"<<interpolationType<<" FMM Proc (ORDER="<< ORDER << ") ... " << std::endl;

    time.tic();

    // Kernels to use (pointer because of the limited size of the stack)

    FAbstractAlgorithm * algorithm  = nullptr;
    FAlgorithmTimers   * timer      = nullptr;
    // non periodic FMM algorithm
    std::unique_ptr<KernelClass> kernelsNoPer(new KernelClass(TreeHeight, loader.getBoxWidth(),
                                                              loader.getCenterOfBox(),&MatrixKernel));
    FmmClassProc    algoNoPer(app.global(),&tree, kernelsNoPer.get());
    //
    // periodic FMM algorithm
    FmmClassProcPER algoPer(app.global(),&tree, aboveTree);
    KernelClass kernelsPer(algoPer.extendedTreeHeight(), algoPer.extendedBoxWidth(),
                           algoPer.extendedBoxCenter(),&MatrixKernel);
    algoPer.setKernel(&kernelsPer);
    ///////////////////////////////////////////////////////////////////////////////////////////////////
    if(! periodicCondition) {// Non periodic case
        algorithm  = &algoNoPer ;
        timer      = &algoNoPer ;
      }
    else {  // Periodic case
        algorithm  = &algoPer ;
        timer      = &algoPer ;
      }
    //
    // FMM exectution  FFmmFarField
    algorithm->execute();
    //

    time.tac();
    double timeUsed = time.elapsed();
    double minTime,maxTime;
    std::cout << "Done  " << "(@Algorithm = " << time.elapsed() << " s)." << std::endl;
    MPI_Reduce(&timeUsed,&minTime,1,MPI_DOUBLE,MPI_MIN,0,app.global().getComm());
    MPI_Reduce(&timeUsed,&maxTime,1,MPI_DOUBLE,MPI_MAX,0,app.global().getComm());
    if(app.global().processId() == 0){
        std::cout << "exec-time-min:" << minTime
                  << " exec-time-max:" << maxTime
                  << std::endl;
  }
  // -----------------------------------------------------
  //
  // Some output
  //
  //
  { // -----------------------------------------------------
    FSize N1=0, N2= loader.getNumberOfParticles()/2, N3= (loader.getNumberOfParticles()-1); ;
    FReal energy =0.0 ;
    //
    //   Loop over all leaves
    //
    std::cout <<std::endl<<" &&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&& "<<std::endl;
    std::cout << std::scientific;
    std::cout.precision(10) ;

    tree.forEachLeaf([&](LeafClass* leaf){
      const FReal*const posX = leaf->getTargets()->getPositions()[0];
      const FReal*const posY = leaf->getTargets()->getPositions()[1];
      const FReal*const posZ = leaf->getTargets()->getPositions()[2];

      const FReal*const potentials = leaf->getTargets()->getPotentials();
      const FReal*const forcesX = leaf->getTargets()->getForcesX();
      const FReal*const forcesY = leaf->getTargets()->getForcesY();
      const FReal*const forcesZ = leaf->getTargets()->getForcesZ();
      const FSize nbParticlesInLeaf = leaf->getTargets()->getNbParticles();
      const FReal*const physicalValues = leaf->getTargets()->getPhysicalValues();

      const FVector<FSize>& indexes = leaf->getTargets()->getIndexes();

      for(FSize idxPart = 0 ; idxPart < nbParticlesInLeaf ; ++idxPart){
          const FSize indexPartOrig = indexes[idxPart];
          if ((indexPartOrig == N1) || (indexPartOrig == N2) || (indexPartOrig == N3)  ) {
              std::cout << "Proc "<< app.global().processId() << " Index "<< indexPartOrig <<"  potential  " << potentials[idxPart]
                           << " Pos "<<posX[idxPart]<<" "<<posY[idxPart]<<" "<<posZ[idxPart]
                              << "   Forces: " << forcesX[idxPart] << " " << forcesY[idxPart] << " "<< forcesZ[idxPart] <<std::endl;
            }
          energy += potentials[idxPart]*physicalValues[idxPart] ;
        }
    });
    FReal gloEnergy = app.global().reduceSum(energy);
    if(0 == app.global().processId()){
        std::cout <<std::endl << "Proc "<< app.global().processId() << " Energy: "<< gloEnergy <<std::endl;
        std::cout <<std::endl <<" &&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&& "<<std::endl<<std::endl;
      }
  }
  // -----------------------------------------------------
  if(FParameters::existParameter(argc, argv, FParameterDefinitions::OutputFile.options)){
      algorithm->getAndBuildMortonIndexAtLeaf(mortonLeafDistribution);
      //
      if(app.global().processId() == 0)
        {
          std::cout << " Morton distribution "<< std::endl ;
          for(auto v : mortonLeafDistribution)
            std::cout << v << " ";

          std::cout <<  std::endl;
        }
      std::string name(FParameters::getStr(argc,argv,FParameterDefinitions::OutputFile.options, "output.fma"));
      FMpiFmaGenericWriter<FReal> paraWriter(name,app);
      paraWriter.writeDistributionOfParticlesFromOctree(tree,loader.getNumberOfParticles(),localParticlesNumber,mortonLeafDistribution);

    }
  return 0;
}