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vlasiator.cpp
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/*
* This file is part of Vlasiator.
* Copyright 2010-2016 Finnish Meteorological Institute
*
* For details of usage, see the COPYING file and read the "Rules of the Road"
* at http://www.physics.helsinki.fi/vlasiator/
*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 2 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along
* with this program; if not, write to the Free Software Foundation, Inc.,
* 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
*/
#include <cstdlib>
#include <iostream>
#include <cmath>
#include <vector>
#include <sstream>
#include <ctime>
#ifdef _OPENMP
#include <omp.h>
#endif
#ifdef USE_GPU
#include "arch/gpu_base.hpp"
#endif
#include <fsgrid.hpp>
#include "vlasovmover.h"
#include "vlasovsolver/vec.h"
#include "definitions.h"
#include "mpiconversion.h"
#include "logger.h"
#include "parameters.h"
#include "readparameters.h"
#include "spatial_cell.hpp"
#include "datareduction/datareducer.h"
#include "sysboundary/sysboundary.h"
#include "fieldtracing/fieldtracing.h"
#include "fieldsolver/fs_common.h"
#include "projects/project.h"
#include "grid.h"
#include "iowrite.h"
#include "ioread.h"
#include "object_wrapper.h"
#include "velocity_mesh_parameters.h"
#include "fieldsolver/gridGlue.hpp"
#include "fieldsolver/derivatives.hpp"
#ifdef CATCH_FPE
#include <fenv.h>
#include <signal.h>
/*! Function used to abort the program upon detecting a floating point exception. Which exceptions are caught is defined using the function feenableexcept.
*/
void fpehandler(int sig_num)
{
signal(SIGFPE, fpehandler);
printf("SIGFPE: floating point exception occured, exiting.\n");
abort();
}
#endif
#include "phiprof.hpp"
Logger logFile, diagnostic;
static dccrg::Dccrg<SpatialCell,dccrg::Cartesian_Geometry> mpiGrid;
using namespace std;
int globalflags::bailingOut = 0;
bool globalflags::writeRestart = 0;
bool globalflags::balanceLoad = 0;
bool globalflags::ionosphereJustSolved = false;
ObjectWrapper objectWrapper;
void addTimedBarrier(string name){
#ifdef NDEBUG
//let's not do a barrier
return;
#endif
int bt=phiprof::initializeTimer(name,"Barriers","MPI");
phiprof::start(bt);
MPI_Barrier(MPI_COMM_WORLD);
phiprof::stop(bt);
}
void computeNewTimeStep(dccrg::Dccrg<SpatialCell,dccrg::Cartesian_Geometry>& mpiGrid,
FsGrid< fsgrids::technical, FS_STENCIL_WIDTH> & technicalGrid, Real &newDt, bool &isChanged) {
phiprof::start("compute-timestep");
// Compute maximum time step. This cannot be done at the first step as the solvers compute the limits for each cell.
isChanged = false;
const vector<CellID>& cells = getLocalCells();
/* Arrays for storing local (per process) and global max dt
0th position stores ordinary space propagation dt
1st position stores velocity space propagation dt
2nd position stores field propagation dt
*/
Real dtMaxLocal[3];
Real dtMaxGlobal[3];
dtMaxLocal[0] = numeric_limits<Real>::max();
dtMaxLocal[1] = numeric_limits<Real>::max();
dtMaxLocal[2] = numeric_limits<Real>::max();
for (vector<CellID>::const_iterator cell_id = cells.begin(); cell_id != cells.end(); ++cell_id) {
SpatialCell* cell = mpiGrid[*cell_id];
const Real dx = cell->parameters[CellParams::DX];
const Real dy = cell->parameters[CellParams::DY];
const Real dz = cell->parameters[CellParams::DZ];
cell->parameters[CellParams::MAXRDT] = numeric_limits<Real>::max();
for (uint popID = 0; popID < getObjectWrapper().particleSpecies.size(); ++popID) {
cell->set_max_r_dt(popID, numeric_limits<Real>::max());
const Realf* block_data = cell->get_data(popID);
const Real *parameters = cell->get_block_parameters(popID);
const Real HALF = 0.5;
Real popMin = std::numeric_limits<Real>::max();
#pragma omp parallel
{
Real threadMin = std::numeric_limits<Real>::max();
arch::parallel_reduce<arch::min>({WID, WID, WID, (uint)cell->get_number_of_velocity_blocks(popID)},
ARCH_LOOP_LAMBDA (const uint i, const uint j, const uint k, const uint n, Real *lthreadMin){
const Real VX
= parameters[n * BlockParams::N_VELOCITY_BLOCK_PARAMS + BlockParams::VXCRD]
+ (i + HALF)*parameters[n * BlockParams::N_VELOCITY_BLOCK_PARAMS + BlockParams::DVX];
const Real VY
= parameters[n * BlockParams::N_VELOCITY_BLOCK_PARAMS + BlockParams::VYCRD]
+ (j + HALF)*parameters[n * BlockParams::N_VELOCITY_BLOCK_PARAMS + BlockParams::DVY];
const Real VZ
= parameters[n * BlockParams::N_VELOCITY_BLOCK_PARAMS + BlockParams::VZCRD]
+ (k + HALF)*parameters[n * BlockParams::N_VELOCITY_BLOCK_PARAMS + BlockParams::DVZ];
lthreadMin[0] = min(dx / fabs(VX), lthreadMin[0]);
lthreadMin[0] = min(dy / fabs(VY), lthreadMin[0]);
lthreadMin[0] = min(dz / fabs(VZ), lthreadMin[0]);
}, threadMin);
#pragma omp critical
{
popMin = min(threadMin, popMin);
}
}
cell->set_max_r_dt(popID, popMin);
cell->parameters[CellParams::MAXRDT] = min(popMin, cell->parameters[CellParams::MAXRDT]);
}
if (cell->sysBoundaryFlag == sysboundarytype::NOT_SYSBOUNDARY ||
(cell->sysBoundaryLayer == 1 && cell->sysBoundaryFlag != sysboundarytype::NOT_SYSBOUNDARY)) {
// spatial fluxes computed also for boundary cells
dtMaxLocal[0] = min(dtMaxLocal[0], cell->parameters[CellParams::MAXRDT]);
}
if (cell->parameters[CellParams::MAXVDT] != 0 &&
(cell->sysBoundaryFlag == sysboundarytype::NOT_SYSBOUNDARY ||
(P::vlasovAccelerateMaxwellianBoundaries && cell->sysBoundaryFlag == sysboundarytype::SET_MAXWELLIAN))) {
// acceleration only done on non-boundary cells
dtMaxLocal[1] = min(dtMaxLocal[1], cell->parameters[CellParams::MAXVDT]);
}
}
// compute max dt for fieldsolver
const std::array<int, 3> gridDims(technicalGrid.getLocalSize());
for (int k = 0; k < gridDims[2]; k++) {
for (int j = 0; j < gridDims[1]; j++) {
for (int i = 0; i < gridDims[0]; i++) {
fsgrids::technical* cell = technicalGrid.get(i, j, k);
if (cell->sysBoundaryFlag == sysboundarytype::NOT_SYSBOUNDARY ||
(cell->sysBoundaryLayer == 1 && cell->sysBoundaryFlag != sysboundarytype::NOT_SYSBOUNDARY)) {
dtMaxLocal[2] = min(dtMaxLocal[2], cell->maxFsDt);
}
}
}
}
MPI_Allreduce(&(dtMaxLocal[0]), &(dtMaxGlobal[0]), 3, MPI_Type<Real>(), MPI_MIN, MPI_COMM_WORLD);
// If any of the solvers are disabled there should be no limits in timespace from it
if (!P::propagateVlasovTranslation)
dtMaxGlobal[0] = numeric_limits<Real>::max();
if (!P::propagateVlasovAcceleration)
dtMaxGlobal[1] = numeric_limits<Real>::max();
if (!P::propagateField)
dtMaxGlobal[2] = numeric_limits<Real>::max();
creal meanVlasovCFL = 0.5 * (P::vlasovSolverMaxCFL + P::vlasovSolverMinCFL);
creal meanFieldsCFL = 0.5 * (P::fieldSolverMaxCFL + P::fieldSolverMinCFL);
Real subcycleDt;
// reduce/increase dt if it is too high for any of the three propagators or too low for all propagators
if ((P::dt > dtMaxGlobal[0] * P::vlasovSolverMaxCFL ||
P::dt > dtMaxGlobal[1] * P::vlasovSolverMaxCFL * P::maxSlAccelerationSubcycles ||
P::dt > dtMaxGlobal[2] * P::fieldSolverMaxCFL * P::maxFieldSolverSubcycles) ||
(P::dt < dtMaxGlobal[0] * P::vlasovSolverMinCFL &&
P::dt < dtMaxGlobal[1] * P::vlasovSolverMinCFL * P::maxSlAccelerationSubcycles &&
P::dt < dtMaxGlobal[2] * P::fieldSolverMinCFL * P::maxFieldSolverSubcycles)) {
// new dt computed
isChanged = true;
// set new timestep to the lowest one of all interval-midpoints
newDt = meanVlasovCFL * dtMaxGlobal[0];
newDt = min(newDt, meanVlasovCFL * dtMaxGlobal[1] * P::maxSlAccelerationSubcycles);
newDt = min(newDt, meanFieldsCFL * dtMaxGlobal[2] * P::maxFieldSolverSubcycles);
logFile << "(TIMESTEP) New dt = " << newDt << " computed on step " << P::tstep << " at " << P::t
<< "s Maximum possible dt (not including vlasovsolver CFL " << P::vlasovSolverMinCFL << "-"
<< P::vlasovSolverMaxCFL << " or fieldsolver CFL " << P::fieldSolverMinCFL << "-" << P::fieldSolverMaxCFL
<< ") in {r, v, BE} was " << dtMaxGlobal[0] << " " << dtMaxGlobal[1] << " " << dtMaxGlobal[2] << " "
<< " Including subcycling { v, BE} was " << dtMaxGlobal[1] * P::maxSlAccelerationSubcycles << " "
<< dtMaxGlobal[2] * P::maxFieldSolverSubcycles << " " << endl
<< writeVerbose;
if (P::dynamicTimestep) {
subcycleDt = newDt;
} else {
logFile << "(TIMESTEP) However, fixed timestep in config overrides dt = " << P::dt << endl << writeVerbose;
subcycleDt = P::dt;
}
} else {
subcycleDt = P::dt;
}
// Subcycle if field solver dt < global dt (including CFL) (new or old dt hence the hassle with subcycleDt
if (meanFieldsCFL * dtMaxGlobal[2] < subcycleDt && P::propagateField) {
P::fieldSolverSubcycles =
min(convert<uint>(ceil(subcycleDt / (meanFieldsCFL * dtMaxGlobal[2]))), P::maxFieldSolverSubcycles);
} else {
P::fieldSolverSubcycles = 1;
}
phiprof::stop("compute-timestep");
}
ObjectWrapper& getObjectWrapper() {
return objectWrapper;
}
/** Get local cell IDs. This function creates a cached copy of the
* cell ID lists to significantly improve performance. The cell ID
* cache is recalculated every time the mesh partitioning changes.
* @return Local cell IDs.*/
const std::vector<CellID>& getLocalCells() {
return Parameters::localCells;
}
void recalculateLocalCellsCache() {
{
vector<CellID> dummy;
dummy.swap(Parameters::localCells);
}
Parameters::localCells = mpiGrid.get_cells();
}
int main(int argn,char* args[]) {
int myRank, doBailout=0;
const creal DT_EPSILON=1e-12;
typedef Parameters P;
Real newDt;
bool dtIsChanged;
// Init MPI:
int required=MPI_THREAD_FUNNELED;
int provided;
MPI_Init_thread(&argn,&args,required,&provided);
if (required > provided){
MPI_Comm_rank(MPI_COMM_WORLD,&myRank);
if(myRank==MASTER_RANK)
cerr << "(MAIN): MPI_Init_thread failed! Got " << provided << ", need "<<required <<endl;
exit(1);
}
phiprof::initialize();
double initialWtime = MPI_Wtime();
SysBoundary& sysBoundaryContainer = getObjectWrapper().sysBoundaryContainer;
MPI_Comm comm = MPI_COMM_WORLD;
MPI_Comm_rank(comm,&myRank);
#ifdef CATCH_FPE
// WARNING FE_INEXACT is too sensitive to be used. See man fenv.
//feenableexcept(FE_DIVBYZERO|FE_INVALID|FE_OVERFLOW|FE_UNDERFLOW);
feenableexcept(FE_DIVBYZERO|FE_INVALID|FE_OVERFLOW);
//feenableexcept(FE_DIVBYZERO|FE_INVALID);
signal(SIGFPE, fpehandler);
#endif
phiprof::start("main");
phiprof::start("Initialization");
#ifdef USE_GPU
// Activate device, create streams
gpu_init_device();
#endif
phiprof::start("Read parameters");
// Allocate velocity mesh wrapper
vmesh::allocMeshWrapper();
//init parameter file reader
Readparameters readparameters(argn,args);
P::addParameters();
// Add parameters for number of populations
getObjectWrapper().addParameters();
readparameters.parse();
P::getParameters();
getObjectWrapper().addPopulationParameters();
sysBoundaryContainer.addParameters();
projects::Project::addParameters();
Project* project = projects::createProject();
getObjectWrapper().project = project;
readparameters.parse(true, false); // 2nd parsing for specific population parameters
readparameters.helpMessage(); // Call after last parse, exits after printing help if help requested
getObjectWrapper().getPopulationParameters();
sysBoundaryContainer.getParameters();
project->getParameters();
vmesh::getMeshWrapper()->initVelocityMeshes(getObjectWrapper().particleSpecies.size());
phiprof::stop("Read parameters");
// Check for correct application of vectorclass values:
if ( (VECL<WID) ||
(VECL*VEC_PER_PLANE != WID2) ||
(VECL*VEC_PER_BLOCK != WID3) ||
//(VPREC > VECL) ||
(VECL != (int)VECL) ||
(VPREC != (int)VPREC) ||
(VEC_PER_PLANE != (int)VEC_PER_PLANE) ||
(VEC_PER_BLOCK != (int)VEC_PER_BLOCK) ) {
if (myRank == MASTER_RANK) {
cerr << "(MAIN) ERROR: Vectorclass definition mismatch!" << endl;
cerr << "VECL " << VECL <<" VEC_PER_PLANE " << VEC_PER_PLANE <<" WID " << WID <<" VEC_PER_BLOCK " << VEC_PER_BLOCK << " VPREC "<< VPREC<<endl;
}
exit(1);
}
//Get version and config info here
std::string version;
std::string config;
//Only master needs the info
if (myRank==MASTER_RANK){
version=readparameters.versionInfo();
config=readparameters.configInfo();
}
// Init parallel logger:
phiprof::start("open logFile & diagnostic");
//if restarting we will append to logfiles
if (logFile.open(MPI_COMM_WORLD,MASTER_RANK,"logfile.txt",P::isRestart) == false) {
if(myRank == MASTER_RANK) cerr << "(MAIN) ERROR: Logger failed to open logfile!" << endl;
exit(1);
}
if (P::diagnosticInterval != 0) {
if (diagnostic.open(MPI_COMM_WORLD,MASTER_RANK,"diagnostic.txt",P::isRestart) == false) {
if(myRank == MASTER_RANK) cerr << "(MAIN) ERROR: Logger failed to open diagnostic file!" << endl;
exit(1);
}
}
{
int mpiProcs;
MPI_Comm_size(MPI_COMM_WORLD,&mpiProcs);
logFile << "(MAIN) Starting simulation with " << mpiProcs << " MPI processes ";
#ifdef _OPENMP
logFile << "and " << omp_get_max_threads();
#else
logFile << "and 0";
#endif
logFile << " OpenMP threads per process" << endl << writeVerbose;
}
phiprof::stop("open logFile & diagnostic");
// Init project
phiprof::start("Init project");
if (project->initialize() == false) {
if(myRank == MASTER_RANK) cerr << "(MAIN): Project did not initialize correctly!" << endl;
exit(1);
}
if (project->initialized() == false) {
if (myRank == MASTER_RANK) {
cerr << "(MAIN): Project base class was not initialized!" << endl;
cerr << "\t Call Project::initialize() in your project's initialize()-function." << endl;
exit(1);
}
}
phiprof::stop("Init project");
// Add VAMR refinement criterias:
#ifdef VAMR
vamr_ref_criteria::addRefinementCriteria();
#endif
// Initialize simplified Fieldsolver grids.
// Needs to be done here already ad the background field will be set right away, before going to initializeGrid even
phiprof::start("Init fieldsolver grids");
const std::array<int,3> fsGridDimensions = {convert<int>(P::xcells_ini * pow(2,P::amrMaxSpatialRefLevel)),
convert<int>(P::ycells_ini * pow(2,P::amrMaxSpatialRefLevel)),
convert<int>(P::zcells_ini * pow(2,P::amrMaxSpatialRefLevel))};
std::array<bool,3> periodicity{sysBoundaryContainer.isBoundaryPeriodic(0),
sysBoundaryContainer.isBoundaryPeriodic(1),
sysBoundaryContainer.isBoundaryPeriodic(2)};
FsGridCouplingInformation gridCoupling;
FsGrid< std::array<Real, fsgrids::bfield::N_BFIELD>, FS_STENCIL_WIDTH> perBGrid(fsGridDimensions, comm, periodicity,gridCoupling);
FsGrid< std::array<Real, fsgrids::bfield::N_BFIELD>, FS_STENCIL_WIDTH> perBDt2Grid(fsGridDimensions, comm, periodicity,gridCoupling);
FsGrid< std::array<Real, fsgrids::efield::N_EFIELD>, FS_STENCIL_WIDTH> EGrid(fsGridDimensions, comm, periodicity,gridCoupling);
FsGrid< std::array<Real, fsgrids::efield::N_EFIELD>, FS_STENCIL_WIDTH> EDt2Grid(fsGridDimensions, comm, periodicity,gridCoupling);
FsGrid< std::array<Real, fsgrids::ehall::N_EHALL>, FS_STENCIL_WIDTH> EHallGrid(fsGridDimensions, comm, periodicity,gridCoupling);
FsGrid< std::array<Real, fsgrids::egradpe::N_EGRADPE>, FS_STENCIL_WIDTH> EGradPeGrid(fsGridDimensions, comm, periodicity,gridCoupling);
FsGrid< std::array<Real, fsgrids::moments::N_MOMENTS>, FS_STENCIL_WIDTH> momentsGrid(fsGridDimensions, comm, periodicity,gridCoupling);
FsGrid< std::array<Real, fsgrids::moments::N_MOMENTS>, FS_STENCIL_WIDTH> momentsDt2Grid(fsGridDimensions, comm, periodicity,gridCoupling);
FsGrid< std::array<Real, fsgrids::dperb::N_DPERB>, FS_STENCIL_WIDTH> dPerBGrid(fsGridDimensions, comm, periodicity,gridCoupling);
FsGrid< std::array<Real, fsgrids::dmoments::N_DMOMENTS>, FS_STENCIL_WIDTH> dMomentsGrid(fsGridDimensions, comm, periodicity,gridCoupling);
FsGrid< std::array<Real, fsgrids::bgbfield::N_BGB>, FS_STENCIL_WIDTH> BgBGrid(fsGridDimensions, comm, periodicity,gridCoupling);
FsGrid< std::array<Real, fsgrids::volfields::N_VOL>, FS_STENCIL_WIDTH> volGrid(fsGridDimensions, comm, periodicity,gridCoupling);
FsGrid< fsgrids::technical, FS_STENCIL_WIDTH> technicalGrid(fsGridDimensions, comm, periodicity,gridCoupling);
// Set DX, DY and DZ
// TODO: This is currently just taking the values from cell 1, and assuming them to be
// constant throughout the simulation.
perBGrid.DX = perBDt2Grid.DX = EGrid.DX = EDt2Grid.DX = EHallGrid.DX = EGradPeGrid.DX = momentsGrid.DX
= momentsDt2Grid.DX = dPerBGrid.DX = dMomentsGrid.DX = BgBGrid.DX = volGrid.DX = technicalGrid.DX
= P::dx_ini / pow(2, P::amrMaxSpatialRefLevel);
perBGrid.DY = perBDt2Grid.DY = EGrid.DY = EDt2Grid.DY = EHallGrid.DY = EGradPeGrid.DY = momentsGrid.DY
= momentsDt2Grid.DY = dPerBGrid.DY = dMomentsGrid.DY = BgBGrid.DY = volGrid.DY = technicalGrid.DY
= P::dy_ini / pow(2, P::amrMaxSpatialRefLevel);
perBGrid.DZ = perBDt2Grid.DZ = EGrid.DZ = EDt2Grid.DZ = EHallGrid.DZ = EGradPeGrid.DZ = momentsGrid.DZ
= momentsDt2Grid.DZ = dPerBGrid.DZ = dMomentsGrid.DZ = BgBGrid.DZ = volGrid.DZ = technicalGrid.DZ
= P::dz_ini / pow(2, P::amrMaxSpatialRefLevel);
// Set the physical start (lower left corner) X, Y, Z
perBGrid.physicalGlobalStart = perBDt2Grid.physicalGlobalStart = EGrid.physicalGlobalStart = EDt2Grid.physicalGlobalStart
= EHallGrid.physicalGlobalStart = EGradPeGrid.physicalGlobalStart = momentsGrid.physicalGlobalStart
= momentsDt2Grid.physicalGlobalStart = dPerBGrid.physicalGlobalStart = dMomentsGrid.physicalGlobalStart
= BgBGrid.physicalGlobalStart = volGrid.physicalGlobalStart = technicalGrid.physicalGlobalStart
= {P::xmin, P::ymin, P::zmin};
// Checking that spatial cells are cubic, otherwise field solver is incorrect (cf. derivatives in E, Hall term)
if ((abs((technicalGrid.DX - technicalGrid.DY) / technicalGrid.DX) > 0.001) ||
(abs((technicalGrid.DX - technicalGrid.DZ) / technicalGrid.DX) > 0.001) ||
(abs((technicalGrid.DY - technicalGrid.DZ) / technicalGrid.DY) > 0.001)) {
if (myRank == MASTER_RANK) {
std::cerr << "WARNING: Your spatial cells seem not to be cubic. However the field solver is assuming them to "
"be. Use at your own risk and responsibility!"
<< std::endl;
}
}
phiprof::stop("Init fieldsolver grids");
// Initialize grid. After initializeGrid local cells have dist
// functions, and B fields set. Cells have also been classified for
// the various sys boundary conditions. All remote cells have been
// created. All spatial date computed this far is up to date for
// FULL_NEIGHBORHOOD. Block lists up to date for
// VLASOV_SOLVER_NEIGHBORHOOD (but dist function has not been communicated)
phiprof::start("Init grids");
initializeGrids(
argn,
args,
mpiGrid,
perBGrid,
BgBGrid,
momentsGrid,
momentsDt2Grid,
EGrid,
EGradPeGrid,
volGrid,
technicalGrid,
sysBoundaryContainer,
*project
);
const std::vector<CellID>& cells = getLocalCells();
phiprof::stop("Init grids");
// Initialize data reduction operators. This should be done elsewhere in order to initialize
// user-defined operators:
phiprof::start("Init DROs");
DataReducer outputReducer, diagnosticReducer;
initializeDataReducers(&outputReducer, &diagnosticReducer);
phiprof::stop("Init DROs");
// Free up memory:
readparameters.~Readparameters();
// Run the field solver once with zero dt. This will initialize
// Fieldsolver dt limits, and also calculate volumetric B-fields.
// At restart, all we need at this stage has been read from the restart, the rest will be recomputed in due time.
if(P::isRestart == false) {
propagateFields(
perBGrid,
perBDt2Grid,
EGrid,
EDt2Grid,
EHallGrid,
EGradPeGrid,
momentsGrid,
momentsDt2Grid,
dPerBGrid,
dMomentsGrid,
BgBGrid,
volGrid,
technicalGrid,
sysBoundaryContainer, 0.0, 1.0
);
}
phiprof::start("getFieldsFromFsGrid");
volGrid.updateGhostCells();
getFieldsFromFsGrid(volGrid, BgBGrid, EGradPeGrid, technicalGrid, mpiGrid, cells);
phiprof::stop("getFieldsFromFsGrid");
// Build communicator for ionosphere solving
SBC::ionosphereGrid.updateIonosphereCommunicator(mpiGrid, technicalGrid);
FieldTracing::calculateIonosphereFsgridCoupling(technicalGrid, perBGrid, dPerBGrid, SBC::ionosphereGrid.nodes, SBC::Ionosphere::radius);
SBC::ionosphereGrid.initSolver(!P::isRestart); // If it is a restart we do not want to zero out everything
if(SBC::Ionosphere::couplingInterval > 0 && P::isRestart) {
SBC::Ionosphere::solveCount = floor(P::t / SBC::Ionosphere::couplingInterval)+1;
} else {
SBC::Ionosphere::solveCount = 1;
}
if (P::isRestart == false) {
phiprof::start("compute-dt");
// Run Vlasov solver once with zero dt to initialize
// per-cell dt limits. In restarts, we read the dt from file.
calculateSpatialTranslation(mpiGrid,0.0);
calculateAcceleration(mpiGrid,0.0);
phiprof::stop("compute-dt");
}
// Save restart data
if (P::writeInitialState) {
FieldTracing::reduceData(technicalGrid, perBGrid, dPerBGrid, mpiGrid, SBC::ionosphereGrid.nodes); /*!< Call the reductions (e.g. field tracing) */
phiprof::start("write-initial-state");
if (myRank == MASTER_RANK)
logFile << "(IO): Writing initial state to disk, tstep = " << endl << writeVerbose;
P::systemWriteDistributionWriteStride.push_back(1);
P::systemWriteName.push_back("initial-grid");
P::systemWriteDistributionWriteXlineStride.push_back(0);
P::systemWriteDistributionWriteYlineStride.push_back(0);
P::systemWriteDistributionWriteZlineStride.push_back(0);
P::systemWritePath.push_back("./");
P::systemWriteFsGrid.push_back(true);
for(uint si=0; si<P::systemWriteName.size(); si++) {
P::systemWrites.push_back(0);
}
const bool writeGhosts = true;
if( writeGrid(mpiGrid,
perBGrid, // TODO: Merge all the fsgrids passed here into one meta-object
EGrid,
EHallGrid,
EGradPeGrid,
momentsGrid,
dPerBGrid,
dMomentsGrid,
BgBGrid,
volGrid,
technicalGrid,
version,
config,
&outputReducer,
P::systemWriteName.size()-1,
P::restartStripeFactor,
writeGhosts
) == false
) {
cerr << "FAILED TO WRITE GRID AT " << __FILE__ << " " << __LINE__ << endl;
}
P::systemWriteDistributionWriteStride.pop_back();
P::systemWriteName.pop_back();
P::systemWriteDistributionWriteXlineStride.pop_back();
P::systemWriteDistributionWriteYlineStride.pop_back();
P::systemWriteDistributionWriteZlineStride.pop_back();
P::systemWritePath.pop_back();
P::systemWriteFsGrid.pop_back();
phiprof::stop("write-initial-state");
}
if (P::isRestart == false) {
//compute new dt
phiprof::start("compute-dt");
computeNewTimeStep(mpiGrid, technicalGrid, newDt, dtIsChanged);
if (P::dynamicTimestep == true && dtIsChanged == true) {
// Only actually update the timestep if dynamicTimestep is on
P::dt=newDt;
}
phiprof::stop("compute-dt");
//go forward by dt/2 in V, initializes leapfrog split. In restarts the
//the distribution function is already propagated forward in time by dt/2
phiprof::start("propagate-velocity-space-dt/2");
if (P::propagateVlasovAcceleration) {
calculateAcceleration(mpiGrid, 0.5*P::dt);
} else {
//zero step to set up moments _v
calculateAcceleration(mpiGrid, 0.0);
}
phiprof::stop("propagate-velocity-space-dt/2");
// Apply boundary conditions
if (P::propagateVlasovTranslation || P::propagateVlasovAcceleration ) {
phiprof::start("Update system boundaries (Vlasov post-acceleration)");
sysBoundaryContainer.applySysBoundaryVlasovConditions(mpiGrid, 0.5*P::dt, true);
phiprof::stop("Update system boundaries (Vlasov post-acceleration)");
addTimedBarrier("barrier-boundary-conditions");
}
// Also update all moments. They won't be transmitted to FSgrid until the field solver is called, though.
phiprof::start("Compute interp moments");
calculateInterpolatedVelocityMoments(
mpiGrid,
CellParams::RHOM,
CellParams::VX,
CellParams::VY,
CellParams::VZ,
CellParams::RHOQ,
CellParams::P_11,
CellParams::P_22,
CellParams::P_33
);
phiprof::stop("Compute interp moments");
}
phiprof::stop("Initialization");
// ***********************************
// ***** INITIALIZATION COMPLETE *****
// ***********************************
// Main simulation loop:
if (myRank == MASTER_RANK){
logFile << "(MAIN): Starting main simulation loop." << endl << writeVerbose;
//report filtering if we are in an AMR run
if (P::amrMaxSpatialRefLevel>0){
logFile<<"Filtering Report: "<<endl;
for (uint refLevel=0 ; refLevel<= P::amrMaxSpatialRefLevel; refLevel++){
logFile<<"\tRefinement Level " <<refLevel<<"==> Passes "<<P::numPasses.at(refLevel)<<endl;
}
logFile<<endl;
}
}
phiprof::start("report-memory-consumption");
report_process_memory_consumption();
phiprof::stop("report-memory-consumption");
unsigned int computedCells=0;
unsigned int computedTotalCells=0;
//Compute here based on time what the file intervals are
P::systemWrites.clear();
for(uint i=0;i< P::systemWriteTimeInterval.size();i++){
int index=(int)(P::t_min/P::systemWriteTimeInterval[i]);
//if we are already over 1% further than the time interval time that
//is requested for writing, then jump to next writing index. This is to
//make sure that at restart we do not write in the middle of
//the interval.
if(P::t_min>(index+0.01)*P::systemWriteTimeInterval[i]) {
index++;
// Special case for large timesteps
int index2=(int)((P::t_min+P::dt)/P::systemWriteTimeInterval[i]);
if (index2>index) index=index2;
}
P::systemWrites.push_back(index);
}
// Invalidate cached cell lists just to be sure (might not be needed)
P::meshRepartitioned = true;
unsigned int wallTimeRestartCounter=1;
int doNow[2] = {0}; // 0: writeRestartNow, 1: balanceLoadNow ; declared outside main loop
int writeRestartNow; // declared outside main loop
bool overrideRebalanceNow = false; // declared outside main loop
addTimedBarrier("barrier-end-initialization");
phiprof::start("Simulation");
double startTime= MPI_Wtime();
double beforeTime = MPI_Wtime();
double beforeSimulationTime=P::t_min;
double beforeStep=P::tstep_min;
while(P::tstep <= P::tstep_max &&
P::t-P::dt <= P::t_max+DT_EPSILON &&
wallTimeRestartCounter <= P::exitAfterRestarts) {
addTimedBarrier("barrier-loop-start");
phiprof::start("IO");
phiprof::start("checkExternalCommands");
if(myRank == MASTER_RANK) {
// check whether STOP or KILL or SAVE has been passed, should be done by MASTER_RANK only as it can reset P::bailout_write_restart
checkExternalCommands();
}
phiprof::stop("checkExternalCommands");
//write out phiprof profiles and logs with a lower interval than normal
//diagnostic (every 10 diagnostic intervals).
phiprof::start("logfile-io");
logFile << "---------- tstep = " << P::tstep << " t = " << P::t <<" dt = " << P::dt << " FS cycles = " << P::fieldSolverSubcycles << " ----------" << endl;
if (P::diagnosticInterval != 0 &&
P::tstep % (P::diagnosticInterval*10) == 0 &&
P::tstep-P::tstep_min >0) {
phiprof::print(MPI_COMM_WORLD,"phiprof");
double currentTime=MPI_Wtime();
double timePerStep=double(currentTime - beforeTime) / (P::tstep-beforeStep);
double timePerSecond=double(currentTime - beforeTime) / (P::t-beforeSimulationTime + DT_EPSILON);
double remainingTime=min(timePerStep*(P::tstep_max-P::tstep),timePerSecond*(P::t_max-P::t));
time_t finalWallTime=time(NULL)+(time_t)remainingTime; //assume time_t is in seconds, as it is almost always
struct tm *finalWallTimeInfo=localtime(&finalWallTime);
logFile << "(TIME) current walltime/step " << timePerStep<< " s" <<endl;
logFile << "(TIME) current walltime/simusecond " << timePerSecond<<" s" <<endl;
logFile << "(TIME) Estimated completion time is " <<asctime(finalWallTimeInfo)<<endl;
//reset before values, we want to report speed since last report of speed.
beforeTime = MPI_Wtime();
beforeSimulationTime=P::t;
beforeStep=P::tstep;
//report_grid_memory_consumption(mpiGrid);
report_process_memory_consumption();
}
logFile << writeVerbose;
phiprof::stop("logfile-io");
// Check whether diagnostic output has to be produced
if (P::diagnosticInterval != 0 && P::tstep % P::diagnosticInterval == 0) {
phiprof::start("diagnostic-io");
if (writeDiagnostic(mpiGrid, diagnosticReducer) == false) {
if(myRank == MASTER_RANK) cerr << "ERROR with diagnostic computation" << endl;
}
phiprof::stop("diagnostic-io");
}
// write system, loop through write classes
for (uint i = 0; i < P::systemWriteTimeInterval.size(); i++) {
if (P::systemWriteTimeInterval[i] >= 0.0 &&
P::t >= P::systemWrites[i] * P::systemWriteTimeInterval[i] - DT_EPSILON) {
// If we have only just restarted, the bulk file should already exist from the previous slot.
if ((P::tstep == P::tstep_min) && (P::tstep>0)) {
P::systemWrites[i]++;
// Special case for large timesteps
int index2=(int)((P::t+P::dt)/P::systemWriteTimeInterval[i]);
if (index2>P::systemWrites[i]) P::systemWrites[i]=index2;
continue;
}
// Calculate these so refinement parameters can be tuned based on the vlsv
calculateScaledDeltasSimple(mpiGrid);
FieldTracing::reduceData(technicalGrid, perBGrid, dPerBGrid, mpiGrid, SBC::ionosphereGrid.nodes); /*!< Call the reductions (e.g. field tracing) */
phiprof::start("write-system");
logFile << "(IO): Writing spatial cell and reduced system data to disk, tstep = " << P::tstep << " t = " << P::t << endl << writeVerbose;
const bool writeGhosts = true;
if(writeGrid(mpiGrid,
perBGrid, // TODO: Merge all the fsgrids passed here into one meta-object
EGrid,
EHallGrid,
EGradPeGrid,
momentsGrid,
dPerBGrid,
dMomentsGrid,
BgBGrid,
volGrid,
technicalGrid,
version,
config,
&outputReducer,
i,
P::systemStripeFactor,
writeGhosts
) == false
) {
cerr << "FAILED TO WRITE GRID AT" << __FILE__ << " " << __LINE__ << endl;
}
P::systemWrites[i]++;
// Special case for large timesteps
int index2=(int)((P::t+P::dt)/P::systemWriteTimeInterval[i]);
if (index2>P::systemWrites[i]) P::systemWrites[i]=index2;
logFile << "(IO): .... done!" << endl << writeVerbose;
phiprof::stop("write-system");
}
}
// Reduce globalflags::bailingOut from all processes
phiprof::start("Bailout-allreduce");
MPI_Allreduce(&(globalflags::bailingOut), &(doBailout), 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
phiprof::stop("Bailout-allreduce");
// Write restart data if needed
// Combined with checking of additional load balancing to have only one collective call.
phiprof::start("compute-is-restart-written-and-extra-LB");
if (myRank == MASTER_RANK) {
if ( (P::saveRestartWalltimeInterval >= 0.0
&& (P::saveRestartWalltimeInterval*wallTimeRestartCounter <= MPI_Wtime()-initialWtime
|| P::tstep == P::tstep_max
|| P::t >= P::t_max))
|| (doBailout > 0 && P::bailout_write_restart)
|| globalflags::writeRestart
) {
doNow[0] = 1;
if (globalflags::writeRestart == true) {
doNow[0] = 2; // Setting to 2 so as to not increment the restart count below.
globalflags::writeRestart = false; // This flag is only used by MASTER_RANK here and it needs to be reset after a restart write has been issued.
}
}
else {
doNow[0] = 0;
}
if (globalflags::balanceLoad == true) {
doNow[1] = 1;
globalflags::balanceLoad = false;
}
}
MPI_Bcast( &doNow, 2 , MPI_INT , MASTER_RANK ,MPI_COMM_WORLD);
writeRestartNow = doNow[0];
doNow[0] = 0;
if (doNow[1] == 1) {
P::prepareForRebalance = true;
doNow[1] = 0;
}
phiprof::stop("compute-is-restart-written-and-extra-LB");
if (writeRestartNow >= 1){
phiprof::start("write-restart");
if (writeRestartNow == 1) {
wallTimeRestartCounter++;
}
if (myRank == MASTER_RANK)
logFile << "(IO): Writing restart data to disk, tstep = " << P::tstep << " t = " << P::t << endl << writeVerbose;
//Write the restart:
if( writeRestart(mpiGrid,
perBGrid, // TODO: Merge all the fsgrids passed here into one meta-object
EGrid,
EHallGrid,
EGradPeGrid,
momentsGrid,
dPerBGrid,
dMomentsGrid,
BgBGrid,
volGrid,
technicalGrid,
version,
config,
outputReducer,"restart",(uint)P::t,P::restartStripeFactor) == false ) {
logFile << "(IO): ERROR Failed to write restart!" << endl << writeVerbose;
cerr << "FAILED TO WRITE RESTART" << endl;
}
if (myRank == MASTER_RANK)
logFile << "(IO): .... done!"<< endl << writeVerbose;
phiprof::stop("write-restart");
}
phiprof::stop("IO");
addTimedBarrier("barrier-end-io");
//no need to propagate if we are on the final step, we just
//wanted to make sure all IO is done even for final step
if(P::tstep == P::tstep_max ||
P::t >= P::t_max ||
doBailout > 0) {
break;
}
//Re-loadbalance if needed
//TODO - add LB measure and do LB if it exceeds threshold
if(((P::tstep % P::rebalanceInterval == 0 && P::tstep > P::tstep_min) || overrideRebalanceNow)) {
logFile << "(LB): Start load balance, tstep = " << P::tstep << " t = " << P::t << endl << writeVerbose;
// Refinement includes LB
if (!dtIsChanged && P::adaptRefinement && P::tstep % (P::rebalanceInterval * P::refineMultiplier) == 0 && P::t > P::refineAfter) {
logFile << "(AMR): Adapting refinement!" << endl << writeVerbose;
if (!adaptRefinement(mpiGrid, technicalGrid, sysBoundaryContainer, *project))
continue; // Refinement failed and we're bailing out
// Calculate new dt limits since we might break CFL when refining
phiprof::start("compute-dt");
calculateSpatialTranslation(mpiGrid,0.0);
calculateAcceleration(mpiGrid,0.0);
phiprof::stop("compute-dt");
}
balanceLoad(mpiGrid, sysBoundaryContainer);
addTimedBarrier("barrier-end-load-balance");
phiprof::start("Shrink_to_fit");
// * shrink to fit after LB * //
shrink_to_fit_grid_data(mpiGrid);
phiprof::stop("Shrink_to_fit");
logFile << "(LB): ... done!" << endl << writeVerbose;
P::prepareForRebalance = false;
overrideRebalanceNow = false;
// Make sure the ionosphere communicator is up-to-date, in case inner boundary cells
// moved.
SBC::ionosphereGrid.updateIonosphereCommunicator(mpiGrid, technicalGrid);
}
//get local cells
const vector<CellID>& cells = getLocalCells();
//compute how many spatial cells we solve for this step
computedCells=0;
for(size_t i=0; i<cells.size(); i++) {
for (uint popID=0; popID<getObjectWrapper().particleSpecies.size(); ++popID)
computedCells += mpiGrid[cells[i]]->get_number_of_velocity_blocks(popID)*WID3;
}
computedTotalCells+=computedCells;
//Check if dt needs to be changed, and propagate V back a half-step to change dt and set up new situation
//do not compute new dt on first step (in restarts dt comes from file, otherwise it was initialized before we entered
//simulation loop
// FIXME what if dt changes at a restart??
if(P::dynamicTimestep && P::tstep > P::tstep_min) {
computeNewTimeStep(mpiGrid, technicalGrid, newDt, dtIsChanged);
addTimedBarrier("barrier-check-dt");
if(dtIsChanged) {
phiprof::start("update-dt");
//propagate velocity space back to real-time
if( P::propagateVlasovAcceleration ) {
// Back half dt to real time, forward by new half dt
calculateAcceleration(mpiGrid,-0.5*P::dt + 0.5*newDt);
}
else {
//zero step to set up moments _v
calculateAcceleration(mpiGrid, 0.0);
}
P::dt=newDt;
logFile <<" dt changed to "<<P::dt <<"s, distribution function was half-stepped to real-time and back"<<endl<<writeVerbose;
phiprof::stop("update-dt");
continue; //
//addTimedBarrier("barrier-new-dt-set");
}
}
if (P::tstep % P::rebalanceInterval == P::rebalanceInterval-1 || P::prepareForRebalance == true) {
if(P::prepareForRebalance == true) {
overrideRebalanceNow = true;
} else {
P::prepareForRebalance = true;
}
#pragma omp parallel for
for (size_t c=0; c<cells.size(); ++c) {
mpiGrid[cells[c]]->get_cell_parameters()[CellParams::LBWEIGHTCOUNTER] = 0;
}
}
phiprof::start("Propagate");
//Propagate the state of simulation forward in time by dt:
phiprof::start("Spatial-space");
if( P::propagateVlasovTranslation) {
calculateSpatialTranslation(mpiGrid,P::dt);
} else {
calculateSpatialTranslation(mpiGrid,0.0);
}
phiprof::stop("Spatial-space",computedCells,"Cells");
// Apply boundary conditions
if (P::propagateVlasovTranslation || P::propagateVlasovAcceleration ) {
phiprof::start("Update system boundaries (Vlasov post-translation)");
sysBoundaryContainer.applySysBoundaryVlasovConditions(mpiGrid, P::t+0.5*P::dt, false);
phiprof::stop("Update system boundaries (Vlasov post-translation)");
addTimedBarrier("barrier-boundary-conditions");
}
phiprof::start("Compute interp moments");
calculateInterpolatedVelocityMoments(
mpiGrid,
CellParams::RHOM_DT2,
CellParams::VX_DT2,