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vlasiator.cpp
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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>
#include <omp.h>
#ifdef _OPENMP
#include <omp.h>
#endif
#include <fsgrid.hpp>
#include "vlasovmover.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 "fieldsolver/fs_common.h"
#include "projects/project.h"
#include "grid.h"
#include "iowrite.h"
#include "ioread.h"
#include "object_wrapper.h"
#include "fieldsolver/gridGlue.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;
using namespace phiprof;
int globalflags::bailingOut = 0;
bool globalflags::writeRestart = 0;
bool globalflags::balanceLoad = 0;
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);
}
bool computeNewTimeStep(dccrg::Dccrg<SpatialCell,dccrg::Cartesian_Geometry>& mpiGrid,
FsGrid< fsgrids::technical, 2>& 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];
for (uint popID=0; popID<getObjectWrapper().particleSpecies.size(); ++popID) {
vmesh::VelocityBlockContainer<vmesh::LocalID>& blockContainer = cell->get_velocity_blocks(popID);
const Real* blockParams = blockContainer.getParameters();
const Real EPS = numeric_limits<Real>::min()*1000;
for (vmesh::LocalID blockLID=0; blockLID<blockContainer.size(); ++blockLID) {
for (unsigned int i=0; i<WID;i+=WID-1) {
const Real Vx
= blockParams[blockLID*BlockParams::N_VELOCITY_BLOCK_PARAMS+BlockParams::VXCRD]
+ (i+HALF)*blockParams[blockLID*BlockParams::N_VELOCITY_BLOCK_PARAMS+BlockParams::DVX]
+ EPS;
const Real Vy
= blockParams[blockLID*BlockParams::N_VELOCITY_BLOCK_PARAMS+BlockParams::VYCRD]
+ (i+HALF)*blockParams[blockLID*BlockParams::N_VELOCITY_BLOCK_PARAMS+BlockParams::DVY]
+ EPS;
const Real Vz
= blockParams[blockLID*BlockParams::N_VELOCITY_BLOCK_PARAMS+BlockParams::VZCRD]
+ (i+HALF)*blockParams[blockLID*BlockParams::N_VELOCITY_BLOCK_PARAMS+BlockParams::DVZ]
+ EPS;
const Real dt_max_cell = min(dx/fabs(Vx),min(dy/fabs(Vy),dz/fabs(Vz)));
cell->parameters[CellParams::MAXRDT] = min(dt_max_cell,cell->parameters[CellParams::MAXRDT]);
cell->set_max_r_dt(popID,min(dt_max_cell,cell->get_max_r_dt(popID)));
}
}
}
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->sysBoundaryFlag == sysboundarytype::NOT_SYSBOUNDARY && cell->parameters[CellParams::MAXVDT] != 0) {
//Acceleration only done on non sysboundary 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 == false)
dtMaxGlobal[0]=numeric_limits<Real>::max();
if (P::propagateVlasovAcceleration == false)
dtMaxGlobal[1]=numeric_limits<Real>::max();
if (P::propagateField == false)
dtMaxGlobal[2]=numeric_limits<Real>::max();
creal meanVlasovCFL = 0.5*(P::vlasovSolverMaxCFL+ P::vlasovSolverMinCFL);
creal meanFieldsCFL = 0.5*(P::fieldSolverMaxCFL+ P::fieldSolverMinCFL);
Real subcycleDt;
// cout << dtMaxGlobal[0];
// cout << " ";
// cout << dtMaxGlobal[1];
// cout << " ";
// cout << dtMaxGlobal[2];
// cout << " ";
// cout << P::vlasovSolverMaxCFL;
// cout << " ";
// cout << P::vlasovSolverMinCFL;
// cout << " ";
// cout << P::fieldSolverMaxCFL;
// cout << " ";
// cout << P::fieldSolverMinCFL;
// cout << endl;
//reduce 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
const Real half = 0.5;
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 == true) {
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");
return true;
}
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[]) {
bool success = true;
int myRank, doBailout;
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();
MPI_Comm comm = MPI_COMM_WORLD;
MPI_Comm_rank(comm,&myRank);
SysBoundary sysBoundaries;
bool isSysBoundaryCondDynamic;
#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");
phiprof::start("Read parameters");
//init parameter file reader
Readparameters readparameters(argn,args,MPI_COMM_WORLD);
P::addParameters();
getObjectWrapper().addParameters();
readparameters.parse(); // First pass parsing
if (P::getParameters() == false) {
if (myRank == MASTER_RANK) {
cerr << "(MAIN) ERROR: getParameters failed!" << endl;
}
exit(1);
}
getObjectWrapper().addPopulationParameters();
sysBoundaries.addParameters();
projects::Project::addParameters();
Project* project = projects::createProject();
getObjectWrapper().project = project;
readparameters.parse(); // Second pass parsing: specific population parameters
readparameters.helpMessage(); // Call after last parse, exits after printing help if help requested
getObjectWrapper().getParameters();
project->getParameters();
sysBoundaries.getParameters();
phiprof::stop("Read parameters");
// 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 AMR refinement criterias:
amr_ref_criteria::addRefinementCriteria();
// 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{sysBoundaries.isBoundaryPeriodic(0),
sysBoundaries.isBoundaryPeriodic(1),
sysBoundaries.isBoundaryPeriodic(2)};
FsGridCouplingInformation gridCoupling;
FsGrid< std::array<Real, fsgrids::bfield::N_BFIELD>, 2> perBGrid(fsGridDimensions, comm, periodicity,gridCoupling);
FsGrid< std::array<Real, fsgrids::bfield::N_BFIELD>, 2> perBDt2Grid(fsGridDimensions, comm, periodicity,gridCoupling);
FsGrid< std::array<Real, fsgrids::efield::N_EFIELD>, 2> EGrid(fsGridDimensions, comm, periodicity,gridCoupling);
FsGrid< std::array<Real, fsgrids::efield::N_EFIELD>, 2> EDt2Grid(fsGridDimensions, comm, periodicity,gridCoupling);
FsGrid< std::array<Real, fsgrids::ehall::N_EHALL>, 2> EHallGrid(fsGridDimensions, comm, periodicity,gridCoupling);
FsGrid< std::array<Real, fsgrids::egradpe::N_EGRADPE>, 2> EGradPeGrid(fsGridDimensions, comm, periodicity,gridCoupling);
FsGrid< std::array<Real, fsgrids::moments::N_MOMENTS>, 2> momentsGrid(fsGridDimensions, comm, periodicity,gridCoupling);
FsGrid< std::array<Real, fsgrids::moments::N_MOMENTS>, 2> momentsDt2Grid(fsGridDimensions, comm, periodicity,gridCoupling);
FsGrid< std::array<Real, fsgrids::dperb::N_DPERB>, 2> dPerBGrid(fsGridDimensions, comm, periodicity,gridCoupling);
FsGrid< std::array<Real, fsgrids::dmoments::N_DMOMENTS>, 2> dMomentsGrid(fsGridDimensions, comm, periodicity,gridCoupling);
FsGrid< std::array<Real, fsgrids::bgbfield::N_BGB>, 2> BgBGrid(fsGridDimensions, comm, periodicity,gridCoupling);
FsGrid< std::array<Real, fsgrids::volfields::N_VOL>, 2> volGrid(fsGridDimensions, comm, periodicity,gridCoupling);
FsGrid< fsgrids::technical, 2> 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};
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,
sysBoundaries,
*project
);
isSysBoundaryCondDynamic = sysBoundaries.isDynamic();
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");
phiprof::start("getFieldsFromFsGrid");
volGrid.updateGhostCells();
getFieldsFromFsGrid(volGrid, BgBGrid, EGradPeGrid, technicalGrid, mpiGrid, cells);
phiprof::stop("getFieldsFromFsGrid");
// Free up memory:
readparameters.finalize();
if (P::isRestart == false) {
// Run Vlasov solver once with zero dt to initialize
//per-cell dt limits. In restarts, we read the dt from file.
phiprof::start("compute-dt");
if(P::propagateField) {
propagateFields(
perBGrid,
perBDt2Grid,
EGrid,
EDt2Grid,
EHallGrid,
EGradPeGrid,
momentsGrid,
momentsDt2Grid,
dPerBGrid,
dMomentsGrid,
BgBGrid,
volGrid,
technicalGrid,
sysBoundaries, 0.0, 1.0
);
}
calculateSpatialTranslation(mpiGrid,0.0);
calculateAcceleration(mpiGrid,0.0);
phiprof::stop("compute-dt");
}
// Save restart data
if (P::writeInitialState) {
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("./");
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,
&outputReducer,P::systemWriteName.size()-1, 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();
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");
}
if (!P::isRestart) {
//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");
}
phiprof::stop("Initialization");
// ***********************************
// ***** INITIALIZATION COMPLETE *****
// ***********************************
// Main simulation loop:
if (myRank == MASTER_RANK) logFile << "(MAIN): Starting main simulation loop." << endl << writeVerbose;
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++;
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: 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) {
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,
&outputReducer, i, writeGhosts) == false ) {
cerr << "FAILED TO WRITE GRID AT" << __FILE__ << " " << __LINE__ << endl;
}
P::systemWrites[i]++;
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,
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
#warning Re-loadbalance has been disabled temporarily for amr debugging
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;
balanceLoad(mpiGrid, sysBoundaries);
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;
}
//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:
if (P::propagateVlasovTranslation || P::propagateVlasovAcceleration ) {
phiprof::start("Update system boundaries (Vlasov pre-translation)");
sysBoundaries.applySysBoundaryVlasovConditions(mpiGrid, P::t+0.5*P::dt);
phiprof::stop("Update system boundaries (Vlasov pre-translation)");
addTimedBarrier("barrier-boundary-conditions");
}
phiprof::start("Spatial-space");
if( P::propagateVlasovTranslation) {
calculateSpatialTranslation(mpiGrid,P::dt);
} else {
calculateSpatialTranslation(mpiGrid,0.0);
}
phiprof::stop("Spatial-space",computedCells,"Cells");
phiprof::start("Compute interp moments");
calculateInterpolatedVelocityMoments(
mpiGrid,
CellParams::RHOM_DT2,
CellParams::VX_DT2,
CellParams::VY_DT2,
CellParams::VZ_DT2,
CellParams::RHOQ_DT2,
CellParams::P_11_DT2,
CellParams::P_22_DT2,
CellParams::P_33_DT2
);
phiprof::stop("Compute interp moments");
// Apply boundary conditions
if (P::propagateVlasovTranslation || P::propagateVlasovAcceleration ) {
phiprof::start("Update system boundaries (Vlasov post-translation)");
sysBoundaries.applySysBoundaryVlasovConditions(mpiGrid, P::t+0.5*P::dt);
phiprof::stop("Update system boundaries (Vlasov post-translation)");
addTimedBarrier("barrier-boundary-conditions");
}
// Propagate fields forward in time by dt. This needs to be done before the
// moments for t + dt are computed (field uses t and t+0.5dt)
if (P::propagateField) {
phiprof::start("Propagate Fields");
phiprof::start("fsgrid-coupling-in");
// Copy moments over into the fsgrid.
//setupTechnicalFsGrid(mpiGrid, cells, technicalGrid);
feedMomentsIntoFsGrid(mpiGrid, cells, momentsGrid,false);
feedMomentsIntoFsGrid(mpiGrid, cells, momentsDt2Grid,true);
phiprof::stop("fsgrid-coupling-in");
propagateFields(
perBGrid,
perBDt2Grid,
EGrid,
EDt2Grid,
EHallGrid,
EGradPeGrid,
momentsGrid,
momentsDt2Grid,
dPerBGrid,
dMomentsGrid,
BgBGrid,
volGrid,
technicalGrid,
sysBoundaries,
P::dt,
P::fieldSolverSubcycles
);
phiprof::start("getFieldsFromFsGrid");
// Copy results back from fsgrid.
volGrid.updateGhostCells();
technicalGrid.updateGhostCells();
getFieldsFromFsGrid(volGrid, BgBGrid, EGradPeGrid, technicalGrid, mpiGrid, cells);
phiprof::stop("getFieldsFromFsGrid");
phiprof::stop("Propagate Fields",cells.size(),"SpatialCells");
addTimedBarrier("barrier-after-field-solver");
}
phiprof::start("Velocity-space");
if ( P::propagateVlasovAcceleration ) {
calculateAcceleration(mpiGrid,P::dt);
addTimedBarrier("barrier-after-ad just-blocks");
} else {
//zero step to set up moments _v
calculateAcceleration(mpiGrid, 0.0);
}
phiprof::stop("Velocity-space",computedCells,"Cells");
addTimedBarrier("barrier-after-acceleration");
phiprof::start("Compute interp moments");
// *here we compute rho and rho_v for timestep t + dt, so next
// timestep * //
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("Propagate",computedCells,"Cells");
phiprof::start("Project endTimeStep");
project->hook(hook::END_OF_TIME_STEP, mpiGrid);
phiprof::stop("Project endTimeStep");
// Check timestep
if (P::dt < P::bailout_min_dt) {
stringstream s;
s << "The timestep dt=" << P::dt << " went below bailout.bailout_min_dt (" << to_string(P::bailout_min_dt) << ")." << endl;
bailout(true, s.str(), __FILE__, __LINE__);
}
//Move forward in time
P::meshRepartitioned = false;
++P::tstep;
P::t += P::dt;
}
double after = MPI_Wtime();
phiprof::stop("Simulation");
phiprof::start("Finalization");
if (P::propagateField ) {
finalizeFieldPropagator();
}
if (myRank == MASTER_RANK) {
if (doBailout > 0) {
logFile << "(BAILOUT): Bailing out, see error log for details." << endl;
}
double timePerStep;
if (P::tstep == P::tstep_min) {
timePerStep=0.0;
} else {
timePerStep=double(after - startTime) / (P::tstep-P::tstep_min);
}
double timePerSecond=double(after - startTime) / (P::t-P::t_min+DT_EPSILON);
logFile << "(MAIN): All timesteps calculated." << endl;
logFile << "\t (TIME) total run time " << after - startTime << " s, total simulated time " << P::t -P::t_min<< " s" << endl;