void Simulation::readCheckpoint() {
int checkpointNum = readCheckpointNum();
// Open the latest file
ostringstream name;
name << CHECKPOINT << checkpointNum; // try uncompressed
ifstream in(name.str().c_str(), ios::in | ios::binary);
if (in.good()) {
checkpoint (in, checkpointNum);
in.close();
} else {
name << ".gz"; // then compressed
igzstream in(name.str().c_str(), ios::in | ios::binary);
if (!in.good())
throw util::checkpoint_error ("Unable to read file");
checkpoint (in, checkpointNum);
in.close();
}
cerr << "Loaded checkpoint from: " << name.str() << endl;
// On resume, write a checkpoint so we can tell whether we have identical checkpointed state
if (util::CommandLine::option (util::CommandLine::TEST_CHECKPOINTING))
writeCheckpoint();
}
static int runSystem(const NBodyCtx* ctx, NBodyState* st, const NBodyFlags* nbf)
{
const real tstop = ctx->timeEvolve - ctx->timestep / 1024.0;
if (nbf->visualizer)
{
launchVisualizer(st, nbf->visArgs);
}
while (st->tnow < tstop)
{
updateDisplayedBodies(st);
if (stepSystem(ctx, st)) /* advance N-body system */
return 1;
nbodyCheckpoint(ctx, st);
}
if (BOINC_APPLICATION || ctx->checkpointT >= 0)
{
mw_report("Making final checkpoint\n");
if (writeCheckpoint(ctx, st))
return warn1("Failed to write final checkpoint\n");
}
return 0;
}
static void finalCheckpoint(EvaluationState* es)
{
#if BOINC_APPLICATION
boinc_begin_critical_section();
#endif
if (writeCheckpoint(es))
fail("Failed to write final checkpoint\n");
#if BOINC_APPLICATION
boinc_end_critical_section();
#endif
}
static CALresult checkpointCAL(SeparationCALMem* cm, const IntegralArea* ia, EvaluationState* es)
{
CALresult err;
readResults(cm, ia, es);
err = writeCheckpoint(es) ? CAL_RESULT_ERROR : CAL_RESULT_OK;
#if BOINC_APPLICATION
boinc_checkpoint_completed();
#endif
return err;
}
static cl_int checkpointCL(CLInfo* ci, SeparationCLMem* cm, const IntegralArea* ia, EvaluationState* es)
{
cl_int err;
err = readKernelResults(ci, cm, es, ia);
if (err != CL_SUCCESS)
return err;
err = writeCheckpoint(es) ? MW_CL_ERROR : CL_SUCCESS;
mw_checkpoint_completed();
return err;
}
static inline void nbodyCheckpoint(const NBodyCtx* ctx, NBodyState* st)
{
if (nbodyTimeToCheckpoint(ctx, st))
{
if (writeCheckpoint(ctx, st))
fail("Failed to write checkpoint\n");
#if BOINC_APPLICATION
boinc_checkpoint_completed();
#endif /* BOINC_APPLICATION */
}
#if BOINC_APPLICATION
boinc_fraction_done(st->tnow / ctx->timeEvolve);
#endif /* BOINC_APPLICATION */
}
/*
* This is the basic entry point for most IO operations. It should be called
* once per iteration of the code, and it will determine which types of IO
* IO should be performed. The different types of IO are:
*
* 1. Spatial dumps
* 2. Checkpoint dumps
* 3. Scalar reductions
* 4. Status file updates
*
* The frequency of each of these is controlled by parameters read in from the
* configuration file.
*/
void performOutput()
{
if(crank == 0)
{
//update the status file?
if(iteration % statusRate == 0)
{
status = fopen("status", "a");
fprintf(status, "Iteration %d:\n dt = %g\tElapsed Time = %g\nMax Vel: %g %g %g\n", iteration, dt, elapsedTime, maxVel[0], maxVel[1], maxVel[2]);
fclose(status);
}
}
/*
* The scalars are single values that result from a global operation on the
* domain. The scalars are:
*
* [0] -- iteration
* [1] -- elapsed time
* [2] -- min u
* [3] -- max u
* [4] -- mean u
* [5] -- min v
* [6] -- max v
* [7] -- mean v
* [8] -- min w
* [9] -- max w
* [10] -- mean w
* [11] -- mean kinetic energy density
* [12] -- max kinetic energy density
*
* ------------ Only present if magnetic fields are included:
* [13] -- min Bx
* [14] -- max Bx
* [15] -- mean Bx
* [16] -- min By
* [17] -- max By
* [18] -- mean By
* [19] -- min Bz
* [20] -- max Bz
* [21] -- mean Bz
* [22] -- mean magnetic energy density
* [23] -- max magnetic energy density*
*/
if(compute_node)
{
if(iteration % scalarRate == 0)
{
PRECISION * local = (PRECISION*)malloc(sizeof(PRECISION)*numScalar);
int i;
PRECISION * datax = u->vec->x->spatial;
PRECISION * datay = u->vec->y->spatial;
PRECISION * dataz = u->vec->z->spatial;
PRECISION temp;
//I feel like there should be an MPI operation that doesn't require
//me to manually take a local min/max/etc, but I'm failing to find
//it. The general MPI_Reduce does an element by element reduction,
//which is not what we want.
local[0] = iteration;
local[1] = elapsedTime;
local[2] = datax[0];
local[3] = datax[0];
local[4] = datax[0];
local[5] = datay[0];
local[6] = datay[0];
local[7] = datay[0];
local[8] = dataz[0];
local[9] = dataz[0];
local[10] = dataz[0];
temp = pow(datax[0],2) + pow(datay[0],2) + pow(dataz[0],2);
local[11] = temp;
local[12] = temp;
for(i = 1; i < spatialCount; i++)
{
local[2] = fmin(local[2], datax[i]);
local[3] = fmax(local[3], datax[i]);
local[4] += datax[i];
local[5] = fmin(local[5], datay[i]);
local[6] = fmax(local[6], datay[i]);
local[7] += datay[i];
local[8] = fmin(local[8], dataz[i]);
local[9] = fmax(local[9], dataz[i]);
local[10] += dataz[i];
temp = pow(datax[i],2) + pow(datay[i],2) + pow(dataz[i],2);
local[11] += temp;
local[12] = fmax(temp, local[12]);
}
if(crank == 0)
{
piScalarData[0] = local[0];
piScalarData[1] = local[1];
}
MPI_Reduce(local+2, piScalarData+2, 1, MPI_PRECISION, MPI_MIN, 0, ccomm);
MPI_Reduce(local+3, piScalarData+3, 1, MPI_PRECISION, MPI_MAX, 0, ccomm);
MPI_Reduce(local+4, piScalarData+4, 1, MPI_PRECISION, MPI_SUM, 0, ccomm);
MPI_Reduce(local+5, piScalarData+5, 1, MPI_PRECISION, MPI_MIN, 0, ccomm);
MPI_Reduce(local+6, piScalarData+6, 1, MPI_PRECISION, MPI_MAX, 0, ccomm);
MPI_Reduce(local+7, piScalarData+7, 1, MPI_PRECISION, MPI_SUM, 0, ccomm);
MPI_Reduce(local+8, piScalarData+8, 1, MPI_PRECISION, MPI_MIN, 0, ccomm);
MPI_Reduce(local+9, piScalarData+9, 1, MPI_PRECISION, MPI_MAX, 0, ccomm);
MPI_Reduce(local+10, piScalarData+10, 1, MPI_PRECISION, MPI_SUM, 0, ccomm);
MPI_Reduce(local+11, piScalarData+11, 1, MPI_PRECISION, MPI_SUM, 0, ccomm);
MPI_Reduce(local+12, piScalarData+12, 1, MPI_PRECISION, MPI_MAX, 0, ccomm);
if(magEquation)
{
datax = B->vec->x->spatial;
datay = B->vec->y->spatial;
dataz = B->vec->z->spatial;
local[13] = datax[0];
local[14] = datax[0];
local[15] = datax[0];
local[16] = datay[0];
local[17] = datay[0];
local[18] = datay[0];
local[19] = dataz[0];
local[20] = dataz[0];
local[21] = dataz[0];
temp = pow(datax[0],2) + pow(datay[0],2) + pow(dataz[0],2);
local[22] = temp;
local[23] = temp;
for(i = 1; i < spatialCount; i++)
{
local[13] = fmin(local[13], datax[i]);
local[14] = fmax(local[14], datax[i]);
local[15] += datax[i];
local[16] = fmin(local[16], datay[i]);
local[17] = fmax(local[17], datay[i]);
local[18] += datay[i];
local[19] = fmin(local[19], dataz[i]);
local[20] = fmax(local[20], dataz[i]);
local[21] += dataz[i];
temp = pow(datax[i],2) + pow(datay[i],2) + pow(dataz[i],2);
local[22] += temp;
local[23] = fmax(temp, local[21]);
}
MPI_Reduce(local+13, piScalarData+13, 1, MPI_PRECISION, MPI_MIN, 0, ccomm);
MPI_Reduce(local+14, piScalarData+14, 1, MPI_PRECISION, MPI_MAX, 0, ccomm);
MPI_Reduce(local+15, piScalarData+15, 1, MPI_PRECISION, MPI_SUM, 0, ccomm);
MPI_Reduce(local+16, piScalarData+16, 1, MPI_PRECISION, MPI_MIN, 0, ccomm);
MPI_Reduce(local+17, piScalarData+17, 1, MPI_PRECISION, MPI_MAX, 0, ccomm);
MPI_Reduce(local+18, piScalarData+18, 1, MPI_PRECISION, MPI_SUM, 0, ccomm);
MPI_Reduce(local+19, piScalarData+19, 1, MPI_PRECISION, MPI_MIN, 0, ccomm);
MPI_Reduce(local+20, piScalarData+20, 1, MPI_PRECISION, MPI_MAX, 0, ccomm);
MPI_Reduce(local+21, piScalarData+21, 1, MPI_PRECISION, MPI_SUM, 0, ccomm);
MPI_Reduce(local+22, piScalarData+22, 1, MPI_PRECISION, MPI_SUM, 0, ccomm);
MPI_Reduce(local+23, piScalarData+23, 1, MPI_PRECISION, MPI_MAX, 0, ccomm);
}
free(local);
//Either store our data for later output, or perform the write to
//file
if(crank == 0)
{
//make the means means and not sums
piScalarData[4] /= (nx*ny*nz);
piScalarData[7] /= (nx*ny*nz);
piScalarData[10] /= (nx*ny*nz);
if(magEquation)
{
piScalarData[15] /= (nx*ny*nz);
piScalarData[18] /= (nx*ny*nz);
piScalarData[21] /= (nx*ny*nz);
}
scalarCount++;
piScalarData += numScalar;
//no reason to send this small amount of data to an IO node.
//our root compute node will just quickly take care of this.
if(scalarCount >= scalarPerF)
{
char fileName[100];
sprintf(fileName, "Scalars/%08d",iteration);
FILE * out = fopen(fileName, "w");
fwrite(scalarData, sizeof(PRECISION), numScalar * scalarPerF, out);
fclose(out);
scalarCount = 0;
piScalarData = scalarData;
}
}
}
}
//Time for spatial file output?
if(iteration % spatialRate == 0)
{
char * name = (char *)malloc(100);
//create the directory
if(crank == 0)
{
sprintf(name, "Spatial/%08d",iteration);
mkdir(name, S_IRWXU);
//Record the simulation time that this snapshot belongs to
sprintf(name, "Spatial/%08d/info",iteration);
FILE * info;
info = fopen(name, "w");
fprintf(info, infostro, elapsedTime);
fclose(info);
}
MPI_Barrier(MPI_COMM_WORLD);
if(compute_node)
{
if(momEquation || kinematic)
{
trace("Outputing u\n");
writeSpatial(u->vec->x,0);
trace("Outputing v\n");
writeSpatial(u->vec->y,0);
trace("Outputing w\n");
writeSpatial(u->vec->z,0);
}
if(tEquation)
{
trace("Outputting T\n");
writeSpatial(T, 0);
}
if(magEquation)
{
trace("Outputing Bx\n");
writeSpatial(B->vec->x,0);
trace("Outputing By\n");
writeSpatial(B->vec->y,0);
trace("Outputing Bz\n");
writeSpatial(B->vec->z,0);
}
}
else if(io_node)
{
if(momEquation || kinematic)
{
sprintf(name, "Spatial/%08d/u", iteration);
trace("Writing to file %s\n", name);
writeSpatial(0, name);
sprintf(name, "Spatial/%08d/v", iteration);
trace("Writing to file %s\n", name);
writeSpatial(0, name);
sprintf(name, "Spatial/%08d/w", iteration);
trace("Writing to file %s\n", name);
writeSpatial(0, name);
}
if(tEquation)
{
sprintf(name, "Spatial/%08d/T", iteration);
trace("Writing to file %s\n", name);
writeSpatial(0, name);
}
if(magEquation)
{
sprintf(name, "Spatial/%08d/Bx", iteration);
trace("Writing to file %s\n", name);
writeSpatial(0, name);
sprintf(name, "Spatial/%08d/By", iteration);
trace("Writing to file %s\n", name);
writeSpatial(0, name);
sprintf(name, "Spatial/%08d/Bz", iteration);
trace("Writing to file %s\n", name);
writeSpatial(0, name);
}
}
free(name);
}
if(iteration % checkRate == 0)
{
if(compute_node)
writeCheckpoint();
}
}
int main(int argc, char **argv)
{
cout << "Greetings, [INSERT_SUBJECT_NAME_HERE]!\n"
"Welcome to the Log-Indexed File Emulator, or L.I.F.E.\n"
"Wait just a moment while we set up a few things...\n\n";
initDrive();
checkPointInit();
readFileMap();
cout << "\nDone! Now it's time for you to grab L.I.F.E. by the horns!\n"
"Enter a command, or enter 'help' for usage information.\n"
"\n{epic prompt} ";
string command;
vector<string> args;
while(getline(cin, command))
{
args.clear();
split(command, ' ', args);
if(!command.empty()){
if((args[0] == "import" || args[0] == "i") && args.size() == 3)
{
import(args[1], args[2]);
}
else if((args[0] == "remove" || args[0] == "r") && args.size() == 2)
{
remove(args[1]);
}
else if((args[0] == "cat" || args[0] == "r") && args.size() == 2)
{
cat(args[1]);
}
else if((args[0] == "list" || args[0] == "l") && args.size() == 1)
{
list();
}
else if((args[0] == "exit" || args[0] == "q") && args.size() == 1)
{
cout << "Getting L.I.F.E. together...\n\n";
writeCheckpoint();
wbuffer.writeToDisk();
writeFileMap();
cout << "\nQuitting L.I.F.E.\n\u0CA0_\u0CA0\n";
exit(0);
}
else if((args[0] == "overwrite" || args[0] == "o") && args.size() == 5)
{
cout<<"overwriting...\n";
overwrite(args[1],args[2], args[3],args[4]);
}
else if((args[0] == "display" || args[0] == "d") && args.size() == 4)
{
cout<<"displaying...\n";
//display(args[1],args[2], args[3]);
}
else if((args[0] == "help" || args[0] == "h"))
{
if(args.size() == 1){
cout << "Thanks for calling L.I.F.E. help.\nHeaven knows we all need it from time to time.\nValid L.I.F.E. commands:\n"
"\timport <filename> <lfs_filename>\n"
"\tremove <lfs_filename>\n"
"\tlist\n"
"\texit\n"
"For more details on a command, enter 'help <command>'.\n";
}else if(args.size() == 2){
if(args[1] == "import"){
cout << "Usage: import <filepath> <lfs_filename>\n"
"Info: Imports a file from a filepath to the DRIVE, using the given filename.\n";
}
else if(args[1] == "remove"){
cout << "Usage: remove <lfs_filename>\n"
"Info: Removes a file from the DRIVE.\n";
}
else if(args[1] == "list"){
cout << "Usage: list\n"
"Info: Lists the names and sizes of all files currently in the DRIVE.\n";
}
else if(args[1] == "exit"){
cout << "Usage: exit\n"
"Info: C'mon bro. Take a good guess.\n";
}
else if(args[1] == "help"){
cout << "Usage: help <command>\n"
"Info: Prints usage info for all commands, and optionally prints specific info for one command.\n";
}else if(args[1] == "me"){
cout << "You're not alone; many of us have had suicidal thoughts at some point in our lives. "
"Feeling suicidal is not a character defect, and it doesn't mean that you are crazy, or weak, or flawed. "
"It only means that you have more pain than you can cope with right now. "
"This pain seems overwhelming and permanent at the moment. "
"But with time and support, you can overcome your problems and the pain and suicidal feelings will pass.\n"
"If you’re feeling suicidal right now, please call for help!\n\n"
"Call 1-800-273-TALK in the U.S.\n"
"Or visit IASP(http://www.iasp.info/resources/Crisis_Centres) to find a helpline in your country. "
"Alternatively, talk to someone you trust and let them know how bad things are.\n";
}else{
cout << "'" << args[1] << "' is not a command... Take your funny business elsewhere. This is a serious, real-world program.\n";
}
}else{
cout << "Hey, don't get too crazy, now.\n";
}
}
else
{
cout << "Invalid command and/or parameters. Enter 'help' for...y'know...help.\n";
}
}
cout << "\n{epic prompt} ";
}
return 0;
}
int Simulation::start(){
// +1 to let final survey run
totalSimDuration = _population->_transmissionModel->vectorInitDuration() + Global::maxAgeIntervals + Surveys.getFinalTimestep() + 1;
int testCheckpointStep = -1; // declare here so goto doesn't cross initialization
if (isCheckpoint()) {
readCheckpoint();
} else {
_population->createInitialHumans();
}
// phase loop
while (true) {
// loop for steps within a phase
while (Global::simulationTime < simPeriodEnd) {
// checkpoint
if (util::BoincWrapper::timeToCheckpoint() || Global::simulationTime == testCheckpointStep) {
writeCheckpoint();
util::BoincWrapper::checkpointCompleted();
if (Global::simulationTime == testCheckpointStep)
throw util::cmd_exit ("Checkpoint test: checkpoint written");
}
// interventions
if (Global::timeStep == Surveys.currentTimestep) {
_population->newSurvey();
Surveys.incrementSurveyPeriod();
}
_population->implementIntervention(Global::timeStep);
// update
++Global::simulationTime;
_population->update1();
++Global::timeStep;
util::BoincWrapper::reportProgress (double(Global::simulationTime) / totalSimDuration);
}
// phase transition: end of one phase to start of next
if (phase == STARTING_PHASE) {
simPeriodEnd = _population->_transmissionModel->vectorInitDuration();
phase = VECTOR_FITTING;
} else if (phase == VECTOR_FITTING) {
int extend = _population->_transmissionModel->vectorInitIterate ();
if (extend > 0) { // repeat phase
simPeriodEnd += extend;
totalSimDuration += extend;
} else { // next phase
simPeriodEnd += Global::maxAgeIntervals;
phase = ONE_LIFE_SPAN;
}
} else if (phase == ONE_LIFE_SPAN) {
simPeriodEnd = totalSimDuration;
Global::timeStep=0;
_population->preMainSimInit();
_population->newSurvey(); // Only to reset TransmissionModel::innoculationsPerAgeGroup
Surveys.incrementSurveyPeriod();
phase = MAIN_PHASE;
} else if (phase == MAIN_PHASE) {
phase = END_SIM;
break;
}
testCheckpointStep = -1;
if (util::CommandLine::option (util::CommandLine::TEST_CHECKPOINTING))
testCheckpointStep = Global::simulationTime + (simPeriodEnd - Global::simulationTime) / 2;
}
delete _population; // must destroy all Human instances to make sure they reported past events
Surveys.writeSummaryArrays();
// Write scenario checksum, only if simulation completed.
cksum.writeToFile (util::BoincWrapper::resolveFile ("scenario.sum"));
return 0;
}