| 1 |
#define _FILE_OFFSET_BITS 64 |
| 2 |
|
| 3 |
#include <string.h> |
| 4 |
#include <iostream> |
| 5 |
#include <fstream> |
| 6 |
#include <algorithm> |
| 7 |
#include <utility> |
| 8 |
|
| 9 |
#ifdef IS_MPI |
| 10 |
#include <mpi.h> |
| 11 |
#include "mpiSimulation.hpp" |
| 12 |
|
| 13 |
namespace dWrite{ |
| 14 |
void DieDieDie( void ); |
| 15 |
} |
| 16 |
|
| 17 |
using namespace dWrite; |
| 18 |
#endif //is_mpi |
| 19 |
|
| 20 |
#include "ReadWrite.hpp" |
| 21 |
#include "simError.h" |
| 22 |
|
| 23 |
DumpWriter::DumpWriter( SimInfo* the_entry_plug ){ |
| 24 |
|
| 25 |
entry_plug = the_entry_plug; |
| 26 |
|
| 27 |
#ifdef IS_MPI |
| 28 |
if(worldRank == 0 ){ |
| 29 |
#endif // is_mpi |
| 30 |
|
| 31 |
|
| 32 |
dumpFile.open(entry_plug->sampleName, ios::out | ios::trunc ); |
| 33 |
|
| 34 |
if( !dumpFile ){ |
| 35 |
|
| 36 |
sprintf( painCave.errMsg, |
| 37 |
"Could not open \"%s\" for dump output.\n", |
| 38 |
entry_plug->sampleName); |
| 39 |
painCave.isFatal = 1; |
| 40 |
simError(); |
| 41 |
} |
| 42 |
|
| 43 |
#ifdef IS_MPI |
| 44 |
} |
| 45 |
|
| 46 |
//sort the local atoms by global index |
| 47 |
sortByGlobalIndex(); |
| 48 |
|
| 49 |
sprintf( checkPointMsg, |
| 50 |
"Sucessfully opened output file for dumping.\n"); |
| 51 |
MPIcheckPoint(); |
| 52 |
#endif // is_mpi |
| 53 |
} |
| 54 |
|
| 55 |
DumpWriter::~DumpWriter( ){ |
| 56 |
|
| 57 |
#ifdef IS_MPI |
| 58 |
if(worldRank == 0 ){ |
| 59 |
#endif // is_mpi |
| 60 |
|
| 61 |
dumpFile.close(); |
| 62 |
|
| 63 |
#ifdef IS_MPI |
| 64 |
} |
| 65 |
#endif // is_mpi |
| 66 |
} |
| 67 |
|
| 68 |
#ifdef IS_MPI |
| 69 |
|
| 70 |
/** |
| 71 |
* A hook function to load balancing |
| 72 |
*/ |
| 73 |
|
| 74 |
void DumpWriter::update(){ |
| 75 |
sortByGlobalIndex(); |
| 76 |
} |
| 77 |
|
| 78 |
/** |
| 79 |
* Auxiliary sorting function |
| 80 |
*/ |
| 81 |
|
| 82 |
bool indexSortingCriterion(const pair<int, int>& p1, const pair<int, int>& p2){ |
| 83 |
return p1.second < p2.second; |
| 84 |
} |
| 85 |
|
| 86 |
/** |
| 87 |
* Sorting the local index by global index |
| 88 |
*/ |
| 89 |
|
| 90 |
void DumpWriter::sortByGlobalIndex(){ |
| 91 |
Atom** atoms = entry_plug->atoms; |
| 92 |
|
| 93 |
indexArray.clear(); |
| 94 |
|
| 95 |
for(int i = 0; i < mpiSim->getMyNlocal();i++) |
| 96 |
indexArray.push_back(make_pair(i, atoms[i]->getGlobalIndex())); |
| 97 |
|
| 98 |
sort(indexArray.begin(), indexArray.end(), indexSortingCriterion); |
| 99 |
} |
| 100 |
#endif |
| 101 |
|
| 102 |
void DumpWriter::writeDump(double currentTime){ |
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|
| 104 |
ofstream finalOut; |
| 105 |
vector<ofstream*> fileStreams; |
| 106 |
|
| 107 |
#ifdef IS_MPI |
| 108 |
if(worldRank == 0 ){ |
| 109 |
|
| 110 |
finalOut.open( entry_plug->finalName, ios::out | ios::trunc ); |
| 111 |
if( !finalOut ){ |
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sprintf( painCave.errMsg, |
| 113 |
"Could not open \"%s\" for final dump output.\n", |
| 114 |
entry_plug->finalName ); |
| 115 |
painCave.isFatal = 1; |
| 116 |
simError(); |
| 117 |
} |
| 118 |
} |
| 119 |
#endif // is_mpi |
| 120 |
|
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fileStreams.push_back(&finalOut); |
| 122 |
fileStreams.push_back(&dumpFile); |
| 123 |
|
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writeFrame(fileStreams, currentTime); |
| 125 |
|
| 126 |
#ifdef IS_MPI |
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finalOut.close(); |
| 128 |
#endif |
| 129 |
|
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} |
| 131 |
|
| 132 |
void DumpWriter::writeFinal(double currentTime){ |
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|
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ofstream finalOut; |
| 135 |
vector<ofstream*> fileStreams; |
| 136 |
|
| 137 |
#ifdef IS_MPI |
| 138 |
if(worldRank == 0 ){ |
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|
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finalOut.open( entry_plug->finalName, ios::out | ios::trunc ); |
| 141 |
|
| 142 |
if( !finalOut ){ |
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sprintf( painCave.errMsg, |
| 144 |
"Could not open \"%s\" for final dump output.\n", |
| 145 |
entry_plug->finalName ); |
| 146 |
painCave.isFatal = 1; |
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simError(); |
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} |
| 149 |
|
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} |
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#endif // is_mpi |
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|
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fileStreams.push_back(&finalOut); |
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writeFrame(fileStreams, currentTime); |
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|
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#ifdef IS_MPI |
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finalOut.close(); |
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#endif |
| 159 |
|
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} |
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|
| 162 |
void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){ |
| 163 |
|
| 164 |
const int BUFFERSIZE = 2000; |
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const int MINIBUFFERSIZE = 100; |
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|
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char tempBuffer[BUFFERSIZE]; |
| 168 |
char writeLine[BUFFERSIZE]; |
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|
| 170 |
int i, k; |
| 171 |
|
| 172 |
#ifdef IS_MPI |
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|
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int *potatoes; |
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int myPotato; |
| 176 |
|
| 177 |
int nProc; |
| 178 |
int j, which_node, done, which_atom, local_index, currentIndex; |
| 179 |
double atomData6[6]; |
| 180 |
double atomData13[13]; |
| 181 |
int isDirectional; |
| 182 |
char* atomTypeString; |
| 183 |
char MPIatomTypeString[MINIBUFFERSIZE]; |
| 184 |
|
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#else //is_mpi |
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int nAtoms = entry_plug->n_atoms; |
| 187 |
#endif //is_mpi |
| 188 |
|
| 189 |
double q[4]; |
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DirectionalAtom* dAtom; |
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Atom** atoms = entry_plug->atoms; |
| 192 |
double pos[3], vel[3]; |
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|
| 194 |
#ifndef IS_MPI |
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|
| 196 |
for(k = 0; k < outFile.size(); k++){ |
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*outFile[k] << nAtoms << "\n"; |
| 198 |
|
| 199 |
*outFile[k] << currentTime << ";\t" |
| 200 |
<< entry_plug->Hmat[0][0] << "\t" |
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<< entry_plug->Hmat[1][0] << "\t" |
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<< entry_plug->Hmat[2][0] << ";\t" |
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|
| 204 |
<< entry_plug->Hmat[0][1] << "\t" |
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<< entry_plug->Hmat[1][1] << "\t" |
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<< entry_plug->Hmat[2][1] << ";\t" |
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|
| 208 |
<< entry_plug->Hmat[0][2] << "\t" |
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<< entry_plug->Hmat[1][2] << "\t" |
| 210 |
<< entry_plug->Hmat[2][2] << ";"; |
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|
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//write out additional parameters, such as chi and eta |
| 213 |
*outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl; |
| 214 |
} |
| 215 |
|
| 216 |
for( i=0; i<nAtoms; i++ ){ |
| 217 |
|
| 218 |
atoms[i]->getPos(pos); |
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atoms[i]->getVel(vel); |
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|
| 221 |
sprintf( tempBuffer, |
| 222 |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
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atoms[i]->getType(), |
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pos[0], |
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pos[1], |
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pos[2], |
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vel[0], |
| 228 |
vel[1], |
| 229 |
vel[2]); |
| 230 |
strcpy( writeLine, tempBuffer ); |
| 231 |
|
| 232 |
if( atoms[i]->isDirectional() ){ |
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|
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dAtom = (DirectionalAtom *)atoms[i]; |
| 235 |
dAtom->getQ( q ); |
| 236 |
|
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sprintf( tempBuffer, |
| 238 |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
| 239 |
q[0], |
| 240 |
q[1], |
| 241 |
q[2], |
| 242 |
q[3], |
| 243 |
dAtom->getJx(), |
| 244 |
dAtom->getJy(), |
| 245 |
dAtom->getJz()); |
| 246 |
strcat( writeLine, tempBuffer ); |
| 247 |
} |
| 248 |
else |
| 249 |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
| 250 |
|
| 251 |
for(k = 0; k < outFile.size(); k++) |
| 252 |
*outFile[k] << writeLine; |
| 253 |
} |
| 254 |
|
| 255 |
#else // is_mpi |
| 256 |
|
| 257 |
/* code to find maximum tag value */ |
| 258 |
|
| 259 |
int *tagub, flag, MAXTAG; |
| 260 |
MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag); |
| 261 |
if (flag) { |
| 262 |
MAXTAG = *tagub; |
| 263 |
} else { |
| 264 |
MAXTAG = 32767; |
| 265 |
} |
| 266 |
|
| 267 |
int haveError; |
| 268 |
|
| 269 |
MPI_Status istatus; |
| 270 |
int *AtomToProcMap = mpiSim->getAtomToProcMap(); |
| 271 |
|
| 272 |
// write out header and node 0's coordinates |
| 273 |
|
| 274 |
if( worldRank == 0 ){ |
| 275 |
|
| 276 |
// Node 0 needs a list of the magic potatoes for each processor; |
| 277 |
|
| 278 |
nProc = mpiSim->getNumberProcessors(); |
| 279 |
potatoes = new int[nProc]; |
| 280 |
|
| 281 |
//write out the comment lines |
| 282 |
for (i = 0; i < nProc; i++) |
| 283 |
potatoes[i] = 0; |
| 284 |
|
| 285 |
for(k = 0; k < outFile.size(); k++){ |
| 286 |
*outFile[k] << mpiSim->getTotAtoms() << "\n"; |
| 287 |
|
| 288 |
*outFile[k] << currentTime << ";\t" |
| 289 |
<< entry_plug->Hmat[0][0] << "\t" |
| 290 |
<< entry_plug->Hmat[1][0] << "\t" |
| 291 |
<< entry_plug->Hmat[2][0] << ";\t" |
| 292 |
|
| 293 |
<< entry_plug->Hmat[0][1] << "\t" |
| 294 |
<< entry_plug->Hmat[1][1] << "\t" |
| 295 |
<< entry_plug->Hmat[2][1] << ";\t" |
| 296 |
|
| 297 |
<< entry_plug->Hmat[0][2] << "\t" |
| 298 |
<< entry_plug->Hmat[1][2] << "\t" |
| 299 |
<< entry_plug->Hmat[2][2] << ";"; |
| 300 |
|
| 301 |
*outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl; |
| 302 |
} |
| 303 |
|
| 304 |
currentIndex = 0; |
| 305 |
|
| 306 |
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
| 307 |
|
| 308 |
// Get the Node number which has this atom; |
| 309 |
|
| 310 |
which_node = AtomToProcMap[i]; |
| 311 |
|
| 312 |
if (which_node != 0) { |
| 313 |
|
| 314 |
if (potatoes[which_node] + 3 >= MAXTAG) { |
| 315 |
// The potato was going to exceed the maximum value, |
| 316 |
// so wrap this processor potato back to 0: |
| 317 |
|
| 318 |
potatoes[which_node] = 0; |
| 319 |
MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD); |
| 320 |
|
| 321 |
} |
| 322 |
|
| 323 |
myPotato = potatoes[which_node]; |
| 324 |
|
| 325 |
MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node, |
| 326 |
myPotato, MPI_COMM_WORLD, &istatus); |
| 327 |
|
| 328 |
atomTypeString = MPIatomTypeString; |
| 329 |
|
| 330 |
myPotato++; |
| 331 |
|
| 332 |
MPI_Recv(&isDirectional, 1, MPI_INT, which_node, |
| 333 |
myPotato, MPI_COMM_WORLD, &istatus); |
| 334 |
|
| 335 |
myPotato++; |
| 336 |
|
| 337 |
if (isDirectional) { |
| 338 |
MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node, |
| 339 |
myPotato, MPI_COMM_WORLD, &istatus); |
| 340 |
} else { |
| 341 |
MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node, |
| 342 |
myPotato, MPI_COMM_WORLD, &istatus); |
| 343 |
} |
| 344 |
|
| 345 |
myPotato++; |
| 346 |
potatoes[which_node] = myPotato; |
| 347 |
|
| 348 |
} else { |
| 349 |
|
| 350 |
haveError = 0; |
| 351 |
which_atom = i; |
| 352 |
|
| 353 |
local_index = indexArray[currentIndex].first; |
| 354 |
|
| 355 |
if (which_atom == indexArray[currentIndex].second) { |
| 356 |
|
| 357 |
atomTypeString = atoms[local_index]->getType(); |
| 358 |
|
| 359 |
atoms[local_index]->getPos(pos); |
| 360 |
atoms[local_index]->getVel(vel); |
| 361 |
|
| 362 |
atomData6[0] = pos[0]; |
| 363 |
atomData6[1] = pos[1]; |
| 364 |
atomData6[2] = pos[2]; |
| 365 |
|
| 366 |
atomData6[3] = vel[0]; |
| 367 |
atomData6[4] = vel[1]; |
| 368 |
atomData6[5] = vel[2]; |
| 369 |
|
| 370 |
isDirectional = 0; |
| 371 |
|
| 372 |
if( atoms[local_index]->isDirectional() ){ |
| 373 |
|
| 374 |
isDirectional = 1; |
| 375 |
|
| 376 |
dAtom = (DirectionalAtom *)atoms[local_index]; |
| 377 |
dAtom->getQ( q ); |
| 378 |
|
| 379 |
for (int j = 0; j < 6 ; j++) |
| 380 |
atomData13[j] = atomData6[j]; |
| 381 |
|
| 382 |
atomData13[6] = q[0]; |
| 383 |
atomData13[7] = q[1]; |
| 384 |
atomData13[8] = q[2]; |
| 385 |
atomData13[9] = q[3]; |
| 386 |
|
| 387 |
atomData13[10] = dAtom->getJx(); |
| 388 |
atomData13[11] = dAtom->getJy(); |
| 389 |
atomData13[12] = dAtom->getJz(); |
| 390 |
} |
| 391 |
|
| 392 |
} else { |
| 393 |
sprintf(painCave.errMsg, |
| 394 |
"Atom %d not found on processor %d\n", |
| 395 |
i, worldRank ); |
| 396 |
haveError= 1; |
| 397 |
simError(); |
| 398 |
} |
| 399 |
|
| 400 |
if(haveError) DieDieDie(); |
| 401 |
|
| 402 |
currentIndex ++; |
| 403 |
} |
| 404 |
// If we've survived to here, format the line: |
| 405 |
|
| 406 |
if (!isDirectional) { |
| 407 |
|
| 408 |
sprintf( writeLine, |
| 409 |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
| 410 |
atomTypeString, |
| 411 |
atomData6[0], |
| 412 |
atomData6[1], |
| 413 |
atomData6[2], |
| 414 |
atomData6[3], |
| 415 |
atomData6[4], |
| 416 |
atomData6[5]); |
| 417 |
|
| 418 |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
| 419 |
|
| 420 |
} else { |
| 421 |
|
| 422 |
sprintf( writeLine, |
| 423 |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
| 424 |
atomTypeString, |
| 425 |
atomData13[0], |
| 426 |
atomData13[1], |
| 427 |
atomData13[2], |
| 428 |
atomData13[3], |
| 429 |
atomData13[4], |
| 430 |
atomData13[5], |
| 431 |
atomData13[6], |
| 432 |
atomData13[7], |
| 433 |
atomData13[8], |
| 434 |
atomData13[9], |
| 435 |
atomData13[10], |
| 436 |
atomData13[11], |
| 437 |
atomData13[12]); |
| 438 |
|
| 439 |
} |
| 440 |
|
| 441 |
for(k = 0; k < outFile.size(); k++) |
| 442 |
*outFile[k] << writeLine; |
| 443 |
} |
| 444 |
|
| 445 |
for(k = 0; k < outFile.size(); k++) |
| 446 |
outFile[k]->flush(); |
| 447 |
|
| 448 |
sprintf( checkPointMsg, |
| 449 |
"Sucessfully took a dump.\n"); |
| 450 |
|
| 451 |
MPIcheckPoint(); |
| 452 |
|
| 453 |
delete[] potatoes; |
| 454 |
|
| 455 |
} else { |
| 456 |
|
| 457 |
// worldRank != 0, so I'm a remote node. |
| 458 |
|
| 459 |
// Set my magic potato to 0: |
| 460 |
|
| 461 |
myPotato = 0; |
| 462 |
currentIndex = 0; |
| 463 |
|
| 464 |
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
| 465 |
|
| 466 |
// Am I the node which has this atom? |
| 467 |
|
| 468 |
if (AtomToProcMap[i] == worldRank) { |
| 469 |
|
| 470 |
if (myPotato + 3 >= MAXTAG) { |
| 471 |
|
| 472 |
// The potato was going to exceed the maximum value, |
| 473 |
// so wrap this processor potato back to 0 (and block until |
| 474 |
// node 0 says we can go: |
| 475 |
|
| 476 |
MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus); |
| 477 |
|
| 478 |
} |
| 479 |
which_atom = i; |
| 480 |
local_index = indexArray[currentIndex].first; |
| 481 |
|
| 482 |
if (which_atom == indexArray[currentIndex].second) { |
| 483 |
|
| 484 |
atomTypeString = atoms[local_index]->getType(); |
| 485 |
|
| 486 |
atoms[local_index]->getPos(pos); |
| 487 |
atoms[local_index]->getVel(vel); |
| 488 |
|
| 489 |
atomData6[0] = pos[0]; |
| 490 |
atomData6[1] = pos[1]; |
| 491 |
atomData6[2] = pos[2]; |
| 492 |
|
| 493 |
atomData6[3] = vel[0]; |
| 494 |
atomData6[4] = vel[1]; |
| 495 |
atomData6[5] = vel[2]; |
| 496 |
|
| 497 |
isDirectional = 0; |
| 498 |
|
| 499 |
if( atoms[local_index]->isDirectional() ){ |
| 500 |
|
| 501 |
isDirectional = 1; |
| 502 |
|
| 503 |
dAtom = (DirectionalAtom *)atoms[local_index]; |
| 504 |
dAtom->getQ( q ); |
| 505 |
|
| 506 |
for (int j = 0; j < 6 ; j++) |
| 507 |
atomData13[j] = atomData6[j]; |
| 508 |
|
| 509 |
atomData13[6] = q[0]; |
| 510 |
atomData13[7] = q[1]; |
| 511 |
atomData13[8] = q[2]; |
| 512 |
atomData13[9] = q[3]; |
| 513 |
|
| 514 |
atomData13[10] = dAtom->getJx(); |
| 515 |
atomData13[11] = dAtom->getJy(); |
| 516 |
atomData13[12] = dAtom->getJz(); |
| 517 |
} |
| 518 |
|
| 519 |
} else { |
| 520 |
sprintf(painCave.errMsg, |
| 521 |
"Atom %d not found on processor %d\n", |
| 522 |
i, worldRank ); |
| 523 |
haveError= 1; |
| 524 |
simError(); |
| 525 |
} |
| 526 |
|
| 527 |
strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE); |
| 528 |
|
| 529 |
// null terminate the string before sending (just in case): |
| 530 |
MPIatomTypeString[MINIBUFFERSIZE-1] = '\0'; |
| 531 |
|
| 532 |
MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0, |
| 533 |
myPotato, MPI_COMM_WORLD); |
| 534 |
|
| 535 |
myPotato++; |
| 536 |
|
| 537 |
MPI_Send(&isDirectional, 1, MPI_INT, 0, |
| 538 |
myPotato, MPI_COMM_WORLD); |
| 539 |
|
| 540 |
myPotato++; |
| 541 |
|
| 542 |
if (isDirectional) { |
| 543 |
|
| 544 |
MPI_Send(atomData13, 13, MPI_DOUBLE, 0, |
| 545 |
myPotato, MPI_COMM_WORLD); |
| 546 |
|
| 547 |
} else { |
| 548 |
|
| 549 |
MPI_Send(atomData6, 6, MPI_DOUBLE, 0, |
| 550 |
myPotato, MPI_COMM_WORLD); |
| 551 |
} |
| 552 |
|
| 553 |
myPotato++; |
| 554 |
currentIndex++; |
| 555 |
} |
| 556 |
} |
| 557 |
|
| 558 |
sprintf( checkPointMsg, |
| 559 |
"Sucessfully took a dump.\n"); |
| 560 |
MPIcheckPoint(); |
| 561 |
|
| 562 |
} |
| 563 |
|
| 564 |
#endif // is_mpi |
| 565 |
} |
| 566 |
|
| 567 |
#ifdef IS_MPI |
| 568 |
|
| 569 |
// a couple of functions to let us escape the write loop |
| 570 |
|
| 571 |
void dWrite::DieDieDie( void ){ |
| 572 |
|
| 573 |
MPI_Finalize(); |
| 574 |
exit (0); |
| 575 |
} |
| 576 |
|
| 577 |
#endif //is_mpi |
