| 1 |
#include "io/DumpWrite.hpp" |
| 2 |
#include "utils/simError.h" |
| 3 |
|
| 4 |
#ifdef IS_MPI |
| 5 |
#include <mpi.h> |
| 6 |
#endif //is_mpi |
| 7 |
namespace oopse { |
| 8 |
DumpWriter::DumpWriter(SimInfo* info, const std::string& filename) |
| 9 |
: info_(info), filename_(filename){ |
| 10 |
#ifdef IS_MPI |
| 11 |
|
| 12 |
if (worldRank == 0) { |
| 13 |
#endif // is_mpi |
| 14 |
|
| 15 |
dumpFile.open(filename_.c_str(), ios::out | ios::trunc); |
| 16 |
|
| 17 |
if (!dumpFile) { |
| 18 |
sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n", |
| 19 |
info_->filename_.c_str()); |
| 20 |
painCave.isFatal = 1; |
| 21 |
simError(); |
| 22 |
} |
| 23 |
|
| 24 |
#ifdef IS_MPI |
| 25 |
|
| 26 |
} |
| 27 |
|
| 28 |
sprintf(checkPointMsg, "Sucessfully opened output file for dumping.\n"); |
| 29 |
MPIcheckPoint(); |
| 30 |
|
| 31 |
#endif // is_mpi |
| 32 |
|
| 33 |
} |
| 34 |
|
| 35 |
DumpWriter::~DumpWriter() { |
| 36 |
|
| 37 |
#ifdef IS_MPI |
| 38 |
|
| 39 |
if (worldRank == 0) { |
| 40 |
#endif // is_mpi |
| 41 |
|
| 42 |
dumpFile.close(); |
| 43 |
|
| 44 |
#ifdef IS_MPI |
| 45 |
|
| 46 |
} |
| 47 |
|
| 48 |
#endif // is_mpi |
| 49 |
|
| 50 |
} |
| 51 |
|
| 52 |
void writeCommentLine(Snapshot* s) { |
| 53 |
|
| 54 |
double currentTime; |
| 55 |
Mat3x3d hmat; |
| 56 |
double chi; |
| 57 |
double integralOfChiDt; |
| 58 |
Mat3x3d eta; |
| 59 |
|
| 60 |
currentTime = s->getTime(); |
| 61 |
hmat = s->getHmat(); |
| 62 |
chi = s->getChi(); |
| 63 |
integralOfChiDt = s->getIntegralOfChiDt(); |
| 64 |
eta = s->getEta(); |
| 65 |
|
| 66 |
os << currentTime << ";\t" |
| 67 |
<< hmat[0][0] << "\t" << hmat[1][0] << "\t" << hmat[2][0] << ";\t" |
| 68 |
<< hmat[0][1] << "\t" << hmat[1][1] << "\t" << hmat[2][1] << ";\t" |
| 69 |
<< hmat[0][2] << "\t" << hmat[1][2] << "\t" << hmat[2][2] << ";"; |
| 70 |
|
| 71 |
//write out additional parameters, such as chi and eta |
| 72 |
|
| 73 |
os << chi << "\t" << integralOfChiDt << "\t;" |
| 74 |
|
| 75 |
os << eta[0][0] << "\t" << eta[1][0] << "\t" << eta[2][0] << ";\t" |
| 76 |
<< eta[0][1] << "\t" << eta[1][1] << "\t" << eta[2][1] << ";\t" |
| 77 |
<< eta[0][2] << "\t" << eta[1][2] << "\t" << eta[2][2] << ";"; |
| 78 |
|
| 79 |
os << endl; |
| 80 |
} |
| 81 |
|
| 82 |
void DumpWriter::writeFrame(std::ostream& os) { |
| 83 |
const int BUFFERSIZE = 2000; |
| 84 |
const int MINIBUFFERSIZE = 100; |
| 85 |
|
| 86 |
char tempBuffer[BUFFERSIZE]; |
| 87 |
char writeLine[BUFFERSIZE]; |
| 88 |
|
| 89 |
Quat4d q; |
| 90 |
Vector3d ji; |
| 91 |
Vector3d pos; |
| 92 |
Vector3d vel; |
| 93 |
|
| 94 |
Molecule* mol; |
| 95 |
StuntDouble* integrableObject; |
| 96 |
typename SimInfo::MoleculeIterator mi; |
| 97 |
typename Molecule::IntegrableObjectIterator ii; |
| 98 |
|
| 99 |
int nTotObjects; |
| 100 |
nTotObjects = info_->getNGlobalIntegrableObjects(); |
| 101 |
|
| 102 |
#ifndef IS_MPI |
| 103 |
|
| 104 |
|
| 105 |
os << nTotObjects << "\n"; |
| 106 |
|
| 107 |
writeCommentLine(info_->getSnapshotManager()->getCurrentSnapshot()); |
| 108 |
|
| 109 |
for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { |
| 110 |
|
| 111 |
for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; |
| 112 |
integrableObject = mol->nextIntegrableObject(ii)) { |
| 113 |
|
| 114 |
|
| 115 |
pos = integrableObject->getPos(); |
| 116 |
vel = integrableObject->getVel(); |
| 117 |
|
| 118 |
sprintf(tempBuffer, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
| 119 |
integrableObject->getType(), |
| 120 |
pos[0], pos[1], pos[2], |
| 121 |
vel[0], vel[1], vel[2]); |
| 122 |
|
| 123 |
strcpy(writeLine, tempBuffer); |
| 124 |
|
| 125 |
if (integrableObject->isDirectional()) { |
| 126 |
q = integrableObject->getQ(); |
| 127 |
ji = integrableObject->getJ(); |
| 128 |
|
| 129 |
sprintf(tempBuffer, "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
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q[0], q[1], q[2], q[3], |
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ji[0], ji[1], ji[2]); |
| 132 |
strcat(writeLine, tempBuffer); |
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} else { |
| 134 |
strcat(writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n"); |
| 135 |
} |
| 136 |
|
| 137 |
os << writeLine; |
| 138 |
|
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} |
| 140 |
} |
| 141 |
|
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#else // is_mpi |
| 143 |
/********************************************************************* |
| 144 |
* Documentation? You want DOCUMENTATION? |
| 145 |
* |
| 146 |
* Why all the potatoes below? |
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* |
| 148 |
* To make a long story short, the original version of DumpWriter |
| 149 |
* worked in the most inefficient way possible. Node 0 would |
| 150 |
* poke each of the node for an individual atom's formatted data |
| 151 |
* as node 0 worked its way down the global index. This was particularly |
| 152 |
* inefficient since the method blocked all processors at every atom |
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* (and did it twice!). |
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* |
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* An intermediate version of DumpWriter could be described from Node |
| 156 |
* zero's perspective as follows: |
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* |
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* 1) Have 100 of your friends stand in a circle. |
| 159 |
* 2) When you say go, have all of them start tossing potatoes at |
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* you (one at a time). |
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* 3) Catch the potatoes. |
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* |
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* It was an improvement, but MPI has buffers and caches that could |
| 164 |
* best be described in this analogy as "potato nets", so there's no |
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* need to block the processors atom-by-atom. |
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* |
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* This new and improved DumpWriter works in an even more efficient |
| 168 |
* way: |
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* |
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* 1) Have 100 of your friend stand in a circle. |
| 171 |
* 2) When you say go, have them start tossing 5-pound bags of |
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* potatoes at you. |
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* 3) Once you've caught a friend's bag of potatoes, |
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* toss them a spud to let them know they can toss another bag. |
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* |
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* How's THAT for documentation? |
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* |
| 178 |
*********************************************************************/ |
| 179 |
const int masterNode = 0; |
| 180 |
|
| 181 |
int * potatoes; |
| 182 |
int myPotato; |
| 183 |
int nProc; |
| 184 |
int which_node; |
| 185 |
double atomData[13]; |
| 186 |
int isDirectional; |
| 187 |
const char * atomTypeString; |
| 188 |
char MPIatomTypeString[MINIBUFFERSIZE]; |
| 189 |
int msgLen; // the length of message actually recieved at master nodes |
| 190 |
int haveError; |
| 191 |
MPI_Status istatus; |
| 192 |
int nCurObj; |
| 193 |
|
| 194 |
// code to find maximum tag value |
| 195 |
int * tagub; |
| 196 |
int flag; |
| 197 |
int MAXTAG; |
| 198 |
MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag); |
| 199 |
|
| 200 |
if (flag) { |
| 201 |
MAXTAG = *tagub; |
| 202 |
} else { |
| 203 |
MAXTAG = 32767; |
| 204 |
} |
| 205 |
|
| 206 |
if (worldRank == masterNode) { //master node (node 0) is responsible for writing the dump file |
| 207 |
|
| 208 |
// Node 0 needs a list of the magic potatoes for each processor; |
| 209 |
|
| 210 |
MPI_Comm_size(MPI_COMM_WORLD, &nProc); |
| 211 |
potatoes = new int[nProc]; |
| 212 |
|
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//write out the comment lines |
| 214 |
for(i = 0; i < nProc; i++) { |
| 215 |
potatoes[i] = 0; |
| 216 |
} |
| 217 |
|
| 218 |
|
| 219 |
os << nTotObjects << "\n"; |
| 220 |
writeCommentLine(info_->getSnapshotManager()->getCurrentSnapshot()); |
| 221 |
|
| 222 |
for(i = 0; i < info_->getNGlobalMolecules(); i++) { |
| 223 |
|
| 224 |
// Get the Node number which has this atom; |
| 225 |
|
| 226 |
which_node = info_->getMolToProc(i); |
| 227 |
|
| 228 |
if (which_node != masterNode) { //current molecule is in slave node |
| 229 |
if (potatoes[which_node] + 1 >= MAXTAG) { |
| 230 |
// The potato was going to exceed the maximum value, |
| 231 |
// so wrap this processor potato back to 0: |
| 232 |
|
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potatoes[which_node] = 0; |
| 234 |
MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0, |
| 235 |
MPI_COMM_WORLD); |
| 236 |
} |
| 237 |
|
| 238 |
myPotato = potatoes[which_node]; |
| 239 |
|
| 240 |
//recieve the number of integrableObject in current molecule |
| 241 |
MPI_Recv(&nCurObj, 1, MPI_INT, which_node, myPotato, |
| 242 |
MPI_COMM_WORLD, &istatus); |
| 243 |
myPotato++; |
| 244 |
|
| 245 |
for(int l = 0; l < nCurObj; l++) { |
| 246 |
if (potatoes[which_node] + 2 >= MAXTAG) { |
| 247 |
// The potato was going to exceed the maximum value, |
| 248 |
// so wrap this processor potato back to 0: |
| 249 |
|
| 250 |
potatoes[which_node] = 0; |
| 251 |
MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, |
| 252 |
0, MPI_COMM_WORLD); |
| 253 |
} |
| 254 |
|
| 255 |
MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, |
| 256 |
which_node, myPotato, MPI_COMM_WORLD, |
| 257 |
&istatus); |
| 258 |
|
| 259 |
atomTypeString = MPIatomTypeString; |
| 260 |
|
| 261 |
myPotato++; |
| 262 |
|
| 263 |
MPI_Recv(atomData, 13, MPI_DOUBLE, which_node, myPotato, |
| 264 |
MPI_COMM_WORLD, &istatus); |
| 265 |
myPotato++; |
| 266 |
|
| 267 |
MPI_Get_count(&istatus, MPI_DOUBLE, &msgLen); |
| 268 |
|
| 269 |
if (msgLen == 13) |
| 270 |
isDirectional = 1; |
| 271 |
else |
| 272 |
isDirectional = 0; |
| 273 |
|
| 274 |
// If we've survived to here, format the line: |
| 275 |
|
| 276 |
if (!isDirectional) { |
| 277 |
sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
| 278 |
atomTypeString, atomData[0], |
| 279 |
atomData[1], atomData[2], |
| 280 |
atomData[3], atomData[4], |
| 281 |
atomData[5]); |
| 282 |
|
| 283 |
strcat(writeLine, |
| 284 |
"0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n"); |
| 285 |
} else { |
| 286 |
sprintf(writeLine, |
| 287 |
"%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", |
| 288 |
atomTypeString, |
| 289 |
atomData[0], |
| 290 |
atomData[1], |
| 291 |
atomData[2], |
| 292 |
atomData[3], |
| 293 |
atomData[4], |
| 294 |
atomData[5], |
| 295 |
atomData[6], |
| 296 |
atomData[7], |
| 297 |
atomData[8], |
| 298 |
atomData[9], |
| 299 |
atomData[10], |
| 300 |
atomData[11], |
| 301 |
atomData[12]); |
| 302 |
} |
| 303 |
|
| 304 |
os << writeLine; |
| 305 |
|
| 306 |
} // end for(int l =0) |
| 307 |
|
| 308 |
potatoes[which_node] = myPotato; |
| 309 |
} else { //master node has current molecule |
| 310 |
|
| 311 |
mol = info_->getMoleculeByGlobalIndex(i); |
| 312 |
|
| 313 |
if (mol == NULL) { |
| 314 |
strcpy(painCave.errMsg, "Molecule not found on node %d!", worldRank); |
| 315 |
painCave.isFatal = 1; |
| 316 |
simError(); |
| 317 |
} |
| 318 |
|
| 319 |
for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; |
| 320 |
integrableObject = mol->nextIntegrableObject(ii)) { |
| 321 |
|
| 322 |
atomTypeString = integrableObject->getType().c_str(); |
| 323 |
|
| 324 |
pos = integrableObject->getPos(); |
| 325 |
vel = integrableObject->getVel(); |
| 326 |
|
| 327 |
atomData[0] = pos[0]; |
| 328 |
atomData[1] = pos[1]; |
| 329 |
atomData[2] = pos[2]; |
| 330 |
|
| 331 |
atomData[3] = vel[0]; |
| 332 |
atomData[4] = vel[1]; |
| 333 |
atomData[5] = vel[2]; |
| 334 |
|
| 335 |
isDirectional = 0; |
| 336 |
|
| 337 |
if (integrableObject->isDirectional()) { |
| 338 |
isDirectional = 1; |
| 339 |
|
| 340 |
q = integrableObject->getQ(); |
| 341 |
ji = integrableObject->getJ(); |
| 342 |
|
| 343 |
for(int j = 0; j < 6; j++) { |
| 344 |
atomData[j] = atomData[j]; |
| 345 |
} |
| 346 |
|
| 347 |
atomData[6] = q[0]; |
| 348 |
atomData[7] = q[1]; |
| 349 |
atomData[8] = q[2]; |
| 350 |
atomData[9] = q[3]; |
| 351 |
|
| 352 |
atomData[10] = ji[0]; |
| 353 |
atomData[11] = ji[1]; |
| 354 |
atomData[12] = ji[2]; |
| 355 |
} |
| 356 |
|
| 357 |
// If we've survived to here, format the line: |
| 358 |
|
| 359 |
if (!isDirectional) { |
| 360 |
sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
| 361 |
atomTypeString, atomData[0], |
| 362 |
atomData[1], atomData[2], |
| 363 |
atomData[3], atomData[4], |
| 364 |
atomData[5]); |
| 365 |
|
| 366 |
strcat(writeLine, |
| 367 |
"0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n"); |
| 368 |
} else { |
| 369 |
sprintf(writeLine, |
| 370 |
"%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", |
| 371 |
atomTypeString, |
| 372 |
atomData[0], |
| 373 |
atomData[1], |
| 374 |
atomData[2], |
| 375 |
atomData[3], |
| 376 |
atomData[4], |
| 377 |
atomData[5], |
| 378 |
atomData[6], |
| 379 |
atomData[7], |
| 380 |
atomData[8], |
| 381 |
atomData[9], |
| 382 |
atomData[10], |
| 383 |
atomData[11], |
| 384 |
atomData[12]); |
| 385 |
} |
| 386 |
|
| 387 |
|
| 388 |
os << writeLine; |
| 389 |
|
| 390 |
} //end for(iter = integrableObject.begin()) |
| 391 |
} |
| 392 |
} //end for(i = 0; i < mpiSim->getNmol()) |
| 393 |
|
| 394 |
os.flush(); |
| 395 |
|
| 396 |
sprintf(checkPointMsg, "Sucessfully took a dump.\n"); |
| 397 |
|
| 398 |
MPIcheckPoint(); |
| 399 |
|
| 400 |
delete [] potatoes; |
| 401 |
} else { |
| 402 |
|
| 403 |
// worldRank != 0, so I'm a remote node. |
| 404 |
|
| 405 |
// Set my magic potato to 0: |
| 406 |
|
| 407 |
myPotato = 0; |
| 408 |
|
| 409 |
for(i = 0; i < info_->getNGlobalMolecules(); i++) { |
| 410 |
|
| 411 |
// Am I the node which has this integrableObject? |
| 412 |
whichNode = info_->getMolToProc(i); |
| 413 |
if (whichNode == worldRank) { |
| 414 |
if (myPotato + 1 >= MAXTAG) { |
| 415 |
|
| 416 |
// The potato was going to exceed the maximum value, |
| 417 |
// so wrap this processor potato back to 0 (and block until |
| 418 |
// node 0 says we can go: |
| 419 |
|
| 420 |
MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, |
| 421 |
&istatus); |
| 422 |
} |
| 423 |
|
| 424 |
mol = info_->getMoleculeByGlobalIndex(i); |
| 425 |
|
| 426 |
|
| 427 |
nCurObj = mol->getNIntegrableObjects(); |
| 428 |
|
| 429 |
MPI_Send(&nCurObj, 1, MPI_INT, 0, myPotato, MPI_COMM_WORLD); |
| 430 |
myPotato++; |
| 431 |
|
| 432 |
for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; |
| 433 |
integrableObject = mol->nextIntegrableObject(ii)) { |
| 434 |
|
| 435 |
if (myPotato + 2 >= MAXTAG) { |
| 436 |
|
| 437 |
// The potato was going to exceed the maximum value, |
| 438 |
// so wrap this processor potato back to 0 (and block until |
| 439 |
// node 0 says we can go: |
| 440 |
|
| 441 |
MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, |
| 442 |
&istatus); |
| 443 |
} |
| 444 |
|
| 445 |
atomTypeString = integrableObject->getType().c_str(); |
| 446 |
|
| 447 |
pos = integrableObject->getPos(); |
| 448 |
vel = integrableObject->getVel(); |
| 449 |
|
| 450 |
atomData[0] = pos[0]; |
| 451 |
atomData[1] = pos[1]; |
| 452 |
atomData[2] = pos[2]; |
| 453 |
|
| 454 |
atomData[3] = vel[0]; |
| 455 |
atomData[4] = vel[1]; |
| 456 |
atomData[5] = vel[2]; |
| 457 |
|
| 458 |
isDirectional = 0; |
| 459 |
|
| 460 |
if (integrableObject->isDirectional()) { |
| 461 |
isDirectional = 1; |
| 462 |
|
| 463 |
q = integrableObject->getQ(); |
| 464 |
ji = integrableObject->getJ(); |
| 465 |
|
| 466 |
atomData[6] = q[0]; |
| 467 |
atomData[7] = q[1]; |
| 468 |
atomData[8] = q[2]; |
| 469 |
atomData[9] = q[3]; |
| 470 |
|
| 471 |
atomData[10] = ji[0]; |
| 472 |
atomData[11] = ji[1]; |
| 473 |
atomData[12] = ji[2]; |
| 474 |
} |
| 475 |
|
| 476 |
strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE); |
| 477 |
|
| 478 |
// null terminate the string before sending (just in case): |
| 479 |
MPIatomTypeString[MINIBUFFERSIZE - 1] = '\0'; |
| 480 |
|
| 481 |
MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0, |
| 482 |
myPotato, MPI_COMM_WORLD); |
| 483 |
|
| 484 |
myPotato++; |
| 485 |
|
| 486 |
if (isDirectional) { |
| 487 |
MPI_Send(atomData, 13, MPI_DOUBLE, 0, myPotato, |
| 488 |
MPI_COMM_WORLD); |
| 489 |
} else { |
| 490 |
MPI_Send(atomData, 6, MPI_DOUBLE, 0, myPotato, |
| 491 |
MPI_COMM_WORLD); |
| 492 |
} |
| 493 |
|
| 494 |
myPotato++; |
| 495 |
} |
| 496 |
|
| 497 |
} |
| 498 |
|
| 499 |
} |
| 500 |
|
| 501 |
sprintf(checkPointMsg, "Sucessfully took a dump.\n"); |
| 502 |
MPIcheckPoint(); |
| 503 |
} |
| 504 |
|
| 505 |
#endif // is_mpi |
| 506 |
|
| 507 |
} |
| 508 |
|
| 509 |
}//end namespace oopse |
