66 |
|
void DumpWriter::writeDump( double currentTime ){ |
67 |
|
|
68 |
|
const int BUFFERSIZE = 2000; |
69 |
< |
const int MINIBUFFERSIZE = 10; |
69 |
> |
const int MINIBUFFERSIZE = 100; |
70 |
|
|
71 |
|
char tempBuffer[BUFFERSIZE]; |
72 |
|
char writeLine[BUFFERSIZE]; |
73 |
|
|
74 |
|
int i; |
75 |
+ |
|
76 |
|
#ifdef IS_MPI |
77 |
+ |
|
78 |
+ |
int *potatoes; |
79 |
+ |
int myPotato; |
80 |
+ |
|
81 |
+ |
int nProc; |
82 |
|
int j, which_node, done, which_atom, local_index; |
83 |
< |
double atomTransData[6]; |
84 |
< |
double atomOrientData[7]; |
83 |
> |
double atomData6[6]; |
84 |
> |
double atomData13[13]; |
85 |
|
int isDirectional; |
86 |
|
char* atomTypeString; |
87 |
< |
int me; |
88 |
< |
int atomTypeTag; |
83 |
< |
int atomIsDirectionalTag; |
84 |
< |
int atomTransDataTag; |
85 |
< |
int atomOrientDataTag; |
87 |
> |
char MPIatomTypeString[MINIBUFFERSIZE]; |
88 |
> |
|
89 |
|
#else //is_mpi |
90 |
|
int nAtoms = entry_plug->n_atoms; |
91 |
|
#endif //is_mpi |
160 |
|
|
161 |
|
#else // is_mpi |
162 |
|
|
163 |
< |
// first thing first, suspend fatalities. |
164 |
< |
painCave.isEventLoop = 1; |
163 |
> |
cout << "master" <<endl; |
164 |
> |
/* code to find maximum tag value */ |
165 |
> |
|
166 |
> |
int tagub, flag, MAXTAG; |
167 |
> |
MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag); |
168 |
> |
if (flag) { |
169 |
> |
MAXTAG = tagub; |
170 |
> |
} else { |
171 |
> |
MAXTAG = 32767; |
172 |
> |
} |
173 |
|
|
163 |
– |
int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone |
174 |
|
int haveError; |
175 |
|
|
176 |
|
MPI_Status istatus; |
179 |
|
// write out header and node 0's coordinates |
180 |
|
|
181 |
|
if( worldRank == 0 ){ |
182 |
+ |
|
183 |
+ |
// Node 0 needs a list of the magic potatoes for each processor; |
184 |
+ |
|
185 |
+ |
nProc = mpiSim->getNumberProcessors(); |
186 |
+ |
potatoes = new int[nProc]; |
187 |
+ |
|
188 |
+ |
for (i = 0; i < nProc; i++) |
189 |
+ |
potatoes[i] = 0; |
190 |
+ |
|
191 |
|
outFile << mpiSim->getTotAtoms() << "\n"; |
192 |
|
|
193 |
|
outFile << currentTime << ";\t" |
206 |
|
outFile << entry_plug->the_integrator->getAdditionalParameters(); |
207 |
|
outFile << endl; |
208 |
|
outFile.flush(); |
209 |
+ |
|
210 |
|
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
211 |
+ |
|
212 |
|
// Get the Node number which has this atom; |
213 |
< |
|
213 |
> |
|
214 |
|
which_node = AtomToProcMap[i]; |
215 |
< |
|
215 |
> |
|
216 |
|
if (which_node != 0) { |
196 |
– |
|
197 |
– |
atomTypeTag = 4*i; |
198 |
– |
atomIsDirectionalTag = 4*i + 1; |
199 |
– |
atomTransDataTag = 4*i + 2; |
200 |
– |
atomOrientDataTag = 4*i + 3; |
217 |
|
|
218 |
< |
MPI_Recv(atomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node, |
219 |
< |
atomTypeTag, MPI_COMM_WORLD, &istatus); |
218 |
> |
if (potatoes[which_node] + 3 >= MAXTAG) { |
219 |
> |
// The potato was going to exceed the maximum value, |
220 |
> |
// so wrap this processor potato back to 0: |
221 |
> |
|
222 |
> |
potatoes[which_node] = 0; |
223 |
> |
MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD); |
224 |
> |
|
225 |
> |
} |
226 |
> |
|
227 |
> |
myPotato = potatoes[which_node]; |
228 |
|
|
229 |
< |
MPI_Recv(&isDirectional, 1, MPI_INT, which_node, |
230 |
< |
atomIsDirectionalTag, MPI_COMM_WORLD, &istatus); |
229 |
> |
MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node, |
230 |
> |
myPotato, MPI_COMM_WORLD, &istatus); |
231 |
|
|
232 |
< |
MPI_Recv(atomTransData, 6, MPI_DOUBLE, which_node, |
233 |
< |
atomTransDataTag, MPI_COMM_WORLD, &istatus); |
232 |
> |
strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE); |
233 |
> |
|
234 |
> |
// Null terminate the atomTypeString just in case: |
235 |
|
|
236 |
< |
if (isDirectional) { |
236 |
> |
atomTypeString[strlen(atomTypeString) - 1] = '\0'; |
237 |
|
|
238 |
< |
MPI_Recv(atomOrientData, 7, MPI_DOUBLE, which_node, |
214 |
< |
atomOrientDataTag, MPI_COMM_WORLD, &istatus); |
238 |
> |
myPotato++; |
239 |
|
|
240 |
+ |
MPI_Recv(&isDirectional, 1, MPI_INT, which_node, |
241 |
+ |
myPotato, MPI_COMM_WORLD, &istatus); |
242 |
+ |
|
243 |
+ |
myPotato++; |
244 |
+ |
|
245 |
+ |
if (isDirectional) { |
246 |
+ |
MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node, |
247 |
+ |
myPotato, MPI_COMM_WORLD, &istatus); |
248 |
+ |
} else { |
249 |
+ |
MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node, |
250 |
+ |
myPotato, MPI_COMM_WORLD, &istatus); |
251 |
|
} |
252 |
+ |
|
253 |
+ |
myPotato++; |
254 |
+ |
potatoes[which_node] = myPotato; |
255 |
|
|
256 |
|
} else { |
257 |
|
|
258 |
|
haveError = 0; |
259 |
|
which_atom = i; |
260 |
|
local_index=-1; |
261 |
< |
|
261 |
> |
|
262 |
|
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
263 |
|
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
264 |
|
} |
265 |
< |
|
265 |
> |
|
266 |
|
if (local_index != -1) { |
267 |
< |
|
267 |
> |
|
268 |
|
atomTypeString = atoms[local_index]->getType(); |
269 |
|
|
270 |
|
atoms[local_index]->getPos(pos); |
271 |
< |
atoms[local_index]->getVel(vel); |
271 |
> |
atoms[local_index]->getVel(vel); |
272 |
|
|
273 |
< |
atomTransData[0] = pos[0]; |
274 |
< |
atomTransData[1] = pos[1]; |
275 |
< |
atomTransData[2] = pos[2]; |
273 |
> |
atomData6[0] = pos[0]; |
274 |
> |
atomData6[1] = pos[1]; |
275 |
> |
atomData6[2] = pos[2]; |
276 |
|
|
277 |
< |
atomTransData[3] = vel[0]; |
278 |
< |
atomTransData[4] = vel[1]; |
279 |
< |
atomTransData[5] = vel[2]; |
277 |
> |
atomData6[3] = vel[0]; |
278 |
> |
atomData6[4] = vel[1]; |
279 |
> |
atomData6[5] = vel[2]; |
280 |
|
|
281 |
|
isDirectional = 0; |
282 |
|
|
286 |
|
|
287 |
|
dAtom = (DirectionalAtom *)atoms[local_index]; |
288 |
|
dAtom->getQ( q ); |
251 |
– |
|
252 |
– |
atomOrientData[0] = q[0]; |
253 |
– |
atomOrientData[1] = q[1]; |
254 |
– |
atomOrientData[2] = q[2]; |
255 |
– |
atomOrientData[3] = q[3]; |
289 |
|
|
290 |
< |
atomOrientData[4] = dAtom->getJx(); |
291 |
< |
atomOrientData[5] = dAtom->getJy(); |
292 |
< |
atomOrientData[6] = dAtom->getJz(); |
290 |
> |
for (int j = 0; j < 6 ; j++) |
291 |
> |
atomData13[j] = atomData6[j]; |
292 |
> |
|
293 |
> |
atomData13[6] = q[0]; |
294 |
> |
atomData13[7] = q[1]; |
295 |
> |
atomData13[8] = q[2]; |
296 |
> |
atomData13[9] = q[3]; |
297 |
> |
|
298 |
> |
atomData13[10] = dAtom->getJx(); |
299 |
> |
atomData13[11] = dAtom->getJy(); |
300 |
> |
atomData13[12] = dAtom->getJz(); |
301 |
|
} |
302 |
< |
|
302 |
> |
|
303 |
|
} else { |
304 |
|
sprintf(painCave.errMsg, |
305 |
|
"Atom %d not found on processor %d\n", |
307 |
|
haveError= 1; |
308 |
|
simError(); |
309 |
|
} |
310 |
< |
|
310 |
> |
|
311 |
|
if(haveError) DieDieDie(); |
312 |
< |
|
312 |
> |
|
313 |
|
// If we've survived to here, format the line: |
314 |
|
|
315 |
< |
sprintf( tempBuffer, |
275 |
< |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
276 |
< |
atomTypeString, |
277 |
< |
atomTransData[0], |
278 |
< |
atomTransData[1], |
279 |
< |
atomTransData[2], |
280 |
< |
atomTransData[3], |
281 |
< |
atomTransData[4], |
282 |
< |
atomTransData[5]); |
315 |
> |
if (!isDirectional) { |
316 |
|
|
317 |
< |
strcpy( writeLine, tempBuffer ); |
318 |
< |
|
319 |
< |
if (isDirectional) { |
317 |
> |
sprintf( tempBuffer, |
318 |
> |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
319 |
> |
atomTypeString, |
320 |
> |
atomData6[0], |
321 |
> |
atomData6[1], |
322 |
> |
atomData6[2], |
323 |
> |
atomData6[3], |
324 |
> |
atomData6[4], |
325 |
> |
atomData6[5]); |
326 |
> |
|
327 |
> |
strcpy( writeLine, tempBuffer ); |
328 |
> |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
329 |
|
|
330 |
+ |
} else { |
331 |
+ |
|
332 |
|
sprintf( tempBuffer, |
333 |
< |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
334 |
< |
atomOrientData[0], |
335 |
< |
atomOrientData[1], |
336 |
< |
atomOrientData[2], |
337 |
< |
atomOrientData[3], |
338 |
< |
atomOrientData[4], |
339 |
< |
atomOrientData[5], |
340 |
< |
atomOrientData[6]); |
333 |
> |
"%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", |
334 |
> |
atomTypeString, |
335 |
> |
atomData13[0], |
336 |
> |
atomData13[1], |
337 |
> |
atomData13[2], |
338 |
> |
atomData13[3], |
339 |
> |
atomData13[4], |
340 |
> |
atomData13[5], |
341 |
> |
atomData13[6], |
342 |
> |
atomData13[7], |
343 |
> |
atomData13[8], |
344 |
> |
atomData13[9], |
345 |
> |
atomData13[10], |
346 |
> |
atomData13[11], |
347 |
> |
atomData13[12]); |
348 |
> |
|
349 |
|
strcat( writeLine, tempBuffer ); |
350 |
< |
|
299 |
< |
} else { |
300 |
< |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
350 |
> |
|
351 |
|
} |
352 |
< |
|
352 |
> |
|
353 |
|
outFile << writeLine; |
354 |
|
outFile.flush(); |
355 |
|
} |
359 |
|
sprintf( checkPointMsg, |
360 |
|
"Sucessfully took a dump.\n"); |
361 |
|
MPIcheckPoint(); |
362 |
< |
|
362 |
> |
delete[] potatoes; |
363 |
|
} else { |
364 |
|
|
365 |
|
// worldRank != 0, so I'm a remote node. |
366 |
+ |
|
367 |
+ |
// Set my magic potato to 0: |
368 |
+ |
|
369 |
+ |
myPotato = 0; |
370 |
|
|
371 |
|
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
372 |
|
|
374 |
|
|
375 |
|
if (AtomToProcMap[i] == worldRank) { |
376 |
|
|
377 |
< |
local_index=-1; |
377 |
> |
if (myPotato + 3 >= MAXTAG) { |
378 |
> |
|
379 |
> |
// The potato was going to exceed the maximum value, |
380 |
> |
// so wrap this processor potato back to 0 (and block until |
381 |
> |
// node 0 says we can go: |
382 |
> |
|
383 |
> |
MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus); |
384 |
> |
|
385 |
> |
} |
386 |
> |
which_atom = i; |
387 |
> |
local_index=-1; |
388 |
|
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
389 |
|
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
390 |
|
} |
395 |
|
atoms[local_index]->getPos(pos); |
396 |
|
atoms[local_index]->getVel(vel); |
397 |
|
|
398 |
< |
atomTransData[0] = pos[0]; |
399 |
< |
atomTransData[1] = pos[1]; |
400 |
< |
atomTransData[2] = pos[2]; |
398 |
> |
atomData6[0] = pos[0]; |
399 |
> |
atomData6[1] = pos[1]; |
400 |
> |
atomData6[2] = pos[2]; |
401 |
|
|
402 |
< |
atomTransData[3] = vel[0]; |
403 |
< |
atomTransData[4] = vel[1]; |
404 |
< |
atomTransData[5] = vel[2]; |
402 |
> |
atomData6[3] = vel[0]; |
403 |
> |
atomData6[4] = vel[1]; |
404 |
> |
atomData6[5] = vel[2]; |
405 |
|
|
406 |
|
isDirectional = 0; |
407 |
|
|
412 |
|
dAtom = (DirectionalAtom *)atoms[local_index]; |
413 |
|
dAtom->getQ( q ); |
414 |
|
|
415 |
< |
atomOrientData[0] = q[0]; |
416 |
< |
atomOrientData[1] = q[1]; |
417 |
< |
atomOrientData[2] = q[2]; |
418 |
< |
atomOrientData[3] = q[3]; |
415 |
> |
for (int j = 0; j < 6 ; j++) |
416 |
> |
atomData13[j] = atomData6[j]; |
417 |
> |
|
418 |
> |
atomData13[6] = q[0]; |
419 |
> |
atomData13[7] = q[1]; |
420 |
> |
atomData13[8] = q[2]; |
421 |
> |
atomData13[9] = q[3]; |
422 |
|
|
423 |
< |
atomOrientData[4] = dAtom->getJx(); |
424 |
< |
atomOrientData[5] = dAtom->getJy(); |
425 |
< |
atomOrientData[6] = dAtom->getJz(); |
423 |
> |
atomData13[10] = dAtom->getJx(); |
424 |
> |
atomData13[11] = dAtom->getJy(); |
425 |
> |
atomData13[12] = dAtom->getJz(); |
426 |
|
} |
427 |
|
|
428 |
|
} else { |
433 |
|
simError(); |
434 |
|
} |
435 |
|
|
436 |
< |
// I've survived this far, so send off the data! |
436 |
> |
strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE); |
437 |
|
|
438 |
< |
atomTypeTag = 4*i; |
439 |
< |
atomIsDirectionalTag = 4*i + 1; |
373 |
< |
atomTransDataTag = 4*i + 2; |
374 |
< |
atomOrientDataTag = 4*i + 3; |
438 |
> |
// null terminate the string before sending (just in case): |
439 |
> |
MPIatomTypeString[MINIBUFFERSIZE-1] = '\0'; |
440 |
|
|
441 |
< |
MPI_Send(atomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0, |
442 |
< |
atomTypeTag, MPI_COMM_WORLD); |
441 |
> |
MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0, |
442 |
> |
myPotato, MPI_COMM_WORLD); |
443 |
|
|
444 |
+ |
myPotato++; |
445 |
+ |
|
446 |
|
MPI_Send(&isDirectional, 1, MPI_INT, 0, |
447 |
< |
atomIsDirectionalTag, MPI_COMM_WORLD); |
447 |
> |
myPotato, MPI_COMM_WORLD); |
448 |
|
|
449 |
< |
MPI_Send(atomTransData, 6, MPI_DOUBLE, 0, |
450 |
< |
atomTransDataTag, MPI_COMM_WORLD); |
384 |
< |
|
449 |
> |
myPotato++; |
450 |
> |
|
451 |
|
if (isDirectional) { |
452 |
|
|
453 |
< |
MPI_Send(atomOrientData, 7, MPI_DOUBLE, 0, |
454 |
< |
atomOrientDataTag, MPI_COMM_WORLD); |
453 |
> |
MPI_Send(atomData13, 13, MPI_DOUBLE, 0, |
454 |
> |
myPotato, MPI_COMM_WORLD); |
455 |
|
|
456 |
+ |
} else { |
457 |
+ |
|
458 |
+ |
MPI_Send(atomData6, 6, MPI_DOUBLE, 0, |
459 |
+ |
myPotato, MPI_COMM_WORLD); |
460 |
|
} |
461 |
< |
|
461 |
> |
|
462 |
> |
myPotato++; |
463 |
|
} |
464 |
|
} |
465 |
|
|
467 |
|
"Sucessfully took a dump.\n"); |
468 |
|
MPIcheckPoint(); |
469 |
|
|
470 |
< |
} |
470 |
> |
} |
471 |
|
|
401 |
– |
painCave.isEventLoop = 0; |
402 |
– |
|
472 |
|
#endif // is_mpi |
473 |
|
} |
474 |
|
|
478 |
|
ofstream finalOut; |
479 |
|
|
480 |
|
const int BUFFERSIZE = 2000; |
481 |
< |
const int MINIBUFFERSIZE = 10; |
481 |
> |
const int MINIBUFFERSIZE = 100; |
482 |
|
char tempBuffer[BUFFERSIZE]; |
483 |
|
char writeLine[BUFFERSIZE]; |
484 |
|
|
487 |
|
Atom** atoms = entry_plug->atoms; |
488 |
|
int i; |
489 |
|
#ifdef IS_MPI |
490 |
+ |
|
491 |
+ |
int *potatoes; |
492 |
+ |
int myPotato; |
493 |
+ |
|
494 |
+ |
int nProc; |
495 |
|
int j, which_node, done, which_atom, local_index; |
496 |
< |
double atomTransData[6]; |
497 |
< |
double atomOrientData[7]; |
496 |
> |
double atomData6[6]; |
497 |
> |
double atomData13[13]; |
498 |
|
int isDirectional; |
499 |
|
char* atomTypeString; |
500 |
< |
int atomTypeTag; |
501 |
< |
int atomIsDirectionalTag; |
428 |
< |
int atomTransDataTag; |
429 |
< |
int atomOrientDataTag; |
500 |
> |
char MPIatomTypeString[MINIBUFFERSIZE]; |
501 |
> |
|
502 |
|
#else //is_mpi |
503 |
|
int nAtoms = entry_plug->n_atoms; |
504 |
|
#endif //is_mpi |
594 |
|
|
595 |
|
#else // is_mpi |
596 |
|
|
597 |
< |
// first thing first, suspend fatalities. |
598 |
< |
painCave.isEventLoop = 1; |
597 |
> |
/* code to find maximum tag value */ |
598 |
> |
int *tagub, flag, MAXTAG; |
599 |
> |
MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag); |
600 |
> |
if (flag) { |
601 |
> |
MAXTAG = *tagub; |
602 |
> |
} else { |
603 |
> |
MAXTAG = 32767; |
604 |
> |
} |
605 |
|
|
528 |
– |
int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone |
606 |
|
int haveError; |
607 |
|
|
608 |
|
MPI_Status istatus; |
611 |
|
// write out header and node 0's coordinates |
612 |
|
|
613 |
|
if( worldRank == 0 ){ |
614 |
+ |
|
615 |
+ |
// Node 0 needs a list of the magic potatoes for each processor; |
616 |
+ |
|
617 |
+ |
nProc = mpiSim->getNumberProcessors(); |
618 |
+ |
potatoes = new int[nProc]; |
619 |
+ |
|
620 |
+ |
for (i = 0; i < nProc; i++) |
621 |
+ |
potatoes[i] = 0; |
622 |
+ |
|
623 |
|
finalOut << mpiSim->getTotAtoms() << "\n"; |
624 |
|
|
625 |
|
finalOut << finalTime << ";\t" |
638 |
|
finalOut << entry_plug->the_integrator->getAdditionalParameters(); |
639 |
|
finalOut << endl; |
640 |
|
finalOut.flush(); |
641 |
+ |
|
642 |
|
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
643 |
+ |
|
644 |
|
// Get the Node number which has this atom; |
645 |
< |
|
645 |
> |
|
646 |
|
which_node = AtomToProcMap[i]; |
647 |
< |
|
647 |
> |
|
648 |
|
if (which_node != 0) { |
561 |
– |
|
562 |
– |
atomTypeTag = 4*i; |
563 |
– |
atomIsDirectionalTag = 4*i + 1; |
564 |
– |
atomTransDataTag = 4*i + 2; |
565 |
– |
atomOrientDataTag = 4*i + 3; |
649 |
|
|
650 |
< |
MPI_Recv(atomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node, |
651 |
< |
atomTypeTag, MPI_COMM_WORLD, &istatus); |
650 |
> |
if (potatoes[which_node] + 3 >= MAXTAG) { |
651 |
> |
// The potato was going to exceed the maximum value, |
652 |
> |
// so wrap this processor potato back to 0: |
653 |
> |
|
654 |
> |
potatoes[which_node] = 0; |
655 |
> |
MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD); |
656 |
> |
|
657 |
> |
} |
658 |
> |
|
659 |
> |
myPotato = potatoes[which_node]; |
660 |
|
|
661 |
< |
MPI_Recv(&isDirectional, 1, MPI_INT, which_node, |
662 |
< |
atomIsDirectionalTag, MPI_COMM_WORLD, &istatus); |
661 |
> |
MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node, |
662 |
> |
myPotato, MPI_COMM_WORLD, &istatus); |
663 |
|
|
664 |
< |
MPI_Recv(atomTransData, 6, MPI_DOUBLE, which_node, |
665 |
< |
atomTransDataTag, MPI_COMM_WORLD, &istatus); |
664 |
> |
strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE); |
665 |
> |
|
666 |
> |
// Null terminate the atomTypeString just in case: |
667 |
|
|
668 |
< |
if (isDirectional) { |
668 |
> |
atomTypeString[strlen(atomTypeString) - 1] = '\0'; |
669 |
|
|
670 |
< |
MPI_Recv(atomOrientData, 7, MPI_DOUBLE, which_node, |
579 |
< |
atomOrientDataTag, MPI_COMM_WORLD, &istatus); |
670 |
> |
myPotato++; |
671 |
|
|
672 |
+ |
MPI_Recv(&isDirectional, 1, MPI_INT, which_node, |
673 |
+ |
myPotato, MPI_COMM_WORLD, &istatus); |
674 |
+ |
|
675 |
+ |
myPotato++; |
676 |
+ |
|
677 |
+ |
if (isDirectional) { |
678 |
+ |
MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node, |
679 |
+ |
myPotato, MPI_COMM_WORLD, &istatus); |
680 |
+ |
} else { |
681 |
+ |
MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node, |
682 |
+ |
myPotato, MPI_COMM_WORLD, &istatus); |
683 |
|
} |
684 |
+ |
|
685 |
+ |
myPotato++; |
686 |
+ |
potatoes[which_node] = myPotato; |
687 |
|
|
688 |
|
} else { |
689 |
|
|
690 |
|
haveError = 0; |
691 |
|
which_atom = i; |
692 |
|
local_index=-1; |
693 |
< |
|
693 |
> |
|
694 |
|
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
695 |
|
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
696 |
|
} |
697 |
< |
|
697 |
> |
|
698 |
|
if (local_index != -1) { |
699 |
< |
|
699 |
> |
|
700 |
|
atomTypeString = atoms[local_index]->getType(); |
701 |
|
|
702 |
|
atoms[local_index]->getPos(pos); |
703 |
< |
atoms[local_index]->getVel(vel); |
703 |
> |
atoms[local_index]->getVel(vel); |
704 |
|
|
705 |
< |
atomTransData[0] = pos[0]; |
706 |
< |
atomTransData[1] = pos[1]; |
707 |
< |
atomTransData[2] = pos[2]; |
705 |
> |
atomData6[0] = pos[0]; |
706 |
> |
atomData6[1] = pos[1]; |
707 |
> |
atomData6[2] = pos[2]; |
708 |
|
|
709 |
< |
atomTransData[3] = vel[0]; |
710 |
< |
atomTransData[4] = vel[1]; |
711 |
< |
atomTransData[5] = vel[2]; |
709 |
> |
atomData6[3] = vel[0]; |
710 |
> |
atomData6[4] = vel[1]; |
711 |
> |
atomData6[5] = vel[2]; |
712 |
|
|
713 |
|
isDirectional = 0; |
714 |
|
|
718 |
|
|
719 |
|
dAtom = (DirectionalAtom *)atoms[local_index]; |
720 |
|
dAtom->getQ( q ); |
616 |
– |
|
617 |
– |
atomOrientData[0] = q[0]; |
618 |
– |
atomOrientData[1] = q[1]; |
619 |
– |
atomOrientData[2] = q[2]; |
620 |
– |
atomOrientData[3] = q[3]; |
721 |
|
|
722 |
< |
atomOrientData[4] = dAtom->getJx(); |
723 |
< |
atomOrientData[5] = dAtom->getJy(); |
724 |
< |
atomOrientData[6] = dAtom->getJz(); |
722 |
> |
for (int j = 0; j < 6 ; j++) |
723 |
> |
atomData13[j] = atomData6[j]; |
724 |
> |
|
725 |
> |
atomData13[6] = q[0]; |
726 |
> |
atomData13[7] = q[1]; |
727 |
> |
atomData13[8] = q[2]; |
728 |
> |
atomData13[9] = q[3]; |
729 |
> |
|
730 |
> |
atomData13[10] = dAtom->getJx(); |
731 |
> |
atomData13[11] = dAtom->getJy(); |
732 |
> |
atomData13[12] = dAtom->getJz(); |
733 |
|
} |
734 |
< |
|
734 |
> |
|
735 |
|
} else { |
736 |
|
sprintf(painCave.errMsg, |
737 |
|
"Atom %d not found on processor %d\n", |
739 |
|
haveError= 1; |
740 |
|
simError(); |
741 |
|
} |
742 |
< |
|
742 |
> |
|
743 |
|
if(haveError) DieDieDie(); |
744 |
< |
|
744 |
> |
|
745 |
|
// If we've survived to here, format the line: |
746 |
|
|
747 |
< |
sprintf( tempBuffer, |
640 |
< |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
641 |
< |
atomTypeString, |
642 |
< |
atomTransData[0], |
643 |
< |
atomTransData[1], |
644 |
< |
atomTransData[2], |
645 |
< |
atomTransData[3], |
646 |
< |
atomTransData[4], |
647 |
< |
atomTransData[5]); |
747 |
> |
if (!isDirectional) { |
748 |
|
|
749 |
< |
strcpy( writeLine, tempBuffer ); |
750 |
< |
|
751 |
< |
if (isDirectional) { |
749 |
> |
sprintf( tempBuffer, |
750 |
> |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
751 |
> |
atomTypeString, |
752 |
> |
atomData6[0], |
753 |
> |
atomData6[1], |
754 |
> |
atomData6[2], |
755 |
> |
atomData6[3], |
756 |
> |
atomData6[4], |
757 |
> |
atomData6[5]); |
758 |
> |
|
759 |
> |
strcpy( writeLine, tempBuffer ); |
760 |
> |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
761 |
|
|
762 |
+ |
} else { |
763 |
+ |
|
764 |
|
sprintf( tempBuffer, |
765 |
< |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
766 |
< |
atomOrientData[0], |
767 |
< |
atomOrientData[1], |
768 |
< |
atomOrientData[2], |
769 |
< |
atomOrientData[3], |
770 |
< |
atomOrientData[4], |
771 |
< |
atomOrientData[5], |
772 |
< |
atomOrientData[6]); |
765 |
> |
"%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", |
766 |
> |
atomTypeString, |
767 |
> |
atomData13[0], |
768 |
> |
atomData13[1], |
769 |
> |
atomData13[2], |
770 |
> |
atomData13[3], |
771 |
> |
atomData13[4], |
772 |
> |
atomData13[5], |
773 |
> |
atomData13[6], |
774 |
> |
atomData13[7], |
775 |
> |
atomData13[8], |
776 |
> |
atomData13[9], |
777 |
> |
atomData13[10], |
778 |
> |
atomData13[11], |
779 |
> |
atomData13[12]); |
780 |
> |
|
781 |
|
strcat( writeLine, tempBuffer ); |
782 |
< |
|
664 |
< |
} else { |
665 |
< |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
782 |
> |
|
783 |
|
} |
784 |
< |
|
784 |
> |
|
785 |
|
finalOut << writeLine; |
786 |
|
finalOut.flush(); |
787 |
|
} |
790 |
|
finalOut.flush(); |
791 |
|
sprintf( checkPointMsg, |
792 |
|
"Sucessfully took a dump.\n"); |
793 |
+ |
delete[] potatoes; |
794 |
+ |
|
795 |
|
MPIcheckPoint(); |
796 |
|
|
797 |
|
} else { |
798 |
|
|
799 |
|
// worldRank != 0, so I'm a remote node. |
800 |
+ |
|
801 |
+ |
// Set my magic potato to 0: |
802 |
+ |
|
803 |
+ |
myPotato = 0; |
804 |
|
|
805 |
|
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
806 |
|
|
808 |
|
|
809 |
|
if (AtomToProcMap[i] == worldRank) { |
810 |
|
|
811 |
+ |
if (myPotato + 3 >= MAXTAG) { |
812 |
+ |
|
813 |
+ |
// The potato was going to exceed the maximum value, |
814 |
+ |
// so wrap this processor potato back to 0 (and block until |
815 |
+ |
// node 0 says we can go: |
816 |
+ |
|
817 |
+ |
MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus); |
818 |
+ |
|
819 |
+ |
} |
820 |
+ |
which_atom = i; |
821 |
|
local_index=-1; |
822 |
|
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
823 |
|
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
829 |
|
atoms[local_index]->getPos(pos); |
830 |
|
atoms[local_index]->getVel(vel); |
831 |
|
|
832 |
< |
atomTransData[0] = pos[0]; |
833 |
< |
atomTransData[1] = pos[1]; |
834 |
< |
atomTransData[2] = pos[2]; |
832 |
> |
atomData6[0] = pos[0]; |
833 |
> |
atomData6[1] = pos[1]; |
834 |
> |
atomData6[2] = pos[2]; |
835 |
|
|
836 |
< |
atomTransData[3] = vel[0]; |
837 |
< |
atomTransData[4] = vel[1]; |
838 |
< |
atomTransData[5] = vel[2]; |
836 |
> |
atomData6[3] = vel[0]; |
837 |
> |
atomData6[4] = vel[1]; |
838 |
> |
atomData6[5] = vel[2]; |
839 |
|
|
840 |
|
isDirectional = 0; |
841 |
|
|
846 |
|
dAtom = (DirectionalAtom *)atoms[local_index]; |
847 |
|
dAtom->getQ( q ); |
848 |
|
|
849 |
< |
atomOrientData[0] = q[0]; |
850 |
< |
atomOrientData[1] = q[1]; |
851 |
< |
atomOrientData[2] = q[2]; |
852 |
< |
atomOrientData[3] = q[3]; |
849 |
> |
for (int j = 0; j < 6 ; j++) |
850 |
> |
atomData13[j] = atomData6[j]; |
851 |
> |
|
852 |
> |
atomData13[6] = q[0]; |
853 |
> |
atomData13[7] = q[1]; |
854 |
> |
atomData13[8] = q[2]; |
855 |
> |
atomData13[9] = q[3]; |
856 |
|
|
857 |
< |
atomOrientData[4] = dAtom->getJx(); |
858 |
< |
atomOrientData[5] = dAtom->getJy(); |
859 |
< |
atomOrientData[6] = dAtom->getJz(); |
857 |
> |
atomData13[10] = dAtom->getJx(); |
858 |
> |
atomData13[11] = dAtom->getJy(); |
859 |
> |
atomData13[12] = dAtom->getJz(); |
860 |
|
} |
861 |
|
|
862 |
|
} else { |
867 |
|
simError(); |
868 |
|
} |
869 |
|
|
870 |
< |
// I've survived this far, so send off the data! |
870 |
> |
strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE); |
871 |
|
|
872 |
< |
atomTypeTag = 4*i; |
873 |
< |
atomIsDirectionalTag = 4*i + 1; |
738 |
< |
atomTransDataTag = 4*i + 2; |
739 |
< |
atomOrientDataTag = 4*i + 3; |
872 |
> |
// null terminate the string before sending (just in case): |
873 |
> |
MPIatomTypeString[MINIBUFFERSIZE-1] = '\0'; |
874 |
|
|
875 |
< |
MPI_Send(atomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0, |
876 |
< |
atomTypeTag, MPI_COMM_WORLD); |
875 |
> |
MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0, |
876 |
> |
myPotato, MPI_COMM_WORLD); |
877 |
|
|
878 |
+ |
myPotato++; |
879 |
+ |
|
880 |
|
MPI_Send(&isDirectional, 1, MPI_INT, 0, |
881 |
< |
atomIsDirectionalTag, MPI_COMM_WORLD); |
881 |
> |
myPotato, MPI_COMM_WORLD); |
882 |
|
|
883 |
< |
MPI_Send(atomTransData, 6, MPI_DOUBLE, 0, |
884 |
< |
atomTransDataTag, MPI_COMM_WORLD); |
749 |
< |
|
883 |
> |
myPotato++; |
884 |
> |
|
885 |
|
if (isDirectional) { |
886 |
|
|
887 |
< |
MPI_Send(atomOrientData, 7, MPI_DOUBLE, 0, |
888 |
< |
atomOrientDataTag, MPI_COMM_WORLD); |
887 |
> |
MPI_Send(atomData13, 13, MPI_DOUBLE, 0, |
888 |
> |
myPotato, MPI_COMM_WORLD); |
889 |
|
|
890 |
+ |
} else { |
891 |
+ |
|
892 |
+ |
MPI_Send(atomData6, 6, MPI_DOUBLE, 0, |
893 |
+ |
myPotato, MPI_COMM_WORLD); |
894 |
|
} |
895 |
< |
|
895 |
> |
|
896 |
> |
myPotato++; |
897 |
|
} |
898 |
|
} |
899 |
|
|
900 |
|
sprintf( checkPointMsg, |
901 |
< |
"Sucessfully wrote final file.\n"); |
901 |
> |
"Sucessfully took a dump.\n"); |
902 |
|
MPIcheckPoint(); |
903 |
|
|
904 |
< |
} |
904 |
> |
} |
905 |
|
|
766 |
– |
painCave.isEventLoop = 0; |
767 |
– |
|
906 |
|
if( worldRank == 0 ) finalOut.close(); |
907 |
|
#endif // is_mpi |
908 |
|
} |