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 |
|
char MPIatomTypeString[MINIBUFFERSIZE]; |
88 |
< |
int me; |
83 |
< |
int atomTypeTag; |
84 |
< |
int atomIsDirectionalTag; |
85 |
< |
int atomTransDataTag; |
86 |
< |
int atomOrientDataTag; |
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 |
> |
/* code to find maximum tag value */ |
164 |
> |
int *tagub, flag, MAXTAG; |
165 |
> |
MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag); |
166 |
> |
if (flag) { |
167 |
> |
MAXTAG = *tagub; |
168 |
> |
} else { |
169 |
> |
MAXTAG = 32767; |
170 |
> |
} |
171 |
|
|
164 |
– |
int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone |
172 |
|
int haveError; |
173 |
|
|
174 |
|
MPI_Status istatus; |
177 |
|
// write out header and node 0's coordinates |
178 |
|
|
179 |
|
if( worldRank == 0 ){ |
180 |
+ |
|
181 |
+ |
// Node 0 needs a list of the magic potatoes for each processor; |
182 |
+ |
|
183 |
+ |
nProc = mpiSim->getNumberProcessors(); |
184 |
+ |
potatoes = new int[nProc]; |
185 |
+ |
|
186 |
+ |
for (i = 0; i < nProc; i++) |
187 |
+ |
potatoes[i] = 0; |
188 |
+ |
|
189 |
|
outFile << mpiSim->getTotAtoms() << "\n"; |
190 |
|
|
191 |
|
outFile << currentTime << ";\t" |
204 |
|
outFile << entry_plug->the_integrator->getAdditionalParameters(); |
205 |
|
outFile << endl; |
206 |
|
outFile.flush(); |
207 |
+ |
|
208 |
|
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
209 |
+ |
|
210 |
|
// Get the Node number which has this atom; |
211 |
< |
|
211 |
> |
|
212 |
|
which_node = AtomToProcMap[i]; |
213 |
< |
|
213 |
> |
|
214 |
|
if (which_node != 0) { |
197 |
– |
|
198 |
– |
atomTypeTag = 4*i; |
199 |
– |
atomIsDirectionalTag = 4*i + 1; |
200 |
– |
atomTransDataTag = 4*i + 2; |
201 |
– |
atomOrientDataTag = 4*i + 3; |
215 |
|
|
216 |
+ |
if (potatoes[which_node] + 3 >= MAXTAG) { |
217 |
+ |
// The potato was going to exceed the maximum value, |
218 |
+ |
// so wrap this processor potato back to 0: |
219 |
+ |
|
220 |
+ |
potatoes[which_node] = 0; |
221 |
+ |
MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD); |
222 |
+ |
|
223 |
+ |
} |
224 |
+ |
|
225 |
+ |
myPotato = potatoes[which_node]; |
226 |
+ |
|
227 |
|
MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node, |
228 |
< |
atomTypeTag, MPI_COMM_WORLD, &istatus); |
228 |
> |
myPotato, MPI_COMM_WORLD, &istatus); |
229 |
|
|
230 |
|
strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE); |
231 |
|
|
233 |
|
|
234 |
|
atomTypeString[strlen(atomTypeString) - 1] = '\0'; |
235 |
|
|
236 |
+ |
myPotato++; |
237 |
+ |
|
238 |
|
MPI_Recv(&isDirectional, 1, MPI_INT, which_node, |
239 |
< |
atomIsDirectionalTag, MPI_COMM_WORLD, &istatus); |
240 |
< |
|
241 |
< |
MPI_Recv(atomTransData, 6, MPI_DOUBLE, which_node, |
216 |
< |
atomTransDataTag, MPI_COMM_WORLD, &istatus); |
239 |
> |
myPotato, MPI_COMM_WORLD, &istatus); |
240 |
> |
|
241 |
> |
myPotato++; |
242 |
|
|
243 |
< |
if (isDirectional) { |
244 |
< |
|
245 |
< |
MPI_Recv(atomOrientData, 7, MPI_DOUBLE, which_node, |
246 |
< |
atomOrientDataTag, MPI_COMM_WORLD, &istatus); |
247 |
< |
|
243 |
> |
if (isDirectional) { |
244 |
> |
MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node, |
245 |
> |
myPotato, MPI_COMM_WORLD, &istatus); |
246 |
> |
} else { |
247 |
> |
MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node, |
248 |
> |
myPotato, MPI_COMM_WORLD, &istatus); |
249 |
|
} |
250 |
+ |
|
251 |
+ |
myPotato++; |
252 |
+ |
potatoes[which_node] = myPotato; |
253 |
|
|
254 |
|
} else { |
255 |
|
|
256 |
|
haveError = 0; |
257 |
|
which_atom = i; |
258 |
|
local_index=-1; |
259 |
< |
|
259 |
> |
|
260 |
|
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
261 |
|
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
262 |
|
} |
263 |
< |
|
263 |
> |
|
264 |
|
if (local_index != -1) { |
265 |
< |
|
265 |
> |
|
266 |
|
atomTypeString = atoms[local_index]->getType(); |
267 |
|
|
268 |
|
atoms[local_index]->getPos(pos); |
269 |
< |
atoms[local_index]->getVel(vel); |
269 |
> |
atoms[local_index]->getVel(vel); |
270 |
|
|
271 |
< |
atomTransData[0] = pos[0]; |
272 |
< |
atomTransData[1] = pos[1]; |
273 |
< |
atomTransData[2] = pos[2]; |
271 |
> |
atomData6[0] = pos[0]; |
272 |
> |
atomData6[1] = pos[1]; |
273 |
> |
atomData6[2] = pos[2]; |
274 |
|
|
275 |
< |
atomTransData[3] = vel[0]; |
276 |
< |
atomTransData[4] = vel[1]; |
277 |
< |
atomTransData[5] = vel[2]; |
275 |
> |
atomData6[3] = vel[0]; |
276 |
> |
atomData6[4] = vel[1]; |
277 |
> |
atomData6[5] = vel[2]; |
278 |
|
|
279 |
|
isDirectional = 0; |
280 |
|
|
284 |
|
|
285 |
|
dAtom = (DirectionalAtom *)atoms[local_index]; |
286 |
|
dAtom->getQ( q ); |
258 |
– |
|
259 |
– |
atomOrientData[0] = q[0]; |
260 |
– |
atomOrientData[1] = q[1]; |
261 |
– |
atomOrientData[2] = q[2]; |
262 |
– |
atomOrientData[3] = q[3]; |
287 |
|
|
288 |
< |
atomOrientData[4] = dAtom->getJx(); |
289 |
< |
atomOrientData[5] = dAtom->getJy(); |
290 |
< |
atomOrientData[6] = dAtom->getJz(); |
288 |
> |
for (int j = 0; j < 6 ; j++) |
289 |
> |
atomData13[j] = atomData6[j]; |
290 |
> |
|
291 |
> |
atomData13[6] = q[0]; |
292 |
> |
atomData13[7] = q[1]; |
293 |
> |
atomData13[8] = q[2]; |
294 |
> |
atomData13[9] = q[3]; |
295 |
> |
|
296 |
> |
atomData13[10] = dAtom->getJx(); |
297 |
> |
atomData13[11] = dAtom->getJy(); |
298 |
> |
atomData13[12] = dAtom->getJz(); |
299 |
|
} |
300 |
< |
|
300 |
> |
|
301 |
|
} else { |
302 |
|
sprintf(painCave.errMsg, |
303 |
|
"Atom %d not found on processor %d\n", |
305 |
|
haveError= 1; |
306 |
|
simError(); |
307 |
|
} |
308 |
< |
|
308 |
> |
|
309 |
|
if(haveError) DieDieDie(); |
310 |
< |
|
310 |
> |
|
311 |
|
// If we've survived to here, format the line: |
312 |
|
|
313 |
< |
sprintf( tempBuffer, |
282 |
< |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
283 |
< |
atomTypeString, |
284 |
< |
atomTransData[0], |
285 |
< |
atomTransData[1], |
286 |
< |
atomTransData[2], |
287 |
< |
atomTransData[3], |
288 |
< |
atomTransData[4], |
289 |
< |
atomTransData[5]); |
313 |
> |
if (!isDirectional) { |
314 |
|
|
315 |
< |
strcpy( writeLine, tempBuffer ); |
316 |
< |
|
317 |
< |
if (isDirectional) { |
315 |
> |
sprintf( tempBuffer, |
316 |
> |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
317 |
> |
atomTypeString, |
318 |
> |
atomData6[0], |
319 |
> |
atomData6[1], |
320 |
> |
atomData6[2], |
321 |
> |
atomData6[3], |
322 |
> |
atomData6[4], |
323 |
> |
atomData6[5]); |
324 |
> |
|
325 |
> |
strcpy( writeLine, tempBuffer ); |
326 |
> |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
327 |
|
|
328 |
+ |
} else { |
329 |
+ |
|
330 |
|
sprintf( tempBuffer, |
331 |
< |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
332 |
< |
atomOrientData[0], |
333 |
< |
atomOrientData[1], |
334 |
< |
atomOrientData[2], |
335 |
< |
atomOrientData[3], |
336 |
< |
atomOrientData[4], |
337 |
< |
atomOrientData[5], |
338 |
< |
atomOrientData[6]); |
331 |
> |
"%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", |
332 |
> |
atomTypeString, |
333 |
> |
atomData13[0], |
334 |
> |
atomData13[1], |
335 |
> |
atomData13[2], |
336 |
> |
atomData13[3], |
337 |
> |
atomData13[4], |
338 |
> |
atomData13[5], |
339 |
> |
atomData13[6], |
340 |
> |
atomData13[7], |
341 |
> |
atomData13[8], |
342 |
> |
atomData13[9], |
343 |
> |
atomData13[10], |
344 |
> |
atomData13[11], |
345 |
> |
atomData13[12]); |
346 |
> |
|
347 |
|
strcat( writeLine, tempBuffer ); |
348 |
< |
|
306 |
< |
} else { |
307 |
< |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
348 |
> |
|
349 |
|
} |
350 |
< |
|
350 |
> |
|
351 |
|
outFile << writeLine; |
352 |
|
outFile.flush(); |
353 |
|
} |
361 |
|
} else { |
362 |
|
|
363 |
|
// worldRank != 0, so I'm a remote node. |
364 |
+ |
|
365 |
+ |
// Set my magic potato to 0: |
366 |
+ |
|
367 |
+ |
myPotato = 0; |
368 |
|
|
369 |
|
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
370 |
|
|
372 |
|
|
373 |
|
if (AtomToProcMap[i] == worldRank) { |
374 |
|
|
375 |
+ |
if (myPotato + 3 >= MAXTAG) { |
376 |
+ |
|
377 |
+ |
// The potato was going to exceed the maximum value, |
378 |
+ |
// so wrap this processor potato back to 0 (and block until |
379 |
+ |
// node 0 says we can go: |
380 |
+ |
|
381 |
+ |
MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus); |
382 |
+ |
|
383 |
+ |
} |
384 |
+ |
|
385 |
|
local_index=-1; |
386 |
|
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
387 |
|
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
393 |
|
atoms[local_index]->getPos(pos); |
394 |
|
atoms[local_index]->getVel(vel); |
395 |
|
|
396 |
< |
atomTransData[0] = pos[0]; |
397 |
< |
atomTransData[1] = pos[1]; |
398 |
< |
atomTransData[2] = pos[2]; |
396 |
> |
atomData6[0] = pos[0]; |
397 |
> |
atomData6[1] = pos[1]; |
398 |
> |
atomData6[2] = pos[2]; |
399 |
|
|
400 |
< |
atomTransData[3] = vel[0]; |
401 |
< |
atomTransData[4] = vel[1]; |
402 |
< |
atomTransData[5] = vel[2]; |
400 |
> |
atomData6[3] = vel[0]; |
401 |
> |
atomData6[4] = vel[1]; |
402 |
> |
atomData6[5] = vel[2]; |
403 |
|
|
404 |
|
isDirectional = 0; |
405 |
|
|
410 |
|
dAtom = (DirectionalAtom *)atoms[local_index]; |
411 |
|
dAtom->getQ( q ); |
412 |
|
|
413 |
< |
atomOrientData[0] = q[0]; |
414 |
< |
atomOrientData[1] = q[1]; |
415 |
< |
atomOrientData[2] = q[2]; |
416 |
< |
atomOrientData[3] = q[3]; |
413 |
> |
for (int j = 0; j < 6 ; j++) |
414 |
> |
atomData13[j] = atomData6[j]; |
415 |
> |
|
416 |
> |
atomData13[6] = q[0]; |
417 |
> |
atomData13[7] = q[1]; |
418 |
> |
atomData13[8] = q[2]; |
419 |
> |
atomData13[9] = q[3]; |
420 |
|
|
421 |
< |
atomOrientData[4] = dAtom->getJx(); |
422 |
< |
atomOrientData[5] = dAtom->getJy(); |
423 |
< |
atomOrientData[6] = dAtom->getJz(); |
421 |
> |
atomData13[10] = dAtom->getJx(); |
422 |
> |
atomData13[11] = dAtom->getJy(); |
423 |
> |
atomData13[12] = dAtom->getJz(); |
424 |
|
} |
425 |
|
|
426 |
|
} else { |
431 |
|
simError(); |
432 |
|
} |
433 |
|
|
376 |
– |
// I've survived this far, so send off the data! |
377 |
– |
|
378 |
– |
atomTypeTag = 4*i; |
379 |
– |
atomIsDirectionalTag = 4*i + 1; |
380 |
– |
atomTransDataTag = 4*i + 2; |
381 |
– |
atomOrientDataTag = 4*i + 3; |
382 |
– |
|
383 |
– |
|
434 |
|
strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE); |
435 |
|
|
436 |
|
// null terminate the string before sending (just in case): |
437 |
|
MPIatomTypeString[MINIBUFFERSIZE-1] = '\0'; |
438 |
|
|
439 |
|
MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0, |
440 |
< |
atomTypeTag, MPI_COMM_WORLD); |
440 |
> |
myPotato, MPI_COMM_WORLD); |
441 |
|
|
442 |
+ |
myPotato++; |
443 |
+ |
|
444 |
|
MPI_Send(&isDirectional, 1, MPI_INT, 0, |
445 |
< |
atomIsDirectionalTag, MPI_COMM_WORLD); |
445 |
> |
myPotato, MPI_COMM_WORLD); |
446 |
|
|
447 |
< |
MPI_Send(atomTransData, 6, MPI_DOUBLE, 0, |
448 |
< |
atomTransDataTag, MPI_COMM_WORLD); |
397 |
< |
|
447 |
> |
myPotato++; |
448 |
> |
|
449 |
|
if (isDirectional) { |
450 |
|
|
451 |
< |
MPI_Send(atomOrientData, 7, MPI_DOUBLE, 0, |
452 |
< |
atomOrientDataTag, MPI_COMM_WORLD); |
451 |
> |
MPI_Send(atomData13, 13, MPI_DOUBLE, 0, |
452 |
> |
myPotato, MPI_COMM_WORLD); |
453 |
|
|
454 |
+ |
} else { |
455 |
+ |
|
456 |
+ |
MPI_Send(atomData6, 6, MPI_DOUBLE, 0, |
457 |
+ |
myPotato, MPI_COMM_WORLD); |
458 |
|
} |
459 |
< |
|
459 |
> |
|
460 |
> |
myPotato++; |
461 |
|
} |
462 |
|
} |
463 |
|
|
465 |
|
"Sucessfully took a dump.\n"); |
466 |
|
MPIcheckPoint(); |
467 |
|
|
468 |
< |
} |
468 |
> |
} |
469 |
|
|
414 |
– |
painCave.isEventLoop = 0; |
415 |
– |
|
470 |
|
#endif // is_mpi |
471 |
|
} |
472 |
|
|
485 |
|
Atom** atoms = entry_plug->atoms; |
486 |
|
int i; |
487 |
|
#ifdef IS_MPI |
488 |
+ |
|
489 |
+ |
int *potatoes; |
490 |
+ |
int myPotato; |
491 |
+ |
|
492 |
+ |
int nProc; |
493 |
|
int j, which_node, done, which_atom, local_index; |
494 |
< |
double atomTransData[6]; |
495 |
< |
double atomOrientData[7]; |
494 |
> |
double atomData6[6]; |
495 |
> |
double atomData13[13]; |
496 |
|
int isDirectional; |
497 |
|
char* atomTypeString; |
498 |
|
char MPIatomTypeString[MINIBUFFERSIZE]; |
499 |
< |
int atomTypeTag; |
441 |
< |
int atomIsDirectionalTag; |
442 |
< |
int atomTransDataTag; |
443 |
< |
int atomOrientDataTag; |
499 |
> |
|
500 |
|
#else //is_mpi |
501 |
|
int nAtoms = entry_plug->n_atoms; |
502 |
|
#endif //is_mpi |
592 |
|
|
593 |
|
#else // is_mpi |
594 |
|
|
595 |
< |
// first thing first, suspend fatalities. |
596 |
< |
painCave.isEventLoop = 1; |
595 |
> |
/* code to find maximum tag value */ |
596 |
> |
int *tagub, flag, MAXTAG; |
597 |
> |
MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag); |
598 |
> |
if (flag) { |
599 |
> |
MAXTAG = *tagub; |
600 |
> |
} else { |
601 |
> |
MAXTAG = 32767; |
602 |
> |
} |
603 |
|
|
542 |
– |
int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone |
604 |
|
int haveError; |
605 |
|
|
606 |
|
MPI_Status istatus; |
609 |
|
// write out header and node 0's coordinates |
610 |
|
|
611 |
|
if( worldRank == 0 ){ |
612 |
+ |
|
613 |
+ |
// Node 0 needs a list of the magic potatoes for each processor; |
614 |
+ |
|
615 |
+ |
nProc = mpiSim->getNumberProcessors(); |
616 |
+ |
potatoes = new int[nProc]; |
617 |
+ |
|
618 |
+ |
for (i = 0; i < nProc; i++) |
619 |
+ |
potatoes[i] = 0; |
620 |
+ |
|
621 |
|
finalOut << mpiSim->getTotAtoms() << "\n"; |
622 |
|
|
623 |
|
finalOut << finalTime << ";\t" |
636 |
|
finalOut << entry_plug->the_integrator->getAdditionalParameters(); |
637 |
|
finalOut << endl; |
638 |
|
finalOut.flush(); |
639 |
+ |
|
640 |
|
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
641 |
+ |
|
642 |
|
// Get the Node number which has this atom; |
643 |
< |
|
643 |
> |
|
644 |
|
which_node = AtomToProcMap[i]; |
645 |
< |
|
645 |
> |
|
646 |
|
if (which_node != 0) { |
575 |
– |
|
576 |
– |
atomTypeTag = 4*i; |
577 |
– |
atomIsDirectionalTag = 4*i + 1; |
578 |
– |
atomTransDataTag = 4*i + 2; |
579 |
– |
atomOrientDataTag = 4*i + 3; |
647 |
|
|
648 |
+ |
if (potatoes[which_node] + 3 >= MAXTAG) { |
649 |
+ |
// The potato was going to exceed the maximum value, |
650 |
+ |
// so wrap this processor potato back to 0: |
651 |
+ |
|
652 |
+ |
potatoes[which_node] = 0; |
653 |
+ |
MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD); |
654 |
+ |
|
655 |
+ |
} |
656 |
+ |
|
657 |
+ |
myPotato = potatoes[which_node]; |
658 |
+ |
|
659 |
|
MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node, |
660 |
< |
atomTypeTag, MPI_COMM_WORLD, &istatus); |
660 |
> |
myPotato, MPI_COMM_WORLD, &istatus); |
661 |
|
|
662 |
|
strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE); |
585 |
– |
|
586 |
– |
MPI_Recv(&isDirectional, 1, MPI_INT, which_node, |
587 |
– |
atomIsDirectionalTag, MPI_COMM_WORLD, &istatus); |
663 |
|
|
664 |
< |
MPI_Recv(atomTransData, 6, MPI_DOUBLE, which_node, |
590 |
< |
atomTransDataTag, MPI_COMM_WORLD, &istatus); |
664 |
> |
// Null terminate the atomTypeString just in case: |
665 |
|
|
666 |
< |
if (isDirectional) { |
666 |
> |
atomTypeString[strlen(atomTypeString) - 1] = '\0'; |
667 |
|
|
668 |
< |
MPI_Recv(atomOrientData, 7, MPI_DOUBLE, which_node, |
595 |
< |
atomOrientDataTag, MPI_COMM_WORLD, &istatus); |
668 |
> |
myPotato++; |
669 |
|
|
670 |
+ |
MPI_Recv(&isDirectional, 1, MPI_INT, which_node, |
671 |
+ |
myPotato, MPI_COMM_WORLD, &istatus); |
672 |
+ |
|
673 |
+ |
myPotato++; |
674 |
+ |
|
675 |
+ |
if (isDirectional) { |
676 |
+ |
MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node, |
677 |
+ |
myPotato, MPI_COMM_WORLD, &istatus); |
678 |
+ |
} else { |
679 |
+ |
MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node, |
680 |
+ |
myPotato, MPI_COMM_WORLD, &istatus); |
681 |
|
} |
682 |
+ |
|
683 |
+ |
myPotato++; |
684 |
+ |
potatoes[which_node] = myPotato; |
685 |
|
|
686 |
|
} else { |
687 |
|
|
688 |
|
haveError = 0; |
689 |
|
which_atom = i; |
690 |
|
local_index=-1; |
691 |
< |
|
691 |
> |
|
692 |
|
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
693 |
|
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
694 |
|
} |
695 |
< |
|
695 |
> |
|
696 |
|
if (local_index != -1) { |
697 |
< |
|
697 |
> |
|
698 |
|
atomTypeString = atoms[local_index]->getType(); |
699 |
|
|
700 |
|
atoms[local_index]->getPos(pos); |
701 |
< |
atoms[local_index]->getVel(vel); |
701 |
> |
atoms[local_index]->getVel(vel); |
702 |
|
|
703 |
< |
atomTransData[0] = pos[0]; |
704 |
< |
atomTransData[1] = pos[1]; |
705 |
< |
atomTransData[2] = pos[2]; |
703 |
> |
atomData6[0] = pos[0]; |
704 |
> |
atomData6[1] = pos[1]; |
705 |
> |
atomData6[2] = pos[2]; |
706 |
|
|
707 |
< |
atomTransData[3] = vel[0]; |
708 |
< |
atomTransData[4] = vel[1]; |
709 |
< |
atomTransData[5] = vel[2]; |
707 |
> |
atomData6[3] = vel[0]; |
708 |
> |
atomData6[4] = vel[1]; |
709 |
> |
atomData6[5] = vel[2]; |
710 |
|
|
711 |
|
isDirectional = 0; |
712 |
|
|
716 |
|
|
717 |
|
dAtom = (DirectionalAtom *)atoms[local_index]; |
718 |
|
dAtom->getQ( q ); |
632 |
– |
|
633 |
– |
atomOrientData[0] = q[0]; |
634 |
– |
atomOrientData[1] = q[1]; |
635 |
– |
atomOrientData[2] = q[2]; |
636 |
– |
atomOrientData[3] = q[3]; |
719 |
|
|
720 |
< |
atomOrientData[4] = dAtom->getJx(); |
721 |
< |
atomOrientData[5] = dAtom->getJy(); |
722 |
< |
atomOrientData[6] = dAtom->getJz(); |
720 |
> |
for (int j = 0; j < 6 ; j++) |
721 |
> |
atomData13[j] = atomData6[j]; |
722 |
> |
|
723 |
> |
atomData13[6] = q[0]; |
724 |
> |
atomData13[7] = q[1]; |
725 |
> |
atomData13[8] = q[2]; |
726 |
> |
atomData13[9] = q[3]; |
727 |
> |
|
728 |
> |
atomData13[10] = dAtom->getJx(); |
729 |
> |
atomData13[11] = dAtom->getJy(); |
730 |
> |
atomData13[12] = dAtom->getJz(); |
731 |
|
} |
732 |
< |
|
732 |
> |
|
733 |
|
} else { |
734 |
|
sprintf(painCave.errMsg, |
735 |
|
"Atom %d not found on processor %d\n", |
737 |
|
haveError= 1; |
738 |
|
simError(); |
739 |
|
} |
740 |
< |
|
740 |
> |
|
741 |
|
if(haveError) DieDieDie(); |
742 |
< |
|
742 |
> |
|
743 |
|
// If we've survived to here, format the line: |
744 |
|
|
745 |
< |
sprintf( tempBuffer, |
656 |
< |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
657 |
< |
atomTypeString, |
658 |
< |
atomTransData[0], |
659 |
< |
atomTransData[1], |
660 |
< |
atomTransData[2], |
661 |
< |
atomTransData[3], |
662 |
< |
atomTransData[4], |
663 |
< |
atomTransData[5]); |
745 |
> |
if (!isDirectional) { |
746 |
|
|
747 |
< |
strcpy( writeLine, tempBuffer ); |
748 |
< |
|
749 |
< |
if (isDirectional) { |
747 |
> |
sprintf( tempBuffer, |
748 |
> |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
749 |
> |
atomTypeString, |
750 |
> |
atomData6[0], |
751 |
> |
atomData6[1], |
752 |
> |
atomData6[2], |
753 |
> |
atomData6[3], |
754 |
> |
atomData6[4], |
755 |
> |
atomData6[5]); |
756 |
> |
|
757 |
> |
strcpy( writeLine, tempBuffer ); |
758 |
> |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
759 |
|
|
760 |
+ |
} else { |
761 |
+ |
|
762 |
|
sprintf( tempBuffer, |
763 |
< |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
764 |
< |
atomOrientData[0], |
765 |
< |
atomOrientData[1], |
766 |
< |
atomOrientData[2], |
767 |
< |
atomOrientData[3], |
768 |
< |
atomOrientData[4], |
769 |
< |
atomOrientData[5], |
770 |
< |
atomOrientData[6]); |
763 |
> |
"%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", |
764 |
> |
atomTypeString, |
765 |
> |
atomData13[0], |
766 |
> |
atomData13[1], |
767 |
> |
atomData13[2], |
768 |
> |
atomData13[3], |
769 |
> |
atomData13[4], |
770 |
> |
atomData13[5], |
771 |
> |
atomData13[6], |
772 |
> |
atomData13[7], |
773 |
> |
atomData13[8], |
774 |
> |
atomData13[9], |
775 |
> |
atomData13[10], |
776 |
> |
atomData13[11], |
777 |
> |
atomData13[12]); |
778 |
> |
|
779 |
|
strcat( writeLine, tempBuffer ); |
780 |
< |
|
680 |
< |
} else { |
681 |
< |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
780 |
> |
|
781 |
|
} |
782 |
< |
|
782 |
> |
|
783 |
|
finalOut << writeLine; |
784 |
|
finalOut.flush(); |
785 |
|
} |
793 |
|
} else { |
794 |
|
|
795 |
|
// worldRank != 0, so I'm a remote node. |
796 |
+ |
|
797 |
+ |
// Set my magic potato to 0: |
798 |
+ |
|
799 |
+ |
myPotato = 0; |
800 |
|
|
801 |
|
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
802 |
|
|
804 |
|
|
805 |
|
if (AtomToProcMap[i] == worldRank) { |
806 |
|
|
807 |
+ |
if (myPotato + 3 >= MAXTAG) { |
808 |
+ |
|
809 |
+ |
// The potato was going to exceed the maximum value, |
810 |
+ |
// so wrap this processor potato back to 0 (and block until |
811 |
+ |
// node 0 says we can go: |
812 |
+ |
|
813 |
+ |
MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus); |
814 |
+ |
|
815 |
+ |
} |
816 |
+ |
|
817 |
|
local_index=-1; |
818 |
|
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
819 |
|
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
825 |
|
atoms[local_index]->getPos(pos); |
826 |
|
atoms[local_index]->getVel(vel); |
827 |
|
|
828 |
< |
atomTransData[0] = pos[0]; |
829 |
< |
atomTransData[1] = pos[1]; |
830 |
< |
atomTransData[2] = pos[2]; |
828 |
> |
atomData6[0] = pos[0]; |
829 |
> |
atomData6[1] = pos[1]; |
830 |
> |
atomData6[2] = pos[2]; |
831 |
|
|
832 |
< |
atomTransData[3] = vel[0]; |
833 |
< |
atomTransData[4] = vel[1]; |
834 |
< |
atomTransData[5] = vel[2]; |
832 |
> |
atomData6[3] = vel[0]; |
833 |
> |
atomData6[4] = vel[1]; |
834 |
> |
atomData6[5] = vel[2]; |
835 |
|
|
836 |
|
isDirectional = 0; |
837 |
|
|
842 |
|
dAtom = (DirectionalAtom *)atoms[local_index]; |
843 |
|
dAtom->getQ( q ); |
844 |
|
|
845 |
< |
atomOrientData[0] = q[0]; |
846 |
< |
atomOrientData[1] = q[1]; |
847 |
< |
atomOrientData[2] = q[2]; |
848 |
< |
atomOrientData[3] = q[3]; |
845 |
> |
for (int j = 0; j < 6 ; j++) |
846 |
> |
atomData13[j] = atomData6[j]; |
847 |
> |
|
848 |
> |
atomData13[6] = q[0]; |
849 |
> |
atomData13[7] = q[1]; |
850 |
> |
atomData13[8] = q[2]; |
851 |
> |
atomData13[9] = q[3]; |
852 |
|
|
853 |
< |
atomOrientData[4] = dAtom->getJx(); |
854 |
< |
atomOrientData[5] = dAtom->getJy(); |
855 |
< |
atomOrientData[6] = dAtom->getJz(); |
853 |
> |
atomData13[10] = dAtom->getJx(); |
854 |
> |
atomData13[11] = dAtom->getJy(); |
855 |
> |
atomData13[12] = dAtom->getJz(); |
856 |
|
} |
857 |
|
|
858 |
|
} else { |
863 |
|
simError(); |
864 |
|
} |
865 |
|
|
750 |
– |
// I've survived this far, so send off the data! |
751 |
– |
|
752 |
– |
atomTypeTag = 4*i; |
753 |
– |
atomIsDirectionalTag = 4*i + 1; |
754 |
– |
atomTransDataTag = 4*i + 2; |
755 |
– |
atomOrientDataTag = 4*i + 3; |
756 |
– |
|
866 |
|
strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE); |
867 |
|
|
868 |
+ |
// null terminate the string before sending (just in case): |
869 |
+ |
MPIatomTypeString[MINIBUFFERSIZE-1] = '\0'; |
870 |
+ |
|
871 |
|
MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0, |
872 |
< |
atomTypeTag, MPI_COMM_WORLD); |
872 |
> |
myPotato, MPI_COMM_WORLD); |
873 |
|
|
874 |
+ |
myPotato++; |
875 |
+ |
|
876 |
|
MPI_Send(&isDirectional, 1, MPI_INT, 0, |
877 |
< |
atomIsDirectionalTag, MPI_COMM_WORLD); |
877 |
> |
myPotato, MPI_COMM_WORLD); |
878 |
|
|
879 |
< |
MPI_Send(atomTransData, 6, MPI_DOUBLE, 0, |
880 |
< |
atomTransDataTag, MPI_COMM_WORLD); |
767 |
< |
|
879 |
> |
myPotato++; |
880 |
> |
|
881 |
|
if (isDirectional) { |
882 |
|
|
883 |
< |
MPI_Send(atomOrientData, 7, MPI_DOUBLE, 0, |
884 |
< |
atomOrientDataTag, MPI_COMM_WORLD); |
883 |
> |
MPI_Send(atomData13, 13, MPI_DOUBLE, 0, |
884 |
> |
myPotato, MPI_COMM_WORLD); |
885 |
|
|
886 |
+ |
} else { |
887 |
+ |
|
888 |
+ |
MPI_Send(atomData6, 6, MPI_DOUBLE, 0, |
889 |
+ |
myPotato, MPI_COMM_WORLD); |
890 |
|
} |
891 |
< |
|
891 |
> |
|
892 |
> |
myPotato++; |
893 |
|
} |
894 |
|
} |
895 |
|
|
896 |
|
sprintf( checkPointMsg, |
897 |
< |
"Sucessfully wrote final file.\n"); |
897 |
> |
"Sucessfully took a dump.\n"); |
898 |
|
MPIcheckPoint(); |
899 |
|
|
900 |
< |
} |
900 |
> |
} |
901 |
|
|
784 |
– |
painCave.isEventLoop = 0; |
785 |
– |
|
902 |
|
if( worldRank == 0 ) finalOut.close(); |
903 |
|
#endif // is_mpi |
904 |
|
} |