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 |
|
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 |
> |
|
165 |
> |
int *tagub, flag, MAXTAG; |
166 |
> |
MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag); |
167 |
> |
if (flag) { |
168 |
> |
MAXTAG = *tagub; |
169 |
> |
} else { |
170 |
> |
MAXTAG = 32767; |
171 |
> |
} |
172 |
|
|
164 |
– |
int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone |
173 |
|
int haveError; |
174 |
|
|
175 |
|
MPI_Status istatus; |
178 |
|
// write out header and node 0's coordinates |
179 |
|
|
180 |
|
if( worldRank == 0 ){ |
181 |
+ |
|
182 |
+ |
// Node 0 needs a list of the magic potatoes for each processor; |
183 |
+ |
|
184 |
+ |
nProc = mpiSim->getNumberProcessors(); |
185 |
+ |
potatoes = new int[nProc]; |
186 |
+ |
|
187 |
+ |
for (i = 0; i < nProc; i++) |
188 |
+ |
potatoes[i] = 0; |
189 |
+ |
|
190 |
|
outFile << mpiSim->getTotAtoms() << "\n"; |
191 |
|
|
192 |
|
outFile << currentTime << ";\t" |
205 |
|
outFile << entry_plug->the_integrator->getAdditionalParameters(); |
206 |
|
outFile << endl; |
207 |
|
outFile.flush(); |
208 |
+ |
|
209 |
|
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
210 |
+ |
|
211 |
|
// Get the Node number which has this atom; |
212 |
< |
|
212 |
> |
|
213 |
|
which_node = AtomToProcMap[i]; |
214 |
< |
|
214 |
> |
|
215 |
|
if (which_node != 0) { |
197 |
– |
|
198 |
– |
atomTypeTag = 4*i; |
199 |
– |
atomIsDirectionalTag = 4*i + 1; |
200 |
– |
atomTransDataTag = 4*i + 2; |
201 |
– |
atomOrientDataTag = 4*i + 3; |
216 |
|
|
217 |
+ |
if (potatoes[which_node] + 3 >= MAXTAG) { |
218 |
+ |
// The potato was going to exceed the maximum value, |
219 |
+ |
// so wrap this processor potato back to 0: |
220 |
+ |
|
221 |
+ |
potatoes[which_node] = 0; |
222 |
+ |
MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD); |
223 |
+ |
|
224 |
+ |
} |
225 |
+ |
|
226 |
+ |
myPotato = potatoes[which_node]; |
227 |
+ |
|
228 |
|
MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node, |
229 |
< |
atomTypeTag, MPI_COMM_WORLD, &istatus); |
229 |
> |
myPotato, MPI_COMM_WORLD, &istatus); |
230 |
|
|
231 |
< |
strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE); |
207 |
< |
|
208 |
< |
MPI_Recv(&isDirectional, 1, MPI_INT, which_node, |
209 |
< |
atomIsDirectionalTag, MPI_COMM_WORLD, &istatus); |
231 |
> |
//strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE); |
232 |
|
|
233 |
< |
MPI_Recv(atomTransData, 6, MPI_DOUBLE, which_node, |
212 |
< |
atomTransDataTag, MPI_COMM_WORLD, &istatus); |
233 |
> |
// Null terminate the atomTypeString just in case: |
234 |
|
|
235 |
< |
if (isDirectional) { |
235 |
> |
//atomTypeString[strlen(atomTypeString) - 1] = '\0'; |
236 |
> |
atomTypeString = MPIatomTypeString; |
237 |
> |
|
238 |
> |
myPotato++; |
239 |
|
|
240 |
< |
MPI_Recv(atomOrientData, 7, MPI_DOUBLE, which_node, |
241 |
< |
atomOrientDataTag, MPI_COMM_WORLD, &istatus); |
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 ); |
254 |
– |
|
255 |
– |
atomOrientData[0] = q[0]; |
256 |
– |
atomOrientData[1] = q[1]; |
257 |
– |
atomOrientData[2] = q[2]; |
258 |
– |
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(); |
274 |
– |
|
275 |
– |
// If we've survived to here, format the line: |
312 |
|
|
313 |
< |
sprintf( tempBuffer, |
314 |
< |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
315 |
< |
atomTypeString, |
316 |
< |
atomTransData[0], |
317 |
< |
atomTransData[1], |
318 |
< |
atomTransData[2], |
319 |
< |
atomTransData[3], |
320 |
< |
atomTransData[4], |
321 |
< |
atomTransData[5]); |
322 |
< |
|
323 |
< |
strcpy( writeLine, tempBuffer ); |
324 |
< |
|
325 |
< |
if (isDirectional) { |
326 |
< |
|
327 |
< |
sprintf( tempBuffer, |
328 |
< |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
329 |
< |
atomOrientData[0], |
330 |
< |
atomOrientData[1], |
331 |
< |
atomOrientData[2], |
332 |
< |
atomOrientData[3], |
333 |
< |
atomOrientData[4], |
334 |
< |
atomOrientData[5], |
335 |
< |
atomOrientData[6]); |
336 |
< |
strcat( writeLine, tempBuffer ); |
337 |
< |
|
338 |
< |
} else { |
339 |
< |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
340 |
< |
} |
341 |
< |
|
342 |
< |
outFile << writeLine; |
343 |
< |
outFile.flush(); |
313 |
> |
} |
314 |
> |
// If we've survived to here, format the line: |
315 |
> |
|
316 |
> |
if (!isDirectional) { |
317 |
> |
|
318 |
> |
sprintf( tempBuffer, |
319 |
> |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
320 |
> |
atomTypeString, |
321 |
> |
atomData6[0], |
322 |
> |
atomData6[1], |
323 |
> |
atomData6[2], |
324 |
> |
atomData6[3], |
325 |
> |
atomData6[4], |
326 |
> |
atomData6[5]); |
327 |
> |
|
328 |
> |
strcpy( writeLine, tempBuffer ); |
329 |
> |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
330 |
> |
|
331 |
> |
} else { |
332 |
> |
|
333 |
> |
sprintf( tempBuffer, |
334 |
> |
"%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", |
335 |
> |
atomTypeString, |
336 |
> |
atomData13[0], |
337 |
> |
atomData13[1], |
338 |
> |
atomData13[2], |
339 |
> |
atomData13[3], |
340 |
> |
atomData13[4], |
341 |
> |
atomData13[5], |
342 |
> |
atomData13[6], |
343 |
> |
atomData13[7], |
344 |
> |
atomData13[8], |
345 |
> |
atomData13[9], |
346 |
> |
atomData13[10], |
347 |
> |
atomData13[11], |
348 |
> |
atomData13[12]); |
349 |
> |
|
350 |
> |
strcpy( writeLine, tempBuffer ); |
351 |
> |
|
352 |
|
} |
353 |
+ |
|
354 |
+ |
outFile << writeLine; |
355 |
+ |
outFile.flush(); |
356 |
|
} |
357 |
+ |
|
358 |
|
|
359 |
|
outFile.flush(); |
360 |
|
sprintf( checkPointMsg, |
361 |
|
"Sucessfully took a dump.\n"); |
362 |
|
MPIcheckPoint(); |
363 |
< |
|
363 |
> |
delete[] potatoes; |
364 |
|
} else { |
365 |
|
|
366 |
|
// worldRank != 0, so I'm a remote node. |
367 |
+ |
|
368 |
+ |
// Set my magic potato to 0: |
369 |
+ |
|
370 |
+ |
myPotato = 0; |
371 |
|
|
372 |
|
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
373 |
|
|
375 |
|
|
376 |
|
if (AtomToProcMap[i] == worldRank) { |
377 |
|
|
378 |
< |
local_index=-1; |
378 |
> |
if (myPotato + 3 >= MAXTAG) { |
379 |
> |
|
380 |
> |
// The potato was going to exceed the maximum value, |
381 |
> |
// so wrap this processor potato back to 0 (and block until |
382 |
> |
// node 0 says we can go: |
383 |
> |
|
384 |
> |
MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus); |
385 |
> |
|
386 |
> |
} |
387 |
> |
which_atom = i; |
388 |
> |
local_index=-1; |
389 |
|
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
390 |
|
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
391 |
|
} |
396 |
|
atoms[local_index]->getPos(pos); |
397 |
|
atoms[local_index]->getVel(vel); |
398 |
|
|
399 |
< |
atomTransData[0] = pos[0]; |
400 |
< |
atomTransData[1] = pos[1]; |
401 |
< |
atomTransData[2] = pos[2]; |
399 |
> |
atomData6[0] = pos[0]; |
400 |
> |
atomData6[1] = pos[1]; |
401 |
> |
atomData6[2] = pos[2]; |
402 |
|
|
403 |
< |
atomTransData[3] = vel[0]; |
404 |
< |
atomTransData[4] = vel[1]; |
405 |
< |
atomTransData[5] = vel[2]; |
403 |
> |
atomData6[3] = vel[0]; |
404 |
> |
atomData6[4] = vel[1]; |
405 |
> |
atomData6[5] = vel[2]; |
406 |
|
|
407 |
|
isDirectional = 0; |
408 |
|
|
413 |
|
dAtom = (DirectionalAtom *)atoms[local_index]; |
414 |
|
dAtom->getQ( q ); |
415 |
|
|
416 |
< |
atomOrientData[0] = q[0]; |
417 |
< |
atomOrientData[1] = q[1]; |
418 |
< |
atomOrientData[2] = q[2]; |
419 |
< |
atomOrientData[3] = q[3]; |
416 |
> |
for (int j = 0; j < 6 ; j++) |
417 |
> |
atomData13[j] = atomData6[j]; |
418 |
> |
|
419 |
> |
atomData13[6] = q[0]; |
420 |
> |
atomData13[7] = q[1]; |
421 |
> |
atomData13[8] = q[2]; |
422 |
> |
atomData13[9] = q[3]; |
423 |
|
|
424 |
< |
atomOrientData[4] = dAtom->getJx(); |
425 |
< |
atomOrientData[5] = dAtom->getJy(); |
426 |
< |
atomOrientData[6] = dAtom->getJz(); |
424 |
> |
atomData13[10] = dAtom->getJx(); |
425 |
> |
atomData13[11] = dAtom->getJy(); |
426 |
> |
atomData13[12] = dAtom->getJz(); |
427 |
|
} |
428 |
|
|
429 |
|
} else { |
434 |
|
simError(); |
435 |
|
} |
436 |
|
|
372 |
– |
// I've survived this far, so send off the data! |
373 |
– |
|
374 |
– |
atomTypeTag = 4*i; |
375 |
– |
atomIsDirectionalTag = 4*i + 1; |
376 |
– |
atomTransDataTag = 4*i + 2; |
377 |
– |
atomOrientDataTag = 4*i + 3; |
378 |
– |
|
379 |
– |
|
437 |
|
strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE); |
438 |
|
|
439 |
+ |
// null terminate the string before sending (just in case): |
440 |
+ |
MPIatomTypeString[MINIBUFFERSIZE-1] = '\0'; |
441 |
+ |
|
442 |
|
MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0, |
443 |
< |
atomTypeTag, MPI_COMM_WORLD); |
443 |
> |
myPotato, MPI_COMM_WORLD); |
444 |
|
|
445 |
+ |
myPotato++; |
446 |
+ |
|
447 |
|
MPI_Send(&isDirectional, 1, MPI_INT, 0, |
448 |
< |
atomIsDirectionalTag, MPI_COMM_WORLD); |
448 |
> |
myPotato, MPI_COMM_WORLD); |
449 |
|
|
450 |
< |
MPI_Send(atomTransData, 6, MPI_DOUBLE, 0, |
451 |
< |
atomTransDataTag, MPI_COMM_WORLD); |
390 |
< |
|
450 |
> |
myPotato++; |
451 |
> |
|
452 |
|
if (isDirectional) { |
453 |
|
|
454 |
< |
MPI_Send(atomOrientData, 7, MPI_DOUBLE, 0, |
455 |
< |
atomOrientDataTag, MPI_COMM_WORLD); |
454 |
> |
MPI_Send(atomData13, 13, MPI_DOUBLE, 0, |
455 |
> |
myPotato, MPI_COMM_WORLD); |
456 |
|
|
457 |
+ |
} else { |
458 |
+ |
|
459 |
+ |
MPI_Send(atomData6, 6, MPI_DOUBLE, 0, |
460 |
+ |
myPotato, MPI_COMM_WORLD); |
461 |
|
} |
462 |
< |
|
462 |
> |
|
463 |
> |
myPotato++; |
464 |
|
} |
465 |
|
} |
466 |
|
|
468 |
|
"Sucessfully took a dump.\n"); |
469 |
|
MPIcheckPoint(); |
470 |
|
|
471 |
< |
} |
471 |
> |
} |
472 |
|
|
407 |
– |
painCave.isEventLoop = 0; |
408 |
– |
|
473 |
|
#endif // is_mpi |
474 |
|
} |
475 |
|
|
479 |
|
ofstream finalOut; |
480 |
|
|
481 |
|
const int BUFFERSIZE = 2000; |
482 |
< |
const int MINIBUFFERSIZE = 10; |
482 |
> |
const int MINIBUFFERSIZE = 100; |
483 |
|
char tempBuffer[BUFFERSIZE]; |
484 |
|
char writeLine[BUFFERSIZE]; |
485 |
|
|
488 |
|
Atom** atoms = entry_plug->atoms; |
489 |
|
int i; |
490 |
|
#ifdef IS_MPI |
491 |
+ |
|
492 |
+ |
int *potatoes; |
493 |
+ |
int myPotato; |
494 |
+ |
|
495 |
+ |
int nProc; |
496 |
|
int j, which_node, done, which_atom, local_index; |
497 |
< |
double atomTransData[6]; |
498 |
< |
double atomOrientData[7]; |
497 |
> |
double atomData6[6]; |
498 |
> |
double atomData13[13]; |
499 |
|
int isDirectional; |
500 |
|
char* atomTypeString; |
501 |
|
char MPIatomTypeString[MINIBUFFERSIZE]; |
502 |
< |
int atomTypeTag; |
434 |
< |
int atomIsDirectionalTag; |
435 |
< |
int atomTransDataTag; |
436 |
< |
int atomOrientDataTag; |
502 |
> |
|
503 |
|
#else //is_mpi |
504 |
|
int nAtoms = entry_plug->n_atoms; |
505 |
|
#endif //is_mpi |
595 |
|
|
596 |
|
#else // is_mpi |
597 |
|
|
598 |
< |
// first thing first, suspend fatalities. |
599 |
< |
painCave.isEventLoop = 1; |
598 |
> |
/* code to find maximum tag value */ |
599 |
> |
int *tagub, flag, MAXTAG; |
600 |
> |
MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag); |
601 |
> |
if (flag) { |
602 |
> |
MAXTAG = *tagub; |
603 |
> |
} else { |
604 |
> |
MAXTAG = 32767; |
605 |
> |
} |
606 |
|
|
535 |
– |
int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone |
607 |
|
int haveError; |
608 |
|
|
609 |
|
MPI_Status istatus; |
612 |
|
// write out header and node 0's coordinates |
613 |
|
|
614 |
|
if( worldRank == 0 ){ |
615 |
+ |
|
616 |
+ |
// Node 0 needs a list of the magic potatoes for each processor; |
617 |
+ |
|
618 |
+ |
nProc = mpiSim->getNumberProcessors(); |
619 |
+ |
potatoes = new int[nProc]; |
620 |
+ |
|
621 |
+ |
for (i = 0; i < nProc; i++) |
622 |
+ |
potatoes[i] = 0; |
623 |
+ |
|
624 |
|
finalOut << mpiSim->getTotAtoms() << "\n"; |
625 |
|
|
626 |
|
finalOut << finalTime << ";\t" |
639 |
|
finalOut << entry_plug->the_integrator->getAdditionalParameters(); |
640 |
|
finalOut << endl; |
641 |
|
finalOut.flush(); |
642 |
+ |
|
643 |
|
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
644 |
+ |
|
645 |
|
// Get the Node number which has this atom; |
646 |
< |
|
646 |
> |
|
647 |
|
which_node = AtomToProcMap[i]; |
648 |
< |
|
648 |
> |
|
649 |
|
if (which_node != 0) { |
568 |
– |
|
569 |
– |
atomTypeTag = 4*i; |
570 |
– |
atomIsDirectionalTag = 4*i + 1; |
571 |
– |
atomTransDataTag = 4*i + 2; |
572 |
– |
atomOrientDataTag = 4*i + 3; |
650 |
|
|
651 |
+ |
if (potatoes[which_node] + 3 >= MAXTAG) { |
652 |
+ |
// The potato was going to exceed the maximum value, |
653 |
+ |
// so wrap this processor potato back to 0: |
654 |
+ |
|
655 |
+ |
potatoes[which_node] = 0; |
656 |
+ |
MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD); |
657 |
+ |
|
658 |
+ |
} |
659 |
+ |
|
660 |
+ |
myPotato = potatoes[which_node]; |
661 |
+ |
|
662 |
|
MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node, |
663 |
< |
atomTypeTag, MPI_COMM_WORLD, &istatus); |
663 |
> |
myPotato, MPI_COMM_WORLD, &istatus); |
664 |
|
|
665 |
< |
strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE); |
665 |
> |
atomTypeString = MPIatomTypeString; |
666 |
> |
|
667 |
> |
myPotato++; |
668 |
|
|
669 |
|
MPI_Recv(&isDirectional, 1, MPI_INT, which_node, |
670 |
< |
atomIsDirectionalTag, MPI_COMM_WORLD, &istatus); |
671 |
< |
|
672 |
< |
MPI_Recv(atomTransData, 6, MPI_DOUBLE, which_node, |
583 |
< |
atomTransDataTag, MPI_COMM_WORLD, &istatus); |
670 |
> |
myPotato, MPI_COMM_WORLD, &istatus); |
671 |
> |
|
672 |
> |
myPotato++; |
673 |
|
|
674 |
< |
if (isDirectional) { |
675 |
< |
|
676 |
< |
MPI_Recv(atomOrientData, 7, MPI_DOUBLE, which_node, |
677 |
< |
atomOrientDataTag, MPI_COMM_WORLD, &istatus); |
678 |
< |
|
674 |
> |
if (isDirectional) { |
675 |
> |
MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node, |
676 |
> |
myPotato, MPI_COMM_WORLD, &istatus); |
677 |
> |
} else { |
678 |
> |
MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node, |
679 |
> |
myPotato, MPI_COMM_WORLD, &istatus); |
680 |
|
} |
681 |
+ |
|
682 |
+ |
myPotato++; |
683 |
+ |
potatoes[which_node] = myPotato; |
684 |
|
|
685 |
|
} else { |
686 |
|
|
687 |
|
haveError = 0; |
688 |
|
which_atom = i; |
689 |
|
local_index=-1; |
690 |
< |
|
690 |
> |
|
691 |
|
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
692 |
|
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
693 |
|
} |
694 |
< |
|
694 |
> |
|
695 |
|
if (local_index != -1) { |
696 |
< |
|
696 |
> |
|
697 |
|
atomTypeString = atoms[local_index]->getType(); |
698 |
|
|
699 |
|
atoms[local_index]->getPos(pos); |
700 |
< |
atoms[local_index]->getVel(vel); |
700 |
> |
atoms[local_index]->getVel(vel); |
701 |
|
|
702 |
< |
atomTransData[0] = pos[0]; |
703 |
< |
atomTransData[1] = pos[1]; |
704 |
< |
atomTransData[2] = pos[2]; |
702 |
> |
atomData6[0] = pos[0]; |
703 |
> |
atomData6[1] = pos[1]; |
704 |
> |
atomData6[2] = pos[2]; |
705 |
|
|
706 |
< |
atomTransData[3] = vel[0]; |
707 |
< |
atomTransData[4] = vel[1]; |
708 |
< |
atomTransData[5] = vel[2]; |
706 |
> |
atomData6[3] = vel[0]; |
707 |
> |
atomData6[4] = vel[1]; |
708 |
> |
atomData6[5] = vel[2]; |
709 |
|
|
710 |
|
isDirectional = 0; |
711 |
|
|
715 |
|
|
716 |
|
dAtom = (DirectionalAtom *)atoms[local_index]; |
717 |
|
dAtom->getQ( q ); |
625 |
– |
|
626 |
– |
atomOrientData[0] = q[0]; |
627 |
– |
atomOrientData[1] = q[1]; |
628 |
– |
atomOrientData[2] = q[2]; |
629 |
– |
atomOrientData[3] = q[3]; |
718 |
|
|
719 |
< |
atomOrientData[4] = dAtom->getJx(); |
720 |
< |
atomOrientData[5] = dAtom->getJy(); |
721 |
< |
atomOrientData[6] = dAtom->getJz(); |
719 |
> |
for (int j = 0; j < 6 ; j++) |
720 |
> |
atomData13[j] = atomData6[j]; |
721 |
> |
|
722 |
> |
atomData13[6] = q[0]; |
723 |
> |
atomData13[7] = q[1]; |
724 |
> |
atomData13[8] = q[2]; |
725 |
> |
atomData13[9] = q[3]; |
726 |
> |
|
727 |
> |
atomData13[10] = dAtom->getJx(); |
728 |
> |
atomData13[11] = dAtom->getJy(); |
729 |
> |
atomData13[12] = dAtom->getJz(); |
730 |
|
} |
731 |
< |
|
731 |
> |
|
732 |
|
} else { |
733 |
|
sprintf(painCave.errMsg, |
734 |
|
"Atom %d not found on processor %d\n", |
736 |
|
haveError= 1; |
737 |
|
simError(); |
738 |
|
} |
739 |
< |
|
739 |
> |
|
740 |
|
if(haveError) DieDieDie(); |
645 |
– |
|
646 |
– |
// If we've survived to here, format the line: |
741 |
|
|
742 |
< |
sprintf( tempBuffer, |
649 |
< |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
650 |
< |
atomTypeString, |
651 |
< |
atomTransData[0], |
652 |
< |
atomTransData[1], |
653 |
< |
atomTransData[2], |
654 |
< |
atomTransData[3], |
655 |
< |
atomTransData[4], |
656 |
< |
atomTransData[5]); |
742 |
> |
} |
743 |
|
|
658 |
– |
strcpy( writeLine, tempBuffer ); |
744 |
|
|
745 |
< |
if (isDirectional) { |
746 |
< |
|
747 |
< |
sprintf( tempBuffer, |
748 |
< |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
749 |
< |
atomOrientData[0], |
750 |
< |
atomOrientData[1], |
751 |
< |
atomOrientData[2], |
752 |
< |
atomOrientData[3], |
753 |
< |
atomOrientData[4], |
754 |
< |
atomOrientData[5], |
755 |
< |
atomOrientData[6]); |
756 |
< |
strcat( writeLine, tempBuffer ); |
757 |
< |
|
758 |
< |
} else { |
759 |
< |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
760 |
< |
} |
761 |
< |
|
762 |
< |
finalOut << writeLine; |
763 |
< |
finalOut.flush(); |
745 |
> |
// If we've survived to here, format the line: |
746 |
> |
|
747 |
> |
if (!isDirectional) { |
748 |
> |
|
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 |
> |
"%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 |
> |
strcpy( writeLine, tempBuffer ); |
782 |
> |
|
783 |
|
} |
784 |
+ |
|
785 |
+ |
finalOut << writeLine; |
786 |
+ |
finalOut.flush(); |
787 |
|
} |
788 |
< |
|
788 |
> |
|
789 |
|
finalOut.flush(); |
790 |
|
sprintf( checkPointMsg, |
791 |
|
"Sucessfully took a dump.\n"); |
792 |
+ |
delete[] potatoes; |
793 |
+ |
|
794 |
|
MPIcheckPoint(); |
795 |
|
|
796 |
|
} else { |
797 |
|
|
798 |
|
// worldRank != 0, so I'm a remote node. |
799 |
+ |
|
800 |
+ |
// Set my magic potato to 0: |
801 |
+ |
|
802 |
+ |
myPotato = 0; |
803 |
|
|
804 |
|
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
805 |
|
|
807 |
|
|
808 |
|
if (AtomToProcMap[i] == worldRank) { |
809 |
|
|
810 |
+ |
if (myPotato + 3 >= MAXTAG) { |
811 |
+ |
|
812 |
+ |
// The potato was going to exceed the maximum value, |
813 |
+ |
// so wrap this processor potato back to 0 (and block until |
814 |
+ |
// node 0 says we can go: |
815 |
+ |
|
816 |
+ |
MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus); |
817 |
+ |
|
818 |
+ |
} |
819 |
+ |
which_atom = i; |
820 |
|
local_index=-1; |
821 |
|
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
822 |
|
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
828 |
|
atoms[local_index]->getPos(pos); |
829 |
|
atoms[local_index]->getVel(vel); |
830 |
|
|
831 |
< |
atomTransData[0] = pos[0]; |
832 |
< |
atomTransData[1] = pos[1]; |
833 |
< |
atomTransData[2] = pos[2]; |
831 |
> |
atomData6[0] = pos[0]; |
832 |
> |
atomData6[1] = pos[1]; |
833 |
> |
atomData6[2] = pos[2]; |
834 |
|
|
835 |
< |
atomTransData[3] = vel[0]; |
836 |
< |
atomTransData[4] = vel[1]; |
837 |
< |
atomTransData[5] = vel[2]; |
835 |
> |
atomData6[3] = vel[0]; |
836 |
> |
atomData6[4] = vel[1]; |
837 |
> |
atomData6[5] = vel[2]; |
838 |
|
|
839 |
|
isDirectional = 0; |
840 |
|
|
845 |
|
dAtom = (DirectionalAtom *)atoms[local_index]; |
846 |
|
dAtom->getQ( q ); |
847 |
|
|
848 |
< |
atomOrientData[0] = q[0]; |
849 |
< |
atomOrientData[1] = q[1]; |
850 |
< |
atomOrientData[2] = q[2]; |
851 |
< |
atomOrientData[3] = q[3]; |
848 |
> |
for (int j = 0; j < 6 ; j++) |
849 |
> |
atomData13[j] = atomData6[j]; |
850 |
> |
|
851 |
> |
atomData13[6] = q[0]; |
852 |
> |
atomData13[7] = q[1]; |
853 |
> |
atomData13[8] = q[2]; |
854 |
> |
atomData13[9] = q[3]; |
855 |
|
|
856 |
< |
atomOrientData[4] = dAtom->getJx(); |
857 |
< |
atomOrientData[5] = dAtom->getJy(); |
858 |
< |
atomOrientData[6] = dAtom->getJz(); |
856 |
> |
atomData13[10] = dAtom->getJx(); |
857 |
> |
atomData13[11] = dAtom->getJy(); |
858 |
> |
atomData13[12] = dAtom->getJz(); |
859 |
|
} |
860 |
|
|
861 |
|
} else { |
866 |
|
simError(); |
867 |
|
} |
868 |
|
|
743 |
– |
// I've survived this far, so send off the data! |
744 |
– |
|
745 |
– |
atomTypeTag = 4*i; |
746 |
– |
atomIsDirectionalTag = 4*i + 1; |
747 |
– |
atomTransDataTag = 4*i + 2; |
748 |
– |
atomOrientDataTag = 4*i + 3; |
749 |
– |
|
869 |
|
strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE); |
870 |
|
|
871 |
+ |
// null terminate the string before sending (just in case): |
872 |
+ |
MPIatomTypeString[MINIBUFFERSIZE-1] = '\0'; |
873 |
+ |
|
874 |
|
MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0, |
875 |
< |
atomTypeTag, MPI_COMM_WORLD); |
875 |
> |
myPotato, MPI_COMM_WORLD); |
876 |
|
|
877 |
+ |
myPotato++; |
878 |
+ |
|
879 |
|
MPI_Send(&isDirectional, 1, MPI_INT, 0, |
880 |
< |
atomIsDirectionalTag, MPI_COMM_WORLD); |
880 |
> |
myPotato, MPI_COMM_WORLD); |
881 |
|
|
882 |
< |
MPI_Send(atomTransData, 6, MPI_DOUBLE, 0, |
883 |
< |
atomTransDataTag, MPI_COMM_WORLD); |
760 |
< |
|
882 |
> |
myPotato++; |
883 |
> |
|
884 |
|
if (isDirectional) { |
885 |
|
|
886 |
< |
MPI_Send(atomOrientData, 7, MPI_DOUBLE, 0, |
887 |
< |
atomOrientDataTag, MPI_COMM_WORLD); |
886 |
> |
MPI_Send(atomData13, 13, MPI_DOUBLE, 0, |
887 |
> |
myPotato, MPI_COMM_WORLD); |
888 |
|
|
889 |
+ |
} else { |
890 |
+ |
|
891 |
+ |
MPI_Send(atomData6, 6, MPI_DOUBLE, 0, |
892 |
+ |
myPotato, MPI_COMM_WORLD); |
893 |
|
} |
894 |
< |
|
894 |
> |
|
895 |
> |
myPotato++; |
896 |
|
} |
897 |
|
} |
898 |
|
|
899 |
|
sprintf( checkPointMsg, |
900 |
< |
"Sucessfully wrote final file.\n"); |
900 |
> |
"Sucessfully took a dump.\n"); |
901 |
|
MPIcheckPoint(); |
902 |
|
|
903 |
< |
} |
903 |
> |
} |
904 |
|
|
777 |
– |
painCave.isEventLoop = 0; |
778 |
– |
|
905 |
|
if( worldRank == 0 ) finalOut.close(); |
906 |
|
#endif // is_mpi |
907 |
|
} |