28 |
|
if(worldRank == 0 ){ |
29 |
|
#endif // is_mpi |
30 |
|
|
31 |
– |
|
31 |
|
dumpFile.open(entry_plug->sampleName, ios::out | ios::trunc ); |
32 |
|
|
33 |
|
if( !dumpFile ){ |
91 |
|
|
92 |
|
indexArray.clear(); |
93 |
|
|
94 |
< |
for(int i = 0; i < mpiSim->getMyNlocal();i++) |
94 |
> |
for(int i = 0; i < mpiSim->getMyNlocal();i++) |
95 |
|
indexArray.push_back(make_pair(i, atoms[i]->getGlobalIndex())); |
96 |
|
|
97 |
|
sort(indexArray.begin(), indexArray.end(), indexSortingCriterion); |
98 |
+ |
|
99 |
+ |
//for (int i = 0; i < mpiSim->getMyNlocal(); i++) { |
100 |
+ |
// printf("node %d has global %d at local %d\n", worldRank, indexArray[i].second, indexArray[i].first); |
101 |
+ |
//} |
102 |
+ |
|
103 |
|
} |
104 |
+ |
|
105 |
|
#endif |
106 |
|
|
107 |
|
void DumpWriter::writeDump(double currentTime){ |
110 |
|
vector<ofstream*> fileStreams; |
111 |
|
|
112 |
|
#ifdef IS_MPI |
113 |
+ |
printf("Hello from node %d\n", worldRank); |
114 |
+ |
sortByGlobalIndex(); |
115 |
|
if(worldRank == 0 ){ |
116 |
|
|
117 |
|
finalOut.open( entry_plug->finalName, ios::out | ios::trunc ); |
143 |
|
|
144 |
|
#ifdef IS_MPI |
145 |
|
if(worldRank == 0 ){ |
146 |
+ |
#endif // is_mpi |
147 |
|
|
148 |
|
finalOut.open( entry_plug->finalName, ios::out | ios::trunc ); |
149 |
|
|
155 |
|
simError(); |
156 |
|
} |
157 |
|
|
158 |
+ |
#ifdef IS_MPI |
159 |
|
} |
160 |
|
#endif // is_mpi |
161 |
|
|
180 |
|
|
181 |
|
#ifdef IS_MPI |
182 |
|
|
183 |
+ |
/********************************************************************* |
184 |
+ |
* Documentation? You want DOCUMENTATION? |
185 |
+ |
* |
186 |
+ |
* Why all the potatoes below? |
187 |
+ |
* |
188 |
+ |
* To make a long story short, the original version of DumpWriter |
189 |
+ |
* worked in the most inefficient way possible. Node 0 would |
190 |
+ |
* poke each of the node for an individual atom's formatted data |
191 |
+ |
* as node 0 worked its way down the global index. This was particularly |
192 |
+ |
* inefficient since the method blocked all processors at every atom |
193 |
+ |
* (and did it twice!). |
194 |
+ |
* |
195 |
+ |
* An intermediate version of DumpWriter could be described from Node |
196 |
+ |
* zero's perspective as follows: |
197 |
+ |
* |
198 |
+ |
* 1) Have 100 of your friends stand in a circle. |
199 |
+ |
* 2) When you say go, have all of them start tossing potatoes at |
200 |
+ |
* you (one at a time). |
201 |
+ |
* 3) Catch the potatoes. |
202 |
+ |
* |
203 |
+ |
* It was an improvement, but MPI has buffers and caches that could |
204 |
+ |
* best be described in this analogy as "potato nets", so there's no |
205 |
+ |
* need to block the processors atom-by-atom. |
206 |
+ |
* |
207 |
+ |
* This new and improved DumpWriter works in an even more efficient |
208 |
+ |
* way: |
209 |
+ |
* |
210 |
+ |
* 1) Have 100 of your friend stand in a circle. |
211 |
+ |
* 2) When you say go, have them start tossing 5-pound bags of |
212 |
+ |
* potatoes at you. |
213 |
+ |
* 3) Once you've caught a friend's bag of potatoes, |
214 |
+ |
* toss them a spud to let them know they can toss another bag. |
215 |
+ |
* |
216 |
+ |
* How's THAT for documentation? |
217 |
+ |
* |
218 |
+ |
*********************************************************************/ |
219 |
+ |
|
220 |
|
int *potatoes; |
221 |
|
int myPotato; |
222 |
|
|
394 |
|
} else { |
395 |
|
|
396 |
|
haveError = 0; |
397 |
< |
which_atom = i; |
397 |
> |
which_atom = i; |
398 |
|
|
399 |
< |
local_index = indexArray[currentIndex].first; |
354 |
< |
|
355 |
< |
if (which_atom == indexArray[currentIndex].second) { |
356 |
< |
|
357 |
< |
atomTypeString = atoms[local_index]->getType(); |
399 |
> |
//local_index = -1; |
400 |
|
|
401 |
< |
atoms[local_index]->getPos(pos); |
402 |
< |
atoms[local_index]->getVel(vel); |
403 |
< |
|
401 |
> |
//for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
402 |
> |
// if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
403 |
> |
//} |
404 |
> |
|
405 |
> |
//if (local_index != -1) { |
406 |
> |
|
407 |
> |
local_index = indexArray[currentIndex].first; |
408 |
> |
|
409 |
> |
if (which_atom == indexArray[currentIndex].second) { |
410 |
> |
|
411 |
> |
atomTypeString = atoms[local_index]->getType(); |
412 |
> |
|
413 |
> |
atoms[local_index]->getPos(pos); |
414 |
> |
atoms[local_index]->getVel(vel); |
415 |
> |
|
416 |
|
atomData6[0] = pos[0]; |
417 |
|
atomData6[1] = pos[1]; |
418 |
|
atomData6[2] = pos[2]; |
444 |
|
} |
445 |
|
|
446 |
|
} else { |
447 |
< |
sprintf(painCave.errMsg, |
448 |
< |
"Atom %d not found on processor %d\n", |
449 |
< |
i, worldRank ); |
450 |
< |
haveError= 1; |
451 |
< |
simError(); |
452 |
< |
} |
447 |
> |
sprintf(painCave.errMsg, |
448 |
> |
"Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n", |
449 |
> |
which_atom, worldRank, currentIndex, local_index ); |
450 |
> |
haveError= 1; |
451 |
> |
simError(); |
452 |
> |
} |
453 |
|
|
454 |
|
if(haveError) DieDieDie(); |
455 |
|
|
456 |
< |
currentIndex ++; |
456 |
> |
currentIndex++; |
457 |
|
} |
458 |
|
// If we've survived to here, format the line: |
459 |
|
|
460 |
|
if (!isDirectional) { |
461 |
|
|
462 |
|
sprintf( writeLine, |
463 |
< |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
464 |
< |
atomTypeString, |
465 |
< |
atomData6[0], |
466 |
< |
atomData6[1], |
467 |
< |
atomData6[2], |
468 |
< |
atomData6[3], |
469 |
< |
atomData6[4], |
470 |
< |
atomData6[5]); |
417 |
< |
|
418 |
< |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
463 |
> |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
464 |
> |
atomTypeString, |
465 |
> |
atomData6[0], |
466 |
> |
atomData6[1], |
467 |
> |
atomData6[2], |
468 |
> |
atomData6[3], |
469 |
> |
atomData6[4], |
470 |
> |
atomData6[5]); |
471 |
|
|
472 |
+ |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
473 |
+ |
|
474 |
|
} else { |
475 |
|
|
476 |
< |
sprintf( writeLine, |
477 |
< |
"%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", |
478 |
< |
atomTypeString, |
479 |
< |
atomData13[0], |
480 |
< |
atomData13[1], |
481 |
< |
atomData13[2], |
482 |
< |
atomData13[3], |
483 |
< |
atomData13[4], |
484 |
< |
atomData13[5], |
485 |
< |
atomData13[6], |
486 |
< |
atomData13[7], |
487 |
< |
atomData13[8], |
488 |
< |
atomData13[9], |
489 |
< |
atomData13[10], |
490 |
< |
atomData13[11], |
491 |
< |
atomData13[12]); |
476 |
> |
sprintf( writeLine, |
477 |
> |
"%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", |
478 |
> |
atomTypeString, |
479 |
> |
atomData13[0], |
480 |
> |
atomData13[1], |
481 |
> |
atomData13[2], |
482 |
> |
atomData13[3], |
483 |
> |
atomData13[4], |
484 |
> |
atomData13[5], |
485 |
> |
atomData13[6], |
486 |
> |
atomData13[7], |
487 |
> |
atomData13[8], |
488 |
> |
atomData13[9], |
489 |
> |
atomData13[10], |
490 |
> |
atomData13[11], |
491 |
> |
atomData13[12]); |
492 |
|
|
493 |
|
} |
494 |
|
|
501 |
|
|
502 |
|
sprintf( checkPointMsg, |
503 |
|
"Sucessfully took a dump.\n"); |
504 |
< |
|
504 |
> |
|
505 |
|
MPIcheckPoint(); |
506 |
< |
|
506 |
> |
|
507 |
|
delete[] potatoes; |
508 |
< |
|
508 |
> |
|
509 |
|
} else { |
510 |
|
|
511 |
|
// worldRank != 0, so I'm a remote node. |
522 |
|
if (AtomToProcMap[i] == worldRank) { |
523 |
|
|
524 |
|
if (myPotato + 3 >= MAXTAG) { |
525 |
< |
|
525 |
> |
|
526 |
|
// The potato was going to exceed the maximum value, |
527 |
|
// so wrap this processor potato back to 0 (and block until |
528 |
|
// node 0 says we can go: |
529 |
< |
|
529 |
> |
|
530 |
|
MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus); |
531 |
|
|
532 |
|
} |
533 |
|
which_atom = i; |
534 |
< |
local_index = indexArray[currentIndex].first; |
534 |
> |
|
535 |
> |
//local_index = -1; |
536 |
> |
|
537 |
> |
//for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
538 |
> |
// if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
539 |
> |
//} |
540 |
> |
|
541 |
> |
//if (local_index != -1) { |
542 |
> |
|
543 |
> |
local_index = indexArray[currentIndex].first; |
544 |
|
|
545 |
< |
if (which_atom == indexArray[currentIndex].second) { |
545 |
> |
if (which_atom == indexArray[currentIndex].second) { |
546 |
|
|
547 |
|
atomTypeString = atoms[local_index]->getType(); |
548 |
< |
|
549 |
< |
atoms[local_index]->getPos(pos); |
550 |
< |
atoms[local_index]->getVel(vel); |
551 |
< |
|
548 |
> |
|
549 |
> |
atoms[local_index]->getPos(pos); |
550 |
> |
atoms[local_index]->getVel(vel); |
551 |
> |
|
552 |
|
atomData6[0] = pos[0]; |
553 |
|
atomData6[1] = pos[1]; |
554 |
|
atomData6[2] = pos[2]; |
580 |
|
} |
581 |
|
|
582 |
|
} else { |
583 |
< |
sprintf(painCave.errMsg, |
584 |
< |
"Atom %d not found on processor %d\n", |
585 |
< |
i, worldRank ); |
586 |
< |
haveError= 1; |
587 |
< |
simError(); |
588 |
< |
} |
589 |
< |
|
583 |
> |
sprintf(painCave.errMsg, |
584 |
> |
"Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n", |
585 |
> |
which_atom, worldRank, currentIndex, local_index ); |
586 |
> |
haveError= 1; |
587 |
> |
simError(); |
588 |
> |
} |
589 |
> |
|
590 |
|
strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE); |
591 |
|
|
592 |
|
// null terminate the string before sending (just in case): |