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 |
+ |
|
100 |
|
#endif |
101 |
|
|
102 |
|
void DumpWriter::writeDump(double currentTime){ |
106 |
|
|
107 |
|
#ifdef IS_MPI |
108 |
|
if(worldRank == 0 ){ |
109 |
< |
|
109 |
> |
#endif |
110 |
|
finalOut.open( entry_plug->finalName, ios::out | ios::trunc ); |
111 |
|
if( !finalOut ){ |
112 |
|
sprintf( painCave.errMsg, |
115 |
|
painCave.isFatal = 1; |
116 |
|
simError(); |
117 |
|
} |
118 |
+ |
#ifdef IS_MPI |
119 |
|
} |
120 |
|
#endif // is_mpi |
121 |
|
|
137 |
|
|
138 |
|
#ifdef IS_MPI |
139 |
|
if(worldRank == 0 ){ |
140 |
+ |
#endif // is_mpi |
141 |
|
|
142 |
|
finalOut.open( entry_plug->finalName, ios::out | ios::trunc ); |
143 |
|
|
149 |
|
simError(); |
150 |
|
} |
151 |
|
|
152 |
+ |
#ifdef IS_MPI |
153 |
|
} |
154 |
|
#endif // is_mpi |
155 |
|
|
174 |
|
|
175 |
|
#ifdef IS_MPI |
176 |
|
|
177 |
+ |
/********************************************************************* |
178 |
+ |
* Documentation? You want DOCUMENTATION? |
179 |
+ |
* |
180 |
+ |
* Why all the potatoes below? |
181 |
+ |
* |
182 |
+ |
* To make a long story short, the original version of DumpWriter |
183 |
+ |
* worked in the most inefficient way possible. Node 0 would |
184 |
+ |
* poke each of the node for an individual atom's formatted data |
185 |
+ |
* as node 0 worked its way down the global index. This was particularly |
186 |
+ |
* inefficient since the method blocked all processors at every atom |
187 |
+ |
* (and did it twice!). |
188 |
+ |
* |
189 |
+ |
* An intermediate version of DumpWriter could be described from Node |
190 |
+ |
* zero's perspective as follows: |
191 |
+ |
* |
192 |
+ |
* 1) Have 100 of your friends stand in a circle. |
193 |
+ |
* 2) When you say go, have all of them start tossing potatoes at |
194 |
+ |
* you (one at a time). |
195 |
+ |
* 3) Catch the potatoes. |
196 |
+ |
* |
197 |
+ |
* It was an improvement, but MPI has buffers and caches that could |
198 |
+ |
* best be described in this analogy as "potato nets", so there's no |
199 |
+ |
* need to block the processors atom-by-atom. |
200 |
+ |
* |
201 |
+ |
* This new and improved DumpWriter works in an even more efficient |
202 |
+ |
* way: |
203 |
+ |
* |
204 |
+ |
* 1) Have 100 of your friend stand in a circle. |
205 |
+ |
* 2) When you say go, have them start tossing 5-pound bags of |
206 |
+ |
* potatoes at you. |
207 |
+ |
* 3) Once you've caught a friend's bag of potatoes, |
208 |
+ |
* toss them a spud to let them know they can toss another bag. |
209 |
+ |
* |
210 |
+ |
* How's THAT for documentation? |
211 |
+ |
* |
212 |
+ |
*********************************************************************/ |
213 |
+ |
|
214 |
|
int *potatoes; |
215 |
|
int myPotato; |
216 |
|
|
388 |
|
} else { |
389 |
|
|
390 |
|
haveError = 0; |
391 |
< |
which_atom = i; |
391 |
> |
which_atom = i; |
392 |
|
|
393 |
< |
local_index = indexArray[currentIndex].first; |
354 |
< |
|
355 |
< |
if (which_atom == indexArray[currentIndex].second) { |
393 |
> |
local_index = indexArray[currentIndex].first; |
394 |
|
|
395 |
< |
atomTypeString = atoms[local_index]->getType(); |
396 |
< |
|
397 |
< |
atoms[local_index]->getPos(pos); |
398 |
< |
atoms[local_index]->getVel(vel); |
399 |
< |
|
395 |
> |
if (which_atom == indexArray[currentIndex].second) { |
396 |
> |
|
397 |
> |
atomTypeString = atoms[local_index]->getType(); |
398 |
> |
|
399 |
> |
atoms[local_index]->getPos(pos); |
400 |
> |
atoms[local_index]->getVel(vel); |
401 |
> |
|
402 |
|
atomData6[0] = pos[0]; |
403 |
|
atomData6[1] = pos[1]; |
404 |
|
atomData6[2] = pos[2]; |
430 |
|
} |
431 |
|
|
432 |
|
} else { |
433 |
< |
sprintf(painCave.errMsg, |
434 |
< |
"Atom %d not found on processor %d\n", |
435 |
< |
i, worldRank ); |
436 |
< |
haveError= 1; |
437 |
< |
simError(); |
438 |
< |
} |
433 |
> |
sprintf(painCave.errMsg, |
434 |
> |
"Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n", |
435 |
> |
which_atom, worldRank, currentIndex, local_index ); |
436 |
> |
haveError= 1; |
437 |
> |
simError(); |
438 |
> |
} |
439 |
|
|
440 |
|
if(haveError) DieDieDie(); |
441 |
|
|
442 |
< |
currentIndex ++; |
442 |
> |
currentIndex++; |
443 |
|
} |
444 |
|
// If we've survived to here, format the line: |
445 |
|
|
446 |
|
if (!isDirectional) { |
447 |
|
|
448 |
|
sprintf( writeLine, |
449 |
< |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
450 |
< |
atomTypeString, |
451 |
< |
atomData6[0], |
452 |
< |
atomData6[1], |
453 |
< |
atomData6[2], |
454 |
< |
atomData6[3], |
455 |
< |
atomData6[4], |
456 |
< |
atomData6[5]); |
417 |
< |
|
418 |
< |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
449 |
> |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
450 |
> |
atomTypeString, |
451 |
> |
atomData6[0], |
452 |
> |
atomData6[1], |
453 |
> |
atomData6[2], |
454 |
> |
atomData6[3], |
455 |
> |
atomData6[4], |
456 |
> |
atomData6[5]); |
457 |
|
|
458 |
+ |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
459 |
+ |
|
460 |
|
} else { |
461 |
|
|
462 |
< |
sprintf( writeLine, |
463 |
< |
"%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", |
464 |
< |
atomTypeString, |
465 |
< |
atomData13[0], |
466 |
< |
atomData13[1], |
467 |
< |
atomData13[2], |
468 |
< |
atomData13[3], |
469 |
< |
atomData13[4], |
470 |
< |
atomData13[5], |
471 |
< |
atomData13[6], |
472 |
< |
atomData13[7], |
473 |
< |
atomData13[8], |
474 |
< |
atomData13[9], |
475 |
< |
atomData13[10], |
476 |
< |
atomData13[11], |
477 |
< |
atomData13[12]); |
462 |
> |
sprintf( writeLine, |
463 |
> |
"%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", |
464 |
> |
atomTypeString, |
465 |
> |
atomData13[0], |
466 |
> |
atomData13[1], |
467 |
> |
atomData13[2], |
468 |
> |
atomData13[3], |
469 |
> |
atomData13[4], |
470 |
> |
atomData13[5], |
471 |
> |
atomData13[6], |
472 |
> |
atomData13[7], |
473 |
> |
atomData13[8], |
474 |
> |
atomData13[9], |
475 |
> |
atomData13[10], |
476 |
> |
atomData13[11], |
477 |
> |
atomData13[12]); |
478 |
|
|
479 |
|
} |
480 |
|
|
487 |
|
|
488 |
|
sprintf( checkPointMsg, |
489 |
|
"Sucessfully took a dump.\n"); |
490 |
< |
|
490 |
> |
|
491 |
|
MPIcheckPoint(); |
492 |
< |
|
492 |
> |
|
493 |
|
delete[] potatoes; |
494 |
< |
|
494 |
> |
|
495 |
|
} else { |
496 |
|
|
497 |
|
// worldRank != 0, so I'm a remote node. |
508 |
|
if (AtomToProcMap[i] == worldRank) { |
509 |
|
|
510 |
|
if (myPotato + 3 >= MAXTAG) { |
511 |
< |
|
511 |
> |
|
512 |
|
// The potato was going to exceed the maximum value, |
513 |
|
// so wrap this processor potato back to 0 (and block until |
514 |
|
// node 0 says we can go: |
515 |
< |
|
515 |
> |
|
516 |
|
MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus); |
517 |
|
|
518 |
|
} |
519 |
|
which_atom = i; |
520 |
< |
local_index = indexArray[currentIndex].first; |
520 |
> |
|
521 |
> |
local_index = indexArray[currentIndex].first; |
522 |
|
|
523 |
< |
if (which_atom == indexArray[currentIndex].second) { |
523 |
> |
if (which_atom == indexArray[currentIndex].second) { |
524 |
|
|
525 |
|
atomTypeString = atoms[local_index]->getType(); |
526 |
< |
|
527 |
< |
atoms[local_index]->getPos(pos); |
528 |
< |
atoms[local_index]->getVel(vel); |
529 |
< |
|
526 |
> |
|
527 |
> |
atoms[local_index]->getPos(pos); |
528 |
> |
atoms[local_index]->getVel(vel); |
529 |
> |
|
530 |
|
atomData6[0] = pos[0]; |
531 |
|
atomData6[1] = pos[1]; |
532 |
|
atomData6[2] = pos[2]; |
558 |
|
} |
559 |
|
|
560 |
|
} else { |
561 |
< |
sprintf(painCave.errMsg, |
562 |
< |
"Atom %d not found on processor %d\n", |
563 |
< |
i, worldRank ); |
564 |
< |
haveError= 1; |
565 |
< |
simError(); |
566 |
< |
} |
567 |
< |
|
561 |
> |
sprintf(painCave.errMsg, |
562 |
> |
"Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n", |
563 |
> |
which_atom, worldRank, currentIndex, local_index ); |
564 |
> |
haveError= 1; |
565 |
> |
simError(); |
566 |
> |
} |
567 |
> |
|
568 |
|
strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE); |
569 |
|
|
570 |
|
// null terminate the string before sending (just in case): |