40 |
|
simError(); |
41 |
|
} |
42 |
|
|
43 |
– |
//outFile.setf( ios::scientific ); |
44 |
– |
|
43 |
|
#ifdef IS_MPI |
44 |
|
} |
45 |
|
|
100 |
|
#endif |
101 |
|
|
102 |
|
void DumpWriter::writeDump(double currentTime){ |
105 |
– |
|
106 |
– |
// write to eor file |
107 |
– |
writeFinal(currentTime); |
103 |
|
|
104 |
< |
//write to dump file |
105 |
< |
writeFrame(dumpFile, currentTime); |
104 |
> |
ofstream finalOut; |
105 |
> |
vector<ofstream*> fileStreams; |
106 |
> |
|
107 |
> |
#ifdef IS_MPI |
108 |
> |
if(worldRank == 0 ){ |
109 |
> |
|
110 |
> |
finalOut.open( entry_plug->finalName, ios::out | ios::trunc ); |
111 |
> |
if( !finalOut ){ |
112 |
> |
sprintf( painCave.errMsg, |
113 |
> |
"Could not open \"%s\" for final dump output.\n", |
114 |
> |
entry_plug->finalName ); |
115 |
> |
painCave.isFatal = 1; |
116 |
> |
simError(); |
117 |
> |
} |
118 |
> |
} |
119 |
> |
#endif // is_mpi |
120 |
> |
|
121 |
> |
fileStreams.push_back(&finalOut); |
122 |
> |
fileStreams.push_back(&dumpFile); |
123 |
> |
|
124 |
> |
writeFrame(fileStreams, currentTime); |
125 |
> |
|
126 |
> |
#ifdef IS_MPI |
127 |
> |
finalOut.close(); |
128 |
> |
#endif |
129 |
|
|
130 |
|
} |
131 |
|
|
132 |
|
void DumpWriter::writeFinal(double currentTime){ |
133 |
|
|
134 |
< |
ofstream finalOut; |
135 |
< |
|
136 |
< |
//Open eor file |
134 |
> |
ofstream finalOut; |
135 |
> |
vector<ofstream*> fileStreams; |
136 |
> |
|
137 |
|
#ifdef IS_MPI |
138 |
|
if(worldRank == 0 ){ |
121 |
– |
#endif // is_mpi |
139 |
|
|
140 |
|
finalOut.open( entry_plug->finalName, ios::out | ios::trunc ); |
141 |
+ |
|
142 |
|
if( !finalOut ){ |
143 |
|
sprintf( painCave.errMsg, |
144 |
|
"Could not open \"%s\" for final dump output.\n", |
146 |
|
painCave.isFatal = 1; |
147 |
|
simError(); |
148 |
|
} |
149 |
< |
|
132 |
< |
#ifdef IS_MPI |
149 |
> |
|
150 |
|
} |
134 |
– |
#endif |
135 |
– |
|
136 |
– |
//write to eor file |
137 |
– |
writeFrame(finalOut, currentTime); |
138 |
– |
|
139 |
– |
//close eor file |
140 |
– |
#ifdef IS_MPI |
141 |
– |
if(worldRank == 0 ){ |
142 |
– |
finalOut.close(); |
143 |
– |
} |
151 |
|
#endif // is_mpi |
152 |
+ |
|
153 |
+ |
fileStreams.push_back(&finalOut); |
154 |
+ |
writeFrame(fileStreams, currentTime); |
155 |
|
|
156 |
+ |
#ifdef IS_MPI |
157 |
+ |
finalOut.close(); |
158 |
+ |
#endif |
159 |
+ |
|
160 |
|
} |
161 |
|
|
162 |
< |
void DumpWriter::writeFrame( ofstream& outFile, double currentTime ){ |
162 |
> |
void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){ |
163 |
|
|
164 |
|
const int BUFFERSIZE = 2000; |
165 |
|
const int MINIBUFFERSIZE = 100; |
166 |
|
|
167 |
< |
char tempBuffer[BUFFERSIZE]; |
167 |
> |
char tempBuffer[BUFFERSIZE]; |
168 |
|
char writeLine[BUFFERSIZE]; |
169 |
|
|
170 |
< |
int i; |
170 |
> |
int i, k; |
171 |
|
|
172 |
|
#ifdef IS_MPI |
173 |
|
|
174 |
+ |
/********************************************************************* |
175 |
+ |
* Documentation? You want DOCUMENTATION? |
176 |
+ |
* |
177 |
+ |
* Why all the potatoes below? |
178 |
+ |
* |
179 |
+ |
* To make a long story short, the original version of DumpWriter |
180 |
+ |
* worked in the most inefficient way possible. Node 0 would |
181 |
+ |
* poke each of the node for an individual atom's formatted data |
182 |
+ |
* as node 0 worked its way down the global index. This was particularly |
183 |
+ |
* inefficient since the method blocked all processors at every atom |
184 |
+ |
* (and did it twice!). |
185 |
+ |
* |
186 |
+ |
* An intermediate version of DumpWriter could be described from Node |
187 |
+ |
* zero's perspective as follows: |
188 |
+ |
* |
189 |
+ |
* 1) Have 100 of your friends stand in a circle. |
190 |
+ |
* 2) When you say go, have all of them start tossing potatoes at |
191 |
+ |
* you (one at a time). |
192 |
+ |
* 3) Catch the potatoes. |
193 |
+ |
* |
194 |
+ |
* It was an improvement, but MPI has buffers and caches that could |
195 |
+ |
* best be described in this analogy as "potato nets", so there's no |
196 |
+ |
* need to block the processors atom-by-atom. |
197 |
+ |
* |
198 |
+ |
* This new and improved DumpWriter works in an even more efficient |
199 |
+ |
* way: |
200 |
+ |
* |
201 |
+ |
* 1) Have 100 of your friend stand in a circle. |
202 |
+ |
* 2) When you say go, have them start tossing 5-pound bags of |
203 |
+ |
* potatoes at you. |
204 |
+ |
* 3) Once you've caught a friend's bag of potatoes, |
205 |
+ |
* toss them a spud to let them know they can toss another bag. |
206 |
+ |
* |
207 |
+ |
* How's THAT for documentation? |
208 |
+ |
* |
209 |
+ |
*********************************************************************/ |
210 |
+ |
|
211 |
|
int *potatoes; |
212 |
|
int myPotato; |
213 |
|
|
229 |
|
double pos[3], vel[3]; |
230 |
|
|
231 |
|
#ifndef IS_MPI |
232 |
+ |
|
233 |
+ |
for(k = 0; k < outFile.size(); k++){ |
234 |
+ |
*outFile[k] << nAtoms << "\n"; |
235 |
|
|
236 |
< |
outFile << nAtoms << "\n"; |
236 |
> |
*outFile[k] << currentTime << ";\t" |
237 |
> |
<< entry_plug->Hmat[0][0] << "\t" |
238 |
> |
<< entry_plug->Hmat[1][0] << "\t" |
239 |
> |
<< entry_plug->Hmat[2][0] << ";\t" |
240 |
> |
|
241 |
> |
<< entry_plug->Hmat[0][1] << "\t" |
242 |
> |
<< entry_plug->Hmat[1][1] << "\t" |
243 |
> |
<< entry_plug->Hmat[2][1] << ";\t" |
244 |
|
|
245 |
< |
outFile << currentTime << ";\t" |
246 |
< |
<< entry_plug->Hmat[0][0] << "\t" |
247 |
< |
<< entry_plug->Hmat[1][0] << "\t" |
187 |
< |
<< entry_plug->Hmat[2][0] << ";\t" |
245 |
> |
<< entry_plug->Hmat[0][2] << "\t" |
246 |
> |
<< entry_plug->Hmat[1][2] << "\t" |
247 |
> |
<< entry_plug->Hmat[2][2] << ";"; |
248 |
|
|
249 |
< |
<< entry_plug->Hmat[0][1] << "\t" |
250 |
< |
<< entry_plug->Hmat[1][1] << "\t" |
251 |
< |
<< entry_plug->Hmat[2][1] << ";\t" |
252 |
< |
|
193 |
< |
<< entry_plug->Hmat[0][2] << "\t" |
194 |
< |
<< entry_plug->Hmat[1][2] << "\t" |
195 |
< |
<< entry_plug->Hmat[2][2] << ";"; |
196 |
< |
//write out additional parameters, such as chi and eta |
197 |
< |
outFile << entry_plug->the_integrator->getAdditionalParameters(); |
198 |
< |
outFile << endl; |
199 |
< |
|
249 |
> |
//write out additional parameters, such as chi and eta |
250 |
> |
*outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl; |
251 |
> |
} |
252 |
> |
|
253 |
|
for( i=0; i<nAtoms; i++ ){ |
254 |
|
|
255 |
|
atoms[i]->getPos(pos); |
285 |
|
else |
286 |
|
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
287 |
|
|
288 |
< |
outFile << writeLine; |
288 |
> |
for(k = 0; k < outFile.size(); k++) |
289 |
> |
*outFile[k] << writeLine; |
290 |
|
} |
291 |
|
|
292 |
|
#else // is_mpi |
315 |
|
nProc = mpiSim->getNumberProcessors(); |
316 |
|
potatoes = new int[nProc]; |
317 |
|
|
318 |
+ |
//write out the comment lines |
319 |
|
for (i = 0; i < nProc; i++) |
320 |
|
potatoes[i] = 0; |
321 |
|
|
322 |
< |
outFile << mpiSim->getTotAtoms() << "\n"; |
322 |
> |
for(k = 0; k < outFile.size(); k++){ |
323 |
> |
*outFile[k] << mpiSim->getTotAtoms() << "\n"; |
324 |
|
|
325 |
< |
outFile << currentTime << ";\t" |
326 |
< |
<< entry_plug->Hmat[0][0] << "\t" |
327 |
< |
<< entry_plug->Hmat[1][0] << "\t" |
328 |
< |
<< entry_plug->Hmat[2][0] << ";\t" |
325 |
> |
*outFile[k] << currentTime << ";\t" |
326 |
> |
<< entry_plug->Hmat[0][0] << "\t" |
327 |
> |
<< entry_plug->Hmat[1][0] << "\t" |
328 |
> |
<< entry_plug->Hmat[2][0] << ";\t" |
329 |
|
|
330 |
< |
<< entry_plug->Hmat[0][1] << "\t" |
331 |
< |
<< entry_plug->Hmat[1][1] << "\t" |
332 |
< |
<< entry_plug->Hmat[2][1] << ";\t" |
330 |
> |
<< entry_plug->Hmat[0][1] << "\t" |
331 |
> |
<< entry_plug->Hmat[1][1] << "\t" |
332 |
> |
<< entry_plug->Hmat[2][1] << ";\t" |
333 |
|
|
334 |
< |
<< entry_plug->Hmat[0][2] << "\t" |
335 |
< |
<< entry_plug->Hmat[1][2] << "\t" |
336 |
< |
<< entry_plug->Hmat[2][2] << ";"; |
334 |
> |
<< entry_plug->Hmat[0][2] << "\t" |
335 |
> |
<< entry_plug->Hmat[1][2] << "\t" |
336 |
> |
<< entry_plug->Hmat[2][2] << ";"; |
337 |
> |
|
338 |
> |
*outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl; |
339 |
> |
} |
340 |
|
|
282 |
– |
outFile << entry_plug->the_integrator->getAdditionalParameters(); |
283 |
– |
outFile << endl; |
284 |
– |
outFile.flush(); |
285 |
– |
|
341 |
|
currentIndex = 0; |
342 |
+ |
|
343 |
|
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
344 |
|
|
345 |
|
// Get the Node number which has this atom; |
384 |
|
|
385 |
|
} else { |
386 |
|
|
387 |
< |
haveError = 0; |
388 |
< |
which_atom = i; |
387 |
> |
haveError = 0; |
388 |
> |
which_atom = i; |
389 |
|
|
390 |
|
local_index = indexArray[currentIndex].first; |
391 |
|
|
393 |
|
|
394 |
|
atomTypeString = atoms[local_index]->getType(); |
395 |
|
|
396 |
< |
atoms[local_index]->getPos(pos); |
397 |
< |
atoms[local_index]->getVel(vel); |
396 |
> |
atoms[local_index]->getPos(pos); |
397 |
> |
atoms[local_index]->getVel(vel); |
398 |
|
|
399 |
|
atomData6[0] = pos[0]; |
400 |
|
atomData6[1] = pos[1]; |
427 |
|
} |
428 |
|
|
429 |
|
} else { |
430 |
< |
sprintf(painCave.errMsg, |
431 |
< |
"Atom %d not found on processor %d\n", |
432 |
< |
i, worldRank ); |
433 |
< |
haveError= 1; |
434 |
< |
simError(); |
435 |
< |
} |
430 |
> |
sprintf(painCave.errMsg, |
431 |
> |
"Atom %d not found on processor %d\n", |
432 |
> |
i, worldRank ); |
433 |
> |
haveError= 1; |
434 |
> |
simError(); |
435 |
> |
} |
436 |
|
|
437 |
< |
if(haveError) DieDieDie(); |
437 |
> |
if(haveError) DieDieDie(); |
438 |
|
|
439 |
|
currentIndex ++; |
440 |
|
} |
442 |
|
|
443 |
|
if (!isDirectional) { |
444 |
|
|
445 |
< |
sprintf( writeLine, |
446 |
< |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
447 |
< |
atomTypeString, |
448 |
< |
atomData6[0], |
449 |
< |
atomData6[1], |
450 |
< |
atomData6[2], |
451 |
< |
atomData6[3], |
452 |
< |
atomData6[4], |
453 |
< |
atomData6[5]); |
445 |
> |
sprintf( writeLine, |
446 |
> |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
447 |
> |
atomTypeString, |
448 |
> |
atomData6[0], |
449 |
> |
atomData6[1], |
450 |
> |
atomData6[2], |
451 |
> |
atomData6[3], |
452 |
> |
atomData6[4], |
453 |
> |
atomData6[5]); |
454 |
|
|
455 |
< |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
455 |
> |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
456 |
|
|
457 |
|
} else { |
458 |
|
|
459 |
< |
sprintf( writeLine, |
460 |
< |
"%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", |
461 |
< |
atomTypeString, |
462 |
< |
atomData13[0], |
463 |
< |
atomData13[1], |
464 |
< |
atomData13[2], |
465 |
< |
atomData13[3], |
466 |
< |
atomData13[4], |
467 |
< |
atomData13[5], |
468 |
< |
atomData13[6], |
469 |
< |
atomData13[7], |
470 |
< |
atomData13[8], |
471 |
< |
atomData13[9], |
472 |
< |
atomData13[10], |
473 |
< |
atomData13[11], |
474 |
< |
atomData13[12]); |
459 |
> |
sprintf( writeLine, |
460 |
> |
"%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", |
461 |
> |
atomTypeString, |
462 |
> |
atomData13[0], |
463 |
> |
atomData13[1], |
464 |
> |
atomData13[2], |
465 |
> |
atomData13[3], |
466 |
> |
atomData13[4], |
467 |
> |
atomData13[5], |
468 |
> |
atomData13[6], |
469 |
> |
atomData13[7], |
470 |
> |
atomData13[8], |
471 |
> |
atomData13[9], |
472 |
> |
atomData13[10], |
473 |
> |
atomData13[11], |
474 |
> |
atomData13[12]); |
475 |
|
|
476 |
|
} |
477 |
|
|
478 |
< |
outFile << writeLine; |
478 |
> |
for(k = 0; k < outFile.size(); k++) |
479 |
> |
*outFile[k] << writeLine; |
480 |
|
} |
481 |
|
|
482 |
< |
|
483 |
< |
outFile.flush(); |
482 |
> |
for(k = 0; k < outFile.size(); k++) |
483 |
> |
outFile[k]->flush(); |
484 |
> |
|
485 |
|
sprintf( checkPointMsg, |
486 |
|
"Sucessfully took a dump.\n"); |
487 |
+ |
|
488 |
|
MPIcheckPoint(); |
489 |
+ |
|
490 |
|
delete[] potatoes; |
491 |
+ |
|
492 |
|
} else { |
493 |
|
|
494 |
|
// worldRank != 0, so I'm a remote node. |
520 |
|
|
521 |
|
atomTypeString = atoms[local_index]->getType(); |
522 |
|
|
523 |
< |
atoms[local_index]->getPos(pos); |
524 |
< |
atoms[local_index]->getVel(vel); |
523 |
> |
atoms[local_index]->getPos(pos); |
524 |
> |
atoms[local_index]->getVel(vel); |
525 |
|
|
526 |
|
atomData6[0] = pos[0]; |
527 |
|
atomData6[1] = pos[1]; |
547 |
|
atomData13[7] = q[1]; |
548 |
|
atomData13[8] = q[2]; |
549 |
|
atomData13[9] = q[3]; |
550 |
< |
|
550 |
> |
|
551 |
|
atomData13[10] = dAtom->getJx(); |
552 |
|
atomData13[11] = dAtom->getJy(); |
553 |
|
atomData13[12] = dAtom->getJz(); |
554 |
|
} |
555 |
|
|
556 |
|
} else { |
557 |
< |
sprintf(painCave.errMsg, |
558 |
< |
"Atom %d not found on processor %d\n", |
559 |
< |
i, worldRank ); |
560 |
< |
haveError= 1; |
561 |
< |
simError(); |
562 |
< |
} |
557 |
> |
sprintf(painCave.errMsg, |
558 |
> |
"Atom %d not found on processor %d\n", |
559 |
> |
i, worldRank ); |
560 |
> |
haveError= 1; |
561 |
> |
simError(); |
562 |
> |
} |
563 |
|
|
564 |
|
strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE); |
565 |
|
|
567 |
|
MPIatomTypeString[MINIBUFFERSIZE-1] = '\0'; |
568 |
|
|
569 |
|
MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0, |
570 |
< |
myPotato, MPI_COMM_WORLD); |
570 |
> |
myPotato, MPI_COMM_WORLD); |
571 |
|
|
572 |
|
myPotato++; |
573 |
|
|
574 |
|
MPI_Send(&isDirectional, 1, MPI_INT, 0, |
575 |
< |
myPotato, MPI_COMM_WORLD); |
575 |
> |
myPotato, MPI_COMM_WORLD); |
576 |
|
|
577 |
|
myPotato++; |
578 |
|
|