3 |
|
#include <string.h> |
4 |
|
#include <iostream> |
5 |
|
#include <fstream> |
6 |
+ |
#include <algorithm> |
7 |
+ |
#include <utility> |
8 |
|
|
9 |
|
#ifdef IS_MPI |
10 |
|
#include <mpi.h> |
28 |
|
if(worldRank == 0 ){ |
29 |
|
#endif // is_mpi |
30 |
|
|
31 |
< |
strcpy( outName, entry_plug->sampleName ); |
31 |
> |
dumpFile.open(entry_plug->sampleName, ios::out | ios::trunc ); |
32 |
|
|
33 |
< |
outFile.open(outName, ios::out | ios::trunc ); |
33 |
> |
if( !dumpFile ){ |
34 |
|
|
33 |
– |
if( !outFile ){ |
34 |
– |
|
35 |
|
sprintf( painCave.errMsg, |
36 |
|
"Could not open \"%s\" for dump output.\n", |
37 |
< |
outName); |
37 |
> |
entry_plug->sampleName); |
38 |
|
painCave.isFatal = 1; |
39 |
|
simError(); |
40 |
|
} |
41 |
|
|
42 |
– |
//outFile.setf( ios::scientific ); |
43 |
– |
|
42 |
|
#ifdef IS_MPI |
43 |
|
} |
44 |
|
|
45 |
+ |
//sort the local atoms by global index |
46 |
+ |
sortByGlobalIndex(); |
47 |
+ |
|
48 |
|
sprintf( checkPointMsg, |
49 |
|
"Sucessfully opened output file for dumping.\n"); |
50 |
|
MPIcheckPoint(); |
57 |
|
if(worldRank == 0 ){ |
58 |
|
#endif // is_mpi |
59 |
|
|
60 |
< |
outFile.close(); |
60 |
> |
dumpFile.close(); |
61 |
|
|
62 |
|
#ifdef IS_MPI |
63 |
|
} |
64 |
|
#endif // is_mpi |
65 |
|
} |
66 |
|
|
67 |
< |
void DumpWriter::writeDump( double currentTime ){ |
67 |
> |
#ifdef IS_MPI |
68 |
|
|
69 |
+ |
/** |
70 |
+ |
* A hook function to load balancing |
71 |
+ |
*/ |
72 |
+ |
|
73 |
+ |
void DumpWriter::update(){ |
74 |
+ |
sortByGlobalIndex(); |
75 |
+ |
} |
76 |
+ |
|
77 |
+ |
/** |
78 |
+ |
* Auxiliary sorting function |
79 |
+ |
*/ |
80 |
+ |
|
81 |
+ |
bool indexSortingCriterion(const pair<int, int>& p1, const pair<int, int>& p2){ |
82 |
+ |
return p1.second < p2.second; |
83 |
+ |
} |
84 |
+ |
|
85 |
+ |
/** |
86 |
+ |
* Sorting the local index by global index |
87 |
+ |
*/ |
88 |
+ |
|
89 |
+ |
void DumpWriter::sortByGlobalIndex(){ |
90 |
+ |
Atom** atoms = entry_plug->atoms; |
91 |
+ |
|
92 |
+ |
indexArray.clear(); |
93 |
+ |
|
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){ |
108 |
+ |
|
109 |
+ |
ofstream finalOut; |
110 |
+ |
vector<ofstream*> fileStreams; |
111 |
+ |
|
112 |
+ |
#ifdef IS_MPI |
113 |
+ |
if(worldRank == 0 ){ |
114 |
+ |
#endif |
115 |
+ |
finalOut.open( entry_plug->finalName, ios::out | ios::trunc ); |
116 |
+ |
if( !finalOut ){ |
117 |
+ |
sprintf( painCave.errMsg, |
118 |
+ |
"Could not open \"%s\" for final dump output.\n", |
119 |
+ |
entry_plug->finalName ); |
120 |
+ |
painCave.isFatal = 1; |
121 |
+ |
simError(); |
122 |
+ |
} |
123 |
+ |
#ifdef IS_MPI |
124 |
+ |
} |
125 |
+ |
#endif // is_mpi |
126 |
+ |
|
127 |
+ |
fileStreams.push_back(&finalOut); |
128 |
+ |
fileStreams.push_back(&dumpFile); |
129 |
+ |
|
130 |
+ |
writeFrame(fileStreams, currentTime); |
131 |
+ |
|
132 |
+ |
#ifdef IS_MPI |
133 |
+ |
finalOut.close(); |
134 |
+ |
#endif |
135 |
+ |
|
136 |
+ |
} |
137 |
+ |
|
138 |
+ |
void DumpWriter::writeFinal(double currentTime){ |
139 |
+ |
|
140 |
+ |
ofstream finalOut; |
141 |
+ |
vector<ofstream*> fileStreams; |
142 |
+ |
|
143 |
+ |
#ifdef IS_MPI |
144 |
+ |
if(worldRank == 0 ){ |
145 |
+ |
#endif // is_mpi |
146 |
+ |
|
147 |
+ |
finalOut.open( entry_plug->finalName, ios::out | ios::trunc ); |
148 |
+ |
|
149 |
+ |
if( !finalOut ){ |
150 |
+ |
sprintf( painCave.errMsg, |
151 |
+ |
"Could not open \"%s\" for final dump output.\n", |
152 |
+ |
entry_plug->finalName ); |
153 |
+ |
painCave.isFatal = 1; |
154 |
+ |
simError(); |
155 |
+ |
} |
156 |
+ |
|
157 |
+ |
#ifdef IS_MPI |
158 |
+ |
} |
159 |
+ |
#endif // is_mpi |
160 |
+ |
|
161 |
+ |
fileStreams.push_back(&finalOut); |
162 |
+ |
writeFrame(fileStreams, currentTime); |
163 |
+ |
|
164 |
+ |
#ifdef IS_MPI |
165 |
+ |
finalOut.close(); |
166 |
+ |
#endif |
167 |
+ |
|
168 |
+ |
} |
169 |
+ |
|
170 |
+ |
void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){ |
171 |
+ |
|
172 |
|
const int BUFFERSIZE = 2000; |
173 |
|
const int MINIBUFFERSIZE = 100; |
174 |
|
|
175 |
< |
char tempBuffer[BUFFERSIZE]; |
175 |
> |
char tempBuffer[BUFFERSIZE]; |
176 |
|
char writeLine[BUFFERSIZE]; |
177 |
|
|
178 |
< |
int i; |
178 |
> |
int i, k; |
179 |
|
|
180 |
|
#ifdef IS_MPI |
181 |
|
|
182 |
+ |
/********************************************************************* |
183 |
+ |
* Documentation? You want DOCUMENTATION? |
184 |
+ |
* |
185 |
+ |
* Why all the potatoes below? |
186 |
+ |
* |
187 |
+ |
* To make a long story short, the original version of DumpWriter |
188 |
+ |
* worked in the most inefficient way possible. Node 0 would |
189 |
+ |
* poke each of the node for an individual atom's formatted data |
190 |
+ |
* as node 0 worked its way down the global index. This was particularly |
191 |
+ |
* inefficient since the method blocked all processors at every atom |
192 |
+ |
* (and did it twice!). |
193 |
+ |
* |
194 |
+ |
* An intermediate version of DumpWriter could be described from Node |
195 |
+ |
* zero's perspective as follows: |
196 |
+ |
* |
197 |
+ |
* 1) Have 100 of your friends stand in a circle. |
198 |
+ |
* 2) When you say go, have all of them start tossing potatoes at |
199 |
+ |
* you (one at a time). |
200 |
+ |
* 3) Catch the potatoes. |
201 |
+ |
* |
202 |
+ |
* It was an improvement, but MPI has buffers and caches that could |
203 |
+ |
* best be described in this analogy as "potato nets", so there's no |
204 |
+ |
* need to block the processors atom-by-atom. |
205 |
+ |
* |
206 |
+ |
* This new and improved DumpWriter works in an even more efficient |
207 |
+ |
* way: |
208 |
+ |
* |
209 |
+ |
* 1) Have 100 of your friend stand in a circle. |
210 |
+ |
* 2) When you say go, have them start tossing 5-pound bags of |
211 |
+ |
* potatoes at you. |
212 |
+ |
* 3) Once you've caught a friend's bag of potatoes, |
213 |
+ |
* toss them a spud to let them know they can toss another bag. |
214 |
+ |
* |
215 |
+ |
* How's THAT for documentation? |
216 |
+ |
* |
217 |
+ |
*********************************************************************/ |
218 |
+ |
|
219 |
|
int *potatoes; |
220 |
|
int myPotato; |
221 |
|
|
222 |
|
int nProc; |
223 |
< |
int j, which_node, done, which_atom, local_index; |
223 |
> |
int j, which_node, done, which_atom, local_index, currentIndex; |
224 |
|
double atomData6[6]; |
225 |
|
double atomData13[13]; |
226 |
|
int isDirectional; |
236 |
|
Atom** atoms = entry_plug->atoms; |
237 |
|
double pos[3], vel[3]; |
238 |
|
|
98 |
– |
// write current frame to the eor file |
99 |
– |
|
100 |
– |
this->writeFinal( currentTime ); |
101 |
– |
|
239 |
|
#ifndef IS_MPI |
240 |
+ |
|
241 |
+ |
for(k = 0; k < outFile.size(); k++){ |
242 |
+ |
*outFile[k] << nAtoms << "\n"; |
243 |
|
|
244 |
< |
outFile << nAtoms << "\n"; |
244 |
> |
*outFile[k] << currentTime << ";\t" |
245 |
> |
<< entry_plug->Hmat[0][0] << "\t" |
246 |
> |
<< entry_plug->Hmat[1][0] << "\t" |
247 |
> |
<< entry_plug->Hmat[2][0] << ";\t" |
248 |
> |
|
249 |
> |
<< entry_plug->Hmat[0][1] << "\t" |
250 |
> |
<< entry_plug->Hmat[1][1] << "\t" |
251 |
> |
<< entry_plug->Hmat[2][1] << ";\t" |
252 |
|
|
253 |
< |
outFile << currentTime << ";\t" |
254 |
< |
<< entry_plug->Hmat[0][0] << "\t" |
255 |
< |
<< entry_plug->Hmat[1][0] << "\t" |
109 |
< |
<< entry_plug->Hmat[2][0] << ";\t" |
253 |
> |
<< entry_plug->Hmat[0][2] << "\t" |
254 |
> |
<< entry_plug->Hmat[1][2] << "\t" |
255 |
> |
<< entry_plug->Hmat[2][2] << ";"; |
256 |
|
|
257 |
< |
<< entry_plug->Hmat[0][1] << "\t" |
258 |
< |
<< entry_plug->Hmat[1][1] << "\t" |
259 |
< |
<< entry_plug->Hmat[2][1] << ";\t" |
260 |
< |
|
115 |
< |
<< entry_plug->Hmat[0][2] << "\t" |
116 |
< |
<< entry_plug->Hmat[1][2] << "\t" |
117 |
< |
<< entry_plug->Hmat[2][2] << ";"; |
118 |
< |
//write out additional parameters, such as chi and eta |
119 |
< |
outFile << entry_plug->the_integrator->getAdditionalParameters(); |
120 |
< |
outFile << endl; |
121 |
< |
|
257 |
> |
//write out additional parameters, such as chi and eta |
258 |
> |
*outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl; |
259 |
> |
} |
260 |
> |
|
261 |
|
for( i=0; i<nAtoms; i++ ){ |
262 |
|
|
263 |
|
atoms[i]->getPos(pos); |
293 |
|
else |
294 |
|
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
295 |
|
|
296 |
< |
outFile << writeLine; |
296 |
> |
for(k = 0; k < outFile.size(); k++) |
297 |
> |
*outFile[k] << writeLine; |
298 |
|
} |
159 |
– |
outFile.flush(); |
299 |
|
|
300 |
|
#else // is_mpi |
301 |
|
|
323 |
|
nProc = mpiSim->getNumberProcessors(); |
324 |
|
potatoes = new int[nProc]; |
325 |
|
|
326 |
+ |
//write out the comment lines |
327 |
|
for (i = 0; i < nProc; i++) |
328 |
|
potatoes[i] = 0; |
329 |
|
|
330 |
< |
outFile << mpiSim->getTotAtoms() << "\n"; |
330 |
> |
for(k = 0; k < outFile.size(); k++){ |
331 |
> |
*outFile[k] << mpiSim->getTotAtoms() << "\n"; |
332 |
|
|
333 |
< |
outFile << currentTime << ";\t" |
334 |
< |
<< entry_plug->Hmat[0][0] << "\t" |
335 |
< |
<< entry_plug->Hmat[1][0] << "\t" |
336 |
< |
<< entry_plug->Hmat[2][0] << ";\t" |
333 |
> |
*outFile[k] << currentTime << ";\t" |
334 |
> |
<< entry_plug->Hmat[0][0] << "\t" |
335 |
> |
<< entry_plug->Hmat[1][0] << "\t" |
336 |
> |
<< entry_plug->Hmat[2][0] << ";\t" |
337 |
|
|
338 |
< |
<< entry_plug->Hmat[0][1] << "\t" |
339 |
< |
<< entry_plug->Hmat[1][1] << "\t" |
340 |
< |
<< entry_plug->Hmat[2][1] << ";\t" |
338 |
> |
<< entry_plug->Hmat[0][1] << "\t" |
339 |
> |
<< entry_plug->Hmat[1][1] << "\t" |
340 |
> |
<< entry_plug->Hmat[2][1] << ";\t" |
341 |
|
|
342 |
< |
<< entry_plug->Hmat[0][2] << "\t" |
343 |
< |
<< entry_plug->Hmat[1][2] << "\t" |
344 |
< |
<< entry_plug->Hmat[2][2] << ";"; |
342 |
> |
<< entry_plug->Hmat[0][2] << "\t" |
343 |
> |
<< entry_plug->Hmat[1][2] << "\t" |
344 |
> |
<< entry_plug->Hmat[2][2] << ";"; |
345 |
> |
|
346 |
> |
*outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl; |
347 |
> |
} |
348 |
|
|
349 |
< |
outFile << entry_plug->the_integrator->getAdditionalParameters(); |
206 |
< |
outFile << endl; |
207 |
< |
outFile.flush(); |
349 |
> |
currentIndex = 0; |
350 |
|
|
351 |
|
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
352 |
|
|
370 |
|
MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node, |
371 |
|
myPotato, MPI_COMM_WORLD, &istatus); |
372 |
|
|
231 |
– |
//strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE); |
232 |
– |
|
233 |
– |
// Null terminate the atomTypeString just in case: |
234 |
– |
|
235 |
– |
//atomTypeString[strlen(atomTypeString) - 1] = '\0'; |
373 |
|
atomTypeString = MPIatomTypeString; |
374 |
|
|
375 |
|
myPotato++; |
392 |
|
|
393 |
|
} else { |
394 |
|
|
395 |
< |
haveError = 0; |
395 |
> |
haveError = 0; |
396 |
|
which_atom = i; |
260 |
– |
local_index=-1; |
397 |
|
|
398 |
< |
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
399 |
< |
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
400 |
< |
} |
398 |
> |
//local_index = -1; |
399 |
> |
|
400 |
> |
//for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
401 |
> |
// if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
402 |
> |
//} |
403 |
|
|
404 |
< |
if (local_index != -1) { |
404 |
> |
//if (local_index != -1) { |
405 |
> |
|
406 |
> |
local_index = indexArray[currentIndex].first; |
407 |
|
|
408 |
< |
atomTypeString = atoms[local_index]->getType(); |
409 |
< |
|
408 |
> |
if (which_atom == indexArray[currentIndex].second) { |
409 |
> |
|
410 |
> |
atomTypeString = atoms[local_index]->getType(); |
411 |
> |
|
412 |
|
atoms[local_index]->getPos(pos); |
413 |
|
atoms[local_index]->getVel(vel); |
414 |
< |
|
414 |
> |
|
415 |
|
atomData6[0] = pos[0]; |
416 |
|
atomData6[1] = pos[1]; |
417 |
|
atomData6[2] = pos[2]; |
444 |
|
|
445 |
|
} else { |
446 |
|
sprintf(painCave.errMsg, |
447 |
< |
"Atom %d not found on processor %d\n", |
448 |
< |
i, worldRank ); |
447 |
> |
"Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n", |
448 |
> |
which_atom, worldRank, currentIndex, local_index ); |
449 |
|
haveError= 1; |
450 |
|
simError(); |
451 |
|
} |
452 |
|
|
453 |
< |
if(haveError) DieDieDie(); |
453 |
> |
if(haveError) DieDieDie(); |
454 |
|
|
455 |
+ |
currentIndex++; |
456 |
|
} |
457 |
|
// If we've survived to here, format the line: |
458 |
|
|
459 |
|
if (!isDirectional) { |
460 |
|
|
461 |
< |
sprintf( tempBuffer, |
461 |
> |
sprintf( writeLine, |
462 |
|
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
463 |
|
atomTypeString, |
464 |
|
atomData6[0], |
468 |
|
atomData6[4], |
469 |
|
atomData6[5]); |
470 |
|
|
328 |
– |
strcpy( writeLine, tempBuffer ); |
471 |
|
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
472 |
|
|
473 |
|
} else { |
474 |
|
|
475 |
< |
sprintf( tempBuffer, |
475 |
> |
sprintf( writeLine, |
476 |
|
"%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", |
477 |
|
atomTypeString, |
478 |
|
atomData13[0], |
488 |
|
atomData13[10], |
489 |
|
atomData13[11], |
490 |
|
atomData13[12]); |
349 |
– |
|
350 |
– |
strcat( writeLine, tempBuffer ); |
491 |
|
|
492 |
|
} |
493 |
|
|
494 |
< |
outFile << writeLine; |
495 |
< |
outFile.flush(); |
494 |
> |
for(k = 0; k < outFile.size(); k++) |
495 |
> |
*outFile[k] << writeLine; |
496 |
|
} |
497 |
|
|
498 |
< |
|
499 |
< |
outFile.flush(); |
498 |
> |
for(k = 0; k < outFile.size(); k++) |
499 |
> |
outFile[k]->flush(); |
500 |
> |
|
501 |
|
sprintf( checkPointMsg, |
502 |
|
"Sucessfully took a dump.\n"); |
503 |
+ |
|
504 |
|
MPIcheckPoint(); |
505 |
+ |
|
506 |
|
delete[] potatoes; |
507 |
+ |
|
508 |
|
} else { |
509 |
|
|
510 |
|
// worldRank != 0, so I'm a remote node. |
512 |
|
// Set my magic potato to 0: |
513 |
|
|
514 |
|
myPotato = 0; |
515 |
+ |
currentIndex = 0; |
516 |
|
|
517 |
|
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
518 |
|
|
521 |
|
if (AtomToProcMap[i] == worldRank) { |
522 |
|
|
523 |
|
if (myPotato + 3 >= MAXTAG) { |
524 |
< |
|
524 |
> |
|
525 |
|
// The potato was going to exceed the maximum value, |
526 |
|
// so wrap this processor potato back to 0 (and block until |
527 |
|
// node 0 says we can go: |
528 |
< |
|
528 |
> |
|
529 |
|
MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus); |
530 |
|
|
531 |
|
} |
532 |
|
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 |
– |
} |
392 |
– |
if (local_index != -1) { |
393 |
– |
|
394 |
– |
atomTypeString = atoms[local_index]->getType(); |
533 |
|
|
534 |
< |
atoms[local_index]->getPos(pos); |
397 |
< |
atoms[local_index]->getVel(vel); |
534 |
> |
//local_index = -1; |
535 |
|
|
536 |
< |
atomData6[0] = pos[0]; |
537 |
< |
atomData6[1] = pos[1]; |
538 |
< |
atomData6[2] = pos[2]; |
402 |
< |
|
403 |
< |
atomData6[3] = vel[0]; |
404 |
< |
atomData6[4] = vel[1]; |
405 |
< |
atomData6[5] = vel[2]; |
406 |
< |
|
407 |
< |
isDirectional = 0; |
408 |
< |
|
409 |
< |
if( atoms[local_index]->isDirectional() ){ |
410 |
< |
|
411 |
< |
isDirectional = 1; |
412 |
< |
|
413 |
< |
dAtom = (DirectionalAtom *)atoms[local_index]; |
414 |
< |
dAtom->getQ( q ); |
415 |
< |
|
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 |
< |
atomData13[10] = dAtom->getJx(); |
425 |
< |
atomData13[11] = dAtom->getJy(); |
426 |
< |
atomData13[12] = dAtom->getJz(); |
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 |
< |
} |
436 |
< |
|
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 |
< |
myPotato, MPI_COMM_WORLD); |
536 |
> |
//for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
537 |
> |
// if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
538 |
> |
//} |
539 |
|
|
540 |
< |
myPotato++; |
540 |
> |
//if (local_index != -1) { |
541 |
|
|
542 |
< |
MPI_Send(&isDirectional, 1, MPI_INT, 0, |
448 |
< |
myPotato, MPI_COMM_WORLD); |
449 |
< |
|
450 |
< |
myPotato++; |
451 |
< |
|
452 |
< |
if (isDirectional) { |
453 |
< |
|
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 |
< |
|
463 |
< |
myPotato++; |
464 |
< |
} |
465 |
< |
} |
466 |
< |
|
467 |
< |
sprintf( checkPointMsg, |
468 |
< |
"Sucessfully took a dump.\n"); |
469 |
< |
MPIcheckPoint(); |
470 |
< |
|
471 |
< |
} |
472 |
< |
|
473 |
< |
#endif // is_mpi |
474 |
< |
} |
475 |
< |
|
476 |
< |
void DumpWriter::writeFinal(double finalTime){ |
477 |
< |
|
478 |
< |
char finalName[500]; |
479 |
< |
ofstream finalOut; |
480 |
< |
|
481 |
< |
const int BUFFERSIZE = 2000; |
482 |
< |
const int MINIBUFFERSIZE = 100; |
483 |
< |
char tempBuffer[BUFFERSIZE]; |
484 |
< |
char writeLine[BUFFERSIZE]; |
485 |
< |
|
486 |
< |
double q[4]; |
487 |
< |
DirectionalAtom* dAtom; |
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 atomData6[6]; |
498 |
< |
double atomData13[13]; |
499 |
< |
int isDirectional; |
500 |
< |
char* atomTypeString; |
501 |
< |
char MPIatomTypeString[MINIBUFFERSIZE]; |
502 |
< |
|
503 |
< |
#else //is_mpi |
504 |
< |
int nAtoms = entry_plug->n_atoms; |
505 |
< |
#endif //is_mpi |
506 |
< |
|
507 |
< |
double pos[3], vel[3]; |
508 |
< |
|
509 |
< |
#ifdef IS_MPI |
510 |
< |
if(worldRank == 0 ){ |
511 |
< |
#endif // is_mpi |
512 |
< |
|
513 |
< |
strcpy( finalName, entry_plug->finalName ); |
514 |
< |
|
515 |
< |
finalOut.open( finalName, ios::out | ios::trunc ); |
516 |
< |
if( !finalOut ){ |
517 |
< |
sprintf( painCave.errMsg, |
518 |
< |
"Could not open \"%s\" for final dump output.\n", |
519 |
< |
finalName ); |
520 |
< |
painCave.isFatal = 1; |
521 |
< |
simError(); |
522 |
< |
} |
523 |
< |
|
524 |
< |
// finalOut.setf( ios::scientific ); |
525 |
< |
|
526 |
< |
#ifdef IS_MPI |
527 |
< |
} |
528 |
< |
|
529 |
< |
sprintf(checkPointMsg,"Opened file for final configuration\n"); |
530 |
< |
MPIcheckPoint(); |
531 |
< |
|
532 |
< |
#endif //is_mpi |
533 |
< |
|
534 |
< |
|
535 |
< |
#ifndef IS_MPI |
536 |
< |
|
537 |
< |
finalOut << nAtoms << "\n"; |
538 |
< |
|
539 |
< |
finalOut << finalTime << ";\t" |
540 |
< |
<< entry_plug->Hmat[0][0] << "\t" |
541 |
< |
<< entry_plug->Hmat[1][0] << "\t" |
542 |
< |
<< entry_plug->Hmat[2][0] << ";\t" |
543 |
< |
|
544 |
< |
<< entry_plug->Hmat[0][1] << "\t" |
545 |
< |
<< entry_plug->Hmat[1][1] << "\t" |
546 |
< |
<< entry_plug->Hmat[2][1] << ";\t" |
547 |
< |
|
548 |
< |
<< entry_plug->Hmat[0][2] << "\t" |
549 |
< |
<< entry_plug->Hmat[1][2] << "\t" |
550 |
< |
<< entry_plug->Hmat[2][2] << ";"; |
551 |
< |
|
552 |
< |
//write out additional parameters, such as chi and eta |
553 |
< |
finalOut << entry_plug->the_integrator->getAdditionalParameters(); |
554 |
< |
finalOut << endl; |
555 |
< |
|
556 |
< |
for( i=0; i<nAtoms; i++ ){ |
557 |
< |
|
558 |
< |
atoms[i]->getPos(pos); |
559 |
< |
atoms[i]->getVel(vel); |
560 |
< |
|
561 |
< |
sprintf( tempBuffer, |
562 |
< |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
563 |
< |
atoms[i]->getType(), |
564 |
< |
pos[0], |
565 |
< |
pos[1], |
566 |
< |
pos[2], |
567 |
< |
vel[0], |
568 |
< |
vel[1], |
569 |
< |
vel[2]); |
570 |
< |
strcpy( writeLine, tempBuffer ); |
571 |
< |
|
572 |
< |
if( atoms[i]->isDirectional() ){ |
573 |
< |
|
574 |
< |
dAtom = (DirectionalAtom *)atoms[i]; |
575 |
< |
dAtom->getQ( q ); |
576 |
< |
|
577 |
< |
sprintf( tempBuffer, |
578 |
< |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
579 |
< |
q[0], |
580 |
< |
q[1], |
581 |
< |
q[2], |
582 |
< |
q[3], |
583 |
< |
dAtom->getJx(), |
584 |
< |
dAtom->getJy(), |
585 |
< |
dAtom->getJz()); |
586 |
< |
strcat( writeLine, tempBuffer ); |
587 |
< |
} |
588 |
< |
else |
589 |
< |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
590 |
< |
|
591 |
< |
finalOut << writeLine; |
592 |
< |
} |
593 |
< |
finalOut.flush(); |
594 |
< |
finalOut.close(); |
595 |
< |
|
596 |
< |
#else // is_mpi |
597 |
< |
|
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 |
< |
|
607 |
< |
int haveError; |
608 |
< |
|
609 |
< |
MPI_Status istatus; |
610 |
< |
int *AtomToProcMap = mpiSim->getAtomToProcMap(); |
611 |
< |
|
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" |
627 |
< |
<< entry_plug->Hmat[0][0] << "\t" |
628 |
< |
<< entry_plug->Hmat[1][0] << "\t" |
629 |
< |
<< entry_plug->Hmat[2][0] << ";\t" |
630 |
< |
|
631 |
< |
<< entry_plug->Hmat[0][1] << "\t" |
632 |
< |
<< entry_plug->Hmat[1][1] << "\t" |
633 |
< |
<< entry_plug->Hmat[2][1] << ";\t" |
634 |
< |
|
635 |
< |
<< entry_plug->Hmat[0][2] << "\t" |
636 |
< |
<< entry_plug->Hmat[1][2] << "\t" |
637 |
< |
<< entry_plug->Hmat[2][2] << ";"; |
638 |
< |
|
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 |
< |
|
647 |
< |
which_node = AtomToProcMap[i]; |
648 |
< |
|
649 |
< |
if (which_node != 0) { |
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 |
< |
myPotato, MPI_COMM_WORLD, &istatus); |
664 |
< |
|
665 |
< |
atomTypeString = MPIatomTypeString; |
542 |
> |
local_index = indexArray[currentIndex].first; |
543 |
|
|
544 |
< |
myPotato++; |
668 |
< |
|
669 |
< |
MPI_Recv(&isDirectional, 1, MPI_INT, which_node, |
670 |
< |
myPotato, MPI_COMM_WORLD, &istatus); |
671 |
< |
|
672 |
< |
myPotato++; |
673 |
< |
|
674 |
< |
if (isDirectional) { |
675 |
< |
MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node, |
676 |
< |
myPotato, MPI_COMM_WORLD, &istatus); |
677 |
< |
} else { |
678 |
< |
printf("inside \n"); |
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 |
< |
|
692 |
< |
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
693 |
< |
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
694 |
< |
} |
695 |
< |
|
696 |
< |
if (local_index != -1) { |
697 |
< |
|
698 |
< |
atomTypeString = atoms[local_index]->getType(); |
699 |
< |
|
700 |
< |
atoms[local_index]->getPos(pos); |
701 |
< |
atoms[local_index]->getVel(vel); |
702 |
< |
|
703 |
< |
atomData6[0] = pos[0]; |
704 |
< |
atomData6[1] = pos[1]; |
705 |
< |
atomData6[2] = pos[2]; |
706 |
< |
|
707 |
< |
atomData6[3] = vel[0]; |
708 |
< |
atomData6[4] = vel[1]; |
709 |
< |
atomData6[5] = vel[2]; |
710 |
< |
|
711 |
< |
isDirectional = 0; |
712 |
< |
|
713 |
< |
if( atoms[local_index]->isDirectional() ){ |
714 |
< |
|
715 |
< |
isDirectional = 1; |
716 |
< |
|
717 |
< |
dAtom = (DirectionalAtom *)atoms[local_index]; |
718 |
< |
dAtom->getQ( q ); |
719 |
< |
|
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 |
< |
|
733 |
< |
} else { |
734 |
< |
sprintf(painCave.errMsg, |
735 |
< |
"Atom %d not found on processor %d\n", |
736 |
< |
i, worldRank ); |
737 |
< |
haveError= 1; |
738 |
< |
simError(); |
739 |
< |
} |
740 |
< |
|
741 |
< |
if(haveError) DieDieDie(); |
742 |
< |
|
743 |
< |
} |
744 |
< |
|
745 |
< |
|
746 |
< |
// If we've survived to here, format the line: |
747 |
< |
|
748 |
< |
if (!isDirectional) { |
749 |
< |
|
750 |
< |
sprintf( tempBuffer, |
751 |
< |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
752 |
< |
atomTypeString, |
753 |
< |
atomData6[0], |
754 |
< |
atomData6[1], |
755 |
< |
atomData6[2], |
756 |
< |
atomData6[3], |
757 |
< |
atomData6[4], |
758 |
< |
atomData6[5]); |
759 |
< |
|
760 |
< |
strcpy( writeLine, tempBuffer ); |
761 |
< |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
762 |
< |
|
763 |
< |
} else { |
764 |
< |
|
765 |
< |
sprintf( tempBuffer, |
766 |
< |
"%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", |
767 |
< |
atomTypeString, |
768 |
< |
atomData13[0], |
769 |
< |
atomData13[1], |
770 |
< |
atomData13[2], |
771 |
< |
atomData13[3], |
772 |
< |
atomData13[4], |
773 |
< |
atomData13[5], |
774 |
< |
atomData13[6], |
775 |
< |
atomData13[7], |
776 |
< |
atomData13[8], |
777 |
< |
atomData13[9], |
778 |
< |
atomData13[10], |
779 |
< |
atomData13[11], |
780 |
< |
atomData13[12]); |
781 |
< |
|
782 |
< |
strcat( writeLine, tempBuffer ); |
783 |
< |
|
784 |
< |
} |
785 |
< |
|
786 |
< |
finalOut << writeLine; |
787 |
< |
finalOut.flush(); |
788 |
< |
} |
789 |
< |
|
790 |
< |
finalOut.flush(); |
791 |
< |
sprintf( checkPointMsg, |
792 |
< |
"Sucessfully took a dump.\n"); |
793 |
< |
delete[] potatoes; |
794 |
< |
|
795 |
< |
MPIcheckPoint(); |
796 |
< |
|
797 |
< |
} else { |
798 |
< |
|
799 |
< |
// worldRank != 0, so I'm a remote node. |
800 |
< |
|
801 |
< |
// Set my magic potato to 0: |
802 |
< |
|
803 |
< |
myPotato = 0; |
804 |
< |
|
805 |
< |
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
806 |
< |
|
807 |
< |
// Am I the node which has this atom? |
808 |
< |
|
809 |
< |
if (AtomToProcMap[i] == worldRank) { |
810 |
< |
|
811 |
< |
if (myPotato + 3 >= MAXTAG) { |
812 |
< |
|
813 |
< |
// The potato was going to exceed the maximum value, |
814 |
< |
// so wrap this processor potato back to 0 (and block until |
815 |
< |
// node 0 says we can go: |
816 |
< |
|
817 |
< |
MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus); |
818 |
< |
|
819 |
< |
} |
820 |
< |
which_atom = i; |
821 |
< |
local_index=-1; |
822 |
< |
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
823 |
< |
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
824 |
< |
} |
825 |
< |
if (local_index != -1) { |
544 |
> |
if (which_atom == indexArray[currentIndex].second) { |
545 |
|
|
546 |
|
atomTypeString = atoms[local_index]->getType(); |
547 |
< |
|
547 |
> |
|
548 |
|
atoms[local_index]->getPos(pos); |
549 |
|
atoms[local_index]->getVel(vel); |
550 |
< |
|
550 |
> |
|
551 |
|
atomData6[0] = pos[0]; |
552 |
|
atomData6[1] = pos[1]; |
553 |
|
atomData6[2] = pos[2]; |
572 |
|
atomData13[7] = q[1]; |
573 |
|
atomData13[8] = q[2]; |
574 |
|
atomData13[9] = q[3]; |
575 |
< |
|
575 |
> |
|
576 |
|
atomData13[10] = dAtom->getJx(); |
577 |
|
atomData13[11] = dAtom->getJy(); |
578 |
|
atomData13[12] = dAtom->getJz(); |
580 |
|
|
581 |
|
} else { |
582 |
|
sprintf(painCave.errMsg, |
583 |
< |
"Atom %d not found on processor %d\n", |
584 |
< |
i, worldRank ); |
583 |
> |
"Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n", |
584 |
> |
which_atom, worldRank, currentIndex, local_index ); |
585 |
|
haveError= 1; |
586 |
|
simError(); |
587 |
|
} |
588 |
< |
|
588 |
> |
|
589 |
|
strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE); |
590 |
|
|
591 |
|
// null terminate the string before sending (just in case): |
592 |
|
MPIatomTypeString[MINIBUFFERSIZE-1] = '\0'; |
593 |
|
|
594 |
|
MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0, |
595 |
< |
myPotato, MPI_COMM_WORLD); |
595 |
> |
myPotato, MPI_COMM_WORLD); |
596 |
|
|
597 |
|
myPotato++; |
598 |
|
|
599 |
|
MPI_Send(&isDirectional, 1, MPI_INT, 0, |
600 |
< |
myPotato, MPI_COMM_WORLD); |
600 |
> |
myPotato, MPI_COMM_WORLD); |
601 |
|
|
602 |
|
myPotato++; |
603 |
|
|
612 |
|
myPotato, MPI_COMM_WORLD); |
613 |
|
} |
614 |
|
|
615 |
< |
myPotato++; |
615 |
> |
myPotato++; |
616 |
> |
currentIndex++; |
617 |
|
} |
618 |
|
} |
619 |
|
|
623 |
|
|
624 |
|
} |
625 |
|
|
906 |
– |
if( worldRank == 0 ) finalOut.close(); |
626 |
|
#endif // is_mpi |
627 |
|
} |
628 |
|
|
910 |
– |
|
911 |
– |
|
629 |
|
#ifdef IS_MPI |
630 |
|
|
631 |
|
// a couple of functions to let us escape the write loop |