1 |
#define _LARGEFILE_SOURCE64 |
2 |
#define _FILE_OFFSET_BITS 64 |
3 |
|
4 |
#include <string.h> |
5 |
#include <iostream> |
6 |
#include <fstream> |
7 |
#include <algorithm> |
8 |
#include <utility> |
9 |
|
10 |
#ifdef IS_MPI |
11 |
#include <mpi.h> |
12 |
#include "mpiSimulation.hpp" |
13 |
|
14 |
namespace dWrite{ |
15 |
void DieDieDie( void ); |
16 |
} |
17 |
|
18 |
using namespace dWrite; |
19 |
#endif //is_mpi |
20 |
|
21 |
#include "ReadWrite.hpp" |
22 |
#include "simError.h" |
23 |
|
24 |
DumpWriter::DumpWriter( SimInfo* the_entry_plug ){ |
25 |
|
26 |
entry_plug = the_entry_plug; |
27 |
|
28 |
#ifdef IS_MPI |
29 |
if(worldRank == 0 ){ |
30 |
#endif // is_mpi |
31 |
|
32 |
dumpFile.open(entry_plug->sampleName, ios::out | ios::trunc ); |
33 |
|
34 |
if( !dumpFile ){ |
35 |
|
36 |
sprintf( painCave.errMsg, |
37 |
"Could not open \"%s\" for dump output.\n", |
38 |
entry_plug->sampleName); |
39 |
painCave.isFatal = 1; |
40 |
simError(); |
41 |
} |
42 |
|
43 |
#ifdef IS_MPI |
44 |
} |
45 |
|
46 |
//sort the local atoms by global index |
47 |
sortByGlobalIndex(); |
48 |
|
49 |
sprintf( checkPointMsg, |
50 |
"Sucessfully opened output file for dumping.\n"); |
51 |
MPIcheckPoint(); |
52 |
#endif // is_mpi |
53 |
} |
54 |
|
55 |
DumpWriter::~DumpWriter( ){ |
56 |
|
57 |
#ifdef IS_MPI |
58 |
if(worldRank == 0 ){ |
59 |
#endif // is_mpi |
60 |
|
61 |
dumpFile.close(); |
62 |
|
63 |
#ifdef IS_MPI |
64 |
} |
65 |
#endif // is_mpi |
66 |
} |
67 |
|
68 |
#ifdef IS_MPI |
69 |
|
70 |
/** |
71 |
* A hook function to load balancing |
72 |
*/ |
73 |
|
74 |
void DumpWriter::update(){ |
75 |
sortByGlobalIndex(); |
76 |
} |
77 |
|
78 |
/** |
79 |
* Auxiliary sorting function |
80 |
*/ |
81 |
|
82 |
bool indexSortingCriterion(const pair<int, int>& p1, const pair<int, int>& p2){ |
83 |
return p1.second < p2.second; |
84 |
} |
85 |
|
86 |
/** |
87 |
* Sorting the local index by global index |
88 |
*/ |
89 |
|
90 |
void DumpWriter::sortByGlobalIndex(){ |
91 |
Molecule* mols = entry_plug->molecules; |
92 |
indexArray.clear(); |
93 |
|
94 |
for(int i = 0; i < entry_plug->n_mol;i++) |
95 |
indexArray.push_back(make_pair(i, mols[i].getGlobalIndex())); |
96 |
|
97 |
sort(indexArray.begin(), indexArray.end(), indexSortingCriterion); |
98 |
} |
99 |
|
100 |
#endif |
101 |
|
102 |
void DumpWriter::writeDump(double currentTime){ |
103 |
|
104 |
ofstream finalOut; |
105 |
vector<ofstream*> fileStreams; |
106 |
|
107 |
#ifdef IS_MPI |
108 |
if(worldRank == 0 ){ |
109 |
#endif |
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 |
#ifdef IS_MPI |
119 |
} |
120 |
#endif // is_mpi |
121 |
|
122 |
fileStreams.push_back(&finalOut); |
123 |
fileStreams.push_back(&dumpFile); |
124 |
|
125 |
writeFrame(fileStreams, currentTime); |
126 |
|
127 |
#ifdef IS_MPI |
128 |
finalOut.close(); |
129 |
#endif |
130 |
|
131 |
} |
132 |
|
133 |
void DumpWriter::writeFinal(double currentTime){ |
134 |
|
135 |
ofstream finalOut; |
136 |
vector<ofstream*> fileStreams; |
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 |
|
144 |
if( !finalOut ){ |
145 |
sprintf( painCave.errMsg, |
146 |
"Could not open \"%s\" for final dump output.\n", |
147 |
entry_plug->finalName ); |
148 |
painCave.isFatal = 1; |
149 |
simError(); |
150 |
} |
151 |
|
152 |
#ifdef IS_MPI |
153 |
} |
154 |
#endif // is_mpi |
155 |
|
156 |
fileStreams.push_back(&finalOut); |
157 |
writeFrame(fileStreams, currentTime); |
158 |
|
159 |
#ifdef IS_MPI |
160 |
finalOut.close(); |
161 |
#endif |
162 |
|
163 |
} |
164 |
|
165 |
void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){ |
166 |
|
167 |
const int BUFFERSIZE = 2000; |
168 |
const int MINIBUFFERSIZE = 100; |
169 |
|
170 |
char tempBuffer[BUFFERSIZE]; |
171 |
char writeLine[BUFFERSIZE]; |
172 |
|
173 |
int i, k; |
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. |
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* 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 |
|
217 |
int nProc; |
218 |
int j, which_node, done, which_atom, local_index, currentIndex; |
219 |
double atomData6[6]; |
220 |
double atomData13[13]; |
221 |
int isDirectional; |
222 |
char* atomTypeString; |
223 |
char MPIatomTypeString[MINIBUFFERSIZE]; |
224 |
int nObjects; |
225 |
#endif //is_mpi |
226 |
|
227 |
double q[4], ji[3]; |
228 |
DirectionalAtom* dAtom; |
229 |
double pos[3], vel[3]; |
230 |
int nTotObjects; |
231 |
StuntDouble* sd; |
232 |
char* molName; |
233 |
vector<StuntDouble*> integrableObjects; |
234 |
vector<StuntDouble*>::iterator iter; |
235 |
nTotObjects = entry_plug->getTotIntegrableObjects(); |
236 |
#ifndef IS_MPI |
237 |
|
238 |
for(k = 0; k < outFile.size(); k++){ |
239 |
*outFile[k] << nTotObjects << "\n"; |
240 |
|
241 |
*outFile[k] << currentTime << ";\t" |
242 |
<< entry_plug->Hmat[0][0] << "\t" |
243 |
<< entry_plug->Hmat[1][0] << "\t" |
244 |
<< entry_plug->Hmat[2][0] << ";\t" |
245 |
|
246 |
<< entry_plug->Hmat[0][1] << "\t" |
247 |
<< entry_plug->Hmat[1][1] << "\t" |
248 |
<< entry_plug->Hmat[2][1] << ";\t" |
249 |
|
250 |
<< entry_plug->Hmat[0][2] << "\t" |
251 |
<< entry_plug->Hmat[1][2] << "\t" |
252 |
<< entry_plug->Hmat[2][2] << ";"; |
253 |
|
254 |
//write out additional parameters, such as chi and eta |
255 |
*outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl; |
256 |
} |
257 |
|
258 |
for( i=0; i< entry_plug->n_mol; i++ ){ |
259 |
|
260 |
integrableObjects = entry_plug->molecules[i].getIntegrableObjects(); |
261 |
molName = (entry_plug->compStamps[entry_plug->molecules[i].getStampID()])->getID(); |
262 |
|
263 |
for( iter = integrableObjects.begin();iter != integrableObjects.end(); ++iter){ |
264 |
sd = *iter; |
265 |
sd->getPos(pos); |
266 |
sd->getVel(vel); |
267 |
|
268 |
sprintf( tempBuffer, |
269 |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
270 |
sd->getType(), |
271 |
pos[0], |
272 |
pos[1], |
273 |
pos[2], |
274 |
vel[0], |
275 |
vel[1], |
276 |
vel[2]); |
277 |
strcpy( writeLine, tempBuffer ); |
278 |
|
279 |
if( sd->isDirectional() ){ |
280 |
|
281 |
sd->getQ( q ); |
282 |
sd->getJ( ji ); |
283 |
|
284 |
sprintf( tempBuffer, |
285 |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
286 |
q[0], |
287 |
q[1], |
288 |
q[2], |
289 |
q[3], |
290 |
ji[0], |
291 |
ji[1], |
292 |
ji[2]); |
293 |
strcat( writeLine, tempBuffer ); |
294 |
} |
295 |
else |
296 |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
297 |
} |
298 |
|
299 |
|
300 |
for(k = 0; k < outFile.size(); k++) |
301 |
*outFile[k] << writeLine; |
302 |
} |
303 |
|
304 |
#else // is_mpi |
305 |
|
306 |
/* code to find maximum tag value */ |
307 |
|
308 |
int *tagub, flag, MAXTAG; |
309 |
MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag); |
310 |
if (flag) { |
311 |
MAXTAG = *tagub; |
312 |
} else { |
313 |
MAXTAG = 32767; |
314 |
} |
315 |
|
316 |
int haveError; |
317 |
|
318 |
MPI_Status istatus; |
319 |
int nCurObj; |
320 |
int *MolToProcMap = mpiSim->getMolToProcMap(); |
321 |
|
322 |
// write out header and node 0's coordinates |
323 |
|
324 |
if( worldRank == 0 ){ |
325 |
|
326 |
// Node 0 needs a list of the magic potatoes for each processor; |
327 |
|
328 |
nProc = mpiSim->getNumberProcessors(); |
329 |
potatoes = new int[nProc]; |
330 |
|
331 |
//write out the comment lines |
332 |
for (i = 0; i < nProc; i++) |
333 |
potatoes[i] = 0; |
334 |
|
335 |
for(k = 0; k < outFile.size(); k++){ |
336 |
*outFile[k] << nTotObjects << "\n"; |
337 |
|
338 |
*outFile[k] << currentTime << ";\t" |
339 |
<< entry_plug->Hmat[0][0] << "\t" |
340 |
<< entry_plug->Hmat[1][0] << "\t" |
341 |
<< entry_plug->Hmat[2][0] << ";\t" |
342 |
|
343 |
<< entry_plug->Hmat[0][1] << "\t" |
344 |
<< entry_plug->Hmat[1][1] << "\t" |
345 |
<< entry_plug->Hmat[2][1] << ";\t" |
346 |
|
347 |
<< entry_plug->Hmat[0][2] << "\t" |
348 |
<< entry_plug->Hmat[1][2] << "\t" |
349 |
<< entry_plug->Hmat[2][2] << ";"; |
350 |
|
351 |
*outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl; |
352 |
} |
353 |
|
354 |
currentIndex = 0; |
355 |
|
356 |
for (i = 0 ; i < mpiSim->getTotNmol(); i++ ) { |
357 |
|
358 |
// Get the Node number which has this atom; |
359 |
|
360 |
which_node = MolToProcMap[i]; |
361 |
|
362 |
if (which_node != 0) { |
363 |
|
364 |
if (potatoes[which_node] + 1 >= MAXTAG) { |
365 |
// The potato was going to exceed the maximum value, |
366 |
// so wrap this processor potato back to 0: |
367 |
|
368 |
potatoes[which_node] = 0; |
369 |
MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0, MPI_COMM_WORLD); |
370 |
|
371 |
} |
372 |
|
373 |
myPotato = potatoes[which_node]; |
374 |
|
375 |
//recieve the number of integrableObject in current molecule |
376 |
MPI_Recv(&nCurObj, 1, MPI_INT, which_node, |
377 |
myPotato, MPI_COMM_WORLD, &istatus); |
378 |
myPotato++; |
379 |
|
380 |
for(int l = 0; l < nCurObj; l++){ |
381 |
|
382 |
if (potatoes[which_node] + 3 >= MAXTAG) { |
383 |
// The potato was going to exceed the maximum value, |
384 |
// so wrap this processor potato back to 0: |
385 |
|
386 |
potatoes[which_node] = 0; |
387 |
MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0, MPI_COMM_WORLD); |
388 |
|
389 |
} |
390 |
|
391 |
MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node, |
392 |
myPotato, MPI_COMM_WORLD, &istatus); |
393 |
|
394 |
atomTypeString = MPIatomTypeString; |
395 |
|
396 |
myPotato++; |
397 |
|
398 |
MPI_Recv(&isDirectional, 1, MPI_INT, which_node, |
399 |
myPotato, MPI_COMM_WORLD, &istatus); |
400 |
|
401 |
myPotato++; |
402 |
|
403 |
if (isDirectional) { |
404 |
MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node, |
405 |
myPotato, MPI_COMM_WORLD, &istatus); |
406 |
} else { |
407 |
MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node, |
408 |
myPotato, MPI_COMM_WORLD, &istatus); |
409 |
} |
410 |
|
411 |
myPotato++; |
412 |
} |
413 |
potatoes[which_node] = myPotato; |
414 |
|
415 |
} else { |
416 |
|
417 |
haveError = 0; |
418 |
|
419 |
local_index = indexArray[currentIndex].first; |
420 |
|
421 |
integrableObjects = (entry_plug->molecules[local_index]).getIntegrableObjects(); |
422 |
|
423 |
for(iter= integrableObjects.begin(); iter != integrableObjects.end(); ++iter){ |
424 |
sd = *iter; |
425 |
atomTypeString = sd->getType(); |
426 |
|
427 |
sd->getPos(pos); |
428 |
sd->getVel(vel); |
429 |
|
430 |
atomData6[0] = pos[0]; |
431 |
atomData6[1] = pos[1]; |
432 |
atomData6[2] = pos[2]; |
433 |
|
434 |
atomData6[3] = vel[0]; |
435 |
atomData6[4] = vel[1]; |
436 |
atomData6[5] = vel[2]; |
437 |
|
438 |
isDirectional = 0; |
439 |
|
440 |
if( sd->isDirectional() ){ |
441 |
|
442 |
isDirectional = 1; |
443 |
|
444 |
sd->getQ( q ); |
445 |
sd->getJ( ji ); |
446 |
|
447 |
for (int j = 0; j < 6 ; j++) |
448 |
atomData13[j] = atomData6[j]; |
449 |
|
450 |
atomData13[6] = q[0]; |
451 |
atomData13[7] = q[1]; |
452 |
atomData13[8] = q[2]; |
453 |
atomData13[9] = q[3]; |
454 |
|
455 |
atomData13[10] = ji[0]; |
456 |
atomData13[11] = ji[1]; |
457 |
atomData13[12] = ji[2]; |
458 |
} |
459 |
|
460 |
} |
461 |
|
462 |
currentIndex++; |
463 |
} |
464 |
// If we've survived to here, format the line: |
465 |
|
466 |
if (!isDirectional) { |
467 |
|
468 |
sprintf( writeLine, |
469 |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
470 |
atomTypeString, |
471 |
atomData6[0], |
472 |
atomData6[1], |
473 |
atomData6[2], |
474 |
atomData6[3], |
475 |
atomData6[4], |
476 |
atomData6[5]); |
477 |
|
478 |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
479 |
|
480 |
} else { |
481 |
|
482 |
sprintf( writeLine, |
483 |
"%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", |
484 |
atomTypeString, |
485 |
atomData13[0], |
486 |
atomData13[1], |
487 |
atomData13[2], |
488 |
atomData13[3], |
489 |
atomData13[4], |
490 |
atomData13[5], |
491 |
atomData13[6], |
492 |
atomData13[7], |
493 |
atomData13[8], |
494 |
atomData13[9], |
495 |
atomData13[10], |
496 |
atomData13[11], |
497 |
atomData13[12]); |
498 |
|
499 |
} |
500 |
|
501 |
for(k = 0; k < outFile.size(); k++) |
502 |
*outFile[k] << writeLine; |
503 |
} |
504 |
|
505 |
for(k = 0; k < outFile.size(); k++) |
506 |
outFile[k]->flush(); |
507 |
|
508 |
sprintf( checkPointMsg, |
509 |
"Sucessfully took a dump.\n"); |
510 |
|
511 |
MPIcheckPoint(); |
512 |
|
513 |
delete[] potatoes; |
514 |
|
515 |
} else { |
516 |
|
517 |
// worldRank != 0, so I'm a remote node. |
518 |
|
519 |
// Set my magic potato to 0: |
520 |
|
521 |
myPotato = 0; |
522 |
currentIndex = 0; |
523 |
|
524 |
for (i = 0 ; i < mpiSim->getTotNmol(); i++ ) { |
525 |
|
526 |
// Am I the node which has this integrableObject? |
527 |
|
528 |
if (MolToProcMap[i] == worldRank) { |
529 |
|
530 |
|
531 |
if (myPotato + 1 >= MAXTAG) { |
532 |
|
533 |
// The potato was going to exceed the maximum value, |
534 |
// so wrap this processor potato back to 0 (and block until |
535 |
// node 0 says we can go: |
536 |
|
537 |
MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus); |
538 |
|
539 |
} |
540 |
|
541 |
local_index = indexArray[currentIndex].first; |
542 |
integrableObjects = entry_plug->molecules[local_index].getIntegrableObjects(); |
543 |
|
544 |
nCurObj = integrableObjects.size(); |
545 |
|
546 |
MPI_Send(&nCurObj, 1, MPI_INT, 0, |
547 |
myPotato, MPI_COMM_WORLD); |
548 |
myPotato++; |
549 |
|
550 |
for( iter = integrableObjects.begin(); iter != integrableObjects.end(); iter++){ |
551 |
|
552 |
if (myPotato + 3 >= MAXTAG) { |
553 |
|
554 |
// The potato was going to exceed the maximum value, |
555 |
// so wrap this processor potato back to 0 (and block until |
556 |
// node 0 says we can go: |
557 |
|
558 |
MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus); |
559 |
|
560 |
} |
561 |
|
562 |
sd = *iter; |
563 |
|
564 |
atomTypeString = sd->getType(); |
565 |
|
566 |
sd->getPos(pos); |
567 |
sd->getVel(vel); |
568 |
|
569 |
atomData6[0] = pos[0]; |
570 |
atomData6[1] = pos[1]; |
571 |
atomData6[2] = pos[2]; |
572 |
|
573 |
atomData6[3] = vel[0]; |
574 |
atomData6[4] = vel[1]; |
575 |
atomData6[5] = vel[2]; |
576 |
|
577 |
isDirectional = 0; |
578 |
|
579 |
if( sd->isDirectional() ){ |
580 |
|
581 |
isDirectional = 1; |
582 |
|
583 |
sd->getQ( q ); |
584 |
sd->getJ( ji ); |
585 |
|
586 |
for (int j = 0; j < 6 ; j++) |
587 |
atomData13[j] = atomData6[j]; |
588 |
|
589 |
atomData13[6] = q[0]; |
590 |
atomData13[7] = q[1]; |
591 |
atomData13[8] = q[2]; |
592 |
atomData13[9] = q[3]; |
593 |
|
594 |
atomData13[10] = ji[0]; |
595 |
atomData13[11] = ji[1]; |
596 |
atomData13[12] = ji[2]; |
597 |
} |
598 |
|
599 |
|
600 |
strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE); |
601 |
|
602 |
// null terminate the string before sending (just in case): |
603 |
MPIatomTypeString[MINIBUFFERSIZE-1] = '\0'; |
604 |
|
605 |
MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0, |
606 |
myPotato, MPI_COMM_WORLD); |
607 |
|
608 |
myPotato++; |
609 |
|
610 |
MPI_Send(&isDirectional, 1, MPI_INT, 0, |
611 |
myPotato, MPI_COMM_WORLD); |
612 |
|
613 |
myPotato++; |
614 |
|
615 |
if (isDirectional) { |
616 |
|
617 |
MPI_Send(atomData13, 13, MPI_DOUBLE, 0, |
618 |
myPotato, MPI_COMM_WORLD); |
619 |
|
620 |
} else { |
621 |
|
622 |
MPI_Send(atomData6, 6, MPI_DOUBLE, 0, |
623 |
myPotato, MPI_COMM_WORLD); |
624 |
} |
625 |
|
626 |
myPotato++; |
627 |
|
628 |
} |
629 |
|
630 |
currentIndex++; |
631 |
|
632 |
} |
633 |
|
634 |
} |
635 |
|
636 |
sprintf( checkPointMsg, |
637 |
"Sucessfully took a dump.\n"); |
638 |
MPIcheckPoint(); |
639 |
|
640 |
} |
641 |
|
642 |
|
643 |
|
644 |
#endif // is_mpi |
645 |
} |
646 |
|
647 |
#ifdef IS_MPI |
648 |
|
649 |
// a couple of functions to let us escape the write loop |
650 |
|
651 |
void dWrite::DieDieDie( void ){ |
652 |
|
653 |
MPI_Finalize(); |
654 |
exit (0); |
655 |
} |
656 |
|
657 |
#endif //is_mpi |