1 |
#include <cstring> |
2 |
#include <iostream> |
3 |
#include <fstream> |
4 |
|
5 |
#ifdef IS_MPI |
6 |
#include <mpi.h> |
7 |
#include <mpi++.h> |
8 |
#include "mpiSimulation.hpp" |
9 |
#define TAKE_THIS_TAG_CHAR 1 |
10 |
#define TAKE_THIS_TAG_INT 2 |
11 |
|
12 |
namespace dWrite{ |
13 |
void nodeZeroError( void ); |
14 |
void anonymousNodeDie( void ); |
15 |
} |
16 |
|
17 |
using namespace dWrite; |
18 |
#endif //is_mpi |
19 |
|
20 |
#include "ReadWrite.hpp" |
21 |
#include "simError.h" |
22 |
|
23 |
DumpWriter::DumpWriter( SimInfo* the_entry_plug ){ |
24 |
|
25 |
entry_plug = the_entry_plug; |
26 |
|
27 |
#ifdef IS_MPI |
28 |
if(worldRank == 0 ){ |
29 |
#endif // is_mpi |
30 |
|
31 |
|
32 |
|
33 |
strcpy( outName, entry_plug->sampleName ); |
34 |
|
35 |
outFile.open(outName, ios::out | ios::trunc ); |
36 |
|
37 |
if( !outFile ){ |
38 |
|
39 |
sprintf( painCave.errMsg, |
40 |
"Could not open \"%s\" for dump output.\n", |
41 |
outName); |
42 |
painCave.isFatal = 1; |
43 |
simError(); |
44 |
} |
45 |
|
46 |
//outFile.setf( ios::scientific ); |
47 |
|
48 |
#ifdef IS_MPI |
49 |
} |
50 |
|
51 |
sprintf( checkPointMsg, |
52 |
"Sucessfully opened output file for dumping.\n"); |
53 |
MPIcheckPoint(); |
54 |
#endif // is_mpi |
55 |
} |
56 |
|
57 |
DumpWriter::~DumpWriter( ){ |
58 |
|
59 |
#ifdef IS_MPI |
60 |
if(worldRank == 0 ){ |
61 |
#endif // is_mpi |
62 |
|
63 |
outFile.close(); |
64 |
|
65 |
#ifdef IS_MPI |
66 |
} |
67 |
#endif // is_mpi |
68 |
} |
69 |
|
70 |
void DumpWriter::writeDump( double currentTime ){ |
71 |
|
72 |
const int BUFFERSIZE = 2000; |
73 |
char tempBuffer[BUFFERSIZE]; |
74 |
char writeLine[BUFFERSIZE]; |
75 |
|
76 |
int i, j, which_node, done, game_over, which_atom, local_index; |
77 |
double q[4]; |
78 |
DirectionalAtom* dAtom; |
79 |
int nAtoms = entry_plug->n_atoms; |
80 |
Atom** atoms = entry_plug->atoms; |
81 |
|
82 |
|
83 |
#ifndef IS_MPI |
84 |
|
85 |
outFile << nAtoms << "\n"; |
86 |
|
87 |
outFile << currentTime << "\t" |
88 |
<< entry_plug->box_x << "\t" |
89 |
<< entry_plug->box_y << "\t" |
90 |
<< entry_plug->box_z << "\n"; |
91 |
|
92 |
for( i=0; i<nAtoms; i++ ){ |
93 |
|
94 |
|
95 |
sprintf( tempBuffer, |
96 |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
97 |
atoms[i]->getType(), |
98 |
atoms[i]->getX(), |
99 |
atoms[i]->getY(), |
100 |
atoms[i]->getZ(), |
101 |
atoms[i]->get_vx(), |
102 |
atoms[i]->get_vy(), |
103 |
atoms[i]->get_vz()); |
104 |
strcpy( writeLine, tempBuffer ); |
105 |
|
106 |
if( atoms[i]->isDirectional() ){ |
107 |
|
108 |
dAtom = (DirectionalAtom *)atoms[i]; |
109 |
dAtom->getQ( q ); |
110 |
|
111 |
sprintf( tempBuffer, |
112 |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
113 |
q[0], |
114 |
q[1], |
115 |
q[2], |
116 |
q[3], |
117 |
dAtom->getJx(), |
118 |
dAtom->getJy(), |
119 |
dAtom->getJz()); |
120 |
strcat( writeLine, tempBuffer ); |
121 |
} |
122 |
else |
123 |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
124 |
|
125 |
outFile << writeLine; |
126 |
} |
127 |
outFile.flush(); |
128 |
|
129 |
#else // is_mpi |
130 |
|
131 |
// first thing first, suspend fatalities. |
132 |
painCave.isEventLoop = 1; |
133 |
|
134 |
int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone |
135 |
int haveError; |
136 |
|
137 |
MPI::Status istatus; |
138 |
int *AtomToProcMap = mpiSim->getAtomToProcMap(); |
139 |
|
140 |
// write out header and node 0's coordinates |
141 |
|
142 |
if( worldRank == 0 ){ |
143 |
outFile << mpiSim->getTotAtoms() << "\n"; |
144 |
|
145 |
outFile << currentTime << "\t" |
146 |
<< entry_plug->box_x << "\t" |
147 |
<< entry_plug->box_y << "\t" |
148 |
<< entry_plug->box_z << "\n"; |
149 |
outFile.flush(); |
150 |
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
151 |
// Get the Node number which has this atom; |
152 |
|
153 |
which_node = AtomToProcMap[i]; |
154 |
|
155 |
if (which_node == 0 ) { |
156 |
|
157 |
haveError = 0; |
158 |
which_atom = i; |
159 |
local_index=-1; |
160 |
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
161 |
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
162 |
} |
163 |
if (local_index != -1) { |
164 |
//format the line |
165 |
sprintf( tempBuffer, |
166 |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
167 |
atoms[local_index]->getType(), |
168 |
atoms[local_index]->getX(), |
169 |
atoms[local_index]->getY(), |
170 |
atoms[local_index]->getZ(), |
171 |
atoms[local_index]->get_vx(), |
172 |
atoms[local_index]->get_vy(), |
173 |
atoms[local_index]->get_vz()); // check here. |
174 |
strcpy( writeLine, tempBuffer ); |
175 |
|
176 |
if( atoms[local_index]->isDirectional() ){ |
177 |
|
178 |
dAtom = (DirectionalAtom *)atoms[local_index]; |
179 |
dAtom->getQ( q ); |
180 |
|
181 |
sprintf( tempBuffer, |
182 |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
183 |
q[0], |
184 |
q[1], |
185 |
q[2], |
186 |
q[3], |
187 |
dAtom->getJx(), |
188 |
dAtom->getJy(), |
189 |
dAtom->getJz()); |
190 |
strcat( writeLine, tempBuffer ); |
191 |
|
192 |
} |
193 |
else |
194 |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
195 |
} |
196 |
else { |
197 |
sprintf(painCave.errMsg, |
198 |
"Atom %d not found on processor %d\n", |
199 |
i, worldRank ); |
200 |
haveError= 1; |
201 |
simError(); |
202 |
} |
203 |
|
204 |
if(haveError) nodeZeroError(); |
205 |
|
206 |
} |
207 |
else { |
208 |
myStatus = 1; |
209 |
MPI::COMM_WORLD.Send(&myStatus, 1, MPI_INT, which_node, |
210 |
TAKE_THIS_TAG_INT); |
211 |
MPI::COMM_WORLD.Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT); |
212 |
MPI::COMM_WORLD.Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node, |
213 |
TAKE_THIS_TAG_CHAR, istatus); |
214 |
MPI::COMM_WORLD.Recv(&myStatus, 1, MPI_INT, which_node, |
215 |
TAKE_THIS_TAG_INT, istatus); |
216 |
|
217 |
if(!myStatus) nodeZeroError(); |
218 |
|
219 |
} |
220 |
|
221 |
outFile << writeLine; |
222 |
outFile.flush(); |
223 |
} |
224 |
|
225 |
// kill everyone off: |
226 |
myStatus = -1; |
227 |
for (j = 0; j < mpiSim->getNumberProcessors(); j++) { |
228 |
MPI::COMM_WORLD.Send(&myStatus, 1, MPI_INT, j, |
229 |
TAKE_THIS_TAG_INT); |
230 |
} |
231 |
|
232 |
} else { |
233 |
|
234 |
done = 0; |
235 |
while (!done) { |
236 |
|
237 |
MPI::COMM_WORLD.Recv(&myStatus, 1, MPI_INT, 0, |
238 |
TAKE_THIS_TAG_INT, istatus); |
239 |
|
240 |
if(!myStatus) anonymousNodeDie(); |
241 |
|
242 |
if(myStatus < 0) break; |
243 |
|
244 |
MPI::COMM_WORLD.Recv(&which_atom, 1, MPI_INT, 0, |
245 |
TAKE_THIS_TAG_INT, istatus); |
246 |
|
247 |
myStatus = 1; |
248 |
local_index=-1; |
249 |
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
250 |
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
251 |
} |
252 |
if (local_index != -1) { |
253 |
//format the line |
254 |
sprintf( tempBuffer, |
255 |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
256 |
atoms[local_index]->getType(), |
257 |
atoms[local_index]->getX(), |
258 |
atoms[local_index]->getY(), |
259 |
atoms[local_index]->getZ(), |
260 |
atoms[local_index]->get_vx(), |
261 |
atoms[local_index]->get_vy(), |
262 |
atoms[local_index]->get_vz()); // check here. |
263 |
strcpy( writeLine, tempBuffer ); |
264 |
|
265 |
if( atoms[local_index]->isDirectional() ){ |
266 |
|
267 |
dAtom = (DirectionalAtom *)atoms[local_index]; |
268 |
dAtom->getQ( q ); |
269 |
|
270 |
sprintf( tempBuffer, |
271 |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
272 |
q[0], |
273 |
q[1], |
274 |
q[2], |
275 |
q[3], |
276 |
dAtom->getJx(), |
277 |
dAtom->getJy(), |
278 |
dAtom->getJz()); |
279 |
strcat( writeLine, tempBuffer ); |
280 |
} |
281 |
else{ |
282 |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
283 |
} |
284 |
} |
285 |
else { |
286 |
sprintf(painCave.errMsg, |
287 |
"Atom %d not found on processor %d\n", |
288 |
which_atom, worldRank ); |
289 |
myStatus = 0; |
290 |
simError(); |
291 |
|
292 |
strcpy( writeLine, "Hello, I'm an error.\n"); |
293 |
} |
294 |
|
295 |
MPI::COMM_WORLD.Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, |
296 |
TAKE_THIS_TAG_CHAR); |
297 |
MPI::COMM_WORLD.Send( &myStatus, 1, MPI_INT, 0, |
298 |
TAKE_THIS_TAG_INT); |
299 |
} |
300 |
} |
301 |
outFile.flush(); |
302 |
sprintf( checkPointMsg, |
303 |
"Sucessfully took a dump.\n"); |
304 |
MPIcheckPoint(); |
305 |
|
306 |
// last thing last, enable fatalities. |
307 |
painCave.isEventLoop = 0; |
308 |
|
309 |
#endif // is_mpi |
310 |
} |
311 |
|
312 |
void DumpWriter::writeFinal(){ |
313 |
|
314 |
char finalName[500]; |
315 |
ofstream finalOut; |
316 |
|
317 |
const int BUFFERSIZE = 2000; |
318 |
char tempBuffer[BUFFERSIZE]; |
319 |
char writeLine[BUFFERSIZE]; |
320 |
|
321 |
double q[4]; |
322 |
DirectionalAtom* dAtom; |
323 |
int nAtoms = entry_plug->n_atoms; |
324 |
Atom** atoms = entry_plug->atoms; |
325 |
int i, j, which_node, done, game_over, which_atom, local_index; |
326 |
|
327 |
|
328 |
#ifdef IS_MPI |
329 |
if(worldRank == 0 ){ |
330 |
#endif // is_mpi |
331 |
|
332 |
strcpy( finalName, entry_plug->finalName ); |
333 |
|
334 |
finalOut.open( finalName, ios::out | ios::trunc ); |
335 |
if( !finalOut ){ |
336 |
sprintf( painCave.errMsg, |
337 |
"Could not open \"%s\" for final dump output.\n", |
338 |
finalName ); |
339 |
painCave.isFatal = 1; |
340 |
simError(); |
341 |
} |
342 |
|
343 |
// finalOut.setf( ios::scientific ); |
344 |
|
345 |
#ifdef IS_MPI |
346 |
} |
347 |
|
348 |
sprintf(checkPointMsg,"Opened file for final configuration\n"); |
349 |
MPIcheckPoint(); |
350 |
|
351 |
#endif //is_mpi |
352 |
|
353 |
|
354 |
#ifndef IS_MPI |
355 |
|
356 |
finalOut << nAtoms << "\n"; |
357 |
|
358 |
finalOut << entry_plug->box_x << "\t" |
359 |
<< entry_plug->box_y << "\t" |
360 |
<< entry_plug->box_z << "\n"; |
361 |
|
362 |
for( i=0; i<nAtoms; i++ ){ |
363 |
|
364 |
sprintf( tempBuffer, |
365 |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
366 |
atoms[i]->getType(), |
367 |
atoms[i]->getX(), |
368 |
atoms[i]->getY(), |
369 |
atoms[i]->getZ(), |
370 |
atoms[i]->get_vx(), |
371 |
atoms[i]->get_vy(), |
372 |
atoms[i]->get_vz()); |
373 |
strcpy( writeLine, tempBuffer ); |
374 |
|
375 |
if( atoms[i]->isDirectional() ){ |
376 |
|
377 |
dAtom = (DirectionalAtom *)atoms[i]; |
378 |
dAtom->getQ( q ); |
379 |
|
380 |
sprintf( tempBuffer, |
381 |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
382 |
q[0], |
383 |
q[1], |
384 |
q[2], |
385 |
q[3], |
386 |
dAtom->getJx(), |
387 |
dAtom->getJy(), |
388 |
dAtom->getJz()); |
389 |
strcat( writeLine, tempBuffer ); |
390 |
} |
391 |
else |
392 |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
393 |
|
394 |
finalOut << writeLine; |
395 |
} |
396 |
finalOut.flush(); |
397 |
finalOut.close(); |
398 |
|
399 |
#else // is_mpi |
400 |
|
401 |
// first thing first, suspend fatalities. |
402 |
painCave.isEventLoop = 1; |
403 |
|
404 |
int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone |
405 |
int haveError; |
406 |
|
407 |
MPI::Status istatus; |
408 |
int *AtomToProcMap = mpiSim->getAtomToProcMap(); |
409 |
|
410 |
// write out header and node 0's coordinates |
411 |
|
412 |
haveError = 0; |
413 |
if( worldRank == 0 ){ |
414 |
finalOut << mpiSim->getTotAtoms() << "\n"; |
415 |
|
416 |
finalOut << entry_plug->box_x << "\t" |
417 |
<< entry_plug->box_y << "\t" |
418 |
<< entry_plug->box_z << "\n"; |
419 |
|
420 |
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
421 |
// Get the Node number which has this molecule: |
422 |
|
423 |
which_node = AtomToProcMap[i]; |
424 |
|
425 |
if (which_node == mpiSim->getMyNode()) { |
426 |
|
427 |
which_atom = i; |
428 |
local_index=-1; |
429 |
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
430 |
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
431 |
} |
432 |
if (local_index != -1) { |
433 |
sprintf( tempBuffer, |
434 |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
435 |
atoms[local_index]->getType(), |
436 |
atoms[local_index]->getX(), |
437 |
atoms[local_index]->getY(), |
438 |
atoms[local_index]->getZ(), |
439 |
atoms[local_index]->get_vx(), |
440 |
atoms[local_index]->get_vy(), |
441 |
atoms[local_index]->get_vz()); |
442 |
strcpy( writeLine, tempBuffer ); |
443 |
|
444 |
if( atoms[local_index]->isDirectional() ){ |
445 |
|
446 |
dAtom = (DirectionalAtom *)atoms[local_index]; |
447 |
dAtom->getQ( q ); |
448 |
|
449 |
sprintf( tempBuffer, |
450 |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
451 |
q[0], |
452 |
q[1], |
453 |
q[2], |
454 |
q[3], |
455 |
dAtom->getJx(), |
456 |
dAtom->getJy(), |
457 |
dAtom->getJz()); |
458 |
strcat( writeLine, tempBuffer ); |
459 |
} |
460 |
else |
461 |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
462 |
} |
463 |
else { |
464 |
sprintf(painCave.errMsg, |
465 |
"Atom %d not found on processor %d\n", |
466 |
i, worldRank ); |
467 |
haveError= 1; |
468 |
simError(); |
469 |
} |
470 |
|
471 |
if(haveError) nodeZeroError(); |
472 |
|
473 |
} |
474 |
else { |
475 |
|
476 |
myStatus = 1; |
477 |
MPI::COMM_WORLD.Send(&myStatus, 1, MPI_INT, which_node, |
478 |
TAKE_THIS_TAG_INT); |
479 |
MPI::COMM_WORLD.Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT); |
480 |
MPI::COMM_WORLD.Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node, |
481 |
TAKE_THIS_TAG_CHAR, istatus); |
482 |
MPI::COMM_WORLD.Recv(&myStatus, 1, MPI_INT, which_node, |
483 |
TAKE_THIS_TAG_INT, istatus); |
484 |
|
485 |
if(!myStatus) nodeZeroError(); |
486 |
} |
487 |
|
488 |
finalOut << writeLine; |
489 |
} |
490 |
|
491 |
// kill everyone off: |
492 |
myStatus = -1; |
493 |
for (j = 0; j < mpiSim->getNumberProcessors(); j++) { |
494 |
MPI::COMM_WORLD.Send(&myStatus, 1, MPI_INT, j, |
495 |
TAKE_THIS_TAG_INT); |
496 |
} |
497 |
|
498 |
} else { |
499 |
|
500 |
done = 0; |
501 |
while (!done) { |
502 |
|
503 |
MPI::COMM_WORLD.Recv(&myStatus, 1, MPI_INT, 0, |
504 |
TAKE_THIS_TAG_INT, istatus); |
505 |
|
506 |
if(!myStatus) anonymousNodeDie(); |
507 |
|
508 |
if(myStatus < 0) break; |
509 |
|
510 |
MPI::COMM_WORLD.Recv(&which_atom, 1, MPI_INT, 0, |
511 |
TAKE_THIS_TAG_INT, istatus); |
512 |
|
513 |
myStatus = 1; |
514 |
local_index=-1; |
515 |
for (j=0; j < mpiSim->getMyNlocal(); j++) { |
516 |
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
517 |
} |
518 |
if (local_index != -1) { |
519 |
|
520 |
//format the line |
521 |
sprintf( tempBuffer, |
522 |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
523 |
atoms[local_index]->getType(), |
524 |
atoms[local_index]->getX(), |
525 |
atoms[local_index]->getY(), |
526 |
atoms[local_index]->getZ(), |
527 |
atoms[local_index]->get_vx(), |
528 |
atoms[local_index]->get_vy(), |
529 |
atoms[local_index]->get_vz()); // check here. |
530 |
strcpy( writeLine, tempBuffer ); |
531 |
|
532 |
if( atoms[local_index]->isDirectional() ){ |
533 |
|
534 |
dAtom = (DirectionalAtom *)atoms[local_index]; |
535 |
dAtom->getQ( q ); |
536 |
|
537 |
sprintf( tempBuffer, |
538 |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
539 |
q[0], |
540 |
q[1], |
541 |
q[2], |
542 |
q[3], |
543 |
dAtom->getJx(), |
544 |
dAtom->getJy(), |
545 |
dAtom->getJz()); |
546 |
strcat( writeLine, tempBuffer ); |
547 |
} |
548 |
else{ |
549 |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
550 |
} |
551 |
} |
552 |
else { |
553 |
sprintf(painCave.errMsg, |
554 |
"Atom %d not found on processor %d\n", |
555 |
which_atom, worldRank ); |
556 |
myStatus = 0; |
557 |
simError(); |
558 |
|
559 |
strcpy( writeLine, "Hello, I'm an error.\n"); |
560 |
} |
561 |
|
562 |
MPI::COMM_WORLD.Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, |
563 |
TAKE_THIS_TAG_CHAR); |
564 |
MPI::COMM_WORLD.Send( &myStatus, 1, MPI_INT, 0, |
565 |
TAKE_THIS_TAG_INT); |
566 |
} |
567 |
} |
568 |
finalOut.flush(); |
569 |
sprintf( checkPointMsg, |
570 |
"Sucessfully took a dump.\n"); |
571 |
MPIcheckPoint(); |
572 |
|
573 |
if( worldRank == 0 ) finalOut.close(); |
574 |
#endif // is_mpi |
575 |
} |
576 |
|
577 |
|
578 |
|
579 |
#ifdef IS_MPI |
580 |
|
581 |
// a couple of functions to let us escape the write loop |
582 |
|
583 |
void dWrite::nodeZeroError( void ){ |
584 |
int j, myStatus; |
585 |
|
586 |
myStatus = 0; |
587 |
for (j = 0; j < mpiSim->getNumberProcessors(); j++) { |
588 |
MPI::COMM_WORLD.Send( &myStatus, 1, MPI_INT, j, |
589 |
TAKE_THIS_TAG_INT); |
590 |
} |
591 |
|
592 |
|
593 |
MPI_Finalize(); |
594 |
exit (0); |
595 |
|
596 |
} |
597 |
|
598 |
void dWrite::anonymousNodeDie( void ){ |
599 |
|
600 |
MPI_Finalize(); |
601 |
exit (0); |
602 |
} |
603 |
|
604 |
#endif //is_mpi |