4 |
|
|
5 |
|
#ifdef IS_MPI |
6 |
|
#include <mpi.h> |
7 |
– |
#include <mpi++.h> |
7 |
|
#include "mpiSimulation.hpp" |
8 |
|
#define TAKE_THIS_TAG_CHAR 1 |
9 |
|
#define TAKE_THIS_TAG_INT 2 |
27 |
|
if(worldRank == 0 ){ |
28 |
|
#endif // is_mpi |
29 |
|
|
31 |
– |
|
32 |
– |
|
30 |
|
strcpy( outName, entry_plug->sampleName ); |
31 |
|
|
32 |
|
outFile.open(outName, ios::out | ios::trunc ); |
39 |
|
painCave.isFatal = 1; |
40 |
|
simError(); |
41 |
|
} |
42 |
< |
|
42 |
> |
|
43 |
|
//outFile.setf( ios::scientific ); |
44 |
|
|
45 |
|
#ifdef IS_MPI |
70 |
|
char tempBuffer[BUFFERSIZE]; |
71 |
|
char writeLine[BUFFERSIZE]; |
72 |
|
|
73 |
< |
int i, j, which_node, done, game_over, which_atom, local_index; |
73 |
> |
int i, j, which_node, done, which_atom, local_index; |
74 |
|
double q[4]; |
75 |
|
DirectionalAtom* dAtom; |
76 |
|
int nAtoms = entry_plug->n_atoms; |
82 |
|
outFile << nAtoms << "\n"; |
83 |
|
|
84 |
|
outFile << currentTime << "\t" |
85 |
< |
<< entry_plug->box_x << "\t" |
86 |
< |
<< entry_plug->box_y << "\t" |
87 |
< |
<< entry_plug->box_z << "\n"; |
85 |
> |
<< entry_plug->Hmat[0] << "\t" |
86 |
> |
<< entry_plug->Hmat[1] << "\t" |
87 |
> |
<< entry_plug->Hmat[2] << "\t" |
88 |
> |
|
89 |
> |
<< entry_plug->Hmat[3] << "\t" |
90 |
> |
<< entry_plug->Hmat[4] << "\t" |
91 |
> |
<< entry_plug->Hmat[5] << "\t" |
92 |
> |
|
93 |
> |
<< entry_plug->Hmat[6] << "\t" |
94 |
> |
<< entry_plug->Hmat[7] << "\t" |
95 |
> |
<< entry_plug->Hmat[8] << "\n"; |
96 |
|
|
97 |
|
for( i=0; i<nAtoms; i++ ){ |
98 |
|
|
139 |
|
int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone |
140 |
|
int haveError; |
141 |
|
|
142 |
< |
MPI::Status istatus; |
142 |
> |
MPI_Status istatus; |
143 |
|
int *AtomToProcMap = mpiSim->getAtomToProcMap(); |
144 |
|
|
145 |
|
// write out header and node 0's coordinates |
146 |
|
|
147 |
|
if( worldRank == 0 ){ |
148 |
|
outFile << mpiSim->getTotAtoms() << "\n"; |
149 |
< |
|
149 |
> |
|
150 |
|
outFile << currentTime << "\t" |
151 |
< |
<< entry_plug->box_x << "\t" |
152 |
< |
<< entry_plug->box_y << "\t" |
153 |
< |
<< entry_plug->box_z << "\n"; |
151 |
> |
<< entry_plug->Hmat[0] << "\t" |
152 |
> |
<< entry_plug->Hmat[1] << "\t" |
153 |
> |
<< entry_plug->Hmat[2] << "\t" |
154 |
> |
|
155 |
> |
<< entry_plug->Hmat[3] << "\t" |
156 |
> |
<< entry_plug->Hmat[4] << "\t" |
157 |
> |
<< entry_plug->Hmat[5] << "\t" |
158 |
> |
|
159 |
> |
<< entry_plug->Hmat[6] << "\t" |
160 |
> |
<< entry_plug->Hmat[7] << "\t" |
161 |
> |
<< entry_plug->Hmat[8] << "\n"; |
162 |
> |
; |
163 |
|
outFile.flush(); |
164 |
|
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
165 |
|
// Get the Node number which has this atom; |
220 |
|
} |
221 |
|
else { |
222 |
|
myStatus = 1; |
223 |
< |
MPI::COMM_WORLD.Send(&myStatus, 1, MPI_INT, which_node, |
224 |
< |
TAKE_THIS_TAG_INT); |
225 |
< |
MPI::COMM_WORLD.Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT); |
226 |
< |
MPI::COMM_WORLD.Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node, |
227 |
< |
TAKE_THIS_TAG_CHAR, istatus); |
228 |
< |
MPI::COMM_WORLD.Recv(&myStatus, 1, MPI_INT, which_node, |
229 |
< |
TAKE_THIS_TAG_INT, istatus); |
223 |
> |
MPI_Send(&myStatus, 1, MPI_INT, which_node, |
224 |
> |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
225 |
> |
MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, |
226 |
> |
MPI_COMM_WORLD); |
227 |
> |
MPI_Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node, |
228 |
> |
TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus); |
229 |
> |
MPI_Recv(&myStatus, 1, MPI_INT, which_node, |
230 |
> |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
231 |
|
|
232 |
|
if(!myStatus) nodeZeroError(); |
233 |
|
|
240 |
|
// kill everyone off: |
241 |
|
myStatus = -1; |
242 |
|
for (j = 0; j < mpiSim->getNumberProcessors(); j++) { |
243 |
< |
MPI::COMM_WORLD.Send(&myStatus, 1, MPI_INT, j, |
244 |
< |
TAKE_THIS_TAG_INT); |
243 |
> |
MPI_Send(&myStatus, 1, MPI_INT, j, |
244 |
> |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
245 |
|
} |
246 |
|
|
247 |
|
} else { |
249 |
|
done = 0; |
250 |
|
while (!done) { |
251 |
|
|
252 |
< |
MPI::COMM_WORLD.Recv(&myStatus, 1, MPI_INT, 0, |
253 |
< |
TAKE_THIS_TAG_INT, istatus); |
252 |
> |
MPI_Recv(&myStatus, 1, MPI_INT, 0, |
253 |
> |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
254 |
|
|
255 |
|
if(!myStatus) anonymousNodeDie(); |
256 |
|
|
257 |
|
if(myStatus < 0) break; |
258 |
|
|
259 |
< |
MPI::COMM_WORLD.Recv(&which_atom, 1, MPI_INT, 0, |
260 |
< |
TAKE_THIS_TAG_INT, istatus); |
259 |
> |
MPI_Recv(&which_atom, 1, MPI_INT, 0, |
260 |
> |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
261 |
|
|
262 |
|
myStatus = 1; |
263 |
|
local_index=-1; |
307 |
|
strcpy( writeLine, "Hello, I'm an error.\n"); |
308 |
|
} |
309 |
|
|
310 |
< |
MPI::COMM_WORLD.Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, |
311 |
< |
TAKE_THIS_TAG_CHAR); |
312 |
< |
MPI::COMM_WORLD.Send( &myStatus, 1, MPI_INT, 0, |
313 |
< |
TAKE_THIS_TAG_INT); |
310 |
> |
MPI_Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, |
311 |
> |
TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD); |
312 |
> |
MPI_Send( &myStatus, 1, MPI_INT, 0, |
313 |
> |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
314 |
|
} |
315 |
|
} |
316 |
|
outFile.flush(); |
324 |
|
#endif // is_mpi |
325 |
|
} |
326 |
|
|
327 |
< |
void DumpWriter::writeFinal(){ |
327 |
> |
void DumpWriter::writeFinal(double finalTime){ |
328 |
|
|
329 |
|
char finalName[500]; |
330 |
|
ofstream finalOut; |
370 |
|
|
371 |
|
finalOut << nAtoms << "\n"; |
372 |
|
|
373 |
< |
finalOut << entry_plug->box_x << "\t" |
374 |
< |
<< entry_plug->box_y << "\t" |
375 |
< |
<< entry_plug->box_z << "\n"; |
373 |
> |
finalOut << finalTime << "\t" |
374 |
> |
<< entry_plug->Hmat[0] << "\t" |
375 |
> |
<< entry_plug->Hmat[1] << "\t" |
376 |
> |
<< entry_plug->Hmat[2] << "\t" |
377 |
> |
|
378 |
> |
<< entry_plug->Hmat[3] << "\t" |
379 |
> |
<< entry_plug->Hmat[4] << "\t" |
380 |
> |
<< entry_plug->Hmat[5] << "\t" |
381 |
> |
|
382 |
> |
<< entry_plug->Hmat[6] << "\t" |
383 |
> |
<< entry_plug->Hmat[7] << "\t" |
384 |
> |
<< entry_plug->Hmat[8] << "\n"; |
385 |
|
|
386 |
|
for( i=0; i<nAtoms; i++ ){ |
387 |
|
|
428 |
|
int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone |
429 |
|
int haveError; |
430 |
|
|
431 |
< |
MPI::Status istatus; |
431 |
> |
MPI_Status istatus; |
432 |
|
int *AtomToProcMap = mpiSim->getAtomToProcMap(); |
433 |
|
|
434 |
|
// write out header and node 0's coordinates |
437 |
|
if( worldRank == 0 ){ |
438 |
|
finalOut << mpiSim->getTotAtoms() << "\n"; |
439 |
|
|
440 |
< |
finalOut << entry_plug->box_x << "\t" |
441 |
< |
<< entry_plug->box_y << "\t" |
442 |
< |
<< entry_plug->box_z << "\n"; |
440 |
> |
finalOut << finalTime << "\t" |
441 |
> |
<< entry_plug->Hmat[0] << "\t" |
442 |
> |
<< entry_plug->Hmat[1] << "\t" |
443 |
> |
<< entry_plug->Hmat[2] << "\t" |
444 |
> |
|
445 |
> |
<< entry_plug->Hmat[3] << "\t" |
446 |
> |
<< entry_plug->Hmat[4] << "\t" |
447 |
> |
<< entry_plug->Hmat[5] << "\t" |
448 |
> |
|
449 |
> |
<< entry_plug->Hmat[6] << "\t" |
450 |
> |
<< entry_plug->Hmat[7] << "\t" |
451 |
> |
<< entry_plug->Hmat[8] << "\n"; |
452 |
|
|
453 |
|
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
454 |
|
// Get the Node number which has this molecule: |
507 |
|
else { |
508 |
|
|
509 |
|
myStatus = 1; |
510 |
< |
MPI::COMM_WORLD.Send(&myStatus, 1, MPI_INT, which_node, |
511 |
< |
TAKE_THIS_TAG_INT); |
512 |
< |
MPI::COMM_WORLD.Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT); |
513 |
< |
MPI::COMM_WORLD.Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node, |
514 |
< |
TAKE_THIS_TAG_CHAR, istatus); |
515 |
< |
MPI::COMM_WORLD.Recv(&myStatus, 1, MPI_INT, which_node, |
516 |
< |
TAKE_THIS_TAG_INT, istatus); |
510 |
> |
MPI_Send(&myStatus, 1, MPI_INT, which_node, |
511 |
> |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
512 |
> |
MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, |
513 |
> |
MPI_COMM_WORLD); |
514 |
> |
MPI_Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node, |
515 |
> |
TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus); |
516 |
> |
MPI_Recv(&myStatus, 1, MPI_INT, which_node, |
517 |
> |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
518 |
|
|
519 |
|
if(!myStatus) nodeZeroError(); |
520 |
|
} |
525 |
|
// kill everyone off: |
526 |
|
myStatus = -1; |
527 |
|
for (j = 0; j < mpiSim->getNumberProcessors(); j++) { |
528 |
< |
MPI::COMM_WORLD.Send(&myStatus, 1, MPI_INT, j, |
529 |
< |
TAKE_THIS_TAG_INT); |
528 |
> |
MPI_Send(&myStatus, 1, MPI_INT, j, |
529 |
> |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
530 |
|
} |
531 |
|
|
532 |
|
} else { |
534 |
|
done = 0; |
535 |
|
while (!done) { |
536 |
|
|
537 |
< |
MPI::COMM_WORLD.Recv(&myStatus, 1, MPI_INT, 0, |
538 |
< |
TAKE_THIS_TAG_INT, istatus); |
537 |
> |
MPI_Recv(&myStatus, 1, MPI_INT, 0, |
538 |
> |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
539 |
|
|
540 |
|
if(!myStatus) anonymousNodeDie(); |
541 |
|
|
542 |
|
if(myStatus < 0) break; |
543 |
|
|
544 |
< |
MPI::COMM_WORLD.Recv(&which_atom, 1, MPI_INT, 0, |
545 |
< |
TAKE_THIS_TAG_INT, istatus); |
544 |
> |
MPI_Recv(&which_atom, 1, MPI_INT, 0, |
545 |
> |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
546 |
|
|
547 |
|
myStatus = 1; |
548 |
|
local_index=-1; |
593 |
|
strcpy( writeLine, "Hello, I'm an error.\n"); |
594 |
|
} |
595 |
|
|
596 |
< |
MPI::COMM_WORLD.Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, |
597 |
< |
TAKE_THIS_TAG_CHAR); |
598 |
< |
MPI::COMM_WORLD.Send( &myStatus, 1, MPI_INT, 0, |
599 |
< |
TAKE_THIS_TAG_INT); |
596 |
> |
MPI_Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, |
597 |
> |
TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD); |
598 |
> |
MPI_Send( &myStatus, 1, MPI_INT, 0, |
599 |
> |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
600 |
|
} |
601 |
|
} |
602 |
|
finalOut.flush(); |
619 |
|
|
620 |
|
myStatus = 0; |
621 |
|
for (j = 0; j < mpiSim->getNumberProcessors(); j++) { |
622 |
< |
MPI::COMM_WORLD.Send( &myStatus, 1, MPI_INT, j, |
623 |
< |
TAKE_THIS_TAG_INT); |
622 |
> |
MPI_Send( &myStatus, 1, MPI_INT, j, |
623 |
> |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
624 |
|
} |
625 |
|
|
626 |
|
|