7 |
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#ifdef IS_MPI |
8 |
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#include <mpi.h> |
9 |
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#include "mpiSimulation.hpp" |
10 |
– |
#define TAKE_THIS_TAG_CHAR 15 |
11 |
– |
#define TAKE_THIS_TAG_INT 20 |
10 |
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|
11 |
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namespace dWrite{ |
12 |
< |
void nodeZeroError( void ); |
15 |
< |
void anonymousNodeDie( void ); |
12 |
> |
void DieDieDie( void ); |
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} |
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|
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using namespace dWrite; |
66 |
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void DumpWriter::writeDump( double currentTime ){ |
67 |
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|
68 |
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const int BUFFERSIZE = 2000; |
69 |
+ |
const int MINIBUFFERSIZE = 10; |
70 |
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|
71 |
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char tempBuffer[BUFFERSIZE]; |
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char writeLine[BUFFERSIZE]; |
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|
74 |
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int i; |
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#ifdef IS_MPI |
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int j, which_node, done, which_atom, local_index; |
77 |
+ |
double atomTransData[6]; |
78 |
+ |
double atomOrientData[7]; |
79 |
+ |
int isDirectional; |
80 |
+ |
char* atomTypeString; |
81 |
+ |
char MPIatomTypeString[MINIBUFFERSIZE]; |
82 |
+ |
int me; |
83 |
+ |
int atomTypeTag; |
84 |
+ |
int atomIsDirectionalTag; |
85 |
+ |
int atomTransDataTag; |
86 |
+ |
int atomOrientDataTag; |
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#else //is_mpi |
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int nAtoms = entry_plug->n_atoms; |
89 |
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#endif //is_mpi |
93 |
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Atom** atoms = entry_plug->atoms; |
94 |
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double pos[3], vel[3]; |
95 |
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|
87 |
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|
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// write current frame to the eor file |
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|
98 |
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this->writeFinal( currentTime ); |
193 |
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|
194 |
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which_node = AtomToProcMap[i]; |
195 |
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|
196 |
< |
if (which_node == 0 ) { |
196 |
> |
if (which_node != 0) { |
197 |
> |
|
198 |
> |
atomTypeTag = 4*i; |
199 |
> |
atomIsDirectionalTag = 4*i + 1; |
200 |
> |
atomTransDataTag = 4*i + 2; |
201 |
> |
atomOrientDataTag = 4*i + 3; |
202 |
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|
203 |
+ |
MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node, |
204 |
+ |
atomTypeTag, MPI_COMM_WORLD, &istatus); |
205 |
+ |
|
206 |
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strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE); |
207 |
+ |
|
208 |
+ |
MPI_Recv(&isDirectional, 1, MPI_INT, which_node, |
209 |
+ |
atomIsDirectionalTag, MPI_COMM_WORLD, &istatus); |
210 |
+ |
|
211 |
+ |
MPI_Recv(atomTransData, 6, MPI_DOUBLE, which_node, |
212 |
+ |
atomTransDataTag, MPI_COMM_WORLD, &istatus); |
213 |
+ |
|
214 |
+ |
if (isDirectional) { |
215 |
+ |
|
216 |
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MPI_Recv(atomOrientData, 7, MPI_DOUBLE, which_node, |
217 |
+ |
atomOrientDataTag, MPI_COMM_WORLD, &istatus); |
218 |
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|
219 |
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} |
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|
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} else { |
222 |
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|
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haveError = 0; |
224 |
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which_atom = i; |
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local_index=-1; |
226 |
+ |
|
227 |
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for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
228 |
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if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
229 |
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} |
230 |
+ |
|
231 |
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if (local_index != -1) { |
197 |
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//format the line |
232 |
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|
233 |
+ |
atomTypeString = atoms[local_index]->getType(); |
234 |
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|
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atoms[local_index]->getPos(pos); |
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atoms[local_index]->getVel(vel); |
237 |
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|
238 |
< |
sprintf( tempBuffer, |
239 |
< |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
240 |
< |
atoms[local_index]->getType(), |
205 |
< |
pos[0], |
206 |
< |
pos[1], |
207 |
< |
pos[2], |
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< |
vel[0], |
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< |
vel[1], |
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< |
vel[2]); // check here. |
211 |
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strcpy( writeLine, tempBuffer ); |
238 |
> |
atomTransData[0] = pos[0]; |
239 |
> |
atomTransData[1] = pos[1]; |
240 |
> |
atomTransData[2] = pos[2]; |
241 |
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|
242 |
+ |
atomTransData[3] = vel[0]; |
243 |
+ |
atomTransData[4] = vel[1]; |
244 |
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atomTransData[5] = vel[2]; |
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+ |
|
246 |
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isDirectional = 0; |
247 |
+ |
|
248 |
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if( atoms[local_index]->isDirectional() ){ |
249 |
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|
250 |
+ |
isDirectional = 1; |
251 |
+ |
|
252 |
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dAtom = (DirectionalAtom *)atoms[local_index]; |
253 |
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dAtom->getQ( q ); |
254 |
+ |
|
255 |
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atomOrientData[0] = q[0]; |
256 |
+ |
atomOrientData[1] = q[1]; |
257 |
+ |
atomOrientData[2] = q[2]; |
258 |
+ |
atomOrientData[3] = q[3]; |
259 |
|
|
260 |
< |
sprintf( tempBuffer, |
261 |
< |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
262 |
< |
q[0], |
263 |
< |
q[1], |
222 |
< |
q[2], |
223 |
< |
q[3], |
224 |
< |
dAtom->getJx(), |
225 |
< |
dAtom->getJy(), |
226 |
< |
dAtom->getJz()); |
227 |
< |
strcat( writeLine, tempBuffer ); |
260 |
> |
atomOrientData[4] = dAtom->getJx(); |
261 |
> |
atomOrientData[5] = dAtom->getJy(); |
262 |
> |
atomOrientData[6] = dAtom->getJz(); |
263 |
> |
} |
264 |
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|
265 |
< |
} |
230 |
< |
else |
231 |
< |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
232 |
< |
} |
233 |
< |
else { |
265 |
> |
} else { |
266 |
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sprintf(painCave.errMsg, |
267 |
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"Atom %d not found on processor %d\n", |
268 |
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i, worldRank ); |
270 |
|
simError(); |
271 |
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} |
272 |
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|
273 |
< |
if(haveError) nodeZeroError(); |
273 |
> |
if(haveError) DieDieDie(); |
274 |
> |
|
275 |
> |
// If we've survived to here, format the line: |
276 |
> |
|
277 |
> |
sprintf( tempBuffer, |
278 |
> |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
279 |
> |
atomTypeString, |
280 |
> |
atomTransData[0], |
281 |
> |
atomTransData[1], |
282 |
> |
atomTransData[2], |
283 |
> |
atomTransData[3], |
284 |
> |
atomTransData[4], |
285 |
> |
atomTransData[5]); |
286 |
|
|
287 |
< |
} |
244 |
< |
else { |
245 |
< |
myStatus = 1; |
246 |
< |
MPI_Send(&myStatus, 1, MPI_INT, which_node, |
247 |
< |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
248 |
< |
MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, |
249 |
< |
MPI_COMM_WORLD); |
250 |
< |
MPI_Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node, |
251 |
< |
TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus); |
252 |
< |
MPI_Recv(&myStatus, 1, MPI_INT, which_node, |
253 |
< |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
287 |
> |
strcpy( writeLine, tempBuffer ); |
288 |
|
|
289 |
< |
if(!myStatus) nodeZeroError(); |
289 |
> |
if (isDirectional) { |
290 |
|
|
291 |
< |
} |
291 |
> |
sprintf( tempBuffer, |
292 |
> |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
293 |
> |
atomOrientData[0], |
294 |
> |
atomOrientData[1], |
295 |
> |
atomOrientData[2], |
296 |
> |
atomOrientData[3], |
297 |
> |
atomOrientData[4], |
298 |
> |
atomOrientData[5], |
299 |
> |
atomOrientData[6]); |
300 |
> |
strcat( writeLine, tempBuffer ); |
301 |
|
|
302 |
< |
outFile << writeLine; |
303 |
< |
outFile.flush(); |
304 |
< |
} |
302 |
> |
} else { |
303 |
> |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
304 |
> |
} |
305 |
|
|
306 |
< |
// kill everyone off: |
307 |
< |
myStatus = -1; |
308 |
< |
for (j = 1; j < mpiSim->getNumberProcessors(); j++) { |
266 |
< |
MPI_Send(&myStatus, 1, MPI_INT, j, |
267 |
< |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
306 |
> |
outFile << writeLine; |
307 |
> |
outFile.flush(); |
308 |
> |
} |
309 |
|
} |
310 |
|
|
311 |
+ |
outFile.flush(); |
312 |
+ |
sprintf( checkPointMsg, |
313 |
+ |
"Sucessfully took a dump.\n"); |
314 |
+ |
MPIcheckPoint(); |
315 |
+ |
|
316 |
|
} else { |
317 |
|
|
318 |
< |
done = 0; |
319 |
< |
while (!done) { |
318 |
> |
// worldRank != 0, so I'm a remote node. |
319 |
> |
|
320 |
> |
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
321 |
> |
|
322 |
> |
// Am I the node which has this atom? |
323 |
> |
|
324 |
> |
if (AtomToProcMap[i] == worldRank) { |
325 |
|
|
326 |
< |
MPI_Recv(&myStatus, 1, MPI_INT, 0, |
327 |
< |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
326 |
> |
local_index=-1; |
327 |
> |
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
328 |
> |
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
329 |
> |
} |
330 |
> |
if (local_index != -1) { |
331 |
> |
|
332 |
> |
atomTypeString = atoms[local_index]->getType(); |
333 |
|
|
334 |
< |
if(!myStatus) anonymousNodeDie(); |
335 |
< |
|
280 |
< |
if(myStatus < 0) break; |
334 |
> |
atoms[local_index]->getPos(pos); |
335 |
> |
atoms[local_index]->getVel(vel); |
336 |
|
|
337 |
< |
MPI_Recv(&which_atom, 1, MPI_INT, 0, |
338 |
< |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
337 |
> |
atomTransData[0] = pos[0]; |
338 |
> |
atomTransData[1] = pos[1]; |
339 |
> |
atomTransData[2] = pos[2]; |
340 |
|
|
341 |
< |
myStatus = 1; |
342 |
< |
local_index=-1; |
343 |
< |
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
344 |
< |
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
345 |
< |
} |
290 |
< |
if (local_index != -1) { |
291 |
< |
//format the line |
341 |
> |
atomTransData[3] = vel[0]; |
342 |
> |
atomTransData[4] = vel[1]; |
343 |
> |
atomTransData[5] = vel[2]; |
344 |
> |
|
345 |
> |
isDirectional = 0; |
346 |
|
|
347 |
< |
atoms[local_index]->getPos(pos); |
294 |
< |
atoms[local_index]->getVel(vel); |
347 |
> |
if( atoms[local_index]->isDirectional() ){ |
348 |
|
|
349 |
< |
sprintf( tempBuffer, |
350 |
< |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
351 |
< |
atoms[local_index]->getType(), |
352 |
< |
pos[0], |
353 |
< |
pos[1], |
354 |
< |
pos[2], |
355 |
< |
vel[0], |
356 |
< |
vel[1], |
357 |
< |
vel[2]); // check here. |
305 |
< |
strcpy( writeLine, tempBuffer ); |
349 |
> |
isDirectional = 1; |
350 |
> |
|
351 |
> |
dAtom = (DirectionalAtom *)atoms[local_index]; |
352 |
> |
dAtom->getQ( q ); |
353 |
> |
|
354 |
> |
atomOrientData[0] = q[0]; |
355 |
> |
atomOrientData[1] = q[1]; |
356 |
> |
atomOrientData[2] = q[2]; |
357 |
> |
atomOrientData[3] = q[3]; |
358 |
|
|
359 |
< |
if( atoms[local_index]->isDirectional() ){ |
359 |
> |
atomOrientData[4] = dAtom->getJx(); |
360 |
> |
atomOrientData[5] = dAtom->getJy(); |
361 |
> |
atomOrientData[6] = dAtom->getJz(); |
362 |
> |
} |
363 |
|
|
364 |
< |
dAtom = (DirectionalAtom *)atoms[local_index]; |
365 |
< |
dAtom->getQ( q ); |
366 |
< |
|
367 |
< |
sprintf( tempBuffer, |
368 |
< |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
369 |
< |
q[0], |
315 |
< |
q[1], |
316 |
< |
q[2], |
317 |
< |
q[3], |
318 |
< |
dAtom->getJx(), |
319 |
< |
dAtom->getJy(), |
320 |
< |
dAtom->getJz()); |
321 |
< |
strcat( writeLine, tempBuffer ); |
364 |
> |
} else { |
365 |
> |
sprintf(painCave.errMsg, |
366 |
> |
"Atom %d not found on processor %d\n", |
367 |
> |
i, worldRank ); |
368 |
> |
haveError= 1; |
369 |
> |
simError(); |
370 |
|
} |
323 |
– |
else{ |
324 |
– |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
325 |
– |
} |
326 |
– |
} |
327 |
– |
else { |
328 |
– |
sprintf(painCave.errMsg, |
329 |
– |
"Atom %d not found on processor %d\n", |
330 |
– |
which_atom, worldRank ); |
331 |
– |
myStatus = 0; |
332 |
– |
simError(); |
371 |
|
|
372 |
< |
strcpy( writeLine, "Hello, I'm an error.\n"); |
335 |
< |
} |
372 |
> |
// I've survived this far, so send off the data! |
373 |
|
|
374 |
< |
MPI_Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, |
375 |
< |
TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD); |
376 |
< |
MPI_Send( &myStatus, 1, MPI_INT, 0, |
377 |
< |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
374 |
> |
atomTypeTag = 4*i; |
375 |
> |
atomIsDirectionalTag = 4*i + 1; |
376 |
> |
atomTransDataTag = 4*i + 2; |
377 |
> |
atomOrientDataTag = 4*i + 3; |
378 |
> |
|
379 |
> |
|
380 |
> |
strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE); |
381 |
> |
|
382 |
> |
MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0, |
383 |
> |
atomTypeTag, MPI_COMM_WORLD); |
384 |
> |
|
385 |
> |
MPI_Send(&isDirectional, 1, MPI_INT, 0, |
386 |
> |
atomIsDirectionalTag, MPI_COMM_WORLD); |
387 |
> |
|
388 |
> |
MPI_Send(atomTransData, 6, MPI_DOUBLE, 0, |
389 |
> |
atomTransDataTag, MPI_COMM_WORLD); |
390 |
> |
|
391 |
> |
if (isDirectional) { |
392 |
> |
|
393 |
> |
MPI_Send(atomOrientData, 7, MPI_DOUBLE, 0, |
394 |
> |
atomOrientDataTag, MPI_COMM_WORLD); |
395 |
> |
|
396 |
> |
} |
397 |
> |
|
398 |
> |
} |
399 |
|
} |
342 |
– |
} |
343 |
– |
outFile.flush(); |
344 |
– |
sprintf( checkPointMsg, |
345 |
– |
"Sucessfully took a dump.\n"); |
346 |
– |
MPIcheckPoint(); |
400 |
|
|
401 |
< |
// last thing last, enable fatalities. |
401 |
> |
sprintf( checkPointMsg, |
402 |
> |
"Sucessfully took a dump.\n"); |
403 |
> |
MPIcheckPoint(); |
404 |
> |
|
405 |
> |
} |
406 |
> |
|
407 |
|
painCave.isEventLoop = 0; |
408 |
|
|
409 |
|
#endif // is_mpi |
415 |
|
ofstream finalOut; |
416 |
|
|
417 |
|
const int BUFFERSIZE = 2000; |
418 |
+ |
const int MINIBUFFERSIZE = 10; |
419 |
|
char tempBuffer[BUFFERSIZE]; |
420 |
|
char writeLine[BUFFERSIZE]; |
421 |
|
|
425 |
|
int i; |
426 |
|
#ifdef IS_MPI |
427 |
|
int j, which_node, done, which_atom, local_index; |
428 |
+ |
double atomTransData[6]; |
429 |
+ |
double atomOrientData[7]; |
430 |
+ |
int isDirectional; |
431 |
+ |
char* atomTypeString; |
432 |
+ |
char MPIatomTypeString[MINIBUFFERSIZE]; |
433 |
+ |
int atomTypeTag; |
434 |
+ |
int atomIsDirectionalTag; |
435 |
+ |
int atomTransDataTag; |
436 |
+ |
int atomOrientDataTag; |
437 |
|
#else //is_mpi |
438 |
|
int nAtoms = entry_plug->n_atoms; |
439 |
|
#endif //is_mpi |
540 |
|
|
541 |
|
// write out header and node 0's coordinates |
542 |
|
|
475 |
– |
haveError = 0; |
543 |
|
if( worldRank == 0 ){ |
544 |
|
finalOut << mpiSim->getTotAtoms() << "\n"; |
545 |
|
|
546 |
|
finalOut << finalTime << ";\t" |
547 |
< |
<< entry_plug->Hmat[0][0] << "\t" |
548 |
< |
<< entry_plug->Hmat[1][0] << "\t" |
549 |
< |
<< entry_plug->Hmat[2][0] << ";\t" |
547 |
> |
<< entry_plug->Hmat[0][0] << "\t" |
548 |
> |
<< entry_plug->Hmat[1][0] << "\t" |
549 |
> |
<< entry_plug->Hmat[2][0] << ";\t" |
550 |
|
|
551 |
< |
<< entry_plug->Hmat[0][1] << "\t" |
552 |
< |
<< entry_plug->Hmat[1][1] << "\t" |
553 |
< |
<< entry_plug->Hmat[2][1] << ";\t" |
551 |
> |
<< entry_plug->Hmat[0][1] << "\t" |
552 |
> |
<< entry_plug->Hmat[1][1] << "\t" |
553 |
> |
<< entry_plug->Hmat[2][1] << ";\t" |
554 |
|
|
555 |
< |
<< entry_plug->Hmat[0][2] << "\t" |
556 |
< |
<< entry_plug->Hmat[1][2] << "\t" |
557 |
< |
<< entry_plug->Hmat[2][2] << ";"; |
555 |
> |
<< entry_plug->Hmat[0][2] << "\t" |
556 |
> |
<< entry_plug->Hmat[1][2] << "\t" |
557 |
> |
<< entry_plug->Hmat[2][2] << ";"; |
558 |
|
|
492 |
– |
//write out additional parameters, such as chi and eta |
559 |
|
finalOut << entry_plug->the_integrator->getAdditionalParameters(); |
560 |
|
finalOut << endl; |
561 |
< |
|
561 |
> |
finalOut.flush(); |
562 |
|
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
563 |
< |
// Get the Node number which has this molecule: |
563 |
> |
// Get the Node number which has this atom; |
564 |
|
|
565 |
|
which_node = AtomToProcMap[i]; |
566 |
|
|
567 |
< |
if (which_node == mpiSim->getMyNode()) { |
567 |
> |
if (which_node != 0) { |
568 |
> |
|
569 |
> |
atomTypeTag = 4*i; |
570 |
> |
atomIsDirectionalTag = 4*i + 1; |
571 |
> |
atomTransDataTag = 4*i + 2; |
572 |
> |
atomOrientDataTag = 4*i + 3; |
573 |
|
|
574 |
+ |
MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node, |
575 |
+ |
atomTypeTag, MPI_COMM_WORLD, &istatus); |
576 |
+ |
|
577 |
+ |
strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE); |
578 |
+ |
|
579 |
+ |
MPI_Recv(&isDirectional, 1, MPI_INT, which_node, |
580 |
+ |
atomIsDirectionalTag, MPI_COMM_WORLD, &istatus); |
581 |
+ |
|
582 |
+ |
MPI_Recv(atomTransData, 6, MPI_DOUBLE, which_node, |
583 |
+ |
atomTransDataTag, MPI_COMM_WORLD, &istatus); |
584 |
+ |
|
585 |
+ |
if (isDirectional) { |
586 |
+ |
|
587 |
+ |
MPI_Recv(atomOrientData, 7, MPI_DOUBLE, which_node, |
588 |
+ |
atomOrientDataTag, MPI_COMM_WORLD, &istatus); |
589 |
+ |
|
590 |
+ |
} |
591 |
+ |
|
592 |
+ |
} else { |
593 |
+ |
|
594 |
+ |
haveError = 0; |
595 |
|
which_atom = i; |
596 |
|
local_index=-1; |
597 |
+ |
|
598 |
|
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
599 |
|
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
600 |
|
} |
601 |
+ |
|
602 |
|
if (local_index != -1) { |
603 |
|
|
604 |
+ |
atomTypeString = atoms[local_index]->getType(); |
605 |
+ |
|
606 |
|
atoms[local_index]->getPos(pos); |
607 |
|
atoms[local_index]->getVel(vel); |
608 |
|
|
609 |
< |
sprintf( tempBuffer, |
610 |
< |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
611 |
< |
atoms[local_index]->getType(), |
516 |
< |
pos[0], |
517 |
< |
pos[1], |
518 |
< |
pos[2], |
519 |
< |
vel[0], |
520 |
< |
vel[1], |
521 |
< |
vel[2]); |
522 |
< |
strcpy( writeLine, tempBuffer ); |
609 |
> |
atomTransData[0] = pos[0]; |
610 |
> |
atomTransData[1] = pos[1]; |
611 |
> |
atomTransData[2] = pos[2]; |
612 |
|
|
613 |
< |
if( atoms[local_index]->isDirectional() ){ |
613 |
> |
atomTransData[3] = vel[0]; |
614 |
> |
atomTransData[4] = vel[1]; |
615 |
> |
atomTransData[5] = vel[2]; |
616 |
> |
|
617 |
> |
isDirectional = 0; |
618 |
|
|
619 |
< |
dAtom = (DirectionalAtom *)atoms[local_index]; |
527 |
< |
dAtom->getQ( q ); |
619 |
> |
if( atoms[local_index]->isDirectional() ){ |
620 |
|
|
621 |
< |
sprintf( tempBuffer, |
622 |
< |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
623 |
< |
q[0], |
624 |
< |
q[1], |
625 |
< |
q[2], |
626 |
< |
q[3], |
627 |
< |
dAtom->getJx(), |
628 |
< |
dAtom->getJy(), |
629 |
< |
dAtom->getJz()); |
630 |
< |
strcat( writeLine, tempBuffer ); |
631 |
< |
} |
632 |
< |
else |
633 |
< |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
634 |
< |
} |
635 |
< |
else { |
621 |
> |
isDirectional = 1; |
622 |
> |
|
623 |
> |
dAtom = (DirectionalAtom *)atoms[local_index]; |
624 |
> |
dAtom->getQ( q ); |
625 |
> |
|
626 |
> |
atomOrientData[0] = q[0]; |
627 |
> |
atomOrientData[1] = q[1]; |
628 |
> |
atomOrientData[2] = q[2]; |
629 |
> |
atomOrientData[3] = q[3]; |
630 |
> |
|
631 |
> |
atomOrientData[4] = dAtom->getJx(); |
632 |
> |
atomOrientData[5] = dAtom->getJy(); |
633 |
> |
atomOrientData[6] = dAtom->getJz(); |
634 |
> |
} |
635 |
> |
|
636 |
> |
} else { |
637 |
|
sprintf(painCave.errMsg, |
638 |
|
"Atom %d not found on processor %d\n", |
639 |
|
i, worldRank ); |
641 |
|
simError(); |
642 |
|
} |
643 |
|
|
644 |
< |
if(haveError) nodeZeroError(); |
644 |
> |
if(haveError) DieDieDie(); |
645 |
> |
|
646 |
> |
// If we've survived to here, format the line: |
647 |
> |
|
648 |
> |
sprintf( tempBuffer, |
649 |
> |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
650 |
> |
atomTypeString, |
651 |
> |
atomTransData[0], |
652 |
> |
atomTransData[1], |
653 |
> |
atomTransData[2], |
654 |
> |
atomTransData[3], |
655 |
> |
atomTransData[4], |
656 |
> |
atomTransData[5]); |
657 |
|
|
658 |
< |
} |
554 |
< |
else { |
658 |
> |
strcpy( writeLine, tempBuffer ); |
659 |
|
|
660 |
< |
myStatus = 1; |
557 |
< |
MPI_Send(&myStatus, 1, MPI_INT, which_node, |
558 |
< |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
559 |
< |
MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, |
560 |
< |
MPI_COMM_WORLD); |
561 |
< |
MPI_Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node, |
562 |
< |
TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus); |
563 |
< |
MPI_Recv(&myStatus, 1, MPI_INT, which_node, |
564 |
< |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
660 |
> |
if (isDirectional) { |
661 |
|
|
662 |
< |
if(!myStatus) nodeZeroError(); |
663 |
< |
} |
662 |
> |
sprintf( tempBuffer, |
663 |
> |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
664 |
> |
atomOrientData[0], |
665 |
> |
atomOrientData[1], |
666 |
> |
atomOrientData[2], |
667 |
> |
atomOrientData[3], |
668 |
> |
atomOrientData[4], |
669 |
> |
atomOrientData[5], |
670 |
> |
atomOrientData[6]); |
671 |
> |
strcat( writeLine, tempBuffer ); |
672 |
|
|
673 |
< |
finalOut << writeLine; |
674 |
< |
} |
673 |
> |
} else { |
674 |
> |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
675 |
> |
} |
676 |
|
|
677 |
< |
// kill everyone off: |
678 |
< |
myStatus = -1; |
679 |
< |
for (j = 1; j < mpiSim->getNumberProcessors(); j++) { |
575 |
< |
MPI_Send(&myStatus, 1, MPI_INT, j, |
576 |
< |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
677 |
> |
finalOut << writeLine; |
678 |
> |
finalOut.flush(); |
679 |
> |
} |
680 |
|
} |
681 |
|
|
682 |
+ |
finalOut.flush(); |
683 |
+ |
sprintf( checkPointMsg, |
684 |
+ |
"Sucessfully took a dump.\n"); |
685 |
+ |
MPIcheckPoint(); |
686 |
+ |
|
687 |
|
} else { |
688 |
|
|
689 |
< |
done = 0; |
690 |
< |
while (!done) { |
689 |
> |
// worldRank != 0, so I'm a remote node. |
690 |
> |
|
691 |
> |
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
692 |
> |
|
693 |
> |
// Am I the node which has this atom? |
694 |
> |
|
695 |
> |
if (AtomToProcMap[i] == worldRank) { |
696 |
|
|
697 |
< |
MPI_Recv(&myStatus, 1, MPI_INT, 0, |
698 |
< |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
697 |
> |
local_index=-1; |
698 |
> |
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
699 |
> |
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
700 |
> |
} |
701 |
> |
if (local_index != -1) { |
702 |
> |
|
703 |
> |
atomTypeString = atoms[local_index]->getType(); |
704 |
|
|
705 |
< |
if(!myStatus) anonymousNodeDie(); |
705 |
> |
atoms[local_index]->getPos(pos); |
706 |
> |
atoms[local_index]->getVel(vel); |
707 |
|
|
708 |
< |
if(myStatus < 0) break; |
708 |
> |
atomTransData[0] = pos[0]; |
709 |
> |
atomTransData[1] = pos[1]; |
710 |
> |
atomTransData[2] = pos[2]; |
711 |
|
|
712 |
< |
MPI_Recv(&which_atom, 1, MPI_INT, 0, |
713 |
< |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
712 |
> |
atomTransData[3] = vel[0]; |
713 |
> |
atomTransData[4] = vel[1]; |
714 |
> |
atomTransData[5] = vel[2]; |
715 |
> |
|
716 |
> |
isDirectional = 0; |
717 |
|
|
718 |
< |
myStatus = 1; |
595 |
< |
local_index=-1; |
596 |
< |
for (j=0; j < mpiSim->getMyNlocal(); j++) { |
597 |
< |
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
598 |
< |
} |
599 |
< |
if (local_index != -1) { |
718 |
> |
if( atoms[local_index]->isDirectional() ){ |
719 |
|
|
720 |
< |
atoms[local_index]->getPos(pos); |
721 |
< |
atoms[local_index]->getVel(vel); |
720 |
> |
isDirectional = 1; |
721 |
> |
|
722 |
> |
dAtom = (DirectionalAtom *)atoms[local_index]; |
723 |
> |
dAtom->getQ( q ); |
724 |
> |
|
725 |
> |
atomOrientData[0] = q[0]; |
726 |
> |
atomOrientData[1] = q[1]; |
727 |
> |
atomOrientData[2] = q[2]; |
728 |
> |
atomOrientData[3] = q[3]; |
729 |
|
|
730 |
< |
//format the line |
731 |
< |
sprintf( tempBuffer, |
732 |
< |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
733 |
< |
atoms[local_index]->getType(), |
608 |
< |
pos[0], |
609 |
< |
pos[1], |
610 |
< |
pos[2], |
611 |
< |
vel[0], |
612 |
< |
vel[1], |
613 |
< |
vel[2]); // check here. |
614 |
< |
strcpy( writeLine, tempBuffer ); |
730 |
> |
atomOrientData[4] = dAtom->getJx(); |
731 |
> |
atomOrientData[5] = dAtom->getJy(); |
732 |
> |
atomOrientData[6] = dAtom->getJz(); |
733 |
> |
} |
734 |
|
|
735 |
< |
if( atoms[local_index]->isDirectional() ){ |
735 |
> |
} else { |
736 |
> |
sprintf(painCave.errMsg, |
737 |
> |
"Atom %d not found on processor %d\n", |
738 |
> |
i, worldRank ); |
739 |
> |
haveError= 1; |
740 |
> |
simError(); |
741 |
> |
} |
742 |
|
|
743 |
< |
dAtom = (DirectionalAtom *)atoms[local_index]; |
619 |
< |
dAtom->getQ( q ); |
743 |
> |
// I've survived this far, so send off the data! |
744 |
|
|
745 |
< |
sprintf( tempBuffer, |
746 |
< |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
747 |
< |
q[0], |
748 |
< |
q[1], |
625 |
< |
q[2], |
626 |
< |
q[3], |
627 |
< |
dAtom->getJx(), |
628 |
< |
dAtom->getJy(), |
629 |
< |
dAtom->getJz()); |
630 |
< |
strcat( writeLine, tempBuffer ); |
631 |
< |
} |
632 |
< |
else{ |
633 |
< |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
634 |
< |
} |
635 |
< |
} |
636 |
< |
else { |
637 |
< |
sprintf(painCave.errMsg, |
638 |
< |
"Atom %d not found on processor %d\n", |
639 |
< |
which_atom, worldRank ); |
640 |
< |
myStatus = 0; |
641 |
< |
simError(); |
745 |
> |
atomTypeTag = 4*i; |
746 |
> |
atomIsDirectionalTag = 4*i + 1; |
747 |
> |
atomTransDataTag = 4*i + 2; |
748 |
> |
atomOrientDataTag = 4*i + 3; |
749 |
|
|
750 |
< |
strcpy( writeLine, "Hello, I'm an error.\n"); |
644 |
< |
} |
750 |
> |
strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE); |
751 |
|
|
752 |
< |
MPI_Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, |
753 |
< |
TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD); |
754 |
< |
MPI_Send( &myStatus, 1, MPI_INT, 0, |
755 |
< |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
752 |
> |
MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0, |
753 |
> |
atomTypeTag, MPI_COMM_WORLD); |
754 |
> |
|
755 |
> |
MPI_Send(&isDirectional, 1, MPI_INT, 0, |
756 |
> |
atomIsDirectionalTag, MPI_COMM_WORLD); |
757 |
> |
|
758 |
> |
MPI_Send(atomTransData, 6, MPI_DOUBLE, 0, |
759 |
> |
atomTransDataTag, MPI_COMM_WORLD); |
760 |
> |
|
761 |
> |
if (isDirectional) { |
762 |
> |
|
763 |
> |
MPI_Send(atomOrientData, 7, MPI_DOUBLE, 0, |
764 |
> |
atomOrientDataTag, MPI_COMM_WORLD); |
765 |
> |
|
766 |
> |
} |
767 |
> |
|
768 |
> |
} |
769 |
|
} |
770 |
+ |
|
771 |
+ |
sprintf( checkPointMsg, |
772 |
+ |
"Sucessfully wrote final file.\n"); |
773 |
+ |
MPIcheckPoint(); |
774 |
+ |
|
775 |
|
} |
776 |
< |
finalOut.flush(); |
777 |
< |
sprintf( checkPointMsg, |
654 |
< |
"Sucessfully took a dump.\n"); |
655 |
< |
MPIcheckPoint(); |
776 |
> |
|
777 |
> |
painCave.isEventLoop = 0; |
778 |
|
|
779 |
|
if( worldRank == 0 ) finalOut.close(); |
780 |
|
#endif // is_mpi |
786 |
|
|
787 |
|
// a couple of functions to let us escape the write loop |
788 |
|
|
789 |
< |
void dWrite::nodeZeroError( void ){ |
668 |
< |
int j, myStatus; |
789 |
> |
void dWrite::DieDieDie( void ){ |
790 |
|
|
670 |
– |
myStatus = 0; |
671 |
– |
for (j = 0; j < mpiSim->getNumberProcessors(); j++) { |
672 |
– |
MPI_Send( &myStatus, 1, MPI_INT, j, |
673 |
– |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
674 |
– |
} |
675 |
– |
|
676 |
– |
|
791 |
|
MPI_Finalize(); |
792 |
|
exit (0); |
679 |
– |
|
793 |
|
} |
794 |
|
|
682 |
– |
void dWrite::anonymousNodeDie( void ){ |
683 |
– |
|
684 |
– |
MPI_Finalize(); |
685 |
– |
exit (0); |
686 |
– |
} |
687 |
– |
|
795 |
|
#endif //is_mpi |