183 |
|
} |
184 |
|
|
185 |
|
#ifdef IS_MPI |
186 |
< |
void SimCreator::mpiMolDivide(){ |
187 |
< |
|
188 |
< |
mpiSim = new mpiSimulation(info); |
186 |
> |
void SimCreator::divideMolecules(SimInfo* info){ |
187 |
> |
int nComponents; |
188 |
> |
MoleculeStamp ** compStamps; |
189 |
> |
randomSPRNG * myRandom; |
190 |
> |
int * componentsNmol; |
191 |
> |
int * AtomsPerProc; |
192 |
|
|
193 |
< |
mpiSim->divideLabor(); |
193 |
> |
double numerator; |
194 |
> |
double denominator; |
195 |
> |
double precast; |
196 |
> |
double x; |
197 |
> |
double y; |
198 |
> |
double a; |
199 |
> |
int old_atoms; |
200 |
> |
int add_atoms; |
201 |
> |
int new_atoms; |
202 |
|
|
203 |
+ |
int nTarget; |
204 |
+ |
int molIndex; |
205 |
+ |
int atomIndex; |
206 |
+ |
int done; |
207 |
+ |
int i; |
208 |
+ |
int j; |
209 |
+ |
int loops; |
210 |
+ |
int which_proc; |
211 |
+ |
int nmol_global, |
212 |
+ |
nmol_local; |
213 |
+ |
int natoms_global, |
214 |
+ |
|
215 |
+ |
int baseSeed = info->getSeed(); |
216 |
+ |
CutoffGroupStamp * cg; |
217 |
+ |
|
218 |
+ |
nComponents = info->nComponents; |
219 |
+ |
compStamps = info->compStamps; |
220 |
+ |
componentsNmol = info->componentsNmol; |
221 |
+ |
AtomsPerProc = new int[parallelData->nProcessors]; |
222 |
+ |
|
223 |
+ |
parallelData->nMolGlobal = info->n_mol; |
224 |
+ |
|
225 |
+ |
if (parallelData->nProcessors > parallelData->nMolGlobal) { |
226 |
+ |
sprintf(painCave.errMsg, |
227 |
+ |
"nProcessors (%d) > nMol (%d)\n" |
228 |
+ |
"\tThe number of processors is larger than\n" |
229 |
+ |
"\tthe number of molecules. This will not result in a \n" |
230 |
+ |
"\tusable division of atoms for force decomposition.\n" |
231 |
+ |
"\tEither try a smaller number of processors, or run the\n" |
232 |
+ |
"\tsingle-processor version of OOPSE.\n", |
233 |
+ |
parallelData->nProcessors, |
234 |
+ |
parallelData->nMolGlobal); |
235 |
+ |
|
236 |
+ |
painCave.isFatal = 1; |
237 |
+ |
simError(); |
238 |
+ |
} |
239 |
+ |
|
240 |
+ |
myRandom = new randomSPRNG(baseSeed); |
241 |
+ |
|
242 |
+ |
a = 3.0 * parallelData->nMolGlobal / parallelData->nAtomsGlobal; |
243 |
+ |
|
244 |
+ |
// Initialize things that we'll send out later: |
245 |
+ |
for( i = 0; i < parallelData->nProcessors; i++ ) { |
246 |
+ |
AtomsPerProc[i] = 0; |
247 |
+ |
} |
248 |
+ |
|
249 |
+ |
for( i = 0; i < parallelData->nMolGlobal; i++ ) { |
250 |
+ |
// default to an error condition: |
251 |
+ |
MolToProcMap[i] = -1; |
252 |
+ |
} |
253 |
+ |
|
254 |
+ |
if (parallelData->myNode == 0) { |
255 |
+ |
numerator = info->n_atoms; |
256 |
+ |
denominator = parallelData->nProcessors; |
257 |
+ |
precast = numerator / denominator; |
258 |
+ |
nTarget = (int)(precast + 0.5); |
259 |
+ |
|
260 |
+ |
// Build the array of molecule component types first |
261 |
+ |
molIndex = 0; |
262 |
+ |
|
263 |
+ |
for( i = 0; i < nComponents; i++ ) { |
264 |
+ |
for( j = 0; j < componentsNmol[i]; j++ ) { |
265 |
+ |
molIndex++; |
266 |
+ |
} |
267 |
+ |
} |
268 |
+ |
|
269 |
+ |
for( i = 0; i < molIndex; i++ ) { |
270 |
+ |
done = 0; |
271 |
+ |
loops = 0; |
272 |
+ |
|
273 |
+ |
while (!done) { |
274 |
+ |
loops++; |
275 |
+ |
|
276 |
+ |
// Pick a processor at random |
277 |
+ |
|
278 |
+ |
which_proc |
279 |
+ |
|
280 |
+ |
= (int) (myRandom->getRandom() * parallelData->nProcessors); |
281 |
+ |
|
282 |
+ |
// How many atoms does this processor have? |
283 |
+ |
|
284 |
+ |
old_atoms = AtomsPerProc[which_proc]; |
285 |
+ |
add_atoms = compStamps[MolComponentType[i]]->getNAtoms(); |
286 |
+ |
new_atoms = old_atoms + add_atoms; |
287 |
+ |
|
288 |
+ |
// If we've been through this loop too many times, we need |
289 |
+ |
// to just give up and assign the molecule to this processor |
290 |
+ |
// and be done with it. |
291 |
+ |
|
292 |
+ |
if (loops > 100) { |
293 |
+ |
sprintf( |
294 |
+ |
painCave.errMsg, |
295 |
+ |
"I've tried 100 times to assign molecule %d to a " |
296 |
+ |
" processor, but can't find a good spot.\n" |
297 |
+ |
"I'm assigning it at random to processor %d.\n", |
298 |
+ |
i, |
299 |
+ |
which_proc); |
300 |
+ |
|
301 |
+ |
painCave.isFatal = 0; |
302 |
+ |
simError(); |
303 |
+ |
|
304 |
+ |
MolToProcMap[i] = which_proc; |
305 |
+ |
AtomsPerProc[which_proc] += add_atoms; |
306 |
+ |
|
307 |
+ |
done = 1; |
308 |
+ |
continue; |
309 |
+ |
} |
310 |
+ |
|
311 |
+ |
// If we can add this molecule to this processor without sending |
312 |
+ |
// it above nTarget, then go ahead and do it: |
313 |
+ |
|
314 |
+ |
if (new_atoms <= nTarget) { |
315 |
+ |
MolToProcMap[i] = which_proc; |
316 |
+ |
AtomsPerProc[which_proc] += add_atoms; |
317 |
+ |
|
318 |
+ |
done = 1; |
319 |
+ |
continue; |
320 |
+ |
} |
321 |
+ |
|
322 |
+ |
// The only situation left is when new_atoms > nTarget. We |
323 |
+ |
// want to accept this with some probability that dies off the |
324 |
+ |
// farther we are from nTarget |
325 |
+ |
|
326 |
+ |
// roughly: x = new_atoms - nTarget |
327 |
+ |
// Pacc(x) = exp(- a * x) |
328 |
+ |
// where a = penalty / (average atoms per molecule) |
329 |
+ |
|
330 |
+ |
x = (double)(new_atoms - nTarget); |
331 |
+ |
y = myRandom->getRandom(); |
332 |
+ |
|
333 |
+ |
if (y < exp(- a * x)) { |
334 |
+ |
MolToProcMap[i] = which_proc; |
335 |
+ |
AtomsPerProc[which_proc] += add_atoms; |
336 |
+ |
|
337 |
+ |
done = 1; |
338 |
+ |
continue; |
339 |
+ |
} else { continue; } |
340 |
+ |
} |
341 |
+ |
} |
342 |
+ |
|
343 |
+ |
// Spray out this nonsense to all other processors: |
344 |
+ |
|
345 |
+ |
MPI_Bcast(MolToProcMap, parallelData->nMolGlobal, MPI_INT, 0, |
346 |
+ |
MPI_COMM_WORLD); |
347 |
+ |
} else { |
348 |
+ |
|
349 |
+ |
// Listen to your marching orders from processor 0: |
350 |
+ |
|
351 |
+ |
MPI_Bcast(MolToProcMap, parallelData->nMolGlobal, MPI_INT, 0, |
352 |
+ |
MPI_COMM_WORLD); } |
353 |
+ |
|
354 |
+ |
// Let's all check for sanity: |
355 |
+ |
|
356 |
+ |
nmol_local = 0; |
357 |
+ |
|
358 |
+ |
for( i = 0; i < parallelData->nMolGlobal; i++ ) { |
359 |
+ |
if (MolToProcMap[i] == parallelData->myNode) { |
360 |
+ |
nmol_local++; |
361 |
+ |
} |
362 |
+ |
} |
363 |
+ |
|
364 |
+ |
MPI_Allreduce(&nmol_local, &nmol_global, 1, MPI_INT, MPI_SUM, |
365 |
+ |
MPI_COMM_WORLD); |
366 |
+ |
|
367 |
+ |
if (nmol_global != info->n_mol) { |
368 |
+ |
sprintf(painCave.errMsg, |
369 |
+ |
"The sum of all nmol_local, %d, did not equal the " |
370 |
+ |
"total number of molecules, %d.\n", |
371 |
+ |
nmol_global, |
372 |
+ |
info->n_mol); |
373 |
+ |
|
374 |
+ |
painCave.isFatal = 1; |
375 |
+ |
simError(); |
376 |
+ |
} |
377 |
+ |
|
378 |
+ |
sprintf(checkPointMsg, |
379 |
+ |
"Successfully divided the molecules among the processors.\n"); |
380 |
+ |
MPIcheckPoint(); |
381 |
+ |
|
382 |
|
} |
383 |
|
#endif |
384 |
|
|
400 |
|
|
401 |
|
} |
402 |
|
|
213 |
– |
|
403 |
|
void SimSetup::compList(MakeStamps* stamps,SimInfo* info) { |
404 |
|
int i; |
405 |
|
char* id; |