3 |
|
#include <string.h> |
4 |
|
#include <iostream> |
5 |
|
#include <fstream> |
6 |
+ |
#include <algorithm> |
7 |
+ |
#include <utility> |
8 |
|
|
9 |
|
#ifdef IS_MPI |
10 |
|
#include <mpi.h> |
28 |
|
if(worldRank == 0 ){ |
29 |
|
#endif // is_mpi |
30 |
|
|
31 |
< |
strcpy( outName, entry_plug->sampleName ); |
31 |
> |
dumpFile.open(entry_plug->sampleName, ios::out | ios::trunc ); |
32 |
|
|
33 |
< |
outFile.open(outName, ios::out | ios::trunc ); |
33 |
> |
if( !dumpFile ){ |
34 |
|
|
33 |
– |
if( !outFile ){ |
34 |
– |
|
35 |
|
sprintf( painCave.errMsg, |
36 |
|
"Could not open \"%s\" for dump output.\n", |
37 |
< |
outName); |
37 |
> |
entry_plug->sampleName); |
38 |
|
painCave.isFatal = 1; |
39 |
|
simError(); |
40 |
|
} |
41 |
|
|
42 |
– |
//outFile.setf( ios::scientific ); |
43 |
– |
|
42 |
|
#ifdef IS_MPI |
43 |
|
} |
44 |
|
|
45 |
+ |
//sort the local atoms by global index |
46 |
+ |
sortByGlobalIndex(); |
47 |
+ |
|
48 |
|
sprintf( checkPointMsg, |
49 |
|
"Sucessfully opened output file for dumping.\n"); |
50 |
|
MPIcheckPoint(); |
57 |
|
if(worldRank == 0 ){ |
58 |
|
#endif // is_mpi |
59 |
|
|
60 |
< |
outFile.close(); |
60 |
> |
dumpFile.close(); |
61 |
|
|
62 |
|
#ifdef IS_MPI |
63 |
|
} |
64 |
|
#endif // is_mpi |
65 |
|
} |
66 |
|
|
67 |
< |
void DumpWriter::writeDump( double currentTime ){ |
67 |
> |
#ifdef IS_MPI |
68 |
|
|
69 |
< |
const int BUFFERSIZE = 2000; |
70 |
< |
const int MINIBUFFERSIZE = 10; |
69 |
> |
/** |
70 |
> |
* A hook function to load balancing |
71 |
> |
*/ |
72 |
|
|
73 |
< |
char tempBuffer[BUFFERSIZE]; |
74 |
< |
char writeLine[BUFFERSIZE]; |
73 |
> |
void DumpWriter::update(){ |
74 |
> |
sortByGlobalIndex(); |
75 |
> |
} |
76 |
> |
|
77 |
> |
/** |
78 |
> |
* Auxiliary sorting function |
79 |
> |
*/ |
80 |
> |
|
81 |
> |
bool indexSortingCriterion(const pair<int, int>& p1, const pair<int, int>& p2){ |
82 |
> |
return p1.second < p2.second; |
83 |
> |
} |
84 |
|
|
85 |
< |
int i; |
86 |
< |
#ifdef IS_MPI |
87 |
< |
int j, which_node, done, which_atom, local_index; |
88 |
< |
double atomTransData[6]; |
89 |
< |
double atomOrientData[7]; |
79 |
< |
int isDirectional; |
80 |
< |
char* atomTypeString; |
81 |
< |
int me; |
82 |
< |
int atomTypeTag; |
83 |
< |
int atomIsDirectionalTag; |
84 |
< |
int atomTransDataTag; |
85 |
< |
int atomOrientDataTag; |
86 |
< |
#else //is_mpi |
87 |
< |
int nAtoms = entry_plug->n_atoms; |
88 |
< |
#endif //is_mpi |
89 |
< |
|
90 |
< |
double q[4]; |
91 |
< |
DirectionalAtom* dAtom; |
85 |
> |
/** |
86 |
> |
* Sorting the local index by global index |
87 |
> |
*/ |
88 |
> |
|
89 |
> |
void DumpWriter::sortByGlobalIndex(){ |
90 |
|
Atom** atoms = entry_plug->atoms; |
91 |
< |
double pos[3], vel[3]; |
91 |
> |
|
92 |
> |
indexArray.clear(); |
93 |
> |
|
94 |
> |
for(int i = 0; i < mpiSim->getMyNlocal();i++) |
95 |
> |
indexArray.push_back(make_pair(i, atoms[i]->getGlobalIndex())); |
96 |
> |
|
97 |
> |
sort(indexArray.begin(), indexArray.end(), indexSortingCriterion); |
98 |
|
|
99 |
< |
// write current frame to the eor file |
99 |
> |
//for (int i = 0; i < mpiSim->getMyNlocal(); i++) { |
100 |
> |
// printf("node %d has global %d at local %d\n", worldRank, indexArray[i].second, indexArray[i].first); |
101 |
> |
//} |
102 |
> |
|
103 |
> |
} |
104 |
|
|
105 |
< |
this->writeFinal( currentTime ); |
105 |
> |
#endif |
106 |
|
|
107 |
< |
#ifndef IS_MPI |
107 |
> |
void DumpWriter::writeDump(double currentTime){ |
108 |
|
|
109 |
< |
outFile << nAtoms << "\n"; |
109 |
> |
ofstream finalOut; |
110 |
> |
vector<ofstream*> fileStreams; |
111 |
|
|
112 |
< |
outFile << currentTime << ";\t" |
113 |
< |
<< entry_plug->Hmat[0][0] << "\t" |
114 |
< |
<< entry_plug->Hmat[1][0] << "\t" |
115 |
< |
<< entry_plug->Hmat[2][0] << ";\t" |
116 |
< |
|
117 |
< |
<< entry_plug->Hmat[0][1] << "\t" |
118 |
< |
<< entry_plug->Hmat[1][1] << "\t" |
119 |
< |
<< entry_plug->Hmat[2][1] << ";\t" |
120 |
< |
|
121 |
< |
<< entry_plug->Hmat[0][2] << "\t" |
122 |
< |
<< entry_plug->Hmat[1][2] << "\t" |
123 |
< |
<< entry_plug->Hmat[2][2] << ";"; |
115 |
< |
//write out additional parameters, such as chi and eta |
116 |
< |
outFile << entry_plug->the_integrator->getAdditionalParameters(); |
117 |
< |
outFile << endl; |
118 |
< |
|
119 |
< |
for( i=0; i<nAtoms; i++ ){ |
120 |
< |
|
121 |
< |
atoms[i]->getPos(pos); |
122 |
< |
atoms[i]->getVel(vel); |
123 |
< |
|
124 |
< |
sprintf( tempBuffer, |
125 |
< |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
126 |
< |
atoms[i]->getType(), |
127 |
< |
pos[0], |
128 |
< |
pos[1], |
129 |
< |
pos[2], |
130 |
< |
vel[0], |
131 |
< |
vel[1], |
132 |
< |
vel[2]); |
133 |
< |
strcpy( writeLine, tempBuffer ); |
134 |
< |
|
135 |
< |
if( atoms[i]->isDirectional() ){ |
136 |
< |
|
137 |
< |
dAtom = (DirectionalAtom *)atoms[i]; |
138 |
< |
dAtom->getQ( q ); |
139 |
< |
|
140 |
< |
sprintf( tempBuffer, |
141 |
< |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
142 |
< |
q[0], |
143 |
< |
q[1], |
144 |
< |
q[2], |
145 |
< |
q[3], |
146 |
< |
dAtom->getJx(), |
147 |
< |
dAtom->getJy(), |
148 |
< |
dAtom->getJz()); |
149 |
< |
strcat( writeLine, tempBuffer ); |
112 |
> |
#ifdef IS_MPI |
113 |
> |
printf("Hello from node %d\n", worldRank); |
114 |
> |
sortByGlobalIndex(); |
115 |
> |
if(worldRank == 0 ){ |
116 |
> |
|
117 |
> |
finalOut.open( entry_plug->finalName, ios::out | ios::trunc ); |
118 |
> |
if( !finalOut ){ |
119 |
> |
sprintf( painCave.errMsg, |
120 |
> |
"Could not open \"%s\" for final dump output.\n", |
121 |
> |
entry_plug->finalName ); |
122 |
> |
painCave.isFatal = 1; |
123 |
> |
simError(); |
124 |
|
} |
151 |
– |
else |
152 |
– |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
153 |
– |
|
154 |
– |
outFile << writeLine; |
125 |
|
} |
126 |
< |
outFile.flush(); |
126 |
> |
#endif // is_mpi |
127 |
|
|
128 |
< |
#else // is_mpi |
128 |
> |
fileStreams.push_back(&finalOut); |
129 |
> |
fileStreams.push_back(&dumpFile); |
130 |
|
|
131 |
< |
// first thing first, suspend fatalities. |
161 |
< |
painCave.isEventLoop = 1; |
131 |
> |
writeFrame(fileStreams, currentTime); |
132 |
|
|
133 |
< |
int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone |
134 |
< |
int haveError; |
133 |
> |
#ifdef IS_MPI |
134 |
> |
finalOut.close(); |
135 |
> |
#endif |
136 |
> |
|
137 |
> |
} |
138 |
|
|
139 |
< |
MPI_Status istatus; |
167 |
< |
int *AtomToProcMap = mpiSim->getAtomToProcMap(); |
139 |
> |
void DumpWriter::writeFinal(double currentTime){ |
140 |
|
|
169 |
– |
// write out header and node 0's coordinates |
170 |
– |
|
171 |
– |
if( worldRank == 0 ){ |
172 |
– |
outFile << mpiSim->getTotAtoms() << "\n"; |
173 |
– |
|
174 |
– |
outFile << currentTime << ";\t" |
175 |
– |
<< entry_plug->Hmat[0][0] << "\t" |
176 |
– |
<< entry_plug->Hmat[1][0] << "\t" |
177 |
– |
<< entry_plug->Hmat[2][0] << ";\t" |
178 |
– |
|
179 |
– |
<< entry_plug->Hmat[0][1] << "\t" |
180 |
– |
<< entry_plug->Hmat[1][1] << "\t" |
181 |
– |
<< entry_plug->Hmat[2][1] << ";\t" |
182 |
– |
|
183 |
– |
<< entry_plug->Hmat[0][2] << "\t" |
184 |
– |
<< entry_plug->Hmat[1][2] << "\t" |
185 |
– |
<< entry_plug->Hmat[2][2] << ";"; |
186 |
– |
|
187 |
– |
outFile << entry_plug->the_integrator->getAdditionalParameters(); |
188 |
– |
outFile << endl; |
189 |
– |
outFile.flush(); |
190 |
– |
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
191 |
– |
// Get the Node number which has this atom; |
192 |
– |
|
193 |
– |
which_node = AtomToProcMap[i]; |
194 |
– |
|
195 |
– |
if (which_node != 0) { |
196 |
– |
|
197 |
– |
atomTypeTag = 4*i; |
198 |
– |
atomIsDirectionalTag = 4*i + 1; |
199 |
– |
atomTransDataTag = 4*i + 2; |
200 |
– |
atomOrientDataTag = 4*i + 3; |
201 |
– |
|
202 |
– |
MPI_Recv(atomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node, |
203 |
– |
atomTypeTag, MPI_COMM_WORLD, &istatus); |
204 |
– |
|
205 |
– |
MPI_Recv(&isDirectional, 1, MPI_INT, which_node, |
206 |
– |
atomIsDirectionalTag, MPI_COMM_WORLD, &istatus); |
207 |
– |
|
208 |
– |
MPI_Recv(atomTransData, 6, MPI_DOUBLE, which_node, |
209 |
– |
atomTransDataTag, MPI_COMM_WORLD, &istatus); |
210 |
– |
|
211 |
– |
if (isDirectional) { |
212 |
– |
|
213 |
– |
MPI_Recv(atomOrientData, 7, MPI_DOUBLE, which_node, |
214 |
– |
atomOrientDataTag, MPI_COMM_WORLD, &istatus); |
215 |
– |
|
216 |
– |
} |
217 |
– |
|
218 |
– |
} else { |
219 |
– |
|
220 |
– |
haveError = 0; |
221 |
– |
which_atom = i; |
222 |
– |
local_index=-1; |
223 |
– |
|
224 |
– |
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
225 |
– |
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
226 |
– |
} |
227 |
– |
|
228 |
– |
if (local_index != -1) { |
229 |
– |
|
230 |
– |
atomTypeString = atoms[local_index]->getType(); |
231 |
– |
|
232 |
– |
atoms[local_index]->getPos(pos); |
233 |
– |
atoms[local_index]->getVel(vel); |
234 |
– |
|
235 |
– |
atomTransData[0] = pos[0]; |
236 |
– |
atomTransData[1] = pos[1]; |
237 |
– |
atomTransData[2] = pos[2]; |
238 |
– |
|
239 |
– |
atomTransData[3] = vel[0]; |
240 |
– |
atomTransData[4] = vel[1]; |
241 |
– |
atomTransData[5] = vel[2]; |
242 |
– |
|
243 |
– |
isDirectional = 0; |
244 |
– |
|
245 |
– |
if( atoms[local_index]->isDirectional() ){ |
246 |
– |
|
247 |
– |
isDirectional = 1; |
248 |
– |
|
249 |
– |
dAtom = (DirectionalAtom *)atoms[local_index]; |
250 |
– |
dAtom->getQ( q ); |
251 |
– |
|
252 |
– |
atomOrientData[0] = q[0]; |
253 |
– |
atomOrientData[1] = q[1]; |
254 |
– |
atomOrientData[2] = q[2]; |
255 |
– |
atomOrientData[3] = q[3]; |
256 |
– |
|
257 |
– |
atomOrientData[4] = dAtom->getJx(); |
258 |
– |
atomOrientData[5] = dAtom->getJy(); |
259 |
– |
atomOrientData[6] = dAtom->getJz(); |
260 |
– |
} |
261 |
– |
|
262 |
– |
} else { |
263 |
– |
sprintf(painCave.errMsg, |
264 |
– |
"Atom %d not found on processor %d\n", |
265 |
– |
i, worldRank ); |
266 |
– |
haveError= 1; |
267 |
– |
simError(); |
268 |
– |
} |
269 |
– |
|
270 |
– |
if(haveError) DieDieDie(); |
271 |
– |
|
272 |
– |
// If we've survived to here, format the line: |
273 |
– |
|
274 |
– |
sprintf( tempBuffer, |
275 |
– |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
276 |
– |
atomTypeString, |
277 |
– |
atomTransData[0], |
278 |
– |
atomTransData[1], |
279 |
– |
atomTransData[2], |
280 |
– |
atomTransData[3], |
281 |
– |
atomTransData[4], |
282 |
– |
atomTransData[5]); |
283 |
– |
|
284 |
– |
strcpy( writeLine, tempBuffer ); |
285 |
– |
|
286 |
– |
if (isDirectional) { |
287 |
– |
|
288 |
– |
sprintf( tempBuffer, |
289 |
– |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
290 |
– |
atomOrientData[0], |
291 |
– |
atomOrientData[1], |
292 |
– |
atomOrientData[2], |
293 |
– |
atomOrientData[3], |
294 |
– |
atomOrientData[4], |
295 |
– |
atomOrientData[5], |
296 |
– |
atomOrientData[6]); |
297 |
– |
strcat( writeLine, tempBuffer ); |
298 |
– |
|
299 |
– |
} else { |
300 |
– |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
301 |
– |
} |
302 |
– |
|
303 |
– |
outFile << writeLine; |
304 |
– |
outFile.flush(); |
305 |
– |
} |
306 |
– |
} |
307 |
– |
|
308 |
– |
outFile.flush(); |
309 |
– |
sprintf( checkPointMsg, |
310 |
– |
"Sucessfully took a dump.\n"); |
311 |
– |
MPIcheckPoint(); |
312 |
– |
|
313 |
– |
} else { |
314 |
– |
|
315 |
– |
// worldRank != 0, so I'm a remote node. |
316 |
– |
|
317 |
– |
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
318 |
– |
|
319 |
– |
// Am I the node which has this atom? |
320 |
– |
|
321 |
– |
if (AtomToProcMap[i] == worldRank) { |
322 |
– |
|
323 |
– |
local_index=-1; |
324 |
– |
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
325 |
– |
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
326 |
– |
} |
327 |
– |
if (local_index != -1) { |
328 |
– |
|
329 |
– |
atomTypeString = atoms[local_index]->getType(); |
330 |
– |
|
331 |
– |
atoms[local_index]->getPos(pos); |
332 |
– |
atoms[local_index]->getVel(vel); |
333 |
– |
|
334 |
– |
atomTransData[0] = pos[0]; |
335 |
– |
atomTransData[1] = pos[1]; |
336 |
– |
atomTransData[2] = pos[2]; |
337 |
– |
|
338 |
– |
atomTransData[3] = vel[0]; |
339 |
– |
atomTransData[4] = vel[1]; |
340 |
– |
atomTransData[5] = vel[2]; |
341 |
– |
|
342 |
– |
isDirectional = 0; |
343 |
– |
|
344 |
– |
if( atoms[local_index]->isDirectional() ){ |
345 |
– |
|
346 |
– |
isDirectional = 1; |
347 |
– |
|
348 |
– |
dAtom = (DirectionalAtom *)atoms[local_index]; |
349 |
– |
dAtom->getQ( q ); |
350 |
– |
|
351 |
– |
atomOrientData[0] = q[0]; |
352 |
– |
atomOrientData[1] = q[1]; |
353 |
– |
atomOrientData[2] = q[2]; |
354 |
– |
atomOrientData[3] = q[3]; |
355 |
– |
|
356 |
– |
atomOrientData[4] = dAtom->getJx(); |
357 |
– |
atomOrientData[5] = dAtom->getJy(); |
358 |
– |
atomOrientData[6] = dAtom->getJz(); |
359 |
– |
} |
360 |
– |
|
361 |
– |
} else { |
362 |
– |
sprintf(painCave.errMsg, |
363 |
– |
"Atom %d not found on processor %d\n", |
364 |
– |
i, worldRank ); |
365 |
– |
haveError= 1; |
366 |
– |
simError(); |
367 |
– |
} |
368 |
– |
|
369 |
– |
// I've survived this far, so send off the data! |
370 |
– |
|
371 |
– |
atomTypeTag = 4*i; |
372 |
– |
atomIsDirectionalTag = 4*i + 1; |
373 |
– |
atomTransDataTag = 4*i + 2; |
374 |
– |
atomOrientDataTag = 4*i + 3; |
375 |
– |
|
376 |
– |
MPI_Send(atomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0, |
377 |
– |
atomTypeTag, MPI_COMM_WORLD); |
378 |
– |
|
379 |
– |
MPI_Send(&isDirectional, 1, MPI_INT, 0, |
380 |
– |
atomIsDirectionalTag, MPI_COMM_WORLD); |
381 |
– |
|
382 |
– |
MPI_Send(atomTransData, 6, MPI_DOUBLE, 0, |
383 |
– |
atomTransDataTag, MPI_COMM_WORLD); |
384 |
– |
|
385 |
– |
if (isDirectional) { |
386 |
– |
|
387 |
– |
MPI_Send(atomOrientData, 7, MPI_DOUBLE, 0, |
388 |
– |
atomOrientDataTag, MPI_COMM_WORLD); |
389 |
– |
|
390 |
– |
} |
391 |
– |
|
392 |
– |
} |
393 |
– |
} |
394 |
– |
|
395 |
– |
sprintf( checkPointMsg, |
396 |
– |
"Sucessfully took a dump.\n"); |
397 |
– |
MPIcheckPoint(); |
398 |
– |
|
399 |
– |
} |
400 |
– |
|
401 |
– |
painCave.isEventLoop = 0; |
402 |
– |
|
403 |
– |
#endif // is_mpi |
404 |
– |
} |
405 |
– |
|
406 |
– |
void DumpWriter::writeFinal(double finalTime){ |
407 |
– |
|
408 |
– |
char finalName[500]; |
141 |
|
ofstream finalOut; |
142 |
+ |
vector<ofstream*> fileStreams; |
143 |
|
|
411 |
– |
const int BUFFERSIZE = 2000; |
412 |
– |
const int MINIBUFFERSIZE = 10; |
413 |
– |
char tempBuffer[BUFFERSIZE]; |
414 |
– |
char writeLine[BUFFERSIZE]; |
415 |
– |
|
416 |
– |
double q[4]; |
417 |
– |
DirectionalAtom* dAtom; |
418 |
– |
Atom** atoms = entry_plug->atoms; |
419 |
– |
int i; |
144 |
|
#ifdef IS_MPI |
421 |
– |
int j, which_node, done, which_atom, local_index; |
422 |
– |
double atomTransData[6]; |
423 |
– |
double atomOrientData[7]; |
424 |
– |
int isDirectional; |
425 |
– |
char* atomTypeString; |
426 |
– |
int atomTypeTag; |
427 |
– |
int atomIsDirectionalTag; |
428 |
– |
int atomTransDataTag; |
429 |
– |
int atomOrientDataTag; |
430 |
– |
#else //is_mpi |
431 |
– |
int nAtoms = entry_plug->n_atoms; |
432 |
– |
#endif //is_mpi |
433 |
– |
|
434 |
– |
double pos[3], vel[3]; |
435 |
– |
|
436 |
– |
#ifdef IS_MPI |
145 |
|
if(worldRank == 0 ){ |
146 |
|
#endif // is_mpi |
147 |
|
|
148 |
< |
strcpy( finalName, entry_plug->finalName ); |
148 |
> |
finalOut.open( entry_plug->finalName, ios::out | ios::trunc ); |
149 |
|
|
442 |
– |
finalOut.open( finalName, ios::out | ios::trunc ); |
150 |
|
if( !finalOut ){ |
151 |
|
sprintf( painCave.errMsg, |
152 |
|
"Could not open \"%s\" for final dump output.\n", |
153 |
< |
finalName ); |
153 |
> |
entry_plug->finalName ); |
154 |
|
painCave.isFatal = 1; |
155 |
|
simError(); |
156 |
|
} |
157 |
|
|
451 |
– |
// finalOut.setf( ios::scientific ); |
452 |
– |
|
158 |
|
#ifdef IS_MPI |
159 |
|
} |
160 |
+ |
#endif // is_mpi |
161 |
+ |
|
162 |
+ |
fileStreams.push_back(&finalOut); |
163 |
+ |
writeFrame(fileStreams, currentTime); |
164 |
|
|
165 |
< |
sprintf(checkPointMsg,"Opened file for final configuration\n"); |
166 |
< |
MPIcheckPoint(); |
165 |
> |
#ifdef IS_MPI |
166 |
> |
finalOut.close(); |
167 |
> |
#endif |
168 |
> |
|
169 |
> |
} |
170 |
|
|
171 |
< |
#endif //is_mpi |
171 |
> |
void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){ |
172 |
|
|
173 |
+ |
const int BUFFERSIZE = 2000; |
174 |
+ |
const int MINIBUFFERSIZE = 100; |
175 |
|
|
176 |
< |
#ifndef IS_MPI |
176 |
> |
char tempBuffer[BUFFERSIZE]; |
177 |
> |
char writeLine[BUFFERSIZE]; |
178 |
|
|
179 |
< |
finalOut << nAtoms << "\n"; |
179 |
> |
int i, k; |
180 |
|
|
181 |
< |
finalOut << finalTime << ";\t" |
182 |
< |
<< entry_plug->Hmat[0][0] << "\t" |
183 |
< |
<< entry_plug->Hmat[1][0] << "\t" |
184 |
< |
<< entry_plug->Hmat[2][0] << ";\t" |
185 |
< |
|
186 |
< |
<< entry_plug->Hmat[0][1] << "\t" |
187 |
< |
<< entry_plug->Hmat[1][1] << "\t" |
188 |
< |
<< entry_plug->Hmat[2][1] << ";\t" |
189 |
< |
|
190 |
< |
<< entry_plug->Hmat[0][2] << "\t" |
191 |
< |
<< entry_plug->Hmat[1][2] << "\t" |
192 |
< |
<< entry_plug->Hmat[2][2] << ";"; |
193 |
< |
|
194 |
< |
//write out additional parameters, such as chi and eta |
195 |
< |
finalOut << entry_plug->the_integrator->getAdditionalParameters(); |
196 |
< |
finalOut << endl; |
181 |
> |
#ifdef IS_MPI |
182 |
> |
|
183 |
> |
/********************************************************************* |
184 |
> |
* Documentation? You want DOCUMENTATION? |
185 |
> |
* |
186 |
> |
* Why all the potatoes below? |
187 |
> |
* |
188 |
> |
* To make a long story short, the original version of DumpWriter |
189 |
> |
* worked in the most inefficient way possible. Node 0 would |
190 |
> |
* poke each of the node for an individual atom's formatted data |
191 |
> |
* as node 0 worked its way down the global index. This was particularly |
192 |
> |
* inefficient since the method blocked all processors at every atom |
193 |
> |
* (and did it twice!). |
194 |
> |
* |
195 |
> |
* An intermediate version of DumpWriter could be described from Node |
196 |
> |
* zero's perspective as follows: |
197 |
> |
* |
198 |
> |
* 1) Have 100 of your friends stand in a circle. |
199 |
> |
* 2) When you say go, have all of them start tossing potatoes at |
200 |
> |
* you (one at a time). |
201 |
> |
* 3) Catch the potatoes. |
202 |
> |
* |
203 |
> |
* It was an improvement, but MPI has buffers and caches that could |
204 |
> |
* best be described in this analogy as "potato nets", so there's no |
205 |
> |
* need to block the processors atom-by-atom. |
206 |
> |
* |
207 |
> |
* This new and improved DumpWriter works in an even more efficient |
208 |
> |
* way: |
209 |
> |
* |
210 |
> |
* 1) Have 100 of your friend stand in a circle. |
211 |
> |
* 2) When you say go, have them start tossing 5-pound bags of |
212 |
> |
* potatoes at you. |
213 |
> |
* 3) Once you've caught a friend's bag of potatoes, |
214 |
> |
* toss them a spud to let them know they can toss another bag. |
215 |
> |
* |
216 |
> |
* How's THAT for documentation? |
217 |
> |
* |
218 |
> |
*********************************************************************/ |
219 |
|
|
220 |
+ |
int *potatoes; |
221 |
+ |
int myPotato; |
222 |
+ |
|
223 |
+ |
int nProc; |
224 |
+ |
int j, which_node, done, which_atom, local_index, currentIndex; |
225 |
+ |
double atomData6[6]; |
226 |
+ |
double atomData13[13]; |
227 |
+ |
int isDirectional; |
228 |
+ |
char* atomTypeString; |
229 |
+ |
char MPIatomTypeString[MINIBUFFERSIZE]; |
230 |
+ |
|
231 |
+ |
#else //is_mpi |
232 |
+ |
int nAtoms = entry_plug->n_atoms; |
233 |
+ |
#endif //is_mpi |
234 |
+ |
|
235 |
+ |
double q[4]; |
236 |
+ |
DirectionalAtom* dAtom; |
237 |
+ |
Atom** atoms = entry_plug->atoms; |
238 |
+ |
double pos[3], vel[3]; |
239 |
+ |
|
240 |
+ |
#ifndef IS_MPI |
241 |
+ |
|
242 |
+ |
for(k = 0; k < outFile.size(); k++){ |
243 |
+ |
*outFile[k] << nAtoms << "\n"; |
244 |
+ |
|
245 |
+ |
*outFile[k] << currentTime << ";\t" |
246 |
+ |
<< entry_plug->Hmat[0][0] << "\t" |
247 |
+ |
<< entry_plug->Hmat[1][0] << "\t" |
248 |
+ |
<< entry_plug->Hmat[2][0] << ";\t" |
249 |
+ |
|
250 |
+ |
<< entry_plug->Hmat[0][1] << "\t" |
251 |
+ |
<< entry_plug->Hmat[1][1] << "\t" |
252 |
+ |
<< entry_plug->Hmat[2][1] << ";\t" |
253 |
+ |
|
254 |
+ |
<< entry_plug->Hmat[0][2] << "\t" |
255 |
+ |
<< entry_plug->Hmat[1][2] << "\t" |
256 |
+ |
<< entry_plug->Hmat[2][2] << ";"; |
257 |
+ |
|
258 |
+ |
//write out additional parameters, such as chi and eta |
259 |
+ |
*outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl; |
260 |
+ |
} |
261 |
+ |
|
262 |
|
for( i=0; i<nAtoms; i++ ){ |
263 |
|
|
264 |
|
atoms[i]->getPos(pos); |
294 |
|
else |
295 |
|
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
296 |
|
|
297 |
< |
finalOut << writeLine; |
297 |
> |
for(k = 0; k < outFile.size(); k++) |
298 |
> |
*outFile[k] << writeLine; |
299 |
|
} |
520 |
– |
finalOut.flush(); |
521 |
– |
finalOut.close(); |
300 |
|
|
301 |
|
#else // is_mpi |
302 |
|
|
303 |
< |
// first thing first, suspend fatalities. |
304 |
< |
painCave.isEventLoop = 1; |
303 |
> |
/* code to find maximum tag value */ |
304 |
> |
|
305 |
> |
int *tagub, flag, MAXTAG; |
306 |
> |
MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag); |
307 |
> |
if (flag) { |
308 |
> |
MAXTAG = *tagub; |
309 |
> |
} else { |
310 |
> |
MAXTAG = 32767; |
311 |
> |
} |
312 |
|
|
528 |
– |
int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone |
313 |
|
int haveError; |
314 |
|
|
315 |
|
MPI_Status istatus; |
318 |
|
// write out header and node 0's coordinates |
319 |
|
|
320 |
|
if( worldRank == 0 ){ |
537 |
– |
finalOut << mpiSim->getTotAtoms() << "\n"; |
321 |
|
|
322 |
< |
finalOut << finalTime << ";\t" |
540 |
< |
<< entry_plug->Hmat[0][0] << "\t" |
541 |
< |
<< entry_plug->Hmat[1][0] << "\t" |
542 |
< |
<< entry_plug->Hmat[2][0] << ";\t" |
322 |
> |
// Node 0 needs a list of the magic potatoes for each processor; |
323 |
|
|
324 |
< |
<< entry_plug->Hmat[0][1] << "\t" |
325 |
< |
<< entry_plug->Hmat[1][1] << "\t" |
546 |
< |
<< entry_plug->Hmat[2][1] << ";\t" |
324 |
> |
nProc = mpiSim->getNumberProcessors(); |
325 |
> |
potatoes = new int[nProc]; |
326 |
|
|
327 |
< |
<< entry_plug->Hmat[0][2] << "\t" |
328 |
< |
<< entry_plug->Hmat[1][2] << "\t" |
329 |
< |
<< entry_plug->Hmat[2][2] << ";"; |
327 |
> |
//write out the comment lines |
328 |
> |
for (i = 0; i < nProc; i++) |
329 |
> |
potatoes[i] = 0; |
330 |
> |
|
331 |
> |
for(k = 0; k < outFile.size(); k++){ |
332 |
> |
*outFile[k] << mpiSim->getTotAtoms() << "\n"; |
333 |
|
|
334 |
< |
finalOut << entry_plug->the_integrator->getAdditionalParameters(); |
335 |
< |
finalOut << endl; |
336 |
< |
finalOut.flush(); |
334 |
> |
*outFile[k] << currentTime << ";\t" |
335 |
> |
<< entry_plug->Hmat[0][0] << "\t" |
336 |
> |
<< entry_plug->Hmat[1][0] << "\t" |
337 |
> |
<< entry_plug->Hmat[2][0] << ";\t" |
338 |
> |
|
339 |
> |
<< entry_plug->Hmat[0][1] << "\t" |
340 |
> |
<< entry_plug->Hmat[1][1] << "\t" |
341 |
> |
<< entry_plug->Hmat[2][1] << ";\t" |
342 |
> |
|
343 |
> |
<< entry_plug->Hmat[0][2] << "\t" |
344 |
> |
<< entry_plug->Hmat[1][2] << "\t" |
345 |
> |
<< entry_plug->Hmat[2][2] << ";"; |
346 |
> |
|
347 |
> |
*outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl; |
348 |
> |
} |
349 |
> |
|
350 |
> |
currentIndex = 0; |
351 |
> |
|
352 |
|
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
353 |
+ |
|
354 |
|
// Get the Node number which has this atom; |
355 |
< |
|
355 |
> |
|
356 |
|
which_node = AtomToProcMap[i]; |
357 |
< |
|
357 |
> |
|
358 |
|
if (which_node != 0) { |
561 |
– |
|
562 |
– |
atomTypeTag = 4*i; |
563 |
– |
atomIsDirectionalTag = 4*i + 1; |
564 |
– |
atomTransDataTag = 4*i + 2; |
565 |
– |
atomOrientDataTag = 4*i + 3; |
359 |
|
|
360 |
< |
MPI_Recv(atomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node, |
361 |
< |
atomTypeTag, MPI_COMM_WORLD, &istatus); |
360 |
> |
if (potatoes[which_node] + 3 >= MAXTAG) { |
361 |
> |
// The potato was going to exceed the maximum value, |
362 |
> |
// so wrap this processor potato back to 0: |
363 |
> |
|
364 |
> |
potatoes[which_node] = 0; |
365 |
> |
MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD); |
366 |
> |
|
367 |
> |
} |
368 |
> |
|
369 |
> |
myPotato = potatoes[which_node]; |
370 |
|
|
371 |
< |
MPI_Recv(&isDirectional, 1, MPI_INT, which_node, |
372 |
< |
atomIsDirectionalTag, MPI_COMM_WORLD, &istatus); |
371 |
> |
MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node, |
372 |
> |
myPotato, MPI_COMM_WORLD, &istatus); |
373 |
|
|
374 |
< |
MPI_Recv(atomTransData, 6, MPI_DOUBLE, which_node, |
375 |
< |
atomTransDataTag, MPI_COMM_WORLD, &istatus); |
374 |
> |
atomTypeString = MPIatomTypeString; |
375 |
> |
|
376 |
> |
myPotato++; |
377 |
|
|
378 |
< |
if (isDirectional) { |
378 |
> |
MPI_Recv(&isDirectional, 1, MPI_INT, which_node, |
379 |
> |
myPotato, MPI_COMM_WORLD, &istatus); |
380 |
> |
|
381 |
> |
myPotato++; |
382 |
|
|
383 |
< |
MPI_Recv(atomOrientData, 7, MPI_DOUBLE, which_node, |
384 |
< |
atomOrientDataTag, MPI_COMM_WORLD, &istatus); |
385 |
< |
|
383 |
> |
if (isDirectional) { |
384 |
> |
MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node, |
385 |
> |
myPotato, MPI_COMM_WORLD, &istatus); |
386 |
> |
} else { |
387 |
> |
MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node, |
388 |
> |
myPotato, MPI_COMM_WORLD, &istatus); |
389 |
|
} |
390 |
+ |
|
391 |
+ |
myPotato++; |
392 |
+ |
potatoes[which_node] = myPotato; |
393 |
|
|
394 |
|
} else { |
395 |
|
|
396 |
< |
haveError = 0; |
396 |
> |
haveError = 0; |
397 |
|
which_atom = i; |
398 |
< |
local_index=-1; |
398 |
> |
|
399 |
> |
//local_index = -1; |
400 |
|
|
401 |
< |
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
402 |
< |
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
403 |
< |
} |
404 |
< |
|
405 |
< |
if (local_index != -1) { |
406 |
< |
|
407 |
< |
atomTypeString = atoms[local_index]->getType(); |
408 |
< |
|
401 |
> |
//for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
402 |
> |
// if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
403 |
> |
//} |
404 |
> |
|
405 |
> |
//if (local_index != -1) { |
406 |
> |
|
407 |
> |
local_index = indexArray[currentIndex].first; |
408 |
> |
|
409 |
> |
if (which_atom == indexArray[currentIndex].second) { |
410 |
> |
|
411 |
> |
atomTypeString = atoms[local_index]->getType(); |
412 |
> |
|
413 |
|
atoms[local_index]->getPos(pos); |
414 |
< |
atoms[local_index]->getVel(vel); |
414 |
> |
atoms[local_index]->getVel(vel); |
415 |
> |
|
416 |
> |
atomData6[0] = pos[0]; |
417 |
> |
atomData6[1] = pos[1]; |
418 |
> |
atomData6[2] = pos[2]; |
419 |
|
|
420 |
< |
atomTransData[0] = pos[0]; |
421 |
< |
atomTransData[1] = pos[1]; |
422 |
< |
atomTransData[2] = pos[2]; |
603 |
< |
|
604 |
< |
atomTransData[3] = vel[0]; |
605 |
< |
atomTransData[4] = vel[1]; |
606 |
< |
atomTransData[5] = vel[2]; |
420 |
> |
atomData6[3] = vel[0]; |
421 |
> |
atomData6[4] = vel[1]; |
422 |
> |
atomData6[5] = vel[2]; |
423 |
|
|
424 |
|
isDirectional = 0; |
425 |
|
|
429 |
|
|
430 |
|
dAtom = (DirectionalAtom *)atoms[local_index]; |
431 |
|
dAtom->getQ( q ); |
616 |
– |
|
617 |
– |
atomOrientData[0] = q[0]; |
618 |
– |
atomOrientData[1] = q[1]; |
619 |
– |
atomOrientData[2] = q[2]; |
620 |
– |
atomOrientData[3] = q[3]; |
432 |
|
|
433 |
< |
atomOrientData[4] = dAtom->getJx(); |
434 |
< |
atomOrientData[5] = dAtom->getJy(); |
435 |
< |
atomOrientData[6] = dAtom->getJz(); |
433 |
> |
for (int j = 0; j < 6 ; j++) |
434 |
> |
atomData13[j] = atomData6[j]; |
435 |
> |
|
436 |
> |
atomData13[6] = q[0]; |
437 |
> |
atomData13[7] = q[1]; |
438 |
> |
atomData13[8] = q[2]; |
439 |
> |
atomData13[9] = q[3]; |
440 |
> |
|
441 |
> |
atomData13[10] = dAtom->getJx(); |
442 |
> |
atomData13[11] = dAtom->getJy(); |
443 |
> |
atomData13[12] = dAtom->getJz(); |
444 |
|
} |
445 |
< |
|
445 |
> |
|
446 |
|
} else { |
447 |
|
sprintf(painCave.errMsg, |
448 |
< |
"Atom %d not found on processor %d\n", |
449 |
< |
i, worldRank ); |
448 |
> |
"Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n", |
449 |
> |
which_atom, worldRank, currentIndex, local_index ); |
450 |
|
haveError= 1; |
451 |
|
simError(); |
452 |
|
} |
634 |
– |
|
635 |
– |
if(haveError) DieDieDie(); |
636 |
– |
|
637 |
– |
// If we've survived to here, format the line: |
453 |
|
|
454 |
< |
sprintf( tempBuffer, |
455 |
< |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
456 |
< |
atomTypeString, |
642 |
< |
atomTransData[0], |
643 |
< |
atomTransData[1], |
644 |
< |
atomTransData[2], |
645 |
< |
atomTransData[3], |
646 |
< |
atomTransData[4], |
647 |
< |
atomTransData[5]); |
648 |
< |
|
649 |
< |
strcpy( writeLine, tempBuffer ); |
650 |
< |
|
651 |
< |
if (isDirectional) { |
652 |
< |
|
653 |
< |
sprintf( tempBuffer, |
654 |
< |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
655 |
< |
atomOrientData[0], |
656 |
< |
atomOrientData[1], |
657 |
< |
atomOrientData[2], |
658 |
< |
atomOrientData[3], |
659 |
< |
atomOrientData[4], |
660 |
< |
atomOrientData[5], |
661 |
< |
atomOrientData[6]); |
662 |
< |
strcat( writeLine, tempBuffer ); |
663 |
< |
|
664 |
< |
} else { |
665 |
< |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
666 |
< |
} |
667 |
< |
|
668 |
< |
finalOut << writeLine; |
669 |
< |
finalOut.flush(); |
454 |
> |
if(haveError) DieDieDie(); |
455 |
> |
|
456 |
> |
currentIndex++; |
457 |
|
} |
458 |
+ |
// If we've survived to here, format the line: |
459 |
+ |
|
460 |
+ |
if (!isDirectional) { |
461 |
+ |
|
462 |
+ |
sprintf( writeLine, |
463 |
+ |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
464 |
+ |
atomTypeString, |
465 |
+ |
atomData6[0], |
466 |
+ |
atomData6[1], |
467 |
+ |
atomData6[2], |
468 |
+ |
atomData6[3], |
469 |
+ |
atomData6[4], |
470 |
+ |
atomData6[5]); |
471 |
+ |
|
472 |
+ |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
473 |
+ |
|
474 |
+ |
} else { |
475 |
+ |
|
476 |
+ |
sprintf( writeLine, |
477 |
+ |
"%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", |
478 |
+ |
atomTypeString, |
479 |
+ |
atomData13[0], |
480 |
+ |
atomData13[1], |
481 |
+ |
atomData13[2], |
482 |
+ |
atomData13[3], |
483 |
+ |
atomData13[4], |
484 |
+ |
atomData13[5], |
485 |
+ |
atomData13[6], |
486 |
+ |
atomData13[7], |
487 |
+ |
atomData13[8], |
488 |
+ |
atomData13[9], |
489 |
+ |
atomData13[10], |
490 |
+ |
atomData13[11], |
491 |
+ |
atomData13[12]); |
492 |
+ |
|
493 |
+ |
} |
494 |
+ |
|
495 |
+ |
for(k = 0; k < outFile.size(); k++) |
496 |
+ |
*outFile[k] << writeLine; |
497 |
|
} |
498 |
< |
|
499 |
< |
finalOut.flush(); |
498 |
> |
|
499 |
> |
for(k = 0; k < outFile.size(); k++) |
500 |
> |
outFile[k]->flush(); |
501 |
> |
|
502 |
|
sprintf( checkPointMsg, |
503 |
|
"Sucessfully took a dump.\n"); |
504 |
+ |
|
505 |
|
MPIcheckPoint(); |
506 |
|
|
507 |
+ |
delete[] potatoes; |
508 |
+ |
|
509 |
|
} else { |
510 |
|
|
511 |
|
// worldRank != 0, so I'm a remote node. |
512 |
+ |
|
513 |
+ |
// Set my magic potato to 0: |
514 |
+ |
|
515 |
+ |
myPotato = 0; |
516 |
+ |
currentIndex = 0; |
517 |
|
|
518 |
|
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
519 |
|
|
521 |
|
|
522 |
|
if (AtomToProcMap[i] == worldRank) { |
523 |
|
|
524 |
< |
local_index=-1; |
525 |
< |
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
526 |
< |
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
524 |
> |
if (myPotato + 3 >= MAXTAG) { |
525 |
> |
|
526 |
> |
// The potato was going to exceed the maximum value, |
527 |
> |
// so wrap this processor potato back to 0 (and block until |
528 |
> |
// node 0 says we can go: |
529 |
> |
|
530 |
> |
MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus); |
531 |
> |
|
532 |
|
} |
533 |
< |
if (local_index != -1) { |
533 |
> |
which_atom = i; |
534 |
> |
|
535 |
> |
//local_index = -1; |
536 |
> |
|
537 |
> |
//for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
538 |
> |
// if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
539 |
> |
//} |
540 |
> |
|
541 |
> |
//if (local_index != -1) { |
542 |
> |
|
543 |
> |
local_index = indexArray[currentIndex].first; |
544 |
> |
|
545 |
> |
if (which_atom == indexArray[currentIndex].second) { |
546 |
|
|
547 |
|
atomTypeString = atoms[local_index]->getType(); |
548 |
< |
|
548 |
> |
|
549 |
|
atoms[local_index]->getPos(pos); |
550 |
|
atoms[local_index]->getVel(vel); |
551 |
+ |
|
552 |
+ |
atomData6[0] = pos[0]; |
553 |
+ |
atomData6[1] = pos[1]; |
554 |
+ |
atomData6[2] = pos[2]; |
555 |
|
|
556 |
< |
atomTransData[0] = pos[0]; |
557 |
< |
atomTransData[1] = pos[1]; |
558 |
< |
atomTransData[2] = pos[2]; |
702 |
< |
|
703 |
< |
atomTransData[3] = vel[0]; |
704 |
< |
atomTransData[4] = vel[1]; |
705 |
< |
atomTransData[5] = vel[2]; |
556 |
> |
atomData6[3] = vel[0]; |
557 |
> |
atomData6[4] = vel[1]; |
558 |
> |
atomData6[5] = vel[2]; |
559 |
|
|
560 |
|
isDirectional = 0; |
561 |
|
|
566 |
|
dAtom = (DirectionalAtom *)atoms[local_index]; |
567 |
|
dAtom->getQ( q ); |
568 |
|
|
569 |
< |
atomOrientData[0] = q[0]; |
570 |
< |
atomOrientData[1] = q[1]; |
571 |
< |
atomOrientData[2] = q[2]; |
572 |
< |
atomOrientData[3] = q[3]; |
573 |
< |
|
574 |
< |
atomOrientData[4] = dAtom->getJx(); |
575 |
< |
atomOrientData[5] = dAtom->getJy(); |
576 |
< |
atomOrientData[6] = dAtom->getJz(); |
569 |
> |
for (int j = 0; j < 6 ; j++) |
570 |
> |
atomData13[j] = atomData6[j]; |
571 |
> |
|
572 |
> |
atomData13[6] = q[0]; |
573 |
> |
atomData13[7] = q[1]; |
574 |
> |
atomData13[8] = q[2]; |
575 |
> |
atomData13[9] = q[3]; |
576 |
> |
|
577 |
> |
atomData13[10] = dAtom->getJx(); |
578 |
> |
atomData13[11] = dAtom->getJy(); |
579 |
> |
atomData13[12] = dAtom->getJz(); |
580 |
|
} |
581 |
|
|
582 |
|
} else { |
583 |
|
sprintf(painCave.errMsg, |
584 |
< |
"Atom %d not found on processor %d\n", |
585 |
< |
i, worldRank ); |
584 |
> |
"Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n", |
585 |
> |
which_atom, worldRank, currentIndex, local_index ); |
586 |
|
haveError= 1; |
587 |
|
simError(); |
588 |
|
} |
589 |
+ |
|
590 |
+ |
strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE); |
591 |
|
|
592 |
< |
// I've survived this far, so send off the data! |
592 |
> |
// null terminate the string before sending (just in case): |
593 |
> |
MPIatomTypeString[MINIBUFFERSIZE-1] = '\0'; |
594 |
|
|
595 |
< |
atomTypeTag = 4*i; |
596 |
< |
atomIsDirectionalTag = 4*i + 1; |
738 |
< |
atomTransDataTag = 4*i + 2; |
739 |
< |
atomOrientDataTag = 4*i + 3; |
740 |
< |
|
741 |
< |
MPI_Send(atomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0, |
742 |
< |
atomTypeTag, MPI_COMM_WORLD); |
595 |
> |
MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0, |
596 |
> |
myPotato, MPI_COMM_WORLD); |
597 |
|
|
598 |
+ |
myPotato++; |
599 |
+ |
|
600 |
|
MPI_Send(&isDirectional, 1, MPI_INT, 0, |
601 |
< |
atomIsDirectionalTag, MPI_COMM_WORLD); |
601 |
> |
myPotato, MPI_COMM_WORLD); |
602 |
|
|
603 |
< |
MPI_Send(atomTransData, 6, MPI_DOUBLE, 0, |
604 |
< |
atomTransDataTag, MPI_COMM_WORLD); |
749 |
< |
|
603 |
> |
myPotato++; |
604 |
> |
|
605 |
|
if (isDirectional) { |
606 |
|
|
607 |
< |
MPI_Send(atomOrientData, 7, MPI_DOUBLE, 0, |
608 |
< |
atomOrientDataTag, MPI_COMM_WORLD); |
607 |
> |
MPI_Send(atomData13, 13, MPI_DOUBLE, 0, |
608 |
> |
myPotato, MPI_COMM_WORLD); |
609 |
|
|
610 |
+ |
} else { |
611 |
+ |
|
612 |
+ |
MPI_Send(atomData6, 6, MPI_DOUBLE, 0, |
613 |
+ |
myPotato, MPI_COMM_WORLD); |
614 |
|
} |
615 |
< |
|
615 |
> |
|
616 |
> |
myPotato++; |
617 |
> |
currentIndex++; |
618 |
|
} |
619 |
|
} |
620 |
|
|
621 |
|
sprintf( checkPointMsg, |
622 |
< |
"Sucessfully wrote final file.\n"); |
622 |
> |
"Sucessfully took a dump.\n"); |
623 |
|
MPIcheckPoint(); |
624 |
|
|
625 |
< |
} |
625 |
> |
} |
626 |
|
|
766 |
– |
painCave.isEventLoop = 0; |
767 |
– |
|
768 |
– |
if( worldRank == 0 ) finalOut.close(); |
627 |
|
#endif // is_mpi |
628 |
|
} |
629 |
|
|
772 |
– |
|
773 |
– |
|
630 |
|
#ifdef IS_MPI |
631 |
|
|
632 |
|
// a couple of functions to let us escape the write loop |