3 |
|
#include <string.h> |
4 |
|
#include <iostream> |
5 |
|
#include <fstream> |
6 |
+ |
#include <algorithm> |
7 |
+ |
#include <utility> |
8 |
|
|
9 |
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#ifdef IS_MPI |
10 |
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#include <mpi.h> |
28 |
|
if(worldRank == 0 ){ |
29 |
|
#endif // is_mpi |
30 |
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|
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 |
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|
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 = 100; |
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 |
< |
char MPIatomTypeString[MINIBUFFERSIZE]; |
82 |
< |
int me; |
83 |
< |
int atomTypeTag; |
84 |
< |
int atomIsDirectionalTag; |
85 |
< |
int atomTransDataTag; |
86 |
< |
int atomOrientDataTag; |
87 |
< |
#else //is_mpi |
88 |
< |
int nAtoms = entry_plug->n_atoms; |
89 |
< |
#endif //is_mpi |
90 |
< |
|
91 |
< |
double q[4]; |
92 |
< |
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 |
|
|
100 |
< |
// write current frame to the eor file |
100 |
> |
#endif |
101 |
|
|
102 |
< |
this->writeFinal( currentTime ); |
102 |
> |
void DumpWriter::writeDump(double currentTime){ |
103 |
|
|
104 |
< |
#ifndef IS_MPI |
104 |
> |
ofstream finalOut; |
105 |
> |
vector<ofstream*> fileStreams; |
106 |
|
|
107 |
< |
outFile << nAtoms << "\n"; |
108 |
< |
|
109 |
< |
outFile << currentTime << ";\t" |
110 |
< |
<< entry_plug->Hmat[0][0] << "\t" |
111 |
< |
<< entry_plug->Hmat[1][0] << "\t" |
112 |
< |
<< entry_plug->Hmat[2][0] << ";\t" |
113 |
< |
|
114 |
< |
<< entry_plug->Hmat[0][1] << "\t" |
115 |
< |
<< entry_plug->Hmat[1][1] << "\t" |
116 |
< |
<< entry_plug->Hmat[2][1] << ";\t" |
112 |
< |
|
113 |
< |
<< entry_plug->Hmat[0][2] << "\t" |
114 |
< |
<< entry_plug->Hmat[1][2] << "\t" |
115 |
< |
<< entry_plug->Hmat[2][2] << ";"; |
116 |
< |
//write out additional parameters, such as chi and eta |
117 |
< |
outFile << entry_plug->the_integrator->getAdditionalParameters(); |
118 |
< |
outFile << endl; |
119 |
< |
|
120 |
< |
for( i=0; i<nAtoms; i++ ){ |
121 |
< |
|
122 |
< |
atoms[i]->getPos(pos); |
123 |
< |
atoms[i]->getVel(vel); |
124 |
< |
|
125 |
< |
sprintf( tempBuffer, |
126 |
< |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
127 |
< |
atoms[i]->getType(), |
128 |
< |
pos[0], |
129 |
< |
pos[1], |
130 |
< |
pos[2], |
131 |
< |
vel[0], |
132 |
< |
vel[1], |
133 |
< |
vel[2]); |
134 |
< |
strcpy( writeLine, tempBuffer ); |
135 |
< |
|
136 |
< |
if( atoms[i]->isDirectional() ){ |
137 |
< |
|
138 |
< |
dAtom = (DirectionalAtom *)atoms[i]; |
139 |
< |
dAtom->getQ( q ); |
140 |
< |
|
141 |
< |
sprintf( tempBuffer, |
142 |
< |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
143 |
< |
q[0], |
144 |
< |
q[1], |
145 |
< |
q[2], |
146 |
< |
q[3], |
147 |
< |
dAtom->getJx(), |
148 |
< |
dAtom->getJy(), |
149 |
< |
dAtom->getJz()); |
150 |
< |
strcat( writeLine, tempBuffer ); |
107 |
> |
#ifdef IS_MPI |
108 |
> |
if(worldRank == 0 ){ |
109 |
> |
#endif |
110 |
> |
finalOut.open( entry_plug->finalName, ios::out | ios::trunc ); |
111 |
> |
if( !finalOut ){ |
112 |
> |
sprintf( painCave.errMsg, |
113 |
> |
"Could not open \"%s\" for final dump output.\n", |
114 |
> |
entry_plug->finalName ); |
115 |
> |
painCave.isFatal = 1; |
116 |
> |
simError(); |
117 |
|
} |
118 |
< |
else |
153 |
< |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
154 |
< |
|
155 |
< |
outFile << writeLine; |
118 |
> |
#ifdef IS_MPI |
119 |
|
} |
120 |
< |
outFile.flush(); |
120 |
> |
#endif // is_mpi |
121 |
|
|
122 |
< |
#else // is_mpi |
122 |
> |
fileStreams.push_back(&finalOut); |
123 |
> |
fileStreams.push_back(&dumpFile); |
124 |
|
|
125 |
< |
// first thing first, suspend fatalities. |
162 |
< |
painCave.isEventLoop = 1; |
125 |
> |
writeFrame(fileStreams, currentTime); |
126 |
|
|
127 |
< |
int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone |
128 |
< |
int haveError; |
127 |
> |
#ifdef IS_MPI |
128 |
> |
finalOut.close(); |
129 |
> |
#endif |
130 |
> |
|
131 |
> |
} |
132 |
|
|
133 |
< |
MPI_Status istatus; |
168 |
< |
int *AtomToProcMap = mpiSim->getAtomToProcMap(); |
133 |
> |
void DumpWriter::writeFinal(double currentTime){ |
134 |
|
|
135 |
< |
// write out header and node 0's coordinates |
135 |
> |
ofstream finalOut; |
136 |
> |
vector<ofstream*> fileStreams; |
137 |
|
|
138 |
< |
if( worldRank == 0 ){ |
139 |
< |
outFile << mpiSim->getTotAtoms() << "\n"; |
138 |
> |
#ifdef IS_MPI |
139 |
> |
if(worldRank == 0 ){ |
140 |
> |
#endif // is_mpi |
141 |
|
|
142 |
< |
outFile << currentTime << ";\t" |
176 |
< |
<< entry_plug->Hmat[0][0] << "\t" |
177 |
< |
<< entry_plug->Hmat[1][0] << "\t" |
178 |
< |
<< entry_plug->Hmat[2][0] << ";\t" |
142 |
> |
finalOut.open( entry_plug->finalName, ios::out | ios::trunc ); |
143 |
|
|
144 |
< |
<< entry_plug->Hmat[0][1] << "\t" |
145 |
< |
<< entry_plug->Hmat[1][1] << "\t" |
146 |
< |
<< entry_plug->Hmat[2][1] << ";\t" |
144 |
> |
if( !finalOut ){ |
145 |
> |
sprintf( painCave.errMsg, |
146 |
> |
"Could not open \"%s\" for final dump output.\n", |
147 |
> |
entry_plug->finalName ); |
148 |
> |
painCave.isFatal = 1; |
149 |
> |
simError(); |
150 |
> |
} |
151 |
|
|
152 |
< |
<< entry_plug->Hmat[0][2] << "\t" |
185 |
< |
<< entry_plug->Hmat[1][2] << "\t" |
186 |
< |
<< entry_plug->Hmat[2][2] << ";"; |
187 |
< |
|
188 |
< |
outFile << entry_plug->the_integrator->getAdditionalParameters(); |
189 |
< |
outFile << endl; |
190 |
< |
outFile.flush(); |
191 |
< |
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
192 |
< |
// Get the Node number which has this atom; |
193 |
< |
|
194 |
< |
which_node = AtomToProcMap[i]; |
195 |
< |
|
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 |
< |
|
203 |
< |
MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node, |
204 |
< |
atomTypeTag, MPI_COMM_WORLD, &istatus); |
205 |
< |
|
206 |
< |
strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE); |
207 |
< |
|
208 |
< |
// Null terminate the atomTypeString just in case: |
209 |
< |
|
210 |
< |
atomTypeString[strlen(atomTypeString) - 1] = '\0'; |
211 |
< |
|
212 |
< |
MPI_Recv(&isDirectional, 1, MPI_INT, which_node, |
213 |
< |
atomIsDirectionalTag, MPI_COMM_WORLD, &istatus); |
214 |
< |
|
215 |
< |
MPI_Recv(atomTransData, 6, MPI_DOUBLE, which_node, |
216 |
< |
atomTransDataTag, MPI_COMM_WORLD, &istatus); |
217 |
< |
|
218 |
< |
if (isDirectional) { |
219 |
< |
|
220 |
< |
MPI_Recv(atomOrientData, 7, MPI_DOUBLE, which_node, |
221 |
< |
atomOrientDataTag, MPI_COMM_WORLD, &istatus); |
222 |
< |
|
223 |
< |
} |
224 |
< |
|
225 |
< |
} else { |
226 |
< |
|
227 |
< |
haveError = 0; |
228 |
< |
which_atom = i; |
229 |
< |
local_index=-1; |
230 |
< |
|
231 |
< |
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
232 |
< |
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
233 |
< |
} |
234 |
< |
|
235 |
< |
if (local_index != -1) { |
236 |
< |
|
237 |
< |
atomTypeString = atoms[local_index]->getType(); |
238 |
< |
|
239 |
< |
atoms[local_index]->getPos(pos); |
240 |
< |
atoms[local_index]->getVel(vel); |
241 |
< |
|
242 |
< |
atomTransData[0] = pos[0]; |
243 |
< |
atomTransData[1] = pos[1]; |
244 |
< |
atomTransData[2] = pos[2]; |
245 |
< |
|
246 |
< |
atomTransData[3] = vel[0]; |
247 |
< |
atomTransData[4] = vel[1]; |
248 |
< |
atomTransData[5] = vel[2]; |
249 |
< |
|
250 |
< |
isDirectional = 0; |
251 |
< |
|
252 |
< |
if( atoms[local_index]->isDirectional() ){ |
253 |
< |
|
254 |
< |
isDirectional = 1; |
255 |
< |
|
256 |
< |
dAtom = (DirectionalAtom *)atoms[local_index]; |
257 |
< |
dAtom->getQ( q ); |
258 |
< |
|
259 |
< |
atomOrientData[0] = q[0]; |
260 |
< |
atomOrientData[1] = q[1]; |
261 |
< |
atomOrientData[2] = q[2]; |
262 |
< |
atomOrientData[3] = q[3]; |
263 |
< |
|
264 |
< |
atomOrientData[4] = dAtom->getJx(); |
265 |
< |
atomOrientData[5] = dAtom->getJy(); |
266 |
< |
atomOrientData[6] = dAtom->getJz(); |
267 |
< |
} |
268 |
< |
|
269 |
< |
} else { |
270 |
< |
sprintf(painCave.errMsg, |
271 |
< |
"Atom %d not found on processor %d\n", |
272 |
< |
i, worldRank ); |
273 |
< |
haveError= 1; |
274 |
< |
simError(); |
275 |
< |
} |
276 |
< |
|
277 |
< |
if(haveError) DieDieDie(); |
278 |
< |
|
279 |
< |
// If we've survived to here, format the line: |
280 |
< |
|
281 |
< |
sprintf( tempBuffer, |
282 |
< |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
283 |
< |
atomTypeString, |
284 |
< |
atomTransData[0], |
285 |
< |
atomTransData[1], |
286 |
< |
atomTransData[2], |
287 |
< |
atomTransData[3], |
288 |
< |
atomTransData[4], |
289 |
< |
atomTransData[5]); |
290 |
< |
|
291 |
< |
strcpy( writeLine, tempBuffer ); |
292 |
< |
|
293 |
< |
if (isDirectional) { |
294 |
< |
|
295 |
< |
sprintf( tempBuffer, |
296 |
< |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
297 |
< |
atomOrientData[0], |
298 |
< |
atomOrientData[1], |
299 |
< |
atomOrientData[2], |
300 |
< |
atomOrientData[3], |
301 |
< |
atomOrientData[4], |
302 |
< |
atomOrientData[5], |
303 |
< |
atomOrientData[6]); |
304 |
< |
strcat( writeLine, tempBuffer ); |
305 |
< |
|
306 |
< |
} else { |
307 |
< |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
308 |
< |
} |
309 |
< |
|
310 |
< |
outFile << writeLine; |
311 |
< |
outFile.flush(); |
312 |
< |
} |
313 |
< |
} |
314 |
< |
|
315 |
< |
outFile.flush(); |
316 |
< |
sprintf( checkPointMsg, |
317 |
< |
"Sucessfully took a dump.\n"); |
318 |
< |
MPIcheckPoint(); |
319 |
< |
|
320 |
< |
} else { |
321 |
< |
|
322 |
< |
// worldRank != 0, so I'm a remote node. |
323 |
< |
|
324 |
< |
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
325 |
< |
|
326 |
< |
// Am I the node which has this atom? |
327 |
< |
|
328 |
< |
if (AtomToProcMap[i] == worldRank) { |
329 |
< |
|
330 |
< |
local_index=-1; |
331 |
< |
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
332 |
< |
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
333 |
< |
} |
334 |
< |
if (local_index != -1) { |
335 |
< |
|
336 |
< |
atomTypeString = atoms[local_index]->getType(); |
337 |
< |
|
338 |
< |
atoms[local_index]->getPos(pos); |
339 |
< |
atoms[local_index]->getVel(vel); |
340 |
< |
|
341 |
< |
atomTransData[0] = pos[0]; |
342 |
< |
atomTransData[1] = pos[1]; |
343 |
< |
atomTransData[2] = pos[2]; |
344 |
< |
|
345 |
< |
atomTransData[3] = vel[0]; |
346 |
< |
atomTransData[4] = vel[1]; |
347 |
< |
atomTransData[5] = vel[2]; |
348 |
< |
|
349 |
< |
isDirectional = 0; |
350 |
< |
|
351 |
< |
if( atoms[local_index]->isDirectional() ){ |
352 |
< |
|
353 |
< |
isDirectional = 1; |
354 |
< |
|
355 |
< |
dAtom = (DirectionalAtom *)atoms[local_index]; |
356 |
< |
dAtom->getQ( q ); |
357 |
< |
|
358 |
< |
atomOrientData[0] = q[0]; |
359 |
< |
atomOrientData[1] = q[1]; |
360 |
< |
atomOrientData[2] = q[2]; |
361 |
< |
atomOrientData[3] = q[3]; |
362 |
< |
|
363 |
< |
atomOrientData[4] = dAtom->getJx(); |
364 |
< |
atomOrientData[5] = dAtom->getJy(); |
365 |
< |
atomOrientData[6] = dAtom->getJz(); |
366 |
< |
} |
367 |
< |
|
368 |
< |
} else { |
369 |
< |
sprintf(painCave.errMsg, |
370 |
< |
"Atom %d not found on processor %d\n", |
371 |
< |
i, worldRank ); |
372 |
< |
haveError= 1; |
373 |
< |
simError(); |
374 |
< |
} |
375 |
< |
|
376 |
< |
// I've survived this far, so send off the data! |
377 |
< |
|
378 |
< |
atomTypeTag = 4*i; |
379 |
< |
atomIsDirectionalTag = 4*i + 1; |
380 |
< |
atomTransDataTag = 4*i + 2; |
381 |
< |
atomOrientDataTag = 4*i + 3; |
382 |
< |
|
383 |
< |
|
384 |
< |
strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE); |
385 |
< |
|
386 |
< |
// null terminate the string before sending (just in case): |
387 |
< |
MPIatomTypeString[MINIBUFFERSIZE-1] = '\0'; |
388 |
< |
|
389 |
< |
MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0, |
390 |
< |
atomTypeTag, MPI_COMM_WORLD); |
391 |
< |
|
392 |
< |
MPI_Send(&isDirectional, 1, MPI_INT, 0, |
393 |
< |
atomIsDirectionalTag, MPI_COMM_WORLD); |
394 |
< |
|
395 |
< |
MPI_Send(atomTransData, 6, MPI_DOUBLE, 0, |
396 |
< |
atomTransDataTag, MPI_COMM_WORLD); |
397 |
< |
|
398 |
< |
if (isDirectional) { |
399 |
< |
|
400 |
< |
MPI_Send(atomOrientData, 7, MPI_DOUBLE, 0, |
401 |
< |
atomOrientDataTag, MPI_COMM_WORLD); |
402 |
< |
|
403 |
< |
} |
404 |
< |
|
405 |
< |
} |
406 |
< |
} |
407 |
< |
|
408 |
< |
sprintf( checkPointMsg, |
409 |
< |
"Sucessfully took a dump.\n"); |
410 |
< |
MPIcheckPoint(); |
411 |
< |
|
152 |
> |
#ifdef IS_MPI |
153 |
|
} |
154 |
+ |
#endif // is_mpi |
155 |
|
|
156 |
< |
painCave.isEventLoop = 0; |
156 |
> |
fileStreams.push_back(&finalOut); |
157 |
> |
writeFrame(fileStreams, currentTime); |
158 |
|
|
159 |
< |
#endif // is_mpi |
159 |
> |
#ifdef IS_MPI |
160 |
> |
finalOut.close(); |
161 |
> |
#endif |
162 |
> |
|
163 |
|
} |
164 |
|
|
165 |
< |
void DumpWriter::writeFinal(double finalTime){ |
165 |
> |
void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){ |
166 |
|
|
421 |
– |
char finalName[500]; |
422 |
– |
ofstream finalOut; |
423 |
– |
|
167 |
|
const int BUFFERSIZE = 2000; |
168 |
|
const int MINIBUFFERSIZE = 100; |
169 |
< |
char tempBuffer[BUFFERSIZE]; |
169 |
> |
|
170 |
> |
char tempBuffer[BUFFERSIZE]; |
171 |
|
char writeLine[BUFFERSIZE]; |
172 |
|
|
173 |
< |
double q[4]; |
174 |
< |
DirectionalAtom* dAtom; |
431 |
< |
Atom** atoms = entry_plug->atoms; |
432 |
< |
int i; |
173 |
> |
int i, k; |
174 |
> |
|
175 |
|
#ifdef IS_MPI |
176 |
< |
int j, which_node, done, which_atom, local_index; |
177 |
< |
double atomTransData[6]; |
178 |
< |
double atomOrientData[7]; |
176 |
> |
|
177 |
> |
/********************************************************************* |
178 |
> |
* Documentation? You want DOCUMENTATION? |
179 |
> |
* |
180 |
> |
* Why all the potatoes below? |
181 |
> |
* |
182 |
> |
* To make a long story short, the original version of DumpWriter |
183 |
> |
* worked in the most inefficient way possible. Node 0 would |
184 |
> |
* poke each of the node for an individual atom's formatted data |
185 |
> |
* as node 0 worked its way down the global index. This was particularly |
186 |
> |
* inefficient since the method blocked all processors at every atom |
187 |
> |
* (and did it twice!). |
188 |
> |
* |
189 |
> |
* An intermediate version of DumpWriter could be described from Node |
190 |
> |
* zero's perspective as follows: |
191 |
> |
* |
192 |
> |
* 1) Have 100 of your friends stand in a circle. |
193 |
> |
* 2) When you say go, have all of them start tossing potatoes at |
194 |
> |
* you (one at a time). |
195 |
> |
* 3) Catch the potatoes. |
196 |
> |
* |
197 |
> |
* It was an improvement, but MPI has buffers and caches that could |
198 |
> |
* best be described in this analogy as "potato nets", so there's no |
199 |
> |
* need to block the processors atom-by-atom. |
200 |
> |
* |
201 |
> |
* This new and improved DumpWriter works in an even more efficient |
202 |
> |
* way: |
203 |
> |
* |
204 |
> |
* 1) Have 100 of your friend stand in a circle. |
205 |
> |
* 2) When you say go, have them start tossing 5-pound bags of |
206 |
> |
* potatoes at you. |
207 |
> |
* 3) Once you've caught a friend's bag of potatoes, |
208 |
> |
* toss them a spud to let them know they can toss another bag. |
209 |
> |
* |
210 |
> |
* How's THAT for documentation? |
211 |
> |
* |
212 |
> |
*********************************************************************/ |
213 |
> |
|
214 |
> |
int *potatoes; |
215 |
> |
int myPotato; |
216 |
> |
|
217 |
> |
int nProc; |
218 |
> |
int j, which_node, done, which_atom, local_index, currentIndex; |
219 |
> |
double atomData6[6]; |
220 |
> |
double atomData13[13]; |
221 |
|
int isDirectional; |
222 |
|
char* atomTypeString; |
223 |
|
char MPIatomTypeString[MINIBUFFERSIZE]; |
224 |
< |
int atomTypeTag; |
441 |
< |
int atomIsDirectionalTag; |
442 |
< |
int atomTransDataTag; |
443 |
< |
int atomOrientDataTag; |
224 |
> |
|
225 |
|
#else //is_mpi |
226 |
|
int nAtoms = entry_plug->n_atoms; |
227 |
|
#endif //is_mpi |
228 |
|
|
229 |
+ |
double q[4]; |
230 |
+ |
DirectionalAtom* dAtom; |
231 |
+ |
Atom** atoms = entry_plug->atoms; |
232 |
|
double pos[3], vel[3]; |
233 |
|
|
450 |
– |
#ifdef IS_MPI |
451 |
– |
if(worldRank == 0 ){ |
452 |
– |
#endif // is_mpi |
453 |
– |
|
454 |
– |
strcpy( finalName, entry_plug->finalName ); |
455 |
– |
|
456 |
– |
finalOut.open( finalName, ios::out | ios::trunc ); |
457 |
– |
if( !finalOut ){ |
458 |
– |
sprintf( painCave.errMsg, |
459 |
– |
"Could not open \"%s\" for final dump output.\n", |
460 |
– |
finalName ); |
461 |
– |
painCave.isFatal = 1; |
462 |
– |
simError(); |
463 |
– |
} |
464 |
– |
|
465 |
– |
// finalOut.setf( ios::scientific ); |
466 |
– |
|
467 |
– |
#ifdef IS_MPI |
468 |
– |
} |
469 |
– |
|
470 |
– |
sprintf(checkPointMsg,"Opened file for final configuration\n"); |
471 |
– |
MPIcheckPoint(); |
472 |
– |
|
473 |
– |
#endif //is_mpi |
474 |
– |
|
475 |
– |
|
234 |
|
#ifndef IS_MPI |
235 |
+ |
|
236 |
+ |
for(k = 0; k < outFile.size(); k++){ |
237 |
+ |
*outFile[k] << nAtoms << "\n"; |
238 |
|
|
239 |
< |
finalOut << nAtoms << "\n"; |
239 |
> |
*outFile[k] << currentTime << ";\t" |
240 |
> |
<< entry_plug->Hmat[0][0] << "\t" |
241 |
> |
<< entry_plug->Hmat[1][0] << "\t" |
242 |
> |
<< entry_plug->Hmat[2][0] << ";\t" |
243 |
> |
|
244 |
> |
<< entry_plug->Hmat[0][1] << "\t" |
245 |
> |
<< entry_plug->Hmat[1][1] << "\t" |
246 |
> |
<< entry_plug->Hmat[2][1] << ";\t" |
247 |
|
|
248 |
< |
finalOut << finalTime << ";\t" |
249 |
< |
<< entry_plug->Hmat[0][0] << "\t" |
250 |
< |
<< entry_plug->Hmat[1][0] << "\t" |
483 |
< |
<< entry_plug->Hmat[2][0] << ";\t" |
248 |
> |
<< entry_plug->Hmat[0][2] << "\t" |
249 |
> |
<< entry_plug->Hmat[1][2] << "\t" |
250 |
> |
<< entry_plug->Hmat[2][2] << ";"; |
251 |
|
|
252 |
< |
<< entry_plug->Hmat[0][1] << "\t" |
253 |
< |
<< entry_plug->Hmat[1][1] << "\t" |
254 |
< |
<< entry_plug->Hmat[2][1] << ";\t" |
255 |
< |
|
489 |
< |
<< entry_plug->Hmat[0][2] << "\t" |
490 |
< |
<< entry_plug->Hmat[1][2] << "\t" |
491 |
< |
<< entry_plug->Hmat[2][2] << ";"; |
492 |
< |
|
493 |
< |
//write out additional parameters, such as chi and eta |
494 |
< |
finalOut << entry_plug->the_integrator->getAdditionalParameters(); |
495 |
< |
finalOut << endl; |
496 |
< |
|
252 |
> |
//write out additional parameters, such as chi and eta |
253 |
> |
*outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl; |
254 |
> |
} |
255 |
> |
|
256 |
|
for( i=0; i<nAtoms; i++ ){ |
257 |
|
|
258 |
|
atoms[i]->getPos(pos); |
288 |
|
else |
289 |
|
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
290 |
|
|
291 |
< |
finalOut << writeLine; |
291 |
> |
for(k = 0; k < outFile.size(); k++) |
292 |
> |
*outFile[k] << writeLine; |
293 |
|
} |
534 |
– |
finalOut.flush(); |
535 |
– |
finalOut.close(); |
294 |
|
|
295 |
|
#else // is_mpi |
296 |
|
|
297 |
< |
// first thing first, suspend fatalities. |
298 |
< |
painCave.isEventLoop = 1; |
297 |
> |
/* code to find maximum tag value */ |
298 |
> |
|
299 |
> |
int *tagub, flag, MAXTAG; |
300 |
> |
MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag); |
301 |
> |
if (flag) { |
302 |
> |
MAXTAG = *tagub; |
303 |
> |
} else { |
304 |
> |
MAXTAG = 32767; |
305 |
> |
} |
306 |
|
|
542 |
– |
int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone |
307 |
|
int haveError; |
308 |
|
|
309 |
|
MPI_Status istatus; |
312 |
|
// write out header and node 0's coordinates |
313 |
|
|
314 |
|
if( worldRank == 0 ){ |
551 |
– |
finalOut << mpiSim->getTotAtoms() << "\n"; |
315 |
|
|
316 |
< |
finalOut << finalTime << ";\t" |
554 |
< |
<< entry_plug->Hmat[0][0] << "\t" |
555 |
< |
<< entry_plug->Hmat[1][0] << "\t" |
556 |
< |
<< entry_plug->Hmat[2][0] << ";\t" |
316 |
> |
// Node 0 needs a list of the magic potatoes for each processor; |
317 |
|
|
318 |
< |
<< entry_plug->Hmat[0][1] << "\t" |
319 |
< |
<< entry_plug->Hmat[1][1] << "\t" |
560 |
< |
<< entry_plug->Hmat[2][1] << ";\t" |
318 |
> |
nProc = mpiSim->getNumberProcessors(); |
319 |
> |
potatoes = new int[nProc]; |
320 |
|
|
321 |
< |
<< entry_plug->Hmat[0][2] << "\t" |
322 |
< |
<< entry_plug->Hmat[1][2] << "\t" |
323 |
< |
<< entry_plug->Hmat[2][2] << ";"; |
321 |
> |
//write out the comment lines |
322 |
> |
for (i = 0; i < nProc; i++) |
323 |
> |
potatoes[i] = 0; |
324 |
> |
|
325 |
> |
for(k = 0; k < outFile.size(); k++){ |
326 |
> |
*outFile[k] << mpiSim->getTotAtoms() << "\n"; |
327 |
|
|
328 |
< |
finalOut << entry_plug->the_integrator->getAdditionalParameters(); |
329 |
< |
finalOut << endl; |
330 |
< |
finalOut.flush(); |
328 |
> |
*outFile[k] << currentTime << ";\t" |
329 |
> |
<< entry_plug->Hmat[0][0] << "\t" |
330 |
> |
<< entry_plug->Hmat[1][0] << "\t" |
331 |
> |
<< entry_plug->Hmat[2][0] << ";\t" |
332 |
> |
|
333 |
> |
<< entry_plug->Hmat[0][1] << "\t" |
334 |
> |
<< entry_plug->Hmat[1][1] << "\t" |
335 |
> |
<< entry_plug->Hmat[2][1] << ";\t" |
336 |
> |
|
337 |
> |
<< entry_plug->Hmat[0][2] << "\t" |
338 |
> |
<< entry_plug->Hmat[1][2] << "\t" |
339 |
> |
<< entry_plug->Hmat[2][2] << ";"; |
340 |
> |
|
341 |
> |
*outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl; |
342 |
> |
} |
343 |
> |
|
344 |
> |
currentIndex = 0; |
345 |
> |
|
346 |
|
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
347 |
+ |
|
348 |
|
// Get the Node number which has this atom; |
349 |
< |
|
349 |
> |
|
350 |
|
which_node = AtomToProcMap[i]; |
351 |
< |
|
351 |
> |
|
352 |
|
if (which_node != 0) { |
575 |
– |
|
576 |
– |
atomTypeTag = 4*i; |
577 |
– |
atomIsDirectionalTag = 4*i + 1; |
578 |
– |
atomTransDataTag = 4*i + 2; |
579 |
– |
atomOrientDataTag = 4*i + 3; |
353 |
|
|
354 |
+ |
if (potatoes[which_node] + 3 >= MAXTAG) { |
355 |
+ |
// The potato was going to exceed the maximum value, |
356 |
+ |
// so wrap this processor potato back to 0: |
357 |
+ |
|
358 |
+ |
potatoes[which_node] = 0; |
359 |
+ |
MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD); |
360 |
+ |
|
361 |
+ |
} |
362 |
+ |
|
363 |
+ |
myPotato = potatoes[which_node]; |
364 |
+ |
|
365 |
|
MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node, |
366 |
< |
atomTypeTag, MPI_COMM_WORLD, &istatus); |
366 |
> |
myPotato, MPI_COMM_WORLD, &istatus); |
367 |
|
|
368 |
< |
strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE); |
368 |
> |
atomTypeString = MPIatomTypeString; |
369 |
> |
|
370 |
> |
myPotato++; |
371 |
|
|
372 |
|
MPI_Recv(&isDirectional, 1, MPI_INT, which_node, |
373 |
< |
atomIsDirectionalTag, MPI_COMM_WORLD, &istatus); |
374 |
< |
|
375 |
< |
MPI_Recv(atomTransData, 6, MPI_DOUBLE, which_node, |
590 |
< |
atomTransDataTag, MPI_COMM_WORLD, &istatus); |
373 |
> |
myPotato, MPI_COMM_WORLD, &istatus); |
374 |
> |
|
375 |
> |
myPotato++; |
376 |
|
|
377 |
< |
if (isDirectional) { |
378 |
< |
|
379 |
< |
MPI_Recv(atomOrientData, 7, MPI_DOUBLE, which_node, |
380 |
< |
atomOrientDataTag, MPI_COMM_WORLD, &istatus); |
381 |
< |
|
377 |
> |
if (isDirectional) { |
378 |
> |
MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node, |
379 |
> |
myPotato, MPI_COMM_WORLD, &istatus); |
380 |
> |
} else { |
381 |
> |
MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node, |
382 |
> |
myPotato, MPI_COMM_WORLD, &istatus); |
383 |
|
} |
384 |
+ |
|
385 |
+ |
myPotato++; |
386 |
+ |
potatoes[which_node] = myPotato; |
387 |
|
|
388 |
|
} else { |
389 |
|
|
390 |
< |
haveError = 0; |
390 |
> |
haveError = 0; |
391 |
|
which_atom = i; |
392 |
< |
local_index=-1; |
393 |
< |
|
394 |
< |
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
395 |
< |
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
396 |
< |
} |
397 |
< |
|
398 |
< |
if (local_index != -1) { |
610 |
< |
|
611 |
< |
atomTypeString = atoms[local_index]->getType(); |
612 |
< |
|
392 |
> |
|
393 |
> |
local_index = indexArray[currentIndex].first; |
394 |
> |
|
395 |
> |
if (which_atom == indexArray[currentIndex].second) { |
396 |
> |
|
397 |
> |
atomTypeString = atoms[local_index]->getType(); |
398 |
> |
|
399 |
|
atoms[local_index]->getPos(pos); |
400 |
< |
atoms[local_index]->getVel(vel); |
400 |
> |
atoms[local_index]->getVel(vel); |
401 |
> |
|
402 |
> |
atomData6[0] = pos[0]; |
403 |
> |
atomData6[1] = pos[1]; |
404 |
> |
atomData6[2] = pos[2]; |
405 |
|
|
406 |
< |
atomTransData[0] = pos[0]; |
407 |
< |
atomTransData[1] = pos[1]; |
408 |
< |
atomTransData[2] = pos[2]; |
619 |
< |
|
620 |
< |
atomTransData[3] = vel[0]; |
621 |
< |
atomTransData[4] = vel[1]; |
622 |
< |
atomTransData[5] = vel[2]; |
406 |
> |
atomData6[3] = vel[0]; |
407 |
> |
atomData6[4] = vel[1]; |
408 |
> |
atomData6[5] = vel[2]; |
409 |
|
|
410 |
|
isDirectional = 0; |
411 |
|
|
415 |
|
|
416 |
|
dAtom = (DirectionalAtom *)atoms[local_index]; |
417 |
|
dAtom->getQ( q ); |
418 |
+ |
|
419 |
+ |
for (int j = 0; j < 6 ; j++) |
420 |
+ |
atomData13[j] = atomData6[j]; |
421 |
|
|
422 |
< |
atomOrientData[0] = q[0]; |
423 |
< |
atomOrientData[1] = q[1]; |
424 |
< |
atomOrientData[2] = q[2]; |
425 |
< |
atomOrientData[3] = q[3]; |
426 |
< |
|
427 |
< |
atomOrientData[4] = dAtom->getJx(); |
428 |
< |
atomOrientData[5] = dAtom->getJy(); |
429 |
< |
atomOrientData[6] = dAtom->getJz(); |
422 |
> |
atomData13[6] = q[0]; |
423 |
> |
atomData13[7] = q[1]; |
424 |
> |
atomData13[8] = q[2]; |
425 |
> |
atomData13[9] = q[3]; |
426 |
> |
|
427 |
> |
atomData13[10] = dAtom->getJx(); |
428 |
> |
atomData13[11] = dAtom->getJy(); |
429 |
> |
atomData13[12] = dAtom->getJz(); |
430 |
|
} |
431 |
< |
|
431 |
> |
|
432 |
|
} else { |
433 |
|
sprintf(painCave.errMsg, |
434 |
< |
"Atom %d not found on processor %d\n", |
435 |
< |
i, worldRank ); |
434 |
> |
"Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n", |
435 |
> |
which_atom, worldRank, currentIndex, local_index ); |
436 |
|
haveError= 1; |
437 |
|
simError(); |
438 |
|
} |
650 |
– |
|
651 |
– |
if(haveError) DieDieDie(); |
652 |
– |
|
653 |
– |
// If we've survived to here, format the line: |
439 |
|
|
440 |
< |
sprintf( tempBuffer, |
441 |
< |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
442 |
< |
atomTypeString, |
658 |
< |
atomTransData[0], |
659 |
< |
atomTransData[1], |
660 |
< |
atomTransData[2], |
661 |
< |
atomTransData[3], |
662 |
< |
atomTransData[4], |
663 |
< |
atomTransData[5]); |
664 |
< |
|
665 |
< |
strcpy( writeLine, tempBuffer ); |
666 |
< |
|
667 |
< |
if (isDirectional) { |
668 |
< |
|
669 |
< |
sprintf( tempBuffer, |
670 |
< |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
671 |
< |
atomOrientData[0], |
672 |
< |
atomOrientData[1], |
673 |
< |
atomOrientData[2], |
674 |
< |
atomOrientData[3], |
675 |
< |
atomOrientData[4], |
676 |
< |
atomOrientData[5], |
677 |
< |
atomOrientData[6]); |
678 |
< |
strcat( writeLine, tempBuffer ); |
679 |
< |
|
680 |
< |
} else { |
681 |
< |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
682 |
< |
} |
683 |
< |
|
684 |
< |
finalOut << writeLine; |
685 |
< |
finalOut.flush(); |
440 |
> |
if(haveError) DieDieDie(); |
441 |
> |
|
442 |
> |
currentIndex++; |
443 |
|
} |
444 |
+ |
// If we've survived to here, format the line: |
445 |
+ |
|
446 |
+ |
if (!isDirectional) { |
447 |
+ |
|
448 |
+ |
sprintf( writeLine, |
449 |
+ |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
450 |
+ |
atomTypeString, |
451 |
+ |
atomData6[0], |
452 |
+ |
atomData6[1], |
453 |
+ |
atomData6[2], |
454 |
+ |
atomData6[3], |
455 |
+ |
atomData6[4], |
456 |
+ |
atomData6[5]); |
457 |
+ |
|
458 |
+ |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
459 |
+ |
|
460 |
+ |
} else { |
461 |
+ |
|
462 |
+ |
sprintf( writeLine, |
463 |
+ |
"%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", |
464 |
+ |
atomTypeString, |
465 |
+ |
atomData13[0], |
466 |
+ |
atomData13[1], |
467 |
+ |
atomData13[2], |
468 |
+ |
atomData13[3], |
469 |
+ |
atomData13[4], |
470 |
+ |
atomData13[5], |
471 |
+ |
atomData13[6], |
472 |
+ |
atomData13[7], |
473 |
+ |
atomData13[8], |
474 |
+ |
atomData13[9], |
475 |
+ |
atomData13[10], |
476 |
+ |
atomData13[11], |
477 |
+ |
atomData13[12]); |
478 |
+ |
|
479 |
+ |
} |
480 |
+ |
|
481 |
+ |
for(k = 0; k < outFile.size(); k++) |
482 |
+ |
*outFile[k] << writeLine; |
483 |
|
} |
484 |
< |
|
485 |
< |
finalOut.flush(); |
484 |
> |
|
485 |
> |
for(k = 0; k < outFile.size(); k++) |
486 |
> |
outFile[k]->flush(); |
487 |
> |
|
488 |
|
sprintf( checkPointMsg, |
489 |
|
"Sucessfully took a dump.\n"); |
490 |
+ |
|
491 |
|
MPIcheckPoint(); |
492 |
|
|
493 |
+ |
delete[] potatoes; |
494 |
+ |
|
495 |
|
} else { |
496 |
|
|
497 |
|
// worldRank != 0, so I'm a remote node. |
498 |
+ |
|
499 |
+ |
// Set my magic potato to 0: |
500 |
+ |
|
501 |
+ |
myPotato = 0; |
502 |
+ |
currentIndex = 0; |
503 |
|
|
504 |
|
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
505 |
|
|
507 |
|
|
508 |
|
if (AtomToProcMap[i] == worldRank) { |
509 |
|
|
510 |
< |
local_index=-1; |
511 |
< |
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
512 |
< |
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
510 |
> |
if (myPotato + 3 >= MAXTAG) { |
511 |
> |
|
512 |
> |
// The potato was going to exceed the maximum value, |
513 |
> |
// so wrap this processor potato back to 0 (and block until |
514 |
> |
// node 0 says we can go: |
515 |
> |
|
516 |
> |
MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus); |
517 |
> |
|
518 |
|
} |
519 |
< |
if (local_index != -1) { |
519 |
> |
which_atom = i; |
520 |
> |
|
521 |
> |
local_index = indexArray[currentIndex].first; |
522 |
> |
|
523 |
> |
if (which_atom == indexArray[currentIndex].second) { |
524 |
|
|
525 |
|
atomTypeString = atoms[local_index]->getType(); |
526 |
< |
|
526 |
> |
|
527 |
|
atoms[local_index]->getPos(pos); |
528 |
|
atoms[local_index]->getVel(vel); |
529 |
+ |
|
530 |
+ |
atomData6[0] = pos[0]; |
531 |
+ |
atomData6[1] = pos[1]; |
532 |
+ |
atomData6[2] = pos[2]; |
533 |
|
|
534 |
< |
atomTransData[0] = pos[0]; |
535 |
< |
atomTransData[1] = pos[1]; |
536 |
< |
atomTransData[2] = pos[2]; |
718 |
< |
|
719 |
< |
atomTransData[3] = vel[0]; |
720 |
< |
atomTransData[4] = vel[1]; |
721 |
< |
atomTransData[5] = vel[2]; |
534 |
> |
atomData6[3] = vel[0]; |
535 |
> |
atomData6[4] = vel[1]; |
536 |
> |
atomData6[5] = vel[2]; |
537 |
|
|
538 |
|
isDirectional = 0; |
539 |
|
|
544 |
|
dAtom = (DirectionalAtom *)atoms[local_index]; |
545 |
|
dAtom->getQ( q ); |
546 |
|
|
547 |
< |
atomOrientData[0] = q[0]; |
548 |
< |
atomOrientData[1] = q[1]; |
549 |
< |
atomOrientData[2] = q[2]; |
550 |
< |
atomOrientData[3] = q[3]; |
551 |
< |
|
552 |
< |
atomOrientData[4] = dAtom->getJx(); |
553 |
< |
atomOrientData[5] = dAtom->getJy(); |
554 |
< |
atomOrientData[6] = dAtom->getJz(); |
547 |
> |
for (int j = 0; j < 6 ; j++) |
548 |
> |
atomData13[j] = atomData6[j]; |
549 |
> |
|
550 |
> |
atomData13[6] = q[0]; |
551 |
> |
atomData13[7] = q[1]; |
552 |
> |
atomData13[8] = q[2]; |
553 |
> |
atomData13[9] = q[3]; |
554 |
> |
|
555 |
> |
atomData13[10] = dAtom->getJx(); |
556 |
> |
atomData13[11] = dAtom->getJy(); |
557 |
> |
atomData13[12] = dAtom->getJz(); |
558 |
|
} |
559 |
|
|
560 |
|
} else { |
561 |
|
sprintf(painCave.errMsg, |
562 |
< |
"Atom %d not found on processor %d\n", |
563 |
< |
i, worldRank ); |
562 |
> |
"Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n", |
563 |
> |
which_atom, worldRank, currentIndex, local_index ); |
564 |
|
haveError= 1; |
565 |
|
simError(); |
566 |
|
} |
567 |
< |
|
750 |
< |
// I've survived this far, so send off the data! |
751 |
< |
|
752 |
< |
atomTypeTag = 4*i; |
753 |
< |
atomIsDirectionalTag = 4*i + 1; |
754 |
< |
atomTransDataTag = 4*i + 2; |
755 |
< |
atomOrientDataTag = 4*i + 3; |
756 |
< |
|
567 |
> |
|
568 |
|
strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE); |
569 |
|
|
570 |
+ |
// null terminate the string before sending (just in case): |
571 |
+ |
MPIatomTypeString[MINIBUFFERSIZE-1] = '\0'; |
572 |
+ |
|
573 |
|
MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0, |
574 |
< |
atomTypeTag, MPI_COMM_WORLD); |
574 |
> |
myPotato, MPI_COMM_WORLD); |
575 |
|
|
576 |
+ |
myPotato++; |
577 |
+ |
|
578 |
|
MPI_Send(&isDirectional, 1, MPI_INT, 0, |
579 |
< |
atomIsDirectionalTag, MPI_COMM_WORLD); |
579 |
> |
myPotato, MPI_COMM_WORLD); |
580 |
|
|
581 |
< |
MPI_Send(atomTransData, 6, MPI_DOUBLE, 0, |
582 |
< |
atomTransDataTag, MPI_COMM_WORLD); |
767 |
< |
|
581 |
> |
myPotato++; |
582 |
> |
|
583 |
|
if (isDirectional) { |
584 |
|
|
585 |
< |
MPI_Send(atomOrientData, 7, MPI_DOUBLE, 0, |
586 |
< |
atomOrientDataTag, MPI_COMM_WORLD); |
585 |
> |
MPI_Send(atomData13, 13, MPI_DOUBLE, 0, |
586 |
> |
myPotato, MPI_COMM_WORLD); |
587 |
|
|
588 |
+ |
} else { |
589 |
+ |
|
590 |
+ |
MPI_Send(atomData6, 6, MPI_DOUBLE, 0, |
591 |
+ |
myPotato, MPI_COMM_WORLD); |
592 |
|
} |
593 |
< |
|
593 |
> |
|
594 |
> |
myPotato++; |
595 |
> |
currentIndex++; |
596 |
|
} |
597 |
|
} |
598 |
|
|
599 |
|
sprintf( checkPointMsg, |
600 |
< |
"Sucessfully wrote final file.\n"); |
600 |
> |
"Sucessfully took a dump.\n"); |
601 |
|
MPIcheckPoint(); |
602 |
|
|
603 |
< |
} |
603 |
> |
} |
604 |
|
|
784 |
– |
painCave.isEventLoop = 0; |
785 |
– |
|
786 |
– |
if( worldRank == 0 ) finalOut.close(); |
605 |
|
#endif // is_mpi |
606 |
|
} |
607 |
|
|
790 |
– |
|
791 |
– |
|
608 |
|
#ifdef IS_MPI |
609 |
|
|
610 |
|
// a couple of functions to let us escape the write loop |