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 |
|
|
29 |
– |
strcpy( outName, entry_plug->sampleName ); |
31 |
|
|
32 |
< |
outFile.open(outName, ios::out | ios::trunc ); |
32 |
> |
dumpFile.open(entry_plug->sampleName, ios::out | ios::trunc ); |
33 |
|
|
34 |
< |
if( !outFile ){ |
34 |
> |
if( !dumpFile ){ |
35 |
|
|
36 |
|
sprintf( painCave.errMsg, |
37 |
|
"Could not open \"%s\" for dump output.\n", |
38 |
< |
outName); |
38 |
> |
entry_plug->sampleName); |
39 |
|
painCave.isFatal = 1; |
40 |
|
simError(); |
41 |
|
} |
42 |
|
|
42 |
– |
//outFile.setf( ios::scientific ); |
43 |
– |
|
43 |
|
#ifdef IS_MPI |
44 |
|
} |
45 |
|
|
46 |
+ |
//sort the local atoms by global index |
47 |
+ |
sortByGlobalIndex(); |
48 |
+ |
|
49 |
|
sprintf( checkPointMsg, |
50 |
|
"Sucessfully opened output file for dumping.\n"); |
51 |
|
MPIcheckPoint(); |
58 |
|
if(worldRank == 0 ){ |
59 |
|
#endif // is_mpi |
60 |
|
|
61 |
< |
outFile.close(); |
61 |
> |
dumpFile.close(); |
62 |
|
|
63 |
|
#ifdef IS_MPI |
64 |
|
} |
65 |
|
#endif // is_mpi |
66 |
|
} |
67 |
|
|
68 |
< |
void DumpWriter::writeDump( double currentTime ){ |
68 |
> |
#ifdef IS_MPI |
69 |
|
|
70 |
< |
const int BUFFERSIZE = 2000; |
71 |
< |
const int MINIBUFFERSIZE = 100; |
70 |
> |
/** |
71 |
> |
* A hook function to load balancing |
72 |
> |
*/ |
73 |
|
|
74 |
< |
char tempBuffer[BUFFERSIZE]; |
75 |
< |
char writeLine[BUFFERSIZE]; |
76 |
< |
|
74 |
< |
int i; |
75 |
< |
|
76 |
< |
#ifdef IS_MPI |
74 |
> |
void DumpWriter::update(){ |
75 |
> |
sortByGlobalIndex(); |
76 |
> |
} |
77 |
|
|
78 |
< |
int *potatoes; |
79 |
< |
int myPotato; |
78 |
> |
/** |
79 |
> |
* Auxiliary sorting function |
80 |
> |
*/ |
81 |
> |
|
82 |
> |
bool indexSortingCriterion(const pair<int, int>& p1, const pair<int, int>& p2){ |
83 |
> |
return p1.second < p2.second; |
84 |
> |
} |
85 |
|
|
86 |
< |
int nProc; |
87 |
< |
int j, which_node, done, which_atom, local_index; |
88 |
< |
double atomData6[6]; |
89 |
< |
double atomData13[13]; |
90 |
< |
int isDirectional; |
86 |
< |
char* atomTypeString; |
87 |
< |
char MPIatomTypeString[MINIBUFFERSIZE]; |
88 |
< |
|
89 |
< |
#else //is_mpi |
90 |
< |
int nAtoms = entry_plug->n_atoms; |
91 |
< |
#endif //is_mpi |
92 |
< |
|
93 |
< |
double q[4]; |
94 |
< |
DirectionalAtom* dAtom; |
86 |
> |
/** |
87 |
> |
* Sorting the local index by global index |
88 |
> |
*/ |
89 |
> |
|
90 |
> |
void DumpWriter::sortByGlobalIndex(){ |
91 |
|
Atom** atoms = entry_plug->atoms; |
92 |
< |
double pos[3], vel[3]; |
92 |
> |
|
93 |
> |
indexArray.clear(); |
94 |
> |
|
95 |
> |
for(int i = 0; i < mpiSim->getMyNlocal();i++) |
96 |
> |
indexArray.push_back(make_pair(i, atoms[i]->getGlobalIndex())); |
97 |
> |
|
98 |
> |
sort(indexArray.begin(), indexArray.end(), indexSortingCriterion); |
99 |
> |
} |
100 |
> |
#endif |
101 |
|
|
102 |
< |
// write current frame to the eor file |
102 |
> |
void DumpWriter::writeDump(double currentTime){ |
103 |
|
|
104 |
< |
this->writeFinal( currentTime ); |
104 |
> |
ofstream finalOut; |
105 |
> |
vector<ofstream*> fileStreams; |
106 |
|
|
107 |
< |
#ifndef IS_MPI |
108 |
< |
|
109 |
< |
outFile << nAtoms << "\n"; |
110 |
< |
|
111 |
< |
outFile << currentTime << ";\t" |
112 |
< |
<< entry_plug->Hmat[0][0] << "\t" |
113 |
< |
<< entry_plug->Hmat[1][0] << "\t" |
114 |
< |
<< entry_plug->Hmat[2][0] << ";\t" |
115 |
< |
|
116 |
< |
<< entry_plug->Hmat[0][1] << "\t" |
112 |
< |
<< entry_plug->Hmat[1][1] << "\t" |
113 |
< |
<< entry_plug->Hmat[2][1] << ";\t" |
114 |
< |
|
115 |
< |
<< entry_plug->Hmat[0][2] << "\t" |
116 |
< |
<< entry_plug->Hmat[1][2] << "\t" |
117 |
< |
<< entry_plug->Hmat[2][2] << ";"; |
118 |
< |
//write out additional parameters, such as chi and eta |
119 |
< |
outFile << entry_plug->the_integrator->getAdditionalParameters(); |
120 |
< |
outFile << endl; |
121 |
< |
|
122 |
< |
for( i=0; i<nAtoms; i++ ){ |
123 |
< |
|
124 |
< |
atoms[i]->getPos(pos); |
125 |
< |
atoms[i]->getVel(vel); |
126 |
< |
|
127 |
< |
sprintf( tempBuffer, |
128 |
< |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
129 |
< |
atoms[i]->getType(), |
130 |
< |
pos[0], |
131 |
< |
pos[1], |
132 |
< |
pos[2], |
133 |
< |
vel[0], |
134 |
< |
vel[1], |
135 |
< |
vel[2]); |
136 |
< |
strcpy( writeLine, tempBuffer ); |
137 |
< |
|
138 |
< |
if( atoms[i]->isDirectional() ){ |
139 |
< |
|
140 |
< |
dAtom = (DirectionalAtom *)atoms[i]; |
141 |
< |
dAtom->getQ( q ); |
142 |
< |
|
143 |
< |
sprintf( tempBuffer, |
144 |
< |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
145 |
< |
q[0], |
146 |
< |
q[1], |
147 |
< |
q[2], |
148 |
< |
q[3], |
149 |
< |
dAtom->getJx(), |
150 |
< |
dAtom->getJy(), |
151 |
< |
dAtom->getJz()); |
152 |
< |
strcat( writeLine, tempBuffer ); |
107 |
> |
#ifdef IS_MPI |
108 |
> |
if(worldRank == 0 ){ |
109 |
> |
|
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 |
|
} |
154 |
– |
else |
155 |
– |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
156 |
– |
|
157 |
– |
outFile << writeLine; |
118 |
|
} |
119 |
< |
outFile.flush(); |
119 |
> |
#endif // is_mpi |
120 |
|
|
121 |
< |
#else // is_mpi |
121 |
> |
fileStreams.push_back(&finalOut); |
122 |
> |
fileStreams.push_back(&dumpFile); |
123 |
|
|
124 |
< |
/* code to find maximum tag value */ |
164 |
< |
int *tagub, flag, MAXTAG; |
165 |
< |
MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag); |
166 |
< |
if (flag) { |
167 |
< |
MAXTAG = *tagub; |
168 |
< |
} else { |
169 |
< |
MAXTAG = 32767; |
170 |
< |
} |
124 |
> |
writeFrame(fileStreams, currentTime); |
125 |
|
|
126 |
< |
int haveError; |
126 |
> |
#ifdef IS_MPI |
127 |
> |
finalOut.close(); |
128 |
> |
#endif |
129 |
> |
|
130 |
> |
} |
131 |
|
|
132 |
< |
MPI_Status istatus; |
175 |
< |
int *AtomToProcMap = mpiSim->getAtomToProcMap(); |
132 |
> |
void DumpWriter::writeFinal(double currentTime){ |
133 |
|
|
134 |
< |
// write out header and node 0's coordinates |
134 |
> |
ofstream finalOut; |
135 |
> |
vector<ofstream*> fileStreams; |
136 |
|
|
137 |
< |
if( worldRank == 0 ){ |
137 |
> |
#ifdef IS_MPI |
138 |
> |
if(worldRank == 0 ){ |
139 |
|
|
140 |
< |
// Node 0 needs a list of the magic potatoes for each processor; |
182 |
< |
|
183 |
< |
nProc = mpiSim->getNumberProcessors(); |
184 |
< |
potatoes = new int[nProc]; |
185 |
< |
|
186 |
< |
for (i = 0; i < nProc; i++) |
187 |
< |
potatoes[i] = 0; |
188 |
< |
|
189 |
< |
outFile << mpiSim->getTotAtoms() << "\n"; |
190 |
< |
|
191 |
< |
outFile << currentTime << ";\t" |
192 |
< |
<< entry_plug->Hmat[0][0] << "\t" |
193 |
< |
<< entry_plug->Hmat[1][0] << "\t" |
194 |
< |
<< entry_plug->Hmat[2][0] << ";\t" |
195 |
< |
|
196 |
< |
<< entry_plug->Hmat[0][1] << "\t" |
197 |
< |
<< entry_plug->Hmat[1][1] << "\t" |
198 |
< |
<< entry_plug->Hmat[2][1] << ";\t" |
199 |
< |
|
200 |
< |
<< entry_plug->Hmat[0][2] << "\t" |
201 |
< |
<< entry_plug->Hmat[1][2] << "\t" |
202 |
< |
<< entry_plug->Hmat[2][2] << ";"; |
203 |
< |
|
204 |
< |
outFile << entry_plug->the_integrator->getAdditionalParameters(); |
205 |
< |
outFile << endl; |
206 |
< |
outFile.flush(); |
207 |
< |
|
208 |
< |
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
209 |
< |
|
210 |
< |
// Get the Node number which has this atom; |
211 |
< |
|
212 |
< |
which_node = AtomToProcMap[i]; |
213 |
< |
|
214 |
< |
if (which_node != 0) { |
215 |
< |
|
216 |
< |
if (potatoes[which_node] + 3 >= MAXTAG) { |
217 |
< |
// The potato was going to exceed the maximum value, |
218 |
< |
// so wrap this processor potato back to 0: |
140 |
> |
finalOut.open( entry_plug->finalName, ios::out | ios::trunc ); |
141 |
|
|
142 |
< |
potatoes[which_node] = 0; |
143 |
< |
MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD); |
144 |
< |
|
145 |
< |
} |
146 |
< |
|
147 |
< |
myPotato = potatoes[which_node]; |
226 |
< |
|
227 |
< |
MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node, |
228 |
< |
myPotato, MPI_COMM_WORLD, &istatus); |
229 |
< |
|
230 |
< |
strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE); |
231 |
< |
|
232 |
< |
// Null terminate the atomTypeString just in case: |
233 |
< |
|
234 |
< |
atomTypeString[strlen(atomTypeString) - 1] = '\0'; |
235 |
< |
|
236 |
< |
myPotato++; |
237 |
< |
|
238 |
< |
MPI_Recv(&isDirectional, 1, MPI_INT, which_node, |
239 |
< |
myPotato, MPI_COMM_WORLD, &istatus); |
240 |
< |
|
241 |
< |
myPotato++; |
242 |
< |
|
243 |
< |
if (isDirectional) { |
244 |
< |
MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node, |
245 |
< |
myPotato, MPI_COMM_WORLD, &istatus); |
246 |
< |
} else { |
247 |
< |
MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node, |
248 |
< |
myPotato, MPI_COMM_WORLD, &istatus); |
249 |
< |
} |
250 |
< |
|
251 |
< |
myPotato++; |
252 |
< |
potatoes[which_node] = myPotato; |
253 |
< |
|
254 |
< |
} else { |
255 |
< |
|
256 |
< |
haveError = 0; |
257 |
< |
which_atom = i; |
258 |
< |
local_index=-1; |
259 |
< |
|
260 |
< |
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
261 |
< |
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
262 |
< |
} |
263 |
< |
|
264 |
< |
if (local_index != -1) { |
265 |
< |
|
266 |
< |
atomTypeString = atoms[local_index]->getType(); |
267 |
< |
|
268 |
< |
atoms[local_index]->getPos(pos); |
269 |
< |
atoms[local_index]->getVel(vel); |
270 |
< |
|
271 |
< |
atomData6[0] = pos[0]; |
272 |
< |
atomData6[1] = pos[1]; |
273 |
< |
atomData6[2] = pos[2]; |
274 |
< |
|
275 |
< |
atomData6[3] = vel[0]; |
276 |
< |
atomData6[4] = vel[1]; |
277 |
< |
atomData6[5] = vel[2]; |
278 |
< |
|
279 |
< |
isDirectional = 0; |
280 |
< |
|
281 |
< |
if( atoms[local_index]->isDirectional() ){ |
282 |
< |
|
283 |
< |
isDirectional = 1; |
284 |
< |
|
285 |
< |
dAtom = (DirectionalAtom *)atoms[local_index]; |
286 |
< |
dAtom->getQ( q ); |
287 |
< |
|
288 |
< |
for (int j = 0; j < 6 ; j++) |
289 |
< |
atomData13[j] = atomData6[j]; |
290 |
< |
|
291 |
< |
atomData13[6] = q[0]; |
292 |
< |
atomData13[7] = q[1]; |
293 |
< |
atomData13[8] = q[2]; |
294 |
< |
atomData13[9] = q[3]; |
295 |
< |
|
296 |
< |
atomData13[10] = dAtom->getJx(); |
297 |
< |
atomData13[11] = dAtom->getJy(); |
298 |
< |
atomData13[12] = dAtom->getJz(); |
299 |
< |
} |
300 |
< |
|
301 |
< |
} else { |
302 |
< |
sprintf(painCave.errMsg, |
303 |
< |
"Atom %d not found on processor %d\n", |
304 |
< |
i, worldRank ); |
305 |
< |
haveError= 1; |
306 |
< |
simError(); |
307 |
< |
} |
308 |
< |
|
309 |
< |
if(haveError) DieDieDie(); |
310 |
< |
|
311 |
< |
// If we've survived to here, format the line: |
312 |
< |
|
313 |
< |
if (!isDirectional) { |
314 |
< |
|
315 |
< |
sprintf( tempBuffer, |
316 |
< |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
317 |
< |
atomTypeString, |
318 |
< |
atomData6[0], |
319 |
< |
atomData6[1], |
320 |
< |
atomData6[2], |
321 |
< |
atomData6[3], |
322 |
< |
atomData6[4], |
323 |
< |
atomData6[5]); |
324 |
< |
|
325 |
< |
strcpy( writeLine, tempBuffer ); |
326 |
< |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
327 |
< |
|
328 |
< |
} else { |
329 |
< |
|
330 |
< |
sprintf( tempBuffer, |
331 |
< |
"%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", |
332 |
< |
atomTypeString, |
333 |
< |
atomData13[0], |
334 |
< |
atomData13[1], |
335 |
< |
atomData13[2], |
336 |
< |
atomData13[3], |
337 |
< |
atomData13[4], |
338 |
< |
atomData13[5], |
339 |
< |
atomData13[6], |
340 |
< |
atomData13[7], |
341 |
< |
atomData13[8], |
342 |
< |
atomData13[9], |
343 |
< |
atomData13[10], |
344 |
< |
atomData13[11], |
345 |
< |
atomData13[12]); |
346 |
< |
|
347 |
< |
strcat( writeLine, tempBuffer ); |
348 |
< |
|
349 |
< |
} |
350 |
< |
|
351 |
< |
outFile << writeLine; |
352 |
< |
outFile.flush(); |
353 |
< |
} |
142 |
> |
if( !finalOut ){ |
143 |
> |
sprintf( painCave.errMsg, |
144 |
> |
"Could not open \"%s\" for final dump output.\n", |
145 |
> |
entry_plug->finalName ); |
146 |
> |
painCave.isFatal = 1; |
147 |
> |
simError(); |
148 |
|
} |
149 |
|
|
150 |
< |
outFile.flush(); |
151 |
< |
sprintf( checkPointMsg, |
152 |
< |
"Sucessfully took a dump.\n"); |
153 |
< |
MPIcheckPoint(); |
154 |
< |
|
361 |
< |
} else { |
150 |
> |
} |
151 |
> |
#endif // is_mpi |
152 |
> |
|
153 |
> |
fileStreams.push_back(&finalOut); |
154 |
> |
writeFrame(fileStreams, currentTime); |
155 |
|
|
156 |
< |
// worldRank != 0, so I'm a remote node. |
157 |
< |
|
158 |
< |
// Set my magic potato to 0: |
366 |
< |
|
367 |
< |
myPotato = 0; |
368 |
< |
|
369 |
< |
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
370 |
< |
|
371 |
< |
// Am I the node which has this atom? |
372 |
< |
|
373 |
< |
if (AtomToProcMap[i] == worldRank) { |
374 |
< |
|
375 |
< |
if (myPotato + 3 >= MAXTAG) { |
376 |
< |
|
377 |
< |
// The potato was going to exceed the maximum value, |
378 |
< |
// so wrap this processor potato back to 0 (and block until |
379 |
< |
// node 0 says we can go: |
380 |
< |
|
381 |
< |
MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus); |
382 |
< |
|
383 |
< |
} |
384 |
< |
|
385 |
< |
local_index=-1; |
386 |
< |
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
387 |
< |
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
388 |
< |
} |
389 |
< |
if (local_index != -1) { |
390 |
< |
|
391 |
< |
atomTypeString = atoms[local_index]->getType(); |
392 |
< |
|
393 |
< |
atoms[local_index]->getPos(pos); |
394 |
< |
atoms[local_index]->getVel(vel); |
395 |
< |
|
396 |
< |
atomData6[0] = pos[0]; |
397 |
< |
atomData6[1] = pos[1]; |
398 |
< |
atomData6[2] = pos[2]; |
399 |
< |
|
400 |
< |
atomData6[3] = vel[0]; |
401 |
< |
atomData6[4] = vel[1]; |
402 |
< |
atomData6[5] = vel[2]; |
403 |
< |
|
404 |
< |
isDirectional = 0; |
405 |
< |
|
406 |
< |
if( atoms[local_index]->isDirectional() ){ |
407 |
< |
|
408 |
< |
isDirectional = 1; |
409 |
< |
|
410 |
< |
dAtom = (DirectionalAtom *)atoms[local_index]; |
411 |
< |
dAtom->getQ( q ); |
412 |
< |
|
413 |
< |
for (int j = 0; j < 6 ; j++) |
414 |
< |
atomData13[j] = atomData6[j]; |
415 |
< |
|
416 |
< |
atomData13[6] = q[0]; |
417 |
< |
atomData13[7] = q[1]; |
418 |
< |
atomData13[8] = q[2]; |
419 |
< |
atomData13[9] = q[3]; |
420 |
< |
|
421 |
< |
atomData13[10] = dAtom->getJx(); |
422 |
< |
atomData13[11] = dAtom->getJy(); |
423 |
< |
atomData13[12] = dAtom->getJz(); |
424 |
< |
} |
425 |
< |
|
426 |
< |
} else { |
427 |
< |
sprintf(painCave.errMsg, |
428 |
< |
"Atom %d not found on processor %d\n", |
429 |
< |
i, worldRank ); |
430 |
< |
haveError= 1; |
431 |
< |
simError(); |
432 |
< |
} |
433 |
< |
|
434 |
< |
strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE); |
435 |
< |
|
436 |
< |
// null terminate the string before sending (just in case): |
437 |
< |
MPIatomTypeString[MINIBUFFERSIZE-1] = '\0'; |
438 |
< |
|
439 |
< |
MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0, |
440 |
< |
myPotato, MPI_COMM_WORLD); |
441 |
< |
|
442 |
< |
myPotato++; |
443 |
< |
|
444 |
< |
MPI_Send(&isDirectional, 1, MPI_INT, 0, |
445 |
< |
myPotato, MPI_COMM_WORLD); |
446 |
< |
|
447 |
< |
myPotato++; |
448 |
< |
|
449 |
< |
if (isDirectional) { |
450 |
< |
|
451 |
< |
MPI_Send(atomData13, 13, MPI_DOUBLE, 0, |
452 |
< |
myPotato, MPI_COMM_WORLD); |
453 |
< |
|
454 |
< |
} else { |
455 |
< |
|
456 |
< |
MPI_Send(atomData6, 6, MPI_DOUBLE, 0, |
457 |
< |
myPotato, MPI_COMM_WORLD); |
458 |
< |
} |
459 |
< |
|
460 |
< |
myPotato++; |
461 |
< |
} |
462 |
< |
} |
463 |
< |
|
464 |
< |
sprintf( checkPointMsg, |
465 |
< |
"Sucessfully took a dump.\n"); |
466 |
< |
MPIcheckPoint(); |
467 |
< |
|
468 |
< |
} |
156 |
> |
#ifdef IS_MPI |
157 |
> |
finalOut.close(); |
158 |
> |
#endif |
159 |
|
|
470 |
– |
#endif // is_mpi |
160 |
|
} |
161 |
|
|
162 |
< |
void DumpWriter::writeFinal(double finalTime){ |
162 |
> |
void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){ |
163 |
|
|
475 |
– |
char finalName[500]; |
476 |
– |
ofstream finalOut; |
477 |
– |
|
164 |
|
const int BUFFERSIZE = 2000; |
165 |
|
const int MINIBUFFERSIZE = 100; |
166 |
< |
char tempBuffer[BUFFERSIZE]; |
166 |
> |
|
167 |
> |
char tempBuffer[BUFFERSIZE]; |
168 |
|
char writeLine[BUFFERSIZE]; |
169 |
|
|
170 |
< |
double q[4]; |
171 |
< |
DirectionalAtom* dAtom; |
485 |
< |
Atom** atoms = entry_plug->atoms; |
486 |
< |
int i; |
170 |
> |
int i, k; |
171 |
> |
|
172 |
|
#ifdef IS_MPI |
173 |
|
|
174 |
+ |
/********************************************************************* |
175 |
+ |
* Documentation? You want DOCUMENTATION? |
176 |
+ |
* |
177 |
+ |
* Why all the potatoes below? |
178 |
+ |
* |
179 |
+ |
* To make a long story short, the original version of DumpWriter |
180 |
+ |
* worked in the most inefficient way possible. Node 0 would |
181 |
+ |
* poke each of the node for an individual atom's formatted data |
182 |
+ |
* as node 0 worked its way down the global index. This was particularly |
183 |
+ |
* inefficient since the method blocked all processors at every atom |
184 |
+ |
* (and did it twice!). |
185 |
+ |
* |
186 |
+ |
* An intermediate version of DumpWriter could be described from Node |
187 |
+ |
* zero's perspective as follows: |
188 |
+ |
* |
189 |
+ |
* 1) Have 100 of your friends stand in a circle. |
190 |
+ |
* 2) When you say go, have all of them start tossing potatoes at |
191 |
+ |
* you (one at a time). |
192 |
+ |
* 3) Catch the potatoes. |
193 |
+ |
* |
194 |
+ |
* It was an improvement, but MPI has buffers and caches that could |
195 |
+ |
* best be described in this analogy as "potato nets", so there's no |
196 |
+ |
* need to block the processors atom-by-atom. |
197 |
+ |
* |
198 |
+ |
* This new and improved DumpWriter works in an even more efficient |
199 |
+ |
* way: |
200 |
+ |
* |
201 |
+ |
* 1) Have 100 of your friend stand in a circle. |
202 |
+ |
* 2) When you say go, have them start tossing 5-pound bags of |
203 |
+ |
* potatoes at you. |
204 |
+ |
* 3) Once you've caught a friend's bag of potatoes, |
205 |
+ |
* toss them a spud to let them know they can toss another bag. |
206 |
+ |
* |
207 |
+ |
* How's THAT for documentation? |
208 |
+ |
* |
209 |
+ |
*********************************************************************/ |
210 |
+ |
|
211 |
|
int *potatoes; |
212 |
|
int myPotato; |
213 |
|
|
214 |
|
int nProc; |
215 |
< |
int j, which_node, done, which_atom, local_index; |
215 |
> |
int j, which_node, done, which_atom, local_index, currentIndex; |
216 |
|
double atomData6[6]; |
217 |
|
double atomData13[13]; |
218 |
|
int isDirectional; |
223 |
|
int nAtoms = entry_plug->n_atoms; |
224 |
|
#endif //is_mpi |
225 |
|
|
226 |
+ |
double q[4]; |
227 |
+ |
DirectionalAtom* dAtom; |
228 |
+ |
Atom** atoms = entry_plug->atoms; |
229 |
|
double pos[3], vel[3]; |
230 |
|
|
506 |
– |
#ifdef IS_MPI |
507 |
– |
if(worldRank == 0 ){ |
508 |
– |
#endif // is_mpi |
509 |
– |
|
510 |
– |
strcpy( finalName, entry_plug->finalName ); |
511 |
– |
|
512 |
– |
finalOut.open( finalName, ios::out | ios::trunc ); |
513 |
– |
if( !finalOut ){ |
514 |
– |
sprintf( painCave.errMsg, |
515 |
– |
"Could not open \"%s\" for final dump output.\n", |
516 |
– |
finalName ); |
517 |
– |
painCave.isFatal = 1; |
518 |
– |
simError(); |
519 |
– |
} |
520 |
– |
|
521 |
– |
// finalOut.setf( ios::scientific ); |
522 |
– |
|
523 |
– |
#ifdef IS_MPI |
524 |
– |
} |
525 |
– |
|
526 |
– |
sprintf(checkPointMsg,"Opened file for final configuration\n"); |
527 |
– |
MPIcheckPoint(); |
528 |
– |
|
529 |
– |
#endif //is_mpi |
530 |
– |
|
531 |
– |
|
231 |
|
#ifndef IS_MPI |
232 |
+ |
|
233 |
+ |
for(k = 0; k < outFile.size(); k++){ |
234 |
+ |
*outFile[k] << nAtoms << "\n"; |
235 |
|
|
236 |
< |
finalOut << nAtoms << "\n"; |
236 |
> |
*outFile[k] << currentTime << ";\t" |
237 |
> |
<< entry_plug->Hmat[0][0] << "\t" |
238 |
> |
<< entry_plug->Hmat[1][0] << "\t" |
239 |
> |
<< entry_plug->Hmat[2][0] << ";\t" |
240 |
> |
|
241 |
> |
<< entry_plug->Hmat[0][1] << "\t" |
242 |
> |
<< entry_plug->Hmat[1][1] << "\t" |
243 |
> |
<< entry_plug->Hmat[2][1] << ";\t" |
244 |
|
|
245 |
< |
finalOut << finalTime << ";\t" |
246 |
< |
<< entry_plug->Hmat[0][0] << "\t" |
247 |
< |
<< entry_plug->Hmat[1][0] << "\t" |
539 |
< |
<< entry_plug->Hmat[2][0] << ";\t" |
245 |
> |
<< entry_plug->Hmat[0][2] << "\t" |
246 |
> |
<< entry_plug->Hmat[1][2] << "\t" |
247 |
> |
<< entry_plug->Hmat[2][2] << ";"; |
248 |
|
|
249 |
< |
<< entry_plug->Hmat[0][1] << "\t" |
250 |
< |
<< entry_plug->Hmat[1][1] << "\t" |
251 |
< |
<< entry_plug->Hmat[2][1] << ";\t" |
252 |
< |
|
545 |
< |
<< entry_plug->Hmat[0][2] << "\t" |
546 |
< |
<< entry_plug->Hmat[1][2] << "\t" |
547 |
< |
<< entry_plug->Hmat[2][2] << ";"; |
548 |
< |
|
549 |
< |
//write out additional parameters, such as chi and eta |
550 |
< |
finalOut << entry_plug->the_integrator->getAdditionalParameters(); |
551 |
< |
finalOut << endl; |
552 |
< |
|
249 |
> |
//write out additional parameters, such as chi and eta |
250 |
> |
*outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl; |
251 |
> |
} |
252 |
> |
|
253 |
|
for( i=0; i<nAtoms; i++ ){ |
254 |
|
|
255 |
|
atoms[i]->getPos(pos); |
285 |
|
else |
286 |
|
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
287 |
|
|
288 |
< |
finalOut << writeLine; |
288 |
> |
for(k = 0; k < outFile.size(); k++) |
289 |
> |
*outFile[k] << writeLine; |
290 |
|
} |
590 |
– |
finalOut.flush(); |
591 |
– |
finalOut.close(); |
291 |
|
|
292 |
|
#else // is_mpi |
293 |
|
|
294 |
|
/* code to find maximum tag value */ |
295 |
+ |
|
296 |
|
int *tagub, flag, MAXTAG; |
297 |
|
MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag); |
298 |
|
if (flag) { |
315 |
|
nProc = mpiSim->getNumberProcessors(); |
316 |
|
potatoes = new int[nProc]; |
317 |
|
|
318 |
+ |
//write out the comment lines |
319 |
|
for (i = 0; i < nProc; i++) |
320 |
|
potatoes[i] = 0; |
321 |
|
|
322 |
< |
finalOut << mpiSim->getTotAtoms() << "\n"; |
322 |
> |
for(k = 0; k < outFile.size(); k++){ |
323 |
> |
*outFile[k] << mpiSim->getTotAtoms() << "\n"; |
324 |
|
|
325 |
< |
finalOut << finalTime << ";\t" |
326 |
< |
<< entry_plug->Hmat[0][0] << "\t" |
327 |
< |
<< entry_plug->Hmat[1][0] << "\t" |
328 |
< |
<< entry_plug->Hmat[2][0] << ";\t" |
627 |
< |
|
628 |
< |
<< entry_plug->Hmat[0][1] << "\t" |
629 |
< |
<< entry_plug->Hmat[1][1] << "\t" |
630 |
< |
<< entry_plug->Hmat[2][1] << ";\t" |
325 |
> |
*outFile[k] << currentTime << ";\t" |
326 |
> |
<< entry_plug->Hmat[0][0] << "\t" |
327 |
> |
<< entry_plug->Hmat[1][0] << "\t" |
328 |
> |
<< entry_plug->Hmat[2][0] << ";\t" |
329 |
|
|
330 |
< |
<< entry_plug->Hmat[0][2] << "\t" |
331 |
< |
<< entry_plug->Hmat[1][2] << "\t" |
332 |
< |
<< entry_plug->Hmat[2][2] << ";"; |
330 |
> |
<< entry_plug->Hmat[0][1] << "\t" |
331 |
> |
<< entry_plug->Hmat[1][1] << "\t" |
332 |
> |
<< entry_plug->Hmat[2][1] << ";\t" |
333 |
|
|
334 |
< |
finalOut << entry_plug->the_integrator->getAdditionalParameters(); |
335 |
< |
finalOut << endl; |
336 |
< |
finalOut.flush(); |
334 |
> |
<< entry_plug->Hmat[0][2] << "\t" |
335 |
> |
<< entry_plug->Hmat[1][2] << "\t" |
336 |
> |
<< entry_plug->Hmat[2][2] << ";"; |
337 |
> |
|
338 |
> |
*outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl; |
339 |
> |
} |
340 |
|
|
341 |
+ |
currentIndex = 0; |
342 |
+ |
|
343 |
|
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
344 |
|
|
345 |
|
// Get the Node number which has this atom; |
362 |
|
MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node, |
363 |
|
myPotato, MPI_COMM_WORLD, &istatus); |
364 |
|
|
365 |
< |
strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE); |
366 |
< |
|
664 |
< |
// Null terminate the atomTypeString just in case: |
665 |
< |
|
666 |
< |
atomTypeString[strlen(atomTypeString) - 1] = '\0'; |
667 |
< |
|
365 |
> |
atomTypeString = MPIatomTypeString; |
366 |
> |
|
367 |
|
myPotato++; |
368 |
|
|
369 |
|
MPI_Recv(&isDirectional, 1, MPI_INT, which_node, |
384 |
|
|
385 |
|
} else { |
386 |
|
|
387 |
< |
haveError = 0; |
388 |
< |
which_atom = i; |
690 |
< |
local_index=-1; |
387 |
> |
haveError = 0; |
388 |
> |
which_atom = i; |
389 |
|
|
390 |
< |
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
391 |
< |
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
392 |
< |
} |
695 |
< |
|
696 |
< |
if (local_index != -1) { |
390 |
> |
local_index = indexArray[currentIndex].first; |
391 |
> |
|
392 |
> |
if (which_atom == indexArray[currentIndex].second) { |
393 |
|
|
394 |
|
atomTypeString = atoms[local_index]->getType(); |
395 |
|
|
396 |
< |
atoms[local_index]->getPos(pos); |
397 |
< |
atoms[local_index]->getVel(vel); |
396 |
> |
atoms[local_index]->getPos(pos); |
397 |
> |
atoms[local_index]->getVel(vel); |
398 |
|
|
399 |
|
atomData6[0] = pos[0]; |
400 |
|
atomData6[1] = pos[1]; |
427 |
|
} |
428 |
|
|
429 |
|
} else { |
430 |
< |
sprintf(painCave.errMsg, |
431 |
< |
"Atom %d not found on processor %d\n", |
432 |
< |
i, worldRank ); |
433 |
< |
haveError= 1; |
434 |
< |
simError(); |
435 |
< |
} |
430 |
> |
sprintf(painCave.errMsg, |
431 |
> |
"Atom %d not found on processor %d\n", |
432 |
> |
i, worldRank ); |
433 |
> |
haveError= 1; |
434 |
> |
simError(); |
435 |
> |
} |
436 |
|
|
437 |
< |
if(haveError) DieDieDie(); |
437 |
> |
if(haveError) DieDieDie(); |
438 |
|
|
439 |
< |
// If we've survived to here, format the line: |
440 |
< |
|
441 |
< |
if (!isDirectional) { |
439 |
> |
currentIndex ++; |
440 |
> |
} |
441 |
> |
// If we've survived to here, format the line: |
442 |
> |
|
443 |
> |
if (!isDirectional) { |
444 |
> |
|
445 |
> |
sprintf( writeLine, |
446 |
> |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
447 |
> |
atomTypeString, |
448 |
> |
atomData6[0], |
449 |
> |
atomData6[1], |
450 |
> |
atomData6[2], |
451 |
> |
atomData6[3], |
452 |
> |
atomData6[4], |
453 |
> |
atomData6[5]); |
454 |
|
|
455 |
< |
sprintf( tempBuffer, |
456 |
< |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
457 |
< |
atomTypeString, |
458 |
< |
atomData6[0], |
459 |
< |
atomData6[1], |
460 |
< |
atomData6[2], |
461 |
< |
atomData6[3], |
462 |
< |
atomData6[4], |
463 |
< |
atomData6[5]); |
464 |
< |
|
465 |
< |
strcpy( writeLine, tempBuffer ); |
466 |
< |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
467 |
< |
|
468 |
< |
} else { |
469 |
< |
|
470 |
< |
sprintf( tempBuffer, |
471 |
< |
"%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", |
472 |
< |
atomTypeString, |
473 |
< |
atomData13[0], |
474 |
< |
atomData13[1], |
767 |
< |
atomData13[2], |
768 |
< |
atomData13[3], |
769 |
< |
atomData13[4], |
770 |
< |
atomData13[5], |
771 |
< |
atomData13[6], |
772 |
< |
atomData13[7], |
773 |
< |
atomData13[8], |
774 |
< |
atomData13[9], |
775 |
< |
atomData13[10], |
776 |
< |
atomData13[11], |
777 |
< |
atomData13[12]); |
778 |
< |
|
779 |
< |
strcat( writeLine, tempBuffer ); |
780 |
< |
|
781 |
< |
} |
455 |
> |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
456 |
> |
|
457 |
> |
} else { |
458 |
> |
|
459 |
> |
sprintf( writeLine, |
460 |
> |
"%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", |
461 |
> |
atomTypeString, |
462 |
> |
atomData13[0], |
463 |
> |
atomData13[1], |
464 |
> |
atomData13[2], |
465 |
> |
atomData13[3], |
466 |
> |
atomData13[4], |
467 |
> |
atomData13[5], |
468 |
> |
atomData13[6], |
469 |
> |
atomData13[7], |
470 |
> |
atomData13[8], |
471 |
> |
atomData13[9], |
472 |
> |
atomData13[10], |
473 |
> |
atomData13[11], |
474 |
> |
atomData13[12]); |
475 |
|
|
783 |
– |
finalOut << writeLine; |
784 |
– |
finalOut.flush(); |
476 |
|
} |
477 |
+ |
|
478 |
+ |
for(k = 0; k < outFile.size(); k++) |
479 |
+ |
*outFile[k] << writeLine; |
480 |
|
} |
481 |
< |
|
482 |
< |
finalOut.flush(); |
481 |
> |
|
482 |
> |
for(k = 0; k < outFile.size(); k++) |
483 |
> |
outFile[k]->flush(); |
484 |
> |
|
485 |
|
sprintf( checkPointMsg, |
486 |
|
"Sucessfully took a dump.\n"); |
487 |
+ |
|
488 |
|
MPIcheckPoint(); |
489 |
< |
|
489 |
> |
|
490 |
> |
delete[] potatoes; |
491 |
> |
|
492 |
|
} else { |
493 |
|
|
494 |
|
// worldRank != 0, so I'm a remote node. |
496 |
|
// Set my magic potato to 0: |
497 |
|
|
498 |
|
myPotato = 0; |
499 |
+ |
currentIndex = 0; |
500 |
|
|
501 |
|
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
502 |
|
|
513 |
|
MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus); |
514 |
|
|
515 |
|
} |
516 |
< |
|
517 |
< |
local_index=-1; |
518 |
< |
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
519 |
< |
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
820 |
< |
} |
821 |
< |
if (local_index != -1) { |
516 |
> |
which_atom = i; |
517 |
> |
local_index = indexArray[currentIndex].first; |
518 |
> |
|
519 |
> |
if (which_atom == indexArray[currentIndex].second) { |
520 |
|
|
521 |
|
atomTypeString = atoms[local_index]->getType(); |
522 |
|
|
523 |
< |
atoms[local_index]->getPos(pos); |
524 |
< |
atoms[local_index]->getVel(vel); |
523 |
> |
atoms[local_index]->getPos(pos); |
524 |
> |
atoms[local_index]->getVel(vel); |
525 |
|
|
526 |
|
atomData6[0] = pos[0]; |
527 |
|
atomData6[1] = pos[1]; |
547 |
|
atomData13[7] = q[1]; |
548 |
|
atomData13[8] = q[2]; |
549 |
|
atomData13[9] = q[3]; |
550 |
< |
|
550 |
> |
|
551 |
|
atomData13[10] = dAtom->getJx(); |
552 |
|
atomData13[11] = dAtom->getJy(); |
553 |
|
atomData13[12] = dAtom->getJz(); |
554 |
|
} |
555 |
|
|
556 |
|
} else { |
557 |
< |
sprintf(painCave.errMsg, |
558 |
< |
"Atom %d not found on processor %d\n", |
559 |
< |
i, worldRank ); |
560 |
< |
haveError= 1; |
561 |
< |
simError(); |
562 |
< |
} |
557 |
> |
sprintf(painCave.errMsg, |
558 |
> |
"Atom %d not found on processor %d\n", |
559 |
> |
i, worldRank ); |
560 |
> |
haveError= 1; |
561 |
> |
simError(); |
562 |
> |
} |
563 |
|
|
564 |
|
strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE); |
565 |
|
|
567 |
|
MPIatomTypeString[MINIBUFFERSIZE-1] = '\0'; |
568 |
|
|
569 |
|
MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0, |
570 |
< |
myPotato, MPI_COMM_WORLD); |
570 |
> |
myPotato, MPI_COMM_WORLD); |
571 |
|
|
572 |
|
myPotato++; |
573 |
|
|
574 |
|
MPI_Send(&isDirectional, 1, MPI_INT, 0, |
575 |
< |
myPotato, MPI_COMM_WORLD); |
575 |
> |
myPotato, MPI_COMM_WORLD); |
576 |
|
|
577 |
|
myPotato++; |
578 |
|
|
587 |
|
myPotato, MPI_COMM_WORLD); |
588 |
|
} |
589 |
|
|
590 |
< |
myPotato++; |
590 |
> |
myPotato++; |
591 |
> |
currentIndex++; |
592 |
|
} |
593 |
|
} |
594 |
|
|
598 |
|
|
599 |
|
} |
600 |
|
|
902 |
– |
if( worldRank == 0 ) finalOut.close(); |
601 |
|
#endif // is_mpi |
602 |
|
} |
603 |
|
|
906 |
– |
|
907 |
– |
|
604 |
|
#ifdef IS_MPI |
605 |
|
|
606 |
|
// a couple of functions to let us escape the write loop |