# | Line 3 | Line 3 | |
---|---|---|
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> | |
# | Line 26 | Line 28 | DumpWriter::DumpWriter( SimInfo* the_entry_plug ){ | |
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 | β | if( !outFile ){ |
34 | β | |
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 | β | //outFile.setf( ios::scientific ); |
43 | β | |
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(); | |
# | Line 56 | Line 57 | DumpWriter::~DumpWriter( ){ | |
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 | + | /** |
70 | + | * A hook function to load balancing |
71 | + | */ |
72 | + | |
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 | + | /** |
86 | + | * Sorting the local index by global index |
87 | + | */ |
88 | + | |
89 | + | void DumpWriter::sortByGlobalIndex(){ |
90 | + | Atom** atoms = entry_plug->atoms; |
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 | + | #endif |
101 | + | |
102 | + | void DumpWriter::writeDump(double currentTime){ |
103 | + | |
104 | + | ofstream finalOut; |
105 | + | vector<ofstream*> fileStreams; |
106 | + | |
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 | + | #ifdef IS_MPI |
119 | + | } |
120 | + | #endif // is_mpi |
121 | + | |
122 | + | fileStreams.push_back(&finalOut); |
123 | + | fileStreams.push_back(&dumpFile); |
124 | + | |
125 | + | writeFrame(fileStreams, currentTime); |
126 | + | |
127 | + | #ifdef IS_MPI |
128 | + | finalOut.close(); |
129 | + | #endif |
130 | + | |
131 | + | } |
132 | + | |
133 | + | void DumpWriter::writeFinal(double currentTime){ |
134 | + | |
135 | + | ofstream finalOut; |
136 | + | vector<ofstream*> fileStreams; |
137 | + | |
138 | + | #ifdef IS_MPI |
139 | + | if(worldRank == 0 ){ |
140 | + | #endif // is_mpi |
141 | + | |
142 | + | finalOut.open( entry_plug->finalName, ios::out | ios::trunc ); |
143 | + | |
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 | + | #ifdef IS_MPI |
153 | + | } |
154 | + | #endif // is_mpi |
155 | + | |
156 | + | fileStreams.push_back(&finalOut); |
157 | + | writeFrame(fileStreams, currentTime); |
158 | + | |
159 | + | #ifdef IS_MPI |
160 | + | finalOut.close(); |
161 | + | #endif |
162 | + | |
163 | + | } |
164 | + | |
165 | + | void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){ |
166 | + | |
167 | const int BUFFERSIZE = 2000; | |
168 | const int MINIBUFFERSIZE = 100; | |
169 | ||
170 | < | char tempBuffer[BUFFERSIZE]; |
170 | > | char tempBuffer[BUFFERSIZE]; |
171 | char writeLine[BUFFERSIZE]; | |
172 | ||
173 | < | 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 me; |
83 | < | int atomTypeTag; |
84 | < | int atomIsDirectionalTag; |
85 | < | int atomTransDataTag; |
86 | < | int atomOrientDataTag; |
224 | > | |
225 | #else //is_mpi | |
226 | int nAtoms = entry_plug->n_atoms; | |
227 | #endif //is_mpi | |
# | Line 93 | Line 231 | void DumpWriter::writeDump( double currentTime ){ | |
231 | Atom** atoms = entry_plug->atoms; | |
232 | double pos[3], vel[3]; | |
233 | ||
96 | β | // write current frame to the eor file |
97 | β | |
98 | β | this->writeFinal( currentTime ); |
99 | β | |
234 | #ifndef IS_MPI | |
235 | + | |
236 | + | for(k = 0; k < outFile.size(); k++){ |
237 | + | *outFile[k] << nAtoms << "\n"; |
238 | ||
239 | < | outFile << 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 | < | outFile << currentTime << ";\t" |
249 | < | << entry_plug->Hmat[0][0] << "\t" |
250 | < | << entry_plug->Hmat[1][0] << "\t" |
107 | < | << 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 | < | |
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 | < | |
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); | |
# | Line 152 | Line 288 | void DumpWriter::writeDump( double currentTime ){ | |
288 | else | |
289 | strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); | |
290 | ||
291 | < | outFile << writeLine; |
291 | > | for(k = 0; k < outFile.size(); k++) |
292 | > | *outFile[k] << writeLine; |
293 | } | |
157 | β | outFile.flush(); |
294 | ||
295 | #else // is_mpi | |
296 | ||
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 | < | } |
305 | > | } |
306 | ||
307 | int haveError; | |
308 | ||
# | Line 175 | Line 312 | void DumpWriter::writeDump( double currentTime ){ | |
312 | // write out header and node 0's coordinates | |
313 | ||
314 | if( worldRank == 0 ){ | |
178 | β | outFile << mpiSim->getTotAtoms() << "\n"; |
315 | ||
316 | < | outFile << currentTime << ";\t" |
181 | < | << entry_plug->Hmat[0][0] << "\t" |
182 | < | << entry_plug->Hmat[1][0] << "\t" |
183 | < | << 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" |
187 | < | << 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 | < | outFile << entry_plug->the_integrator->getAdditionalParameters(); |
329 | < | outFile << endl; |
330 | < | outFile.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 | < | tag = 0; |
333 | > | << entry_plug->Hmat[0][1] << "\t" |
334 | > | << entry_plug->Hmat[1][1] << "\t" |
335 | > | << entry_plug->Hmat[2][1] << ";\t" |
336 | ||
337 | < | for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
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 | < | if (tag + 2 >= MAXTAG) { |
345 | < | // The tag was going to exceed the maximum value, so wrap around to 0: |
346 | < | tag = 0; |
204 | < | // Send the newly zeroed tag on to the other nodes: |
205 | < | MPI_Bcast(&tag, 1, MPI_INT, 0, MPI_COMM_WORLD); |
206 | < | } |
344 | > | currentIndex = 0; |
345 | > | |
346 | > | for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
347 | ||
348 | // Get the Node number which has this atom; | |
349 | ||
350 | which_node = AtomToProcMap[i]; | |
351 | ||
352 | if (which_node != 0) { | |
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); |
369 | < | |
370 | < | // Null terminate the atomTypeString just in case: |
368 | > | atomTypeString = MPIatomTypeString; |
369 | > | |
370 | > | myPotato++; |
371 | ||
221 | β | atomTypeString[strlen(atomTypeString) - 1] = '\0'; |
222 | β | |
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, |
227 | < | 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) { |
247 | < | |
248 | < | atomTypeString = atoms[local_index]->getType(); |
249 | < | |
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]; |
256 | < | |
257 | < | atomTransData[3] = vel[0]; |
258 | < | atomTransData[4] = vel[1]; |
259 | < | atomTransData[5] = vel[2]; |
406 | > | atomData6[3] = vel[0]; |
407 | > | atomData6[4] = vel[1]; |
408 | > | atomData6[5] = vel[2]; |
409 | ||
410 | isDirectional = 0; | |
411 | ||
# | Line 266 | Line 415 | void DumpWriter::writeDump( double currentTime ){ | |
415 | ||
416 | dAtom = (DirectionalAtom *)atoms[local_index]; | |
417 | dAtom->getQ( q ); | |
269 | β | |
270 | β | atomOrientData[0] = q[0]; |
271 | β | atomOrientData[1] = q[1]; |
272 | β | atomOrientData[2] = q[2]; |
273 | β | atomOrientData[3] = q[3]; |
418 | ||
419 | < | atomOrientData[4] = dAtom->getJx(); |
420 | < | atomOrientData[5] = dAtom->getJy(); |
421 | < | atomOrientData[6] = dAtom->getJz(); |
419 | > | for (int j = 0; j < 6 ; j++) |
420 | > | atomData13[j] = atomData6[j]; |
421 | > | |
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 | } | |
287 | β | |
288 | β | if(haveError) DieDieDie(); |
289 | β | |
290 | β | // 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, |
295 | < | atomTransData[0], |
296 | < | atomTransData[1], |
297 | < | atomTransData[2], |
298 | < | atomTransData[3], |
299 | < | atomTransData[4], |
300 | < | atomTransData[5]); |
301 | < | |
302 | < | strcpy( writeLine, tempBuffer ); |
303 | < | |
304 | < | if (isDirectional) { |
305 | < | |
306 | < | sprintf( tempBuffer, |
307 | < | "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
308 | < | atomOrientData[0], |
309 | < | atomOrientData[1], |
310 | < | atomOrientData[2], |
311 | < | atomOrientData[3], |
312 | < | atomOrientData[4], |
313 | < | atomOrientData[5], |
314 | < | atomOrientData[6]); |
315 | < | strcat( writeLine, tempBuffer ); |
316 | < | |
317 | < | } else { |
318 | < | strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
319 | < | } |
320 | < | |
321 | < | outFile << writeLine; |
322 | < | outFile.flush(); |
440 | > | if(haveError) DieDieDie(); |
441 | > | |
442 | > | currentIndex++; |
443 | } | |
444 | < | } |
325 | < | |
326 | < | outFile.flush(); |
327 | < | sprintf( checkPointMsg, |
328 | < | "Sucessfully took a dump.\n"); |
329 | < | MPIcheckPoint(); |
330 | < | |
331 | < | } else { |
332 | < | |
333 | < | // worldRank != 0, so I'm a remote node. |
334 | < | |
335 | < | for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
444 | > | // If we've survived to here, format the line: |
445 | ||
446 | < | // Am I the node which has this atom? |
447 | < | |
448 | < | if (AtomToProcMap[i] == worldRank) { |
449 | < | |
450 | < | local_index=-1; |
451 | < | for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
452 | < | if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
453 | < | } |
454 | < | if (local_index != -1) { |
455 | < | |
456 | < | atomTypeString = atoms[local_index]->getType(); |
457 | < | |
458 | < | atoms[local_index]->getPos(pos); |
459 | < | atoms[local_index]->getVel(vel); |
351 | < | |
352 | < | atomTransData[0] = pos[0]; |
353 | < | atomTransData[1] = pos[1]; |
354 | < | atomTransData[2] = pos[2]; |
355 | < | |
356 | < | atomTransData[3] = vel[0]; |
357 | < | atomTransData[4] = vel[1]; |
358 | < | atomTransData[5] = vel[2]; |
359 | < | |
360 | < | isDirectional = 0; |
361 | < | |
362 | < | if( atoms[local_index]->isDirectional() ){ |
363 | < | |
364 | < | isDirectional = 1; |
365 | < | |
366 | < | dAtom = (DirectionalAtom *)atoms[local_index]; |
367 | < | dAtom->getQ( q ); |
368 | < | |
369 | < | atomOrientData[0] = q[0]; |
370 | < | atomOrientData[1] = q[1]; |
371 | < | atomOrientData[2] = q[2]; |
372 | < | atomOrientData[3] = q[3]; |
373 | < | |
374 | < | atomOrientData[4] = dAtom->getJx(); |
375 | < | atomOrientData[5] = dAtom->getJy(); |
376 | < | atomOrientData[6] = dAtom->getJz(); |
377 | < | } |
378 | < | |
379 | < | } else { |
380 | < | sprintf(painCave.errMsg, |
381 | < | "Atom %d not found on processor %d\n", |
382 | < | i, worldRank ); |
383 | < | haveError= 1; |
384 | < | simError(); |
385 | < | } |
386 | < | |
387 | < | // I've survived this far, so send off the data! |
388 | < | |
389 | < | atomTypeTag = 4*i; |
390 | < | atomIsDirectionalTag = 4*i + 1; |
391 | < | atomTransDataTag = 4*i + 2; |
392 | < | atomOrientDataTag = 4*i + 3; |
393 | < | |
394 | < | |
395 | < | strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE); |
396 | < | |
397 | < | // null terminate the string before sending (just in case): |
398 | < | MPIatomTypeString[MINIBUFFERSIZE-1] = '\0'; |
399 | < | |
400 | < | MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0, |
401 | < | atomTypeTag, MPI_COMM_WORLD); |
402 | < | |
403 | < | MPI_Send(&isDirectional, 1, MPI_INT, 0, |
404 | < | atomIsDirectionalTag, MPI_COMM_WORLD); |
405 | < | |
406 | < | MPI_Send(atomTransData, 6, MPI_DOUBLE, 0, |
407 | < | atomTransDataTag, MPI_COMM_WORLD); |
408 | < | |
409 | < | if (isDirectional) { |
410 | < | |
411 | < | MPI_Send(atomOrientData, 7, MPI_DOUBLE, 0, |
412 | < | atomOrientDataTag, MPI_COMM_WORLD); |
413 | < | |
414 | < | } |
415 | < | |
416 | < | } |
417 | < | } |
418 | < | |
419 | < | sprintf( checkPointMsg, |
420 | < | "Sucessfully took a dump.\n"); |
421 | < | MPIcheckPoint(); |
422 | < | |
423 | < | } |
424 | < | |
425 | < | painCave.isEventLoop = 0; |
426 | < | |
427 | < | #endif // is_mpi |
428 | < | } |
429 | < | |
430 | < | void DumpWriter::writeFinal(double finalTime){ |
431 | < | |
432 | < | char finalName[500]; |
433 | < | ofstream finalOut; |
434 | < | |
435 | < | const int BUFFERSIZE = 2000; |
436 | < | const int MINIBUFFERSIZE = 100; |
437 | < | char tempBuffer[BUFFERSIZE]; |
438 | < | char writeLine[BUFFERSIZE]; |
439 | < | |
440 | < | double q[4]; |
441 | < | DirectionalAtom* dAtom; |
442 | < | Atom** atoms = entry_plug->atoms; |
443 | < | int i; |
444 | < | #ifdef IS_MPI |
445 | < | int j, which_node, done, which_atom, local_index; |
446 | < | double atomTransData[6]; |
447 | < | double atomOrientData[7]; |
448 | < | int isDirectional; |
449 | < | char* atomTypeString; |
450 | < | char MPIatomTypeString[MINIBUFFERSIZE]; |
451 | < | int atomTypeTag; |
452 | < | int atomIsDirectionalTag; |
453 | < | int atomTransDataTag; |
454 | < | int atomOrientDataTag; |
455 | < | #else //is_mpi |
456 | < | int nAtoms = entry_plug->n_atoms; |
457 | < | #endif //is_mpi |
458 | < | |
459 | < | double pos[3], vel[3]; |
460 | < | |
461 | < | #ifdef IS_MPI |
462 | < | if(worldRank == 0 ){ |
463 | < | #endif // is_mpi |
464 | < | |
465 | < | strcpy( finalName, entry_plug->finalName ); |
466 | < | |
467 | < | finalOut.open( finalName, ios::out | ios::trunc ); |
468 | < | if( !finalOut ){ |
469 | < | sprintf( painCave.errMsg, |
470 | < | "Could not open \"%s\" for final dump output.\n", |
471 | < | finalName ); |
472 | < | painCave.isFatal = 1; |
473 | < | simError(); |
474 | < | } |
475 | < | |
476 | < | // finalOut.setf( ios::scientific ); |
477 | < | |
478 | < | #ifdef IS_MPI |
479 | < | } |
480 | < | |
481 | < | sprintf(checkPointMsg,"Opened file for final configuration\n"); |
482 | < | MPIcheckPoint(); |
483 | < | |
484 | < | #endif //is_mpi |
485 | < | |
486 | < | |
487 | < | #ifndef IS_MPI |
488 | < | |
489 | < | finalOut << nAtoms << "\n"; |
490 | < | |
491 | < | finalOut << finalTime << ";\t" |
492 | < | << entry_plug->Hmat[0][0] << "\t" |
493 | < | << entry_plug->Hmat[1][0] << "\t" |
494 | < | << entry_plug->Hmat[2][0] << ";\t" |
495 | < | |
496 | < | << entry_plug->Hmat[0][1] << "\t" |
497 | < | << entry_plug->Hmat[1][1] << "\t" |
498 | < | << entry_plug->Hmat[2][1] << ";\t" |
499 | < | |
500 | < | << entry_plug->Hmat[0][2] << "\t" |
501 | < | << entry_plug->Hmat[1][2] << "\t" |
502 | < | << entry_plug->Hmat[2][2] << ";"; |
503 | < | |
504 | < | //write out additional parameters, such as chi and eta |
505 | < | finalOut << entry_plug->the_integrator->getAdditionalParameters(); |
506 | < | finalOut << endl; |
507 | < | |
508 | < | for( i=0; i<nAtoms; i++ ){ |
509 | < | |
510 | < | atoms[i]->getPos(pos); |
511 | < | atoms[i]->getVel(vel); |
512 | < | |
513 | < | sprintf( tempBuffer, |
514 | < | "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
515 | < | atoms[i]->getType(), |
516 | < | pos[0], |
517 | < | pos[1], |
518 | < | pos[2], |
519 | < | vel[0], |
520 | < | vel[1], |
521 | < | vel[2]); |
522 | < | strcpy( writeLine, tempBuffer ); |
523 | < | |
524 | < | if( atoms[i]->isDirectional() ){ |
525 | < | |
526 | < | dAtom = (DirectionalAtom *)atoms[i]; |
527 | < | dAtom->getQ( q ); |
528 | < | |
529 | < | sprintf( tempBuffer, |
530 | < | "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
531 | < | q[0], |
532 | < | q[1], |
533 | < | q[2], |
534 | < | q[3], |
535 | < | dAtom->getJx(), |
536 | < | dAtom->getJy(), |
537 | < | dAtom->getJz()); |
538 | < | strcat( writeLine, tempBuffer ); |
539 | < | } |
540 | < | else |
541 | < | strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
542 | < | |
543 | < | finalOut << writeLine; |
544 | < | } |
545 | < | finalOut.flush(); |
546 | < | finalOut.close(); |
547 | < | |
548 | < | #else // is_mpi |
549 | < | |
550 | < | // first thing first, suspend fatalities. |
551 | < | painCave.isEventLoop = 1; |
552 | < | |
553 | < | int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone |
554 | < | int haveError; |
555 | < | |
556 | < | MPI_Status istatus; |
557 | < | int *AtomToProcMap = mpiSim->getAtomToProcMap(); |
558 | < | |
559 | < | // write out header and node 0's coordinates |
560 | < | |
561 | < | if( worldRank == 0 ){ |
562 | < | finalOut << mpiSim->getTotAtoms() << "\n"; |
563 | < | |
564 | < | finalOut << finalTime << ";\t" |
565 | < | << entry_plug->Hmat[0][0] << "\t" |
566 | < | << entry_plug->Hmat[1][0] << "\t" |
567 | < | << entry_plug->Hmat[2][0] << ";\t" |
568 | < | |
569 | < | << entry_plug->Hmat[0][1] << "\t" |
570 | < | << entry_plug->Hmat[1][1] << "\t" |
571 | < | << entry_plug->Hmat[2][1] << ";\t" |
572 | < | |
573 | < | << entry_plug->Hmat[0][2] << "\t" |
574 | < | << entry_plug->Hmat[1][2] << "\t" |
575 | < | << entry_plug->Hmat[2][2] << ";"; |
576 | < | |
577 | < | finalOut << entry_plug->the_integrator->getAdditionalParameters(); |
578 | < | finalOut << endl; |
579 | < | finalOut.flush(); |
580 | < | for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
581 | < | // Get the Node number which has this atom; |
582 | < | |
583 | < | which_node = AtomToProcMap[i]; |
584 | < | |
585 | < | if (which_node != 0) { |
586 | < | |
587 | < | atomTypeTag = 4*i; |
588 | < | atomIsDirectionalTag = 4*i + 1; |
589 | < | atomTransDataTag = 4*i + 2; |
590 | < | atomOrientDataTag = 4*i + 3; |
591 | < | |
592 | < | MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node, |
593 | < | atomTypeTag, MPI_COMM_WORLD, &istatus); |
594 | < | |
595 | < | strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE); |
596 | < | |
597 | < | MPI_Recv(&isDirectional, 1, MPI_INT, which_node, |
598 | < | atomIsDirectionalTag, MPI_COMM_WORLD, &istatus); |
599 | < | |
600 | < | MPI_Recv(atomTransData, 6, MPI_DOUBLE, which_node, |
601 | < | atomTransDataTag, MPI_COMM_WORLD, &istatus); |
602 | < | |
603 | < | if (isDirectional) { |
604 | < | |
605 | < | MPI_Recv(atomOrientData, 7, MPI_DOUBLE, which_node, |
606 | < | atomOrientDataTag, MPI_COMM_WORLD, &istatus); |
607 | < | |
608 | < | } |
609 | < | |
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 | ||
612 | β | haveError = 0; |
613 | β | which_atom = i; |
614 | β | local_index=-1; |
615 | β | |
616 | β | for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
617 | β | if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
618 | β | } |
619 | β | |
620 | β | if (local_index != -1) { |
621 | β | |
622 | β | atomTypeString = atoms[local_index]->getType(); |
623 | β | |
624 | β | atoms[local_index]->getPos(pos); |
625 | β | atoms[local_index]->getVel(vel); |
626 | β | |
627 | β | atomTransData[0] = pos[0]; |
628 | β | atomTransData[1] = pos[1]; |
629 | β | atomTransData[2] = pos[2]; |
630 | β | |
631 | β | atomTransData[3] = vel[0]; |
632 | β | atomTransData[4] = vel[1]; |
633 | β | atomTransData[5] = vel[2]; |
634 | β | |
635 | β | isDirectional = 0; |
636 | β | |
637 | β | if( atoms[local_index]->isDirectional() ){ |
638 | β | |
639 | β | isDirectional = 1; |
640 | β | |
641 | β | dAtom = (DirectionalAtom *)atoms[local_index]; |
642 | β | dAtom->getQ( q ); |
643 | β | |
644 | β | atomOrientData[0] = q[0]; |
645 | β | atomOrientData[1] = q[1]; |
646 | β | atomOrientData[2] = q[2]; |
647 | β | atomOrientData[3] = q[3]; |
648 | β | |
649 | β | atomOrientData[4] = dAtom->getJx(); |
650 | β | atomOrientData[5] = dAtom->getJy(); |
651 | β | atomOrientData[6] = dAtom->getJz(); |
652 | β | } |
653 | β | |
654 | β | } else { |
655 | β | sprintf(painCave.errMsg, |
656 | β | "Atom %d not found on processor %d\n", |
657 | β | i, worldRank ); |
658 | β | haveError= 1; |
659 | β | simError(); |
660 | β | } |
661 | β | |
662 | β | if(haveError) DieDieDie(); |
663 | β | |
664 | β | // If we've survived to here, format the line: |
665 | β | |
666 | β | sprintf( tempBuffer, |
667 | β | "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
668 | β | atomTypeString, |
669 | β | atomTransData[0], |
670 | β | atomTransData[1], |
671 | β | atomTransData[2], |
672 | β | atomTransData[3], |
673 | β | atomTransData[4], |
674 | β | atomTransData[5]); |
675 | β | |
676 | β | strcpy( writeLine, tempBuffer ); |
677 | β | |
678 | β | if (isDirectional) { |
679 | β | |
680 | β | sprintf( tempBuffer, |
681 | β | "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
682 | β | atomOrientData[0], |
683 | β | atomOrientData[1], |
684 | β | atomOrientData[2], |
685 | β | atomOrientData[3], |
686 | β | atomOrientData[4], |
687 | β | atomOrientData[5], |
688 | β | atomOrientData[6]); |
689 | β | strcat( writeLine, tempBuffer ); |
690 | β | |
691 | β | } else { |
692 | β | strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
693 | β | } |
694 | β | |
695 | β | finalOut << writeLine; |
696 | β | finalOut.flush(); |
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 | ||
# | Line 712 | Line 507 | void DumpWriter::writeFinal(double finalTime){ | |
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]; |
729 | < | |
730 | < | atomTransData[3] = vel[0]; |
731 | < | atomTransData[4] = vel[1]; |
732 | < | atomTransData[5] = vel[2]; |
534 | > | atomData6[3] = vel[0]; |
535 | > | atomData6[4] = vel[1]; |
536 | > | atomData6[5] = vel[2]; |
537 | ||
538 | isDirectional = 0; | |
539 | ||
# | Line 740 | Line 544 | void DumpWriter::writeFinal(double finalTime){ | |
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 | < | |
761 | < | // I've survived this far, so send off the data! |
762 | < | |
763 | < | atomTypeTag = 4*i; |
764 | < | atomIsDirectionalTag = 4*i + 1; |
765 | < | atomTransDataTag = 4*i + 2; |
766 | < | atomOrientDataTag = 4*i + 3; |
767 | < | |
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); |
778 | < | |
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 | ||
795 | β | painCave.isEventLoop = 0; |
796 | β | |
797 | β | if( worldRank == 0 ) finalOut.close(); |
605 | #endif // is_mpi | |
606 | } | |
607 | ||
801 | β | |
802 | β | |
608 | #ifdef IS_MPI | |
609 | ||
610 | // a couple of functions to let us escape the write loop |
β | Removed lines |
+ | Added lines |
< | Changed lines |
> | Changed lines |