# | 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 | – | if( !outFile ){ |
34 | – | |
35 | sprintf( painCave.errMsg, | |
36 | "Could not open \"%s\" for dump output.\n", | |
37 | < | outName); |
37 | > | entry_plug->sampleName); |
38 | painCave.isFatal = 1; | |
39 | simError(); | |
40 | } | |
41 | ||
42 | – | //outFile.setf( ios::scientific ); |
43 | – | |
42 | #ifdef IS_MPI | |
43 | } | |
44 | ||
45 | + | //sort the local atoms by global index |
46 | + | sortByGlobalIndex(); |
47 | + | |
48 | sprintf( checkPointMsg, | |
49 | "Sucessfully opened output file for dumping.\n"); | |
50 | MPIcheckPoint(); | |
# | 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 | < | 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 | < | // write current frame to the eor file |
99 | > | //for (int i = 0; i < mpiSim->getMyNlocal(); i++) { |
100 | > | // printf("node %d has global %d at local %d\n", worldRank, indexArray[i].second, indexArray[i].first); |
101 | > | //} |
102 | > | |
103 | > | } |
104 | ||
105 | < | this->writeFinal( currentTime ); |
105 | > | #endif |
106 | ||
107 | < | #ifndef IS_MPI |
107 | > | void DumpWriter::writeDump(double currentTime){ |
108 | ||
109 | < | outFile << nAtoms << "\n"; |
109 | > | ofstream finalOut; |
110 | > | vector<ofstream*> fileStreams; |
111 | ||
112 | < | outFile << currentTime << ";\t" |
113 | < | << entry_plug->Hmat[0][0] << "\t" |
114 | < | << entry_plug->Hmat[1][0] << "\t" |
115 | < | << entry_plug->Hmat[2][0] << ";\t" |
116 | < | |
117 | < | << entry_plug->Hmat[0][1] << "\t" |
118 | < | << entry_plug->Hmat[1][1] << "\t" |
119 | < | << entry_plug->Hmat[2][1] << ";\t" |
120 | < | |
121 | < | << entry_plug->Hmat[0][2] << "\t" |
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 ); |
112 | > | #ifdef IS_MPI |
113 | > | if(worldRank == 0 ){ |
114 | > | #endif |
115 | > | finalOut.open( entry_plug->finalName, ios::out | ios::trunc ); |
116 | > | if( !finalOut ){ |
117 | > | sprintf( painCave.errMsg, |
118 | > | "Could not open \"%s\" for final dump output.\n", |
119 | > | entry_plug->finalName ); |
120 | > | painCave.isFatal = 1; |
121 | > | simError(); |
122 | } | |
123 | < | else |
153 | < | strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
154 | < | |
155 | < | outFile << writeLine; |
123 | > | #ifdef IS_MPI |
124 | } | |
125 | < | outFile.flush(); |
125 | > | #endif // is_mpi |
126 | ||
127 | < | #else // is_mpi |
127 | > | fileStreams.push_back(&finalOut); |
128 | > | fileStreams.push_back(&dumpFile); |
129 | ||
130 | < | // first thing first, suspend fatalities. |
162 | < | painCave.isEventLoop = 1; |
130 | > | writeFrame(fileStreams, currentTime); |
131 | ||
132 | < | int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone |
133 | < | int haveError; |
132 | > | #ifdef IS_MPI |
133 | > | finalOut.close(); |
134 | > | #endif |
135 | > | |
136 | > | } |
137 | ||
138 | < | MPI_Status istatus; |
168 | < | int *AtomToProcMap = mpiSim->getAtomToProcMap(); |
138 | > | void DumpWriter::writeFinal(double currentTime){ |
139 | ||
140 | < | // write out header and node 0's coordinates |
140 | > | ofstream finalOut; |
141 | > | vector<ofstream*> fileStreams; |
142 | ||
143 | < | if( worldRank == 0 ){ |
144 | < | outFile << mpiSim->getTotAtoms() << "\n"; |
143 | > | #ifdef IS_MPI |
144 | > | if(worldRank == 0 ){ |
145 | > | #endif // is_mpi |
146 | ||
147 | < | outFile << currentTime << ";\t" |
176 | < | << entry_plug->Hmat[0][0] << "\t" |
177 | < | << entry_plug->Hmat[1][0] << "\t" |
178 | < | << entry_plug->Hmat[2][0] << ";\t" |
147 | > | finalOut.open( entry_plug->finalName, ios::out | ios::trunc ); |
148 | ||
149 | < | << entry_plug->Hmat[0][1] << "\t" |
150 | < | << entry_plug->Hmat[1][1] << "\t" |
151 | < | << entry_plug->Hmat[2][1] << ";\t" |
149 | > | if( !finalOut ){ |
150 | > | sprintf( painCave.errMsg, |
151 | > | "Could not open \"%s\" for final dump output.\n", |
152 | > | entry_plug->finalName ); |
153 | > | painCave.isFatal = 1; |
154 | > | simError(); |
155 | > | } |
156 | ||
157 | < | << entry_plug->Hmat[0][2] << "\t" |
158 | < | << entry_plug->Hmat[1][2] << "\t" |
159 | < | << 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 | < | |
412 | < | } |
157 | > | #ifdef IS_MPI |
158 | > | } |
159 | > | #endif // is_mpi |
160 | ||
161 | < | painCave.isEventLoop = 0; |
161 | > | fileStreams.push_back(&finalOut); |
162 | > | writeFrame(fileStreams, currentTime); |
163 | ||
164 | < | #endif // is_mpi |
164 | > | #ifdef IS_MPI |
165 | > | finalOut.close(); |
166 | > | #endif |
167 | > | |
168 | } | |
169 | ||
170 | < | void DumpWriter::writeFinal(double finalTime){ |
170 | > | void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){ |
171 | ||
421 | – | char finalName[500]; |
422 | – | ofstream finalOut; |
423 | – | |
172 | const int BUFFERSIZE = 2000; | |
173 | const int MINIBUFFERSIZE = 100; | |
174 | < | char tempBuffer[BUFFERSIZE]; |
174 | > | |
175 | > | char tempBuffer[BUFFERSIZE]; |
176 | char writeLine[BUFFERSIZE]; | |
177 | ||
178 | < | double q[4]; |
179 | < | DirectionalAtom* dAtom; |
431 | < | Atom** atoms = entry_plug->atoms; |
432 | < | int i; |
178 | > | int i, k; |
179 | > | |
180 | #ifdef IS_MPI | |
181 | < | int j, which_node, done, which_atom, local_index; |
182 | < | double atomTransData[6]; |
183 | < | double atomOrientData[7]; |
181 | > | |
182 | > | /********************************************************************* |
183 | > | * Documentation? You want DOCUMENTATION? |
184 | > | * |
185 | > | * Why all the potatoes below? |
186 | > | * |
187 | > | * To make a long story short, the original version of DumpWriter |
188 | > | * worked in the most inefficient way possible. Node 0 would |
189 | > | * poke each of the node for an individual atom's formatted data |
190 | > | * as node 0 worked its way down the global index. This was particularly |
191 | > | * inefficient since the method blocked all processors at every atom |
192 | > | * (and did it twice!). |
193 | > | * |
194 | > | * An intermediate version of DumpWriter could be described from Node |
195 | > | * zero's perspective as follows: |
196 | > | * |
197 | > | * 1) Have 100 of your friends stand in a circle. |
198 | > | * 2) When you say go, have all of them start tossing potatoes at |
199 | > | * you (one at a time). |
200 | > | * 3) Catch the potatoes. |
201 | > | * |
202 | > | * It was an improvement, but MPI has buffers and caches that could |
203 | > | * best be described in this analogy as "potato nets", so there's no |
204 | > | * need to block the processors atom-by-atom. |
205 | > | * |
206 | > | * This new and improved DumpWriter works in an even more efficient |
207 | > | * way: |
208 | > | * |
209 | > | * 1) Have 100 of your friend stand in a circle. |
210 | > | * 2) When you say go, have them start tossing 5-pound bags of |
211 | > | * potatoes at you. |
212 | > | * 3) Once you've caught a friend's bag of potatoes, |
213 | > | * toss them a spud to let them know they can toss another bag. |
214 | > | * |
215 | > | * How's THAT for documentation? |
216 | > | * |
217 | > | *********************************************************************/ |
218 | > | |
219 | > | int *potatoes; |
220 | > | int myPotato; |
221 | > | |
222 | > | int nProc; |
223 | > | int j, which_node, done, which_atom, local_index, currentIndex; |
224 | > | double atomData6[6]; |
225 | > | double atomData13[13]; |
226 | int isDirectional; | |
227 | char* atomTypeString; | |
228 | char MPIatomTypeString[MINIBUFFERSIZE]; | |
229 | < | int atomTypeTag; |
441 | < | int atomIsDirectionalTag; |
442 | < | int atomTransDataTag; |
443 | < | int atomOrientDataTag; |
229 | > | |
230 | #else //is_mpi | |
231 | int nAtoms = entry_plug->n_atoms; | |
232 | #endif //is_mpi | |
233 | ||
234 | + | double q[4]; |
235 | + | DirectionalAtom* dAtom; |
236 | + | Atom** atoms = entry_plug->atoms; |
237 | double pos[3], vel[3]; | |
238 | ||
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 | – | |
239 | #ifndef IS_MPI | |
240 | + | |
241 | + | for(k = 0; k < outFile.size(); k++){ |
242 | + | *outFile[k] << nAtoms << "\n"; |
243 | ||
244 | < | finalOut << nAtoms << "\n"; |
244 | > | *outFile[k] << currentTime << ";\t" |
245 | > | << entry_plug->Hmat[0][0] << "\t" |
246 | > | << entry_plug->Hmat[1][0] << "\t" |
247 | > | << entry_plug->Hmat[2][0] << ";\t" |
248 | > | |
249 | > | << entry_plug->Hmat[0][1] << "\t" |
250 | > | << entry_plug->Hmat[1][1] << "\t" |
251 | > | << entry_plug->Hmat[2][1] << ";\t" |
252 | ||
253 | < | finalOut << finalTime << ";\t" |
254 | < | << entry_plug->Hmat[0][0] << "\t" |
255 | < | << entry_plug->Hmat[1][0] << "\t" |
483 | < | << entry_plug->Hmat[2][0] << ";\t" |
253 | > | << entry_plug->Hmat[0][2] << "\t" |
254 | > | << entry_plug->Hmat[1][2] << "\t" |
255 | > | << entry_plug->Hmat[2][2] << ";"; |
256 | ||
257 | < | << entry_plug->Hmat[0][1] << "\t" |
258 | < | << entry_plug->Hmat[1][1] << "\t" |
259 | < | << entry_plug->Hmat[2][1] << ";\t" |
260 | < | |
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 | < | |
257 | > | //write out additional parameters, such as chi and eta |
258 | > | *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl; |
259 | > | } |
260 | > | |
261 | for( i=0; i<nAtoms; i++ ){ | |
262 | ||
263 | atoms[i]->getPos(pos); | |
# | Line 529 | Line 293 | void DumpWriter::writeFinal(double finalTime){ | |
293 | else | |
294 | strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); | |
295 | ||
296 | < | finalOut << writeLine; |
296 | > | for(k = 0; k < outFile.size(); k++) |
297 | > | *outFile[k] << writeLine; |
298 | } | |
534 | – | finalOut.flush(); |
535 | – | finalOut.close(); |
299 | ||
300 | #else // is_mpi | |
301 | ||
302 | < | // first thing first, suspend fatalities. |
303 | < | painCave.isEventLoop = 1; |
302 | > | /* code to find maximum tag value */ |
303 | > | |
304 | > | int *tagub, flag, MAXTAG; |
305 | > | MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag); |
306 | > | if (flag) { |
307 | > | MAXTAG = *tagub; |
308 | > | } else { |
309 | > | MAXTAG = 32767; |
310 | > | } |
311 | ||
542 | – | int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone |
312 | int haveError; | |
313 | ||
314 | MPI_Status istatus; | |
# | Line 548 | Line 317 | void DumpWriter::writeFinal(double finalTime){ | |
317 | // write out header and node 0's coordinates | |
318 | ||
319 | if( worldRank == 0 ){ | |
551 | – | finalOut << mpiSim->getTotAtoms() << "\n"; |
320 | ||
321 | < | finalOut << finalTime << ";\t" |
554 | < | << entry_plug->Hmat[0][0] << "\t" |
555 | < | << entry_plug->Hmat[1][0] << "\t" |
556 | < | << entry_plug->Hmat[2][0] << ";\t" |
321 | > | // Node 0 needs a list of the magic potatoes for each processor; |
322 | ||
323 | < | << entry_plug->Hmat[0][1] << "\t" |
324 | < | << entry_plug->Hmat[1][1] << "\t" |
560 | < | << entry_plug->Hmat[2][1] << ";\t" |
323 | > | nProc = mpiSim->getNumberProcessors(); |
324 | > | potatoes = new int[nProc]; |
325 | ||
326 | < | << entry_plug->Hmat[0][2] << "\t" |
327 | < | << entry_plug->Hmat[1][2] << "\t" |
328 | < | << entry_plug->Hmat[2][2] << ";"; |
326 | > | //write out the comment lines |
327 | > | for (i = 0; i < nProc; i++) |
328 | > | potatoes[i] = 0; |
329 | > | |
330 | > | for(k = 0; k < outFile.size(); k++){ |
331 | > | *outFile[k] << mpiSim->getTotAtoms() << "\n"; |
332 | ||
333 | < | finalOut << entry_plug->the_integrator->getAdditionalParameters(); |
334 | < | finalOut << endl; |
335 | < | finalOut.flush(); |
333 | > | *outFile[k] << currentTime << ";\t" |
334 | > | << entry_plug->Hmat[0][0] << "\t" |
335 | > | << entry_plug->Hmat[1][0] << "\t" |
336 | > | << entry_plug->Hmat[2][0] << ";\t" |
337 | > | |
338 | > | << entry_plug->Hmat[0][1] << "\t" |
339 | > | << entry_plug->Hmat[1][1] << "\t" |
340 | > | << entry_plug->Hmat[2][1] << ";\t" |
341 | > | |
342 | > | << entry_plug->Hmat[0][2] << "\t" |
343 | > | << entry_plug->Hmat[1][2] << "\t" |
344 | > | << entry_plug->Hmat[2][2] << ";"; |
345 | > | |
346 | > | *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl; |
347 | > | } |
348 | > | |
349 | > | currentIndex = 0; |
350 | > | |
351 | for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { | |
352 | + | |
353 | // Get the Node number which has this atom; | |
354 | < | |
354 | > | |
355 | which_node = AtomToProcMap[i]; | |
356 | < | |
356 | > | |
357 | if (which_node != 0) { | |
575 | – | |
576 | – | atomTypeTag = 4*i; |
577 | – | atomIsDirectionalTag = 4*i + 1; |
578 | – | atomTransDataTag = 4*i + 2; |
579 | – | atomOrientDataTag = 4*i + 3; |
358 | ||
359 | + | if (potatoes[which_node] + 3 >= MAXTAG) { |
360 | + | // The potato was going to exceed the maximum value, |
361 | + | // so wrap this processor potato back to 0: |
362 | + | |
363 | + | potatoes[which_node] = 0; |
364 | + | MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD); |
365 | + | |
366 | + | } |
367 | + | |
368 | + | myPotato = potatoes[which_node]; |
369 | + | |
370 | MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node, | |
371 | < | atomTypeTag, MPI_COMM_WORLD, &istatus); |
371 | > | myPotato, MPI_COMM_WORLD, &istatus); |
372 | ||
373 | < | strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE); |
373 | > | atomTypeString = MPIatomTypeString; |
374 | > | |
375 | > | myPotato++; |
376 | ||
377 | MPI_Recv(&isDirectional, 1, MPI_INT, which_node, | |
378 | < | atomIsDirectionalTag, MPI_COMM_WORLD, &istatus); |
379 | < | |
380 | < | MPI_Recv(atomTransData, 6, MPI_DOUBLE, which_node, |
590 | < | atomTransDataTag, MPI_COMM_WORLD, &istatus); |
378 | > | myPotato, MPI_COMM_WORLD, &istatus); |
379 | > | |
380 | > | myPotato++; |
381 | ||
382 | < | if (isDirectional) { |
383 | < | |
384 | < | MPI_Recv(atomOrientData, 7, MPI_DOUBLE, which_node, |
385 | < | atomOrientDataTag, MPI_COMM_WORLD, &istatus); |
386 | < | |
382 | > | if (isDirectional) { |
383 | > | MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node, |
384 | > | myPotato, MPI_COMM_WORLD, &istatus); |
385 | > | } else { |
386 | > | MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node, |
387 | > | myPotato, MPI_COMM_WORLD, &istatus); |
388 | } | |
389 | + | |
390 | + | myPotato++; |
391 | + | potatoes[which_node] = myPotato; |
392 | ||
393 | } else { | |
394 | ||
395 | < | haveError = 0; |
395 | > | haveError = 0; |
396 | which_atom = i; | |
397 | < | local_index=-1; |
397 | > | |
398 | > | //local_index = -1; |
399 | ||
400 | < | for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
401 | < | if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
402 | < | } |
403 | < | |
404 | < | if (local_index != -1) { |
405 | < | |
406 | < | atomTypeString = atoms[local_index]->getType(); |
407 | < | |
400 | > | //for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
401 | > | // if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
402 | > | //} |
403 | > | |
404 | > | //if (local_index != -1) { |
405 | > | |
406 | > | local_index = indexArray[currentIndex].first; |
407 | > | |
408 | > | if (which_atom == indexArray[currentIndex].second) { |
409 | > | |
410 | > | atomTypeString = atoms[local_index]->getType(); |
411 | > | |
412 | atoms[local_index]->getPos(pos); | |
413 | < | atoms[local_index]->getVel(vel); |
413 | > | atoms[local_index]->getVel(vel); |
414 | > | |
415 | > | atomData6[0] = pos[0]; |
416 | > | atomData6[1] = pos[1]; |
417 | > | atomData6[2] = pos[2]; |
418 | ||
419 | < | atomTransData[0] = pos[0]; |
420 | < | atomTransData[1] = pos[1]; |
421 | < | atomTransData[2] = pos[2]; |
619 | < | |
620 | < | atomTransData[3] = vel[0]; |
621 | < | atomTransData[4] = vel[1]; |
622 | < | atomTransData[5] = vel[2]; |
419 | > | atomData6[3] = vel[0]; |
420 | > | atomData6[4] = vel[1]; |
421 | > | atomData6[5] = vel[2]; |
422 | ||
423 | isDirectional = 0; | |
424 | ||
# | Line 629 | Line 428 | void DumpWriter::writeFinal(double finalTime){ | |
428 | ||
429 | dAtom = (DirectionalAtom *)atoms[local_index]; | |
430 | dAtom->getQ( q ); | |
632 | – | |
633 | – | atomOrientData[0] = q[0]; |
634 | – | atomOrientData[1] = q[1]; |
635 | – | atomOrientData[2] = q[2]; |
636 | – | atomOrientData[3] = q[3]; |
431 | ||
432 | < | atomOrientData[4] = dAtom->getJx(); |
433 | < | atomOrientData[5] = dAtom->getJy(); |
434 | < | atomOrientData[6] = dAtom->getJz(); |
432 | > | for (int j = 0; j < 6 ; j++) |
433 | > | atomData13[j] = atomData6[j]; |
434 | > | |
435 | > | atomData13[6] = q[0]; |
436 | > | atomData13[7] = q[1]; |
437 | > | atomData13[8] = q[2]; |
438 | > | atomData13[9] = q[3]; |
439 | > | |
440 | > | atomData13[10] = dAtom->getJx(); |
441 | > | atomData13[11] = dAtom->getJy(); |
442 | > | atomData13[12] = dAtom->getJz(); |
443 | } | |
444 | < | |
444 | > | |
445 | } else { | |
446 | sprintf(painCave.errMsg, | |
447 | < | "Atom %d not found on processor %d\n", |
448 | < | i, worldRank ); |
447 | > | "Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n", |
448 | > | which_atom, worldRank, currentIndex, local_index ); |
449 | haveError= 1; | |
450 | simError(); | |
451 | } | |
650 | – | |
651 | – | if(haveError) DieDieDie(); |
652 | – | |
653 | – | // If we've survived to here, format the line: |
452 | ||
453 | < | sprintf( tempBuffer, |
454 | < | "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
455 | < | 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(); |
453 | > | if(haveError) DieDieDie(); |
454 | > | |
455 | > | currentIndex++; |
456 | } | |
457 | + | // If we've survived to here, format the line: |
458 | + | |
459 | + | if (!isDirectional) { |
460 | + | |
461 | + | sprintf( writeLine, |
462 | + | "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
463 | + | atomTypeString, |
464 | + | atomData6[0], |
465 | + | atomData6[1], |
466 | + | atomData6[2], |
467 | + | atomData6[3], |
468 | + | atomData6[4], |
469 | + | atomData6[5]); |
470 | + | |
471 | + | strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
472 | + | |
473 | + | } else { |
474 | + | |
475 | + | sprintf( writeLine, |
476 | + | "%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", |
477 | + | atomTypeString, |
478 | + | atomData13[0], |
479 | + | atomData13[1], |
480 | + | atomData13[2], |
481 | + | atomData13[3], |
482 | + | atomData13[4], |
483 | + | atomData13[5], |
484 | + | atomData13[6], |
485 | + | atomData13[7], |
486 | + | atomData13[8], |
487 | + | atomData13[9], |
488 | + | atomData13[10], |
489 | + | atomData13[11], |
490 | + | atomData13[12]); |
491 | + | |
492 | + | } |
493 | + | |
494 | + | for(k = 0; k < outFile.size(); k++) |
495 | + | *outFile[k] << writeLine; |
496 | } | |
497 | < | |
498 | < | finalOut.flush(); |
497 | > | |
498 | > | for(k = 0; k < outFile.size(); k++) |
499 | > | outFile[k]->flush(); |
500 | > | |
501 | sprintf( checkPointMsg, | |
502 | "Sucessfully took a dump.\n"); | |
503 | + | |
504 | MPIcheckPoint(); | |
505 | ||
506 | + | delete[] potatoes; |
507 | + | |
508 | } else { | |
509 | ||
510 | // worldRank != 0, so I'm a remote node. | |
511 | + | |
512 | + | // Set my magic potato to 0: |
513 | + | |
514 | + | myPotato = 0; |
515 | + | currentIndex = 0; |
516 | ||
517 | for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { | |
518 | ||
# | Line 701 | Line 520 | void DumpWriter::writeFinal(double finalTime){ | |
520 | ||
521 | if (AtomToProcMap[i] == worldRank) { | |
522 | ||
523 | < | local_index=-1; |
524 | < | for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
525 | < | if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
523 | > | if (myPotato + 3 >= MAXTAG) { |
524 | > | |
525 | > | // The potato was going to exceed the maximum value, |
526 | > | // so wrap this processor potato back to 0 (and block until |
527 | > | // node 0 says we can go: |
528 | > | |
529 | > | MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus); |
530 | > | |
531 | } | |
532 | < | if (local_index != -1) { |
532 | > | which_atom = i; |
533 | > | |
534 | > | //local_index = -1; |
535 | > | |
536 | > | //for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
537 | > | // if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
538 | > | //} |
539 | > | |
540 | > | //if (local_index != -1) { |
541 | > | |
542 | > | local_index = indexArray[currentIndex].first; |
543 | > | |
544 | > | if (which_atom == indexArray[currentIndex].second) { |
545 | ||
546 | atomTypeString = atoms[local_index]->getType(); | |
547 | < | |
547 | > | |
548 | atoms[local_index]->getPos(pos); | |
549 | atoms[local_index]->getVel(vel); | |
550 | + | |
551 | + | atomData6[0] = pos[0]; |
552 | + | atomData6[1] = pos[1]; |
553 | + | atomData6[2] = pos[2]; |
554 | ||
555 | < | atomTransData[0] = pos[0]; |
556 | < | atomTransData[1] = pos[1]; |
557 | < | atomTransData[2] = pos[2]; |
718 | < | |
719 | < | atomTransData[3] = vel[0]; |
720 | < | atomTransData[4] = vel[1]; |
721 | < | atomTransData[5] = vel[2]; |
555 | > | atomData6[3] = vel[0]; |
556 | > | atomData6[4] = vel[1]; |
557 | > | atomData6[5] = vel[2]; |
558 | ||
559 | isDirectional = 0; | |
560 | ||
# | Line 729 | Line 565 | void DumpWriter::writeFinal(double finalTime){ | |
565 | dAtom = (DirectionalAtom *)atoms[local_index]; | |
566 | dAtom->getQ( q ); | |
567 | ||
568 | < | atomOrientData[0] = q[0]; |
569 | < | atomOrientData[1] = q[1]; |
570 | < | atomOrientData[2] = q[2]; |
571 | < | atomOrientData[3] = q[3]; |
572 | < | |
573 | < | atomOrientData[4] = dAtom->getJx(); |
574 | < | atomOrientData[5] = dAtom->getJy(); |
575 | < | atomOrientData[6] = dAtom->getJz(); |
568 | > | for (int j = 0; j < 6 ; j++) |
569 | > | atomData13[j] = atomData6[j]; |
570 | > | |
571 | > | atomData13[6] = q[0]; |
572 | > | atomData13[7] = q[1]; |
573 | > | atomData13[8] = q[2]; |
574 | > | atomData13[9] = q[3]; |
575 | > | |
576 | > | atomData13[10] = dAtom->getJx(); |
577 | > | atomData13[11] = dAtom->getJy(); |
578 | > | atomData13[12] = dAtom->getJz(); |
579 | } | |
580 | ||
581 | } else { | |
582 | sprintf(painCave.errMsg, | |
583 | < | "Atom %d not found on processor %d\n", |
584 | < | i, worldRank ); |
583 | > | "Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n", |
584 | > | which_atom, worldRank, currentIndex, local_index ); |
585 | haveError= 1; | |
586 | simError(); | |
587 | } | |
588 | < | |
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 | < | |
588 | > | |
589 | strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE); | |
590 | ||
591 | + | // null terminate the string before sending (just in case): |
592 | + | MPIatomTypeString[MINIBUFFERSIZE-1] = '\0'; |
593 | + | |
594 | MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0, | |
595 | < | atomTypeTag, MPI_COMM_WORLD); |
595 | > | myPotato, MPI_COMM_WORLD); |
596 | ||
597 | + | myPotato++; |
598 | + | |
599 | MPI_Send(&isDirectional, 1, MPI_INT, 0, | |
600 | < | atomIsDirectionalTag, MPI_COMM_WORLD); |
600 | > | myPotato, MPI_COMM_WORLD); |
601 | ||
602 | < | MPI_Send(atomTransData, 6, MPI_DOUBLE, 0, |
603 | < | atomTransDataTag, MPI_COMM_WORLD); |
767 | < | |
602 | > | myPotato++; |
603 | > | |
604 | if (isDirectional) { | |
605 | ||
606 | < | MPI_Send(atomOrientData, 7, MPI_DOUBLE, 0, |
607 | < | atomOrientDataTag, MPI_COMM_WORLD); |
606 | > | MPI_Send(atomData13, 13, MPI_DOUBLE, 0, |
607 | > | myPotato, MPI_COMM_WORLD); |
608 | ||
609 | + | } else { |
610 | + | |
611 | + | MPI_Send(atomData6, 6, MPI_DOUBLE, 0, |
612 | + | myPotato, MPI_COMM_WORLD); |
613 | } | |
614 | < | |
614 | > | |
615 | > | myPotato++; |
616 | > | currentIndex++; |
617 | } | |
618 | } | |
619 | ||
620 | sprintf( checkPointMsg, | |
621 | < | "Sucessfully wrote final file.\n"); |
621 | > | "Sucessfully took a dump.\n"); |
622 | MPIcheckPoint(); | |
623 | ||
624 | < | } |
624 | > | } |
625 | ||
784 | – | painCave.isEventLoop = 0; |
785 | – | |
786 | – | if( worldRank == 0 ) finalOut.close(); |
626 | #endif // is_mpi | |
627 | } | |
628 | ||
790 | – | |
791 | – | |
629 | #ifdef IS_MPI | |
630 | ||
631 | // a couple of functions to let us escape the write loop |
– | Removed lines |
+ | Added lines |
< | Changed lines |
> | Changed lines |