# | Line 1 | Line 1 | |
---|---|---|
1 | < | #include <cstring> |
1 | > | #define _FILE_OFFSET_BITS 64 |
2 | > | |
3 | > | #include <string.h> |
4 | #include <iostream> | |
5 | #include <fstream> | |
6 | ||
7 | #ifdef IS_MPI | |
8 | #include <mpi.h> | |
7 | – | #include <mpi++.h> |
9 | #include "mpiSimulation.hpp" | |
10 | < | #define TAKE_THIS_TAG 0 |
10 | > | |
11 | > | namespace dWrite{ |
12 | > | void DieDieDie( void ); |
13 | > | } |
14 | > | |
15 | > | using namespace dWrite; |
16 | #endif //is_mpi | |
17 | ||
18 | #include "ReadWrite.hpp" | |
# | Line 19 | Line 25 | DumpWriter::DumpWriter( SimInfo* the_entry_plug ){ | |
25 | #ifdef IS_MPI | |
26 | if(worldRank == 0 ){ | |
27 | #endif // is_mpi | |
28 | < | |
23 | < | |
24 | < | |
28 | > | |
29 | strcpy( outName, entry_plug->sampleName ); | |
30 | < | |
30 | > | |
31 | outFile.open(outName, ios::out | ios::trunc ); | |
32 | < | |
32 | > | |
33 | if( !outFile ){ | |
34 | < | |
34 | > | |
35 | sprintf( painCave.errMsg, | |
36 | "Could not open \"%s\" for dump output.\n", | |
37 | outName); | |
38 | painCave.isFatal = 1; | |
39 | simError(); | |
40 | } | |
41 | < | |
41 | > | |
42 | //outFile.setf( ios::scientific ); | |
43 | ||
44 | #ifdef IS_MPI | |
# | Line 60 | Line 64 | void DumpWriter::writeDump( double currentTime ){ | |
64 | } | |
65 | ||
66 | void DumpWriter::writeDump( double currentTime ){ | |
67 | < | |
67 | > | |
68 | const int BUFFERSIZE = 2000; | |
69 | + | const int MINIBUFFERSIZE = 100; |
70 | + | |
71 | char tempBuffer[BUFFERSIZE]; | |
72 | char writeLine[BUFFERSIZE]; | |
73 | ||
74 | < | int i, j, which_node, done, game_over, which_atom, local_index; |
74 | > | int i; |
75 | > | |
76 | > | #ifdef IS_MPI |
77 | > | |
78 | > | int *potatoes; |
79 | > | int myPotato; |
80 | > | |
81 | > | int nProc; |
82 | > | int j, which_node, done, which_atom, local_index; |
83 | > | double atomData6[6]; |
84 | > | double atomData13[13]; |
85 | > | 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; | |
71 | – | int nAtoms = entry_plug->n_atoms; |
95 | Atom** atoms = entry_plug->atoms; | |
96 | < | |
96 | > | double pos[3], vel[3]; |
97 | ||
98 | + | // write current frame to the eor file |
99 | + | |
100 | + | this->writeFinal( currentTime ); |
101 | + | |
102 | #ifndef IS_MPI | |
103 | < | |
103 | > | |
104 | outFile << nAtoms << "\n"; | |
105 | < | |
106 | < | outFile << currentTime << "\t" |
107 | < | << entry_plug->box_x << "\t" |
108 | < | << entry_plug->box_y << "\t" |
109 | < | << entry_plug->box_z << "\n"; |
110 | < | |
105 | > | |
106 | > | outFile << currentTime << ";\t" |
107 | > | << entry_plug->Hmat[0][0] << "\t" |
108 | > | << entry_plug->Hmat[1][0] << "\t" |
109 | > | << entry_plug->Hmat[2][0] << ";\t" |
110 | > | |
111 | > | << 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++ ){ | |
85 | – | |
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 | < | atoms[i]->getX(), |
131 | < | atoms[i]->getY(), |
132 | < | atoms[i]->getZ(), |
133 | < | atoms[i]->get_vx(), |
134 | < | atoms[i]->get_vy(), |
135 | < | atoms[i]->get_vz()); |
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 | < | |
139 | > | |
140 | dAtom = (DirectionalAtom *)atoms[i]; | |
141 | dAtom->getQ( q ); | |
142 | < | |
142 | > | |
143 | sprintf( tempBuffer, | |
144 | "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", | |
145 | q[0], | |
# | Line 113 | Line 153 | void DumpWriter::writeDump( double currentTime ){ | |
153 | } | |
154 | else | |
155 | strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); | |
156 | < | |
156 | > | |
157 | outFile << writeLine; | |
158 | } | |
159 | outFile.flush(); | |
160 | ||
161 | #else // is_mpi | |
162 | ||
163 | < | MPI::Status istatus; |
164 | < | int *AtomToProcMap = mpiSim->getAtomToProcMap(); |
163 | > | cout << "master" <<endl; |
164 | > | /* code to find maximum tag value */ |
165 | ||
166 | + | int tagub, flag, MAXTAG; |
167 | + | MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag); |
168 | + | if (flag) { |
169 | + | MAXTAG = tagub; |
170 | + | } else { |
171 | + | MAXTAG = 32767; |
172 | + | } |
173 | + | |
174 | + | int haveError; |
175 | + | |
176 | + | MPI_Status istatus; |
177 | + | int *AtomToProcMap = mpiSim->getAtomToProcMap(); |
178 | + | |
179 | // write out header and node 0's coordinates | |
180 | < | |
180 | > | |
181 | if( worldRank == 0 ){ | |
182 | < | outFile << mpiSim->getTotAtoms() << "\n"; |
182 | > | |
183 | > | // Node 0 needs a list of the magic potatoes for each processor; |
184 | > | |
185 | > | nProc = mpiSim->getNumberProcessors(); |
186 | > | potatoes = new int[nProc]; |
187 | > | |
188 | > | for (i = 0; i < nProc; i++) |
189 | > | potatoes[i] = 0; |
190 | ||
191 | < | outFile << currentTime << "\t" |
192 | < | << entry_plug->box_x << "\t" |
193 | < | << entry_plug->box_y << "\t" |
194 | < | << entry_plug->box_z << "\n"; |
195 | < | |
191 | > | outFile << mpiSim->getTotAtoms() << "\n"; |
192 | > | |
193 | > | outFile << currentTime << ";\t" |
194 | > | << entry_plug->Hmat[0][0] << "\t" |
195 | > | << entry_plug->Hmat[1][0] << "\t" |
196 | > | << entry_plug->Hmat[2][0] << ";\t" |
197 | > | |
198 | > | << entry_plug->Hmat[0][1] << "\t" |
199 | > | << entry_plug->Hmat[1][1] << "\t" |
200 | > | << entry_plug->Hmat[2][1] << ";\t" |
201 | > | |
202 | > | << entry_plug->Hmat[0][2] << "\t" |
203 | > | << entry_plug->Hmat[1][2] << "\t" |
204 | > | << entry_plug->Hmat[2][2] << ";"; |
205 | > | |
206 | > | outFile << entry_plug->the_integrator->getAdditionalParameters(); |
207 | > | outFile << endl; |
208 | > | outFile.flush(); |
209 | > | |
210 | for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { | |
211 | + | |
212 | // Get the Node number which has this atom; | |
213 | ||
214 | < | which_node = AtomToProcMap[i]; |
214 | > | which_node = AtomToProcMap[i]; |
215 | ||
216 | < | if (which_node == mpiSim->getMyNode()) { |
216 | > | if (which_node != 0) { |
217 | > | |
218 | > | if (potatoes[which_node] + 3 >= MAXTAG) { |
219 | > | // The potato was going to exceed the maximum value, |
220 | > | // so wrap this processor potato back to 0: |
221 | > | |
222 | > | potatoes[which_node] = 0; |
223 | > | MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD); |
224 | > | |
225 | > | } |
226 | > | |
227 | > | myPotato = potatoes[which_node]; |
228 | ||
229 | < | sprintf( tempBuffer, |
230 | < | "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
231 | < | atoms[i]->getType(), |
232 | < | atoms[i]->getX(), |
233 | < | atoms[i]->getY(), |
234 | < | atoms[i]->getZ(), |
235 | < | atoms[i]->get_vx(), |
236 | < | atoms[i]->get_vy(), |
237 | < | atoms[i]->get_vz()); |
238 | < | strcpy( writeLine, tempBuffer ); |
239 | < | |
240 | < | if( atoms[i]->isDirectional() ){ |
241 | < | |
242 | < | dAtom = (DirectionalAtom *)atoms[i]; |
243 | < | dAtom->getQ( q ); |
244 | < | |
245 | < | sprintf( tempBuffer, |
246 | < | "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
247 | < | q[0], |
248 | < | q[1], |
249 | < | q[2], |
250 | < | q[3], |
165 | < | dAtom->getJx(), |
166 | < | dAtom->getJy(), |
167 | < | dAtom->getJz()); |
168 | < | strcat( writeLine, tempBuffer ); |
229 | > | MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node, |
230 | > | myPotato, MPI_COMM_WORLD, &istatus); |
231 | > | |
232 | > | strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE); |
233 | > | |
234 | > | // Null terminate the atomTypeString just in case: |
235 | > | |
236 | > | atomTypeString[strlen(atomTypeString) - 1] = '\0'; |
237 | > | |
238 | > | myPotato++; |
239 | > | |
240 | > | MPI_Recv(&isDirectional, 1, MPI_INT, which_node, |
241 | > | myPotato, MPI_COMM_WORLD, &istatus); |
242 | > | |
243 | > | myPotato++; |
244 | > | |
245 | > | if (isDirectional) { |
246 | > | MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node, |
247 | > | myPotato, MPI_COMM_WORLD, &istatus); |
248 | > | } else { |
249 | > | MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node, |
250 | > | myPotato, MPI_COMM_WORLD, &istatus); |
251 | } | |
170 | – | else |
171 | – | strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
252 | ||
253 | + | myPotato++; |
254 | + | potatoes[which_node] = myPotato; |
255 | + | |
256 | } else { | |
257 | ||
258 | < | MPI::COMM_WORLD.Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG); |
259 | < | MPI::COMM_WORLD.Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node, |
260 | < | TAKE_THIS_TAG, istatus); |
258 | > | haveError = 0; |
259 | > | which_atom = i; |
260 | > | local_index=-1; |
261 | > | |
262 | > | for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
263 | > | if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
264 | > | } |
265 | > | |
266 | > | if (local_index != -1) { |
267 | > | |
268 | > | atomTypeString = atoms[local_index]->getType(); |
269 | > | |
270 | > | atoms[local_index]->getPos(pos); |
271 | > | atoms[local_index]->getVel(vel); |
272 | > | |
273 | > | atomData6[0] = pos[0]; |
274 | > | atomData6[1] = pos[1]; |
275 | > | atomData6[2] = pos[2]; |
276 | > | |
277 | > | atomData6[3] = vel[0]; |
278 | > | atomData6[4] = vel[1]; |
279 | > | atomData6[5] = vel[2]; |
280 | > | |
281 | > | isDirectional = 0; |
282 | > | |
283 | > | if( atoms[local_index]->isDirectional() ){ |
284 | > | |
285 | > | isDirectional = 1; |
286 | > | |
287 | > | dAtom = (DirectionalAtom *)atoms[local_index]; |
288 | > | dAtom->getQ( q ); |
289 | > | |
290 | > | for (int j = 0; j < 6 ; j++) |
291 | > | atomData13[j] = atomData6[j]; |
292 | > | |
293 | > | atomData13[6] = q[0]; |
294 | > | atomData13[7] = q[1]; |
295 | > | atomData13[8] = q[2]; |
296 | > | atomData13[9] = q[3]; |
297 | > | |
298 | > | atomData13[10] = dAtom->getJx(); |
299 | > | atomData13[11] = dAtom->getJy(); |
300 | > | atomData13[12] = dAtom->getJz(); |
301 | > | } |
302 | > | |
303 | > | } else { |
304 | > | sprintf(painCave.errMsg, |
305 | > | "Atom %d not found on processor %d\n", |
306 | > | i, worldRank ); |
307 | > | haveError= 1; |
308 | > | simError(); |
309 | > | } |
310 | > | |
311 | > | if(haveError) DieDieDie(); |
312 | > | |
313 | > | // If we've survived to here, format the line: |
314 | > | |
315 | > | if (!isDirectional) { |
316 | > | |
317 | > | sprintf( tempBuffer, |
318 | > | "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
319 | > | atomTypeString, |
320 | > | atomData6[0], |
321 | > | atomData6[1], |
322 | > | atomData6[2], |
323 | > | atomData6[3], |
324 | > | atomData6[4], |
325 | > | atomData6[5]); |
326 | > | |
327 | > | strcpy( writeLine, tempBuffer ); |
328 | > | strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
329 | > | |
330 | > | } else { |
331 | > | |
332 | > | sprintf( tempBuffer, |
333 | > | "%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", |
334 | > | atomTypeString, |
335 | > | atomData13[0], |
336 | > | atomData13[1], |
337 | > | atomData13[2], |
338 | > | atomData13[3], |
339 | > | atomData13[4], |
340 | > | atomData13[5], |
341 | > | atomData13[6], |
342 | > | atomData13[7], |
343 | > | atomData13[8], |
344 | > | atomData13[9], |
345 | > | atomData13[10], |
346 | > | atomData13[11], |
347 | > | atomData13[12]); |
348 | > | |
349 | > | strcat( writeLine, tempBuffer ); |
350 | > | |
351 | > | } |
352 | > | |
353 | > | outFile << writeLine; |
354 | > | outFile.flush(); |
355 | } | |
179 | – | |
180 | – | outFile << writeLine; |
356 | } | |
182 | – | |
183 | – | // kill everyone off: |
184 | – | game_over = -1; |
185 | – | for (j = 0; j < mpiSim->getNumberProcessors(); j++) { |
186 | – | MPI::COMM_WORLD.Send(&game_over, 1, MPI_INT, j, TAKE_THIS_TAG); |
187 | – | } |
357 | ||
358 | + | outFile.flush(); |
359 | + | sprintf( checkPointMsg, |
360 | + | "Sucessfully took a dump.\n"); |
361 | + | MPIcheckPoint(); |
362 | + | delete[] potatoes; |
363 | } else { | |
364 | + | |
365 | + | // worldRank != 0, so I'm a remote node. |
366 | + | |
367 | + | // Set my magic potato to 0: |
368 | + | |
369 | + | myPotato = 0; |
370 | ||
371 | < | done = 0; |
192 | < | while (!done) { |
193 | < | MPI::COMM_WORLD.Recv(&which_atom, 1, MPI_INT, 0, |
194 | < | TAKE_THIS_TAG, istatus); |
371 | > | for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
372 | ||
373 | < | if (which_atom == -1) { |
374 | < | done=1; |
375 | < | continue; |
376 | < | } else { |
377 | < | local_index=-1; |
378 | < | for (j=0; j < mpiSim->getMyNlocal(); j++) { |
373 | > | // Am I the node which has this atom? |
374 | > | |
375 | > | if (AtomToProcMap[i] == worldRank) { |
376 | > | |
377 | > | if (myPotato + 3 >= MAXTAG) { |
378 | > | |
379 | > | // The potato was going to exceed the maximum value, |
380 | > | // so wrap this processor potato back to 0 (and block until |
381 | > | // node 0 says we can go: |
382 | > | |
383 | > | MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus); |
384 | > | |
385 | > | } |
386 | > | which_atom = i; |
387 | > | local_index=-1; |
388 | > | for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
389 | if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; | |
390 | } | |
391 | if (local_index != -1) { | |
392 | < | //format the line |
393 | < | sprintf( tempBuffer, |
394 | < | "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
395 | < | atoms[local_index]->getType(), |
396 | < | atoms[local_index]->getX(), |
397 | < | atoms[local_index]->getY(), |
398 | < | atoms[local_index]->getZ(), |
399 | < | atoms[local_index]->get_vx(), |
400 | < | atoms[local_index]->get_vy(), |
401 | < | atoms[local_index]->get_vz()); // check here. |
402 | < | strcpy( writeLine, tempBuffer ); |
403 | < | |
392 | > | |
393 | > | atomTypeString = atoms[local_index]->getType(); |
394 | > | |
395 | > | atoms[local_index]->getPos(pos); |
396 | > | atoms[local_index]->getVel(vel); |
397 | > | |
398 | > | atomData6[0] = pos[0]; |
399 | > | atomData6[1] = pos[1]; |
400 | > | atomData6[2] = pos[2]; |
401 | > | |
402 | > | atomData6[3] = vel[0]; |
403 | > | atomData6[4] = vel[1]; |
404 | > | atomData6[5] = vel[2]; |
405 | > | |
406 | > | isDirectional = 0; |
407 | > | |
408 | if( atoms[local_index]->isDirectional() ){ | |
409 | + | |
410 | + | isDirectional = 1; |
411 | ||
412 | dAtom = (DirectionalAtom *)atoms[local_index]; | |
413 | dAtom->getQ( q ); | |
414 | ||
415 | < | sprintf( tempBuffer, |
416 | < | "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
417 | < | q[0], |
418 | < | q[1], |
419 | < | q[2], |
420 | < | q[3], |
421 | < | dAtom->getJx(), |
422 | < | dAtom->getJy(), |
423 | < | dAtom->getJz()); |
424 | < | strcat( writeLine, tempBuffer ); |
415 | > | for (int j = 0; j < 6 ; j++) |
416 | > | atomData13[j] = atomData6[j]; |
417 | > | |
418 | > | atomData13[6] = q[0]; |
419 | > | atomData13[7] = q[1]; |
420 | > | atomData13[8] = q[2]; |
421 | > | atomData13[9] = q[3]; |
422 | > | |
423 | > | atomData13[10] = dAtom->getJx(); |
424 | > | atomData13[11] = dAtom->getJy(); |
425 | > | atomData13[12] = dAtom->getJz(); |
426 | } | |
427 | < | else |
428 | < | strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
427 | > | |
428 | > | } else { |
429 | > | sprintf(painCave.errMsg, |
430 | > | "Atom %d not found on processor %d\n", |
431 | > | i, worldRank ); |
432 | > | haveError= 1; |
433 | > | simError(); |
434 | > | } |
435 | > | |
436 | > | strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE); |
437 | > | |
438 | > | // null terminate the string before sending (just in case): |
439 | > | MPIatomTypeString[MINIBUFFERSIZE-1] = '\0'; |
440 | > | |
441 | > | MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0, |
442 | > | myPotato, MPI_COMM_WORLD); |
443 | > | |
444 | > | myPotato++; |
445 | > | |
446 | > | MPI_Send(&isDirectional, 1, MPI_INT, 0, |
447 | > | myPotato, MPI_COMM_WORLD); |
448 | > | |
449 | > | myPotato++; |
450 | > | |
451 | > | if (isDirectional) { |
452 | > | |
453 | > | MPI_Send(atomData13, 13, MPI_DOUBLE, 0, |
454 | > | myPotato, MPI_COMM_WORLD); |
455 | ||
236 | – | MPI::COMM_WORLD.Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, |
237 | – | TAKE_THIS_TAG); |
456 | } else { | |
457 | < | strcpy( writeLine, "ATOM NOT FOUND ON THIS PROCESSOR"); |
458 | < | MPI::COMM_WORLD.Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, |
459 | < | TAKE_THIS_TAG); |
457 | > | |
458 | > | MPI_Send(atomData6, 6, MPI_DOUBLE, 0, |
459 | > | myPotato, MPI_COMM_WORLD); |
460 | } | |
461 | + | |
462 | + | myPotato++; |
463 | } | |
464 | } | |
465 | < | } |
466 | < | outFile.flush(); |
467 | < | sprintf( checkPointMsg, |
468 | < | "Sucessfully took a dump.\n"); |
469 | < | MPIcheckPoint(); |
465 | > | |
466 | > | sprintf( checkPointMsg, |
467 | > | "Sucessfully took a dump.\n"); |
468 | > | MPIcheckPoint(); |
469 | > | |
470 | > | } |
471 | > | |
472 | #endif // is_mpi | |
473 | } | |
474 | ||
475 | < | void DumpWriter::writeFinal(){ |
475 | > | void DumpWriter::writeFinal(double finalTime){ |
476 | ||
477 | char finalName[500]; | |
478 | ofstream finalOut; | |
479 | ||
480 | const int BUFFERSIZE = 2000; | |
481 | + | const int MINIBUFFERSIZE = 100; |
482 | char tempBuffer[BUFFERSIZE]; | |
483 | < | char writeLine[BUFFERSIZE]; |
483 | > | char writeLine[BUFFERSIZE]; |
484 | ||
485 | double q[4]; | |
486 | DirectionalAtom* dAtom; | |
264 | – | int nAtoms = entry_plug->n_atoms; |
487 | Atom** atoms = entry_plug->atoms; | |
488 | < | int i, j, which_node, done, game_over, which_atom, local_index; |
488 | > | int i; |
489 | > | #ifdef IS_MPI |
490 | ||
491 | < | |
491 | > | int *potatoes; |
492 | > | int myPotato; |
493 | > | |
494 | > | int nProc; |
495 | > | int j, which_node, done, which_atom, local_index; |
496 | > | double atomData6[6]; |
497 | > | double atomData13[13]; |
498 | > | int isDirectional; |
499 | > | char* atomTypeString; |
500 | > | char MPIatomTypeString[MINIBUFFERSIZE]; |
501 | > | |
502 | > | #else //is_mpi |
503 | > | int nAtoms = entry_plug->n_atoms; |
504 | > | #endif //is_mpi |
505 | > | |
506 | > | double pos[3], vel[3]; |
507 | > | |
508 | #ifdef IS_MPI | |
509 | if(worldRank == 0 ){ | |
510 | #endif // is_mpi | |
511 | < | |
511 | > | |
512 | strcpy( finalName, entry_plug->finalName ); | |
513 | < | |
513 | > | |
514 | finalOut.open( finalName, ios::out | ios::trunc ); | |
515 | if( !finalOut ){ | |
516 | sprintf( painCave.errMsg, | |
# | Line 280 | Line 519 | void DumpWriter::writeFinal(){ | |
519 | painCave.isFatal = 1; | |
520 | simError(); | |
521 | } | |
522 | < | |
522 | > | |
523 | // finalOut.setf( ios::scientific ); | |
524 | < | |
524 | > | |
525 | #ifdef IS_MPI | |
526 | } | |
527 | < | |
527 | > | |
528 | sprintf(checkPointMsg,"Opened file for final configuration\n"); | |
529 | < | MPIcheckPoint(); |
530 | < | |
529 | > | MPIcheckPoint(); |
530 | > | |
531 | #endif //is_mpi | |
532 | ||
533 | < | |
533 | > | |
534 | #ifndef IS_MPI | |
535 | < | |
535 | > | |
536 | finalOut << nAtoms << "\n"; | |
537 | < | |
538 | < | finalOut << entry_plug->box_x << "\t" |
539 | < | << entry_plug->box_y << "\t" |
540 | < | << entry_plug->box_z << "\n"; |
541 | < | |
537 | > | |
538 | > | finalOut << finalTime << ";\t" |
539 | > | << entry_plug->Hmat[0][0] << "\t" |
540 | > | << entry_plug->Hmat[1][0] << "\t" |
541 | > | << entry_plug->Hmat[2][0] << ";\t" |
542 | > | |
543 | > | << entry_plug->Hmat[0][1] << "\t" |
544 | > | << entry_plug->Hmat[1][1] << "\t" |
545 | > | << entry_plug->Hmat[2][1] << ";\t" |
546 | > | |
547 | > | << entry_plug->Hmat[0][2] << "\t" |
548 | > | << entry_plug->Hmat[1][2] << "\t" |
549 | > | << entry_plug->Hmat[2][2] << ";"; |
550 | > | |
551 | > | //write out additional parameters, such as chi and eta |
552 | > | finalOut << entry_plug->the_integrator->getAdditionalParameters(); |
553 | > | finalOut << endl; |
554 | > | |
555 | for( i=0; i<nAtoms; i++ ){ | |
556 | < | |
556 | > | |
557 | > | atoms[i]->getPos(pos); |
558 | > | atoms[i]->getVel(vel); |
559 | > | |
560 | sprintf( tempBuffer, | |
561 | "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", | |
562 | atoms[i]->getType(), | |
563 | < | atoms[i]->getX(), |
564 | < | atoms[i]->getY(), |
565 | < | atoms[i]->getZ(), |
566 | < | atoms[i]->get_vx(), |
567 | < | atoms[i]->get_vy(), |
568 | < | atoms[i]->get_vz()); |
563 | > | pos[0], |
564 | > | pos[1], |
565 | > | pos[2], |
566 | > | vel[0], |
567 | > | vel[1], |
568 | > | vel[2]); |
569 | strcpy( writeLine, tempBuffer ); | |
570 | ||
571 | if( atoms[i]->isDirectional() ){ | |
572 | < | |
572 | > | |
573 | dAtom = (DirectionalAtom *)atoms[i]; | |
574 | dAtom->getQ( q ); | |
575 | < | |
575 | > | |
576 | sprintf( tempBuffer, | |
577 | "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", | |
578 | q[0], | |
# | Line 331 | Line 586 | void DumpWriter::writeFinal(){ | |
586 | } | |
587 | else | |
588 | strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); | |
589 | < | |
589 | > | |
590 | finalOut << writeLine; | |
591 | } | |
592 | finalOut.flush(); | |
593 | finalOut.close(); | |
594 | ||
595 | #else // is_mpi | |
596 | < | |
597 | < | MPI::Status istatus; |
596 | > | |
597 | > | /* code to find maximum tag value */ |
598 | > | int *tagub, flag, MAXTAG; |
599 | > | MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag); |
600 | > | if (flag) { |
601 | > | MAXTAG = *tagub; |
602 | > | } else { |
603 | > | MAXTAG = 32767; |
604 | > | } |
605 | > | |
606 | > | int haveError; |
607 | > | |
608 | > | MPI_Status istatus; |
609 | int *AtomToProcMap = mpiSim->getAtomToProcMap(); | |
610 | ||
611 | // write out header and node 0's coordinates | |
612 | < | |
612 | > | |
613 | if( worldRank == 0 ){ | |
614 | < | finalOut << mpiSim->getTotAtoms() << "\n"; |
614 | > | |
615 | > | // Node 0 needs a list of the magic potatoes for each processor; |
616 | > | |
617 | > | nProc = mpiSim->getNumberProcessors(); |
618 | > | potatoes = new int[nProc]; |
619 | > | |
620 | > | for (i = 0; i < nProc; i++) |
621 | > | potatoes[i] = 0; |
622 | ||
623 | < | finalOut << entry_plug->box_x << "\t" |
624 | < | << entry_plug->box_y << "\t" |
625 | < | << entry_plug->box_z << "\n"; |
626 | < | |
623 | > | finalOut << mpiSim->getTotAtoms() << "\n"; |
624 | > | |
625 | > | finalOut << finalTime << ";\t" |
626 | > | << entry_plug->Hmat[0][0] << "\t" |
627 | > | << entry_plug->Hmat[1][0] << "\t" |
628 | > | << entry_plug->Hmat[2][0] << ";\t" |
629 | > | |
630 | > | << entry_plug->Hmat[0][1] << "\t" |
631 | > | << entry_plug->Hmat[1][1] << "\t" |
632 | > | << entry_plug->Hmat[2][1] << ";\t" |
633 | > | |
634 | > | << entry_plug->Hmat[0][2] << "\t" |
635 | > | << entry_plug->Hmat[1][2] << "\t" |
636 | > | << entry_plug->Hmat[2][2] << ";"; |
637 | > | |
638 | > | finalOut << entry_plug->the_integrator->getAdditionalParameters(); |
639 | > | finalOut << endl; |
640 | > | finalOut.flush(); |
641 | > | |
642 | for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { | |
355 | – | // Get the Node number which has this molecule: |
643 | ||
644 | < | which_node = AtomToProcMap[i]; |
644 | > | // Get the Node number which has this atom; |
645 | ||
646 | < | if (which_node == mpiSim->getMyNode()) { |
646 | > | which_node = AtomToProcMap[i]; |
647 | > | |
648 | > | if (which_node != 0) { |
649 | > | |
650 | > | if (potatoes[which_node] + 3 >= MAXTAG) { |
651 | > | // The potato was going to exceed the maximum value, |
652 | > | // so wrap this processor potato back to 0: |
653 | > | |
654 | > | potatoes[which_node] = 0; |
655 | > | MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD); |
656 | > | |
657 | > | } |
658 | > | |
659 | > | myPotato = potatoes[which_node]; |
660 | ||
661 | < | sprintf( tempBuffer, |
662 | < | "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
663 | < | atoms[i]->getType(), |
664 | < | atoms[i]->getX(), |
665 | < | atoms[i]->getY(), |
666 | < | atoms[i]->getZ(), |
667 | < | atoms[i]->get_vx(), |
668 | < | atoms[i]->get_vy(), |
669 | < | atoms[i]->get_vz()); |
670 | < | strcpy( writeLine, tempBuffer ); |
671 | < | |
672 | < | if( atoms[i]->isDirectional() ){ |
673 | < | |
674 | < | dAtom = (DirectionalAtom *)atoms[i]; |
675 | < | dAtom->getQ( q ); |
676 | < | |
677 | < | sprintf( tempBuffer, |
678 | < | "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
679 | < | q[0], |
680 | < | q[1], |
681 | < | q[2], |
682 | < | q[3], |
383 | < | dAtom->getJx(), |
384 | < | dAtom->getJy(), |
385 | < | dAtom->getJz()); |
386 | < | strcat( writeLine, tempBuffer ); |
661 | > | MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node, |
662 | > | myPotato, MPI_COMM_WORLD, &istatus); |
663 | > | |
664 | > | strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE); |
665 | > | |
666 | > | // Null terminate the atomTypeString just in case: |
667 | > | |
668 | > | atomTypeString[strlen(atomTypeString) - 1] = '\0'; |
669 | > | |
670 | > | myPotato++; |
671 | > | |
672 | > | MPI_Recv(&isDirectional, 1, MPI_INT, which_node, |
673 | > | myPotato, MPI_COMM_WORLD, &istatus); |
674 | > | |
675 | > | myPotato++; |
676 | > | |
677 | > | if (isDirectional) { |
678 | > | MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node, |
679 | > | myPotato, MPI_COMM_WORLD, &istatus); |
680 | > | } else { |
681 | > | MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node, |
682 | > | myPotato, MPI_COMM_WORLD, &istatus); |
683 | } | |
388 | – | else |
389 | – | strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
684 | ||
685 | + | myPotato++; |
686 | + | potatoes[which_node] = myPotato; |
687 | + | |
688 | } else { | |
689 | ||
690 | < | MPI::COMM_WORLD.Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG); |
691 | < | MPI::COMM_WORLD.Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node, |
692 | < | TAKE_THIS_TAG, istatus); |
690 | > | haveError = 0; |
691 | > | which_atom = i; |
692 | > | local_index=-1; |
693 | > | |
694 | > | for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
695 | > | if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
696 | > | } |
697 | > | |
698 | > | if (local_index != -1) { |
699 | > | |
700 | > | atomTypeString = atoms[local_index]->getType(); |
701 | > | |
702 | > | atoms[local_index]->getPos(pos); |
703 | > | atoms[local_index]->getVel(vel); |
704 | > | |
705 | > | atomData6[0] = pos[0]; |
706 | > | atomData6[1] = pos[1]; |
707 | > | atomData6[2] = pos[2]; |
708 | > | |
709 | > | atomData6[3] = vel[0]; |
710 | > | atomData6[4] = vel[1]; |
711 | > | atomData6[5] = vel[2]; |
712 | > | |
713 | > | isDirectional = 0; |
714 | > | |
715 | > | if( atoms[local_index]->isDirectional() ){ |
716 | > | |
717 | > | isDirectional = 1; |
718 | > | |
719 | > | dAtom = (DirectionalAtom *)atoms[local_index]; |
720 | > | dAtom->getQ( q ); |
721 | > | |
722 | > | for (int j = 0; j < 6 ; j++) |
723 | > | atomData13[j] = atomData6[j]; |
724 | > | |
725 | > | atomData13[6] = q[0]; |
726 | > | atomData13[7] = q[1]; |
727 | > | atomData13[8] = q[2]; |
728 | > | atomData13[9] = q[3]; |
729 | > | |
730 | > | atomData13[10] = dAtom->getJx(); |
731 | > | atomData13[11] = dAtom->getJy(); |
732 | > | atomData13[12] = dAtom->getJz(); |
733 | > | } |
734 | > | |
735 | > | } else { |
736 | > | sprintf(painCave.errMsg, |
737 | > | "Atom %d not found on processor %d\n", |
738 | > | i, worldRank ); |
739 | > | haveError= 1; |
740 | > | simError(); |
741 | > | } |
742 | > | |
743 | > | if(haveError) DieDieDie(); |
744 | > | |
745 | > | // If we've survived to here, format the line: |
746 | > | |
747 | > | if (!isDirectional) { |
748 | > | |
749 | > | sprintf( tempBuffer, |
750 | > | "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
751 | > | atomTypeString, |
752 | > | atomData6[0], |
753 | > | atomData6[1], |
754 | > | atomData6[2], |
755 | > | atomData6[3], |
756 | > | atomData6[4], |
757 | > | atomData6[5]); |
758 | > | |
759 | > | strcpy( writeLine, tempBuffer ); |
760 | > | strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
761 | > | |
762 | > | } else { |
763 | > | |
764 | > | sprintf( tempBuffer, |
765 | > | "%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", |
766 | > | atomTypeString, |
767 | > | atomData13[0], |
768 | > | atomData13[1], |
769 | > | atomData13[2], |
770 | > | atomData13[3], |
771 | > | atomData13[4], |
772 | > | atomData13[5], |
773 | > | atomData13[6], |
774 | > | atomData13[7], |
775 | > | atomData13[8], |
776 | > | atomData13[9], |
777 | > | atomData13[10], |
778 | > | atomData13[11], |
779 | > | atomData13[12]); |
780 | > | |
781 | > | strcat( writeLine, tempBuffer ); |
782 | > | |
783 | > | } |
784 | > | |
785 | > | finalOut << writeLine; |
786 | > | finalOut.flush(); |
787 | } | |
397 | – | |
398 | – | finalOut << writeLine; |
788 | } | |
400 | – | |
401 | – | // kill everyone off: |
402 | – | game_over = -1; |
403 | – | for (j = 0; j < mpiSim->getNumberProcessors(); j++) { |
404 | – | MPI::COMM_WORLD.Send(&game_over, 1, MPI_INT, j, TAKE_THIS_TAG); |
405 | – | } |
789 | ||
790 | + | finalOut.flush(); |
791 | + | sprintf( checkPointMsg, |
792 | + | "Sucessfully took a dump.\n"); |
793 | + | delete[] potatoes; |
794 | + | |
795 | + | MPIcheckPoint(); |
796 | + | |
797 | } else { | |
798 | + | |
799 | + | // worldRank != 0, so I'm a remote node. |
800 | + | |
801 | + | // Set my magic potato to 0: |
802 | + | |
803 | + | myPotato = 0; |
804 | ||
805 | < | done = 0; |
806 | < | while (!done) { |
807 | < | MPI::COMM_WORLD.Recv(&which_atom, 1, MPI_INT, 0, |
808 | < | TAKE_THIS_TAG, istatus); |
805 | > | for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
806 | > | |
807 | > | // Am I the node which has this atom? |
808 | > | |
809 | > | if (AtomToProcMap[i] == worldRank) { |
810 | ||
811 | < | if (which_atom == -1) { |
415 | < | done=1; |
416 | < | continue; |
417 | < | } else { |
811 | > | if (myPotato + 3 >= MAXTAG) { |
812 | ||
813 | < | local_index=-1; |
814 | < | for (j=0; j < mpiSim->getMyNlocal(); j++) { |
813 | > | // The potato was going to exceed the maximum value, |
814 | > | // so wrap this processor potato back to 0 (and block until |
815 | > | // node 0 says we can go: |
816 | > | |
817 | > | MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus); |
818 | > | |
819 | > | } |
820 | > | which_atom = i; |
821 | > | local_index=-1; |
822 | > | for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
823 | if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; | |
824 | } | |
825 | if (local_index != -1) { | |
826 | + | |
827 | + | atomTypeString = atoms[local_index]->getType(); |
828 | ||
829 | < | //format the line |
830 | < | sprintf( tempBuffer, |
831 | < | "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
832 | < | atoms[local_index]->getType(), |
833 | < | atoms[local_index]->getX(), |
834 | < | atoms[local_index]->getY(), |
835 | < | atoms[local_index]->getZ(), |
836 | < | atoms[local_index]->get_vx(), |
837 | < | atoms[local_index]->get_vy(), |
838 | < | atoms[local_index]->get_vz()); // check here. |
839 | < | strcpy( writeLine, tempBuffer ); |
840 | < | |
829 | > | atoms[local_index]->getPos(pos); |
830 | > | atoms[local_index]->getVel(vel); |
831 | > | |
832 | > | atomData6[0] = pos[0]; |
833 | > | atomData6[1] = pos[1]; |
834 | > | atomData6[2] = pos[2]; |
835 | > | |
836 | > | atomData6[3] = vel[0]; |
837 | > | atomData6[4] = vel[1]; |
838 | > | atomData6[5] = vel[2]; |
839 | > | |
840 | > | isDirectional = 0; |
841 | > | |
842 | if( atoms[local_index]->isDirectional() ){ | |
843 | + | |
844 | + | isDirectional = 1; |
845 | ||
846 | dAtom = (DirectionalAtom *)atoms[local_index]; | |
847 | dAtom->getQ( q ); | |
848 | < | |
849 | < | sprintf( tempBuffer, |
850 | < | "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
851 | < | q[0], |
852 | < | q[1], |
853 | < | q[2], |
854 | < | q[3], |
855 | < | dAtom->getJx(), |
856 | < | dAtom->getJy(), |
857 | < | dAtom->getJz()); |
858 | < | strcat( writeLine, tempBuffer ); |
848 | > | |
849 | > | for (int j = 0; j < 6 ; j++) |
850 | > | atomData13[j] = atomData6[j]; |
851 | > | |
852 | > | atomData13[6] = q[0]; |
853 | > | atomData13[7] = q[1]; |
854 | > | atomData13[8] = q[2]; |
855 | > | atomData13[9] = q[3]; |
856 | > | |
857 | > | atomData13[10] = dAtom->getJx(); |
858 | > | atomData13[11] = dAtom->getJy(); |
859 | > | atomData13[12] = dAtom->getJz(); |
860 | } | |
861 | < | else |
862 | < | strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
861 | > | |
862 | > | } else { |
863 | > | sprintf(painCave.errMsg, |
864 | > | "Atom %d not found on processor %d\n", |
865 | > | i, worldRank ); |
866 | > | haveError= 1; |
867 | > | simError(); |
868 | > | } |
869 | > | |
870 | > | strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE); |
871 | > | |
872 | > | // null terminate the string before sending (just in case): |
873 | > | MPIatomTypeString[MINIBUFFERSIZE-1] = '\0'; |
874 | > | |
875 | > | MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0, |
876 | > | myPotato, MPI_COMM_WORLD); |
877 | > | |
878 | > | myPotato++; |
879 | > | |
880 | > | MPI_Send(&isDirectional, 1, MPI_INT, 0, |
881 | > | myPotato, MPI_COMM_WORLD); |
882 | > | |
883 | > | myPotato++; |
884 | > | |
885 | > | if (isDirectional) { |
886 | > | |
887 | > | MPI_Send(atomData13, 13, MPI_DOUBLE, 0, |
888 | > | myPotato, MPI_COMM_WORLD); |
889 | ||
456 | – | MPI::COMM_WORLD.Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, |
457 | – | TAKE_THIS_TAG); |
890 | } else { | |
891 | < | strcpy( writeLine, "ATOM NOT FOUND ON THIS PROCESSOR"); |
892 | < | MPI::COMM_WORLD.Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, |
893 | < | TAKE_THIS_TAG); |
891 | > | |
892 | > | MPI_Send(atomData6, 6, MPI_DOUBLE, 0, |
893 | > | myPotato, MPI_COMM_WORLD); |
894 | } | |
895 | + | |
896 | + | myPotato++; |
897 | } | |
898 | } | |
465 | – | } |
466 | – | finalOut.flush(); |
467 | – | sprintf( checkPointMsg, |
468 | – | "Sucessfully took a dump.\n"); |
469 | – | MPIcheckPoint(); |
899 | ||
900 | < | if( worldRank == 0 ) finalOut.close(); |
900 | > | sprintf( checkPointMsg, |
901 | > | "Sucessfully took a dump.\n"); |
902 | > | MPIcheckPoint(); |
903 | > | |
904 | > | } |
905 | > | |
906 | > | if( worldRank == 0 ) finalOut.close(); |
907 | #endif // is_mpi | |
908 | } | |
909 | + | |
910 | + | |
911 | + | |
912 | + | #ifdef IS_MPI |
913 | + | |
914 | + | // a couple of functions to let us escape the write loop |
915 | + | |
916 | + | void dWrite::DieDieDie( void ){ |
917 | + | |
918 | + | MPI_Finalize(); |
919 | + | exit (0); |
920 | + | } |
921 | + | |
922 | + | #endif //is_mpi |
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