# | 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" | |
9 | – | #define TAKE_THIS_TAG_CHAR 1 |
10 | – | #define TAKE_THIS_TAG_INT 2 |
10 | ||
11 | namespace dWrite{ | |
12 | < | void nodeZeroError( void ); |
14 | < | void anonymousNodeDie( void ); |
12 | > | void DieDieDie( void ); |
13 | } | |
14 | ||
15 | using namespace dWrite; | |
# | Line 27 | Line 25 | DumpWriter::DumpWriter( SimInfo* the_entry_plug ){ | |
25 | #ifdef IS_MPI | |
26 | if(worldRank == 0 ){ | |
27 | #endif // is_mpi | |
28 | < | |
31 | < | |
32 | < | |
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 68 | 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; | |
79 | – | 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++ ){ | |
93 | – | |
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 121 | 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 | < | // first thing first, suspend fatalities. |
164 | < | painCave.isEventLoop = 1; |
163 | > | /* code to find maximum tag value */ |
164 | > | |
165 | > | int *tagub, flag, MAXTAG; |
166 | > | MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag); |
167 | > | if (flag) { |
168 | > | MAXTAG = *tagub; |
169 | > | } else { |
170 | > | MAXTAG = 32767; |
171 | > | } |
172 | ||
134 | – | int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone |
173 | int haveError; | |
174 | ||
175 | < | MPI::Status istatus; |
175 | > | MPI_Status istatus; |
176 | int *AtomToProcMap = mpiSim->getAtomToProcMap(); | |
177 | < | |
177 | > | |
178 | // write out header and node 0's coordinates | |
179 | < | |
179 | > | |
180 | if( worldRank == 0 ){ | |
181 | < | outFile << mpiSim->getTotAtoms() << "\n"; |
181 | > | |
182 | > | // Node 0 needs a list of the magic potatoes for each processor; |
183 | > | |
184 | > | nProc = mpiSim->getNumberProcessors(); |
185 | > | potatoes = new int[nProc]; |
186 | > | |
187 | > | for (i = 0; i < nProc; i++) |
188 | > | potatoes[i] = 0; |
189 | ||
190 | < | outFile << currentTime << "\t" |
191 | < | << entry_plug->box_x << "\t" |
192 | < | << entry_plug->box_y << "\t" |
193 | < | << entry_plug->box_z << "\n"; |
190 | > | outFile << mpiSim->getTotAtoms() << "\n"; |
191 | > | |
192 | > | outFile << currentTime << ";\t" |
193 | > | << entry_plug->Hmat[0][0] << "\t" |
194 | > | << entry_plug->Hmat[1][0] << "\t" |
195 | > | << entry_plug->Hmat[2][0] << ";\t" |
196 | > | |
197 | > | << entry_plug->Hmat[0][1] << "\t" |
198 | > | << entry_plug->Hmat[1][1] << "\t" |
199 | > | << entry_plug->Hmat[2][1] << ";\t" |
200 | > | |
201 | > | << entry_plug->Hmat[0][2] << "\t" |
202 | > | << entry_plug->Hmat[1][2] << "\t" |
203 | > | << entry_plug->Hmat[2][2] << ";"; |
204 | > | |
205 | > | outFile << entry_plug->the_integrator->getAdditionalParameters(); |
206 | > | outFile << endl; |
207 | outFile.flush(); | |
208 | + | |
209 | for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { | |
210 | + | |
211 | // Get the Node number which has this atom; | |
212 | ||
213 | < | which_node = AtomToProcMap[i]; |
213 | > | which_node = AtomToProcMap[i]; |
214 | ||
215 | < | if (which_node == 0 ) { |
215 | > | if (which_node != 0) { |
216 | > | |
217 | > | if (potatoes[which_node] + 3 >= MAXTAG) { |
218 | > | // The potato was going to exceed the maximum value, |
219 | > | // so wrap this processor potato back to 0: |
220 | > | |
221 | > | potatoes[which_node] = 0; |
222 | > | MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD); |
223 | > | |
224 | > | } |
225 | > | |
226 | > | myPotato = potatoes[which_node]; |
227 | > | |
228 | > | MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node, |
229 | > | myPotato, MPI_COMM_WORLD, &istatus); |
230 | > | |
231 | > | //strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE); |
232 | > | |
233 | > | // Null terminate the atomTypeString just in case: |
234 | > | |
235 | > | //atomTypeString[strlen(atomTypeString) - 1] = '\0'; |
236 | > | atomTypeString = MPIatomTypeString; |
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 | + | } |
252 | + | |
253 | + | myPotato++; |
254 | + | potatoes[which_node] = myPotato; |
255 | + | |
256 | + | } else { |
257 | + | |
258 | haveError = 0; | |
259 | which_atom = i; | |
260 | < | local_index=-1; |
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 | < | //format the line |
268 | < | sprintf( tempBuffer, |
269 | < | "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
270 | < | atoms[local_index]->getType(), |
271 | < | atoms[local_index]->getX(), |
272 | < | atoms[local_index]->getY(), |
273 | < | atoms[local_index]->getZ(), |
274 | < | atoms[local_index]->get_vx(), |
275 | < | atoms[local_index]->get_vy(), |
276 | < | atoms[local_index]->get_vz()); // check here. |
277 | < | strcpy( writeLine, tempBuffer ); |
278 | < | |
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 | < | sprintf( tempBuffer, |
294 | < | "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
295 | < | q[0], |
296 | < | q[1], |
297 | < | q[2], |
298 | < | q[3], |
299 | < | dAtom->getJx(), |
300 | < | dAtom->getJy(), |
301 | < | dAtom->getJz()); |
302 | < | strcat( writeLine, tempBuffer ); |
303 | < | |
192 | < | } |
193 | < | else |
194 | < | strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
195 | < | } |
196 | < | else { |
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) nodeZeroError(); |
312 | < | |
313 | < | } |
314 | < | else { |
315 | < | myStatus = 1; |
209 | < | MPI::COMM_WORLD.Send(&myStatus, 1, MPI_INT, which_node, |
210 | < | TAKE_THIS_TAG_INT); |
211 | < | MPI::COMM_WORLD.Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT); |
212 | < | MPI::COMM_WORLD.Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node, |
213 | < | TAKE_THIS_TAG_CHAR, istatus); |
214 | < | MPI::COMM_WORLD.Recv(&myStatus, 1, MPI_INT, which_node, |
215 | < | TAKE_THIS_TAG_INT, istatus); |
216 | < | |
217 | < | if(!myStatus) nodeZeroError(); |
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 | } | |
220 | – | |
221 | – | outFile << writeLine; |
222 | – | outFile.flush(); |
356 | } | |
224 | – | |
225 | – | // kill everyone off: |
226 | – | myStatus = -1; |
227 | – | for (j = 0; j < mpiSim->getNumberProcessors(); j++) { |
228 | – | MPI::COMM_WORLD.Send(&myStatus, 1, MPI_INT, j, |
229 | – | TAKE_THIS_TAG_INT); |
230 | – | } |
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; |
235 | < | while (!done) { |
371 | > | for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
372 | ||
373 | < | MPI::COMM_WORLD.Recv(&myStatus, 1, MPI_INT, 0, |
238 | < | TAKE_THIS_TAG_INT, istatus); |
239 | < | |
240 | < | if(!myStatus) anonymousNodeDie(); |
373 | > | // Am I the node which has this atom? |
374 | ||
375 | < | if(myStatus < 0) break; |
375 | > | if (AtomToProcMap[i] == worldRank) { |
376 | ||
377 | < | MPI::COMM_WORLD.Recv(&which_atom, 1, MPI_INT, 0, |
378 | < | TAKE_THIS_TAG_INT, istatus); |
379 | < | |
380 | < | myStatus = 1; |
381 | < | local_index=-1; |
382 | < | for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
383 | < | if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
384 | < | } |
385 | < | if (local_index != -1) { |
386 | < | //format the line |
387 | < | sprintf( tempBuffer, |
388 | < | "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
389 | < | atoms[local_index]->getType(), |
390 | < | atoms[local_index]->getX(), |
391 | < | atoms[local_index]->getY(), |
392 | < | atoms[local_index]->getZ(), |
393 | < | atoms[local_index]->get_vx(), |
394 | < | atoms[local_index]->get_vy(), |
395 | < | atoms[local_index]->get_vz()); // check here. |
396 | < | strcpy( writeLine, tempBuffer ); |
397 | < | |
398 | < | if( atoms[local_index]->isDirectional() ){ |
399 | < | |
400 | < | dAtom = (DirectionalAtom *)atoms[local_index]; |
401 | < | dAtom->getQ( q ); |
402 | < | |
403 | < | sprintf( tempBuffer, |
404 | < | "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
405 | < | q[0], |
406 | < | q[1], |
407 | < | q[2], |
408 | < | q[3], |
409 | < | dAtom->getJx(), |
410 | < | dAtom->getJy(), |
411 | < | dAtom->getJz()); |
412 | < | strcat( writeLine, tempBuffer ); |
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 | > | |
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 | > | 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 | > | |
428 | > | } else { |
429 | > | sprintf(painCave.errMsg, |
430 | > | "Atom %d not found on processor %d\n", |
431 | > | i, worldRank ); |
432 | > | haveError= 1; |
433 | > | simError(); |
434 | } | |
281 | – | else{ |
282 | – | strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
283 | – | } |
284 | – | } |
285 | – | else { |
286 | – | sprintf(painCave.errMsg, |
287 | – | "Atom %d not found on processor %d\n", |
288 | – | which_atom, worldRank ); |
289 | – | myStatus = 0; |
290 | – | simError(); |
435 | ||
436 | < | strcpy( writeLine, "Hello, I'm an error.\n"); |
293 | < | } |
436 | > | strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE); |
437 | ||
438 | < | MPI::COMM_WORLD.Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, |
439 | < | TAKE_THIS_TAG_CHAR); |
297 | < | MPI::COMM_WORLD.Send( &myStatus, 1, MPI_INT, 0, |
298 | < | TAKE_THIS_TAG_INT); |
299 | < | } |
300 | < | } |
301 | < | outFile.flush(); |
302 | < | sprintf( checkPointMsg, |
303 | < | "Sucessfully took a dump.\n"); |
304 | < | MPIcheckPoint(); |
438 | > | // null terminate the string before sending (just in case): |
439 | > | MPIatomTypeString[MINIBUFFERSIZE-1] = '\0'; |
440 | ||
441 | < | // last thing last, enable fatalities. |
442 | < | painCave.isEventLoop = 0; |
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 | + | |
456 | + | } else { |
457 | + | |
458 | + | MPI_Send(atomData6, 6, MPI_DOUBLE, 0, |
459 | + | myPotato, MPI_COMM_WORLD); |
460 | + | } |
461 | + | |
462 | + | myPotato++; |
463 | + | } |
464 | + | } |
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; | |
323 | – | 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 339 | 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 390 | 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 | |
400 | – | |
401 | – | // first thing first, suspend fatalities. |
402 | – | painCave.isEventLoop = 1; |
596 | ||
597 | < | int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone |
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; |
608 | > | MPI_Status istatus; |
609 | int *AtomToProcMap = mpiSim->getAtomToProcMap(); | |
610 | ||
611 | // write out header and node 0's coordinates | |
612 | < | |
412 | < | haveError = 0; |
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++ ) { | |
421 | – | // 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 | + | MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node, |
662 | + | myPotato, MPI_COMM_WORLD, &istatus); |
663 | + | |
664 | + | atomTypeString = MPIatomTypeString; |
665 | + | |
666 | + | myPotato++; |
667 | + | |
668 | + | MPI_Recv(&isDirectional, 1, MPI_INT, which_node, |
669 | + | myPotato, MPI_COMM_WORLD, &istatus); |
670 | + | |
671 | + | myPotato++; |
672 | + | |
673 | + | if (isDirectional) { |
674 | + | MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node, |
675 | + | myPotato, MPI_COMM_WORLD, &istatus); |
676 | + | } else { |
677 | + | MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node, |
678 | + | myPotato, MPI_COMM_WORLD, &istatus); |
679 | + | } |
680 | + | |
681 | + | myPotato++; |
682 | + | potatoes[which_node] = myPotato; |
683 | + | |
684 | + | } else { |
685 | + | |
686 | + | haveError = 0; |
687 | which_atom = i; | |
688 | < | local_index=-1; |
688 | > | local_index=-1; |
689 | > | |
690 | for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { | |
691 | if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; | |
692 | } | |
693 | < | if (local_index != -1) { |
694 | < | sprintf( tempBuffer, |
695 | < | "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
696 | < | atoms[local_index]->getType(), |
697 | < | atoms[local_index]->getX(), |
698 | < | atoms[local_index]->getY(), |
699 | < | atoms[local_index]->getZ(), |
700 | < | atoms[local_index]->get_vx(), |
701 | < | atoms[local_index]->get_vy(), |
702 | < | atoms[local_index]->get_vz()); |
703 | < | strcpy( writeLine, tempBuffer ); |
704 | < | |
705 | < | if( atoms[local_index]->isDirectional() ){ |
706 | < | |
707 | < | dAtom = (DirectionalAtom *)atoms[local_index]; |
708 | < | dAtom->getQ( q ); |
709 | < | |
710 | < | sprintf( tempBuffer, |
711 | < | "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
712 | < | q[0], |
713 | < | q[1], |
714 | < | q[2], |
715 | < | q[3], |
716 | < | dAtom->getJx(), |
717 | < | dAtom->getJy(), |
718 | < | dAtom->getJz()); |
719 | < | strcat( writeLine, tempBuffer ); |
720 | < | } |
721 | < | else |
722 | < | strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
723 | < | } |
724 | < | else { |
693 | > | |
694 | > | if (local_index != -1) { |
695 | > | |
696 | > | atomTypeString = atoms[local_index]->getType(); |
697 | > | |
698 | > | atoms[local_index]->getPos(pos); |
699 | > | atoms[local_index]->getVel(vel); |
700 | > | |
701 | > | atomData6[0] = pos[0]; |
702 | > | atomData6[1] = pos[1]; |
703 | > | atomData6[2] = pos[2]; |
704 | > | |
705 | > | atomData6[3] = vel[0]; |
706 | > | atomData6[4] = vel[1]; |
707 | > | atomData6[5] = vel[2]; |
708 | > | |
709 | > | isDirectional = 0; |
710 | > | |
711 | > | if( atoms[local_index]->isDirectional() ){ |
712 | > | |
713 | > | isDirectional = 1; |
714 | > | |
715 | > | dAtom = (DirectionalAtom *)atoms[local_index]; |
716 | > | dAtom->getQ( q ); |
717 | > | |
718 | > | for (int j = 0; j < 6 ; j++) |
719 | > | atomData13[j] = atomData6[j]; |
720 | > | |
721 | > | atomData13[6] = q[0]; |
722 | > | atomData13[7] = q[1]; |
723 | > | atomData13[8] = q[2]; |
724 | > | atomData13[9] = q[3]; |
725 | > | |
726 | > | atomData13[10] = dAtom->getJx(); |
727 | > | atomData13[11] = dAtom->getJy(); |
728 | > | atomData13[12] = dAtom->getJz(); |
729 | > | } |
730 | > | |
731 | > | } else { |
732 | sprintf(painCave.errMsg, | |
733 | "Atom %d not found on processor %d\n", | |
734 | i, worldRank ); | |
735 | haveError= 1; | |
736 | simError(); | |
737 | < | } |
737 | > | } |
738 | > | |
739 | > | if(haveError) DieDieDie(); |
740 | > | |
741 | > | // If we've survived to here, format the line: |
742 | > | |
743 | > | if (!isDirectional) { |
744 | ||
745 | < | if(haveError) nodeZeroError(); |
746 | < | |
747 | < | } |
748 | < | else { |
745 | > | sprintf( tempBuffer, |
746 | > | "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
747 | > | atomTypeString, |
748 | > | atomData6[0], |
749 | > | atomData6[1], |
750 | > | atomData6[2], |
751 | > | atomData6[3], |
752 | > | atomData6[4], |
753 | > | atomData6[5]); |
754 | > | |
755 | > | strcpy( writeLine, tempBuffer ); |
756 | > | strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
757 | > | |
758 | > | } else { |
759 | > | |
760 | > | sprintf( tempBuffer, |
761 | > | "%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", |
762 | > | atomTypeString, |
763 | > | atomData13[0], |
764 | > | atomData13[1], |
765 | > | atomData13[2], |
766 | > | atomData13[3], |
767 | > | atomData13[4], |
768 | > | atomData13[5], |
769 | > | atomData13[6], |
770 | > | atomData13[7], |
771 | > | atomData13[8], |
772 | > | atomData13[9], |
773 | > | atomData13[10], |
774 | > | atomData13[11], |
775 | > | atomData13[12]); |
776 | > | |
777 | > | strcat( writeLine, tempBuffer ); |
778 | > | |
779 | > | } |
780 | ||
781 | < | myStatus = 1; |
782 | < | MPI::COMM_WORLD.Send(&myStatus, 1, MPI_INT, which_node, |
478 | < | TAKE_THIS_TAG_INT); |
479 | < | MPI::COMM_WORLD.Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT); |
480 | < | MPI::COMM_WORLD.Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node, |
481 | < | TAKE_THIS_TAG_CHAR, istatus); |
482 | < | MPI::COMM_WORLD.Recv(&myStatus, 1, MPI_INT, which_node, |
483 | < | TAKE_THIS_TAG_INT, istatus); |
484 | < | |
485 | < | if(!myStatus) nodeZeroError(); |
781 | > | finalOut << writeLine; |
782 | > | finalOut.flush(); |
783 | } | |
487 | – | |
488 | – | finalOut << writeLine; |
784 | } | |
490 | – | |
491 | – | // kill everyone off: |
492 | – | myStatus = -1; |
493 | – | for (j = 0; j < mpiSim->getNumberProcessors(); j++) { |
494 | – | MPI::COMM_WORLD.Send(&myStatus, 1, MPI_INT, j, |
495 | – | TAKE_THIS_TAG_INT); |
496 | – | } |
785 | ||
786 | < | } else { |
786 | > | finalOut.flush(); |
787 | > | sprintf( checkPointMsg, |
788 | > | "Sucessfully took a dump.\n"); |
789 | > | delete[] potatoes; |
790 | > | |
791 | > | MPIcheckPoint(); |
792 | ||
793 | < | done = 0; |
501 | < | while (!done) { |
793 | > | } else { |
794 | ||
795 | < | MPI::COMM_WORLD.Recv(&myStatus, 1, MPI_INT, 0, |
796 | < | TAKE_THIS_TAG_INT, istatus); |
795 | > | // worldRank != 0, so I'm a remote node. |
796 | > | |
797 | > | // Set my magic potato to 0: |
798 | > | |
799 | > | myPotato = 0; |
800 | > | |
801 | > | for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
802 | ||
803 | < | if(!myStatus) anonymousNodeDie(); |
803 | > | // Am I the node which has this atom? |
804 | ||
805 | < | if(myStatus < 0) break; |
509 | < | |
510 | < | MPI::COMM_WORLD.Recv(&which_atom, 1, MPI_INT, 0, |
511 | < | TAKE_THIS_TAG_INT, istatus); |
512 | < | |
513 | < | myStatus = 1; |
514 | < | local_index=-1; |
515 | < | for (j=0; j < mpiSim->getMyNlocal(); j++) { |
516 | < | if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
517 | < | } |
518 | < | if (local_index != -1) { |
805 | > | if (AtomToProcMap[i] == worldRank) { |
806 | ||
807 | < | //format the line |
808 | < | sprintf( tempBuffer, |
809 | < | "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
810 | < | atoms[local_index]->getType(), |
811 | < | atoms[local_index]->getX(), |
812 | < | atoms[local_index]->getY(), |
813 | < | atoms[local_index]->getZ(), |
814 | < | atoms[local_index]->get_vx(), |
815 | < | atoms[local_index]->get_vy(), |
816 | < | atoms[local_index]->get_vz()); // check here. |
817 | < | strcpy( writeLine, tempBuffer ); |
818 | < | |
819 | < | if( atoms[local_index]->isDirectional() ){ |
820 | < | |
821 | < | dAtom = (DirectionalAtom *)atoms[local_index]; |
822 | < | dAtom->getQ( q ); |
823 | < | |
824 | < | sprintf( tempBuffer, |
825 | < | "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
826 | < | q[0], |
827 | < | q[1], |
828 | < | q[2], |
829 | < | q[3], |
830 | < | dAtom->getJx(), |
831 | < | dAtom->getJy(), |
832 | < | dAtom->getJz()); |
833 | < | strcat( writeLine, tempBuffer ); |
807 | > | if (myPotato + 3 >= MAXTAG) { |
808 | > | |
809 | > | // The potato was going to exceed the maximum value, |
810 | > | // so wrap this processor potato back to 0 (and block until |
811 | > | // node 0 says we can go: |
812 | > | |
813 | > | MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus); |
814 | > | |
815 | > | } |
816 | > | which_atom = i; |
817 | > | local_index=-1; |
818 | > | for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
819 | > | if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
820 | > | } |
821 | > | if (local_index != -1) { |
822 | > | |
823 | > | atomTypeString = atoms[local_index]->getType(); |
824 | > | |
825 | > | atoms[local_index]->getPos(pos); |
826 | > | atoms[local_index]->getVel(vel); |
827 | > | |
828 | > | atomData6[0] = pos[0]; |
829 | > | atomData6[1] = pos[1]; |
830 | > | atomData6[2] = pos[2]; |
831 | > | |
832 | > | atomData6[3] = vel[0]; |
833 | > | atomData6[4] = vel[1]; |
834 | > | atomData6[5] = vel[2]; |
835 | > | |
836 | > | isDirectional = 0; |
837 | > | |
838 | > | if( atoms[local_index]->isDirectional() ){ |
839 | > | |
840 | > | isDirectional = 1; |
841 | > | |
842 | > | dAtom = (DirectionalAtom *)atoms[local_index]; |
843 | > | dAtom->getQ( q ); |
844 | > | |
845 | > | for (int j = 0; j < 6 ; j++) |
846 | > | atomData13[j] = atomData6[j]; |
847 | > | |
848 | > | atomData13[6] = q[0]; |
849 | > | atomData13[7] = q[1]; |
850 | > | atomData13[8] = q[2]; |
851 | > | atomData13[9] = q[3]; |
852 | > | |
853 | > | atomData13[10] = dAtom->getJx(); |
854 | > | atomData13[11] = dAtom->getJy(); |
855 | > | atomData13[12] = dAtom->getJz(); |
856 | > | } |
857 | > | |
858 | > | } else { |
859 | > | sprintf(painCave.errMsg, |
860 | > | "Atom %d not found on processor %d\n", |
861 | > | i, worldRank ); |
862 | > | haveError= 1; |
863 | > | simError(); |
864 | } | |
548 | – | else{ |
549 | – | strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
550 | – | } |
551 | – | } |
552 | – | else { |
553 | – | sprintf(painCave.errMsg, |
554 | – | "Atom %d not found on processor %d\n", |
555 | – | which_atom, worldRank ); |
556 | – | myStatus = 0; |
557 | – | simError(); |
558 | – | |
559 | – | strcpy( writeLine, "Hello, I'm an error.\n"); |
560 | – | } |
865 | ||
866 | < | MPI::COMM_WORLD.Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, |
867 | < | TAKE_THIS_TAG_CHAR); |
868 | < | MPI::COMM_WORLD.Send( &myStatus, 1, MPI_INT, 0, |
869 | < | TAKE_THIS_TAG_INT); |
866 | > | strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE); |
867 | > | |
868 | > | // null terminate the string before sending (just in case): |
869 | > | MPIatomTypeString[MINIBUFFERSIZE-1] = '\0'; |
870 | > | |
871 | > | MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0, |
872 | > | myPotato, MPI_COMM_WORLD); |
873 | > | |
874 | > | myPotato++; |
875 | > | |
876 | > | MPI_Send(&isDirectional, 1, MPI_INT, 0, |
877 | > | myPotato, MPI_COMM_WORLD); |
878 | > | |
879 | > | myPotato++; |
880 | > | |
881 | > | if (isDirectional) { |
882 | > | |
883 | > | MPI_Send(atomData13, 13, MPI_DOUBLE, 0, |
884 | > | myPotato, MPI_COMM_WORLD); |
885 | > | |
886 | > | } else { |
887 | > | |
888 | > | MPI_Send(atomData6, 6, MPI_DOUBLE, 0, |
889 | > | myPotato, MPI_COMM_WORLD); |
890 | > | } |
891 | > | |
892 | > | myPotato++; |
893 | > | } |
894 | } | |
895 | < | } |
896 | < | finalOut.flush(); |
897 | < | sprintf( checkPointMsg, |
898 | < | "Sucessfully took a dump.\n"); |
899 | < | MPIcheckPoint(); |
895 | > | |
896 | > | sprintf( checkPointMsg, |
897 | > | "Sucessfully took a dump.\n"); |
898 | > | MPIcheckPoint(); |
899 | > | |
900 | > | } |
901 | ||
902 | < | if( worldRank == 0 ) finalOut.close(); |
902 | > | if( worldRank == 0 ) finalOut.close(); |
903 | #endif // is_mpi | |
904 | } | |
905 | ||
# | Line 580 | Line 909 | void DumpWriter::writeFinal(){ | |
909 | ||
910 | // a couple of functions to let us escape the write loop | |
911 | ||
912 | < | void dWrite::nodeZeroError( void ){ |
584 | < | int j, myStatus; |
585 | < | |
586 | < | myStatus = 0; |
587 | < | for (j = 0; j < mpiSim->getNumberProcessors(); j++) { |
588 | < | MPI::COMM_WORLD.Send( &myStatus, 1, MPI_INT, j, |
589 | < | TAKE_THIS_TAG_INT); |
590 | < | } |
591 | < | |
912 | > | void dWrite::DieDieDie( void ){ |
913 | ||
914 | MPI_Finalize(); | |
915 | exit (0); | |
595 | – | |
916 | } | |
917 | ||
598 | – | void dWrite::anonymousNodeDie( void ){ |
599 | – | |
600 | – | MPI_Finalize(); |
601 | – | exit (0); |
602 | – | } |
603 | – | |
918 | #endif //is_mpi |
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