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root/group/trunk/OOPSE/libmdtools/DumpWriter.cpp
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Comparing trunk/OOPSE/libmdtools/DumpWriter.cpp (file contents):
Revision 912 by gezelter, Thu Jan 8 18:59:36 2004 UTC vs.
Revision 951 by mmeineke, Fri Jan 16 21:51:51 2004 UTC

# 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"
122 <          << entry_plug->Hmat[1][2] << "\t"
123 <          << 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 >  printf("Hello from node %d\n", worldRank);
114 >  sortByGlobalIndex();
115 >  if(worldRank == 0 ){
116 >    
117 >    finalOut.open( entry_plug->finalName, ios::out | ios::trunc );
118 >    if( !finalOut ){
119 >      sprintf( painCave.errMsg,
120 >               "Could not open \"%s\" for final dump output.\n",
121 >               entry_plug->finalName );
122 >      painCave.isFatal = 1;
123 >      simError();
124      }
152 –    else
153 –      strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
154 –
155 –    outFile << writeLine;
125    }
126 <  outFile.flush();
126 > #endif // is_mpi
127  
128 < #else // is_mpi
128 >  fileStreams.push_back(&finalOut);
129 >  fileStreams.push_back(&dumpFile);
130  
131 <  // first thing first, suspend fatalities.
162 <  painCave.isEventLoop = 1;
131 >  writeFrame(fileStreams, currentTime);
132  
133 <  int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
134 <  int haveError;
133 > #ifdef IS_MPI
134 >  finalOut.close();
135 > #endif
136 >        
137 > }
138  
139 <  MPI_Status istatus;
168 <  int *AtomToProcMap = mpiSim->getAtomToProcMap();
139 > void DumpWriter::writeFinal(double currentTime){
140  
141 <  // write out header and node 0's coordinates
141 >  ofstream finalOut;
142 >  vector<ofstream*> fileStreams;
143  
144 <  if( worldRank == 0 ){
145 <    outFile << mpiSim->getTotAtoms() << "\n";
144 > #ifdef IS_MPI
145 >  if(worldRank == 0 ){
146 > #endif // is_mpi
147  
148 <    outFile << currentTime << ";\t"
176 <            << entry_plug->Hmat[0][0] << "\t"
177 <            << entry_plug->Hmat[1][0] << "\t"
178 <            << entry_plug->Hmat[2][0] << ";\t"
148 >    finalOut.open( entry_plug->finalName, ios::out | ios::trunc );
149  
150 <            << entry_plug->Hmat[0][1] << "\t"
151 <            << entry_plug->Hmat[1][1] << "\t"
152 <            << entry_plug->Hmat[2][1] << ";\t"
150 >    if( !finalOut ){
151 >      sprintf( painCave.errMsg,
152 >               "Could not open \"%s\" for final dump output.\n",
153 >               entry_plug->finalName );
154 >      painCave.isFatal = 1;
155 >      simError();
156 >    }
157  
158 <            << entry_plug->Hmat[0][2] << "\t"
159 <            << entry_plug->Hmat[1][2] << "\t"
160 <            << 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 <  }
158 > #ifdef IS_MPI
159 >  }
160 > #endif // is_mpi
161    
162 <  painCave.isEventLoop = 0;
162 >  fileStreams.push_back(&finalOut);  
163 >  writeFrame(fileStreams, currentTime);
164  
165 < #endif // is_mpi
165 > #ifdef IS_MPI
166 >  finalOut.close();
167 > #endif
168 >  
169   }
170  
171 < void DumpWriter::writeFinal(double finalTime){
171 > void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){
172  
421 –  char finalName[500];
422 –  ofstream finalOut;
423 –
173    const int BUFFERSIZE = 2000;
174    const int MINIBUFFERSIZE = 100;
175 <  char tempBuffer[BUFFERSIZE];
175 >
176 >  char tempBuffer[BUFFERSIZE];  
177    char writeLine[BUFFERSIZE];
178  
179 <  double q[4];
180 <  DirectionalAtom* dAtom;
431 <  Atom** atoms = entry_plug->atoms;
432 <  int i;
179 >  int i, k;
180 >
181   #ifdef IS_MPI
182 <  int j, which_node, done, which_atom, local_index;
183 <  double atomTransData[6];
184 <  double atomOrientData[7];
182 >  
183 >  /*********************************************************************
184 >   * Documentation?  You want DOCUMENTATION?
185 >   *
186 >   * Why all the potatoes below?  
187 >   *
188 >   * To make a long story short, the original version of DumpWriter
189 >   * worked in the most inefficient way possible.  Node 0 would
190 >   * poke each of the node for an individual atom's formatted data
191 >   * as node 0 worked its way down the global index. This was particularly
192 >   * inefficient since the method blocked all processors at every atom
193 >   * (and did it twice!).
194 >   *
195 >   * An intermediate version of DumpWriter could be described from Node
196 >   * zero's perspective as follows:
197 >   *
198 >   *  1) Have 100 of your friends stand in a circle.
199 >   *  2) When you say go, have all of them start tossing potatoes at
200 >   *     you (one at a time).
201 >   *  3) Catch the potatoes.
202 >   *
203 >   * It was an improvement, but MPI has buffers and caches that could
204 >   * best be described in this analogy as "potato nets", so there's no
205 >   * need to block the processors atom-by-atom.
206 >   *
207 >   * This new and improved DumpWriter works in an even more efficient
208 >   * way:
209 >   *
210 >   *  1) Have 100 of your friend stand in a circle.
211 >   *  2) When you say go, have them start tossing 5-pound bags of
212 >   *     potatoes at you.
213 >   *  3) Once you've caught a friend's bag of potatoes,
214 >   *     toss them a spud to let them know they can toss another bag.
215 >   *
216 >   * How's THAT for documentation?
217 >   *
218 >   *********************************************************************/
219 >
220 >  int *potatoes;
221 >  int myPotato;
222 >
223 >  int nProc;
224 >  int j, which_node, done, which_atom, local_index, currentIndex;
225 >  double atomData6[6];
226 >  double atomData13[13];
227    int isDirectional;
228    char* atomTypeString;
229    char MPIatomTypeString[MINIBUFFERSIZE];
230 <  int atomTypeTag;
441 <  int atomIsDirectionalTag;
442 <  int atomTransDataTag;
443 <  int atomOrientDataTag;
230 >
231   #else //is_mpi
232    int nAtoms = entry_plug->n_atoms;
233   #endif //is_mpi
234  
235 +  double q[4];
236 +  DirectionalAtom* dAtom;
237 +  Atom** atoms = entry_plug->atoms;
238    double pos[3], vel[3];
239  
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 –
240   #ifndef IS_MPI
241 +  
242 +  for(k = 0; k < outFile.size(); k++){
243 +    *outFile[k] << nAtoms << "\n";
244  
245 <  finalOut << nAtoms << "\n";
245 >    *outFile[k] << currentTime << ";\t"
246 >               << entry_plug->Hmat[0][0] << "\t"
247 >                     << entry_plug->Hmat[1][0] << "\t"
248 >                     << entry_plug->Hmat[2][0] << ";\t"
249 >              
250 >               << entry_plug->Hmat[0][1] << "\t"
251 >                     << entry_plug->Hmat[1][1] << "\t"
252 >                     << entry_plug->Hmat[2][1] << ";\t"
253  
254 <  finalOut << finalTime << ";\t"
255 <           << entry_plug->Hmat[0][0] << "\t"
256 <           << entry_plug->Hmat[1][0] << "\t"
483 <           << entry_plug->Hmat[2][0] << ";\t"
254 >                     << entry_plug->Hmat[0][2] << "\t"
255 >                     << entry_plug->Hmat[1][2] << "\t"
256 >                     << entry_plug->Hmat[2][2] << ";";
257  
258 <           << entry_plug->Hmat[0][1] << "\t"
259 <           << entry_plug->Hmat[1][1] << "\t"
260 <           << entry_plug->Hmat[2][1] << ";\t"
261 <
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 <
258 >    //write out additional parameters, such as chi and eta
259 >    *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
260 >  }
261 >  
262    for( i=0; i<nAtoms; i++ ){
263  
264      atoms[i]->getPos(pos);
# Line 529 | Line 294 | void DumpWriter::writeFinal(double finalTime){
294      else
295        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
296  
297 <    finalOut << writeLine;
297 >    for(k = 0; k < outFile.size(); k++)
298 >      *outFile[k] << writeLine;
299    }
534 –  finalOut.flush();
535 –  finalOut.close();
300  
301   #else // is_mpi
302  
303 <  // first thing first, suspend fatalities.
304 <  painCave.isEventLoop = 1;
303 >  /* code to find maximum tag value */
304 >  
305 >  int *tagub, flag, MAXTAG;
306 >  MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
307 >  if (flag) {
308 >    MAXTAG = *tagub;
309 >  } else {
310 >    MAXTAG = 32767;
311 >  }  
312  
542 –  int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
313    int haveError;
314  
315    MPI_Status istatus;
# Line 548 | Line 318 | void DumpWriter::writeFinal(double finalTime){
318    // write out header and node 0's coordinates
319  
320    if( worldRank == 0 ){
551 –    finalOut << mpiSim->getTotAtoms() << "\n";
321  
322 <    finalOut << finalTime << ";\t"
554 <            << entry_plug->Hmat[0][0] << "\t"
555 <            << entry_plug->Hmat[1][0] << "\t"
556 <            << entry_plug->Hmat[2][0] << ";\t"
322 >    // Node 0 needs a list of the magic potatoes for each processor;
323  
324 <            << entry_plug->Hmat[0][1] << "\t"
325 <            << entry_plug->Hmat[1][1] << "\t"
560 <            << entry_plug->Hmat[2][1] << ";\t"
324 >    nProc = mpiSim->getNumberProcessors();
325 >    potatoes = new int[nProc];
326  
327 <            << entry_plug->Hmat[0][2] << "\t"
328 <            << entry_plug->Hmat[1][2] << "\t"
329 <            << entry_plug->Hmat[2][2] << ";";
327 >    //write out the comment lines
328 >    for (i = 0; i < nProc; i++)
329 >      potatoes[i] = 0;
330 >    
331 >      for(k = 0; k < outFile.size(); k++){
332 >        *outFile[k] << mpiSim->getTotAtoms() << "\n";
333  
334 <    finalOut << entry_plug->the_integrator->getAdditionalParameters();
335 <    finalOut << endl;
336 <    finalOut.flush();
334 >        *outFile[k] << currentTime << ";\t"
335 >                         << entry_plug->Hmat[0][0] << "\t"
336 >                         << entry_plug->Hmat[1][0] << "\t"
337 >                         << entry_plug->Hmat[2][0] << ";\t"
338 >
339 >                         << entry_plug->Hmat[0][1] << "\t"
340 >                         << entry_plug->Hmat[1][1] << "\t"
341 >                         << entry_plug->Hmat[2][1] << ";\t"
342 >
343 >                         << entry_plug->Hmat[0][2] << "\t"
344 >                         << entry_plug->Hmat[1][2] << "\t"
345 >                         << entry_plug->Hmat[2][2] << ";";
346 >  
347 >        *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
348 >    }
349 >
350 >    currentIndex = 0;
351 >
352      for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
353 +      
354        // Get the Node number which has this atom;
355 <
355 >      
356        which_node = AtomToProcMap[i];
357 <
357 >      
358        if (which_node != 0) {
575 –        
576 –        atomTypeTag          = 4*i;
577 –        atomIsDirectionalTag = 4*i + 1;
578 –        atomTransDataTag     = 4*i + 2;
579 –        atomOrientDataTag    = 4*i + 3;
359  
360 +        if (potatoes[which_node] + 3 >= MAXTAG) {
361 +          // The potato was going to exceed the maximum value,
362 +          // so wrap this processor potato back to 0:        
363 +
364 +          potatoes[which_node] = 0;          
365 +          MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
366 +          
367 +        }
368 +
369 +        myPotato = potatoes[which_node];        
370 +        
371          MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
372 <                 atomTypeTag, MPI_COMM_WORLD, &istatus);
372 >                 myPotato, MPI_COMM_WORLD, &istatus);
373          
374 <        strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE);
374 >        atomTypeString = MPIatomTypeString;
375 >        
376 >        myPotato++;
377  
378          MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
379 <                 atomIsDirectionalTag, MPI_COMM_WORLD, &istatus);
380 <        
381 <        MPI_Recv(atomTransData, 6, MPI_DOUBLE, which_node,
590 <                 atomTransDataTag, MPI_COMM_WORLD, &istatus);
379 >                 myPotato, MPI_COMM_WORLD, &istatus);
380 >              
381 >        myPotato++;
382  
383 <        if (isDirectional) {
384 <
385 <          MPI_Recv(atomOrientData, 7, MPI_DOUBLE, which_node,
386 <                   atomOrientDataTag, MPI_COMM_WORLD, &istatus);
387 <
383 >        if (isDirectional) {          
384 >          MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node,
385 >                   myPotato, MPI_COMM_WORLD, &istatus);
386 >        } else {
387 >          MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node,
388 >                   myPotato, MPI_COMM_WORLD, &istatus);          
389          }
390 +        
391 +        myPotato++;
392 +        potatoes[which_node] = myPotato;
393  
394        } else {
395          
396 <        haveError = 0;
396 >        haveError = 0;
397          which_atom = i;
398 <        local_index=-1;
398 >        
399 >        //local_index = -1;
400  
401 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
402 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
403 <        }
404 <
405 <        if (local_index != -1) {
406 <
407 <          atomTypeString = atoms[local_index]->getType();
408 <
401 >        //for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
402 >        //  if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
403 >        //}
404 >        
405 >        //if (local_index != -1) {
406 >          
407 >          local_index = indexArray[currentIndex].first;        
408 >          
409 >          if (which_atom == indexArray[currentIndex].second) {
410 >            
411 >            atomTypeString = atoms[local_index]->getType();
412 >            
413            atoms[local_index]->getPos(pos);
414 <          atoms[local_index]->getVel(vel);
414 >          atoms[local_index]->getVel(vel);          
415 >          
416 >          atomData6[0] = pos[0];
417 >          atomData6[1] = pos[1];
418 >          atomData6[2] = pos[2];
419  
420 <          atomTransData[0] = pos[0];
421 <          atomTransData[1] = pos[1];
422 <          atomTransData[2] = pos[2];
619 <
620 <          atomTransData[3] = vel[0];
621 <          atomTransData[4] = vel[1];
622 <          atomTransData[5] = vel[2];
420 >          atomData6[3] = vel[0];
421 >          atomData6[4] = vel[1];
422 >          atomData6[5] = vel[2];
423            
424            isDirectional = 0;
425  
# Line 629 | Line 429 | void DumpWriter::writeFinal(double finalTime){
429              
430              dAtom = (DirectionalAtom *)atoms[local_index];
431              dAtom->getQ( q );
632 –            
633 –            atomOrientData[0] = q[0];
634 –            atomOrientData[1] = q[1];
635 –            atomOrientData[2] = q[2];
636 –            atomOrientData[3] = q[3];
432  
433 <            atomOrientData[4] = dAtom->getJx();
434 <            atomOrientData[5] = dAtom->getJy();
435 <            atomOrientData[6] = dAtom->getJz();
433 >            for (int j = 0; j < 6 ; j++)
434 >              atomData13[j] = atomData6[j];            
435 >            
436 >            atomData13[6] = q[0];
437 >            atomData13[7] = q[1];
438 >            atomData13[8] = q[2];
439 >            atomData13[9] = q[3];
440 >            
441 >            atomData13[10] = dAtom->getJx();
442 >            atomData13[11] = dAtom->getJy();
443 >            atomData13[12] = dAtom->getJz();
444            }
445 <
445 >          
446          } else {
447            sprintf(painCave.errMsg,
448 <                  "Atom %d not found on processor %d\n",
449 <                  i, worldRank );
448 >                  "Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n",
449 >                  which_atom, worldRank, currentIndex, local_index );
450            haveError= 1;
451            simError();
452          }
650 –
651 –        if(haveError) DieDieDie();
652 –                              
653 –        // If we've survived to here, format the line:
453          
454 <        sprintf( tempBuffer,
455 <                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
456 <                 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();
454 >        if(haveError) DieDieDie();
455 >        
456 >        currentIndex++;
457        }
458 +      // If we've survived to here, format the line:
459 +      
460 +      if (!isDirectional) {
461 +        
462 +        sprintf( writeLine,
463 +                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
464 +                 atomTypeString,
465 +                 atomData6[0],
466 +                 atomData6[1],
467 +                 atomData6[2],
468 +                 atomData6[3],
469 +                 atomData6[4],
470 +                 atomData6[5]);
471 +        
472 +        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
473 +        
474 +      } else {
475 +        
476 +        sprintf( writeLine,
477 +                 "%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",
478 +                 atomTypeString,
479 +                 atomData13[0],
480 +                 atomData13[1],
481 +                 atomData13[2],
482 +                 atomData13[3],
483 +                 atomData13[4],
484 +                 atomData13[5],
485 +                 atomData13[6],
486 +                 atomData13[7],
487 +                 atomData13[8],
488 +                 atomData13[9],
489 +                 atomData13[10],
490 +                 atomData13[11],
491 +                 atomData13[12]);
492 +        
493 +      }
494 +      
495 +      for(k = 0; k < outFile.size(); k++)
496 +        *outFile[k] << writeLine;
497      }
498 <
499 <    finalOut.flush();
498 >    
499 >    for(k = 0; k < outFile.size(); k++)
500 >      outFile[k]->flush();
501 >    
502      sprintf( checkPointMsg,
503               "Sucessfully took a dump.\n");
504 +    
505      MPIcheckPoint();        
506      
507 +    delete[] potatoes;
508 +    
509    } else {
510  
511      // worldRank != 0, so I'm a remote node.  
512 +
513 +    // Set my magic potato to 0:
514 +
515 +    myPotato = 0;
516 +    currentIndex = 0;
517      
518      for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
519        
# Line 701 | Line 521 | void DumpWriter::writeFinal(double finalTime){
521        
522        if (AtomToProcMap[i] == worldRank) {
523  
524 <        local_index=-1;
525 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
526 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
524 >        if (myPotato + 3 >= MAXTAG) {
525 >          
526 >          // The potato was going to exceed the maximum value,
527 >          // so wrap this processor potato back to 0 (and block until
528 >          // node 0 says we can go:
529 >          
530 >          MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
531 >          
532          }
533 <        if (local_index != -1) {
533 >        which_atom = i;
534 >
535 >        //local_index = -1;
536 >
537 >        //for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
538 >        // if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
539 >        //}
540 >        
541 >        //if (local_index != -1) {
542 >
543 >        local_index = indexArray[currentIndex].first;        
544 >                
545 >        if (which_atom == indexArray[currentIndex].second) {
546          
547            atomTypeString = atoms[local_index]->getType();
548 <
548 >          
549            atoms[local_index]->getPos(pos);
550            atoms[local_index]->getVel(vel);
551 +          
552 +          atomData6[0] = pos[0];
553 +          atomData6[1] = pos[1];
554 +          atomData6[2] = pos[2];
555  
556 <          atomTransData[0] = pos[0];
557 <          atomTransData[1] = pos[1];
558 <          atomTransData[2] = pos[2];
718 <
719 <          atomTransData[3] = vel[0];
720 <          atomTransData[4] = vel[1];
721 <          atomTransData[5] = vel[2];
556 >          atomData6[3] = vel[0];
557 >          atomData6[4] = vel[1];
558 >          atomData6[5] = vel[2];
559            
560            isDirectional = 0;
561  
# Line 729 | Line 566 | void DumpWriter::writeFinal(double finalTime){
566              dAtom = (DirectionalAtom *)atoms[local_index];
567              dAtom->getQ( q );
568              
569 <            atomOrientData[0] = q[0];
570 <            atomOrientData[1] = q[1];
571 <            atomOrientData[2] = q[2];
572 <            atomOrientData[3] = q[3];
573 <
574 <            atomOrientData[4] = dAtom->getJx();
575 <            atomOrientData[5] = dAtom->getJy();
576 <            atomOrientData[6] = dAtom->getJz();
569 >            for (int j = 0; j < 6 ; j++)
570 >              atomData13[j] = atomData6[j];
571 >            
572 >            atomData13[6] = q[0];
573 >            atomData13[7] = q[1];
574 >            atomData13[8] = q[2];
575 >            atomData13[9] = q[3];
576 >  
577 >            atomData13[10] = dAtom->getJx();
578 >            atomData13[11] = dAtom->getJy();
579 >            atomData13[12] = dAtom->getJz();
580            }
581  
582          } else {
583            sprintf(painCave.errMsg,
584 <                  "Atom %d not found on processor %d\n",
585 <                  i, worldRank );
584 >                  "Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n",
585 >                  which_atom, worldRank, currentIndex, local_index );
586            haveError= 1;
587            simError();
588          }
589 <
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 <
589 >        
590          strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
591  
592 +        // null terminate the string before sending (just in case):
593 +        MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
594 +
595          MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
596 <                 atomTypeTag, MPI_COMM_WORLD);
596 >                             myPotato, MPI_COMM_WORLD);
597          
598 +        myPotato++;
599 +
600          MPI_Send(&isDirectional, 1, MPI_INT, 0,
601 <                 atomIsDirectionalTag, MPI_COMM_WORLD);
601 >                             myPotato, MPI_COMM_WORLD);
602          
603 <        MPI_Send(atomTransData, 6, MPI_DOUBLE, 0,
604 <                 atomTransDataTag, MPI_COMM_WORLD);
767 <
603 >        myPotato++;
604 >        
605          if (isDirectional) {
606  
607 <          MPI_Send(atomOrientData, 7, MPI_DOUBLE, 0,
608 <                   atomOrientDataTag, MPI_COMM_WORLD);
607 >          MPI_Send(atomData13, 13, MPI_DOUBLE, 0,
608 >                   myPotato, MPI_COMM_WORLD);
609            
610 +        } else {
611 +
612 +          MPI_Send(atomData6, 6, MPI_DOUBLE, 0,
613 +                   myPotato, MPI_COMM_WORLD);
614          }
615 <      
615 >
616 >        myPotato++;  
617 >        currentIndex++;    
618        }
619      }
620  
621      sprintf( checkPointMsg,
622 <             "Sucessfully wrote final file.\n");
622 >             "Sucessfully took a dump.\n");
623      MPIcheckPoint();        
624      
625 <  }
625 >  }
626    
784 –  painCave.isEventLoop = 0;
785 –
786 –  if( worldRank == 0 ) finalOut.close();
627   #endif // is_mpi
628   }
629  
790 –
791 –
630   #ifdef IS_MPI
631  
632   // a couple of functions to let us escape the write loop

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