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root/group/trunk/OOPSE/libmdtools/DumpWriter.cpp
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Comparing trunk/OOPSE/libmdtools/DumpWriter.cpp (file contents):
Revision 910 by gezelter, Thu Jan 8 18:05:37 2004 UTC vs.
Revision 1097 by gezelter, Mon Apr 12 20:32:20 2004 UTC

# Line 1 | Line 1
1 + #define _LARGEFILE_SOURCE64
2   #define _FILE_OFFSET_BITS 64
3  
4   #include <string.h>
5   #include <iostream>
6   #include <fstream>
7 + #include <algorithm>
8 + #include <utility>
9  
10   #ifdef IS_MPI
11   #include <mpi.h>
# Line 26 | Line 29 | DumpWriter::DumpWriter( SimInfo* the_entry_plug ){
29    if(worldRank == 0 ){
30   #endif // is_mpi
31  
32 <    strcpy( outName, entry_plug->sampleName );
32 >    dumpFile.open(entry_plug->sampleName, ios::out | ios::trunc );
33  
34 <    outFile.open(outName, ios::out | ios::trunc );
34 >    if( !dumpFile ){
35  
33 –    if( !outFile ){
34 –
36        sprintf( painCave.errMsg,
37                 "Could not open \"%s\" for dump output.\n",
38 <               outName);
38 >               entry_plug->sampleName);
39        painCave.isFatal = 1;
40        simError();
41      }
42  
42 –    //outFile.setf( ios::scientific );
43 –
43   #ifdef IS_MPI
44    }
45  
46 +  //sort the local atoms by global index
47 +  sortByGlobalIndex();
48 +  
49    sprintf( checkPointMsg,
50             "Sucessfully opened output file for dumping.\n");
51    MPIcheckPoint();
# Line 56 | Line 58 | DumpWriter::~DumpWriter( ){
58    if(worldRank == 0 ){
59   #endif // is_mpi
60  
61 <    outFile.close();
61 >    dumpFile.close();
62  
63   #ifdef IS_MPI
64    }
65   #endif // is_mpi
66   }
67  
68 < void DumpWriter::writeDump( double currentTime ){
68 > #ifdef IS_MPI
69  
70 <  const int BUFFERSIZE = 2000;
71 <  const int MINIBUFFERSIZE = 10;
70 > /**
71 > * A hook function to load balancing
72 > */
73  
74 <  char tempBuffer[BUFFERSIZE];
75 <  char writeLine[BUFFERSIZE];
74 > void DumpWriter::update(){
75 >  sortByGlobalIndex();          
76 > }
77 >  
78 > /**
79 > * Auxiliary sorting function
80 > */
81 >
82 > bool indexSortingCriterion(const pair<int, int>& p1, const pair<int, int>& p2){
83 >  return p1.second < p2.second;
84 > }
85  
86 <  int i;
87 < #ifdef IS_MPI
88 <  int j, which_node, done, which_atom, local_index;
89 <  double atomTransData[6];
90 <  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;
86 > /**
87 > * Sorting the local index by global index
88 > */
89 >
90 > void DumpWriter::sortByGlobalIndex(){
91    Atom** atoms = entry_plug->atoms;
92 <  double pos[3], vel[3];
92 >  
93 >  indexArray.clear();
94 >  
95 >  for(int i = 0; i < mpiSim->getMyNlocal();i++)
96 >    indexArray.push_back(make_pair(i, atoms[i]->getGlobalIndex()));
97 >  
98 >  sort(indexArray.begin(), indexArray.end(), indexSortingCriterion);    
99 > }
100  
101 <  // write current frame to the eor file
101 > #endif
102  
103 <  this->writeFinal( currentTime );
103 > void DumpWriter::writeDump(double currentTime){
104  
105 < #ifndef IS_MPI
105 >  ofstream finalOut;
106 >  vector<ofstream*> fileStreams;
107  
108 <  outFile << nAtoms << "\n";
108 > #ifdef IS_MPI
109 >  if(worldRank == 0 ){
110 > #endif    
111 >    finalOut.open( entry_plug->finalName, ios::out | ios::trunc );
112 >    if( !finalOut ){
113 >      sprintf( painCave.errMsg,
114 >               "Could not open \"%s\" for final dump output.\n",
115 >               entry_plug->finalName );
116 >      painCave.isFatal = 1;
117 >      simError();
118 >    }
119 > #ifdef IS_MPI
120 >  }
121 > #endif // is_mpi
122  
123 <  outFile << currentTime << ";\t"
124 <          << entry_plug->Hmat[0][0] << "\t"
106 <          << entry_plug->Hmat[1][0] << "\t"
107 <          << entry_plug->Hmat[2][0] << ";\t"
123 >  fileStreams.push_back(&finalOut);
124 >  fileStreams.push_back(&dumpFile);
125  
126 <          << entry_plug->Hmat[0][1] << "\t"
110 <          << entry_plug->Hmat[1][1] << "\t"
111 <          << entry_plug->Hmat[2][1] << ";\t"
126 >  writeFrame(fileStreams, currentTime);
127  
128 <          << entry_plug->Hmat[0][2] << "\t"
129 <          << entry_plug->Hmat[1][2] << "\t"
130 <          << entry_plug->Hmat[2][2] << ";";
131 <  //write out additional parameters, such as chi and eta
132 <  outFile << entry_plug->the_integrator->getAdditionalParameters();
118 <  outFile << endl;
128 > #ifdef IS_MPI
129 >  finalOut.close();
130 > #endif
131 >        
132 > }
133  
134 <  for( i=0; i<nAtoms; i++ ){
134 > void DumpWriter::writeFinal(double currentTime){
135  
136 <    atoms[i]->getPos(pos);
137 <    atoms[i]->getVel(vel);
136 >  ofstream finalOut;
137 >  vector<ofstream*> fileStreams;
138  
139 <    sprintf( tempBuffer,
140 <             "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
141 <             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 );
139 > #ifdef IS_MPI
140 >  if(worldRank == 0 ){
141 > #endif // is_mpi
142  
143 <    if( atoms[i]->isDirectional() ){
143 >    finalOut.open( entry_plug->finalName, ios::out | ios::trunc );
144  
145 <      dAtom = (DirectionalAtom *)atoms[i];
146 <      dAtom->getQ( q );
147 <
148 <      sprintf( tempBuffer,
149 <               "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
150 <               q[0],
144 <               q[1],
145 <               q[2],
146 <               q[3],
147 <               dAtom->getJx(),
148 <               dAtom->getJy(),
149 <               dAtom->getJz());
150 <      strcat( writeLine, tempBuffer );
145 >    if( !finalOut ){
146 >      sprintf( painCave.errMsg,
147 >               "Could not open \"%s\" for final dump output.\n",
148 >               entry_plug->finalName );
149 >      painCave.isFatal = 1;
150 >      simError();
151      }
152 –    else
153 –      strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
152  
153 <    outFile << writeLine;
153 > #ifdef IS_MPI
154    }
155 <  outFile.flush();
155 > #endif // is_mpi
156 >  
157 >  fileStreams.push_back(&finalOut);  
158 >  writeFrame(fileStreams, currentTime);
159  
160 < #else // is_mpi
160 > #ifdef IS_MPI
161 >  finalOut.close();
162 > #endif
163 >  
164 > }
165  
166 <  // first thing first, suspend fatalities.
162 <  painCave.isEventLoop = 1;
166 > void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){
167  
168 <  int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
169 <  int haveError;
168 >  const int BUFFERSIZE = 2000;
169 >  const int MINIBUFFERSIZE = 100;
170  
171 <  MPI_Status istatus;
172 <  int *AtomToProcMap = mpiSim->getAtomToProcMap();
171 >  char tempBuffer[BUFFERSIZE];  
172 >  char writeLine[BUFFERSIZE];
173  
174 <  // write out header and node 0's coordinates
174 >  int i, k;
175  
176 <  if( worldRank == 0 ){
177 <    outFile << mpiSim->getTotAtoms() << "\n";
176 > #ifdef IS_MPI
177 >  
178 >  /*********************************************************************
179 >   * Documentation?  You want DOCUMENTATION?
180 >   *
181 >   * Why all the potatoes below?  
182 >   *
183 >   * To make a long story short, the original version of DumpWriter
184 >   * worked in the most inefficient way possible.  Node 0 would
185 >   * poke each of the node for an individual atom's formatted data
186 >   * as node 0 worked its way down the global index. This was particularly
187 >   * inefficient since the method blocked all processors at every atom
188 >   * (and did it twice!).
189 >   *
190 >   * An intermediate version of DumpWriter could be described from Node
191 >   * zero's perspective as follows:
192 >   *
193 >   *  1) Have 100 of your friends stand in a circle.
194 >   *  2) When you say go, have all of them start tossing potatoes at
195 >   *     you (one at a time).
196 >   *  3) Catch the potatoes.
197 >   *
198 >   * It was an improvement, but MPI has buffers and caches that could
199 >   * best be described in this analogy as "potato nets", so there's no
200 >   * need to block the processors atom-by-atom.
201 >   *
202 >   * This new and improved DumpWriter works in an even more efficient
203 >   * way:
204 >   *
205 >   *  1) Have 100 of your friend stand in a circle.
206 >   *  2) When you say go, have them start tossing 5-pound bags of
207 >   *     potatoes at you.
208 >   *  3) Once you've caught a friend's bag of potatoes,
209 >   *     toss them a spud to let them know they can toss another bag.
210 >   *
211 >   * How's THAT for documentation?
212 >   *
213 >   *********************************************************************/
214  
215 <    outFile << currentTime << ";\t"
216 <            << entry_plug->Hmat[0][0] << "\t"
177 <            << entry_plug->Hmat[1][0] << "\t"
178 <            << entry_plug->Hmat[2][0] << ";\t"
179 <
180 <            << entry_plug->Hmat[0][1] << "\t"
181 <            << entry_plug->Hmat[1][1] << "\t"
182 <            << entry_plug->Hmat[2][1] << ";\t"
183 <
184 <            << entry_plug->Hmat[0][2] << "\t"
185 <            << entry_plug->Hmat[1][2] << "\t"
186 <            << 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;
215 >  int *potatoes;
216 >  int myPotato;
217  
218 <      which_node = AtomToProcMap[i];
219 <
220 <      if (which_node != 0) {
221 <        
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 <        MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
209 <                 atomIsDirectionalTag, MPI_COMM_WORLD, &istatus);
210 <        
211 <        MPI_Recv(atomTransData, 6, MPI_DOUBLE, which_node,
212 <                 atomTransDataTag, MPI_COMM_WORLD, &istatus);
213 <
214 <        if (isDirectional) {
215 <
216 <          MPI_Recv(atomOrientData, 7, MPI_DOUBLE, which_node,
217 <                   atomOrientDataTag, MPI_COMM_WORLD, &istatus);
218 <
219 <        }
220 <
221 <      } else {
222 <        
223 <        haveError = 0;
224 <        which_atom = i;
225 <        local_index=-1;
226 <
227 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
228 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
229 <        }
230 <
231 <        if (local_index != -1) {
232 <
233 <          atomTypeString = atoms[local_index]->getType();
234 <
235 <          atoms[local_index]->getPos(pos);
236 <          atoms[local_index]->getVel(vel);
237 <
238 <          atomTransData[0] = pos[0];
239 <          atomTransData[1] = pos[1];
240 <          atomTransData[2] = pos[2];
241 <
242 <          atomTransData[3] = vel[0];
243 <          atomTransData[4] = vel[1];
244 <          atomTransData[5] = vel[2];
245 <          
246 <          isDirectional = 0;
247 <
248 <          if( atoms[local_index]->isDirectional() ){
249 <
250 <            isDirectional = 1;
251 <            
252 <            dAtom = (DirectionalAtom *)atoms[local_index];
253 <            dAtom->getQ( q );
254 <            
255 <            atomOrientData[0] = q[0];
256 <            atomOrientData[1] = q[1];
257 <            atomOrientData[2] = q[2];
258 <            atomOrientData[3] = q[3];
259 <
260 <            atomOrientData[4] = dAtom->getJx();
261 <            atomOrientData[5] = dAtom->getJy();
262 <            atomOrientData[6] = dAtom->getJz();
263 <          }
264 <
265 <        } else {
266 <          sprintf(painCave.errMsg,
267 <                  "Atom %d not found on processor %d\n",
268 <                  i, worldRank );
269 <          haveError= 1;
270 <          simError();
271 <        }
272 <
273 <        if(haveError) DieDieDie();
274 <                              
275 <        // If we've survived to here, format the line:
276 <        
277 <        sprintf( tempBuffer,
278 <                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
279 <                 atomTypeString,
280 <                 atomTransData[0],
281 <                 atomTransData[1],
282 <                 atomTransData[2],
283 <                 atomTransData[3],
284 <                 atomTransData[4],
285 <                 atomTransData[5]);
286 <
287 <        strcpy( writeLine, tempBuffer );
288 <
289 <        if (isDirectional) {
290 <
291 <          sprintf( tempBuffer,
292 <                   "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
293 <                   atomOrientData[0],
294 <                   atomOrientData[1],
295 <                   atomOrientData[2],
296 <                   atomOrientData[3],
297 <                   atomOrientData[4],
298 <                   atomOrientData[5],
299 <                   atomOrientData[6]);
300 <          strcat( writeLine, tempBuffer );
301 <
302 <        } else {
303 <          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
304 <        }
305 <
306 <        outFile << writeLine;
307 <        outFile.flush();
308 <      }
309 <    }
310 <
311 <    outFile.flush();
312 <    sprintf( checkPointMsg,
313 <             "Sucessfully took a dump.\n");
314 <    MPIcheckPoint();        
315 <    
316 <  } else {
317 <
318 <    // worldRank != 0, so I'm a remote node.  
319 <    
320 <    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
321 <      
322 <      // Am I the node which has this atom?
323 <      
324 <      if (AtomToProcMap[i] == worldRank) {
325 <
326 <        local_index=-1;
327 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
328 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
329 <        }
330 <        if (local_index != -1) {
331 <        
332 <          atomTypeString = atoms[local_index]->getType();
333 <
334 <          atoms[local_index]->getPos(pos);
335 <          atoms[local_index]->getVel(vel);
336 <
337 <          atomTransData[0] = pos[0];
338 <          atomTransData[1] = pos[1];
339 <          atomTransData[2] = pos[2];
340 <
341 <          atomTransData[3] = vel[0];
342 <          atomTransData[4] = vel[1];
343 <          atomTransData[5] = vel[2];
344 <          
345 <          isDirectional = 0;
346 <
347 <          if( atoms[local_index]->isDirectional() ){
348 <
349 <            isDirectional = 1;
350 <            
351 <            dAtom = (DirectionalAtom *)atoms[local_index];
352 <            dAtom->getQ( q );
353 <            
354 <            atomOrientData[0] = q[0];
355 <            atomOrientData[1] = q[1];
356 <            atomOrientData[2] = q[2];
357 <            atomOrientData[3] = q[3];
358 <
359 <            atomOrientData[4] = dAtom->getJx();
360 <            atomOrientData[5] = dAtom->getJy();
361 <            atomOrientData[6] = dAtom->getJz();
362 <          }
363 <
364 <        } else {
365 <          sprintf(painCave.errMsg,
366 <                  "Atom %d not found on processor %d\n",
367 <                  i, worldRank );
368 <          haveError= 1;
369 <          simError();
370 <        }
371 <
372 <        // I've survived this far, so send off the data!
373 <
374 <        atomTypeTag          = 4*i;
375 <        atomIsDirectionalTag = 4*i + 1;
376 <        atomTransDataTag     = 4*i + 2;
377 <        atomOrientDataTag    = 4*i + 3;
378 <
379 <
380 <        strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
381 <
382 <        MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
383 <                 atomTypeTag, MPI_COMM_WORLD);
384 <        
385 <        MPI_Send(&isDirectional, 1, MPI_INT, 0,
386 <                 atomIsDirectionalTag, MPI_COMM_WORLD);
387 <        
388 <        MPI_Send(atomTransData, 6, MPI_DOUBLE, 0,
389 <                 atomTransDataTag, MPI_COMM_WORLD);
390 <
391 <        if (isDirectional) {
392 <
393 <          MPI_Send(atomOrientData, 7, MPI_DOUBLE, 0,
394 <                   atomOrientDataTag, MPI_COMM_WORLD);
395 <          
396 <        }
397 <      
398 <      }
399 <    }
400 <
401 <    sprintf( checkPointMsg,
402 <             "Sucessfully took a dump.\n");
403 <    MPIcheckPoint();        
404 <    
405 <  }
406 <  
407 <  painCave.isEventLoop = 0;
408 <
409 < #endif // is_mpi
410 < }
411 <
412 < void DumpWriter::writeFinal(double finalTime){
413 <
414 <  char finalName[500];
415 <  ofstream finalOut;
416 <
417 <  const int BUFFERSIZE = 2000;
418 <  const int MINIBUFFERSIZE = 10;
419 <  char tempBuffer[BUFFERSIZE];
420 <  char writeLine[BUFFERSIZE];
421 <
422 <  double q[4];
423 <  DirectionalAtom* dAtom;
424 <  Atom** atoms = entry_plug->atoms;
425 <  int i;
426 < #ifdef IS_MPI
427 <  int j, which_node, done, which_atom, local_index;
428 <  double atomTransData[6];
429 <  double atomOrientData[7];
218 >  int nProc;
219 >  int j, which_node, done, which_atom, local_index, currentIndex;
220 >  double atomData6[6];
221 >  double atomData13[13];
222    int isDirectional;
223    char* atomTypeString;
224    char MPIatomTypeString[MINIBUFFERSIZE];
225 <  int atomTypeTag;
434 <  int atomIsDirectionalTag;
435 <  int atomTransDataTag;
436 <  int atomOrientDataTag;
225 >
226   #else //is_mpi
227    int nAtoms = entry_plug->n_atoms;
228   #endif //is_mpi
229  
230 +  double q[4], ji[3];
231 +  DirectionalAtom* dAtom;
232 +  Atom** atoms = entry_plug->atoms;
233    double pos[3], vel[3];
234  
443 – #ifdef IS_MPI
444 –  if(worldRank == 0 ){
445 – #endif // is_mpi
446 –
447 –    strcpy( finalName, entry_plug->finalName );
448 –
449 –    finalOut.open( finalName, ios::out | ios::trunc );
450 –    if( !finalOut ){
451 –      sprintf( painCave.errMsg,
452 –               "Could not open \"%s\" for final dump output.\n",
453 –               finalName );
454 –      painCave.isFatal = 1;
455 –      simError();
456 –    }
457 –
458 –    // finalOut.setf( ios::scientific );
459 –
460 – #ifdef IS_MPI
461 –  }
462 –
463 –  sprintf(checkPointMsg,"Opened file for final configuration\n");
464 –  MPIcheckPoint();
465 –
466 – #endif //is_mpi
467 –
468 –
235   #ifndef IS_MPI
236 +  
237 +  for(k = 0; k < outFile.size(); k++){
238 +    *outFile[k] << nAtoms << "\n";
239  
240 <  finalOut << nAtoms << "\n";
240 >    *outFile[k] << currentTime << ";\t"
241 >               << entry_plug->Hmat[0][0] << "\t"
242 >                     << entry_plug->Hmat[1][0] << "\t"
243 >                     << entry_plug->Hmat[2][0] << ";\t"
244 >              
245 >               << entry_plug->Hmat[0][1] << "\t"
246 >                     << entry_plug->Hmat[1][1] << "\t"
247 >                     << entry_plug->Hmat[2][1] << ";\t"
248  
249 <  finalOut << finalTime << ";\t"
250 <           << entry_plug->Hmat[0][0] << "\t"
251 <           << entry_plug->Hmat[1][0] << "\t"
476 <           << entry_plug->Hmat[2][0] << ";\t"
249 >                     << entry_plug->Hmat[0][2] << "\t"
250 >                     << entry_plug->Hmat[1][2] << "\t"
251 >                     << entry_plug->Hmat[2][2] << ";";
252  
253 <           << entry_plug->Hmat[0][1] << "\t"
254 <           << entry_plug->Hmat[1][1] << "\t"
255 <           << entry_plug->Hmat[2][1] << ";\t"
256 <
482 <           << entry_plug->Hmat[0][2] << "\t"
483 <           << entry_plug->Hmat[1][2] << "\t"
484 <           << entry_plug->Hmat[2][2] << ";";
485 <
486 <  //write out additional parameters, such as chi and eta
487 <  finalOut << entry_plug->the_integrator->getAdditionalParameters();
488 <  finalOut << endl;
489 <
253 >    //write out additional parameters, such as chi and eta
254 >    *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
255 >  }
256 >  
257    for( i=0; i<nAtoms; i++ ){
258  
259      atoms[i]->getPos(pos);
# Line 507 | Line 274 | void DumpWriter::writeFinal(double finalTime){
274  
275        dAtom = (DirectionalAtom *)atoms[i];
276        dAtom->getQ( q );
277 +      dAtom->getJ( ji );
278  
279        sprintf( tempBuffer,
280                 "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
# Line 514 | Line 282 | void DumpWriter::writeFinal(double finalTime){
282                 q[1],
283                 q[2],
284                 q[3],
285 <               dAtom->getJx(),
286 <               dAtom->getJy(),
287 <               dAtom->getJz());
285 >               ji[0],
286 >               ji[1],
287 >               ji[2]);
288        strcat( writeLine, tempBuffer );
289      }
290      else
291        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
292  
293 <    finalOut << writeLine;
293 >    for(k = 0; k < outFile.size(); k++)
294 >      *outFile[k] << writeLine;
295    }
527 –  finalOut.flush();
528 –  finalOut.close();
296  
297   #else // is_mpi
298  
299 <  // first thing first, suspend fatalities.
300 <  painCave.isEventLoop = 1;
299 >  /* code to find maximum tag value */
300 >  
301 >  int *tagub, flag, MAXTAG;
302 >  MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
303 >  if (flag) {
304 >    MAXTAG = *tagub;
305 >  } else {
306 >    MAXTAG = 32767;
307 >  }  
308  
535 –  int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
309    int haveError;
310  
311    MPI_Status istatus;
# Line 541 | Line 314 | void DumpWriter::writeFinal(double finalTime){
314    // write out header and node 0's coordinates
315  
316    if( worldRank == 0 ){
544 –    finalOut << mpiSim->getTotAtoms() << "\n";
317  
318 <    finalOut << finalTime << ";\t"
547 <            << entry_plug->Hmat[0][0] << "\t"
548 <            << entry_plug->Hmat[1][0] << "\t"
549 <            << entry_plug->Hmat[2][0] << ";\t"
318 >    // Node 0 needs a list of the magic potatoes for each processor;
319  
320 <            << entry_plug->Hmat[0][1] << "\t"
321 <            << entry_plug->Hmat[1][1] << "\t"
553 <            << entry_plug->Hmat[2][1] << ";\t"
320 >    nProc = mpiSim->getNumberProcessors();
321 >    potatoes = new int[nProc];
322  
323 <            << entry_plug->Hmat[0][2] << "\t"
324 <            << entry_plug->Hmat[1][2] << "\t"
325 <            << entry_plug->Hmat[2][2] << ";";
323 >    //write out the comment lines
324 >    for (i = 0; i < nProc; i++)
325 >      potatoes[i] = 0;
326 >    
327 >      for(k = 0; k < outFile.size(); k++){
328 >        *outFile[k] << mpiSim->getTotAtoms() << "\n";
329  
330 <    finalOut << entry_plug->the_integrator->getAdditionalParameters();
331 <    finalOut << endl;
332 <    finalOut.flush();
330 >        *outFile[k] << currentTime << ";\t"
331 >                         << entry_plug->Hmat[0][0] << "\t"
332 >                         << entry_plug->Hmat[1][0] << "\t"
333 >                         << entry_plug->Hmat[2][0] << ";\t"
334 >
335 >                         << entry_plug->Hmat[0][1] << "\t"
336 >                         << entry_plug->Hmat[1][1] << "\t"
337 >                         << entry_plug->Hmat[2][1] << ";\t"
338 >
339 >                         << entry_plug->Hmat[0][2] << "\t"
340 >                         << entry_plug->Hmat[1][2] << "\t"
341 >                         << entry_plug->Hmat[2][2] << ";";
342 >  
343 >        *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
344 >    }
345 >
346 >    currentIndex = 0;
347 >
348      for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
349 +      
350        // Get the Node number which has this atom;
351 <
351 >      
352        which_node = AtomToProcMap[i];
353 <
353 >      
354        if (which_node != 0) {
568 –        
569 –        atomTypeTag          = 4*i;
570 –        atomIsDirectionalTag = 4*i + 1;
571 –        atomTransDataTag     = 4*i + 2;
572 –        atomOrientDataTag    = 4*i + 3;
355  
356 +        if (potatoes[which_node] + 3 >= MAXTAG) {
357 +          // The potato was going to exceed the maximum value,
358 +          // so wrap this processor potato back to 0:        
359 +
360 +          potatoes[which_node] = 0;          
361 +          MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
362 +          
363 +        }
364 +
365 +        myPotato = potatoes[which_node];        
366 +        
367          MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
368 <                 atomTypeTag, MPI_COMM_WORLD, &istatus);
368 >                 myPotato, MPI_COMM_WORLD, &istatus);
369          
370 <        strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE);
370 >        atomTypeString = MPIatomTypeString;
371 >        
372 >        myPotato++;
373  
374          MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
375 <                 atomIsDirectionalTag, MPI_COMM_WORLD, &istatus);
376 <        
377 <        MPI_Recv(atomTransData, 6, MPI_DOUBLE, which_node,
583 <                 atomTransDataTag, MPI_COMM_WORLD, &istatus);
375 >                 myPotato, MPI_COMM_WORLD, &istatus);
376 >              
377 >        myPotato++;
378  
379 <        if (isDirectional) {
380 <
381 <          MPI_Recv(atomOrientData, 7, MPI_DOUBLE, which_node,
382 <                   atomOrientDataTag, MPI_COMM_WORLD, &istatus);
383 <
379 >        if (isDirectional) {          
380 >          MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node,
381 >                   myPotato, MPI_COMM_WORLD, &istatus);
382 >        } else {
383 >          MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node,
384 >                   myPotato, MPI_COMM_WORLD, &istatus);          
385          }
386 +        
387 +        myPotato++;
388 +        potatoes[which_node] = myPotato;
389  
390        } else {
391          
392 <        haveError = 0;
392 >        haveError = 0;
393          which_atom = i;
394 <        local_index=-1;
395 <
396 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
397 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
398 <        }
399 <
400 <        if (local_index != -1) {
603 <
604 <          atomTypeString = atoms[local_index]->getType();
605 <
394 >        
395 >          local_index = indexArray[currentIndex].first;        
396 >          
397 >          if (which_atom == indexArray[currentIndex].second) {
398 >            
399 >            atomTypeString = atoms[local_index]->getType();
400 >            
401            atoms[local_index]->getPos(pos);
402 <          atoms[local_index]->getVel(vel);
402 >          atoms[local_index]->getVel(vel);          
403 >          
404 >          atomData6[0] = pos[0];
405 >          atomData6[1] = pos[1];
406 >          atomData6[2] = pos[2];
407  
408 <          atomTransData[0] = pos[0];
409 <          atomTransData[1] = pos[1];
410 <          atomTransData[2] = pos[2];
612 <
613 <          atomTransData[3] = vel[0];
614 <          atomTransData[4] = vel[1];
615 <          atomTransData[5] = vel[2];
408 >          atomData6[3] = vel[0];
409 >          atomData6[4] = vel[1];
410 >          atomData6[5] = vel[2];
411            
412            isDirectional = 0;
413  
# Line 622 | Line 417 | void DumpWriter::writeFinal(double finalTime){
417              
418              dAtom = (DirectionalAtom *)atoms[local_index];
419              dAtom->getQ( q );
420 +            dAtom->getJ( ji );
421 +
422 +            for (int j = 0; j < 6 ; j++)
423 +              atomData13[j] = atomData6[j];            
424 +            
425 +            atomData13[6] = q[0];
426 +            atomData13[7] = q[1];
427 +            atomData13[8] = q[2];
428 +            atomData13[9] = q[3];
429              
430 <            atomOrientData[0] = q[0];
431 <            atomOrientData[1] = q[1];
432 <            atomOrientData[2] = q[2];
629 <            atomOrientData[3] = q[3];
630 <
631 <            atomOrientData[4] = dAtom->getJx();
632 <            atomOrientData[5] = dAtom->getJy();
633 <            atomOrientData[6] = dAtom->getJz();
430 >            atomData13[10] = ji[0];
431 >            atomData13[11] = ji[1];
432 >            atomData13[12] = ji[2];
433            }
434 <
434 >          
435          } else {
436            sprintf(painCave.errMsg,
437 <                  "Atom %d not found on processor %d\n",
438 <                  i, worldRank );
437 >                  "Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n",
438 >                  which_atom, worldRank, currentIndex, local_index );
439            haveError= 1;
440            simError();
441          }
643 –
644 –        if(haveError) DieDieDie();
645 –                              
646 –        // If we've survived to here, format the line:
442          
443 <        sprintf( tempBuffer,
444 <                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
445 <                 atomTypeString,
651 <                 atomTransData[0],
652 <                 atomTransData[1],
653 <                 atomTransData[2],
654 <                 atomTransData[3],
655 <                 atomTransData[4],
656 <                 atomTransData[5]);
657 <
658 <        strcpy( writeLine, tempBuffer );
659 <
660 <        if (isDirectional) {
661 <
662 <          sprintf( tempBuffer,
663 <                   "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
664 <                   atomOrientData[0],
665 <                   atomOrientData[1],
666 <                   atomOrientData[2],
667 <                   atomOrientData[3],
668 <                   atomOrientData[4],
669 <                   atomOrientData[5],
670 <                   atomOrientData[6]);
671 <          strcat( writeLine, tempBuffer );
672 <
673 <        } else {
674 <          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
675 <        }
676 <
677 <        finalOut << writeLine;
678 <        finalOut.flush();
443 >        if(haveError) DieDieDie();
444 >        
445 >        currentIndex++;
446        }
447 +      // If we've survived to here, format the line:
448 +      
449 +      if (!isDirectional) {
450 +        
451 +        sprintf( writeLine,
452 +                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
453 +                 atomTypeString,
454 +                 atomData6[0],
455 +                 atomData6[1],
456 +                 atomData6[2],
457 +                 atomData6[3],
458 +                 atomData6[4],
459 +                 atomData6[5]);
460 +        
461 +        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
462 +        
463 +      } else {
464 +        
465 +        sprintf( writeLine,
466 +                 "%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",
467 +                 atomTypeString,
468 +                 atomData13[0],
469 +                 atomData13[1],
470 +                 atomData13[2],
471 +                 atomData13[3],
472 +                 atomData13[4],
473 +                 atomData13[5],
474 +                 atomData13[6],
475 +                 atomData13[7],
476 +                 atomData13[8],
477 +                 atomData13[9],
478 +                 atomData13[10],
479 +                 atomData13[11],
480 +                 atomData13[12]);
481 +        
482 +      }
483 +      
484 +      for(k = 0; k < outFile.size(); k++)
485 +        *outFile[k] << writeLine;
486      }
487 <
488 <    finalOut.flush();
487 >    
488 >    for(k = 0; k < outFile.size(); k++)
489 >      outFile[k]->flush();
490 >    
491      sprintf( checkPointMsg,
492               "Sucessfully took a dump.\n");
493 +    
494      MPIcheckPoint();        
495      
496 +    delete[] potatoes;
497 +    
498    } else {
499  
500      // worldRank != 0, so I'm a remote node.  
501 +
502 +    // Set my magic potato to 0:
503 +
504 +    myPotato = 0;
505 +    currentIndex = 0;
506      
507      for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
508        
# Line 694 | Line 510 | void DumpWriter::writeFinal(double finalTime){
510        
511        if (AtomToProcMap[i] == worldRank) {
512  
513 <        local_index=-1;
514 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
515 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
513 >        if (myPotato + 3 >= MAXTAG) {
514 >          
515 >          // The potato was going to exceed the maximum value,
516 >          // so wrap this processor potato back to 0 (and block until
517 >          // node 0 says we can go:
518 >          
519 >          MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
520 >          
521          }
522 <        if (local_index != -1) {
522 >        which_atom = i;
523 >
524 >        local_index = indexArray[currentIndex].first;        
525 >                
526 >        if (which_atom == indexArray[currentIndex].second) {
527          
528            atomTypeString = atoms[local_index]->getType();
529 <
529 >          
530            atoms[local_index]->getPos(pos);
531            atoms[local_index]->getVel(vel);
532 +          
533 +          atomData6[0] = pos[0];
534 +          atomData6[1] = pos[1];
535 +          atomData6[2] = pos[2];
536  
537 <          atomTransData[0] = pos[0];
538 <          atomTransData[1] = pos[1];
539 <          atomTransData[2] = pos[2];
711 <
712 <          atomTransData[3] = vel[0];
713 <          atomTransData[4] = vel[1];
714 <          atomTransData[5] = vel[2];
537 >          atomData6[3] = vel[0];
538 >          atomData6[4] = vel[1];
539 >          atomData6[5] = vel[2];
540            
541            isDirectional = 0;
542  
# Line 721 | Line 546 | void DumpWriter::writeFinal(double finalTime){
546              
547              dAtom = (DirectionalAtom *)atoms[local_index];
548              dAtom->getQ( q );
549 +            dAtom->getJ( ji );
550              
551 <            atomOrientData[0] = q[0];
552 <            atomOrientData[1] = q[1];
553 <            atomOrientData[2] = q[2];
554 <            atomOrientData[3] = q[3];
555 <
556 <            atomOrientData[4] = dAtom->getJx();
557 <            atomOrientData[5] = dAtom->getJy();
558 <            atomOrientData[6] = dAtom->getJz();
551 >            for (int j = 0; j < 6 ; j++)
552 >              atomData13[j] = atomData6[j];
553 >            
554 >            atomData13[6] = q[0];
555 >            atomData13[7] = q[1];
556 >            atomData13[8] = q[2];
557 >            atomData13[9] = q[3];
558 >  
559 >            atomData13[10] = ji[0];
560 >            atomData13[11] = ji[1];
561 >            atomData13[12] = ji[2];
562            }
563  
564          } else {
565            sprintf(painCave.errMsg,
566 <                  "Atom %d not found on processor %d\n",
567 <                  i, worldRank );
566 >                  "Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n",
567 >                  which_atom, worldRank, currentIndex, local_index );
568            haveError= 1;
569            simError();
570          }
571 <
743 <        // I've survived this far, so send off the data!
744 <
745 <        atomTypeTag          = 4*i;
746 <        atomIsDirectionalTag = 4*i + 1;
747 <        atomTransDataTag     = 4*i + 2;
748 <        atomOrientDataTag    = 4*i + 3;
749 <
571 >        
572          strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
573  
574 +        // null terminate the string before sending (just in case):
575 +        MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
576 +
577          MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
578 <                 atomTypeTag, MPI_COMM_WORLD);
578 >                             myPotato, MPI_COMM_WORLD);
579          
580 +        myPotato++;
581 +
582          MPI_Send(&isDirectional, 1, MPI_INT, 0,
583 <                 atomIsDirectionalTag, MPI_COMM_WORLD);
583 >                             myPotato, MPI_COMM_WORLD);
584          
585 <        MPI_Send(atomTransData, 6, MPI_DOUBLE, 0,
586 <                 atomTransDataTag, MPI_COMM_WORLD);
760 <
585 >        myPotato++;
586 >        
587          if (isDirectional) {
588  
589 <          MPI_Send(atomOrientData, 7, MPI_DOUBLE, 0,
590 <                   atomOrientDataTag, MPI_COMM_WORLD);
589 >          MPI_Send(atomData13, 13, MPI_DOUBLE, 0,
590 >                   myPotato, MPI_COMM_WORLD);
591            
592 +        } else {
593 +
594 +          MPI_Send(atomData6, 6, MPI_DOUBLE, 0,
595 +                   myPotato, MPI_COMM_WORLD);
596          }
597 <      
597 >
598 >        myPotato++;  
599 >        currentIndex++;    
600        }
601      }
602  
603      sprintf( checkPointMsg,
604 <             "Sucessfully wrote final file.\n");
604 >             "Sucessfully took a dump.\n");
605      MPIcheckPoint();        
606      
607 <  }
607 >  }
608    
777 –  painCave.isEventLoop = 0;
778 –
779 –  if( worldRank == 0 ) finalOut.close();
609   #endif // is_mpi
610   }
611  
783 –
784 –
612   #ifdef IS_MPI
613  
614   // a couple of functions to let us escape the write loop

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