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root/group/trunk/OOPSE/libmdtools/DumpWriter.cpp
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Comparing trunk/OOPSE/libmdtools/DumpWriter.cpp (file contents):
Revision 929 by tim, Tue Jan 13 15:46:49 2004 UTC vs.
Revision 951 by mmeineke, Fri Jan 16 21:51:51 2004 UTC

# Line 28 | Line 28 | DumpWriter::DumpWriter( SimInfo* the_entry_plug ){
28    if(worldRank == 0 ){
29   #endif // is_mpi
30  
31 –
31      dumpFile.open(entry_plug->sampleName, ios::out | ios::trunc );
32  
33      if( !dumpFile ){
# Line 40 | Line 39 | DumpWriter::DumpWriter( SimInfo* the_entry_plug ){
39        simError();
40      }
41  
43 –    //outFile.setf( ios::scientific );
44 –
42   #ifdef IS_MPI
43    }
44  
# Line 94 | Line 91 | void DumpWriter::sortByGlobalIndex(){
91    
92    indexArray.clear();
93    
94 <  for(int i = 0; i < mpiSim->getMyNlocal();i++)
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 +  //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   #endif
106  
107   void DumpWriter::writeDump(double currentTime){
105 –  
106 – // write to eor file
107 –  writeFinal(currentTime);
108  
109 < //write to dump file
110 <  writeFrame(dumpFile, currentTime);
109 >  ofstream finalOut;
110 >  vector<ofstream*> fileStreams;
111 >
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 >    }
125 >  }
126 > #endif // is_mpi
127 >
128 >  fileStreams.push_back(&finalOut);
129 >  fileStreams.push_back(&dumpFile);
130 >
131 >  writeFrame(fileStreams, currentTime);
132 >
133 > #ifdef IS_MPI
134 >  finalOut.close();
135 > #endif
136          
137   }
138  
139   void DumpWriter::writeFinal(double currentTime){
140  
141 <  ofstream finalOut;    
142 <  
143 <  //Open eor file
141 >  ofstream finalOut;
142 >  vector<ofstream*> fileStreams;
143 >
144   #ifdef IS_MPI
145    if(worldRank == 0 ){
146   #endif // is_mpi
147  
148      finalOut.open( entry_plug->finalName, ios::out | ios::trunc );
149 +
150      if( !finalOut ){
151        sprintf( painCave.errMsg,
152                 "Could not open \"%s\" for final dump output.\n",
# Line 128 | Line 154 | void DumpWriter::writeFinal(double currentTime){
154        painCave.isFatal = 1;
155        simError();
156      }
157 <    
157 >
158   #ifdef IS_MPI
159    }
134 – #endif
135 –  
136 –  //write to eor file  
137 –  writeFrame(finalOut, currentTime);
138 –  
139 –  //close eor file      
140 – #ifdef IS_MPI
141 –  if(worldRank == 0 ){
142 –    finalOut.close();
143 –  }
160   #endif // is_mpi
161 +  
162 +  fileStreams.push_back(&finalOut);  
163 +  writeFrame(fileStreams, currentTime);
164  
165 + #ifdef IS_MPI
166 +  finalOut.close();
167 + #endif
168 +  
169   }
170  
171 < void DumpWriter::writeFrame( ofstream& outFile, double currentTime ){
171 > void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){
172  
173    const int BUFFERSIZE = 2000;
174    const int MINIBUFFERSIZE = 100;
175  
176 <  char tempBuffer[BUFFERSIZE];
176 >  char tempBuffer[BUFFERSIZE];  
177    char writeLine[BUFFERSIZE];
178  
179 <  int i;
179 >  int i, k;
180  
181   #ifdef IS_MPI
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  
# Line 178 | Line 238 | void DumpWriter::writeFrame( ofstream& outFile, double
238    double pos[3], vel[3];
239  
240   #ifndef IS_MPI
241 +  
242 +  for(k = 0; k < outFile.size(); k++){
243 +    *outFile[k] << nAtoms << "\n";
244  
245 <  outFile << 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 <  outFile << currentTime << ";\t"
255 <          << entry_plug->Hmat[0][0] << "\t"
256 <          << entry_plug->Hmat[1][0] << "\t"
187 <          << 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 <
193 <          << entry_plug->Hmat[0][2] << "\t"
194 <          << entry_plug->Hmat[1][2] << "\t"
195 <          << entry_plug->Hmat[2][2] << ";";
196 <  //write out additional parameters, such as chi and eta
197 <  outFile << entry_plug->the_integrator->getAdditionalParameters();
198 <  outFile << endl;
199 <
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 232 | Line 294 | void DumpWriter::writeFrame( ofstream& outFile, double
294      else
295        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
296  
297 <    outFile << writeLine;
297 >    for(k = 0; k < outFile.size(); k++)
298 >      *outFile[k] << writeLine;
299    }
300  
301   #else // is_mpi
# Line 261 | Line 324 | void DumpWriter::writeFrame( ofstream& outFile, double
324      nProc = mpiSim->getNumberProcessors();
325      potatoes = new int[nProc];
326  
327 +    //write out the comment lines
328      for (i = 0; i < nProc; i++)
329        potatoes[i] = 0;
330      
331 <    outFile << mpiSim->getTotAtoms() << "\n";
331 >      for(k = 0; k < outFile.size(); k++){
332 >        *outFile[k] << mpiSim->getTotAtoms() << "\n";
333  
334 <    outFile << currentTime << ";\t"
335 <            << entry_plug->Hmat[0][0] << "\t"
336 <            << entry_plug->Hmat[1][0] << "\t"
337 <            << entry_plug->Hmat[2][0] << ";\t"
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"
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] << ";";
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  
282 –    outFile << entry_plug->the_integrator->getAdditionalParameters();
283 –    outFile << endl;
284 –    outFile.flush();
285 –    
350      currentIndex = 0;
351 +
352      for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
353        
354        // Get the Node number which has this atom;
# Line 328 | Line 393 | void DumpWriter::writeFrame( ofstream& outFile, double
393  
394        } else {
395          
396 <        haveError = 0;
396 >        haveError = 0;
397          which_atom = i;
398          
399 <        local_index = indexArray[currentIndex].first;        
335 <                
336 <        if (which_atom == indexArray[currentIndex].second) {
337 <          
338 <          atomTypeString = atoms[local_index]->getType();
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 +          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);          
415 <
415 >          
416            atomData6[0] = pos[0];
417            atomData6[1] = pos[1];
418            atomData6[2] = pos[2];
# Line 372 | Line 445 | void DumpWriter::writeFrame( ofstream& outFile, double
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          }
453          
454 <        if(haveError) DieDieDie();
454 >        if(haveError) DieDieDie();
455          
456 <        currentIndex ++;
456 >        currentIndex++;
457        }
458        // If we've survived to here, format the line:
459        
460        if (!isDirectional) {
461          
462 <        sprintf( writeLine,
462 >        sprintf( writeLine,
463                   "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
464                   atomTypeString,
465                   atomData6[0],
# Line 395 | Line 468 | void DumpWriter::writeFrame( ofstream& outFile, double
468                   atomData6[3],
469                   atomData6[4],
470                   atomData6[5]);
471 <
471 >        
472          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
473          
474        } else {
# Line 419 | Line 492 | void DumpWriter::writeFrame( ofstream& outFile, double
492          
493        }
494        
495 <      outFile << writeLine;
495 >      for(k = 0; k < outFile.size(); k++)
496 >        *outFile[k] << writeLine;
497      }
498      
499 <
500 <    outFile.flush();
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.  
# Line 444 | Line 522 | void DumpWriter::writeFrame( ofstream& outFile, double
522        if (AtomToProcMap[i] == worldRank) {
523  
524          if (myPotato + 3 >= MAXTAG) {
525 <
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 <
529 >          
530            MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
531            
532          }
533          which_atom = i;
534 <        local_index = indexArray[currentIndex].first;        
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) {
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 <
551 >          
552            atomData6[0] = pos[0];
553            atomData6[1] = pos[1];
554            atomData6[2] = pos[2];
# Line 486 | Line 573 | void DumpWriter::writeFrame( ofstream& outFile, double
573              atomData13[7] = q[1];
574              atomData13[8] = q[2];
575              atomData13[9] = q[3];
576 <
576 >  
577              atomData13[10] = dAtom->getJx();
578              atomData13[11] = dAtom->getJy();
579              atomData13[12] = dAtom->getJz();
# Line 494 | Line 581 | void DumpWriter::writeFrame( ofstream& outFile, double
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 <
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 <                 myPotato, MPI_COMM_WORLD);
596 >                             myPotato, MPI_COMM_WORLD);
597          
598          myPotato++;
599  
600          MPI_Send(&isDirectional, 1, MPI_INT, 0,
601 <                 myPotato, MPI_COMM_WORLD);
601 >                             myPotato, MPI_COMM_WORLD);
602          
603          myPotato++;
604          

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