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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 949 by chuckv, Thu Jan 15 21:57:10 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 ){
121 – #endif // is_mpi
146  
147      finalOut.open( entry_plug->finalName, ios::out | ios::trunc );
148 +
149      if( !finalOut ){
150        sprintf( painCave.errMsg,
151                 "Could not open \"%s\" for final dump output.\n",
# Line 128 | Line 153 | void DumpWriter::writeFinal(double currentTime){
153        painCave.isFatal = 1;
154        simError();
155      }
156 <    
132 < #ifdef IS_MPI
156 >
157    }
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 –  }
158   #endif // is_mpi
159 +  
160 +  fileStreams.push_back(&finalOut);  
161 +  writeFrame(fileStreams, currentTime);
162  
163 + #ifdef IS_MPI
164 +  finalOut.close();
165 + #endif
166 +  
167   }
168  
169 < void DumpWriter::writeFrame( ofstream& outFile, double currentTime ){
169 > void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){
170  
171    const int BUFFERSIZE = 2000;
172    const int MINIBUFFERSIZE = 100;
173  
174 <  char tempBuffer[BUFFERSIZE];
174 >  char tempBuffer[BUFFERSIZE];  
175    char writeLine[BUFFERSIZE];
176  
177 <  int i;
177 >  int i, k;
178  
179   #ifdef IS_MPI
180    
181 +  /*********************************************************************
182 +   * Documentation?  You want DOCUMENTATION?
183 +   *
184 +   * Why all the potatoes below?  
185 +   *
186 +   * To make a long story short, the original version of DumpWriter
187 +   * worked in the most inefficient way possible.  Node 0 would
188 +   * poke each of the node for an individual atom's formatted data
189 +   * as node 0 worked its way down the global index. This was particularly
190 +   * inefficient since the method blocked all processors at every atom
191 +   * (and did it twice!).
192 +   *
193 +   * An intermediate version of DumpWriter could be described from Node
194 +   * zero's perspective as follows:
195 +   *
196 +   *  1) Have 100 of your friends stand in a circle.
197 +   *  2) When you say go, have all of them start tossing potatoes at
198 +   *     you (one at a time).
199 +   *  3) Catch the potatoes.
200 +   *
201 +   * It was an improvement, but MPI has buffers and caches that could
202 +   * best be described in this analogy as "potato nets", so there's no
203 +   * need to block the processors atom-by-atom.
204 +   *
205 +   * This new and improved DumpWriter works in an even more efficient
206 +   * way:
207 +   *
208 +   *  1) Have 100 of your friend stand in a circle.
209 +   *  2) When you say go, have them start tossing 5-pound bags of
210 +   *     potatoes at you.
211 +   *  3) Once you've caught a friend's bag of potatoes,
212 +   *     toss them a spud to let them know they can toss another bag.
213 +   *
214 +   * How's THAT for documentation?
215 +   *
216 +   *********************************************************************/
217 +
218    int *potatoes;
219    int myPotato;
220  
# Line 178 | Line 236 | void DumpWriter::writeFrame( ofstream& outFile, double
236    double pos[3], vel[3];
237  
238   #ifndef IS_MPI
239 +  
240 +  for(k = 0; k < outFile.size(); k++){
241 +    *outFile[k] << nAtoms << "\n";
242  
243 <  outFile << nAtoms << "\n";
243 >    *outFile[k] << currentTime << ";\t"
244 >               << entry_plug->Hmat[0][0] << "\t"
245 >                     << entry_plug->Hmat[1][0] << "\t"
246 >                     << entry_plug->Hmat[2][0] << ";\t"
247 >              
248 >               << entry_plug->Hmat[0][1] << "\t"
249 >                     << entry_plug->Hmat[1][1] << "\t"
250 >                     << entry_plug->Hmat[2][1] << ";\t"
251  
252 <  outFile << currentTime << ";\t"
253 <          << entry_plug->Hmat[0][0] << "\t"
254 <          << entry_plug->Hmat[1][0] << "\t"
187 <          << entry_plug->Hmat[2][0] << ";\t"
252 >                     << entry_plug->Hmat[0][2] << "\t"
253 >                     << entry_plug->Hmat[1][2] << "\t"
254 >                     << entry_plug->Hmat[2][2] << ";";
255  
256 <          << entry_plug->Hmat[0][1] << "\t"
257 <          << entry_plug->Hmat[1][1] << "\t"
258 <          << entry_plug->Hmat[2][1] << ";\t"
259 <
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 <
256 >    //write out additional parameters, such as chi and eta
257 >    *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
258 >  }
259 >  
260    for( i=0; i<nAtoms; i++ ){
261  
262      atoms[i]->getPos(pos);
# Line 232 | Line 292 | void DumpWriter::writeFrame( ofstream& outFile, double
292      else
293        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
294  
295 <    outFile << writeLine;
295 >    for(k = 0; k < outFile.size(); k++)
296 >      *outFile[k] << writeLine;
297    }
298  
299   #else // is_mpi
# Line 261 | Line 322 | void DumpWriter::writeFrame( ofstream& outFile, double
322      nProc = mpiSim->getNumberProcessors();
323      potatoes = new int[nProc];
324  
325 +    //write out the comment lines
326      for (i = 0; i < nProc; i++)
327        potatoes[i] = 0;
328      
329 <    outFile << mpiSim->getTotAtoms() << "\n";
329 >      for(k = 0; k < outFile.size(); k++){
330 >        *outFile[k] << mpiSim->getTotAtoms() << "\n";
331  
332 <    outFile << currentTime << ";\t"
333 <            << entry_plug->Hmat[0][0] << "\t"
334 <            << entry_plug->Hmat[1][0] << "\t"
335 <            << entry_plug->Hmat[2][0] << ";\t"
332 >        *outFile[k] << currentTime << ";\t"
333 >                         << entry_plug->Hmat[0][0] << "\t"
334 >                         << entry_plug->Hmat[1][0] << "\t"
335 >                         << entry_plug->Hmat[2][0] << ";\t"
336  
337 <            << entry_plug->Hmat[0][1] << "\t"
338 <            << entry_plug->Hmat[1][1] << "\t"
339 <            << entry_plug->Hmat[2][1] << ";\t"
337 >                         << entry_plug->Hmat[0][1] << "\t"
338 >                         << entry_plug->Hmat[1][1] << "\t"
339 >                         << entry_plug->Hmat[2][1] << ";\t"
340  
341 <            << entry_plug->Hmat[0][2] << "\t"
342 <            << entry_plug->Hmat[1][2] << "\t"
343 <            << entry_plug->Hmat[2][2] << ";";
341 >                         << entry_plug->Hmat[0][2] << "\t"
342 >                         << entry_plug->Hmat[1][2] << "\t"
343 >                         << entry_plug->Hmat[2][2] << ";";
344 >  
345 >        *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
346 >    }
347  
282 –    outFile << entry_plug->the_integrator->getAdditionalParameters();
283 –    outFile << endl;
284 –    outFile.flush();
285 –    
348      currentIndex = 0;
349 +
350      for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
351        
352        // Get the Node number which has this atom;
# Line 328 | Line 391 | void DumpWriter::writeFrame( ofstream& outFile, double
391  
392        } else {
393          
394 <        haveError = 0;
394 >        haveError = 0;
395          which_atom = i;
396          
397 <        local_index = indexArray[currentIndex].first;        
335 <                
336 <        if (which_atom == indexArray[currentIndex].second) {
337 <          
338 <          atomTypeString = atoms[local_index]->getType();
397 >        //local_index = -1;
398  
399 +        //for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
400 +        //  if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
401 +        //}
402 +        
403 +        //if (local_index != -1) {
404 +          
405 +          local_index = indexArray[currentIndex].first;        
406 +          
407 +          if (which_atom == indexArray[currentIndex].second) {
408 +            
409 +            atomTypeString = atoms[local_index]->getType();
410 +            
411            atoms[local_index]->getPos(pos);
412            atoms[local_index]->getVel(vel);          
413 <
413 >          
414            atomData6[0] = pos[0];
415            atomData6[1] = pos[1];
416            atomData6[2] = pos[2];
# Line 372 | Line 443 | void DumpWriter::writeFrame( ofstream& outFile, double
443            
444          } else {
445            sprintf(painCave.errMsg,
446 <                  "Atom %d not found on processor %d\n",
447 <                  i, worldRank );
446 >                  "Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n",
447 >                  which_atom, worldRank, currentIndex, local_index );
448            haveError= 1;
449            simError();
450          }
451          
452 <        if(haveError) DieDieDie();
452 >        if(haveError) DieDieDie();
453          
454 <        currentIndex ++;
454 >        currentIndex++;
455        }
456        // If we've survived to here, format the line:
457        
458        if (!isDirectional) {
459          
460 <        sprintf( writeLine,
460 >        sprintf( writeLine,
461                   "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
462                   atomTypeString,
463                   atomData6[0],
# Line 395 | Line 466 | void DumpWriter::writeFrame( ofstream& outFile, double
466                   atomData6[3],
467                   atomData6[4],
468                   atomData6[5]);
469 <
469 >        
470          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
471          
472        } else {
# Line 419 | Line 490 | void DumpWriter::writeFrame( ofstream& outFile, double
490          
491        }
492        
493 <      outFile << writeLine;
493 >      for(k = 0; k < outFile.size(); k++)
494 >        *outFile[k] << writeLine;
495      }
496      
497 <
498 <    outFile.flush();
497 >    for(k = 0; k < outFile.size(); k++)
498 >      outFile[k]->flush();
499 >    
500      sprintf( checkPointMsg,
501               "Sucessfully took a dump.\n");
502 +    
503      MPIcheckPoint();        
504 +    
505      delete[] potatoes;
506 +    
507    } else {
508  
509      // worldRank != 0, so I'm a remote node.  
# Line 444 | Line 520 | void DumpWriter::writeFrame( ofstream& outFile, double
520        if (AtomToProcMap[i] == worldRank) {
521  
522          if (myPotato + 3 >= MAXTAG) {
523 <
523 >          
524            // The potato was going to exceed the maximum value,
525            // so wrap this processor potato back to 0 (and block until
526            // node 0 says we can go:
527 <
527 >          
528            MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
529            
530          }
531          which_atom = i;
532 <        local_index = indexArray[currentIndex].first;        
532 >
533 >        //local_index = -1;
534 >
535 >        //for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
536 >        // if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
537 >        //}
538 >        
539 >        //if (local_index != -1) {
540 >
541 >        local_index = indexArray[currentIndex].first;        
542                  
543 <        if (which_atom == indexArray[currentIndex].second) {
543 >        if (which_atom == indexArray[currentIndex].second) {
544          
545            atomTypeString = atoms[local_index]->getType();
546 <
546 >          
547            atoms[local_index]->getPos(pos);
548            atoms[local_index]->getVel(vel);
549 <
549 >          
550            atomData6[0] = pos[0];
551            atomData6[1] = pos[1];
552            atomData6[2] = pos[2];
# Line 486 | Line 571 | void DumpWriter::writeFrame( ofstream& outFile, double
571              atomData13[7] = q[1];
572              atomData13[8] = q[2];
573              atomData13[9] = q[3];
574 <
574 >  
575              atomData13[10] = dAtom->getJx();
576              atomData13[11] = dAtom->getJy();
577              atomData13[12] = dAtom->getJz();
# Line 494 | Line 579 | void DumpWriter::writeFrame( ofstream& outFile, double
579  
580          } else {
581            sprintf(painCave.errMsg,
582 <                  "Atom %d not found on processor %d\n",
583 <                  i, worldRank );
582 >                  "Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n",
583 >                  which_atom, worldRank, currentIndex, local_index );
584            haveError= 1;
585            simError();
586          }
587 <
587 >        
588          strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
589  
590          // null terminate the string before sending (just in case):
591          MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
592  
593          MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
594 <                 myPotato, MPI_COMM_WORLD);
594 >                             myPotato, MPI_COMM_WORLD);
595          
596          myPotato++;
597  
598          MPI_Send(&isDirectional, 1, MPI_INT, 0,
599 <                 myPotato, MPI_COMM_WORLD);
599 >                             myPotato, MPI_COMM_WORLD);
600          
601          myPotato++;
602          

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