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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 1000 by tim, Fri Jan 30 21:47:22 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 +
100   #endif
101  
102   void DumpWriter::writeDump(double currentTime){
105 –  
106 – // write to eor file
107 –  writeFinal(currentTime);
103  
104 < //write to dump file
105 <  writeFrame(dumpFile, currentTime);
104 >  ofstream finalOut;
105 >  vector<ofstream*> fileStreams;
106 >
107 > #ifdef IS_MPI
108 >  if(worldRank == 0 ){
109 > #endif    
110 >    finalOut.open( entry_plug->finalName, ios::out | ios::trunc );
111 >    if( !finalOut ){
112 >      sprintf( painCave.errMsg,
113 >               "Could not open \"%s\" for final dump output.\n",
114 >               entry_plug->finalName );
115 >      painCave.isFatal = 1;
116 >      simError();
117 >    }
118 > #ifdef IS_MPI
119 >  }
120 > #endif // is_mpi
121 >
122 >  fileStreams.push_back(&finalOut);
123 >  fileStreams.push_back(&dumpFile);
124 >
125 >  writeFrame(fileStreams, currentTime);
126 >
127 > #ifdef IS_MPI
128 >  finalOut.close();
129 > #endif
130          
131   }
132  
133   void DumpWriter::writeFinal(double currentTime){
134  
135 <  ofstream finalOut;    
136 <  
137 <  //Open eor file
135 >  ofstream finalOut;
136 >  vector<ofstream*> fileStreams;
137 >
138   #ifdef IS_MPI
139    if(worldRank == 0 ){
140   #endif // is_mpi
141  
142      finalOut.open( entry_plug->finalName, ios::out | ios::trunc );
143 +
144      if( !finalOut ){
145        sprintf( painCave.errMsg,
146                 "Could not open \"%s\" for final dump output.\n",
# Line 128 | Line 148 | void DumpWriter::writeFinal(double currentTime){
148        painCave.isFatal = 1;
149        simError();
150      }
151 <    
151 >
152   #ifdef IS_MPI
153    }
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 –  }
154   #endif // is_mpi
155 +  
156 +  fileStreams.push_back(&finalOut);  
157 +  writeFrame(fileStreams, currentTime);
158  
159 + #ifdef IS_MPI
160 +  finalOut.close();
161 + #endif
162 +  
163   }
164  
165 < void DumpWriter::writeFrame( ofstream& outFile, double currentTime ){
165 > void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){
166  
167    const int BUFFERSIZE = 2000;
168    const int MINIBUFFERSIZE = 100;
169  
170 <  char tempBuffer[BUFFERSIZE];
170 >  char tempBuffer[BUFFERSIZE];  
171    char writeLine[BUFFERSIZE];
172  
173 <  int i;
173 >  int i, k;
174  
175   #ifdef IS_MPI
176    
177 +  /*********************************************************************
178 +   * Documentation?  You want DOCUMENTATION?
179 +   *
180 +   * Why all the potatoes below?  
181 +   *
182 +   * To make a long story short, the original version of DumpWriter
183 +   * worked in the most inefficient way possible.  Node 0 would
184 +   * poke each of the node for an individual atom's formatted data
185 +   * as node 0 worked its way down the global index. This was particularly
186 +   * inefficient since the method blocked all processors at every atom
187 +   * (and did it twice!).
188 +   *
189 +   * An intermediate version of DumpWriter could be described from Node
190 +   * zero's perspective as follows:
191 +   *
192 +   *  1) Have 100 of your friends stand in a circle.
193 +   *  2) When you say go, have all of them start tossing potatoes at
194 +   *     you (one at a time).
195 +   *  3) Catch the potatoes.
196 +   *
197 +   * It was an improvement, but MPI has buffers and caches that could
198 +   * best be described in this analogy as "potato nets", so there's no
199 +   * need to block the processors atom-by-atom.
200 +   *
201 +   * This new and improved DumpWriter works in an even more efficient
202 +   * way:
203 +   *
204 +   *  1) Have 100 of your friend stand in a circle.
205 +   *  2) When you say go, have them start tossing 5-pound bags of
206 +   *     potatoes at you.
207 +   *  3) Once you've caught a friend's bag of potatoes,
208 +   *     toss them a spud to let them know they can toss another bag.
209 +   *
210 +   * How's THAT for documentation?
211 +   *
212 +   *********************************************************************/
213 +
214    int *potatoes;
215    int myPotato;
216  
# Line 178 | Line 232 | void DumpWriter::writeFrame( ofstream& outFile, double
232    double pos[3], vel[3];
233  
234   #ifndef IS_MPI
235 +  
236 +  for(k = 0; k < outFile.size(); k++){
237 +    *outFile[k] << nAtoms << "\n";
238  
239 <  outFile << nAtoms << "\n";
239 >    *outFile[k] << currentTime << ";\t"
240 >               << entry_plug->Hmat[0][0] << "\t"
241 >                     << entry_plug->Hmat[1][0] << "\t"
242 >                     << entry_plug->Hmat[2][0] << ";\t"
243 >              
244 >               << entry_plug->Hmat[0][1] << "\t"
245 >                     << entry_plug->Hmat[1][1] << "\t"
246 >                     << entry_plug->Hmat[2][1] << ";\t"
247  
248 <  outFile << currentTime << ";\t"
249 <          << entry_plug->Hmat[0][0] << "\t"
250 <          << entry_plug->Hmat[1][0] << "\t"
187 <          << entry_plug->Hmat[2][0] << ";\t"
188 <
189 <          << entry_plug->Hmat[0][1] << "\t"
190 <          << entry_plug->Hmat[1][1] << "\t"
191 <          << entry_plug->Hmat[2][1] << ";\t"
248 >                     << entry_plug->Hmat[0][2] << "\t"
249 >                     << entry_plug->Hmat[1][2] << "\t"
250 >                     << entry_plug->Hmat[2][2] << ";";
251  
252 <          << entry_plug->Hmat[0][2] << "\t"
253 <          << entry_plug->Hmat[1][2] << "\t"
254 <          << entry_plug->Hmat[2][2] << ";";
255 <  //write out additional parameters, such as chi and eta
197 <  outFile << entry_plug->the_integrator->getAdditionalParameters();
198 <  outFile << endl;
199 <
252 >    //write out additional parameters, such as chi and eta
253 >    *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
254 >  }
255 >  
256    for( i=0; i<nAtoms; i++ ){
257  
258      atoms[i]->getPos(pos);
# Line 232 | Line 288 | void DumpWriter::writeFrame( ofstream& outFile, double
288      else
289        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
290  
291 <    outFile << writeLine;
291 >    for(k = 0; k < outFile.size(); k++)
292 >      *outFile[k] << writeLine;
293    }
294  
295   #else // is_mpi
# Line 261 | Line 318 | void DumpWriter::writeFrame( ofstream& outFile, double
318      nProc = mpiSim->getNumberProcessors();
319      potatoes = new int[nProc];
320  
321 +    //write out the comment lines
322      for (i = 0; i < nProc; i++)
323        potatoes[i] = 0;
324      
325 <    outFile << mpiSim->getTotAtoms() << "\n";
325 >      for(k = 0; k < outFile.size(); k++){
326 >        *outFile[k] << mpiSim->getTotAtoms() << "\n";
327  
328 <    outFile << currentTime << ";\t"
329 <            << entry_plug->Hmat[0][0] << "\t"
330 <            << entry_plug->Hmat[1][0] << "\t"
331 <            << entry_plug->Hmat[2][0] << ";\t"
328 >        *outFile[k] << currentTime << ";\t"
329 >                         << entry_plug->Hmat[0][0] << "\t"
330 >                         << entry_plug->Hmat[1][0] << "\t"
331 >                         << entry_plug->Hmat[2][0] << ";\t"
332  
333 <            << entry_plug->Hmat[0][1] << "\t"
334 <            << entry_plug->Hmat[1][1] << "\t"
335 <            << entry_plug->Hmat[2][1] << ";\t"
333 >                         << entry_plug->Hmat[0][1] << "\t"
334 >                         << entry_plug->Hmat[1][1] << "\t"
335 >                         << entry_plug->Hmat[2][1] << ";\t"
336  
337 <            << entry_plug->Hmat[0][2] << "\t"
338 <            << entry_plug->Hmat[1][2] << "\t"
339 <            << entry_plug->Hmat[2][2] << ";";
337 >                         << entry_plug->Hmat[0][2] << "\t"
338 >                         << entry_plug->Hmat[1][2] << "\t"
339 >                         << entry_plug->Hmat[2][2] << ";";
340 >  
341 >        *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
342 >    }
343  
282 –    outFile << entry_plug->the_integrator->getAdditionalParameters();
283 –    outFile << endl;
284 –    outFile.flush();
285 –    
344      currentIndex = 0;
345 +
346      for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
347        
348        // Get the Node number which has this atom;
# Line 328 | Line 387 | void DumpWriter::writeFrame( ofstream& outFile, double
387  
388        } else {
389          
390 <        haveError = 0;
390 >        haveError = 0;
391          which_atom = i;
392          
393 <        local_index = indexArray[currentIndex].first;        
335 <                
336 <        if (which_atom == indexArray[currentIndex].second) {
393 >          local_index = indexArray[currentIndex].first;        
394            
395 <          atomTypeString = atoms[local_index]->getType();
396 <
395 >          if (which_atom == indexArray[currentIndex].second) {
396 >            
397 >            atomTypeString = atoms[local_index]->getType();
398 >            
399            atoms[local_index]->getPos(pos);
400            atoms[local_index]->getVel(vel);          
401 <
401 >          
402            atomData6[0] = pos[0];
403            atomData6[1] = pos[1];
404            atomData6[2] = pos[2];
# Line 372 | Line 431 | void DumpWriter::writeFrame( ofstream& outFile, double
431            
432          } else {
433            sprintf(painCave.errMsg,
434 <                  "Atom %d not found on processor %d\n",
435 <                  i, worldRank );
434 >                  "Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n",
435 >                  which_atom, worldRank, currentIndex, local_index );
436            haveError= 1;
437            simError();
438          }
439          
440 <        if(haveError) DieDieDie();
440 >        if(haveError) DieDieDie();
441          
442 <        currentIndex ++;
442 >        currentIndex++;
443        }
444        // If we've survived to here, format the line:
445        
446        if (!isDirectional) {
447          
448 <        sprintf( writeLine,
448 >        sprintf( writeLine,
449                   "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
450                   atomTypeString,
451                   atomData6[0],
# Line 395 | Line 454 | void DumpWriter::writeFrame( ofstream& outFile, double
454                   atomData6[3],
455                   atomData6[4],
456                   atomData6[5]);
457 <
457 >        
458          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
459          
460        } else {
# Line 419 | Line 478 | void DumpWriter::writeFrame( ofstream& outFile, double
478          
479        }
480        
481 <      outFile << writeLine;
481 >      for(k = 0; k < outFile.size(); k++)
482 >        *outFile[k] << writeLine;
483      }
484      
485 <
486 <    outFile.flush();
485 >    for(k = 0; k < outFile.size(); k++)
486 >      outFile[k]->flush();
487 >    
488      sprintf( checkPointMsg,
489               "Sucessfully took a dump.\n");
490 +    
491      MPIcheckPoint();        
492 +    
493      delete[] potatoes;
494 +    
495    } else {
496  
497      // worldRank != 0, so I'm a remote node.  
# Line 444 | Line 508 | void DumpWriter::writeFrame( ofstream& outFile, double
508        if (AtomToProcMap[i] == worldRank) {
509  
510          if (myPotato + 3 >= MAXTAG) {
511 <
511 >          
512            // The potato was going to exceed the maximum value,
513            // so wrap this processor potato back to 0 (and block until
514            // node 0 says we can go:
515 <
515 >          
516            MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
517            
518          }
519          which_atom = i;
520 <        local_index = indexArray[currentIndex].first;        
520 >
521 >        local_index = indexArray[currentIndex].first;        
522                  
523 <        if (which_atom == indexArray[currentIndex].second) {
523 >        if (which_atom == indexArray[currentIndex].second) {
524          
525            atomTypeString = atoms[local_index]->getType();
526 <
526 >          
527            atoms[local_index]->getPos(pos);
528            atoms[local_index]->getVel(vel);
529 <
529 >          
530            atomData6[0] = pos[0];
531            atomData6[1] = pos[1];
532            atomData6[2] = pos[2];
# Line 486 | Line 551 | void DumpWriter::writeFrame( ofstream& outFile, double
551              atomData13[7] = q[1];
552              atomData13[8] = q[2];
553              atomData13[9] = q[3];
554 <
554 >  
555              atomData13[10] = dAtom->getJx();
556              atomData13[11] = dAtom->getJy();
557              atomData13[12] = dAtom->getJz();
# Line 494 | Line 559 | void DumpWriter::writeFrame( ofstream& outFile, double
559  
560          } else {
561            sprintf(painCave.errMsg,
562 <                  "Atom %d not found on processor %d\n",
563 <                  i, worldRank );
562 >                  "Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n",
563 >                  which_atom, worldRank, currentIndex, local_index );
564            haveError= 1;
565            simError();
566          }
567 <
567 >        
568          strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
569  
570          // null terminate the string before sending (just in case):
571          MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
572  
573          MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
574 <                 myPotato, MPI_COMM_WORLD);
574 >                             myPotato, MPI_COMM_WORLD);
575          
576          myPotato++;
577  
578          MPI_Send(&isDirectional, 1, MPI_INT, 0,
579 <                 myPotato, MPI_COMM_WORLD);
579 >                             myPotato, MPI_COMM_WORLD);
580          
581          myPotato++;
582          

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