ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/group/trunk/OOPSE/libmdtools/DumpWriter.cpp
(Generate patch)

Comparing trunk/OOPSE/libmdtools/DumpWriter.cpp (file contents):
Revision 929 by tim, Tue Jan 13 15:46:49 2004 UTC vs.
Revision 952 by tim, Fri Jan 16 21:55:39 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 >  if(worldRank == 0 ){
114 > #endif    
115 >    finalOut.open( entry_plug->finalName, ios::out | ios::trunc );
116 >    if( !finalOut ){
117 >      sprintf( painCave.errMsg,
118 >               "Could not open \"%s\" for final dump output.\n",
119 >               entry_plug->finalName );
120 >      painCave.isFatal = 1;
121 >      simError();
122 >    }
123 > #ifdef IS_MPI
124 >  }
125 > #endif // is_mpi
126 >
127 >  fileStreams.push_back(&finalOut);
128 >  fileStreams.push_back(&dumpFile);
129 >
130 >  writeFrame(fileStreams, currentTime);
131 >
132 > #ifdef IS_MPI
133 >  finalOut.close();
134 > #endif
135          
136   }
137  
138   void DumpWriter::writeFinal(double currentTime){
139  
140 <  ofstream finalOut;    
141 <  
142 <  //Open eor file
140 >  ofstream finalOut;
141 >  vector<ofstream*> fileStreams;
142 >
143   #ifdef IS_MPI
144    if(worldRank == 0 ){
145   #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 <    
156 >
157   #ifdef IS_MPI
158    }
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 –  }
159   #endif // is_mpi
160 +  
161 +  fileStreams.push_back(&finalOut);  
162 +  writeFrame(fileStreams, currentTime);
163  
164 + #ifdef IS_MPI
165 +  finalOut.close();
166 + #endif
167 +  
168   }
169  
170 < void DumpWriter::writeFrame( ofstream& outFile, double currentTime ){
170 > void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){
171  
172    const int BUFFERSIZE = 2000;
173    const int MINIBUFFERSIZE = 100;
174  
175 <  char tempBuffer[BUFFERSIZE];
175 >  char tempBuffer[BUFFERSIZE];  
176    char writeLine[BUFFERSIZE];
177  
178 <  int i;
178 >  int i, k;
179  
180   #ifdef IS_MPI
181    
182 +  /*********************************************************************
183 +   * Documentation?  You want DOCUMENTATION?
184 +   *
185 +   * Why all the potatoes below?  
186 +   *
187 +   * To make a long story short, the original version of DumpWriter
188 +   * worked in the most inefficient way possible.  Node 0 would
189 +   * poke each of the node for an individual atom's formatted data
190 +   * as node 0 worked its way down the global index. This was particularly
191 +   * inefficient since the method blocked all processors at every atom
192 +   * (and did it twice!).
193 +   *
194 +   * An intermediate version of DumpWriter could be described from Node
195 +   * zero's perspective as follows:
196 +   *
197 +   *  1) Have 100 of your friends stand in a circle.
198 +   *  2) When you say go, have all of them start tossing potatoes at
199 +   *     you (one at a time).
200 +   *  3) Catch the potatoes.
201 +   *
202 +   * It was an improvement, but MPI has buffers and caches that could
203 +   * best be described in this analogy as "potato nets", so there's no
204 +   * need to block the processors atom-by-atom.
205 +   *
206 +   * This new and improved DumpWriter works in an even more efficient
207 +   * way:
208 +   *
209 +   *  1) Have 100 of your friend stand in a circle.
210 +   *  2) When you say go, have them start tossing 5-pound bags of
211 +   *     potatoes at you.
212 +   *  3) Once you've caught a friend's bag of potatoes,
213 +   *     toss them a spud to let them know they can toss another bag.
214 +   *
215 +   * How's THAT for documentation?
216 +   *
217 +   *********************************************************************/
218 +
219    int *potatoes;
220    int myPotato;
221  
# Line 178 | Line 237 | void DumpWriter::writeFrame( ofstream& outFile, double
237    double pos[3], vel[3];
238  
239   #ifndef IS_MPI
240 +  
241 +  for(k = 0; k < outFile.size(); k++){
242 +    *outFile[k] << nAtoms << "\n";
243  
244 <  outFile << nAtoms << "\n";
244 >    *outFile[k] << currentTime << ";\t"
245 >               << entry_plug->Hmat[0][0] << "\t"
246 >                     << entry_plug->Hmat[1][0] << "\t"
247 >                     << entry_plug->Hmat[2][0] << ";\t"
248 >              
249 >               << entry_plug->Hmat[0][1] << "\t"
250 >                     << entry_plug->Hmat[1][1] << "\t"
251 >                     << entry_plug->Hmat[2][1] << ";\t"
252  
253 <  outFile << currentTime << ";\t"
254 <          << entry_plug->Hmat[0][0] << "\t"
255 <          << entry_plug->Hmat[1][0] << "\t"
187 <          << entry_plug->Hmat[2][0] << ";\t"
253 >                     << entry_plug->Hmat[0][2] << "\t"
254 >                     << entry_plug->Hmat[1][2] << "\t"
255 >                     << entry_plug->Hmat[2][2] << ";";
256  
257 <          << entry_plug->Hmat[0][1] << "\t"
258 <          << entry_plug->Hmat[1][1] << "\t"
259 <          << entry_plug->Hmat[2][1] << ";\t"
260 <
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 <
257 >    //write out additional parameters, such as chi and eta
258 >    *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
259 >  }
260 >  
261    for( i=0; i<nAtoms; i++ ){
262  
263      atoms[i]->getPos(pos);
# Line 232 | Line 293 | void DumpWriter::writeFrame( ofstream& outFile, double
293      else
294        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
295  
296 <    outFile << writeLine;
296 >    for(k = 0; k < outFile.size(); k++)
297 >      *outFile[k] << writeLine;
298    }
299  
300   #else // is_mpi
# Line 261 | Line 323 | void DumpWriter::writeFrame( ofstream& outFile, double
323      nProc = mpiSim->getNumberProcessors();
324      potatoes = new int[nProc];
325  
326 +    //write out the comment lines
327      for (i = 0; i < nProc; i++)
328        potatoes[i] = 0;
329      
330 <    outFile << mpiSim->getTotAtoms() << "\n";
330 >      for(k = 0; k < outFile.size(); k++){
331 >        *outFile[k] << mpiSim->getTotAtoms() << "\n";
332  
333 <    outFile << currentTime << ";\t"
334 <            << entry_plug->Hmat[0][0] << "\t"
335 <            << entry_plug->Hmat[1][0] << "\t"
336 <            << entry_plug->Hmat[2][0] << ";\t"
333 >        *outFile[k] << currentTime << ";\t"
334 >                         << entry_plug->Hmat[0][0] << "\t"
335 >                         << entry_plug->Hmat[1][0] << "\t"
336 >                         << entry_plug->Hmat[2][0] << ";\t"
337  
338 <            << entry_plug->Hmat[0][1] << "\t"
339 <            << entry_plug->Hmat[1][1] << "\t"
340 <            << entry_plug->Hmat[2][1] << ";\t"
338 >                         << entry_plug->Hmat[0][1] << "\t"
339 >                         << entry_plug->Hmat[1][1] << "\t"
340 >                         << entry_plug->Hmat[2][1] << ";\t"
341  
342 <            << entry_plug->Hmat[0][2] << "\t"
343 <            << entry_plug->Hmat[1][2] << "\t"
344 <            << entry_plug->Hmat[2][2] << ";";
342 >                         << entry_plug->Hmat[0][2] << "\t"
343 >                         << entry_plug->Hmat[1][2] << "\t"
344 >                         << entry_plug->Hmat[2][2] << ";";
345 >  
346 >        *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
347 >    }
348  
282 –    outFile << entry_plug->the_integrator->getAdditionalParameters();
283 –    outFile << endl;
284 –    outFile.flush();
285 –    
349      currentIndex = 0;
350 +
351      for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
352        
353        // Get the Node number which has this atom;
# Line 328 | Line 392 | void DumpWriter::writeFrame( ofstream& outFile, double
392  
393        } else {
394          
395 <        haveError = 0;
395 >        haveError = 0;
396          which_atom = i;
397          
398 <        local_index = indexArray[currentIndex].first;        
335 <                
336 <        if (which_atom == indexArray[currentIndex].second) {
337 <          
338 <          atomTypeString = atoms[local_index]->getType();
398 >        //local_index = -1;
399  
400 +        //for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
401 +        //  if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
402 +        //}
403 +        
404 +        //if (local_index != -1) {
405 +          
406 +          local_index = indexArray[currentIndex].first;        
407 +          
408 +          if (which_atom == indexArray[currentIndex].second) {
409 +            
410 +            atomTypeString = atoms[local_index]->getType();
411 +            
412            atoms[local_index]->getPos(pos);
413            atoms[local_index]->getVel(vel);          
414 <
414 >          
415            atomData6[0] = pos[0];
416            atomData6[1] = pos[1];
417            atomData6[2] = pos[2];
# Line 372 | Line 444 | void DumpWriter::writeFrame( ofstream& outFile, double
444            
445          } else {
446            sprintf(painCave.errMsg,
447 <                  "Atom %d not found on processor %d\n",
448 <                  i, worldRank );
447 >                  "Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n",
448 >                  which_atom, worldRank, currentIndex, local_index );
449            haveError= 1;
450            simError();
451          }
452          
453 <        if(haveError) DieDieDie();
453 >        if(haveError) DieDieDie();
454          
455 <        currentIndex ++;
455 >        currentIndex++;
456        }
457        // If we've survived to here, format the line:
458        
459        if (!isDirectional) {
460          
461 <        sprintf( writeLine,
461 >        sprintf( writeLine,
462                   "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
463                   atomTypeString,
464                   atomData6[0],
# Line 395 | Line 467 | void DumpWriter::writeFrame( ofstream& outFile, double
467                   atomData6[3],
468                   atomData6[4],
469                   atomData6[5]);
470 <
470 >        
471          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
472          
473        } else {
# Line 419 | Line 491 | void DumpWriter::writeFrame( ofstream& outFile, double
491          
492        }
493        
494 <      outFile << writeLine;
494 >      for(k = 0; k < outFile.size(); k++)
495 >        *outFile[k] << writeLine;
496      }
497      
498 <
499 <    outFile.flush();
498 >    for(k = 0; k < outFile.size(); k++)
499 >      outFile[k]->flush();
500 >    
501      sprintf( checkPointMsg,
502               "Sucessfully took a dump.\n");
503 +    
504      MPIcheckPoint();        
505 +    
506      delete[] potatoes;
507 +    
508    } else {
509  
510      // worldRank != 0, so I'm a remote node.  
# Line 444 | Line 521 | void DumpWriter::writeFrame( ofstream& outFile, double
521        if (AtomToProcMap[i] == worldRank) {
522  
523          if (myPotato + 3 >= MAXTAG) {
524 <
524 >          
525            // The potato was going to exceed the maximum value,
526            // so wrap this processor potato back to 0 (and block until
527            // node 0 says we can go:
528 <
528 >          
529            MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
530            
531          }
532          which_atom = i;
533 <        local_index = indexArray[currentIndex].first;        
533 >
534 >        //local_index = -1;
535 >
536 >        //for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
537 >        // if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
538 >        //}
539 >        
540 >        //if (local_index != -1) {
541 >
542 >        local_index = indexArray[currentIndex].first;        
543                  
544 <        if (which_atom == indexArray[currentIndex].second) {
544 >        if (which_atom == indexArray[currentIndex].second) {
545          
546            atomTypeString = atoms[local_index]->getType();
547 <
547 >          
548            atoms[local_index]->getPos(pos);
549            atoms[local_index]->getVel(vel);
550 <
550 >          
551            atomData6[0] = pos[0];
552            atomData6[1] = pos[1];
553            atomData6[2] = pos[2];
# Line 486 | Line 572 | void DumpWriter::writeFrame( ofstream& outFile, double
572              atomData13[7] = q[1];
573              atomData13[8] = q[2];
574              atomData13[9] = q[3];
575 <
575 >  
576              atomData13[10] = dAtom->getJx();
577              atomData13[11] = dAtom->getJy();
578              atomData13[12] = dAtom->getJz();
# Line 494 | Line 580 | void DumpWriter::writeFrame( ofstream& outFile, double
580  
581          } else {
582            sprintf(painCave.errMsg,
583 <                  "Atom %d not found on processor %d\n",
584 <                  i, worldRank );
583 >                  "Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n",
584 >                  which_atom, worldRank, currentIndex, local_index );
585            haveError= 1;
586            simError();
587          }
588 <
588 >        
589          strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
590  
591          // null terminate the string before sending (just in case):
592          MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
593  
594          MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
595 <                 myPotato, MPI_COMM_WORLD);
595 >                             myPotato, MPI_COMM_WORLD);
596          
597          myPotato++;
598  
599          MPI_Send(&isDirectional, 1, MPI_INT, 0,
600 <                 myPotato, MPI_COMM_WORLD);
600 >                             myPotato, MPI_COMM_WORLD);
601          
602          myPotato++;
603          

Diff Legend

– Removed lines
+ Added lines
< Changed lines
> Changed lines