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root/group/trunk/OOPSE/libmdtools/DumpWriter.cpp
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Comparing trunk/OOPSE/libmdtools/DumpWriter.cpp (file contents):
Revision 936 by tim, Tue Jan 13 20:35:25 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 92 | 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){
# Line 105 | Line 110 | void DumpWriter::writeDump(double currentTime){
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 );
# Line 136 | Line 143 | void DumpWriter::writeFinal(double currentTime){
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  
# Line 147 | Line 155 | void DumpWriter::writeFinal(double currentTime){
155        simError();
156      }
157  
158 + #ifdef IS_MPI
159    }
160   #endif // is_mpi
161    
# Line 171 | Line 180 | void DumpWriter::writeFrame( vector<ofstream*>& outFil
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 348 | Line 394 | void DumpWriter::writeFrame( vector<ofstream*>& outFil
394        } else {
395          
396          haveError = 0;
397 <              which_atom = i;
397 >        which_atom = i;
398          
399 <        local_index = indexArray[currentIndex].first;        
354 <                
355 <        if (which_atom == indexArray[currentIndex].second) {
356 <          
357 <          atomTypeString = atoms[local_index]->getType();
399 >        //local_index = -1;
400  
401 <                atoms[local_index]->getPos(pos);
402 <                atoms[local_index]->getVel(vel);          
403 <
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 >          
416            atomData6[0] = pos[0];
417            atomData6[1] = pos[1];
418            atomData6[2] = pos[2];
# Line 390 | Line 444 | void DumpWriter::writeFrame( vector<ofstream*>& outFil
444            }
445            
446          } else {
447 <          sprintf(painCave.errMsg,
448 <                              "Atom %d not found on processor %d\n",
449 <                              i, worldRank );
450 <                haveError= 1;
451 <                simError();
452 <              }
447 >          sprintf(painCave.errMsg,
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();
455          
456 <        currentIndex ++;
456 >        currentIndex++;
457        }
458        // If we've survived to here, format the line:
459        
460        if (!isDirectional) {
461          
462          sprintf( writeLine,
463 <                             "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
464 <                             atomTypeString,
465 <                             atomData6[0],
466 <                             atomData6[1],
467 <                             atomData6[2],
468 <                             atomData6[3],
469 <                             atomData6[4],
470 <                             atomData6[5]);
417 <
418 <              strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
463 >                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
464 >                 atomTypeString,
465 >                 atomData6[0],
466 >                 atomData6[1],
467 >                 atomData6[2],
468 >                 atomData6[3],
469 >                 atomData6[4],
470 >                 atomData6[5]);
471          
472 +        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
473 +        
474        } else {
475          
476 <              sprintf( writeLine,
477 <                             "%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",
478 <                             atomTypeString,
479 <                             atomData13[0],
480 <                             atomData13[1],
481 <                             atomData13[2],
482 <                             atomData13[3],
483 <                             atomData13[4],
484 <                             atomData13[5],
485 <                             atomData13[6],
486 <                             atomData13[7],
487 <                             atomData13[8],
488 <                             atomData13[9],
489 <                             atomData13[10],
490 <                             atomData13[11],
491 <                             atomData13[12]);
476 >        sprintf( writeLine,
477 >                 "%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",
478 >                 atomTypeString,
479 >                 atomData13[0],
480 >                 atomData13[1],
481 >                 atomData13[2],
482 >                 atomData13[3],
483 >                 atomData13[4],
484 >                 atomData13[5],
485 >                 atomData13[6],
486 >                 atomData13[7],
487 >                 atomData13[8],
488 >                 atomData13[9],
489 >                 atomData13[10],
490 >                 atomData13[11],
491 >                 atomData13[12]);
492          
493        }
494        
# Line 447 | Line 501 | void DumpWriter::writeFrame( vector<ofstream*>& outFil
501      
502      sprintf( checkPointMsg,
503               "Sucessfully took a dump.\n");
504 <
504 >    
505      MPIcheckPoint();        
506 <
506 >    
507      delete[] potatoes;
508 <
508 >    
509    } else {
510  
511      // worldRank != 0, so I'm a remote node.  
# Line 468 | Line 522 | void DumpWriter::writeFrame( vector<ofstream*>& outFil
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 <
549 <                atoms[local_index]->getPos(pos);
550 <                atoms[local_index]->getVel(vel);
551 <
548 >          
549 >          atoms[local_index]->getPos(pos);
550 >          atoms[local_index]->getVel(vel);
551 >          
552            atomData6[0] = pos[0];
553            atomData6[1] = pos[1];
554            atomData6[2] = pos[2];
# Line 517 | Line 580 | void DumpWriter::writeFrame( vector<ofstream*>& outFil
580            }
581  
582          } else {
583 <                sprintf(painCave.errMsg,
584 <                              "Atom %d not found on processor %d\n",
585 <                              i, worldRank );
586 <                haveError= 1;
587 <                simError();
588 <              }
589 <
583 >          sprintf(painCave.errMsg,
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 >        
590          strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
591  
592          // null terminate the string before sending (just in case):

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