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root/group/trunk/OOPSE/libmdtools/DumpWriter.cpp
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Comparing trunk/OOPSE/libmdtools/DumpWriter.cpp (file contents):
Revision 934 by tim, Tue Jan 13 20:04:28 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 –    finalOut.open( entry_plug->finalName, ios::out | ios::trunc );
44 –    if( !finalOut ){
45 –      sprintf( painCave.errMsg,
46 –               "Could not open \"%s\" for final dump output.\n",
47 –               entry_plug->finalName );
48 –      painCave.isFatal = 1;
49 –      simError();
50 –    }
51 –
42   #ifdef IS_MPI
43    }
44  
# Line 68 | Line 58 | DumpWriter::~DumpWriter( ){
58   #endif // is_mpi
59  
60      dumpFile.close();
71 –    finalOut.close();
61  
62   #ifdef IS_MPI
63    }
# Line 102 | 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){
108  
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 <    finalOut.seekp(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  
# Line 123 | Line 129 | void DumpWriter::writeDump(double currentTime){
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    vector<ofstream*> fileStreams;
143  
144   #ifdef IS_MPI
145    if(worldRank == 0 ){
146 <    finalOut.seekp(0);
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",
152 >               entry_plug->finalName );
153 >      painCave.isFatal = 1;
154 >      simError();
155 >    }
156 >
157    }
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  
# Line 146 | Line 171 | void DumpWriter::writeFrame( vector<ofstream*>& outFil
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, 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 330 | Line 392 | void DumpWriter::writeFrame( vector<ofstream*>& outFil
392        } else {
393          
394          haveError = 0;
395 <              which_atom = i;
395 >        which_atom = i;
396          
397 <        local_index = indexArray[currentIndex].first;        
336 <                
337 <        if (which_atom == indexArray[currentIndex].second) {
338 <          
339 <          atomTypeString = atoms[local_index]->getType();
397 >        //local_index = -1;
398  
399 <                atoms[local_index]->getPos(pos);
400 <                atoms[local_index]->getVel(vel);          
401 <
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 >          
414            atomData6[0] = pos[0];
415            atomData6[1] = pos[1];
416            atomData6[2] = pos[2];
# Line 372 | Line 442 | void DumpWriter::writeFrame( vector<ofstream*>& outFil
442            }
443            
444          } else {
445 <          sprintf(painCave.errMsg,
446 <                              "Atom %d not found on processor %d\n",
447 <                              i, worldRank );
448 <                haveError= 1;
449 <                simError();
450 <              }
445 >          sprintf(painCave.errMsg,
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();
453          
454 <        currentIndex ++;
454 >        currentIndex++;
455        }
456        // If we've survived to here, format the line:
457        
458        if (!isDirectional) {
459          
460          sprintf( writeLine,
461 <                             "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
462 <                             atomTypeString,
463 <                             atomData6[0],
464 <                             atomData6[1],
465 <                             atomData6[2],
466 <                             atomData6[3],
467 <                             atomData6[4],
468 <                             atomData6[5]);
399 <
400 <              strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
461 >                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
462 >                 atomTypeString,
463 >                 atomData6[0],
464 >                 atomData6[1],
465 >                 atomData6[2],
466 >                 atomData6[3],
467 >                 atomData6[4],
468 >                 atomData6[5]);
469          
470 +        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
471 +        
472        } else {
473          
474 <              sprintf( writeLine,
475 <                             "%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",
476 <                             atomTypeString,
477 <                             atomData13[0],
478 <                             atomData13[1],
479 <                             atomData13[2],
480 <                             atomData13[3],
481 <                             atomData13[4],
482 <                             atomData13[5],
483 <                             atomData13[6],
484 <                             atomData13[7],
485 <                             atomData13[8],
486 <                             atomData13[9],
487 <                             atomData13[10],
488 <                             atomData13[11],
489 <                             atomData13[12]);
474 >        sprintf( writeLine,
475 >                 "%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",
476 >                 atomTypeString,
477 >                 atomData13[0],
478 >                 atomData13[1],
479 >                 atomData13[2],
480 >                 atomData13[3],
481 >                 atomData13[4],
482 >                 atomData13[5],
483 >                 atomData13[6],
484 >                 atomData13[7],
485 >                 atomData13[8],
486 >                 atomData13[9],
487 >                 atomData13[10],
488 >                 atomData13[11],
489 >                 atomData13[12]);
490          
491        }
492        
# Line 429 | Line 499 | void DumpWriter::writeFrame( vector<ofstream*>& outFil
499      
500      sprintf( checkPointMsg,
501               "Sucessfully took a dump.\n");
502 <
502 >    
503      MPIcheckPoint();        
504 <
504 >    
505      delete[] potatoes;
506 <
506 >    
507    } else {
508  
509      // worldRank != 0, so I'm a remote node.  
# Line 450 | Line 520 | void DumpWriter::writeFrame( vector<ofstream*>& outFil
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 <
547 <                atoms[local_index]->getPos(pos);
548 <                atoms[local_index]->getVel(vel);
549 <
546 >          
547 >          atoms[local_index]->getPos(pos);
548 >          atoms[local_index]->getVel(vel);
549 >          
550            atomData6[0] = pos[0];
551            atomData6[1] = pos[1];
552            atomData6[2] = pos[2];
# Line 499 | Line 578 | void DumpWriter::writeFrame( vector<ofstream*>& outFil
578            }
579  
580          } else {
581 <                sprintf(painCave.errMsg,
582 <                              "Atom %d not found on processor %d\n",
583 <                              i, worldRank );
584 <                haveError= 1;
585 <                simError();
586 <              }
587 <
581 >          sprintf(painCave.errMsg,
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 >        
588          strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
589  
590          // null terminate the string before sending (just in case):

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