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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 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 –    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    if(worldRank == 0 ){
114 <    finalOut.seekp(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  
# Line 123 | Line 128 | void DumpWriter::writeDump(double currentTime){
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    vector<ofstream*> fileStreams;
142  
143   #ifdef IS_MPI
144    if(worldRank == 0 ){
145 <    finalOut.seekp(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",
152 >               entry_plug->finalName );
153 >      painCave.isFatal = 1;
154 >      simError();
155 >    }
156 >
157 > #ifdef IS_MPI
158    }
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  
# Line 146 | Line 172 | void DumpWriter::writeFrame( vector<ofstream*>& outFil
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, 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 330 | Line 393 | void DumpWriter::writeFrame( vector<ofstream*>& outFil
393        } else {
394          
395          haveError = 0;
396 <              which_atom = i;
396 >        which_atom = i;
397          
398 <        local_index = indexArray[currentIndex].first;        
336 <                
337 <        if (which_atom == indexArray[currentIndex].second) {
338 <          
339 <          atomTypeString = atoms[local_index]->getType();
398 >        //local_index = -1;
399  
400 <                atoms[local_index]->getPos(pos);
401 <                atoms[local_index]->getVel(vel);          
402 <
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 >          
415            atomData6[0] = pos[0];
416            atomData6[1] = pos[1];
417            atomData6[2] = pos[2];
# Line 372 | Line 443 | void DumpWriter::writeFrame( vector<ofstream*>& outFil
443            }
444            
445          } else {
446 <          sprintf(painCave.errMsg,
447 <                              "Atom %d not found on processor %d\n",
448 <                              i, worldRank );
449 <                haveError= 1;
450 <                simError();
451 <              }
446 >          sprintf(painCave.errMsg,
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();
454          
455 <        currentIndex ++;
455 >        currentIndex++;
456        }
457        // If we've survived to here, format the line:
458        
459        if (!isDirectional) {
460          
461          sprintf( writeLine,
462 <                             "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
463 <                             atomTypeString,
464 <                             atomData6[0],
465 <                             atomData6[1],
466 <                             atomData6[2],
467 <                             atomData6[3],
468 <                             atomData6[4],
469 <                             atomData6[5]);
399 <
400 <              strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
462 >                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
463 >                 atomTypeString,
464 >                 atomData6[0],
465 >                 atomData6[1],
466 >                 atomData6[2],
467 >                 atomData6[3],
468 >                 atomData6[4],
469 >                 atomData6[5]);
470          
471 +        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
472 +        
473        } else {
474          
475 <              sprintf( writeLine,
476 <                             "%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",
477 <                             atomTypeString,
478 <                             atomData13[0],
479 <                             atomData13[1],
480 <                             atomData13[2],
481 <                             atomData13[3],
482 <                             atomData13[4],
483 <                             atomData13[5],
484 <                             atomData13[6],
485 <                             atomData13[7],
486 <                             atomData13[8],
487 <                             atomData13[9],
488 <                             atomData13[10],
489 <                             atomData13[11],
490 <                             atomData13[12]);
475 >        sprintf( writeLine,
476 >                 "%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",
477 >                 atomTypeString,
478 >                 atomData13[0],
479 >                 atomData13[1],
480 >                 atomData13[2],
481 >                 atomData13[3],
482 >                 atomData13[4],
483 >                 atomData13[5],
484 >                 atomData13[6],
485 >                 atomData13[7],
486 >                 atomData13[8],
487 >                 atomData13[9],
488 >                 atomData13[10],
489 >                 atomData13[11],
490 >                 atomData13[12]);
491          
492        }
493        
# Line 429 | Line 500 | void DumpWriter::writeFrame( vector<ofstream*>& outFil
500      
501      sprintf( checkPointMsg,
502               "Sucessfully took a dump.\n");
503 <
503 >    
504      MPIcheckPoint();        
505 <
505 >    
506      delete[] potatoes;
507 <
507 >    
508    } else {
509  
510      // worldRank != 0, so I'm a remote node.  
# Line 450 | Line 521 | void DumpWriter::writeFrame( vector<ofstream*>& outFil
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 <
548 <                atoms[local_index]->getPos(pos);
549 <                atoms[local_index]->getVel(vel);
550 <
547 >          
548 >          atoms[local_index]->getPos(pos);
549 >          atoms[local_index]->getVel(vel);
550 >          
551            atomData6[0] = pos[0];
552            atomData6[1] = pos[1];
553            atomData6[2] = pos[2];
# Line 499 | Line 579 | void DumpWriter::writeFrame( vector<ofstream*>& outFil
579            }
580  
581          } else {
582 <                sprintf(painCave.errMsg,
583 <                              "Atom %d not found on processor %d\n",
584 <                              i, worldRank );
585 <                haveError= 1;
586 <                simError();
587 <              }
588 <
582 >          sprintf(painCave.errMsg,
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 >        
589          strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
590  
591          // null terminate the string before sending (just in case):

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