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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 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 –    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 +
100   #endif
101  
102   void DumpWriter::writeDump(double currentTime){
103  
104 +  ofstream finalOut;
105    vector<ofstream*> fileStreams;
106  
107   #ifdef IS_MPI
108    if(worldRank == 0 ){
109 <    finalOut.seekp(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  
# Line 123 | Line 123 | void DumpWriter::writeDump(double currentTime){
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    vector<ofstream*> fileStreams;
137  
138   #ifdef IS_MPI
139    if(worldRank == 0 ){
140 <    finalOut.seekp(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",
147 >               entry_plug->finalName );
148 >      painCave.isFatal = 1;
149 >      simError();
150 >    }
151 >
152 > #ifdef IS_MPI
153    }
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  
# Line 146 | Line 167 | void DumpWriter::writeFrame( vector<ofstream*>& outFil
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, 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 330 | Line 388 | void DumpWriter::writeFrame( vector<ofstream*>& outFil
388        } else {
389          
390          haveError = 0;
391 <              which_atom = i;
391 >        which_atom = i;
392          
393 <        local_index = indexArray[currentIndex].first;        
336 <                
337 <        if (which_atom == indexArray[currentIndex].second) {
393 >          local_index = indexArray[currentIndex].first;        
394            
395 <          atomTypeString = atoms[local_index]->getType();
396 <
397 <                atoms[local_index]->getPos(pos);
398 <                atoms[local_index]->getVel(vel);          
399 <
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 >          
402            atomData6[0] = pos[0];
403            atomData6[1] = pos[1];
404            atomData6[2] = pos[2];
# Line 372 | Line 430 | void DumpWriter::writeFrame( vector<ofstream*>& outFil
430            }
431            
432          } else {
433 <          sprintf(painCave.errMsg,
434 <                              "Atom %d not found on processor %d\n",
435 <                              i, worldRank );
436 <                haveError= 1;
437 <                simError();
438 <              }
433 >          sprintf(painCave.errMsg,
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();
441          
442 <        currentIndex ++;
442 >        currentIndex++;
443        }
444        // If we've survived to here, format the line:
445        
446        if (!isDirectional) {
447          
448          sprintf( writeLine,
449 <                             "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
450 <                             atomTypeString,
451 <                             atomData6[0],
452 <                             atomData6[1],
453 <                             atomData6[2],
454 <                             atomData6[3],
455 <                             atomData6[4],
456 <                             atomData6[5]);
399 <
400 <              strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
449 >                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
450 >                 atomTypeString,
451 >                 atomData6[0],
452 >                 atomData6[1],
453 >                 atomData6[2],
454 >                 atomData6[3],
455 >                 atomData6[4],
456 >                 atomData6[5]);
457          
458 +        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
459 +        
460        } else {
461          
462 <              sprintf( writeLine,
463 <                             "%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",
464 <                             atomTypeString,
465 <                             atomData13[0],
466 <                             atomData13[1],
467 <                             atomData13[2],
468 <                             atomData13[3],
469 <                             atomData13[4],
470 <                             atomData13[5],
471 <                             atomData13[6],
472 <                             atomData13[7],
473 <                             atomData13[8],
474 <                             atomData13[9],
475 <                             atomData13[10],
476 <                             atomData13[11],
477 <                             atomData13[12]);
462 >        sprintf( writeLine,
463 >                 "%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",
464 >                 atomTypeString,
465 >                 atomData13[0],
466 >                 atomData13[1],
467 >                 atomData13[2],
468 >                 atomData13[3],
469 >                 atomData13[4],
470 >                 atomData13[5],
471 >                 atomData13[6],
472 >                 atomData13[7],
473 >                 atomData13[8],
474 >                 atomData13[9],
475 >                 atomData13[10],
476 >                 atomData13[11],
477 >                 atomData13[12]);
478          
479        }
480        
# Line 429 | Line 487 | void DumpWriter::writeFrame( vector<ofstream*>& outFil
487      
488      sprintf( checkPointMsg,
489               "Sucessfully took a dump.\n");
490 <
490 >    
491      MPIcheckPoint();        
492 <
492 >    
493      delete[] potatoes;
494 <
494 >    
495    } else {
496  
497      // worldRank != 0, so I'm a remote node.  
# Line 450 | Line 508 | void DumpWriter::writeFrame( vector<ofstream*>& outFil
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 <
527 <                atoms[local_index]->getPos(pos);
528 <                atoms[local_index]->getVel(vel);
529 <
526 >          
527 >          atoms[local_index]->getPos(pos);
528 >          atoms[local_index]->getVel(vel);
529 >          
530            atomData6[0] = pos[0];
531            atomData6[1] = pos[1];
532            atomData6[2] = pos[2];
# Line 499 | Line 558 | void DumpWriter::writeFrame( vector<ofstream*>& outFil
558            }
559  
560          } else {
561 <                sprintf(painCave.errMsg,
562 <                              "Atom %d not found on processor %d\n",
563 <                              i, worldRank );
564 <                haveError= 1;
565 <                simError();
566 <              }
567 <
561 >          sprintf(painCave.errMsg,
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 >        
568          strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
569  
570          // null terminate the string before sending (just in case):

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