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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 1078 by tim, Tue Mar 2 20:32:40 2004 UTC

# Line 1 | Line 1
1 + #define _LARGEFILE_SOURCE64
2   #define _FILE_OFFSET_BITS 64
3  
4   #include <string.h>
# Line 28 | Line 29 | DumpWriter::DumpWriter( SimInfo* the_entry_plug ){
29    if(worldRank == 0 ){
30   #endif // is_mpi
31  
31 –
32      dumpFile.open(entry_plug->sampleName, ios::out | ios::trunc );
33  
34      if( !dumpFile ){
# Line 40 | Line 40 | DumpWriter::DumpWriter( SimInfo* the_entry_plug ){
40        simError();
41      }
42  
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 –
43   #ifdef IS_MPI
44    }
45  
# Line 68 | Line 59 | DumpWriter::~DumpWriter( ){
59   #endif // is_mpi
60  
61      dumpFile.close();
71 –    finalOut.close();
62  
63   #ifdef IS_MPI
64    }
# Line 102 | Line 92 | void DumpWriter::sortByGlobalIndex(){
92    
93    indexArray.clear();
94    
95 <  for(int i = 0; i < mpiSim->getMyNlocal();i++)
95 >  for(int i = 0; i < mpiSim->getMyNlocal();i++)
96      indexArray.push_back(make_pair(i, atoms[i]->getGlobalIndex()));
97    
98    sort(indexArray.begin(), indexArray.end(), indexSortingCriterion);    
99   }
100 +
101   #endif
102  
103   void DumpWriter::writeDump(double currentTime){
104  
105 +  ofstream finalOut;
106    vector<ofstream*> fileStreams;
107  
108   #ifdef IS_MPI
109    if(worldRank == 0 ){
110 <    finalOut.seekp(0);
110 > #endif    
111 >    finalOut.open( entry_plug->finalName, ios::out | ios::trunc );
112 >    if( !finalOut ){
113 >      sprintf( painCave.errMsg,
114 >               "Could not open \"%s\" for final dump output.\n",
115 >               entry_plug->finalName );
116 >      painCave.isFatal = 1;
117 >      simError();
118 >    }
119 > #ifdef IS_MPI
120    }
121   #endif // is_mpi
122  
# Line 123 | Line 124 | void DumpWriter::writeDump(double currentTime){
124    fileStreams.push_back(&dumpFile);
125  
126    writeFrame(fileStreams, currentTime);
127 +
128 + #ifdef IS_MPI
129 +  finalOut.close();
130 + #endif
131          
132   }
133  
134   void DumpWriter::writeFinal(double currentTime){
135  
136 +  ofstream finalOut;
137    vector<ofstream*> fileStreams;
138  
139   #ifdef IS_MPI
140    if(worldRank == 0 ){
141 <    finalOut.seekp(0);
141 > #endif // is_mpi
142 >
143 >    finalOut.open( entry_plug->finalName, ios::out | ios::trunc );
144 >
145 >    if( !finalOut ){
146 >      sprintf( painCave.errMsg,
147 >               "Could not open \"%s\" for final dump output.\n",
148 >               entry_plug->finalName );
149 >      painCave.isFatal = 1;
150 >      simError();
151 >    }
152 >
153 > #ifdef IS_MPI
154    }
155   #endif // is_mpi
156    
157    fileStreams.push_back(&finalOut);  
158    writeFrame(fileStreams, currentTime);
159 +
160 + #ifdef IS_MPI
161 +  finalOut.close();
162 + #endif
163    
164   }
165  
# Line 146 | Line 168 | void DumpWriter::writeFrame( vector<ofstream*>& outFil
168    const int BUFFERSIZE = 2000;
169    const int MINIBUFFERSIZE = 100;
170  
171 <  char tempBuffer[BUFFERSIZE];
171 >  char tempBuffer[BUFFERSIZE];  
172    char writeLine[BUFFERSIZE];
173  
174    int i, k;
175  
176   #ifdef IS_MPI
177    
178 +  /*********************************************************************
179 +   * Documentation?  You want DOCUMENTATION?
180 +   *
181 +   * Why all the potatoes below?  
182 +   *
183 +   * To make a long story short, the original version of DumpWriter
184 +   * worked in the most inefficient way possible.  Node 0 would
185 +   * poke each of the node for an individual atom's formatted data
186 +   * as node 0 worked its way down the global index. This was particularly
187 +   * inefficient since the method blocked all processors at every atom
188 +   * (and did it twice!).
189 +   *
190 +   * An intermediate version of DumpWriter could be described from Node
191 +   * zero's perspective as follows:
192 +   *
193 +   *  1) Have 100 of your friends stand in a circle.
194 +   *  2) When you say go, have all of them start tossing potatoes at
195 +   *     you (one at a time).
196 +   *  3) Catch the potatoes.
197 +   *
198 +   * It was an improvement, but MPI has buffers and caches that could
199 +   * best be described in this analogy as "potato nets", so there's no
200 +   * need to block the processors atom-by-atom.
201 +   *
202 +   * This new and improved DumpWriter works in an even more efficient
203 +   * way:
204 +   *
205 +   *  1) Have 100 of your friend stand in a circle.
206 +   *  2) When you say go, have them start tossing 5-pound bags of
207 +   *     potatoes at you.
208 +   *  3) Once you've caught a friend's bag of potatoes,
209 +   *     toss them a spud to let them know they can toss another bag.
210 +   *
211 +   * How's THAT for documentation?
212 +   *
213 +   *********************************************************************/
214 +
215    int *potatoes;
216    int myPotato;
217  
# Line 330 | Line 389 | void DumpWriter::writeFrame( vector<ofstream*>& outFil
389        } else {
390          
391          haveError = 0;
392 <              which_atom = i;
392 >        which_atom = i;
393          
394 <        local_index = indexArray[currentIndex].first;        
336 <                
337 <        if (which_atom == indexArray[currentIndex].second) {
394 >          local_index = indexArray[currentIndex].first;        
395            
396 <          atomTypeString = atoms[local_index]->getType();
397 <
398 <                atoms[local_index]->getPos(pos);
399 <                atoms[local_index]->getVel(vel);          
400 <
396 >          if (which_atom == indexArray[currentIndex].second) {
397 >            
398 >            atomTypeString = atoms[local_index]->getType();
399 >            
400 >          atoms[local_index]->getPos(pos);
401 >          atoms[local_index]->getVel(vel);          
402 >          
403            atomData6[0] = pos[0];
404            atomData6[1] = pos[1];
405            atomData6[2] = pos[2];
# Line 372 | Line 431 | void DumpWriter::writeFrame( vector<ofstream*>& outFil
431            }
432            
433          } else {
434 <          sprintf(painCave.errMsg,
435 <                              "Atom %d not found on processor %d\n",
436 <                              i, worldRank );
437 <                haveError= 1;
438 <                simError();
439 <              }
434 >          sprintf(painCave.errMsg,
435 >                  "Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n",
436 >                  which_atom, worldRank, currentIndex, local_index );
437 >          haveError= 1;
438 >          simError();
439 >        }
440          
441          if(haveError) DieDieDie();
442          
443 <        currentIndex ++;
443 >        currentIndex++;
444        }
445        // If we've survived to here, format the line:
446        
447        if (!isDirectional) {
448          
449          sprintf( writeLine,
450 <                             "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
451 <                             atomTypeString,
452 <                             atomData6[0],
453 <                             atomData6[1],
454 <                             atomData6[2],
455 <                             atomData6[3],
456 <                             atomData6[4],
457 <                             atomData6[5]);
399 <
400 <              strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
450 >                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
451 >                 atomTypeString,
452 >                 atomData6[0],
453 >                 atomData6[1],
454 >                 atomData6[2],
455 >                 atomData6[3],
456 >                 atomData6[4],
457 >                 atomData6[5]);
458          
459 +        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
460 +        
461        } else {
462          
463 <              sprintf( writeLine,
464 <                             "%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",
465 <                             atomTypeString,
466 <                             atomData13[0],
467 <                             atomData13[1],
468 <                             atomData13[2],
469 <                             atomData13[3],
470 <                             atomData13[4],
471 <                             atomData13[5],
472 <                             atomData13[6],
473 <                             atomData13[7],
474 <                             atomData13[8],
475 <                             atomData13[9],
476 <                             atomData13[10],
477 <                             atomData13[11],
478 <                             atomData13[12]);
463 >        sprintf( writeLine,
464 >                 "%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",
465 >                 atomTypeString,
466 >                 atomData13[0],
467 >                 atomData13[1],
468 >                 atomData13[2],
469 >                 atomData13[3],
470 >                 atomData13[4],
471 >                 atomData13[5],
472 >                 atomData13[6],
473 >                 atomData13[7],
474 >                 atomData13[8],
475 >                 atomData13[9],
476 >                 atomData13[10],
477 >                 atomData13[11],
478 >                 atomData13[12]);
479          
480        }
481        
# Line 429 | Line 488 | void DumpWriter::writeFrame( vector<ofstream*>& outFil
488      
489      sprintf( checkPointMsg,
490               "Sucessfully took a dump.\n");
491 <
491 >    
492      MPIcheckPoint();        
493 <
493 >    
494      delete[] potatoes;
495 <
495 >    
496    } else {
497  
498      // worldRank != 0, so I'm a remote node.  
# Line 450 | Line 509 | void DumpWriter::writeFrame( vector<ofstream*>& outFil
509        if (AtomToProcMap[i] == worldRank) {
510  
511          if (myPotato + 3 >= MAXTAG) {
512 <
512 >          
513            // The potato was going to exceed the maximum value,
514            // so wrap this processor potato back to 0 (and block until
515            // node 0 says we can go:
516 <
516 >          
517            MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
518            
519          }
520          which_atom = i;
521 <        local_index = indexArray[currentIndex].first;        
521 >
522 >        local_index = indexArray[currentIndex].first;        
523                  
524 <        if (which_atom == indexArray[currentIndex].second) {
524 >        if (which_atom == indexArray[currentIndex].second) {
525          
526            atomTypeString = atoms[local_index]->getType();
527 <
528 <                atoms[local_index]->getPos(pos);
529 <                atoms[local_index]->getVel(vel);
530 <
527 >          
528 >          atoms[local_index]->getPos(pos);
529 >          atoms[local_index]->getVel(vel);
530 >          
531            atomData6[0] = pos[0];
532            atomData6[1] = pos[1];
533            atomData6[2] = pos[2];
# Line 499 | Line 559 | void DumpWriter::writeFrame( vector<ofstream*>& outFil
559            }
560  
561          } else {
562 <                sprintf(painCave.errMsg,
563 <                              "Atom %d not found on processor %d\n",
564 <                              i, worldRank );
565 <                haveError= 1;
566 <                simError();
567 <              }
568 <
562 >          sprintf(painCave.errMsg,
563 >                  "Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n",
564 >                  which_atom, worldRank, currentIndex, local_index );
565 >          haveError= 1;
566 >          simError();
567 >        }
568 >        
569          strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
570  
571          // null terminate the string before sending (just in case):

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