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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 1097 by gezelter, Mon Apr 12 20:32:20 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 168 | Line 227 | void DumpWriter::writeFrame( vector<ofstream*>& outFil
227    int nAtoms = entry_plug->n_atoms;
228   #endif //is_mpi
229  
230 <  double q[4];
230 >  double q[4], ji[3];
231    DirectionalAtom* dAtom;
232    Atom** atoms = entry_plug->atoms;
233    double pos[3], vel[3];
# Line 215 | Line 274 | void DumpWriter::writeFrame( vector<ofstream*>& outFil
274  
275        dAtom = (DirectionalAtom *)atoms[i];
276        dAtom->getQ( q );
277 +      dAtom->getJ( ji );
278  
279        sprintf( tempBuffer,
280                 "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
# Line 222 | Line 282 | void DumpWriter::writeFrame( vector<ofstream*>& outFil
282                 q[1],
283                 q[2],
284                 q[3],
285 <               dAtom->getJx(),
286 <               dAtom->getJy(),
287 <               dAtom->getJz());
285 >               ji[0],
286 >               ji[1],
287 >               ji[2]);
288        strcat( writeLine, tempBuffer );
289      }
290      else
# Line 330 | Line 390 | void DumpWriter::writeFrame( vector<ofstream*>& outFil
390        } else {
391          
392          haveError = 0;
393 <              which_atom = i;
393 >        which_atom = i;
394          
395 <        local_index = indexArray[currentIndex].first;        
336 <                
337 <        if (which_atom == indexArray[currentIndex].second) {
395 >          local_index = indexArray[currentIndex].first;        
396            
397 <          atomTypeString = atoms[local_index]->getType();
398 <
399 <                atoms[local_index]->getPos(pos);
400 <                atoms[local_index]->getVel(vel);          
401 <
397 >          if (which_atom == indexArray[currentIndex].second) {
398 >            
399 >            atomTypeString = atoms[local_index]->getType();
400 >            
401 >          atoms[local_index]->getPos(pos);
402 >          atoms[local_index]->getVel(vel);          
403 >          
404            atomData6[0] = pos[0];
405            atomData6[1] = pos[1];
406            atomData6[2] = pos[2];
# Line 357 | Line 417 | void DumpWriter::writeFrame( vector<ofstream*>& outFil
417              
418              dAtom = (DirectionalAtom *)atoms[local_index];
419              dAtom->getQ( q );
420 +            dAtom->getJ( ji );
421  
422              for (int j = 0; j < 6 ; j++)
423                atomData13[j] = atomData6[j];            
# Line 366 | Line 427 | void DumpWriter::writeFrame( vector<ofstream*>& outFil
427              atomData13[8] = q[2];
428              atomData13[9] = q[3];
429              
430 <            atomData13[10] = dAtom->getJx();
431 <            atomData13[11] = dAtom->getJy();
432 <            atomData13[12] = dAtom->getJz();
430 >            atomData13[10] = ji[0];
431 >            atomData13[11] = ji[1];
432 >            atomData13[12] = ji[2];
433            }
434            
435          } else {
436 <          sprintf(painCave.errMsg,
437 <                              "Atom %d not found on processor %d\n",
438 <                              i, worldRank );
439 <                haveError= 1;
440 <                simError();
441 <              }
436 >          sprintf(painCave.errMsg,
437 >                  "Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n",
438 >                  which_atom, worldRank, currentIndex, local_index );
439 >          haveError= 1;
440 >          simError();
441 >        }
442          
443          if(haveError) DieDieDie();
444          
445 <        currentIndex ++;
445 >        currentIndex++;
446        }
447        // If we've survived to here, format the line:
448        
449        if (!isDirectional) {
450          
451          sprintf( writeLine,
452 <                             "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
453 <                             atomTypeString,
454 <                             atomData6[0],
455 <                             atomData6[1],
456 <                             atomData6[2],
457 <                             atomData6[3],
458 <                             atomData6[4],
459 <                             atomData6[5]);
399 <
400 <              strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
452 >                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
453 >                 atomTypeString,
454 >                 atomData6[0],
455 >                 atomData6[1],
456 >                 atomData6[2],
457 >                 atomData6[3],
458 >                 atomData6[4],
459 >                 atomData6[5]);
460          
461 +        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
462 +        
463        } else {
464          
465 <              sprintf( writeLine,
466 <                             "%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",
467 <                             atomTypeString,
468 <                             atomData13[0],
469 <                             atomData13[1],
470 <                             atomData13[2],
471 <                             atomData13[3],
472 <                             atomData13[4],
473 <                             atomData13[5],
474 <                             atomData13[6],
475 <                             atomData13[7],
476 <                             atomData13[8],
477 <                             atomData13[9],
478 <                             atomData13[10],
479 <                             atomData13[11],
480 <                             atomData13[12]);
465 >        sprintf( writeLine,
466 >                 "%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",
467 >                 atomTypeString,
468 >                 atomData13[0],
469 >                 atomData13[1],
470 >                 atomData13[2],
471 >                 atomData13[3],
472 >                 atomData13[4],
473 >                 atomData13[5],
474 >                 atomData13[6],
475 >                 atomData13[7],
476 >                 atomData13[8],
477 >                 atomData13[9],
478 >                 atomData13[10],
479 >                 atomData13[11],
480 >                 atomData13[12]);
481          
482        }
483        
# Line 429 | Line 490 | void DumpWriter::writeFrame( vector<ofstream*>& outFil
490      
491      sprintf( checkPointMsg,
492               "Sucessfully took a dump.\n");
493 <
493 >    
494      MPIcheckPoint();        
495 <
495 >    
496      delete[] potatoes;
497 <
497 >    
498    } else {
499  
500      // worldRank != 0, so I'm a remote node.  
# Line 450 | Line 511 | void DumpWriter::writeFrame( vector<ofstream*>& outFil
511        if (AtomToProcMap[i] == worldRank) {
512  
513          if (myPotato + 3 >= MAXTAG) {
514 <
514 >          
515            // The potato was going to exceed the maximum value,
516            // so wrap this processor potato back to 0 (and block until
517            // node 0 says we can go:
518 <
518 >          
519            MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
520            
521          }
522          which_atom = i;
523 <        local_index = indexArray[currentIndex].first;        
523 >
524 >        local_index = indexArray[currentIndex].first;        
525                  
526 <        if (which_atom == indexArray[currentIndex].second) {
526 >        if (which_atom == indexArray[currentIndex].second) {
527          
528            atomTypeString = atoms[local_index]->getType();
529 <
530 <                atoms[local_index]->getPos(pos);
531 <                atoms[local_index]->getVel(vel);
532 <
529 >          
530 >          atoms[local_index]->getPos(pos);
531 >          atoms[local_index]->getVel(vel);
532 >          
533            atomData6[0] = pos[0];
534            atomData6[1] = pos[1];
535            atomData6[2] = pos[2];
# Line 484 | Line 546 | void DumpWriter::writeFrame( vector<ofstream*>& outFil
546              
547              dAtom = (DirectionalAtom *)atoms[local_index];
548              dAtom->getQ( q );
549 +            dAtom->getJ( ji );
550              
551              for (int j = 0; j < 6 ; j++)
552                atomData13[j] = atomData6[j];
# Line 493 | Line 556 | void DumpWriter::writeFrame( vector<ofstream*>& outFil
556              atomData13[8] = q[2];
557              atomData13[9] = q[3];
558    
559 <            atomData13[10] = dAtom->getJx();
560 <            atomData13[11] = dAtom->getJy();
561 <            atomData13[12] = dAtom->getJz();
559 >            atomData13[10] = ji[0];
560 >            atomData13[11] = ji[1];
561 >            atomData13[12] = ji[2];
562            }
563  
564          } else {
565 <                sprintf(painCave.errMsg,
566 <                              "Atom %d not found on processor %d\n",
567 <                              i, worldRank );
568 <                haveError= 1;
569 <                simError();
570 <              }
571 <
565 >          sprintf(painCave.errMsg,
566 >                  "Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n",
567 >                  which_atom, worldRank, currentIndex, local_index );
568 >          haveError= 1;
569 >          simError();
570 >        }
571 >        
572          strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
573  
574          // null terminate the string before sending (just in case):

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