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root/group/trunk/OOPSE/libmdtools/DumpWriter.cpp
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Comparing trunk/OOPSE/libmdtools/DumpWriter.cpp (file contents):
Revision 913 by chuckv, Thu Jan 8 22:25:52 2004 UTC vs.
Revision 947 by gezelter, Thu Jan 15 14:22:16 2004 UTC

# Line 3 | Line 3
3   #include <string.h>
4   #include <iostream>
5   #include <fstream>
6 + #include <algorithm>
7 + #include <utility>
8  
9   #ifdef IS_MPI
10   #include <mpi.h>
# Line 26 | Line 28 | DumpWriter::DumpWriter( SimInfo* the_entry_plug ){
28    if(worldRank == 0 ){
29   #endif // is_mpi
30  
29 –    strcpy( outName, entry_plug->sampleName );
31  
32 <    outFile.open(outName, ios::out | ios::trunc );
32 >    dumpFile.open(entry_plug->sampleName, ios::out | ios::trunc );
33  
34 <    if( !outFile ){
34 >    if( !dumpFile ){
35  
36        sprintf( painCave.errMsg,
37                 "Could not open \"%s\" for dump output.\n",
38 <               outName);
38 >               entry_plug->sampleName);
39        painCave.isFatal = 1;
40        simError();
41      }
42  
42 –    //outFile.setf( ios::scientific );
43 –
43   #ifdef IS_MPI
44    }
45  
46 +  //sort the local atoms by global index
47 +  sortByGlobalIndex();
48 +  
49    sprintf( checkPointMsg,
50             "Sucessfully opened output file for dumping.\n");
51    MPIcheckPoint();
# Line 56 | Line 58 | DumpWriter::~DumpWriter( ){
58    if(worldRank == 0 ){
59   #endif // is_mpi
60  
61 <    outFile.close();
61 >    dumpFile.close();
62  
63   #ifdef IS_MPI
64    }
65   #endif // is_mpi
66   }
67  
68 < void DumpWriter::writeDump( double currentTime ){
68 > #ifdef IS_MPI
69  
70 + /**
71 + * A hook function to load balancing
72 + */
73 +
74 + void DumpWriter::update(){
75 +  sortByGlobalIndex();          
76 + }
77 +  
78 + /**
79 + * Auxiliary sorting function
80 + */
81 +
82 + bool indexSortingCriterion(const pair<int, int>& p1, const pair<int, int>& p2){
83 +  return p1.second < p2.second;
84 + }
85 +
86 + /**
87 + * Sorting the local index by global index
88 + */
89 +
90 + void DumpWriter::sortByGlobalIndex(){
91 +  Atom** atoms = entry_plug->atoms;
92 +  
93 +  indexArray.clear();
94 +  
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 + #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 +    
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 +  }
119 + #endif // is_mpi
120 +
121 +  fileStreams.push_back(&finalOut);
122 +  fileStreams.push_back(&dumpFile);
123 +
124 +  writeFrame(fileStreams, currentTime);
125 +
126 + #ifdef IS_MPI
127 +  finalOut.close();
128 + #endif
129 +        
130 + }
131 +
132 + void DumpWriter::writeFinal(double currentTime){
133 +
134 +  ofstream finalOut;
135 +  vector<ofstream*> fileStreams;
136 +
137 + #ifdef IS_MPI
138 +  if(worldRank == 0 ){
139 +
140 +    finalOut.open( entry_plug->finalName, ios::out | ios::trunc );
141 +
142 +    if( !finalOut ){
143 +      sprintf( painCave.errMsg,
144 +               "Could not open \"%s\" for final dump output.\n",
145 +               entry_plug->finalName );
146 +      painCave.isFatal = 1;
147 +      simError();
148 +    }
149 +
150 +  }
151 + #endif // is_mpi
152 +  
153 +  fileStreams.push_back(&finalOut);  
154 +  writeFrame(fileStreams, currentTime);
155 +
156 + #ifdef IS_MPI
157 +  finalOut.close();
158 + #endif
159 +  
160 + }
161 +
162 + void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){
163 +
164    const int BUFFERSIZE = 2000;
165    const int MINIBUFFERSIZE = 100;
166  
167 <  char tempBuffer[BUFFERSIZE];
167 >  char tempBuffer[BUFFERSIZE];  
168    char writeLine[BUFFERSIZE];
169  
170 <  int i;
170 >  int i, k;
171 >
172   #ifdef IS_MPI
173 <  int j, which_node, done, which_atom, local_index;
174 <  double atomTransData[6];
175 <  double atomOrientData[7];
173 >  
174 >  /*********************************************************************
175 >   * Documentation?  You want DOCUMENTATION?
176 >   *
177 >   * Why all the potatoes below?  
178 >   *
179 >   * To make a long story short, the original version of DumpWriter
180 >   * worked in the most inefficient way possible.  Node 0 would
181 >   * poke each of the node for an individual atom's formatted data
182 >   * as node 0 worked its way down the global index. This was particularly
183 >   * inefficient since the method blocked all processors at every atom
184 >   * (and did it twice!).
185 >   *
186 >   * An intermediate version of DumpWriter could be described from Node
187 >   * zero's perspective as follows:
188 >   *
189 >   *  1) Have 100 of your friends stand in a circle.
190 >   *  2) When you say go, have all of them start tossing potatoes at
191 >   *     you (one at a time).
192 >   *  3) Catch the potatoes.
193 >   *
194 >   * It was an improvement, but MPI has buffers and caches that could
195 >   * best be described in this analogy as "potato nets", so there's no
196 >   * need to block the processors atom-by-atom.
197 >   *
198 >   * This new and improved DumpWriter works in an even more efficient
199 >   * way:
200 >   *
201 >   *  1) Have 100 of your friend stand in a circle.
202 >   *  2) When you say go, have them start tossing 5-pound bags of
203 >   *     potatoes at you.
204 >   *  3) Once you've caught a friend's bag of potatoes,
205 >   *     toss them a spud to let them know they can toss another bag.
206 >   *
207 >   * How's THAT for documentation?
208 >   *
209 >   *********************************************************************/
210 >
211 >  int *potatoes;
212 >  int myPotato;
213 >
214 >  int nProc;
215 >  int j, which_node, done, which_atom, local_index, currentIndex;
216 >  double atomData6[6];
217 >  double atomData13[13];
218    int isDirectional;
219    char* atomTypeString;
220    char MPIatomTypeString[MINIBUFFERSIZE];
221 <  int me;
83 <  int atomTypeTag;
84 <  int atomIsDirectionalTag;
85 <  int atomTransDataTag;
86 <  int atomOrientDataTag;
221 >
222   #else //is_mpi
223    int nAtoms = entry_plug->n_atoms;
224   #endif //is_mpi
# Line 93 | Line 228 | void DumpWriter::writeDump( double currentTime ){
228    Atom** atoms = entry_plug->atoms;
229    double pos[3], vel[3];
230  
96 –  // write current frame to the eor file
97 –
98 –  this->writeFinal( currentTime );
99 –
231   #ifndef IS_MPI
232 +  
233 +  for(k = 0; k < outFile.size(); k++){
234 +    *outFile[k] << nAtoms << "\n";
235  
236 <  outFile << nAtoms << "\n";
236 >    *outFile[k] << currentTime << ";\t"
237 >               << entry_plug->Hmat[0][0] << "\t"
238 >                     << entry_plug->Hmat[1][0] << "\t"
239 >                     << entry_plug->Hmat[2][0] << ";\t"
240 >              
241 >               << entry_plug->Hmat[0][1] << "\t"
242 >                     << entry_plug->Hmat[1][1] << "\t"
243 >                     << entry_plug->Hmat[2][1] << ";\t"
244  
245 <  outFile << currentTime << ";\t"
246 <          << entry_plug->Hmat[0][0] << "\t"
247 <          << entry_plug->Hmat[1][0] << "\t"
107 <          << entry_plug->Hmat[2][0] << ";\t"
245 >                     << entry_plug->Hmat[0][2] << "\t"
246 >                     << entry_plug->Hmat[1][2] << "\t"
247 >                     << entry_plug->Hmat[2][2] << ";";
248  
249 <          << entry_plug->Hmat[0][1] << "\t"
250 <          << entry_plug->Hmat[1][1] << "\t"
251 <          << entry_plug->Hmat[2][1] << ";\t"
252 <
113 <          << entry_plug->Hmat[0][2] << "\t"
114 <          << entry_plug->Hmat[1][2] << "\t"
115 <          << entry_plug->Hmat[2][2] << ";";
116 <  //write out additional parameters, such as chi and eta
117 <  outFile << entry_plug->the_integrator->getAdditionalParameters();
118 <  outFile << endl;
119 <
249 >    //write out additional parameters, such as chi and eta
250 >    *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
251 >  }
252 >  
253    for( i=0; i<nAtoms; i++ ){
254  
255      atoms[i]->getPos(pos);
# Line 152 | Line 285 | void DumpWriter::writeDump( double currentTime ){
285      else
286        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
287  
288 <    outFile << writeLine;
288 >    for(k = 0; k < outFile.size(); k++)
289 >      *outFile[k] << writeLine;
290    }
157 –  outFile.flush();
291  
292   #else // is_mpi
293  
294    /* code to find maximum tag value */
295 +  
296    int *tagub, flag, MAXTAG;
297    MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
298    if (flag) {
299      MAXTAG = *tagub;
300    } else {
301      MAXTAG = 32767;
302 <  }
302 >  }  
303  
304    int haveError;
305  
# Line 175 | Line 309 | void DumpWriter::writeDump( double currentTime ){
309    // write out header and node 0's coordinates
310  
311    if( worldRank == 0 ){
178 –    outFile << mpiSim->getTotAtoms() << "\n";
312  
313 <    outFile << currentTime << ";\t"
181 <            << entry_plug->Hmat[0][0] << "\t"
182 <            << entry_plug->Hmat[1][0] << "\t"
183 <            << entry_plug->Hmat[2][0] << ";\t"
313 >    // Node 0 needs a list of the magic potatoes for each processor;
314  
315 <            << entry_plug->Hmat[0][1] << "\t"
316 <            << entry_plug->Hmat[1][1] << "\t"
187 <            << entry_plug->Hmat[2][1] << ";\t"
315 >    nProc = mpiSim->getNumberProcessors();
316 >    potatoes = new int[nProc];
317  
318 <            << entry_plug->Hmat[0][2] << "\t"
319 <            << entry_plug->Hmat[1][2] << "\t"
320 <            << entry_plug->Hmat[2][2] << ";";
318 >    //write out the comment lines
319 >    for (i = 0; i < nProc; i++)
320 >      potatoes[i] = 0;
321 >    
322 >      for(k = 0; k < outFile.size(); k++){
323 >        *outFile[k] << mpiSim->getTotAtoms() << "\n";
324  
325 <    outFile << entry_plug->the_integrator->getAdditionalParameters();
326 <    outFile << endl;
327 <    outFile.flush();
325 >        *outFile[k] << currentTime << ";\t"
326 >                         << entry_plug->Hmat[0][0] << "\t"
327 >                         << entry_plug->Hmat[1][0] << "\t"
328 >                         << entry_plug->Hmat[2][0] << ";\t"
329  
330 <    tag = 0;
330 >                         << entry_plug->Hmat[0][1] << "\t"
331 >                         << entry_plug->Hmat[1][1] << "\t"
332 >                         << entry_plug->Hmat[2][1] << ";\t"
333  
334 <    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
334 >                         << entry_plug->Hmat[0][2] << "\t"
335 >                         << entry_plug->Hmat[1][2] << "\t"
336 >                         << entry_plug->Hmat[2][2] << ";";
337 >  
338 >        *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
339 >    }
340  
341 <      if (tag + 2 >= MAXTAG) {
342 <        // The tag was going to exceed the maximum value, so wrap around to 0:
343 <        tag = 0;
204 <        // Send the newly zeroed tag on to the other nodes:
205 <        MPI_Bcast(&tag, 1, MPI_INT, 0, MPI_COMM_WORLD);
206 <      }
341 >    currentIndex = 0;
342 >
343 >    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
344        
345        // Get the Node number which has this atom;
346        
347        which_node = AtomToProcMap[i];
348        
349        if (which_node != 0) {
350 +
351 +        if (potatoes[which_node] + 3 >= MAXTAG) {
352 +          // The potato was going to exceed the maximum value,
353 +          // so wrap this processor potato back to 0:        
354 +
355 +          potatoes[which_node] = 0;          
356 +          MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
357 +          
358 +        }
359 +
360 +        myPotato = potatoes[which_node];        
361          
362          MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
363 <                 atomTypeTag, MPI_COMM_WORLD, &istatus);
363 >                 myPotato, MPI_COMM_WORLD, &istatus);
364          
365 <        strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE);
366 <        
367 <        // Null terminate the atomTypeString just in case:
365 >        atomTypeString = MPIatomTypeString;
366 >        
367 >        myPotato++;
368  
221 –        atomTypeString[strlen(atomTypeString) - 1] = '\0';
222 –
369          MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
370 <                 atomIsDirectionalTag, MPI_COMM_WORLD, &istatus);
371 <        
372 <        MPI_Recv(atomTransData, 6, MPI_DOUBLE, which_node,
227 <                 atomTransDataTag, MPI_COMM_WORLD, &istatus);
370 >                 myPotato, MPI_COMM_WORLD, &istatus);
371 >              
372 >        myPotato++;
373  
374 <        if (isDirectional) {
375 <
376 <          MPI_Recv(atomOrientData, 7, MPI_DOUBLE, which_node,
377 <                   atomOrientDataTag, MPI_COMM_WORLD, &istatus);
378 <
374 >        if (isDirectional) {          
375 >          MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node,
376 >                   myPotato, MPI_COMM_WORLD, &istatus);
377 >        } else {
378 >          MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node,
379 >                   myPotato, MPI_COMM_WORLD, &istatus);          
380          }
381 +        
382 +        myPotato++;
383 +        potatoes[which_node] = myPotato;
384  
385        } else {
386          
387 <        haveError = 0;
388 <        which_atom = i;
389 <        local_index=-1;
390 <
391 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
392 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
393 <        }
245 <
246 <        if (local_index != -1) {
247 <
387 >        haveError = 0;
388 >              which_atom = i;
389 >        
390 >        local_index = indexArray[currentIndex].first;        
391 >                
392 >        if (which_atom == indexArray[currentIndex].second) {
393 >          
394            atomTypeString = atoms[local_index]->getType();
395  
396 <          atoms[local_index]->getPos(pos);
397 <          atoms[local_index]->getVel(vel);
396 >                atoms[local_index]->getPos(pos);
397 >                atoms[local_index]->getVel(vel);          
398  
399 <          atomTransData[0] = pos[0];
400 <          atomTransData[1] = pos[1];
401 <          atomTransData[2] = pos[2];
399 >          atomData6[0] = pos[0];
400 >          atomData6[1] = pos[1];
401 >          atomData6[2] = pos[2];
402  
403 <          atomTransData[3] = vel[0];
404 <          atomTransData[4] = vel[1];
405 <          atomTransData[5] = vel[2];
403 >          atomData6[3] = vel[0];
404 >          atomData6[4] = vel[1];
405 >          atomData6[5] = vel[2];
406            
407            isDirectional = 0;
408  
# Line 266 | Line 412 | void DumpWriter::writeDump( double currentTime ){
412              
413              dAtom = (DirectionalAtom *)atoms[local_index];
414              dAtom->getQ( q );
269 –            
270 –            atomOrientData[0] = q[0];
271 –            atomOrientData[1] = q[1];
272 –            atomOrientData[2] = q[2];
273 –            atomOrientData[3] = q[3];
415  
416 <            atomOrientData[4] = dAtom->getJx();
417 <            atomOrientData[5] = dAtom->getJy();
418 <            atomOrientData[6] = dAtom->getJz();
416 >            for (int j = 0; j < 6 ; j++)
417 >              atomData13[j] = atomData6[j];            
418 >            
419 >            atomData13[6] = q[0];
420 >            atomData13[7] = q[1];
421 >            atomData13[8] = q[2];
422 >            atomData13[9] = q[3];
423 >            
424 >            atomData13[10] = dAtom->getJx();
425 >            atomData13[11] = dAtom->getJy();
426 >            atomData13[12] = dAtom->getJz();
427            }
428 <
428 >          
429          } else {
430 <          sprintf(painCave.errMsg,
431 <                  "Atom %d not found on processor %d\n",
432 <                  i, worldRank );
433 <          haveError= 1;
434 <          simError();
435 <        }
287 <
288 <        if(haveError) DieDieDie();
289 <                              
290 <        // If we've survived to here, format the line:
430 >          sprintf(painCave.errMsg,
431 >                              "Atom %d not found on processor %d\n",
432 >                              i, worldRank );
433 >                haveError= 1;
434 >                simError();
435 >              }
436          
437 <        sprintf( tempBuffer,
438 <                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
439 <                 atomTypeString,
295 <                 atomTransData[0],
296 <                 atomTransData[1],
297 <                 atomTransData[2],
298 <                 atomTransData[3],
299 <                 atomTransData[4],
300 <                 atomTransData[5]);
301 <
302 <        strcpy( writeLine, tempBuffer );
303 <
304 <        if (isDirectional) {
305 <
306 <          sprintf( tempBuffer,
307 <                   "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
308 <                   atomOrientData[0],
309 <                   atomOrientData[1],
310 <                   atomOrientData[2],
311 <                   atomOrientData[3],
312 <                   atomOrientData[4],
313 <                   atomOrientData[5],
314 <                   atomOrientData[6]);
315 <          strcat( writeLine, tempBuffer );
316 <
317 <        } else {
318 <          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
319 <        }
320 <
321 <        outFile << writeLine;
322 <        outFile.flush();
437 >        if(haveError) DieDieDie();
438 >        
439 >        currentIndex ++;
440        }
441 <    }
325 <
326 <    outFile.flush();
327 <    sprintf( checkPointMsg,
328 <             "Sucessfully took a dump.\n");
329 <    MPIcheckPoint();        
330 <    
331 <  } else {
332 <
333 <    // worldRank != 0, so I'm a remote node.  
334 <    
335 <    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
441 >      // If we've survived to here, format the line:
442        
443 <      // Am I the node which has this atom?
444 <      
445 <      if (AtomToProcMap[i] == worldRank) {
446 <
447 <        local_index=-1;
448 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
449 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
450 <        }
451 <        if (local_index != -1) {
452 <        
453 <          atomTypeString = atoms[local_index]->getType();
348 <
349 <          atoms[local_index]->getPos(pos);
350 <          atoms[local_index]->getVel(vel);
351 <
352 <          atomTransData[0] = pos[0];
353 <          atomTransData[1] = pos[1];
354 <          atomTransData[2] = pos[2];
355 <
356 <          atomTransData[3] = vel[0];
357 <          atomTransData[4] = vel[1];
358 <          atomTransData[5] = vel[2];
359 <          
360 <          isDirectional = 0;
361 <
362 <          if( atoms[local_index]->isDirectional() ){
363 <
364 <            isDirectional = 1;
365 <            
366 <            dAtom = (DirectionalAtom *)atoms[local_index];
367 <            dAtom->getQ( q );
368 <            
369 <            atomOrientData[0] = q[0];
370 <            atomOrientData[1] = q[1];
371 <            atomOrientData[2] = q[2];
372 <            atomOrientData[3] = q[3];
373 <
374 <            atomOrientData[4] = dAtom->getJx();
375 <            atomOrientData[5] = dAtom->getJy();
376 <            atomOrientData[6] = dAtom->getJz();
377 <          }
378 <
379 <        } else {
380 <          sprintf(painCave.errMsg,
381 <                  "Atom %d not found on processor %d\n",
382 <                  i, worldRank );
383 <          haveError= 1;
384 <          simError();
385 <        }
443 >      if (!isDirectional) {
444 >        
445 >        sprintf( writeLine,
446 >                             "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
447 >                             atomTypeString,
448 >                             atomData6[0],
449 >                             atomData6[1],
450 >                             atomData6[2],
451 >                             atomData6[3],
452 >                             atomData6[4],
453 >                             atomData6[5]);
454  
455 <        // I've survived this far, so send off the data!
456 <
457 <        atomTypeTag          = 4*i;
458 <        atomIsDirectionalTag = 4*i + 1;
459 <        atomTransDataTag     = 4*i + 2;
460 <        atomOrientDataTag    = 4*i + 3;
461 <
462 <
463 <        strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
464 <
465 <        // null terminate the string before sending (just in case):
466 <        MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
467 <
468 <        MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
469 <                 atomTypeTag, MPI_COMM_WORLD);
455 >              strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
456 >        
457 >      } else {
458 >        
459 >              sprintf( writeLine,
460 >                             "%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",
461 >                             atomTypeString,
462 >                             atomData13[0],
463 >                             atomData13[1],
464 >                             atomData13[2],
465 >                             atomData13[3],
466 >                             atomData13[4],
467 >                             atomData13[5],
468 >                             atomData13[6],
469 >                             atomData13[7],
470 >                             atomData13[8],
471 >                             atomData13[9],
472 >                             atomData13[10],
473 >                             atomData13[11],
474 >                             atomData13[12]);
475          
403 –        MPI_Send(&isDirectional, 1, MPI_INT, 0,
404 –                 atomIsDirectionalTag, MPI_COMM_WORLD);
405 –        
406 –        MPI_Send(atomTransData, 6, MPI_DOUBLE, 0,
407 –                 atomTransDataTag, MPI_COMM_WORLD);
408 –
409 –        if (isDirectional) {
410 –
411 –          MPI_Send(atomOrientData, 7, MPI_DOUBLE, 0,
412 –                   atomOrientDataTag, MPI_COMM_WORLD);
413 –          
414 –        }
415 –      
476        }
477 +      
478 +      for(k = 0; k < outFile.size(); k++)
479 +        *outFile[k] << writeLine;
480      }
481 <
481 >    
482 >    for(k = 0; k < outFile.size(); k++)
483 >      outFile[k]->flush();
484 >    
485      sprintf( checkPointMsg,
486               "Sucessfully took a dump.\n");
421 –    MPIcheckPoint();        
422 –    
423 –  }
424 –  
425 –  painCave.isEventLoop = 0;
487  
488 < #endif // is_mpi
428 < }
429 <
430 < void DumpWriter::writeFinal(double finalTime){
431 <
432 <  char finalName[500];
433 <  ofstream finalOut;
434 <
435 <  const int BUFFERSIZE = 2000;
436 <  const int MINIBUFFERSIZE = 100;
437 <  char tempBuffer[BUFFERSIZE];
438 <  char writeLine[BUFFERSIZE];
439 <
440 <  double q[4];
441 <  DirectionalAtom* dAtom;
442 <  Atom** atoms = entry_plug->atoms;
443 <  int i;
444 < #ifdef IS_MPI
445 <  int j, which_node, done, which_atom, local_index;
446 <  double atomTransData[6];
447 <  double atomOrientData[7];
448 <  int isDirectional;
449 <  char* atomTypeString;
450 <  char MPIatomTypeString[MINIBUFFERSIZE];
451 <  int atomTypeTag;
452 <  int atomIsDirectionalTag;
453 <  int atomTransDataTag;
454 <  int atomOrientDataTag;
455 < #else //is_mpi
456 <  int nAtoms = entry_plug->n_atoms;
457 < #endif //is_mpi
458 <
459 <  double pos[3], vel[3];
460 <
461 < #ifdef IS_MPI
462 <  if(worldRank == 0 ){
463 < #endif // is_mpi
464 <
465 <    strcpy( finalName, entry_plug->finalName );
466 <
467 <    finalOut.open( finalName, ios::out | ios::trunc );
468 <    if( !finalOut ){
469 <      sprintf( painCave.errMsg,
470 <               "Could not open \"%s\" for final dump output.\n",
471 <               finalName );
472 <      painCave.isFatal = 1;
473 <      simError();
474 <    }
475 <
476 <    // finalOut.setf( ios::scientific );
477 <
478 < #ifdef IS_MPI
479 <  }
480 <
481 <  sprintf(checkPointMsg,"Opened file for final configuration\n");
482 <  MPIcheckPoint();
483 <
484 < #endif //is_mpi
485 <
486 <
487 < #ifndef IS_MPI
488 <
489 <  finalOut << nAtoms << "\n";
490 <
491 <  finalOut << finalTime << ";\t"
492 <           << entry_plug->Hmat[0][0] << "\t"
493 <           << entry_plug->Hmat[1][0] << "\t"
494 <           << entry_plug->Hmat[2][0] << ";\t"
495 <
496 <           << entry_plug->Hmat[0][1] << "\t"
497 <           << entry_plug->Hmat[1][1] << "\t"
498 <           << entry_plug->Hmat[2][1] << ";\t"
499 <
500 <           << entry_plug->Hmat[0][2] << "\t"
501 <           << entry_plug->Hmat[1][2] << "\t"
502 <           << entry_plug->Hmat[2][2] << ";";
503 <
504 <  //write out additional parameters, such as chi and eta
505 <  finalOut << entry_plug->the_integrator->getAdditionalParameters();
506 <  finalOut << endl;
507 <
508 <  for( i=0; i<nAtoms; i++ ){
509 <
510 <    atoms[i]->getPos(pos);
511 <    atoms[i]->getVel(vel);
512 <
513 <    sprintf( tempBuffer,
514 <             "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
515 <             atoms[i]->getType(),
516 <             pos[0],
517 <             pos[1],
518 <             pos[2],
519 <             vel[0],
520 <             vel[1],
521 <             vel[2]);
522 <    strcpy( writeLine, tempBuffer );
523 <
524 <    if( atoms[i]->isDirectional() ){
525 <
526 <      dAtom = (DirectionalAtom *)atoms[i];
527 <      dAtom->getQ( q );
528 <
529 <      sprintf( tempBuffer,
530 <               "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
531 <               q[0],
532 <               q[1],
533 <               q[2],
534 <               q[3],
535 <               dAtom->getJx(),
536 <               dAtom->getJy(),
537 <               dAtom->getJz());
538 <      strcat( writeLine, tempBuffer );
539 <    }
540 <    else
541 <      strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
542 <
543 <    finalOut << writeLine;
544 <  }
545 <  finalOut.flush();
546 <  finalOut.close();
547 <
548 < #else // is_mpi
549 <
550 <  // first thing first, suspend fatalities.
551 <  painCave.isEventLoop = 1;
552 <
553 <  int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
554 <  int haveError;
555 <
556 <  MPI_Status istatus;
557 <  int *AtomToProcMap = mpiSim->getAtomToProcMap();
558 <
559 <  // write out header and node 0's coordinates
560 <
561 <  if( worldRank == 0 ){
562 <    finalOut << mpiSim->getTotAtoms() << "\n";
563 <
564 <    finalOut << finalTime << ";\t"
565 <            << entry_plug->Hmat[0][0] << "\t"
566 <            << entry_plug->Hmat[1][0] << "\t"
567 <            << entry_plug->Hmat[2][0] << ";\t"
568 <
569 <            << entry_plug->Hmat[0][1] << "\t"
570 <            << entry_plug->Hmat[1][1] << "\t"
571 <            << entry_plug->Hmat[2][1] << ";\t"
572 <
573 <            << entry_plug->Hmat[0][2] << "\t"
574 <            << entry_plug->Hmat[1][2] << "\t"
575 <            << entry_plug->Hmat[2][2] << ";";
576 <
577 <    finalOut << entry_plug->the_integrator->getAdditionalParameters();
578 <    finalOut << endl;
579 <    finalOut.flush();
580 <    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
581 <      // Get the Node number which has this atom;
582 <
583 <      which_node = AtomToProcMap[i];
584 <
585 <      if (which_node != 0) {
586 <        
587 <        atomTypeTag          = 4*i;
588 <        atomIsDirectionalTag = 4*i + 1;
589 <        atomTransDataTag     = 4*i + 2;
590 <        atomOrientDataTag    = 4*i + 3;
488 >    MPIcheckPoint();        
489  
490 <        MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
593 <                 atomTypeTag, MPI_COMM_WORLD, &istatus);
594 <        
595 <        strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE);
490 >    delete[] potatoes;
491  
492 <        MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
598 <                 atomIsDirectionalTag, MPI_COMM_WORLD, &istatus);
599 <        
600 <        MPI_Recv(atomTransData, 6, MPI_DOUBLE, which_node,
601 <                 atomTransDataTag, MPI_COMM_WORLD, &istatus);
492 >  } else {
493  
494 <        if (isDirectional) {
494 >    // worldRank != 0, so I'm a remote node.  
495  
496 <          MPI_Recv(atomOrientData, 7, MPI_DOUBLE, which_node,
606 <                   atomOrientDataTag, MPI_COMM_WORLD, &istatus);
496 >    // Set my magic potato to 0:
497  
498 <        }
499 <
610 <      } else {
611 <        
612 <        haveError = 0;
613 <        which_atom = i;
614 <        local_index=-1;
615 <
616 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
617 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
618 <        }
619 <
620 <        if (local_index != -1) {
621 <
622 <          atomTypeString = atoms[local_index]->getType();
623 <
624 <          atoms[local_index]->getPos(pos);
625 <          atoms[local_index]->getVel(vel);
626 <
627 <          atomTransData[0] = pos[0];
628 <          atomTransData[1] = pos[1];
629 <          atomTransData[2] = pos[2];
630 <
631 <          atomTransData[3] = vel[0];
632 <          atomTransData[4] = vel[1];
633 <          atomTransData[5] = vel[2];
634 <          
635 <          isDirectional = 0;
636 <
637 <          if( atoms[local_index]->isDirectional() ){
638 <
639 <            isDirectional = 1;
640 <            
641 <            dAtom = (DirectionalAtom *)atoms[local_index];
642 <            dAtom->getQ( q );
643 <            
644 <            atomOrientData[0] = q[0];
645 <            atomOrientData[1] = q[1];
646 <            atomOrientData[2] = q[2];
647 <            atomOrientData[3] = q[3];
648 <
649 <            atomOrientData[4] = dAtom->getJx();
650 <            atomOrientData[5] = dAtom->getJy();
651 <            atomOrientData[6] = dAtom->getJz();
652 <          }
653 <
654 <        } else {
655 <          sprintf(painCave.errMsg,
656 <                  "Atom %d not found on processor %d\n",
657 <                  i, worldRank );
658 <          haveError= 1;
659 <          simError();
660 <        }
661 <
662 <        if(haveError) DieDieDie();
663 <                              
664 <        // If we've survived to here, format the line:
665 <        
666 <        sprintf( tempBuffer,
667 <                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
668 <                 atomTypeString,
669 <                 atomTransData[0],
670 <                 atomTransData[1],
671 <                 atomTransData[2],
672 <                 atomTransData[3],
673 <                 atomTransData[4],
674 <                 atomTransData[5]);
675 <
676 <        strcpy( writeLine, tempBuffer );
677 <
678 <        if (isDirectional) {
679 <
680 <          sprintf( tempBuffer,
681 <                   "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
682 <                   atomOrientData[0],
683 <                   atomOrientData[1],
684 <                   atomOrientData[2],
685 <                   atomOrientData[3],
686 <                   atomOrientData[4],
687 <                   atomOrientData[5],
688 <                   atomOrientData[6]);
689 <          strcat( writeLine, tempBuffer );
690 <
691 <        } else {
692 <          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
693 <        }
694 <
695 <        finalOut << writeLine;
696 <        finalOut.flush();
697 <      }
698 <    }
699 <
700 <    finalOut.flush();
701 <    sprintf( checkPointMsg,
702 <             "Sucessfully took a dump.\n");
703 <    MPIcheckPoint();        
498 >    myPotato = 0;
499 >    currentIndex = 0;
500      
705 –  } else {
706 –
707 –    // worldRank != 0, so I'm a remote node.  
708 –    
501      for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
502        
503        // Am I the node which has this atom?
504        
505        if (AtomToProcMap[i] == worldRank) {
506  
507 <        local_index=-1;
508 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
509 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
507 >        if (myPotato + 3 >= MAXTAG) {
508 >
509 >          // The potato was going to exceed the maximum value,
510 >          // so wrap this processor potato back to 0 (and block until
511 >          // node 0 says we can go:
512 >
513 >          MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
514 >          
515          }
516 <        if (local_index != -1) {
516 >        which_atom = i;
517 >        local_index = indexArray[currentIndex].first;        
518 >                
519 >        if (which_atom == indexArray[currentIndex].second) {
520          
521            atomTypeString = atoms[local_index]->getType();
522  
523 <          atoms[local_index]->getPos(pos);
524 <          atoms[local_index]->getVel(vel);
523 >                atoms[local_index]->getPos(pos);
524 >                atoms[local_index]->getVel(vel);
525  
526 <          atomTransData[0] = pos[0];
527 <          atomTransData[1] = pos[1];
528 <          atomTransData[2] = pos[2];
526 >          atomData6[0] = pos[0];
527 >          atomData6[1] = pos[1];
528 >          atomData6[2] = pos[2];
529  
530 <          atomTransData[3] = vel[0];
531 <          atomTransData[4] = vel[1];
532 <          atomTransData[5] = vel[2];
530 >          atomData6[3] = vel[0];
531 >          atomData6[4] = vel[1];
532 >          atomData6[5] = vel[2];
533            
534            isDirectional = 0;
535  
# Line 740 | Line 540 | void DumpWriter::writeFinal(double finalTime){
540              dAtom = (DirectionalAtom *)atoms[local_index];
541              dAtom->getQ( q );
542              
543 <            atomOrientData[0] = q[0];
544 <            atomOrientData[1] = q[1];
545 <            atomOrientData[2] = q[2];
546 <            atomOrientData[3] = q[3];
547 <
548 <            atomOrientData[4] = dAtom->getJx();
549 <            atomOrientData[5] = dAtom->getJy();
550 <            atomOrientData[6] = dAtom->getJz();
543 >            for (int j = 0; j < 6 ; j++)
544 >              atomData13[j] = atomData6[j];
545 >            
546 >            atomData13[6] = q[0];
547 >            atomData13[7] = q[1];
548 >            atomData13[8] = q[2];
549 >            atomData13[9] = q[3];
550 >  
551 >            atomData13[10] = dAtom->getJx();
552 >            atomData13[11] = dAtom->getJy();
553 >            atomData13[12] = dAtom->getJz();
554            }
555  
556          } else {
557 <          sprintf(painCave.errMsg,
558 <                  "Atom %d not found on processor %d\n",
559 <                  i, worldRank );
560 <          haveError= 1;
561 <          simError();
562 <        }
557 >                sprintf(painCave.errMsg,
558 >                              "Atom %d not found on processor %d\n",
559 >                              i, worldRank );
560 >                haveError= 1;
561 >                simError();
562 >              }
563  
761 –        // I've survived this far, so send off the data!
762 –
763 –        atomTypeTag          = 4*i;
764 –        atomIsDirectionalTag = 4*i + 1;
765 –        atomTransDataTag     = 4*i + 2;
766 –        atomOrientDataTag    = 4*i + 3;
767 –
564          strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
565  
566 +        // null terminate the string before sending (just in case):
567 +        MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
568 +
569          MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
570 <                 atomTypeTag, MPI_COMM_WORLD);
570 >                             myPotato, MPI_COMM_WORLD);
571          
572 +        myPotato++;
573 +
574          MPI_Send(&isDirectional, 1, MPI_INT, 0,
575 <                 atomIsDirectionalTag, MPI_COMM_WORLD);
575 >                             myPotato, MPI_COMM_WORLD);
576          
577 <        MPI_Send(atomTransData, 6, MPI_DOUBLE, 0,
578 <                 atomTransDataTag, MPI_COMM_WORLD);
778 <
577 >        myPotato++;
578 >        
579          if (isDirectional) {
580  
581 <          MPI_Send(atomOrientData, 7, MPI_DOUBLE, 0,
582 <                   atomOrientDataTag, MPI_COMM_WORLD);
581 >          MPI_Send(atomData13, 13, MPI_DOUBLE, 0,
582 >                   myPotato, MPI_COMM_WORLD);
583            
584 +        } else {
585 +
586 +          MPI_Send(atomData6, 6, MPI_DOUBLE, 0,
587 +                   myPotato, MPI_COMM_WORLD);
588          }
589 <      
589 >
590 >        myPotato++;  
591 >        currentIndex++;    
592        }
593      }
594  
595      sprintf( checkPointMsg,
596 <             "Sucessfully wrote final file.\n");
596 >             "Sucessfully took a dump.\n");
597      MPIcheckPoint();        
598      
599 <  }
599 >  }
600    
795 –  painCave.isEventLoop = 0;
796 –
797 –  if( worldRank == 0 ) finalOut.close();
601   #endif // is_mpi
602   }
603  
801 –
802 –
604   #ifdef IS_MPI
605  
606   // a couple of functions to let us escape the write loop

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