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root/group/trunk/OOPSE/libmdtools/DumpWriter.cpp
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Comparing trunk/OOPSE/libmdtools/DumpWriter.cpp (file contents):
Revision 905 by tim, Wed Jan 7 19:26:12 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>
11   #include "mpiSimulation.hpp"
10 – #define TAKE_THIS_TAG_CHAR 15
11 – #define TAKE_THIS_TAG_INT 20
12  
13   namespace dWrite{
14 <  void nodeZeroError( void );
15 <  void anonymousNodeDie( void );
14 >  void DieDieDie( void );
15   }
16  
17   using namespace dWrite;
# Line 29 | Line 28 | DumpWriter::DumpWriter( SimInfo* the_entry_plug ){
28    if(worldRank == 0 ){
29   #endif // is_mpi
30  
32 –    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  
45 –    //outFile.setf( ios::scientific );
46 –
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 59 | 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 <  char tempBuffer[BUFFERSIZE];
165 >  const int MINIBUFFERSIZE = 100;
166 >
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;
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 >
222   #else //is_mpi
223    int nAtoms = entry_plug->n_atoms;
224   #endif //is_mpi
# Line 84 | Line 228 | void DumpWriter::writeDump( double currentTime ){
228    Atom** atoms = entry_plug->atoms;
229    double pos[3], vel[3];
230  
87 –
88 –  // write current frame to the eor file
89 –
90 –  this->writeFinal( currentTime );
91 –
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"
99 <          << 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 <
105 <          << entry_plug->Hmat[0][2] << "\t"
106 <          << entry_plug->Hmat[1][2] << "\t"
107 <          << entry_plug->Hmat[2][2] << ";";
108 <  //write out additional parameters, such as chi and eta
109 <  outFile << entry_plug->the_integrator->getAdditionalParameters();
110 <  outFile << endl;
111 <
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 144 | 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    }
149 –  outFile.flush();
291  
292   #else // is_mpi
293  
294 <  // first thing first, suspend fatalities.
295 <  painCave.isEventLoop = 1;
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 >  }  
303  
156 –  int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
304    int haveError;
305  
306    MPI_Status istatus;
# Line 162 | Line 309 | void DumpWriter::writeDump( double currentTime ){
309    // write out header and node 0's coordinates
310  
311    if( worldRank == 0 ){
165 –    outFile << mpiSim->getTotAtoms() << "\n";
312  
313 <    outFile << currentTime << ";\t"
168 <            << entry_plug->Hmat[0][0] << "\t"
169 <            << entry_plug->Hmat[1][0] << "\t"
170 <            << 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"
174 <            << 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] << ";";
321 <
322 <    outFile << entry_plug->the_integrator->getAdditionalParameters();
323 <    outFile << endl;
324 <    outFile.flush();
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[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 >                         << entry_plug->Hmat[0][1] << "\t"
331 >                         << entry_plug->Hmat[1][1] << "\t"
332 >                         << entry_plug->Hmat[2][1] << ";\t"
333 >
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 >    currentIndex = 0;
342 >
343      for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
344 +      
345        // Get the Node number which has this atom;
346 <
346 >      
347        which_node = AtomToProcMap[i];
348 +      
349 +      if (which_node != 0) {
350  
351 <      if (which_node == 0 ) {
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 <        haveError = 0;
356 <        which_atom = i;
357 <        local_index=-1;
193 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
194 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
355 >          potatoes[which_node] = 0;          
356 >          MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
357 >          
358          }
196 –        if (local_index != -1) {
197 –          //format the line
359  
360 <          atoms[local_index]->getPos(pos);
361 <          atoms[local_index]->getVel(vel);
360 >        myPotato = potatoes[which_node];        
361 >        
362 >        MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
363 >                 myPotato, MPI_COMM_WORLD, &istatus);
364 >        
365 >        atomTypeString = MPIatomTypeString;
366 >        
367 >        myPotato++;
368  
369 <          sprintf( tempBuffer,
370 <                   "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
371 <                   atoms[local_index]->getType(),
372 <                   pos[0],
206 <                   pos[1],
207 <                   pos[2],
208 <                   vel[0],
209 <                   vel[1],
210 <                   vel[2]); // check here.
211 <          strcpy( writeLine, tempBuffer );
369 >        MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
370 >                 myPotato, MPI_COMM_WORLD, &istatus);
371 >              
372 >        myPotato++;
373  
374 <          if( atoms[local_index]->isDirectional() ){
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 <            dAtom = (DirectionalAtom *)atoms[local_index];
386 <            dAtom->getQ( q );
385 >      } else {
386 >        
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 <            sprintf( tempBuffer,
397 <                     "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
220 <                     q[0],
221 <                     q[1],
222 <                     q[2],
223 <                     q[3],
224 <                     dAtom->getJx(),
225 <                     dAtom->getJy(),
226 <                     dAtom->getJz());
227 <            strcat( writeLine, tempBuffer );
396 >                atoms[local_index]->getPos(pos);
397 >                atoms[local_index]->getVel(vel);          
398  
399 <          }
400 <          else
401 <            strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
232 <        }
233 <        else {
234 <          sprintf(painCave.errMsg,
235 <                  "Atom %d not found on processor %d\n",
236 <                  i, worldRank );
237 <          haveError= 1;
238 <          simError();
239 <        }
399 >          atomData6[0] = pos[0];
400 >          atomData6[1] = pos[1];
401 >          atomData6[2] = pos[2];
402  
403 <        if(haveError) nodeZeroError();
403 >          atomData6[3] = vel[0];
404 >          atomData6[4] = vel[1];
405 >          atomData6[5] = vel[2];
406 >          
407 >          isDirectional = 0;
408  
409 <      }
244 <      else {
245 <        myStatus = 1;
246 <        MPI_Send(&myStatus, 1, MPI_INT, which_node,
247 <                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
248 <        MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
249 <                 MPI_COMM_WORLD);
250 <        MPI_Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node,
251 <                 TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
252 <        MPI_Recv(&myStatus, 1, MPI_INT, which_node,
253 <                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
409 >          if( atoms[local_index]->isDirectional() ){
410  
411 <        if(!myStatus) nodeZeroError();
411 >            isDirectional = 1;
412 >            
413 >            dAtom = (DirectionalAtom *)atoms[local_index];
414 >            dAtom->getQ( q );
415  
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 +          
429 +        } else {
430 +          sprintf(painCave.errMsg,
431 +                              "Atom %d not found on processor %d\n",
432 +                              i, worldRank );
433 +                haveError= 1;
434 +                simError();
435 +              }
436 +        
437 +        if(haveError) DieDieDie();
438 +        
439 +        currentIndex ++;
440        }
441 +      // If we've survived to here, format the line:
442 +      
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 <      outFile << writeLine;
456 <      outFile.flush();
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 >        
476 >      }
477 >      
478 >      for(k = 0; k < outFile.size(); k++)
479 >        *outFile[k] << writeLine;
480      }
481 +    
482 +    for(k = 0; k < outFile.size(); k++)
483 +      outFile[k]->flush();
484 +    
485 +    sprintf( checkPointMsg,
486 +             "Sucessfully took a dump.\n");
487  
488 <    // kill everyone off:
264 <    myStatus = -1;
265 <    for (j = 1; j < mpiSim->getNumberProcessors(); j++) {
266 <      MPI_Send(&myStatus, 1, MPI_INT, j,
267 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
268 <    }
488 >    MPIcheckPoint();        
489  
490 +    delete[] potatoes;
491 +
492    } else {
493  
494 <    done = 0;
273 <    while (!done) {
494 >    // worldRank != 0, so I'm a remote node.  
495  
496 <      MPI_Recv(&myStatus, 1, MPI_INT, 0,
276 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
496 >    // Set my magic potato to 0:
497  
498 <      if(!myStatus) anonymousNodeDie();
498 >    myPotato = 0;
499 >    currentIndex = 0;
500 >    
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 <      if(myStatus < 0) break;
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(&which_atom, 1, MPI_INT, 0,
514 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
513 >          MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
514 >          
515 >        }
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 <      myStatus = 1;
524 <      local_index=-1;
287 <      for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
288 <        if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
289 <      }
290 <      if (local_index != -1) {
291 <        //format the line
523 >                atoms[local_index]->getPos(pos);
524 >                atoms[local_index]->getVel(vel);
525  
526 <        atoms[local_index]->getPos(pos);
527 <        atoms[local_index]->getVel(vel);
526 >          atomData6[0] = pos[0];
527 >          atomData6[1] = pos[1];
528 >          atomData6[2] = pos[2];
529  
530 <        sprintf( tempBuffer,
531 <                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
532 <                 atoms[local_index]->getType(),
533 <                 pos[0],
534 <                 pos[1],
301 <                 pos[2],
302 <                 vel[0],
303 <                 vel[1],
304 <                 vel[2]); // check here.
305 <        strcpy( writeLine, tempBuffer );
530 >          atomData6[3] = vel[0];
531 >          atomData6[4] = vel[1];
532 >          atomData6[5] = vel[2];
533 >          
534 >          isDirectional = 0;
535  
536 <        if( atoms[local_index]->isDirectional() ){
536 >          if( atoms[local_index]->isDirectional() ){
537  
538 <          dAtom = (DirectionalAtom *)atoms[local_index];
539 <          dAtom->getQ( q );
538 >            isDirectional = 1;
539 >            
540 >            dAtom = (DirectionalAtom *)atoms[local_index];
541 >            dAtom->getQ( q );
542 >            
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 <          sprintf( tempBuffer,
557 <                   "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
558 <                   q[0],
559 <                   q[1],
560 <                   q[2],
561 <                   q[3],
562 <                   dAtom->getJx(),
319 <                   dAtom->getJy(),
320 <                   dAtom->getJz());
321 <          strcat( writeLine, tempBuffer );
322 <        }
323 <        else{
324 <          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
325 <        }
326 <      }
327 <      else {
328 <        sprintf(painCave.errMsg,
329 <                "Atom %d not found on processor %d\n",
330 <                which_atom, worldRank );
331 <        myStatus = 0;
332 <        simError();
556 >        } else {
557 >                sprintf(painCave.errMsg,
558 >                              "Atom %d not found on processor %d\n",
559 >                              i, worldRank );
560 >                haveError= 1;
561 >                simError();
562 >              }
563  
564 <        strcpy( writeLine, "Hello, I'm an error.\n");
335 <      }
564 >        strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
565  
566 <      MPI_Send(writeLine, BUFFERSIZE, MPI_CHAR, 0,
567 <               TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
339 <      MPI_Send( &myStatus, 1, MPI_INT, 0,
340 <                TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
341 <    }
342 <  }
343 <  outFile.flush();
344 <  sprintf( checkPointMsg,
345 <           "Sucessfully took a dump.\n");
346 <  MPIcheckPoint();
566 >        // null terminate the string before sending (just in case):
567 >        MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
568  
569 < // last  thing last, enable  fatalities.
570 <  painCave.isEventLoop = 0;
569 >        MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
570 >                             myPotato, MPI_COMM_WORLD);
571 >        
572 >        myPotato++;
573  
574 < #endif // is_mpi
575 < }
574 >        MPI_Send(&isDirectional, 1, MPI_INT, 0,
575 >                             myPotato, MPI_COMM_WORLD);
576 >        
577 >        myPotato++;
578 >        
579 >        if (isDirectional) {
580  
581 < void DumpWriter::writeFinal(double finalTime){
581 >          MPI_Send(atomData13, 13, MPI_DOUBLE, 0,
582 >                   myPotato, MPI_COMM_WORLD);
583 >          
584 >        } else {
585  
586 <  char finalName[500];
587 <  ofstream finalOut;
358 <
359 <  const int BUFFERSIZE = 2000;
360 <  char tempBuffer[BUFFERSIZE];
361 <  char writeLine[BUFFERSIZE];
362 <
363 <  double q[4];
364 <  DirectionalAtom* dAtom;
365 <  Atom** atoms = entry_plug->atoms;
366 <  int i;
367 < #ifdef IS_MPI
368 <  int j, which_node, done, which_atom, local_index;
369 < #else //is_mpi
370 <  int nAtoms = entry_plug->n_atoms;
371 < #endif //is_mpi
372 <
373 <  double pos[3], vel[3];
374 <
375 < #ifdef IS_MPI
376 <  if(worldRank == 0 ){
377 < #endif // is_mpi
378 <
379 <    strcpy( finalName, entry_plug->finalName );
380 <
381 <    finalOut.open( finalName, ios::out | ios::trunc );
382 <    if( !finalOut ){
383 <      sprintf( painCave.errMsg,
384 <               "Could not open \"%s\" for final dump output.\n",
385 <               finalName );
386 <      painCave.isFatal = 1;
387 <      simError();
388 <    }
389 <
390 <    // finalOut.setf( ios::scientific );
391 <
392 < #ifdef IS_MPI
393 <  }
394 <
395 <  sprintf(checkPointMsg,"Opened file for final configuration\n");
396 <  MPIcheckPoint();
397 <
398 < #endif //is_mpi
399 <
400 <
401 < #ifndef IS_MPI
402 <
403 <  finalOut << nAtoms << "\n";
404 <
405 <  finalOut << finalTime << ";\t"
406 <           << entry_plug->Hmat[0][0] << "\t"
407 <           << entry_plug->Hmat[1][0] << "\t"
408 <           << entry_plug->Hmat[2][0] << ";\t"
409 <
410 <           << entry_plug->Hmat[0][1] << "\t"
411 <           << entry_plug->Hmat[1][1] << "\t"
412 <           << entry_plug->Hmat[2][1] << ";\t"
413 <
414 <           << entry_plug->Hmat[0][2] << "\t"
415 <           << entry_plug->Hmat[1][2] << "\t"
416 <           << entry_plug->Hmat[2][2] << ";";
417 <
418 <  //write out additional parameters, such as chi and eta
419 <  finalOut << entry_plug->the_integrator->getAdditionalParameters();
420 <  finalOut << endl;
421 <
422 <  for( i=0; i<nAtoms; i++ ){
423 <
424 <    atoms[i]->getPos(pos);
425 <    atoms[i]->getVel(vel);
426 <
427 <    sprintf( tempBuffer,
428 <             "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
429 <             atoms[i]->getType(),
430 <             pos[0],
431 <             pos[1],
432 <             pos[2],
433 <             vel[0],
434 <             vel[1],
435 <             vel[2]);
436 <    strcpy( writeLine, tempBuffer );
437 <
438 <    if( atoms[i]->isDirectional() ){
439 <
440 <      dAtom = (DirectionalAtom *)atoms[i];
441 <      dAtom->getQ( q );
442 <
443 <      sprintf( tempBuffer,
444 <               "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
445 <               q[0],
446 <               q[1],
447 <               q[2],
448 <               q[3],
449 <               dAtom->getJx(),
450 <               dAtom->getJy(),
451 <               dAtom->getJz());
452 <      strcat( writeLine, tempBuffer );
453 <    }
454 <    else
455 <      strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
456 <
457 <    finalOut << writeLine;
458 <  }
459 <  finalOut.flush();
460 <  finalOut.close();
461 <
462 < #else // is_mpi
463 <
464 <  // first thing first, suspend fatalities.
465 <  painCave.isEventLoop = 1;
466 <
467 <  int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
468 <  int haveError;
469 <
470 <  MPI_Status istatus;
471 <  int *AtomToProcMap = mpiSim->getAtomToProcMap();
472 <
473 <  // write out header and node 0's coordinates
474 <
475 <  haveError = 0;
476 <  if( worldRank == 0 ){
477 <    finalOut << mpiSim->getTotAtoms() << "\n";
478 <
479 <    finalOut << finalTime << ";\t"
480 <             << entry_plug->Hmat[0][0] << "\t"
481 <             << entry_plug->Hmat[1][0] << "\t"
482 <             << entry_plug->Hmat[2][0] << ";\t"
483 <
484 <             << entry_plug->Hmat[0][1] << "\t"
485 <             << entry_plug->Hmat[1][1] << "\t"
486 <             << entry_plug->Hmat[2][1] << ";\t"
487 <
488 <             << entry_plug->Hmat[0][2] << "\t"
489 <             << entry_plug->Hmat[1][2] << "\t"
490 <             << entry_plug->Hmat[2][2] << ";";
491 <
492 <    //write out additional parameters, such as chi and eta
493 <    finalOut << entry_plug->the_integrator->getAdditionalParameters();
494 <    finalOut << endl;
495 <
496 <    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
497 <      // Get the Node number which has this molecule:
498 <
499 <      which_node = AtomToProcMap[i];
500 <
501 <      if (which_node == mpiSim->getMyNode()) {
502 <
503 <        which_atom = i;
504 <        local_index=-1;
505 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
506 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
586 >          MPI_Send(atomData6, 6, MPI_DOUBLE, 0,
587 >                   myPotato, MPI_COMM_WORLD);
588          }
508 –        if (local_index != -1) {
589  
590 <          atoms[local_index]->getPos(pos);
591 <          atoms[local_index]->getVel(vel);
512 <
513 <          sprintf( tempBuffer,
514 <                   "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
515 <                   atoms[local_index]->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[local_index]->isDirectional() ){
525 <
526 <            dAtom = (DirectionalAtom *)atoms[local_index];
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 <        else {
544 <          sprintf(painCave.errMsg,
545 <                  "Atom %d not found on processor %d\n",
546 <                  i, worldRank );
547 <          haveError= 1;
548 <          simError();
549 <        }
550 <
551 <        if(haveError) nodeZeroError();
552 <
590 >        myPotato++;  
591 >        currentIndex++;    
592        }
554 –      else {
555 –
556 –        myStatus = 1;
557 –        MPI_Send(&myStatus, 1, MPI_INT, which_node,
558 –                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
559 –        MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
560 –                 MPI_COMM_WORLD);
561 –        MPI_Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node,
562 –                 TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
563 –        MPI_Recv(&myStatus, 1, MPI_INT, which_node,
564 –                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
565 –
566 –        if(!myStatus) nodeZeroError();
567 –      }
568 –
569 –      finalOut << writeLine;
593      }
594  
595 <    // kill everyone off:
596 <    myStatus = -1;
597 <    for (j = 1; j < mpiSim->getNumberProcessors(); j++) {
598 <      MPI_Send(&myStatus, 1, MPI_INT, j,
599 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
600 <    }
578 <
579 <  } else {
580 <
581 <    done = 0;
582 <    while (!done) {
583 <
584 <      MPI_Recv(&myStatus, 1, MPI_INT, 0,
585 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
586 <
587 <      if(!myStatus) anonymousNodeDie();
588 <
589 <      if(myStatus < 0) break;
590 <
591 <      MPI_Recv(&which_atom, 1, MPI_INT, 0,
592 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
593 <
594 <      myStatus = 1;
595 <      local_index=-1;
596 <      for (j=0; j < mpiSim->getMyNlocal(); j++) {
597 <        if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
598 <      }
599 <      if (local_index != -1) {
600 <
601 <        atoms[local_index]->getPos(pos);
602 <        atoms[local_index]->getVel(vel);
603 <
604 <        //format the line
605 <        sprintf( tempBuffer,
606 <                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
607 <                 atoms[local_index]->getType(),
608 <                 pos[0],
609 <                 pos[1],
610 <                 pos[2],
611 <                 vel[0],
612 <                 vel[1],
613 <                 vel[2]); // check here.
614 <        strcpy( writeLine, tempBuffer );
615 <
616 <        if( atoms[local_index]->isDirectional() ){
617 <
618 <          dAtom = (DirectionalAtom *)atoms[local_index];
619 <          dAtom->getQ( q );
620 <
621 <          sprintf( tempBuffer,
622 <                   "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
623 <                   q[0],
624 <                   q[1],
625 <                   q[2],
626 <                   q[3],
627 <                   dAtom->getJx(),
628 <                   dAtom->getJy(),
629 <                   dAtom->getJz());
630 <          strcat( writeLine, tempBuffer );
631 <        }
632 <        else{
633 <          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
634 <        }
635 <      }
636 <      else {
637 <        sprintf(painCave.errMsg,
638 <                "Atom %d not found on processor %d\n",
639 <                which_atom, worldRank );
640 <        myStatus = 0;
641 <        simError();
642 <
643 <        strcpy( writeLine, "Hello, I'm an error.\n");
644 <      }
645 <
646 <      MPI_Send(writeLine, BUFFERSIZE, MPI_CHAR, 0,
647 <               TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
648 <      MPI_Send( &myStatus, 1, MPI_INT, 0,
649 <                TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
650 <    }
651 <  }
652 <  finalOut.flush();
653 <  sprintf( checkPointMsg,
654 <           "Sucessfully took a dump.\n");
655 <  MPIcheckPoint();
656 <
657 <  if( worldRank == 0 ) finalOut.close();
595 >    sprintf( checkPointMsg,
596 >             "Sucessfully took a dump.\n");
597 >    MPIcheckPoint();        
598 >    
599 >  }
600 >  
601   #endif // is_mpi
602   }
603  
661 –
662 –
604   #ifdef IS_MPI
605  
606   // a couple of functions to let us escape the write loop
607  
608 < void dWrite::nodeZeroError( void ){
668 <  int j, myStatus;
608 > void dWrite::DieDieDie( void ){
609  
670 –  myStatus = 0;
671 –  for (j = 0; j < mpiSim->getNumberProcessors(); j++) {
672 –    MPI_Send( &myStatus, 1, MPI_INT, j,
673 –              TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
674 –  }
675 –
676 –
610    MPI_Finalize();
611    exit (0);
679 –
612   }
613  
682 – void dWrite::anonymousNodeDie( void ){
683 –
684 –  MPI_Finalize();
685 –  exit (0);
686 – }
687 –
614   #endif //is_mpi

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