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root/group/trunk/OOPSE/libmdtools/DumpWriter.cpp
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Comparing trunk/OOPSE/libmdtools/DumpWriter.cpp (file contents):
Revision 907 by gezelter, Thu Jan 8 17:40:56 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 = 10;
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 <  int me;
221 <  int atomTypeTag;
83 <  int atomIsDirectionalTag;
84 <  int atomTransDataTag;
85 <  int atomOrientDataTag;
220 >  char MPIatomTypeString[MINIBUFFERSIZE];
221 >
222   #else //is_mpi
223    int nAtoms = entry_plug->n_atoms;
224   #endif //is_mpi
# Line 92 | Line 228 | void DumpWriter::writeDump( double currentTime ){
228    Atom** atoms = entry_plug->atoms;
229    double pos[3], vel[3];
230  
95 –  // write current frame to the eor file
96 –
97 –  this->writeFinal( currentTime );
98 –
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"
106 <          << 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 <
112 <          << entry_plug->Hmat[0][2] << "\t"
113 <          << entry_plug->Hmat[1][2] << "\t"
114 <          << entry_plug->Hmat[2][2] << ";";
115 <  //write out additional parameters, such as chi and eta
116 <  outFile << entry_plug->the_integrator->getAdditionalParameters();
117 <  outFile << endl;
118 <
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 151 | 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    }
156 –  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  
163 –  int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
304    int haveError;
305  
306    MPI_Status istatus;
# Line 169 | Line 309 | void DumpWriter::writeDump( double currentTime ){
309    // write out header and node 0's coordinates
310  
311    if( worldRank == 0 ){
172 –    outFile << mpiSim->getTotAtoms() << "\n";
312  
313 <    outFile << currentTime << ";\t"
175 <            << entry_plug->Hmat[0][0] << "\t"
176 <            << entry_plug->Hmat[1][0] << "\t"
177 <            << 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"
181 <            << 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 >                         << 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 <
348 >      
349        if (which_node != 0) {
196 –        
197 –        atomTypeTag          = 4*i;
198 –        atomIsDirectionalTag = 4*i + 1;
199 –        atomTransDataTag     = 4*i + 2;
200 –        atomOrientDataTag    = 4*i + 3;
350  
351 <        MPI_Recv(atomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
352 <                 atomTypeTag, MPI_COMM_WORLD, &istatus);
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(&isDirectional, 1, MPI_INT, which_node,
363 <                 atomIsDirectionalTag, MPI_COMM_WORLD, &istatus);
362 >        MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
363 >                 myPotato, MPI_COMM_WORLD, &istatus);
364          
365 <        MPI_Recv(atomTransData, 6, MPI_DOUBLE, which_node,
366 <                 atomTransDataTag, MPI_COMM_WORLD, &istatus);
365 >        atomTypeString = MPIatomTypeString;
366 >        
367 >        myPotato++;
368  
369 <        if (isDirectional) {
369 >        MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
370 >                 myPotato, MPI_COMM_WORLD, &istatus);
371 >              
372 >        myPotato++;
373  
374 <          MPI_Recv(atomOrientData, 7, MPI_DOUBLE, which_node,
375 <                   atomOrientDataTag, MPI_COMM_WORLD, &istatus);
376 <
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 <        }
227 <
228 <        if (local_index != -1) {
229 <
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 248 | Line 412 | void DumpWriter::writeDump( double currentTime ){
412              
413              dAtom = (DirectionalAtom *)atoms[local_index];
414              dAtom->getQ( q );
251 –            
252 –            atomOrientData[0] = q[0];
253 –            atomOrientData[1] = q[1];
254 –            atomOrientData[2] = q[2];
255 –            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 <        }
269 <
270 <        if(haveError) DieDieDie();
271 <                              
272 <        // 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,
277 <                 atomTransData[0],
278 <                 atomTransData[1],
279 <                 atomTransData[2],
280 <                 atomTransData[3],
281 <                 atomTransData[4],
282 <                 atomTransData[5]);
283 <
284 <        strcpy( writeLine, tempBuffer );
285 <
286 <        if (isDirectional) {
287 <
288 <          sprintf( tempBuffer,
289 <                   "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
290 <                   atomOrientData[0],
291 <                   atomOrientData[1],
292 <                   atomOrientData[2],
293 <                   atomOrientData[3],
294 <                   atomOrientData[4],
295 <                   atomOrientData[5],
296 <                   atomOrientData[6]);
297 <          strcat( writeLine, tempBuffer );
298 <
299 <        } else {
300 <          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
301 <        }
302 <
303 <        outFile << writeLine;
304 <        outFile.flush();
437 >        if(haveError) DieDieDie();
438 >        
439 >        currentIndex ++;
440        }
441 <    }
307 <
308 <    outFile.flush();
309 <    sprintf( checkPointMsg,
310 <             "Sucessfully took a dump.\n");
311 <    MPIcheckPoint();        
312 <    
313 <  } else {
314 <
315 <    // worldRank != 0, so I'm a remote node.  
316 <    
317 <    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();
330 <
331 <          atoms[local_index]->getPos(pos);
332 <          atoms[local_index]->getVel(vel);
333 <
334 <          atomTransData[0] = pos[0];
335 <          atomTransData[1] = pos[1];
336 <          atomTransData[2] = pos[2];
337 <
338 <          atomTransData[3] = vel[0];
339 <          atomTransData[4] = vel[1];
340 <          atomTransData[5] = vel[2];
341 <          
342 <          isDirectional = 0;
343 <
344 <          if( atoms[local_index]->isDirectional() ){
345 <
346 <            isDirectional = 1;
347 <            
348 <            dAtom = (DirectionalAtom *)atoms[local_index];
349 <            dAtom->getQ( q );
350 <            
351 <            atomOrientData[0] = q[0];
352 <            atomOrientData[1] = q[1];
353 <            atomOrientData[2] = q[2];
354 <            atomOrientData[3] = q[3];
355 <
356 <            atomOrientData[4] = dAtom->getJx();
357 <            atomOrientData[5] = dAtom->getJy();
358 <            atomOrientData[6] = dAtom->getJz();
359 <          }
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 <        } else {
456 <          sprintf(painCave.errMsg,
457 <                  "Atom %d not found on processor %d\n",
458 <                  i, worldRank );
459 <          haveError= 1;
460 <          simError();
461 <        }
462 <
463 <        // I've survived this far, so send off the data!
464 <
465 <        atomTypeTag          = 4*i;
466 <        atomIsDirectionalTag = 4*i + 1;
467 <        atomTransDataTag     = 4*i + 2;
468 <        atomOrientDataTag    = 4*i + 3;
469 <
470 <        MPI_Send(atomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
471 <                 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          
379 –        MPI_Send(&isDirectional, 1, MPI_INT, 0,
380 –                 atomIsDirectionalTag, MPI_COMM_WORLD);
381 –        
382 –        MPI_Send(atomTransData, 6, MPI_DOUBLE, 0,
383 –                 atomTransDataTag, MPI_COMM_WORLD);
384 –
385 –        if (isDirectional) {
386 –
387 –          MPI_Send(atomOrientData, 7, MPI_DOUBLE, 0,
388 –                   atomOrientDataTag, MPI_COMM_WORLD);
389 –          
390 –        }
391 –      
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");
487 +
488      MPIcheckPoint();        
398 –    
399 –  }
400 –  
401 –  painCave.isEventLoop = 0;
489  
490 < #endif // is_mpi
404 < }
405 <
406 < void DumpWriter::writeFinal(double finalTime){
407 <
408 <  char finalName[500];
409 <  ofstream finalOut;
410 <
411 <  const int BUFFERSIZE = 2000;
412 <  const int MINIBUFFERSIZE = 10;
413 <  char tempBuffer[BUFFERSIZE];
414 <  char writeLine[BUFFERSIZE];
415 <
416 <  double q[4];
417 <  DirectionalAtom* dAtom;
418 <  Atom** atoms = entry_plug->atoms;
419 <  int i;
420 < #ifdef IS_MPI
421 <  int j, which_node, done, which_atom, local_index;
422 <  double atomTransData[6];
423 <  double atomOrientData[7];
424 <  int isDirectional;
425 <  char* atomTypeString;
426 <  int atomTypeTag;
427 <  int atomIsDirectionalTag;
428 <  int atomTransDataTag;
429 <  int atomOrientDataTag;
430 < #else //is_mpi
431 <  int nAtoms = entry_plug->n_atoms;
432 < #endif //is_mpi
433 <
434 <  double pos[3], vel[3];
435 <
436 < #ifdef IS_MPI
437 <  if(worldRank == 0 ){
438 < #endif // is_mpi
439 <
440 <    strcpy( finalName, entry_plug->finalName );
441 <
442 <    finalOut.open( finalName, ios::out | ios::trunc );
443 <    if( !finalOut ){
444 <      sprintf( painCave.errMsg,
445 <               "Could not open \"%s\" for final dump output.\n",
446 <               finalName );
447 <      painCave.isFatal = 1;
448 <      simError();
449 <    }
450 <
451 <    // finalOut.setf( ios::scientific );
452 <
453 < #ifdef IS_MPI
454 <  }
455 <
456 <  sprintf(checkPointMsg,"Opened file for final configuration\n");
457 <  MPIcheckPoint();
458 <
459 < #endif //is_mpi
460 <
461 <
462 < #ifndef IS_MPI
463 <
464 <  finalOut << nAtoms << "\n";
465 <
466 <  finalOut << finalTime << ";\t"
467 <           << entry_plug->Hmat[0][0] << "\t"
468 <           << entry_plug->Hmat[1][0] << "\t"
469 <           << entry_plug->Hmat[2][0] << ";\t"
470 <
471 <           << entry_plug->Hmat[0][1] << "\t"
472 <           << entry_plug->Hmat[1][1] << "\t"
473 <           << entry_plug->Hmat[2][1] << ";\t"
474 <
475 <           << entry_plug->Hmat[0][2] << "\t"
476 <           << entry_plug->Hmat[1][2] << "\t"
477 <           << entry_plug->Hmat[2][2] << ";";
478 <
479 <  //write out additional parameters, such as chi and eta
480 <  finalOut << entry_plug->the_integrator->getAdditionalParameters();
481 <  finalOut << endl;
482 <
483 <  for( i=0; i<nAtoms; i++ ){
484 <
485 <    atoms[i]->getPos(pos);
486 <    atoms[i]->getVel(vel);
487 <
488 <    sprintf( tempBuffer,
489 <             "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
490 <             atoms[i]->getType(),
491 <             pos[0],
492 <             pos[1],
493 <             pos[2],
494 <             vel[0],
495 <             vel[1],
496 <             vel[2]);
497 <    strcpy( writeLine, tempBuffer );
498 <
499 <    if( atoms[i]->isDirectional() ){
500 <
501 <      dAtom = (DirectionalAtom *)atoms[i];
502 <      dAtom->getQ( q );
503 <
504 <      sprintf( tempBuffer,
505 <               "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
506 <               q[0],
507 <               q[1],
508 <               q[2],
509 <               q[3],
510 <               dAtom->getJx(),
511 <               dAtom->getJy(),
512 <               dAtom->getJz());
513 <      strcat( writeLine, tempBuffer );
514 <    }
515 <    else
516 <      strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
517 <
518 <    finalOut << writeLine;
519 <  }
520 <  finalOut.flush();
521 <  finalOut.close();
522 <
523 < #else // is_mpi
524 <
525 <  // first thing first, suspend fatalities.
526 <  painCave.isEventLoop = 1;
527 <
528 <  int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
529 <  int haveError;
530 <
531 <  MPI_Status istatus;
532 <  int *AtomToProcMap = mpiSim->getAtomToProcMap();
533 <
534 <  // write out header and node 0's coordinates
535 <
536 <  if( worldRank == 0 ){
537 <    finalOut << mpiSim->getTotAtoms() << "\n";
538 <
539 <    finalOut << finalTime << ";\t"
540 <            << entry_plug->Hmat[0][0] << "\t"
541 <            << entry_plug->Hmat[1][0] << "\t"
542 <            << entry_plug->Hmat[2][0] << ";\t"
543 <
544 <            << entry_plug->Hmat[0][1] << "\t"
545 <            << entry_plug->Hmat[1][1] << "\t"
546 <            << entry_plug->Hmat[2][1] << ";\t"
547 <
548 <            << entry_plug->Hmat[0][2] << "\t"
549 <            << entry_plug->Hmat[1][2] << "\t"
550 <            << entry_plug->Hmat[2][2] << ";";
551 <
552 <    finalOut << entry_plug->the_integrator->getAdditionalParameters();
553 <    finalOut << endl;
554 <    finalOut.flush();
555 <    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
556 <      // Get the Node number which has this atom;
557 <
558 <      which_node = AtomToProcMap[i];
559 <
560 <      if (which_node != 0) {
561 <        
562 <        atomTypeTag          = 4*i;
563 <        atomIsDirectionalTag = 4*i + 1;
564 <        atomTransDataTag     = 4*i + 2;
565 <        atomOrientDataTag    = 4*i + 3;
566 <
567 <        MPI_Recv(atomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
568 <                 atomTypeTag, MPI_COMM_WORLD, &istatus);
569 <        
570 <        MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
571 <                 atomIsDirectionalTag, MPI_COMM_WORLD, &istatus);
572 <        
573 <        MPI_Recv(atomTransData, 6, MPI_DOUBLE, which_node,
574 <                 atomTransDataTag, MPI_COMM_WORLD, &istatus);
490 >    delete[] potatoes;
491  
492 <        if (isDirectional) {
492 >  } else {
493  
494 <          MPI_Recv(atomOrientData, 7, MPI_DOUBLE, which_node,
579 <                   atomOrientDataTag, MPI_COMM_WORLD, &istatus);
494 >    // worldRank != 0, so I'm a remote node.  
495  
496 <        }
496 >    // Set my magic potato to 0:
497  
498 <      } else {
499 <        
585 <        haveError = 0;
586 <        which_atom = i;
587 <        local_index=-1;
588 <
589 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
590 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
591 <        }
592 <
593 <        if (local_index != -1) {
594 <
595 <          atomTypeString = atoms[local_index]->getType();
596 <
597 <          atoms[local_index]->getPos(pos);
598 <          atoms[local_index]->getVel(vel);
599 <
600 <          atomTransData[0] = pos[0];
601 <          atomTransData[1] = pos[1];
602 <          atomTransData[2] = pos[2];
603 <
604 <          atomTransData[3] = vel[0];
605 <          atomTransData[4] = vel[1];
606 <          atomTransData[5] = vel[2];
607 <          
608 <          isDirectional = 0;
609 <
610 <          if( atoms[local_index]->isDirectional() ){
611 <
612 <            isDirectional = 1;
613 <            
614 <            dAtom = (DirectionalAtom *)atoms[local_index];
615 <            dAtom->getQ( q );
616 <            
617 <            atomOrientData[0] = q[0];
618 <            atomOrientData[1] = q[1];
619 <            atomOrientData[2] = q[2];
620 <            atomOrientData[3] = q[3];
621 <
622 <            atomOrientData[4] = dAtom->getJx();
623 <            atomOrientData[5] = dAtom->getJy();
624 <            atomOrientData[6] = dAtom->getJz();
625 <          }
626 <
627 <        } else {
628 <          sprintf(painCave.errMsg,
629 <                  "Atom %d not found on processor %d\n",
630 <                  i, worldRank );
631 <          haveError= 1;
632 <          simError();
633 <        }
634 <
635 <        if(haveError) DieDieDie();
636 <                              
637 <        // If we've survived to here, format the line:
638 <        
639 <        sprintf( tempBuffer,
640 <                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
641 <                 atomTypeString,
642 <                 atomTransData[0],
643 <                 atomTransData[1],
644 <                 atomTransData[2],
645 <                 atomTransData[3],
646 <                 atomTransData[4],
647 <                 atomTransData[5]);
648 <
649 <        strcpy( writeLine, tempBuffer );
650 <
651 <        if (isDirectional) {
652 <
653 <          sprintf( tempBuffer,
654 <                   "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
655 <                   atomOrientData[0],
656 <                   atomOrientData[1],
657 <                   atomOrientData[2],
658 <                   atomOrientData[3],
659 <                   atomOrientData[4],
660 <                   atomOrientData[5],
661 <                   atomOrientData[6]);
662 <          strcat( writeLine, tempBuffer );
663 <
664 <        } else {
665 <          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
666 <        }
667 <
668 <        finalOut << writeLine;
669 <        finalOut.flush();
670 <      }
671 <    }
672 <
673 <    finalOut.flush();
674 <    sprintf( checkPointMsg,
675 <             "Sucessfully took a dump.\n");
676 <    MPIcheckPoint();        
498 >    myPotato = 0;
499 >    currentIndex = 0;
500      
678 –  } else {
679 –
680 –    // worldRank != 0, so I'm a remote node.  
681 –    
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 713 | 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  
564 <        // I've survived this far, so send off the data!
564 >        strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
565  
566 <        atomTypeTag          = 4*i;
567 <        atomIsDirectionalTag = 4*i + 1;
738 <        atomTransDataTag     = 4*i + 2;
739 <        atomOrientDataTag    = 4*i + 3;
566 >        // null terminate the string before sending (just in case):
567 >        MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
568  
569 <        MPI_Send(atomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
570 <                 atomTypeTag, MPI_COMM_WORLD);
569 >        MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
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);
749 <
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    
766 –  painCave.isEventLoop = 0;
767 –
768 –  if( worldRank == 0 ) finalOut.close();
601   #endif // is_mpi
602   }
603  
772 –
773 –
604   #ifdef IS_MPI
605  
606   // a couple of functions to let us escape the write loop

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