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root/group/trunk/OOPSE/libmdtools/DumpWriter.cpp
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Comparing trunk/OOPSE/libmdtools/DumpWriter.cpp (file contents):
Revision 804 by mmeineke, Thu Oct 16 19:16:24 2003 UTC vs.
Revision 951 by mmeineke, Fri Jan 16 21:51:51 2004 UTC

# Line 1 | Line 1
1   #define _FILE_OFFSET_BITS 64
2  
3 < #include <cstring>
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 1
11 – #define TAKE_THIS_TAG_INT 2
12  
13   namespace dWrite{
14 <  void nodeZeroError( void );
15 <  void anonymousNodeDie( void );
14 >  void DieDieDie( void );
15   }
16  
17   using namespace dWrite;
# Line 28 | Line 27 | DumpWriter::DumpWriter( SimInfo* the_entry_plug ){
27   #ifdef IS_MPI
28    if(worldRank == 0 ){
29   #endif // is_mpi
30 <    
31 <    strcpy( outName, entry_plug->sampleName );
32 <    
33 <    outFile.open(outName, ios::out | ios::trunc );
34 <    
36 <    if( !outFile ){
37 <      
30 >
31 >    dumpFile.open(entry_plug->sampleName, ios::out | ios::trunc );
32 >
33 >    if( !dumpFile ){
34 >
35        sprintf( painCave.errMsg,
36                 "Could not open \"%s\" for dump output.\n",
37 <               outName);
37 >               entry_plug->sampleName);
38        painCave.isFatal = 1;
39        simError();
40      }
41  
45 –    //outFile.setf( ios::scientific );
46 –
42   #ifdef IS_MPI
43    }
44  
45 +  //sort the local atoms by global index
46 +  sortByGlobalIndex();
47 +  
48    sprintf( checkPointMsg,
49             "Sucessfully opened output file for dumping.\n");
50    MPIcheckPoint();
# Line 59 | Line 57 | DumpWriter::~DumpWriter( ){
57    if(worldRank == 0 ){
58   #endif // is_mpi
59  
60 <    outFile.close();
60 >    dumpFile.close();
61  
62   #ifdef IS_MPI
63    }
64   #endif // is_mpi
65   }
66  
67 < void DumpWriter::writeDump( double currentTime ){
67 > #ifdef IS_MPI
68 >
69 > /**
70 > * A hook function to load balancing
71 > */
72 >
73 > void DumpWriter::update(){
74 >  sortByGlobalIndex();          
75 > }
76    
77 + /**
78 + * Auxiliary sorting function
79 + */
80 +
81 + bool indexSortingCriterion(const pair<int, int>& p1, const pair<int, int>& p2){
82 +  return p1.second < p2.second;
83 + }
84 +
85 + /**
86 + * Sorting the local index by global index
87 + */
88 +
89 + void DumpWriter::sortByGlobalIndex(){
90 +  Atom** atoms = entry_plug->atoms;
91 +  
92 +  indexArray.clear();
93 +  
94 +  for(int i = 0; i < mpiSim->getMyNlocal();i++)
95 +    indexArray.push_back(make_pair(i, atoms[i]->getGlobalIndex()));
96 +  
97 +  sort(indexArray.begin(), indexArray.end(), indexSortingCriterion);    
98 +
99 +  //for (int i = 0; i < mpiSim->getMyNlocal(); i++) {
100 +  //  printf("node %d has global %d at local %d\n", worldRank, indexArray[i].second, indexArray[i].first);
101 +  //}
102 +    
103 + }
104 +
105 + #endif
106 +
107 + void DumpWriter::writeDump(double currentTime){
108 +
109 +  ofstream finalOut;
110 +  vector<ofstream*> fileStreams;
111 +
112 + #ifdef IS_MPI
113 +  printf("Hello from node %d\n", worldRank);
114 +  sortByGlobalIndex();
115 +  if(worldRank == 0 ){
116 +    
117 +    finalOut.open( entry_plug->finalName, ios::out | ios::trunc );
118 +    if( !finalOut ){
119 +      sprintf( painCave.errMsg,
120 +               "Could not open \"%s\" for final dump output.\n",
121 +               entry_plug->finalName );
122 +      painCave.isFatal = 1;
123 +      simError();
124 +    }
125 +  }
126 + #endif // is_mpi
127 +
128 +  fileStreams.push_back(&finalOut);
129 +  fileStreams.push_back(&dumpFile);
130 +
131 +  writeFrame(fileStreams, currentTime);
132 +
133 + #ifdef IS_MPI
134 +  finalOut.close();
135 + #endif
136 +        
137 + }
138 +
139 + void DumpWriter::writeFinal(double currentTime){
140 +
141 +  ofstream finalOut;
142 +  vector<ofstream*> fileStreams;
143 +
144 + #ifdef IS_MPI
145 +  if(worldRank == 0 ){
146 + #endif // is_mpi
147 +
148 +    finalOut.open( entry_plug->finalName, ios::out | ios::trunc );
149 +
150 +    if( !finalOut ){
151 +      sprintf( painCave.errMsg,
152 +               "Could not open \"%s\" for final dump output.\n",
153 +               entry_plug->finalName );
154 +      painCave.isFatal = 1;
155 +      simError();
156 +    }
157 +
158 + #ifdef IS_MPI
159 +  }
160 + #endif // is_mpi
161 +  
162 +  fileStreams.push_back(&finalOut);  
163 +  writeFrame(fileStreams, currentTime);
164 +
165 + #ifdef IS_MPI
166 +  finalOut.close();
167 + #endif
168 +  
169 + }
170 +
171 + void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){
172 +
173    const int BUFFERSIZE = 2000;
174 <  char tempBuffer[BUFFERSIZE];
174 >  const int MINIBUFFERSIZE = 100;
175 >
176 >  char tempBuffer[BUFFERSIZE];  
177    char writeLine[BUFFERSIZE];
178  
179 <  int i;
179 >  int i, k;
180 >
181   #ifdef IS_MPI
182 <  int j, which_node, done, which_atom, local_index;
182 >  
183 >  /*********************************************************************
184 >   * Documentation?  You want DOCUMENTATION?
185 >   *
186 >   * Why all the potatoes below?  
187 >   *
188 >   * To make a long story short, the original version of DumpWriter
189 >   * worked in the most inefficient way possible.  Node 0 would
190 >   * poke each of the node for an individual atom's formatted data
191 >   * as node 0 worked its way down the global index. This was particularly
192 >   * inefficient since the method blocked all processors at every atom
193 >   * (and did it twice!).
194 >   *
195 >   * An intermediate version of DumpWriter could be described from Node
196 >   * zero's perspective as follows:
197 >   *
198 >   *  1) Have 100 of your friends stand in a circle.
199 >   *  2) When you say go, have all of them start tossing potatoes at
200 >   *     you (one at a time).
201 >   *  3) Catch the potatoes.
202 >   *
203 >   * It was an improvement, but MPI has buffers and caches that could
204 >   * best be described in this analogy as "potato nets", so there's no
205 >   * need to block the processors atom-by-atom.
206 >   *
207 >   * This new and improved DumpWriter works in an even more efficient
208 >   * way:
209 >   *
210 >   *  1) Have 100 of your friend stand in a circle.
211 >   *  2) When you say go, have them start tossing 5-pound bags of
212 >   *     potatoes at you.
213 >   *  3) Once you've caught a friend's bag of potatoes,
214 >   *     toss them a spud to let them know they can toss another bag.
215 >   *
216 >   * How's THAT for documentation?
217 >   *
218 >   *********************************************************************/
219 >
220 >  int *potatoes;
221 >  int myPotato;
222 >
223 >  int nProc;
224 >  int j, which_node, done, which_atom, local_index, currentIndex;
225 >  double atomData6[6];
226 >  double atomData13[13];
227 >  int isDirectional;
228 >  char* atomTypeString;
229 >  char MPIatomTypeString[MINIBUFFERSIZE];
230 >
231   #else //is_mpi
232    int nAtoms = entry_plug->n_atoms;
233   #endif //is_mpi
# Line 83 | Line 236 | void DumpWriter::writeDump( double currentTime ){
236    DirectionalAtom* dAtom;
237    Atom** atoms = entry_plug->atoms;
238    double pos[3], vel[3];
86 –    
87 –  
88 –  // write current frame to the eor file
239  
90 –  this->writeFinal( currentTime );
91 –
240   #ifndef IS_MPI
241 <    
242 <  outFile << nAtoms << "\n";
243 <    
96 <  outFile << currentTime << ";\t"
97 <          << entry_plug->Hmat[0][0] << "\t"
98 <          << entry_plug->Hmat[1][0] << "\t"
99 <          << entry_plug->Hmat[2][0] << ";\t"
241 >  
242 >  for(k = 0; k < outFile.size(); k++){
243 >    *outFile[k] << nAtoms << "\n";
244  
245 <          << entry_plug->Hmat[0][1] << "\t"
246 <          << entry_plug->Hmat[1][1] << "\t"
247 <          << entry_plug->Hmat[2][1] << ";\t"
245 >    *outFile[k] << currentTime << ";\t"
246 >               << entry_plug->Hmat[0][0] << "\t"
247 >                     << entry_plug->Hmat[1][0] << "\t"
248 >                     << entry_plug->Hmat[2][0] << ";\t"
249 >              
250 >               << entry_plug->Hmat[0][1] << "\t"
251 >                     << entry_plug->Hmat[1][1] << "\t"
252 >                     << entry_plug->Hmat[2][1] << ";\t"
253  
254 <          << entry_plug->Hmat[0][2] << "\t"
255 <          << entry_plug->Hmat[1][2] << "\t"
256 <          << entry_plug->Hmat[2][2] << ";\n";
257 <    
254 >                     << entry_plug->Hmat[0][2] << "\t"
255 >                     << entry_plug->Hmat[1][2] << "\t"
256 >                     << entry_plug->Hmat[2][2] << ";";
257 >
258 >    //write out additional parameters, such as chi and eta
259 >    *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
260 >  }
261 >  
262    for( i=0; i<nAtoms; i++ ){
263 <      
263 >
264      atoms[i]->getPos(pos);
265      atoms[i]->getVel(vel);
266  
# Line 123 | Line 276 | void DumpWriter::writeDump( double currentTime ){
276      strcpy( writeLine, tempBuffer );
277  
278      if( atoms[i]->isDirectional() ){
279 <        
279 >
280        dAtom = (DirectionalAtom *)atoms[i];
281        dAtom->getQ( q );
282 <        
282 >
283        sprintf( tempBuffer,
284                 "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
285                 q[0],
# Line 140 | Line 293 | void DumpWriter::writeDump( double currentTime ){
293      }
294      else
295        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
296 <      
297 <    outFile << writeLine;
296 >
297 >    for(k = 0; k < outFile.size(); k++)
298 >      *outFile[k] << writeLine;
299    }
146 –  outFile.flush();
300  
301   #else // is_mpi
302  
303 <  // first thing first, suspend fatalities.
304 <  painCave.isEventLoop = 1;
303 >  /* code to find maximum tag value */
304 >  
305 >  int *tagub, flag, MAXTAG;
306 >  MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
307 >  if (flag) {
308 >    MAXTAG = *tagub;
309 >  } else {
310 >    MAXTAG = 32767;
311 >  }  
312  
153 –  int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
313    int haveError;
314  
315    MPI_Status istatus;
316    int *AtomToProcMap = mpiSim->getAtomToProcMap();
317 <  
317 >
318    // write out header and node 0's coordinates
319 <  
319 >
320    if( worldRank == 0 ){
321 <    outFile << mpiSim->getTotAtoms() << "\n";
322 <  
323 <    outFile << currentTime << ";\t"
324 <            << entry_plug->Hmat[0][0] << "\t"
325 <            << entry_plug->Hmat[1][0] << "\t"
326 <            << entry_plug->Hmat[2][0] << ";\t"
327 <      
328 <            << entry_plug->Hmat[0][1] << "\t"
329 <            << entry_plug->Hmat[1][1] << "\t"
171 <            << entry_plug->Hmat[2][1] << ";\t"
172 <      
173 <            << entry_plug->Hmat[0][2] << "\t"
174 <            << entry_plug->Hmat[1][2] << "\t"
175 <            << entry_plug->Hmat[2][2] << ";\n";
321 >
322 >    // Node 0 needs a list of the magic potatoes for each processor;
323 >
324 >    nProc = mpiSim->getNumberProcessors();
325 >    potatoes = new int[nProc];
326 >
327 >    //write out the comment lines
328 >    for (i = 0; i < nProc; i++)
329 >      potatoes[i] = 0;
330      
331 <    outFile.flush();
331 >      for(k = 0; k < outFile.size(); k++){
332 >        *outFile[k] << mpiSim->getTotAtoms() << "\n";
333 >
334 >        *outFile[k] << currentTime << ";\t"
335 >                         << entry_plug->Hmat[0][0] << "\t"
336 >                         << entry_plug->Hmat[1][0] << "\t"
337 >                         << entry_plug->Hmat[2][0] << ";\t"
338 >
339 >                         << entry_plug->Hmat[0][1] << "\t"
340 >                         << entry_plug->Hmat[1][1] << "\t"
341 >                         << entry_plug->Hmat[2][1] << ";\t"
342 >
343 >                         << entry_plug->Hmat[0][2] << "\t"
344 >                         << entry_plug->Hmat[1][2] << "\t"
345 >                         << entry_plug->Hmat[2][2] << ";";
346 >  
347 >        *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
348 >    }
349 >
350 >    currentIndex = 0;
351 >
352      for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
353 +      
354        // Get the Node number which has this atom;
355        
356 <      which_node = AtomToProcMap[i];    
356 >      which_node = AtomToProcMap[i];
357        
358 <      if (which_node == 0 ) {
358 >      if (which_node != 0) {
359 >
360 >        if (potatoes[which_node] + 3 >= MAXTAG) {
361 >          // The potato was going to exceed the maximum value,
362 >          // so wrap this processor potato back to 0:        
363 >
364 >          potatoes[which_node] = 0;          
365 >          MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
366 >          
367 >        }
368 >
369 >        myPotato = potatoes[which_node];        
370 >        
371 >        MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
372 >                 myPotato, MPI_COMM_WORLD, &istatus);
373 >        
374 >        atomTypeString = MPIatomTypeString;
375          
376 <        haveError = 0;
377 <        which_atom = i;
378 <        local_index=-1;        
379 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
380 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
376 >        myPotato++;
377 >
378 >        MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
379 >                 myPotato, MPI_COMM_WORLD, &istatus);
380 >              
381 >        myPotato++;
382 >
383 >        if (isDirectional) {          
384 >          MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node,
385 >                   myPotato, MPI_COMM_WORLD, &istatus);
386 >        } else {
387 >          MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node,
388 >                   myPotato, MPI_COMM_WORLD, &istatus);          
389          }
390 <        if (local_index != -1) {
391 <          //format the line
390 >        
391 >        myPotato++;
392 >        potatoes[which_node] = myPotato;
393 >
394 >      } else {
395 >        
396 >        haveError = 0;
397 >        which_atom = i;
398 >        
399 >        //local_index = -1;
400 >
401 >        //for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
402 >        //  if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
403 >        //}
404 >        
405 >        //if (local_index != -1) {
406            
407 +          local_index = indexArray[currentIndex].first;        
408 +          
409 +          if (which_atom == indexArray[currentIndex].second) {
410 +            
411 +            atomTypeString = atoms[local_index]->getType();
412 +            
413            atoms[local_index]->getPos(pos);
414 <          atoms[local_index]->getVel(vel);
196 <
197 <          sprintf( tempBuffer,
198 <                   "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
199 <                   atoms[local_index]->getType(),
200 <                   pos[0],
201 <                   pos[1],
202 <                   pos[2],
203 <                   vel[0],
204 <                   vel[1],
205 <                   vel[2]); // check here.
206 <          strcpy( writeLine, tempBuffer );
414 >          atoms[local_index]->getVel(vel);          
415            
416 +          atomData6[0] = pos[0];
417 +          atomData6[1] = pos[1];
418 +          atomData6[2] = pos[2];
419 +
420 +          atomData6[3] = vel[0];
421 +          atomData6[4] = vel[1];
422 +          atomData6[5] = vel[2];
423 +          
424 +          isDirectional = 0;
425 +
426            if( atoms[local_index]->isDirectional() ){
427 +
428 +            isDirectional = 1;
429              
430              dAtom = (DirectionalAtom *)atoms[local_index];
431              dAtom->getQ( q );
432 +
433 +            for (int j = 0; j < 6 ; j++)
434 +              atomData13[j] = atomData6[j];            
435              
436 <            sprintf( tempBuffer,
437 <                     "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
438 <                     q[0],
439 <                     q[1],
440 <                     q[2],
441 <                     q[3],
442 <                     dAtom->getJx(),
443 <                     dAtom->getJy(),
444 <                     dAtom->getJz());
445 <            strcat( writeLine, tempBuffer );
446 <            
224 <          }
225 <          else
226 <            strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );      
227 <        }
228 <        else {
436 >            atomData13[6] = q[0];
437 >            atomData13[7] = q[1];
438 >            atomData13[8] = q[2];
439 >            atomData13[9] = q[3];
440 >            
441 >            atomData13[10] = dAtom->getJx();
442 >            atomData13[11] = dAtom->getJy();
443 >            atomData13[12] = dAtom->getJz();
444 >          }
445 >          
446 >        } else {
447            sprintf(painCave.errMsg,
448 <                  "Atom %d not found on processor %d\n",
449 <                  i, worldRank );
448 >                  "Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n",
449 >                  which_atom, worldRank, currentIndex, local_index );
450            haveError= 1;
451            simError();
452 <        }
453 <        
454 <        if(haveError) nodeZeroError();
455 <
452 >        }
453 >        
454 >        if(haveError) DieDieDie();
455 >        
456 >        currentIndex++;
457        }
458 <      else {
459 <        myStatus = 1;
460 <        MPI_Send(&myStatus, 1, MPI_INT, which_node,
242 <                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
243 <        MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
244 <                 MPI_COMM_WORLD);
245 <        MPI_Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node,
246 <                 TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
247 <        MPI_Recv(&myStatus, 1, MPI_INT, which_node,
248 <                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
458 >      // If we've survived to here, format the line:
459 >      
460 >      if (!isDirectional) {
461          
462 <        if(!myStatus) nodeZeroError();
463 <
462 >        sprintf( writeLine,
463 >                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
464 >                 atomTypeString,
465 >                 atomData6[0],
466 >                 atomData6[1],
467 >                 atomData6[2],
468 >                 atomData6[3],
469 >                 atomData6[4],
470 >                 atomData6[5]);
471 >        
472 >        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
473 >        
474 >      } else {
475 >        
476 >        sprintf( writeLine,
477 >                 "%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",
478 >                 atomTypeString,
479 >                 atomData13[0],
480 >                 atomData13[1],
481 >                 atomData13[2],
482 >                 atomData13[3],
483 >                 atomData13[4],
484 >                 atomData13[5],
485 >                 atomData13[6],
486 >                 atomData13[7],
487 >                 atomData13[8],
488 >                 atomData13[9],
489 >                 atomData13[10],
490 >                 atomData13[11],
491 >                 atomData13[12]);
492 >        
493        }
494        
495 <      outFile << writeLine;
496 <      outFile.flush();
495 >      for(k = 0; k < outFile.size(); k++)
496 >        *outFile[k] << writeLine;
497      }
498      
499 <    // kill everyone off:
500 <    myStatus = -1;
260 <    for (j = 0; j < mpiSim->getNumberProcessors(); j++) {      
261 <      MPI_Send(&myStatus, 1, MPI_INT, j,
262 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
263 <    }
264 <
265 <  } else {
499 >    for(k = 0; k < outFile.size(); k++)
500 >      outFile[k]->flush();
501      
502 <    done = 0;
503 <    while (!done) {
269 <      
270 <      MPI_Recv(&myStatus, 1, MPI_INT, 0,
271 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
272 <
273 <      if(!myStatus) anonymousNodeDie();
274 <      
275 <      if(myStatus < 0) break;
276 <
277 <      MPI_Recv(&which_atom, 1, MPI_INT, 0,
278 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
279 <      
280 <      myStatus = 1;
281 <      local_index=-1;        
282 <      for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
283 <        if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
284 <      }
285 <      if (local_index != -1) {
286 <        //format the line
287 <
288 <        atoms[local_index]->getPos(pos);
289 <        atoms[local_index]->getVel(vel);
290 <
291 <        sprintf( tempBuffer,
292 <                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
293 <                 atoms[local_index]->getType(),
294 <                 pos[0],
295 <                 pos[1],
296 <                 pos[2],
297 <                 vel[0],
298 <                 vel[1],
299 <                 vel[2]); // check here.
300 <        strcpy( writeLine, tempBuffer );
301 <        
302 <        if( atoms[local_index]->isDirectional() ){
303 <          
304 <          dAtom = (DirectionalAtom *)atoms[local_index];
305 <          dAtom->getQ( q );
306 <          
307 <          sprintf( tempBuffer,
308 <                   "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
309 <                   q[0],
310 <                   q[1],
311 <                   q[2],
312 <                   q[3],
313 <                   dAtom->getJx(),
314 <                   dAtom->getJy(),
315 <                   dAtom->getJz());
316 <          strcat( writeLine, tempBuffer );
317 <        }
318 <        else{
319 <          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
320 <        }
321 <      }
322 <      else {
323 <        sprintf(painCave.errMsg,
324 <                "Atom %d not found on processor %d\n",
325 <                which_atom, worldRank );
326 <        myStatus = 0;
327 <        simError();
328 <
329 <        strcpy( writeLine, "Hello, I'm an error.\n");
330 <      }
331 <
332 <      MPI_Send(writeLine, BUFFERSIZE, MPI_CHAR, 0,
333 <               TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
334 <      MPI_Send( &myStatus, 1, MPI_INT, 0,
335 <                TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
336 <    }
337 <  }  
338 <  outFile.flush();
339 <  sprintf( checkPointMsg,
340 <           "Sucessfully took a dump.\n");
341 <  MPIcheckPoint();
342 <
343 < // last  thing last, enable  fatalities.
344 <  painCave.isEventLoop = 0;
345 <
346 < #endif // is_mpi
347 < }
348 <
349 < void DumpWriter::writeFinal(double finalTime){
350 <
351 <  char finalName[500];
352 <  ofstream finalOut;
353 <
354 <  const int BUFFERSIZE = 2000;
355 <  char tempBuffer[BUFFERSIZE];
356 <  char writeLine[BUFFERSIZE];  
357 <
358 <  double q[4];
359 <  DirectionalAtom* dAtom;
360 <  Atom** atoms = entry_plug->atoms;
361 <  int i;
362 < #ifdef IS_MPI
363 <  int j, which_node, done, which_atom, local_index;
364 < #else //is_mpi
365 <  int nAtoms = entry_plug->n_atoms;
366 < #endif //is_mpi
367 <  
368 <  double pos[3], vel[3];
369 <  
370 < #ifdef IS_MPI
371 <  if(worldRank == 0 ){
372 < #endif // is_mpi
502 >    sprintf( checkPointMsg,
503 >             "Sucessfully took a dump.\n");
504      
505 <    strcpy( finalName, entry_plug->finalName );
505 >    MPIcheckPoint();        
506      
507 <    finalOut.open( finalName, ios::out | ios::trunc );
377 <    if( !finalOut ){
378 <      sprintf( painCave.errMsg,
379 <               "Could not open \"%s\" for final dump output.\n",
380 <               finalName );
381 <      painCave.isFatal = 1;
382 <      simError();
383 <    }
507 >    delete[] potatoes;
508      
509 <    // finalOut.setf( ios::scientific );
386 <    
387 < #ifdef IS_MPI
388 <  }
389 <  
390 <  sprintf(checkPointMsg,"Opened file for final configuration\n");
391 <  MPIcheckPoint();  
392 <  
393 < #endif //is_mpi
509 >  } else {
510  
511 <  
396 < #ifndef IS_MPI
397 <    
398 <  finalOut << nAtoms << "\n";
399 <    
400 <  finalOut << finalTime << ";\t"
401 <           << entry_plug->Hmat[0][0] << "\t"
402 <           << entry_plug->Hmat[1][0] << "\t"
403 <           << entry_plug->Hmat[2][0] << ";\t"
404 <    
405 <           << entry_plug->Hmat[0][1] << "\t"
406 <           << entry_plug->Hmat[1][1] << "\t"
407 <           << entry_plug->Hmat[2][1] << ";\t"
408 <    
409 <           << entry_plug->Hmat[0][2] << "\t"
410 <           << entry_plug->Hmat[1][2] << "\t"
411 <           << entry_plug->Hmat[2][2] << ";\n";
412 <  
413 <  for( i=0; i<nAtoms; i++ ){
414 <      
415 <    atoms[i]->getPos(pos);
416 <    atoms[i]->getVel(vel);
417 <    
418 <    sprintf( tempBuffer,
419 <             "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
420 <             atoms[i]->getType(),
421 <             pos[0],
422 <             pos[1],
423 <             pos[2],
424 <             vel[0],
425 <             vel[1],
426 <             vel[2]);
427 <    strcpy( writeLine, tempBuffer );
511 >    // worldRank != 0, so I'm a remote node.  
512  
513 <    if( atoms[i]->isDirectional() ){
430 <        
431 <      dAtom = (DirectionalAtom *)atoms[i];
432 <      dAtom->getQ( q );
433 <        
434 <      sprintf( tempBuffer,
435 <               "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
436 <               q[0],
437 <               q[1],
438 <               q[2],
439 <               q[3],
440 <               dAtom->getJx(),
441 <               dAtom->getJy(),
442 <               dAtom->getJz());
443 <      strcat( writeLine, tempBuffer );
444 <    }
445 <    else
446 <      strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
447 <      
448 <    finalOut << writeLine;
449 <  }
450 <  finalOut.flush();
451 <  finalOut.close();
513 >    // Set my magic potato to 0:
514  
515 < #else // is_mpi
516 <  
455 <  // first thing first, suspend fatalities.
456 <  painCave.isEventLoop = 1;
457 <
458 <  int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
459 <  int haveError;
460 <
461 <  MPI_Status istatus;
462 <  int *AtomToProcMap = mpiSim->getAtomToProcMap();
463 <
464 <  // write out header and node 0's coordinates
465 <  
466 <  haveError = 0;
467 <  if( worldRank == 0 ){
468 <    finalOut << mpiSim->getTotAtoms() << "\n";
515 >    myPotato = 0;
516 >    currentIndex = 0;
517      
470 –    finalOut << finalTime << ";\t"
471 –             << entry_plug->Hmat[0][0] << "\t"
472 –             << entry_plug->Hmat[1][0] << "\t"
473 –             << entry_plug->Hmat[2][0] << ";\t"
474 –      
475 –             << entry_plug->Hmat[0][1] << "\t"
476 –             << entry_plug->Hmat[1][1] << "\t"
477 –             << entry_plug->Hmat[2][1] << ";\t"
478 –      
479 –             << entry_plug->Hmat[0][2] << "\t"
480 –             << entry_plug->Hmat[1][2] << "\t"
481 –             << entry_plug->Hmat[2][2] << ";\n";
482 –    
518      for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
484 –      // Get the Node number which has this molecule:
519        
520 <      which_node = AtomToProcMap[i];    
520 >      // Am I the node which has this atom?
521        
522 <      if (which_node == mpiSim->getMyNode()) {
522 >      if (AtomToProcMap[i] == worldRank) {
523  
524 <        which_atom = i;
525 <        local_index=-1;        
526 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
527 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
524 >        if (myPotato + 3 >= MAXTAG) {
525 >          
526 >          // The potato was going to exceed the maximum value,
527 >          // so wrap this processor potato back to 0 (and block until
528 >          // node 0 says we can go:
529 >          
530 >          MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
531 >          
532          }
533 <        if (local_index != -1) {    
533 >        which_atom = i;
534  
535 +        //local_index = -1;
536 +
537 +        //for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
538 +        // if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
539 +        //}
540 +        
541 +        //if (local_index != -1) {
542 +
543 +        local_index = indexArray[currentIndex].first;        
544 +                
545 +        if (which_atom == indexArray[currentIndex].second) {
546 +        
547 +          atomTypeString = atoms[local_index]->getType();
548 +          
549            atoms[local_index]->getPos(pos);
550            atoms[local_index]->getVel(vel);
551            
552 <          sprintf( tempBuffer,
553 <                   "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
554 <                   atoms[local_index]->getType(),
555 <                   pos[0],
556 <                   pos[1],
557 <                   pos[2],
558 <                   vel[0],
559 <                   vel[1],
560 <                   vel[2]);
561 <          strcpy( writeLine, tempBuffer );
562 <          
563 <          if( atoms[local_index]->isDirectional() ){
564 <            
565 <            dAtom = (DirectionalAtom *)atoms[local_index];
566 <            dAtom->getQ( q );
567 <            
568 <            sprintf( tempBuffer,
569 <                     "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
570 <                     q[0],
571 <                     q[1],
572 <                     q[2],
573 <                     q[3],
574 <                     dAtom->getJx(),
575 <                     dAtom->getJy(),
576 <                     dAtom->getJz());
577 <            strcat( writeLine, tempBuffer );
578 <          }
579 <          else
580 <            strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );      
581 <        }
582 <        else {
552 >          atomData6[0] = pos[0];
553 >          atomData6[1] = pos[1];
554 >          atomData6[2] = pos[2];
555 >
556 >          atomData6[3] = vel[0];
557 >          atomData6[4] = vel[1];
558 >          atomData6[5] = vel[2];
559 >          
560 >          isDirectional = 0;
561 >
562 >          if( atoms[local_index]->isDirectional() ){
563 >
564 >            isDirectional = 1;
565 >            
566 >            dAtom = (DirectionalAtom *)atoms[local_index];
567 >            dAtom->getQ( q );
568 >            
569 >            for (int j = 0; j < 6 ; j++)
570 >              atomData13[j] = atomData6[j];
571 >            
572 >            atomData13[6] = q[0];
573 >            atomData13[7] = q[1];
574 >            atomData13[8] = q[2];
575 >            atomData13[9] = q[3];
576 >  
577 >            atomData13[10] = dAtom->getJx();
578 >            atomData13[11] = dAtom->getJy();
579 >            atomData13[12] = dAtom->getJz();
580 >          }
581 >
582 >        } else {
583            sprintf(painCave.errMsg,
584 <                  "Atom %d not found on processor %d\n",
585 <                  i, worldRank );
584 >                  "Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n",
585 >                  which_atom, worldRank, currentIndex, local_index );
586            haveError= 1;
587            simError();
588 <        }
588 >        }
589 >        
590 >        strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
591  
592 <        if(haveError) nodeZeroError();
593 <    
594 <      }
595 <      else {
592 >        // null terminate the string before sending (just in case):
593 >        MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
594 >
595 >        MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
596 >                             myPotato, MPI_COMM_WORLD);
597          
598 <        myStatus = 1;
544 <        MPI_Send(&myStatus, 1, MPI_INT, which_node,
545 <                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
546 <        MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
547 <                 MPI_COMM_WORLD);
548 <        MPI_Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node,
549 <                 TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
550 <        MPI_Recv(&myStatus, 1, MPI_INT, which_node,
551 <                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
552 <        
553 <        if(!myStatus) nodeZeroError();
554 <      }
555 <      
556 <      finalOut << writeLine;
557 <    }
558 <    
559 <    // kill everyone off:
560 <    myStatus = -1;
561 <    for (j = 0; j < mpiSim->getNumberProcessors(); j++) {      
562 <      MPI_Send(&myStatus, 1, MPI_INT, j,
563 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
564 <    }
598 >        myPotato++;
599  
600 <  } else {
601 <    
602 <    done = 0;
603 <    while (!done) {
600 >        MPI_Send(&isDirectional, 1, MPI_INT, 0,
601 >                             myPotato, MPI_COMM_WORLD);
602 >        
603 >        myPotato++;
604 >        
605 >        if (isDirectional) {
606  
607 <      MPI_Recv(&myStatus, 1, MPI_INT, 0,
608 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
609 <      
610 <      if(!myStatus) anonymousNodeDie();
575 <      
576 <      if(myStatus < 0) break;
577 <      
578 <      MPI_Recv(&which_atom, 1, MPI_INT, 0,
579 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
580 <      
581 <      myStatus = 1;
582 <      local_index=-1;        
583 <      for (j=0; j < mpiSim->getMyNlocal(); j++) {
584 <        if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
585 <      }
586 <      if (local_index != -1) {
607 >          MPI_Send(atomData13, 13, MPI_DOUBLE, 0,
608 >                   myPotato, MPI_COMM_WORLD);
609 >          
610 >        } else {
611  
612 <        atoms[local_index]->getPos(pos);
613 <        atoms[local_index]->getVel(vel);
612 >          MPI_Send(atomData6, 6, MPI_DOUBLE, 0,
613 >                   myPotato, MPI_COMM_WORLD);
614 >        }
615  
616 <        //format the line
617 <        sprintf( tempBuffer,
593 <                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
594 <                 atoms[local_index]->getType(),
595 <                 pos[0],
596 <                 pos[1],
597 <                 pos[2],
598 <                 vel[0],
599 <                 vel[1],
600 <                 vel[2]); // check here.
601 <        strcpy( writeLine, tempBuffer );
602 <        
603 <        if( atoms[local_index]->isDirectional() ){
604 <          
605 <          dAtom = (DirectionalAtom *)atoms[local_index];
606 <          dAtom->getQ( q );
607 <          
608 <          sprintf( tempBuffer,
609 <                   "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
610 <                   q[0],
611 <                   q[1],
612 <                   q[2],
613 <                   q[3],
614 <                   dAtom->getJx(),
615 <                   dAtom->getJy(),
616 <                   dAtom->getJz());
617 <          strcat( writeLine, tempBuffer );
618 <        }
619 <        else{
620 <          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
621 <        }
622 <      }
623 <      else {
624 <        sprintf(painCave.errMsg,
625 <                "Atom %d not found on processor %d\n",
626 <                which_atom, worldRank );
627 <        myStatus = 0;
628 <        simError();
629 <        
630 <        strcpy( writeLine, "Hello, I'm an error.\n");
616 >        myPotato++;  
617 >        currentIndex++;    
618        }
632 –
633 –      MPI_Send(writeLine, BUFFERSIZE, MPI_CHAR, 0,
634 –               TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
635 –      MPI_Send( &myStatus, 1, MPI_INT, 0,
636 –                TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
619      }
620 <  }
621 <  finalOut.flush();
622 <  sprintf( checkPointMsg,
623 <           "Sucessfully took a dump.\n");
624 <  MPIcheckPoint();
620 >
621 >    sprintf( checkPointMsg,
622 >             "Sucessfully took a dump.\n");
623 >    MPIcheckPoint();        
624 >    
625 >  }
626    
644 –  if( worldRank == 0 ) finalOut.close();    
627   #endif // is_mpi
628   }
629  
648 –
649 –
630   #ifdef IS_MPI
631  
632   // a couple of functions to let us escape the write loop
633  
634 < void dWrite::nodeZeroError( void ){
655 <  int j, myStatus;
656 <  
657 <  myStatus = 0;
658 <  for (j = 0; j < mpiSim->getNumberProcessors(); j++) {      
659 <    MPI_Send( &myStatus, 1, MPI_INT, j,
660 <              TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
661 <  }  
662 <  
634 > void dWrite::DieDieDie( void ){
635  
636    MPI_Finalize();
637    exit (0);
666 –  
638   }
639  
669 – void dWrite::anonymousNodeDie( void ){
670 –
671 –  MPI_Finalize();
672 –  exit (0);
673 – }
674 –
640   #endif //is_mpi

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