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root/group/trunk/OOPSE/libmdtools/DumpWriter.cpp
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Comparing trunk/OOPSE/libmdtools/DumpWriter.cpp (file contents):
Revision 787 by mmeineke, Thu Sep 25 19:27:15 2003 UTC vs.
Revision 1078 by tim, Tue Mar 2 20:32:40 2004 UTC

# Line 1 | Line 1
1 + #define _LARGEFILE_SOURCE64
2   #define _FILE_OFFSET_BITS 64
3  
4 < #include <cstring>
4 > #include <string.h>
5   #include <iostream>
6   #include <fstream>
7 + #include <algorithm>
8 + #include <utility>
9  
10   #ifdef IS_MPI
11   #include <mpi.h>
12   #include "mpiSimulation.hpp"
10 – #define TAKE_THIS_TAG_CHAR 1
11 – #define TAKE_THIS_TAG_INT 2
13  
14   namespace dWrite{
15 <  void nodeZeroError( void );
15 <  void anonymousNodeDie( void );
15 >  void DieDieDie( void );
16   }
17  
18   using namespace dWrite;
# Line 28 | Line 28 | DumpWriter::DumpWriter( SimInfo* the_entry_plug ){
28   #ifdef IS_MPI
29    if(worldRank == 0 ){
30   #endif // is_mpi
31 <    
32 <    strcpy( outName, entry_plug->sampleName );
33 <    
34 <    outFile.open(outName, ios::out | ios::trunc );
35 <    
36 <    if( !outFile ){
37 <      
31 >
32 >    dumpFile.open(entry_plug->sampleName, ios::out | ios::trunc );
33 >
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 +
101 + #endif
102 +
103 + void DumpWriter::writeDump(double currentTime){
104 +
105 +  ofstream finalOut;
106 +  vector<ofstream*> fileStreams;
107 +
108 + #ifdef IS_MPI
109 +  if(worldRank == 0 ){
110 + #endif    
111 +    finalOut.open( entry_plug->finalName, ios::out | ios::trunc );
112 +    if( !finalOut ){
113 +      sprintf( painCave.errMsg,
114 +               "Could not open \"%s\" for final dump output.\n",
115 +               entry_plug->finalName );
116 +      painCave.isFatal = 1;
117 +      simError();
118 +    }
119 + #ifdef IS_MPI
120 +  }
121 + #endif // is_mpi
122 +
123 +  fileStreams.push_back(&finalOut);
124 +  fileStreams.push_back(&dumpFile);
125 +
126 +  writeFrame(fileStreams, currentTime);
127 +
128 + #ifdef IS_MPI
129 +  finalOut.close();
130 + #endif
131 +        
132 + }
133 +
134 + void DumpWriter::writeFinal(double currentTime){
135 +
136 +  ofstream finalOut;
137 +  vector<ofstream*> fileStreams;
138 +
139 + #ifdef IS_MPI
140 +  if(worldRank == 0 ){
141 + #endif // is_mpi
142 +
143 +    finalOut.open( entry_plug->finalName, ios::out | ios::trunc );
144 +
145 +    if( !finalOut ){
146 +      sprintf( painCave.errMsg,
147 +               "Could not open \"%s\" for final dump output.\n",
148 +               entry_plug->finalName );
149 +      painCave.isFatal = 1;
150 +      simError();
151 +    }
152 +
153 + #ifdef IS_MPI
154 +  }
155 + #endif // is_mpi
156 +  
157 +  fileStreams.push_back(&finalOut);  
158 +  writeFrame(fileStreams, currentTime);
159 +
160 + #ifdef IS_MPI
161 +  finalOut.close();
162 + #endif
163 +  
164 + }
165 +
166 + void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){
167 +
168    const int BUFFERSIZE = 2000;
169 <  char tempBuffer[BUFFERSIZE];
169 >  const int MINIBUFFERSIZE = 100;
170 >
171 >  char tempBuffer[BUFFERSIZE];  
172    char writeLine[BUFFERSIZE];
173  
174 <  int i;
174 >  int i, k;
175 >
176   #ifdef IS_MPI
177 <  int j, which_node, done, which_atom, local_index;
177 >  
178 >  /*********************************************************************
179 >   * Documentation?  You want DOCUMENTATION?
180 >   *
181 >   * Why all the potatoes below?  
182 >   *
183 >   * To make a long story short, the original version of DumpWriter
184 >   * worked in the most inefficient way possible.  Node 0 would
185 >   * poke each of the node for an individual atom's formatted data
186 >   * as node 0 worked its way down the global index. This was particularly
187 >   * inefficient since the method blocked all processors at every atom
188 >   * (and did it twice!).
189 >   *
190 >   * An intermediate version of DumpWriter could be described from Node
191 >   * zero's perspective as follows:
192 >   *
193 >   *  1) Have 100 of your friends stand in a circle.
194 >   *  2) When you say go, have all of them start tossing potatoes at
195 >   *     you (one at a time).
196 >   *  3) Catch the potatoes.
197 >   *
198 >   * It was an improvement, but MPI has buffers and caches that could
199 >   * best be described in this analogy as "potato nets", so there's no
200 >   * need to block the processors atom-by-atom.
201 >   *
202 >   * This new and improved DumpWriter works in an even more efficient
203 >   * way:
204 >   *
205 >   *  1) Have 100 of your friend stand in a circle.
206 >   *  2) When you say go, have them start tossing 5-pound bags of
207 >   *     potatoes at you.
208 >   *  3) Once you've caught a friend's bag of potatoes,
209 >   *     toss them a spud to let them know they can toss another bag.
210 >   *
211 >   * How's THAT for documentation?
212 >   *
213 >   *********************************************************************/
214 >
215 >  int *potatoes;
216 >  int myPotato;
217 >
218 >  int nProc;
219 >  int j, which_node, done, which_atom, local_index, currentIndex;
220 >  double atomData6[6];
221 >  double atomData13[13];
222 >  int isDirectional;
223 >  char* atomTypeString;
224 >  char MPIatomTypeString[MINIBUFFERSIZE];
225 >
226   #else //is_mpi
227    int nAtoms = entry_plug->n_atoms;
228   #endif //is_mpi
# Line 83 | Line 231 | void DumpWriter::writeDump( double currentTime ){
231    DirectionalAtom* dAtom;
232    Atom** atoms = entry_plug->atoms;
233    double pos[3], vel[3];
86 –    
234  
235   #ifndef IS_MPI
236 <    
237 <  outFile << nAtoms << "\n";
238 <    
92 <  outFile << currentTime << ";\t"
93 <          << entry_plug->Hmat[0][0] << "\t"
94 <          << entry_plug->Hmat[1][0] << "\t"
95 <          << entry_plug->Hmat[2][0] << ";\t"
236 >  
237 >  for(k = 0; k < outFile.size(); k++){
238 >    *outFile[k] << nAtoms << "\n";
239  
240 <          << entry_plug->Hmat[0][1] << "\t"
241 <          << entry_plug->Hmat[1][1] << "\t"
242 <          << entry_plug->Hmat[2][1] << ";\t"
240 >    *outFile[k] << currentTime << ";\t"
241 >               << entry_plug->Hmat[0][0] << "\t"
242 >                     << entry_plug->Hmat[1][0] << "\t"
243 >                     << entry_plug->Hmat[2][0] << ";\t"
244 >              
245 >               << entry_plug->Hmat[0][1] << "\t"
246 >                     << entry_plug->Hmat[1][1] << "\t"
247 >                     << entry_plug->Hmat[2][1] << ";\t"
248  
249 <          << entry_plug->Hmat[0][2] << "\t"
250 <          << entry_plug->Hmat[1][2] << "\t"
251 <          << entry_plug->Hmat[2][2] << ";\n";
252 <    
249 >                     << entry_plug->Hmat[0][2] << "\t"
250 >                     << entry_plug->Hmat[1][2] << "\t"
251 >                     << entry_plug->Hmat[2][2] << ";";
252 >
253 >    //write out additional parameters, such as chi and eta
254 >    *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
255 >  }
256 >  
257    for( i=0; i<nAtoms; i++ ){
258 <      
258 >
259      atoms[i]->getPos(pos);
260      atoms[i]->getVel(vel);
261  
# Line 119 | Line 271 | void DumpWriter::writeDump( double currentTime ){
271      strcpy( writeLine, tempBuffer );
272  
273      if( atoms[i]->isDirectional() ){
274 <        
274 >
275        dAtom = (DirectionalAtom *)atoms[i];
276        dAtom->getQ( q );
277 <        
277 >
278        sprintf( tempBuffer,
279                 "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
280                 q[0],
# Line 136 | Line 288 | void DumpWriter::writeDump( double currentTime ){
288      }
289      else
290        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
291 <      
292 <    outFile << writeLine;
291 >
292 >    for(k = 0; k < outFile.size(); k++)
293 >      *outFile[k] << writeLine;
294    }
142 –  outFile.flush();
295  
296   #else // is_mpi
297  
298 <  // first thing first, suspend fatalities.
299 <  painCave.isEventLoop = 1;
298 >  /* code to find maximum tag value */
299 >  
300 >  int *tagub, flag, MAXTAG;
301 >  MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
302 >  if (flag) {
303 >    MAXTAG = *tagub;
304 >  } else {
305 >    MAXTAG = 32767;
306 >  }  
307  
149 –  int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
308    int haveError;
309  
310    MPI_Status istatus;
311    int *AtomToProcMap = mpiSim->getAtomToProcMap();
312 <  
312 >
313    // write out header and node 0's coordinates
314 <  
314 >
315    if( worldRank == 0 ){
316 <    outFile << mpiSim->getTotAtoms() << "\n";
317 <  
318 <    outFile << currentTime << ";\t"
319 <            << entry_plug->Hmat[0][0] << "\t"
320 <            << entry_plug->Hmat[1][0] << "\t"
321 <            << entry_plug->Hmat[2][0] << ";\t"
322 <      
323 <            << entry_plug->Hmat[0][1] << "\t"
324 <            << entry_plug->Hmat[1][1] << "\t"
167 <            << entry_plug->Hmat[2][1] << ";\t"
168 <      
169 <            << entry_plug->Hmat[0][2] << "\t"
170 <            << entry_plug->Hmat[1][2] << "\t"
171 <            << entry_plug->Hmat[2][2] << ";\n";
316 >
317 >    // Node 0 needs a list of the magic potatoes for each processor;
318 >
319 >    nProc = mpiSim->getNumberProcessors();
320 >    potatoes = new int[nProc];
321 >
322 >    //write out the comment lines
323 >    for (i = 0; i < nProc; i++)
324 >      potatoes[i] = 0;
325      
326 <    outFile.flush();
326 >      for(k = 0; k < outFile.size(); k++){
327 >        *outFile[k] << mpiSim->getTotAtoms() << "\n";
328 >
329 >        *outFile[k] << currentTime << ";\t"
330 >                         << entry_plug->Hmat[0][0] << "\t"
331 >                         << entry_plug->Hmat[1][0] << "\t"
332 >                         << entry_plug->Hmat[2][0] << ";\t"
333 >
334 >                         << entry_plug->Hmat[0][1] << "\t"
335 >                         << entry_plug->Hmat[1][1] << "\t"
336 >                         << entry_plug->Hmat[2][1] << ";\t"
337 >
338 >                         << entry_plug->Hmat[0][2] << "\t"
339 >                         << entry_plug->Hmat[1][2] << "\t"
340 >                         << entry_plug->Hmat[2][2] << ";";
341 >  
342 >        *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
343 >    }
344 >
345 >    currentIndex = 0;
346 >
347      for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
348 +      
349        // Get the Node number which has this atom;
350        
351 <      which_node = AtomToProcMap[i];    
351 >      which_node = AtomToProcMap[i];
352        
353 <      if (which_node == 0 ) {
353 >      if (which_node != 0) {
354 >
355 >        if (potatoes[which_node] + 3 >= MAXTAG) {
356 >          // The potato was going to exceed the maximum value,
357 >          // so wrap this processor potato back to 0:        
358 >
359 >          potatoes[which_node] = 0;          
360 >          MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
361 >          
362 >        }
363 >
364 >        myPotato = potatoes[which_node];        
365 >        
366 >        MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
367 >                 myPotato, MPI_COMM_WORLD, &istatus);
368 >        
369 >        atomTypeString = MPIatomTypeString;
370          
371 <        haveError = 0;
372 <        which_atom = i;
373 <        local_index=-1;        
374 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
375 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
371 >        myPotato++;
372 >
373 >        MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
374 >                 myPotato, MPI_COMM_WORLD, &istatus);
375 >              
376 >        myPotato++;
377 >
378 >        if (isDirectional) {          
379 >          MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node,
380 >                   myPotato, MPI_COMM_WORLD, &istatus);
381 >        } else {
382 >          MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node,
383 >                   myPotato, MPI_COMM_WORLD, &istatus);          
384          }
385 <        if (local_index != -1) {
386 <          //format the line
387 <          
190 <          atoms[local_index]->getPos(pos);
191 <          atoms[local_index]->getVel(vel);
385 >        
386 >        myPotato++;
387 >        potatoes[which_node] = myPotato;
388  
389 <          sprintf( tempBuffer,
390 <                   "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
391 <                   atoms[local_index]->getType(),
392 <                   pos[0],
393 <                   pos[1],
394 <                   pos[2],
395 <                   vel[0],
396 <                   vel[1],
397 <                   vel[2]); // check here.
398 <          strcpy( writeLine, tempBuffer );
389 >      } else {
390 >        
391 >        haveError = 0;
392 >        which_atom = i;
393 >        
394 >          local_index = indexArray[currentIndex].first;        
395 >          
396 >          if (which_atom == indexArray[currentIndex].second) {
397 >            
398 >            atomTypeString = atoms[local_index]->getType();
399 >            
400 >          atoms[local_index]->getPos(pos);
401 >          atoms[local_index]->getVel(vel);          
402            
403 +          atomData6[0] = pos[0];
404 +          atomData6[1] = pos[1];
405 +          atomData6[2] = pos[2];
406 +
407 +          atomData6[3] = vel[0];
408 +          atomData6[4] = vel[1];
409 +          atomData6[5] = vel[2];
410 +          
411 +          isDirectional = 0;
412 +
413            if( atoms[local_index]->isDirectional() ){
414 +
415 +            isDirectional = 1;
416              
417              dAtom = (DirectionalAtom *)atoms[local_index];
418              dAtom->getQ( q );
419 +
420 +            for (int j = 0; j < 6 ; j++)
421 +              atomData13[j] = atomData6[j];            
422              
423 <            sprintf( tempBuffer,
424 <                     "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
425 <                     q[0],
426 <                     q[1],
427 <                     q[2],
428 <                     q[3],
429 <                     dAtom->getJx(),
430 <                     dAtom->getJy(),
431 <                     dAtom->getJz());
432 <            strcat( writeLine, tempBuffer );
433 <            
220 <          }
221 <          else
222 <            strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );      
223 <        }
224 <        else {
423 >            atomData13[6] = q[0];
424 >            atomData13[7] = q[1];
425 >            atomData13[8] = q[2];
426 >            atomData13[9] = q[3];
427 >            
428 >            atomData13[10] = dAtom->getJx();
429 >            atomData13[11] = dAtom->getJy();
430 >            atomData13[12] = dAtom->getJz();
431 >          }
432 >          
433 >        } else {
434            sprintf(painCave.errMsg,
435 <                  "Atom %d not found on processor %d\n",
436 <                  i, worldRank );
435 >                  "Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n",
436 >                  which_atom, worldRank, currentIndex, local_index );
437            haveError= 1;
438            simError();
439 <        }
440 <        
441 <        if(haveError) nodeZeroError();
442 <
439 >        }
440 >        
441 >        if(haveError) DieDieDie();
442 >        
443 >        currentIndex++;
444        }
445 <      else {
446 <        myStatus = 1;
447 <        MPI_Send(&myStatus, 1, MPI_INT, which_node,
238 <                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
239 <        MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
240 <                 MPI_COMM_WORLD);
241 <        MPI_Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node,
242 <                 TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
243 <        MPI_Recv(&myStatus, 1, MPI_INT, which_node,
244 <                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
445 >      // If we've survived to here, format the line:
446 >      
447 >      if (!isDirectional) {
448          
449 <        if(!myStatus) nodeZeroError();
450 <
449 >        sprintf( writeLine,
450 >                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
451 >                 atomTypeString,
452 >                 atomData6[0],
453 >                 atomData6[1],
454 >                 atomData6[2],
455 >                 atomData6[3],
456 >                 atomData6[4],
457 >                 atomData6[5]);
458 >        
459 >        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
460 >        
461 >      } else {
462 >        
463 >        sprintf( writeLine,
464 >                 "%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",
465 >                 atomTypeString,
466 >                 atomData13[0],
467 >                 atomData13[1],
468 >                 atomData13[2],
469 >                 atomData13[3],
470 >                 atomData13[4],
471 >                 atomData13[5],
472 >                 atomData13[6],
473 >                 atomData13[7],
474 >                 atomData13[8],
475 >                 atomData13[9],
476 >                 atomData13[10],
477 >                 atomData13[11],
478 >                 atomData13[12]);
479 >        
480        }
481        
482 <      outFile << writeLine;
483 <      outFile.flush();
482 >      for(k = 0; k < outFile.size(); k++)
483 >        *outFile[k] << writeLine;
484      }
485      
486 <    // kill everyone off:
487 <    myStatus = -1;
256 <    for (j = 0; j < mpiSim->getNumberProcessors(); j++) {      
257 <      MPI_Send(&myStatus, 1, MPI_INT, j,
258 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
259 <    }
260 <
261 <  } else {
486 >    for(k = 0; k < outFile.size(); k++)
487 >      outFile[k]->flush();
488      
489 <    done = 0;
490 <    while (!done) {
265 <      
266 <      MPI_Recv(&myStatus, 1, MPI_INT, 0,
267 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
268 <
269 <      if(!myStatus) anonymousNodeDie();
270 <      
271 <      if(myStatus < 0) break;
272 <
273 <      MPI_Recv(&which_atom, 1, MPI_INT, 0,
274 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
275 <      
276 <      myStatus = 1;
277 <      local_index=-1;        
278 <      for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
279 <        if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
280 <      }
281 <      if (local_index != -1) {
282 <        //format the line
283 <
284 <        atoms[local_index]->getPos(pos);
285 <        atoms[local_index]->getVel(vel);
286 <
287 <        sprintf( tempBuffer,
288 <                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
289 <                 atoms[local_index]->getType(),
290 <                 pos[0],
291 <                 pos[1],
292 <                 pos[2],
293 <                 vel[0],
294 <                 vel[1],
295 <                 vel[2]); // check here.
296 <        strcpy( writeLine, tempBuffer );
297 <        
298 <        if( atoms[local_index]->isDirectional() ){
299 <          
300 <          dAtom = (DirectionalAtom *)atoms[local_index];
301 <          dAtom->getQ( q );
302 <          
303 <          sprintf( tempBuffer,
304 <                   "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
305 <                   q[0],
306 <                   q[1],
307 <                   q[2],
308 <                   q[3],
309 <                   dAtom->getJx(),
310 <                   dAtom->getJy(),
311 <                   dAtom->getJz());
312 <          strcat( writeLine, tempBuffer );
313 <        }
314 <        else{
315 <          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
316 <        }
317 <      }
318 <      else {
319 <        sprintf(painCave.errMsg,
320 <                "Atom %d not found on processor %d\n",
321 <                which_atom, worldRank );
322 <        myStatus = 0;
323 <        simError();
324 <
325 <        strcpy( writeLine, "Hello, I'm an error.\n");
326 <      }
327 <
328 <      MPI_Send(writeLine, BUFFERSIZE, MPI_CHAR, 0,
329 <               TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
330 <      MPI_Send( &myStatus, 1, MPI_INT, 0,
331 <                TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
332 <    }
333 <  }  
334 <  outFile.flush();
335 <  sprintf( checkPointMsg,
336 <           "Sucessfully took a dump.\n");
337 <  MPIcheckPoint();
338 <
339 < // last  thing last, enable  fatalities.
340 <  painCave.isEventLoop = 0;
341 <
342 < #endif // is_mpi
343 < }
344 <
345 < void DumpWriter::writeFinal(double finalTime){
346 <
347 <  char finalName[500];
348 <  ofstream finalOut;
349 <
350 <  const int BUFFERSIZE = 2000;
351 <  char tempBuffer[BUFFERSIZE];
352 <  char writeLine[BUFFERSIZE];  
353 <
354 <  double q[4];
355 <  DirectionalAtom* dAtom;
356 <  Atom** atoms = entry_plug->atoms;
357 <  int i;
358 < #ifdef IS_MPI
359 <  int j, which_node, done, which_atom, local_index;
360 < #else //is_mpi
361 <  int nAtoms = entry_plug->n_atoms;
362 < #endif //is_mpi
363 <  
364 <  double pos[3], vel[3];
365 <  
366 < #ifdef IS_MPI
367 <  if(worldRank == 0 ){
368 < #endif // is_mpi
489 >    sprintf( checkPointMsg,
490 >             "Sucessfully took a dump.\n");
491      
492 <    strcpy( finalName, entry_plug->finalName );
492 >    MPIcheckPoint();        
493      
494 <    finalOut.open( finalName, ios::out | ios::trunc );
373 <    if( !finalOut ){
374 <      sprintf( painCave.errMsg,
375 <               "Could not open \"%s\" for final dump output.\n",
376 <               finalName );
377 <      painCave.isFatal = 1;
378 <      simError();
379 <    }
494 >    delete[] potatoes;
495      
496 <    // finalOut.setf( ios::scientific );
382 <    
383 < #ifdef IS_MPI
384 <  }
385 <  
386 <  sprintf(checkPointMsg,"Opened file for final configuration\n");
387 <  MPIcheckPoint();  
388 <  
389 < #endif //is_mpi
496 >  } else {
497  
498 <  
392 < #ifndef IS_MPI
393 <    
394 <  finalOut << nAtoms << "\n";
395 <    
396 <  finalOut << finalTime << ";\t"
397 <           << entry_plug->Hmat[0][0] << "\t"
398 <           << entry_plug->Hmat[1][0] << "\t"
399 <           << entry_plug->Hmat[2][0] << ";\t"
400 <    
401 <           << entry_plug->Hmat[0][1] << "\t"
402 <           << entry_plug->Hmat[1][1] << "\t"
403 <           << entry_plug->Hmat[2][1] << ";\t"
404 <    
405 <           << entry_plug->Hmat[0][2] << "\t"
406 <           << entry_plug->Hmat[1][2] << "\t"
407 <           << entry_plug->Hmat[2][2] << ";\n";
408 <  
409 <  for( i=0; i<nAtoms; i++ ){
410 <      
411 <    atoms[i]->getPos(pos);
412 <    atoms[i]->getVel(vel);
413 <    
414 <    sprintf( tempBuffer,
415 <             "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
416 <             atoms[i]->getType(),
417 <             pos[0],
418 <             pos[1],
419 <             pos[2],
420 <             vel[0],
421 <             vel[1],
422 <             vel[2]);
423 <    strcpy( writeLine, tempBuffer );
498 >    // worldRank != 0, so I'm a remote node.  
499  
500 <    if( atoms[i]->isDirectional() ){
426 <        
427 <      dAtom = (DirectionalAtom *)atoms[i];
428 <      dAtom->getQ( q );
429 <        
430 <      sprintf( tempBuffer,
431 <               "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
432 <               q[0],
433 <               q[1],
434 <               q[2],
435 <               q[3],
436 <               dAtom->getJx(),
437 <               dAtom->getJy(),
438 <               dAtom->getJz());
439 <      strcat( writeLine, tempBuffer );
440 <    }
441 <    else
442 <      strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
443 <      
444 <    finalOut << writeLine;
445 <  }
446 <  finalOut.flush();
447 <  finalOut.close();
500 >    // Set my magic potato to 0:
501  
502 < #else // is_mpi
503 <  
451 <  // first thing first, suspend fatalities.
452 <  painCave.isEventLoop = 1;
453 <
454 <  int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
455 <  int haveError;
456 <
457 <  MPI_Status istatus;
458 <  int *AtomToProcMap = mpiSim->getAtomToProcMap();
459 <
460 <  // write out header and node 0's coordinates
461 <  
462 <  haveError = 0;
463 <  if( worldRank == 0 ){
464 <    finalOut << mpiSim->getTotAtoms() << "\n";
502 >    myPotato = 0;
503 >    currentIndex = 0;
504      
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] << ";\n";
478 –    
505      for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
480 –      // Get the Node number which has this molecule:
506        
507 <      which_node = AtomToProcMap[i];    
507 >      // Am I the node which has this atom?
508        
509 <      if (which_node == mpiSim->getMyNode()) {
509 >      if (AtomToProcMap[i] == worldRank) {
510  
511 <        which_atom = i;
512 <        local_index=-1;        
513 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
514 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
511 >        if (myPotato + 3 >= MAXTAG) {
512 >          
513 >          // The potato was going to exceed the maximum value,
514 >          // so wrap this processor potato back to 0 (and block until
515 >          // node 0 says we can go:
516 >          
517 >          MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
518 >          
519          }
520 <        if (local_index != -1) {    
520 >        which_atom = i;
521  
522 +        local_index = indexArray[currentIndex].first;        
523 +                
524 +        if (which_atom == indexArray[currentIndex].second) {
525 +        
526 +          atomTypeString = atoms[local_index]->getType();
527 +          
528            atoms[local_index]->getPos(pos);
529            atoms[local_index]->getVel(vel);
530            
531 <          sprintf( tempBuffer,
532 <                   "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
533 <                   atoms[local_index]->getType(),
534 <                   pos[0],
535 <                   pos[1],
536 <                   pos[2],
537 <                   vel[0],
538 <                   vel[1],
539 <                   vel[2]);
540 <          strcpy( writeLine, tempBuffer );
541 <          
542 <          if( atoms[local_index]->isDirectional() ){
543 <            
544 <            dAtom = (DirectionalAtom *)atoms[local_index];
545 <            dAtom->getQ( q );
546 <            
547 <            sprintf( tempBuffer,
548 <                     "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
549 <                     q[0],
550 <                     q[1],
551 <                     q[2],
552 <                     q[3],
553 <                     dAtom->getJx(),
554 <                     dAtom->getJy(),
555 <                     dAtom->getJz());
556 <            strcat( writeLine, tempBuffer );
557 <          }
558 <          else
559 <            strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );      
560 <        }
561 <        else {
531 >          atomData6[0] = pos[0];
532 >          atomData6[1] = pos[1];
533 >          atomData6[2] = pos[2];
534 >
535 >          atomData6[3] = vel[0];
536 >          atomData6[4] = vel[1];
537 >          atomData6[5] = vel[2];
538 >          
539 >          isDirectional = 0;
540 >
541 >          if( atoms[local_index]->isDirectional() ){
542 >
543 >            isDirectional = 1;
544 >            
545 >            dAtom = (DirectionalAtom *)atoms[local_index];
546 >            dAtom->getQ( q );
547 >            
548 >            for (int j = 0; j < 6 ; j++)
549 >              atomData13[j] = atomData6[j];
550 >            
551 >            atomData13[6] = q[0];
552 >            atomData13[7] = q[1];
553 >            atomData13[8] = q[2];
554 >            atomData13[9] = q[3];
555 >  
556 >            atomData13[10] = dAtom->getJx();
557 >            atomData13[11] = dAtom->getJy();
558 >            atomData13[12] = dAtom->getJz();
559 >          }
560 >
561 >        } else {
562            sprintf(painCave.errMsg,
563 <                  "Atom %d not found on processor %d\n",
564 <                  i, worldRank );
563 >                  "Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n",
564 >                  which_atom, worldRank, currentIndex, local_index );
565            haveError= 1;
566            simError();
567 <        }
567 >        }
568 >        
569 >        strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
570  
571 <        if(haveError) nodeZeroError();
572 <    
573 <      }
574 <      else {
571 >        // null terminate the string before sending (just in case):
572 >        MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
573 >
574 >        MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
575 >                             myPotato, MPI_COMM_WORLD);
576          
577 <        myStatus = 1;
540 <        MPI_Send(&myStatus, 1, MPI_INT, which_node,
541 <                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
542 <        MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
543 <                 MPI_COMM_WORLD);
544 <        MPI_Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node,
545 <                 TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
546 <        MPI_Recv(&myStatus, 1, MPI_INT, which_node,
547 <                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
548 <        
549 <        if(!myStatus) nodeZeroError();
550 <      }
551 <      
552 <      finalOut << writeLine;
553 <    }
554 <    
555 <    // kill everyone off:
556 <    myStatus = -1;
557 <    for (j = 0; j < mpiSim->getNumberProcessors(); j++) {      
558 <      MPI_Send(&myStatus, 1, MPI_INT, j,
559 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
560 <    }
577 >        myPotato++;
578  
579 <  } else {
580 <    
581 <    done = 0;
582 <    while (!done) {
579 >        MPI_Send(&isDirectional, 1, MPI_INT, 0,
580 >                             myPotato, MPI_COMM_WORLD);
581 >        
582 >        myPotato++;
583 >        
584 >        if (isDirectional) {
585  
586 <      MPI_Recv(&myStatus, 1, MPI_INT, 0,
587 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
588 <      
589 <      if(!myStatus) anonymousNodeDie();
571 <      
572 <      if(myStatus < 0) break;
573 <      
574 <      MPI_Recv(&which_atom, 1, MPI_INT, 0,
575 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
576 <      
577 <      myStatus = 1;
578 <      local_index=-1;        
579 <      for (j=0; j < mpiSim->getMyNlocal(); j++) {
580 <        if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
581 <      }
582 <      if (local_index != -1) {
586 >          MPI_Send(atomData13, 13, MPI_DOUBLE, 0,
587 >                   myPotato, MPI_COMM_WORLD);
588 >          
589 >        } else {
590  
591 <        atoms[local_index]->getPos(pos);
592 <        atoms[local_index]->getVel(vel);
591 >          MPI_Send(atomData6, 6, MPI_DOUBLE, 0,
592 >                   myPotato, MPI_COMM_WORLD);
593 >        }
594  
595 <        //format the line
596 <        sprintf( tempBuffer,
589 <                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
590 <                 atoms[local_index]->getType(),
591 <                 pos[0],
592 <                 pos[1],
593 <                 pos[2],
594 <                 vel[0],
595 <                 vel[1],
596 <                 vel[2]); // check here.
597 <        strcpy( writeLine, tempBuffer );
598 <        
599 <        if( atoms[local_index]->isDirectional() ){
600 <          
601 <          dAtom = (DirectionalAtom *)atoms[local_index];
602 <          dAtom->getQ( q );
603 <          
604 <          sprintf( tempBuffer,
605 <                   "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
606 <                   q[0],
607 <                   q[1],
608 <                   q[2],
609 <                   q[3],
610 <                   dAtom->getJx(),
611 <                   dAtom->getJy(),
612 <                   dAtom->getJz());
613 <          strcat( writeLine, tempBuffer );
614 <        }
615 <        else{
616 <          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
617 <        }
618 <      }
619 <      else {
620 <        sprintf(painCave.errMsg,
621 <                "Atom %d not found on processor %d\n",
622 <                which_atom, worldRank );
623 <        myStatus = 0;
624 <        simError();
625 <        
626 <        strcpy( writeLine, "Hello, I'm an error.\n");
595 >        myPotato++;  
596 >        currentIndex++;    
597        }
628 –
629 –      MPI_Send(writeLine, BUFFERSIZE, MPI_CHAR, 0,
630 –               TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
631 –      MPI_Send( &myStatus, 1, MPI_INT, 0,
632 –                TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
598      }
599 <  }
600 <  finalOut.flush();
601 <  sprintf( checkPointMsg,
602 <           "Sucessfully took a dump.\n");
603 <  MPIcheckPoint();
599 >
600 >    sprintf( checkPointMsg,
601 >             "Sucessfully took a dump.\n");
602 >    MPIcheckPoint();        
603 >    
604 >  }
605    
640 –  if( worldRank == 0 ) finalOut.close();    
606   #endif // is_mpi
607   }
608  
644 –
645 –
609   #ifdef IS_MPI
610  
611   // a couple of functions to let us escape the write loop
612  
613 < void dWrite::nodeZeroError( void ){
651 <  int j, myStatus;
652 <  
653 <  myStatus = 0;
654 <  for (j = 0; j < mpiSim->getNumberProcessors(); j++) {      
655 <    MPI_Send( &myStatus, 1, MPI_INT, j,
656 <              TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
657 <  }  
658 <  
613 > void dWrite::DieDieDie( void ){
614  
615    MPI_Finalize();
616    exit (0);
662 –  
617   }
618  
665 – void dWrite::anonymousNodeDie( void ){
666 –
667 –  MPI_Finalize();
668 –  exit (0);
669 – }
670 –
619   #endif //is_mpi

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