ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/group/trunk/OOPSE/libmdtools/DumpWriter.cpp
(Generate patch)

Comparing trunk/OOPSE/libmdtools/DumpWriter.cpp (file contents):
Revision 670 by mmeineke, Thu Aug 7 21:47:18 2003 UTC vs.
Revision 1000 by tim, Fri Jan 30 21:47:22 2004 UTC

# Line 1 | Line 1
1 < #include <cstring>
1 > #define _FILE_OFFSET_BITS 64
2 >
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"
8 – #define TAKE_THIS_TAG_CHAR 1
9 – #define TAKE_THIS_TAG_INT 2
12  
13   namespace dWrite{
14 <  void nodeZeroError( void );
13 <  void anonymousNodeDie( void );
14 >  void DieDieDie( void );
15   }
16  
17   using namespace dWrite;
# Line 26 | 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 <    
34 <    if( !outFile ){
35 <      
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  
43 –    //outFile.setf( ios::scientific );
44 –
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 57 | 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 +
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 + #endif    
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 + #ifdef IS_MPI
119 +  }
120 + #endif // is_mpi
121 +
122 +  fileStreams.push_back(&finalOut);
123 +  fileStreams.push_back(&dumpFile);
124 +
125 +  writeFrame(fileStreams, currentTime);
126 +
127 + #ifdef IS_MPI
128 +  finalOut.close();
129 + #endif
130 +        
131 + }
132 +
133 + void DumpWriter::writeFinal(double currentTime){
134 +
135 +  ofstream finalOut;
136 +  vector<ofstream*> fileStreams;
137 +
138 + #ifdef IS_MPI
139 +  if(worldRank == 0 ){
140 + #endif // is_mpi
141 +
142 +    finalOut.open( entry_plug->finalName, ios::out | ios::trunc );
143 +
144 +    if( !finalOut ){
145 +      sprintf( painCave.errMsg,
146 +               "Could not open \"%s\" for final dump output.\n",
147 +               entry_plug->finalName );
148 +      painCave.isFatal = 1;
149 +      simError();
150 +    }
151 +
152 + #ifdef IS_MPI
153 +  }
154 + #endif // is_mpi
155 +  
156 +  fileStreams.push_back(&finalOut);  
157 +  writeFrame(fileStreams, currentTime);
158 +
159 + #ifdef IS_MPI
160 +  finalOut.close();
161 + #endif
162 +  
163 + }
164 +
165 + void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){
166 +
167    const int BUFFERSIZE = 2000;
168 <  char tempBuffer[BUFFERSIZE];
168 >  const int MINIBUFFERSIZE = 100;
169 >
170 >  char tempBuffer[BUFFERSIZE];  
171    char writeLine[BUFFERSIZE];
172  
173 <  int i, j, which_node, done, which_atom, local_index;
173 >  int i, k;
174 >
175 > #ifdef IS_MPI
176 >  
177 >  /*********************************************************************
178 >   * Documentation?  You want DOCUMENTATION?
179 >   *
180 >   * Why all the potatoes below?  
181 >   *
182 >   * To make a long story short, the original version of DumpWriter
183 >   * worked in the most inefficient way possible.  Node 0 would
184 >   * poke each of the node for an individual atom's formatted data
185 >   * as node 0 worked its way down the global index. This was particularly
186 >   * inefficient since the method blocked all processors at every atom
187 >   * (and did it twice!).
188 >   *
189 >   * An intermediate version of DumpWriter could be described from Node
190 >   * zero's perspective as follows:
191 >   *
192 >   *  1) Have 100 of your friends stand in a circle.
193 >   *  2) When you say go, have all of them start tossing potatoes at
194 >   *     you (one at a time).
195 >   *  3) Catch the potatoes.
196 >   *
197 >   * It was an improvement, but MPI has buffers and caches that could
198 >   * best be described in this analogy as "potato nets", so there's no
199 >   * need to block the processors atom-by-atom.
200 >   *
201 >   * This new and improved DumpWriter works in an even more efficient
202 >   * way:
203 >   *
204 >   *  1) Have 100 of your friend stand in a circle.
205 >   *  2) When you say go, have them start tossing 5-pound bags of
206 >   *     potatoes at you.
207 >   *  3) Once you've caught a friend's bag of potatoes,
208 >   *     toss them a spud to let them know they can toss another bag.
209 >   *
210 >   * How's THAT for documentation?
211 >   *
212 >   *********************************************************************/
213 >
214 >  int *potatoes;
215 >  int myPotato;
216 >
217 >  int nProc;
218 >  int j, which_node, done, which_atom, local_index, currentIndex;
219 >  double atomData6[6];
220 >  double atomData13[13];
221 >  int isDirectional;
222 >  char* atomTypeString;
223 >  char MPIatomTypeString[MINIBUFFERSIZE];
224 >
225 > #else //is_mpi
226 >  int nAtoms = entry_plug->n_atoms;
227 > #endif //is_mpi
228 >
229    double q[4];
230    DirectionalAtom* dAtom;
76 –  int nAtoms = entry_plug->n_atoms;
231    Atom** atoms = entry_plug->atoms;
78 –
232    double pos[3], vel[3];
80 –    
233  
234   #ifndef IS_MPI
235 <    
236 <  outFile << nAtoms << "\n";
237 <    
86 <  outFile << currentTime << ";\t"
87 <          << entry_plug->Hmat[0][0] << "\t"
88 <          << entry_plug->Hmat[1][0] << "\t"
89 <          << entry_plug->Hmat[2][0] << ";\t"
235 >  
236 >  for(k = 0; k < outFile.size(); k++){
237 >    *outFile[k] << nAtoms << "\n";
238  
239 <          << entry_plug->Hmat[0][1] << "\t"
240 <          << entry_plug->Hmat[1][1] << "\t"
241 <          << entry_plug->Hmat[2][1] << ";\t"
239 >    *outFile[k] << currentTime << ";\t"
240 >               << entry_plug->Hmat[0][0] << "\t"
241 >                     << entry_plug->Hmat[1][0] << "\t"
242 >                     << entry_plug->Hmat[2][0] << ";\t"
243 >              
244 >               << entry_plug->Hmat[0][1] << "\t"
245 >                     << entry_plug->Hmat[1][1] << "\t"
246 >                     << entry_plug->Hmat[2][1] << ";\t"
247  
248 <          << entry_plug->Hmat[0][2] << "\t"
249 <          << entry_plug->Hmat[1][2] << "\t"
250 <          << entry_plug->Hmat[2][2] << ";\n";
251 <    
248 >                     << entry_plug->Hmat[0][2] << "\t"
249 >                     << entry_plug->Hmat[1][2] << "\t"
250 >                     << entry_plug->Hmat[2][2] << ";";
251 >
252 >    //write out additional parameters, such as chi and eta
253 >    *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
254 >  }
255 >  
256    for( i=0; i<nAtoms; i++ ){
257 <      
257 >
258      atoms[i]->getPos(pos);
259      atoms[i]->getVel(vel);
260  
# Line 113 | Line 270 | void DumpWriter::writeDump( double currentTime ){
270      strcpy( writeLine, tempBuffer );
271  
272      if( atoms[i]->isDirectional() ){
273 <        
273 >
274        dAtom = (DirectionalAtom *)atoms[i];
275        dAtom->getQ( q );
276 <        
276 >
277        sprintf( tempBuffer,
278                 "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
279                 q[0],
# Line 130 | Line 287 | void DumpWriter::writeDump( double currentTime ){
287      }
288      else
289        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
290 <      
291 <    outFile << writeLine;
290 >
291 >    for(k = 0; k < outFile.size(); k++)
292 >      *outFile[k] << writeLine;
293    }
136 –  outFile.flush();
294  
295   #else // is_mpi
296  
297 <  // first thing first, suspend fatalities.
298 <  painCave.isEventLoop = 1;
297 >  /* code to find maximum tag value */
298 >  
299 >  int *tagub, flag, MAXTAG;
300 >  MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
301 >  if (flag) {
302 >    MAXTAG = *tagub;
303 >  } else {
304 >    MAXTAG = 32767;
305 >  }  
306  
143 –  int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
307    int haveError;
308  
309    MPI_Status istatus;
310    int *AtomToProcMap = mpiSim->getAtomToProcMap();
311 <  
311 >
312    // write out header and node 0's coordinates
313 <  
313 >
314    if( worldRank == 0 ){
315 <    outFile << mpiSim->getTotAtoms() << "\n";
316 <  
317 <    outFile << currentTime << ";\t"
318 <            << entry_plug->Hmat[0][0] << "\t"
319 <            << entry_plug->Hmat[1][0] << "\t"
320 <            << entry_plug->Hmat[2][0] << ";\t"
321 <      
322 <            << entry_plug->Hmat[0][1] << "\t"
323 <            << entry_plug->Hmat[1][1] << "\t"
161 <            << entry_plug->Hmat[2][1] << ";\t"
162 <      
163 <            << entry_plug->Hmat[0][2] << "\t"
164 <            << entry_plug->Hmat[1][2] << "\t"
165 <            << entry_plug->Hmat[2][2] << ";\n";
315 >
316 >    // Node 0 needs a list of the magic potatoes for each processor;
317 >
318 >    nProc = mpiSim->getNumberProcessors();
319 >    potatoes = new int[nProc];
320 >
321 >    //write out the comment lines
322 >    for (i = 0; i < nProc; i++)
323 >      potatoes[i] = 0;
324      
325 <    outFile.flush();
325 >      for(k = 0; k < outFile.size(); k++){
326 >        *outFile[k] << mpiSim->getTotAtoms() << "\n";
327 >
328 >        *outFile[k] << currentTime << ";\t"
329 >                         << entry_plug->Hmat[0][0] << "\t"
330 >                         << entry_plug->Hmat[1][0] << "\t"
331 >                         << entry_plug->Hmat[2][0] << ";\t"
332 >
333 >                         << entry_plug->Hmat[0][1] << "\t"
334 >                         << entry_plug->Hmat[1][1] << "\t"
335 >                         << entry_plug->Hmat[2][1] << ";\t"
336 >
337 >                         << entry_plug->Hmat[0][2] << "\t"
338 >                         << entry_plug->Hmat[1][2] << "\t"
339 >                         << entry_plug->Hmat[2][2] << ";";
340 >  
341 >        *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
342 >    }
343 >
344 >    currentIndex = 0;
345 >
346      for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
347 +      
348        // Get the Node number which has this atom;
349        
350 <      which_node = AtomToProcMap[i];    
350 >      which_node = AtomToProcMap[i];
351        
352 <      if (which_node == 0 ) {
352 >      if (which_node != 0) {
353 >
354 >        if (potatoes[which_node] + 3 >= MAXTAG) {
355 >          // The potato was going to exceed the maximum value,
356 >          // so wrap this processor potato back to 0:        
357 >
358 >          potatoes[which_node] = 0;          
359 >          MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
360 >          
361 >        }
362 >
363 >        myPotato = potatoes[which_node];        
364 >        
365 >        MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
366 >                 myPotato, MPI_COMM_WORLD, &istatus);
367 >        
368 >        atomTypeString = MPIatomTypeString;
369          
370 <        haveError = 0;
371 <        which_atom = i;
372 <        local_index=-1;        
373 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
374 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
370 >        myPotato++;
371 >
372 >        MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
373 >                 myPotato, MPI_COMM_WORLD, &istatus);
374 >              
375 >        myPotato++;
376 >
377 >        if (isDirectional) {          
378 >          MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node,
379 >                   myPotato, MPI_COMM_WORLD, &istatus);
380 >        } else {
381 >          MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node,
382 >                   myPotato, MPI_COMM_WORLD, &istatus);          
383          }
384 <        if (local_index != -1) {
385 <          //format the line
386 <          
184 <          atoms[local_index]->getPos(pos);
185 <          atoms[local_index]->getVel(vel);
384 >        
385 >        myPotato++;
386 >        potatoes[which_node] = myPotato;
387  
388 <          sprintf( tempBuffer,
389 <                   "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
390 <                   atoms[local_index]->getType(),
391 <                   pos[0],
392 <                   pos[1],
393 <                   pos[2],
394 <                   vel[0],
395 <                   vel[1],
396 <                   vel[2]); // check here.
397 <          strcpy( writeLine, tempBuffer );
388 >      } else {
389 >        
390 >        haveError = 0;
391 >        which_atom = i;
392 >        
393 >          local_index = indexArray[currentIndex].first;        
394 >          
395 >          if (which_atom == indexArray[currentIndex].second) {
396 >            
397 >            atomTypeString = atoms[local_index]->getType();
398 >            
399 >          atoms[local_index]->getPos(pos);
400 >          atoms[local_index]->getVel(vel);          
401            
402 +          atomData6[0] = pos[0];
403 +          atomData6[1] = pos[1];
404 +          atomData6[2] = pos[2];
405 +
406 +          atomData6[3] = vel[0];
407 +          atomData6[4] = vel[1];
408 +          atomData6[5] = vel[2];
409 +          
410 +          isDirectional = 0;
411 +
412            if( atoms[local_index]->isDirectional() ){
413 +
414 +            isDirectional = 1;
415              
416              dAtom = (DirectionalAtom *)atoms[local_index];
417              dAtom->getQ( q );
418 +
419 +            for (int j = 0; j < 6 ; j++)
420 +              atomData13[j] = atomData6[j];            
421              
422 <            sprintf( tempBuffer,
423 <                     "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
424 <                     q[0],
425 <                     q[1],
426 <                     q[2],
427 <                     q[3],
428 <                     dAtom->getJx(),
429 <                     dAtom->getJy(),
430 <                     dAtom->getJz());
431 <            strcat( writeLine, tempBuffer );
432 <            
214 <          }
215 <          else
216 <            strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );      
217 <        }
218 <        else {
422 >            atomData13[6] = q[0];
423 >            atomData13[7] = q[1];
424 >            atomData13[8] = q[2];
425 >            atomData13[9] = q[3];
426 >            
427 >            atomData13[10] = dAtom->getJx();
428 >            atomData13[11] = dAtom->getJy();
429 >            atomData13[12] = dAtom->getJz();
430 >          }
431 >          
432 >        } else {
433            sprintf(painCave.errMsg,
434 <                  "Atom %d not found on processor %d\n",
435 <                  i, worldRank );
434 >                  "Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n",
435 >                  which_atom, worldRank, currentIndex, local_index );
436            haveError= 1;
437            simError();
438 <        }
439 <        
440 <        if(haveError) nodeZeroError();
441 <
438 >        }
439 >        
440 >        if(haveError) DieDieDie();
441 >        
442 >        currentIndex++;
443        }
444 <      else {
445 <        myStatus = 1;
446 <        MPI_Send(&myStatus, 1, MPI_INT, which_node,
232 <                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
233 <        MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
234 <                 MPI_COMM_WORLD);
235 <        MPI_Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node,
236 <                 TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
237 <        MPI_Recv(&myStatus, 1, MPI_INT, which_node,
238 <                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
444 >      // If we've survived to here, format the line:
445 >      
446 >      if (!isDirectional) {
447          
448 <        if(!myStatus) nodeZeroError();
449 <
448 >        sprintf( writeLine,
449 >                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
450 >                 atomTypeString,
451 >                 atomData6[0],
452 >                 atomData6[1],
453 >                 atomData6[2],
454 >                 atomData6[3],
455 >                 atomData6[4],
456 >                 atomData6[5]);
457 >        
458 >        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
459 >        
460 >      } else {
461 >        
462 >        sprintf( writeLine,
463 >                 "%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",
464 >                 atomTypeString,
465 >                 atomData13[0],
466 >                 atomData13[1],
467 >                 atomData13[2],
468 >                 atomData13[3],
469 >                 atomData13[4],
470 >                 atomData13[5],
471 >                 atomData13[6],
472 >                 atomData13[7],
473 >                 atomData13[8],
474 >                 atomData13[9],
475 >                 atomData13[10],
476 >                 atomData13[11],
477 >                 atomData13[12]);
478 >        
479        }
480        
481 <      outFile << writeLine;
482 <      outFile.flush();
481 >      for(k = 0; k < outFile.size(); k++)
482 >        *outFile[k] << writeLine;
483      }
484      
485 <    // kill everyone off:
486 <    myStatus = -1;
487 <    for (j = 0; j < mpiSim->getNumberProcessors(); j++) {      
488 <      MPI_Send(&myStatus, 1, MPI_INT, j,
489 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
490 <    }
491 <
485 >    for(k = 0; k < outFile.size(); k++)
486 >      outFile[k]->flush();
487 >    
488 >    sprintf( checkPointMsg,
489 >             "Sucessfully took a dump.\n");
490 >    
491 >    MPIcheckPoint();        
492 >    
493 >    delete[] potatoes;
494 >    
495    } else {
496 +
497 +    // worldRank != 0, so I'm a remote node.  
498 +
499 +    // Set my magic potato to 0:
500 +
501 +    myPotato = 0;
502 +    currentIndex = 0;
503      
504 <    done = 0;
258 <    while (!done) {
504 >    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
505        
506 <      MPI_Recv(&myStatus, 1, MPI_INT, 0,
261 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
262 <
263 <      if(!myStatus) anonymousNodeDie();
506 >      // Am I the node which has this atom?
507        
508 <      if(myStatus < 0) break;
508 >      if (AtomToProcMap[i] == worldRank) {
509  
510 <      MPI_Recv(&which_atom, 1, MPI_INT, 0,
511 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
512 <      
513 <      myStatus = 1;
514 <      local_index=-1;        
515 <      for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
516 <        if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
517 <      }
518 <      if (local_index != -1) {
519 <        //format the line
510 >        if (myPotato + 3 >= MAXTAG) {
511 >          
512 >          // The potato was going to exceed the maximum value,
513 >          // so wrap this processor potato back to 0 (and block until
514 >          // node 0 says we can go:
515 >          
516 >          MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
517 >          
518 >        }
519 >        which_atom = i;
520  
521 <        atoms[local_index]->getPos(pos);
522 <        atoms[local_index]->getVel(vel);
523 <
524 <        sprintf( tempBuffer,
525 <                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
283 <                 atoms[local_index]->getType(),
284 <                 pos[0],
285 <                 pos[1],
286 <                 pos[2],
287 <                 vel[0],
288 <                 vel[1],
289 <                 vel[2]); // check here.
290 <        strcpy( writeLine, tempBuffer );
291 <        
292 <        if( atoms[local_index]->isDirectional() ){
521 >        local_index = indexArray[currentIndex].first;        
522 >                
523 >        if (which_atom == indexArray[currentIndex].second) {
524 >        
525 >          atomTypeString = atoms[local_index]->getType();
526            
527 <          dAtom = (DirectionalAtom *)atoms[local_index];
528 <          dAtom->getQ( q );
527 >          atoms[local_index]->getPos(pos);
528 >          atoms[local_index]->getVel(vel);
529            
530 <          sprintf( tempBuffer,
531 <                   "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
532 <                   q[0],
300 <                   q[1],
301 <                   q[2],
302 <                   q[3],
303 <                   dAtom->getJx(),
304 <                   dAtom->getJy(),
305 <                   dAtom->getJz());
306 <          strcat( writeLine, tempBuffer );
307 <        }
308 <        else{
309 <          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
310 <        }
311 <      }
312 <      else {
313 <        sprintf(painCave.errMsg,
314 <                "Atom %d not found on processor %d\n",
315 <                which_atom, worldRank );
316 <        myStatus = 0;
317 <        simError();
530 >          atomData6[0] = pos[0];
531 >          atomData6[1] = pos[1];
532 >          atomData6[2] = pos[2];
533  
534 <        strcpy( writeLine, "Hello, I'm an error.\n");
535 <      }
534 >          atomData6[3] = vel[0];
535 >          atomData6[4] = vel[1];
536 >          atomData6[5] = vel[2];
537 >          
538 >          isDirectional = 0;
539  
540 <      MPI_Send(writeLine, BUFFERSIZE, MPI_CHAR, 0,
323 <               TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
324 <      MPI_Send( &myStatus, 1, MPI_INT, 0,
325 <                TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
326 <    }
327 <  }  
328 <  outFile.flush();
329 <  sprintf( checkPointMsg,
330 <           "Sucessfully took a dump.\n");
331 <  MPIcheckPoint();
540 >          if( atoms[local_index]->isDirectional() ){
541  
542 < // last  thing last, enable  fatalities.
543 <  painCave.isEventLoop = 0;
542 >            isDirectional = 1;
543 >            
544 >            dAtom = (DirectionalAtom *)atoms[local_index];
545 >            dAtom->getQ( q );
546 >            
547 >            for (int j = 0; j < 6 ; j++)
548 >              atomData13[j] = atomData6[j];
549 >            
550 >            atomData13[6] = q[0];
551 >            atomData13[7] = q[1];
552 >            atomData13[8] = q[2];
553 >            atomData13[9] = q[3];
554 >  
555 >            atomData13[10] = dAtom->getJx();
556 >            atomData13[11] = dAtom->getJy();
557 >            atomData13[12] = dAtom->getJz();
558 >          }
559  
560 < #endif // is_mpi
561 < }
560 >        } else {
561 >          sprintf(painCave.errMsg,
562 >                  "Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n",
563 >                  which_atom, worldRank, currentIndex, local_index );
564 >          haveError= 1;
565 >          simError();
566 >        }
567 >        
568 >        strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
569  
570 < void DumpWriter::writeFinal(double finalTime){
570 >        // null terminate the string before sending (just in case):
571 >        MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
572  
573 <  char finalName[500];
574 <  ofstream finalOut;
573 >        MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
574 >                             myPotato, MPI_COMM_WORLD);
575 >        
576 >        myPotato++;
577  
578 <  const int BUFFERSIZE = 2000;
579 <  char tempBuffer[BUFFERSIZE];
580 <  char writeLine[BUFFERSIZE];  
578 >        MPI_Send(&isDirectional, 1, MPI_INT, 0,
579 >                             myPotato, MPI_COMM_WORLD);
580 >        
581 >        myPotato++;
582 >        
583 >        if (isDirectional) {
584  
585 <  double q[4];
586 <  DirectionalAtom* dAtom;
587 <  int nAtoms = entry_plug->n_atoms;
588 <  Atom** atoms = entry_plug->atoms;
352 <  int i, j, which_node, done, game_over, which_atom, local_index;
353 <  
354 <  double pos[3], vel[3];
355 <  
356 < #ifdef IS_MPI
357 <  if(worldRank == 0 ){
358 < #endif // is_mpi
359 <    
360 <    strcpy( finalName, entry_plug->finalName );
361 <    
362 <    finalOut.open( finalName, ios::out | ios::trunc );
363 <    if( !finalOut ){
364 <      sprintf( painCave.errMsg,
365 <               "Could not open \"%s\" for final dump output.\n",
366 <               finalName );
367 <      painCave.isFatal = 1;
368 <      simError();
369 <    }
370 <    
371 <    // finalOut.setf( ios::scientific );
372 <    
373 < #ifdef IS_MPI
374 <  }
375 <  
376 <  sprintf(checkPointMsg,"Opened file for final configuration\n");
377 <  MPIcheckPoint();  
378 <  
379 < #endif //is_mpi
585 >          MPI_Send(atomData13, 13, MPI_DOUBLE, 0,
586 >                   myPotato, MPI_COMM_WORLD);
587 >          
588 >        } else {
589  
590 <  
591 < #ifndef IS_MPI
383 <    
384 <  finalOut << nAtoms << "\n";
385 <    
386 <  finalOut << finalTime << ";\t"
387 <           << entry_plug->Hmat[0][0] << "\t"
388 <           << entry_plug->Hmat[1][0] << "\t"
389 <           << entry_plug->Hmat[2][0] << ";\t"
390 <    
391 <           << entry_plug->Hmat[0][1] << "\t"
392 <           << entry_plug->Hmat[1][1] << "\t"
393 <           << entry_plug->Hmat[2][1] << ";\t"
394 <    
395 <           << entry_plug->Hmat[0][2] << "\t"
396 <           << entry_plug->Hmat[1][2] << "\t"
397 <           << entry_plug->Hmat[2][2] << ";\n";
398 <  
399 <  for( i=0; i<nAtoms; i++ ){
400 <      
401 <    atoms[i]->getPos(pos);
402 <    atoms[i]->getVel(vel);
403 <    
404 <    sprintf( tempBuffer,
405 <             "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
406 <             atoms[i]->getType(),
407 <             pos[0],
408 <             pos[1],
409 <             pos[2],
410 <             vel[0],
411 <             vel[1],
412 <             vel[2]);
413 <    strcpy( writeLine, tempBuffer );
414 <
415 <    if( atoms[i]->isDirectional() ){
416 <        
417 <      dAtom = (DirectionalAtom *)atoms[i];
418 <      dAtom->getQ( q );
419 <        
420 <      sprintf( tempBuffer,
421 <               "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
422 <               q[0],
423 <               q[1],
424 <               q[2],
425 <               q[3],
426 <               dAtom->getJx(),
427 <               dAtom->getJy(),
428 <               dAtom->getJz());
429 <      strcat( writeLine, tempBuffer );
430 <    }
431 <    else
432 <      strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
433 <      
434 <    finalOut << writeLine;
435 <  }
436 <  finalOut.flush();
437 <  finalOut.close();
438 <
439 < #else // is_mpi
440 <  
441 <  // first thing first, suspend fatalities.
442 <  painCave.isEventLoop = 1;
443 <
444 <  int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
445 <  int haveError;
446 <
447 <  MPI_Status istatus;
448 <  int *AtomToProcMap = mpiSim->getAtomToProcMap();
449 <
450 <  // write out header and node 0's coordinates
451 <  
452 <  haveError = 0;
453 <  if( worldRank == 0 ){
454 <    finalOut << mpiSim->getTotAtoms() << "\n";
455 <    
456 <    finalOut << finalTime << ";\t"
457 <             << entry_plug->Hmat[0][0] << "\t"
458 <             << entry_plug->Hmat[1][0] << "\t"
459 <             << entry_plug->Hmat[2][0] << ";\t"
460 <      
461 <             << entry_plug->Hmat[0][1] << "\t"
462 <             << entry_plug->Hmat[1][1] << "\t"
463 <             << entry_plug->Hmat[2][1] << ";\t"
464 <      
465 <             << entry_plug->Hmat[0][2] << "\t"
466 <             << entry_plug->Hmat[1][2] << "\t"
467 <             << entry_plug->Hmat[2][2] << ";\n";
468 <    
469 <    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
470 <      // Get the Node number which has this molecule:
471 <      
472 <      which_node = AtomToProcMap[i];    
473 <      
474 <      if (which_node == mpiSim->getMyNode()) {
475 <
476 <        which_atom = i;
477 <        local_index=-1;        
478 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
479 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
590 >          MPI_Send(atomData6, 6, MPI_DOUBLE, 0,
591 >                   myPotato, MPI_COMM_WORLD);
592          }
481 –        if (local_index != -1) {    
593  
594 <          atoms[local_index]->getPos(pos);
595 <          atoms[local_index]->getVel(vel);
485 <          
486 <          sprintf( tempBuffer,
487 <                   "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
488 <                   atoms[local_index]->getType(),
489 <                   pos[0],
490 <                   pos[1],
491 <                   pos[2],
492 <                   vel[0],
493 <                   vel[1],
494 <                   vel[2]);
495 <          strcpy( writeLine, tempBuffer );
496 <          
497 <          if( atoms[local_index]->isDirectional() ){
498 <            
499 <            dAtom = (DirectionalAtom *)atoms[local_index];
500 <            dAtom->getQ( q );
501 <            
502 <            sprintf( tempBuffer,
503 <                     "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
504 <                     q[0],
505 <                     q[1],
506 <                     q[2],
507 <                     q[3],
508 <                     dAtom->getJx(),
509 <                     dAtom->getJy(),
510 <                     dAtom->getJz());
511 <            strcat( writeLine, tempBuffer );
512 <          }
513 <          else
514 <            strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );      
515 <        }
516 <        else {
517 <          sprintf(painCave.errMsg,
518 <                  "Atom %d not found on processor %d\n",
519 <                  i, worldRank );
520 <          haveError= 1;
521 <          simError();
522 <        }
523 <
524 <        if(haveError) nodeZeroError();
525 <    
526 <      }
527 <      else {
528 <        
529 <        myStatus = 1;
530 <        MPI_Send(&myStatus, 1, MPI_INT, which_node,
531 <                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
532 <        MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
533 <                 MPI_COMM_WORLD);
534 <        MPI_Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node,
535 <                 TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
536 <        MPI_Recv(&myStatus, 1, MPI_INT, which_node,
537 <                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
538 <        
539 <        if(!myStatus) nodeZeroError();
594 >        myPotato++;  
595 >        currentIndex++;    
596        }
541 –      
542 –      finalOut << writeLine;
597      }
544 –    
545 –    // kill everyone off:
546 –    myStatus = -1;
547 –    for (j = 0; j < mpiSim->getNumberProcessors(); j++) {      
548 –      MPI_Send(&myStatus, 1, MPI_INT, j,
549 –               TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
550 –    }
598  
599 <  } else {
599 >    sprintf( checkPointMsg,
600 >             "Sucessfully took a dump.\n");
601 >    MPIcheckPoint();        
602      
603 <    done = 0;
555 <    while (!done) {
556 <
557 <      MPI_Recv(&myStatus, 1, MPI_INT, 0,
558 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
559 <      
560 <      if(!myStatus) anonymousNodeDie();
561 <      
562 <      if(myStatus < 0) break;
563 <      
564 <      MPI_Recv(&which_atom, 1, MPI_INT, 0,
565 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
566 <      
567 <      myStatus = 1;
568 <      local_index=-1;        
569 <      for (j=0; j < mpiSim->getMyNlocal(); j++) {
570 <        if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
571 <      }
572 <      if (local_index != -1) {
573 <
574 <        atoms[local_index]->getPos(pos);
575 <        atoms[local_index]->getVel(vel);
576 <
577 <        //format the line
578 <        sprintf( tempBuffer,
579 <                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
580 <                 atoms[local_index]->getType(),
581 <                 pos[0],
582 <                 pos[1],
583 <                 pos[2],
584 <                 vel[0],
585 <                 vel[1],
586 <                 vel[2]); // check here.
587 <        strcpy( writeLine, tempBuffer );
588 <        
589 <        if( atoms[local_index]->isDirectional() ){
590 <          
591 <          dAtom = (DirectionalAtom *)atoms[local_index];
592 <          dAtom->getQ( q );
593 <          
594 <          sprintf( tempBuffer,
595 <                   "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
596 <                   q[0],
597 <                   q[1],
598 <                   q[2],
599 <                   q[3],
600 <                   dAtom->getJx(),
601 <                   dAtom->getJy(),
602 <                   dAtom->getJz());
603 <          strcat( writeLine, tempBuffer );
604 <        }
605 <        else{
606 <          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
607 <        }
608 <      }
609 <      else {
610 <        sprintf(painCave.errMsg,
611 <                "Atom %d not found on processor %d\n",
612 <                which_atom, worldRank );
613 <        myStatus = 0;
614 <        simError();
615 <        
616 <        strcpy( writeLine, "Hello, I'm an error.\n");
617 <      }
618 <
619 <      MPI_Send(writeLine, BUFFERSIZE, MPI_CHAR, 0,
620 <               TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
621 <      MPI_Send( &myStatus, 1, MPI_INT, 0,
622 <                TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
623 <    }
624 <  }
625 <  finalOut.flush();
626 <  sprintf( checkPointMsg,
627 <           "Sucessfully took a dump.\n");
628 <  MPIcheckPoint();
603 >  }
604    
630 –  if( worldRank == 0 ) finalOut.close();    
605   #endif // is_mpi
606   }
607  
634 –
635 –
608   #ifdef IS_MPI
609  
610   // a couple of functions to let us escape the write loop
611  
612 < void dWrite::nodeZeroError( void ){
641 <  int j, myStatus;
642 <  
643 <  myStatus = 0;
644 <  for (j = 0; j < mpiSim->getNumberProcessors(); j++) {      
645 <    MPI_Send( &myStatus, 1, MPI_INT, j,
646 <              TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
647 <  }  
648 <  
612 > void dWrite::DieDieDie( void ){
613  
614    MPI_Finalize();
615    exit (0);
652 –  
616   }
617  
655 – void dWrite::anonymousNodeDie( void ){
656 –
657 –  MPI_Finalize();
658 –  exit (0);
659 – }
660 –
618   #endif //is_mpi

Diff Legend

– Removed lines
+ Added lines
< Changed lines
> Changed lines