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root/group/trunk/mdtools/md_code/DumpWriter.cpp
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Comparing trunk/mdtools/md_code/DumpWriter.cpp (file contents):
Revision 214 by mmeineke, Mon Dec 16 21:42:14 2002 UTC vs.
Revision 261 by chuckv, Mon Feb 3 21:15:59 2003 UTC

# Line 1 | Line 1
1   #include <cstring>
2   #include <iostream>
3   #include <fstream>
4 +
5 + #ifdef IS_MPI
6   #include <mpi.h>
7 + #include "mpiSimulation.hpp"
8 + #define TAKE_THIS_TAG 0
9 + #endif //is_mpi
10  
11   #include "ReadWrite.hpp"
12   #include "simError.h"
13  
14  
15 +
16 +
17 +
18   DumpWriter::DumpWriter( SimInfo* the_entry_plug ){
19  
20 +  entry_plug = the_entry_plug;
21 +
22   #ifdef IS_MPI
23    if(worldRank == 0 ){
24   #endif // is_mpi
25      
26 <    entry_plug = the_entry_plug;
26 >
27      
28      strcpy( outName, entry_plug->sampleName );
29      
20 –    std::cerr << "Opening " << outName << " for dumping.\n";
21 –
30      outFile.open(outName, ios::out | ios::trunc );
31      
32      if( !outFile ){
# Line 34 | Line 42 | DumpWriter::DumpWriter( SimInfo* the_entry_plug ){
42  
43   #ifdef IS_MPI
44    }
45 +
46 +  sprintf( checkPointMsg,
47 +           "Sucessfully opened output file for dumping.\n");
48 +  MPIcheckPoint();
49   #endif // is_mpi
50   }
51  
# Line 53 | Line 65 | void DumpWriter::writeDump( double currentTime ){
65   void DumpWriter::writeDump( double currentTime ){
66    
67    const int BUFFERSIZE = 2000;
68 <  char tempBuffer[500];
68 >  char tempBuffer[BUFFERSIZE];
69    char writeLine[BUFFERSIZE];
70  
71    int i;
# Line 74 | Line 86 | void DumpWriter::writeDump( double currentTime ){
86      
87    for( i=0; i<nAtoms; i++ ){
88        
89 +
90      sprintf( tempBuffer,
91               "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
92               atoms[i]->getType(),
# Line 123 | Line 136 | void DumpWriter::writeDump( double currentTime ){
136    // write out header and node 0's coordinates
137  
138    if( worldRank == 0 ){
139 <    outFile << entry_plug->mpiSim->getTotAtoms() << "\n";
139 >    outFile << mpiSim->getTotAtoms() << "\n";
140        
141      outFile << currentTime << "\t"
142              << entry_plug->box_x << "\t"
# Line 163 | Line 176 | void DumpWriter::writeDump( double currentTime ){
176        else
177          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
178          
179 <      outfile << writeLine;
179 >      outFile << writeLine;
180        masterIndex++;
181      }
182      outFile.flush();
183    }
184 +
185 +  sprintf( checkPointMsg,
186 +           "Sucessfully wrote node 0's dump configuration.\n");
187 +  MPIcheckPoint();
188      
189 <  for (procIndex = 1; procIndex < entry_plug->mpiSim->getNumberProcessors();
189 >  for (procIndex = 1; procIndex < mpiSim->getNumberProcessors();
190         procIndex++){
191  
192      if( worldRank == 0 ){
193 <        
193 >      
194        mpiErr = MPI_Recv(&nodeAtomsStart,1,MPI_INT,procIndex,
195 <                        MPI_ANY_TAG,MPI_COMM_WORLD,istatus);
196 <
195 >                        TAKE_THIS_TAG,MPI_COMM_WORLD,istatus);
196 >      
197        mpiErr = MPI_Recv(&nodeAtomsEnd,1,MPI_INT,procIndex,
198 <                        MPI_ANY_TAG,MPI_COMM_WORLD, istatus);
199 <        
198 >                        TAKE_THIS_TAG,MPI_COMM_WORLD, istatus);
199 >      
200        // Make sure where node 0 is writing to, matches where the
201        // receiving node expects it to be.
202 <        
202 >      
203        if (masterIndex != nodeAtomsStart){
204          sendError = 1;
205 <        mpiErr = MPI_Send(&sendError,1,MPI_INT,procIndex,MPI_ANY_TAG,
205 >        mpiErr = MPI_Send(&sendError,1,MPI_INT,procIndex,TAKE_THIS_TAG,
206                            MPI_COMM_WORLD);
207          sprintf(painCave.errMsg,
208                  "DumpWriter error: atoms start index (%d) for "
# Line 194 | Line 211 | void DumpWriter::writeDump( double currentTime ){
211          painCave.isFatal = 1;
212          simError();
213        }
214 <        
214 >      
215        sendError = 0;
216 <      mpiErr = MPI_Send(&sendError,1,MPI_INT,procIndex,MPI_ANY_TAG,
216 >      mpiErr = MPI_Send(&sendError,1,MPI_INT,procIndex,TAKE_THIS_TAG,
217                          MPI_COMM_WORLD);
218 <
218 >      
219        // recieve the nodes writeLines
220 <
221 <      for ( i = nodeAtomStart; i <= nodeAtomEnd, i++){
222 <          
223 <        mpiErr = MPI_Recv(&read_buffer,BUFFERSIZE,MPI_CHAR,procIndex,
224 <                          MPI_ANY_TAG,MPI_COMM_WORLD,istatus );
225 <
220 >      
221 >      for ( i = nodeAtomsStart; i <= nodeAtomsEnd; i++){
222 >        
223 >        mpiErr = MPI_Recv(writeLine,BUFFERSIZE,MPI_CHAR,procIndex,
224 >                          TAKE_THIS_TAG,MPI_COMM_WORLD,istatus );
225 >        
226          outFile << writeLine;
227          masterIndex++;
228        }
# Line 213 | Line 230 | void DumpWriter::writeDump( double currentTime ){
230  
231      else if( worldRank == procIndex ){
232  
233 <      nodeAtomStart = entry_plug->mpiSim->getMyAtomStart();
234 <      nodeAtomEnd = entry_plug->mpiSim->getMyAtomEnd();
235 <        
236 <      mpiErr = MPI_Send(&nodeAtomsStart,1,MPI_INT,0,MPI_ANY_TAG,
233 >      nodeAtomsStart = mpiSim->getMyAtomStart();
234 >      nodeAtomsEnd = mpiSim->getMyAtomEnd();
235 >
236 >      mpiErr = MPI_Send(&nodeAtomsStart,1,MPI_INT,0,TAKE_THIS_TAG,
237                          MPI_COMM_WORLD);
238 <      mpiErr = MPI_Send(&nodeAtomsEnd,1,MPI_INT,0,MPI_ANY_TAG,
238 >      mpiErr = MPI_Send(&nodeAtomsEnd,1,MPI_INT,0,TAKE_THIS_TAG,
239                          MPI_COMM_WORLD);
240          
241 <      mpiErr = MPI_Recv(&sendError,1,MPI_INT,0,MPI_ANY_TAG,
241 >      sendError = -1;
242 >      mpiErr = MPI_Recv(&sendError,1,MPI_INT,0,TAKE_THIS_TAG,
243                          MPI_COMM_WORLD, istatus);
244 <      if (sendError) mpiCheckpoint();
244 >
245 >      if (sendError) MPIcheckPoint();
246  
247        // send current node's configuration line by line.
248  
249        for( i=0; i<nAtoms; i++ ){
250 <          
250 >
251          sprintf( tempBuffer,
252                   "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
253                   atoms[i]->getType(),
# Line 237 | Line 256 | void DumpWriter::writeDump( double currentTime ){
256                   atoms[i]->getZ(),
257                   atoms[i]->get_vx(),
258                   atoms[i]->get_vy(),
259 <                 atoms[i]->get_vz());
259 >                 atoms[i]->get_vz()); // check here.
260          strcpy( writeLine, tempBuffer );
261            
262          if( atoms[i]->isDirectional() ){
# Line 259 | Line 278 | void DumpWriter::writeDump( double currentTime ){
278          else
279            strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
280            
281 <        mpiErr = MPI_Send(writeLine,BUFFERSIZE,MPI_CHAR,0,MPI_ANY_TAG,
281 >        mpiErr = MPI_Send(writeLine,BUFFERSIZE,MPI_CHAR,0,TAKE_THIS_TAG,
282                            MPI_COMM_WORLD);
283        }
284      }
285        
286      sprintf(checkPointMsg,"Node %d sent dump configuration.",
287              procIndex);
288 <    mpiCheckPoint();
288 >    MPIcheckPoint();
289    }
290      
291   #endif // is_mpi
# Line 311 | Line 330 | void DumpWriter::writeFinal(){
330   #ifdef IS_MPI
331    }
332    
333 <  sprintf(checkPointMsg,"Opened file for final configuration\n",procIndex);
334 <  mpiCheckPoint();  
333 >  sprintf(checkPointMsg,"Opened file for final configuration\n");
334 >  MPIcheckPoint();  
335    
336   #endif //is_mpi
337  
# Line 322 | Line 341 | void DumpWriter::writeFinal(){
341      
342    finalOut << nAtoms << "\n";
343      
344 <  finalOut << currentTime << "\t"
345 <          << entry_plug->box_x << "\t"
346 <          << entry_plug->box_y << "\t"
328 <          << entry_plug->box_z << "\n";
344 >  finalOut << entry_plug->box_x << "\t"
345 >           << entry_plug->box_y << "\t"
346 >           << entry_plug->box_z << "\n";
347      
348    for( i=0; i<nAtoms; i++ ){
349        
# Line 378 | Line 396 | void DumpWriter::writeFinal(){
396    // write out header and node 0's coordinates
397  
398    if( worldRank == 0 ){
399 <    finalOut << entry_plug->mpiSim->getTotAtoms() << "\n";
399 >    finalOut << mpiSim->getTotAtoms() << "\n";
400        
401 <    finalOut << currentTime << "\t"
402 <            << entry_plug->box_x << "\t"
403 <            << entry_plug->box_y << "\t"
404 <            << entry_plug->box_z << "\n";
387 <
401 >    finalOut << entry_plug->box_x << "\t"
402 >             << entry_plug->box_y << "\t"
403 >             << entry_plug->box_z << "\n";
404 >    
405      masterIndex = 0;
406 +    
407      for( i=0; i<nAtoms; i++ ){
408        
409        sprintf( tempBuffer,
# Line 418 | Line 436 | void DumpWriter::writeFinal(){
436        else
437          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
438          
439 <      outfile << writeLine;
439 >      finalOut << writeLine;
440        masterIndex++;
441      }
442      finalOut.flush();
443    }
444      
445 <  for (procIndex = 1; procIndex < entry_plug->mpiSim->getNumberProcessors();
445 >  for (procIndex = 1; procIndex < mpiSim->getNumberProcessors();
446         procIndex++){
447  
448      if( worldRank == 0 ){
449          
450        mpiErr = MPI_Recv(&nodeAtomsStart,1,MPI_INT,procIndex,
451 <                        MPI_ANY_TAG,MPI_COMM_WORLD,istatus);
451 >                        TAKE_THIS_TAG,MPI_COMM_WORLD,istatus);
452  
453        mpiErr = MPI_Recv(&nodeAtomsEnd,1,MPI_INT,procIndex,
454 <                        MPI_ANY_TAG,MPI_COMM_WORLD, istatus);
454 >                        TAKE_THIS_TAG,MPI_COMM_WORLD, istatus);
455          
456        // Make sure where node 0 is writing to, matches where the
457        // receiving node expects it to be.
458          
459        if (masterIndex != nodeAtomsStart){
460          sendError = 1;
461 <        mpiErr = MPI_Send(&sendError,1,MPI_INT,procIndex,MPI_ANY_TAG,
461 >        mpiErr = MPI_Send(&sendError,1,MPI_INT,procIndex,TAKE_THIS_TAG,
462                            MPI_COMM_WORLD);
463          sprintf(painCave.errMsg,
464                  "DumpWriter error: atoms start index (%d) for "
# Line 451 | Line 469 | void DumpWriter::writeFinal(){
469        }
470          
471        sendError = 0;
472 <      mpiErr = MPI_Send(&sendError,1,MPI_INT,procIndex,MPI_ANY_TAG,
472 >      mpiErr = MPI_Send(&sendError,1,MPI_INT,procIndex,TAKE_THIS_TAG,
473                          MPI_COMM_WORLD);
474  
475        // recieve the nodes writeLines
476  
477 <      for ( i = nodeAtomStart; i <= nodeAtomEnd, i++){
477 >      for ( i = nodeAtomsStart; i <= nodeAtomsEnd; i++){
478            
479 <        mpiErr = MPI_Recv(&read_buffer,BUFFERSIZE,MPI_CHAR,procIndex,
480 <                          MPI_ANY_TAG,MPI_COMM_WORLD,istatus );
479 >        mpiErr = MPI_Recv(writeLine,BUFFERSIZE,MPI_CHAR,procIndex,
480 >                          TAKE_THIS_TAG,MPI_COMM_WORLD,istatus );
481  
482          finalOut << writeLine;
483          masterIndex++;
# Line 470 | Line 488 | void DumpWriter::writeFinal(){
488  
489      else if( worldRank == procIndex ){
490  
491 <      nodeAtomStart = entry_plug->mpiSim->getMyAtomStart();
492 <      nodeAtomEnd = entry_plug->mpiSim->getMyAtomEnd();
491 >      nodeAtomsStart = mpiSim->getMyAtomStart();
492 >      nodeAtomsEnd = mpiSim->getMyAtomEnd();
493          
494 <      mpiErr = MPI_Send(&nodeAtomsStart,1,MPI_INT,0,MPI_ANY_TAG,
494 >      mpiErr = MPI_Send(&nodeAtomsStart,1,MPI_INT,0,TAKE_THIS_TAG,
495                          MPI_COMM_WORLD);
496 <      mpiErr = MPI_Send(&nodeAtomsEnd,1,MPI_INT,0,MPI_ANY_TAG,
496 >      mpiErr = MPI_Send(&nodeAtomsEnd,1,MPI_INT,0,TAKE_THIS_TAG,
497                          MPI_COMM_WORLD);
498          
499 <      mpiErr = MPI_Recv(&sendError,1,MPI_INT,0,MPI_ANY_TAG,
499 >      mpiErr = MPI_Recv(&sendError,1,MPI_INT,0,TAKE_THIS_TAG,
500                          MPI_COMM_WORLD, istatus);
501 <      if (sendError) mpiCheckpoint();
501 >      if (sendError) MPIcheckPoint();
502  
503        // send current node's configuration line by line.
504  
# Line 516 | Line 534 | void DumpWriter::writeFinal(){
534          else
535            strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
536            
537 <        mpiErr = MPI_Send(writeLine,BUFFERSIZE,MPI_CHAR,0,MPI_ANY_TAG,
537 >        mpiErr = MPI_Send(writeLine,BUFFERSIZE,MPI_CHAR,0,TAKE_THIS_TAG,
538                            MPI_COMM_WORLD);
539        }
540      }
541        
542      sprintf(checkPointMsg,"Node %d sent dump configuration.",
543              procIndex);
544 <    mpiCheckPoint();
544 >    MPIcheckPoint();
545    }
546  
547    if( worldRank == 0 ) finalOut.close();

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