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Comparing branches/development/src/io/DumpWriter.cpp (file contents):
Revision 1769 by gezelter, Mon Jul 9 14:15:52 2012 UTC vs.
Revision 1874 by gezelter, Wed May 15 15:09:35 2013 UTC

# Line 35 | Line 35
35   *                                                                      
36   * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).            
37   * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
38 < * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
38 > * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).          
39   * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40   * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41   */
# Line 302 | Line 302 | namespace OpenMD {
302    void DumpWriter::writeFrame(std::ostream& os) {
303  
304   #ifdef IS_MPI
305 <    MPI_Status istatus;
305 >    MPI::Status istatus;
306   #endif
307  
308      Molecule* mol;
# Line 331 | Line 331 | namespace OpenMD {
331  
332      if (doSiteData_) {
333        os << "    <SiteData>\n";
334 <      for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
334 >      for (mol = info_->beginMolecule(mi); mol != NULL;
335 >           mol = info_->nextMolecule(mi)) {
336                
337          for (sd = mol->beginIntegrableObject(ii); sd != NULL;  
338             sd = mol->nextIntegrableObject(ii)) {        
# Line 358 | Line 359 | namespace OpenMD {
359  
360      os.flush();
361   #else
361 –    //every node prepares the dump lines for integrable objects belong to itself
362 –    std::string buffer;
363 –    for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
362  
363 +    const int masterNode = 0;
364 +    int worldRank = MPI::COMM_WORLD.Get_rank();
365 +    int nProc = MPI::COMM_WORLD.Get_size();
366  
366 –      for (sd = mol->beginIntegrableObject(ii); sd != NULL;
367 –           sd = mol->nextIntegrableObject(ii)) {        
368 –          buffer += prepareDumpLine(sd);
369 –      }
370 –    }
371 –    
372 –    const int masterNode = 0;
373 –    int nProc;
374 –    MPI_Comm_size(MPI_COMM_WORLD, &nProc);
367      if (worldRank == masterNode) {      
368        os << "  <Snapshot>\n";  
369 <      writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
369 >      writeFrameProperties(os,
370 >                           info_->getSnapshotManager()->getCurrentSnapshot());
371        os << "    <StuntDoubles>\n";
372 <        
380 <      os << buffer;
372 >    }
373  
374 +    //every node prepares the dump lines for integrable objects belong to itself
375 +    std::string buffer;
376 +    for (mol = info_->beginMolecule(mi); mol != NULL;
377 +         mol = info_->nextMolecule(mi)) {
378 +      for (sd = mol->beginIntegrableObject(ii); sd != NULL;
379 +           sd = mol->nextIntegrableObject(ii)) {        
380 +        buffer += prepareDumpLine(sd);
381 +      }
382 +    }
383 +    
384 +    if (worldRank == masterNode) {      
385 +      os << buffer;
386 +      
387        for (int i = 1; i < nProc; ++i) {
388 +        // tell processor i to start sending us data:
389 +        MPI::COMM_WORLD.Bcast(&i, 1, MPI::INT, masterNode);
390  
391          // receive the length of the string buffer that was
392 <        // prepared by processor i
386 <
387 <        MPI_Bcast(&i, 1, MPI_INT,masterNode,MPI_COMM_WORLD);
392 >        // prepared by processor i:        
393          int recvLength;
394 <        MPI_Recv(&recvLength, 1, MPI_INT, i, 0, MPI_COMM_WORLD, &istatus);
394 >        MPI::COMM_WORLD.Recv(&recvLength, 1, MPI::INT, i, MPI::ANY_TAG,
395 >                             istatus);
396 >
397 >        // create a buffer to receive the data
398          char* recvBuffer = new char[recvLength];
399          if (recvBuffer == NULL) {
400          } else {
401 <          MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i, 0, MPI_COMM_WORLD, &istatus);
401 >          // receive the data:
402 >          MPI::COMM_WORLD.Recv(recvBuffer, recvLength, MPI::CHAR, i,
403 >                               MPI::ANY_TAG, istatus);
404 >          // send it to the file:
405            os << recvBuffer;
406 +          // get rid of the receive buffer:
407            delete [] recvBuffer;
408          }
409        }
398 –      os << "    </StuntDoubles>\n";
399 –      
400 –      os << "  </Snapshot>\n";
401 –      os.flush();
410      } else {
411        int sendBufferLength = buffer.size() + 1;
412        int myturn = 0;
413        for (int i = 1; i < nProc; ++i){
414 <        MPI_Bcast(&myturn,1, MPI_INT,masterNode,MPI_COMM_WORLD);
414 >        // wait for the master node to call our number:
415 >        MPI::COMM_WORLD.Bcast(&myturn, 1, MPI::INT, masterNode);
416          if (myturn == worldRank){
417 <          MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
418 <          MPI_Send((void *)buffer.c_str(), sendBufferLength, MPI_CHAR, masterNode, 0, MPI_COMM_WORLD);
417 >          // send the length of our buffer:
418 >          MPI::COMM_WORLD.Send(&sendBufferLength, 1, MPI::INT, masterNode, 0);
419 >
420 >          // send our buffer:
421 >          MPI::COMM_WORLD.Send((void *)buffer.c_str(), sendBufferLength,
422 >                               MPI::CHAR, masterNode, 0);
423          }
424        }
425      }
426 +    
427 +    if (worldRank == masterNode) {      
428 +      os << "    </StuntDoubles>\n";
429 +    }
430  
431 < #endif // is_mpi
431 >    if (doSiteData_) {
432 >      if (worldRank == masterNode) {
433 >        os << "    <SiteData>\n";
434 >      }
435 >      buffer.clear();
436 >      for (mol = info_->beginMolecule(mi); mol != NULL;
437 >           mol = info_->nextMolecule(mi)) {
438 >              
439 >        for (sd = mol->beginIntegrableObject(ii); sd != NULL;  
440 >             sd = mol->nextIntegrableObject(ii)) {      
441 >          
442 >          int ioIndex = sd->getGlobalIntegrableObjectIndex();
443 >          // do one for the IO itself
444 >          buffer += prepareSiteLine(sd, ioIndex, 0);
445  
446 +          if (sd->isRigidBody()) {
447 +            
448 +            RigidBody* rb = static_cast<RigidBody*>(sd);
449 +            int siteIndex = 0;
450 +            for (atom = rb->beginAtom(ai); atom != NULL;  
451 +                 atom = rb->nextAtom(ai)) {                                            
452 +              buffer += prepareSiteLine(atom, ioIndex, siteIndex);
453 +              siteIndex++;
454 +            }
455 +          }
456 +        }
457 +      }
458 +
459 +      if (worldRank == masterNode) {    
460 +        os << buffer;
461 +        
462 +        for (int i = 1; i < nProc; ++i) {
463 +          
464 +          // tell processor i to start sending us data:
465 +          MPI::COMM_WORLD.Bcast(&i, 1, MPI::INT, masterNode);
466 +          
467 +          // receive the length of the string buffer that was
468 +          // prepared by processor i:        
469 +          int recvLength;
470 +          MPI::COMM_WORLD.Recv(&recvLength, 1, MPI::INT, i, MPI::ANY_TAG,
471 +                               istatus);
472 +          
473 +          // create a buffer to receive the data
474 +          char* recvBuffer = new char[recvLength];
475 +          if (recvBuffer == NULL) {
476 +          } else {
477 +            // receive the data:
478 +            MPI::COMM_WORLD.Recv(recvBuffer, recvLength, MPI::CHAR, i,
479 +                                 MPI::ANY_TAG, istatus);
480 +            // send it to the file:
481 +            os << recvBuffer;
482 +            // get rid of the receive buffer:
483 +            delete [] recvBuffer;
484 +          }
485 +        }      
486 +      } else {
487 +        int sendBufferLength = buffer.size() + 1;
488 +        int myturn = 0;
489 +        for (int i = 1; i < nProc; ++i){
490 +          // wait for the master node to call our number:
491 +          MPI::COMM_WORLD.Bcast(&myturn, 1, MPI::INT, masterNode);
492 +          if (myturn == worldRank){
493 +            // send the length of our buffer:
494 +            MPI::COMM_WORLD.Send(&sendBufferLength, 1, MPI::INT, masterNode, 0);
495 +            // send our buffer:
496 +            MPI::COMM_WORLD.Send((void *)buffer.c_str(), sendBufferLength,
497 +                                 MPI::CHAR, masterNode, 0);
498 +          }
499 +        }
500 +      }
501 +      
502 +      if (worldRank == masterNode) {    
503 +        os << "    </SiteData>\n";
504 +      }
505 +    }
506 +    
507 +    if (worldRank == masterNode) {
508 +      os << "  </Snapshot>\n";
509 +      os.flush();
510 +    }
511 +    
512 + #endif // is_mpi
513 +    
514    }
515  
516    std::string DumpWriter::prepareDumpLine(StuntDouble* sd) {
# Line 628 | Line 726 | namespace OpenMD {
726   #ifdef IS_MPI
727      if (worldRank == 0) {
728   #endif // is_mpi
729 <
729 >      
730        eorStream = createOStream(eorFilename_);
731 <
731 >      writeFrame(*eorStream);
732 >      
733   #ifdef IS_MPI
734      }
636 – #endif // is_mpi    
637 –
638 –    writeFrame(*eorStream);
639 –
640 – #ifdef IS_MPI
735      if (worldRank == 0) {
736   #endif // is_mpi
737 +
738        writeClosing(*eorStream);
739        delete eorStream;
740 +
741   #ifdef IS_MPI
742      }
743   #endif // is_mpi  

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