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root/OpenMD/trunk/src/io/DumpWriter.cpp
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Comparing trunk/src/io/DumpWriter.cpp (file contents):
Revision 1921 by gezelter, Thu Aug 1 18:23:07 2013 UTC vs.
Revision 1983 by gezelter, Tue Apr 15 20:36:19 2014 UTC

# Line 39 | Line 39
39   * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40   * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41   */
42 +
43 + #include "config.h"
44 +
45 + #ifdef IS_MPI
46 + #include <mpi.h>
47 + #endif
48  
49   #include "io/DumpWriter.hpp"
50   #include "primitives/Molecule.hpp"
# Line 54 | Line 60
60   #define isinf(x) (!_finite(x) && !_isnan(x))
61   #endif
62  
57 – #ifdef IS_MPI
58 – #include <mpi.h>
59 – #endif
60 –
63   using namespace std;
64   namespace OpenMD {
65  
# Line 302 | Line 304 | namespace OpenMD {
304    void DumpWriter::writeFrame(std::ostream& os) {
305  
306   #ifdef IS_MPI
307 <    MPI::Status istatus;
307 >    MPI_Status istatus;
308   #endif
309  
310      Molecule* mol;
# Line 360 | Line 362 | namespace OpenMD {
362   #else
363  
364      const int masterNode = 0;
365 <    int worldRank = MPI::COMM_WORLD.Get_rank();
366 <    int nProc = MPI::COMM_WORLD.Get_size();
365 >    int worldRank;
366 >    int nProc;
367  
368 +    MPI_Comm_size( MPI_COMM_WORLD, &nProc);
369 +    MPI_Comm_rank( MPI_COMM_WORLD, &worldRank);
370 +
371 +
372      if (worldRank == masterNode) {      
373        os << "  <Snapshot>\n";  
374        writeFrameProperties(os,
# Line 385 | Line 391 | namespace OpenMD {
391        
392        for (int i = 1; i < nProc; ++i) {
393          // tell processor i to start sending us data:
394 <        MPI::COMM_WORLD.Bcast(&i, 1, MPI::INT, masterNode);
394 >        MPI_Bcast(&i, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
395  
396          // receive the length of the string buffer that was
397          // prepared by processor i:        
398          int recvLength;
399 <        MPI::COMM_WORLD.Recv(&recvLength, 1, MPI::INT, i, MPI::ANY_TAG,
400 <                             istatus);
399 >        MPI_Recv(&recvLength, 1, MPI_INT, i, MPI_ANY_TAG, MPI_COMM_WORLD,
400 >                 &istatus);
401  
402          // create a buffer to receive the data
403          char* recvBuffer = new char[recvLength];
404          if (recvBuffer == NULL) {
405          } else {
406            // receive the data:
407 <          MPI::COMM_WORLD.Recv(recvBuffer, recvLength, MPI::CHAR, i,
408 <                               MPI::ANY_TAG, istatus);
407 >          MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i,
408 >                               MPI_ANY_TAG, MPI_COMM_WORLD, &istatus);
409            // send it to the file:
410            os << recvBuffer;
411            // get rid of the receive buffer:
# Line 411 | Line 417 | namespace OpenMD {
417        int myturn = 0;
418        for (int i = 1; i < nProc; ++i){
419          // wait for the master node to call our number:
420 <        MPI::COMM_WORLD.Bcast(&myturn, 1, MPI::INT, masterNode);
420 >        MPI_Bcast(&myturn, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
421          if (myturn == worldRank){
422            // send the length of our buffer:
423 <          MPI::COMM_WORLD.Send(&sendBufferLength, 1, MPI::INT, masterNode, 0);
423 >          MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
424  
425            // send our buffer:
426 <          MPI::COMM_WORLD.Send((void *)buffer.c_str(), sendBufferLength,
427 <                               MPI::CHAR, masterNode, 0);
426 >          MPI_Send((void *)buffer.c_str(), sendBufferLength,
427 >                   MPI_CHAR, masterNode, 0, MPI_COMM_WORLD);
428  
429          }
430        }
# Line 462 | Line 468 | namespace OpenMD {
468          for (int i = 1; i < nProc; ++i) {
469            
470            // tell processor i to start sending us data:
471 <          MPI::COMM_WORLD.Bcast(&i, 1, MPI::INT, masterNode);
471 >          MPI_Bcast(&i, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
472            
473            // receive the length of the string buffer that was
474            // prepared by processor i:        
475            int recvLength;
476 <          MPI::COMM_WORLD.Recv(&recvLength, 1, MPI::INT, i, MPI::ANY_TAG,
477 <                               istatus);
476 >          MPI_Recv(&recvLength, 1, MPI_INT, i, MPI_ANY_TAG, MPI_COMM_WORLD,
477 >                   &istatus);
478            
479            // create a buffer to receive the data
480            char* recvBuffer = new char[recvLength];
481            if (recvBuffer == NULL) {
482            } else {
483              // receive the data:
484 <            MPI::COMM_WORLD.Recv(recvBuffer, recvLength, MPI::CHAR, i,
485 <                                 MPI::ANY_TAG, istatus);
484 >            MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i,
485 >                     MPI_ANY_TAG, MPI_COMM_WORLD, &istatus);
486              // send it to the file:
487              os << recvBuffer;
488              // get rid of the receive buffer:
# Line 488 | Line 494 | namespace OpenMD {
494          int myturn = 0;
495          for (int i = 1; i < nProc; ++i){
496            // wait for the master node to call our number:
497 <          MPI::COMM_WORLD.Bcast(&myturn, 1, MPI::INT, masterNode);
497 >          MPI_Bcast(&myturn, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
498            if (myturn == worldRank){
499              // send the length of our buffer:
500 <            MPI::COMM_WORLD.Send(&sendBufferLength, 1, MPI::INT, masterNode, 0);
500 >            MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
501              // send our buffer:
502 <            MPI::COMM_WORLD.Send((void *)buffer.c_str(), sendBufferLength,
503 <                                 MPI::CHAR, masterNode, 0);
502 >            MPI_Send((void *)buffer.c_str(), sendBufferLength,
503 >                     MPI_CHAR, masterNode, 0, MPI_COMM_WORLD);
504            }
505          }
506        }
# Line 731 | Line 737 | namespace OpenMD {
737    }
738  
739    void DumpWriter::writeEor() {
740 <    std::ostream* eorStream;
741 <    
740 >
741 >    std::ostream* eorStream = NULL;
742 >
743   #ifdef IS_MPI
744      if (worldRank == 0) {
745   #endif // is_mpi
# Line 765 | Line 772 | namespace OpenMD {
772   #ifdef IS_MPI
773      if (worldRank == 0) {
774   #endif // is_mpi
768 –
775        buffers.push_back(dumpFile_->rdbuf());
770 –
776        eorStream = createOStream(eorFilename_);
772 –
777        buffers.push_back(eorStream->rdbuf());
774 –        
778   #ifdef IS_MPI
779      }
780   #endif // is_mpi    
781  
782      TeeBuf tbuf(buffers.begin(), buffers.end());
783      std::ostream os(&tbuf);
781 –
784      writeFrame(os);
785  
786   #ifdef IS_MPI
# Line 788 | Line 790 | namespace OpenMD {
790        delete eorStream;
791   #ifdef IS_MPI
792      }
793 < #endif // is_mpi  
792 <    
793 > #endif // is_mpi      
794    }
795  
796    std::ostream* DumpWriter::createOStream(const std::string& filename) {

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