src/io/DumpWriter.cpp

/*
 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Acknowledgement of the program authors must be made in any
 *    publication of scientific results based in part on use of the
 *    program.  An acceptable form of acknowledgement is citation of
 *    the article in which the program was described (Matthew
 *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
 *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
 *    Parallel Simulation Engine for Molecular Dynamics,"
 *    J. Comput. Chem. 26, pp. 252-271 (2005))
 *
 * 2. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 */
 
#include "io/DumpWriter.hpp"
#include "primitives/Molecule.hpp"
#include "utils/simError.h"
#include "io/basic_teebuf.hpp"
#include "io/gzstream.hpp"
#include "io/Globals.hpp"

#ifdef IS_MPI
#include <mpi.h>
#endif //is_mpi

namespace oopse {

  DumpWriter::DumpWriter(SimInfo* info) 
    : info_(info), filename_(info->getDumpFileName()), eorFilename_(info->getFinalConfigFileName()){

    Globals* simParams = info->getSimParams();
    needCompression_ = simParams->getCompressDumpFile();

    if (needCompression_) {
        filename_ += ".gz";
        eorFilename_ += ".gz";
    }
    
#ifdef IS_MPI

      if (worldRank == 0) {
#endif // is_mpi


        dumpFile_ = createOStream(filename_);

        if (!dumpFile_) {
          sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
                  filename_.c_str());
          painCave.isFatal = 1;
          simError();
        }

#ifdef IS_MPI

      }

      sprintf(checkPointMsg, "Sucessfully opened output file for dumping.\n");
      MPIcheckPoint();

#endif // is_mpi

    }


  DumpWriter::DumpWriter(SimInfo* info, const std::string& filename) 
    : info_(info), filename_(filename){

    Globals* simParams = info->getSimParams();
    eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";    

    needCompression_ = simParams->getCompressDumpFile();
    if (needCompression_) {
        filename_ += ".gz";
        eorFilename_ += ".gz";
    }
    
#ifdef IS_MPI

      if (worldRank == 0) {
#endif // is_mpi


        dumpFile_ = createOStream(filename_);

        if (!dumpFile_) {
          sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
                  filename_.c_str());
          painCave.isFatal = 1;
          simError();
        }

#ifdef IS_MPI

      }

      sprintf(checkPointMsg, "Sucessfully opened output file for dumping.\n");
      MPIcheckPoint();

#endif // is_mpi

    }

  DumpWriter::~DumpWriter() {

#ifdef IS_MPI

    if (worldRank == 0) {
#endif // is_mpi

      delete dumpFile_;

#ifdef IS_MPI

    }

#endif // is_mpi

  }

  void DumpWriter::writeCommentLine(std::ostream& os, Snapshot* s) {

    double currentTime;
    Mat3x3d hmat;
    double chi;
    double integralOfChiDt;
    Mat3x3d eta;
    
    currentTime = s->getTime();
    hmat = s->getHmat();
    chi = s->getChi();
    integralOfChiDt = s->getIntegralOfChiDt();
    eta = s->getEta();
    
    os << currentTime << ";\t" 
       << hmat(0, 0) << "\t" << hmat(1, 0) << "\t" << hmat(2, 0) << ";\t" 
       << hmat(0, 1) << "\t" << hmat(1, 1) << "\t" << hmat(2, 1) << ";\t"
       << hmat(0, 2) << "\t" << hmat(1, 2) << "\t" << hmat(2, 2) << ";\t";

    //write out additional parameters, such as chi and eta

    os << chi << "\t" << integralOfChiDt << "\t;";

    os << eta(0, 0) << "\t" << eta(1, 0) << "\t" << eta(2, 0) << ";\t" 
       << eta(0, 1) << "\t" << eta(1, 1) << "\t" << eta(2, 1) << ";\t"
       << eta(0, 2) << "\t" << eta(1, 2) << "\t" << eta(2, 2) << ";";
        
    os << "\n";
  }

  void DumpWriter::writeFrame(std::ostream& os) {
    const int BUFFERSIZE = 2000;
    const int MINIBUFFERSIZE = 100;

    char tempBuffer[BUFFERSIZE];
    char writeLine[BUFFERSIZE];

    Quat4d q;
    Vector3d ji;
    Vector3d pos;
    Vector3d vel;

    Molecule* mol;
    StuntDouble* integrableObject;
    SimInfo::MoleculeIterator mi;
    Molecule::IntegrableObjectIterator ii;
  
    int nTotObjects;    
    nTotObjects = info_->getNGlobalIntegrableObjects();

#ifndef IS_MPI


    os << nTotObjects << "\n";
        
    writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot());

    for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {

      for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; 
           integrableObject = mol->nextIntegrableObject(ii)) { 
                

        pos = integrableObject->getPos();
        vel = integrableObject->getVel();

        sprintf(tempBuffer, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
                integrableObject->getType().c_str(), 
                pos[0], pos[1], pos[2],
                vel[0], vel[1], vel[2]);

        strcpy(writeLine, tempBuffer);

        if (integrableObject->isDirectional()) {
          q = integrableObject->getQ();
          ji = integrableObject->getJ();

          sprintf(tempBuffer, "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", 
                  q[0], q[1], q[2], q[3],
                  ji[0], ji[1], ji[2]);
          strcat(writeLine, tempBuffer);
        } else {
          strcat(writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n");
        }

        os << writeLine;

      }
    }

    os.flush();
#else // is_mpi
    /*********************************************************************
     * Documentation?  You want DOCUMENTATION?
     * 
     * Why all the potatoes below?  
     *
     * To make a long story short, the original version of DumpWriter
     * worked in the most inefficient way possible.  Node 0 would 
     * poke each of the node for an individual atom's formatted data 
     * as node 0 worked its way down the global index. This was particularly 
     * inefficient since the method blocked all processors at every atom 
     * (and did it twice!).
     *
     * An intermediate version of DumpWriter could be described from Node
     * zero's perspective as follows:
     * 
     *  1) Have 100 of your friends stand in a circle.
     *  2) When you say go, have all of them start tossing potatoes at
     *     you (one at a time).
     *  3) Catch the potatoes.
     *
     * It was an improvement, but MPI has buffers and caches that could 
     * best be described in this analogy as "potato nets", so there's no 
     * need to block the processors atom-by-atom.
     * 
     * This new and improved DumpWriter works in an even more efficient 
     * way:
     * 
     *  1) Have 100 of your friend stand in a circle.
     *  2) When you say go, have them start tossing 5-pound bags of 
     *     potatoes at you.
     *  3) Once you've caught a friend's bag of potatoes,
     *     toss them a spud to let them know they can toss another bag.
     *
     * How's THAT for documentation?
     *
     *********************************************************************/
    const int masterNode = 0;

    int * potatoes;
    int myPotato;
    int nProc;
    int which_node;
    double atomData[13];
    int isDirectional;
    char MPIatomTypeString[MINIBUFFERSIZE];
    int msgLen; // the length of message actually recieved at master nodes
    int haveError;
    MPI_Status istatus;
    int nCurObj;
    
    // code to find maximum tag value
    int * tagub;
    int flag;
    int MAXTAG;
    MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);

    if (flag) {
      MAXTAG = *tagub;
    } else {
      MAXTAG = 32767;
    }

    if (worldRank == masterNode) { //master node (node 0) is responsible for writing the dump file

      // Node 0 needs a list of the magic potatoes for each processor;

      MPI_Comm_size(MPI_COMM_WORLD, &nProc);
      potatoes = new int[nProc];

      //write out the comment lines
      for(int i = 0; i < nProc; i++) {
        potatoes[i] = 0;
      }


      os << nTotObjects << "\n";
      writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot());

      for(int i = 0; i < info_->getNGlobalMolecules(); i++) {

        // Get the Node number which has this atom;

        which_node = info_->getMolToProc(i);

        if (which_node != masterNode) { //current molecule is in slave node
          if (potatoes[which_node] + 1 >= MAXTAG) {
            // The potato was going to exceed the maximum value, 
            // so wrap this processor potato back to 0:         

            potatoes[which_node] = 0;
            MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0,
                     MPI_COMM_WORLD);
          }

          myPotato = potatoes[which_node];

          //recieve the number of integrableObject in current molecule
          MPI_Recv(&nCurObj, 1, MPI_INT, which_node, myPotato,
                   MPI_COMM_WORLD, &istatus);
          myPotato++;

          for(int l = 0; l < nCurObj; l++) {
            if (potatoes[which_node] + 2 >= MAXTAG) {
              // The potato was going to exceed the maximum value, 
              // so wrap this processor potato back to 0:         

              potatoes[which_node] = 0;
              MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node,
                       0, MPI_COMM_WORLD);
            }

            MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR,
                     which_node, myPotato, MPI_COMM_WORLD,
                     &istatus);

            myPotato++;

            MPI_Recv(atomData, 13, MPI_DOUBLE, which_node, myPotato,
                     MPI_COMM_WORLD, &istatus);
            myPotato++;

            MPI_Get_count(&istatus, MPI_DOUBLE, &msgLen);

            if (msgLen == 13)
              isDirectional = 1;
            else
              isDirectional = 0;

            // If we've survived to here, format the line:

            if (!isDirectional) {
              sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
                      MPIatomTypeString, atomData[0],
                      atomData[1], atomData[2],
                      atomData[3], atomData[4],
                      atomData[5]);

              strcat(writeLine,
                     "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n");
            } else {
              sprintf(writeLine,
                      "%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",
                      MPIatomTypeString,
                      atomData[0],
                      atomData[1],
                      atomData[2],
                      atomData[3],
                      atomData[4],
                      atomData[5],
                      atomData[6],
                      atomData[7],
                      atomData[8],
                      atomData[9],
                      atomData[10],
                      atomData[11],
                      atomData[12]);
            }

            os << writeLine;

          } // end for(int l =0)

          potatoes[which_node] = myPotato;
        } else { //master node has current molecule

          mol = info_->getMoleculeByGlobalIndex(i);

          if (mol == NULL) {
            sprintf(painCave.errMsg, "Molecule not found on node %d!", worldRank);
            painCave.isFatal = 1;
            simError();
          }
                
          for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; 
               integrableObject = mol->nextIntegrableObject(ii)) {      

            pos = integrableObject->getPos();
            vel = integrableObject->getVel();

            atomData[0] = pos[0];
            atomData[1] = pos[1];
            atomData[2] = pos[2];

            atomData[3] = vel[0];
            atomData[4] = vel[1];
            atomData[5] = vel[2];

            isDirectional = 0;

            if (integrableObject->isDirectional()) {
              isDirectional = 1;

              q = integrableObject->getQ();
              ji = integrableObject->getJ();

              for(int j = 0; j < 6; j++) {
                atomData[j] = atomData[j];
              }

              atomData[6] = q[0];
              atomData[7] = q[1];
              atomData[8] = q[2];
              atomData[9] = q[3];

              atomData[10] = ji[0];
              atomData[11] = ji[1];
              atomData[12] = ji[2];
            }

            // If we've survived to here, format the line:

            if (!isDirectional) {
              sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
                      integrableObject->getType().c_str(), atomData[0],
                      atomData[1], atomData[2],
                      atomData[3], atomData[4],
                      atomData[5]);

              strcat(writeLine,
                     "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n");
            } else {
              sprintf(writeLine,
                      "%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",
                      integrableObject->getType().c_str(),
                      atomData[0],
                      atomData[1],
                      atomData[2],
                      atomData[3],
                      atomData[4],
                      atomData[5],
                      atomData[6],
                      atomData[7],
                      atomData[8],
                      atomData[9],
                      atomData[10],
                      atomData[11],
                      atomData[12]);
            }


            os << writeLine;

          } //end for(iter = integrableObject.begin())
        }
      } //end for(i = 0; i < mpiSim->getNmol())

      os.flush();
        
      sprintf(checkPointMsg, "Sucessfully took a dump.\n");
      MPIcheckPoint();

      delete [] potatoes;
    } else {

      // worldRank != 0, so I'm a remote node.  

      // Set my magic potato to 0:

      myPotato = 0;

      for(int i = 0; i < info_->getNGlobalMolecules(); i++) {

        // Am I the node which has this integrableObject?
        int whichNode = info_->getMolToProc(i);
        if (whichNode == worldRank) {
          if (myPotato + 1 >= MAXTAG) {

            // The potato was going to exceed the maximum value, 
            // so wrap this processor potato back to 0 (and block until
            // node 0 says we can go:

            MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD,
                     &istatus);
          }

          mol = info_->getMoleculeByGlobalIndex(i);

                
          nCurObj = mol->getNIntegrableObjects();

          MPI_Send(&nCurObj, 1, MPI_INT, 0, myPotato, MPI_COMM_WORLD);
          myPotato++;

          for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; 
               integrableObject = mol->nextIntegrableObject(ii)) {

            if (myPotato + 2 >= MAXTAG) {

              // The potato was going to exceed the maximum value, 
              // so wrap this processor potato back to 0 (and block until
              // node 0 says we can go:

              MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD,
                       &istatus);
            }

            pos = integrableObject->getPos();
            vel = integrableObject->getVel();

            atomData[0] = pos[0];
            atomData[1] = pos[1];
            atomData[2] = pos[2];

            atomData[3] = vel[0];
            atomData[4] = vel[1];
            atomData[5] = vel[2];

            isDirectional = 0;

            if (integrableObject->isDirectional()) {
              isDirectional = 1;

              q = integrableObject->getQ();
              ji = integrableObject->getJ();

              atomData[6] = q[0];
              atomData[7] = q[1];
              atomData[8] = q[2];
              atomData[9] = q[3];

              atomData[10] = ji[0];
              atomData[11] = ji[1];
              atomData[12] = ji[2];
            }

            strncpy(MPIatomTypeString, integrableObject->getType().c_str(), MINIBUFFERSIZE);

            // null terminate the  std::string before sending (just in case):
            MPIatomTypeString[MINIBUFFERSIZE - 1] = '\0';

            MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
                     myPotato, MPI_COMM_WORLD);

            myPotato++;

            if (isDirectional) {
              MPI_Send(atomData, 13, MPI_DOUBLE, 0, myPotato,
                       MPI_COMM_WORLD);
            } else {
              MPI_Send(atomData, 6, MPI_DOUBLE, 0, myPotato,
                       MPI_COMM_WORLD);
            }

            myPotato++;
          }
                    
        }
            
      }
      sprintf(checkPointMsg, "Sucessfully took a dump.\n");
      MPIcheckPoint();
    }

#endif // is_mpi

  }

  void DumpWriter::writeDump() {
    writeFrame(*dumpFile_);
  }

  void DumpWriter::writeEor() {
    std::ostream* eorStream;
    
#ifdef IS_MPI
    if (worldRank == 0) {
#endif // is_mpi

      eorStream = createOStream(eorFilename_);

#ifdef IS_MPI
    }
#endif // is_mpi    

    writeFrame(*eorStream);

#ifdef IS_MPI
    if (worldRank == 0) {
#endif // is_mpi
    delete eorStream;

#ifdef IS_MPI
    }
#endif // is_mpi  

  }


  void DumpWriter::writeDumpAndEor() {
    std::vector<std::streambuf*> buffers;
    std::ostream* eorStream;
#ifdef IS_MPI
    if (worldRank == 0) {
#endif // is_mpi

      buffers.push_back(dumpFile_->rdbuf());

      eorStream = createOStream(eorFilename_);

      buffers.push_back(eorStream->rdbuf());
        
#ifdef IS_MPI
    }
#endif // is_mpi    

    TeeBuf tbuf(buffers.begin(), buffers.end());
    std::ostream os(&tbuf);

    writeFrame(os);

#ifdef IS_MPI
    if (worldRank == 0) {
#endif // is_mpi
    delete eorStream;

#ifdef IS_MPI
    }
#endif // is_mpi  
    
  }

std::ostream* DumpWriter::createOStream(const std::string& filename) {
    std::ostream* newOStream;
    if (needCompression_) {
        newOStream = new ogzstream(filename.c_str());
    } else {
        newOStream = new std::ofstream(filename.c_str());
    }
    return newOStream;
}

}//end namespace oopse
Revision:	615
Committed:	Tue Sep 20 21:22:38 2005 UTC (19 years, 7 months ago) by tim
File size:	17523 byte(s)
Log Message:	adding zlib support for DumpWriter
#	User	Rev	Content
1	gezelter	507	/*
2	gezelter	246	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3			*
4			* The University of Notre Dame grants you ("Licensee") a
5			* non-exclusive, royalty free, license to use, modify and
6			* redistribute this software in source and binary code form, provided
7			* that the following conditions are met:
8			*
9			* 1. Acknowledgement of the program authors must be made in any
10			* publication of scientific results based in part on use of the
11			* program. An acceptable form of acknowledgement is citation of
12			* the article in which the program was described (Matthew
13			* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14			* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15			* Parallel Simulation Engine for Molecular Dynamics,"
16			* J. Comput. Chem. 26, pp. 252-271 (2005))
17			*
18			* 2. Redistributions of source code must retain the above copyright
19			* notice, this list of conditions and the following disclaimer.
20			*
21			* 3. Redistributions in binary form must reproduce the above copyright
22			* notice, this list of conditions and the following disclaimer in the
23			* documentation and/or other materials provided with the
24			* distribution.
25			*
26			* This software is provided "AS IS," without a warranty of any
27			* kind. All express or implied conditions, representations and
28			* warranties, including any implied warranty of merchantability,
29			* fitness for a particular purpose or non-infringement, are hereby
30			* excluded. The University of Notre Dame and its licensors shall not
31			* be liable for any damages suffered by licensee as a result of
32			* using, modifying or distributing the software or its
33			* derivatives. In no event will the University of Notre Dame or its
34			* licensors be liable for any lost revenue, profit or data, or for
35			* direct, indirect, special, consequential, incidental or punitive
36			* damages, however caused and regardless of the theory of liability,
37			* arising out of the use of or inability to use software, even if the
38			* University of Notre Dame has been advised of the possibility of
39			* such damages.
40			*/
41
42			#include "io/DumpWriter.hpp"
43			#include "primitives/Molecule.hpp"
44			#include "utils/simError.h"
45	tim	376	#include "io/basic_teebuf.hpp"
46	tim	615	#include "io/gzstream.hpp"
47			#include "io/Globals.hpp"
48
49	gezelter	2	#ifdef IS_MPI
50			#include <mpi.h>
51	gezelter	246	#endif //is_mpi
52	gezelter	2
53	gezelter	246	namespace oopse {
54	gezelter	2
55	gezelter	507	DumpWriter::DumpWriter(SimInfo* info)
56			: info_(info), filename_(info->getDumpFileName()), eorFilename_(info->getFinalConfigFileName()){
57	tim	615
58			Globals* simParams = info->getSimParams();
59			needCompression_ = simParams->getCompressDumpFile();
60
61			if (needCompression_) {
62			filename_ += ".gz";
63			eorFilename_ += ".gz";
64			}
65
66	tim	376	#ifdef IS_MPI
67
68	gezelter	507	if (worldRank == 0) {
69	tim	376	#endif // is_mpi
70
71
72	tim	615	dumpFile_ = createOStream(filename_);
73
74	tim	376	if (!dumpFile_) {
75	gezelter	507	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
76			filename_.c_str());
77			painCave.isFatal = 1;
78			simError();
79	tim	376	}
80
81			#ifdef IS_MPI
82
83	gezelter	507	}
84	tim	376
85	gezelter	507	sprintf(checkPointMsg, "Sucessfully opened output file for dumping.\n");
86			MPIcheckPoint();
87	tim	376
88			#endif // is_mpi
89
90	gezelter	507	}
91	tim	376
92
93	gezelter	507	DumpWriter::DumpWriter(SimInfo* info, const std::string& filename)
94			: info_(info), filename_(filename){
95	tim	615
96			Globals* simParams = info->getSimParams();
97			eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";
98
99			needCompression_ = simParams->getCompressDumpFile();
100			if (needCompression_) {
101			filename_ += ".gz";
102			eorFilename_ += ".gz";
103			}
104
105	gezelter	246	#ifdef IS_MPI
106	gezelter	2
107	gezelter	507	if (worldRank == 0) {
108	gezelter	246	#endif // is_mpi
109	gezelter	2
110
111	tim	615	dumpFile_ = createOStream(filename_);
112
113	gezelter	246	if (!dumpFile_) {
114	gezelter	507	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
115			filename_.c_str());
116			painCave.isFatal = 1;
117			simError();
118	gezelter	246	}
119	gezelter	2
120			#ifdef IS_MPI
121
122	gezelter	507	}
123	gezelter	2
124	gezelter	507	sprintf(checkPointMsg, "Sucessfully opened output file for dumping.\n");
125			MPIcheckPoint();
126	gezelter	2
127			#endif // is_mpi
128	gezelter	246
129	gezelter	507	}
130	gezelter	2
131	gezelter	507	DumpWriter::~DumpWriter() {
132	gezelter	2
133			#ifdef IS_MPI
134	gezelter	246
135			if (worldRank == 0) {
136	gezelter	2	#endif // is_mpi
137
138	tim	615	delete dumpFile_;
139	gezelter	2
140			#ifdef IS_MPI
141	gezelter	246
142			}
143
144	gezelter	2	#endif // is_mpi
145	gezelter	246
146	gezelter	507	}
147	gezelter	2
148	gezelter	507	void DumpWriter::writeCommentLine(std::ostream& os, Snapshot* s) {
149	gezelter	2
150	gezelter	246	double currentTime;
151			Mat3x3d hmat;
152			double chi;
153			double integralOfChiDt;
154			Mat3x3d eta;
155
156			currentTime = s->getTime();
157			hmat = s->getHmat();
158			chi = s->getChi();
159			integralOfChiDt = s->getIntegralOfChiDt();
160			eta = s->getEta();
161
162			os << currentTime << ";\t"
163	gezelter	507	<< hmat(0, 0) << "\t" << hmat(1, 0) << "\t" << hmat(2, 0) << ";\t"
164			<< hmat(0, 1) << "\t" << hmat(1, 1) << "\t" << hmat(2, 1) << ";\t"
165			<< hmat(0, 2) << "\t" << hmat(1, 2) << "\t" << hmat(2, 2) << ";\t";
166	gezelter	2
167	gezelter	246	//write out additional parameters, such as chi and eta
168
169			os << chi << "\t" << integralOfChiDt << "\t;";
170
171			os << eta(0, 0) << "\t" << eta(1, 0) << "\t" << eta(2, 0) << ";\t"
172	gezelter	507	<< eta(0, 1) << "\t" << eta(1, 1) << "\t" << eta(2, 1) << ";\t"
173			<< eta(0, 2) << "\t" << eta(1, 2) << "\t" << eta(2, 2) << ";";
174	gezelter	246
175	tim	376	os << "\n";
176	gezelter	507	}
177	gezelter	2
178	gezelter	507	void DumpWriter::writeFrame(std::ostream& os) {
179	gezelter	246	const int BUFFERSIZE = 2000;
180			const int MINIBUFFERSIZE = 100;
181
182			char tempBuffer[BUFFERSIZE];
183			char writeLine[BUFFERSIZE];
184
185			Quat4d q;
186			Vector3d ji;
187			Vector3d pos;
188			Vector3d vel;
189
190			Molecule* mol;
191			StuntDouble* integrableObject;
192			SimInfo::MoleculeIterator mi;
193			Molecule::IntegrableObjectIterator ii;
194	gezelter	2
195	gezelter	246	int nTotObjects;
196			nTotObjects = info_->getNGlobalIntegrableObjects();
197	gezelter	2
198	gezelter	246	#ifndef IS_MPI
199	gezelter	2
200
201	gezelter	246	os << nTotObjects << "\n";
202
203			writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot());
204	gezelter	2
205	gezelter	246	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
206	gezelter	2
207	gezelter	507	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
208			integrableObject = mol->nextIntegrableObject(ii)) {
209	gezelter	246
210	gezelter	2
211	gezelter	507	pos = integrableObject->getPos();
212			vel = integrableObject->getVel();
213	gezelter	2
214	gezelter	507	sprintf(tempBuffer, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
215			integrableObject->getType().c_str(),
216			pos[0], pos[1], pos[2],
217			vel[0], vel[1], vel[2]);
218	gezelter	2
219	gezelter	507	strcpy(writeLine, tempBuffer);
220	gezelter	2
221	gezelter	507	if (integrableObject->isDirectional()) {
222			q = integrableObject->getQ();
223			ji = integrableObject->getJ();
224	gezelter	2
225	gezelter	507	sprintf(tempBuffer, "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
226			q[0], q[1], q[2], q[3],
227			ji[0], ji[1], ji[2]);
228			strcat(writeLine, tempBuffer);
229			} else {
230			strcat(writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n");
231			}
232	gezelter	2
233	gezelter	507	os << writeLine;
234	gezelter	2
235	gezelter	507	}
236	gezelter	2	}
237
238	tim	324	os.flush();
239	gezelter	246	#else // is_mpi
240			/*********************************************************************
241			* Documentation? You want DOCUMENTATION?
242			*
243			* Why all the potatoes below?
244			*
245			* To make a long story short, the original version of DumpWriter
246			* worked in the most inefficient way possible. Node 0 would
247			* poke each of the node for an individual atom's formatted data
248			* as node 0 worked its way down the global index. This was particularly
249			* inefficient since the method blocked all processors at every atom
250			* (and did it twice!).
251			*
252			* An intermediate version of DumpWriter could be described from Node
253			* zero's perspective as follows:
254			*
255			* 1) Have 100 of your friends stand in a circle.
256			* 2) When you say go, have all of them start tossing potatoes at
257			* you (one at a time).
258			* 3) Catch the potatoes.
259			*
260			* It was an improvement, but MPI has buffers and caches that could
261			* best be described in this analogy as "potato nets", so there's no
262			* need to block the processors atom-by-atom.
263			*
264			* This new and improved DumpWriter works in an even more efficient
265			* way:
266			*
267			* 1) Have 100 of your friend stand in a circle.
268			* 2) When you say go, have them start tossing 5-pound bags of
269			* potatoes at you.
270			* 3) Once you've caught a friend's bag of potatoes,
271			* toss them a spud to let them know they can toss another bag.
272			*
273			* How's THAT for documentation?
274			*
275			*********************************************************************/
276			const int masterNode = 0;
277	gezelter	2
278	gezelter	246	int * potatoes;
279			int myPotato;
280			int nProc;
281			int which_node;
282			double atomData[13];
283			int isDirectional;
284			char MPIatomTypeString[MINIBUFFERSIZE];
285			int msgLen; // the length of message actually recieved at master nodes
286			int haveError;
287			MPI_Status istatus;
288			int nCurObj;
289
290			// code to find maximum tag value
291			int * tagub;
292			int flag;
293			int MAXTAG;
294			MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
295	gezelter	2
296	gezelter	246	if (flag) {
297	gezelter	507	MAXTAG = *tagub;
298	gezelter	246	} else {
299	gezelter	507	MAXTAG = 32767;
300	gezelter	246	}
301	gezelter	2
302	gezelter	246	if (worldRank == masterNode) { //master node (node 0) is responsible for writing the dump file
303	gezelter	2
304	gezelter	507	// Node 0 needs a list of the magic potatoes for each processor;
305	gezelter	2
306	gezelter	507	MPI_Comm_size(MPI_COMM_WORLD, &nProc);
307			potatoes = new int[nProc];
308	gezelter	2
309	gezelter	507	//write out the comment lines
310			for(int i = 0; i < nProc; i++) {
311			potatoes[i] = 0;
312			}
313	gezelter	2
314
315	gezelter	507	os << nTotObjects << "\n";
316			writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot());
317	gezelter	2
318	gezelter	507	for(int i = 0; i < info_->getNGlobalMolecules(); i++) {
319	gezelter	2
320	gezelter	507	// Get the Node number which has this atom;
321	gezelter	2
322	gezelter	507	which_node = info_->getMolToProc(i);
323	gezelter	2
324	gezelter	507	if (which_node != masterNode) { //current molecule is in slave node
325			if (potatoes[which_node] + 1 >= MAXTAG) {
326			// The potato was going to exceed the maximum value,
327			// so wrap this processor potato back to 0:
328	gezelter	2
329	gezelter	507	potatoes[which_node] = 0;
330			MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0,
331			MPI_COMM_WORLD);
332			}
333	gezelter	2
334	gezelter	507	myPotato = potatoes[which_node];
335	gezelter	2
336	gezelter	507	//recieve the number of integrableObject in current molecule
337			MPI_Recv(&nCurObj, 1, MPI_INT, which_node, myPotato,
338			MPI_COMM_WORLD, &istatus);
339			myPotato++;
340	gezelter	2
341	gezelter	507	for(int l = 0; l < nCurObj; l++) {
342			if (potatoes[which_node] + 2 >= MAXTAG) {
343			// The potato was going to exceed the maximum value,
344			// so wrap this processor potato back to 0:
345	gezelter	2
346	gezelter	507	potatoes[which_node] = 0;
347			MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node,
348			0, MPI_COMM_WORLD);
349			}
350	gezelter	2
351	gezelter	507	MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR,
352			which_node, myPotato, MPI_COMM_WORLD,
353			&istatus);
354	gezelter	2
355	gezelter	507	myPotato++;
356	gezelter	2
357	gezelter	507	MPI_Recv(atomData, 13, MPI_DOUBLE, which_node, myPotato,
358			MPI_COMM_WORLD, &istatus);
359			myPotato++;
360	gezelter	2
361	gezelter	507	MPI_Get_count(&istatus, MPI_DOUBLE, &msgLen);
362	gezelter	2
363	gezelter	507	if (msgLen == 13)
364			isDirectional = 1;
365			else
366			isDirectional = 0;
367	gezelter	2
368	gezelter	507	// If we've survived to here, format the line:
369	gezelter	2
370	gezelter	507	if (!isDirectional) {
371			sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
372			MPIatomTypeString, atomData[0],
373			atomData[1], atomData[2],
374			atomData[3], atomData[4],
375			atomData[5]);
376	gezelter	2
377	gezelter	507	strcat(writeLine,
378			"0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n");
379			} else {
380			sprintf(writeLine,
381			"%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",
382			MPIatomTypeString,
383			atomData[0],
384			atomData[1],
385			atomData[2],
386			atomData[3],
387			atomData[4],
388			atomData[5],
389			atomData[6],
390			atomData[7],
391			atomData[8],
392			atomData[9],
393			atomData[10],
394			atomData[11],
395			atomData[12]);
396			}
397	gezelter	2
398	gezelter	507	os << writeLine;
399	gezelter	2
400	gezelter	507	} // end for(int l =0)
401	gezelter	2
402	gezelter	507	potatoes[which_node] = myPotato;
403			} else { //master node has current molecule
404	gezelter	2
405	gezelter	507	mol = info_->getMoleculeByGlobalIndex(i);
406	gezelter	2
407	gezelter	507	if (mol == NULL) {
408			sprintf(painCave.errMsg, "Molecule not found on node %d!", worldRank);
409			painCave.isFatal = 1;
410			simError();
411			}
412	gezelter	246
413	gezelter	507	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
414			integrableObject = mol->nextIntegrableObject(ii)) {
415	gezelter	2
416	gezelter	507	pos = integrableObject->getPos();
417			vel = integrableObject->getVel();
418	gezelter	2
419	gezelter	507	atomData[0] = pos[0];
420			atomData[1] = pos[1];
421			atomData[2] = pos[2];
422	gezelter	2
423	gezelter	507	atomData[3] = vel[0];
424			atomData[4] = vel[1];
425			atomData[5] = vel[2];
426	gezelter	2
427	gezelter	507	isDirectional = 0;
428	gezelter	2
429	gezelter	507	if (integrableObject->isDirectional()) {
430			isDirectional = 1;
431	gezelter	2
432	gezelter	507	q = integrableObject->getQ();
433			ji = integrableObject->getJ();
434	gezelter	2
435	gezelter	507	for(int j = 0; j < 6; j++) {
436			atomData[j] = atomData[j];
437			}
438	gezelter	2
439	gezelter	507	atomData[6] = q[0];
440			atomData[7] = q[1];
441			atomData[8] = q[2];
442			atomData[9] = q[3];
443	gezelter	2
444	gezelter	507	atomData[10] = ji[0];
445			atomData[11] = ji[1];
446			atomData[12] = ji[2];
447			}
448	gezelter	2
449	gezelter	507	// If we've survived to here, format the line:
450	gezelter	2
451	gezelter	507	if (!isDirectional) {
452			sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
453			integrableObject->getType().c_str(), atomData[0],
454			atomData[1], atomData[2],
455			atomData[3], atomData[4],
456			atomData[5]);
457	gezelter	2
458	gezelter	507	strcat(writeLine,
459			"0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n");
460			} else {
461			sprintf(writeLine,
462			"%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",
463			integrableObject->getType().c_str(),
464			atomData[0],
465			atomData[1],
466			atomData[2],
467			atomData[3],
468			atomData[4],
469			atomData[5],
470			atomData[6],
471			atomData[7],
472			atomData[8],
473			atomData[9],
474			atomData[10],
475			atomData[11],
476			atomData[12]);
477			}
478	gezelter	2
479
480	gezelter	507	os << writeLine;
481	gezelter	2
482	gezelter	507	} //end for(iter = integrableObject.begin())
483			}
484			} //end for(i = 0; i < mpiSim->getNmol())
485	gezelter	2
486	gezelter	507	os.flush();
487	tim	251
488	gezelter	507	sprintf(checkPointMsg, "Sucessfully took a dump.\n");
489			MPIcheckPoint();
490	gezelter	2
491	gezelter	507	delete [] potatoes;
492	gezelter	246	} else {
493	gezelter	2
494	gezelter	507	// worldRank != 0, so I'm a remote node.
495	gezelter	2
496	gezelter	507	// Set my magic potato to 0:
497	gezelter	2
498	gezelter	507	myPotato = 0;
499	gezelter	2
500	gezelter	507	for(int i = 0; i < info_->getNGlobalMolecules(); i++) {
501	gezelter	2
502	gezelter	507	// Am I the node which has this integrableObject?
503			int whichNode = info_->getMolToProc(i);
504			if (whichNode == worldRank) {
505			if (myPotato + 1 >= MAXTAG) {
506	gezelter	2
507	gezelter	507	// The potato was going to exceed the maximum value,
508			// so wrap this processor potato back to 0 (and block until
509			// node 0 says we can go:
510	gezelter	2
511	gezelter	507	MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD,
512			&istatus);
513			}
514	gezelter	2
515	gezelter	507	mol = info_->getMoleculeByGlobalIndex(i);
516	gezelter	246
517	gezelter	2
518	gezelter	507	nCurObj = mol->getNIntegrableObjects();
519	gezelter	2
520	gezelter	507	MPI_Send(&nCurObj, 1, MPI_INT, 0, myPotato, MPI_COMM_WORLD);
521			myPotato++;
522	gezelter	2
523	gezelter	507	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
524			integrableObject = mol->nextIntegrableObject(ii)) {
525	gezelter	2
526	gezelter	507	if (myPotato + 2 >= MAXTAG) {
527	gezelter	2
528	gezelter	507	// The potato was going to exceed the maximum value,
529			// so wrap this processor potato back to 0 (and block until
530			// node 0 says we can go:
531	gezelter	2
532	gezelter	507	MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD,
533			&istatus);
534			}
535	gezelter	2
536	gezelter	507	pos = integrableObject->getPos();
537			vel = integrableObject->getVel();
538	gezelter	2
539	gezelter	507	atomData[0] = pos[0];
540			atomData[1] = pos[1];
541			atomData[2] = pos[2];
542	gezelter	2
543	gezelter	507	atomData[3] = vel[0];
544			atomData[4] = vel[1];
545			atomData[5] = vel[2];
546	gezelter	2
547	gezelter	507	isDirectional = 0;
548	gezelter	2
549	gezelter	507	if (integrableObject->isDirectional()) {
550			isDirectional = 1;
551	gezelter	2
552	gezelter	507	q = integrableObject->getQ();
553			ji = integrableObject->getJ();
554	gezelter	2
555	gezelter	507	atomData[6] = q[0];
556			atomData[7] = q[1];
557			atomData[8] = q[2];
558			atomData[9] = q[3];
559	gezelter	246
560	gezelter	507	atomData[10] = ji[0];
561			atomData[11] = ji[1];
562			atomData[12] = ji[2];
563			}
564	gezelter	246
565	gezelter	507	strncpy(MPIatomTypeString, integrableObject->getType().c_str(), MINIBUFFERSIZE);
566	gezelter	246
567	gezelter	507	// null terminate the std::string before sending (just in case):
568			MPIatomTypeString[MINIBUFFERSIZE - 1] = '\0';
569	gezelter	246
570	gezelter	507	MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
571			myPotato, MPI_COMM_WORLD);
572	gezelter	246
573	gezelter	507	myPotato++;
574	gezelter	246
575	gezelter	507	if (isDirectional) {
576			MPI_Send(atomData, 13, MPI_DOUBLE, 0, myPotato,
577			MPI_COMM_WORLD);
578			} else {
579			MPI_Send(atomData, 6, MPI_DOUBLE, 0, myPotato,
580			MPI_COMM_WORLD);
581			}
582	gezelter	246
583	gezelter	507	myPotato++;
584			}
585	gezelter	246
586	gezelter	507	}
587	gezelter	246
588	gezelter	507	}
589			sprintf(checkPointMsg, "Sucessfully took a dump.\n");
590			MPIcheckPoint();
591	gezelter	246	}
592
593			#endif // is_mpi
594
595	gezelter	507	}
596	gezelter	2
597	gezelter	507	void DumpWriter::writeDump() {
598	tim	615	writeFrame(*dumpFile_);
599	gezelter	507	}
600	tim	376
601	gezelter	507	void DumpWriter::writeEor() {
602	tim	615	std::ostream* eorStream;
603	tim	376
604			#ifdef IS_MPI
605			if (worldRank == 0) {
606			#endif // is_mpi
607
608	tim	615	eorStream = createOStream(eorFilename_);
609	tim	376
610			#ifdef IS_MPI
611			}
612			#endif // is_mpi
613
614	tim	615	writeFrame(*eorStream);
615
616			#ifdef IS_MPI
617			if (worldRank == 0) {
618			#endif // is_mpi
619			delete eorStream;
620
621			#ifdef IS_MPI
622			}
623			#endif // is_mpi
624
625	gezelter	507	}
626	tim	376
627
628	gezelter	507	void DumpWriter::writeDumpAndEor() {
629	tim	376	std::vector<std::streambuf*> buffers;
630	tim	615	std::ostream* eorStream;
631	tim	376	#ifdef IS_MPI
632			if (worldRank == 0) {
633			#endif // is_mpi
634
635	tim	615	buffers.push_back(dumpFile_->rdbuf());
636	tim	376
637	tim	615	eorStream = createOStream(eorFilename_);
638	tim	376
639	tim	615	buffers.push_back(eorStream->rdbuf());
640	tim	376
641			#ifdef IS_MPI
642			}
643			#endif // is_mpi
644
645			TeeBuf tbuf(buffers.begin(), buffers.end());
646			std::ostream os(&tbuf);
647
648			writeFrame(os);
649	tim	615
650			#ifdef IS_MPI
651			if (worldRank == 0) {
652			#endif // is_mpi
653			delete eorStream;
654
655			#ifdef IS_MPI
656			}
657			#endif // is_mpi
658	tim	376
659	gezelter	507	}
660	tim	376
661	tim	615	std::ostream* DumpWriter::createOStream(const std::string& filename) {
662			std::ostream* newOStream;
663			if (needCompression_) {
664			newOStream = new ogzstream(filename.c_str());
665			} else {
666			newOStream = new std::ofstream(filename.c_str());
667			}
668			return newOStream;
669			}
670	tim	376
671	gezelter	246	}//end namespace oopse