OOPSE/libmdtools/DumpWriter.cpp

#define _LARGEFILE_SOURCE64
#define _FILE_OFFSET_BITS 64

#include <string.h>
#include <iostream>
#include <fstream>
#include <algorithm>
#include <utility>

#ifdef IS_MPI
#include <mpi.h>
#include "mpiSimulation.hpp"

namespace dWrite{
  void DieDieDie( void );
}

using namespace dWrite;
#endif //is_mpi

#include "ReadWrite.hpp"
#include "simError.h"

DumpWriter::DumpWriter( SimInfo* the_entry_plug ){

  entry_plug = the_entry_plug;

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

    dumpFile.open(entry_plug->sampleName, ios::out | ios::trunc );

    if( !dumpFile ){

      sprintf( painCave.errMsg,
               "Could not open \"%s\" for dump output.\n",
               entry_plug->sampleName);
      painCave.isFatal = 1;
      simError();
    }

#ifdef IS_MPI
  }

  //sort the local atoms by global index
  sortByGlobalIndex();
  
  sprintf( checkPointMsg,
           "Sucessfully opened output file for dumping.\n");
  MPIcheckPoint();
#endif // is_mpi
}

DumpWriter::~DumpWriter( ){

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

    dumpFile.close();

#ifdef IS_MPI
  }
#endif // is_mpi
}

#ifdef IS_MPI

/**
 * A hook function to load balancing
 */

void DumpWriter::update(){
  sortByGlobalIndex();          
}
  
/**
 * Auxiliary sorting function
 */
 
bool indexSortingCriterion(const pair<int, int>& p1, const pair<int, int>& p2){
  return p1.second < p2.second;
}

/**
 * Sorting the local index by global index
 */
 
void DumpWriter::sortByGlobalIndex(){
  Molecule* mols = entry_plug->molecules;  
  indexArray.clear();
  
  for(int i = 0; i < entry_plug->n_mol;i++) 
    indexArray.push_back(make_pair(i, mols[i].getGlobalIndex()));
  
  sort(indexArray.begin(), indexArray.end(), indexSortingCriterion);    
}

#endif

void DumpWriter::writeDump(double currentTime){

  ofstream finalOut;
  vector<ofstream*> fileStreams;

#ifdef IS_MPI
  if(worldRank == 0 ){
#endif    
    finalOut.open( entry_plug->finalName, ios::out | ios::trunc );
    if( !finalOut ){
      sprintf( painCave.errMsg,
               "Could not open \"%s\" for final dump output.\n",
               entry_plug->finalName );
      painCave.isFatal = 1;
      simError();
    }
#ifdef IS_MPI
  }
#endif // is_mpi

  fileStreams.push_back(&finalOut); 
  fileStreams.push_back(&dumpFile);

  writeFrame(fileStreams, currentTime);

#ifdef IS_MPI
  finalOut.close();
#endif
        
}

void DumpWriter::writeFinal(double currentTime){

  ofstream finalOut;
  vector<ofstream*> fileStreams;

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

    finalOut.open( entry_plug->finalName, ios::out | ios::trunc );

    if( !finalOut ){
      sprintf( painCave.errMsg,
               "Could not open \"%s\" for final dump output.\n",
               entry_plug->finalName );
      painCave.isFatal = 1;
      simError();
    }

#ifdef IS_MPI
  }
#endif // is_mpi
  
  fileStreams.push_back(&finalOut);  
  writeFrame(fileStreams, currentTime);

#ifdef IS_MPI
  finalOut.close();
#endif
  
}

void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){

  const int BUFFERSIZE = 2000;
  const int MINIBUFFERSIZE = 100;

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

  int i;
  unsigned int k;

#ifdef 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?
   *
   *********************************************************************/

  int *potatoes;
  int myPotato;

  int nProc;
  int j, which_node, done, which_atom, local_index, currentIndex;
  double atomData[13];
  int isDirectional;
  char* atomTypeString;
  char MPIatomTypeString[MINIBUFFERSIZE];
  int nObjects;
  int msgLen; // the length of message actually recieved at master nodes
#endif //is_mpi

  double q[4], ji[3];
  DirectionalAtom* dAtom;
  double pos[3], vel[3];
  int nTotObjects;
  StuntDouble* sd;
  char* molName;
  vector<StuntDouble*> integrableObjects;
  vector<StuntDouble*>::iterator iter;
  nTotObjects = entry_plug->getTotIntegrableObjects();
#ifndef IS_MPI
  
  for(k = 0; k < outFile.size(); k++){
    *outFile[k] << nTotObjects << "\n";

    *outFile[k] << currentTime << ";\t"
               << entry_plug->Hmat[0][0] << "\t"
                     << entry_plug->Hmat[1][0] << "\t"
                     << entry_plug->Hmat[2][0] << ";\t"
               
               << entry_plug->Hmat[0][1] << "\t"
                     << entry_plug->Hmat[1][1] << "\t"
                     << entry_plug->Hmat[2][1] << ";\t"

                     << entry_plug->Hmat[0][2] << "\t"
                     << entry_plug->Hmat[1][2] << "\t"
                     << entry_plug->Hmat[2][2] << ";";

    //write out additional parameters, such as chi and eta
    *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
  }
  
  for( i=0; i< entry_plug->n_mol; i++ ){

    integrableObjects = entry_plug->molecules[i].getIntegrableObjects();
    molName = (entry_plug->compStamps[entry_plug->molecules[i].getStampID()])->getID();
    
    for( iter = integrableObjects.begin();iter !=  integrableObjects.end(); ++iter){
      sd = *iter;
      sd->getPos(pos);
      sd->getVel(vel);

      sprintf( tempBuffer,
             "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
             sd->getType(),
             pos[0],
             pos[1],
             pos[2],
             vel[0],
             vel[1],
             vel[2]);
      strcpy( writeLine, tempBuffer );

      if( sd->isDirectional() ){

        sd->getQ( q );
        sd->getJ( ji );

        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" );
    
      for(k = 0; k < outFile.size(); k++)
        *outFile[k] << writeLine;      
    }

}

#else // is_mpi

  /* code to find maximum tag value */
  
  int *tagub, flag, MAXTAG;
  MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
  if (flag) {
    MAXTAG = *tagub;
  } else {
    MAXTAG = 32767;
  }  

  int haveError;

  MPI_Status istatus;
  int nCurObj;
  int *MolToProcMap = mpiSim->getMolToProcMap();

  // write out header and node 0's coordinates

  if( worldRank == 0 ){

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

    nProc = mpiSim->getNProcessors();
    potatoes = new int[nProc];

    //write out the comment lines
    for (i = 0; i < nProc; i++) 
      potatoes[i] = 0;
    
      for(k = 0; k < outFile.size(); k++){
        *outFile[k] << nTotObjects << "\n";

        *outFile[k] << currentTime << ";\t"
                         << entry_plug->Hmat[0][0] << "\t"
                         << entry_plug->Hmat[1][0] << "\t"
                         << entry_plug->Hmat[2][0] << ";\t"

                         << entry_plug->Hmat[0][1] << "\t"
                         << entry_plug->Hmat[1][1] << "\t"
                         << entry_plug->Hmat[2][1] << ";\t"

                         << entry_plug->Hmat[0][2] << "\t"
                         << entry_plug->Hmat[1][2] << "\t"
                         << entry_plug->Hmat[2][2] << ";";
  
        *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
    }

    currentIndex = 0;

    for (i = 0 ; i < mpiSim->getNMolGlobal(); i++ ) {
      
      // Get the Node number which has this atom;
      
      which_node = MolToProcMap[i];
      
      if (which_node != 0) {
        
        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);

          atomTypeString = MPIatomTypeString;

          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",
                 atomTypeString,
                 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",
                         atomTypeString,
                         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]);
            
          }
          
          for(k = 0; k < outFile.size(); k++)
            *outFile[k] << writeLine;            

        }// end for(int l =0)
        potatoes[which_node] = myPotato;

      }
      else {
        
        haveError = 0;
        
            local_index = indexArray[currentIndex].first;        

        integrableObjects = (entry_plug->molecules[local_index]).getIntegrableObjects(); 

        for(iter= integrableObjects.begin(); iter != integrableObjects.end(); ++iter){    
                sd = *iter;
            atomTypeString = sd->getType();
            
            sd->getPos(pos);
            sd->getVel(vel);          
          
            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( sd->isDirectional() ){

              isDirectional = 1;
                
              sd->getQ( q );
              sd->getJ( ji );

              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",
                 atomTypeString,
                 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",
                         atomTypeString,
                         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]);
              
            }
            
            for(k = 0; k < outFile.size(); k++)
              *outFile[k] << writeLine;
            
            
        }//end for(iter = integrableObject.begin())
        
      currentIndex++;
      }

    }//end for(i = 0; i < mpiSim->getNmol())
    
    for(k = 0; k < outFile.size(); k++)
      outFile[k]->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;
    currentIndex = 0;
    
    for (i = 0 ; i < mpiSim->getNMolGlobal(); i++ ) {
      
      // Am I the node which has this integrableObject?
      
      if (MolToProcMap[i] == 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);
          
        }

          local_index = indexArray[currentIndex].first;        
          integrableObjects = entry_plug->molecules[local_index].getIntegrableObjects();
          
          nCurObj = integrableObjects.size();
                      
          MPI_Send(&nCurObj, 1, MPI_INT, 0,
                             myPotato, MPI_COMM_WORLD);
          myPotato++;

          for( iter = integrableObjects.begin(); iter  != integrableObjects.end(); iter++){

            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);
              
            }
            
            sd = *iter;
            
            atomTypeString = sd->getType();

            sd->getPos(pos);
            sd->getVel(vel);

            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( sd->isDirectional() ){

                isDirectional = 1;
                
                sd->getQ( q );
                sd->getJ( ji );
                
                
                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, atomTypeString, MINIBUFFERSIZE);

            // null terminate the 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++;  

          }

          currentIndex++;    
          
        }
      
      }

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


#endif // is_mpi
}

#ifdef IS_MPI

// a couple of functions to let us escape the write loop

void dWrite::DieDieDie( void ){

  MPI_Finalize();
  exit (0);
}

#endif //is_mpi
Revision:	1252
Committed:	Mon Jun 7 14:26:33 2004 UTC (20 years, 1 month ago) by gezelter
File size:	17418 byte(s)
Log Message:	Fixes from gcc -Wall
#	User	Rev	Content
1	tim	1078	#define _LARGEFILE_SOURCE64
2	mmeineke	723	#define _FILE_OFFSET_BITS 64
3
4	gezelter	829	#include <string.h>
5	mmeineke	377	#include <iostream>
6			#include <fstream>
7	tim	929	#include <algorithm>
8			#include <utility>
9	mmeineke	377
10			#ifdef IS_MPI
11			#include <mpi.h>
12			#include "mpiSimulation.hpp"
13	mmeineke	440
14			namespace dWrite{
15	gezelter	907	void DieDieDie( void );
16	mmeineke	440	}
17
18			using namespace dWrite;
19	mmeineke	377	#endif //is_mpi
20
21			#include "ReadWrite.hpp"
22			#include "simError.h"
23
24			DumpWriter::DumpWriter( SimInfo* the_entry_plug ){
25
26			entry_plug = the_entry_plug;
27
28			#ifdef IS_MPI
29			if(worldRank == 0 ){
30			#endif // is_mpi
31	tim	837
32	tim	929	dumpFile.open(entry_plug->sampleName, ios::out \| ios::trunc );
33	tim	837
34	tim	929	if( !dumpFile ){
35	tim	837
36	mmeineke	377	sprintf( painCave.errMsg,
37			"Could not open \"%s\" for dump output.\n",
38	tim	929	entry_plug->sampleName);
39	mmeineke	377	painCave.isFatal = 1;
40			simError();
41			}
42	mmeineke	469
43	mmeineke	377	#ifdef IS_MPI
44			}
45
46	tim	929	//sort the local atoms by global index
47			sortByGlobalIndex();
48
49	mmeineke	377	sprintf( checkPointMsg,
50			"Sucessfully opened output file for dumping.\n");
51			MPIcheckPoint();
52			#endif // is_mpi
53			}
54
55			DumpWriter::~DumpWriter( ){
56
57			#ifdef IS_MPI
58			if(worldRank == 0 ){
59			#endif // is_mpi
60
61	tim	929	dumpFile.close();
62	mmeineke	377
63			#ifdef IS_MPI
64			}
65			#endif // is_mpi
66			}
67
68	tim	929	#ifdef IS_MPI
69	tim	837
70	tim	929	/**
71			* A hook function to load balancing
72			*/
73
74			void DumpWriter::update(){
75			sortByGlobalIndex();
76			}
77
78			/**
79			* Auxiliary sorting function
80			*/
81
82			bool indexSortingCriterion(const pair<int, int>& p1, const pair<int, int>& p2){
83			return p1.second < p2.second;
84			}
85
86			/**
87			* Sorting the local index by global index
88			*/
89
90			void DumpWriter::sortByGlobalIndex(){
91	tim	1108	Molecule* mols = entry_plug->molecules;
92	tim	929	indexArray.clear();
93
94	tim	1129	for(int i = 0; i < entry_plug->n_mol;i++)
95	tim	1108	indexArray.push_back(make_pair(i, mols[i].getGlobalIndex()));
96	tim	929
97			sort(indexArray.begin(), indexArray.end(), indexSortingCriterion);
98			}
99	chuckv	949
100	tim	929	#endif
101
102			void DumpWriter::writeDump(double currentTime){
103
104	tim	936	ofstream finalOut;
105	tim	934	vector<ofstream*> fileStreams;
106
107			#ifdef IS_MPI
108			if(worldRank == 0 ){
109	tim	952	#endif
110	tim	936	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	tim	952	#ifdef IS_MPI
119	tim	934	}
120			#endif // is_mpi
121
122			fileStreams.push_back(&finalOut);
123			fileStreams.push_back(&dumpFile);
124
125			writeFrame(fileStreams, currentTime);
126	tim	936
127			#ifdef IS_MPI
128			finalOut.close();
129			#endif
130	tim	929
131			}
132
133			void DumpWriter::writeFinal(double currentTime){
134
135	tim	936	ofstream finalOut;
136	tim	934	vector<ofstream*> fileStreams;
137
138	tim	929	#ifdef IS_MPI
139			if(worldRank == 0 ){
140	mmeineke	951	#endif // is_mpi
141	tim	936
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	mmeineke	951	#ifdef IS_MPI
153	tim	934	}
154	tim	929	#endif // is_mpi
155
156	tim	934	fileStreams.push_back(&finalOut);
157			writeFrame(fileStreams, currentTime);
158	tim	936
159			#ifdef IS_MPI
160			finalOut.close();
161			#endif
162	tim	929
163			}
164
165	tim	934	void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){
166	tim	929
167	mmeineke	377	const int BUFFERSIZE = 2000;
168	gezelter	912	const int MINIBUFFERSIZE = 100;
169	gezelter	907
170	tim	936	char tempBuffer[BUFFERSIZE];
171	mmeineke	377	char writeLine[BUFFERSIZE];
172
173	gezelter	1252	int i;
174			unsigned int k;
175	gezelter	916
176	mmeineke	787	#ifdef IS_MPI
177	gezelter	916
178	gezelter	947	/*********************************************************************
179			* Documentation? You want DOCUMENTATION?
180			*
181			* Why all the potatoes below?
182			*
183			* To make a long story short, the original version of DumpWriter
184			* worked in the most inefficient way possible. Node 0 would
185			* poke each of the node for an individual atom's formatted data
186			* as node 0 worked its way down the global index. This was particularly
187			* inefficient since the method blocked all processors at every atom
188			* (and did it twice!).
189			*
190			* An intermediate version of DumpWriter could be described from Node
191			* zero's perspective as follows:
192			*
193			* 1) Have 100 of your friends stand in a circle.
194			* 2) When you say go, have all of them start tossing potatoes at
195			* you (one at a time).
196			* 3) Catch the potatoes.
197			*
198			* It was an improvement, but MPI has buffers and caches that could
199			* best be described in this analogy as "potato nets", so there's no
200			* need to block the processors atom-by-atom.
201			*
202			* This new and improved DumpWriter works in an even more efficient
203			* way:
204			*
205			* 1) Have 100 of your friend stand in a circle.
206			* 2) When you say go, have them start tossing 5-pound bags of
207			* potatoes at you.
208			* 3) Once you've caught a friend's bag of potatoes,
209			* toss them a spud to let them know they can toss another bag.
210			*
211			* How's THAT for documentation?
212			*
213			*********************************************************************/
214
215	gezelter	916	int *potatoes;
216			int myPotato;
217
218			int nProc;
219	tim	929	int j, which_node, done, which_atom, local_index, currentIndex;
220	tim	1152	double atomData[13];
221	gezelter	907	int isDirectional;
222			char* atomTypeString;
223	gezelter	910	char MPIatomTypeString[MINIBUFFERSIZE];
224	tim	1108	int nObjects;
225	tim	1152	int msgLen; // the length of message actually recieved at master nodes
226	mmeineke	787	#endif //is_mpi
227
228	gezelter	1097	double q[4], ji[3];
229	mmeineke	377	DirectionalAtom* dAtom;
230	mmeineke	670	double pos[3], vel[3];
231	tim	1108	int nTotObjects;
232			StuntDouble* sd;
233			char* molName;
234			vector<StuntDouble*> integrableObjects;
235			vector<StuntDouble*>::iterator iter;
236			nTotObjects = entry_plug->getTotIntegrableObjects();
237	mmeineke	377	#ifndef IS_MPI
238	tim	934
239			for(k = 0; k < outFile.size(); k++){
240	tim	1108	*outFile[k] << nTotObjects << "\n";
241	tim	837
242	tim	934	*outFile[k] << currentTime << ";\t"
243			<< entry_plug->Hmat[0][0] << "\t"
244			<< entry_plug->Hmat[1][0] << "\t"
245			<< entry_plug->Hmat[2][0] << ";\t"
246
247			<< entry_plug->Hmat[0][1] << "\t"
248			<< entry_plug->Hmat[1][1] << "\t"
249			<< entry_plug->Hmat[2][1] << ";\t"
250	tim	837
251	tim	934	<< entry_plug->Hmat[0][2] << "\t"
252			<< entry_plug->Hmat[1][2] << "\t"
253			<< entry_plug->Hmat[2][2] << ";";
254	mmeineke	572
255	tim	934	//write out additional parameters, such as chi and eta
256			*outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
257			}
258
259	tim	1108	for( i=0; i< entry_plug->n_mol; i++ ){
260	tim	837
261	tim	1108	integrableObjects = entry_plug->molecules[i].getIntegrableObjects();
262			molName = (entry_plug->compStamps[entry_plug->molecules[i].getStampID()])->getID();
263
264			for( iter = integrableObjects.begin();iter != integrableObjects.end(); ++iter){
265			sd = *iter;
266			sd->getPos(pos);
267			sd->getVel(vel);
268	mmeineke	377
269	tim	1108	sprintf( tempBuffer,
270			"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
271			sd->getType(),
272			pos[0],
273			pos[1],
274			pos[2],
275			vel[0],
276			vel[1],
277			vel[2]);
278			strcpy( writeLine, tempBuffer );
279	mmeineke	377
280	tim	1108	if( sd->isDirectional() ){
281	tim	837
282	tim	1108	sd->getQ( q );
283			sd->getJ( ji );
284	tim	837
285	tim	1108	sprintf( tempBuffer,
286			"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
287			q[0],
288			q[1],
289			q[2],
290			q[3],
291			ji[0],
292			ji[1],
293			ji[2]);
294			strcat( writeLine, tempBuffer );
295			}
296			else
297			strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
298	tim	1231
299			for(k = 0; k < outFile.size(); k++)
300			*outFile[k] << writeLine;
301	mmeineke	377	}
302	tim	837
303	tim	1108	}
304	mmeineke	377
305			#else // is_mpi
306	gezelter	416
307	chuckv	913	/* code to find maximum tag value */
308	tim	919
309	tim	920	int *tagub, flag, MAXTAG;
310	chuckv	913	MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
311			if (flag) {
312	tim	920	MAXTAG = *tagub;
313	chuckv	913	} else {
314			MAXTAG = 32767;
315	gezelter	916	}
316	mmeineke	440
317			int haveError;
318
319	mmeineke	447	MPI_Status istatus;
320	tim	1108	int nCurObj;
321			int *MolToProcMap = mpiSim->getMolToProcMap();
322	tim	837
323	mmeineke	377	// write out header and node 0's coordinates
324	tim	837
325	mmeineke	377	if( worldRank == 0 ){
326	gezelter	916
327			// Node 0 needs a list of the magic potatoes for each processor;
328
329	gezelter	1203	nProc = mpiSim->getNProcessors();
330	gezelter	916	potatoes = new int[nProc];
331
332	tim	934	//write out the comment lines
333	gezelter	916	for (i = 0; i < nProc; i++)
334			potatoes[i] = 0;
335
336	tim	934	for(k = 0; k < outFile.size(); k++){
337	tim	1108	*outFile[k] << nTotObjects << "\n";
338	tim	837
339	tim	934	*outFile[k] << currentTime << ";\t"
340			<< entry_plug->Hmat[0][0] << "\t"
341			<< entry_plug->Hmat[1][0] << "\t"
342			<< entry_plug->Hmat[2][0] << ";\t"
343	tim	837
344	tim	934	<< entry_plug->Hmat[0][1] << "\t"
345			<< entry_plug->Hmat[1][1] << "\t"
346			<< entry_plug->Hmat[2][1] << ";\t"
347	tim	837
348	tim	934	<< entry_plug->Hmat[0][2] << "\t"
349			<< entry_plug->Hmat[1][2] << "\t"
350			<< entry_plug->Hmat[2][2] << ";";
351
352			*outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
353			}
354	tim	837
355	tim	929	currentIndex = 0;
356	tim	934
357	gezelter	1203	for (i = 0 ; i < mpiSim->getNMolGlobal(); i++ ) {
358	chuckv	913
359	gezelter	417	// Get the Node number which has this atom;
360	chuckv	913
361	tim	1108	which_node = MolToProcMap[i];
362	chuckv	913
363	gezelter	907	if (which_node != 0) {
364	tim	1108
365			if (potatoes[which_node] + 1 >= MAXTAG) {
366	gezelter	916	// The potato was going to exceed the maximum value,
367			// so wrap this processor potato back to 0:
368
369			potatoes[which_node] = 0;
370	tim	1129	MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
371	gezelter	916
372			}
373
374			myPotato = potatoes[which_node];
375	tim	1108
376			//recieve the number of integrableObject in current molecule
377			MPI_Recv(&nCurObj, 1, MPI_INT, which_node,
378	gezelter	916	myPotato, MPI_COMM_WORLD, &istatus);
379	tim	1129	myPotato++;
380	gezelter	907
381	tim	1108	for(int l = 0; l < nCurObj; l++){
382	gezelter	916
383	tim	1152	if (potatoes[which_node] + 2 >= MAXTAG) {
384	tim	1108	// The potato was going to exceed the maximum value,
385			// so wrap this processor potato back to 0:
386
387			potatoes[which_node] = 0;
388	tim	1129	MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
389	tim	1108
390			}
391
392			MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
393			myPotato, MPI_COMM_WORLD, &istatus);
394
395			atomTypeString = MPIatomTypeString;
396
397			myPotato++;
398
399	tim	1152	MPI_Recv(atomData, 13, MPI_DOUBLE, which_node, myPotato, MPI_COMM_WORLD, &istatus);
400	tim	1108	myPotato++;
401	gezelter	907
402	tim	1152	MPI_Get_count(&istatus, MPI_DOUBLE, &msgLen);
403	tim	1108
404	tim	1152	if(msgLen == 13)
405			isDirectional = 1;
406			else
407			isDirectional = 0;
408	tim	1231
409			// If we've survived to here, format the line:
410	tim	1152
411	tim	1231	if (!isDirectional) {
412
413			sprintf( writeLine,
414			"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
415			atomTypeString,
416			atomData[0],
417			atomData[1],
418			atomData[2],
419			atomData[3],
420			atomData[4],
421			atomData[5]);
422
423			strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
424
425			}
426			else {
427
428			sprintf( writeLine,
429			"%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",
430			atomTypeString,
431			atomData[0],
432			atomData[1],
433			atomData[2],
434			atomData[3],
435			atomData[4],
436			atomData[5],
437			atomData[6],
438			atomData[7],
439			atomData[8],
440			atomData[9],
441			atomData[10],
442			atomData[11],
443			atomData[12]);
444
445			}
446
447			for(k = 0; k < outFile.size(); k++)
448			*outFile[k] << writeLine;
449
450			}// end for(int l =0)
451	gezelter	916	potatoes[which_node] = myPotato;
452	gezelter	907
453	tim	1231	}
454			else {
455	gezelter	907
456	tim	934	haveError = 0;
457	gezelter	916
458	tim	1108	local_index = indexArray[currentIndex].first;
459	tim	837
460	tim	1108	integrableObjects = (entry_plug->molecules[local_index]).getIntegrableObjects();
461	gezelter	907
462	tim	1108	for(iter= integrableObjects.begin(); iter != integrableObjects.end(); ++iter){
463			sd = *iter;
464			atomTypeString = sd->getType();
465
466			sd->getPos(pos);
467			sd->getVel(vel);
468
469	tim	1152	atomData[0] = pos[0];
470			atomData[1] = pos[1];
471			atomData[2] = pos[2];
472	tim	837
473	tim	1152	atomData[3] = vel[0];
474			atomData[4] = vel[1];
475			atomData[5] = vel[2];
476	tim	1108
477			isDirectional = 0;
478	gezelter	916
479	tim	1108	if( sd->isDirectional() ){
480
481			isDirectional = 1;
482
483			sd->getQ( q );
484			sd->getJ( ji );
485
486			for (int j = 0; j < 6 ; j++)
487	tim	1152	atomData[j] = atomData[j];
488	tim	1108
489	tim	1152	atomData[6] = q[0];
490			atomData[7] = q[1];
491			atomData[8] = q[2];
492			atomData[9] = q[3];
493	tim	1108
494	tim	1152	atomData[10] = ji[0];
495			atomData[11] = ji[1];
496			atomData[12] = ji[2];
497	tim	1108	}
498	gezelter	907
499	tim	1231	// If we've survived to here, format the line:
500
501			if (!isDirectional) {
502
503			sprintf( writeLine,
504			"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
505			atomTypeString,
506			atomData[0],
507			atomData[1],
508			atomData[2],
509			atomData[3],
510			atomData[4],
511			atomData[5]);
512
513			strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
514
515			}
516			else {
517
518			sprintf( writeLine,
519			"%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",
520			atomTypeString,
521			atomData[0],
522			atomData[1],
523			atomData[2],
524			atomData[3],
525			atomData[4],
526			atomData[5],
527			atomData[6],
528			atomData[7],
529			atomData[8],
530			atomData[9],
531			atomData[10],
532			atomData[11],
533			atomData[12]);
534
535			}
536
537			for(k = 0; k < outFile.size(); k++)
538			*outFile[k] << writeLine;
539
540
541			}//end for(iter = integrableObject.begin())
542	gezelter	916
543	tim	1108	currentIndex++;
544	tim	926	}
545	tim	1231
546			}//end for(i = 0; i < mpiSim->getNmol())
547	tim	926
548	tim	934	for(k = 0; k < outFile.size(); k++)
549			outFile[k]->flush();
550
551	gezelter	907	sprintf( checkPointMsg,
552			"Sucessfully took a dump.\n");
553	chuckv	949
554	gezelter	907	MPIcheckPoint();
555	chuckv	949
556	tim	919	delete[] potatoes;
557	chuckv	949
558	gezelter	415	} else {
559	tim	837
560	gezelter	907	// worldRank != 0, so I'm a remote node.
561	gezelter	916
562			// Set my magic potato to 0:
563
564			myPotato = 0;
565	tim	929	currentIndex = 0;
566	gezelter	907
567	gezelter	1203	for (i = 0 ; i < mpiSim->getNMolGlobal(); i++ ) {
568	gezelter	907
569	tim	1108	// Am I the node which has this integrableObject?
570	gezelter	907
571	tim	1108	if (MolToProcMap[i] == worldRank) {
572	tim	837
573	tim	1108
574			if (myPotato + 1 >= MAXTAG) {
575	chuckv	949
576	gezelter	916	// The potato was going to exceed the maximum value,
577			// so wrap this processor potato back to 0 (and block until
578			// node 0 says we can go:
579	chuckv	949
580	gezelter	916	MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
581
582			}
583	chuckv	949
584	tim	1108	local_index = indexArray[currentIndex].first;
585			integrableObjects = entry_plug->molecules[local_index].getIntegrableObjects();
586
587			nCurObj = integrableObjects.size();
588
589			MPI_Send(&nCurObj, 1, MPI_INT, 0,
590			myPotato, MPI_COMM_WORLD);
591	tim	1129	myPotato++;
592	tim	1108
593			for( iter = integrableObjects.begin(); iter != integrableObjects.end(); iter++){
594
595	tim	1152	if (myPotato + 2 >= MAXTAG) {
596	tim	1108
597			// The potato was going to exceed the maximum value,
598			// so wrap this processor potato back to 0 (and block until
599			// node 0 says we can go:
600
601			MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
602
603			}
604
605			sd = *iter;
606
607			atomTypeString = sd->getType();
608
609			sd->getPos(pos);
610			sd->getVel(vel);
611
612	tim	1152	atomData[0] = pos[0];
613			atomData[1] = pos[1];
614			atomData[2] = pos[2];
615	tim	1108
616	tim	1152	atomData[3] = vel[0];
617			atomData[4] = vel[1];
618			atomData[5] = vel[2];
619	tim	1108
620			isDirectional = 0;
621
622			if( sd->isDirectional() ){
623
624			isDirectional = 1;
625	tim	920
626	tim	1108	sd->getQ( q );
627			sd->getJ( ji );
628
629
630	tim	1152	atomData[6] = q[0];
631			atomData[7] = q[1];
632			atomData[8] = q[2];
633			atomData[9] = q[3];
634	tim	1108
635	tim	1152	atomData[10] = ji[0];
636			atomData[11] = ji[1];
637			atomData[12] = ji[2];
638	tim	1108	}
639	tim	837
640	tim	1108
641			strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
642	tim	837
643	tim	1108	// null terminate the string before sending (just in case):
644			MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
645	mmeineke	377
646	tim	1108	MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
647			myPotato, MPI_COMM_WORLD);
648	gezelter	907
649	tim	1108	myPotato++;
650	gezelter	907
651	tim	1108	if (isDirectional) {
652	tim	837
653	tim	1152	MPI_Send(atomData, 13, MPI_DOUBLE, 0,
654	tim	1108	myPotato, MPI_COMM_WORLD);
655
656			} else {
657	tim	837
658	tim	1152	MPI_Send(atomData, 6, MPI_DOUBLE, 0,
659	tim	1108	myPotato, MPI_COMM_WORLD);
660			}
661	tim	837
662	tim	1108	myPotato++;
663	gezelter	916
664	tim	1108	}
665	gezelter	907
666	tim	1108	currentIndex++;
667	gezelter	907
668			}
669	tim	1108
670	mmeineke	377	}
671	mmeineke	440
672	gezelter	907	sprintf( checkPointMsg,
673	gezelter	916	"Sucessfully took a dump.\n");
674	tim	1129	MPIcheckPoint();
675	gezelter	907
676	tim	1129	}
677
678
679	gezelter	907
680	mmeineke	377	#endif // is_mpi
681			}
682	mmeineke	440
683			#ifdef IS_MPI
684
685			// a couple of functions to let us escape the write loop
686
687	gezelter	907	void dWrite::DieDieDie( void ){
688	tim	837
689	mmeineke	440	MPI_Finalize();
690			exit (0);
691			}
692
693			#endif //is_mpi