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Comparing trunk/src/io/DumpWriter.cpp (file contents):
Revision 2 by gezelter, Fri Sep 24 04:16:43 2004 UTC vs.
Revision 619 by tim, Wed Sep 21 20:59:31 2005 UTC

# Line 1 | Line 1
1 < #define _LARGEFILE_SOURCE64
2 < #define _FILE_OFFSET_BITS 64
1 > /*
2 > * 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 > #include "io/basic_teebuf.hpp"
46 > #include "io/gzstream.hpp"
47 > #include "io/Globals.hpp"
48  
4 – #include <string.h>
5 – #include <iostream>
6 – #include <fstream>
7 – #include <algorithm>
8 – #include <utility>
9 –
49   #ifdef IS_MPI
50   #include <mpi.h>
12 – #include "mpiSimulation.hpp"
13 –
14 – namespace dWrite{
15 –  void DieDieDie( void );
16 – }
17 –
18 – using namespace dWrite;
51   #endif //is_mpi
52  
53 < #include "ReadWrite.hpp"
22 < #include "simError.h"
53 > namespace oopse {
54  
55 < DumpWriter::DumpWriter( SimInfo* the_entry_plug ){
55 >  DumpWriter::DumpWriter(SimInfo* info)
56 >    : info_(info), filename_(info->getDumpFileName()), eorFilename_(info->getFinalConfigFileName()){
57  
58 <  entry_plug = the_entry_plug;
58 >    Globals* simParams = info->getSimParams();
59 >    needCompression_ = simParams->getCompressDumpFile();
60  
61 + #ifdef HAVE_LIBZ
62 +    if (needCompression_) {
63 +        filename_ += ".gz";
64 +        eorFilename_ += ".gz";
65 +    }
66 + #endif
67 +    
68   #ifdef IS_MPI
69 <  if(worldRank == 0 ){
69 >
70 >      if (worldRank == 0) {
71   #endif // is_mpi
72  
32 –    dumpFile.open(entry_plug->sampleName.c_str(), ios::out | ios::trunc );
73  
74 <    if( !dumpFile ){
74 >        dumpFile_ = createOStream(filename_);
75  
76 <      sprintf( painCave.errMsg,
77 <               "Could not open \"%s\" for dump output.\n",
78 <               entry_plug->sampleName.c_str());
79 <      painCave.isFatal = 1;
80 <      simError();
81 <    }
76 >        if (!dumpFile_) {
77 >          sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
78 >                  filename_.c_str());
79 >          painCave.isFatal = 1;
80 >          simError();
81 >        }
82  
83   #ifdef IS_MPI
44 –  }
84  
85 <  //sort the local atoms by global index
47 <  sortByGlobalIndex();
48 <  
49 <  sprintf( checkPointMsg,
50 <           "Sucessfully opened output file for dumping.\n");
51 <  MPIcheckPoint();
52 < #endif // is_mpi
53 < }
85 >      }
86  
87 < DumpWriter::~DumpWriter( ){
87 >      sprintf(checkPointMsg, "Sucessfully opened output file for dumping.\n");
88 >      MPIcheckPoint();
89  
57 – #ifdef IS_MPI
58 –  if(worldRank == 0 ){
90   #endif // is_mpi
91  
92 <    dumpFile.close();
92 >    }
93  
63 – #ifdef IS_MPI
64 –  }
65 – #endif // is_mpi
66 – }
94  
95 < #ifdef IS_MPI
95 >  DumpWriter::DumpWriter(SimInfo* info, const std::string& filename)
96 >    : info_(info), filename_(filename){
97  
98 < /**
99 < * A hook function to load balancing
72 < */
98 >    Globals* simParams = info->getSimParams();
99 >    eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";    
100  
101 < 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 < }
101 >    needCompression_ = simParams->getCompressDumpFile();
102  
103 < /**
104 < * Sorting the local index by global index
105 < */
106 <
107 < void DumpWriter::sortByGlobalIndex(){
91 <  Molecule* mols = entry_plug->molecules;  
92 <  indexArray.clear();
93 <  
94 <  for(int i = 0; i < entry_plug->n_mol;i++)
95 <    indexArray.push_back(make_pair(i, mols[i].getGlobalIndex()));
96 <  
97 <  sort(indexArray.begin(), indexArray.end(), indexSortingCriterion);    
98 < }
99 <
103 > #ifdef HAVE_LIBZ
104 >    if (needCompression_) {
105 >        filename_ += ".gz";
106 >        eorFilename_ += ".gz";
107 >    }
108   #endif
109 <
102 < void DumpWriter::writeDump(double currentTime){
103 <
104 <  ofstream finalOut;
105 <  vector<ofstream*> fileStreams;
106 <
109 >    
110   #ifdef IS_MPI
111 <  if(worldRank == 0 ){
112 < #endif    
110 <    finalOut.open( entry_plug->finalName.c_str(), 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.c_str() );
115 <      painCave.isFatal = 1;
116 <      simError();
117 <    }
118 < #ifdef IS_MPI
119 <  }
111 >
112 >      if (worldRank == 0) {
113   #endif // is_mpi
114  
122 –  fileStreams.push_back(&finalOut);
123 –  fileStreams.push_back(&dumpFile);
115  
116 <  writeFrame(fileStreams, currentTime);
116 >        dumpFile_ = createOStream(filename_);
117  
118 +        if (!dumpFile_) {
119 +          sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
120 +                  filename_.c_str());
121 +          painCave.isFatal = 1;
122 +          simError();
123 +        }
124 +
125   #ifdef IS_MPI
128 –  finalOut.close();
129 – #endif
130 –        
131 – }
126  
127 < void DumpWriter::writeFinal(double currentTime){
127 >      }
128  
129 <  ofstream finalOut;
130 <  vector<ofstream*> fileStreams;
129 >      sprintf(checkPointMsg, "Sucessfully opened output file for dumping.\n");
130 >      MPIcheckPoint();
131  
138 – #ifdef IS_MPI
139 –  if(worldRank == 0 ){
132   #endif // is_mpi
133  
142 –    finalOut.open( entry_plug->finalName.c_str(), 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.c_str() );
148 –      painCave.isFatal = 1;
149 –      simError();
134      }
135  
136 < #ifdef IS_MPI
153 <  }
154 < #endif // is_mpi
155 <  
156 <  fileStreams.push_back(&finalOut);  
157 <  writeFrame(fileStreams, currentTime);
136 >  DumpWriter::~DumpWriter() {
137  
138   #ifdef IS_MPI
160 –  finalOut.close();
161 – #endif
162 –  
163 – }
139  
140 < void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){
140 >    if (worldRank == 0) {
141 > #endif // is_mpi
142  
143 <  const int BUFFERSIZE = 2000;
168 <  const int MINIBUFFERSIZE = 100;
143 >      delete dumpFile_;
144  
170 –  char tempBuffer[BUFFERSIZE];  
171 –  char writeLine[BUFFERSIZE];
172 –
173 –  int i;
174 –  unsigned int k;
175 –
145   #ifdef IS_MPI
177 –  
178 –  /*********************************************************************
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 –   *********************************************************************/
146  
147 <  int *potatoes;
216 <  int myPotato;
147 >    }
148  
149 <  int nProc;
219 <  int j, which_node, done, which_atom, local_index, currentIndex;
220 <  double atomData[13];
221 <  int isDirectional;
222 <  char* atomTypeString;
223 <  char MPIatomTypeString[MINIBUFFERSIZE];
224 <  int nObjects;
225 <  int msgLen; // the length of message actually recieved at master nodes
226 < #endif //is_mpi
149 > #endif // is_mpi
150  
151 <  double q[4], ji[3];
229 <  DirectionalAtom* dAtom;
230 <  double pos[3], vel[3];
231 <  int nTotObjects;
232 <  StuntDouble* sd;
233 <  char* molName;
234 <  vector<StuntDouble*> integrableObjects;
235 <  vector<StuntDouble*>::iterator iter;
236 <  nTotObjects = entry_plug->getTotIntegrableObjects();
237 < #ifndef IS_MPI
238 <  
239 <  for(k = 0; k < outFile.size(); k++){
240 <    *outFile[k] << nTotObjects << "\n";
151 >  }
152  
153 <    *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"
153 >  void DumpWriter::writeCommentLine(std::ostream& os, Snapshot* s) {
154  
155 <                     << entry_plug->Hmat[0][2] << "\t"
156 <                     << entry_plug->Hmat[1][2] << "\t"
157 <                     << entry_plug->Hmat[2][2] << ";";
155 >    double currentTime;
156 >    Mat3x3d hmat;
157 >    double chi;
158 >    double integralOfChiDt;
159 >    Mat3x3d eta;
160 >    
161 >    currentTime = s->getTime();
162 >    hmat = s->getHmat();
163 >    chi = s->getChi();
164 >    integralOfChiDt = s->getIntegralOfChiDt();
165 >    eta = s->getEta();
166 >    
167 >    os << currentTime << ";\t"
168 >       << hmat(0, 0) << "\t" << hmat(1, 0) << "\t" << hmat(2, 0) << ";\t"
169 >       << hmat(0, 1) << "\t" << hmat(1, 1) << "\t" << hmat(2, 1) << ";\t"
170 >       << hmat(0, 2) << "\t" << hmat(1, 2) << "\t" << hmat(2, 2) << ";\t";
171  
172      //write out additional parameters, such as chi and eta
173 <    *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
173 >
174 >    os << chi << "\t" << integralOfChiDt << "\t;";
175 >
176 >    os << eta(0, 0) << "\t" << eta(1, 0) << "\t" << eta(2, 0) << ";\t"
177 >       << eta(0, 1) << "\t" << eta(1, 1) << "\t" << eta(2, 1) << ";\t"
178 >       << eta(0, 2) << "\t" << eta(1, 2) << "\t" << eta(2, 2) << ";";
179 >        
180 >    os << "\n";
181    }
258 –  
259 –  for( i=0; i< entry_plug->n_mol; i++ ){
182  
183 <    integrableObjects = entry_plug->molecules[i].getIntegrableObjects();
184 <    molName = (entry_plug->compStamps[entry_plug->molecules[i].getStampID()])->getID();
185 <    
264 <    for( iter = integrableObjects.begin();iter !=  integrableObjects.end(); ++iter){
265 <      sd = *iter;
266 <      sd->getPos(pos);
267 <      sd->getVel(vel);
183 >  void DumpWriter::writeFrame(std::ostream& os) {
184 >    const int BUFFERSIZE = 2000;
185 >    const int MINIBUFFERSIZE = 100;
186  
187 <      sprintf( tempBuffer,
188 <             "%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 );
187 >    char tempBuffer[BUFFERSIZE];
188 >    char writeLine[BUFFERSIZE];
189  
190 <      if( sd->isDirectional() ){
190 >    Quat4d q;
191 >    Vector3d ji;
192 >    Vector3d pos;
193 >    Vector3d vel;
194  
195 <        sd->getQ( q );
196 <        sd->getJ( ji );
195 >    Molecule* mol;
196 >    StuntDouble* integrableObject;
197 >    SimInfo::MoleculeIterator mi;
198 >    Molecule::IntegrableObjectIterator ii;
199 >  
200 >    int nTotObjects;    
201 >    nTotObjects = info_->getNGlobalIntegrableObjects();
202  
203 <        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 <    
299 <      for(k = 0; k < outFile.size(); k++)
300 <        *outFile[k] << writeLine;      
301 <    }
203 > #ifndef IS_MPI
204  
303 – }
205  
206 < #else // is_mpi
206 >    os << nTotObjects << "\n";
207 >        
208 >    writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot());
209  
210 <  /* code to find maximum tag value */
308 <  
309 <  int *tagub, flag, MAXTAG;
310 <  MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
311 <  if (flag) {
312 <    MAXTAG = *tagub;
313 <  } else {
314 <    MAXTAG = 32767;
315 <  }  
210 >    for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
211  
212 <  int haveError;
212 >      for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
213 >           integrableObject = mol->nextIntegrableObject(ii)) {
214 >                
215  
216 <  MPI_Status istatus;
217 <  int nCurObj;
321 <  int *MolToProcMap = mpiSim->getMolToProcMap();
216 >        pos = integrableObject->getPos();
217 >        vel = integrableObject->getVel();
218  
219 <  // write out header and node 0's coordinates
219 >        sprintf(tempBuffer, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
220 >                integrableObject->getType().c_str(),
221 >                pos[0], pos[1], pos[2],
222 >                vel[0], vel[1], vel[2]);
223  
224 <  if( worldRank == 0 ){
224 >        strcpy(writeLine, tempBuffer);
225  
226 <    // Node 0 needs a list of the magic potatoes for each processor;
226 >        if (integrableObject->isDirectional()) {
227 >          q = integrableObject->getQ();
228 >          ji = integrableObject->getJ();
229  
230 <    nProc = mpiSim->getNProcessors();
231 <    potatoes = new int[nProc];
230 >          sprintf(tempBuffer, "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
231 >                  q[0], q[1], q[2], q[3],
232 >                  ji[0], ji[1], ji[2]);
233 >          strcat(writeLine, tempBuffer);
234 >        } else {
235 >          strcat(writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n");
236 >        }
237  
238 <    //write out the comment lines
333 <    for (i = 0; i < nProc; i++)
334 <      potatoes[i] = 0;
335 <    
336 <      for(k = 0; k < outFile.size(); k++){
337 <        *outFile[k] << nTotObjects << "\n";
238 >        os << writeLine;
239  
240 <        *outFile[k] << currentTime << ";\t"
241 <                         << entry_plug->Hmat[0][0] << "\t"
341 <                         << entry_plug->Hmat[1][0] << "\t"
342 <                         << entry_plug->Hmat[2][0] << ";\t"
240 >      }
241 >    }
242  
243 <                         << entry_plug->Hmat[0][1] << "\t"
244 <                         << entry_plug->Hmat[1][1] << "\t"
245 <                         << entry_plug->Hmat[2][1] << ";\t"
243 >    os.flush();
244 > #else // is_mpi
245 >    /*********************************************************************
246 >     * Documentation?  You want DOCUMENTATION?
247 >     *
248 >     * Why all the potatoes below?  
249 >     *
250 >     * To make a long story short, the original version of DumpWriter
251 >     * worked in the most inefficient way possible.  Node 0 would
252 >     * poke each of the node for an individual atom's formatted data
253 >     * as node 0 worked its way down the global index. This was particularly
254 >     * inefficient since the method blocked all processors at every atom
255 >     * (and did it twice!).
256 >     *
257 >     * An intermediate version of DumpWriter could be described from Node
258 >     * zero's perspective as follows:
259 >     *
260 >     *  1) Have 100 of your friends stand in a circle.
261 >     *  2) When you say go, have all of them start tossing potatoes at
262 >     *     you (one at a time).
263 >     *  3) Catch the potatoes.
264 >     *
265 >     * It was an improvement, but MPI has buffers and caches that could
266 >     * best be described in this analogy as "potato nets", so there's no
267 >     * need to block the processors atom-by-atom.
268 >     *
269 >     * This new and improved DumpWriter works in an even more efficient
270 >     * way:
271 >     *
272 >     *  1) Have 100 of your friend stand in a circle.
273 >     *  2) When you say go, have them start tossing 5-pound bags of
274 >     *     potatoes at you.
275 >     *  3) Once you've caught a friend's bag of potatoes,
276 >     *     toss them a spud to let them know they can toss another bag.
277 >     *
278 >     * How's THAT for documentation?
279 >     *
280 >     *********************************************************************/
281 >    const int masterNode = 0;
282  
283 <                         << entry_plug->Hmat[0][2] << "\t"
284 <                         << entry_plug->Hmat[1][2] << "\t"
285 <                         << entry_plug->Hmat[2][2] << ";";
286 <  
287 <        *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
283 >    int * potatoes;
284 >    int myPotato;
285 >    int nProc;
286 >    int which_node;
287 >    double atomData[13];
288 >    int isDirectional;
289 >    char MPIatomTypeString[MINIBUFFERSIZE];
290 >    int msgLen; // the length of message actually recieved at master nodes
291 >    int haveError;
292 >    MPI_Status istatus;
293 >    int nCurObj;
294 >    
295 >    // code to find maximum tag value
296 >    int * tagub;
297 >    int flag;
298 >    int MAXTAG;
299 >    MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
300 >
301 >    if (flag) {
302 >      MAXTAG = *tagub;
303 >    } else {
304 >      MAXTAG = 32767;
305      }
306  
307 <    currentIndex = 0;
307 >    if (worldRank == masterNode) { //master node (node 0) is responsible for writing the dump file
308  
309 <    for (i = 0 ; i < mpiSim->getNMolGlobal(); i++ ) {
358 <      
359 <      // Get the Node number which has this atom;
360 <      
361 <      which_node = MolToProcMap[i];
362 <      
363 <      if (which_node != 0) {
364 <        
365 <        if (potatoes[which_node] + 1 >= MAXTAG) {
366 <          // The potato was going to exceed the maximum value,
367 <          // so wrap this processor potato back to 0:        
309 >      // Node 0 needs a list of the magic potatoes for each processor;
310  
311 <          potatoes[which_node] = 0;          
312 <          MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
371 <          
372 <        }
311 >      MPI_Comm_size(MPI_COMM_WORLD, &nProc);
312 >      potatoes = new int[nProc];
313  
314 <        myPotato = potatoes[which_node];        
314 >      //write out the comment lines
315 >      for(int i = 0; i < nProc; i++) {
316 >        potatoes[i] = 0;
317 >      }
318  
376 –        //recieve the number of integrableObject in current molecule
377 –        MPI_Recv(&nCurObj, 1, MPI_INT, which_node,
378 –                 myPotato, MPI_COMM_WORLD, &istatus);
379 –        myPotato++;
380 –        
381 –        for(int l = 0; l < nCurObj; l++){
319  
320 <          if (potatoes[which_node] + 2 >= MAXTAG) {
321 <            // The potato was going to exceed the maximum value,
385 <            // so wrap this processor potato back to 0:        
320 >      os << nTotObjects << "\n";
321 >      writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot());
322  
323 <            potatoes[which_node] = 0;          
388 <            MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
389 <            
390 <          }
323 >      for(int i = 0; i < info_->getNGlobalMolecules(); i++) {
324  
325 <          MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
393 <          myPotato, MPI_COMM_WORLD, &istatus);
325 >        // Get the Node number which has this atom;
326  
327 <          atomTypeString = MPIatomTypeString;
327 >        which_node = info_->getMolToProc(i);
328  
329 <          myPotato++;
329 >        if (which_node != masterNode) { //current molecule is in slave node
330 >          if (potatoes[which_node] + 1 >= MAXTAG) {
331 >            // The potato was going to exceed the maximum value,
332 >            // so wrap this processor potato back to 0:        
333  
334 <          MPI_Recv(atomData, 13, MPI_DOUBLE, which_node, myPotato, MPI_COMM_WORLD, &istatus);
335 <          myPotato++;
334 >            potatoes[which_node] = 0;
335 >            MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0,
336 >                     MPI_COMM_WORLD);
337 >          }
338  
339 <          MPI_Get_count(&istatus, MPI_DOUBLE, &msgLen);
339 >          myPotato = potatoes[which_node];
340  
341 <          if(msgLen  == 13)
342 <            isDirectional = 1;
343 <          else
344 <            isDirectional = 0;
345 <          
346 <          // If we've survived to here, format the line:
347 <            
348 <          if (!isDirectional) {
349 <        
350 <            sprintf( writeLine,
351 <                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
352 <                 atomTypeString,
353 <                 atomData[0],
354 <                 atomData[1],
355 <                 atomData[2],
356 <                 atomData[3],
357 <                 atomData[4],
358 <                 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;            
341 >          //recieve the number of integrableObject in current molecule
342 >          MPI_Recv(&nCurObj, 1, MPI_INT, which_node, myPotato,
343 >                   MPI_COMM_WORLD, &istatus);
344 >          myPotato++;
345 >
346 >          for(int l = 0; l < nCurObj; l++) {
347 >            if (potatoes[which_node] + 2 >= MAXTAG) {
348 >              // The potato was going to exceed the maximum value,
349 >              // so wrap this processor potato back to 0:        
350 >
351 >              potatoes[which_node] = 0;
352 >              MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node,
353 >                       0, MPI_COMM_WORLD);
354 >            }
355 >
356 >            MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR,
357 >                     which_node, myPotato, MPI_COMM_WORLD,
358 >                     &istatus);
359  
360 <        }// end for(int l =0)
451 <        potatoes[which_node] = myPotato;
360 >            myPotato++;
361  
362 <      }
363 <      else {
364 <        
456 <        haveError = 0;
457 <        
458 <            local_index = indexArray[currentIndex].first;        
362 >            MPI_Recv(atomData, 13, MPI_DOUBLE, which_node, myPotato,
363 >                     MPI_COMM_WORLD, &istatus);
364 >            myPotato++;
365  
366 <        integrableObjects = (entry_plug->molecules[local_index]).getIntegrableObjects();
366 >            MPI_Get_count(&istatus, MPI_DOUBLE, &msgLen);
367  
368 <        for(iter= integrableObjects.begin(); iter != integrableObjects.end(); ++iter){    
369 <                sd = *iter;
370 <            atomTypeString = sd->getType();
371 <            
466 <            sd->getPos(pos);
467 <            sd->getVel(vel);          
468 <          
469 <            atomData[0] = pos[0];
470 <            atomData[1] = pos[1];
471 <            atomData[2] = pos[2];
368 >            if (msgLen == 13)
369 >              isDirectional = 1;
370 >            else
371 >              isDirectional = 0;
372  
373 <            atomData[3] = vel[0];
474 <            atomData[4] = vel[1];
475 <            atomData[5] = vel[2];
476 <              
477 <            isDirectional = 0;
373 >            // If we've survived to here, format the line:
374  
375 <            if( sd->isDirectional() ){
375 >            if (!isDirectional) {
376 >              sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
377 >                      MPIatomTypeString, atomData[0],
378 >                      atomData[1], atomData[2],
379 >                      atomData[3], atomData[4],
380 >                      atomData[5]);
381  
382 <              isDirectional = 1;
383 <                
384 <              sd->getQ( q );
385 <              sd->getJ( ji );
382 >              strcat(writeLine,
383 >                     "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n");
384 >            } else {
385 >              sprintf(writeLine,
386 >                      "%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",
387 >                      MPIatomTypeString,
388 >                      atomData[0],
389 >                      atomData[1],
390 >                      atomData[2],
391 >                      atomData[3],
392 >                      atomData[4],
393 >                      atomData[5],
394 >                      atomData[6],
395 >                      atomData[7],
396 >                      atomData[8],
397 >                      atomData[9],
398 >                      atomData[10],
399 >                      atomData[11],
400 >                      atomData[12]);
401 >            }
402  
403 <              for (int j = 0; j < 6 ; j++)
487 <                atomData[j] = atomData[j];            
488 <              
489 <              atomData[6] = q[0];
490 <              atomData[7] = q[1];
491 <              atomData[8] = q[2];
492 <              atomData[9] = q[3];
493 <              
494 <              atomData[10] = ji[0];
495 <              atomData[11] = ji[1];
496 <              atomData[12] = ji[2];
497 <            }
498 <            
499 <            // 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 <        
543 <      currentIndex++;
544 <      }
403 >            os << writeLine;
404  
405 <    }//end for(i = 0; i < mpiSim->getNmol())
547 <    
548 <    for(k = 0; k < outFile.size(); k++)
549 <      outFile[k]->flush();
550 <    
551 <    sprintf( checkPointMsg,
552 <             "Sucessfully took a dump.\n");
553 <    
554 <    MPIcheckPoint();        
555 <    
556 <    delete[] potatoes;
557 <    
558 <  } else {
405 >          } // end for(int l =0)
406  
407 <    // worldRank != 0, so I'm a remote node.  
407 >          potatoes[which_node] = myPotato;
408 >        } else { //master node has current molecule
409  
410 <    // Set my magic potato to 0:
410 >          mol = info_->getMoleculeByGlobalIndex(i);
411  
412 <    myPotato = 0;
413 <    currentIndex = 0;
414 <    
415 <    for (i = 0 ; i < mpiSim->getNMolGlobal(); i++ ) {
416 <      
417 <      // Am I the node which has this integrableObject?
418 <      
419 <      if (MolToProcMap[i] == worldRank) {
412 >          if (mol == NULL) {
413 >            sprintf(painCave.errMsg, "Molecule not found on node %d!", worldRank);
414 >            painCave.isFatal = 1;
415 >            simError();
416 >          }
417 >                
418 >          for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
419 >               integrableObject = mol->nextIntegrableObject(ii)) {      
420  
421 +            pos = integrableObject->getPos();
422 +            vel = integrableObject->getVel();
423  
424 <        if (myPotato + 1 >= MAXTAG) {
425 <          
426 <          // 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 <          
580 <          MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
581 <          
582 <        }
424 >            atomData[0] = pos[0];
425 >            atomData[1] = pos[1];
426 >            atomData[2] = pos[2];
427  
428 <          local_index = indexArray[currentIndex].first;        
429 <          integrableObjects = entry_plug->molecules[local_index].getIntegrableObjects();
430 <          
587 <          nCurObj = integrableObjects.size();
588 <                      
589 <          MPI_Send(&nCurObj, 1, MPI_INT, 0,
590 <                             myPotato, MPI_COMM_WORLD);
591 <          myPotato++;
428 >            atomData[3] = vel[0];
429 >            atomData[4] = vel[1];
430 >            atomData[5] = vel[2];
431  
432 <          for( iter = integrableObjects.begin(); iter  != integrableObjects.end(); iter++){
432 >            isDirectional = 0;
433  
434 <            if (myPotato + 2 >= MAXTAG) {
435 <          
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();
434 >            if (integrableObject->isDirectional()) {
435 >              isDirectional = 1;
436  
437 <            sd->getPos(pos);
438 <            sd->getVel(vel);
437 >              q = integrableObject->getQ();
438 >              ji = integrableObject->getJ();
439  
440 <            atomData[0] = pos[0];
441 <            atomData[1] = pos[1];
442 <            atomData[2] = pos[2];
440 >              for(int j = 0; j < 6; j++) {
441 >                atomData[j] = atomData[j];
442 >              }
443  
444 <            atomData[3] = vel[0];
445 <            atomData[4] = vel[1];
446 <            atomData[5] = vel[2];
447 <              
620 <            isDirectional = 0;
444 >              atomData[6] = q[0];
445 >              atomData[7] = q[1];
446 >              atomData[8] = q[2];
447 >              atomData[9] = q[3];
448  
449 <            if( sd->isDirectional() ){
449 >              atomData[10] = ji[0];
450 >              atomData[11] = ji[1];
451 >              atomData[12] = ji[2];
452 >            }
453  
454 <                isDirectional = 1;
455 <                
456 <                sd->getQ( q );
457 <                sd->getJ( ji );
458 <                
454 >            // If we've survived to here, format the line:
455 >
456 >            if (!isDirectional) {
457 >              sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
458 >                      integrableObject->getType().c_str(), atomData[0],
459 >                      atomData[1], atomData[2],
460 >                      atomData[3], atomData[4],
461 >                      atomData[5]);
462 >
463 >              strcat(writeLine,
464 >                     "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n");
465 >            } else {
466 >              sprintf(writeLine,
467 >                      "%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",
468 >                      integrableObject->getType().c_str(),
469 >                      atomData[0],
470 >                      atomData[1],
471 >                      atomData[2],
472 >                      atomData[3],
473 >                      atomData[4],
474 >                      atomData[5],
475 >                      atomData[6],
476 >                      atomData[7],
477 >                      atomData[8],
478 >                      atomData[9],
479 >                      atomData[10],
480 >                      atomData[11],
481 >                      atomData[12]);
482 >            }
483 >
484 >
485 >            os << writeLine;
486 >
487 >          } //end for(iter = integrableObject.begin())
488 >        }
489 >      } //end for(i = 0; i < mpiSim->getNmol())
490 >
491 >      os.flush();
492 >        
493 >      sprintf(checkPointMsg, "Sucessfully took a dump.\n");
494 >      MPIcheckPoint();
495 >
496 >      delete [] potatoes;
497 >    } else {
498 >
499 >      // worldRank != 0, so I'm a remote node.  
500 >
501 >      // Set my magic potato to 0:
502 >
503 >      myPotato = 0;
504 >
505 >      for(int i = 0; i < info_->getNGlobalMolecules(); i++) {
506 >
507 >        // Am I the node which has this integrableObject?
508 >        int whichNode = info_->getMolToProc(i);
509 >        if (whichNode == worldRank) {
510 >          if (myPotato + 1 >= MAXTAG) {
511 >
512 >            // The potato was going to exceed the maximum value,
513 >            // so wrap this processor potato back to 0 (and block until
514 >            // node 0 says we can go:
515 >
516 >            MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD,
517 >                     &istatus);
518 >          }
519 >
520 >          mol = info_->getMoleculeByGlobalIndex(i);
521 >
522                  
523 <                atomData[6] = q[0];
631 <                atomData[7] = q[1];
632 <                atomData[8] = q[2];
633 <                atomData[9] = q[3];
634 <      
635 <                atomData[10] = ji[0];
636 <                atomData[11] = ji[1];
637 <                atomData[12] = ji[2];
638 <              }
523 >          nCurObj = mol->getNIntegrableObjects();
524  
525 <            
526 <            strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
525 >          MPI_Send(&nCurObj, 1, MPI_INT, 0, myPotato, MPI_COMM_WORLD);
526 >          myPotato++;
527  
528 <            // null terminate the string before sending (just in case):
529 <            MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
528 >          for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
529 >               integrableObject = mol->nextIntegrableObject(ii)) {
530  
531 <            MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
647 <                             myPotato, MPI_COMM_WORLD);
648 <            
649 <            myPotato++;
650 <            
651 <            if (isDirectional) {
531 >            if (myPotato + 2 >= MAXTAG) {
532  
533 <              MPI_Send(atomData, 13, MPI_DOUBLE, 0,
534 <                       myPotato, MPI_COMM_WORLD);
535 <              
656 <            } else {
533 >              // The potato was going to exceed the maximum value,
534 >              // so wrap this processor potato back to 0 (and block until
535 >              // node 0 says we can go:
536  
537 <              MPI_Send(atomData, 6, MPI_DOUBLE, 0,
538 <                       myPotato, MPI_COMM_WORLD);
539 <            }
537 >              MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD,
538 >                       &istatus);
539 >            }
540  
541 <            myPotato++;  
541 >            pos = integrableObject->getPos();
542 >            vel = integrableObject->getVel();
543  
544 <          }
544 >            atomData[0] = pos[0];
545 >            atomData[1] = pos[1];
546 >            atomData[2] = pos[2];
547  
548 <          currentIndex++;    
549 <          
550 <        }
551 <      
548 >            atomData[3] = vel[0];
549 >            atomData[4] = vel[1];
550 >            atomData[5] = vel[2];
551 >
552 >            isDirectional = 0;
553 >
554 >            if (integrableObject->isDirectional()) {
555 >              isDirectional = 1;
556 >
557 >              q = integrableObject->getQ();
558 >              ji = integrableObject->getJ();
559 >
560 >              atomData[6] = q[0];
561 >              atomData[7] = q[1];
562 >              atomData[8] = q[2];
563 >              atomData[9] = q[3];
564 >
565 >              atomData[10] = ji[0];
566 >              atomData[11] = ji[1];
567 >              atomData[12] = ji[2];
568 >            }
569 >
570 >            strncpy(MPIatomTypeString, integrableObject->getType().c_str(), MINIBUFFERSIZE);
571 >
572 >            // null terminate the  std::string before sending (just in case):
573 >            MPIatomTypeString[MINIBUFFERSIZE - 1] = '\0';
574 >
575 >            MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
576 >                     myPotato, MPI_COMM_WORLD);
577 >
578 >            myPotato++;
579 >
580 >            if (isDirectional) {
581 >              MPI_Send(atomData, 13, MPI_DOUBLE, 0, myPotato,
582 >                       MPI_COMM_WORLD);
583 >            } else {
584 >              MPI_Send(atomData, 6, MPI_DOUBLE, 0, myPotato,
585 >                       MPI_COMM_WORLD);
586 >            }
587 >
588 >            myPotato++;
589 >          }
590 >                    
591 >        }
592 >            
593        }
594 +      sprintf(checkPointMsg, "Sucessfully took a dump.\n");
595 +      MPIcheckPoint();
596 +    }
597  
598 <    sprintf( checkPointMsg,
599 <             "Sucessfully took a dump.\n");
600 <    MPIcheckPoint();                
598 > #endif // is_mpi
599 >
600 >  }
601 >
602 >  void DumpWriter::writeDump() {
603 >    writeFrame(*dumpFile_);
604 >  }
605 >
606 >  void DumpWriter::writeEor() {
607 >    std::ostream* eorStream;
608      
609 + #ifdef IS_MPI
610 +    if (worldRank == 0) {
611 + #endif // is_mpi
612 +
613 +      eorStream = createOStream(eorFilename_);
614 +
615 + #ifdef IS_MPI
616      }
617 + #endif // is_mpi    
618  
619 +    writeFrame(*eorStream);
620  
621 <  
621 > #ifdef IS_MPI
622 >    if (worldRank == 0) {
623   #endif // is_mpi
624 < }
624 >    delete eorStream;
625  
626   #ifdef IS_MPI
627 +    }
628 + #endif // is_mpi  
629  
630 < // a couple of functions to let us escape the write loop
630 >  }
631  
687 – void dWrite::DieDieDie( void ){
632  
633 <  MPI_Finalize();
634 <  exit (0);
633 >  void DumpWriter::writeDumpAndEor() {
634 >    std::vector<std::streambuf*> buffers;
635 >    std::ostream* eorStream;
636 > #ifdef IS_MPI
637 >    if (worldRank == 0) {
638 > #endif // is_mpi
639 >
640 >      buffers.push_back(dumpFile_->rdbuf());
641 >
642 >      eorStream = createOStream(eorFilename_);
643 >
644 >      buffers.push_back(eorStream->rdbuf());
645 >        
646 > #ifdef IS_MPI
647 >    }
648 > #endif // is_mpi    
649 >
650 >    TeeBuf tbuf(buffers.begin(), buffers.end());
651 >    std::ostream os(&tbuf);
652 >
653 >    writeFrame(os);
654 >
655 > #ifdef IS_MPI
656 >    if (worldRank == 0) {
657 > #endif // is_mpi
658 >    delete eorStream;
659 >
660 > #ifdef IS_MPI
661 >    }
662 > #endif // is_mpi  
663 >    
664 >  }
665 >
666 > std::ostream* DumpWriter::createOStream(const std::string& filename) {
667 >
668 >    std::ostream* newOStream;
669 > #ifdef HAVE_LIBZ
670 >    if (needCompression_) {
671 >        newOStream = new ogzstream(filename.c_str());
672 >    } else {
673 >        newOStream = new std::ofstream(filename.c_str());
674 >    }
675 > #else
676 >    newOStream = new std::ofstream(filename.c_str());
677 > #endif
678 >    return newOStream;
679   }
680  
681 < #endif //is_mpi
681 > }//end namespace oopse

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