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root/group/trunk/OOPSE/libmdtools/DumpWriter.cpp
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Comparing trunk/OOPSE/libmdtools/DumpWriter.cpp (file contents):
Revision 787 by mmeineke, Thu Sep 25 19:27:15 2003 UTC vs.
Revision 1152 by tim, Mon May 10 20:28:14 2004 UTC

# Line 1 | Line 1
1 + #define _LARGEFILE_SOURCE64
2   #define _FILE_OFFSET_BITS 64
3  
4 < #include <cstring>
4 > #include <string.h>
5   #include <iostream>
6   #include <fstream>
7 + #include <algorithm>
8 + #include <utility>
9  
10   #ifdef IS_MPI
11   #include <mpi.h>
12   #include "mpiSimulation.hpp"
10 – #define TAKE_THIS_TAG_CHAR 1
11 – #define TAKE_THIS_TAG_INT 2
13  
14   namespace dWrite{
15 <  void nodeZeroError( void );
15 <  void anonymousNodeDie( void );
15 >  void DieDieDie( void );
16   }
17  
18   using namespace dWrite;
# Line 28 | Line 28 | DumpWriter::DumpWriter( SimInfo* the_entry_plug ){
28   #ifdef IS_MPI
29    if(worldRank == 0 ){
30   #endif // is_mpi
31 <    
32 <    strcpy( outName, entry_plug->sampleName );
33 <    
34 <    outFile.open(outName, ios::out | ios::trunc );
35 <    
36 <    if( !outFile ){
37 <      
31 >
32 >    dumpFile.open(entry_plug->sampleName, ios::out | ios::trunc );
33 >
34 >    if( !dumpFile ){
35 >
36        sprintf( painCave.errMsg,
37                 "Could not open \"%s\" for dump output.\n",
38 <               outName);
38 >               entry_plug->sampleName);
39        painCave.isFatal = 1;
40        simError();
41      }
42  
45 –    //outFile.setf( ios::scientific );
46 –
43   #ifdef IS_MPI
44    }
45  
46 +  //sort the local atoms by global index
47 +  sortByGlobalIndex();
48 +  
49    sprintf( checkPointMsg,
50             "Sucessfully opened output file for dumping.\n");
51    MPIcheckPoint();
# Line 59 | Line 58 | DumpWriter::~DumpWriter( ){
58    if(worldRank == 0 ){
59   #endif // is_mpi
60  
61 <    outFile.close();
61 >    dumpFile.close();
62  
63   #ifdef IS_MPI
64    }
65   #endif // is_mpi
66   }
67  
69 – void DumpWriter::writeDump( double currentTime ){
70 –  
71 –  const int BUFFERSIZE = 2000;
72 –  char tempBuffer[BUFFERSIZE];
73 –  char writeLine[BUFFERSIZE];
74 –
75 –  int i;
68   #ifdef IS_MPI
77 –  int j, which_node, done, which_atom, local_index;
78 – #else //is_mpi
79 –  int nAtoms = entry_plug->n_atoms;
80 – #endif //is_mpi
69  
70 <  double q[4];
71 <  DirectionalAtom* dAtom;
72 <  Atom** atoms = entry_plug->atoms;
85 <  double pos[3], vel[3];
86 <    
70 > /**
71 > * A hook function to load balancing
72 > */
73  
74 < #ifndef IS_MPI
75 <    
76 <  outFile << nAtoms << "\n";
77 <    
78 <  outFile << currentTime << ";\t"
79 <          << entry_plug->Hmat[0][0] << "\t"
80 <          << entry_plug->Hmat[1][0] << "\t"
81 <          << entry_plug->Hmat[2][0] << ";\t"
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 <          << entry_plug->Hmat[0][1] << "\t"
87 <          << entry_plug->Hmat[1][1] << "\t"
88 <          << entry_plug->Hmat[2][1] << ";\t"
86 > /**
87 > * Sorting the local index by global index
88 > */
89 >
90 > 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  
100 <          << entry_plug->Hmat[0][2] << "\t"
102 <          << entry_plug->Hmat[1][2] << "\t"
103 <          << entry_plug->Hmat[2][2] << ";\n";
104 <    
105 <  for( i=0; i<nAtoms; i++ ){
106 <      
107 <    atoms[i]->getPos(pos);
108 <    atoms[i]->getVel(vel);
100 > #endif
101  
102 <    sprintf( tempBuffer,
111 <             "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
112 <             atoms[i]->getType(),
113 <             pos[0],
114 <             pos[1],
115 <             pos[2],
116 <             vel[0],
117 <             vel[1],
118 <             vel[2]);
119 <    strcpy( writeLine, tempBuffer );
102 > void DumpWriter::writeDump(double currentTime){
103  
104 <    if( atoms[i]->isDirectional() ){
105 <        
106 <      dAtom = (DirectionalAtom *)atoms[i];
107 <      dAtom->getQ( q );
108 <        
109 <      sprintf( tempBuffer,
110 <               "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
111 <               q[0],
112 <               q[1],
113 <               q[2],
114 <               q[3],
115 <               dAtom->getJx(),
116 <               dAtom->getJy(),
134 <               dAtom->getJz());
135 <      strcat( writeLine, tempBuffer );
104 >  ofstream finalOut;
105 >  vector<ofstream*> fileStreams;
106 >
107 > #ifdef IS_MPI
108 >  if(worldRank == 0 ){
109 > #endif    
110 >    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 <    else
138 <      strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
139 <      
140 <    outFile << writeLine;
118 > #ifdef IS_MPI
119    }
120 <  outFile.flush();
120 > #endif // is_mpi
121  
122 < #else // is_mpi
122 >  fileStreams.push_back(&finalOut);
123 >  fileStreams.push_back(&dumpFile);
124  
125 <  // first thing first, suspend fatalities.
147 <  painCave.isEventLoop = 1;
125 >  writeFrame(fileStreams, currentTime);
126  
127 <  int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
128 <  int haveError;
127 > #ifdef IS_MPI
128 >  finalOut.close();
129 > #endif
130 >        
131 > }
132  
133 <  MPI_Status istatus;
153 <  int *AtomToProcMap = mpiSim->getAtomToProcMap();
154 <  
155 <  // write out header and node 0's coordinates
156 <  
157 <  if( worldRank == 0 ){
158 <    outFile << mpiSim->getTotAtoms() << "\n";
159 <  
160 <    outFile << currentTime << ";\t"
161 <            << entry_plug->Hmat[0][0] << "\t"
162 <            << entry_plug->Hmat[1][0] << "\t"
163 <            << entry_plug->Hmat[2][0] << ";\t"
164 <      
165 <            << entry_plug->Hmat[0][1] << "\t"
166 <            << entry_plug->Hmat[1][1] << "\t"
167 <            << entry_plug->Hmat[2][1] << ";\t"
168 <      
169 <            << entry_plug->Hmat[0][2] << "\t"
170 <            << entry_plug->Hmat[1][2] << "\t"
171 <            << entry_plug->Hmat[2][2] << ";\n";
172 <    
173 <    outFile.flush();
174 <    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
175 <      // Get the Node number which has this atom;
176 <      
177 <      which_node = AtomToProcMap[i];    
178 <      
179 <      if (which_node == 0 ) {
180 <        
181 <        haveError = 0;
182 <        which_atom = i;
183 <        local_index=-1;        
184 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
185 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
186 <        }
187 <        if (local_index != -1) {
188 <          //format the line
189 <          
190 <          atoms[local_index]->getPos(pos);
191 <          atoms[local_index]->getVel(vel);
133 > void DumpWriter::writeFinal(double currentTime){
134  
193 –          sprintf( tempBuffer,
194 –                   "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
195 –                   atoms[local_index]->getType(),
196 –                   pos[0],
197 –                   pos[1],
198 –                   pos[2],
199 –                   vel[0],
200 –                   vel[1],
201 –                   vel[2]); // check here.
202 –          strcpy( writeLine, tempBuffer );
203 –          
204 –          if( atoms[local_index]->isDirectional() ){
205 –            
206 –            dAtom = (DirectionalAtom *)atoms[local_index];
207 –            dAtom->getQ( q );
208 –            
209 –            sprintf( tempBuffer,
210 –                     "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
211 –                     q[0],
212 –                     q[1],
213 –                     q[2],
214 –                     q[3],
215 –                     dAtom->getJx(),
216 –                     dAtom->getJy(),
217 –                     dAtom->getJz());
218 –            strcat( writeLine, tempBuffer );
219 –            
220 –          }
221 –          else
222 –            strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );      
223 –        }
224 –        else {
225 –          sprintf(painCave.errMsg,
226 –                  "Atom %d not found on processor %d\n",
227 –                  i, worldRank );
228 –          haveError= 1;
229 –          simError();
230 –        }
231 –        
232 –        if(haveError) nodeZeroError();
233 –
234 –      }
235 –      else {
236 –        myStatus = 1;
237 –        MPI_Send(&myStatus, 1, MPI_INT, which_node,
238 –                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
239 –        MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
240 –                 MPI_COMM_WORLD);
241 –        MPI_Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node,
242 –                 TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
243 –        MPI_Recv(&myStatus, 1, MPI_INT, which_node,
244 –                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
245 –        
246 –        if(!myStatus) nodeZeroError();
247 –
248 –      }
249 –      
250 –      outFile << writeLine;
251 –      outFile.flush();
252 –    }
253 –    
254 –    // kill everyone off:
255 –    myStatus = -1;
256 –    for (j = 0; j < mpiSim->getNumberProcessors(); j++) {      
257 –      MPI_Send(&myStatus, 1, MPI_INT, j,
258 –               TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
259 –    }
260 –
261 –  } else {
262 –    
263 –    done = 0;
264 –    while (!done) {
265 –      
266 –      MPI_Recv(&myStatus, 1, MPI_INT, 0,
267 –               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
268 –
269 –      if(!myStatus) anonymousNodeDie();
270 –      
271 –      if(myStatus < 0) break;
272 –
273 –      MPI_Recv(&which_atom, 1, MPI_INT, 0,
274 –               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
275 –      
276 –      myStatus = 1;
277 –      local_index=-1;        
278 –      for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
279 –        if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
280 –      }
281 –      if (local_index != -1) {
282 –        //format the line
283 –
284 –        atoms[local_index]->getPos(pos);
285 –        atoms[local_index]->getVel(vel);
286 –
287 –        sprintf( tempBuffer,
288 –                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
289 –                 atoms[local_index]->getType(),
290 –                 pos[0],
291 –                 pos[1],
292 –                 pos[2],
293 –                 vel[0],
294 –                 vel[1],
295 –                 vel[2]); // check here.
296 –        strcpy( writeLine, tempBuffer );
297 –        
298 –        if( atoms[local_index]->isDirectional() ){
299 –          
300 –          dAtom = (DirectionalAtom *)atoms[local_index];
301 –          dAtom->getQ( q );
302 –          
303 –          sprintf( tempBuffer,
304 –                   "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
305 –                   q[0],
306 –                   q[1],
307 –                   q[2],
308 –                   q[3],
309 –                   dAtom->getJx(),
310 –                   dAtom->getJy(),
311 –                   dAtom->getJz());
312 –          strcat( writeLine, tempBuffer );
313 –        }
314 –        else{
315 –          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
316 –        }
317 –      }
318 –      else {
319 –        sprintf(painCave.errMsg,
320 –                "Atom %d not found on processor %d\n",
321 –                which_atom, worldRank );
322 –        myStatus = 0;
323 –        simError();
324 –
325 –        strcpy( writeLine, "Hello, I'm an error.\n");
326 –      }
327 –
328 –      MPI_Send(writeLine, BUFFERSIZE, MPI_CHAR, 0,
329 –               TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
330 –      MPI_Send( &myStatus, 1, MPI_INT, 0,
331 –                TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
332 –    }
333 –  }  
334 –  outFile.flush();
335 –  sprintf( checkPointMsg,
336 –           "Sucessfully took a dump.\n");
337 –  MPIcheckPoint();
338 –
339 – // last  thing last, enable  fatalities.
340 –  painCave.isEventLoop = 0;
341 –
342 – #endif // is_mpi
343 – }
344 –
345 – void DumpWriter::writeFinal(double finalTime){
346 –
347 –  char finalName[500];
135    ofstream finalOut;
136 +  vector<ofstream*> fileStreams;
137  
350 –  const int BUFFERSIZE = 2000;
351 –  char tempBuffer[BUFFERSIZE];
352 –  char writeLine[BUFFERSIZE];  
353 –
354 –  double q[4];
355 –  DirectionalAtom* dAtom;
356 –  Atom** atoms = entry_plug->atoms;
357 –  int i;
138   #ifdef IS_MPI
359 –  int j, which_node, done, which_atom, local_index;
360 – #else //is_mpi
361 –  int nAtoms = entry_plug->n_atoms;
362 – #endif //is_mpi
363 –  
364 –  double pos[3], vel[3];
365 –  
366 – #ifdef IS_MPI
139    if(worldRank == 0 ){
140   #endif // is_mpi
141 <    
142 <    strcpy( finalName, entry_plug->finalName );
143 <    
372 <    finalOut.open( finalName, ios::out | ios::trunc );
141 >
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 <               finalName );
147 >               entry_plug->finalName );
148        painCave.isFatal = 1;
149        simError();
150      }
151 <    
381 <    // finalOut.setf( ios::scientific );
382 <    
151 >
152   #ifdef IS_MPI
153    }
154 + #endif // is_mpi
155    
156 <  sprintf(checkPointMsg,"Opened file for final configuration\n");
157 <  MPIcheckPoint();  
156 >  fileStreams.push_back(&finalOut);  
157 >  writeFrame(fileStreams, currentTime);
158 >
159 > #ifdef IS_MPI
160 >  finalOut.close();
161 > #endif
162    
163 < #endif //is_mpi
163 > }
164  
165 + void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){
166 +
167 +  const int BUFFERSIZE = 2000;
168 +  const int MINIBUFFERSIZE = 100;
169 +
170 +  char tempBuffer[BUFFERSIZE];  
171 +  char writeLine[BUFFERSIZE];
172 +
173 +  int i, k;
174 +
175 + #ifdef IS_MPI
176    
177 +  /*********************************************************************
178 +   * Documentation?  You want DOCUMENTATION?
179 +   *
180 +   * Why all the potatoes below?  
181 +   *
182 +   * To make a long story short, the original version of DumpWriter
183 +   * worked in the most inefficient way possible.  Node 0 would
184 +   * poke each of the node for an individual atom's formatted data
185 +   * as node 0 worked its way down the global index. This was particularly
186 +   * inefficient since the method blocked all processors at every atom
187 +   * (and did it twice!).
188 +   *
189 +   * An intermediate version of DumpWriter could be described from Node
190 +   * zero's perspective as follows:
191 +   *
192 +   *  1) Have 100 of your friends stand in a circle.
193 +   *  2) When you say go, have all of them start tossing potatoes at
194 +   *     you (one at a time).
195 +   *  3) Catch the potatoes.
196 +   *
197 +   * It was an improvement, but MPI has buffers and caches that could
198 +   * best be described in this analogy as "potato nets", so there's no
199 +   * need to block the processors atom-by-atom.
200 +   *
201 +   * This new and improved DumpWriter works in an even more efficient
202 +   * way:
203 +   *
204 +   *  1) Have 100 of your friend stand in a circle.
205 +   *  2) When you say go, have them start tossing 5-pound bags of
206 +   *     potatoes at you.
207 +   *  3) Once you've caught a friend's bag of potatoes,
208 +   *     toss them a spud to let them know they can toss another bag.
209 +   *
210 +   * How's THAT for documentation?
211 +   *
212 +   *********************************************************************/
213 +
214 +  int *potatoes;
215 +  int myPotato;
216 +
217 +  int nProc;
218 +  int j, which_node, done, which_atom, local_index, currentIndex;
219 +  double atomData[13];
220 +  int isDirectional;
221 +  char* atomTypeString;
222 +  char MPIatomTypeString[MINIBUFFERSIZE];
223 +  int nObjects;
224 +  int msgLen; // the length of message actually recieved at master nodes
225 + #endif //is_mpi
226 +
227 +  double q[4], ji[3];
228 +  DirectionalAtom* dAtom;
229 +  double pos[3], vel[3];
230 +  int nTotObjects;
231 +  StuntDouble* sd;
232 +  char* molName;
233 +  vector<StuntDouble*> integrableObjects;
234 +  vector<StuntDouble*>::iterator iter;
235 +  nTotObjects = entry_plug->getTotIntegrableObjects();
236   #ifndef IS_MPI
393 –    
394 –  finalOut << nAtoms << "\n";
395 –    
396 –  finalOut << finalTime << ";\t"
397 –           << entry_plug->Hmat[0][0] << "\t"
398 –           << entry_plug->Hmat[1][0] << "\t"
399 –           << entry_plug->Hmat[2][0] << ";\t"
400 –    
401 –           << entry_plug->Hmat[0][1] << "\t"
402 –           << entry_plug->Hmat[1][1] << "\t"
403 –           << entry_plug->Hmat[2][1] << ";\t"
404 –    
405 –           << entry_plug->Hmat[0][2] << "\t"
406 –           << entry_plug->Hmat[1][2] << "\t"
407 –           << entry_plug->Hmat[2][2] << ";\n";
237    
238 <  for( i=0; i<nAtoms; i++ ){
239 <      
240 <    atoms[i]->getPos(pos);
241 <    atoms[i]->getVel(vel);
238 >  for(k = 0; k < outFile.size(); k++){
239 >    *outFile[k] << nTotObjects << "\n";
240 >
241 >    *outFile[k] << currentTime << ";\t"
242 >               << entry_plug->Hmat[0][0] << "\t"
243 >                     << entry_plug->Hmat[1][0] << "\t"
244 >                     << entry_plug->Hmat[2][0] << ";\t"
245 >              
246 >               << entry_plug->Hmat[0][1] << "\t"
247 >                     << entry_plug->Hmat[1][1] << "\t"
248 >                     << entry_plug->Hmat[2][1] << ";\t"
249 >
250 >                     << entry_plug->Hmat[0][2] << "\t"
251 >                     << entry_plug->Hmat[1][2] << "\t"
252 >                     << entry_plug->Hmat[2][2] << ";";
253 >
254 >    //write out additional parameters, such as chi and eta
255 >    *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
256 >  }
257 >  
258 >  for( i=0; i< entry_plug->n_mol; i++ ){
259 >
260 >    integrableObjects = entry_plug->molecules[i].getIntegrableObjects();
261 >    molName = (entry_plug->compStamps[entry_plug->molecules[i].getStampID()])->getID();
262      
263 <    sprintf( tempBuffer,
264 <             "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
265 <             atoms[i]->getType(),
266 <             pos[0],
418 <             pos[1],
419 <             pos[2],
420 <             vel[0],
421 <             vel[1],
422 <             vel[2]);
423 <    strcpy( writeLine, tempBuffer );
263 >    for( iter = integrableObjects.begin();iter !=  integrableObjects.end(); ++iter){
264 >      sd = *iter;
265 >      sd->getPos(pos);
266 >      sd->getVel(vel);
267  
425 –    if( atoms[i]->isDirectional() ){
426 –        
427 –      dAtom = (DirectionalAtom *)atoms[i];
428 –      dAtom->getQ( q );
429 –        
268        sprintf( tempBuffer,
269 <               "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
270 <               q[0],
271 <               q[1],
272 <               q[2],
273 <               q[3],
274 <               dAtom->getJx(),
275 <               dAtom->getJy(),
276 <               dAtom->getJz());
277 <      strcat( writeLine, tempBuffer );
269 >             "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
270 >             sd->getType(),
271 >             pos[0],
272 >             pos[1],
273 >             pos[2],
274 >             vel[0],
275 >             vel[1],
276 >             vel[2]);
277 >      strcpy( writeLine, tempBuffer );
278 >
279 >      if( sd->isDirectional() ){
280 >
281 >        sd->getQ( q );
282 >        sd->getJ( ji );
283 >
284 >        sprintf( tempBuffer,
285 >               "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
286 >               q[0],
287 >               q[1],
288 >               q[2],
289 >               q[3],
290 >                 ji[0],
291 >                 ji[1],
292 >                 ji[2]);
293 >        strcat( writeLine, tempBuffer );
294 >      }
295 >      else
296 >        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
297      }
441 –    else
442 –      strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
443 –      
444 –    finalOut << writeLine;
445 –  }
446 –  finalOut.flush();
447 –  finalOut.close();
298  
299 +    
300 +    for(k = 0; k < outFile.size(); k++)
301 +      *outFile[k] << writeLine;
302 + }
303 +
304   #else // is_mpi
305 +
306 +  /* code to find maximum tag value */
307    
308 <  // first thing first, suspend fatalities.
309 <  painCave.isEventLoop = 1;
308 >  int *tagub, flag, MAXTAG;
309 >  MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
310 >  if (flag) {
311 >    MAXTAG = *tagub;
312 >  } else {
313 >    MAXTAG = 32767;
314 >  }  
315  
454 –  int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
316    int haveError;
317  
318    MPI_Status istatus;
319 <  int *AtomToProcMap = mpiSim->getAtomToProcMap();
319 >  int nCurObj;
320 >  int *MolToProcMap = mpiSim->getMolToProcMap();
321  
322    // write out header and node 0's coordinates
323 <  
462 <  haveError = 0;
323 >
324    if( worldRank == 0 ){
325 <    finalOut << mpiSim->getTotAtoms() << "\n";
325 >
326 >    // Node 0 needs a list of the magic potatoes for each processor;
327 >
328 >    nProc = mpiSim->getNumberProcessors();
329 >    potatoes = new int[nProc];
330 >
331 >    //write out the comment lines
332 >    for (i = 0; i < nProc; i++)
333 >      potatoes[i] = 0;
334      
335 <    finalOut << finalTime << ";\t"
336 <             << entry_plug->Hmat[0][0] << "\t"
337 <             << entry_plug->Hmat[1][0] << "\t"
338 <             << entry_plug->Hmat[2][0] << ";\t"
335 >      for(k = 0; k < outFile.size(); k++){
336 >        *outFile[k] << nTotObjects << "\n";
337 >
338 >        *outFile[k] << currentTime << ";\t"
339 >                         << entry_plug->Hmat[0][0] << "\t"
340 >                         << entry_plug->Hmat[1][0] << "\t"
341 >                         << entry_plug->Hmat[2][0] << ";\t"
342 >
343 >                         << entry_plug->Hmat[0][1] << "\t"
344 >                         << entry_plug->Hmat[1][1] << "\t"
345 >                         << entry_plug->Hmat[2][1] << ";\t"
346 >
347 >                         << entry_plug->Hmat[0][2] << "\t"
348 >                         << entry_plug->Hmat[1][2] << "\t"
349 >                         << entry_plug->Hmat[2][2] << ";";
350 >  
351 >        *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
352 >    }
353 >
354 >    currentIndex = 0;
355 >
356 >    for (i = 0 ; i < mpiSim->getTotNmol(); i++ ) {
357        
358 <             << entry_plug->Hmat[0][1] << "\t"
472 <             << entry_plug->Hmat[1][1] << "\t"
473 <             << entry_plug->Hmat[2][1] << ";\t"
358 >      // Get the Node number which has this atom;
359        
360 <             << entry_plug->Hmat[0][2] << "\t"
476 <             << entry_plug->Hmat[1][2] << "\t"
477 <             << entry_plug->Hmat[2][2] << ";\n";
478 <    
479 <    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
480 <      // Get the Node number which has this molecule:
360 >      which_node = MolToProcMap[i];
361        
362 <      which_node = AtomToProcMap[i];    
363 <      
364 <      if (which_node == mpiSim->getMyNode()) {
362 >      if (which_node != 0) {
363 >        
364 >        if (potatoes[which_node] + 1 >= MAXTAG) {
365 >          // The potato was going to exceed the maximum value,
366 >          // so wrap this processor potato back to 0:        
367  
368 <        which_atom = i;
369 <        local_index=-1;        
370 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
489 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
368 >          potatoes[which_node] = 0;          
369 >          MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
370 >          
371          }
491 –        if (local_index != -1) {    
372  
373 <          atoms[local_index]->getPos(pos);
494 <          atoms[local_index]->getVel(vel);
495 <          
496 <          sprintf( tempBuffer,
497 <                   "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
498 <                   atoms[local_index]->getType(),
499 <                   pos[0],
500 <                   pos[1],
501 <                   pos[2],
502 <                   vel[0],
503 <                   vel[1],
504 <                   vel[2]);
505 <          strcpy( writeLine, tempBuffer );
506 <          
507 <          if( atoms[local_index]->isDirectional() ){
508 <            
509 <            dAtom = (DirectionalAtom *)atoms[local_index];
510 <            dAtom->getQ( q );
511 <            
512 <            sprintf( tempBuffer,
513 <                     "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
514 <                     q[0],
515 <                     q[1],
516 <                     q[2],
517 <                     q[3],
518 <                     dAtom->getJx(),
519 <                     dAtom->getJy(),
520 <                     dAtom->getJz());
521 <            strcat( writeLine, tempBuffer );
522 <          }
523 <          else
524 <            strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );      
525 <        }
526 <        else {
527 <          sprintf(painCave.errMsg,
528 <                  "Atom %d not found on processor %d\n",
529 <                  i, worldRank );
530 <          haveError= 1;
531 <          simError();
532 <        }
373 >        myPotato = potatoes[which_node];        
374  
375 <        if(haveError) nodeZeroError();
376 <    
377 <      }
378 <      else {
375 >        //recieve the number of integrableObject in current molecule
376 >        MPI_Recv(&nCurObj, 1, MPI_INT, which_node,
377 >                 myPotato, MPI_COMM_WORLD, &istatus);
378 >        myPotato++;
379          
380 <        myStatus = 1;
381 <        MPI_Send(&myStatus, 1, MPI_INT, which_node,
382 <                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
383 <        MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
384 <                 MPI_COMM_WORLD);
385 <        MPI_Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node,
386 <                 TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
387 <        MPI_Recv(&myStatus, 1, MPI_INT, which_node,
388 <                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
389 <        
390 <        if(!myStatus) nodeZeroError();
380 >        for(int l = 0; l < nCurObj; l++){
381 >
382 >          if (potatoes[which_node] + 2 >= MAXTAG) {
383 >            // The potato was going to exceed the maximum value,
384 >            // so wrap this processor potato back to 0:        
385 >
386 >            potatoes[which_node] = 0;          
387 >            MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
388 >            
389 >          }
390 >
391 >          MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
392 >          myPotato, MPI_COMM_WORLD, &istatus);
393 >
394 >          atomTypeString = MPIatomTypeString;
395 >
396 >          myPotato++;
397 >
398 >          MPI_Recv(atomData, 13, MPI_DOUBLE, which_node, myPotato, MPI_COMM_WORLD, &istatus);
399 >          myPotato++;
400 >
401 >          MPI_Get_count(&istatus, MPI_DOUBLE, &msgLen);
402 >
403 >          if(msgLen  == 13)
404 >            isDirectional = 1;
405 >          else
406 >            isDirectional = 0;
407 >            
408 >        }
409 >        potatoes[which_node] = myPotato;
410 >
411 >      } else {
412 >        
413 >        haveError = 0;
414 >        
415 >            local_index = indexArray[currentIndex].first;        
416 >
417 >        integrableObjects = (entry_plug->molecules[local_index]).getIntegrableObjects();
418 >
419 >        for(iter= integrableObjects.begin(); iter != integrableObjects.end(); ++iter){    
420 >                sd = *iter;
421 >            atomTypeString = sd->getType();
422 >            
423 >            sd->getPos(pos);
424 >            sd->getVel(vel);          
425 >          
426 >            atomData[0] = pos[0];
427 >            atomData[1] = pos[1];
428 >            atomData[2] = pos[2];
429 >
430 >            atomData[3] = vel[0];
431 >            atomData[4] = vel[1];
432 >            atomData[5] = vel[2];
433 >              
434 >            isDirectional = 0;
435 >
436 >            if( sd->isDirectional() ){
437 >
438 >              isDirectional = 1;
439 >                
440 >              sd->getQ( q );
441 >              sd->getJ( ji );
442 >
443 >              for (int j = 0; j < 6 ; j++)
444 >                atomData[j] = atomData[j];            
445 >              
446 >              atomData[6] = q[0];
447 >              atomData[7] = q[1];
448 >              atomData[8] = q[2];
449 >              atomData[9] = q[3];
450 >              
451 >              atomData[10] = ji[0];
452 >              atomData[11] = ji[1];
453 >              atomData[12] = ji[2];
454 >            }
455 >            
456 >        }
457 >        
458 >      currentIndex++;
459        }
460 +      // If we've survived to here, format the line:
461        
462 <      finalOut << writeLine;
463 <    }
464 <    
465 <    // kill everyone off:
466 <    myStatus = -1;
467 <    for (j = 0; j < mpiSim->getNumberProcessors(); j++) {      
468 <      MPI_Send(&myStatus, 1, MPI_INT, j,
469 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
462 >      if (!isDirectional) {
463 >        
464 >        sprintf( writeLine,
465 >                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
466 >                 atomTypeString,
467 >                 atomData[0],
468 >                 atomData[1],
469 >                 atomData[2],
470 >                 atomData[3],
471 >                 atomData[4],
472 >                 atomData[5]);
473 >        
474 >        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
475 >        
476 >      } else {
477 >        
478 >        sprintf( writeLine,
479 >                 "%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",
480 >                 atomTypeString,
481 >                 atomData[0],
482 >                 atomData[1],
483 >                 atomData[2],
484 >                 atomData[3],
485 >                 atomData[4],
486 >                 atomData[5],
487 >                 atomData[6],
488 >                 atomData[7],
489 >                 atomData[8],
490 >                 atomData[9],
491 >                 atomData[10],
492 >                 atomData[11],
493 >                 atomData[12]);
494 >        
495 >      }
496 >      
497 >      for(k = 0; k < outFile.size(); k++)
498 >        *outFile[k] << writeLine;
499      }
561 –
562 –  } else {
500      
501 <    done = 0;
502 <    while (!done) {
501 >    for(k = 0; k < outFile.size(); k++)
502 >      outFile[k]->flush();
503 >    
504 >    sprintf( checkPointMsg,
505 >             "Sucessfully took a dump.\n");
506 >    
507 >    MPIcheckPoint();        
508 >    
509 >    delete[] potatoes;
510 >    
511 >  } else {
512  
513 <      MPI_Recv(&myStatus, 1, MPI_INT, 0,
514 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
513 >    // worldRank != 0, so I'm a remote node.  
514 >
515 >    // Set my magic potato to 0:
516 >
517 >    myPotato = 0;
518 >    currentIndex = 0;
519 >    
520 >    for (i = 0 ; i < mpiSim->getTotNmol(); i++ ) {
521        
522 <      if(!myStatus) anonymousNodeDie();
522 >      // Am I the node which has this integrableObject?
523        
524 <      if(myStatus < 0) break;
573 <      
574 <      MPI_Recv(&which_atom, 1, MPI_INT, 0,
575 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
576 <      
577 <      myStatus = 1;
578 <      local_index=-1;        
579 <      for (j=0; j < mpiSim->getMyNlocal(); j++) {
580 <        if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
581 <      }
582 <      if (local_index != -1) {
524 >      if (MolToProcMap[i] == worldRank) {
525  
584 –        atoms[local_index]->getPos(pos);
585 –        atoms[local_index]->getVel(vel);
526  
527 <        //format the line
588 <        sprintf( tempBuffer,
589 <                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
590 <                 atoms[local_index]->getType(),
591 <                 pos[0],
592 <                 pos[1],
593 <                 pos[2],
594 <                 vel[0],
595 <                 vel[1],
596 <                 vel[2]); // check here.
597 <        strcpy( writeLine, tempBuffer );
598 <        
599 <        if( atoms[local_index]->isDirectional() ){
527 >        if (myPotato + 1 >= MAXTAG) {
528            
529 <          dAtom = (DirectionalAtom *)atoms[local_index];
530 <          dAtom->getQ( q );
529 >          // The potato was going to exceed the maximum value,
530 >          // so wrap this processor potato back to 0 (and block until
531 >          // node 0 says we can go:
532            
533 <          sprintf( tempBuffer,
534 <                   "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
535 <                   q[0],
536 <                   q[1],
537 <                   q[2],
538 <                   q[3],
539 <                   dAtom->getJx(),
540 <                   dAtom->getJy(),
541 <                   dAtom->getJz());
542 <          strcat( writeLine, tempBuffer );
543 <        }
544 <        else{
545 <          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
546 <        }
547 <      }
548 <      else {
549 <        sprintf(painCave.errMsg,
550 <                "Atom %d not found on processor %d\n",
551 <                which_atom, worldRank );
552 <        myStatus = 0;
553 <        simError();
554 <        
555 <        strcpy( writeLine, "Hello, I'm an error.\n");
533 >          MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
534 >          
535 >        }
536 >
537 >          local_index = indexArray[currentIndex].first;        
538 >          integrableObjects = entry_plug->molecules[local_index].getIntegrableObjects();
539 >          
540 >          nCurObj = integrableObjects.size();
541 >                      
542 >          MPI_Send(&nCurObj, 1, MPI_INT, 0,
543 >                             myPotato, MPI_COMM_WORLD);
544 >          myPotato++;
545 >
546 >          for( iter = integrableObjects.begin(); iter  != integrableObjects.end(); iter++){
547 >
548 >            if (myPotato + 2 >= MAXTAG) {
549 >          
550 >              // The potato was going to exceed the maximum value,
551 >              // so wrap this processor potato back to 0 (and block until
552 >              // node 0 says we can go:
553 >          
554 >              MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
555 >              
556 >            }
557 >            
558 >            sd = *iter;
559 >            
560 >            atomTypeString = sd->getType();
561 >
562 >            sd->getPos(pos);
563 >            sd->getVel(vel);
564 >
565 >            atomData[0] = pos[0];
566 >            atomData[1] = pos[1];
567 >            atomData[2] = pos[2];
568 >
569 >            atomData[3] = vel[0];
570 >            atomData[4] = vel[1];
571 >            atomData[5] = vel[2];
572 >              
573 >            isDirectional = 0;
574 >
575 >            if( sd->isDirectional() ){
576 >
577 >                isDirectional = 1;
578 >                
579 >                sd->getQ( q );
580 >                sd->getJ( ji );
581 >                
582 >                
583 >                atomData[6] = q[0];
584 >                atomData[7] = q[1];
585 >                atomData[8] = q[2];
586 >                atomData[9] = q[3];
587 >      
588 >                atomData[10] = ji[0];
589 >                atomData[11] = ji[1];
590 >                atomData[12] = ji[2];
591 >              }
592 >
593 >            
594 >            strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
595 >
596 >            // null terminate the string before sending (just in case):
597 >            MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
598 >
599 >            MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
600 >                             myPotato, MPI_COMM_WORLD);
601 >            
602 >            myPotato++;
603 >            
604 >            if (isDirectional) {
605 >
606 >              MPI_Send(atomData, 13, MPI_DOUBLE, 0,
607 >                       myPotato, MPI_COMM_WORLD);
608 >              
609 >            } else {
610 >
611 >              MPI_Send(atomData, 6, MPI_DOUBLE, 0,
612 >                       myPotato, MPI_COMM_WORLD);
613 >            }
614 >
615 >            myPotato++;  
616 >
617 >          }
618 >
619 >          currentIndex++;    
620 >          
621 >        }
622 >      
623        }
624  
625 <      MPI_Send(writeLine, BUFFERSIZE, MPI_CHAR, 0,
626 <               TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
627 <      MPI_Send( &myStatus, 1, MPI_INT, 0,
628 <                TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
625 >    sprintf( checkPointMsg,
626 >             "Sucessfully took a dump.\n");
627 >    MPIcheckPoint();                
628 >    
629      }
630 <  }
631 <  finalOut.flush();
636 <  sprintf( checkPointMsg,
637 <           "Sucessfully took a dump.\n");
638 <  MPIcheckPoint();
630 >
631 >
632    
640 –  if( worldRank == 0 ) finalOut.close();    
633   #endif // is_mpi
634   }
635  
644 –
645 –
636   #ifdef IS_MPI
637  
638   // a couple of functions to let us escape the write loop
639  
640 < void dWrite::nodeZeroError( void ){
651 <  int j, myStatus;
652 <  
653 <  myStatus = 0;
654 <  for (j = 0; j < mpiSim->getNumberProcessors(); j++) {      
655 <    MPI_Send( &myStatus, 1, MPI_INT, j,
656 <              TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
657 <  }  
658 <  
640 > void dWrite::DieDieDie( void ){
641  
642    MPI_Finalize();
643    exit (0);
662 –  
644   }
645  
665 – void dWrite::anonymousNodeDie( void ){
666 –
667 –  MPI_Finalize();
668 –  exit (0);
669 – }
670 –
646   #endif //is_mpi

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