ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/group/trunk/OOPSE/libmdtools/DumpWriter.cpp
(Generate patch)

Comparing trunk/OOPSE/libmdtools/DumpWriter.cpp (file contents):
Revision 437 by chuckv, Fri Mar 28 22:34:02 2003 UTC vs.
Revision 1000 by tim, Fri Jan 30 21:47:22 2004 UTC

# Line 1 | Line 1
1 < #include <cstring>
1 > #define _FILE_OFFSET_BITS 64
2 >
3 > #include <string.h>
4   #include <iostream>
5   #include <fstream>
6 + #include <algorithm>
7 + #include <utility>
8  
9   #ifdef IS_MPI
10   #include <mpi.h>
7 – #include <mpi++.h>
11   #include "mpiSimulation.hpp"
12 < #define TAKE_THIS_TAG_CHAR 1
13 < #define TAKE_THIS_TAG_INT 2
12 >
13 > namespace dWrite{
14 >  void DieDieDie( void );
15 > }
16 >
17 > using namespace dWrite;
18   #endif //is_mpi
19  
20   #include "ReadWrite.hpp"
# Line 20 | Line 27 | DumpWriter::DumpWriter( SimInfo* the_entry_plug ){
27   #ifdef IS_MPI
28    if(worldRank == 0 ){
29   #endif // is_mpi
30 <    
31 <
32 <    
33 <    strcpy( outName, entry_plug->sampleName );
34 <    
28 <    outFile.open(outName, ios::out | ios::trunc );
29 <    
30 <    if( !outFile ){
31 <      
30 >
31 >    dumpFile.open(entry_plug->sampleName, ios::out | ios::trunc );
32 >
33 >    if( !dumpFile ){
34 >
35        sprintf( painCave.errMsg,
36                 "Could not open \"%s\" for dump output.\n",
37 <               outName);
37 >               entry_plug->sampleName);
38        painCave.isFatal = 1;
39        simError();
40      }
38 –  
39 –    //outFile.setf( ios::scientific );
41  
42   #ifdef IS_MPI
43    }
44  
45 +  //sort the local atoms by global index
46 +  sortByGlobalIndex();
47 +  
48    sprintf( checkPointMsg,
49             "Sucessfully opened output file for dumping.\n");
50    MPIcheckPoint();
# Line 53 | Line 57 | DumpWriter::~DumpWriter( ){
57    if(worldRank == 0 ){
58   #endif // is_mpi
59  
60 <    outFile.close();
60 >    dumpFile.close();
61  
62   #ifdef IS_MPI
63    }
64   #endif // is_mpi
65   }
66  
67 < void DumpWriter::writeDump( double currentTime ){
67 > #ifdef IS_MPI
68 >
69 > /**
70 > * A hook function to load balancing
71 > */
72 >
73 > void DumpWriter::update(){
74 >  sortByGlobalIndex();          
75 > }
76    
77 <  const int BUFFERSIZE = 2000;
78 <  char tempBuffer[BUFFERSIZE];
79 <  char writeLine[BUFFERSIZE];
77 > /**
78 > * Auxiliary sorting function
79 > */
80 >
81 > bool indexSortingCriterion(const pair<int, int>& p1, const pair<int, int>& p2){
82 >  return p1.second < p2.second;
83 > }
84  
85 <  int i, j, which_node, done, game_over, which_atom, local_index;
86 <  double q[4];
87 <  DirectionalAtom* dAtom;
88 <  int nAtoms = entry_plug->n_atoms;
85 > /**
86 > * Sorting the local index by global index
87 > */
88 >
89 > void DumpWriter::sortByGlobalIndex(){
90    Atom** atoms = entry_plug->atoms;
91 <    
91 >  
92 >  indexArray.clear();
93 >  
94 >  for(int i = 0; i < mpiSim->getMyNlocal();i++)
95 >    indexArray.push_back(make_pair(i, atoms[i]->getGlobalIndex()));
96 >  
97 >  sort(indexArray.begin(), indexArray.end(), indexSortingCriterion);    
98 > }
99  
100 < #ifndef IS_MPI
77 <    
78 <  outFile << nAtoms << "\n";
79 <    
80 <  outFile << currentTime << "\t"
81 <          << entry_plug->box_x << "\t"
82 <          << entry_plug->box_y << "\t"
83 <          << entry_plug->box_z << "\n";
84 <    
85 <  for( i=0; i<nAtoms; i++ ){
86 <      
100 > #endif
101  
102 <    sprintf( tempBuffer,
89 <             "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
90 <             atoms[i]->getType(),
91 <             atoms[i]->getX(),
92 <             atoms[i]->getY(),
93 <             atoms[i]->getZ(),
94 <             atoms[i]->get_vx(),
95 <             atoms[i]->get_vy(),
96 <             atoms[i]->get_vz());
97 <    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(),
112 <               dAtom->getJz());
113 <      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
116 <      strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
117 <      
118 <    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 <  MPI::Status istatus;
125 <  int *AtomToProcMap = mpiSim->getAtomToProcMap();
126 <  
127 <  // write out header and node 0's coordinates
128 <  
129 <  if( worldRank == 0 ){
130 <    outFile << mpiSim->getTotAtoms() << "\n";
131 <    
132 <    outFile << currentTime << "\t"
133 <            << entry_plug->box_x << "\t"
134 <            << entry_plug->box_y << "\t"
135 <            << entry_plug->box_z << "\n";
136 <    outFile.flush();
137 <    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
138 <      // Get the Node number which has this atom;
139 <      
140 <      which_node = AtomToProcMap[i];    
141 <      
142 <      if (which_node == 0 ) {
143 <        
144 <        which_atom = i;
145 <        local_index=-1;        
146 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
147 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
148 <        }
149 <        if (local_index != -1) {
150 <          //format the line
151 <          sprintf( tempBuffer,
152 <                   "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
153 <                   atoms[local_index]->getType(),
154 <                   atoms[local_index]->getX(),
155 <                   atoms[local_index]->getY(),
156 <                   atoms[local_index]->getZ(),
157 <                   atoms[local_index]->get_vx(),
158 <                   atoms[local_index]->get_vy(),
159 <                   atoms[local_index]->get_vz()); // check here.
160 <          strcpy( writeLine, tempBuffer );
161 <          
162 <          if( atoms[local_index]->isDirectional() ){
163 <            
164 <            dAtom = (DirectionalAtom *)atoms[local_index];
165 <            dAtom->getQ( q );
166 <            
167 <            sprintf( tempBuffer,
168 <                     "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
169 <                     q[0],
170 <                     q[1],
171 <                     q[2],
172 <                     q[3],
173 <                     dAtom->getJx(),
174 <                     dAtom->getJy(),
175 <                     dAtom->getJz());
176 <            strcat( writeLine, tempBuffer );
177 <            
178 <          }
179 <          else
180 <            strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );      
181 <        }
182 <        else {
183 <          strcpy( writeLine, "ATOM NOT FOUND ON THIS PROCESSOR");
184 <        }
185 <      }
186 <      else {
187 <        
188 <        //std::cerr << "node 0: sending node " << which_node << " request for atom " << i << "\n";
189 <        MPI::COMM_WORLD.Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT);
190 <        //std::cerr << "node 0: sent!\n";
191 <        MPI::COMM_WORLD.Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node,
192 <                             TAKE_THIS_TAG_CHAR, istatus);
193 <        //std::cerr << "node 0: got this line: " << writeLine;
194 <      }
195 <      
196 <      outFile << writeLine;
197 <      outFile.flush();
198 <    }
199 <    
200 <    // kill everyone off:
201 <    game_over = -1;
202 <    for (j = 0; j < mpiSim->getNumberProcessors(); j++) {      
203 <      MPI::COMM_WORLD.Send(&game_over, 1, MPI_INT, j, TAKE_THIS_TAG_INT);
204 <    }
125 >  writeFrame(fileStreams, currentTime);
126  
127 <  } else {
128 <    
129 <    done = 0;
130 <    while (!done) {
210 <      //std::cerr << "node: " << mpiSim->getMyNode() << " Waiting for receive \n";
211 <      MPI::COMM_WORLD.Recv(&which_atom, 1, MPI_INT, 0,
212 <                           TAKE_THIS_TAG_INT, istatus);
213 <      //std::cerr << "node: " << mpiSim->getMyNode() << " got request for atom " << which_atom << "\n";
214 <      if (which_atom == -1) {
215 <        done=1;
216 <        continue;
217 <      } else {
218 <        local_index=-1;        
219 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
220 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
221 <        }
222 <        if (local_index != -1) {
223 <          //format the line
224 <          sprintf( tempBuffer,
225 <                   "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
226 <                   atoms[local_index]->getType(),
227 <                   atoms[local_index]->getX(),
228 <                   atoms[local_index]->getY(),
229 <                   atoms[local_index]->getZ(),
230 <                   atoms[local_index]->get_vx(),
231 <                   atoms[local_index]->get_vy(),
232 <                   atoms[local_index]->get_vz()); // check here.
233 <          strcpy( writeLine, tempBuffer );
234 <          
235 <          if( atoms[local_index]->isDirectional() ){
236 <            
237 <            dAtom = (DirectionalAtom *)atoms[local_index];
238 <            dAtom->getQ( q );
239 <            
240 <            sprintf( tempBuffer,
241 <                     "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
242 <                     q[0],
243 <                     q[1],
244 <                     q[2],
245 <                     q[3],
246 <                     dAtom->getJx(),
247 <                     dAtom->getJy(),
248 <                     dAtom->getJz());
249 <            strcat( writeLine, tempBuffer );
250 <          }
251 <          else
252 <            strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
253 <          // std::cerr << "node: " << mpiSim->getMyNode() << " sending this line" << writeLine;
254 <          MPI::COMM_WORLD.Send(writeLine, BUFFERSIZE, MPI_CHAR, 0,
255 <                               TAKE_THIS_TAG_CHAR);
256 <        } else {
257 <          strcpy( writeLine, "ATOM NOT FOUND ON THIS PROCESSOR");
258 <          MPI::COMM_WORLD.Send(writeLine, BUFFERSIZE, MPI_CHAR, 0,
259 <                               TAKE_THIS_TAG_CHAR);
260 <        }
261 <      }
262 <    }
263 <  }  
264 <  outFile.flush();
265 <  sprintf( checkPointMsg,
266 <           "Sucessfully took a dump.\n");
267 <  MPIcheckPoint();
268 < #endif // is_mpi
127 > #ifdef IS_MPI
128 >  finalOut.close();
129 > #endif
130 >        
131   }
132  
133 < void DumpWriter::writeFinal(){
133 > void DumpWriter::writeFinal(double currentTime){
134  
273 –  char finalName[500];
135    ofstream finalOut;
136 +  vector<ofstream*> fileStreams;
137  
276 –  const int BUFFERSIZE = 2000;
277 –  char tempBuffer[BUFFERSIZE];
278 –  char writeLine[BUFFERSIZE];  
279 –
280 –  double q[4];
281 –  DirectionalAtom* dAtom;
282 –  int nAtoms = entry_plug->n_atoms;
283 –  Atom** atoms = entry_plug->atoms;
284 –  int i, j, which_node, done, game_over, which_atom, local_index;
285 –  
286 –  
138   #ifdef IS_MPI
139    if(worldRank == 0 ){
140   #endif // is_mpi
141 <    
142 <    strcpy( finalName, entry_plug->finalName );
143 <    
293 <    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 <    
302 <    // finalOut.setf( ios::scientific );
303 <    
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 atomData6[6];
220 +  double atomData13[13];
221 +  int isDirectional;
222 +  char* atomTypeString;
223 +  char MPIatomTypeString[MINIBUFFERSIZE];
224 +
225 + #else //is_mpi
226 +  int nAtoms = entry_plug->n_atoms;
227 + #endif //is_mpi
228 +
229 +  double q[4];
230 +  DirectionalAtom* dAtom;
231 +  Atom** atoms = entry_plug->atoms;
232 +  double pos[3], vel[3];
233 +
234   #ifndef IS_MPI
314 –    
315 –  finalOut << nAtoms << "\n";
316 –    
317 –  finalOut << entry_plug->box_x << "\t"
318 –           << entry_plug->box_y << "\t"
319 –           << entry_plug->box_z << "\n";
235    
236 +  for(k = 0; k < outFile.size(); k++){
237 +    *outFile[k] << nAtoms << "\n";
238 +
239 +    *outFile[k] << currentTime << ";\t"
240 +               << entry_plug->Hmat[0][0] << "\t"
241 +                     << entry_plug->Hmat[1][0] << "\t"
242 +                     << entry_plug->Hmat[2][0] << ";\t"
243 +              
244 +               << entry_plug->Hmat[0][1] << "\t"
245 +                     << entry_plug->Hmat[1][1] << "\t"
246 +                     << entry_plug->Hmat[2][1] << ";\t"
247 +
248 +                     << entry_plug->Hmat[0][2] << "\t"
249 +                     << entry_plug->Hmat[1][2] << "\t"
250 +                     << entry_plug->Hmat[2][2] << ";";
251 +
252 +    //write out additional parameters, such as chi and eta
253 +    *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
254 +  }
255 +  
256    for( i=0; i<nAtoms; i++ ){
257 <      
257 >
258 >    atoms[i]->getPos(pos);
259 >    atoms[i]->getVel(vel);
260 >
261      sprintf( tempBuffer,
262               "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
263               atoms[i]->getType(),
264 <             atoms[i]->getX(),
265 <             atoms[i]->getY(),
266 <             atoms[i]->getZ(),
267 <             atoms[i]->get_vx(),
268 <             atoms[i]->get_vy(),
269 <             atoms[i]->get_vz());
264 >             pos[0],
265 >             pos[1],
266 >             pos[2],
267 >             vel[0],
268 >             vel[1],
269 >             vel[2]);
270      strcpy( writeLine, tempBuffer );
271  
272      if( atoms[i]->isDirectional() ){
273 <        
273 >
274        dAtom = (DirectionalAtom *)atoms[i];
275        dAtom->getQ( q );
276 <        
276 >
277        sprintf( tempBuffer,
278                 "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
279                 q[0],
# Line 349 | Line 287 | void DumpWriter::writeFinal(){
287      }
288      else
289        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
290 <      
291 <    finalOut << writeLine;
290 >
291 >    for(k = 0; k < outFile.size(); k++)
292 >      *outFile[k] << writeLine;
293    }
355 –  finalOut.flush();
356 –  finalOut.close();
294  
295   #else // is_mpi
296 +
297 +  /* code to find maximum tag value */
298    
299 <  MPI::Status istatus;
299 >  int *tagub, flag, MAXTAG;
300 >  MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
301 >  if (flag) {
302 >    MAXTAG = *tagub;
303 >  } else {
304 >    MAXTAG = 32767;
305 >  }  
306 >
307 >  int haveError;
308 >
309 >  MPI_Status istatus;
310    int *AtomToProcMap = mpiSim->getAtomToProcMap();
311  
312    // write out header and node 0's coordinates
313 <  
313 >
314    if( worldRank == 0 ){
315 <    finalOut << mpiSim->getTotAtoms() << "\n";
315 >
316 >    // Node 0 needs a list of the magic potatoes for each processor;
317 >
318 >    nProc = mpiSim->getNumberProcessors();
319 >    potatoes = new int[nProc];
320 >
321 >    //write out the comment lines
322 >    for (i = 0; i < nProc; i++)
323 >      potatoes[i] = 0;
324      
325 <    finalOut << entry_plug->box_x << "\t"
326 <            << entry_plug->box_y << "\t"
327 <            << entry_plug->box_z << "\n";
328 <    
325 >      for(k = 0; k < outFile.size(); k++){
326 >        *outFile[k] << mpiSim->getTotAtoms() << "\n";
327 >
328 >        *outFile[k] << currentTime << ";\t"
329 >                         << entry_plug->Hmat[0][0] << "\t"
330 >                         << entry_plug->Hmat[1][0] << "\t"
331 >                         << entry_plug->Hmat[2][0] << ";\t"
332 >
333 >                         << entry_plug->Hmat[0][1] << "\t"
334 >                         << entry_plug->Hmat[1][1] << "\t"
335 >                         << entry_plug->Hmat[2][1] << ";\t"
336 >
337 >                         << entry_plug->Hmat[0][2] << "\t"
338 >                         << entry_plug->Hmat[1][2] << "\t"
339 >                         << entry_plug->Hmat[2][2] << ";";
340 >  
341 >        *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
342 >    }
343 >
344 >    currentIndex = 0;
345 >
346      for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
373 –      // Get the Node number which has this molecule:
347        
348 <      which_node = AtomToProcMap[i];    
348 >      // Get the Node number which has this atom;
349        
350 <      if (which_node == mpiSim->getMyNode()) {
350 >      which_node = AtomToProcMap[i];
351 >      
352 >      if (which_node != 0) {
353  
354 <        which_atom = i;
355 <        local_index=-1;        
356 <        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
357 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
354 >        if (potatoes[which_node] + 3 >= MAXTAG) {
355 >          // The potato was going to exceed the maximum value,
356 >          // so wrap this processor potato back to 0:        
357 >
358 >          potatoes[which_node] = 0;          
359 >          MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
360 >          
361          }
362 <        if (local_index != -1) {        
363 <          sprintf( tempBuffer,
364 <                   "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
365 <                   atoms[local_index]->getType(),
366 <                   atoms[local_index]->getX(),
367 <                   atoms[local_index]->getY(),
368 <                   atoms[local_index]->getZ(),
369 <                   atoms[local_index]->get_vx(),
370 <                   atoms[local_index]->get_vy(),
371 <                   atoms[local_index]->get_vz());
372 <          strcpy( writeLine, tempBuffer );
373 <          
374 <          if( atoms[local_index]->isDirectional() ){
362 >
363 >        myPotato = potatoes[which_node];        
364 >        
365 >        MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
366 >                 myPotato, MPI_COMM_WORLD, &istatus);
367 >        
368 >        atomTypeString = MPIatomTypeString;
369 >        
370 >        myPotato++;
371 >
372 >        MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
373 >                 myPotato, MPI_COMM_WORLD, &istatus);
374 >              
375 >        myPotato++;
376 >
377 >        if (isDirectional) {          
378 >          MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node,
379 >                   myPotato, MPI_COMM_WORLD, &istatus);
380 >        } else {
381 >          MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node,
382 >                   myPotato, MPI_COMM_WORLD, &istatus);          
383 >        }
384 >        
385 >        myPotato++;
386 >        potatoes[which_node] = myPotato;
387 >
388 >      } else {
389 >        
390 >        haveError = 0;
391 >        which_atom = i;
392 >        
393 >          local_index = indexArray[currentIndex].first;        
394 >          
395 >          if (which_atom == indexArray[currentIndex].second) {
396              
397 <            dAtom = (DirectionalAtom *)atoms[local_index];
399 <            dAtom->getQ( q );
397 >            atomTypeString = atoms[local_index]->getType();
398              
399 <            sprintf( tempBuffer,
400 <                     "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
401 <                     q[0],
402 <                     q[1],
403 <                     q[2],
404 <                     q[3],
405 <                     dAtom->getJx(),
406 <                     dAtom->getJy(),
407 <                     dAtom->getJz());
408 <            strcat( writeLine, tempBuffer );
409 <          }
410 <          else
411 <            strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );      
412 <        }
413 <        else {
414 <          strcpy( writeLine, "ATOM NOT FOUND ON THIS PROCESSOR");
415 <        }
416 <    
399 >          atoms[local_index]->getPos(pos);
400 >          atoms[local_index]->getVel(vel);          
401 >          
402 >          atomData6[0] = pos[0];
403 >          atomData6[1] = pos[1];
404 >          atomData6[2] = pos[2];
405 >
406 >          atomData6[3] = vel[0];
407 >          atomData6[4] = vel[1];
408 >          atomData6[5] = vel[2];
409 >          
410 >          isDirectional = 0;
411 >
412 >          if( atoms[local_index]->isDirectional() ){
413 >
414 >            isDirectional = 1;
415 >            
416 >            dAtom = (DirectionalAtom *)atoms[local_index];
417 >            dAtom->getQ( q );
418 >
419 >            for (int j = 0; j < 6 ; j++)
420 >              atomData13[j] = atomData6[j];            
421 >            
422 >            atomData13[6] = q[0];
423 >            atomData13[7] = q[1];
424 >            atomData13[8] = q[2];
425 >            atomData13[9] = q[3];
426 >            
427 >            atomData13[10] = dAtom->getJx();
428 >            atomData13[11] = dAtom->getJy();
429 >            atomData13[12] = dAtom->getJz();
430 >          }
431 >          
432 >        } else {
433 >          sprintf(painCave.errMsg,
434 >                  "Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n",
435 >                  which_atom, worldRank, currentIndex, local_index );
436 >          haveError= 1;
437 >          simError();
438 >        }
439 >        
440 >        if(haveError) DieDieDie();
441 >        
442 >        currentIndex++;
443 >      }
444 >      // If we've survived to here, format the line:
445 >      
446 >      if (!isDirectional) {
447 >        
448 >        sprintf( writeLine,
449 >                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
450 >                 atomTypeString,
451 >                 atomData6[0],
452 >                 atomData6[1],
453 >                 atomData6[2],
454 >                 atomData6[3],
455 >                 atomData6[4],
456 >                 atomData6[5]);
457 >        
458 >        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
459 >        
460        } else {
461 +        
462 +        sprintf( writeLine,
463 +                 "%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",
464 +                 atomTypeString,
465 +                 atomData13[0],
466 +                 atomData13[1],
467 +                 atomData13[2],
468 +                 atomData13[3],
469 +                 atomData13[4],
470 +                 atomData13[5],
471 +                 atomData13[6],
472 +                 atomData13[7],
473 +                 atomData13[8],
474 +                 atomData13[9],
475 +                 atomData13[10],
476 +                 atomData13[11],
477 +                 atomData13[12]);
478          
421 –        MPI::COMM_WORLD.Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT);
422 –        MPI::COMM_WORLD.Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node,
423 –                                TAKE_THIS_TAG_CHAR, istatus);
479        }
480        
481 <      finalOut << writeLine;
481 >      for(k = 0; k < outFile.size(); k++)
482 >        *outFile[k] << writeLine;
483      }
484      
485 <    // kill everyone off:
486 <    game_over = -1;
431 <    for (j = 0; j < mpiSim->getNumberProcessors(); j++) {
432 <      MPI::COMM_WORLD.Send(&game_over, 1, MPI_INT, j, TAKE_THIS_TAG_INT);
433 <    }
434 <
435 <  } else {
485 >    for(k = 0; k < outFile.size(); k++)
486 >      outFile[k]->flush();
487      
488 <    done = 0;
489 <    while (!done) {
490 <      MPI::COMM_WORLD.Recv(&which_atom, 1, MPI_INT, 0,
491 <                           TAKE_THIS_TAG_INT, istatus);
488 >    sprintf( checkPointMsg,
489 >             "Sucessfully took a dump.\n");
490 >    
491 >    MPIcheckPoint();        
492 >    
493 >    delete[] potatoes;
494 >    
495 >  } else {
496  
497 <      if (which_atom == -1) {
443 <        done=1;
444 <        continue;
445 <      } else {
497 >    // worldRank != 0, so I'm a remote node.  
498  
499 <        local_index=-1;        
500 <        for (j=0; j < mpiSim->getMyNlocal(); j++) {
501 <          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
499 >    // Set my magic potato to 0:
500 >
501 >    myPotato = 0;
502 >    currentIndex = 0;
503 >    
504 >    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
505 >      
506 >      // Am I the node which has this atom?
507 >      
508 >      if (AtomToProcMap[i] == worldRank) {
509 >
510 >        if (myPotato + 3 >= 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, &istatus);
517 >          
518          }
519 <        if (local_index != -1) {
519 >        which_atom = i;
520  
521 <          //format the line
522 <          sprintf( tempBuffer,
523 <                   "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
524 <                   atoms[local_index]->getType(),
525 <                   atoms[local_index]->getX(),
458 <                   atoms[local_index]->getY(),
459 <                   atoms[local_index]->getZ(),
460 <                   atoms[local_index]->get_vx(),
461 <                   atoms[local_index]->get_vy(),
462 <                   atoms[local_index]->get_vz()); // check here.
463 <          strcpy( writeLine, tempBuffer );
521 >        local_index = indexArray[currentIndex].first;        
522 >                
523 >        if (which_atom == indexArray[currentIndex].second) {
524 >        
525 >          atomTypeString = atoms[local_index]->getType();
526            
527 +          atoms[local_index]->getPos(pos);
528 +          atoms[local_index]->getVel(vel);
529 +          
530 +          atomData6[0] = pos[0];
531 +          atomData6[1] = pos[1];
532 +          atomData6[2] = pos[2];
533 +
534 +          atomData6[3] = vel[0];
535 +          atomData6[4] = vel[1];
536 +          atomData6[5] = vel[2];
537 +          
538 +          isDirectional = 0;
539 +
540            if( atoms[local_index]->isDirectional() ){
541 +
542 +            isDirectional = 1;
543              
544              dAtom = (DirectionalAtom *)atoms[local_index];
545              dAtom->getQ( q );
546 <            
547 <            sprintf( tempBuffer,
548 <                     "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
549 <                     q[0],
550 <                     q[1],
551 <                     q[2],
552 <                     q[3],
553 <                     dAtom->getJx(),
554 <                     dAtom->getJy(),
555 <                     dAtom->getJz());
556 <            strcat( writeLine, tempBuffer );
546 >            
547 >            for (int j = 0; j < 6 ; j++)
548 >              atomData13[j] = atomData6[j];
549 >            
550 >            atomData13[6] = q[0];
551 >            atomData13[7] = q[1];
552 >            atomData13[8] = q[2];
553 >            atomData13[9] = q[3];
554 >  
555 >            atomData13[10] = dAtom->getJx();
556 >            atomData13[11] = dAtom->getJy();
557 >            atomData13[12] = dAtom->getJz();
558            }
559 <          else
560 <            strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
559 >
560 >        } else {
561 >          sprintf(painCave.errMsg,
562 >                  "Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n",
563 >                  which_atom, worldRank, currentIndex, local_index );
564 >          haveError= 1;
565 >          simError();
566 >        }
567 >        
568 >        strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
569 >
570 >        // null terminate the string before sending (just in case):
571 >        MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
572 >
573 >        MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
574 >                             myPotato, MPI_COMM_WORLD);
575 >        
576 >        myPotato++;
577 >
578 >        MPI_Send(&isDirectional, 1, MPI_INT, 0,
579 >                             myPotato, MPI_COMM_WORLD);
580 >        
581 >        myPotato++;
582 >        
583 >        if (isDirectional) {
584 >
585 >          MPI_Send(atomData13, 13, MPI_DOUBLE, 0,
586 >                   myPotato, MPI_COMM_WORLD);
587            
484 –          MPI::COMM_WORLD.Send(writeLine, BUFFERSIZE, MPI_CHAR, 0,
485 –                               TAKE_THIS_TAG_CHAR);
588          } else {
589 <          strcpy( writeLine, "ATOM NOT FOUND ON THIS PROCESSOR");
590 <          MPI::COMM_WORLD.Send(writeLine, BUFFERSIZE, MPI_CHAR, 0,
591 <                               TAKE_THIS_TAG_CHAR);
589 >
590 >          MPI_Send(atomData6, 6, MPI_DOUBLE, 0,
591 >                   myPotato, MPI_COMM_WORLD);
592          }
593 +
594 +        myPotato++;  
595 +        currentIndex++;    
596        }
597      }
493 –  }
494 –  finalOut.flush();
495 –  sprintf( checkPointMsg,
496 –           "Sucessfully took a dump.\n");
497 –  MPIcheckPoint();
598  
599 <  if( worldRank == 0 ) finalOut.close();    
599 >    sprintf( checkPointMsg,
600 >             "Sucessfully took a dump.\n");
601 >    MPIcheckPoint();        
602 >    
603 >  }
604 >  
605   #endif // is_mpi
606   }
607 +
608 + #ifdef IS_MPI
609 +
610 + // a couple of functions to let us escape the write loop
611 +
612 + void dWrite::DieDieDie( void ){
613 +
614 +  MPI_Finalize();
615 +  exit (0);
616 + }
617 +
618 + #endif //is_mpi

Diff Legend

– Removed lines
+ Added lines
< Changed lines
> Changed lines