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root/group/branches/no-template-branch/OOPSE/libmdtools/InitializeFromFile.cpp
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Comparing:
branches/mmeineke/OOPSE/libmdtools/InitializeFromFile.cpp (file contents), Revision 377 by mmeineke, Fri Mar 21 17:42:12 2003 UTC vs.
trunk/OOPSE/libmdtools/InitializeFromFile.cpp (file contents), Revision 440 by mmeineke, Tue Apr 1 16:49:17 2003 UTC

# Line 12 | Line 12
12   #include "simError.h"
13  
14   #ifdef IS_MPI
15 + #include <mpi.h>
16 + #include <mpi++.h>
17   #include "mpiSimulation.hpp"
18 + #define TAKE_THIS_TAG_CHAR 0
19 + #define TAKE_THIS_TAG_INT 1
20  
21 < #define TAKE_THIS_TAG 0
21 > namespace initFile{
22 >  void nodeZeroError( void );
23 >  void anonymousNodeDie( void );
24 > }
25 >
26 > using namespace initFile;
27 >
28   #endif // is_mpi
29  
30   InitializeFromFile :: InitializeFromFile( char *in_name ){
# Line 62 | Line 72 | void InitializeFromFile :: read_xyz( SimInfo* the_entr
72  
73   void InitializeFromFile :: read_xyz( SimInfo* the_entry_plug ){
74  
75 <  int i; // loop counter
75 >  int i, j, done, which_node, which_atom; // loop counter
76  
77    const int BUFFERSIZE = 2000; // size of the read buffer
78    int n_atoms; // the number of atoms
# Line 138 | Line 148 | void InitializeFromFile :: read_xyz( SimInfo* the_entr
148    // MPI Section of code..........
149   #else //IS_MPI
150  
151 <  int masterIndex;
152 <  int nodeAtomsStart;
143 <  int nodeAtomsEnd;
144 <  int mpiErr;
145 <  int sendError;
151 >  // first thing first, suspend fatalities.
152 >  painCave.isEventLoop = 1;
153  
154 <  MPI_Status istatus[MPI_STATUS_SIZE];
154 >  int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
155 >  int haveError;
156 >  
157 >  MPI::Status istatus;
158 >  int *AtomToProcMap = mpiSim->getAtomToProcMap();
159  
160 +  
161 +  haveError = 0;
162    if (worldRank == 0) {
163 +
164      eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
165      if( eof_test == NULL ){
166        sprintf( painCave.errMsg,
167                 "Error reading 1st line of %d \n ",c_in_name);
168 <      painCave.isFatal = 1;
168 >      haveError = 1;
169        simError();
170      }
171      
# Line 168 | Line 182 | void InitializeFromFile :: read_xyz( SimInfo* the_entr
182                 "Initialize from File error. %s n_atoms, %d, "
183                 "does not match the BASS file's n_atoms, %d.\n",
184                 c_in_name, n_atoms, entry_plug->n_atoms );
185 <      painCave.isFatal = 1;
185 >      haveError= 1;
186        simError();
187      }
188      
# Line 178 | Line 192 | void InitializeFromFile :: read_xyz( SimInfo* the_entr
192      if(eof_test == NULL){
193        sprintf( painCave.errMsg,
194                 "error in reading commment in %s\n", c_in_name);
195 <      painCave.isFatal = 1;
195 >      haveError= 1;
196        simError();
197      }
198    
199 <    // Read Proc 0 share of the xyz file...
200 <    masterIndex = 0;
201 <    for( i=0; i <= mpiSim->getMyAtomEnd(); i++){
202 <    
199 >    if(haveError) nodeZeroError();
200 >
201 >    for (i=0 ; i < mpiSim->getTotAtoms(); i++) {
202 >      
203        eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
204        if(eof_test == NULL){
205          sprintf(painCave.errMsg,
# Line 193 | Line 207 | void InitializeFromFile :: read_xyz( SimInfo* the_entr
207                  "natoms  = %d; index = %d\n"
208                  "error reading the line from the file.\n",
209                  c_in_name, n_atoms, i );
210 <        painCave.isFatal = 1;
210 >        haveError= 1;
211          simError();
212        }
213      
214 <      parseErr = parseDumpLine( read_buffer, i );
201 <      if( parseErr != NULL ){
202 <        strcpy( painCave.errMsg, parseErr );
203 <        painCave.isFatal = 1;
204 <        simError();
205 <      }    
206 <      masterIndex++;
207 <    }
208 <  }
214 >      if(haveError) nodeZeroError();
215  
216 <  sprintf(checkPointMsg,
217 <          "Node 0 has successfully read positions from input file.");
218 <  MPIcheckPoint();
219 <
220 <  for (procIndex = 1; procIndex < mpiSim->getNumberProcessors();
221 <         procIndex++){
222 <    if (worldRank == 0) {
223 <
224 <      mpiErr = MPI_Recv(&nodeAtomsStart,1,MPI_INT,procIndex,TAKE_THIS_TAG,MPI_COMM_WORLD,
225 <               istatus);
226 <
221 <      mpiErr = MPI_Recv(&nodeAtomsEnd,1,MPI_INT,procIndex,TAKE_THIS_TAG,MPI_COMM_WORLD,
222 <               istatus);
223 <      // Make sure where node 0 is reading from, matches where the receiving node
224 <      // expects it to be.
225 <
226 <      if (masterIndex != nodeAtomsStart){
227 <        sendError = 1;
228 <        mpiErr = MPI_Send(&sendError,1,MPI_INT,procIndex,TAKE_THIS_TAG,MPI_COMM_WORLD);
229 <        sprintf(painCave.errMsg,
230 <                "Initialize from file error: atoms start index (%d) for "
231 <                "node %d not equal to master index (%d)",nodeAtomsStart,procIndex,masterIndex );
232 <        painCave.isFatal = 1;
233 <        simError();
234 <      }
235 <      sendError = 0;
236 <      mpiErr = MPI_Send(&sendError,1,MPI_INT,procIndex,TAKE_THIS_TAG,MPI_COMM_WORLD);
216 >      // Get the Node number which wants this atom:
217 >      which_node = AtomToProcMap[i];    
218 >      if (which_node == 0) {
219 >        parseErr = parseDumpLine( read_buffer, i );
220 >        if( parseErr != NULL ){
221 >          strcpy( painCave.errMsg, parseErr );
222 >          haveError = 1;
223 >          simError();
224 >        }    
225 >        if(haveError) nodeZeroError();
226 >      }
227        
228 <      for ( i = nodeAtomsStart; i <= nodeAtomsEnd; i++){
229 <        eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
230 <        if(eof_test == NULL){
231 <          
232 <          sprintf(read_buffer,"ERROR");
233 <          mpiErr = MPI_Send(read_buffer,BUFFERSIZE,MPI_CHAR,procIndex,TAKE_THIS_TAG,MPI_COMM_WORLD);
234 <          
235 <          sprintf(painCave.errMsg,
236 <                  "error in reading file %s\n"
237 <                  "natoms  = %d; index = %d\n"
238 <                  "error reading the line from the file.\n",
249 <                  c_in_name, n_atoms, i );
250 <          painCave.isFatal = 1;
251 <          simError();
252 <        }
253 <        
254 <        mpiErr = MPI_Send(read_buffer,BUFFERSIZE,MPI_CHAR,procIndex,TAKE_THIS_TAG,MPI_COMM_WORLD);
255 <        mpiErr = MPI_Recv(&sendError,1,MPI_INT,procIndex,TAKE_THIS_TAG,MPI_COMM_WORLD,
256 <                          istatus);
257 <        if (sendError) MPIcheckPoint();
258 <
259 <        masterIndex++;
228 >      else {
229 >      
230 >        myStatus = 1;
231 >        MPI::COMM_WORLD.Send(&myStatus, 1, MPI_INT, which_node,
232 >                             TAKE_THIS_TAG_INT);
233 >        MPI::COMM_WORLD.Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node,
234 >                             TAKE_THIS_TAG_CHAR);
235 >        MPI::COMM_WORLD.Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT);
236 >        MPI::COMM_WORLD.Recv(&myStatus, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, istatus);
237 >        
238 >        if(!myStatus) nodeZeroError();
239        }
240      }
241 +    myStatus = -1;
242 +    for (j = 0; j < mpiSim->getNumberProcessors(); j++) {      
243 +      MPI::COMM_WORLD.Send( &myStatus, 1, MPI_INT, j,
244 +                            TAKE_THIS_TAG_INT);
245 +    }
246 +    
247 +  } else {
248 +    
249 +    done = 0;
250 +    while (!done) {
251  
252 <
253 <    else if(worldRank == procIndex){
265 <      nodeAtomsStart = mpiSim->getMyAtomStart();
266 <      nodeAtomsEnd = mpiSim->getMyAtomEnd();
267 <      mpiErr = MPI_Send(&nodeAtomsStart,1,MPI_INT,0,TAKE_THIS_TAG,MPI_COMM_WORLD);
268 <      mpiErr = MPI_Send(&nodeAtomsEnd,1,MPI_INT,0,TAKE_THIS_TAG,MPI_COMM_WORLD);
252 >      MPI::COMM_WORLD.Recv(&myStatus, 1, MPI_INT, 0,
253 >                           TAKE_THIS_TAG_INT, istatus);
254        
255 <      mpiErr = MPI_Recv(&sendError,1,MPI_INT,0,TAKE_THIS_TAG,MPI_COMM_WORLD,
256 <               istatus);
257 <      if (sendError) MPIcheckPoint();
255 >      if(!myStatus) anonymousNodeDie();
256 >      
257 >      if(myStatus < 0) break;
258  
259 <      for ( i = 0; i < entry_plug->n_atoms; i++){
260 <
261 <        mpiErr = MPI_Recv(&read_buffer,BUFFERSIZE,MPI_CHAR,0,TAKE_THIS_TAG,MPI_COMM_WORLD,
262 <                          istatus);
263 <        
264 <        if(!strcmp(read_buffer, "ERROR")) MPIcheckPoint();
265 <        
266 <        parseErr = parseDumpLine( read_buffer, i );
267 <        if( parseErr != NULL ){
268 <          sendError = 1;
269 <          mpiErr = MPI_Send(&sendError,1,MPI_INT,0,TAKE_THIS_TAG,MPI_COMM_WORLD);
285 <
286 <
287 <          strcpy( painCave.errMsg, parseErr );
288 <          painCave.isFatal = 1;
289 <          simError();
290 <        }
291 <        sendError = 0;
292 <        mpiErr = MPI_Send(&sendError,1,MPI_INT,0,TAKE_THIS_TAG,MPI_COMM_WORLD);
259 >      MPI::COMM_WORLD.Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0,
260 >                           TAKE_THIS_TAG_CHAR, istatus);
261 >      MPI::COMM_WORLD.Recv(&which_atom, 1, MPI_INT, 0,
262 >                           TAKE_THIS_TAG_INT, istatus);
263 >      
264 >      myStatus = 1;
265 >      parseErr = parseDumpLine( read_buffer, which_atom );
266 >      if( parseErr != NULL ){
267 >        strcpy( painCave.errMsg, parseErr );
268 >        myStatus = 0;;
269 >        simError();
270        }
271 +      
272 +      MPI::COMM_WORLD.Send( &myStatus, 1, MPI_INT, 0,
273 +                            TAKE_THIS_TAG_INT);
274 +      
275      }
295 –    sprintf(checkPointMsg,"Node %d received initial configuration.",procIndex);
296 –    MPIcheckPoint();
276    }
277 <
277 >    
278 > // last  thing last, enable  fatalities.
279 >  painCave.isEventLoop = 0;
280 >  
281   #endif
282   }
283  
284 + char* InitializeFromFile::parseDumpLine(char* readLine, int globalIndex){
285  
303 – char* InitializeFromFile::parseDumpLine(char* readLine, int atomIndex){
304 –
286    char *foo; // the pointer to the current string token
287    
288    double rx, ry, rz; // position place holders
# Line 313 | Line 294 | char* InitializeFromFile::parseDumpLine(char* readLine
294    Atom **atoms = entry_plug->atoms;
295    DirectionalAtom* dAtom;
296    
297 <  int n_atoms;
297 >  int j, n_atoms, atomIndex;
298  
299   #ifdef IS_MPI
300    n_atoms = mpiSim->getTotAtoms();
301 +  atomIndex=-1;        
302 +  for (j=0; j < mpiSim->getMyNlocal(); j++) {
303 +    if (atoms[j]->getGlobalIndex() == globalIndex) atomIndex = j;
304 +  }
305 +  if (atomIndex == -1) {
306 +    sprintf( painCave.errMsg,
307 +             "Initialize from file error. Atom at index %d "
308 +             "in file %s does not exist on processor %d .\n",
309 +             globalIndex, c_in_name, mpiSim->getMyNode() );
310 +    return strdup( painCave.errMsg );
311 +  }  
312   #else
313    n_atoms = entry_plug->n_atoms;
314 +  atomIndex = globalIndex;
315   #endif // is_mpi
316  
324 –
317    // set the string tokenizer
318    
319    foo = strtok(readLine, " ,;\t");
# Line 512 | Line 504 | char* InitializeFromFile::parseDumpLine(char* readLine
504  
505    return NULL;
506   }
507 +
508 +
509 + #ifdef IS_MPI
510 +
511 + // a couple of functions to let us escape the read loop
512 +
513 + void initFile::nodeZeroError( void ){
514 +  int j, myStatus;
515 +  
516 +  myStatus = 0;
517 +  for (j = 0; j < mpiSim->getNumberProcessors(); j++) {      
518 +    MPI::COMM_WORLD.Send( &myStatus, 1, MPI_INT, j,
519 +                          TAKE_THIS_TAG_INT);
520 +  }  
521 +  
522 +
523 +  MPI_Finalize();
524 +  exit (0);
525 +  
526 + }
527 +
528 + void initFile::anonymousNodeDie( void ){
529 +
530 +  MPI_Finalize();
531 +  exit (0);
532 + }
533 +
534 + #endif //is_mpi

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