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root/group/trunk/OOPSE/libmdtools/InitializeFromFile.cpp
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Comparing trunk/OOPSE/libmdtools/InitializeFromFile.cpp (file contents):
Revision 378 by mmeineke, Fri Mar 21 17:42:12 2003 UTC vs.
Revision 447 by mmeineke, Thu Apr 3 20:21:54 2003 UTC

# Line 12 | Line 12
12   #include "simError.h"
13  
14   #ifdef IS_MPI
15 + #include <mpi.h>
16   #include "mpiSimulation.hpp"
17 + #define TAKE_THIS_TAG_CHAR 0
18 + #define TAKE_THIS_TAG_INT 1
19  
20 < #define TAKE_THIS_TAG 0
20 > namespace initFile{
21 >  void nodeZeroError( void );
22 >  void anonymousNodeDie( void );
23 > }
24 >
25 > using namespace initFile;
26 >
27   #endif // is_mpi
28  
29   InitializeFromFile :: InitializeFromFile( char *in_name ){
# Line 62 | Line 71 | void InitializeFromFile :: read_xyz( SimInfo* the_entr
71  
72   void InitializeFromFile :: read_xyz( SimInfo* the_entry_plug ){
73  
74 <  int i; // loop counter
74 >  int i, j, done, which_node, which_atom; // loop counter
75  
76    const int BUFFERSIZE = 2000; // size of the read buffer
77    int n_atoms; // the number of atoms
# Line 138 | Line 147 | void InitializeFromFile :: read_xyz( SimInfo* the_entr
147    // MPI Section of code..........
148   #else //IS_MPI
149  
150 <  int masterIndex;
151 <  int nodeAtomsStart;
143 <  int nodeAtomsEnd;
144 <  int mpiErr;
145 <  int sendError;
150 >  // first thing first, suspend fatalities.
151 >  painCave.isEventLoop = 1;
152  
153 <  MPI_Status istatus[MPI_STATUS_SIZE];
153 >  int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
154 >  int haveError;
155 >  
156 >  MPI_Status istatus;
157 >  int *AtomToProcMap = mpiSim->getAtomToProcMap();
158  
159 +  
160 +  haveError = 0;
161    if (worldRank == 0) {
162 +
163      eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
164      if( eof_test == NULL ){
165        sprintf( painCave.errMsg,
166                 "Error reading 1st line of %d \n ",c_in_name);
167 <      painCave.isFatal = 1;
167 >      haveError = 1;
168        simError();
169      }
170      
# Line 168 | Line 181 | void InitializeFromFile :: read_xyz( SimInfo* the_entr
181                 "Initialize from File error. %s n_atoms, %d, "
182                 "does not match the BASS file's n_atoms, %d.\n",
183                 c_in_name, n_atoms, entry_plug->n_atoms );
184 <      painCave.isFatal = 1;
184 >      haveError= 1;
185        simError();
186      }
187      
# Line 178 | Line 191 | void InitializeFromFile :: read_xyz( SimInfo* the_entr
191      if(eof_test == NULL){
192        sprintf( painCave.errMsg,
193                 "error in reading commment in %s\n", c_in_name);
194 <      painCave.isFatal = 1;
194 >      haveError= 1;
195        simError();
196      }
197    
198 <    // Read Proc 0 share of the xyz file...
199 <    masterIndex = 0;
200 <    for( i=0; i <= mpiSim->getMyAtomEnd(); i++){
201 <    
198 >    if(haveError) nodeZeroError();
199 >
200 >    for (i=0 ; i < mpiSim->getTotAtoms(); i++) {
201 >      
202        eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
203        if(eof_test == NULL){
204          sprintf(painCave.errMsg,
# Line 193 | Line 206 | void InitializeFromFile :: read_xyz( SimInfo* the_entr
206                  "natoms  = %d; index = %d\n"
207                  "error reading the line from the file.\n",
208                  c_in_name, n_atoms, i );
209 <        painCave.isFatal = 1;
209 >        haveError= 1;
210          simError();
211        }
212      
213 <      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 <  }
213 >      if(haveError) nodeZeroError();
214  
215 <  sprintf(checkPointMsg,
216 <          "Node 0 has successfully read positions from input file.");
217 <  MPIcheckPoint();
218 <
219 <  for (procIndex = 1; procIndex < mpiSim->getNumberProcessors();
220 <         procIndex++){
221 <    if (worldRank == 0) {
222 <
223 <      mpiErr = MPI_Recv(&nodeAtomsStart,1,MPI_INT,procIndex,TAKE_THIS_TAG,MPI_COMM_WORLD,
224 <               istatus);
225 <
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);
215 >      // Get the Node number which wants this atom:
216 >      which_node = AtomToProcMap[i];    
217 >      if (which_node == 0) {
218 >        parseErr = parseDumpLine( read_buffer, i );
219 >        if( parseErr != NULL ){
220 >          strcpy( painCave.errMsg, parseErr );
221 >          haveError = 1;
222 >          simError();
223 >        }    
224 >        if(haveError) nodeZeroError();
225 >      }
226        
227 <      for ( i = nodeAtomsStart; i <= nodeAtomsEnd; i++){
228 <        eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
229 <        if(eof_test == NULL){
230 <          
231 <          sprintf(read_buffer,"ERROR");
232 <          mpiErr = MPI_Send(read_buffer,BUFFERSIZE,MPI_CHAR,procIndex,TAKE_THIS_TAG,MPI_COMM_WORLD);
233 <          
234 <          sprintf(painCave.errMsg,
235 <                  "error in reading file %s\n"
236 <                  "natoms  = %d; index = %d\n"
237 <                  "error reading the line from the file.\n",
238 <                  c_in_name, n_atoms, i );
239 <          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++;
227 >      else {
228 >      
229 >        myStatus = 1;
230 >        MPI_Send(&myStatus, 1, MPI_INT, which_node,
231 >                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
232 >        MPI_Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node,
233 >                 TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
234 >        MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
235 >                 MPI_COMM_WORLD);
236 >        MPI_Recv(&myStatus, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
237 >                 MPI_COMM_WORLD, &istatus);
238 >        
239 >        if(!myStatus) nodeZeroError();
240        }
241      }
242 +    myStatus = -1;
243 +    for (j = 0; j < mpiSim->getNumberProcessors(); j++) {      
244 +      MPI_Send( &myStatus, 1, MPI_INT, j,
245 +                TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
246 +    }
247 +    
248 +  } else {
249 +    
250 +    done = 0;
251 +    while (!done) {
252  
253 <
254 <    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);
253 >      MPI_Recv(&myStatus, 1, MPI_INT, 0,
254 >               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
255        
256 <      mpiErr = MPI_Recv(&sendError,1,MPI_INT,0,TAKE_THIS_TAG,MPI_COMM_WORLD,
257 <               istatus);
258 <      if (sendError) MPIcheckPoint();
256 >      if(!myStatus) anonymousNodeDie();
257 >      
258 >      if(myStatus < 0) break;
259  
260 <      for ( i = 0; i < entry_plug->n_atoms; i++){
261 <
262 <        mpiErr = MPI_Recv(&read_buffer,BUFFERSIZE,MPI_CHAR,0,TAKE_THIS_TAG,MPI_COMM_WORLD,
263 <                          istatus);
264 <        
265 <        if(!strcmp(read_buffer, "ERROR")) MPIcheckPoint();
266 <        
267 <        parseErr = parseDumpLine( read_buffer, i );
268 <        if( parseErr != NULL ){
269 <          sendError = 1;
270 <          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);
260 >      MPI_Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0,
261 >               TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
262 >      MPI_Recv(&which_atom, 1, MPI_INT, 0,
263 >               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
264 >      
265 >      myStatus = 1;
266 >      parseErr = parseDumpLine( read_buffer, which_atom );
267 >      if( parseErr != NULL ){
268 >        strcpy( painCave.errMsg, parseErr );
269 >        myStatus = 0;;
270 >        simError();
271        }
272 +      
273 +      MPI_Send( &myStatus, 1, MPI_INT, 0,
274 +                TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
275 +      
276      }
295 –    sprintf(checkPointMsg,"Node %d received initial configuration.",procIndex);
296 –    MPIcheckPoint();
277    }
278 <
278 >    
279 > // last  thing last, enable  fatalities.
280 >  painCave.isEventLoop = 0;
281 >  
282   #endif
283   }
284  
285 + char* InitializeFromFile::parseDumpLine(char* readLine, int globalIndex){
286  
303 – char* InitializeFromFile::parseDumpLine(char* readLine, int atomIndex){
304 –
287    char *foo; // the pointer to the current string token
288    
289    double rx, ry, rz; // position place holders
# Line 313 | Line 295 | char* InitializeFromFile::parseDumpLine(char* readLine
295    Atom **atoms = entry_plug->atoms;
296    DirectionalAtom* dAtom;
297    
298 <  int n_atoms;
298 >  int j, n_atoms, atomIndex;
299  
300   #ifdef IS_MPI
301    n_atoms = mpiSim->getTotAtoms();
302 +  atomIndex=-1;        
303 +  for (j=0; j < mpiSim->getMyNlocal(); j++) {
304 +    if (atoms[j]->getGlobalIndex() == globalIndex) atomIndex = j;
305 +  }
306 +  if (atomIndex == -1) {
307 +    sprintf( painCave.errMsg,
308 +             "Initialize from file error. Atom at index %d "
309 +             "in file %s does not exist on processor %d .\n",
310 +             globalIndex, c_in_name, mpiSim->getMyNode() );
311 +    return strdup( painCave.errMsg );
312 +  }  
313   #else
314    n_atoms = entry_plug->n_atoms;
315 +  atomIndex = globalIndex;
316   #endif // is_mpi
317  
324 –
318    // set the string tokenizer
319    
320    foo = strtok(readLine, " ,;\t");
# Line 512 | Line 505 | char* InitializeFromFile::parseDumpLine(char* readLine
505  
506    return NULL;
507   }
508 +
509 +
510 + #ifdef IS_MPI
511 +
512 + // a couple of functions to let us escape the read loop
513 +
514 + void initFile::nodeZeroError( void ){
515 +  int j, myStatus;
516 +  
517 +  myStatus = 0;
518 +  for (j = 0; j < mpiSim->getNumberProcessors(); j++) {      
519 +    MPI_Send( &myStatus, 1, MPI_INT, j,
520 +              TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
521 +  }  
522 +  
523 +
524 +  MPI_Finalize();
525 +  exit (0);
526 +  
527 + }
528 +
529 + void initFile::anonymousNodeDie( void ){
530 +
531 +  MPI_Finalize();
532 +  exit (0);
533 + }
534 +
535 + #endif //is_mpi

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