# | Line 13 | Line 13 | |
---|---|---|
13 | ||
14 | #ifdef IS_MPI | |
15 | #include <mpi.h> | |
16 | – | #include <mpi++.h> |
16 | #include "mpiSimulation.hpp" | |
17 | < | #define TAKE_THIS_TAG 0 |
17 | > | #define TAKE_THIS_TAG_CHAR 0 |
18 | > | #define TAKE_THIS_TAG_INT 1 |
19 | > | |
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 61 | Line 69 | InitializeFromFile :: ~InitializeFromFile( ){ | |
69 | } | |
70 | ||
71 | ||
72 | < | void InitializeFromFile :: read_xyz( SimInfo* the_entry_plug ){ |
72 | > | void InitializeFromFile :: read_xyz( SimInfo* the_simnfo ){ |
73 | ||
74 | int i, j, done, which_node, which_atom; // loop counter | |
75 | ||
# | Line 75 | Line 83 | void InitializeFromFile :: read_xyz( SimInfo* the_entr | |
83 | char *eof_test; // ptr to see when we reach the end of the file | |
84 | char *parseErr; | |
85 | int procIndex; | |
86 | + | double boxMat[9]; |
87 | + | |
88 | ||
89 | < | entry_plug = the_entry_plug; |
89 | > | simnfo = the_simnfo; |
90 | ||
91 | ||
92 | #ifndef IS_MPI | |
# | Line 91 | Line 101 | void InitializeFromFile :: read_xyz( SimInfo* the_entr | |
101 | ||
102 | n_atoms = atoi( read_buffer ); | |
103 | ||
104 | < | Atom **atoms = entry_plug->atoms; |
104 | > | Atom **atoms = simnfo->atoms; |
105 | DirectionalAtom* dAtom; | |
106 | ||
107 | < | if( n_atoms != entry_plug->n_atoms ){ |
107 | > | if( n_atoms != simnfo->n_atoms ){ |
108 | sprintf( painCave.errMsg, | |
109 | "Initialize from File error. %s n_atoms, %d, " | |
110 | "does not match the BASS file's n_atoms, %d.\n", | |
111 | < | c_in_name, n_atoms, entry_plug->n_atoms ); |
111 | > | c_in_name, n_atoms, simnfo->n_atoms ); |
112 | painCave.isFatal = 1; | |
113 | simError(); | |
114 | } | |
115 | ||
116 | < | //read and toss the comment line |
116 | > | //read the box mat from the comment line |
117 | ||
118 | eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); | |
119 | if(eof_test == NULL){ | |
# | Line 113 | Line 123 | void InitializeFromFile :: read_xyz( SimInfo* the_entr | |
123 | simError(); | |
124 | } | |
125 | ||
126 | + | parseErr = parseBoxLine( read_buffer, boxMat ); |
127 | + | if( parseErr != NULL ){ |
128 | + | strcpy( painCave.errMsg, parseErr ); |
129 | + | painCave.isFatal = 1; |
130 | + | simError(); |
131 | + | } |
132 | + | |
133 | + | simnfo->setBoxM( boxMat ); |
134 | + | |
135 | + | |
136 | for( i=0; i < n_atoms; i++){ | |
137 | ||
138 | eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); | |
# | Line 132 | Line 152 | void InitializeFromFile :: read_xyz( SimInfo* the_entr | |
152 | strcpy( painCave.errMsg, parseErr ); | |
153 | painCave.isFatal = 1; | |
154 | simError(); | |
155 | < | } |
155 | > | } |
156 | } | |
157 | ||
158 | ||
159 | // MPI Section of code.......... | |
160 | #else //IS_MPI | |
161 | ||
162 | < | MPI::Status istatus; |
162 | > | // first thing first, suspend fatalities. |
163 | > | painCave.isEventLoop = 1; |
164 | > | |
165 | > | int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone |
166 | > | int haveError; |
167 | > | |
168 | > | MPI_Status istatus; |
169 | int *AtomToProcMap = mpiSim->getAtomToProcMap(); | |
170 | ||
171 | + | |
172 | + | haveError = 0; |
173 | if (worldRank == 0) { | |
174 | + | |
175 | eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); | |
176 | if( eof_test == NULL ){ | |
177 | sprintf( painCave.errMsg, | |
178 | "Error reading 1st line of %d \n ",c_in_name); | |
179 | < | painCave.isFatal = 1; |
179 | > | haveError = 1; |
180 | simError(); | |
181 | } | |
182 | ||
183 | n_atoms = atoi( read_buffer ); | |
184 | ||
185 | < | Atom **atoms = entry_plug->atoms; |
185 | > | Atom **atoms = simnfo->atoms; |
186 | DirectionalAtom* dAtom; | |
187 | ||
188 | // Check to see that the number of atoms in the intial configuration file is the | |
# | Line 163 | Line 192 | void InitializeFromFile :: read_xyz( SimInfo* the_entr | |
192 | sprintf( painCave.errMsg, | |
193 | "Initialize from File error. %s n_atoms, %d, " | |
194 | "does not match the BASS file's n_atoms, %d.\n", | |
195 | < | c_in_name, n_atoms, entry_plug->n_atoms ); |
196 | < | painCave.isFatal = 1; |
195 | > | c_in_name, n_atoms, simnfo->n_atoms ); |
196 | > | haveError= 1; |
197 | simError(); | |
198 | } | |
199 | ||
200 | < | //read and toss the comment line |
200 | > | //read the boxMat from the comment line |
201 | ||
202 | eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); | |
203 | if(eof_test == NULL){ | |
204 | sprintf( painCave.errMsg, | |
205 | "error in reading commment in %s\n", c_in_name); | |
206 | < | painCave.isFatal = 1; |
206 | > | haveError = 1; |
207 | simError(); | |
208 | } | |
209 | + | |
210 | + | parseErr = parseBoxLine( read_buffer, boxMat ); |
211 | + | if( parseErr != NULL ){ |
212 | + | strcpy( painCave.errMsg, parseErr ); |
213 | + | haveError = 1; |
214 | + | simError(); |
215 | + | } |
216 | + | |
217 | + | MPI_Bcast(boxMat, 9, MPI_DOUBLE, 0, MPI_COMM_WORLD ); |
218 | ||
219 | + | if(haveError) nodeZeroError(); |
220 | ||
221 | for (i=0 ; i < mpiSim->getTotAtoms(); i++) { | |
222 | ||
# | Line 188 | Line 227 | void InitializeFromFile :: read_xyz( SimInfo* the_entr | |
227 | "natoms = %d; index = %d\n" | |
228 | "error reading the line from the file.\n", | |
229 | c_in_name, n_atoms, i ); | |
230 | < | painCave.isFatal = 1; |
230 | > | haveError= 1; |
231 | simError(); | |
232 | } | |
233 | ||
234 | + | if(haveError) nodeZeroError(); |
235 | + | |
236 | // Get the Node number which wants this atom: | |
237 | which_node = AtomToProcMap[i]; | |
238 | < | if (which_node == mpiSim->getMyNode()) { |
238 | > | if (which_node == 0) { |
239 | parseErr = parseDumpLine( read_buffer, i ); | |
240 | if( parseErr != NULL ){ | |
241 | strcpy( painCave.errMsg, parseErr ); | |
242 | < | painCave.isFatal = 1; |
242 | > | haveError = 1; |
243 | simError(); | |
244 | } | |
245 | < | } else { |
246 | < | MPI::COMM_WORLD.Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node, |
247 | < | TAKE_THIS_TAG); |
248 | < | MPI::COMM_WORLD.Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG); |
245 | > | if(haveError) nodeZeroError(); |
246 | > | } |
247 | > | |
248 | > | else { |
249 | > | |
250 | > | myStatus = 1; |
251 | > | MPI_Send(&myStatus, 1, MPI_INT, which_node, |
252 | > | TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
253 | > | MPI_Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node, |
254 | > | TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD); |
255 | > | MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, |
256 | > | MPI_COMM_WORLD); |
257 | > | MPI_Recv(&myStatus, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, |
258 | > | MPI_COMM_WORLD, &istatus); |
259 | > | |
260 | > | if(!myStatus) nodeZeroError(); |
261 | } | |
262 | } | |
263 | < | sprintf(read_buffer, "GAMEOVER"); |
263 | > | myStatus = -1; |
264 | for (j = 0; j < mpiSim->getNumberProcessors(); j++) { | |
265 | < | MPI::COMM_WORLD.Send(read_buffer, BUFFERSIZE, MPI_CHAR, j, |
266 | < | TAKE_THIS_TAG); |
265 | > | MPI_Send( &myStatus, 1, MPI_INT, j, |
266 | > | TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
267 | } | |
268 | < | |
268 | > | |
269 | } else { | |
270 | + | |
271 | + | MPI_Bcast(boxMat, 9, MPI_DOUBLE, 0, MPI_COMM_WORLD); |
272 | ||
273 | done = 0; | |
274 | while (!done) { | |
275 | < | MPI::COMM_WORLD.Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0, |
276 | < | TAKE_THIS_TAG, istatus); |
277 | < | if (strcmp(read_buffer, "GAMEOVER")) { |
278 | < | done = 1; |
279 | < | continue; |
280 | < | } else { |
281 | < | MPI::COMM_WORLD.Recv(&which_atom, 1, MPI_INT, 0, |
282 | < | TAKE_THIS_TAG, istatus); |
283 | < | parseErr = parseDumpLine( read_buffer, which_atom ); |
284 | < | if( parseErr != NULL ){ |
285 | < | strcpy( painCave.errMsg, parseErr ); |
286 | < | painCave.isFatal = 1; |
287 | < | simError(); |
288 | < | } |
275 | > | |
276 | > | MPI_Recv(&myStatus, 1, MPI_INT, 0, |
277 | > | TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
278 | > | |
279 | > | if(!myStatus) anonymousNodeDie(); |
280 | > | |
281 | > | if(myStatus < 0) break; |
282 | > | |
283 | > | MPI_Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0, |
284 | > | TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus); |
285 | > | MPI_Recv(&which_atom, 1, MPI_INT, 0, |
286 | > | TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
287 | > | |
288 | > | myStatus = 1; |
289 | > | parseErr = parseDumpLine( read_buffer, which_atom ); |
290 | > | if( parseErr != NULL ){ |
291 | > | strcpy( painCave.errMsg, parseErr ); |
292 | > | myStatus = 0;; |
293 | > | simError(); |
294 | } | |
295 | + | |
296 | + | MPI_Send( &myStatus, 1, MPI_INT, 0, |
297 | + | TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
298 | + | |
299 | } | |
300 | } | |
301 | < | |
301 | > | |
302 | > | // last thing last, enable fatalities. |
303 | > | painCave.isEventLoop = 0; |
304 | > | simnfo->setBoxM( boxMat ); |
305 | > | |
306 | > | |
307 | #endif | |
308 | } | |
309 | ||
310 | < | char* InitializeFromFile::parseDumpLine(char* readLine, int atomIndex){ |
310 | > | char* InitializeFromFile::parseDumpLine(char* readLine, int globalIndex){ |
311 | ||
312 | char *foo; // the pointer to the current string token | |
313 | ||
# | Line 248 | Line 317 | char* InitializeFromFile::parseDumpLine(char* readLine | |
317 | double jx, jy, jz; // angular velocity placeholders; | |
318 | double qSqr, qLength; // needed to normalize the quaternion vector. | |
319 | ||
320 | < | Atom **atoms = entry_plug->atoms; |
320 | > | Atom **atoms = simnfo->atoms; |
321 | DirectionalAtom* dAtom; | |
322 | ||
323 | < | int n_atoms; |
323 | > | int j, n_atoms, atomIndex; |
324 | ||
325 | #ifdef IS_MPI | |
326 | n_atoms = mpiSim->getTotAtoms(); | |
327 | + | atomIndex=-1; |
328 | + | for (j=0; j < mpiSim->getMyNlocal(); j++) { |
329 | + | if (atoms[j]->getGlobalIndex() == globalIndex) atomIndex = j; |
330 | + | } |
331 | + | if (atomIndex == -1) { |
332 | + | sprintf( painCave.errMsg, |
333 | + | "Initialize from file error. Atom at index %d " |
334 | + | "in file %s does not exist on processor %d .\n", |
335 | + | globalIndex, c_in_name, mpiSim->getMyNode() ); |
336 | + | return strdup( painCave.errMsg ); |
337 | + | } |
338 | #else | |
339 | < | n_atoms = entry_plug->n_atoms; |
339 | > | n_atoms = simnfo->n_atoms; |
340 | > | atomIndex = globalIndex; |
341 | #endif // is_mpi | |
342 | ||
262 | – | |
343 | // set the string tokenizer | |
344 | ||
345 | foo = strtok(readLine, " ,;\t"); | |
# | Line 450 | Line 530 | char* InitializeFromFile::parseDumpLine(char* readLine | |
530 | ||
531 | return NULL; | |
532 | } | |
533 | + | |
534 | + | |
535 | + | char* InitializeFromFile::parseBoxLine(char* readLine, double boxMat[9]){ |
536 | + | |
537 | + | char *foo; // the pointer to the current string token |
538 | + | int j; |
539 | + | |
540 | + | // set the string tokenizer |
541 | + | |
542 | + | foo = strtok(readLine, " ,;\t"); |
543 | + | // ignore the first token which is the time stamp. |
544 | + | |
545 | + | |
546 | + | // get the Hx vector |
547 | + | |
548 | + | foo = strtok(NULL, " ,;\t"); |
549 | + | if(foo == NULL){ |
550 | + | sprintf( painCave.errMsg, |
551 | + | "error in reading Hx[0] from %s\n", |
552 | + | c_in_name ); |
553 | + | return strdup( painCave.errMsg ); |
554 | + | } |
555 | + | boxMat[0] = atof( foo ); |
556 | + | |
557 | + | foo = strtok(NULL, " ,;\t"); |
558 | + | if(foo == NULL){ |
559 | + | sprintf( painCave.errMsg, |
560 | + | "error in reading Hx[1] from %s\n", |
561 | + | c_in_name ); |
562 | + | return strdup( painCave.errMsg ); |
563 | + | } |
564 | + | boxMat[1] = atof( foo ); |
565 | + | |
566 | + | foo = strtok(NULL, " ,;\t"); |
567 | + | if(foo == NULL){ |
568 | + | sprintf( painCave.errMsg, |
569 | + | "error in reading Hx[2] from %s\n", |
570 | + | c_in_name ); |
571 | + | return strdup( painCave.errMsg ); |
572 | + | } |
573 | + | boxMat[2] = atof( foo ); |
574 | + | |
575 | + | // get the Hy vector |
576 | + | |
577 | + | foo = strtok(NULL, " ,;\t"); |
578 | + | if(foo == NULL){ |
579 | + | sprintf( painCave.errMsg, |
580 | + | "error in reading Hy[0] from %s\n", |
581 | + | c_in_name ); |
582 | + | return strdup( painCave.errMsg ); |
583 | + | } |
584 | + | boxMat[3] = atof( foo ); |
585 | + | |
586 | + | foo = strtok(NULL, " ,;\t"); |
587 | + | if(foo == NULL){ |
588 | + | sprintf( painCave.errMsg, |
589 | + | "error in reading Hy[1] from %s\n", |
590 | + | c_in_name ); |
591 | + | return strdup( painCave.errMsg ); |
592 | + | } |
593 | + | boxMat[4] = atof( foo ); |
594 | + | |
595 | + | foo = strtok(NULL, " ,;\t"); |
596 | + | if(foo == NULL){ |
597 | + | sprintf( painCave.errMsg, |
598 | + | "error in reading Hy[2] from %s\n", |
599 | + | c_in_name ); |
600 | + | return strdup( painCave.errMsg ); |
601 | + | } |
602 | + | boxMat[5] = atof( foo ); |
603 | + | |
604 | + | // get the Hz vector |
605 | + | |
606 | + | foo = strtok(NULL, " ,;\t"); |
607 | + | if(foo == NULL){ |
608 | + | sprintf( painCave.errMsg, |
609 | + | "error in reading Hz[0] from %s\n", |
610 | + | c_in_name ); |
611 | + | return strdup( painCave.errMsg ); |
612 | + | } |
613 | + | boxMat[6] = atof( foo ); |
614 | + | |
615 | + | foo = strtok(NULL, " ,;\t"); |
616 | + | if(foo == NULL){ |
617 | + | sprintf( painCave.errMsg, |
618 | + | "error in reading Hz[1] from %s\n", |
619 | + | c_in_name ); |
620 | + | return strdup( painCave.errMsg ); |
621 | + | } |
622 | + | boxMat[7] = atof( foo ); |
623 | + | |
624 | + | foo = strtok(NULL, " ,;\t"); |
625 | + | if(foo == NULL){ |
626 | + | sprintf( painCave.errMsg, |
627 | + | "error in reading Hz[2] from %s\n", |
628 | + | c_in_name ); |
629 | + | return strdup( painCave.errMsg ); |
630 | + | } |
631 | + | boxMat[8] = atof( foo ); |
632 | + | |
633 | + | return NULL; |
634 | + | } |
635 | + | |
636 | + | |
637 | + | #ifdef IS_MPI |
638 | + | |
639 | + | // a couple of functions to let us escape the read loop |
640 | + | |
641 | + | void initFile::nodeZeroError( void ){ |
642 | + | int j, myStatus; |
643 | + | |
644 | + | myStatus = 0; |
645 | + | for (j = 0; j < mpiSim->getNumberProcessors(); j++) { |
646 | + | MPI_Send( &myStatus, 1, MPI_INT, j, |
647 | + | TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
648 | + | } |
649 | + | |
650 | + | |
651 | + | MPI_Finalize(); |
652 | + | exit (0); |
653 | + | |
654 | + | } |
655 | + | |
656 | + | void initFile::anonymousNodeDie( void ){ |
657 | + | |
658 | + | MPI_Finalize(); |
659 | + | exit (0); |
660 | + | } |
661 | + | |
662 | + | #endif //is_mpi |
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