# | 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 :: readInit( 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 | + | double theBoxMat3[3][3]; |
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 | + | for(i=0;i<3;i++) |
134 | + | for(j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i]; |
135 | + | |
136 | + | simnfo->setBoxM( theBoxMat3 ); |
137 | + | |
138 | + | |
139 | for( i=0; i < n_atoms; i++){ | |
140 | ||
141 | eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); | |
# | Line 132 | Line 155 | void InitializeFromFile :: read_xyz( SimInfo* the_entr | |
155 | strcpy( painCave.errMsg, parseErr ); | |
156 | painCave.isFatal = 1; | |
157 | simError(); | |
158 | < | } |
158 | > | } |
159 | } | |
160 | ||
161 | ||
162 | // MPI Section of code.......... | |
163 | #else //IS_MPI | |
164 | ||
165 | < | MPI::Status istatus; |
165 | > | // first thing first, suspend fatalities. |
166 | > | painCave.isEventLoop = 1; |
167 | > | |
168 | > | int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone |
169 | > | int haveError; |
170 | > | |
171 | > | MPI_Status istatus; |
172 | int *AtomToProcMap = mpiSim->getAtomToProcMap(); | |
173 | ||
174 | + | |
175 | + | haveError = 0; |
176 | if (worldRank == 0) { | |
177 | + | |
178 | eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); | |
179 | if( eof_test == NULL ){ | |
180 | sprintf( painCave.errMsg, | |
181 | "Error reading 1st line of %d \n ",c_in_name); | |
182 | < | painCave.isFatal = 1; |
182 | > | haveError = 1; |
183 | simError(); | |
184 | } | |
185 | ||
186 | n_atoms = atoi( read_buffer ); | |
187 | ||
188 | < | Atom **atoms = entry_plug->atoms; |
188 | > | Atom **atoms = simnfo->atoms; |
189 | DirectionalAtom* dAtom; | |
190 | ||
191 | // Check to see that the number of atoms in the intial configuration file is the | |
# | Line 163 | Line 195 | void InitializeFromFile :: read_xyz( SimInfo* the_entr | |
195 | sprintf( painCave.errMsg, | |
196 | "Initialize from File error. %s n_atoms, %d, " | |
197 | "does not match the BASS file's n_atoms, %d.\n", | |
198 | < | c_in_name, n_atoms, entry_plug->n_atoms ); |
199 | < | painCave.isFatal = 1; |
198 | > | c_in_name, n_atoms, simnfo->n_atoms ); |
199 | > | haveError= 1; |
200 | simError(); | |
201 | } | |
202 | ||
203 | < | //read and toss the comment line |
203 | > | //read the boxMat from the comment line |
204 | ||
205 | eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); | |
206 | if(eof_test == NULL){ | |
207 | sprintf( painCave.errMsg, | |
208 | "error in reading commment in %s\n", c_in_name); | |
209 | < | painCave.isFatal = 1; |
209 | > | haveError = 1; |
210 | simError(); | |
211 | } | |
212 | + | |
213 | + | parseErr = parseBoxLine( read_buffer, boxMat ); |
214 | + | if( parseErr != NULL ){ |
215 | + | strcpy( painCave.errMsg, parseErr ); |
216 | + | haveError = 1; |
217 | + | simError(); |
218 | + | } |
219 | + | |
220 | + | MPI_Bcast(boxMat, 9, MPI_DOUBLE, 0, MPI_COMM_WORLD ); |
221 | ||
222 | + | if(haveError) nodeZeroError(); |
223 | ||
224 | for (i=0 ; i < mpiSim->getTotAtoms(); i++) { | |
225 | ||
# | Line 188 | Line 230 | void InitializeFromFile :: read_xyz( SimInfo* the_entr | |
230 | "natoms = %d; index = %d\n" | |
231 | "error reading the line from the file.\n", | |
232 | c_in_name, n_atoms, i ); | |
233 | < | painCave.isFatal = 1; |
233 | > | haveError= 1; |
234 | simError(); | |
235 | } | |
236 | ||
237 | + | if(haveError) nodeZeroError(); |
238 | + | |
239 | // Get the Node number which wants this atom: | |
240 | which_node = AtomToProcMap[i]; | |
241 | < | if (which_node == mpiSim->getMyNode()) { |
241 | > | if (which_node == 0) { |
242 | parseErr = parseDumpLine( read_buffer, i ); | |
243 | if( parseErr != NULL ){ | |
244 | strcpy( painCave.errMsg, parseErr ); | |
245 | < | painCave.isFatal = 1; |
245 | > | haveError = 1; |
246 | simError(); | |
247 | } | |
248 | < | } else { |
249 | < | MPI::COMM_WORLD.Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node, |
250 | < | TAKE_THIS_TAG); |
251 | < | MPI::COMM_WORLD.Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG); |
248 | > | if(haveError) nodeZeroError(); |
249 | > | } |
250 | > | |
251 | > | else { |
252 | > | |
253 | > | myStatus = 1; |
254 | > | MPI_Send(&myStatus, 1, MPI_INT, which_node, |
255 | > | TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
256 | > | MPI_Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node, |
257 | > | TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD); |
258 | > | MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, |
259 | > | MPI_COMM_WORLD); |
260 | > | MPI_Recv(&myStatus, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, |
261 | > | MPI_COMM_WORLD, &istatus); |
262 | > | |
263 | > | if(!myStatus) nodeZeroError(); |
264 | } | |
265 | } | |
266 | < | sprintf(read_buffer, "GAMEOVER"); |
266 | > | myStatus = -1; |
267 | for (j = 0; j < mpiSim->getNumberProcessors(); j++) { | |
268 | < | MPI::COMM_WORLD.Send(read_buffer, BUFFERSIZE, MPI_CHAR, j, |
269 | < | TAKE_THIS_TAG); |
268 | > | MPI_Send( &myStatus, 1, MPI_INT, j, |
269 | > | TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
270 | } | |
271 | < | |
271 | > | |
272 | } else { | |
273 | + | |
274 | + | MPI_Bcast(boxMat, 9, MPI_DOUBLE, 0, MPI_COMM_WORLD); |
275 | ||
276 | done = 0; | |
277 | while (!done) { | |
278 | < | MPI::COMM_WORLD.Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0, |
279 | < | TAKE_THIS_TAG, istatus); |
280 | < | if (strcmp(read_buffer, "GAMEOVER")) { |
281 | < | done = 1; |
282 | < | continue; |
283 | < | } else { |
284 | < | MPI::COMM_WORLD.Recv(&which_atom, 1, MPI_INT, 0, |
285 | < | TAKE_THIS_TAG, istatus); |
286 | < | parseErr = parseDumpLine( read_buffer, which_atom ); |
287 | < | if( parseErr != NULL ){ |
288 | < | strcpy( painCave.errMsg, parseErr ); |
289 | < | painCave.isFatal = 1; |
290 | < | simError(); |
291 | < | } |
278 | > | |
279 | > | MPI_Recv(&myStatus, 1, MPI_INT, 0, |
280 | > | TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
281 | > | |
282 | > | if(!myStatus) anonymousNodeDie(); |
283 | > | |
284 | > | if(myStatus < 0) break; |
285 | > | |
286 | > | MPI_Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0, |
287 | > | TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus); |
288 | > | MPI_Recv(&which_atom, 1, MPI_INT, 0, |
289 | > | TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
290 | > | |
291 | > | myStatus = 1; |
292 | > | parseErr = parseDumpLine( read_buffer, which_atom ); |
293 | > | if( parseErr != NULL ){ |
294 | > | strcpy( painCave.errMsg, parseErr ); |
295 | > | myStatus = 0;; |
296 | > | simError(); |
297 | } | |
298 | + | |
299 | + | MPI_Send( &myStatus, 1, MPI_INT, 0, |
300 | + | TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
301 | + | |
302 | } | |
303 | } | |
304 | < | |
304 | > | |
305 | > | // last thing last, enable fatalities. |
306 | > | painCave.isEventLoop = 0; |
307 | > | |
308 | > | for(i=0;i<3;i++) |
309 | > | for(j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i]; |
310 | > | |
311 | > | simnfo->setBoxM( theBoxMat3 ); |
312 | > | |
313 | > | |
314 | #endif | |
315 | } | |
316 | ||
317 | < | char* InitializeFromFile::parseDumpLine(char* readLine, int atomIndex){ |
317 | > | char* InitializeFromFile::parseDumpLine(char* readLine, int globalIndex){ |
318 | ||
319 | char *foo; // the pointer to the current string token | |
320 | ||
# | Line 248 | Line 324 | char* InitializeFromFile::parseDumpLine(char* readLine | |
324 | double jx, jy, jz; // angular velocity placeholders; | |
325 | double qSqr, qLength; // needed to normalize the quaternion vector. | |
326 | ||
327 | < | Atom **atoms = entry_plug->atoms; |
327 | > | Atom **atoms = simnfo->atoms; |
328 | DirectionalAtom* dAtom; | |
329 | ||
330 | < | int n_atoms; |
330 | > | int j, n_atoms, atomIndex; |
331 | ||
332 | #ifdef IS_MPI | |
333 | n_atoms = mpiSim->getTotAtoms(); | |
334 | + | atomIndex=-1; |
335 | + | for (j=0; j < mpiSim->getMyNlocal(); j++) { |
336 | + | if (atoms[j]->getGlobalIndex() == globalIndex) atomIndex = j; |
337 | + | } |
338 | + | if (atomIndex == -1) { |
339 | + | sprintf( painCave.errMsg, |
340 | + | "Initialize from file error. Atom at index %d " |
341 | + | "in file %s does not exist on processor %d .\n", |
342 | + | globalIndex, c_in_name, mpiSim->getMyNode() ); |
343 | + | return strdup( painCave.errMsg ); |
344 | + | } |
345 | #else | |
346 | < | n_atoms = entry_plug->n_atoms; |
346 | > | n_atoms = simnfo->n_atoms; |
347 | > | atomIndex = globalIndex; |
348 | #endif // is_mpi | |
349 | ||
262 | – | |
350 | // set the string tokenizer | |
351 | ||
352 | foo = strtok(readLine, " ,;\t"); | |
# | Line 447 | Line 534 | char* InitializeFromFile::parseDumpLine(char* readLine | |
534 | atoms[atomIndex]->set_vx( vx ); | |
535 | atoms[atomIndex]->set_vy( vy ); | |
536 | atoms[atomIndex]->set_vz( vz ); | |
537 | + | |
538 | + | return NULL; |
539 | + | } |
540 | + | |
541 | + | |
542 | + | char* InitializeFromFile::parseBoxLine(char* readLine, double boxMat[9]){ |
543 | + | |
544 | + | char *foo; // the pointer to the current string token |
545 | + | int j; |
546 | + | |
547 | + | // set the string tokenizer |
548 | + | |
549 | + | foo = strtok(readLine, " ,;\t"); |
550 | + | // set the timeToken. |
551 | + | |
552 | + | if(foo == NULL){ |
553 | + | sprintf( painCave.errMsg, |
554 | + | "error in reading Time from %s\n", |
555 | + | c_in_name ); |
556 | + | return strdup( painCave.errMsg ); |
557 | + | } |
558 | + | simnfo->setTime( atof( foo ) ); |
559 | + | |
560 | + | // get the Hx vector |
561 | + | |
562 | + | foo = strtok(NULL, " ,;\t"); |
563 | + | if(foo == NULL){ |
564 | + | sprintf( painCave.errMsg, |
565 | + | "error in reading Hx[0] from %s\n", |
566 | + | c_in_name ); |
567 | + | return strdup( painCave.errMsg ); |
568 | + | } |
569 | + | boxMat[0] = atof( foo ); |
570 | + | |
571 | + | foo = strtok(NULL, " ,;\t"); |
572 | + | if(foo == NULL){ |
573 | + | sprintf( painCave.errMsg, |
574 | + | "error in reading Hx[1] from %s\n", |
575 | + | c_in_name ); |
576 | + | return strdup( painCave.errMsg ); |
577 | + | } |
578 | + | boxMat[1] = atof( foo ); |
579 | + | |
580 | + | foo = strtok(NULL, " ,;\t"); |
581 | + | if(foo == NULL){ |
582 | + | sprintf( painCave.errMsg, |
583 | + | "error in reading Hx[2] from %s\n", |
584 | + | c_in_name ); |
585 | + | return strdup( painCave.errMsg ); |
586 | + | } |
587 | + | boxMat[2] = atof( foo ); |
588 | + | |
589 | + | // get the Hy vector |
590 | + | |
591 | + | foo = strtok(NULL, " ,;\t"); |
592 | + | if(foo == NULL){ |
593 | + | sprintf( painCave.errMsg, |
594 | + | "error in reading Hy[0] from %s\n", |
595 | + | c_in_name ); |
596 | + | return strdup( painCave.errMsg ); |
597 | + | } |
598 | + | boxMat[3] = atof( foo ); |
599 | + | |
600 | + | foo = strtok(NULL, " ,;\t"); |
601 | + | if(foo == NULL){ |
602 | + | sprintf( painCave.errMsg, |
603 | + | "error in reading Hy[1] from %s\n", |
604 | + | c_in_name ); |
605 | + | return strdup( painCave.errMsg ); |
606 | + | } |
607 | + | boxMat[4] = atof( foo ); |
608 | + | |
609 | + | foo = strtok(NULL, " ,;\t"); |
610 | + | if(foo == NULL){ |
611 | + | sprintf( painCave.errMsg, |
612 | + | "error in reading Hy[2] from %s\n", |
613 | + | c_in_name ); |
614 | + | return strdup( painCave.errMsg ); |
615 | + | } |
616 | + | boxMat[5] = atof( foo ); |
617 | ||
618 | + | // get the Hz vector |
619 | + | |
620 | + | foo = strtok(NULL, " ,;\t"); |
621 | + | if(foo == NULL){ |
622 | + | sprintf( painCave.errMsg, |
623 | + | "error in reading Hz[0] from %s\n", |
624 | + | c_in_name ); |
625 | + | return strdup( painCave.errMsg ); |
626 | + | } |
627 | + | boxMat[6] = atof( foo ); |
628 | + | |
629 | + | foo = strtok(NULL, " ,;\t"); |
630 | + | if(foo == NULL){ |
631 | + | sprintf( painCave.errMsg, |
632 | + | "error in reading Hz[1] from %s\n", |
633 | + | c_in_name ); |
634 | + | return strdup( painCave.errMsg ); |
635 | + | } |
636 | + | boxMat[7] = atof( foo ); |
637 | + | |
638 | + | foo = strtok(NULL, " ,;\t"); |
639 | + | if(foo == NULL){ |
640 | + | sprintf( painCave.errMsg, |
641 | + | "error in reading Hz[2] from %s\n", |
642 | + | c_in_name ); |
643 | + | return strdup( painCave.errMsg ); |
644 | + | } |
645 | + | boxMat[8] = atof( foo ); |
646 | + | |
647 | return NULL; | |
648 | } | |
649 | + | |
650 | + | |
651 | + | #ifdef IS_MPI |
652 | + | |
653 | + | // a couple of functions to let us escape the read loop |
654 | + | |
655 | + | void initFile::nodeZeroError( void ){ |
656 | + | int j, myStatus; |
657 | + | |
658 | + | myStatus = 0; |
659 | + | for (j = 0; j < mpiSim->getNumberProcessors(); j++) { |
660 | + | MPI_Send( &myStatus, 1, MPI_INT, j, |
661 | + | TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
662 | + | } |
663 | + | |
664 | + | |
665 | + | MPI_Finalize(); |
666 | + | exit (0); |
667 | + | |
668 | + | } |
669 | + | |
670 | + | void initFile::anonymousNodeDie( void ){ |
671 | + | |
672 | + | MPI_Finalize(); |
673 | + | exit (0); |
674 | + | } |
675 | + | |
676 | + | #endif //is_mpi |
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