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 ){ |
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 |
|
|
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 |
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){ |
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); |
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 |
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 |
|
|
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 |
|
|
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 |
< |
|
287 |
< |
parseErr = parseDumpLine( read_buffer, which_atom ); |
288 |
< |
if( parseErr != NULL ){ |
289 |
< |
strcpy( painCave.errMsg, parseErr ); |
290 |
< |
painCave.isFatal = 1; |
291 |
< |
simError(); |
292 |
< |
} |
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 |
|
|
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 j, n_atoms, atomIndex; |
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 |
|
|
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->currentTime = 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 |