13 |
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14 |
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#ifdef IS_MPI |
15 |
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#include <mpi.h> |
16 |
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#include <mpi++.h> |
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#include "mpiSimulation.hpp" |
17 |
< |
#define TAKE_THIS_TAG 0 |
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> |
#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 ); |
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> |
} |
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|
25 |
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using namespace initFile; |
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|
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#endif // is_mpi |
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|
29 |
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InitializeFromFile :: InitializeFromFile( char *in_name ){ |
69 |
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} |
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|
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|
72 |
< |
void InitializeFromFile :: read_xyz( SimInfo* the_entry_plug ){ |
72 |
> |
void InitializeFromFile :: readInit( SimInfo* the_simnfo ){ |
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|
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int i, j, done, which_node, which_atom; // loop counter |
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|
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char *eof_test; // ptr to see when we reach the end of the file |
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char *parseErr; |
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int procIndex; |
86 |
+ |
double currTime; |
87 |
+ |
double boxMat[9]; |
88 |
+ |
double theBoxMat3[3][3]; |
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|
90 |
< |
entry_plug = the_entry_plug; |
90 |
> |
simnfo = the_simnfo; |
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|
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|
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#ifndef IS_MPI |
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n_atoms = atoi( read_buffer ); |
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|
105 |
< |
Atom **atoms = entry_plug->atoms; |
105 |
> |
Atom **atoms = simnfo->atoms; |
106 |
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DirectionalAtom* dAtom; |
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|
108 |
< |
if( n_atoms != entry_plug->n_atoms ){ |
108 |
> |
if( n_atoms != simnfo->n_atoms ){ |
109 |
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sprintf( painCave.errMsg, |
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"Initialize from File error. %s n_atoms, %d, " |
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"does not match the BASS file's n_atoms, %d.\n", |
112 |
< |
c_in_name, n_atoms, entry_plug->n_atoms ); |
112 |
> |
c_in_name, n_atoms, simnfo->n_atoms ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
117 |
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//read and toss the comment line |
117 |
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//read the box mat from the comment line |
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|
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eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
120 |
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if(eof_test == NULL){ |
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simError(); |
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} |
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|
127 |
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parseErr = parseBoxLine( read_buffer, boxMat, currTime ); |
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if( parseErr != NULL ){ |
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strcpy( painCave.errMsg, parseErr ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
134 |
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for(i=0;i<3;i++) |
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for(j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i]; |
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|
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simnfo->setBoxM( theBoxMat3 ); |
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simnfo->setTime( currTime ); |
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|
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|
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for( i=0; i < n_atoms; i++){ |
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|
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eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
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strcpy( painCave.errMsg, parseErr ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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} |
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} |
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// MPI Section of code.......... |
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#else //IS_MPI |
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|
167 |
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MPI::Status istatus; |
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// first thing first, suspend fatalities. |
168 |
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painCave.isEventLoop = 1; |
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|
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int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone |
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int haveError; |
172 |
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|
173 |
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MPI_Status istatus; |
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int *AtomToProcMap = mpiSim->getAtomToProcMap(); |
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|
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|
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haveError = 0; |
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if (worldRank == 0) { |
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|
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eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
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if( eof_test == NULL ){ |
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sprintf( painCave.errMsg, |
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"Error reading 1st line of %d \n ",c_in_name); |
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painCave.isFatal = 1; |
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haveError = 1; |
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simError(); |
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} |
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|
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n_atoms = atoi( read_buffer ); |
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|
190 |
< |
Atom **atoms = entry_plug->atoms; |
190 |
> |
Atom **atoms = simnfo->atoms; |
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DirectionalAtom* dAtom; |
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|
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// Check to see that the number of atoms in the intial configuration file is the |
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sprintf( painCave.errMsg, |
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"Initialize from File error. %s n_atoms, %d, " |
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"does not match the BASS file's n_atoms, %d.\n", |
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< |
c_in_name, n_atoms, entry_plug->n_atoms ); |
201 |
< |
painCave.isFatal = 1; |
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> |
c_in_name, n_atoms, simnfo->n_atoms ); |
201 |
> |
haveError= 1; |
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simError(); |
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} |
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|
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//read and toss the comment line |
205 |
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//read the boxMat from the comment line |
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|
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eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
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if(eof_test == NULL){ |
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sprintf( painCave.errMsg, |
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"error in reading commment in %s\n", c_in_name); |
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< |
painCave.isFatal = 1; |
211 |
> |
haveError = 1; |
212 |
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simError(); |
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} |
214 |
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|
215 |
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parseErr = parseBoxLine( read_buffer, boxMat, currTime ); |
216 |
+ |
if( parseErr != NULL ){ |
217 |
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strcpy( painCave.errMsg, parseErr ); |
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+ |
haveError = 1; |
219 |
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simError(); |
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} |
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|
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MPI_Bcast(boxMat, 9, MPI_DOUBLE, 0, MPI_COMM_WORLD ); |
223 |
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MPI_Bcast(&currTime, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD ); |
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|
225 |
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if(haveError) nodeZeroError(); |
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for (i=0 ; i < mpiSim->getTotAtoms(); i++) { |
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|
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"natoms = %d; index = %d\n" |
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"error reading the line from the file.\n", |
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c_in_name, n_atoms, i ); |
236 |
< |
painCave.isFatal = 1; |
236 |
> |
haveError= 1; |
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simError(); |
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} |
239 |
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|
240 |
+ |
if(haveError) nodeZeroError(); |
241 |
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|
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// Get the Node number which wants this atom: |
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which_node = AtomToProcMap[i]; |
244 |
< |
if (which_node == mpiSim->getMyNode()) { |
244 |
> |
if (which_node == 0) { |
245 |
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parseErr = parseDumpLine( read_buffer, i ); |
246 |
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if( parseErr != NULL ){ |
247 |
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strcpy( painCave.errMsg, parseErr ); |
248 |
< |
painCave.isFatal = 1; |
248 |
> |
haveError = 1; |
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simError(); |
250 |
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} |
251 |
< |
} else { |
252 |
< |
MPI::COMM_WORLD.Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node, |
253 |
< |
TAKE_THIS_TAG); |
254 |
< |
MPI::COMM_WORLD.Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG); |
251 |
> |
if(haveError) nodeZeroError(); |
252 |
> |
} |
253 |
> |
|
254 |
> |
else { |
255 |
> |
|
256 |
> |
myStatus = 1; |
257 |
> |
MPI_Send(&myStatus, 1, MPI_INT, which_node, |
258 |
> |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
259 |
> |
MPI_Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node, |
260 |
> |
TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD); |
261 |
> |
MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, |
262 |
> |
MPI_COMM_WORLD); |
263 |
> |
MPI_Recv(&myStatus, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, |
264 |
> |
MPI_COMM_WORLD, &istatus); |
265 |
> |
|
266 |
> |
if(!myStatus) nodeZeroError(); |
267 |
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} |
268 |
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} |
269 |
< |
sprintf(read_buffer, "GAMEOVER"); |
269 |
> |
myStatus = -1; |
270 |
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for (j = 0; j < mpiSim->getNumberProcessors(); j++) { |
271 |
< |
MPI::COMM_WORLD.Send(read_buffer, BUFFERSIZE, MPI_CHAR, j, |
272 |
< |
TAKE_THIS_TAG); |
271 |
> |
MPI_Send( &myStatus, 1, MPI_INT, j, |
272 |
> |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
273 |
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} |
274 |
< |
|
274 |
> |
|
275 |
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} else { |
276 |
+ |
|
277 |
+ |
MPI_Bcast(boxMat, 9, MPI_DOUBLE, 0, MPI_COMM_WORLD); |
278 |
+ |
MPI_Bcast(&currTime, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD); |
279 |
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|
280 |
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done = 0; |
281 |
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while (!done) { |
282 |
< |
MPI::COMM_WORLD.Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0, |
283 |
< |
TAKE_THIS_TAG, istatus); |
284 |
< |
if (strcmp(read_buffer, "GAMEOVER")) { |
285 |
< |
done = 1; |
286 |
< |
continue; |
287 |
< |
} else { |
288 |
< |
MPI::COMM_WORLD.Recv(&which_atom, 1, MPI_INT, 0, |
289 |
< |
TAKE_THIS_TAG, istatus); |
290 |
< |
parseErr = parseDumpLine( read_buffer, which_atom ); |
291 |
< |
if( parseErr != NULL ){ |
292 |
< |
strcpy( painCave.errMsg, parseErr ); |
293 |
< |
painCave.isFatal = 1; |
294 |
< |
simError(); |
295 |
< |
} |
282 |
> |
|
283 |
> |
MPI_Recv(&myStatus, 1, MPI_INT, 0, |
284 |
> |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
285 |
> |
|
286 |
> |
if(!myStatus) anonymousNodeDie(); |
287 |
> |
|
288 |
> |
if(myStatus < 0) break; |
289 |
> |
|
290 |
> |
MPI_Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0, |
291 |
> |
TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus); |
292 |
> |
MPI_Recv(&which_atom, 1, MPI_INT, 0, |
293 |
> |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
294 |
> |
|
295 |
> |
myStatus = 1; |
296 |
> |
parseErr = parseDumpLine( read_buffer, which_atom ); |
297 |
> |
if( parseErr != NULL ){ |
298 |
> |
strcpy( painCave.errMsg, parseErr ); |
299 |
> |
myStatus = 0;; |
300 |
> |
simError(); |
301 |
|
} |
302 |
+ |
|
303 |
+ |
MPI_Send( &myStatus, 1, MPI_INT, 0, |
304 |
+ |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
305 |
+ |
|
306 |
|
} |
307 |
|
} |
308 |
< |
|
308 |
> |
|
309 |
> |
// last thing last, enable fatalities. |
310 |
> |
painCave.isEventLoop = 0; |
311 |
> |
|
312 |
> |
for(i=0;i<3;i++) |
313 |
> |
for(j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i]; |
314 |
> |
|
315 |
> |
simnfo->setBoxM( theBoxMat3 ); |
316 |
> |
simnfo->setTime( currTime ); |
317 |
> |
|
318 |
> |
|
319 |
|
#endif |
320 |
|
} |
321 |
|
|
322 |
< |
char* InitializeFromFile::parseDumpLine(char* readLine, int atomIndex){ |
322 |
> |
char* InitializeFromFile::parseDumpLine(char* readLine, int globalIndex){ |
323 |
|
|
324 |
|
char *foo; // the pointer to the current string token |
325 |
|
|
329 |
|
double jx, jy, jz; // angular velocity placeholders; |
330 |
|
double qSqr, qLength; // needed to normalize the quaternion vector. |
331 |
|
|
332 |
< |
Atom **atoms = entry_plug->atoms; |
332 |
> |
Atom **atoms = simnfo->atoms; |
333 |
|
DirectionalAtom* dAtom; |
334 |
|
|
335 |
< |
int n_atoms; |
335 |
> |
int j, n_atoms, atomIndex; |
336 |
|
|
337 |
|
#ifdef IS_MPI |
338 |
|
n_atoms = mpiSim->getTotAtoms(); |
339 |
+ |
atomIndex=-1; |
340 |
+ |
for (j=0; j < mpiSim->getMyNlocal(); j++) { |
341 |
+ |
if (atoms[j]->getGlobalIndex() == globalIndex) atomIndex = j; |
342 |
+ |
} |
343 |
+ |
if (atomIndex == -1) { |
344 |
+ |
sprintf( painCave.errMsg, |
345 |
+ |
"Initialize from file error. Atom at index %d " |
346 |
+ |
"in file %s does not exist on processor %d .\n", |
347 |
+ |
globalIndex, c_in_name, mpiSim->getMyNode() ); |
348 |
+ |
return strdup( painCave.errMsg ); |
349 |
+ |
} |
350 |
|
#else |
351 |
< |
n_atoms = entry_plug->n_atoms; |
351 |
> |
n_atoms = simnfo->n_atoms; |
352 |
> |
atomIndex = globalIndex; |
353 |
|
#endif // is_mpi |
354 |
|
|
262 |
– |
|
355 |
|
// set the string tokenizer |
356 |
|
|
357 |
|
foo = strtok(readLine, " ,;\t"); |
542 |
|
|
543 |
|
return NULL; |
544 |
|
} |
545 |
+ |
|
546 |
+ |
|
547 |
+ |
char* InitializeFromFile::parseBoxLine(char* readLine, double boxMat[9], |
548 |
+ |
double &time ){ |
549 |
+ |
|
550 |
+ |
char *foo; // the pointer to the current string token |
551 |
+ |
int j; |
552 |
+ |
|
553 |
+ |
// set the string tokenizer |
554 |
+ |
|
555 |
+ |
foo = strtok(readLine, " ,;\t"); |
556 |
+ |
// set the timeToken. |
557 |
+ |
|
558 |
+ |
if(foo == NULL){ |
559 |
+ |
sprintf( painCave.errMsg, |
560 |
+ |
"error in reading Time from %s\n", |
561 |
+ |
c_in_name ); |
562 |
+ |
return strdup( painCave.errMsg ); |
563 |
+ |
} |
564 |
+ |
time = atof( foo ); |
565 |
+ |
|
566 |
+ |
// get the Hx vector |
567 |
+ |
|
568 |
+ |
foo = strtok(NULL, " ,;\t"); |
569 |
+ |
if(foo == NULL){ |
570 |
+ |
sprintf( painCave.errMsg, |
571 |
+ |
"error in reading Hx[0] from %s\n", |
572 |
+ |
c_in_name ); |
573 |
+ |
return strdup( painCave.errMsg ); |
574 |
+ |
} |
575 |
+ |
boxMat[0] = atof( foo ); |
576 |
+ |
|
577 |
+ |
foo = strtok(NULL, " ,;\t"); |
578 |
+ |
if(foo == NULL){ |
579 |
+ |
sprintf( painCave.errMsg, |
580 |
+ |
"error in reading Hx[1] from %s\n", |
581 |
+ |
c_in_name ); |
582 |
+ |
return strdup( painCave.errMsg ); |
583 |
+ |
} |
584 |
+ |
boxMat[1] = atof( foo ); |
585 |
+ |
|
586 |
+ |
foo = strtok(NULL, " ,;\t"); |
587 |
+ |
if(foo == NULL){ |
588 |
+ |
sprintf( painCave.errMsg, |
589 |
+ |
"error in reading Hx[2] from %s\n", |
590 |
+ |
c_in_name ); |
591 |
+ |
return strdup( painCave.errMsg ); |
592 |
+ |
} |
593 |
+ |
boxMat[2] = atof( foo ); |
594 |
+ |
|
595 |
+ |
// get the Hy vector |
596 |
+ |
|
597 |
+ |
foo = strtok(NULL, " ,;\t"); |
598 |
+ |
if(foo == NULL){ |
599 |
+ |
sprintf( painCave.errMsg, |
600 |
+ |
"error in reading Hy[0] from %s\n", |
601 |
+ |
c_in_name ); |
602 |
+ |
return strdup( painCave.errMsg ); |
603 |
+ |
} |
604 |
+ |
boxMat[3] = atof( foo ); |
605 |
+ |
|
606 |
+ |
foo = strtok(NULL, " ,;\t"); |
607 |
+ |
if(foo == NULL){ |
608 |
+ |
sprintf( painCave.errMsg, |
609 |
+ |
"error in reading Hy[1] from %s\n", |
610 |
+ |
c_in_name ); |
611 |
+ |
return strdup( painCave.errMsg ); |
612 |
+ |
} |
613 |
+ |
boxMat[4] = atof( foo ); |
614 |
+ |
|
615 |
+ |
foo = strtok(NULL, " ,;\t"); |
616 |
+ |
if(foo == NULL){ |
617 |
+ |
sprintf( painCave.errMsg, |
618 |
+ |
"error in reading Hy[2] from %s\n", |
619 |
+ |
c_in_name ); |
620 |
+ |
return strdup( painCave.errMsg ); |
621 |
+ |
} |
622 |
+ |
boxMat[5] = atof( foo ); |
623 |
+ |
|
624 |
+ |
// get the Hz vector |
625 |
+ |
|
626 |
+ |
foo = strtok(NULL, " ,;\t"); |
627 |
+ |
if(foo == NULL){ |
628 |
+ |
sprintf( painCave.errMsg, |
629 |
+ |
"error in reading Hz[0] from %s\n", |
630 |
+ |
c_in_name ); |
631 |
+ |
return strdup( painCave.errMsg ); |
632 |
+ |
} |
633 |
+ |
boxMat[6] = atof( foo ); |
634 |
+ |
|
635 |
+ |
foo = strtok(NULL, " ,;\t"); |
636 |
+ |
if(foo == NULL){ |
637 |
+ |
sprintf( painCave.errMsg, |
638 |
+ |
"error in reading Hz[1] from %s\n", |
639 |
+ |
c_in_name ); |
640 |
+ |
return strdup( painCave.errMsg ); |
641 |
+ |
} |
642 |
+ |
boxMat[7] = atof( foo ); |
643 |
+ |
|
644 |
+ |
foo = strtok(NULL, " ,;\t"); |
645 |
+ |
if(foo == NULL){ |
646 |
+ |
sprintf( painCave.errMsg, |
647 |
+ |
"error in reading Hz[2] from %s\n", |
648 |
+ |
c_in_name ); |
649 |
+ |
return strdup( painCave.errMsg ); |
650 |
+ |
} |
651 |
+ |
boxMat[8] = atof( foo ); |
652 |
+ |
|
653 |
+ |
return NULL; |
654 |
+ |
} |
655 |
+ |
|
656 |
+ |
|
657 |
+ |
#ifdef IS_MPI |
658 |
+ |
|
659 |
+ |
// a couple of functions to let us escape the read loop |
660 |
+ |
|
661 |
+ |
void initFile::nodeZeroError( void ){ |
662 |
+ |
int j, myStatus; |
663 |
+ |
|
664 |
+ |
myStatus = 0; |
665 |
+ |
for (j = 0; j < mpiSim->getNumberProcessors(); j++) { |
666 |
+ |
MPI_Send( &myStatus, 1, MPI_INT, j, |
667 |
+ |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
668 |
+ |
} |
669 |
+ |
|
670 |
+ |
|
671 |
+ |
MPI_Finalize(); |
672 |
+ |
exit (0); |
673 |
+ |
|
674 |
+ |
} |
675 |
+ |
|
676 |
+ |
void initFile::anonymousNodeDie( void ){ |
677 |
+ |
|
678 |
+ |
MPI_Finalize(); |
679 |
+ |
exit (0); |
680 |
+ |
} |
681 |
+ |
|
682 |
+ |
#endif //is_mpi |