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#ifdef IS_MPI |
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#include <mpi.h> |
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#include <mpi++.h> |
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#include "mpiSimulation.hpp" |
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< |
#define TAKE_THIS_TAG 0 |
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> |
#define TAKE_THIS_TAG_CHAR 0 |
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> |
#define TAKE_THIS_TAG_INT 1 |
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> |
|
20 |
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namespace initFile{ |
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> |
void nodeZeroError( void ); |
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void anonymousNodeDie( void ); |
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} |
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|
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using namespace initFile; |
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|
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#endif // is_mpi |
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|
29 |
< |
InitializeFromFile :: InitializeFromFile( char *in_name ){ |
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InitializeFromFile::InitializeFromFile( char *in_name ){ |
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|
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#ifdef IS_MPI |
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if (worldRank == 0) { |
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#endif |
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return; |
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} |
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|
52 |
< |
InitializeFromFile :: ~InitializeFromFile( ){ |
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> |
InitializeFromFile::~InitializeFromFile( ){ |
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#ifdef IS_MPI |
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if (worldRank == 0) { |
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#endif |
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} |
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|
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|
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void InitializeFromFile :: read_xyz( SimInfo* the_entry_plug ){ |
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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; |
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+ |
double currTime; |
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double boxMat[9]; |
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double theBoxMat3[3][3]; |
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|
91 |
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entry_plug = the_entry_plug; |
91 |
> |
simnfo = the_simnfo; |
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|
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|
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#ifndef IS_MPI |
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|
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n_atoms = atoi( read_buffer ); |
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|
106 |
< |
Atom **atoms = entry_plug->atoms; |
106 |
> |
Atom **atoms = simnfo->atoms; |
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DirectionalAtom* dAtom; |
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|
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< |
if( n_atoms != entry_plug->n_atoms ){ |
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> |
if( n_atoms != simnfo->n_atoms ){ |
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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 ); |
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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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|
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//read and toss the comment line |
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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); |
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if(eof_test == NULL){ |
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simError(); |
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} |
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|
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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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|
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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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|
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MPI::Status istatus; |
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// first thing first, suspend fatalities. |
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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; |
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|
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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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|
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Atom **atoms = entry_plug->atoms; |
191 |
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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 ); |
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painCave.isFatal = 1; |
201 |
> |
c_in_name, n_atoms, simnfo->n_atoms ); |
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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 |
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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; |
212 |
> |
haveError = 1; |
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simError(); |
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} |
215 |
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|
216 |
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parseErr = parseBoxLine( read_buffer, boxMat, currTime ); |
217 |
+ |
if( parseErr != NULL ){ |
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strcpy( painCave.errMsg, parseErr ); |
219 |
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haveError = 1; |
220 |
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simError(); |
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} |
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|
223 |
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MPI_Bcast(boxMat, 9, MPI_DOUBLE, 0, MPI_COMM_WORLD ); |
224 |
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MPI_Bcast(&currTime, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD ); |
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|
226 |
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if(haveError) nodeZeroError(); |
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|
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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 ); |
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< |
painCave.isFatal = 1; |
237 |
> |
haveError= 1; |
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simError(); |
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} |
240 |
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|
241 |
+ |
if(haveError) nodeZeroError(); |
242 |
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|
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// Get the Node number which wants this atom: |
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which_node = AtomToProcMap[i]; |
245 |
< |
if (which_node == mpiSim->getMyNode()) { |
245 |
> |
if (which_node == 0) { |
246 |
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parseErr = parseDumpLine( read_buffer, i ); |
247 |
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if( parseErr != NULL ){ |
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strcpy( painCave.errMsg, parseErr ); |
249 |
< |
painCave.isFatal = 1; |
249 |
> |
haveError = 1; |
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simError(); |
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} |
252 |
< |
} else { |
253 |
< |
MPI::COMM_WORLD.Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node, |
254 |
< |
TAKE_THIS_TAG); |
255 |
< |
MPI::COMM_WORLD.Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG); |
252 |
> |
if(haveError) nodeZeroError(); |
253 |
> |
} |
254 |
> |
|
255 |
> |
else { |
256 |
> |
|
257 |
> |
myStatus = 1; |
258 |
> |
MPI_Send(&myStatus, 1, MPI_INT, which_node, |
259 |
> |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
260 |
> |
MPI_Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node, |
261 |
> |
TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD); |
262 |
> |
MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, |
263 |
> |
MPI_COMM_WORLD); |
264 |
> |
MPI_Recv(&myStatus, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, |
265 |
> |
MPI_COMM_WORLD, &istatus); |
266 |
> |
|
267 |
> |
if(!myStatus) nodeZeroError(); |
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} |
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} |
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< |
sprintf(read_buffer, "GAMEOVER"); |
270 |
> |
myStatus = -1; |
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for (j = 0; j < mpiSim->getNumberProcessors(); j++) { |
272 |
< |
MPI::COMM_WORLD.Send(read_buffer, BUFFERSIZE, MPI_CHAR, j, |
273 |
< |
TAKE_THIS_TAG); |
272 |
> |
MPI_Send( &myStatus, 1, MPI_INT, j, |
273 |
> |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
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} |
275 |
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|
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} else { |
277 |
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|
278 |
+ |
MPI_Bcast(boxMat, 9, MPI_DOUBLE, 0, MPI_COMM_WORLD); |
279 |
+ |
MPI_Bcast(&currTime, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD); |
280 |
+ |
|
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done = 0; |
282 |
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while (!done) { |
283 |
< |
MPI::COMM_WORLD.Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0, |
284 |
< |
TAKE_THIS_TAG, istatus); |
285 |
< |
if (strcmp(read_buffer, "GAMEOVER")) { |
286 |
< |
done = 1; |
287 |
< |
continue; |
288 |
< |
} else { |
289 |
< |
MPI::COMM_WORLD.Recv(&which_atom, 1, MPI_INT, 0, |
290 |
< |
TAKE_THIS_TAG, istatus); |
291 |
< |
|
292 |
< |
parseErr = parseDumpLine( read_buffer, which_atom ); |
293 |
< |
if( parseErr != NULL ){ |
294 |
< |
strcpy( painCave.errMsg, parseErr ); |
295 |
< |
painCave.isFatal = 1; |
296 |
< |
simError(); |
297 |
< |
} |
283 |
> |
|
284 |
> |
MPI_Recv(&myStatus, 1, MPI_INT, 0, |
285 |
> |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
286 |
> |
|
287 |
> |
if(!myStatus) anonymousNodeDie(); |
288 |
> |
|
289 |
> |
if(myStatus < 0) break; |
290 |
> |
|
291 |
> |
MPI_Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0, |
292 |
> |
TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus); |
293 |
> |
MPI_Recv(&which_atom, 1, MPI_INT, 0, |
294 |
> |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
295 |
> |
|
296 |
> |
myStatus = 1; |
297 |
> |
parseErr = parseDumpLine( read_buffer, which_atom ); |
298 |
> |
if( parseErr != NULL ){ |
299 |
> |
strcpy( painCave.errMsg, parseErr ); |
300 |
> |
myStatus = 0;; |
301 |
> |
simError(); |
302 |
|
} |
303 |
+ |
|
304 |
+ |
MPI_Send( &myStatus, 1, MPI_INT, 0, |
305 |
+ |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
306 |
+ |
|
307 |
|
} |
308 |
|
} |
309 |
< |
|
309 |
> |
|
310 |
> |
// last thing last, enable fatalities. |
311 |
> |
painCave.isEventLoop = 0; |
312 |
> |
|
313 |
> |
for(i=0;i<3;i++) |
314 |
> |
for(j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i]; |
315 |
> |
|
316 |
> |
simnfo->setBoxM( theBoxMat3 ); |
317 |
> |
simnfo->setTime( currTime ); |
318 |
> |
|
319 |
> |
|
320 |
|
#endif |
321 |
|
} |
322 |
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|
324 |
|
|
325 |
|
char *foo; // the pointer to the current string token |
326 |
|
|
327 |
< |
double rx, ry, rz; // position place holders |
328 |
< |
double vx, vy, vz; // velocity placeholders |
327 |
> |
double pos[3]; // position place holders |
328 |
> |
double vel[3]; // velocity placeholders |
329 |
|
double q[4]; // the quaternions |
330 |
|
double jx, jy, jz; // angular velocity placeholders; |
331 |
|
double qSqr, qLength; // needed to normalize the quaternion vector. |
332 |
|
|
333 |
< |
Atom **atoms = entry_plug->atoms; |
333 |
> |
Atom **atoms = simnfo->atoms; |
334 |
|
DirectionalAtom* dAtom; |
335 |
|
|
336 |
|
int j, n_atoms, atomIndex; |
349 |
|
return strdup( painCave.errMsg ); |
350 |
|
} |
351 |
|
#else |
352 |
< |
n_atoms = entry_plug->n_atoms; |
352 |
> |
n_atoms = simnfo->n_atoms; |
353 |
|
atomIndex = globalIndex; |
354 |
|
#endif // is_mpi |
355 |
|
|
378 |
|
c_in_name, n_atoms, atomIndex ); |
379 |
|
return strdup( painCave.errMsg ); |
380 |
|
} |
381 |
< |
rx = atof( foo ); |
381 |
> |
pos[0] = atof( foo ); |
382 |
|
|
383 |
|
foo = strtok(NULL, " ,;\t"); |
384 |
|
if(foo == NULL){ |
388 |
|
c_in_name, n_atoms, atomIndex ); |
389 |
|
return strdup( painCave.errMsg ); |
390 |
|
} |
391 |
< |
ry = atof( foo ); |
391 |
> |
pos[1] = atof( foo ); |
392 |
|
|
393 |
|
foo = strtok(NULL, " ,;\t"); |
394 |
|
if(foo == NULL){ |
398 |
|
c_in_name, n_atoms, atomIndex ); |
399 |
|
return strdup( painCave.errMsg ); |
400 |
|
} |
401 |
< |
rz = atof( foo ); |
401 |
> |
pos[2] = atof( foo ); |
402 |
|
|
403 |
|
|
404 |
|
// get the velocities |
411 |
|
c_in_name, n_atoms, atomIndex ); |
412 |
|
return strdup( painCave.errMsg ); |
413 |
|
} |
414 |
< |
vx = atof( foo ); |
414 |
> |
vel[0] = atof( foo ); |
415 |
|
|
416 |
|
foo = strtok(NULL, " ,;\t"); |
417 |
|
if(foo == NULL){ |
421 |
|
c_in_name, n_atoms, atomIndex ); |
422 |
|
return strdup( painCave.errMsg ); |
423 |
|
} |
424 |
< |
vy = atof( foo ); |
424 |
> |
vel[1] = atof( foo ); |
425 |
|
|
426 |
|
foo = strtok(NULL, " ,;\t"); |
427 |
|
if(foo == NULL){ |
431 |
|
c_in_name, n_atoms, atomIndex ); |
432 |
|
return strdup( painCave.errMsg ); |
433 |
|
} |
434 |
< |
vz = atof( foo ); |
434 |
> |
vel[2] = atof( foo ); |
435 |
|
|
436 |
|
|
437 |
|
// get the quaternions |
533 |
|
|
534 |
|
// add the positions and velocities to the atom |
535 |
|
|
536 |
< |
atoms[atomIndex]->setX( rx ); |
537 |
< |
atoms[atomIndex]->setY( ry ); |
457 |
< |
atoms[atomIndex]->setZ( rz ); |
458 |
< |
|
459 |
< |
atoms[atomIndex]->set_vx( vx ); |
460 |
< |
atoms[atomIndex]->set_vy( vy ); |
461 |
< |
atoms[atomIndex]->set_vz( vz ); |
536 |
> |
atoms[atomIndex]->setPos( pos ); |
537 |
> |
atoms[atomIndex]->setVel( vel ); |
538 |
|
|
539 |
|
return NULL; |
540 |
|
} |
541 |
+ |
|
542 |
+ |
|
543 |
+ |
char* InitializeFromFile::parseBoxLine(char* readLine, double boxMat[9], |
544 |
+ |
double &time ){ |
545 |
+ |
|
546 |
+ |
char *foo; // the pointer to the current string token |
547 |
+ |
int j; |
548 |
+ |
|
549 |
+ |
// set the string tokenizer |
550 |
+ |
|
551 |
+ |
foo = strtok(readLine, " ,;\t"); |
552 |
+ |
// set the timeToken. |
553 |
+ |
|
554 |
+ |
if(foo == NULL){ |
555 |
+ |
sprintf( painCave.errMsg, |
556 |
+ |
"error in reading Time from %s\n", |
557 |
+ |
c_in_name ); |
558 |
+ |
return strdup( painCave.errMsg ); |
559 |
+ |
} |
560 |
+ |
time = atof( foo ); |
561 |
+ |
|
562 |
+ |
// get the Hx vector |
563 |
+ |
|
564 |
+ |
foo = strtok(NULL, " ,;\t"); |
565 |
+ |
if(foo == NULL){ |
566 |
+ |
sprintf( painCave.errMsg, |
567 |
+ |
"error in reading Hx[0] from %s\n", |
568 |
+ |
c_in_name ); |
569 |
+ |
return strdup( painCave.errMsg ); |
570 |
+ |
} |
571 |
+ |
boxMat[0] = atof( foo ); |
572 |
+ |
|
573 |
+ |
foo = strtok(NULL, " ,;\t"); |
574 |
+ |
if(foo == NULL){ |
575 |
+ |
sprintf( painCave.errMsg, |
576 |
+ |
"error in reading Hx[1] from %s\n", |
577 |
+ |
c_in_name ); |
578 |
+ |
return strdup( painCave.errMsg ); |
579 |
+ |
} |
580 |
+ |
boxMat[1] = atof( foo ); |
581 |
+ |
|
582 |
+ |
foo = strtok(NULL, " ,;\t"); |
583 |
+ |
if(foo == NULL){ |
584 |
+ |
sprintf( painCave.errMsg, |
585 |
+ |
"error in reading Hx[2] from %s\n", |
586 |
+ |
c_in_name ); |
587 |
+ |
return strdup( painCave.errMsg ); |
588 |
+ |
} |
589 |
+ |
boxMat[2] = atof( foo ); |
590 |
+ |
|
591 |
+ |
// get the Hy vector |
592 |
+ |
|
593 |
+ |
foo = strtok(NULL, " ,;\t"); |
594 |
+ |
if(foo == NULL){ |
595 |
+ |
sprintf( painCave.errMsg, |
596 |
+ |
"error in reading Hy[0] from %s\n", |
597 |
+ |
c_in_name ); |
598 |
+ |
return strdup( painCave.errMsg ); |
599 |
+ |
} |
600 |
+ |
boxMat[3] = atof( foo ); |
601 |
+ |
|
602 |
+ |
foo = strtok(NULL, " ,;\t"); |
603 |
+ |
if(foo == NULL){ |
604 |
+ |
sprintf( painCave.errMsg, |
605 |
+ |
"error in reading Hy[1] from %s\n", |
606 |
+ |
c_in_name ); |
607 |
+ |
return strdup( painCave.errMsg ); |
608 |
+ |
} |
609 |
+ |
boxMat[4] = atof( foo ); |
610 |
+ |
|
611 |
+ |
foo = strtok(NULL, " ,;\t"); |
612 |
+ |
if(foo == NULL){ |
613 |
+ |
sprintf( painCave.errMsg, |
614 |
+ |
"error in reading Hy[2] from %s\n", |
615 |
+ |
c_in_name ); |
616 |
+ |
return strdup( painCave.errMsg ); |
617 |
+ |
} |
618 |
+ |
boxMat[5] = atof( foo ); |
619 |
+ |
|
620 |
+ |
// get the Hz vector |
621 |
+ |
|
622 |
+ |
foo = strtok(NULL, " ,;\t"); |
623 |
+ |
if(foo == NULL){ |
624 |
+ |
sprintf( painCave.errMsg, |
625 |
+ |
"error in reading Hz[0] from %s\n", |
626 |
+ |
c_in_name ); |
627 |
+ |
return strdup( painCave.errMsg ); |
628 |
+ |
} |
629 |
+ |
boxMat[6] = atof( foo ); |
630 |
+ |
|
631 |
+ |
foo = strtok(NULL, " ,;\t"); |
632 |
+ |
if(foo == NULL){ |
633 |
+ |
sprintf( painCave.errMsg, |
634 |
+ |
"error in reading Hz[1] from %s\n", |
635 |
+ |
c_in_name ); |
636 |
+ |
return strdup( painCave.errMsg ); |
637 |
+ |
} |
638 |
+ |
boxMat[7] = atof( foo ); |
639 |
+ |
|
640 |
+ |
foo = strtok(NULL, " ,;\t"); |
641 |
+ |
if(foo == NULL){ |
642 |
+ |
sprintf( painCave.errMsg, |
643 |
+ |
"error in reading Hz[2] from %s\n", |
644 |
+ |
c_in_name ); |
645 |
+ |
return strdup( painCave.errMsg ); |
646 |
+ |
} |
647 |
+ |
boxMat[8] = atof( foo ); |
648 |
+ |
|
649 |
+ |
return NULL; |
650 |
+ |
} |
651 |
+ |
|
652 |
+ |
|
653 |
+ |
#ifdef IS_MPI |
654 |
+ |
|
655 |
+ |
// a couple of functions to let us escape the read loop |
656 |
+ |
|
657 |
+ |
void initFile::nodeZeroError( void ){ |
658 |
+ |
int j, myStatus; |
659 |
+ |
|
660 |
+ |
myStatus = 0; |
661 |
+ |
for (j = 0; j < mpiSim->getNumberProcessors(); j++) { |
662 |
+ |
MPI_Send( &myStatus, 1, MPI_INT, j, |
663 |
+ |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
664 |
+ |
} |
665 |
+ |
|
666 |
+ |
|
667 |
+ |
MPI_Finalize(); |
668 |
+ |
exit (0); |
669 |
+ |
|
670 |
+ |
} |
671 |
+ |
|
672 |
+ |
void initFile::anonymousNodeDie( void ){ |
673 |
+ |
|
674 |
+ |
MPI_Finalize(); |
675 |
+ |
exit (0); |
676 |
+ |
} |
677 |
+ |
|
678 |
+ |
#endif //is_mpi |