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#include "simError.h" |
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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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|
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#define TAKE_THIS_TAG 0 |
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#endif // is_mpi |
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void InitializeFromFile :: read_xyz( SimInfo* the_entry_plug ){ |
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int i; // loop counter |
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int i, j, done, which_node, which_atom; // loop counter |
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const int BUFFERSIZE = 2000; // size of the read buffer |
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int n_atoms; // the number of atoms |
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// MPI Section of code.......... |
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#else //IS_MPI |
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int masterIndex; |
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int nodeAtomsStart; |
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int nodeAtomsEnd; |
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int mpiErr; |
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int sendError; |
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MPI::Status istatus; |
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int *AtomToProcMap = mpiSim->getAtomToProcMap(); |
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MPI_Status istatus[MPI_STATUS_SIZE]; |
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|
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if (worldRank == 0) { |
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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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// Read Proc 0 share of the xyz file... |
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masterIndex = 0; |
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for( i=0; i <= mpiSim->getMyAtomEnd(); i++){ |
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for (i=0 ; i < mpiSim->getTotAtoms(); i++) { |
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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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simError(); |
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} |
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parseErr = parseDumpLine( read_buffer, i ); |
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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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masterIndex++; |
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} |
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} |
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|
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sprintf(checkPointMsg, |
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"Node 0 has successfully read positions from input file."); |
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MPIcheckPoint(); |
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|
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for (procIndex = 1; procIndex < mpiSim->getNumberProcessors(); |
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procIndex++){ |
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if (worldRank == 0) { |
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|
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mpiErr = MPI_Recv(&nodeAtomsStart,1,MPI_INT,procIndex,TAKE_THIS_TAG,MPI_COMM_WORLD, |
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istatus); |
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|
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mpiErr = MPI_Recv(&nodeAtomsEnd,1,MPI_INT,procIndex,TAKE_THIS_TAG,MPI_COMM_WORLD, |
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istatus); |
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// Make sure where node 0 is reading from, matches where the receiving node |
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// expects it to be. |
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|
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if (masterIndex != nodeAtomsStart){ |
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sendError = 1; |
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mpiErr = MPI_Send(&sendError,1,MPI_INT,procIndex,TAKE_THIS_TAG,MPI_COMM_WORLD); |
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sprintf(painCave.errMsg, |
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"Initialize from file error: atoms start index (%d) for " |
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"node %d not equal to master index (%d)",nodeAtomsStart,procIndex,masterIndex ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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sendError = 0; |
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mpiErr = MPI_Send(&sendError,1,MPI_INT,procIndex,TAKE_THIS_TAG,MPI_COMM_WORLD); |
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|
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for ( i = nodeAtomsStart; i <= nodeAtomsEnd; i++){ |
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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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|
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sprintf(read_buffer,"ERROR"); |
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mpiErr = MPI_Send(read_buffer,BUFFERSIZE,MPI_CHAR,procIndex,TAKE_THIS_TAG,MPI_COMM_WORLD); |
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|
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sprintf(painCave.errMsg, |
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"error in reading file %s\n" |
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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; |
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simError(); |
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} |
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|
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mpiErr = MPI_Send(read_buffer,BUFFERSIZE,MPI_CHAR,procIndex,TAKE_THIS_TAG,MPI_COMM_WORLD); |
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mpiErr = MPI_Recv(&sendError,1,MPI_INT,procIndex,TAKE_THIS_TAG,MPI_COMM_WORLD, |
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istatus); |
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if (sendError) MPIcheckPoint(); |
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|
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masterIndex++; |
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// Get the Node number which wants this atom: |
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which_node = AtomToProcMap[i]; |
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if (which_node == mpiSim->getMyNode()) { |
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parseErr = parseDumpLine( read_buffer, i ); |
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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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} else { |
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MPI::COMM_WORLD.Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node, |
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TAKE_THIS_TAG); |
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MPI::COMM_WORLD.Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG); |
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} |
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} |
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else if(worldRank == procIndex){ |
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nodeAtomsStart = mpiSim->getMyAtomStart(); |
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nodeAtomsEnd = mpiSim->getMyAtomEnd(); |
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mpiErr = MPI_Send(&nodeAtomsStart,1,MPI_INT,0,TAKE_THIS_TAG,MPI_COMM_WORLD); |
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mpiErr = MPI_Send(&nodeAtomsEnd,1,MPI_INT,0,TAKE_THIS_TAG,MPI_COMM_WORLD); |
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|
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mpiErr = MPI_Recv(&sendError,1,MPI_INT,0,TAKE_THIS_TAG,MPI_COMM_WORLD, |
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istatus); |
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if (sendError) MPIcheckPoint(); |
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|
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for ( i = 0; i < entry_plug->n_atoms; i++){ |
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|
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mpiErr = MPI_Recv(&read_buffer,BUFFERSIZE,MPI_CHAR,0,TAKE_THIS_TAG,MPI_COMM_WORLD, |
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istatus); |
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|
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if(!strcmp(read_buffer, "ERROR")) MPIcheckPoint(); |
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|
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parseErr = parseDumpLine( read_buffer, i ); |
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if( parseErr != NULL ){ |
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sendError = 1; |
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mpiErr = MPI_Send(&sendError,1,MPI_INT,0,TAKE_THIS_TAG,MPI_COMM_WORLD); |
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|
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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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sendError = 0; |
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mpiErr = MPI_Send(&sendError,1,MPI_INT,0,TAKE_THIS_TAG,MPI_COMM_WORLD); |
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sprintf(read_buffer, "GAMEOVER"); |
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for (j = 0; j < mpiSim->getNumberProcessors(); j++) { |
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MPI::COMM_WORLD.Send(read_buffer, BUFFERSIZE, MPI_CHAR, j, |
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TAKE_THIS_TAG); |
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} |
215 |
> |
|
216 |
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} else { |
217 |
> |
|
218 |
> |
done = 0; |
219 |
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while (!done) { |
220 |
> |
MPI::COMM_WORLD.Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0, |
221 |
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TAKE_THIS_TAG, istatus); |
222 |
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if (strcmp(read_buffer, "GAMEOVER")) { |
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done = 1; |
224 |
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continue; |
225 |
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} else { |
226 |
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MPI::COMM_WORLD.Recv(&which_atom, 1, MPI_INT, 0, |
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> |
TAKE_THIS_TAG, istatus); |
228 |
> |
|
229 |
> |
parseErr = parseDumpLine( read_buffer, which_atom ); |
230 |
> |
if( parseErr != NULL ){ |
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> |
strcpy( painCave.errMsg, parseErr ); |
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> |
painCave.isFatal = 1; |
233 |
> |
simError(); |
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} |
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} |
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} |
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sprintf(checkPointMsg,"Node %d received initial configuration.",procIndex); |
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MPIcheckPoint(); |
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} |
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|
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#endif |
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} |
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242 |
+ |
char* InitializeFromFile::parseDumpLine(char* readLine, int globalIndex){ |
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303 |
– |
char* InitializeFromFile::parseDumpLine(char* readLine, int atomIndex){ |
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char *foo; // the pointer to the current string token |
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double rx, ry, rz; // position place holders |
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Atom **atoms = entry_plug->atoms; |
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DirectionalAtom* dAtom; |
254 |
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255 |
< |
int n_atoms; |
255 |
> |
int j, n_atoms, atomIndex; |
256 |
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257 |
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#ifdef IS_MPI |
258 |
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n_atoms = mpiSim->getTotAtoms(); |
259 |
+ |
atomIndex=-1; |
260 |
+ |
for (j=0; j < mpiSim->getMyNlocal(); j++) { |
261 |
+ |
if (atoms[j]->getGlobalIndex() == globalIndex) atomIndex = j; |
262 |
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} |
263 |
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if (atomIndex == -1) { |
264 |
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sprintf( painCave.errMsg, |
265 |
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"Initialize from file error. Atom at index %d " |
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"in file %s does not exist on processor %d .\n", |
267 |
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globalIndex, c_in_name, mpiSim->getMyNode() ); |
268 |
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return strdup( painCave.errMsg ); |
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+ |
} |
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#else |
271 |
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n_atoms = entry_plug->n_atoms; |
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+ |
atomIndex = globalIndex; |
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#endif // is_mpi |
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– |
|
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// set the string tokenizer |
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foo = strtok(readLine, " ,;\t"); |