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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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#define TAKE_THIS_TAG_CHAR 0 |
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#define TAKE_THIS_TAG_INT 1 |
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|
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#define TAKE_THIS_TAG 0 |
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void nodeZeroError( void ); |
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void anonymousNodeDie( void ); |
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|
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#endif // is_mpi |
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|
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InitializeFromFile :: InitializeFromFile( char *in_name ){ |
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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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|
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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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// first thing first, suspend fatalities. |
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painCave.isEventLoop = 1; |
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|
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MPI_Status istatus[MPI_STATUS_SIZE]; |
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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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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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"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; |
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haveError= 1; |
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simError(); |
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} |
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|
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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; |
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haveError= 1; |
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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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|
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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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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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"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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haveError= 1; |
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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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if(haveError) nodeZeroError(); |
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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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// Get the Node number which wants this atom: |
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which_node = AtomToProcMap[i]; |
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if (which_node == 0) { |
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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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haveError = 1; |
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simError(); |
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} |
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if(haveError) nodeZeroError(); |
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} |
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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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else { |
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|
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myStatus = 1; |
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MPI::COMM_WORLD.Send(&myStatus, 1, MPI_INT, which_node, |
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TAKE_THIS_TAG_INT); |
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MPI::COMM_WORLD.Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node, |
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TAKE_THIS_TAG_CHAR); |
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MPI::COMM_WORLD.Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT); |
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MPI::COMM_WORLD.Recv(&myStatus, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, istatus); |
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|
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mpiErr = MPI_Send(read_buffer,BUFFERSIZE,MPI_CHAR,procIndex,TAKE_THIS_TAG,MPI_COMM_WORLD); |
255 |
< |
mpiErr = MPI_Recv(&sendError,1,MPI_INT,procIndex,TAKE_THIS_TAG,MPI_COMM_WORLD, |
256 |
< |
istatus); |
257 |
< |
if (sendError) MPIcheckPoint(); |
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|
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masterIndex++; |
234 |
> |
if(!myStatus) nodeZeroError(); |
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} |
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} |
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+ |
myStatus = -1; |
238 |
+ |
for (j = 0; j < mpiSim->getNumberProcessors(); j++) { |
239 |
+ |
MPI::COMM_WORLD.Send( &myStatus, 1, MPI_INT, j, |
240 |
+ |
TAKE_THIS_TAG_INT); |
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} |
242 |
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|
243 |
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} else { |
244 |
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|
245 |
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done = 0; |
246 |
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while (!done) { |
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|
248 |
< |
|
249 |
< |
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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> |
MPI::COMM_WORLD.Recv(&myStatus, 1, MPI_INT, 0, |
249 |
> |
TAKE_THIS_TAG_INT, istatus); |
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|
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< |
mpiErr = MPI_Recv(&sendError,1,MPI_INT,0,TAKE_THIS_TAG,MPI_COMM_WORLD, |
252 |
< |
istatus); |
253 |
< |
if (sendError) MPIcheckPoint(); |
251 |
> |
if(!myStatus) anonymousNodeDie(); |
252 |
> |
|
253 |
> |
if(myStatus < 0) break; |
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|
255 |
< |
for ( i = 0; i < entry_plug->n_atoms; i++){ |
256 |
< |
|
257 |
< |
mpiErr = MPI_Recv(&read_buffer,BUFFERSIZE,MPI_CHAR,0,TAKE_THIS_TAG,MPI_COMM_WORLD, |
258 |
< |
istatus); |
259 |
< |
|
260 |
< |
if(!strcmp(read_buffer, "ERROR")) MPIcheckPoint(); |
261 |
< |
|
262 |
< |
parseErr = parseDumpLine( read_buffer, i ); |
263 |
< |
if( parseErr != NULL ){ |
264 |
< |
sendError = 1; |
265 |
< |
mpiErr = MPI_Send(&sendError,1,MPI_INT,0,TAKE_THIS_TAG,MPI_COMM_WORLD); |
285 |
< |
|
286 |
< |
|
287 |
< |
strcpy( painCave.errMsg, parseErr ); |
288 |
< |
painCave.isFatal = 1; |
289 |
< |
simError(); |
290 |
< |
} |
291 |
< |
sendError = 0; |
292 |
< |
mpiErr = MPI_Send(&sendError,1,MPI_INT,0,TAKE_THIS_TAG,MPI_COMM_WORLD); |
255 |
> |
MPI::COMM_WORLD.Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0, |
256 |
> |
TAKE_THIS_TAG_CHAR, istatus); |
257 |
> |
MPI::COMM_WORLD.Recv(&which_atom, 1, MPI_INT, 0, |
258 |
> |
TAKE_THIS_TAG_INT, istatus); |
259 |
> |
|
260 |
> |
myStatus = 1; |
261 |
> |
parseErr = parseDumpLine( read_buffer, which_atom ); |
262 |
> |
if( parseErr != NULL ){ |
263 |
> |
strcpy( painCave.errMsg, parseErr ); |
264 |
> |
myStatus = 0;; |
265 |
> |
simError(); |
266 |
|
} |
267 |
< |
} |
268 |
< |
sprintf(checkPointMsg,"Node %d received initial configuration.",procIndex); |
269 |
< |
MPIcheckPoint(); |
267 |
> |
|
268 |
> |
MPI::COMM_WORLD.Send( &myStatus, 1, MPI_INT, 0, |
269 |
> |
TAKE_THIS_TAG_INT); |
270 |
> |
|
271 |
> |
} |
272 |
|
} |
273 |
< |
|
273 |
> |
|
274 |
> |
// last thing last, enable fatalities. |
275 |
> |
painCave.isEventLoop = 0; |
276 |
> |
|
277 |
|
#endif |
278 |
|
} |
279 |
|
|
280 |
+ |
char* InitializeFromFile::parseDumpLine(char* readLine, int globalIndex){ |
281 |
|
|
303 |
– |
char* InitializeFromFile::parseDumpLine(char* readLine, int atomIndex){ |
304 |
– |
|
282 |
|
char *foo; // the pointer to the current string token |
283 |
|
|
284 |
|
double rx, ry, rz; // position place holders |
290 |
|
Atom **atoms = entry_plug->atoms; |
291 |
|
DirectionalAtom* dAtom; |
292 |
|
|
293 |
< |
int n_atoms; |
293 |
> |
int j, n_atoms, atomIndex; |
294 |
|
|
295 |
|
#ifdef IS_MPI |
296 |
|
n_atoms = mpiSim->getTotAtoms(); |
297 |
+ |
atomIndex=-1; |
298 |
+ |
for (j=0; j < mpiSim->getMyNlocal(); j++) { |
299 |
+ |
if (atoms[j]->getGlobalIndex() == globalIndex) atomIndex = j; |
300 |
+ |
} |
301 |
+ |
if (atomIndex == -1) { |
302 |
+ |
sprintf( painCave.errMsg, |
303 |
+ |
"Initialize from file error. Atom at index %d " |
304 |
+ |
"in file %s does not exist on processor %d .\n", |
305 |
+ |
globalIndex, c_in_name, mpiSim->getMyNode() ); |
306 |
+ |
return strdup( painCave.errMsg ); |
307 |
+ |
} |
308 |
|
#else |
309 |
|
n_atoms = entry_plug->n_atoms; |
310 |
+ |
atomIndex = globalIndex; |
311 |
|
#endif // is_mpi |
312 |
|
|
324 |
– |
|
313 |
|
// set the string tokenizer |
314 |
|
|
315 |
|
foo = strtok(readLine, " ,;\t"); |
500 |
|
|
501 |
|
return NULL; |
502 |
|
} |
503 |
+ |
|
504 |
+ |
|
505 |
+ |
#ifdef IS_MPI |
506 |
+ |
|
507 |
+ |
// a couple of functions to let us escape the read loop |
508 |
+ |
|
509 |
+ |
void nodeZeroError( void ){ |
510 |
+ |
int j, myStatus; |
511 |
+ |
|
512 |
+ |
myStatus = 0; |
513 |
+ |
for (j = 0; j < mpiSim->getNumberProcessors(); j++) { |
514 |
+ |
MPI::COMM_WORLD.Send( &myStatus, 1, MPI_INT, j, |
515 |
+ |
TAKE_THIS_TAG_INT); |
516 |
+ |
} |
517 |
+ |
|
518 |
+ |
|
519 |
+ |
MPI_Finalize(); |
520 |
+ |
exit (0); |
521 |
+ |
|
522 |
+ |
} |
523 |
+ |
|
524 |
+ |
void anonymousNodeDie( void ){ |
525 |
+ |
|
526 |
+ |
MPI_Finalize(); |
527 |
+ |
exit (0); |
528 |
+ |
} |
529 |
+ |
|
530 |
+ |
#endif //is_mpi |