--- trunk/OOPSE/libmdtools/DumpWriter.cpp 2003/03/21 17:42:12 378 +++ trunk/OOPSE/libmdtools/DumpWriter.cpp 2003/04/03 20:21:54 447 @@ -5,16 +5,20 @@ #ifdef IS_MPI #include #include "mpiSimulation.hpp" -#define TAKE_THIS_TAG 0 +#define TAKE_THIS_TAG_CHAR 1 +#define TAKE_THIS_TAG_INT 2 + +namespace dWrite{ + void nodeZeroError( void ); + void anonymousNodeDie( void ); +} + +using namespace dWrite; #endif //is_mpi #include "ReadWrite.hpp" #include "simError.h" - - - - DumpWriter::DumpWriter( SimInfo* the_entry_plug ){ entry_plug = the_entry_plug; @@ -68,7 +72,7 @@ void DumpWriter::writeDump( double currentTime ){ char tempBuffer[BUFFERSIZE]; char writeLine[BUFFERSIZE]; - int i; + int i, j, which_node, done, game_over, which_atom, local_index; double q[4]; DirectionalAtom* dAtom; int nAtoms = entry_plug->n_atoms; @@ -123,147 +127,146 @@ void DumpWriter::writeDump( double currentTime ){ #else // is_mpi - int masterIndex; - int nodeAtomsStart; - int nodeAtomsEnd; - int mpiErr; - int sendError; - int procIndex; - - MPI_Status istatus[MPI_STATUS_SIZE]; + // first thing first, suspend fatalities. + painCave.isEventLoop = 1; - - // write out header and node 0's coordinates + int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone + int haveError; + MPI_Status istatus; + int *AtomToProcMap = mpiSim->getAtomToProcMap(); + + // write out header and node 0's coordinates + if( worldRank == 0 ){ outFile << mpiSim->getTotAtoms() << "\n"; - + outFile << currentTime << "\t" << entry_plug->box_x << "\t" << entry_plug->box_y << "\t" << entry_plug->box_z << "\n"; - - masterIndex = 0; - for( i=0; igetTotAtoms(); i++ ) { + // Get the Node number which has this atom; - sprintf( tempBuffer, - "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", - atoms[i]->getType(), - atoms[i]->getX(), - atoms[i]->getY(), - atoms[i]->getZ(), - atoms[i]->get_vx(), - atoms[i]->get_vy(), - atoms[i]->get_vz()); - strcpy( writeLine, tempBuffer ); + which_node = AtomToProcMap[i]; + + if (which_node == 0 ) { - if( atoms[i]->isDirectional() ){ + haveError = 0; + which_atom = i; + local_index=-1; + for (j=0; (jgetMyNlocal()) && (local_index < 0); j++) { + if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; + } + if (local_index != -1) { + //format the line + sprintf( tempBuffer, + "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", + atoms[local_index]->getType(), + atoms[local_index]->getX(), + atoms[local_index]->getY(), + atoms[local_index]->getZ(), + atoms[local_index]->get_vx(), + atoms[local_index]->get_vy(), + atoms[local_index]->get_vz()); // check here. + strcpy( writeLine, tempBuffer ); - dAtom = (DirectionalAtom *)atoms[i]; - dAtom->getQ( q ); - - sprintf( tempBuffer, - "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", - q[0], - q[1], - q[2], - q[3], - dAtom->getJx(), - dAtom->getJy(), - dAtom->getJz()); - strcat( writeLine, tempBuffer ); + if( atoms[local_index]->isDirectional() ){ + + dAtom = (DirectionalAtom *)atoms[local_index]; + dAtom->getQ( q ); + + sprintf( tempBuffer, + "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", + q[0], + q[1], + q[2], + q[3], + dAtom->getJx(), + dAtom->getJy(), + dAtom->getJz()); + strcat( writeLine, tempBuffer ); + + } + else + strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); + } + else { + sprintf(painCave.errMsg, + "Atom %d not found on processor %d\n", + i, worldRank ); + haveError= 1; + simError(); + } + + if(haveError) nodeZeroError(); + } - else - strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); + else { + myStatus = 1; + MPI_Send(&myStatus, 1, MPI_INT, which_node, + TAKE_THIS_TAG_INT, MPI_COMM_WORLD); + MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, + MPI_COMM_WORLD); + MPI_Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node, + TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus); + MPI_Recv(&myStatus, 1, MPI_INT, which_node, + TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); + if(!myStatus) nodeZeroError(); + + } + outFile << writeLine; - masterIndex++; + outFile.flush(); } - outFile.flush(); - } + + // kill everyone off: + myStatus = -1; + for (j = 0; j < mpiSim->getNumberProcessors(); j++) { + MPI_Send(&myStatus, 1, MPI_INT, j, + TAKE_THIS_TAG_INT, MPI_COMM_WORLD); + } - sprintf( checkPointMsg, - "Sucessfully wrote node 0's dump configuration.\n"); - MPIcheckPoint(); + } else { - for (procIndex = 1; procIndex < mpiSim->getNumberProcessors(); - procIndex++){ + done = 0; + while (!done) { + + MPI_Recv(&myStatus, 1, MPI_INT, 0, + TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); - if( worldRank == 0 ){ + if(!myStatus) anonymousNodeDie(); - mpiErr = MPI_Recv(&nodeAtomsStart,1,MPI_INT,procIndex, - TAKE_THIS_TAG,MPI_COMM_WORLD,istatus); - - mpiErr = MPI_Recv(&nodeAtomsEnd,1,MPI_INT,procIndex, - TAKE_THIS_TAG,MPI_COMM_WORLD, istatus); + if(myStatus < 0) break; + + MPI_Recv(&which_atom, 1, MPI_INT, 0, + TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); - // Make sure where node 0 is writing to, matches where the - // receiving node expects it to be. - - if (masterIndex != nodeAtomsStart){ - sendError = 1; - mpiErr = MPI_Send(&sendError,1,MPI_INT,procIndex,TAKE_THIS_TAG, - MPI_COMM_WORLD); - sprintf(painCave.errMsg, - "DumpWriter error: atoms start index (%d) for " - "node %d not equal to master index (%d)", - nodeAtomsStart,procIndex,masterIndex ); - painCave.isFatal = 1; - simError(); + myStatus = 1; + local_index=-1; + for (j=0; (jgetMyNlocal()) && (local_index < 0); j++) { + if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; } - - sendError = 0; - mpiErr = MPI_Send(&sendError,1,MPI_INT,procIndex,TAKE_THIS_TAG, - MPI_COMM_WORLD); - - // recieve the nodes writeLines - - for ( i = nodeAtomsStart; i <= nodeAtomsEnd; i++){ - - mpiErr = MPI_Recv(writeLine,BUFFERSIZE,MPI_CHAR,procIndex, - TAKE_THIS_TAG,MPI_COMM_WORLD,istatus ); - - outFile << writeLine; - masterIndex++; - } - } - - else if( worldRank == procIndex ){ - - nodeAtomsStart = mpiSim->getMyAtomStart(); - nodeAtomsEnd = mpiSim->getMyAtomEnd(); - - mpiErr = MPI_Send(&nodeAtomsStart,1,MPI_INT,0,TAKE_THIS_TAG, - MPI_COMM_WORLD); - mpiErr = MPI_Send(&nodeAtomsEnd,1,MPI_INT,0,TAKE_THIS_TAG, - MPI_COMM_WORLD); - - sendError = -1; - mpiErr = MPI_Recv(&sendError,1,MPI_INT,0,TAKE_THIS_TAG, - MPI_COMM_WORLD, istatus); - - if (sendError) MPIcheckPoint(); - - // send current node's configuration line by line. - - for( i=0; igetType(), - atoms[i]->getX(), - atoms[i]->getY(), - atoms[i]->getZ(), - atoms[i]->get_vx(), - atoms[i]->get_vy(), - atoms[i]->get_vz()); // check here. + atoms[local_index]->getType(), + atoms[local_index]->getX(), + atoms[local_index]->getY(), + atoms[local_index]->getZ(), + atoms[local_index]->get_vx(), + atoms[local_index]->get_vy(), + atoms[local_index]->get_vz()); // check here. strcpy( writeLine, tempBuffer ); + + if( atoms[local_index]->isDirectional() ){ - if( atoms[i]->isDirectional() ){ - - dAtom = (DirectionalAtom *)atoms[i]; + dAtom = (DirectionalAtom *)atoms[local_index]; dAtom->getQ( q ); - + sprintf( tempBuffer, "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", q[0], @@ -275,40 +278,52 @@ void DumpWriter::writeDump( double currentTime ){ dAtom->getJz()); strcat( writeLine, tempBuffer ); } - else + else{ strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); - - mpiErr = MPI_Send(writeLine,BUFFERSIZE,MPI_CHAR,0,TAKE_THIS_TAG, - MPI_COMM_WORLD); + } + } + else { + sprintf(painCave.errMsg, + "Atom %d not found on processor %d\n", + which_atom, worldRank ); + myStatus = 0; + simError(); + + strcpy( writeLine, "Hello, I'm an error.\n"); } + + MPI_Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, + TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD); + MPI_Send( &myStatus, 1, MPI_INT, 0, + TAKE_THIS_TAG_INT, MPI_COMM_WORLD); } - - sprintf(checkPointMsg,"Node %d sent dump configuration.", - procIndex); - MPIcheckPoint(); - } - + } + outFile.flush(); + sprintf( checkPointMsg, + "Sucessfully took a dump.\n"); + MPIcheckPoint(); + + // last thing last, enable fatalities. + painCave.isEventLoop = 0; + #endif // is_mpi } - - void DumpWriter::writeFinal(){ + char finalName[500]; + ofstream finalOut; const int BUFFERSIZE = 2000; - char tempBuffer[500]; - char writeLine[BUFFERSIZE]; - - char finalName[500]; + char tempBuffer[BUFFERSIZE]; + char writeLine[BUFFERSIZE]; - int i; double q[4]; DirectionalAtom* dAtom; int nAtoms = entry_plug->n_atoms; Atom** atoms = entry_plug->atoms; + int i, j, which_node, done, game_over, which_atom, local_index; - ofstream finalOut; #ifdef IS_MPI if(worldRank == 0 ){ @@ -335,8 +350,7 @@ void DumpWriter::writeFinal(){ #endif //is_mpi - - + #ifndef IS_MPI finalOut << nAtoms << "\n"; @@ -344,7 +358,7 @@ void DumpWriter::writeFinal(){ finalOut << entry_plug->box_x << "\t" << entry_plug->box_y << "\t" << entry_plug->box_z << "\n"; - + for( i=0; igetAtomToProcMap(); + // write out header and node 0's coordinates + + haveError = 0; if( worldRank == 0 ){ finalOut << mpiSim->getTotAtoms() << "\n"; - + finalOut << entry_plug->box_x << "\t" - << entry_plug->box_y << "\t" - << entry_plug->box_z << "\n"; + << entry_plug->box_y << "\t" + << entry_plug->box_z << "\n"; - masterIndex = 0; - - for( i=0; igetTotAtoms(); i++ ) { + // Get the Node number which has this molecule: - sprintf( tempBuffer, - "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", - atoms[i]->getType(), - atoms[i]->getX(), - atoms[i]->getY(), - atoms[i]->getZ(), - atoms[i]->get_vx(), - atoms[i]->get_vy(), - atoms[i]->get_vz()); - strcpy( writeLine, tempBuffer ); - - if( atoms[i]->isDirectional() ){ + which_node = AtomToProcMap[i]; + + if (which_node == mpiSim->getMyNode()) { + + which_atom = i; + local_index=-1; + for (j=0; (jgetMyNlocal()) && (local_index < 0); j++) { + if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; + } + if (local_index != -1) { + sprintf( tempBuffer, + "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", + atoms[local_index]->getType(), + atoms[local_index]->getX(), + atoms[local_index]->getY(), + atoms[local_index]->getZ(), + atoms[local_index]->get_vx(), + atoms[local_index]->get_vy(), + atoms[local_index]->get_vz()); + strcpy( writeLine, tempBuffer ); - dAtom = (DirectionalAtom *)atoms[i]; - dAtom->getQ( q ); - - sprintf( tempBuffer, - "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", - q[0], - q[1], - q[2], - q[3], - dAtom->getJx(), - dAtom->getJy(), - dAtom->getJz()); - strcat( writeLine, tempBuffer ); - } - else - strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); + if( atoms[local_index]->isDirectional() ){ + + dAtom = (DirectionalAtom *)atoms[local_index]; + dAtom->getQ( q ); + + sprintf( tempBuffer, + "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", + q[0], + q[1], + q[2], + q[3], + dAtom->getJx(), + dAtom->getJy(), + dAtom->getJz()); + strcat( writeLine, tempBuffer ); + } + else + strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); + } + else { + sprintf(painCave.errMsg, + "Atom %d not found on processor %d\n", + i, worldRank ); + haveError= 1; + simError(); + } + + if(haveError) nodeZeroError(); + + } + else { + + myStatus = 1; + MPI_Send(&myStatus, 1, MPI_INT, which_node, + TAKE_THIS_TAG_INT, MPI_COMM_WORLD); + MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, + MPI_COMM_WORLD); + MPI_Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node, + TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus); + MPI_Recv(&myStatus, 1, MPI_INT, which_node, + TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); + if(!myStatus) nodeZeroError(); + } + finalOut << writeLine; - masterIndex++; } - finalOut.flush(); - } - for (procIndex = 1; procIndex < mpiSim->getNumberProcessors(); - procIndex++){ + // kill everyone off: + myStatus = -1; + for (j = 0; j < mpiSim->getNumberProcessors(); j++) { + MPI_Send(&myStatus, 1, MPI_INT, j, + TAKE_THIS_TAG_INT, MPI_COMM_WORLD); + } - if( worldRank == 0 ){ - - mpiErr = MPI_Recv(&nodeAtomsStart,1,MPI_INT,procIndex, - TAKE_THIS_TAG,MPI_COMM_WORLD,istatus); + } else { + + done = 0; + while (!done) { - mpiErr = MPI_Recv(&nodeAtomsEnd,1,MPI_INT,procIndex, - TAKE_THIS_TAG,MPI_COMM_WORLD, istatus); - - // Make sure where node 0 is writing to, matches where the - // receiving node expects it to be. - - if (masterIndex != nodeAtomsStart){ - sendError = 1; - mpiErr = MPI_Send(&sendError,1,MPI_INT,procIndex,TAKE_THIS_TAG, - MPI_COMM_WORLD); - sprintf(painCave.errMsg, - "DumpWriter error: atoms start index (%d) for " - "node %d not equal to master index (%d)", - nodeAtomsStart,procIndex,masterIndex ); - painCave.isFatal = 1; - simError(); + MPI_Recv(&myStatus, 1, MPI_INT, 0, + TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); + + if(!myStatus) anonymousNodeDie(); + + if(myStatus < 0) break; + + MPI_Recv(&which_atom, 1, MPI_INT, 0, + TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); + + myStatus = 1; + local_index=-1; + for (j=0; j < mpiSim->getMyNlocal(); j++) { + if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; } - - sendError = 0; - mpiErr = MPI_Send(&sendError,1,MPI_INT,procIndex,TAKE_THIS_TAG, - MPI_COMM_WORLD); + if (local_index != -1) { - // recieve the nodes writeLines - - for ( i = nodeAtomsStart; i <= nodeAtomsEnd; i++){ - - mpiErr = MPI_Recv(writeLine,BUFFERSIZE,MPI_CHAR,procIndex, - TAKE_THIS_TAG,MPI_COMM_WORLD,istatus ); - - finalOut << writeLine; - masterIndex++; - } - - finalOut.flush(); - } - - else if( worldRank == procIndex ){ - - nodeAtomsStart = mpiSim->getMyAtomStart(); - nodeAtomsEnd = mpiSim->getMyAtomEnd(); - - mpiErr = MPI_Send(&nodeAtomsStart,1,MPI_INT,0,TAKE_THIS_TAG, - MPI_COMM_WORLD); - mpiErr = MPI_Send(&nodeAtomsEnd,1,MPI_INT,0,TAKE_THIS_TAG, - MPI_COMM_WORLD); - - mpiErr = MPI_Recv(&sendError,1,MPI_INT,0,TAKE_THIS_TAG, - MPI_COMM_WORLD, istatus); - if (sendError) MPIcheckPoint(); - - // send current node's configuration line by line. - - for( i=0; igetType(), - atoms[i]->getX(), - atoms[i]->getY(), - atoms[i]->getZ(), - atoms[i]->get_vx(), - atoms[i]->get_vy(), - atoms[i]->get_vz()); + atoms[local_index]->getType(), + atoms[local_index]->getX(), + atoms[local_index]->getY(), + atoms[local_index]->getZ(), + atoms[local_index]->get_vx(), + atoms[local_index]->get_vy(), + atoms[local_index]->get_vz()); // check here. strcpy( writeLine, tempBuffer ); + + if( atoms[local_index]->isDirectional() ){ - if( atoms[i]->isDirectional() ){ - - dAtom = (DirectionalAtom *)atoms[i]; + dAtom = (DirectionalAtom *)atoms[local_index]; dAtom->getQ( q ); - + sprintf( tempBuffer, "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", q[0], @@ -531,21 +546,60 @@ void DumpWriter::writeFinal(){ dAtom->getJz()); strcat( writeLine, tempBuffer ); } - else + else{ strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); - - mpiErr = MPI_Send(writeLine,BUFFERSIZE,MPI_CHAR,0,TAKE_THIS_TAG, - MPI_COMM_WORLD); + } + } + else { + sprintf(painCave.errMsg, + "Atom %d not found on processor %d\n", + which_atom, worldRank ); + myStatus = 0; + simError(); + + strcpy( writeLine, "Hello, I'm an error.\n"); } + + MPI_Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, + TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD); + MPI_Send( &myStatus, 1, MPI_INT, 0, + TAKE_THIS_TAG_INT, MPI_COMM_WORLD); } - - sprintf(checkPointMsg,"Node %d sent dump configuration.", - procIndex); - MPIcheckPoint(); } + finalOut.flush(); + sprintf( checkPointMsg, + "Sucessfully took a dump.\n"); + MPIcheckPoint(); + + if( worldRank == 0 ) finalOut.close(); +#endif // is_mpi +} - if( worldRank == 0 ) finalOut.close(); - -#endif // is_mpi + +#ifdef IS_MPI + +// a couple of functions to let us escape the write loop + +void dWrite::nodeZeroError( void ){ + int j, myStatus; + + myStatus = 0; + for (j = 0; j < mpiSim->getNumberProcessors(); j++) { + MPI_Send( &myStatus, 1, MPI_INT, j, + TAKE_THIS_TAG_INT, MPI_COMM_WORLD); + } + + + MPI_Finalize(); + exit (0); + } + +void dWrite::anonymousNodeDie( void ){ + + MPI_Finalize(); + exit (0); +} + +#endif //is_mpi