--- trunk/OOPSE/libmdtools/DumpWriter.cpp 2003/03/27 01:49:45 417 +++ trunk/OOPSE/libmdtools/DumpWriter.cpp 2003/10/28 16:03:37 829 @@ -1,12 +1,21 @@ -#include +#define _FILE_OFFSET_BITS 64 + +#include #include #include #ifdef IS_MPI #include -#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" @@ -20,8 +29,6 @@ DumpWriter::DumpWriter( SimInfo* the_entry_plug ){ if(worldRank == 0 ){ #endif // is_mpi - - strcpy( outName, entry_plug->sampleName ); outFile.open(outName, ios::out | ios::trunc ); @@ -34,7 +41,7 @@ DumpWriter::DumpWriter( SimInfo* the_entry_plug ){ painCave.isFatal = 1; simError(); } - + //outFile.setf( ios::scientific ); #ifdef IS_MPI @@ -65,34 +72,54 @@ void DumpWriter::writeDump( double currentTime ){ char tempBuffer[BUFFERSIZE]; char writeLine[BUFFERSIZE]; - int i, j, which_node, done, game_over, which_atom; + int i; +#ifdef IS_MPI + int j, which_node, done, which_atom, local_index; +#else //is_mpi + int nAtoms = entry_plug->n_atoms; +#endif //is_mpi + double q[4]; DirectionalAtom* dAtom; - int nAtoms = entry_plug->n_atoms; Atom** atoms = entry_plug->atoms; + double pos[3], vel[3]; + + // write current frame to the eor file + this->writeFinal( currentTime ); + #ifndef IS_MPI outFile << nAtoms << "\n"; - outFile << currentTime << "\t" - << entry_plug->box_x << "\t" - << entry_plug->box_y << "\t" - << entry_plug->box_z << "\n"; + outFile << currentTime << ";\t" + << entry_plug->Hmat[0][0] << "\t" + << entry_plug->Hmat[1][0] << "\t" + << entry_plug->Hmat[2][0] << ";\t" + + << entry_plug->Hmat[0][1] << "\t" + << entry_plug->Hmat[1][1] << "\t" + << entry_plug->Hmat[2][1] << ";\t" + + << entry_plug->Hmat[0][2] << "\t" + << entry_plug->Hmat[1][2] << "\t" + << entry_plug->Hmat[2][2] << ";\n"; for( i=0; igetPos(pos); + atoms[i]->getVel(vel); 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()); + pos[0], + pos[1], + pos[2], + vel[0], + vel[1], + vel[2]); strcpy( writeLine, tempBuffer ); if( atoms[i]->isDirectional() ){ @@ -120,101 +147,163 @@ void DumpWriter::writeDump( double currentTime ){ #else // is_mpi - MPI::Status istatus; + // first thing first, suspend fatalities. + painCave.isEventLoop = 1; + + 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->Hmat[0][0] << "\t" + << entry_plug->Hmat[1][0] << "\t" + << entry_plug->Hmat[2][0] << ";\t" + + << entry_plug->Hmat[0][1] << "\t" + << entry_plug->Hmat[1][1] << "\t" + << entry_plug->Hmat[2][1] << ";\t" + + << entry_plug->Hmat[0][2] << "\t" + << entry_plug->Hmat[1][2] << "\t" + << entry_plug->Hmat[2][2] << ";\n"; - outFile << currentTime << "\t" - << entry_plug->box_x << "\t" - << entry_plug->box_y << "\t" - << entry_plug->box_z << "\n"; - + outFile.flush(); for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { // Get the Node number which has this atom; which_node = AtomToProcMap[i]; - if (which_node == mpiSim->getMyNode()) { - - 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 (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 - dAtom = (DirectionalAtom *)atoms[i]; - dAtom->getQ( q ); - + atoms[local_index]->getPos(pos); + atoms[local_index]->getVel(vel); + 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 { - - MPI::COMM_WORLD.Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG); - MPI::COMM_WORLD.Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node, - TAKE_THIS_TAG, istatus); + "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", + atoms[local_index]->getType(), + pos[0], + pos[1], + pos[2], + vel[0], + vel[1], + vel[2]); // check here. + strcpy( 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 { + 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; + outFile.flush(); } // kill everyone off: - game_over = -1; + myStatus = -1; for (j = 0; j < mpiSim->getNumberProcessors(); j++) { - MPI::COMM_WORLD.Send(&game_over, 1, MPI_INT, j, TAKE_THIS_TAG); + MPI_Send(&myStatus, 1, MPI_INT, j, + TAKE_THIS_TAG_INT, MPI_COMM_WORLD); } } else { done = 0; while (!done) { - MPI::COMM_WORLD.Recv(&which_atom, 1, MPI_INT, 0, - TAKE_THIS_TAG, istatus); + + MPI_Recv(&myStatus, 1, MPI_INT, 0, + TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); - if (which_atom == -1) { - done=1; - continue; - } else { + if(!myStatus) anonymousNodeDie(); + + if(myStatus < 0) break; - //format the line + MPI_Recv(&which_atom, 1, MPI_INT, 0, + TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); + + myStatus = 1; + 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 + + atoms[local_index]->getPos(pos); + atoms[local_index]->getVel(vel); + sprintf( tempBuffer, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", - atoms[which_atom]->getType(), - atoms[which_atom]->getX(), - atoms[which_atom]->getY(), - atoms[which_atom]->getZ(), - atoms[which_atom]->get_vx(), - atoms[which_atom]->get_vy(), - atoms[which_atom]->get_vz()); // check here. + atoms[local_index]->getType(), + pos[0], + pos[1], + pos[2], + vel[0], + vel[1], + vel[2]); // check here. strcpy( writeLine, tempBuffer ); + + if( atoms[local_index]->isDirectional() ){ - if( atoms[which_atom]->isDirectional() ){ - - dAtom = (DirectionalAtom *)atoms[which_atom]; + 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], @@ -226,22 +315,38 @@ 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" ); - - MPI::COMM_WORLD.Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, - TAKE_THIS_TAG); + } + } + 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); } } outFile.flush(); sprintf( checkPointMsg, "Sucessfully took a dump.\n"); MPIcheckPoint(); + + // last thing last, enable fatalities. + painCave.isEventLoop = 0; + #endif // is_mpi } -void DumpWriter::writeFinal(){ +void DumpWriter::writeFinal(double finalTime){ char finalName[500]; ofstream finalOut; @@ -252,10 +357,15 @@ void DumpWriter::writeFinal(){ 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; + int i; +#ifdef IS_MPI + int j, which_node, done, which_atom, local_index; +#else //is_mpi + int nAtoms = entry_plug->n_atoms; +#endif //is_mpi + double pos[3], vel[3]; #ifdef IS_MPI if(worldRank == 0 ){ @@ -287,21 +397,33 @@ void DumpWriter::writeFinal(){ finalOut << nAtoms << "\n"; - finalOut << entry_plug->box_x << "\t" - << entry_plug->box_y << "\t" - << entry_plug->box_z << "\n"; + finalOut << finalTime << ";\t" + << entry_plug->Hmat[0][0] << "\t" + << entry_plug->Hmat[1][0] << "\t" + << entry_plug->Hmat[2][0] << ";\t" + + << entry_plug->Hmat[0][1] << "\t" + << entry_plug->Hmat[1][1] << "\t" + << entry_plug->Hmat[2][1] << ";\t" + + << entry_plug->Hmat[0][2] << "\t" + << entry_plug->Hmat[1][2] << "\t" + << entry_plug->Hmat[2][2] << ";\n"; for( i=0; igetPos(pos); + atoms[i]->getVel(vel); + 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()); + pos[0], + pos[1], + pos[2], + vel[0], + vel[1], + vel[2]); strcpy( writeLine, tempBuffer ); if( atoms[i]->isDirectional() ){ @@ -330,17 +452,33 @@ void DumpWriter::writeFinal(){ #else // is_mpi - MPI::Status istatus; + // first thing first, suspend fatalities. + painCave.isEventLoop = 1; + + 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 + 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"; + finalOut << finalTime << ";\t" + << entry_plug->Hmat[0][0] << "\t" + << entry_plug->Hmat[1][0] << "\t" + << entry_plug->Hmat[2][0] << ";\t" + + << entry_plug->Hmat[0][1] << "\t" + << entry_plug->Hmat[1][1] << "\t" + << entry_plug->Hmat[2][1] << ";\t" + + << entry_plug->Hmat[0][2] << "\t" + << entry_plug->Hmat[1][2] << "\t" + << entry_plug->Hmat[2][2] << ";\n"; for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { // Get the Node number which has this molecule: @@ -348,82 +486,125 @@ void DumpWriter::writeFinal(){ which_node = AtomToProcMap[i]; if (which_node == mpiSim->getMyNode()) { - - 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_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) { + + atoms[local_index]->getPos(pos); + atoms[local_index]->getVel(vel); - dAtom = (DirectionalAtom *)atoms[i]; - dAtom->getQ( q ); + sprintf( tempBuffer, + "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", + atoms[local_index]->getType(), + pos[0], + pos[1], + pos[2], + vel[0], + vel[1], + vel[2]); + strcpy( writeLine, tempBuffer ); - 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 { - } else { - - MPI::COMM_WORLD.Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG); - MPI::COMM_WORLD.Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node, - TAKE_THIS_TAG, istatus); + 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; } // kill everyone off: - game_over = -1; - for (j = 0; j < mpiSim->getNumberProcessors(); j++) { - MPI::COMM_WORLD.Send(&game_over, 1, MPI_INT, j, TAKE_THIS_TAG); + myStatus = -1; + for (j = 0; j < mpiSim->getNumberProcessors(); j++) { + MPI_Send(&myStatus, 1, MPI_INT, j, + TAKE_THIS_TAG_INT, MPI_COMM_WORLD); } } else { done = 0; while (!done) { - MPI::COMM_WORLD.Recv(&which_atom, 1, MPI_INT, 0, - TAKE_THIS_TAG, istatus); - if (which_atom == -1) { - done=1; - continue; - } else { + 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; + } + if (local_index != -1) { - //format the line + atoms[local_index]->getPos(pos); + atoms[local_index]->getVel(vel); + + //format the line sprintf( tempBuffer, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", - atoms[which_atom]->getType(), - atoms[which_atom]->getX(), - atoms[which_atom]->getY(), - atoms[which_atom]->getZ(), - atoms[which_atom]->get_vx(), - atoms[which_atom]->get_vy(), - atoms[which_atom]->get_vz()); // check here. + atoms[local_index]->getType(), + pos[0], + pos[1], + pos[2], + vel[0], + vel[1], + vel[2]); // check here. strcpy( writeLine, tempBuffer ); + + if( atoms[local_index]->isDirectional() ){ - if( atoms[which_atom]->isDirectional() ){ - - dAtom = (DirectionalAtom *)atoms[which_atom]; + 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], @@ -435,19 +616,60 @@ 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" ); - - MPI::COMM_WORLD.Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, - TAKE_THIS_TAG); + } + } + 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); } - } + } finalOut.flush(); sprintf( checkPointMsg, "Sucessfully took a dump.\n"); MPIcheckPoint(); - + 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