--- trunk/OOPSE/libmdtools/DumpWriter.cpp 2003/03/21 17:42:12 378 +++ trunk/OOPSE/libmdtools/DumpWriter.cpp 2004/01/12 20:37:59 926 @@ -1,20 +1,23 @@ -#include +#define _FILE_OFFSET_BITS 64 + +#include #include #include #ifdef IS_MPI #include #include "mpiSimulation.hpp" -#define TAKE_THIS_TAG 0 + +namespace dWrite{ + void DieDieDie( void ); +} + +using namespace dWrite; #endif //is_mpi #include "ReadWrite.hpp" #include "simError.h" - - - - DumpWriter::DumpWriter( SimInfo* the_entry_plug ){ entry_plug = the_entry_plug; @@ -22,22 +25,20 @@ DumpWriter::DumpWriter( SimInfo* the_entry_plug ){ #ifdef IS_MPI if(worldRank == 0 ){ #endif // is_mpi - - - + strcpy( outName, entry_plug->sampleName ); - + outFile.open(outName, ios::out | ios::trunc ); - + if( !outFile ){ - + sprintf( painCave.errMsg, "Could not open \"%s\" for dump output.\n", outName); painCave.isFatal = 1; simError(); } - + //outFile.setf( ios::scientific ); #ifdef IS_MPI @@ -63,46 +64,82 @@ void DumpWriter::writeDump( double currentTime ){ } void DumpWriter::writeDump( double currentTime ){ - + const int BUFFERSIZE = 2000; + const int MINIBUFFERSIZE = 100; + char tempBuffer[BUFFERSIZE]; char writeLine[BUFFERSIZE]; int i; + +#ifdef IS_MPI + + int *potatoes; + int myPotato; + + int nProc; + int j, which_node, done, which_atom, local_index; + double atomData6[6]; + double atomData13[13]; + int isDirectional; + char* atomTypeString; + char MPIatomTypeString[MINIBUFFERSIZE]; + +#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] << ";"; + //write out additional parameters, such as chi and eta + outFile << entry_plug->the_integrator->getAdditionalParameters(); + outFile << endl; + 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() ){ - + 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], @@ -116,206 +153,365 @@ void DumpWriter::writeDump( double currentTime ){ } else strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); - + outFile << writeLine; } outFile.flush(); #else // is_mpi - int masterIndex; - int nodeAtomsStart; - int nodeAtomsEnd; - int mpiErr; - int sendError; - int procIndex; - - MPI_Status istatus[MPI_STATUS_SIZE]; + /* code to find maximum tag value */ + + int *tagub, flag, MAXTAG; + MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag); + if (flag) { + MAXTAG = *tagub; + } else { + MAXTAG = 32767; + } - + 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; igetType(), - 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() ){ - - 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" ); - - outFile << writeLine; - masterIndex++; - } - outFile.flush(); - } + // Node 0 needs a list of the magic potatoes for each processor; - sprintf( checkPointMsg, - "Sucessfully wrote node 0's dump configuration.\n"); - MPIcheckPoint(); + nProc = mpiSim->getNumberProcessors(); + potatoes = new int[nProc]; + + for (i = 0; i < nProc; i++) + potatoes[i] = 0; - for (procIndex = 1; procIndex < mpiSim->getNumberProcessors(); - procIndex++){ + outFile << mpiSim->getTotAtoms() << "\n"; - if( worldRank == 0 ){ + 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] << ";"; + + outFile << entry_plug->the_integrator->getAdditionalParameters(); + outFile << endl; + outFile.flush(); + + for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { - mpiErr = MPI_Recv(&nodeAtomsStart,1,MPI_INT,procIndex, - TAKE_THIS_TAG,MPI_COMM_WORLD,istatus); + // Get the Node number which has this atom; - mpiErr = MPI_Recv(&nodeAtomsEnd,1,MPI_INT,procIndex, - TAKE_THIS_TAG,MPI_COMM_WORLD, istatus); + which_node = AtomToProcMap[i]; - // 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(); - } - - 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++; - } - } + if (which_node != 0) { - else if( worldRank == procIndex ){ + if (potatoes[which_node] + 3 >= MAXTAG) { + // The potato was going to exceed the maximum value, + // so wrap this processor potato back to 0: - nodeAtomsStart = mpiSim->getMyAtomStart(); - nodeAtomsEnd = mpiSim->getMyAtomEnd(); + potatoes[which_node] = 0; + MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD); + + } - 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); + myPotato = potatoes[which_node]; + + MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node, + myPotato, MPI_COMM_WORLD, &istatus); + + //strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE); + + // Null terminate the atomTypeString just in case: + + //atomTypeString[strlen(atomTypeString) - 1] = '\0'; + atomTypeString = MPIatomTypeString; - sendError = -1; - mpiErr = MPI_Recv(&sendError,1,MPI_INT,0,TAKE_THIS_TAG, - MPI_COMM_WORLD, istatus); + myPotato++; - if (sendError) MPIcheckPoint(); + MPI_Recv(&isDirectional, 1, MPI_INT, which_node, + myPotato, MPI_COMM_WORLD, &istatus); + + myPotato++; - // send current node's configuration line by line. + if (isDirectional) { + MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node, + myPotato, MPI_COMM_WORLD, &istatus); + } else { + MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node, + myPotato, MPI_COMM_WORLD, &istatus); + } + + myPotato++; + potatoes[which_node] = myPotato; - for( i=0; igetMyNlocal()) && (local_index < 0); j++) { + if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; + } + + if (local_index != -1) { + + atomTypeString = atoms[local_index]->getType(); + atoms[local_index]->getPos(pos); + atoms[local_index]->getVel(vel); + + atomData6[0] = pos[0]; + atomData6[1] = pos[1]; + atomData6[2] = pos[2]; + + atomData6[3] = vel[0]; + atomData6[4] = vel[1]; + atomData6[5] = vel[2]; + + isDirectional = 0; + + if( atoms[local_index]->isDirectional() ){ + + isDirectional = 1; + + dAtom = (DirectionalAtom *)atoms[local_index]; + dAtom->getQ( q ); + + for (int j = 0; j < 6 ; j++) + atomData13[j] = atomData6[j]; + + atomData13[6] = q[0]; + atomData13[7] = q[1]; + atomData13[8] = q[2]; + atomData13[9] = q[3]; + + atomData13[10] = dAtom->getJx(); + atomData13[11] = dAtom->getJy(); + atomData13[12] = dAtom->getJz(); + } + + } else { + sprintf(painCave.errMsg, + "Atom %d not found on processor %d\n", + i, worldRank ); + haveError= 1; + simError(); + } + + if(haveError) DieDieDie(); + + } + // If we've survived to here, format the line: + + if (!isDirectional) { + 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()); // check here. + atomTypeString, + atomData6[0], + atomData6[1], + atomData6[2], + atomData6[3], + atomData6[4], + atomData6[5]); + strcpy( writeLine, tempBuffer ); - - if( atoms[i]->isDirectional() ){ - - 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" ); - - mpiErr = MPI_Send(writeLine,BUFFERSIZE,MPI_CHAR,0,TAKE_THIS_TAG, - MPI_COMM_WORLD); + strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); + + } else { + + sprintf( tempBuffer, + "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", + atomTypeString, + atomData13[0], + atomData13[1], + atomData13[2], + atomData13[3], + atomData13[4], + atomData13[5], + atomData13[6], + atomData13[7], + atomData13[8], + atomData13[9], + atomData13[10], + atomData13[11], + atomData13[12]); + + strcat( writeLine, tempBuffer ); + } + + outFile << writeLine; + outFile.flush(); } + + + outFile.flush(); + sprintf( checkPointMsg, + "Sucessfully took a dump.\n"); + MPIcheckPoint(); + delete[] potatoes; + } else { + + // worldRank != 0, so I'm a remote node. + + // Set my magic potato to 0: + + myPotato = 0; + + for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { - sprintf(checkPointMsg,"Node %d sent dump configuration.", - procIndex); - MPIcheckPoint(); - } + // Am I the node which has this atom? + + if (AtomToProcMap[i] == worldRank) { + + if (myPotato + 3 >= MAXTAG) { + + // The potato was going to exceed the maximum value, + // so wrap this processor potato back to 0 (and block until + // node 0 says we can go: + + MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus); + + } + 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) { + + atomTypeString = atoms[local_index]->getType(); + + atoms[local_index]->getPos(pos); + atoms[local_index]->getVel(vel); + + atomData6[0] = pos[0]; + atomData6[1] = pos[1]; + atomData6[2] = pos[2]; + + atomData6[3] = vel[0]; + atomData6[4] = vel[1]; + atomData6[5] = vel[2]; + + isDirectional = 0; + + if( atoms[local_index]->isDirectional() ){ + + isDirectional = 1; + + dAtom = (DirectionalAtom *)atoms[local_index]; + dAtom->getQ( q ); + + for (int j = 0; j < 6 ; j++) + atomData13[j] = atomData6[j]; + + atomData13[6] = q[0]; + atomData13[7] = q[1]; + atomData13[8] = q[2]; + atomData13[9] = q[3]; + + atomData13[10] = dAtom->getJx(); + atomData13[11] = dAtom->getJy(); + atomData13[12] = dAtom->getJz(); + } + + } else { + sprintf(painCave.errMsg, + "Atom %d not found on processor %d\n", + i, worldRank ); + haveError= 1; + simError(); + } + + strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE); + + // null terminate the string before sending (just in case): + MPIatomTypeString[MINIBUFFERSIZE-1] = '\0'; + + MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0, + myPotato, MPI_COMM_WORLD); + + myPotato++; + + MPI_Send(&isDirectional, 1, MPI_INT, 0, + myPotato, MPI_COMM_WORLD); + + myPotato++; + + if (isDirectional) { + + MPI_Send(atomData13, 13, MPI_DOUBLE, 0, + myPotato, MPI_COMM_WORLD); + + } else { + + MPI_Send(atomData6, 6, MPI_DOUBLE, 0, + myPotato, MPI_COMM_WORLD); + } + + myPotato++; + } + } + + sprintf( checkPointMsg, + "Sucessfully took a dump.\n"); + MPIcheckPoint(); + } + #endif // is_mpi } +void DumpWriter::writeFinal(double finalTime){ + char finalName[500]; + ofstream finalOut; -void DumpWriter::writeFinal(){ - - const int BUFFERSIZE = 2000; - char tempBuffer[500]; + const int MINIBUFFERSIZE = 100; + char tempBuffer[BUFFERSIZE]; char writeLine[BUFFERSIZE]; - - char finalName[500]; - int i; double q[4]; DirectionalAtom* dAtom; - int nAtoms = entry_plug->n_atoms; Atom** atoms = entry_plug->atoms; + int i; +#ifdef IS_MPI - ofstream finalOut; - + int *potatoes; + int myPotato; + + int nProc; + int j, which_node, done, which_atom, local_index; + double atomData6[6]; + double atomData13[13]; + int isDirectional; + char* atomTypeString; + char MPIatomTypeString[MINIBUFFERSIZE]; + +#else //is_mpi + int nAtoms = entry_plug->n_atoms; +#endif //is_mpi + + double pos[3], vel[3]; + #ifdef IS_MPI if(worldRank == 0 ){ #endif // is_mpi - + strcpy( finalName, entry_plug->finalName ); - + finalOut.open( finalName, ios::out | ios::trunc ); if( !finalOut ){ sprintf( painCave.errMsg, @@ -324,45 +520,60 @@ void DumpWriter::writeFinal(){ painCave.isFatal = 1; simError(); } - + // finalOut.setf( ios::scientific ); - + #ifdef IS_MPI } - + sprintf(checkPointMsg,"Opened file for final configuration\n"); - MPIcheckPoint(); - + MPIcheckPoint(); + #endif //is_mpi - #ifndef IS_MPI - + 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] << ";"; + + //write out additional parameters, such as chi and eta + finalOut << entry_plug->the_integrator->getAdditionalParameters(); + finalOut << endl; + 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() ){ - + 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], @@ -376,176 +587,336 @@ void DumpWriter::writeFinal(){ } else strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); - + finalOut << writeLine; } finalOut.flush(); + finalOut.close(); #else // is_mpi - int masterIndex; - int nodeAtomsStart; - int nodeAtomsEnd; - int mpiErr; - int sendError; - int procIndex; - - MPI_Status istatus[MPI_STATUS_SIZE]; + /* code to find maximum tag value */ + int *tagub, flag, MAXTAG; + MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag); + if (flag) { + MAXTAG = *tagub; + } else { + MAXTAG = 32767; + } - + int haveError; + + MPI_Status istatus; + int *AtomToProcMap = mpiSim->getAtomToProcMap(); + // write out header and node 0's coordinates if( worldRank == 0 ){ - finalOut << mpiSim->getTotAtoms() << "\n"; - - finalOut << entry_plug->box_x << "\t" - << entry_plug->box_y << "\t" - << entry_plug->box_z << "\n"; + + // Node 0 needs a list of the magic potatoes for each processor; + + nProc = mpiSim->getNumberProcessors(); + potatoes = new int[nProc]; + + for (i = 0; i < nProc; i++) + potatoes[i] = 0; - masterIndex = 0; - - 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()); - strcpy( writeLine, tempBuffer ); - - if( atoms[i]->isDirectional() ){ - - 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" ); - - finalOut << writeLine; - masterIndex++; - } - finalOut.flush(); - } - - for (procIndex = 1; procIndex < mpiSim->getNumberProcessors(); - procIndex++){ + finalOut << mpiSim->getTotAtoms() << "\n"; - if( worldRank == 0 ){ - - mpiErr = MPI_Recv(&nodeAtomsStart,1,MPI_INT,procIndex, - TAKE_THIS_TAG,MPI_COMM_WORLD,istatus); + finalOut << finalTime << ";\t" + << entry_plug->Hmat[0][0] << "\t" + << entry_plug->Hmat[1][0] << "\t" + << entry_plug->Hmat[2][0] << ";\t" - 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(); - } - - sendError = 0; - mpiErr = MPI_Send(&sendError,1,MPI_INT,procIndex,TAKE_THIS_TAG, - MPI_COMM_WORLD); + << entry_plug->Hmat[0][1] << "\t" + << entry_plug->Hmat[1][1] << "\t" + << entry_plug->Hmat[2][1] << ";\t" - // recieve the nodes writeLines + << entry_plug->Hmat[0][2] << "\t" + << entry_plug->Hmat[1][2] << "\t" + << entry_plug->Hmat[2][2] << ";"; - for ( i = nodeAtomsStart; i <= nodeAtomsEnd; i++){ - - mpiErr = MPI_Recv(writeLine,BUFFERSIZE,MPI_CHAR,procIndex, - TAKE_THIS_TAG,MPI_COMM_WORLD,istatus ); + finalOut << entry_plug->the_integrator->getAdditionalParameters(); + finalOut << endl; + finalOut.flush(); - finalOut << writeLine; - masterIndex++; - } + for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { + + // Get the Node number which has this atom; + + which_node = AtomToProcMap[i]; + + if (which_node != 0) { - finalOut.flush(); - } + if (potatoes[which_node] + 3 >= MAXTAG) { + // The potato was going to exceed the maximum value, + // so wrap this processor potato back to 0: - else if( worldRank == procIndex ){ + potatoes[which_node] = 0; + MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD); + + } - 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(); + myPotato = potatoes[which_node]; + + MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node, + myPotato, MPI_COMM_WORLD, &istatus); + + atomTypeString = MPIatomTypeString; + + myPotato++; - // send current node's configuration line by line. + MPI_Recv(&isDirectional, 1, MPI_INT, which_node, + myPotato, MPI_COMM_WORLD, &istatus); + + myPotato++; - for( i=0; igetMyNlocal()) && (local_index < 0); j++) { + if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; + } + + if (local_index != -1) { + + atomTypeString = atoms[local_index]->getType(); + + atoms[local_index]->getPos(pos); + atoms[local_index]->getVel(vel); + + atomData6[0] = pos[0]; + atomData6[1] = pos[1]; + atomData6[2] = pos[2]; + + atomData6[3] = vel[0]; + atomData6[4] = vel[1]; + atomData6[5] = vel[2]; + + isDirectional = 0; + + if( atoms[local_index]->isDirectional() ){ + + isDirectional = 1; + + dAtom = (DirectionalAtom *)atoms[local_index]; + dAtom->getQ( q ); + + for (int j = 0; j < 6 ; j++) + atomData13[j] = atomData6[j]; + + atomData13[6] = q[0]; + atomData13[7] = q[1]; + atomData13[8] = q[2]; + atomData13[9] = q[3]; + + atomData13[10] = dAtom->getJx(); + atomData13[11] = dAtom->getJy(); + atomData13[12] = dAtom->getJz(); + } + + } else { + sprintf(painCave.errMsg, + "Atom %d not found on processor %d\n", + i, worldRank ); + haveError= 1; + simError(); + } + + if(haveError) DieDieDie(); + + } + + + // If we've survived to here, format the line: + + if (!isDirectional) { + 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()); + atomTypeString, + atomData6[0], + atomData6[1], + atomData6[2], + atomData6[3], + atomData6[4], + atomData6[5]); + strcpy( writeLine, tempBuffer ); - - if( atoms[i]->isDirectional() ){ - - 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" ); - - mpiErr = MPI_Send(writeLine,BUFFERSIZE,MPI_CHAR,0,TAKE_THIS_TAG, - MPI_COMM_WORLD); + strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); + + } else { + + sprintf( tempBuffer, + "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", + atomTypeString, + atomData13[0], + atomData13[1], + atomData13[2], + atomData13[3], + atomData13[4], + atomData13[5], + atomData13[6], + atomData13[7], + atomData13[8], + atomData13[9], + atomData13[10], + atomData13[11], + atomData13[12]); + + strcat( writeLine, tempBuffer ); + } + + finalOut << writeLine; + finalOut.flush(); } + + finalOut.flush(); + sprintf( checkPointMsg, + "Sucessfully took a dump.\n"); + delete[] potatoes; + + MPIcheckPoint(); + + } else { + + // worldRank != 0, so I'm a remote node. + + // Set my magic potato to 0: + + myPotato = 0; + + for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { - sprintf(checkPointMsg,"Node %d sent dump configuration.", - procIndex); - MPIcheckPoint(); - } + // Am I the node which has this atom? + + if (AtomToProcMap[i] == worldRank) { - if( worldRank == 0 ) finalOut.close(); + if (myPotato + 3 >= MAXTAG) { + // The potato was going to exceed the maximum value, + // so wrap this processor potato back to 0 (and block until + // node 0 says we can go: + + MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus); + + } + 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) { + + atomTypeString = atoms[local_index]->getType(); + + atoms[local_index]->getPos(pos); + atoms[local_index]->getVel(vel); + + atomData6[0] = pos[0]; + atomData6[1] = pos[1]; + atomData6[2] = pos[2]; + + atomData6[3] = vel[0]; + atomData6[4] = vel[1]; + atomData6[5] = vel[2]; + + isDirectional = 0; + + if( atoms[local_index]->isDirectional() ){ + + isDirectional = 1; + + dAtom = (DirectionalAtom *)atoms[local_index]; + dAtom->getQ( q ); + + for (int j = 0; j < 6 ; j++) + atomData13[j] = atomData6[j]; + + atomData13[6] = q[0]; + atomData13[7] = q[1]; + atomData13[8] = q[2]; + atomData13[9] = q[3]; + + atomData13[10] = dAtom->getJx(); + atomData13[11] = dAtom->getJy(); + atomData13[12] = dAtom->getJz(); + } + + } else { + sprintf(painCave.errMsg, + "Atom %d not found on processor %d\n", + i, worldRank ); + haveError= 1; + simError(); + } + + strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE); + + // null terminate the string before sending (just in case): + MPIatomTypeString[MINIBUFFERSIZE-1] = '\0'; + + MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0, + myPotato, MPI_COMM_WORLD); + + myPotato++; + + MPI_Send(&isDirectional, 1, MPI_INT, 0, + myPotato, MPI_COMM_WORLD); + + myPotato++; + + if (isDirectional) { + + MPI_Send(atomData13, 13, MPI_DOUBLE, 0, + myPotato, MPI_COMM_WORLD); + + } else { + + MPI_Send(atomData6, 6, MPI_DOUBLE, 0, + myPotato, MPI_COMM_WORLD); + } + + myPotato++; + } + } + + 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::DieDieDie( void ){ + + MPI_Finalize(); + exit (0); +} + +#endif //is_mpi