--- trunk/OOPSE/libmdtools/DumpWriter.cpp 2003/03/21 17:42:12 378 +++ trunk/OOPSE/libmdtools/DumpWriter.cpp 2004/01/30 21:47:22 1000 @@ -1,20 +1,25 @@ -#include +#define _FILE_OFFSET_BITS 64 + +#include #include #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; @@ -22,27 +27,24 @@ 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 ){ - + + dumpFile.open(entry_plug->sampleName, ios::out | ios::trunc ); + + if( !dumpFile ){ + sprintf( painCave.errMsg, "Could not open \"%s\" for dump output.\n", - outName); + entry_plug->sampleName); painCave.isFatal = 1; simError(); } - - //outFile.setf( ios::scientific ); #ifdef IS_MPI } + //sort the local atoms by global index + sortByGlobalIndex(); + sprintf( checkPointMsg, "Sucessfully opened output file for dumping.\n"); MPIcheckPoint(); @@ -55,314 +57,223 @@ DumpWriter::~DumpWriter( ){ if(worldRank == 0 ){ #endif // is_mpi - outFile.close(); + dumpFile.close(); #ifdef IS_MPI } #endif // is_mpi } -void DumpWriter::writeDump( double currentTime ){ +#ifdef IS_MPI + +/** + * A hook function to load balancing + */ + +void DumpWriter::update(){ + sortByGlobalIndex(); +} - const int BUFFERSIZE = 2000; - char tempBuffer[BUFFERSIZE]; - char writeLine[BUFFERSIZE]; +/** + * Auxiliary sorting function + */ + +bool indexSortingCriterion(const pair& p1, const pair& p2){ + return p1.second < p2.second; +} - int i; - double q[4]; - DirectionalAtom* dAtom; - int nAtoms = entry_plug->n_atoms; +/** + * Sorting the local index by global index + */ + +void DumpWriter::sortByGlobalIndex(){ Atom** atoms = entry_plug->atoms; - + + indexArray.clear(); + + for(int i = 0; i < mpiSim->getMyNlocal();i++) + indexArray.push_back(make_pair(i, atoms[i]->getGlobalIndex())); + + sort(indexArray.begin(), indexArray.end(), indexSortingCriterion); +} -#ifndef IS_MPI - - outFile << nAtoms << "\n"; - - outFile << currentTime << "\t" - << entry_plug->box_x << "\t" - << entry_plug->box_y << "\t" - << entry_plug->box_z << "\n"; - - 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 ); +void DumpWriter::writeDump(double currentTime){ - 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 ); + ofstream finalOut; + vector fileStreams; + +#ifdef IS_MPI + if(worldRank == 0 ){ +#endif + finalOut.open( entry_plug->finalName, ios::out | ios::trunc ); + if( !finalOut ){ + sprintf( painCave.errMsg, + "Could not open \"%s\" for final dump output.\n", + entry_plug->finalName ); + painCave.isFatal = 1; + simError(); } - else - strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); - - outFile << writeLine; +#ifdef IS_MPI } - outFile.flush(); +#endif // is_mpi -#else // is_mpi + fileStreams.push_back(&finalOut); + fileStreams.push_back(&dumpFile); - int masterIndex; - int nodeAtomsStart; - int nodeAtomsEnd; - int mpiErr; - int sendError; - int procIndex; - - MPI_Status istatus[MPI_STATUS_SIZE]; + writeFrame(fileStreams, currentTime); - - // write out header and node 0's coordinates +#ifdef IS_MPI + finalOut.close(); +#endif + +} - 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"; +void DumpWriter::writeFinal(double currentTime){ - 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(); - } + ofstream finalOut; + vector fileStreams; - sprintf( checkPointMsg, - "Sucessfully wrote node 0's dump configuration.\n"); - MPIcheckPoint(); - - for (procIndex = 1; procIndex < mpiSim->getNumberProcessors(); - procIndex++){ +#ifdef IS_MPI + if(worldRank == 0 ){ +#endif // is_mpi - if( worldRank == 0 ){ - - 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); - - // 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++; - } - } + finalOut.open( entry_plug->finalName, ios::out | ios::trunc ); - 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. - 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); - } + if( !finalOut ){ + sprintf( painCave.errMsg, + "Could not open \"%s\" for final dump output.\n", + entry_plug->finalName ); + painCave.isFatal = 1; + simError(); } - - sprintf(checkPointMsg,"Node %d sent dump configuration.", - procIndex); - MPIcheckPoint(); + +#ifdef IS_MPI } - #endif // is_mpi + + fileStreams.push_back(&finalOut); + writeFrame(fileStreams, currentTime); + +#ifdef IS_MPI + finalOut.close(); +#endif + } +void DumpWriter::writeFrame( vector& outFile, double currentTime ){ + const int BUFFERSIZE = 2000; + const int MINIBUFFERSIZE = 100; -void DumpWriter::writeFinal(){ + char tempBuffer[BUFFERSIZE]; + char writeLine[BUFFERSIZE]; + int i, k; - const int BUFFERSIZE = 2000; - char tempBuffer[500]; - char writeLine[BUFFERSIZE]; +#ifdef IS_MPI - char finalName[500]; + /********************************************************************* + * Documentation? You want DOCUMENTATION? + * + * Why all the potatoes below? + * + * To make a long story short, the original version of DumpWriter + * worked in the most inefficient way possible. Node 0 would + * poke each of the node for an individual atom's formatted data + * as node 0 worked its way down the global index. This was particularly + * inefficient since the method blocked all processors at every atom + * (and did it twice!). + * + * An intermediate version of DumpWriter could be described from Node + * zero's perspective as follows: + * + * 1) Have 100 of your friends stand in a circle. + * 2) When you say go, have all of them start tossing potatoes at + * you (one at a time). + * 3) Catch the potatoes. + * + * It was an improvement, but MPI has buffers and caches that could + * best be described in this analogy as "potato nets", so there's no + * need to block the processors atom-by-atom. + * + * This new and improved DumpWriter works in an even more efficient + * way: + * + * 1) Have 100 of your friend stand in a circle. + * 2) When you say go, have them start tossing 5-pound bags of + * potatoes at you. + * 3) Once you've caught a friend's bag of potatoes, + * toss them a spud to let them know they can toss another bag. + * + * How's THAT for documentation? + * + *********************************************************************/ - int i; + int *potatoes; + int myPotato; + + int nProc; + int j, which_node, done, which_atom, local_index, currentIndex; + 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]; + +#ifndef IS_MPI - ofstream finalOut; - -#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, - "Could not open \"%s\" for final dump output.\n", - finalName ); - painCave.isFatal = 1; - simError(); - } - - // finalOut.setf( ios::scientific ); - -#ifdef IS_MPI + for(k = 0; k < outFile.size(); k++){ + *outFile[k] << nAtoms << "\n"; + + *outFile[k] << 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[k] << entry_plug->the_integrator->getAdditionalParameters() << endl; } - sprintf(checkPointMsg,"Opened file for final configuration\n"); - MPIcheckPoint(); - -#endif //is_mpi + for( i=0; igetPos(pos); + atoms[i]->getVel(vel); -#ifndef IS_MPI - - finalOut << nAtoms << "\n"; - - finalOut << entry_plug->box_x << "\t" - << entry_plug->box_y << "\t" - << entry_plug->box_z << "\n"; - - 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()); + 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 +287,332 @@ void DumpWriter::writeFinal(){ } else strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); - - finalOut << writeLine; + + for(k = 0; k < outFile.size(); k++) + *outFile[k] << writeLine; } - finalOut.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 ){ - 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]; + + //write out the comment lines + for (i = 0; i < nProc; i++) + potatoes[i] = 0; - masterIndex = 0; - - for( i=0; igetTotAtoms() << "\n"; + + *outFile[k] << 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[k] << entry_plug->the_integrator->getAdditionalParameters() << endl; + } + + currentIndex = 0; + + for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { - 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 ); + // Get the Node number which has this atom; + + which_node = AtomToProcMap[i]; + + if (which_node != 0) { + + if (potatoes[which_node] + 3 >= MAXTAG) { + // The potato was going to exceed the maximum value, + // so wrap this processor potato back to 0: + + potatoes[which_node] = 0; + MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD); + + } + + myPotato = potatoes[which_node]; + + MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node, + myPotato, MPI_COMM_WORLD, &istatus); + + atomTypeString = MPIatomTypeString; - if( atoms[i]->isDirectional() ){ + myPotato++; + + MPI_Recv(&isDirectional, 1, MPI_INT, which_node, + myPotato, MPI_COMM_WORLD, &istatus); + + myPotato++; + + 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; + + } else { + + haveError = 0; + which_atom = i; + + local_index = indexArray[currentIndex].first; + + if (which_atom == indexArray[currentIndex].second) { + + atomTypeString = atoms[local_index]->getType(); + + atoms[local_index]->getPos(pos); + atoms[local_index]->getVel(vel); - 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 ); + 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, currentIndex = %d, local_index = %d\n", + which_atom, worldRank, currentIndex, local_index ); + haveError= 1; + simError(); + } + + if(haveError) DieDieDie(); + + currentIndex++; } - else + // If we've survived to here, format the line: + + if (!isDirectional) { + + sprintf( writeLine, + "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", + atomTypeString, + atomData6[0], + atomData6[1], + atomData6[2], + atomData6[3], + atomData6[4], + atomData6[5]); + strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); - finalOut << writeLine; - masterIndex++; + } else { + + sprintf( writeLine, + "%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]); + + } + + for(k = 0; k < outFile.size(); k++) + *outFile[k] << writeLine; } - finalOut.flush(); - } - for (procIndex = 1; procIndex < mpiSim->getNumberProcessors(); - procIndex++){ + for(k = 0; k < outFile.size(); k++) + outFile[k]->flush(); + + sprintf( checkPointMsg, + "Sucessfully took a dump.\n"); + + MPIcheckPoint(); + + delete[] potatoes; + + } else { - if( worldRank == 0 ){ - - mpiErr = MPI_Recv(&nodeAtomsStart,1,MPI_INT,procIndex, - TAKE_THIS_TAG,MPI_COMM_WORLD,istatus); + // worldRank != 0, so I'm a remote node. - 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); + // Set my magic potato to 0: - // recieve the nodes writeLines + myPotato = 0; + currentIndex = 0; + + for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { + + // Am I the node which has this atom? + + if (AtomToProcMap[i] == worldRank) { - for ( i = nodeAtomsStart; i <= nodeAtomsEnd; i++){ + if (myPotato + 3 >= MAXTAG) { - mpiErr = MPI_Recv(writeLine,BUFFERSIZE,MPI_CHAR,procIndex, - TAKE_THIS_TAG,MPI_COMM_WORLD,istatus ); + // 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; - finalOut << writeLine; - masterIndex++; - } + local_index = indexArray[currentIndex].first; + + if (which_atom == indexArray[currentIndex].second) { + + 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]; - finalOut.flush(); - } + atomData6[3] = vel[0]; + atomData6[4] = vel[1]; + atomData6[5] = vel[2]; + + isDirectional = 0; - else if( worldRank == procIndex ){ + if( atoms[local_index]->isDirectional() ){ - nodeAtomsStart = mpiSim->getMyAtomStart(); - nodeAtomsEnd = mpiSim->getMyAtomEnd(); + 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, currentIndex = %d, local_index = %d\n", + which_atom, worldRank, currentIndex, local_index ); + haveError= 1; + simError(); + } - 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(); + strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE); - // send current node's configuration line by line. + // null terminate the string before sending (just in case): + MPIatomTypeString[MINIBUFFERSIZE-1] = '\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" ); - - mpiErr = MPI_Send(writeLine,BUFFERSIZE,MPI_CHAR,0,TAKE_THIS_TAG, - MPI_COMM_WORLD); + 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++; + currentIndex++; } } - - sprintf(checkPointMsg,"Node %d sent dump configuration.", - procIndex); - MPIcheckPoint(); - } - if( worldRank == 0 ) finalOut.close(); - + sprintf( checkPointMsg, + "Sucessfully took a dump.\n"); + MPIcheckPoint(); + } + #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