--- trunk/OOPSE/libmdtools/DumpWriter.cpp 2003/04/03 20:21:54 447 +++ trunk/OOPSE/libmdtools/DumpWriter.cpp 2004/05/27 00:48:12 1198 @@ -1,16 +1,18 @@ -#include +#define _LARGEFILE_SOURCE64 +#define _FILE_OFFSET_BITS 64 + +#include #include #include +#include +#include #ifdef IS_MPI #include #include "mpiSimulation.hpp" -#define TAKE_THIS_TAG_CHAR 1 -#define TAKE_THIS_TAG_INT 2 namespace dWrite{ - void nodeZeroError( void ); - void anonymousNodeDie( void ); + void DieDieDie( void ); } using namespace dWrite; @@ -26,27 +28,24 @@ 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(); @@ -59,547 +58,589 @@ 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, j, which_node, done, game_over, which_atom, local_index; - double q[4]; - DirectionalAtom* dAtom; - int nAtoms = entry_plug->n_atoms; - Atom** atoms = entry_plug->atoms; - +/** + * Sorting the local index by global index + */ + +void DumpWriter::sortByGlobalIndex(){ + Molecule* mols = entry_plug->molecules; + indexArray.clear(); + + for(int i = 0; i < entry_plug->n_mol;i++) + indexArray.push_back(make_pair(i, mols[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); - // first thing first, suspend fatalities. - painCave.isEventLoop = 1; + writeFrame(fileStreams, currentTime); - int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone - int haveError; +#ifdef IS_MPI + finalOut.close(); +#endif + +} - 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"; - outFile.flush(); - for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { - // Get the Node number which has this atom; - - which_node = AtomToProcMap[i]; - - if (which_node == 0 ) { - - 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 ); - - 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(); +void DumpWriter::writeFinal(double currentTime){ - } - 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: - 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_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; (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 ); - - 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", - which_atom, worldRank ); - myStatus = 0; - simError(); + ofstream finalOut; + vector fileStreams; - 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(){ - - char finalName[500]; - ofstream finalOut; - - const int BUFFERSIZE = 2000; - char tempBuffer[BUFFERSIZE]; - char writeLine[BUFFERSIZE]; - - 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; - - #ifdef IS_MPI if(worldRank == 0 ){ #endif // is_mpi - - strcpy( finalName, entry_plug->finalName ); - - finalOut.open( finalName, ios::out | ios::trunc ); + + finalOut.open( entry_plug->finalName, ios::out | ios::trunc ); + if( !finalOut ){ sprintf( painCave.errMsg, "Could not open \"%s\" for final dump output.\n", - finalName ); + entry_plug->finalName ); painCave.isFatal = 1; simError(); } - - // finalOut.setf( ios::scientific ); - + #ifdef IS_MPI } +#endif // is_mpi - sprintf(checkPointMsg,"Opened file for final configuration\n"); - MPIcheckPoint(); + fileStreams.push_back(&finalOut); + writeFrame(fileStreams, currentTime); + +#ifdef IS_MPI + finalOut.close(); +#endif -#endif //is_mpi +} +void DumpWriter::writeFrame( vector& outFile, double currentTime ){ + + const int BUFFERSIZE = 2000; + const int MINIBUFFERSIZE = 100; + + char tempBuffer[BUFFERSIZE]; + char writeLine[BUFFERSIZE]; + + int i, k; + +#ifdef IS_MPI + /********************************************************************* + * 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 *potatoes; + int myPotato; + + int nProc; + int j, which_node, done, which_atom, local_index, currentIndex; + double atomData[13]; + int isDirectional; + char* atomTypeString; + char MPIatomTypeString[MINIBUFFERSIZE]; + int nObjects; + int msgLen; // the length of message actually recieved at master nodes +#endif //is_mpi + + double q[4], ji[3]; + DirectionalAtom* dAtom; + double pos[3], vel[3]; + int nTotObjects; + StuntDouble* sd; + char* molName; + vector integrableObjects; + vector::iterator iter; + nTotObjects = entry_plug->getTotIntegrableObjects(); #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()); - strcpy( writeLine, tempBuffer ); + for(k = 0; k < outFile.size(); k++){ + *outFile[k] << nTotObjects << "\n"; - if( atoms[i]->isDirectional() ){ - - dAtom = (DirectionalAtom *)atoms[i]; - dAtom->getQ( q ); - + *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; + } + + for( i=0; i< entry_plug->n_mol; i++ ){ + + integrableObjects = entry_plug->molecules[i].getIntegrableObjects(); + molName = (entry_plug->compStamps[entry_plug->molecules[i].getStampID()])->getID(); + + for( iter = integrableObjects.begin();iter != integrableObjects.end(); ++iter){ + sd = *iter; + sd->getPos(pos); + sd->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 ); + "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", + sd->getType(), + pos[0], + pos[1], + pos[2], + vel[0], + vel[1], + vel[2]); + strcpy( writeLine, tempBuffer ); + + if( sd->isDirectional() ){ + + sd->getQ( q ); + sd->getJ( ji ); + + sprintf( tempBuffer, + "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", + q[0], + q[1], + q[2], + q[3], + ji[0], + ji[1], + ji[2]); + strcat( writeLine, tempBuffer ); + } + else + strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); } - else - strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); - - finalOut << writeLine; - } - finalOut.flush(); - finalOut.close(); + + for(k = 0; k < outFile.size(); k++) + *outFile[k] << writeLine; +} + #else // is_mpi + + /* code to find maximum tag value */ - // first thing first, suspend fatalities. - painCave.isEventLoop = 1; + int *tagub, flag, MAXTAG; + MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag); + if (flag) { + MAXTAG = *tagub; + } else { + MAXTAG = 32767; + } - int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone int haveError; MPI_Status istatus; - int *AtomToProcMap = mpiSim->getAtomToProcMap(); + int nCurObj; + int *MolToProcMap = mpiSim->getMolToProcMap(); // write out header and node 0's coordinates - - haveError = 0; + if( worldRank == 0 ){ - finalOut << mpiSim->getTotAtoms() << "\n"; + + // Node 0 needs a list of the magic potatoes for each processor; + + nProc = mpiSim->getNprocessors(); + potatoes = new int[nProc]; + + //write out the comment lines + for (i = 0; i < nProc; i++) + potatoes[i] = 0; - finalOut << entry_plug->box_x << "\t" - << entry_plug->box_y << "\t" - << entry_plug->box_z << "\n"; - - for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { - // Get the Node number which has this molecule: + for(k = 0; k < outFile.size(); k++){ + *outFile[k] << nTotObjects << "\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->getTotNmol(); i++ ) { - which_node = AtomToProcMap[i]; + // Get the Node number which has this atom; - if (which_node == mpiSim->getMyNode()) { + which_node = MolToProcMap[i]; + + if (which_node != 0) { + + if (potatoes[which_node] + 1 >= MAXTAG) { + // The potato was going to exceed the maximum value, + // so wrap this processor potato back to 0: - which_atom = i; - local_index=-1; - for (j=0; (jgetMyNlocal()) && (local_index < 0); j++) { - if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; + potatoes[which_node] = 0; + MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0, MPI_COMM_WORLD); + } - 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 ); - - 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 { + myPotato = potatoes[which_node]; + + //recieve the number of integrableObject in current molecule + MPI_Recv(&nCurObj, 1, MPI_INT, which_node, + myPotato, MPI_COMM_WORLD, &istatus); + myPotato++; - 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(); + for(int l = 0; l < nCurObj; l++){ + + if (potatoes[which_node] + 2 >= MAXTAG) { + // The potato was going to exceed the maximum value, + // so wrap this processor potato back to 0: + + potatoes[which_node] = 0; + MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0, MPI_COMM_WORLD); + + } + + MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node, + myPotato, MPI_COMM_WORLD, &istatus); + + atomTypeString = MPIatomTypeString; + + myPotato++; + + MPI_Recv(atomData, 13, MPI_DOUBLE, which_node, myPotato, MPI_COMM_WORLD, &istatus); + myPotato++; + + MPI_Get_count(&istatus, MPI_DOUBLE, &msgLen); + + if(msgLen == 13) + isDirectional = 1; + else + isDirectional = 0; + + } + potatoes[which_node] = myPotato; + + } else { + + haveError = 0; + + local_index = indexArray[currentIndex].first; + + integrableObjects = (entry_plug->molecules[local_index]).getIntegrableObjects(); + + for(iter= integrableObjects.begin(); iter != integrableObjects.end(); ++iter){ + sd = *iter; + atomTypeString = sd->getType(); + + sd->getPos(pos); + sd->getVel(vel); + + atomData[0] = pos[0]; + atomData[1] = pos[1]; + atomData[2] = pos[2]; + + atomData[3] = vel[0]; + atomData[4] = vel[1]; + atomData[5] = vel[2]; + + isDirectional = 0; + + if( sd->isDirectional() ){ + + isDirectional = 1; + + sd->getQ( q ); + sd->getJ( ji ); + + for (int j = 0; j < 6 ; j++) + atomData[j] = atomData[j]; + + atomData[6] = q[0]; + atomData[7] = q[1]; + atomData[8] = q[2]; + atomData[9] = q[3]; + + atomData[10] = ji[0]; + atomData[11] = ji[1]; + atomData[12] = ji[2]; + } + + } + + currentIndex++; } + // If we've survived to here, format the line: - finalOut << writeLine; - } - - // 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 (!isDirectional) { + + sprintf( writeLine, + "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", + atomTypeString, + atomData[0], + atomData[1], + atomData[2], + atomData[3], + atomData[4], + atomData[5]); + + strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); + + } 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, + atomData[0], + atomData[1], + atomData[2], + atomData[3], + atomData[4], + atomData[5], + atomData[6], + atomData[7], + atomData[8], + atomData[9], + atomData[10], + atomData[11], + atomData[12]); + + } + + for(k = 0; k < outFile.size(); k++) + *outFile[k] << writeLine; } - - } else { - done = 0; - while (!done) { + for(k = 0; k < outFile.size(); k++) + outFile[k]->flush(); + + sprintf( checkPointMsg, + "Sucessfully took a dump.\n"); + + MPIcheckPoint(); + + delete[] potatoes; + + } else { - MPI_Recv(&myStatus, 1, MPI_INT, 0, - TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); + // worldRank != 0, so I'm a remote node. + + // Set my magic potato to 0: + + myPotato = 0; + currentIndex = 0; + + for (i = 0 ; i < mpiSim->getTotNmol(); i++ ) { - if(!myStatus) anonymousNodeDie(); + // Am I the node which has this integrableObject? - 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) { + if (MolToProcMap[i] == worldRank) { - //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 ); - - if( atoms[local_index]->isDirectional() ){ + + if (myPotato + 1 >= MAXTAG) { - dAtom = (DirectionalAtom *)atoms[local_index]; - dAtom->getQ( q ); + // 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: - 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", - which_atom, worldRank ); - myStatus = 0; - simError(); - - strcpy( writeLine, "Hello, I'm an error.\n"); + MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus); + + } + + local_index = indexArray[currentIndex].first; + integrableObjects = entry_plug->molecules[local_index].getIntegrableObjects(); + + nCurObj = integrableObjects.size(); + + MPI_Send(&nCurObj, 1, MPI_INT, 0, + myPotato, MPI_COMM_WORLD); + myPotato++; + + for( iter = integrableObjects.begin(); iter != integrableObjects.end(); iter++){ + + if (myPotato + 2 >= 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); + + } + + sd = *iter; + + atomTypeString = sd->getType(); + + sd->getPos(pos); + sd->getVel(vel); + + atomData[0] = pos[0]; + atomData[1] = pos[1]; + atomData[2] = pos[2]; + + atomData[3] = vel[0]; + atomData[4] = vel[1]; + atomData[5] = vel[2]; + + isDirectional = 0; + + if( sd->isDirectional() ){ + + isDirectional = 1; + + sd->getQ( q ); + sd->getJ( ji ); + + + atomData[6] = q[0]; + atomData[7] = q[1]; + atomData[8] = q[2]; + atomData[9] = q[3]; + + atomData[10] = ji[0]; + atomData[11] = ji[1]; + atomData[12] = ji[2]; + } + + + 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++; + + if (isDirectional) { + + MPI_Send(atomData, 13, MPI_DOUBLE, 0, + myPotato, MPI_COMM_WORLD); + + } else { + + MPI_Send(atomData, 6, MPI_DOUBLE, 0, + myPotato, MPI_COMM_WORLD); + } + + myPotato++; + + } + + currentIndex++; + + } + } - 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, + "Sucessfully took a dump.\n"); + MPIcheckPoint(); + } - } - 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); - } - +void dWrite::DieDieDie( void ){ MPI_Finalize(); exit (0); - } -void dWrite::anonymousNodeDie( void ){ - - MPI_Finalize(); - exit (0); -} - #endif //is_mpi