--- trunk/OOPSE/libmdtools/DumpWriter.cpp 2004/01/12 20:37:59 926 +++ trunk/OOPSE/libmdtools/DumpWriter.cpp 2004/06/03 21:06:51 1231 @@ -1,8 +1,11 @@ +#define _LARGEFILE_SOURCE64 #define _FILE_OFFSET_BITS 64 #include #include #include +#include +#include #ifdef IS_MPI #include @@ -26,24 +29,23 @@ DumpWriter::DumpWriter( SimInfo* the_entry_plug ){ if(worldRank == 0 ){ #endif // is_mpi - strcpy( outName, entry_plug->sampleName ); + dumpFile.open(entry_plug->sampleName, ios::out | ios::trunc ); - outFile.open(outName, ios::out | ios::trunc ); + if( !dumpFile ){ - if( !outFile ){ - 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(); @@ -56,108 +58,249 @@ 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 - const int BUFFERSIZE = 2000; - const int MINIBUFFERSIZE = 100; +/** + * A hook function to load balancing + */ - char tempBuffer[BUFFERSIZE]; - char writeLine[BUFFERSIZE]; +void DumpWriter::update(){ + sortByGlobalIndex(); +} + +/** + * Auxiliary sorting function + */ + +bool indexSortingCriterion(const pair& p1, const pair& p2){ + return p1.second < p2.second; +} - int i; - -#ifdef IS_MPI +/** + * Sorting the local index by global index + */ + +void DumpWriter::sortByGlobalIndex(){ + Molecule* mols = entry_plug->molecules; + indexArray.clear(); - int *potatoes; - int myPotato; + 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); +} - int nProc; - int j, which_node, done, which_atom, local_index; - double atomData6[6]; - double atomData13[13]; - int isDirectional; - char* atomTypeString; - char MPIatomTypeString[MINIBUFFERSIZE]; +#endif -#else //is_mpi - int nAtoms = entry_plug->n_atoms; -#endif //is_mpi +void DumpWriter::writeDump(double currentTime){ - double q[4]; - DirectionalAtom* dAtom; - Atom** atoms = entry_plug->atoms; - double pos[3], vel[3]; + ofstream finalOut; + vector fileStreams; - // write current frame to the eor file +#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(); + } +#ifdef IS_MPI + } +#endif // is_mpi - this->writeFinal( currentTime ); + fileStreams.push_back(&finalOut); + fileStreams.push_back(&dumpFile); -#ifndef IS_MPI + writeFrame(fileStreams, currentTime); - outFile << nAtoms << "\n"; +#ifdef IS_MPI + finalOut.close(); +#endif + +} - outFile << currentTime << ";\t" - << entry_plug->Hmat[0][0] << "\t" - << entry_plug->Hmat[1][0] << "\t" - << entry_plug->Hmat[2][0] << ";\t" +void DumpWriter::writeFinal(double currentTime){ - << entry_plug->Hmat[0][1] << "\t" - << entry_plug->Hmat[1][1] << "\t" - << entry_plug->Hmat[2][1] << ";\t" + ofstream finalOut; + vector fileStreams; - << 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; +#ifdef IS_MPI + if(worldRank == 0 ){ +#endif // is_mpi - for( i=0; ifinalName, ios::out | ios::trunc ); - atoms[i]->getPos(pos); - atoms[i]->getVel(vel); + if( !finalOut ){ + sprintf( painCave.errMsg, + "Could not open \"%s\" for final dump output.\n", + entry_plug->finalName ); + painCave.isFatal = 1; + simError(); + } - sprintf( tempBuffer, - "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", - atoms[i]->getType(), - pos[0], - pos[1], - pos[2], - vel[0], - vel[1], - vel[2]); - strcpy( writeLine, tempBuffer ); +#ifdef IS_MPI + } +#endif // is_mpi + + fileStreams.push_back(&finalOut); + writeFrame(fileStreams, currentTime); - if( atoms[i]->isDirectional() ){ +#ifdef IS_MPI + finalOut.close(); +#endif + +} - dAtom = (DirectionalAtom *)atoms[i]; - dAtom->getQ( q ); +void DumpWriter::writeFrame( vector& outFile, double currentTime ){ - 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" ); + const int BUFFERSIZE = 2000; + const int MINIBUFFERSIZE = 100; - outFile << writeLine; + 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 + + 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] << ";"; + + //write out additional parameters, such as chi and eta + *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl; } - outFile.flush(); + + 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, + "%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" ); + + for(k = 0; k < outFile.size(); k++) + *outFile[k] << writeLine; + } + +} + #else // is_mpi /* code to find maximum tag value */ @@ -173,7 +316,8 @@ void DumpWriter::writeDump( double currentTime ){ int haveError; MPI_Status istatus; - int *AtomToProcMap = mpiSim->getAtomToProcMap(); + int nCurObj; + int *MolToProcMap = mpiSim->getMolToProcMap(); // write out header and node 0's coordinates @@ -181,734 +325,360 @@ void DumpWriter::writeDump( double currentTime ){ // Node 0 needs a list of the magic potatoes for each processor; - nProc = mpiSim->getNumberProcessors(); + nProc = mpiSim->getNProcessors(); potatoes = new int[nProc]; + //write out the comment lines for (i = 0; i < nProc; i++) potatoes[i] = 0; - outFile << mpiSim->getTotAtoms() << "\n"; + for(k = 0; k < outFile.size(); k++){ + *outFile[k] << nTotObjects << "\n"; - outFile << currentTime << ";\t" - << entry_plug->Hmat[0][0] << "\t" - << entry_plug->Hmat[1][0] << "\t" - << entry_plug->Hmat[2][0] << ";\t" + *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][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] << ";"; + << 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; + } - outFile << entry_plug->the_integrator->getAdditionalParameters(); - outFile << endl; - outFile.flush(); + currentIndex = 0; - for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { + for (i = 0 ; i < mpiSim->getNMolGlobal(); i++ ) { // Get the Node number which has this atom; - which_node = AtomToProcMap[i]; + which_node = MolToProcMap[i]; if (which_node != 0) { - - if (potatoes[which_node] + 3 >= MAXTAG) { + + if (potatoes[which_node] + 1 >= 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); + MPI_Send(&potatoes[which_node], 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); - - //strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE); - - // Null terminate the atomTypeString just in case: - //atomTypeString[strlen(atomTypeString) - 1] = '\0'; - atomTypeString = MPIatomTypeString; - - myPotato++; - - MPI_Recv(&isDirectional, 1, MPI_INT, which_node, + //recieve the number of integrableObject in current molecule + MPI_Recv(&nCurObj, 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; + for(int l = 0; l < nCurObj; l++){ - } else { - - 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) { - - atomTypeString = atoms[local_index]->getType(); + if (potatoes[which_node] + 2 >= MAXTAG) { + // The potato was going to exceed the maximum value, + // so wrap this processor potato back to 0: - atoms[local_index]->getPos(pos); - atoms[local_index]->getVel(vel); + potatoes[which_node] = 0; + MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0, MPI_COMM_WORLD); + + } - atomData6[0] = pos[0]; - atomData6[1] = pos[1]; - atomData6[2] = pos[2]; + MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node, + myPotato, MPI_COMM_WORLD, &istatus); - atomData6[3] = vel[0]; - atomData6[4] = vel[1]; - atomData6[5] = vel[2]; - - isDirectional = 0; + atomTypeString = MPIatomTypeString; - if( atoms[local_index]->isDirectional() ){ + 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; + + // If we've survived to here, format the line: - dAtom = (DirectionalAtom *)atoms[local_index]; - dAtom->getQ( q ); - - for (int j = 0; j < 6 ; j++) - atomData13[j] = atomData6[j]; + 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]); - 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(); - + for(k = 0; k < outFile.size(); k++) + *outFile[k] << writeLine; + + }// end for(int l =0) + potatoes[which_node] = myPotato; + } - // 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", - atomTypeString, - atomData6[0], - atomData6[1], - atomData6[2], - atomData6[3], - atomData6[4], - atomData6[5]); - - strcpy( writeLine, tempBuffer ); - 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 ); + else { - } - - outFile << writeLine; - outFile.flush(); - } - + haveError = 0; + + local_index = indexArray[currentIndex].first; - outFile.flush(); - sprintf( checkPointMsg, - "Sucessfully took a dump.\n"); - MPIcheckPoint(); - delete[] potatoes; - } else { + integrableObjects = (entry_plug->molecules[local_index]).getIntegrableObjects(); - // worldRank != 0, so I'm a remote node. + 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]; - // Set my magic potato to 0: + atomData[3] = vel[0]; + atomData[4] = vel[1]; + atomData[5] = vel[2]; + + isDirectional = 0; - myPotato = 0; - - for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { - - // Am I the node which has this atom? - - if (AtomToProcMap[i] == worldRank) { + if( sd->isDirectional() ){ - if (myPotato + 3 >= MAXTAG) { + isDirectional = 1; + + sd->getQ( q ); + sd->getJ( ji ); - // 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; + 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]; + } - dAtom = (DirectionalAtom *)atoms[local_index]; - dAtom->getQ( q ); + // If we've survived to here, format the line: - 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); + 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; + + + }//end for(iter = integrableObject.begin()) - 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++; } - } + }//end for(i = 0; i < mpiSim->getNmol()) + + for(k = 0; k < outFile.size(); k++) + outFile[k]->flush(); + sprintf( checkPointMsg, "Sucessfully took a dump.\n"); + MPIcheckPoint(); - } - -#endif // is_mpi -} + delete[] potatoes; + + } else { -void DumpWriter::writeFinal(double finalTime){ + // worldRank != 0, so I'm a remote node. - char finalName[500]; - ofstream finalOut; + // Set my magic potato to 0: - const int BUFFERSIZE = 2000; - const int MINIBUFFERSIZE = 100; - char tempBuffer[BUFFERSIZE]; - char writeLine[BUFFERSIZE]; + myPotato = 0; + currentIndex = 0; + + for (i = 0 ; i < mpiSim->getNMolGlobal(); i++ ) { + + // Am I the node which has this integrableObject? + + if (MolToProcMap[i] == worldRank) { - double q[4]; - DirectionalAtom* dAtom; - Atom** atoms = entry_plug->atoms; - 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]; + if (myPotato + 1 >= 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); + + } -#else //is_mpi - int nAtoms = entry_plug->n_atoms; -#endif //is_mpi + 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++; - double pos[3], vel[3]; + for( iter = integrableObjects.begin(); iter != integrableObjects.end(); iter++){ -#ifdef IS_MPI - if(worldRank == 0 ){ -#endif // is_mpi + 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(); - strcpy( finalName, entry_plug->finalName ); + sd->getPos(pos); + sd->getVel(vel); - 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(); - } + atomData[0] = pos[0]; + atomData[1] = pos[1]; + atomData[2] = pos[2]; - // finalOut.setf( ios::scientific ); + atomData[3] = vel[0]; + atomData[4] = vel[1]; + atomData[5] = vel[2]; + + isDirectional = 0; -#ifdef IS_MPI - } + if( sd->isDirectional() ){ - sprintf(checkPointMsg,"Opened file for final configuration\n"); - MPIcheckPoint(); + 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]; + } -#endif //is_mpi + + strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE); + // null terminate the string before sending (just in case): + MPIatomTypeString[MINIBUFFERSIZE-1] = '\0'; -#ifndef IS_MPI + MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0, + myPotato, MPI_COMM_WORLD); + + myPotato++; + + if (isDirectional) { - finalOut << nAtoms << "\n"; + MPI_Send(atomData, 13, MPI_DOUBLE, 0, + myPotato, MPI_COMM_WORLD); + + } else { - finalOut << finalTime << ";\t" - << entry_plug->Hmat[0][0] << "\t" - << entry_plug->Hmat[1][0] << "\t" - << entry_plug->Hmat[2][0] << ";\t" + MPI_Send(atomData, 6, MPI_DOUBLE, 0, + myPotato, MPI_COMM_WORLD); + } - << entry_plug->Hmat[0][1] << "\t" - << entry_plug->Hmat[1][1] << "\t" - << entry_plug->Hmat[2][1] << ";\t" + myPotato++; - << 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(), - 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], - 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; - } - finalOut.flush(); - finalOut.close(); - -#else // is_mpi - - /* 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 ){ - - // 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; - - finalOut << mpiSim->getTotAtoms() << "\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] << ";"; - - finalOut << entry_plug->the_integrator->getAdditionalParameters(); - finalOut << endl; - finalOut.flush(); - - for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { - - // 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); + currentIndex++; } - - myPotato = potatoes[which_node]; - - MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node, - myPotato, MPI_COMM_WORLD, &istatus); - - atomTypeString = MPIatomTypeString; - - 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 { - printf("inside \n"); - 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=-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(); - } - - 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", - atomTypeString, - atomData6[0], - atomData6[1], - atomData6[2], - atomData6[3], - atomData6[4], - atomData6[5]); - - strcpy( writeLine, tempBuffer ); - 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(); - 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++ ) { - - // 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(); - - } + - if( worldRank == 0 ) finalOut.close(); #endif // is_mpi } - - #ifdef IS_MPI // a couple of functions to let us escape the write loop