--- trunk/OOPSE/libmdtools/DumpWriter.cpp 2004/01/10 02:15:35 919 +++ trunk/OOPSE/libmdtools/DumpWriter.cpp 2004/01/15 21:57:10 949 @@ -3,6 +3,8 @@ #include #include #include +#include +#include #ifdef IS_MPI #include @@ -26,24 +28,23 @@ 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(); @@ -56,443 +57,169 @@ 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]; - - int i; - -#ifdef IS_MPI +void DumpWriter::update(){ + sortByGlobalIndex(); +} - int *potatoes; - int myPotato; +/** + * Auxiliary sorting function + */ + +bool indexSortingCriterion(const pair& p1, const pair& p2){ + return p1.second < p2.second; +} - 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; +/** + * Sorting the local index by global index + */ + +void DumpWriter::sortByGlobalIndex(){ Atom** atoms = entry_plug->atoms; - double pos[3], vel[3]; + + 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); - // write current frame to the eor file + //for (int i = 0; i < mpiSim->getMyNlocal(); i++) { + // printf("node %d has global %d at local %d\n", worldRank, indexArray[i].second, indexArray[i].first); + //} + +} - this->writeFinal( currentTime ); +#endif -#ifndef IS_MPI +void DumpWriter::writeDump(double currentTime){ - outFile << nAtoms << "\n"; + ofstream finalOut; + vector fileStreams; - 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(), - 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 ); +#ifdef IS_MPI + printf("Hello from node %d\n", worldRank); + sortByGlobalIndex(); + if(worldRank == 0 ){ + + 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; } - outFile.flush(); +#endif // is_mpi -#else // is_mpi + fileStreams.push_back(&finalOut); + fileStreams.push_back(&dumpFile); - cout << "master" <getAtomToProcMap(); +void DumpWriter::writeFinal(double currentTime){ - // write out header and node 0's coordinates + ofstream finalOut; + vector fileStreams; - 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; - - outFile << mpiSim->getTotAtoms() << "\n"; - - outFile << currentTime << ";\t" - << entry_plug->Hmat[0][0] << "\t" - << entry_plug->Hmat[1][0] << "\t" - << entry_plug->Hmat[2][0] << ";\t" - - << entry_plug->Hmat[0][1] << "\t" - << entry_plug->Hmat[1][1] << "\t" - << entry_plug->Hmat[2][1] << ";\t" - - << entry_plug->Hmat[0][2] << "\t" - << entry_plug->Hmat[1][2] << "\t" - << entry_plug->Hmat[2][2] << ";"; - - outFile << entry_plug->the_integrator->getAdditionalParameters(); - outFile << endl; - 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) { +#ifdef IS_MPI + if(worldRank == 0 ){ - if (potatoes[which_node] + 3 >= MAXTAG) { - // The potato was going to exceed the maximum value, - // so wrap this processor potato back to 0: + finalOut.open( entry_plug->finalName, ios::out | ios::trunc ); - 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); - - strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE); - - // Null terminate the atomTypeString just in case: - - atomTypeString[strlen(atomTypeString) - 1] = '\0'; - - 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=-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 ); - - } - - outFile << writeLine; - outFile.flush(); - } + if( !finalOut ){ + sprintf( painCave.errMsg, + "Could not open \"%s\" for final dump output.\n", + entry_plug->finalName ); + painCave.isFatal = 1; + simError(); } - outFile.flush(); - sprintf( checkPointMsg, - "Sucessfully took a dump.\n"); - MPIcheckPoint(); - delete[] potatoes; - } else { + } +#endif // is_mpi + + fileStreams.push_back(&finalOut); + writeFrame(fileStreams, currentTime); - // 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(); - - } +#ifdef IS_MPI + finalOut.close(); +#endif -#endif // is_mpi } -void DumpWriter::writeFinal(double finalTime){ +void DumpWriter::writeFrame( vector& outFile, double currentTime ){ - char finalName[500]; - ofstream finalOut; - const int BUFFERSIZE = 2000; const int MINIBUFFERSIZE = 100; - char tempBuffer[BUFFERSIZE]; + + char tempBuffer[BUFFERSIZE]; char writeLine[BUFFERSIZE]; - double q[4]; - DirectionalAtom* dAtom; - Atom** atoms = entry_plug->atoms; - int i; + 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; + int j, which_node, done, which_atom, local_index, currentIndex; double atomData6[6]; double atomData13[13]; int isDirectional; @@ -503,55 +230,33 @@ void DumpWriter::writeFinal(double finalTime){ int nAtoms = entry_plug->n_atoms; #endif //is_mpi + double q[4]; + DirectionalAtom* dAtom; + Atom** atoms = entry_plug->atoms; 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, - "Could not open \"%s\" for final dump output.\n", - finalName ); - painCave.isFatal = 1; - simError(); - } - - // finalOut.setf( ios::scientific ); - -#ifdef IS_MPI - } - - sprintf(checkPointMsg,"Opened file for final configuration\n"); - MPIcheckPoint(); - -#endif //is_mpi - - #ifndef IS_MPI + + for(k = 0; k < outFile.size(); k++){ + *outFile[k] << nAtoms << "\n"; - finalOut << 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" - 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][2] << "\t" + << entry_plug->Hmat[1][2] << "\t" + << entry_plug->Hmat[2][2] << ";"; - << 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; - + //write out additional parameters, such as chi and eta + *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl; + } + for( i=0; igetPos(pos); @@ -587,14 +292,14 @@ void DumpWriter::writeFinal(double finalTime){ 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(); - 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) { @@ -617,27 +322,30 @@ void DumpWriter::writeFinal(double finalTime){ nProc = mpiSim->getNumberProcessors(); potatoes = new int[nProc]; + //write out the comment lines for (i = 0; i < nProc; i++) potatoes[i] = 0; - finalOut << mpiSim->getTotAtoms() << "\n"; + for(k = 0; k < outFile.size(); k++){ + *outFile[k] << mpiSim->getTotAtoms() << "\n"; - finalOut << finalTime << ";\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; + } - finalOut << entry_plug->the_integrator->getAdditionalParameters(); - finalOut << endl; - finalOut.flush(); + currentIndex = 0; for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { @@ -661,12 +369,8 @@ void DumpWriter::writeFinal(double finalTime){ 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, @@ -687,21 +391,26 @@ void DumpWriter::writeFinal(double finalTime){ } else { - haveError = 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; - } + //local_index = -1; + + //for (j=0; (jgetMyNlocal()) && (local_index < 0); j++) { + // if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; + //} - if (local_index != -1) { + //if (local_index != -1) { + + local_index = indexArray[currentIndex].first; - atomTypeString = atoms[local_index]->getType(); - + 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]; @@ -734,66 +443,67 @@ void DumpWriter::writeFinal(double finalTime){ } else { sprintf(painCave.errMsg, - "Atom %d not found on processor %d\n", - i, worldRank ); + "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(); + 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 ); - - } + currentIndex++; + } + // 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" ); + + } 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]); - finalOut << writeLine; - finalOut.flush(); } + + for(k = 0; k < outFile.size(); k++) + *outFile[k] << writeLine; } - - finalOut.flush(); + + for(k = 0; k < outFile.size(); k++) + outFile[k]->flush(); + sprintf( checkPointMsg, "Sucessfully took a dump.\n"); - delete[] potatoes; - + MPIcheckPoint(); + delete[] potatoes; + } else { // worldRank != 0, so I'm a remote node. @@ -801,6 +511,7 @@ void DumpWriter::writeFinal(double finalTime){ // Set my magic potato to 0: myPotato = 0; + currentIndex = 0; for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { @@ -809,26 +520,33 @@ void DumpWriter::writeFinal(double finalTime){ 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) { + 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) { + + 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]; @@ -853,7 +571,7 @@ void DumpWriter::writeFinal(double finalTime){ atomData13[7] = q[1]; atomData13[8] = q[2]; atomData13[9] = q[3]; - + atomData13[10] = dAtom->getJx(); atomData13[11] = dAtom->getJy(); atomData13[12] = dAtom->getJz(); @@ -861,24 +579,24 @@ void DumpWriter::writeFinal(double finalTime){ } else { sprintf(painCave.errMsg, - "Atom %d not found on processor %d\n", - i, worldRank ); + "Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n", + which_atom, worldRank, currentIndex, local_index ); 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_COMM_WORLD); myPotato++; MPI_Send(&isDirectional, 1, MPI_INT, 0, - myPotato, MPI_COMM_WORLD); + myPotato, MPI_COMM_WORLD); myPotato++; @@ -893,7 +611,8 @@ void DumpWriter::writeFinal(double finalTime){ myPotato, MPI_COMM_WORLD); } - myPotato++; + myPotato++; + currentIndex++; } } @@ -903,12 +622,9 @@ void DumpWriter::writeFinal(double finalTime){ } - if( worldRank == 0 ) finalOut.close(); #endif // is_mpi } - - #ifdef IS_MPI // a couple of functions to let us escape the write loop