--- trunk/OOPSE/libmdtools/DumpWriter.cpp 2004/01/12 22:54:42 927 +++ trunk/OOPSE/libmdtools/DumpWriter.cpp 2004/01/13 15:46:49 929 @@ -3,6 +3,8 @@ #include #include #include +#include +#include #ifdef IS_MPI #include @@ -26,15 +28,14 @@ DumpWriter::DumpWriter( SimInfo* the_entry_plug ){ if(worldRank == 0 ){ #endif // is_mpi - strcpy( outName, entry_plug->sampleName ); - outFile.open(outName, ios::out | ios::trunc ); + dumpFile.open(entry_plug->sampleName, ios::out | ios::trunc ); - if( !outFile ){ + if( !dumpFile ){ sprintf( painCave.errMsg, "Could not open \"%s\" for dump output.\n", - outName); + entry_plug->sampleName); painCave.isFatal = 1; simError(); } @@ -44,6 +45,9 @@ DumpWriter::DumpWriter( SimInfo* the_entry_plug ){ #ifdef IS_MPI } + //sort the local atoms by global index + sortByGlobalIndex(); + sprintf( checkPointMsg, "Sucessfully opened output file for dumping.\n"); MPIcheckPoint(); @@ -56,15 +60,93 @@ 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(); +} + +/** + * Auxiliary sorting function + */ + +bool indexSortingCriterion(const pair& p1, const pair& p2){ + return p1.second < p2.second; +} + +/** + * 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); +} +#endif + +void DumpWriter::writeDump(double currentTime){ + +// write to eor file + writeFinal(currentTime); + +//write to dump file + writeFrame(dumpFile, currentTime); + +} + +void DumpWriter::writeFinal(double currentTime){ + + ofstream finalOut; + + //Open eor file +#ifdef IS_MPI + if(worldRank == 0 ){ +#endif // is_mpi + + 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 + + //write to eor file + writeFrame(finalOut, currentTime); + + //close eor file +#ifdef IS_MPI + if(worldRank == 0 ){ + finalOut.close(); + } +#endif // is_mpi +} + +void DumpWriter::writeFrame( ofstream& outFile, double currentTime ){ + const int BUFFERSIZE = 2000; const int MINIBUFFERSIZE = 100; @@ -79,7 +161,7 @@ void DumpWriter::writeDump( double currentTime ){ 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; @@ -95,10 +177,6 @@ void DumpWriter::writeDump( double currentTime ){ Atom** atoms = entry_plug->atoms; double pos[3], vel[3]; - // write current frame to the eor file - - this->writeFinal( currentTime ); - #ifndef IS_MPI outFile << nAtoms << "\n"; @@ -156,7 +234,6 @@ void DumpWriter::writeDump( double currentTime ){ outFile << writeLine; } - outFile.flush(); #else // is_mpi @@ -205,7 +282,8 @@ void DumpWriter::writeDump( double currentTime ){ outFile << entry_plug->the_integrator->getAdditionalParameters(); outFile << endl; outFile.flush(); - + + currentIndex = 0; for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { // Get the Node number which has this atom; @@ -228,11 +306,6 @@ void DumpWriter::writeDump( double currentTime ){ 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++; @@ -257,13 +330,10 @@ void DumpWriter::writeDump( double currentTime ){ 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) { + + local_index = indexArray[currentIndex].first; + + if (which_atom == indexArray[currentIndex].second) { atomTypeString = atoms[local_index]->getType(); @@ -310,12 +380,13 @@ void DumpWriter::writeDump( double currentTime ){ if(haveError) DieDieDie(); + currentIndex ++; } // If we've survived to here, format the line: if (!isDirectional) { - sprintf( tempBuffer, + sprintf( writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", atomTypeString, atomData6[0], @@ -324,13 +395,12 @@ void DumpWriter::writeDump( double currentTime ){ 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, + 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], @@ -346,13 +416,10 @@ void DumpWriter::writeDump( double currentTime ){ atomData13[10], atomData13[11], atomData13[12]); - - strcpy( writeLine, tempBuffer ); } outFile << writeLine; - outFile.flush(); } @@ -368,6 +435,7 @@ void DumpWriter::writeDump( double currentTime ){ // Set my magic potato to 0: myPotato = 0; + currentIndex = 0; for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { @@ -385,443 +453,9 @@ void DumpWriter::writeDump( double currentTime ){ } which_atom = i; - local_index=-1; - for (j=0; (jgetMyNlocal()) && (local_index < 0); j++) { - if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; - } - if (local_index != -1) { - - atomTypeString = atoms[local_index]->getType(); - - atoms[local_index]->getPos(pos); - atoms[local_index]->getVel(vel); - - atomData6[0] = pos[0]; - atomData6[1] = pos[1]; - atomData6[2] = pos[2]; - - atomData6[3] = vel[0]; - atomData6[4] = vel[1]; - atomData6[5] = vel[2]; - - isDirectional = 0; - - if( atoms[local_index]->isDirectional() ){ - - isDirectional = 1; - - dAtom = (DirectionalAtom *)atoms[local_index]; - dAtom->getQ( q ); - - for (int j = 0; j < 6 ; j++) - atomData13[j] = atomData6[j]; - - atomData13[6] = q[0]; - atomData13[7] = q[1]; - atomData13[8] = q[2]; - atomData13[9] = q[3]; - - atomData13[10] = dAtom->getJx(); - atomData13[11] = dAtom->getJy(); - atomData13[12] = dAtom->getJz(); - } - - } else { - sprintf(painCave.errMsg, - "Atom %d not found on processor %d\n", - i, worldRank ); - haveError= 1; - simError(); - } - - strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE); - - // null terminate the string before sending (just in case): - MPIatomTypeString[MINIBUFFERSIZE-1] = '\0'; - - MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0, - myPotato, MPI_COMM_WORLD); - - myPotato++; - - MPI_Send(&isDirectional, 1, MPI_INT, 0, - myPotato, MPI_COMM_WORLD); - - myPotato++; - - if (isDirectional) { - - MPI_Send(atomData13, 13, MPI_DOUBLE, 0, - myPotato, MPI_COMM_WORLD); - - } else { - - MPI_Send(atomData6, 6, MPI_DOUBLE, 0, - myPotato, MPI_COMM_WORLD); - } - - myPotato++; - } - } - - sprintf( checkPointMsg, - "Sucessfully took a dump.\n"); - MPIcheckPoint(); - - } - -#endif // is_mpi -} - -void DumpWriter::writeFinal(double finalTime){ - - char finalName[500]; - ofstream finalOut; - - const int BUFFERSIZE = 2000; - const int MINIBUFFERSIZE = 100; - char tempBuffer[BUFFERSIZE]; - char writeLine[BUFFERSIZE]; - - 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]; - -#else //is_mpi - int nAtoms = entry_plug->n_atoms; -#endif //is_mpi - - double pos[3], vel[3]; - -#ifdef IS_MPI - if(worldRank == 0 ){ -#endif // is_mpi - - strcpy( finalName, entry_plug->finalName ); - - finalOut.open( finalName, ios::out | ios::trunc ); - if( !finalOut ){ - sprintf( painCave.errMsg, - "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 - - finalOut << nAtoms << "\n"; - - finalOut << finalTime << ";\t" - << entry_plug->Hmat[0][0] << "\t" - << entry_plug->Hmat[1][0] << "\t" - << entry_plug->Hmat[2][0] << ";\t" - - << entry_plug->Hmat[0][1] << "\t" - << entry_plug->Hmat[1][1] << "\t" - << entry_plug->Hmat[2][1] << ";\t" - - << entry_plug->Hmat[0][2] << "\t" - << entry_plug->Hmat[1][2] << "\t" - << entry_plug->Hmat[2][2] << ";"; - - //write out additional parameters, such as chi and eta - finalOut << entry_plug->the_integrator->getAdditionalParameters(); - finalOut << endl; - - for( i=0; igetPos(pos); - atoms[i]->getVel(vel); - - sprintf( tempBuffer, - "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", - atoms[i]->getType(), - 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); - - } - - myPotato = potatoes[which_node]; - - MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node, - myPotato, MPI_COMM_WORLD, &istatus); - - atomTypeString = MPIatomTypeString; + local_index = indexArray[currentIndex].first; - 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]); - - strcpy( writeLine, tempBuffer ); - - } - - finalOut << writeLine; - finalOut.flush(); - } - - finalOut.flush(); - sprintf( checkPointMsg, - "Sucessfully took a dump.\n"); - delete[] potatoes; - - MPIcheckPoint(); - - } else { - - // worldRank != 0, so I'm a remote node. - - // Set my magic potato to 0: - - myPotato = 0; - - for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { - - // 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) { + if (which_atom == indexArray[currentIndex].second) { atomTypeString = atoms[local_index]->getType(); @@ -892,7 +526,8 @@ void DumpWriter::writeFinal(double finalTime){ myPotato, MPI_COMM_WORLD); } - myPotato++; + myPotato++; + currentIndex++; } } @@ -902,12 +537,9 @@ 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