--- trunk/OOPSE/libmdtools/DumpWriter.cpp 2004/01/13 15:46:49 929 +++ trunk/OOPSE/libmdtools/DumpWriter.cpp 2004/04/22 03:29:30 1129 @@ -1,3 +1,4 @@ +#define _LARGEFILE_SOURCE64 #define _FILE_OFFSET_BITS 64 #include @@ -28,7 +29,6 @@ DumpWriter::DumpWriter( SimInfo* the_entry_plug ){ if(worldRank == 0 ){ #endif // is_mpi - dumpFile.open(entry_plug->sampleName, ios::out | ios::trunc ); if( !dumpFile ){ @@ -40,8 +40,6 @@ DumpWriter::DumpWriter( SimInfo* the_entry_plug ){ simError(); } - //outFile.setf( ios::scientific ); - #ifdef IS_MPI } @@ -90,37 +88,59 @@ void DumpWriter::sortByGlobalIndex(){ */ void DumpWriter::sortByGlobalIndex(){ - Atom** atoms = entry_plug->atoms; - + Molecule* mols = entry_plug->molecules; indexArray.clear(); - for(int i = 0; i < mpiSim->getMyNlocal();i++) - indexArray.push_back(make_pair(i, atoms[i]->getGlobalIndex())); + 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); } + #endif void DumpWriter::writeDump(double currentTime){ - -// write to eor file - writeFinal(currentTime); -//write to dump file - writeFrame(dumpFile, currentTime); + 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(); + } +#ifdef IS_MPI + } +#endif // is_mpi + + fileStreams.push_back(&finalOut); + fileStreams.push_back(&dumpFile); + + writeFrame(fileStreams, currentTime); + +#ifdef IS_MPI + finalOut.close(); +#endif } void DumpWriter::writeFinal(double currentTime){ - ofstream finalOut; - - //Open eor file + ofstream finalOut; + vector fileStreams; + #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", @@ -128,35 +148,69 @@ void DumpWriter::writeFinal(double currentTime){ 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 + + fileStreams.push_back(&finalOut); + writeFrame(fileStreams, currentTime); +#ifdef IS_MPI + finalOut.close(); +#endif + } -void DumpWriter::writeFrame( ofstream& outFile, double currentTime ){ +void DumpWriter::writeFrame( vector& outFile, double currentTime ){ const int BUFFERSIZE = 2000; const int MINIBUFFERSIZE = 100; - char tempBuffer[BUFFERSIZE]; + char tempBuffer[BUFFERSIZE]; char writeLine[BUFFERSIZE]; - 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; @@ -167,73 +221,85 @@ void DumpWriter::writeFrame( ofstream& outFile, double int isDirectional; char* atomTypeString; char MPIatomTypeString[MINIBUFFERSIZE]; - -#else //is_mpi - int nAtoms = entry_plug->n_atoms; + int nObjects; #endif //is_mpi - double q[4]; + double q[4], ji[3]; DirectionalAtom* dAtom; - Atom** atoms = entry_plug->atoms; 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 << 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" - 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][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" + //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++ ){ - << 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; + 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); - for( i=0; igetType(), + pos[0], + pos[1], + pos[2], + vel[0], + vel[1], + vel[2]); + strcpy( writeLine, tempBuffer ); - atoms[i]->getPos(pos); - atoms[i]->getVel(vel); + if( sd->isDirectional() ){ - 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 ); + sd->getQ( q ); + sd->getJ( ji ); - 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 ); + 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" ); - outFile << writeLine; - } + + for(k = 0; k < outFile.size(); k++) + *outFile[k] << writeLine; +} #else // is_mpi @@ -250,7 +316,8 @@ void DumpWriter::writeFrame( ofstream& outFile, double int haveError; MPI_Status istatus; - int *AtomToProcMap = mpiSim->getAtomToProcMap(); + int nCurObj; + int *MolToProcMap = mpiSim->getMolToProcMap(); // write out header and node 0's coordinates @@ -261,132 +328,144 @@ void DumpWriter::writeFrame( ofstream& outFile, double nProc = mpiSim->getNumberProcessors(); 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->getTotNmol(); 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, + + //recieve the number of integrableObject in current molecule + MPI_Recv(&nCurObj, 1, MPI_INT, which_node, myPotato, MPI_COMM_WORLD, &istatus); - - atomTypeString = MPIatomTypeString; - myPotato++; + + for(int l = 0; l < nCurObj; l++){ - MPI_Recv(&isDirectional, 1, MPI_INT, which_node, - myPotato, MPI_COMM_WORLD, &istatus); + 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(&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(&isDirectional, 1, MPI_INT, which_node, + myPotato, MPI_COMM_WORLD, &istatus); - myPotato++; + myPotato++; - if (isDirectional) { + if (isDirectional) { MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node, myPotato, MPI_COMM_WORLD, &istatus); - } else { + } else { MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node, myPotato, MPI_COMM_WORLD, &istatus); + } + + myPotato++; } - - myPotato++; potatoes[which_node] = myPotato; } else { - haveError = 0; - which_atom = i; + haveError = 0; - local_index = indexArray[currentIndex].first; - - if (which_atom == indexArray[currentIndex].second) { - - atomTypeString = atoms[local_index]->getType(); + local_index = indexArray[currentIndex].first; - atoms[local_index]->getPos(pos); - atoms[local_index]->getVel(vel); + integrableObjects = (entry_plug->molecules[local_index]).getIntegrableObjects(); - atomData6[0] = pos[0]; - atomData6[1] = pos[1]; - atomData6[2] = pos[2]; + for(iter= integrableObjects.begin(); iter != integrableObjects.end(); ++iter){ + sd = *iter; + atomTypeString = sd->getType(); + + sd->getPos(pos); + sd->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; + atomData6[3] = vel[0]; + atomData6[4] = vel[1]; + atomData6[5] = vel[2]; + + isDirectional = 0; - if( atoms[local_index]->isDirectional() ){ + if( sd->isDirectional() ){ - isDirectional = 1; - - dAtom = (DirectionalAtom *)atoms[local_index]; - dAtom->getQ( q ); + isDirectional = 1; + + sd->getQ( q ); + sd->getJ( ji ); - for (int j = 0; j < 6 ; j++) - atomData13[j] = atomData6[j]; + 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] = ji[0]; + atomData13[11] = ji[1]; + atomData13[12] = ji[2]; + } - 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(); - - currentIndex ++; + currentIndex++; } // If we've survived to here, format the line: if (!isDirectional) { - sprintf( writeLine, + sprintf( writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", atomTypeString, atomData6[0], @@ -395,7 +474,7 @@ void DumpWriter::writeFrame( ofstream& outFile, double atomData6[3], atomData6[4], atomData6[5]); - + strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); } else { @@ -419,15 +498,20 @@ void DumpWriter::writeFrame( ofstream& outFile, double } - outFile << writeLine; + for(k = 0; k < outFile.size(); k++) + *outFile[k] << writeLine; } - - outFile.flush(); + for(k = 0; k < outFile.size(); k++) + outFile[k]->flush(); + sprintf( checkPointMsg, "Sucessfully took a dump.\n"); + MPIcheckPoint(); + delete[] potatoes; + } else { // worldRank != 0, so I'm a remote node. @@ -437,105 +521,125 @@ void DumpWriter::writeFrame( ofstream& outFile, double myPotato = 0; currentIndex = 0; - for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { + for (i = 0 ; i < mpiSim->getTotNmol(); i++ ) { - // Am I the node which has this atom? + // Am I the node which has this integrableObject? - if (AtomToProcMap[i] == worldRank) { + if (MolToProcMap[i] == worldRank) { - if (myPotato + 3 >= MAXTAG) { + 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); } - 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); - - atomData6[0] = pos[0]; - atomData6[1] = pos[1]; - atomData6[2] = pos[2]; - - atomData6[3] = vel[0]; - atomData6[4] = vel[1]; - atomData6[5] = vel[2]; + local_index = indexArray[currentIndex].first; + integrableObjects = entry_plug->molecules[local_index].getIntegrableObjects(); - isDirectional = 0; + nCurObj = integrableObjects.size(); + + MPI_Send(&nCurObj, 1, MPI_INT, 0, + myPotato, MPI_COMM_WORLD); + myPotato++; - if( atoms[local_index]->isDirectional() ){ + for( iter = integrableObjects.begin(); iter != integrableObjects.end(); iter++){ - isDirectional = 1; + 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); + + } - dAtom = (DirectionalAtom *)atoms[local_index]; - dAtom->getQ( q ); + sd = *iter; - 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]; + atomTypeString = sd->getType(); - atomData13[10] = dAtom->getJx(); - atomData13[11] = dAtom->getJy(); - atomData13[12] = dAtom->getJz(); - } + sd->getPos(pos); + sd->getVel(vel); - } else { - sprintf(painCave.errMsg, - "Atom %d not found on processor %d\n", - i, worldRank ); - haveError= 1; - simError(); - } + atomData6[0] = pos[0]; + atomData6[1] = pos[1]; + atomData6[2] = pos[2]; - strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE); + atomData6[3] = vel[0]; + atomData6[4] = vel[1]; + atomData6[5] = vel[2]; + + isDirectional = 0; - // null terminate the string before sending (just in case): - MPIatomTypeString[MINIBUFFERSIZE-1] = '\0'; + if( sd->isDirectional() ){ - MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0, - myPotato, MPI_COMM_WORLD); - - myPotato++; + isDirectional = 1; + + sd->getQ( q ); + sd->getJ( ji ); + + 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] = ji[0]; + atomData13[11] = ji[1]; + atomData13[12] = ji[2]; + } - MPI_Send(&isDirectional, 1, MPI_INT, 0, - myPotato, MPI_COMM_WORLD); - - myPotato++; - - if (isDirectional) { + + strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE); - MPI_Send(atomData13, 13, MPI_DOUBLE, 0, - myPotato, MPI_COMM_WORLD); - - } else { + // null terminate the string before sending (just in case): + MPIatomTypeString[MINIBUFFERSIZE-1] = '\0'; - MPI_Send(atomData6, 6, MPI_DOUBLE, 0, - myPotato, MPI_COMM_WORLD); - } + MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0, + myPotato, MPI_COMM_WORLD); + + myPotato++; - myPotato++; - currentIndex++; + 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, "Sucessfully took a dump.\n"); - MPIcheckPoint(); + MPIcheckPoint(); - } + } + + #endif // is_mpi }