--- trunk/OOPSE/libmdtools/DumpWriter.cpp 2004/01/13 20:04:28 934 +++ 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 ){ @@ -40,15 +40,6 @@ DumpWriter::DumpWriter( SimInfo* the_entry_plug ){ simError(); } - 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 } @@ -68,7 +59,6 @@ DumpWriter::~DumpWriter( ){ #endif // is_mpi dumpFile.close(); - finalOut.close(); #ifdef IS_MPI } @@ -98,24 +88,34 @@ 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){ + ofstream finalOut; vector fileStreams; #ifdef IS_MPI if(worldRank == 0 ){ - finalOut.seekp(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 @@ -123,21 +123,42 @@ void DumpWriter::writeDump(double currentTime){ fileStreams.push_back(&dumpFile); writeFrame(fileStreams, currentTime); + +#ifdef IS_MPI + finalOut.close(); +#endif } void DumpWriter::writeFinal(double currentTime){ + ofstream finalOut; vector fileStreams; #ifdef IS_MPI if(worldRank == 0 ){ - finalOut.seekp(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 // is_mpi fileStreams.push_back(&finalOut); writeFrame(fileStreams, currentTime); + +#ifdef IS_MPI + finalOut.close(); +#endif } @@ -146,13 +167,50 @@ void DumpWriter::writeFrame( vector& outFil const int BUFFERSIZE = 2000; const int MINIBUFFERSIZE = 100; - char tempBuffer[BUFFERSIZE]; + 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; @@ -163,20 +221,22 @@ void DumpWriter::writeFrame( vector& outFil 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] << nAtoms << "\n"; + *outFile[k] << nTotObjects << "\n"; *outFile[k] << currentTime << ";\t" << entry_plug->Hmat[0][0] << "\t" @@ -195,44 +255,51 @@ void DumpWriter::writeFrame( vector& outFil *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl; } - for( i=0; in_mol; i++ ){ - atoms[i]->getPos(pos); - atoms[i]->getVel(vel); + 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", - atoms[i]->getType(), - pos[0], - pos[1], - pos[2], - vel[0], - vel[1], - vel[2]); - strcpy( writeLine, tempBuffer ); + 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( atoms[i]->isDirectional() ){ + if( sd->isDirectional() ){ - dAtom = (DirectionalAtom *)atoms[i]; - dAtom->getQ( q ); + 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], - 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" ); + for(k = 0; k < outFile.size(); k++) *outFile[k] << writeLine; - } +} #else // is_mpi @@ -249,7 +316,8 @@ void DumpWriter::writeFrame( vector& outFil int haveError; MPI_Status istatus; - int *AtomToProcMap = mpiSim->getAtomToProcMap(); + int nCurObj; + int *MolToProcMap = mpiSim->getMolToProcMap(); // write out header and node 0's coordinates @@ -265,7 +333,7 @@ void DumpWriter::writeFrame( vector& outFil potatoes[i] = 0; for(k = 0; k < outFile.size(); k++){ - *outFile[k] << mpiSim->getTotAtoms() << "\n"; + *outFile[k] << nTotObjects << "\n"; *outFile[k] << currentTime << ";\t" << entry_plug->Hmat[0][0] << "\t" @@ -285,138 +353,148 @@ void DumpWriter::writeFrame( vector& outFil 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; - 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]; - - atomData13[6] = q[0]; - atomData13[7] = q[1]; - atomData13[8] = q[2]; - atomData13[9] = q[3]; + 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[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, - "%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" ); + "%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]); + 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]); } @@ -429,11 +507,11 @@ void DumpWriter::writeFrame( vector& outFil sprintf( checkPointMsg, "Sucessfully took a dump.\n"); - + MPIcheckPoint(); - + delete[] potatoes; - + } else { // worldRank != 0, so I'm a remote node. @@ -443,105 +521,125 @@ void DumpWriter::writeFrame( vector& outFil 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); + 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++; - atomData6[0] = pos[0]; - atomData6[1] = pos[1]; - atomData6[2] = pos[2]; + for( iter = integrableObjects.begin(); iter != integrableObjects.end(); iter++){ - atomData6[3] = vel[0]; - atomData6[4] = vel[1]; - atomData6[5] = vel[2]; - - isDirectional = 0; + 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); + + } + + sd = *iter; + + atomTypeString = sd->getType(); - if( atoms[local_index]->isDirectional() ){ + sd->getPos(pos); + sd->getVel(vel); - isDirectional = 1; + 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( sd->isDirectional() ){ + + 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]; + } + + + 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); - dAtom = (DirectionalAtom *)atoms[local_index]; - dAtom->getQ( q ); + myPotato++; + + MPI_Send(&isDirectional, 1, MPI_INT, 0, + myPotato, MPI_COMM_WORLD); - for (int j = 0; j < 6 ; j++) - atomData13[j] = atomData6[j]; + myPotato++; - 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(); - } + if (isDirectional) { - } else { - sprintf(painCave.errMsg, - "Atom %d not found on processor %d\n", - i, worldRank ); - haveError= 1; - simError(); - } + MPI_Send(atomData13, 13, MPI_DOUBLE, 0, + myPotato, MPI_COMM_WORLD); + + } else { - strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE); + MPI_Send(atomData6, 6, MPI_DOUBLE, 0, + myPotato, MPI_COMM_WORLD); + } - // null terminate the string before sending (just in case): - MPIatomTypeString[MINIBUFFERSIZE-1] = '\0'; + myPotato++; - 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); + currentIndex++; - } 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 }