--- trunk/OOPSE/libmdtools/DumpWriter.cpp 2004/01/13 15:46:49 929 +++ trunk/OOPSE/libmdtools/DumpWriter.cpp 2004/01/16 21:55:39 952 @@ -28,7 +28,6 @@ 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 +39,6 @@ DumpWriter::DumpWriter( SimInfo* the_entry_plug ){ simError(); } - //outFile.setf( ios::scientific ); - #ifdef IS_MPI } @@ -94,33 +91,61 @@ void DumpWriter::sortByGlobalIndex(){ indexArray.clear(); - for(int i = 0; i < mpiSim->getMyNlocal();i++) + for(int i = 0; i < mpiSim->getMyNlocal();i++) indexArray.push_back(make_pair(i, atoms[i]->getGlobalIndex())); sort(indexArray.begin(), indexArray.end(), indexSortingCriterion); + + //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); + //} + } + #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 +153,69 @@ 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; @@ -178,25 +237,27 @@ void DumpWriter::writeFrame( ofstream& outFile, double double pos[3], vel[3]; #ifndef IS_MPI + + for(k = 0; k < outFile.size(); k++){ + *outFile[k] << nAtoms << "\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" - - << 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; - + //write out additional parameters, such as chi and eta + *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl; + } + for( i=0; igetPos(pos); @@ -232,7 +293,8 @@ void DumpWriter::writeFrame( ofstream& outFile, double 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 @@ -261,29 +323,31 @@ 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] << mpiSim->getTotAtoms() << "\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++ ) { // Get the Node number which has this atom; @@ -328,18 +392,26 @@ void DumpWriter::writeFrame( ofstream& outFile, double } else { - haveError = 0; + haveError = 0; which_atom = i; - local_index = indexArray[currentIndex].first; - - if (which_atom == indexArray[currentIndex].second) { - - atomTypeString = atoms[local_index]->getType(); + //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]; @@ -372,21 +444,21 @@ void DumpWriter::writeFrame( ofstream& outFile, double } 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(); - 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 +467,7 @@ 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 +491,20 @@ 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. @@ -444,24 +521,33 @@ void DumpWriter::writeFrame( ofstream& outFile, double 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 = indexArray[currentIndex].first; + + //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) { + 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]; @@ -486,7 +572,7 @@ void DumpWriter::writeFrame( ofstream& outFile, double atomData13[7] = q[1]; atomData13[8] = q[2]; atomData13[9] = q[3]; - + atomData13[10] = dAtom->getJx(); atomData13[11] = dAtom->getJy(); atomData13[12] = dAtom->getJz(); @@ -494,24 +580,24 @@ void DumpWriter::writeFrame( ofstream& outFile, double } 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++;