--- trunk/OOPSE/libmdtools/DumpWriter.cpp 2004/01/13 15:46:49 929 +++ trunk/OOPSE/libmdtools/DumpWriter.cpp 2004/01/15 14:22:16 947 @@ -40,8 +40,6 @@ DumpWriter::DumpWriter( SimInfo* the_entry_plug ){ simError(); } - //outFile.setf( ios::scientific ); - #ifdef IS_MPI } @@ -102,25 +100,45 @@ void DumpWriter::writeDump(double currentTime){ #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 ){ + + 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(); + } + } +#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 +146,68 @@ 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 +229,27 @@ 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 +285,8 @@ 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 +315,31 @@ 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; @@ -328,8 +384,8 @@ void DumpWriter::writeFrame( ofstream& outFile, double } else { - haveError = 0; - which_atom = i; + haveError = 0; + which_atom = i; local_index = indexArray[currentIndex].first; @@ -337,8 +393,8 @@ void DumpWriter::writeFrame( ofstream& outFile, double atomTypeString = atoms[local_index]->getType(); - atoms[local_index]->getPos(pos); - atoms[local_index]->getVel(vel); + atoms[local_index]->getPos(pos); + atoms[local_index]->getVel(vel); atomData6[0] = pos[0]; atomData6[1] = pos[1]; @@ -371,14 +427,14 @@ void DumpWriter::writeFrame( ofstream& outFile, double } } else { - sprintf(painCave.errMsg, - "Atom %d not found on processor %d\n", - i, worldRank ); - haveError= 1; - simError(); - } + sprintf(painCave.errMsg, + "Atom %d not found on processor %d\n", + i, worldRank ); + haveError= 1; + simError(); + } - if(haveError) DieDieDie(); + if(haveError) DieDieDie(); currentIndex ++; } @@ -386,48 +442,53 @@ void DumpWriter::writeFrame( ofstream& outFile, double 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]); + 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" ); + 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]); } - 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. @@ -459,8 +520,8 @@ void DumpWriter::writeFrame( ofstream& outFile, double atomTypeString = atoms[local_index]->getType(); - atoms[local_index]->getPos(pos); - atoms[local_index]->getVel(vel); + atoms[local_index]->getPos(pos); + atoms[local_index]->getVel(vel); atomData6[0] = pos[0]; atomData6[1] = pos[1]; @@ -486,19 +547,19 @@ 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(); } } else { - sprintf(painCave.errMsg, - "Atom %d not found on processor %d\n", - i, worldRank ); - haveError= 1; - simError(); - } + sprintf(painCave.errMsg, + "Atom %d not found on processor %d\n", + i, worldRank ); + haveError= 1; + simError(); + } strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE); @@ -506,12 +567,12 @@ void DumpWriter::writeFrame( ofstream& outFile, double 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++;