--- trunk/OOPSE/libmdtools/DumpWriter.cpp 2004/01/08 22:25:52 913 +++ trunk/OOPSE/libmdtools/DumpWriter.cpp 2004/01/09 20:29:32 916 @@ -72,18 +72,20 @@ void DumpWriter::writeDump( double currentTime ){ char writeLine[BUFFERSIZE]; int i; + #ifdef IS_MPI + + int *potatoes; + int myPotato; + + int nProc; int j, which_node, done, which_atom, local_index; - double atomTransData[6]; - double atomOrientData[7]; + double atomData6[6]; + double atomData13[13]; int isDirectional; char* atomTypeString; char MPIatomTypeString[MINIBUFFERSIZE]; - int me; - int atomTypeTag; - int atomIsDirectionalTag; - int atomTransDataTag; - int atomOrientDataTag; + #else //is_mpi int nAtoms = entry_plug->n_atoms; #endif //is_mpi @@ -165,7 +167,7 @@ void DumpWriter::writeDump( double currentTime ){ MAXTAG = *tagub; } else { MAXTAG = 32767; - } + } int haveError; @@ -175,6 +177,15 @@ void DumpWriter::writeDump( double currentTime ){ // 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; + outFile << mpiSim->getTotAtoms() << "\n"; outFile << currentTime << ";\t" @@ -194,25 +205,27 @@ void DumpWriter::writeDump( double currentTime ){ outFile << endl; outFile.flush(); - tag = 0; - for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { - - if (tag + 2 >= MAXTAG) { - // The tag was going to exceed the maximum value, so wrap around to 0: - tag = 0; - // Send the newly zeroed tag on to the other nodes: - MPI_Bcast(&tag, 1, MPI_INT, 0, MPI_COMM_WORLD); - } // 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, - atomTypeTag, MPI_COMM_WORLD, &istatus); + myPotato, MPI_COMM_WORLD, &istatus); strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE); @@ -220,43 +233,48 @@ void DumpWriter::writeDump( double currentTime ){ atomTypeString[strlen(atomTypeString) - 1] = '\0'; + myPotato++; + MPI_Recv(&isDirectional, 1, MPI_INT, which_node, - atomIsDirectionalTag, MPI_COMM_WORLD, &istatus); - - MPI_Recv(atomTransData, 6, MPI_DOUBLE, which_node, - atomTransDataTag, MPI_COMM_WORLD, &istatus); + myPotato, MPI_COMM_WORLD, &istatus); + + myPotato++; - if (isDirectional) { - - MPI_Recv(atomOrientData, 7, MPI_DOUBLE, which_node, - atomOrientDataTag, MPI_COMM_WORLD, &istatus); - + 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); + atoms[local_index]->getVel(vel); - atomTransData[0] = pos[0]; - atomTransData[1] = pos[1]; - atomTransData[2] = pos[2]; + atomData6[0] = pos[0]; + atomData6[1] = pos[1]; + atomData6[2] = pos[2]; - atomTransData[3] = vel[0]; - atomTransData[4] = vel[1]; - atomTransData[5] = vel[2]; + atomData6[3] = vel[0]; + atomData6[4] = vel[1]; + atomData6[5] = vel[2]; isDirectional = 0; @@ -266,17 +284,20 @@ void DumpWriter::writeDump( double currentTime ){ dAtom = (DirectionalAtom *)atoms[local_index]; dAtom->getQ( q ); - - atomOrientData[0] = q[0]; - atomOrientData[1] = q[1]; - atomOrientData[2] = q[2]; - atomOrientData[3] = q[3]; - atomOrientData[4] = dAtom->getJx(); - atomOrientData[5] = dAtom->getJy(); - atomOrientData[6] = dAtom->getJz(); + 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", @@ -284,40 +305,49 @@ void DumpWriter::writeDump( double currentTime ){ haveError= 1; simError(); } - + if(haveError) DieDieDie(); - + // If we've survived to here, format the line: - sprintf( tempBuffer, - "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", - atomTypeString, - atomTransData[0], - atomTransData[1], - atomTransData[2], - atomTransData[3], - atomTransData[4], - atomTransData[5]); + if (!isDirectional) { - strcpy( writeLine, tempBuffer ); - - if (isDirectional) { - sprintf( tempBuffer, - "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", - atomOrientData[0], - atomOrientData[1], - atomOrientData[2], - atomOrientData[3], - atomOrientData[4], - atomOrientData[5], - atomOrientData[6]); - strcat( writeLine, tempBuffer ); - - } else { + "%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]); + + strcat( writeLine, tempBuffer ); + + } + outFile << writeLine; outFile.flush(); } @@ -331,6 +361,10 @@ void DumpWriter::writeDump( double currentTime ){ } else { // worldRank != 0, so I'm a remote node. + + // Set my magic potato to 0: + + myPotato = 0; for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { @@ -338,6 +372,16 @@ void DumpWriter::writeDump( double currentTime ){ 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); + + } + local_index=-1; for (j=0; (jgetMyNlocal()) && (local_index < 0); j++) { if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; @@ -349,13 +393,13 @@ void DumpWriter::writeDump( double currentTime ){ atoms[local_index]->getPos(pos); atoms[local_index]->getVel(vel); - atomTransData[0] = pos[0]; - atomTransData[1] = pos[1]; - atomTransData[2] = pos[2]; + atomData6[0] = pos[0]; + atomData6[1] = pos[1]; + atomData6[2] = pos[2]; - atomTransData[3] = vel[0]; - atomTransData[4] = vel[1]; - atomTransData[5] = vel[2]; + atomData6[3] = vel[0]; + atomData6[4] = vel[1]; + atomData6[5] = vel[2]; isDirectional = 0; @@ -366,14 +410,17 @@ void DumpWriter::writeDump( double currentTime ){ dAtom = (DirectionalAtom *)atoms[local_index]; dAtom->getQ( q ); - atomOrientData[0] = q[0]; - atomOrientData[1] = q[1]; - atomOrientData[2] = q[2]; - atomOrientData[3] = 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]; - atomOrientData[4] = dAtom->getJx(); - atomOrientData[5] = dAtom->getJy(); - atomOrientData[6] = dAtom->getJz(); + atomData13[10] = dAtom->getJx(); + atomData13[11] = dAtom->getJy(); + atomData13[12] = dAtom->getJz(); } } else { @@ -384,35 +431,33 @@ void DumpWriter::writeDump( double currentTime ){ simError(); } - // I've survived this far, so send off the data! - - atomTypeTag = 4*i; - atomIsDirectionalTag = 4*i + 1; - atomTransDataTag = 4*i + 2; - atomOrientDataTag = 4*i + 3; - - strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE); // null terminate the string before sending (just in case): MPIatomTypeString[MINIBUFFERSIZE-1] = '\0'; MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0, - atomTypeTag, MPI_COMM_WORLD); + myPotato, MPI_COMM_WORLD); + myPotato++; + MPI_Send(&isDirectional, 1, MPI_INT, 0, - atomIsDirectionalTag, MPI_COMM_WORLD); + myPotato, MPI_COMM_WORLD); - MPI_Send(atomTransData, 6, MPI_DOUBLE, 0, - atomTransDataTag, MPI_COMM_WORLD); - + myPotato++; + if (isDirectional) { - MPI_Send(atomOrientData, 7, MPI_DOUBLE, 0, - atomOrientDataTag, MPI_COMM_WORLD); + MPI_Send(atomData13, 13, MPI_DOUBLE, 0, + myPotato, MPI_COMM_WORLD); + } else { + + MPI_Send(atomData6, 6, MPI_DOUBLE, 0, + myPotato, MPI_COMM_WORLD); } - + + myPotato++; } } @@ -420,10 +465,8 @@ void DumpWriter::writeDump( double currentTime ){ "Sucessfully took a dump.\n"); MPIcheckPoint(); - } + } - painCave.isEventLoop = 0; - #endif // is_mpi } @@ -442,16 +485,18 @@ void DumpWriter::writeFinal(double finalTime){ 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 atomTransData[6]; - double atomOrientData[7]; + double atomData6[6]; + double atomData13[13]; int isDirectional; char* atomTypeString; char MPIatomTypeString[MINIBUFFERSIZE]; - int atomTypeTag; - int atomIsDirectionalTag; - int atomTransDataTag; - int atomOrientDataTag; + #else //is_mpi int nAtoms = entry_plug->n_atoms; #endif //is_mpi @@ -547,10 +592,15 @@ void DumpWriter::writeFinal(double finalTime){ #else // is_mpi - // first thing first, suspend fatalities. - painCave.isEventLoop = 1; + /* 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 myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone int haveError; MPI_Status istatus; @@ -559,6 +609,15 @@ void DumpWriter::writeFinal(double finalTime){ // 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" @@ -577,60 +636,77 @@ void DumpWriter::writeFinal(double finalTime){ 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) { - - atomTypeTag = 4*i; - atomIsDirectionalTag = 4*i + 1; - atomTransDataTag = 4*i + 2; - atomOrientDataTag = 4*i + 3; + 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, - atomTypeTag, MPI_COMM_WORLD, &istatus); + myPotato, MPI_COMM_WORLD, &istatus); strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE); - - MPI_Recv(&isDirectional, 1, MPI_INT, which_node, - atomIsDirectionalTag, MPI_COMM_WORLD, &istatus); - MPI_Recv(atomTransData, 6, MPI_DOUBLE, which_node, - atomTransDataTag, MPI_COMM_WORLD, &istatus); + // Null terminate the atomTypeString just in case: - if (isDirectional) { + atomTypeString[strlen(atomTypeString) - 1] = '\0'; - MPI_Recv(atomOrientData, 7, MPI_DOUBLE, which_node, - atomOrientDataTag, MPI_COMM_WORLD, &istatus); + 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); + atoms[local_index]->getVel(vel); - atomTransData[0] = pos[0]; - atomTransData[1] = pos[1]; - atomTransData[2] = pos[2]; + atomData6[0] = pos[0]; + atomData6[1] = pos[1]; + atomData6[2] = pos[2]; - atomTransData[3] = vel[0]; - atomTransData[4] = vel[1]; - atomTransData[5] = vel[2]; + atomData6[3] = vel[0]; + atomData6[4] = vel[1]; + atomData6[5] = vel[2]; isDirectional = 0; @@ -640,17 +716,20 @@ void DumpWriter::writeFinal(double finalTime){ dAtom = (DirectionalAtom *)atoms[local_index]; dAtom->getQ( q ); - - atomOrientData[0] = q[0]; - atomOrientData[1] = q[1]; - atomOrientData[2] = q[2]; - atomOrientData[3] = q[3]; - atomOrientData[4] = dAtom->getJx(); - atomOrientData[5] = dAtom->getJy(); - atomOrientData[6] = dAtom->getJz(); + 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", @@ -658,40 +737,49 @@ void DumpWriter::writeFinal(double finalTime){ haveError= 1; simError(); } - + if(haveError) DieDieDie(); - + // If we've survived to here, format the line: - sprintf( tempBuffer, - "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", - atomTypeString, - atomTransData[0], - atomTransData[1], - atomTransData[2], - atomTransData[3], - atomTransData[4], - atomTransData[5]); + if (!isDirectional) { - strcpy( writeLine, tempBuffer ); - - if (isDirectional) { - sprintf( tempBuffer, - "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", - atomOrientData[0], - atomOrientData[1], - atomOrientData[2], - atomOrientData[3], - atomOrientData[4], - atomOrientData[5], - atomOrientData[6]); - strcat( writeLine, 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 { - strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); + + 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]); + + strcat( writeLine, tempBuffer ); + } - + finalOut << writeLine; finalOut.flush(); } @@ -705,6 +793,10 @@ void DumpWriter::writeFinal(double finalTime){ } else { // worldRank != 0, so I'm a remote node. + + // Set my magic potato to 0: + + myPotato = 0; for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { @@ -712,6 +804,16 @@ void DumpWriter::writeFinal(double finalTime){ 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); + + } + local_index=-1; for (j=0; (jgetMyNlocal()) && (local_index < 0); j++) { if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; @@ -723,13 +825,13 @@ void DumpWriter::writeFinal(double finalTime){ atoms[local_index]->getPos(pos); atoms[local_index]->getVel(vel); - atomTransData[0] = pos[0]; - atomTransData[1] = pos[1]; - atomTransData[2] = pos[2]; + atomData6[0] = pos[0]; + atomData6[1] = pos[1]; + atomData6[2] = pos[2]; - atomTransData[3] = vel[0]; - atomTransData[4] = vel[1]; - atomTransData[5] = vel[2]; + atomData6[3] = vel[0]; + atomData6[4] = vel[1]; + atomData6[5] = vel[2]; isDirectional = 0; @@ -740,14 +842,17 @@ void DumpWriter::writeFinal(double finalTime){ dAtom = (DirectionalAtom *)atoms[local_index]; dAtom->getQ( q ); - atomOrientData[0] = q[0]; - atomOrientData[1] = q[1]; - atomOrientData[2] = q[2]; - atomOrientData[3] = 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]; - atomOrientData[4] = dAtom->getJx(); - atomOrientData[5] = dAtom->getJy(); - atomOrientData[6] = dAtom->getJz(); + atomData13[10] = dAtom->getJx(); + atomData13[11] = dAtom->getJy(); + atomData13[12] = dAtom->getJz(); } } else { @@ -758,42 +863,42 @@ void DumpWriter::writeFinal(double finalTime){ simError(); } - // I've survived this far, so send off the data! - - atomTypeTag = 4*i; - atomIsDirectionalTag = 4*i + 1; - atomTransDataTag = 4*i + 2; - atomOrientDataTag = 4*i + 3; - strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE); + // null terminate the string before sending (just in case): + MPIatomTypeString[MINIBUFFERSIZE-1] = '\0'; + MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0, - atomTypeTag, MPI_COMM_WORLD); + myPotato, MPI_COMM_WORLD); + myPotato++; + MPI_Send(&isDirectional, 1, MPI_INT, 0, - atomIsDirectionalTag, MPI_COMM_WORLD); + myPotato, MPI_COMM_WORLD); - MPI_Send(atomTransData, 6, MPI_DOUBLE, 0, - atomTransDataTag, MPI_COMM_WORLD); - + myPotato++; + if (isDirectional) { - MPI_Send(atomOrientData, 7, MPI_DOUBLE, 0, - atomOrientDataTag, MPI_COMM_WORLD); + 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 wrote final file.\n"); + "Sucessfully took a dump.\n"); MPIcheckPoint(); - } + } - painCave.isEventLoop = 0; - if( worldRank == 0 ) finalOut.close(); #endif // is_mpi }