--- trunk/OOPSE/libmdtools/DumpWriter.cpp 2003/10/16 19:16:24 804 +++ trunk/OOPSE/libmdtools/DumpWriter.cpp 2004/01/10 02:15:35 919 @@ -1,18 +1,15 @@ #define _FILE_OFFSET_BITS 64 -#include +#include #include #include #ifdef IS_MPI #include #include "mpiSimulation.hpp" -#define TAKE_THIS_TAG_CHAR 1 -#define TAKE_THIS_TAG_INT 2 namespace dWrite{ - void nodeZeroError( void ); - void anonymousNodeDie( void ); + void DieDieDie( void ); } using namespace dWrite; @@ -28,13 +25,13 @@ DumpWriter::DumpWriter( SimInfo* the_entry_plug ){ #ifdef IS_MPI if(worldRank == 0 ){ #endif // is_mpi - + strcpy( outName, entry_plug->sampleName ); - + outFile.open(outName, ios::out | ios::trunc ); - + if( !outFile ){ - + sprintf( painCave.errMsg, "Could not open \"%s\" for dump output.\n", outName); @@ -67,14 +64,28 @@ void DumpWriter::writeDump( double currentTime ){ } void DumpWriter::writeDump( double currentTime ){ - + const int BUFFERSIZE = 2000; + const int MINIBUFFERSIZE = 100; + char tempBuffer[BUFFERSIZE]; char writeLine[BUFFERSIZE]; int i; + #ifdef IS_MPI + + int *potatoes; + int myPotato; + + int nProc; int j, which_node, done, which_atom, local_index; + double atomData6[6]; + double atomData13[13]; + int isDirectional; + char* atomTypeString; + char MPIatomTypeString[MINIBUFFERSIZE]; + #else //is_mpi int nAtoms = entry_plug->n_atoms; #endif //is_mpi @@ -83,17 +94,16 @@ void DumpWriter::writeDump( double currentTime ){ DirectionalAtom* dAtom; Atom** atoms = entry_plug->atoms; double pos[3], vel[3]; - - + // write current frame to the eor file this->writeFinal( currentTime ); #ifndef IS_MPI - + outFile << nAtoms << "\n"; - - outFile << currentTime << ";\t" + + outFile << currentTime << ";\t" << entry_plug->Hmat[0][0] << "\t" << entry_plug->Hmat[1][0] << "\t" << entry_plug->Hmat[2][0] << ";\t" @@ -104,10 +114,13 @@ void DumpWriter::writeDump( double currentTime ){ << entry_plug->Hmat[0][2] << "\t" << entry_plug->Hmat[1][2] << "\t" - << entry_plug->Hmat[2][2] << ";\n"; - + << entry_plug->Hmat[2][2] << ";"; + //write out additional parameters, such as chi and eta + outFile << entry_plug->the_integrator->getAdditionalParameters(); + outFile << endl; + for( i=0; igetPos(pos); atoms[i]->getVel(vel); @@ -123,10 +136,10 @@ void DumpWriter::writeDump( double currentTime ){ strcpy( writeLine, tempBuffer ); 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], @@ -140,209 +153,322 @@ void DumpWriter::writeDump( double currentTime ){ } else strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); - + outFile << writeLine; } outFile.flush(); #else // is_mpi - // first thing first, suspend fatalities. - painCave.isEventLoop = 1; + cout << "master" <getAtomToProcMap(); - + // 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" + + 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][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] << ";\n"; - + << entry_plug->Hmat[2][2] << ";"; + + outFile << entry_plug->the_integrator->getAdditionalParameters(); + outFile << endl; outFile.flush(); + for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { + // Get the Node number which has this atom; - which_node = AtomToProcMap[i]; + which_node = AtomToProcMap[i]; - if (which_node == 0 ) { - + 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, + myPotato, MPI_COMM_WORLD, &istatus); + + strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE); + + // Null terminate the atomTypeString just in case: + + atomTypeString[strlen(atomTypeString) - 1] = '\0'; + + 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; + local_index=-1; + for (j=0; (jgetMyNlocal()) && (local_index < 0); j++) { if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; } + if (local_index != -1) { - //format the line - + + atomTypeString = atoms[local_index]->getType(); + atoms[local_index]->getPos(pos); - atoms[local_index]->getVel(vel); + atoms[local_index]->getVel(vel); - sprintf( tempBuffer, - "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", - atoms[local_index]->getType(), - pos[0], - pos[1], - pos[2], - vel[0], - vel[1], - vel[2]); // check here. - strcpy( writeLine, tempBuffer ); - + 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( atoms[local_index]->isDirectional() ){ + + isDirectional = 1; dAtom = (DirectionalAtom *)atoms[local_index]; dAtom->getQ( q ); + + for (int j = 0; j < 6 ; j++) + atomData13[j] = atomData6[j]; - 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 ); - - } - else - strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); - } - else { + 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) nodeZeroError(); + } + + if(haveError) DieDieDie(); + + // If we've survived to here, format the line: + + if (!isDirectional) { - } - else { - myStatus = 1; - MPI_Send(&myStatus, 1, MPI_INT, which_node, - TAKE_THIS_TAG_INT, MPI_COMM_WORLD); - MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, - MPI_COMM_WORLD); - MPI_Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node, - TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus); - MPI_Recv(&myStatus, 1, MPI_INT, which_node, - TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); - - if(!myStatus) nodeZeroError(); + sprintf( 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 { + + 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(); } - - outFile << writeLine; - outFile.flush(); } - - // kill everyone off: - myStatus = -1; - for (j = 0; j < mpiSim->getNumberProcessors(); j++) { - MPI_Send(&myStatus, 1, MPI_INT, j, - TAKE_THIS_TAG_INT, MPI_COMM_WORLD); - } + outFile.flush(); + sprintf( checkPointMsg, + "Sucessfully took a dump.\n"); + MPIcheckPoint(); + delete[] potatoes; } else { + + // worldRank != 0, so I'm a remote node. + + // Set my magic potato to 0: + + myPotato = 0; - done = 0; - while (!done) { + for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { - MPI_Recv(&myStatus, 1, MPI_INT, 0, - TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); - - if(!myStatus) anonymousNodeDie(); + // Am I the node which has this atom? - if(myStatus < 0) break; + if (AtomToProcMap[i] == worldRank) { - MPI_Recv(&which_atom, 1, MPI_INT, 0, - TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); - - myStatus = 1; - local_index=-1; - for (j=0; (jgetMyNlocal()) && (local_index < 0); j++) { - if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; - } - if (local_index != -1) { - //format the line + if (myPotato + 3 >= MAXTAG) { - atoms[local_index]->getPos(pos); - atoms[local_index]->getVel(vel); + // 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: - sprintf( tempBuffer, - "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", - atoms[local_index]->getType(), - pos[0], - pos[1], - pos[2], - vel[0], - vel[1], - vel[2]); // check here. - strcpy( writeLine, tempBuffer ); - - if( atoms[local_index]->isDirectional() ){ - - dAtom = (DirectionalAtom *)atoms[local_index]; - 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 ); + MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus); + + } + 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); + + 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( atoms[local_index]->isDirectional() ){ + + isDirectional = 1; + + dAtom = (DirectionalAtom *)atoms[local_index]; + dAtom->getQ( q ); + + 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", + i, worldRank ); + haveError= 1; + simError(); } - else{ - strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); - } - } - else { - sprintf(painCave.errMsg, - "Atom %d not found on processor %d\n", - which_atom, worldRank ); - myStatus = 0; - simError(); - strcpy( writeLine, "Hello, I'm an error.\n"); - } + strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE); - MPI_Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, - TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD); - MPI_Send( &myStatus, 1, MPI_INT, 0, - TAKE_THIS_TAG_INT, MPI_COMM_WORLD); - } - } - outFile.flush(); - sprintf( checkPointMsg, - "Sucessfully took a dump.\n"); - MPIcheckPoint(); + // null terminate the string before sending (just in case): + MPIatomTypeString[MINIBUFFERSIZE-1] = '\0'; - // last thing last, enable fatalities. - painCave.isEventLoop = 0; + 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); + + } else { + + MPI_Send(atomData6, 6, MPI_DOUBLE, 0, + myPotato, MPI_COMM_WORLD); + } + + myPotato++; + } + } + + sprintf( checkPointMsg, + "Sucessfully took a dump.\n"); + MPIcheckPoint(); + + } + #endif // is_mpi } @@ -352,27 +478,39 @@ void DumpWriter::writeFinal(double finalTime){ ofstream finalOut; const int BUFFERSIZE = 2000; + const int MINIBUFFERSIZE = 100; char tempBuffer[BUFFERSIZE]; - char writeLine[BUFFERSIZE]; + char writeLine[BUFFERSIZE]; double q[4]; DirectionalAtom* dAtom; 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 atomData6[6]; + double atomData13[13]; + int isDirectional; + char* atomTypeString; + char MPIatomTypeString[MINIBUFFERSIZE]; + #else //is_mpi int nAtoms = entry_plug->n_atoms; #endif //is_mpi - + double pos[3], vel[3]; - + #ifdef IS_MPI if(worldRank == 0 ){ #endif // is_mpi - + strcpy( finalName, entry_plug->finalName ); - + finalOut.open( finalName, ios::out | ios::trunc ); if( !finalOut ){ sprintf( painCave.errMsg, @@ -381,40 +519,44 @@ void DumpWriter::writeFinal(double finalTime){ painCave.isFatal = 1; simError(); } - + // finalOut.setf( ios::scientific ); - + #ifdef IS_MPI } - + sprintf(checkPointMsg,"Opened file for final configuration\n"); - MPIcheckPoint(); - + MPIcheckPoint(); + #endif //is_mpi - + #ifndef IS_MPI - + finalOut << nAtoms << "\n"; - + finalOut << finalTime << ";\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][2] << "\t" << entry_plug->Hmat[1][2] << "\t" - << entry_plug->Hmat[2][2] << ";\n"; - + << entry_plug->Hmat[2][2] << ";"; + + //write out additional parameters, such as chi and eta + finalOut << entry_plug->the_integrator->getAdditionalParameters(); + finalOut << endl; + for( i=0; igetPos(pos); atoms[i]->getVel(vel); - + sprintf( tempBuffer, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", atoms[i]->getType(), @@ -427,10 +569,10 @@ void DumpWriter::writeFinal(double finalTime){ strcpy( writeLine, tempBuffer ); 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], @@ -444,204 +586,324 @@ void DumpWriter::writeFinal(double finalTime){ } else strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); - + finalOut << writeLine; } finalOut.flush(); finalOut.close(); #else // is_mpi - - // first thing first, suspend fatalities. - painCave.isEventLoop = 1; - int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone + /* 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 haveError; MPI_Status istatus; int *AtomToProcMap = mpiSim->getAtomToProcMap(); // write out header and node 0's coordinates - - haveError = 0; + if( worldRank == 0 ){ - finalOut << mpiSim->getTotAtoms() << "\n"; + + // 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" - << 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][2] << "\t" - << entry_plug->Hmat[1][2] << "\t" - << entry_plug->Hmat[2][2] << ";\n"; - + << 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][2] << "\t" + << entry_plug->Hmat[1][2] << "\t" + << entry_plug->Hmat[2][2] << ";"; + + finalOut << entry_plug->the_integrator->getAdditionalParameters(); + finalOut << endl; + finalOut.flush(); + for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { - // Get the Node number which has this molecule: - which_node = AtomToProcMap[i]; + // Get the Node number which has this atom; - if (which_node == mpiSim->getMyNode()) { + 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, + myPotato, MPI_COMM_WORLD, &istatus); + + strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE); + + // Null terminate the atomTypeString just in case: + + atomTypeString[strlen(atomTypeString) - 1] = '\0'; + + 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; + local_index=-1; + for (j=0; (jgetMyNlocal()) && (local_index < 0); j++) { if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; } - if (local_index != -1) { + + if (local_index != -1) { + + atomTypeString = atoms[local_index]->getType(); atoms[local_index]->getPos(pos); - atoms[local_index]->getVel(vel); - - sprintf( tempBuffer, - "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", - atoms[local_index]->getType(), - pos[0], - pos[1], - pos[2], - vel[0], - vel[1], - vel[2]); - strcpy( writeLine, tempBuffer ); - - if( atoms[local_index]->isDirectional() ){ - - dAtom = (DirectionalAtom *)atoms[local_index]; - 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 ); - } - else - strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); - } - else { + 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]; + + isDirectional = 0; + + if( atoms[local_index]->isDirectional() ){ + + isDirectional = 1; + + dAtom = (DirectionalAtom *)atoms[local_index]; + dAtom->getQ( q ); + + 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", i, worldRank ); haveError= 1; simError(); - } + } + + if(haveError) DieDieDie(); + + // If we've survived to here, format the line: + + if (!isDirectional) { - if(haveError) nodeZeroError(); - - } - else { + sprintf( 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 { + + 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 ); + + } - myStatus = 1; - MPI_Send(&myStatus, 1, MPI_INT, which_node, - TAKE_THIS_TAG_INT, MPI_COMM_WORLD); - MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, - MPI_COMM_WORLD); - MPI_Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node, - TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus); - MPI_Recv(&myStatus, 1, MPI_INT, which_node, - TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); - - if(!myStatus) nodeZeroError(); + finalOut << writeLine; + finalOut.flush(); } - - finalOut << writeLine; } - - // kill everyone off: - myStatus = -1; - for (j = 0; j < mpiSim->getNumberProcessors(); j++) { - MPI_Send(&myStatus, 1, MPI_INT, j, - TAKE_THIS_TAG_INT, MPI_COMM_WORLD); - } - } else { + finalOut.flush(); + sprintf( checkPointMsg, + "Sucessfully took a dump.\n"); + delete[] potatoes; + + MPIcheckPoint(); - done = 0; - while (!done) { + } else { - MPI_Recv(&myStatus, 1, MPI_INT, 0, - TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); + // worldRank != 0, so I'm a remote node. + + // Set my magic potato to 0: + + myPotato = 0; + + for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { - if(!myStatus) anonymousNodeDie(); + // Am I the node which has this atom? - if(myStatus < 0) break; - - MPI_Recv(&which_atom, 1, MPI_INT, 0, - TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); - - myStatus = 1; - local_index=-1; - for (j=0; j < mpiSim->getMyNlocal(); j++) { - if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; - } - if (local_index != -1) { + if (AtomToProcMap[i] == worldRank) { - atoms[local_index]->getPos(pos); - atoms[local_index]->getVel(vel); + if (myPotato + 3 >= MAXTAG) { - //format the line - sprintf( tempBuffer, - "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", - atoms[local_index]->getType(), - pos[0], - pos[1], - pos[2], - vel[0], - vel[1], - vel[2]); // check here. - strcpy( writeLine, tempBuffer ); - - if( atoms[local_index]->isDirectional() ){ - - dAtom = (DirectionalAtom *)atoms[local_index]; - 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 ); + // 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=-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); + + 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( atoms[local_index]->isDirectional() ){ + + isDirectional = 1; + + dAtom = (DirectionalAtom *)atoms[local_index]; + dAtom->getQ( q ); + + 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", + i, worldRank ); + haveError= 1; + simError(); } - else{ - strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); - } - } - else { - sprintf(painCave.errMsg, - "Atom %d not found on processor %d\n", - which_atom, worldRank ); - myStatus = 0; - simError(); - - strcpy( writeLine, "Hello, I'm an error.\n"); - } - MPI_Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, - TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD); - MPI_Send( &myStatus, 1, MPI_INT, 0, - TAKE_THIS_TAG_INT, MPI_COMM_WORLD); + 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_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++; + } } - } - finalOut.flush(); - sprintf( checkPointMsg, - "Sucessfully took a dump.\n"); - MPIcheckPoint(); + + sprintf( checkPointMsg, + "Sucessfully took a dump.\n"); + MPIcheckPoint(); + + } - if( worldRank == 0 ) finalOut.close(); + if( worldRank == 0 ) finalOut.close(); #endif // is_mpi } @@ -651,25 +913,10 @@ void DumpWriter::writeFinal(double finalTime){ // a couple of functions to let us escape the write loop -void dWrite::nodeZeroError( void ){ - int j, myStatus; - - myStatus = 0; - for (j = 0; j < mpiSim->getNumberProcessors(); j++) { - MPI_Send( &myStatus, 1, MPI_INT, j, - TAKE_THIS_TAG_INT, MPI_COMM_WORLD); - } - +void dWrite::DieDieDie( void ){ MPI_Finalize(); exit (0); - } -void dWrite::anonymousNodeDie( void ){ - - MPI_Finalize(); - exit (0); -} - #endif //is_mpi