7 |
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#ifdef IS_MPI |
8 |
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#include <mpi.h> |
9 |
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#include "mpiSimulation.hpp" |
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#define TAKE_THIS_TAG_CHAR 15 |
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#define TAKE_THIS_TAG_INT 20 |
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|
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namespace dWrite{ |
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< |
void nodeZeroError( void ); |
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< |
void anonymousNodeDie( void ); |
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> |
void DieDieDie( void ); |
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} |
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|
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using namespace dWrite; |
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void DumpWriter::writeDump( double currentTime ){ |
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|
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const int BUFFERSIZE = 2000; |
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const int MINIBUFFERSIZE = 100; |
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|
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char tempBuffer[BUFFERSIZE]; |
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char writeLine[BUFFERSIZE]; |
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|
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int i; |
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|
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#ifdef IS_MPI |
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|
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int *potatoes; |
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int myPotato; |
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|
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int nProc; |
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int j, which_node, done, which_atom, local_index; |
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double atomData6[6]; |
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double atomData13[13]; |
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int isDirectional; |
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char* atomTypeString; |
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char MPIatomTypeString[MINIBUFFERSIZE]; |
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|
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#else //is_mpi |
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int nAtoms = entry_plug->n_atoms; |
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#endif //is_mpi |
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Atom** atoms = entry_plug->atoms; |
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double pos[3], vel[3]; |
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|
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|
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// write current frame to the eor file |
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|
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this->writeFinal( currentTime ); |
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|
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#else // is_mpi |
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|
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// first thing first, suspend fatalities. |
164 |
< |
painCave.isEventLoop = 1; |
163 |
> |
/* code to find maximum tag value */ |
164 |
> |
|
165 |
> |
int *tagub, flag, MAXTAG; |
166 |
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MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag); |
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> |
if (flag) { |
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> |
MAXTAG = *tagub; |
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> |
} else { |
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MAXTAG = 32767; |
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> |
} |
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|
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int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone |
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int haveError; |
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|
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MPI_Status istatus; |
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// write out header and node 0's coordinates |
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|
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if( worldRank == 0 ){ |
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|
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// Node 0 needs a list of the magic potatoes for each processor; |
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|
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nProc = mpiSim->getNumberProcessors(); |
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potatoes = new int[nProc]; |
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|
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for (i = 0; i < nProc; i++) |
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potatoes[i] = 0; |
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|
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outFile << mpiSim->getTotAtoms() << "\n"; |
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|
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outFile << currentTime << ";\t" |
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outFile << entry_plug->the_integrator->getAdditionalParameters(); |
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outFile << endl; |
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outFile.flush(); |
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|
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for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
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|
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// Get the Node number which has this atom; |
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|
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|
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which_node = AtomToProcMap[i]; |
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|
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if (which_node != 0) { |
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|
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< |
if (which_node == 0 ) { |
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if (potatoes[which_node] + 3 >= MAXTAG) { |
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// The potato was going to exceed the maximum value, |
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// so wrap this processor potato back to 0: |
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|
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potatoes[which_node] = 0; |
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MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD); |
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|
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} |
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|
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myPotato = potatoes[which_node]; |
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|
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MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node, |
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myPotato, MPI_COMM_WORLD, &istatus); |
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|
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//strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE); |
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|
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// Null terminate the atomTypeString just in case: |
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|
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//atomTypeString[strlen(atomTypeString) - 1] = '\0'; |
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atomTypeString = MPIatomTypeString; |
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|
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myPotato++; |
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|
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MPI_Recv(&isDirectional, 1, MPI_INT, which_node, |
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myPotato, MPI_COMM_WORLD, &istatus); |
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|
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myPotato++; |
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|
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if (isDirectional) { |
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MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node, |
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myPotato, MPI_COMM_WORLD, &istatus); |
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} else { |
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MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node, |
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myPotato, MPI_COMM_WORLD, &istatus); |
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} |
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|
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myPotato++; |
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potatoes[which_node] = myPotato; |
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|
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} else { |
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|
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haveError = 0; |
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which_atom = i; |
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local_index=-1; |
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|
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for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
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if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
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} |
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|
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if (local_index != -1) { |
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//format the line |
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|
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> |
atomTypeString = atoms[local_index]->getType(); |
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|
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atoms[local_index]->getPos(pos); |
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atoms[local_index]->getVel(vel); |
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atoms[local_index]->getVel(vel); |
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|
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sprintf( tempBuffer, |
274 |
< |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
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< |
atoms[local_index]->getType(), |
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< |
pos[0], |
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pos[1], |
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< |
pos[2], |
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< |
vel[0], |
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vel[1], |
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vel[2]); // check here. |
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strcpy( writeLine, tempBuffer ); |
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> |
atomData6[0] = pos[0]; |
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> |
atomData6[1] = pos[1]; |
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> |
atomData6[2] = pos[2]; |
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> |
|
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> |
atomData6[3] = vel[0]; |
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> |
atomData6[4] = vel[1]; |
279 |
> |
atomData6[5] = vel[2]; |
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> |
|
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> |
isDirectional = 0; |
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|
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if( atoms[local_index]->isDirectional() ){ |
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|
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+ |
isDirectional = 1; |
286 |
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|
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dAtom = (DirectionalAtom *)atoms[local_index]; |
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dAtom->getQ( q ); |
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|
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< |
sprintf( tempBuffer, |
291 |
< |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
292 |
< |
q[0], |
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< |
q[1], |
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< |
q[2], |
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< |
q[3], |
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< |
dAtom->getJx(), |
297 |
< |
dAtom->getJy(), |
298 |
< |
dAtom->getJz()); |
299 |
< |
strcat( writeLine, tempBuffer ); |
300 |
< |
|
301 |
< |
} |
302 |
< |
else |
303 |
< |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
232 |
< |
} |
233 |
< |
else { |
290 |
> |
for (int j = 0; j < 6 ; j++) |
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> |
atomData13[j] = atomData6[j]; |
292 |
> |
|
293 |
> |
atomData13[6] = q[0]; |
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> |
atomData13[7] = q[1]; |
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> |
atomData13[8] = q[2]; |
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> |
atomData13[9] = q[3]; |
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> |
|
298 |
> |
atomData13[10] = dAtom->getJx(); |
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> |
atomData13[11] = dAtom->getJy(); |
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> |
atomData13[12] = dAtom->getJz(); |
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> |
} |
302 |
> |
|
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> |
} else { |
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sprintf(painCave.errMsg, |
305 |
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"Atom %d not found on processor %d\n", |
306 |
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i, worldRank ); |
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haveError= 1; |
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simError(); |
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} |
310 |
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|
311 |
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if(haveError) DieDieDie(); |
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|
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// If we've survived to here, format the line: |
314 |
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|
315 |
+ |
if (!isDirectional) { |
316 |
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|
317 |
< |
if(haveError) nodeZeroError(); |
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> |
sprintf( tempBuffer, |
318 |
> |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
319 |
> |
atomTypeString, |
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> |
atomData6[0], |
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> |
atomData6[1], |
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> |
atomData6[2], |
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> |
atomData6[3], |
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> |
atomData6[4], |
325 |
> |
atomData6[5]); |
326 |
> |
|
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> |
strcpy( writeLine, tempBuffer ); |
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> |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
329 |
|
|
330 |
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} else { |
331 |
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|
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sprintf( tempBuffer, |
333 |
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"%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", |
334 |
+ |
atomTypeString, |
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+ |
atomData13[0], |
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atomData13[1], |
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atomData13[2], |
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atomData13[3], |
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atomData13[4], |
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atomData13[5], |
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+ |
atomData13[6], |
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atomData13[7], |
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+ |
atomData13[8], |
344 |
+ |
atomData13[9], |
345 |
+ |
atomData13[10], |
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+ |
atomData13[11], |
347 |
+ |
atomData13[12]); |
348 |
+ |
|
349 |
+ |
strcat( writeLine, tempBuffer ); |
350 |
+ |
|
351 |
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} |
352 |
+ |
|
353 |
+ |
outFile << writeLine; |
354 |
+ |
outFile.flush(); |
355 |
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} |
356 |
< |
else { |
245 |
< |
myStatus = 1; |
246 |
< |
MPI_Send(&myStatus, 1, MPI_INT, which_node, |
247 |
< |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
248 |
< |
MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, |
249 |
< |
MPI_COMM_WORLD); |
250 |
< |
MPI_Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node, |
251 |
< |
TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus); |
252 |
< |
MPI_Recv(&myStatus, 1, MPI_INT, which_node, |
253 |
< |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
356 |
> |
} |
357 |
|
|
358 |
< |
if(!myStatus) nodeZeroError(); |
358 |
> |
outFile.flush(); |
359 |
> |
sprintf( checkPointMsg, |
360 |
> |
"Sucessfully took a dump.\n"); |
361 |
> |
MPIcheckPoint(); |
362 |
> |
delete[] potatoes; |
363 |
> |
} else { |
364 |
|
|
365 |
< |
} |
365 |
> |
// worldRank != 0, so I'm a remote node. |
366 |
|
|
367 |
< |
outFile << writeLine; |
260 |
< |
outFile.flush(); |
261 |
< |
} |
367 |
> |
// Set my magic potato to 0: |
368 |
|
|
369 |
< |
// kill everyone off: |
370 |
< |
myStatus = -1; |
371 |
< |
for (j = 1; j < mpiSim->getNumberProcessors(); j++) { |
372 |
< |
MPI_Send(&myStatus, 1, MPI_INT, j, |
373 |
< |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
374 |
< |
} |
369 |
> |
myPotato = 0; |
370 |
> |
|
371 |
> |
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
372 |
> |
|
373 |
> |
// Am I the node which has this atom? |
374 |
> |
|
375 |
> |
if (AtomToProcMap[i] == worldRank) { |
376 |
|
|
377 |
< |
} else { |
377 |
> |
if (myPotato + 3 >= MAXTAG) { |
378 |
|
|
379 |
< |
done = 0; |
380 |
< |
while (!done) { |
379 |
> |
// The potato was going to exceed the maximum value, |
380 |
> |
// so wrap this processor potato back to 0 (and block until |
381 |
> |
// node 0 says we can go: |
382 |
|
|
383 |
< |
MPI_Recv(&myStatus, 1, MPI_INT, 0, |
384 |
< |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
383 |
> |
MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus); |
384 |
> |
|
385 |
> |
} |
386 |
> |
which_atom = i; |
387 |
> |
local_index=-1; |
388 |
> |
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
389 |
> |
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
390 |
> |
} |
391 |
> |
if (local_index != -1) { |
392 |
> |
|
393 |
> |
atomTypeString = atoms[local_index]->getType(); |
394 |
|
|
395 |
< |
if(!myStatus) anonymousNodeDie(); |
395 |
> |
atoms[local_index]->getPos(pos); |
396 |
> |
atoms[local_index]->getVel(vel); |
397 |
|
|
398 |
< |
if(myStatus < 0) break; |
398 |
> |
atomData6[0] = pos[0]; |
399 |
> |
atomData6[1] = pos[1]; |
400 |
> |
atomData6[2] = pos[2]; |
401 |
|
|
402 |
< |
MPI_Recv(&which_atom, 1, MPI_INT, 0, |
403 |
< |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
402 |
> |
atomData6[3] = vel[0]; |
403 |
> |
atomData6[4] = vel[1]; |
404 |
> |
atomData6[5] = vel[2]; |
405 |
> |
|
406 |
> |
isDirectional = 0; |
407 |
|
|
408 |
< |
myStatus = 1; |
286 |
< |
local_index=-1; |
287 |
< |
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
288 |
< |
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
289 |
< |
} |
290 |
< |
if (local_index != -1) { |
291 |
< |
//format the line |
408 |
> |
if( atoms[local_index]->isDirectional() ){ |
409 |
|
|
410 |
< |
atoms[local_index]->getPos(pos); |
411 |
< |
atoms[local_index]->getVel(vel); |
410 |
> |
isDirectional = 1; |
411 |
> |
|
412 |
> |
dAtom = (DirectionalAtom *)atoms[local_index]; |
413 |
> |
dAtom->getQ( q ); |
414 |
> |
|
415 |
> |
for (int j = 0; j < 6 ; j++) |
416 |
> |
atomData13[j] = atomData6[j]; |
417 |
> |
|
418 |
> |
atomData13[6] = q[0]; |
419 |
> |
atomData13[7] = q[1]; |
420 |
> |
atomData13[8] = q[2]; |
421 |
> |
atomData13[9] = q[3]; |
422 |
|
|
423 |
< |
sprintf( tempBuffer, |
424 |
< |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
425 |
< |
atoms[local_index]->getType(), |
426 |
< |
pos[0], |
300 |
< |
pos[1], |
301 |
< |
pos[2], |
302 |
< |
vel[0], |
303 |
< |
vel[1], |
304 |
< |
vel[2]); // check here. |
305 |
< |
strcpy( writeLine, tempBuffer ); |
423 |
> |
atomData13[10] = dAtom->getJx(); |
424 |
> |
atomData13[11] = dAtom->getJy(); |
425 |
> |
atomData13[12] = dAtom->getJz(); |
426 |
> |
} |
427 |
|
|
428 |
< |
if( atoms[local_index]->isDirectional() ){ |
428 |
> |
} else { |
429 |
> |
sprintf(painCave.errMsg, |
430 |
> |
"Atom %d not found on processor %d\n", |
431 |
> |
i, worldRank ); |
432 |
> |
haveError= 1; |
433 |
> |
simError(); |
434 |
> |
} |
435 |
|
|
436 |
< |
dAtom = (DirectionalAtom *)atoms[local_index]; |
310 |
< |
dAtom->getQ( q ); |
436 |
> |
strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE); |
437 |
|
|
438 |
< |
sprintf( tempBuffer, |
439 |
< |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
314 |
< |
q[0], |
315 |
< |
q[1], |
316 |
< |
q[2], |
317 |
< |
q[3], |
318 |
< |
dAtom->getJx(), |
319 |
< |
dAtom->getJy(), |
320 |
< |
dAtom->getJz()); |
321 |
< |
strcat( writeLine, tempBuffer ); |
322 |
< |
} |
323 |
< |
else{ |
324 |
< |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
325 |
< |
} |
326 |
< |
} |
327 |
< |
else { |
328 |
< |
sprintf(painCave.errMsg, |
329 |
< |
"Atom %d not found on processor %d\n", |
330 |
< |
which_atom, worldRank ); |
331 |
< |
myStatus = 0; |
332 |
< |
simError(); |
438 |
> |
// null terminate the string before sending (just in case): |
439 |
> |
MPIatomTypeString[MINIBUFFERSIZE-1] = '\0'; |
440 |
|
|
441 |
< |
strcpy( writeLine, "Hello, I'm an error.\n"); |
442 |
< |
} |
441 |
> |
MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0, |
442 |
> |
myPotato, MPI_COMM_WORLD); |
443 |
> |
|
444 |
> |
myPotato++; |
445 |
|
|
446 |
< |
MPI_Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, |
447 |
< |
TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD); |
448 |
< |
MPI_Send( &myStatus, 1, MPI_INT, 0, |
449 |
< |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
450 |
< |
} |
451 |
< |
} |
343 |
< |
outFile.flush(); |
344 |
< |
sprintf( checkPointMsg, |
345 |
< |
"Sucessfully took a dump.\n"); |
346 |
< |
MPIcheckPoint(); |
446 |
> |
MPI_Send(&isDirectional, 1, MPI_INT, 0, |
447 |
> |
myPotato, MPI_COMM_WORLD); |
448 |
> |
|
449 |
> |
myPotato++; |
450 |
> |
|
451 |
> |
if (isDirectional) { |
452 |
|
|
453 |
< |
// last thing last, enable fatalities. |
454 |
< |
painCave.isEventLoop = 0; |
453 |
> |
MPI_Send(atomData13, 13, MPI_DOUBLE, 0, |
454 |
> |
myPotato, MPI_COMM_WORLD); |
455 |
> |
|
456 |
> |
} else { |
457 |
|
|
458 |
+ |
MPI_Send(atomData6, 6, MPI_DOUBLE, 0, |
459 |
+ |
myPotato, MPI_COMM_WORLD); |
460 |
+ |
} |
461 |
+ |
|
462 |
+ |
myPotato++; |
463 |
+ |
} |
464 |
+ |
} |
465 |
+ |
|
466 |
+ |
sprintf( checkPointMsg, |
467 |
+ |
"Sucessfully took a dump.\n"); |
468 |
+ |
MPIcheckPoint(); |
469 |
+ |
|
470 |
+ |
} |
471 |
+ |
|
472 |
|
#endif // is_mpi |
473 |
|
} |
474 |
|
|
478 |
|
ofstream finalOut; |
479 |
|
|
480 |
|
const int BUFFERSIZE = 2000; |
481 |
+ |
const int MINIBUFFERSIZE = 100; |
482 |
|
char tempBuffer[BUFFERSIZE]; |
483 |
|
char writeLine[BUFFERSIZE]; |
484 |
|
|
487 |
|
Atom** atoms = entry_plug->atoms; |
488 |
|
int i; |
489 |
|
#ifdef IS_MPI |
490 |
+ |
|
491 |
+ |
int *potatoes; |
492 |
+ |
int myPotato; |
493 |
+ |
|
494 |
+ |
int nProc; |
495 |
|
int j, which_node, done, which_atom, local_index; |
496 |
+ |
double atomData6[6]; |
497 |
+ |
double atomData13[13]; |
498 |
+ |
int isDirectional; |
499 |
+ |
char* atomTypeString; |
500 |
+ |
char MPIatomTypeString[MINIBUFFERSIZE]; |
501 |
+ |
|
502 |
|
#else //is_mpi |
503 |
|
int nAtoms = entry_plug->n_atoms; |
504 |
|
#endif //is_mpi |
594 |
|
|
595 |
|
#else // is_mpi |
596 |
|
|
597 |
< |
// first thing first, suspend fatalities. |
598 |
< |
painCave.isEventLoop = 1; |
597 |
> |
/* code to find maximum tag value */ |
598 |
> |
int *tagub, flag, MAXTAG; |
599 |
> |
MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag); |
600 |
> |
if (flag) { |
601 |
> |
MAXTAG = *tagub; |
602 |
> |
} else { |
603 |
> |
MAXTAG = 32767; |
604 |
> |
} |
605 |
|
|
467 |
– |
int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone |
606 |
|
int haveError; |
607 |
|
|
608 |
|
MPI_Status istatus; |
610 |
|
|
611 |
|
// write out header and node 0's coordinates |
612 |
|
|
475 |
– |
haveError = 0; |
613 |
|
if( worldRank == 0 ){ |
614 |
+ |
|
615 |
+ |
// Node 0 needs a list of the magic potatoes for each processor; |
616 |
+ |
|
617 |
+ |
nProc = mpiSim->getNumberProcessors(); |
618 |
+ |
potatoes = new int[nProc]; |
619 |
+ |
|
620 |
+ |
for (i = 0; i < nProc; i++) |
621 |
+ |
potatoes[i] = 0; |
622 |
+ |
|
623 |
|
finalOut << mpiSim->getTotAtoms() << "\n"; |
624 |
|
|
625 |
|
finalOut << finalTime << ";\t" |
626 |
< |
<< entry_plug->Hmat[0][0] << "\t" |
627 |
< |
<< entry_plug->Hmat[1][0] << "\t" |
628 |
< |
<< entry_plug->Hmat[2][0] << ";\t" |
483 |
< |
|
484 |
< |
<< entry_plug->Hmat[0][1] << "\t" |
485 |
< |
<< entry_plug->Hmat[1][1] << "\t" |
486 |
< |
<< entry_plug->Hmat[2][1] << ";\t" |
626 |
> |
<< entry_plug->Hmat[0][0] << "\t" |
627 |
> |
<< entry_plug->Hmat[1][0] << "\t" |
628 |
> |
<< entry_plug->Hmat[2][0] << ";\t" |
629 |
|
|
630 |
< |
<< entry_plug->Hmat[0][2] << "\t" |
631 |
< |
<< entry_plug->Hmat[1][2] << "\t" |
632 |
< |
<< entry_plug->Hmat[2][2] << ";"; |
630 |
> |
<< entry_plug->Hmat[0][1] << "\t" |
631 |
> |
<< entry_plug->Hmat[1][1] << "\t" |
632 |
> |
<< entry_plug->Hmat[2][1] << ";\t" |
633 |
|
|
634 |
< |
//write out additional parameters, such as chi and eta |
634 |
> |
<< entry_plug->Hmat[0][2] << "\t" |
635 |
> |
<< entry_plug->Hmat[1][2] << "\t" |
636 |
> |
<< entry_plug->Hmat[2][2] << ";"; |
637 |
> |
|
638 |
|
finalOut << entry_plug->the_integrator->getAdditionalParameters(); |
639 |
|
finalOut << endl; |
640 |
+ |
finalOut.flush(); |
641 |
|
|
642 |
|
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
643 |
< |
// Get the Node number which has this molecule: |
644 |
< |
|
643 |
> |
|
644 |
> |
// Get the Node number which has this atom; |
645 |
> |
|
646 |
|
which_node = AtomToProcMap[i]; |
647 |
+ |
|
648 |
+ |
if (which_node != 0) { |
649 |
|
|
650 |
< |
if (which_node == mpiSim->getMyNode()) { |
650 |
> |
if (potatoes[which_node] + 3 >= MAXTAG) { |
651 |
> |
// The potato was going to exceed the maximum value, |
652 |
> |
// so wrap this processor potato back to 0: |
653 |
|
|
654 |
+ |
potatoes[which_node] = 0; |
655 |
+ |
MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD); |
656 |
+ |
|
657 |
+ |
} |
658 |
+ |
|
659 |
+ |
myPotato = potatoes[which_node]; |
660 |
+ |
|
661 |
+ |
MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node, |
662 |
+ |
myPotato, MPI_COMM_WORLD, &istatus); |
663 |
+ |
|
664 |
+ |
atomTypeString = MPIatomTypeString; |
665 |
+ |
|
666 |
+ |
myPotato++; |
667 |
+ |
|
668 |
+ |
MPI_Recv(&isDirectional, 1, MPI_INT, which_node, |
669 |
+ |
myPotato, MPI_COMM_WORLD, &istatus); |
670 |
+ |
|
671 |
+ |
myPotato++; |
672 |
+ |
|
673 |
+ |
if (isDirectional) { |
674 |
+ |
MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node, |
675 |
+ |
myPotato, MPI_COMM_WORLD, &istatus); |
676 |
+ |
} else { |
677 |
+ |
MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node, |
678 |
+ |
myPotato, MPI_COMM_WORLD, &istatus); |
679 |
+ |
} |
680 |
+ |
|
681 |
+ |
myPotato++; |
682 |
+ |
potatoes[which_node] = myPotato; |
683 |
+ |
|
684 |
+ |
} else { |
685 |
+ |
|
686 |
+ |
haveError = 0; |
687 |
|
which_atom = i; |
688 |
|
local_index=-1; |
689 |
+ |
|
690 |
|
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
691 |
|
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
692 |
|
} |
693 |
+ |
|
694 |
|
if (local_index != -1) { |
695 |
+ |
|
696 |
+ |
atomTypeString = atoms[local_index]->getType(); |
697 |
|
|
698 |
|
atoms[local_index]->getPos(pos); |
699 |
< |
atoms[local_index]->getVel(vel); |
699 |
> |
atoms[local_index]->getVel(vel); |
700 |
|
|
701 |
< |
sprintf( tempBuffer, |
702 |
< |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
703 |
< |
atoms[local_index]->getType(), |
516 |
< |
pos[0], |
517 |
< |
pos[1], |
518 |
< |
pos[2], |
519 |
< |
vel[0], |
520 |
< |
vel[1], |
521 |
< |
vel[2]); |
522 |
< |
strcpy( writeLine, tempBuffer ); |
701 |
> |
atomData6[0] = pos[0]; |
702 |
> |
atomData6[1] = pos[1]; |
703 |
> |
atomData6[2] = pos[2]; |
704 |
|
|
705 |
< |
if( atoms[local_index]->isDirectional() ){ |
705 |
> |
atomData6[3] = vel[0]; |
706 |
> |
atomData6[4] = vel[1]; |
707 |
> |
atomData6[5] = vel[2]; |
708 |
> |
|
709 |
> |
isDirectional = 0; |
710 |
|
|
711 |
< |
dAtom = (DirectionalAtom *)atoms[local_index]; |
527 |
< |
dAtom->getQ( q ); |
711 |
> |
if( atoms[local_index]->isDirectional() ){ |
712 |
|
|
713 |
< |
sprintf( tempBuffer, |
714 |
< |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
715 |
< |
q[0], |
716 |
< |
q[1], |
717 |
< |
q[2], |
718 |
< |
q[3], |
719 |
< |
dAtom->getJx(), |
720 |
< |
dAtom->getJy(), |
721 |
< |
dAtom->getJz()); |
722 |
< |
strcat( writeLine, tempBuffer ); |
723 |
< |
} |
724 |
< |
else |
725 |
< |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
726 |
< |
} |
727 |
< |
else { |
713 |
> |
isDirectional = 1; |
714 |
> |
|
715 |
> |
dAtom = (DirectionalAtom *)atoms[local_index]; |
716 |
> |
dAtom->getQ( q ); |
717 |
> |
|
718 |
> |
for (int j = 0; j < 6 ; j++) |
719 |
> |
atomData13[j] = atomData6[j]; |
720 |
> |
|
721 |
> |
atomData13[6] = q[0]; |
722 |
> |
atomData13[7] = q[1]; |
723 |
> |
atomData13[8] = q[2]; |
724 |
> |
atomData13[9] = q[3]; |
725 |
> |
|
726 |
> |
atomData13[10] = dAtom->getJx(); |
727 |
> |
atomData13[11] = dAtom->getJy(); |
728 |
> |
atomData13[12] = dAtom->getJz(); |
729 |
> |
} |
730 |
> |
|
731 |
> |
} else { |
732 |
|
sprintf(painCave.errMsg, |
733 |
|
"Atom %d not found on processor %d\n", |
734 |
|
i, worldRank ); |
735 |
|
haveError= 1; |
736 |
|
simError(); |
737 |
|
} |
738 |
+ |
|
739 |
+ |
if(haveError) DieDieDie(); |
740 |
+ |
|
741 |
+ |
// If we've survived to here, format the line: |
742 |
+ |
|
743 |
+ |
if (!isDirectional) { |
744 |
|
|
745 |
< |
if(haveError) nodeZeroError(); |
745 |
> |
sprintf( tempBuffer, |
746 |
> |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
747 |
> |
atomTypeString, |
748 |
> |
atomData6[0], |
749 |
> |
atomData6[1], |
750 |
> |
atomData6[2], |
751 |
> |
atomData6[3], |
752 |
> |
atomData6[4], |
753 |
> |
atomData6[5]); |
754 |
> |
|
755 |
> |
strcpy( writeLine, tempBuffer ); |
756 |
> |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
757 |
|
|
758 |
+ |
} else { |
759 |
+ |
|
760 |
+ |
sprintf( tempBuffer, |
761 |
+ |
"%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", |
762 |
+ |
atomTypeString, |
763 |
+ |
atomData13[0], |
764 |
+ |
atomData13[1], |
765 |
+ |
atomData13[2], |
766 |
+ |
atomData13[3], |
767 |
+ |
atomData13[4], |
768 |
+ |
atomData13[5], |
769 |
+ |
atomData13[6], |
770 |
+ |
atomData13[7], |
771 |
+ |
atomData13[8], |
772 |
+ |
atomData13[9], |
773 |
+ |
atomData13[10], |
774 |
+ |
atomData13[11], |
775 |
+ |
atomData13[12]); |
776 |
+ |
|
777 |
+ |
strcat( writeLine, tempBuffer ); |
778 |
+ |
|
779 |
+ |
} |
780 |
+ |
|
781 |
+ |
finalOut << writeLine; |
782 |
+ |
finalOut.flush(); |
783 |
|
} |
784 |
< |
else { |
784 |
> |
} |
785 |
|
|
786 |
< |
myStatus = 1; |
787 |
< |
MPI_Send(&myStatus, 1, MPI_INT, which_node, |
788 |
< |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
789 |
< |
MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, |
790 |
< |
MPI_COMM_WORLD); |
791 |
< |
MPI_Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node, |
792 |
< |
TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus); |
793 |
< |
MPI_Recv(&myStatus, 1, MPI_INT, which_node, |
564 |
< |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
786 |
> |
finalOut.flush(); |
787 |
> |
sprintf( checkPointMsg, |
788 |
> |
"Sucessfully took a dump.\n"); |
789 |
> |
delete[] potatoes; |
790 |
> |
|
791 |
> |
MPIcheckPoint(); |
792 |
> |
|
793 |
> |
} else { |
794 |
|
|
795 |
< |
if(!myStatus) nodeZeroError(); |
567 |
< |
} |
795 |
> |
// worldRank != 0, so I'm a remote node. |
796 |
|
|
797 |
< |
finalOut << writeLine; |
570 |
< |
} |
797 |
> |
// Set my magic potato to 0: |
798 |
|
|
799 |
< |
// kill everyone off: |
800 |
< |
myStatus = -1; |
801 |
< |
for (j = 1; j < mpiSim->getNumberProcessors(); j++) { |
802 |
< |
MPI_Send(&myStatus, 1, MPI_INT, j, |
803 |
< |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
804 |
< |
} |
799 |
> |
myPotato = 0; |
800 |
> |
|
801 |
> |
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
802 |
> |
|
803 |
> |
// Am I the node which has this atom? |
804 |
> |
|
805 |
> |
if (AtomToProcMap[i] == worldRank) { |
806 |
|
|
807 |
< |
} else { |
807 |
> |
if (myPotato + 3 >= MAXTAG) { |
808 |
|
|
809 |
< |
done = 0; |
810 |
< |
while (!done) { |
809 |
> |
// The potato was going to exceed the maximum value, |
810 |
> |
// so wrap this processor potato back to 0 (and block until |
811 |
> |
// node 0 says we can go: |
812 |
|
|
813 |
< |
MPI_Recv(&myStatus, 1, MPI_INT, 0, |
814 |
< |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
813 |
> |
MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus); |
814 |
> |
|
815 |
> |
} |
816 |
> |
which_atom = i; |
817 |
> |
local_index=-1; |
818 |
> |
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
819 |
> |
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
820 |
> |
} |
821 |
> |
if (local_index != -1) { |
822 |
> |
|
823 |
> |
atomTypeString = atoms[local_index]->getType(); |
824 |
|
|
825 |
< |
if(!myStatus) anonymousNodeDie(); |
825 |
> |
atoms[local_index]->getPos(pos); |
826 |
> |
atoms[local_index]->getVel(vel); |
827 |
|
|
828 |
< |
if(myStatus < 0) break; |
828 |
> |
atomData6[0] = pos[0]; |
829 |
> |
atomData6[1] = pos[1]; |
830 |
> |
atomData6[2] = pos[2]; |
831 |
|
|
832 |
< |
MPI_Recv(&which_atom, 1, MPI_INT, 0, |
833 |
< |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
832 |
> |
atomData6[3] = vel[0]; |
833 |
> |
atomData6[4] = vel[1]; |
834 |
> |
atomData6[5] = vel[2]; |
835 |
> |
|
836 |
> |
isDirectional = 0; |
837 |
|
|
838 |
< |
myStatus = 1; |
595 |
< |
local_index=-1; |
596 |
< |
for (j=0; j < mpiSim->getMyNlocal(); j++) { |
597 |
< |
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
598 |
< |
} |
599 |
< |
if (local_index != -1) { |
838 |
> |
if( atoms[local_index]->isDirectional() ){ |
839 |
|
|
840 |
< |
atoms[local_index]->getPos(pos); |
841 |
< |
atoms[local_index]->getVel(vel); |
840 |
> |
isDirectional = 1; |
841 |
> |
|
842 |
> |
dAtom = (DirectionalAtom *)atoms[local_index]; |
843 |
> |
dAtom->getQ( q ); |
844 |
> |
|
845 |
> |
for (int j = 0; j < 6 ; j++) |
846 |
> |
atomData13[j] = atomData6[j]; |
847 |
> |
|
848 |
> |
atomData13[6] = q[0]; |
849 |
> |
atomData13[7] = q[1]; |
850 |
> |
atomData13[8] = q[2]; |
851 |
> |
atomData13[9] = q[3]; |
852 |
|
|
853 |
< |
//format the line |
854 |
< |
sprintf( tempBuffer, |
855 |
< |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
856 |
< |
atoms[local_index]->getType(), |
608 |
< |
pos[0], |
609 |
< |
pos[1], |
610 |
< |
pos[2], |
611 |
< |
vel[0], |
612 |
< |
vel[1], |
613 |
< |
vel[2]); // check here. |
614 |
< |
strcpy( writeLine, tempBuffer ); |
853 |
> |
atomData13[10] = dAtom->getJx(); |
854 |
> |
atomData13[11] = dAtom->getJy(); |
855 |
> |
atomData13[12] = dAtom->getJz(); |
856 |
> |
} |
857 |
|
|
858 |
< |
if( atoms[local_index]->isDirectional() ){ |
858 |
> |
} else { |
859 |
> |
sprintf(painCave.errMsg, |
860 |
> |
"Atom %d not found on processor %d\n", |
861 |
> |
i, worldRank ); |
862 |
> |
haveError= 1; |
863 |
> |
simError(); |
864 |
> |
} |
865 |
|
|
866 |
< |
dAtom = (DirectionalAtom *)atoms[local_index]; |
619 |
< |
dAtom->getQ( q ); |
866 |
> |
strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE); |
867 |
|
|
868 |
< |
sprintf( tempBuffer, |
869 |
< |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
623 |
< |
q[0], |
624 |
< |
q[1], |
625 |
< |
q[2], |
626 |
< |
q[3], |
627 |
< |
dAtom->getJx(), |
628 |
< |
dAtom->getJy(), |
629 |
< |
dAtom->getJz()); |
630 |
< |
strcat( writeLine, tempBuffer ); |
631 |
< |
} |
632 |
< |
else{ |
633 |
< |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
634 |
< |
} |
635 |
< |
} |
636 |
< |
else { |
637 |
< |
sprintf(painCave.errMsg, |
638 |
< |
"Atom %d not found on processor %d\n", |
639 |
< |
which_atom, worldRank ); |
640 |
< |
myStatus = 0; |
641 |
< |
simError(); |
868 |
> |
// null terminate the string before sending (just in case): |
869 |
> |
MPIatomTypeString[MINIBUFFERSIZE-1] = '\0'; |
870 |
|
|
871 |
< |
strcpy( writeLine, "Hello, I'm an error.\n"); |
872 |
< |
} |
871 |
> |
MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0, |
872 |
> |
myPotato, MPI_COMM_WORLD); |
873 |
> |
|
874 |
> |
myPotato++; |
875 |
|
|
876 |
< |
MPI_Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, |
877 |
< |
TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD); |
878 |
< |
MPI_Send( &myStatus, 1, MPI_INT, 0, |
879 |
< |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
876 |
> |
MPI_Send(&isDirectional, 1, MPI_INT, 0, |
877 |
> |
myPotato, MPI_COMM_WORLD); |
878 |
> |
|
879 |
> |
myPotato++; |
880 |
> |
|
881 |
> |
if (isDirectional) { |
882 |
> |
|
883 |
> |
MPI_Send(atomData13, 13, MPI_DOUBLE, 0, |
884 |
> |
myPotato, MPI_COMM_WORLD); |
885 |
> |
|
886 |
> |
} else { |
887 |
> |
|
888 |
> |
MPI_Send(atomData6, 6, MPI_DOUBLE, 0, |
889 |
> |
myPotato, MPI_COMM_WORLD); |
890 |
> |
} |
891 |
> |
|
892 |
> |
myPotato++; |
893 |
> |
} |
894 |
|
} |
651 |
– |
} |
652 |
– |
finalOut.flush(); |
653 |
– |
sprintf( checkPointMsg, |
654 |
– |
"Sucessfully took a dump.\n"); |
655 |
– |
MPIcheckPoint(); |
895 |
|
|
896 |
+ |
sprintf( checkPointMsg, |
897 |
+ |
"Sucessfully took a dump.\n"); |
898 |
+ |
MPIcheckPoint(); |
899 |
+ |
|
900 |
+ |
} |
901 |
+ |
|
902 |
|
if( worldRank == 0 ) finalOut.close(); |
903 |
|
#endif // is_mpi |
904 |
|
} |
909 |
|
|
910 |
|
// a couple of functions to let us escape the write loop |
911 |
|
|
912 |
< |
void dWrite::nodeZeroError( void ){ |
668 |
< |
int j, myStatus; |
912 |
> |
void dWrite::DieDieDie( void ){ |
913 |
|
|
670 |
– |
myStatus = 0; |
671 |
– |
for (j = 0; j < mpiSim->getNumberProcessors(); j++) { |
672 |
– |
MPI_Send( &myStatus, 1, MPI_INT, j, |
673 |
– |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
674 |
– |
} |
675 |
– |
|
676 |
– |
|
914 |
|
MPI_Finalize(); |
915 |
|
exit (0); |
679 |
– |
|
916 |
|
} |
917 |
|
|
682 |
– |
void dWrite::anonymousNodeDie( void ){ |
683 |
– |
|
684 |
– |
MPI_Finalize(); |
685 |
– |
exit (0); |
686 |
– |
} |
687 |
– |
|
918 |
|
#endif //is_mpi |