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#define _FILE_OFFSET_BITS 64 |
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#include <cstring> |
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#include <iostream> |
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#include <fstream> |
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#ifdef IS_MPI |
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#include <mpi.h> |
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#include "mpiSimulation.hpp" |
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#define TAKE_THIS_TAG 0 |
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#define TAKE_THIS_TAG_CHAR 1 |
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#define TAKE_THIS_TAG_INT 2 |
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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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} |
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|
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using namespace dWrite; |
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#endif //is_mpi |
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#include "ReadWrite.hpp" |
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#include "simError.h" |
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|
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DumpWriter::DumpWriter( SimInfo* the_entry_plug ){ |
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entry_plug = the_entry_plug; |
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if(worldRank == 0 ){ |
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#endif // is_mpi |
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strcpy( outName, entry_plug->sampleName ); |
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outFile.open(outName, ios::out | ios::trunc ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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//outFile.setf( ios::scientific ); |
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#ifdef IS_MPI |
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char writeLine[BUFFERSIZE]; |
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|
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int i; |
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#ifdef IS_MPI |
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int j, which_node, done, which_atom, local_index; |
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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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|
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double q[4]; |
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DirectionalAtom* dAtom; |
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int nAtoms = entry_plug->n_atoms; |
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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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#ifndef IS_MPI |
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|
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outFile << nAtoms << "\n"; |
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|
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outFile << currentTime << "\t" |
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<< entry_plug->box_x << "\t" |
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<< entry_plug->box_y << "\t" |
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<< entry_plug->box_z << "\n"; |
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outFile << currentTime << ";\t" |
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<< entry_plug->Hmat[0][0] << "\t" |
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<< entry_plug->Hmat[1][0] << "\t" |
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<< entry_plug->Hmat[2][0] << ";\t" |
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|
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<< entry_plug->Hmat[0][1] << "\t" |
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<< entry_plug->Hmat[1][1] << "\t" |
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<< entry_plug->Hmat[2][1] << ";\t" |
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|
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<< entry_plug->Hmat[0][2] << "\t" |
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<< entry_plug->Hmat[1][2] << "\t" |
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<< entry_plug->Hmat[2][2] << ";\n"; |
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for( i=0; i<nAtoms; i++ ){ |
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atoms[i]->getPos(pos); |
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atoms[i]->getVel(vel); |
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|
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sprintf( tempBuffer, |
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"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
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atoms[i]->getType(), |
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atoms[i]->getX(), |
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atoms[i]->getY(), |
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atoms[i]->getZ(), |
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atoms[i]->get_vx(), |
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atoms[i]->get_vy(), |
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atoms[i]->get_vz()); |
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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]); |
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strcpy( writeLine, tempBuffer ); |
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if( atoms[i]->isDirectional() ){ |
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#else // is_mpi |
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|
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int masterIndex; |
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int nodeAtomsStart; |
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int nodeAtomsEnd; |
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int mpiErr; |
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int sendError; |
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int procIndex; |
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|
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MPI_Status istatus[MPI_STATUS_SIZE]; |
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// first thing first, suspend fatalities. |
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painCave.isEventLoop = 1; |
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|
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|
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// write out header and node 0's coordinates |
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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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int *AtomToProcMap = mpiSim->getAtomToProcMap(); |
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|
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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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outFile << mpiSim->getTotAtoms() << "\n"; |
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|
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outFile << currentTime << ";\t" |
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<< entry_plug->Hmat[0][0] << "\t" |
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<< entry_plug->Hmat[1][0] << "\t" |
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<< entry_plug->Hmat[2][0] << ";\t" |
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|
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outFile << currentTime << "\t" |
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<< entry_plug->box_x << "\t" |
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<< entry_plug->box_y << "\t" |
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<< entry_plug->box_z << "\n"; |
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|
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masterIndex = 0; |
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for( i=0; i<nAtoms; i++ ){ |
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<< entry_plug->Hmat[0][1] << "\t" |
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<< entry_plug->Hmat[1][1] << "\t" |
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<< entry_plug->Hmat[2][1] << ";\t" |
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|
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sprintf( tempBuffer, |
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"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
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atoms[i]->getType(), |
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atoms[i]->getX(), |
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atoms[i]->getY(), |
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atoms[i]->getZ(), |
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atoms[i]->get_vx(), |
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atoms[i]->get_vy(), |
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atoms[i]->get_vz()); |
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strcpy( writeLine, tempBuffer ); |
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|
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if( atoms[i]->isDirectional() ){ |
161 |
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|
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dAtom = (DirectionalAtom *)atoms[i]; |
163 |
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dAtom->getQ( q ); |
164 |
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|
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sprintf( tempBuffer, |
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"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
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< |
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(), |
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dAtom->getJy(), |
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dAtom->getJz()); |
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< |
strcat( writeLine, tempBuffer ); |
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} |
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else |
177 |
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strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
178 |
< |
|
179 |
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outFile << writeLine; |
180 |
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masterIndex++; |
181 |
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} |
182 |
< |
outFile.flush(); |
183 |
< |
} |
184 |
< |
|
185 |
< |
sprintf( checkPointMsg, |
186 |
< |
"Sucessfully wrote node 0's dump configuration.\n"); |
187 |
< |
MPIcheckPoint(); |
173 |
> |
<< entry_plug->Hmat[0][2] << "\t" |
174 |
> |
<< entry_plug->Hmat[1][2] << "\t" |
175 |
> |
<< entry_plug->Hmat[2][2] << ";\n"; |
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|
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< |
for (procIndex = 1; procIndex < mpiSim->getNumberProcessors(); |
178 |
< |
procIndex++){ |
179 |
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|
192 |
< |
if( worldRank == 0 ){ |
177 |
> |
outFile.flush(); |
178 |
> |
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
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> |
// Get the Node number which has this atom; |
180 |
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|
181 |
< |
mpiErr = MPI_Recv(&nodeAtomsStart,1,MPI_INT,procIndex, |
195 |
< |
TAKE_THIS_TAG,MPI_COMM_WORLD,istatus); |
181 |
> |
which_node = AtomToProcMap[i]; |
182 |
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|
183 |
< |
mpiErr = MPI_Recv(&nodeAtomsEnd,1,MPI_INT,procIndex, |
198 |
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TAKE_THIS_TAG,MPI_COMM_WORLD, istatus); |
199 |
< |
|
200 |
< |
// Make sure where node 0 is writing to, matches where the |
201 |
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// receiving node expects it to be. |
202 |
< |
|
203 |
< |
if (masterIndex != nodeAtomsStart){ |
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< |
sendError = 1; |
205 |
< |
mpiErr = MPI_Send(&sendError,1,MPI_INT,procIndex,TAKE_THIS_TAG, |
206 |
< |
MPI_COMM_WORLD); |
207 |
< |
sprintf(painCave.errMsg, |
208 |
< |
"DumpWriter error: atoms start index (%d) for " |
209 |
< |
"node %d not equal to master index (%d)", |
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< |
nodeAtomsStart,procIndex,masterIndex ); |
211 |
< |
painCave.isFatal = 1; |
212 |
< |
simError(); |
213 |
< |
} |
214 |
< |
|
215 |
< |
sendError = 0; |
216 |
< |
mpiErr = MPI_Send(&sendError,1,MPI_INT,procIndex,TAKE_THIS_TAG, |
217 |
< |
MPI_COMM_WORLD); |
218 |
< |
|
219 |
< |
// recieve the nodes writeLines |
220 |
< |
|
221 |
< |
for ( i = nodeAtomsStart; i <= nodeAtomsEnd; i++){ |
183 |
> |
if (which_node == 0 ) { |
184 |
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|
185 |
< |
mpiErr = MPI_Recv(writeLine,BUFFERSIZE,MPI_CHAR,procIndex, |
186 |
< |
TAKE_THIS_TAG,MPI_COMM_WORLD,istatus ); |
187 |
< |
|
188 |
< |
outFile << writeLine; |
189 |
< |
masterIndex++; |
185 |
> |
haveError = 0; |
186 |
> |
which_atom = i; |
187 |
> |
local_index=-1; |
188 |
> |
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
189 |
> |
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
190 |
> |
} |
191 |
> |
if (local_index != -1) { |
192 |
> |
//format the line |
193 |
> |
|
194 |
> |
atoms[local_index]->getPos(pos); |
195 |
> |
atoms[local_index]->getVel(vel); |
196 |
> |
|
197 |
> |
sprintf( tempBuffer, |
198 |
> |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
199 |
> |
atoms[local_index]->getType(), |
200 |
> |
pos[0], |
201 |
> |
pos[1], |
202 |
> |
pos[2], |
203 |
> |
vel[0], |
204 |
> |
vel[1], |
205 |
> |
vel[2]); // check here. |
206 |
> |
strcpy( writeLine, tempBuffer ); |
207 |
> |
|
208 |
> |
if( atoms[local_index]->isDirectional() ){ |
209 |
> |
|
210 |
> |
dAtom = (DirectionalAtom *)atoms[local_index]; |
211 |
> |
dAtom->getQ( q ); |
212 |
> |
|
213 |
> |
sprintf( tempBuffer, |
214 |
> |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
215 |
> |
q[0], |
216 |
> |
q[1], |
217 |
> |
q[2], |
218 |
> |
q[3], |
219 |
> |
dAtom->getJx(), |
220 |
> |
dAtom->getJy(), |
221 |
> |
dAtom->getJz()); |
222 |
> |
strcat( writeLine, tempBuffer ); |
223 |
> |
|
224 |
> |
} |
225 |
> |
else |
226 |
> |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
227 |
> |
} |
228 |
> |
else { |
229 |
> |
sprintf(painCave.errMsg, |
230 |
> |
"Atom %d not found on processor %d\n", |
231 |
> |
i, worldRank ); |
232 |
> |
haveError= 1; |
233 |
> |
simError(); |
234 |
> |
} |
235 |
> |
|
236 |
> |
if(haveError) nodeZeroError(); |
237 |
> |
|
238 |
|
} |
239 |
+ |
else { |
240 |
+ |
myStatus = 1; |
241 |
+ |
MPI_Send(&myStatus, 1, MPI_INT, which_node, |
242 |
+ |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
243 |
+ |
MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, |
244 |
+ |
MPI_COMM_WORLD); |
245 |
+ |
MPI_Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node, |
246 |
+ |
TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus); |
247 |
+ |
MPI_Recv(&myStatus, 1, MPI_INT, which_node, |
248 |
+ |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
249 |
+ |
|
250 |
+ |
if(!myStatus) nodeZeroError(); |
251 |
+ |
|
252 |
+ |
} |
253 |
+ |
|
254 |
+ |
outFile << writeLine; |
255 |
+ |
outFile.flush(); |
256 |
|
} |
257 |
+ |
|
258 |
+ |
// kill everyone off: |
259 |
+ |
myStatus = -1; |
260 |
+ |
for (j = 0; j < mpiSim->getNumberProcessors(); j++) { |
261 |
+ |
MPI_Send(&myStatus, 1, MPI_INT, j, |
262 |
+ |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
263 |
+ |
} |
264 |
|
|
265 |
< |
else if( worldRank == procIndex ){ |
265 |
> |
} else { |
266 |
> |
|
267 |
> |
done = 0; |
268 |
> |
while (!done) { |
269 |
> |
|
270 |
> |
MPI_Recv(&myStatus, 1, MPI_INT, 0, |
271 |
> |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
272 |
|
|
273 |
< |
nodeAtomsStart = mpiSim->getMyAtomStart(); |
274 |
< |
nodeAtomsEnd = mpiSim->getMyAtomEnd(); |
273 |
> |
if(!myStatus) anonymousNodeDie(); |
274 |
> |
|
275 |
> |
if(myStatus < 0) break; |
276 |
|
|
277 |
< |
mpiErr = MPI_Send(&nodeAtomsStart,1,MPI_INT,0,TAKE_THIS_TAG, |
278 |
< |
MPI_COMM_WORLD); |
279 |
< |
mpiErr = MPI_Send(&nodeAtomsEnd,1,MPI_INT,0,TAKE_THIS_TAG, |
280 |
< |
MPI_COMM_WORLD); |
281 |
< |
|
282 |
< |
sendError = -1; |
283 |
< |
mpiErr = MPI_Recv(&sendError,1,MPI_INT,0,TAKE_THIS_TAG, |
284 |
< |
MPI_COMM_WORLD, istatus); |
277 |
> |
MPI_Recv(&which_atom, 1, MPI_INT, 0, |
278 |
> |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
279 |
> |
|
280 |
> |
myStatus = 1; |
281 |
> |
local_index=-1; |
282 |
> |
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
283 |
> |
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
284 |
> |
} |
285 |
> |
if (local_index != -1) { |
286 |
> |
//format the line |
287 |
|
|
288 |
< |
if (sendError) MPIcheckPoint(); |
288 |
> |
atoms[local_index]->getPos(pos); |
289 |
> |
atoms[local_index]->getVel(vel); |
290 |
|
|
247 |
– |
// send current node's configuration line by line. |
248 |
– |
|
249 |
– |
for( i=0; i<nAtoms; i++ ){ |
250 |
– |
|
291 |
|
sprintf( tempBuffer, |
292 |
|
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
293 |
< |
atoms[i]->getType(), |
294 |
< |
atoms[i]->getX(), |
295 |
< |
atoms[i]->getY(), |
296 |
< |
atoms[i]->getZ(), |
297 |
< |
atoms[i]->get_vx(), |
298 |
< |
atoms[i]->get_vy(), |
299 |
< |
atoms[i]->get_vz()); // check here. |
293 |
> |
atoms[local_index]->getType(), |
294 |
> |
pos[0], |
295 |
> |
pos[1], |
296 |
> |
pos[2], |
297 |
> |
vel[0], |
298 |
> |
vel[1], |
299 |
> |
vel[2]); // check here. |
300 |
|
strcpy( writeLine, tempBuffer ); |
301 |
+ |
|
302 |
+ |
if( atoms[local_index]->isDirectional() ){ |
303 |
|
|
304 |
< |
if( atoms[i]->isDirectional() ){ |
263 |
< |
|
264 |
< |
dAtom = (DirectionalAtom *)atoms[i]; |
304 |
> |
dAtom = (DirectionalAtom *)atoms[local_index]; |
305 |
|
dAtom->getQ( q ); |
306 |
< |
|
306 |
> |
|
307 |
|
sprintf( tempBuffer, |
308 |
|
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
309 |
|
q[0], |
315 |
|
dAtom->getJz()); |
316 |
|
strcat( writeLine, tempBuffer ); |
317 |
|
} |
318 |
< |
else |
318 |
> |
else{ |
319 |
|
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
320 |
< |
|
321 |
< |
mpiErr = MPI_Send(writeLine,BUFFERSIZE,MPI_CHAR,0,TAKE_THIS_TAG, |
322 |
< |
MPI_COMM_WORLD); |
320 |
> |
} |
321 |
> |
} |
322 |
> |
else { |
323 |
> |
sprintf(painCave.errMsg, |
324 |
> |
"Atom %d not found on processor %d\n", |
325 |
> |
which_atom, worldRank ); |
326 |
> |
myStatus = 0; |
327 |
> |
simError(); |
328 |
> |
|
329 |
> |
strcpy( writeLine, "Hello, I'm an error.\n"); |
330 |
|
} |
331 |
+ |
|
332 |
+ |
MPI_Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, |
333 |
+ |
TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD); |
334 |
+ |
MPI_Send( &myStatus, 1, MPI_INT, 0, |
335 |
+ |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
336 |
|
} |
337 |
< |
|
338 |
< |
sprintf(checkPointMsg,"Node %d sent dump configuration.", |
339 |
< |
procIndex); |
340 |
< |
MPIcheckPoint(); |
341 |
< |
} |
342 |
< |
|
337 |
> |
} |
338 |
> |
outFile.flush(); |
339 |
> |
sprintf( checkPointMsg, |
340 |
> |
"Sucessfully took a dump.\n"); |
341 |
> |
MPIcheckPoint(); |
342 |
> |
|
343 |
> |
// last thing last, enable fatalities. |
344 |
> |
painCave.isEventLoop = 0; |
345 |
> |
|
346 |
|
#endif // is_mpi |
347 |
|
} |
348 |
|
|
349 |
+ |
void DumpWriter::writeFinal(double finalTime){ |
350 |
|
|
351 |
+ |
char finalName[500]; |
352 |
+ |
ofstream finalOut; |
353 |
|
|
296 |
– |
void DumpWriter::writeFinal(){ |
297 |
– |
|
298 |
– |
|
354 |
|
const int BUFFERSIZE = 2000; |
355 |
< |
char tempBuffer[500]; |
356 |
< |
char writeLine[BUFFERSIZE]; |
302 |
< |
|
303 |
< |
char finalName[500]; |
355 |
> |
char tempBuffer[BUFFERSIZE]; |
356 |
> |
char writeLine[BUFFERSIZE]; |
357 |
|
|
305 |
– |
int i; |
358 |
|
double q[4]; |
359 |
|
DirectionalAtom* dAtom; |
308 |
– |
int nAtoms = entry_plug->n_atoms; |
360 |
|
Atom** atoms = entry_plug->atoms; |
361 |
+ |
int i; |
362 |
+ |
#ifdef IS_MPI |
363 |
+ |
int j, which_node, done, which_atom, local_index; |
364 |
+ |
#else //is_mpi |
365 |
+ |
int nAtoms = entry_plug->n_atoms; |
366 |
+ |
#endif //is_mpi |
367 |
|
|
368 |
< |
ofstream finalOut; |
368 |
> |
double pos[3], vel[3]; |
369 |
|
|
370 |
|
#ifdef IS_MPI |
371 |
|
if(worldRank == 0 ){ |
392 |
|
|
393 |
|
#endif //is_mpi |
394 |
|
|
395 |
< |
|
339 |
< |
|
395 |
> |
|
396 |
|
#ifndef IS_MPI |
397 |
|
|
398 |
|
finalOut << nAtoms << "\n"; |
399 |
|
|
400 |
< |
finalOut << entry_plug->box_x << "\t" |
401 |
< |
<< entry_plug->box_y << "\t" |
402 |
< |
<< entry_plug->box_z << "\n"; |
400 |
> |
finalOut << finalTime << ";\t" |
401 |
> |
<< entry_plug->Hmat[0][0] << "\t" |
402 |
> |
<< entry_plug->Hmat[1][0] << "\t" |
403 |
> |
<< entry_plug->Hmat[2][0] << ";\t" |
404 |
> |
|
405 |
> |
<< entry_plug->Hmat[0][1] << "\t" |
406 |
> |
<< entry_plug->Hmat[1][1] << "\t" |
407 |
> |
<< entry_plug->Hmat[2][1] << ";\t" |
408 |
|
|
409 |
+ |
<< entry_plug->Hmat[0][2] << "\t" |
410 |
+ |
<< entry_plug->Hmat[1][2] << "\t" |
411 |
+ |
<< entry_plug->Hmat[2][2] << ";\n"; |
412 |
+ |
|
413 |
|
for( i=0; i<nAtoms; i++ ){ |
414 |
|
|
415 |
+ |
atoms[i]->getPos(pos); |
416 |
+ |
atoms[i]->getVel(vel); |
417 |
+ |
|
418 |
|
sprintf( tempBuffer, |
419 |
|
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
420 |
|
atoms[i]->getType(), |
421 |
< |
atoms[i]->getX(), |
422 |
< |
atoms[i]->getY(), |
423 |
< |
atoms[i]->getZ(), |
424 |
< |
atoms[i]->get_vx(), |
425 |
< |
atoms[i]->get_vy(), |
426 |
< |
atoms[i]->get_vz()); |
421 |
> |
pos[0], |
422 |
> |
pos[1], |
423 |
> |
pos[2], |
424 |
> |
vel[0], |
425 |
> |
vel[1], |
426 |
> |
vel[2]); |
427 |
|
strcpy( writeLine, tempBuffer ); |
428 |
|
|
429 |
|
if( atoms[i]->isDirectional() ){ |
448 |
|
finalOut << writeLine; |
449 |
|
} |
450 |
|
finalOut.flush(); |
451 |
+ |
finalOut.close(); |
452 |
|
|
453 |
|
#else // is_mpi |
454 |
+ |
|
455 |
+ |
// first thing first, suspend fatalities. |
456 |
+ |
painCave.isEventLoop = 1; |
457 |
|
|
458 |
< |
int masterIndex; |
459 |
< |
int nodeAtomsStart; |
388 |
< |
int nodeAtomsEnd; |
389 |
< |
int mpiErr; |
390 |
< |
int sendError; |
391 |
< |
int procIndex; |
392 |
< |
|
393 |
< |
MPI_Status istatus[MPI_STATUS_SIZE]; |
458 |
> |
int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone |
459 |
> |
int haveError; |
460 |
|
|
461 |
< |
|
462 |
< |
// write out header and node 0's coordinates |
461 |
> |
MPI_Status istatus; |
462 |
> |
int *AtomToProcMap = mpiSim->getAtomToProcMap(); |
463 |
|
|
464 |
+ |
// write out header and node 0's coordinates |
465 |
+ |
|
466 |
+ |
haveError = 0; |
467 |
|
if( worldRank == 0 ){ |
468 |
|
finalOut << mpiSim->getTotAtoms() << "\n"; |
469 |
+ |
|
470 |
+ |
finalOut << finalTime << ";\t" |
471 |
+ |
<< entry_plug->Hmat[0][0] << "\t" |
472 |
+ |
<< entry_plug->Hmat[1][0] << "\t" |
473 |
+ |
<< entry_plug->Hmat[2][0] << ";\t" |
474 |
|
|
475 |
< |
finalOut << entry_plug->box_x << "\t" |
476 |
< |
<< entry_plug->box_y << "\t" |
477 |
< |
<< entry_plug->box_z << "\n"; |
475 |
> |
<< entry_plug->Hmat[0][1] << "\t" |
476 |
> |
<< entry_plug->Hmat[1][1] << "\t" |
477 |
> |
<< entry_plug->Hmat[2][1] << ";\t" |
478 |
> |
|
479 |
> |
<< entry_plug->Hmat[0][2] << "\t" |
480 |
> |
<< entry_plug->Hmat[1][2] << "\t" |
481 |
> |
<< entry_plug->Hmat[2][2] << ";\n"; |
482 |
|
|
483 |
< |
masterIndex = 0; |
484 |
< |
|
407 |
< |
for( i=0; i<nAtoms; i++ ){ |
483 |
> |
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
484 |
> |
// Get the Node number which has this molecule: |
485 |
|
|
486 |
< |
sprintf( tempBuffer, |
487 |
< |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
488 |
< |
atoms[i]->getType(), |
489 |
< |
atoms[i]->getX(), |
490 |
< |
atoms[i]->getY(), |
491 |
< |
atoms[i]->getZ(), |
492 |
< |
atoms[i]->get_vx(), |
493 |
< |
atoms[i]->get_vy(), |
494 |
< |
atoms[i]->get_vz()); |
495 |
< |
strcpy( writeLine, tempBuffer ); |
496 |
< |
|
497 |
< |
if( atoms[i]->isDirectional() ){ |
486 |
> |
which_node = AtomToProcMap[i]; |
487 |
> |
|
488 |
> |
if (which_node == mpiSim->getMyNode()) { |
489 |
> |
|
490 |
> |
which_atom = i; |
491 |
> |
local_index=-1; |
492 |
> |
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
493 |
> |
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
494 |
> |
} |
495 |
> |
if (local_index != -1) { |
496 |
> |
|
497 |
> |
atoms[local_index]->getPos(pos); |
498 |
> |
atoms[local_index]->getVel(vel); |
499 |
|
|
500 |
< |
dAtom = (DirectionalAtom *)atoms[i]; |
501 |
< |
dAtom->getQ( q ); |
500 |
> |
sprintf( tempBuffer, |
501 |
> |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
502 |
> |
atoms[local_index]->getType(), |
503 |
> |
pos[0], |
504 |
> |
pos[1], |
505 |
> |
pos[2], |
506 |
> |
vel[0], |
507 |
> |
vel[1], |
508 |
> |
vel[2]); |
509 |
> |
strcpy( writeLine, tempBuffer ); |
510 |
|
|
511 |
< |
sprintf( tempBuffer, |
512 |
< |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
513 |
< |
q[0], |
514 |
< |
q[1], |
515 |
< |
q[2], |
516 |
< |
q[3], |
517 |
< |
dAtom->getJx(), |
518 |
< |
dAtom->getJy(), |
519 |
< |
dAtom->getJz()); |
520 |
< |
strcat( writeLine, tempBuffer ); |
521 |
< |
} |
522 |
< |
else |
523 |
< |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
511 |
> |
if( atoms[local_index]->isDirectional() ){ |
512 |
> |
|
513 |
> |
dAtom = (DirectionalAtom *)atoms[local_index]; |
514 |
> |
dAtom->getQ( q ); |
515 |
> |
|
516 |
> |
sprintf( tempBuffer, |
517 |
> |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
518 |
> |
q[0], |
519 |
> |
q[1], |
520 |
> |
q[2], |
521 |
> |
q[3], |
522 |
> |
dAtom->getJx(), |
523 |
> |
dAtom->getJy(), |
524 |
> |
dAtom->getJz()); |
525 |
> |
strcat( writeLine, tempBuffer ); |
526 |
> |
} |
527 |
> |
else |
528 |
> |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
529 |
> |
} |
530 |
> |
else { |
531 |
> |
sprintf(painCave.errMsg, |
532 |
> |
"Atom %d not found on processor %d\n", |
533 |
> |
i, worldRank ); |
534 |
> |
haveError= 1; |
535 |
> |
simError(); |
536 |
> |
} |
537 |
> |
|
538 |
> |
if(haveError) nodeZeroError(); |
539 |
> |
|
540 |
> |
} |
541 |
> |
else { |
542 |
> |
|
543 |
> |
myStatus = 1; |
544 |
> |
MPI_Send(&myStatus, 1, MPI_INT, which_node, |
545 |
> |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
546 |
> |
MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, |
547 |
> |
MPI_COMM_WORLD); |
548 |
> |
MPI_Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node, |
549 |
> |
TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus); |
550 |
> |
MPI_Recv(&myStatus, 1, MPI_INT, which_node, |
551 |
> |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
552 |
|
|
553 |
+ |
if(!myStatus) nodeZeroError(); |
554 |
+ |
} |
555 |
+ |
|
556 |
|
finalOut << writeLine; |
440 |
– |
masterIndex++; |
557 |
|
} |
442 |
– |
finalOut.flush(); |
443 |
– |
} |
558 |
|
|
559 |
< |
for (procIndex = 1; procIndex < mpiSim->getNumberProcessors(); |
560 |
< |
procIndex++){ |
559 |
> |
// kill everyone off: |
560 |
> |
myStatus = -1; |
561 |
> |
for (j = 0; j < mpiSim->getNumberProcessors(); j++) { |
562 |
> |
MPI_Send(&myStatus, 1, MPI_INT, j, |
563 |
> |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
564 |
> |
} |
565 |
|
|
566 |
< |
if( worldRank == 0 ){ |
567 |
< |
|
568 |
< |
mpiErr = MPI_Recv(&nodeAtomsStart,1,MPI_INT,procIndex, |
569 |
< |
TAKE_THIS_TAG,MPI_COMM_WORLD,istatus); |
566 |
> |
} else { |
567 |
> |
|
568 |
> |
done = 0; |
569 |
> |
while (!done) { |
570 |
|
|
571 |
< |
mpiErr = MPI_Recv(&nodeAtomsEnd,1,MPI_INT,procIndex, |
572 |
< |
TAKE_THIS_TAG,MPI_COMM_WORLD, istatus); |
573 |
< |
|
574 |
< |
// Make sure where node 0 is writing to, matches where the |
575 |
< |
// receiving node expects it to be. |
576 |
< |
|
577 |
< |
if (masterIndex != nodeAtomsStart){ |
578 |
< |
sendError = 1; |
579 |
< |
mpiErr = MPI_Send(&sendError,1,MPI_INT,procIndex,TAKE_THIS_TAG, |
580 |
< |
MPI_COMM_WORLD); |
581 |
< |
sprintf(painCave.errMsg, |
582 |
< |
"DumpWriter error: atoms start index (%d) for " |
583 |
< |
"node %d not equal to master index (%d)", |
584 |
< |
nodeAtomsStart,procIndex,masterIndex ); |
467 |
< |
painCave.isFatal = 1; |
468 |
< |
simError(); |
571 |
> |
MPI_Recv(&myStatus, 1, MPI_INT, 0, |
572 |
> |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
573 |
> |
|
574 |
> |
if(!myStatus) anonymousNodeDie(); |
575 |
> |
|
576 |
> |
if(myStatus < 0) break; |
577 |
> |
|
578 |
> |
MPI_Recv(&which_atom, 1, MPI_INT, 0, |
579 |
> |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
580 |
> |
|
581 |
> |
myStatus = 1; |
582 |
> |
local_index=-1; |
583 |
> |
for (j=0; j < mpiSim->getMyNlocal(); j++) { |
584 |
> |
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
585 |
|
} |
586 |
< |
|
471 |
< |
sendError = 0; |
472 |
< |
mpiErr = MPI_Send(&sendError,1,MPI_INT,procIndex,TAKE_THIS_TAG, |
473 |
< |
MPI_COMM_WORLD); |
586 |
> |
if (local_index != -1) { |
587 |
|
|
588 |
< |
// recieve the nodes writeLines |
588 |
> |
atoms[local_index]->getPos(pos); |
589 |
> |
atoms[local_index]->getVel(vel); |
590 |
|
|
591 |
< |
for ( i = nodeAtomsStart; i <= nodeAtomsEnd; i++){ |
478 |
< |
|
479 |
< |
mpiErr = MPI_Recv(writeLine,BUFFERSIZE,MPI_CHAR,procIndex, |
480 |
< |
TAKE_THIS_TAG,MPI_COMM_WORLD,istatus ); |
481 |
< |
|
482 |
< |
finalOut << writeLine; |
483 |
< |
masterIndex++; |
484 |
< |
} |
485 |
< |
|
486 |
< |
finalOut.flush(); |
487 |
< |
} |
488 |
< |
|
489 |
< |
else if( worldRank == procIndex ){ |
490 |
< |
|
491 |
< |
nodeAtomsStart = mpiSim->getMyAtomStart(); |
492 |
< |
nodeAtomsEnd = mpiSim->getMyAtomEnd(); |
493 |
< |
|
494 |
< |
mpiErr = MPI_Send(&nodeAtomsStart,1,MPI_INT,0,TAKE_THIS_TAG, |
495 |
< |
MPI_COMM_WORLD); |
496 |
< |
mpiErr = MPI_Send(&nodeAtomsEnd,1,MPI_INT,0,TAKE_THIS_TAG, |
497 |
< |
MPI_COMM_WORLD); |
498 |
< |
|
499 |
< |
mpiErr = MPI_Recv(&sendError,1,MPI_INT,0,TAKE_THIS_TAG, |
500 |
< |
MPI_COMM_WORLD, istatus); |
501 |
< |
if (sendError) MPIcheckPoint(); |
502 |
< |
|
503 |
< |
// send current node's configuration line by line. |
504 |
< |
|
505 |
< |
for( i=0; i<nAtoms; i++ ){ |
506 |
< |
|
591 |
> |
//format the line |
592 |
|
sprintf( tempBuffer, |
593 |
|
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
594 |
< |
atoms[i]->getType(), |
595 |
< |
atoms[i]->getX(), |
596 |
< |
atoms[i]->getY(), |
597 |
< |
atoms[i]->getZ(), |
598 |
< |
atoms[i]->get_vx(), |
599 |
< |
atoms[i]->get_vy(), |
600 |
< |
atoms[i]->get_vz()); |
594 |
> |
atoms[local_index]->getType(), |
595 |
> |
pos[0], |
596 |
> |
pos[1], |
597 |
> |
pos[2], |
598 |
> |
vel[0], |
599 |
> |
vel[1], |
600 |
> |
vel[2]); // check here. |
601 |
|
strcpy( writeLine, tempBuffer ); |
602 |
+ |
|
603 |
+ |
if( atoms[local_index]->isDirectional() ){ |
604 |
|
|
605 |
< |
if( atoms[i]->isDirectional() ){ |
519 |
< |
|
520 |
< |
dAtom = (DirectionalAtom *)atoms[i]; |
605 |
> |
dAtom = (DirectionalAtom *)atoms[local_index]; |
606 |
|
dAtom->getQ( q ); |
607 |
< |
|
607 |
> |
|
608 |
|
sprintf( tempBuffer, |
609 |
|
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
610 |
|
q[0], |
616 |
|
dAtom->getJz()); |
617 |
|
strcat( writeLine, tempBuffer ); |
618 |
|
} |
619 |
< |
else |
619 |
> |
else{ |
620 |
|
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
621 |
< |
|
622 |
< |
mpiErr = MPI_Send(writeLine,BUFFERSIZE,MPI_CHAR,0,TAKE_THIS_TAG, |
623 |
< |
MPI_COMM_WORLD); |
621 |
> |
} |
622 |
> |
} |
623 |
> |
else { |
624 |
> |
sprintf(painCave.errMsg, |
625 |
> |
"Atom %d not found on processor %d\n", |
626 |
> |
which_atom, worldRank ); |
627 |
> |
myStatus = 0; |
628 |
> |
simError(); |
629 |
> |
|
630 |
> |
strcpy( writeLine, "Hello, I'm an error.\n"); |
631 |
|
} |
632 |
+ |
|
633 |
+ |
MPI_Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, |
634 |
+ |
TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD); |
635 |
+ |
MPI_Send( &myStatus, 1, MPI_INT, 0, |
636 |
+ |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
637 |
|
} |
541 |
– |
|
542 |
– |
sprintf(checkPointMsg,"Node %d sent dump configuration.", |
543 |
– |
procIndex); |
544 |
– |
MPIcheckPoint(); |
638 |
|
} |
639 |
+ |
finalOut.flush(); |
640 |
+ |
sprintf( checkPointMsg, |
641 |
+ |
"Sucessfully took a dump.\n"); |
642 |
+ |
MPIcheckPoint(); |
643 |
+ |
|
644 |
+ |
if( worldRank == 0 ) finalOut.close(); |
645 |
+ |
#endif // is_mpi |
646 |
+ |
} |
647 |
|
|
547 |
– |
if( worldRank == 0 ) finalOut.close(); |
648 |
|
|
649 |
< |
|
650 |
< |
#endif // is_mpi |
649 |
> |
|
650 |
> |
#ifdef IS_MPI |
651 |
> |
|
652 |
> |
// a couple of functions to let us escape the write loop |
653 |
> |
|
654 |
> |
void dWrite::nodeZeroError( void ){ |
655 |
> |
int j, myStatus; |
656 |
> |
|
657 |
> |
myStatus = 0; |
658 |
> |
for (j = 0; j < mpiSim->getNumberProcessors(); j++) { |
659 |
> |
MPI_Send( &myStatus, 1, MPI_INT, j, |
660 |
> |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
661 |
> |
} |
662 |
> |
|
663 |
> |
|
664 |
> |
MPI_Finalize(); |
665 |
> |
exit (0); |
666 |
> |
|
667 |
|
} |
668 |
+ |
|
669 |
+ |
void dWrite::anonymousNodeDie( void ){ |
670 |
+ |
|
671 |
+ |
MPI_Finalize(); |
672 |
+ |
exit (0); |
673 |
+ |
} |
674 |
+ |
|
675 |
+ |
#endif //is_mpi |