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#include <cstring> |
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#define _FILE_OFFSET_BITS 64 |
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|
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#include <string.h> |
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#include <iostream> |
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#include <fstream> |
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|
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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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|
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namespace dWrite{ |
12 |
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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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#endif //is_mpi |
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|
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#include "ReadWrite.hpp" |
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#include "simError.h" |
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|
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|
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|
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DumpWriter::DumpWriter( SimInfo* the_entry_plug ){ |
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|
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entry_plug = the_entry_plug; |
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#ifdef IS_MPI |
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if(worldRank == 0 ){ |
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#endif // is_mpi |
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|
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|
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|
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|
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strcpy( outName, entry_plug->sampleName ); |
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|
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outFile.open(outName, ios::out | ios::trunc ); |
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|
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if( !outFile ){ |
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|
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|
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sprintf( painCave.errMsg, |
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"Could not open \"%s\" for dump output.\n", |
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outName); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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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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} |
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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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|
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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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|
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double pos[3], vel[3]; |
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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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|
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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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|
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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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<< 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] << ";"; |
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//write out additional parameters, such as chi and eta |
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outFile << entry_plug->the_integrator->getAdditionalParameters(); |
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outFile << endl; |
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|
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for( i=0; i<nAtoms; i++ ){ |
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|
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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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|
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if( atoms[i]->isDirectional() ){ |
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|
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|
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dAtom = (DirectionalAtom *)atoms[i]; |
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dAtom->getQ( q ); |
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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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} |
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else |
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strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
156 |
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|
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outFile << writeLine; |
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} |
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outFile.flush(); |
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#else // is_mpi |
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|
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int masterIndex; |
164 |
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int nodeAtomsStart; |
165 |
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int nodeAtomsEnd; |
166 |
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int mpiErr; |
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int sendError; |
168 |
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int procIndex; |
169 |
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|
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MPI_Status istatus[MPI_STATUS_SIZE]; |
163 |
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/* code to find maximum tag value */ |
164 |
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int *tagub, flag, MAXTAG; |
165 |
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MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag); |
166 |
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if (flag) { |
167 |
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MAXTAG = *tagub; |
168 |
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} else { |
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MAXTAG = 32767; |
170 |
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} |
171 |
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|
172 |
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|
172 |
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int haveError; |
173 |
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|
174 |
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MPI_Status istatus; |
175 |
> |
int *AtomToProcMap = mpiSim->getAtomToProcMap(); |
176 |
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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 ){ |
139 |
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outFile << mpiSim->getTotAtoms() << "\n"; |
140 |
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|
141 |
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outFile << currentTime << "\t" |
142 |
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<< entry_plug->box_x << "\t" |
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<< entry_plug->box_y << "\t" |
144 |
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<< entry_plug->box_z << "\n"; |
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|
181 |
< |
masterIndex = 0; |
147 |
< |
for( i=0; i<nAtoms; i++ ){ |
148 |
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|
149 |
< |
sprintf( tempBuffer, |
150 |
< |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
151 |
< |
atoms[i]->getType(), |
152 |
< |
atoms[i]->getX(), |
153 |
< |
atoms[i]->getY(), |
154 |
< |
atoms[i]->getZ(), |
155 |
< |
atoms[i]->get_vx(), |
156 |
< |
atoms[i]->get_vy(), |
157 |
< |
atoms[i]->get_vz()); |
158 |
< |
strcpy( writeLine, tempBuffer ); |
159 |
< |
|
160 |
< |
if( atoms[i]->isDirectional() ){ |
161 |
< |
|
162 |
< |
dAtom = (DirectionalAtom *)atoms[i]; |
163 |
< |
dAtom->getQ( q ); |
164 |
< |
|
165 |
< |
sprintf( tempBuffer, |
166 |
< |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
167 |
< |
q[0], |
168 |
< |
q[1], |
169 |
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q[2], |
170 |
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q[3], |
171 |
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dAtom->getJx(), |
172 |
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dAtom->getJy(), |
173 |
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dAtom->getJz()); |
174 |
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strcat( writeLine, tempBuffer ); |
175 |
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} |
176 |
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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 |
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|
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outFile << writeLine; |
180 |
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masterIndex++; |
181 |
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} |
182 |
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outFile.flush(); |
183 |
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} |
181 |
> |
// Node 0 needs a list of the magic potatoes for each processor; |
182 |
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|
183 |
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sprintf( checkPointMsg, |
184 |
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"Sucessfully wrote node 0's dump configuration.\n"); |
185 |
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MPIcheckPoint(); |
183 |
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nProc = mpiSim->getNumberProcessors(); |
184 |
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potatoes = new int[nProc]; |
185 |
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|
186 |
> |
for (i = 0; i < nProc; i++) |
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potatoes[i] = 0; |
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|
189 |
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for (procIndex = 1; procIndex < mpiSim->getNumberProcessors(); |
190 |
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procIndex++){ |
189 |
> |
outFile << mpiSim->getTotAtoms() << "\n"; |
190 |
|
|
191 |
< |
if( worldRank == 0 ){ |
191 |
> |
outFile << currentTime << ";\t" |
192 |
> |
<< entry_plug->Hmat[0][0] << "\t" |
193 |
> |
<< entry_plug->Hmat[1][0] << "\t" |
194 |
> |
<< entry_plug->Hmat[2][0] << ";\t" |
195 |
> |
|
196 |
> |
<< entry_plug->Hmat[0][1] << "\t" |
197 |
> |
<< entry_plug->Hmat[1][1] << "\t" |
198 |
> |
<< entry_plug->Hmat[2][1] << ";\t" |
199 |
> |
|
200 |
> |
<< entry_plug->Hmat[0][2] << "\t" |
201 |
> |
<< entry_plug->Hmat[1][2] << "\t" |
202 |
> |
<< entry_plug->Hmat[2][2] << ";"; |
203 |
> |
|
204 |
> |
outFile << entry_plug->the_integrator->getAdditionalParameters(); |
205 |
> |
outFile << endl; |
206 |
> |
outFile.flush(); |
207 |
> |
|
208 |
> |
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
209 |
|
|
210 |
< |
mpiErr = MPI_Recv(&nodeAtomsStart,1,MPI_INT,procIndex, |
195 |
< |
TAKE_THIS_TAG,MPI_COMM_WORLD,istatus); |
210 |
> |
// Get the Node number which has this atom; |
211 |
|
|
212 |
< |
mpiErr = MPI_Recv(&nodeAtomsEnd,1,MPI_INT,procIndex, |
198 |
< |
TAKE_THIS_TAG,MPI_COMM_WORLD, istatus); |
212 |
> |
which_node = AtomToProcMap[i]; |
213 |
|
|
214 |
< |
// Make sure where node 0 is writing to, matches where the |
201 |
< |
// receiving node expects it to be. |
202 |
< |
|
203 |
< |
if (masterIndex != nodeAtomsStart){ |
204 |
< |
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)", |
210 |
< |
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++){ |
222 |
< |
|
223 |
< |
mpiErr = MPI_Recv(writeLine,BUFFERSIZE,MPI_CHAR,procIndex, |
224 |
< |
TAKE_THIS_TAG,MPI_COMM_WORLD,istatus ); |
225 |
< |
|
226 |
< |
outFile << writeLine; |
227 |
< |
masterIndex++; |
228 |
< |
} |
229 |
< |
} |
214 |
> |
if (which_node != 0) { |
215 |
|
|
216 |
< |
else if( worldRank == procIndex ){ |
216 |
> |
if (potatoes[which_node] + 3 >= MAXTAG) { |
217 |
> |
// The potato was going to exceed the maximum value, |
218 |
> |
// so wrap this processor potato back to 0: |
219 |
|
|
220 |
< |
nodeAtomsStart = mpiSim->getMyAtomStart(); |
221 |
< |
nodeAtomsEnd = mpiSim->getMyAtomEnd(); |
220 |
> |
potatoes[which_node] = 0; |
221 |
> |
MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD); |
222 |
> |
|
223 |
> |
} |
224 |
|
|
225 |
< |
mpiErr = MPI_Send(&nodeAtomsStart,1,MPI_INT,0,TAKE_THIS_TAG, |
226 |
< |
MPI_COMM_WORLD); |
227 |
< |
mpiErr = MPI_Send(&nodeAtomsEnd,1,MPI_INT,0,TAKE_THIS_TAG, |
228 |
< |
MPI_COMM_WORLD); |
229 |
< |
|
230 |
< |
sendError = -1; |
231 |
< |
mpiErr = MPI_Recv(&sendError,1,MPI_INT,0,TAKE_THIS_TAG, |
232 |
< |
MPI_COMM_WORLD, istatus); |
225 |
> |
myPotato = potatoes[which_node]; |
226 |
> |
|
227 |
> |
MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node, |
228 |
> |
myPotato, MPI_COMM_WORLD, &istatus); |
229 |
> |
|
230 |
> |
strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE); |
231 |
> |
|
232 |
> |
// Null terminate the atomTypeString just in case: |
233 |
|
|
234 |
< |
if (sendError) MPIcheckPoint(); |
234 |
> |
atomTypeString[strlen(atomTypeString) - 1] = '\0'; |
235 |
|
|
236 |
< |
// send current node's configuration line by line. |
236 |
> |
myPotato++; |
237 |
|
|
238 |
< |
for( i=0; i<nAtoms; i++ ){ |
238 |
> |
MPI_Recv(&isDirectional, 1, MPI_INT, which_node, |
239 |
> |
myPotato, MPI_COMM_WORLD, &istatus); |
240 |
> |
|
241 |
> |
myPotato++; |
242 |
|
|
243 |
< |
sprintf( tempBuffer, |
244 |
< |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
245 |
< |
atoms[i]->getType(), |
246 |
< |
atoms[i]->getX(), |
247 |
< |
atoms[i]->getY(), |
248 |
< |
atoms[i]->getZ(), |
249 |
< |
atoms[i]->get_vx(), |
250 |
< |
atoms[i]->get_vy(), |
251 |
< |
atoms[i]->get_vz()); // check here. |
252 |
< |
strcpy( writeLine, tempBuffer ); |
253 |
< |
|
254 |
< |
if( atoms[i]->isDirectional() ){ |
255 |
< |
|
256 |
< |
dAtom = (DirectionalAtom *)atoms[i]; |
257 |
< |
dAtom->getQ( q ); |
258 |
< |
|
259 |
< |
sprintf( tempBuffer, |
260 |
< |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
261 |
< |
q[0], |
262 |
< |
q[1], |
263 |
< |
q[2], |
264 |
< |
q[3], |
265 |
< |
dAtom->getJx(), |
266 |
< |
dAtom->getJy(), |
267 |
< |
dAtom->getJz()); |
268 |
< |
strcat( writeLine, tempBuffer ); |
243 |
> |
if (isDirectional) { |
244 |
> |
MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node, |
245 |
> |
myPotato, MPI_COMM_WORLD, &istatus); |
246 |
> |
} else { |
247 |
> |
MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node, |
248 |
> |
myPotato, MPI_COMM_WORLD, &istatus); |
249 |
> |
} |
250 |
> |
|
251 |
> |
myPotato++; |
252 |
> |
potatoes[which_node] = myPotato; |
253 |
> |
|
254 |
> |
} else { |
255 |
> |
|
256 |
> |
haveError = 0; |
257 |
> |
which_atom = i; |
258 |
> |
local_index=-1; |
259 |
> |
|
260 |
> |
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
261 |
> |
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
262 |
> |
} |
263 |
> |
|
264 |
> |
if (local_index != -1) { |
265 |
> |
|
266 |
> |
atomTypeString = atoms[local_index]->getType(); |
267 |
> |
|
268 |
> |
atoms[local_index]->getPos(pos); |
269 |
> |
atoms[local_index]->getVel(vel); |
270 |
> |
|
271 |
> |
atomData6[0] = pos[0]; |
272 |
> |
atomData6[1] = pos[1]; |
273 |
> |
atomData6[2] = pos[2]; |
274 |
> |
|
275 |
> |
atomData6[3] = vel[0]; |
276 |
> |
atomData6[4] = vel[1]; |
277 |
> |
atomData6[5] = vel[2]; |
278 |
> |
|
279 |
> |
isDirectional = 0; |
280 |
> |
|
281 |
> |
if( atoms[local_index]->isDirectional() ){ |
282 |
> |
|
283 |
> |
isDirectional = 1; |
284 |
> |
|
285 |
> |
dAtom = (DirectionalAtom *)atoms[local_index]; |
286 |
> |
dAtom->getQ( q ); |
287 |
> |
|
288 |
> |
for (int j = 0; j < 6 ; j++) |
289 |
> |
atomData13[j] = atomData6[j]; |
290 |
> |
|
291 |
> |
atomData13[6] = q[0]; |
292 |
> |
atomData13[7] = q[1]; |
293 |
> |
atomData13[8] = q[2]; |
294 |
> |
atomData13[9] = q[3]; |
295 |
> |
|
296 |
> |
atomData13[10] = dAtom->getJx(); |
297 |
> |
atomData13[11] = dAtom->getJy(); |
298 |
> |
atomData13[12] = dAtom->getJz(); |
299 |
> |
} |
300 |
> |
|
301 |
> |
} else { |
302 |
> |
sprintf(painCave.errMsg, |
303 |
> |
"Atom %d not found on processor %d\n", |
304 |
> |
i, worldRank ); |
305 |
> |
haveError= 1; |
306 |
> |
simError(); |
307 |
|
} |
308 |
< |
else |
309 |
< |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
310 |
< |
|
311 |
< |
mpiErr = MPI_Send(writeLine,BUFFERSIZE,MPI_CHAR,0,TAKE_THIS_TAG, |
312 |
< |
MPI_COMM_WORLD); |
308 |
> |
|
309 |
> |
if(haveError) DieDieDie(); |
310 |
> |
|
311 |
> |
// If we've survived to here, format the line: |
312 |
> |
|
313 |
> |
if (!isDirectional) { |
314 |
> |
|
315 |
> |
sprintf( tempBuffer, |
316 |
> |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
317 |
> |
atomTypeString, |
318 |
> |
atomData6[0], |
319 |
> |
atomData6[1], |
320 |
> |
atomData6[2], |
321 |
> |
atomData6[3], |
322 |
> |
atomData6[4], |
323 |
> |
atomData6[5]); |
324 |
> |
|
325 |
> |
strcpy( writeLine, tempBuffer ); |
326 |
> |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
327 |
> |
|
328 |
> |
} else { |
329 |
> |
|
330 |
> |
sprintf( tempBuffer, |
331 |
> |
"%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", |
332 |
> |
atomTypeString, |
333 |
> |
atomData13[0], |
334 |
> |
atomData13[1], |
335 |
> |
atomData13[2], |
336 |
> |
atomData13[3], |
337 |
> |
atomData13[4], |
338 |
> |
atomData13[5], |
339 |
> |
atomData13[6], |
340 |
> |
atomData13[7], |
341 |
> |
atomData13[8], |
342 |
> |
atomData13[9], |
343 |
> |
atomData13[10], |
344 |
> |
atomData13[11], |
345 |
> |
atomData13[12]); |
346 |
> |
|
347 |
> |
strcat( writeLine, tempBuffer ); |
348 |
> |
|
349 |
> |
} |
350 |
> |
|
351 |
> |
outFile << writeLine; |
352 |
> |
outFile.flush(); |
353 |
|
} |
354 |
|
} |
355 |
+ |
|
356 |
+ |
outFile.flush(); |
357 |
+ |
sprintf( checkPointMsg, |
358 |
+ |
"Sucessfully took a dump.\n"); |
359 |
+ |
MPIcheckPoint(); |
360 |
+ |
|
361 |
+ |
} else { |
362 |
+ |
|
363 |
+ |
// worldRank != 0, so I'm a remote node. |
364 |
+ |
|
365 |
+ |
// Set my magic potato to 0: |
366 |
+ |
|
367 |
+ |
myPotato = 0; |
368 |
+ |
|
369 |
+ |
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
370 |
|
|
371 |
< |
sprintf(checkPointMsg,"Node %d sent dump configuration.", |
372 |
< |
procIndex); |
373 |
< |
MPIcheckPoint(); |
374 |
< |
} |
371 |
> |
// Am I the node which has this atom? |
372 |
> |
|
373 |
> |
if (AtomToProcMap[i] == worldRank) { |
374 |
> |
|
375 |
> |
if (myPotato + 3 >= MAXTAG) { |
376 |
> |
|
377 |
> |
// The potato was going to exceed the maximum value, |
378 |
> |
// so wrap this processor potato back to 0 (and block until |
379 |
> |
// node 0 says we can go: |
380 |
> |
|
381 |
> |
MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus); |
382 |
> |
|
383 |
> |
} |
384 |
> |
|
385 |
> |
local_index=-1; |
386 |
> |
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
387 |
> |
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
388 |
> |
} |
389 |
> |
if (local_index != -1) { |
390 |
> |
|
391 |
> |
atomTypeString = atoms[local_index]->getType(); |
392 |
> |
|
393 |
> |
atoms[local_index]->getPos(pos); |
394 |
> |
atoms[local_index]->getVel(vel); |
395 |
> |
|
396 |
> |
atomData6[0] = pos[0]; |
397 |
> |
atomData6[1] = pos[1]; |
398 |
> |
atomData6[2] = pos[2]; |
399 |
> |
|
400 |
> |
atomData6[3] = vel[0]; |
401 |
> |
atomData6[4] = vel[1]; |
402 |
> |
atomData6[5] = vel[2]; |
403 |
> |
|
404 |
> |
isDirectional = 0; |
405 |
> |
|
406 |
> |
if( atoms[local_index]->isDirectional() ){ |
407 |
> |
|
408 |
> |
isDirectional = 1; |
409 |
> |
|
410 |
> |
dAtom = (DirectionalAtom *)atoms[local_index]; |
411 |
> |
dAtom->getQ( q ); |
412 |
> |
|
413 |
> |
for (int j = 0; j < 6 ; j++) |
414 |
> |
atomData13[j] = atomData6[j]; |
415 |
> |
|
416 |
> |
atomData13[6] = q[0]; |
417 |
> |
atomData13[7] = q[1]; |
418 |
> |
atomData13[8] = q[2]; |
419 |
> |
atomData13[9] = q[3]; |
420 |
> |
|
421 |
> |
atomData13[10] = dAtom->getJx(); |
422 |
> |
atomData13[11] = dAtom->getJy(); |
423 |
> |
atomData13[12] = dAtom->getJz(); |
424 |
> |
} |
425 |
> |
|
426 |
> |
} else { |
427 |
> |
sprintf(painCave.errMsg, |
428 |
> |
"Atom %d not found on processor %d\n", |
429 |
> |
i, worldRank ); |
430 |
> |
haveError= 1; |
431 |
> |
simError(); |
432 |
> |
} |
433 |
> |
|
434 |
> |
strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE); |
435 |
> |
|
436 |
> |
// null terminate the string before sending (just in case): |
437 |
> |
MPIatomTypeString[MINIBUFFERSIZE-1] = '\0'; |
438 |
> |
|
439 |
> |
MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0, |
440 |
> |
myPotato, MPI_COMM_WORLD); |
441 |
> |
|
442 |
> |
myPotato++; |
443 |
> |
|
444 |
> |
MPI_Send(&isDirectional, 1, MPI_INT, 0, |
445 |
> |
myPotato, MPI_COMM_WORLD); |
446 |
> |
|
447 |
> |
myPotato++; |
448 |
> |
|
449 |
> |
if (isDirectional) { |
450 |
> |
|
451 |
> |
MPI_Send(atomData13, 13, MPI_DOUBLE, 0, |
452 |
> |
myPotato, MPI_COMM_WORLD); |
453 |
> |
|
454 |
> |
} else { |
455 |
> |
|
456 |
> |
MPI_Send(atomData6, 6, MPI_DOUBLE, 0, |
457 |
> |
myPotato, MPI_COMM_WORLD); |
458 |
> |
} |
459 |
> |
|
460 |
> |
myPotato++; |
461 |
> |
} |
462 |
> |
} |
463 |
> |
|
464 |
> |
sprintf( checkPointMsg, |
465 |
> |
"Sucessfully took a dump.\n"); |
466 |
> |
MPIcheckPoint(); |
467 |
|
|
468 |
+ |
} |
469 |
+ |
|
470 |
|
#endif // is_mpi |
471 |
|
} |
472 |
|
|
473 |
+ |
void DumpWriter::writeFinal(double finalTime){ |
474 |
|
|
475 |
+ |
char finalName[500]; |
476 |
+ |
ofstream finalOut; |
477 |
|
|
296 |
– |
void DumpWriter::writeFinal(){ |
297 |
– |
|
298 |
– |
|
478 |
|
const int BUFFERSIZE = 2000; |
479 |
< |
char tempBuffer[500]; |
479 |
> |
const int MINIBUFFERSIZE = 100; |
480 |
> |
char tempBuffer[BUFFERSIZE]; |
481 |
|
char writeLine[BUFFERSIZE]; |
302 |
– |
|
303 |
– |
char finalName[500]; |
482 |
|
|
305 |
– |
int i; |
483 |
|
double q[4]; |
484 |
|
DirectionalAtom* dAtom; |
308 |
– |
int nAtoms = entry_plug->n_atoms; |
485 |
|
Atom** atoms = entry_plug->atoms; |
486 |
+ |
int i; |
487 |
+ |
#ifdef IS_MPI |
488 |
|
|
489 |
< |
ofstream finalOut; |
490 |
< |
|
489 |
> |
int *potatoes; |
490 |
> |
int myPotato; |
491 |
> |
|
492 |
> |
int nProc; |
493 |
> |
int j, which_node, done, which_atom, local_index; |
494 |
> |
double atomData6[6]; |
495 |
> |
double atomData13[13]; |
496 |
> |
int isDirectional; |
497 |
> |
char* atomTypeString; |
498 |
> |
char MPIatomTypeString[MINIBUFFERSIZE]; |
499 |
> |
|
500 |
> |
#else //is_mpi |
501 |
> |
int nAtoms = entry_plug->n_atoms; |
502 |
> |
#endif //is_mpi |
503 |
> |
|
504 |
> |
double pos[3], vel[3]; |
505 |
> |
|
506 |
|
#ifdef IS_MPI |
507 |
|
if(worldRank == 0 ){ |
508 |
|
#endif // is_mpi |
509 |
< |
|
509 |
> |
|
510 |
|
strcpy( finalName, entry_plug->finalName ); |
511 |
< |
|
511 |
> |
|
512 |
|
finalOut.open( finalName, ios::out | ios::trunc ); |
513 |
|
if( !finalOut ){ |
514 |
|
sprintf( painCave.errMsg, |
517 |
|
painCave.isFatal = 1; |
518 |
|
simError(); |
519 |
|
} |
520 |
< |
|
520 |
> |
|
521 |
|
// finalOut.setf( ios::scientific ); |
522 |
< |
|
522 |
> |
|
523 |
|
#ifdef IS_MPI |
524 |
|
} |
525 |
< |
|
525 |
> |
|
526 |
|
sprintf(checkPointMsg,"Opened file for final configuration\n"); |
527 |
< |
MPIcheckPoint(); |
528 |
< |
|
527 |
> |
MPIcheckPoint(); |
528 |
> |
|
529 |
|
#endif //is_mpi |
530 |
|
|
338 |
– |
|
531 |
|
|
532 |
|
#ifndef IS_MPI |
533 |
< |
|
533 |
> |
|
534 |
|
finalOut << nAtoms << "\n"; |
535 |
< |
|
536 |
< |
finalOut << entry_plug->box_x << "\t" |
537 |
< |
<< entry_plug->box_y << "\t" |
538 |
< |
<< entry_plug->box_z << "\n"; |
539 |
< |
|
535 |
> |
|
536 |
> |
finalOut << finalTime << ";\t" |
537 |
> |
<< entry_plug->Hmat[0][0] << "\t" |
538 |
> |
<< entry_plug->Hmat[1][0] << "\t" |
539 |
> |
<< entry_plug->Hmat[2][0] << ";\t" |
540 |
> |
|
541 |
> |
<< entry_plug->Hmat[0][1] << "\t" |
542 |
> |
<< entry_plug->Hmat[1][1] << "\t" |
543 |
> |
<< entry_plug->Hmat[2][1] << ";\t" |
544 |
> |
|
545 |
> |
<< entry_plug->Hmat[0][2] << "\t" |
546 |
> |
<< entry_plug->Hmat[1][2] << "\t" |
547 |
> |
<< entry_plug->Hmat[2][2] << ";"; |
548 |
> |
|
549 |
> |
//write out additional parameters, such as chi and eta |
550 |
> |
finalOut << entry_plug->the_integrator->getAdditionalParameters(); |
551 |
> |
finalOut << endl; |
552 |
> |
|
553 |
|
for( i=0; i<nAtoms; i++ ){ |
554 |
< |
|
554 |
> |
|
555 |
> |
atoms[i]->getPos(pos); |
556 |
> |
atoms[i]->getVel(vel); |
557 |
> |
|
558 |
|
sprintf( tempBuffer, |
559 |
|
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
560 |
|
atoms[i]->getType(), |
561 |
< |
atoms[i]->getX(), |
562 |
< |
atoms[i]->getY(), |
563 |
< |
atoms[i]->getZ(), |
564 |
< |
atoms[i]->get_vx(), |
565 |
< |
atoms[i]->get_vy(), |
566 |
< |
atoms[i]->get_vz()); |
561 |
> |
pos[0], |
562 |
> |
pos[1], |
563 |
> |
pos[2], |
564 |
> |
vel[0], |
565 |
> |
vel[1], |
566 |
> |
vel[2]); |
567 |
|
strcpy( writeLine, tempBuffer ); |
568 |
|
|
569 |
|
if( atoms[i]->isDirectional() ){ |
570 |
< |
|
570 |
> |
|
571 |
|
dAtom = (DirectionalAtom *)atoms[i]; |
572 |
|
dAtom->getQ( q ); |
573 |
< |
|
573 |
> |
|
574 |
|
sprintf( tempBuffer, |
575 |
|
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
576 |
|
q[0], |
584 |
|
} |
585 |
|
else |
586 |
|
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
587 |
< |
|
587 |
> |
|
588 |
|
finalOut << writeLine; |
589 |
|
} |
590 |
|
finalOut.flush(); |
591 |
+ |
finalOut.close(); |
592 |
|
|
593 |
|
#else // is_mpi |
594 |
|
|
595 |
< |
int masterIndex; |
596 |
< |
int nodeAtomsStart; |
597 |
< |
int nodeAtomsEnd; |
598 |
< |
int mpiErr; |
599 |
< |
int sendError; |
600 |
< |
int procIndex; |
601 |
< |
|
602 |
< |
MPI_Status istatus[MPI_STATUS_SIZE]; |
595 |
> |
/* code to find maximum tag value */ |
596 |
> |
int *tagub, flag, MAXTAG; |
597 |
> |
MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag); |
598 |
> |
if (flag) { |
599 |
> |
MAXTAG = *tagub; |
600 |
> |
} else { |
601 |
> |
MAXTAG = 32767; |
602 |
> |
} |
603 |
|
|
604 |
< |
|
604 |
> |
int haveError; |
605 |
> |
|
606 |
> |
MPI_Status istatus; |
607 |
> |
int *AtomToProcMap = mpiSim->getAtomToProcMap(); |
608 |
> |
|
609 |
|
// write out header and node 0's coordinates |
610 |
|
|
611 |
|
if( worldRank == 0 ){ |
612 |
+ |
|
613 |
+ |
// Node 0 needs a list of the magic potatoes for each processor; |
614 |
+ |
|
615 |
+ |
nProc = mpiSim->getNumberProcessors(); |
616 |
+ |
potatoes = new int[nProc]; |
617 |
+ |
|
618 |
+ |
for (i = 0; i < nProc; i++) |
619 |
+ |
potatoes[i] = 0; |
620 |
+ |
|
621 |
|
finalOut << mpiSim->getTotAtoms() << "\n"; |
622 |
+ |
|
623 |
+ |
finalOut << finalTime << ";\t" |
624 |
+ |
<< entry_plug->Hmat[0][0] << "\t" |
625 |
+ |
<< entry_plug->Hmat[1][0] << "\t" |
626 |
+ |
<< entry_plug->Hmat[2][0] << ";\t" |
627 |
+ |
|
628 |
+ |
<< entry_plug->Hmat[0][1] << "\t" |
629 |
+ |
<< entry_plug->Hmat[1][1] << "\t" |
630 |
+ |
<< entry_plug->Hmat[2][1] << ";\t" |
631 |
+ |
|
632 |
+ |
<< entry_plug->Hmat[0][2] << "\t" |
633 |
+ |
<< entry_plug->Hmat[1][2] << "\t" |
634 |
+ |
<< entry_plug->Hmat[2][2] << ";"; |
635 |
+ |
|
636 |
+ |
finalOut << entry_plug->the_integrator->getAdditionalParameters(); |
637 |
+ |
finalOut << endl; |
638 |
+ |
finalOut.flush(); |
639 |
+ |
|
640 |
+ |
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
641 |
|
|
642 |
< |
finalOut << entry_plug->box_x << "\t" |
402 |
< |
<< entry_plug->box_y << "\t" |
403 |
< |
<< entry_plug->box_z << "\n"; |
404 |
< |
|
405 |
< |
masterIndex = 0; |
406 |
< |
|
407 |
< |
for( i=0; i<nAtoms; i++ ){ |
642 |
> |
// Get the Node number which has this atom; |
643 |
|
|
644 |
< |
sprintf( tempBuffer, |
645 |
< |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
646 |
< |
atoms[i]->getType(), |
412 |
< |
atoms[i]->getX(), |
413 |
< |
atoms[i]->getY(), |
414 |
< |
atoms[i]->getZ(), |
415 |
< |
atoms[i]->get_vx(), |
416 |
< |
atoms[i]->get_vy(), |
417 |
< |
atoms[i]->get_vz()); |
418 |
< |
strcpy( writeLine, tempBuffer ); |
419 |
< |
|
420 |
< |
if( atoms[i]->isDirectional() ){ |
421 |
< |
|
422 |
< |
dAtom = (DirectionalAtom *)atoms[i]; |
423 |
< |
dAtom->getQ( q ); |
424 |
< |
|
425 |
< |
sprintf( tempBuffer, |
426 |
< |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
427 |
< |
q[0], |
428 |
< |
q[1], |
429 |
< |
q[2], |
430 |
< |
q[3], |
431 |
< |
dAtom->getJx(), |
432 |
< |
dAtom->getJy(), |
433 |
< |
dAtom->getJz()); |
434 |
< |
strcat( writeLine, tempBuffer ); |
435 |
< |
} |
436 |
< |
else |
437 |
< |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
438 |
< |
|
439 |
< |
finalOut << writeLine; |
440 |
< |
masterIndex++; |
441 |
< |
} |
442 |
< |
finalOut.flush(); |
443 |
< |
} |
444 |
< |
|
445 |
< |
for (procIndex = 1; procIndex < mpiSim->getNumberProcessors(); |
446 |
< |
procIndex++){ |
644 |
> |
which_node = AtomToProcMap[i]; |
645 |
> |
|
646 |
> |
if (which_node != 0) { |
647 |
|
|
648 |
< |
if( worldRank == 0 ){ |
649 |
< |
|
650 |
< |
mpiErr = MPI_Recv(&nodeAtomsStart,1,MPI_INT,procIndex, |
451 |
< |
TAKE_THIS_TAG,MPI_COMM_WORLD,istatus); |
648 |
> |
if (potatoes[which_node] + 3 >= MAXTAG) { |
649 |
> |
// The potato was going to exceed the maximum value, |
650 |
> |
// so wrap this processor potato back to 0: |
651 |
|
|
652 |
< |
mpiErr = MPI_Recv(&nodeAtomsEnd,1,MPI_INT,procIndex, |
653 |
< |
TAKE_THIS_TAG,MPI_COMM_WORLD, istatus); |
654 |
< |
|
655 |
< |
// Make sure where node 0 is writing to, matches where the |
457 |
< |
// receiving node expects it to be. |
458 |
< |
|
459 |
< |
if (masterIndex != nodeAtomsStart){ |
460 |
< |
sendError = 1; |
461 |
< |
mpiErr = MPI_Send(&sendError,1,MPI_INT,procIndex,TAKE_THIS_TAG, |
462 |
< |
MPI_COMM_WORLD); |
463 |
< |
sprintf(painCave.errMsg, |
464 |
< |
"DumpWriter error: atoms start index (%d) for " |
465 |
< |
"node %d not equal to master index (%d)", |
466 |
< |
nodeAtomsStart,procIndex,masterIndex ); |
467 |
< |
painCave.isFatal = 1; |
468 |
< |
simError(); |
469 |
< |
} |
470 |
< |
|
471 |
< |
sendError = 0; |
472 |
< |
mpiErr = MPI_Send(&sendError,1,MPI_INT,procIndex,TAKE_THIS_TAG, |
473 |
< |
MPI_COMM_WORLD); |
652 |
> |
potatoes[which_node] = 0; |
653 |
> |
MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD); |
654 |
> |
|
655 |
> |
} |
656 |
|
|
657 |
< |
// recieve the nodes writeLines |
657 |
> |
myPotato = potatoes[which_node]; |
658 |
> |
|
659 |
> |
MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node, |
660 |
> |
myPotato, MPI_COMM_WORLD, &istatus); |
661 |
> |
|
662 |
> |
strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE); |
663 |
> |
|
664 |
> |
// Null terminate the atomTypeString just in case: |
665 |
|
|
666 |
< |
for ( i = nodeAtomsStart; i <= nodeAtomsEnd; i++){ |
478 |
< |
|
479 |
< |
mpiErr = MPI_Recv(writeLine,BUFFERSIZE,MPI_CHAR,procIndex, |
480 |
< |
TAKE_THIS_TAG,MPI_COMM_WORLD,istatus ); |
666 |
> |
atomTypeString[strlen(atomTypeString) - 1] = '\0'; |
667 |
|
|
668 |
< |
finalOut << writeLine; |
483 |
< |
masterIndex++; |
484 |
< |
} |
668 |
> |
myPotato++; |
669 |
|
|
670 |
< |
finalOut.flush(); |
671 |
< |
} |
670 |
> |
MPI_Recv(&isDirectional, 1, MPI_INT, which_node, |
671 |
> |
myPotato, MPI_COMM_WORLD, &istatus); |
672 |
> |
|
673 |
> |
myPotato++; |
674 |
|
|
675 |
< |
else if( worldRank == procIndex ){ |
675 |
> |
if (isDirectional) { |
676 |
> |
MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node, |
677 |
> |
myPotato, MPI_COMM_WORLD, &istatus); |
678 |
> |
} else { |
679 |
> |
MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node, |
680 |
> |
myPotato, MPI_COMM_WORLD, &istatus); |
681 |
> |
} |
682 |
> |
|
683 |
> |
myPotato++; |
684 |
> |
potatoes[which_node] = myPotato; |
685 |
|
|
686 |
< |
nodeAtomsStart = mpiSim->getMyAtomStart(); |
687 |
< |
nodeAtomsEnd = mpiSim->getMyAtomEnd(); |
688 |
< |
|
689 |
< |
mpiErr = MPI_Send(&nodeAtomsStart,1,MPI_INT,0,TAKE_THIS_TAG, |
690 |
< |
MPI_COMM_WORLD); |
691 |
< |
mpiErr = MPI_Send(&nodeAtomsEnd,1,MPI_INT,0,TAKE_THIS_TAG, |
692 |
< |
MPI_COMM_WORLD); |
693 |
< |
|
694 |
< |
mpiErr = MPI_Recv(&sendError,1,MPI_INT,0,TAKE_THIS_TAG, |
695 |
< |
MPI_COMM_WORLD, istatus); |
696 |
< |
if (sendError) MPIcheckPoint(); |
697 |
< |
|
698 |
< |
// send current node's configuration line by line. |
686 |
> |
} else { |
687 |
> |
|
688 |
> |
haveError = 0; |
689 |
> |
which_atom = i; |
690 |
> |
local_index=-1; |
691 |
> |
|
692 |
> |
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
693 |
> |
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
694 |
> |
} |
695 |
> |
|
696 |
> |
if (local_index != -1) { |
697 |
> |
|
698 |
> |
atomTypeString = atoms[local_index]->getType(); |
699 |
|
|
700 |
< |
for( i=0; i<nAtoms; i++ ){ |
701 |
< |
|
702 |
< |
sprintf( tempBuffer, |
703 |
< |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
704 |
< |
atoms[i]->getType(), |
705 |
< |
atoms[i]->getX(), |
706 |
< |
atoms[i]->getY(), |
707 |
< |
atoms[i]->getZ(), |
708 |
< |
atoms[i]->get_vx(), |
709 |
< |
atoms[i]->get_vy(), |
710 |
< |
atoms[i]->get_vz()); |
711 |
< |
strcpy( writeLine, tempBuffer ); |
712 |
< |
|
713 |
< |
if( atoms[i]->isDirectional() ){ |
714 |
< |
|
715 |
< |
dAtom = (DirectionalAtom *)atoms[i]; |
716 |
< |
dAtom->getQ( q ); |
717 |
< |
|
718 |
< |
sprintf( tempBuffer, |
719 |
< |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
720 |
< |
q[0], |
721 |
< |
q[1], |
722 |
< |
q[2], |
723 |
< |
q[3], |
724 |
< |
dAtom->getJx(), |
725 |
< |
dAtom->getJy(), |
726 |
< |
dAtom->getJz()); |
727 |
< |
strcat( writeLine, tempBuffer ); |
700 |
> |
atoms[local_index]->getPos(pos); |
701 |
> |
atoms[local_index]->getVel(vel); |
702 |
> |
|
703 |
> |
atomData6[0] = pos[0]; |
704 |
> |
atomData6[1] = pos[1]; |
705 |
> |
atomData6[2] = pos[2]; |
706 |
> |
|
707 |
> |
atomData6[3] = vel[0]; |
708 |
> |
atomData6[4] = vel[1]; |
709 |
> |
atomData6[5] = vel[2]; |
710 |
> |
|
711 |
> |
isDirectional = 0; |
712 |
> |
|
713 |
> |
if( atoms[local_index]->isDirectional() ){ |
714 |
> |
|
715 |
> |
isDirectional = 1; |
716 |
> |
|
717 |
> |
dAtom = (DirectionalAtom *)atoms[local_index]; |
718 |
> |
dAtom->getQ( q ); |
719 |
> |
|
720 |
> |
for (int j = 0; j < 6 ; j++) |
721 |
> |
atomData13[j] = atomData6[j]; |
722 |
> |
|
723 |
> |
atomData13[6] = q[0]; |
724 |
> |
atomData13[7] = q[1]; |
725 |
> |
atomData13[8] = q[2]; |
726 |
> |
atomData13[9] = q[3]; |
727 |
> |
|
728 |
> |
atomData13[10] = dAtom->getJx(); |
729 |
> |
atomData13[11] = dAtom->getJy(); |
730 |
> |
atomData13[12] = dAtom->getJz(); |
731 |
> |
} |
732 |
> |
|
733 |
> |
} else { |
734 |
> |
sprintf(painCave.errMsg, |
735 |
> |
"Atom %d not found on processor %d\n", |
736 |
> |
i, worldRank ); |
737 |
> |
haveError= 1; |
738 |
> |
simError(); |
739 |
|
} |
740 |
< |
else |
741 |
< |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
742 |
< |
|
743 |
< |
mpiErr = MPI_Send(writeLine,BUFFERSIZE,MPI_CHAR,0,TAKE_THIS_TAG, |
744 |
< |
MPI_COMM_WORLD); |
740 |
> |
|
741 |
> |
if(haveError) DieDieDie(); |
742 |
> |
|
743 |
> |
// If we've survived to here, format the line: |
744 |
> |
|
745 |
> |
if (!isDirectional) { |
746 |
> |
|
747 |
> |
sprintf( tempBuffer, |
748 |
> |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
749 |
> |
atomTypeString, |
750 |
> |
atomData6[0], |
751 |
> |
atomData6[1], |
752 |
> |
atomData6[2], |
753 |
> |
atomData6[3], |
754 |
> |
atomData6[4], |
755 |
> |
atomData6[5]); |
756 |
> |
|
757 |
> |
strcpy( writeLine, tempBuffer ); |
758 |
> |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
759 |
> |
|
760 |
> |
} else { |
761 |
> |
|
762 |
> |
sprintf( tempBuffer, |
763 |
> |
"%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", |
764 |
> |
atomTypeString, |
765 |
> |
atomData13[0], |
766 |
> |
atomData13[1], |
767 |
> |
atomData13[2], |
768 |
> |
atomData13[3], |
769 |
> |
atomData13[4], |
770 |
> |
atomData13[5], |
771 |
> |
atomData13[6], |
772 |
> |
atomData13[7], |
773 |
> |
atomData13[8], |
774 |
> |
atomData13[9], |
775 |
> |
atomData13[10], |
776 |
> |
atomData13[11], |
777 |
> |
atomData13[12]); |
778 |
> |
|
779 |
> |
strcat( writeLine, tempBuffer ); |
780 |
> |
|
781 |
> |
} |
782 |
> |
|
783 |
> |
finalOut << writeLine; |
784 |
> |
finalOut.flush(); |
785 |
|
} |
786 |
|
} |
787 |
+ |
|
788 |
+ |
finalOut.flush(); |
789 |
+ |
sprintf( checkPointMsg, |
790 |
+ |
"Sucessfully took a dump.\n"); |
791 |
+ |
MPIcheckPoint(); |
792 |
+ |
|
793 |
+ |
} else { |
794 |
+ |
|
795 |
+ |
// worldRank != 0, so I'm a remote node. |
796 |
+ |
|
797 |
+ |
// Set my magic potato to 0: |
798 |
+ |
|
799 |
+ |
myPotato = 0; |
800 |
+ |
|
801 |
+ |
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
802 |
|
|
803 |
< |
sprintf(checkPointMsg,"Node %d sent dump configuration.", |
804 |
< |
procIndex); |
805 |
< |
MPIcheckPoint(); |
545 |
< |
} |
803 |
> |
// Am I the node which has this atom? |
804 |
> |
|
805 |
> |
if (AtomToProcMap[i] == worldRank) { |
806 |
|
|
807 |
< |
if( worldRank == 0 ) finalOut.close(); |
807 |
> |
if (myPotato + 3 >= MAXTAG) { |
808 |
|
|
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(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus); |
814 |
+ |
|
815 |
+ |
} |
816 |
+ |
|
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 |
+ |
atoms[local_index]->getPos(pos); |
826 |
+ |
atoms[local_index]->getVel(vel); |
827 |
+ |
|
828 |
+ |
atomData6[0] = pos[0]; |
829 |
+ |
atomData6[1] = pos[1]; |
830 |
+ |
atomData6[2] = pos[2]; |
831 |
+ |
|
832 |
+ |
atomData6[3] = vel[0]; |
833 |
+ |
atomData6[4] = vel[1]; |
834 |
+ |
atomData6[5] = vel[2]; |
835 |
+ |
|
836 |
+ |
isDirectional = 0; |
837 |
+ |
|
838 |
+ |
if( atoms[local_index]->isDirectional() ){ |
839 |
+ |
|
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 |
+ |
atomData13[10] = dAtom->getJx(); |
854 |
+ |
atomData13[11] = dAtom->getJy(); |
855 |
+ |
atomData13[12] = dAtom->getJz(); |
856 |
+ |
} |
857 |
+ |
|
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 |
+ |
strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE); |
867 |
+ |
|
868 |
+ |
// null terminate the string before sending (just in case): |
869 |
+ |
MPIatomTypeString[MINIBUFFERSIZE-1] = '\0'; |
870 |
+ |
|
871 |
+ |
MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0, |
872 |
+ |
myPotato, MPI_COMM_WORLD); |
873 |
+ |
|
874 |
+ |
myPotato++; |
875 |
+ |
|
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 |
+ |
} |
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 |
|
} |
905 |
+ |
|
906 |
+ |
|
907 |
+ |
|
908 |
+ |
#ifdef IS_MPI |
909 |
+ |
|
910 |
+ |
// a couple of functions to let us escape the write loop |
911 |
+ |
|
912 |
+ |
void dWrite::DieDieDie( void ){ |
913 |
+ |
|
914 |
+ |
MPI_Finalize(); |
915 |
+ |
exit (0); |
916 |
+ |
} |
917 |
+ |
|
918 |
+ |
#endif //is_mpi |