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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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#include <algorithm> |
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#include <utility> |
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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{ |
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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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|
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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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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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dumpFile.open(entry_plug->sampleName, ios::out | ios::trunc ); |
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|
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if( !dumpFile ){ |
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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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entry_plug->sampleName); |
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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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|
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#ifdef IS_MPI |
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} |
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|
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//sort the local atoms by global index |
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sortByGlobalIndex(); |
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|
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sprintf( checkPointMsg, |
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"Sucessfully opened output file for dumping.\n"); |
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MPIcheckPoint(); |
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if(worldRank == 0 ){ |
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#endif // is_mpi |
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|
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outFile.close(); |
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dumpFile.close(); |
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|
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#ifdef IS_MPI |
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} |
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#endif // is_mpi |
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} |
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|
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void DumpWriter::writeDump( double currentTime ){ |
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#ifdef IS_MPI |
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|
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/** |
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* A hook function to load balancing |
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*/ |
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|
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void DumpWriter::update(){ |
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sortByGlobalIndex(); |
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} |
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|
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const int BUFFERSIZE = 2000; |
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char tempBuffer[BUFFERSIZE]; |
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char writeLine[BUFFERSIZE]; |
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/** |
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* Auxiliary sorting function |
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*/ |
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|
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bool indexSortingCriterion(const pair<int, int>& p1, const pair<int, int>& p2){ |
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return p1.second < p2.second; |
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} |
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|
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int i; |
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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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/** |
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* Sorting the local index by global index |
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*/ |
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|
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void DumpWriter::sortByGlobalIndex(){ |
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Atom** atoms = entry_plug->atoms; |
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|
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|
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indexArray.clear(); |
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|
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for(int i = 0; i < mpiSim->getMyNlocal();i++) |
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indexArray.push_back(make_pair(i, atoms[i]->getGlobalIndex())); |
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|
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sort(indexArray.begin(), indexArray.end(), indexSortingCriterion); |
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} |
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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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|
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for( i=0; i<nAtoms; i++ ){ |
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|
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#endif |
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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 ); |
102 |
> |
void DumpWriter::writeDump(double currentTime){ |
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|
104 |
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if( atoms[i]->isDirectional() ){ |
105 |
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|
106 |
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dAtom = (DirectionalAtom *)atoms[i]; |
107 |
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dAtom->getQ( q ); |
108 |
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|
109 |
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sprintf( tempBuffer, |
110 |
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"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
111 |
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q[0], |
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q[1], |
113 |
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q[2], |
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q[3], |
115 |
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dAtom->getJx(), |
116 |
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dAtom->getJy(), |
114 |
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dAtom->getJz()); |
115 |
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strcat( writeLine, tempBuffer ); |
104 |
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ofstream finalOut; |
105 |
> |
vector<ofstream*> fileStreams; |
106 |
> |
|
107 |
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#ifdef IS_MPI |
108 |
> |
if(worldRank == 0 ){ |
109 |
> |
#endif |
110 |
> |
finalOut.open( entry_plug->finalName, ios::out | ios::trunc ); |
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if( !finalOut ){ |
112 |
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sprintf( painCave.errMsg, |
113 |
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"Could not open \"%s\" for final dump output.\n", |
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entry_plug->finalName ); |
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painCave.isFatal = 1; |
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simError(); |
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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" ); |
119 |
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|
120 |
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outFile << writeLine; |
118 |
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#ifdef IS_MPI |
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} |
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outFile.flush(); |
120 |
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#endif // is_mpi |
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|
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#else // is_mpi |
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fileStreams.push_back(&finalOut); |
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fileStreams.push_back(&dumpFile); |
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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; |
132 |
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|
133 |
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MPI_Status istatus[MPI_STATUS_SIZE]; |
125 |
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writeFrame(fileStreams, currentTime); |
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|
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|
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// write out header and node 0's coordinates |
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#ifdef IS_MPI |
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finalOut.close(); |
129 |
> |
#endif |
130 |
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|
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} |
132 |
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|
133 |
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if( worldRank == 0 ){ |
139 |
< |
outFile << mpiSim->getTotAtoms() << "\n"; |
140 |
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|
141 |
< |
outFile << currentTime << "\t" |
142 |
< |
<< entry_plug->box_x << "\t" |
143 |
< |
<< entry_plug->box_y << "\t" |
144 |
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<< entry_plug->box_z << "\n"; |
133 |
> |
void DumpWriter::writeFinal(double currentTime){ |
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|
135 |
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masterIndex = 0; |
136 |
< |
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 |
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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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|
165 |
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sprintf( tempBuffer, |
166 |
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"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
167 |
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q[0], |
168 |
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q[1], |
169 |
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q[2], |
170 |
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q[3], |
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dAtom->getJx(), |
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dAtom->getJy(), |
173 |
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dAtom->getJz()); |
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strcat( writeLine, tempBuffer ); |
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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" ); |
178 |
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|
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outFile << writeLine; |
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masterIndex++; |
181 |
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} |
182 |
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outFile.flush(); |
183 |
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} |
135 |
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ofstream finalOut; |
136 |
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vector<ofstream*> fileStreams; |
137 |
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|
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sprintf( checkPointMsg, |
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"Sucessfully wrote node 0's dump configuration.\n"); |
140 |
< |
MPIcheckPoint(); |
188 |
< |
|
189 |
< |
for (procIndex = 1; procIndex < mpiSim->getNumberProcessors(); |
190 |
< |
procIndex++){ |
138 |
> |
#ifdef IS_MPI |
139 |
> |
if(worldRank == 0 ){ |
140 |
> |
#endif // is_mpi |
141 |
|
|
142 |
< |
if( worldRank == 0 ){ |
193 |
< |
|
194 |
< |
mpiErr = MPI_Recv(&nodeAtomsStart,1,MPI_INT,procIndex, |
195 |
< |
TAKE_THIS_TAG,MPI_COMM_WORLD,istatus); |
196 |
< |
|
197 |
< |
mpiErr = MPI_Recv(&nodeAtomsEnd,1,MPI_INT,procIndex, |
198 |
< |
TAKE_THIS_TAG,MPI_COMM_WORLD, istatus); |
199 |
< |
|
200 |
< |
// 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 |
< |
} |
142 |
> |
finalOut.open( entry_plug->finalName, ios::out | ios::trunc ); |
143 |
|
|
144 |
< |
else if( worldRank == procIndex ){ |
145 |
< |
|
146 |
< |
nodeAtomsStart = mpiSim->getMyAtomStart(); |
147 |
< |
nodeAtomsEnd = mpiSim->getMyAtomEnd(); |
148 |
< |
|
149 |
< |
mpiErr = MPI_Send(&nodeAtomsStart,1,MPI_INT,0,TAKE_THIS_TAG, |
237 |
< |
MPI_COMM_WORLD); |
238 |
< |
mpiErr = MPI_Send(&nodeAtomsEnd,1,MPI_INT,0,TAKE_THIS_TAG, |
239 |
< |
MPI_COMM_WORLD); |
240 |
< |
|
241 |
< |
sendError = -1; |
242 |
< |
mpiErr = MPI_Recv(&sendError,1,MPI_INT,0,TAKE_THIS_TAG, |
243 |
< |
MPI_COMM_WORLD, istatus); |
244 |
< |
|
245 |
< |
if (sendError) MPIcheckPoint(); |
246 |
< |
|
247 |
< |
// send current node's configuration line by line. |
248 |
< |
|
249 |
< |
for( i=0; i<nAtoms; i++ ){ |
250 |
< |
|
251 |
< |
sprintf( tempBuffer, |
252 |
< |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
253 |
< |
atoms[i]->getType(), |
254 |
< |
atoms[i]->getX(), |
255 |
< |
atoms[i]->getY(), |
256 |
< |
atoms[i]->getZ(), |
257 |
< |
atoms[i]->get_vx(), |
258 |
< |
atoms[i]->get_vy(), |
259 |
< |
atoms[i]->get_vz()); // check here. |
260 |
< |
strcpy( writeLine, tempBuffer ); |
261 |
< |
|
262 |
< |
if( atoms[i]->isDirectional() ){ |
263 |
< |
|
264 |
< |
dAtom = (DirectionalAtom *)atoms[i]; |
265 |
< |
dAtom->getQ( q ); |
266 |
< |
|
267 |
< |
sprintf( tempBuffer, |
268 |
< |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
269 |
< |
q[0], |
270 |
< |
q[1], |
271 |
< |
q[2], |
272 |
< |
q[3], |
273 |
< |
dAtom->getJx(), |
274 |
< |
dAtom->getJy(), |
275 |
< |
dAtom->getJz()); |
276 |
< |
strcat( writeLine, tempBuffer ); |
277 |
< |
} |
278 |
< |
else |
279 |
< |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
280 |
< |
|
281 |
< |
mpiErr = MPI_Send(writeLine,BUFFERSIZE,MPI_CHAR,0,TAKE_THIS_TAG, |
282 |
< |
MPI_COMM_WORLD); |
283 |
< |
} |
144 |
> |
if( !finalOut ){ |
145 |
> |
sprintf( painCave.errMsg, |
146 |
> |
"Could not open \"%s\" for final dump output.\n", |
147 |
> |
entry_plug->finalName ); |
148 |
> |
painCave.isFatal = 1; |
149 |
> |
simError(); |
150 |
|
} |
151 |
< |
|
152 |
< |
sprintf(checkPointMsg,"Node %d sent dump configuration.", |
287 |
< |
procIndex); |
288 |
< |
MPIcheckPoint(); |
151 |
> |
|
152 |
> |
#ifdef IS_MPI |
153 |
|
} |
290 |
– |
|
154 |
|
#endif // is_mpi |
155 |
+ |
|
156 |
+ |
fileStreams.push_back(&finalOut); |
157 |
+ |
writeFrame(fileStreams, currentTime); |
158 |
+ |
|
159 |
+ |
#ifdef IS_MPI |
160 |
+ |
finalOut.close(); |
161 |
+ |
#endif |
162 |
+ |
|
163 |
|
} |
164 |
|
|
165 |
+ |
void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){ |
166 |
|
|
167 |
+ |
const int BUFFERSIZE = 2000; |
168 |
+ |
const int MINIBUFFERSIZE = 100; |
169 |
|
|
170 |
< |
void DumpWriter::writeFinal(){ |
170 |
> |
char tempBuffer[BUFFERSIZE]; |
171 |
> |
char writeLine[BUFFERSIZE]; |
172 |
|
|
173 |
+ |
int i, k; |
174 |
|
|
175 |
< |
const int BUFFERSIZE = 2000; |
300 |
< |
char tempBuffer[500]; |
301 |
< |
char writeLine[BUFFERSIZE]; |
175 |
> |
#ifdef IS_MPI |
176 |
|
|
177 |
< |
char finalName[500]; |
177 |
> |
/********************************************************************* |
178 |
> |
* Documentation? You want DOCUMENTATION? |
179 |
> |
* |
180 |
> |
* Why all the potatoes below? |
181 |
> |
* |
182 |
> |
* To make a long story short, the original version of DumpWriter |
183 |
> |
* worked in the most inefficient way possible. Node 0 would |
184 |
> |
* poke each of the node for an individual atom's formatted data |
185 |
> |
* as node 0 worked its way down the global index. This was particularly |
186 |
> |
* inefficient since the method blocked all processors at every atom |
187 |
> |
* (and did it twice!). |
188 |
> |
* |
189 |
> |
* An intermediate version of DumpWriter could be described from Node |
190 |
> |
* zero's perspective as follows: |
191 |
> |
* |
192 |
> |
* 1) Have 100 of your friends stand in a circle. |
193 |
> |
* 2) When you say go, have all of them start tossing potatoes at |
194 |
> |
* you (one at a time). |
195 |
> |
* 3) Catch the potatoes. |
196 |
> |
* |
197 |
> |
* It was an improvement, but MPI has buffers and caches that could |
198 |
> |
* best be described in this analogy as "potato nets", so there's no |
199 |
> |
* need to block the processors atom-by-atom. |
200 |
> |
* |
201 |
> |
* This new and improved DumpWriter works in an even more efficient |
202 |
> |
* way: |
203 |
> |
* |
204 |
> |
* 1) Have 100 of your friend stand in a circle. |
205 |
> |
* 2) When you say go, have them start tossing 5-pound bags of |
206 |
> |
* potatoes at you. |
207 |
> |
* 3) Once you've caught a friend's bag of potatoes, |
208 |
> |
* toss them a spud to let them know they can toss another bag. |
209 |
> |
* |
210 |
> |
* How's THAT for documentation? |
211 |
> |
* |
212 |
> |
*********************************************************************/ |
213 |
|
|
214 |
< |
int i; |
214 |
> |
int *potatoes; |
215 |
> |
int myPotato; |
216 |
> |
|
217 |
> |
int nProc; |
218 |
> |
int j, which_node, done, which_atom, local_index, currentIndex; |
219 |
> |
double atomData6[6]; |
220 |
> |
double atomData13[13]; |
221 |
> |
int isDirectional; |
222 |
> |
char* atomTypeString; |
223 |
> |
char MPIatomTypeString[MINIBUFFERSIZE]; |
224 |
> |
|
225 |
> |
#else //is_mpi |
226 |
> |
int nAtoms = entry_plug->n_atoms; |
227 |
> |
#endif //is_mpi |
228 |
> |
|
229 |
|
double q[4]; |
230 |
|
DirectionalAtom* dAtom; |
308 |
– |
int nAtoms = entry_plug->n_atoms; |
231 |
|
Atom** atoms = entry_plug->atoms; |
232 |
+ |
double pos[3], vel[3]; |
233 |
+ |
|
234 |
+ |
#ifndef IS_MPI |
235 |
|
|
236 |
< |
ofstream finalOut; |
237 |
< |
|
238 |
< |
#ifdef IS_MPI |
239 |
< |
if(worldRank == 0 ){ |
240 |
< |
#endif // is_mpi |
241 |
< |
|
242 |
< |
strcpy( finalName, entry_plug->finalName ); |
243 |
< |
|
244 |
< |
finalOut.open( finalName, ios::out | ios::trunc ); |
245 |
< |
if( !finalOut ){ |
246 |
< |
sprintf( painCave.errMsg, |
247 |
< |
"Could not open \"%s\" for final dump output.\n", |
248 |
< |
finalName ); |
249 |
< |
painCave.isFatal = 1; |
250 |
< |
simError(); |
251 |
< |
} |
252 |
< |
|
253 |
< |
// finalOut.setf( ios::scientific ); |
329 |
< |
|
330 |
< |
#ifdef IS_MPI |
236 |
> |
for(k = 0; k < outFile.size(); k++){ |
237 |
> |
*outFile[k] << nAtoms << "\n"; |
238 |
> |
|
239 |
> |
*outFile[k] << currentTime << ";\t" |
240 |
> |
<< entry_plug->Hmat[0][0] << "\t" |
241 |
> |
<< entry_plug->Hmat[1][0] << "\t" |
242 |
> |
<< entry_plug->Hmat[2][0] << ";\t" |
243 |
> |
|
244 |
> |
<< entry_plug->Hmat[0][1] << "\t" |
245 |
> |
<< entry_plug->Hmat[1][1] << "\t" |
246 |
> |
<< entry_plug->Hmat[2][1] << ";\t" |
247 |
> |
|
248 |
> |
<< entry_plug->Hmat[0][2] << "\t" |
249 |
> |
<< entry_plug->Hmat[1][2] << "\t" |
250 |
> |
<< entry_plug->Hmat[2][2] << ";"; |
251 |
> |
|
252 |
> |
//write out additional parameters, such as chi and eta |
253 |
> |
*outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl; |
254 |
|
} |
255 |
|
|
256 |
< |
sprintf(checkPointMsg,"Opened file for final configuration\n"); |
334 |
< |
MPIcheckPoint(); |
335 |
< |
|
336 |
< |
#endif //is_mpi |
256 |
> |
for( i=0; i<nAtoms; i++ ){ |
257 |
|
|
258 |
< |
|
258 |
> |
atoms[i]->getPos(pos); |
259 |
> |
atoms[i]->getVel(vel); |
260 |
|
|
340 |
– |
#ifndef IS_MPI |
341 |
– |
|
342 |
– |
finalOut << nAtoms << "\n"; |
343 |
– |
|
344 |
– |
finalOut << entry_plug->box_x << "\t" |
345 |
– |
<< entry_plug->box_y << "\t" |
346 |
– |
<< entry_plug->box_z << "\n"; |
347 |
– |
|
348 |
– |
for( i=0; i<nAtoms; i++ ){ |
349 |
– |
|
261 |
|
sprintf( tempBuffer, |
262 |
|
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
263 |
|
atoms[i]->getType(), |
264 |
< |
atoms[i]->getX(), |
265 |
< |
atoms[i]->getY(), |
266 |
< |
atoms[i]->getZ(), |
267 |
< |
atoms[i]->get_vx(), |
268 |
< |
atoms[i]->get_vy(), |
269 |
< |
atoms[i]->get_vz()); |
264 |
> |
pos[0], |
265 |
> |
pos[1], |
266 |
> |
pos[2], |
267 |
> |
vel[0], |
268 |
> |
vel[1], |
269 |
> |
vel[2]); |
270 |
|
strcpy( writeLine, tempBuffer ); |
271 |
|
|
272 |
|
if( atoms[i]->isDirectional() ){ |
273 |
< |
|
273 |
> |
|
274 |
|
dAtom = (DirectionalAtom *)atoms[i]; |
275 |
|
dAtom->getQ( q ); |
276 |
< |
|
276 |
> |
|
277 |
|
sprintf( tempBuffer, |
278 |
|
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
279 |
|
q[0], |
287 |
|
} |
288 |
|
else |
289 |
|
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
290 |
< |
|
291 |
< |
finalOut << writeLine; |
290 |
> |
|
291 |
> |
for(k = 0; k < outFile.size(); k++) |
292 |
> |
*outFile[k] << writeLine; |
293 |
|
} |
382 |
– |
finalOut.flush(); |
294 |
|
|
295 |
|
#else // is_mpi |
296 |
|
|
297 |
< |
int masterIndex; |
298 |
< |
int nodeAtomsStart; |
299 |
< |
int nodeAtomsEnd; |
300 |
< |
int mpiErr; |
301 |
< |
int sendError; |
302 |
< |
int procIndex; |
303 |
< |
|
304 |
< |
MPI_Status istatus[MPI_STATUS_SIZE]; |
297 |
> |
/* code to find maximum tag value */ |
298 |
> |
|
299 |
> |
int *tagub, flag, MAXTAG; |
300 |
> |
MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag); |
301 |
> |
if (flag) { |
302 |
> |
MAXTAG = *tagub; |
303 |
> |
} else { |
304 |
> |
MAXTAG = 32767; |
305 |
> |
} |
306 |
|
|
307 |
< |
|
307 |
> |
int haveError; |
308 |
> |
|
309 |
> |
MPI_Status istatus; |
310 |
> |
int *AtomToProcMap = mpiSim->getAtomToProcMap(); |
311 |
> |
|
312 |
|
// write out header and node 0's coordinates |
313 |
|
|
314 |
|
if( worldRank == 0 ){ |
315 |
< |
finalOut << mpiSim->getTotAtoms() << "\n"; |
316 |
< |
|
317 |
< |
finalOut << entry_plug->box_x << "\t" |
318 |
< |
<< entry_plug->box_y << "\t" |
319 |
< |
<< entry_plug->box_z << "\n"; |
315 |
> |
|
316 |
> |
// Node 0 needs a list of the magic potatoes for each processor; |
317 |
> |
|
318 |
> |
nProc = mpiSim->getNumberProcessors(); |
319 |
> |
potatoes = new int[nProc]; |
320 |
> |
|
321 |
> |
//write out the comment lines |
322 |
> |
for (i = 0; i < nProc; i++) |
323 |
> |
potatoes[i] = 0; |
324 |
|
|
325 |
< |
masterIndex = 0; |
326 |
< |
|
327 |
< |
for( i=0; i<nAtoms; i++ ){ |
325 |
> |
for(k = 0; k < outFile.size(); k++){ |
326 |
> |
*outFile[k] << mpiSim->getTotAtoms() << "\n"; |
327 |
> |
|
328 |
> |
*outFile[k] << currentTime << ";\t" |
329 |
> |
<< entry_plug->Hmat[0][0] << "\t" |
330 |
> |
<< entry_plug->Hmat[1][0] << "\t" |
331 |
> |
<< entry_plug->Hmat[2][0] << ";\t" |
332 |
> |
|
333 |
> |
<< entry_plug->Hmat[0][1] << "\t" |
334 |
> |
<< entry_plug->Hmat[1][1] << "\t" |
335 |
> |
<< entry_plug->Hmat[2][1] << ";\t" |
336 |
> |
|
337 |
> |
<< entry_plug->Hmat[0][2] << "\t" |
338 |
> |
<< entry_plug->Hmat[1][2] << "\t" |
339 |
> |
<< entry_plug->Hmat[2][2] << ";"; |
340 |
> |
|
341 |
> |
*outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl; |
342 |
> |
} |
343 |
> |
|
344 |
> |
currentIndex = 0; |
345 |
> |
|
346 |
> |
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
347 |
|
|
348 |
< |
sprintf( tempBuffer, |
349 |
< |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
350 |
< |
atoms[i]->getType(), |
351 |
< |
atoms[i]->getX(), |
352 |
< |
atoms[i]->getY(), |
353 |
< |
atoms[i]->getZ(), |
354 |
< |
atoms[i]->get_vx(), |
355 |
< |
atoms[i]->get_vy(), |
356 |
< |
atoms[i]->get_vz()); |
357 |
< |
strcpy( writeLine, tempBuffer ); |
348 |
> |
// Get the Node number which has this atom; |
349 |
> |
|
350 |
> |
which_node = AtomToProcMap[i]; |
351 |
> |
|
352 |
> |
if (which_node != 0) { |
353 |
> |
|
354 |
> |
if (potatoes[which_node] + 3 >= MAXTAG) { |
355 |
> |
// The potato was going to exceed the maximum value, |
356 |
> |
// so wrap this processor potato back to 0: |
357 |
> |
|
358 |
> |
potatoes[which_node] = 0; |
359 |
> |
MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD); |
360 |
> |
|
361 |
> |
} |
362 |
> |
|
363 |
> |
myPotato = potatoes[which_node]; |
364 |
> |
|
365 |
> |
MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node, |
366 |
> |
myPotato, MPI_COMM_WORLD, &istatus); |
367 |
> |
|
368 |
> |
atomTypeString = MPIatomTypeString; |
369 |
|
|
370 |
< |
if( atoms[i]->isDirectional() ){ |
370 |
> |
myPotato++; |
371 |
> |
|
372 |
> |
MPI_Recv(&isDirectional, 1, MPI_INT, which_node, |
373 |
> |
myPotato, MPI_COMM_WORLD, &istatus); |
374 |
> |
|
375 |
> |
myPotato++; |
376 |
> |
|
377 |
> |
if (isDirectional) { |
378 |
> |
MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node, |
379 |
> |
myPotato, MPI_COMM_WORLD, &istatus); |
380 |
> |
} else { |
381 |
> |
MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node, |
382 |
> |
myPotato, MPI_COMM_WORLD, &istatus); |
383 |
> |
} |
384 |
> |
|
385 |
> |
myPotato++; |
386 |
> |
potatoes[which_node] = myPotato; |
387 |
> |
|
388 |
> |
} else { |
389 |
> |
|
390 |
> |
haveError = 0; |
391 |
> |
which_atom = i; |
392 |
> |
|
393 |
> |
local_index = indexArray[currentIndex].first; |
394 |
> |
|
395 |
> |
if (which_atom == indexArray[currentIndex].second) { |
396 |
> |
|
397 |
> |
atomTypeString = atoms[local_index]->getType(); |
398 |
> |
|
399 |
> |
atoms[local_index]->getPos(pos); |
400 |
> |
atoms[local_index]->getVel(vel); |
401 |
|
|
402 |
< |
dAtom = (DirectionalAtom *)atoms[i]; |
403 |
< |
dAtom->getQ( q ); |
404 |
< |
|
405 |
< |
sprintf( tempBuffer, |
406 |
< |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
407 |
< |
q[0], |
408 |
< |
q[1], |
409 |
< |
q[2], |
410 |
< |
q[3], |
411 |
< |
dAtom->getJx(), |
412 |
< |
dAtom->getJy(), |
413 |
< |
dAtom->getJz()); |
414 |
< |
strcat( writeLine, tempBuffer ); |
402 |
> |
atomData6[0] = pos[0]; |
403 |
> |
atomData6[1] = pos[1]; |
404 |
> |
atomData6[2] = pos[2]; |
405 |
> |
|
406 |
> |
atomData6[3] = vel[0]; |
407 |
> |
atomData6[4] = vel[1]; |
408 |
> |
atomData6[5] = vel[2]; |
409 |
> |
|
410 |
> |
isDirectional = 0; |
411 |
> |
|
412 |
> |
if( atoms[local_index]->isDirectional() ){ |
413 |
> |
|
414 |
> |
isDirectional = 1; |
415 |
> |
|
416 |
> |
dAtom = (DirectionalAtom *)atoms[local_index]; |
417 |
> |
dAtom->getQ( q ); |
418 |
> |
|
419 |
> |
for (int j = 0; j < 6 ; j++) |
420 |
> |
atomData13[j] = atomData6[j]; |
421 |
> |
|
422 |
> |
atomData13[6] = q[0]; |
423 |
> |
atomData13[7] = q[1]; |
424 |
> |
atomData13[8] = q[2]; |
425 |
> |
atomData13[9] = q[3]; |
426 |
> |
|
427 |
> |
atomData13[10] = dAtom->getJx(); |
428 |
> |
atomData13[11] = dAtom->getJy(); |
429 |
> |
atomData13[12] = dAtom->getJz(); |
430 |
> |
} |
431 |
> |
|
432 |
> |
} else { |
433 |
> |
sprintf(painCave.errMsg, |
434 |
> |
"Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n", |
435 |
> |
which_atom, worldRank, currentIndex, local_index ); |
436 |
> |
haveError= 1; |
437 |
> |
simError(); |
438 |
> |
} |
439 |
> |
|
440 |
> |
if(haveError) DieDieDie(); |
441 |
> |
|
442 |
> |
currentIndex++; |
443 |
|
} |
444 |
< |
else |
444 |
> |
// If we've survived to here, format the line: |
445 |
> |
|
446 |
> |
if (!isDirectional) { |
447 |
> |
|
448 |
> |
sprintf( writeLine, |
449 |
> |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
450 |
> |
atomTypeString, |
451 |
> |
atomData6[0], |
452 |
> |
atomData6[1], |
453 |
> |
atomData6[2], |
454 |
> |
atomData6[3], |
455 |
> |
atomData6[4], |
456 |
> |
atomData6[5]); |
457 |
> |
|
458 |
|
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
459 |
|
|
460 |
< |
finalOut << writeLine; |
461 |
< |
masterIndex++; |
460 |
> |
} else { |
461 |
> |
|
462 |
> |
sprintf( writeLine, |
463 |
> |
"%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", |
464 |
> |
atomTypeString, |
465 |
> |
atomData13[0], |
466 |
> |
atomData13[1], |
467 |
> |
atomData13[2], |
468 |
> |
atomData13[3], |
469 |
> |
atomData13[4], |
470 |
> |
atomData13[5], |
471 |
> |
atomData13[6], |
472 |
> |
atomData13[7], |
473 |
> |
atomData13[8], |
474 |
> |
atomData13[9], |
475 |
> |
atomData13[10], |
476 |
> |
atomData13[11], |
477 |
> |
atomData13[12]); |
478 |
> |
|
479 |
> |
} |
480 |
> |
|
481 |
> |
for(k = 0; k < outFile.size(); k++) |
482 |
> |
*outFile[k] << writeLine; |
483 |
|
} |
442 |
– |
finalOut.flush(); |
443 |
– |
} |
484 |
|
|
485 |
< |
for (procIndex = 1; procIndex < mpiSim->getNumberProcessors(); |
486 |
< |
procIndex++){ |
485 |
> |
for(k = 0; k < outFile.size(); k++) |
486 |
> |
outFile[k]->flush(); |
487 |
> |
|
488 |
> |
sprintf( checkPointMsg, |
489 |
> |
"Sucessfully took a dump.\n"); |
490 |
> |
|
491 |
> |
MPIcheckPoint(); |
492 |
> |
|
493 |
> |
delete[] potatoes; |
494 |
> |
|
495 |
> |
} else { |
496 |
|
|
497 |
< |
if( worldRank == 0 ){ |
449 |
< |
|
450 |
< |
mpiErr = MPI_Recv(&nodeAtomsStart,1,MPI_INT,procIndex, |
451 |
< |
TAKE_THIS_TAG,MPI_COMM_WORLD,istatus); |
497 |
> |
// worldRank != 0, so I'm a remote node. |
498 |
|
|
499 |
< |
mpiErr = MPI_Recv(&nodeAtomsEnd,1,MPI_INT,procIndex, |
454 |
< |
TAKE_THIS_TAG,MPI_COMM_WORLD, istatus); |
455 |
< |
|
456 |
< |
// 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); |
499 |
> |
// Set my magic potato to 0: |
500 |
|
|
501 |
< |
// recieve the nodes writeLines |
501 |
> |
myPotato = 0; |
502 |
> |
currentIndex = 0; |
503 |
> |
|
504 |
> |
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
505 |
> |
|
506 |
> |
// Am I the node which has this atom? |
507 |
> |
|
508 |
> |
if (AtomToProcMap[i] == worldRank) { |
509 |
|
|
510 |
< |
for ( i = nodeAtomsStart; i <= nodeAtomsEnd; i++){ |
510 |
> |
if (myPotato + 3 >= MAXTAG) { |
511 |
|
|
512 |
< |
mpiErr = MPI_Recv(writeLine,BUFFERSIZE,MPI_CHAR,procIndex, |
513 |
< |
TAKE_THIS_TAG,MPI_COMM_WORLD,istatus ); |
512 |
> |
// The potato was going to exceed the maximum value, |
513 |
> |
// so wrap this processor potato back to 0 (and block until |
514 |
> |
// node 0 says we can go: |
515 |
> |
|
516 |
> |
MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus); |
517 |
> |
|
518 |
> |
} |
519 |
> |
which_atom = i; |
520 |
|
|
521 |
< |
finalOut << writeLine; |
522 |
< |
masterIndex++; |
523 |
< |
} |
521 |
> |
local_index = indexArray[currentIndex].first; |
522 |
> |
|
523 |
> |
if (which_atom == indexArray[currentIndex].second) { |
524 |
> |
|
525 |
> |
atomTypeString = atoms[local_index]->getType(); |
526 |
> |
|
527 |
> |
atoms[local_index]->getPos(pos); |
528 |
> |
atoms[local_index]->getVel(vel); |
529 |
> |
|
530 |
> |
atomData6[0] = pos[0]; |
531 |
> |
atomData6[1] = pos[1]; |
532 |
> |
atomData6[2] = pos[2]; |
533 |
|
|
534 |
< |
finalOut.flush(); |
535 |
< |
} |
534 |
> |
atomData6[3] = vel[0]; |
535 |
> |
atomData6[4] = vel[1]; |
536 |
> |
atomData6[5] = vel[2]; |
537 |
> |
|
538 |
> |
isDirectional = 0; |
539 |
|
|
540 |
< |
else if( worldRank == procIndex ){ |
540 |
> |
if( atoms[local_index]->isDirectional() ){ |
541 |
|
|
542 |
< |
nodeAtomsStart = mpiSim->getMyAtomStart(); |
543 |
< |
nodeAtomsEnd = mpiSim->getMyAtomEnd(); |
542 |
> |
isDirectional = 1; |
543 |
> |
|
544 |
> |
dAtom = (DirectionalAtom *)atoms[local_index]; |
545 |
> |
dAtom->getQ( q ); |
546 |
> |
|
547 |
> |
for (int j = 0; j < 6 ; j++) |
548 |
> |
atomData13[j] = atomData6[j]; |
549 |
> |
|
550 |
> |
atomData13[6] = q[0]; |
551 |
> |
atomData13[7] = q[1]; |
552 |
> |
atomData13[8] = q[2]; |
553 |
> |
atomData13[9] = q[3]; |
554 |
> |
|
555 |
> |
atomData13[10] = dAtom->getJx(); |
556 |
> |
atomData13[11] = dAtom->getJy(); |
557 |
> |
atomData13[12] = dAtom->getJz(); |
558 |
> |
} |
559 |
> |
|
560 |
> |
} else { |
561 |
> |
sprintf(painCave.errMsg, |
562 |
> |
"Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n", |
563 |
> |
which_atom, worldRank, currentIndex, local_index ); |
564 |
> |
haveError= 1; |
565 |
> |
simError(); |
566 |
> |
} |
567 |
|
|
568 |
< |
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(); |
568 |
> |
strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE); |
569 |
|
|
570 |
< |
// send current node's configuration line by line. |
570 |
> |
// null terminate the string before sending (just in case): |
571 |
> |
MPIatomTypeString[MINIBUFFERSIZE-1] = '\0'; |
572 |
|
|
573 |
< |
for( i=0; i<nAtoms; i++ ){ |
574 |
< |
|
575 |
< |
sprintf( tempBuffer, |
576 |
< |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
577 |
< |
atoms[i]->getType(), |
578 |
< |
atoms[i]->getX(), |
579 |
< |
atoms[i]->getY(), |
580 |
< |
atoms[i]->getZ(), |
581 |
< |
atoms[i]->get_vx(), |
582 |
< |
atoms[i]->get_vy(), |
583 |
< |
atoms[i]->get_vz()); |
584 |
< |
strcpy( writeLine, tempBuffer ); |
585 |
< |
|
586 |
< |
if( atoms[i]->isDirectional() ){ |
587 |
< |
|
588 |
< |
dAtom = (DirectionalAtom *)atoms[i]; |
589 |
< |
dAtom->getQ( q ); |
590 |
< |
|
591 |
< |
sprintf( tempBuffer, |
592 |
< |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
593 |
< |
q[0], |
594 |
< |
q[1], |
595 |
< |
q[2], |
528 |
< |
q[3], |
529 |
< |
dAtom->getJx(), |
530 |
< |
dAtom->getJy(), |
531 |
< |
dAtom->getJz()); |
532 |
< |
strcat( writeLine, tempBuffer ); |
533 |
< |
} |
534 |
< |
else |
535 |
< |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
536 |
< |
|
537 |
< |
mpiErr = MPI_Send(writeLine,BUFFERSIZE,MPI_CHAR,0,TAKE_THIS_TAG, |
538 |
< |
MPI_COMM_WORLD); |
573 |
> |
MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0, |
574 |
> |
myPotato, MPI_COMM_WORLD); |
575 |
> |
|
576 |
> |
myPotato++; |
577 |
> |
|
578 |
> |
MPI_Send(&isDirectional, 1, MPI_INT, 0, |
579 |
> |
myPotato, MPI_COMM_WORLD); |
580 |
> |
|
581 |
> |
myPotato++; |
582 |
> |
|
583 |
> |
if (isDirectional) { |
584 |
> |
|
585 |
> |
MPI_Send(atomData13, 13, MPI_DOUBLE, 0, |
586 |
> |
myPotato, MPI_COMM_WORLD); |
587 |
> |
|
588 |
> |
} else { |
589 |
> |
|
590 |
> |
MPI_Send(atomData6, 6, MPI_DOUBLE, 0, |
591 |
> |
myPotato, MPI_COMM_WORLD); |
592 |
> |
} |
593 |
> |
|
594 |
> |
myPotato++; |
595 |
> |
currentIndex++; |
596 |
|
} |
597 |
|
} |
541 |
– |
|
542 |
– |
sprintf(checkPointMsg,"Node %d sent dump configuration.", |
543 |
– |
procIndex); |
544 |
– |
MPIcheckPoint(); |
545 |
– |
} |
598 |
|
|
599 |
< |
if( worldRank == 0 ) finalOut.close(); |
600 |
< |
|
599 |
> |
sprintf( checkPointMsg, |
600 |
> |
"Sucessfully took a dump.\n"); |
601 |
> |
MPIcheckPoint(); |
602 |
|
|
603 |
+ |
} |
604 |
+ |
|
605 |
|
#endif // is_mpi |
606 |
|
} |
607 |
+ |
|
608 |
+ |
#ifdef IS_MPI |
609 |
+ |
|
610 |
+ |
// a couple of functions to let us escape the write loop |
611 |
+ |
|
612 |
+ |
void dWrite::DieDieDie( void ){ |
613 |
+ |
|
614 |
+ |
MPI_Finalize(); |
615 |
+ |
exit (0); |
616 |
+ |
} |
617 |
+ |
|
618 |
+ |
#endif //is_mpi |