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#ifdef IS_MPI |
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#include <cstdlib> |
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#include <cstring> |
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#include <iostream> |
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#include <stdlib.h> |
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#include <string.h> |
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#include <math.h> |
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#include <mpi.h> |
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#include <mpi++.h> |
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#include "mpiSimulation.hpp" |
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#include "simError.h" |
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#include "fortranWrappers.hpp" |
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#include "randomSPRNG.hpp" |
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|
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mpiSimulation* mpiSim; |
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mpiSimulation::mpiSimulation(SimInfo* the_entryPlug) |
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entryPlug = the_entryPlug; |
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mpiPlug = new mpiSimData; |
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|
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mpiPlug->numberProcessors = MPI::COMM_WORLD.Get_size(); |
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MPI_Comm_size(MPI_COMM_WORLD, &(mpiPlug->nProcessors) ); |
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mpiPlug->myNode = worldRank; |
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|
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|
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MolToProcMap = new int[entryPlug->n_mol]; |
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MolComponentType = new int[entryPlug->n_mol]; |
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AtomToProcMap = new int[entryPlug->n_atoms]; |
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|
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mpiSim = this; |
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wrapMeSimParallel( this ); |
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} |
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mpiSimulation::~mpiSimulation(){ |
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|
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delete[] MolToProcMap; |
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delete[] MolComponentType; |
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delete[] AtomToProcMap; |
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|
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delete mpiPlug; |
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// perhaps we should let fortran know the party is over. |
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|
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} |
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void mpiSimulation::divideLabor( ){ |
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int* mpiSimulation::divideLabor( void ){ |
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|
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int* globalIndex; |
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|
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int nComponents; |
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MoleculeStamp** compStamps; |
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randomSPRNG *myRandom; |
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int* componentsNmol; |
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int* AtomsPerProc; |
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|
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double numerator; |
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double denominator; |
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double precast; |
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double x, y, a; |
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int old_atoms, add_atoms, new_atoms; |
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|
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int nTarget; |
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int molIndex, atomIndex, compIndex, compStart; |
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int molIndex, atomIndex; |
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int done; |
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int nLocal, molLocal; |
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int i, index; |
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int smallDiff, bigDiff; |
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int i, j, loops, which_proc, nmol_local, natoms_local; |
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int nmol_global, natoms_global; |
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int local_index; |
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int baseSeed = entryPlug->getSeed(); |
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|
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int testSum; |
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|
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nComponents = entryPlug->nComponents; |
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compStamps = entryPlug->compStamps; |
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componentsNmol = entryPlug->componentsNmol; |
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AtomsPerProc = new int[mpiPlug->nProcessors]; |
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|
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mpiPlug->nAtomsGlobal = entryPlug->n_atoms; |
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mpiPlug->nBondsGlobal = entryPlug->n_bonds; |
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mpiPlug->nBendsGlobal = entryPlug->n_bends; |
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mpiPlug->nTorsionsGlobal = entryPlug->n_torsions; |
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mpiPlug->nSRIGlobal = entryPlug->n_SRI; |
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mpiPlug->nMolGlobal = entryPlug->n_mol; |
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mpiPlug->nGroupsGlobal = entryPlug->ngroup; |
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numerator = (double) entryPlug->n_atoms; |
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denominator = (double) mpiPlug->numberProcessors; |
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precast = numerator / denominator; |
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nTarget = (int)( precast + 0.5 ); |
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|
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molIndex = 0; |
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atomIndex = 0; |
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compIndex = 0; |
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compStart = 0; |
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for( i=0; i<(mpiPlug->numberProcessors-1); i++){ |
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myRandom = new randomSPRNG( baseSeed ); |
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|
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a = 3.0 * (double)mpiPlug->nMolGlobal / (double)mpiPlug->nAtomsGlobal; |
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|
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// Initialize things that we'll send out later: |
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for (i = 0; i < mpiPlug->nProcessors; i++ ) { |
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AtomsPerProc[i] = 0; |
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} |
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for (i = 0; i < mpiPlug->nMolGlobal; i++ ) { |
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// default to an error condition: |
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MolToProcMap[i] = -1; |
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MolComponentType[i] = -1; |
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} |
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for (i = 0; i < mpiPlug->nAtomsGlobal; i++ ) { |
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// default to an error condition: |
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AtomToProcMap[i] = -1; |
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} |
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|
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done = 0; |
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nLocal = 0; |
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molLocal = 0; |
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if (mpiPlug->myNode == 0) { |
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numerator = (double) entryPlug->n_atoms; |
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denominator = (double) mpiPlug->nProcessors; |
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precast = numerator / denominator; |
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nTarget = (int)( precast + 0.5 ); |
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|
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if( i == mpiPlug->myNode ){ |
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mpiPlug->myMolStart = molIndex; |
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mpiPlug->myAtomStart = atomIndex; |
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// Build the array of molecule component types first |
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molIndex = 0; |
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for (i=0; i < nComponents; i++) { |
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for (j=0; j < componentsNmol[i]; j++) { |
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MolComponentType[molIndex] = i; |
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molIndex++; |
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} |
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} |
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|
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atomIndex = 0; |
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|
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for (i = 0; i < molIndex; i++ ) { |
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|
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done = 0; |
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loops = 0; |
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|
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while( !done ){ |
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loops++; |
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|
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// Pick a processor at random |
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|
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which_proc = (int) (myRandom->getRandom() * mpiPlug->nProcessors); |
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|
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// How many atoms does this processor have? |
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|
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old_atoms = AtomsPerProc[which_proc]; |
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add_atoms = compStamps[MolComponentType[i]]->getNAtoms(); |
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new_atoms = old_atoms + add_atoms; |
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|
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// If we've been through this loop too many times, we need |
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// to just give up and assign the molecule to this processor |
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// and be done with it. |
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|
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if (loops > 100) { |
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sprintf( painCave.errMsg, |
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"I've tried 100 times to assign molecule %d to a " |
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" processor, but can't find a good spot.\n" |
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"I'm assigning it at random to processor %d.\n", |
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i, which_proc); |
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painCave.isFatal = 0; |
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simError(); |
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|
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MolToProcMap[i] = which_proc; |
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AtomsPerProc[which_proc] += add_atoms; |
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for (j = 0 ; j < add_atoms; j++ ) { |
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AtomToProcMap[atomIndex] = which_proc; |
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atomIndex++; |
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} |
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done = 1; |
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continue; |
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} |
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|
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while( !done ){ |
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|
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if( (molIndex-compStart) >= componentsNmol[compIndex] ){ |
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compStart = molIndex; |
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compIndex++; |
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continue; |
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} |
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// If we can add this molecule to this processor without sending |
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// it above nTarget, then go ahead and do it: |
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|
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if (new_atoms <= nTarget) { |
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MolToProcMap[i] = which_proc; |
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AtomsPerProc[which_proc] += add_atoms; |
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for (j = 0 ; j < add_atoms; j++ ) { |
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AtomToProcMap[atomIndex] = which_proc; |
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atomIndex++; |
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} |
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done = 1; |
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continue; |
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} |
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nLocal += compStamps[compIndex]->getNAtoms(); |
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atomIndex += compStamps[compIndex]->getNAtoms(); |
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molIndex++; |
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molLocal++; |
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|
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// The only situation left is when new_atoms > nTarget. We |
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// want to accept this with some probability that dies off the |
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// farther we are from nTarget |
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|
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// roughly: x = new_atoms - nTarget |
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// Pacc(x) = exp(- a * x) |
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// where a = penalty / (average atoms per molecule) |
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|
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x = (double) (new_atoms - nTarget); |
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y = myRandom->getRandom(); |
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|
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if ( nLocal == nTarget ) done = 1; |
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|
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else if( nLocal < nTarget ){ |
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smallDiff = nTarget - nLocal; |
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} |
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else if( nLocal > nTarget ){ |
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bigDiff = nLocal - nTarget; |
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|
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if( bigDiff < smallDiff ) done = 1; |
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else{ |
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molIndex--; |
191 |
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molLocal--; |
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atomIndex -= compStamps[compIndex]->getNAtoms(); |
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nLocal -= compStamps[compIndex]->getNAtoms(); |
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done = 1; |
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} |
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if (y < exp(- a * x)) { |
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MolToProcMap[i] = which_proc; |
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AtomsPerProc[which_proc] += add_atoms; |
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for (j = 0 ; j < add_atoms; j++ ) { |
184 |
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AtomToProcMap[atomIndex] = which_proc; |
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atomIndex++; |
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} |
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done = 1; |
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continue; |
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} else { |
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continue; |
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} |
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|
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} |
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} |
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|
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// Spray out this nonsense to all other processors: |
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|
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MPI_Bcast(MolToProcMap, mpiPlug->nMolGlobal, |
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MPI_INT, 0, MPI_COMM_WORLD); |
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|
201 |
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MPI_Bcast(AtomToProcMap, mpiPlug->nAtomsGlobal, |
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MPI_INT, 0, MPI_COMM_WORLD); |
203 |
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|
204 |
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MPI_Bcast(MolComponentType, mpiPlug->nMolGlobal, |
205 |
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MPI_INT, 0, MPI_COMM_WORLD); |
206 |
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|
207 |
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MPI_Bcast(AtomsPerProc, mpiPlug->nProcessors, |
208 |
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MPI_INT, 0, MPI_COMM_WORLD); |
209 |
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} else { |
210 |
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|
211 |
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// Listen to your marching orders from processor 0: |
212 |
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|
213 |
< |
if( i == mpiPlug->myNode ){ |
214 |
< |
mpiPlug->myMolEnd = (molIndex - 1); |
125 |
< |
mpiPlug->myAtomEnd = (atomIndex - 1); |
126 |
< |
mpiPlug->myNlocal = nLocal; |
127 |
< |
mpiPlug->myMol = molLocal; |
128 |
< |
} |
213 |
> |
MPI_Bcast(MolToProcMap, mpiPlug->nMolGlobal, |
214 |
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MPI_INT, 0, MPI_COMM_WORLD); |
215 |
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|
216 |
< |
numerator = (double)( entryPlug->n_atoms - atomIndex ); |
217 |
< |
denominator = (double)( mpiPlug->numberProcessors - (i+1) ); |
218 |
< |
precast = numerator / denominator; |
219 |
< |
nTarget = (int)( precast + 0.5 ); |
216 |
> |
MPI_Bcast(AtomToProcMap, mpiPlug->nAtomsGlobal, |
217 |
> |
MPI_INT, 0, MPI_COMM_WORLD); |
218 |
> |
|
219 |
> |
MPI_Bcast(MolComponentType, mpiPlug->nMolGlobal, |
220 |
> |
MPI_INT, 0, MPI_COMM_WORLD); |
221 |
> |
|
222 |
> |
MPI_Bcast(AtomsPerProc, mpiPlug->nProcessors, |
223 |
> |
MPI_INT, 0, MPI_COMM_WORLD); |
224 |
> |
|
225 |
> |
|
226 |
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} |
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|
136 |
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if( mpiPlug->myNode == mpiPlug->numberProcessors-1 ){ |
137 |
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mpiPlug->myMolStart = molIndex; |
138 |
– |
mpiPlug->myAtomStart = atomIndex; |
227 |
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|
140 |
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nLocal = 0; |
141 |
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molLocal = 0; |
142 |
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while( compIndex < nComponents ){ |
143 |
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|
144 |
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if( (molIndex-compStart) >= componentsNmol[compIndex] ){ |
145 |
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compStart = molIndex; |
146 |
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compIndex++; |
147 |
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continue; |
148 |
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} |
228 |
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|
229 |
< |
nLocal += compStamps[compIndex]->getNAtoms(); |
230 |
< |
atomIndex += compStamps[compIndex]->getNAtoms(); |
231 |
< |
molIndex++; |
232 |
< |
molLocal++; |
233 |
< |
} |
234 |
< |
|
235 |
< |
mpiPlug->myMolEnd = (molIndex - 1); |
157 |
< |
mpiPlug->myAtomEnd = (atomIndex - 1); |
158 |
< |
mpiPlug->myNlocal = nLocal; |
159 |
< |
mpiPlug->myMol = molLocal; |
229 |
> |
// Let's all check for sanity: |
230 |
> |
|
231 |
> |
nmol_local = 0; |
232 |
> |
for (i = 0 ; i < mpiPlug->nMolGlobal; i++ ) { |
233 |
> |
if (MolToProcMap[i] == mpiPlug->myNode) { |
234 |
> |
nmol_local++; |
235 |
> |
} |
236 |
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} |
237 |
|
|
238 |
+ |
natoms_local = 0; |
239 |
+ |
for (i = 0; i < mpiPlug->nAtomsGlobal; i++) { |
240 |
+ |
if (AtomToProcMap[i] == mpiPlug->myNode) { |
241 |
+ |
natoms_local++; |
242 |
+ |
} |
243 |
+ |
} |
244 |
|
|
245 |
< |
MPI_Allreduce( &nLocal, &testSum, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD ); |
245 |
> |
MPI_Allreduce(&nmol_local,&nmol_global,1,MPI_INT,MPI_SUM, |
246 |
> |
MPI_COMM_WORLD); |
247 |
> |
MPI_Allreduce(&natoms_local,&natoms_global,1,MPI_INT, |
248 |
> |
MPI_SUM, MPI_COMM_WORLD); |
249 |
|
|
250 |
< |
if( mpiPlug->myNode == 0 ){ |
251 |
< |
if( testSum != entryPlug->n_atoms ){ |
252 |
< |
sprintf( painCave.errMsg, |
253 |
< |
"The summ of all nLocals, %d, did not equal the total number of atoms, %d.\n", |
254 |
< |
testSum, entryPlug->n_atoms ); |
255 |
< |
painCave.isFatal = 1; |
256 |
< |
simError(); |
172 |
< |
} |
250 |
> |
if( nmol_global != entryPlug->n_mol ){ |
251 |
> |
sprintf( painCave.errMsg, |
252 |
> |
"The sum of all nmol_local, %d, did not equal the " |
253 |
> |
"total number of molecules, %d.\n", |
254 |
> |
nmol_global, entryPlug->n_mol ); |
255 |
> |
painCave.isFatal = 1; |
256 |
> |
simError(); |
257 |
|
} |
258 |
+ |
|
259 |
+ |
if( natoms_global != entryPlug->n_atoms ){ |
260 |
+ |
sprintf( painCave.errMsg, |
261 |
+ |
"The sum of all natoms_local, %d, did not equal the " |
262 |
+ |
"total number of atoms, %d.\n", |
263 |
+ |
natoms_global, entryPlug->n_atoms ); |
264 |
+ |
painCave.isFatal = 1; |
265 |
+ |
simError(); |
266 |
+ |
} |
267 |
|
|
268 |
|
sprintf( checkPointMsg, |
269 |
|
"Successfully divided the molecules among the processors.\n" ); |
270 |
|
MPIcheckPoint(); |
271 |
|
|
272 |
< |
// lets create the identity array |
272 |
> |
mpiPlug->nMolLocal = nmol_local; |
273 |
> |
mpiPlug->nAtomsLocal = natoms_local; |
274 |
|
|
275 |
< |
globalIndex = new int[mpiPlug->myNlocal]; |
276 |
< |
index = mpiPlug->myAtomStart; |
277 |
< |
for( i=0; i<mpiPlug->myNlocal; i++){ |
278 |
< |
globalIndex[i] = index; |
279 |
< |
index++; |
275 |
> |
globalAtomIndex.resize(mpiPlug->nAtomsLocal); |
276 |
> |
globalToLocalAtom.resize(mpiPlug->nAtomsGlobal); |
277 |
> |
local_index = 0; |
278 |
> |
for (i = 0; i < mpiPlug->nAtomsGlobal; i++) { |
279 |
> |
if (AtomToProcMap[i] == mpiPlug->myNode) { |
280 |
> |
globalAtomIndex[local_index] = i; |
281 |
> |
|
282 |
> |
globalToLocalAtom[i] = local_index; |
283 |
> |
local_index++; |
284 |
> |
|
285 |
> |
} |
286 |
> |
else |
287 |
> |
globalToLocalAtom[i] = -1; |
288 |
|
} |
289 |
|
|
290 |
< |
return globalIndex; |
290 |
> |
globalMolIndex.resize(mpiPlug->nMolLocal); |
291 |
> |
globalToLocalMol.resize(mpiPlug->nMolGlobal); |
292 |
> |
|
293 |
> |
local_index = 0; |
294 |
> |
for (i = 0; i < mpiPlug->nMolGlobal; i++) { |
295 |
> |
if (MolToProcMap[i] == mpiPlug->myNode) { |
296 |
> |
globalMolIndex[local_index] = i; |
297 |
> |
globalToLocalMol[i] = local_index; |
298 |
> |
local_index++; |
299 |
> |
} |
300 |
> |
else |
301 |
> |
globalToLocalMol[i] = -1; |
302 |
> |
} |
303 |
> |
|
304 |
|
} |
305 |
|
|
306 |
|
|
307 |
|
void mpiSimulation::mpiRefresh( void ){ |
308 |
|
|
309 |
|
int isError, i; |
310 |
< |
int *globalIndex = new int[mpiPlug->myNlocal]; |
310 |
> |
int *globalIndex = new int[mpiPlug->nAtomsLocal]; |
311 |
|
|
312 |
< |
for(i=0; i<mpiPlug->myNlocal; i++) globalIndex[i] = entryPlug->atoms[i]->getGlobalIndex(); |
312 |
> |
// Fortran indexing needs to be increased by 1 in order to get the 2 languages to |
313 |
> |
// not barf |
314 |
|
|
315 |
+ |
for(i=0; i<mpiPlug->nAtomsLocal; i++) globalIndex[i] = entryPlug->atoms[i]->getGlobalIndex()+1; |
316 |
+ |
|
317 |
|
|
318 |
|
isError = 0; |
319 |
|
setFsimParallel( mpiPlug, &(entryPlug->n_atoms), globalIndex, &isError ); |