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#ifdef IS_MPI |
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#include <iostream> |
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#include <cstdlib> |
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#include <cstring> |
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#include <cmath> |
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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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#define BASE_SEED 123456789 |
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mpiSimulation* mpiSim; |
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mpiSimulation::mpiSimulation(SimInfo* the_entryPlug) |
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mpiPlug->numberProcessors = MPI::COMM_WORLD.Get_size(); |
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mpiPlug->myNode = worldRank; |
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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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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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int* mpiSimulation::divideLabor( void ){ |
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int* globalIndex; |
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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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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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int nTarget; |
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int molIndex, atomIndex, compIndex, compStart; |
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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 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, index; |
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int smallDiff, bigDiff; |
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int baseSeed = BASE_SEED; |
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int testSum; |
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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->numberProcessors]; |
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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->nSRIGlobal = entryPlug->n_SRI; |
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mpiPlug->nMolGlobal = entryPlug->n_mol; |
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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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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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done = 0; |
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nLocal = 0; |
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molLocal = 0; |
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myRandom = new randomSPRNG( baseSeed ); |
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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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} |
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while( !done ){ |
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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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a = (double)mpiPlug->nMolGlobal / (double)mpiPlug->nAtomsGlobal; |
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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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if ( nLocal == nTarget ) done = 1; |
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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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if( bigDiff < smallDiff ) done = 1; |
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else{ |
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molIndex--; |
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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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} |
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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->numberProcessors; 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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if( i == mpiPlug->myNode ){ |
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mpiPlug->myMolEnd = (molIndex - 1); |
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mpiPlug->myAtomEnd = (atomIndex - 1); |
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mpiPlug->myNlocal = nLocal; |
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mpiPlug->myMol = molLocal; |
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} |
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numerator = (double)( entryPlug->n_atoms - atomIndex ); |
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denominator = (double)( mpiPlug->numberProcessors - (i+1) ); |
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if (mpiPlug->myNode == 0) { |
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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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if( mpiPlug->myNode == mpiPlug->numberProcessors-1 ){ |
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mpiPlug->myMolStart = molIndex; |
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mpiPlug->myAtomStart = atomIndex; |
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nLocal = 0; |
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molLocal = 0; |
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while( compIndex < nComponents ){ |
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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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// 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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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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atomIndex = 0; |
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for (i = 0; i < molIndex; i++ ) { |
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done = 0; |
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loops = 0; |
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while( !done ){ |
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loops++; |
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// Pick a processor at random |
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which_proc = (int) (myRandom->getRandom() * mpiPlug->numberProcessors); |
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// How many atoms does this processor have? |
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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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// If the processor already had too many atoms, just skip this |
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// processor and try again. |
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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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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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if (old_atoms >= nTarget) continue; |
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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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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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// The only situation left is where old_atoms < nTarget, but |
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// new_atoms > nTarget. We want to accept this with some |
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// probability that dies off the 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 = 1 / (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 (exp(- a * x) > y) { |
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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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} 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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mpiPlug->myMolEnd = (molIndex - 1); |
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mpiPlug->myAtomEnd = (atomIndex - 1); |
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mpiPlug->myNlocal = nLocal; |
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mpiPlug->myMol = molLocal; |
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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::COMM_WORLD.Bcast(MolToProcMap, mpiPlug->nMolGlobal, |
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MPI_INT, 0); |
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|
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MPI::COMM_WORLD.Bcast(AtomToProcMap, mpiPlug->nAtomsGlobal, |
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MPI_INT, 0); |
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> |
|
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MPI::COMM_WORLD.Bcast(MolComponentType, mpiPlug->nMolGlobal, |
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MPI_INT, 0); |
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> |
|
| 220 |
> |
MPI::COMM_WORLD.Bcast(AtomsPerProc, mpiPlug->numberProcessors, |
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MPI_INT, 0); |
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} else { |
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> |
|
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// Listen to your marching orders from processor 0: |
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> |
|
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> |
MPI::COMM_WORLD.Bcast(MolToProcMap, mpiPlug->nMolGlobal, |
| 227 |
> |
MPI_INT, 0); |
| 228 |
> |
|
| 229 |
> |
MPI::COMM_WORLD.Bcast(AtomToProcMap, mpiPlug->nAtomsGlobal, |
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> |
MPI_INT, 0); |
| 231 |
> |
|
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> |
MPI::COMM_WORLD.Bcast(MolComponentType, mpiPlug->nMolGlobal, |
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> |
MPI_INT, 0); |
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> |
|
| 235 |
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MPI::COMM_WORLD.Bcast(AtomsPerProc, mpiPlug->numberProcessors, |
| 236 |
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MPI_INT, 0); |
| 237 |
> |
|
| 238 |
> |
|
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} |
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< |
MPI_Allreduce( &nLocal, &testSum, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD ); |
| 243 |
< |
|
| 244 |
< |
if( mpiPlug->myNode == 0 ){ |
| 245 |
< |
if( testSum != entryPlug->n_atoms ){ |
| 246 |
< |
sprintf( painCave.errMsg, |
| 247 |
< |
"The summ of all nLocals, %d, did not equal the total number of atoms, %d.\n", |
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testSum, entryPlug->n_atoms ); |
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painCave.isFatal = 1; |
| 171 |
< |
simError(); |
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> |
// Let's all check for sanity: |
| 243 |
> |
|
| 244 |
> |
nmol_local = 0; |
| 245 |
> |
for (i = 0 ; i < mpiPlug->nMolGlobal; i++ ) { |
| 246 |
> |
if (MolToProcMap[i] == mpiPlug->myNode) { |
| 247 |
> |
nmol_local++; |
| 248 |
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} |
| 249 |
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} |
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|
| 251 |
+ |
natoms_local = 0; |
| 252 |
+ |
for (i = 0; i < mpiPlug->nAtomsGlobal; i++) { |
| 253 |
+ |
if (AtomToProcMap[i] == mpiPlug->myNode) { |
| 254 |
+ |
natoms_local++; |
| 255 |
+ |
} |
| 256 |
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} |
| 257 |
+ |
|
| 258 |
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std::cerr << "proc = " << mpiPlug->myNode << " atoms = " << natoms_local << "\n"; |
| 259 |
+ |
|
| 260 |
+ |
MPI::COMM_WORLD.Allreduce(&nmol_local,&nmol_global,1,MPI_INT,MPI_SUM); |
| 261 |
+ |
MPI::COMM_WORLD.Allreduce(&natoms_local,&natoms_global,1,MPI_INT,MPI_SUM); |
| 262 |
+ |
|
| 263 |
+ |
if( nmol_global != entryPlug->n_mol ){ |
| 264 |
+ |
sprintf( painCave.errMsg, |
| 265 |
+ |
"The sum of all nmol_local, %d, did not equal the " |
| 266 |
+ |
"total number of molecules, %d.\n", |
| 267 |
+ |
nmol_global, entryPlug->n_mol ); |
| 268 |
+ |
painCave.isFatal = 1; |
| 269 |
+ |
simError(); |
| 270 |
+ |
} |
| 271 |
+ |
|
| 272 |
+ |
if( natoms_global != entryPlug->n_atoms ){ |
| 273 |
+ |
sprintf( painCave.errMsg, |
| 274 |
+ |
"The sum of all natoms_local, %d, did not equal the " |
| 275 |
+ |
"total number of atoms, %d.\n", |
| 276 |
+ |
natoms_global, entryPlug->n_atoms ); |
| 277 |
+ |
painCave.isFatal = 1; |
| 278 |
+ |
simError(); |
| 279 |
+ |
} |
| 280 |
+ |
|
| 281 |
|
sprintf( checkPointMsg, |
| 282 |
|
"Successfully divided the molecules among the processors.\n" ); |
| 283 |
|
MPIcheckPoint(); |
| 284 |
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|
| 285 |
< |
// lets create the identity array |
| 285 |
> |
mpiPlug->myNMol = nmol_local; |
| 286 |
> |
mpiPlug->myNlocal = natoms_local; |
| 287 |
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|
| 288 |
|
globalIndex = new int[mpiPlug->myNlocal]; |
| 289 |
< |
index = mpiPlug->myAtomStart; |
| 290 |
< |
for( i=0; i<mpiPlug->myNlocal; i++){ |
| 291 |
< |
globalIndex[i] = index; |
| 292 |
< |
index++; |
| 289 |
> |
local_index = 0; |
| 290 |
> |
for (i = 0; i < mpiPlug->nAtomsGlobal; i++) { |
| 291 |
> |
if (AtomToProcMap[i] == mpiPlug->myNode) { |
| 292 |
> |
globalIndex[local_index] = i; |
| 293 |
> |
local_index++; |
| 294 |
> |
} |
| 295 |
|
} |
| 296 |
< |
|
| 296 |
> |
|
| 297 |
|
return globalIndex; |
| 298 |
|
} |
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|
