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#ifdef IS_MPI |
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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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|
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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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|
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mpiSimulation::mpiSimulation(SimInfo* the_entryPlug) |
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{ |
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entryPlug = the_entryPlug; |
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mpiPlug = new mpiSimData; |
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|
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MPI_Comm_size(MPI_COMM_WORLD, &(mpiPlug->numberProcessors) ); |
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mpiPlug->myNode = worldRank; |
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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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|
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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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|
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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; |
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int done; |
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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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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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|
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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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|
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|
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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->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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|
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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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// 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->numberProcessors); |
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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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// 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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|
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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 (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++ ) { |
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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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|
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MPI_Bcast(AtomToProcMap, mpiPlug->nAtomsGlobal, |
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MPI_INT, 0, MPI_COMM_WORLD); |
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|
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MPI_Bcast(MolComponentType, mpiPlug->nMolGlobal, |
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MPI_INT, 0, MPI_COMM_WORLD); |
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|
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MPI_Bcast(AtomsPerProc, mpiPlug->numberProcessors, |
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MPI_INT, 0, MPI_COMM_WORLD); |
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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_Bcast(MolToProcMap, mpiPlug->nMolGlobal, |
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MPI_INT, 0, MPI_COMM_WORLD); |
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|
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MPI_Bcast(AtomToProcMap, mpiPlug->nAtomsGlobal, |
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MPI_INT, 0, MPI_COMM_WORLD); |
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|
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MPI_Bcast(MolComponentType, mpiPlug->nMolGlobal, |
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MPI_INT, 0, MPI_COMM_WORLD); |
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|
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MPI_Bcast(AtomsPerProc, mpiPlug->numberProcessors, |
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MPI_INT, 0, MPI_COMM_WORLD); |
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|
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|
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} |
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|
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|
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// Let's all check for sanity: |
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|
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nmol_local = 0; |
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for (i = 0 ; i < mpiPlug->nMolGlobal; i++ ) { |
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if (MolToProcMap[i] == mpiPlug->myNode) { |
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nmol_local++; |
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} |
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} |
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|
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natoms_local = 0; |
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for (i = 0; i < mpiPlug->nAtomsGlobal; i++) { |
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if (AtomToProcMap[i] == mpiPlug->myNode) { |
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natoms_local++; |
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} |
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} |
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|
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MPI_Allreduce(&nmol_local,&nmol_global,1,MPI_INT,MPI_SUM, |
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MPI_COMM_WORLD); |
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MPI_Allreduce(&natoms_local,&natoms_global,1,MPI_INT, |
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MPI_SUM, MPI_COMM_WORLD); |
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|
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if( nmol_global != entryPlug->n_mol ){ |
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sprintf( painCave.errMsg, |
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"The sum of all nmol_local, %d, did not equal the " |
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"total number of molecules, %d.\n", |
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nmol_global, entryPlug->n_mol ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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if( natoms_global != entryPlug->n_atoms ){ |
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sprintf( painCave.errMsg, |
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"The sum of all natoms_local, %d, did not equal the " |
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"total number of atoms, %d.\n", |
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natoms_global, entryPlug->n_atoms ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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sprintf( checkPointMsg, |
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"Successfully divided the molecules among the processors.\n" ); |
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MPIcheckPoint(); |
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|
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mpiPlug->myNMol = nmol_local; |
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mpiPlug->myNlocal = natoms_local; |
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|
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globalIndex = new int[mpiPlug->myNlocal]; |
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local_index = 0; |
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for (i = 0; i < mpiPlug->nAtomsGlobal; i++) { |
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if (AtomToProcMap[i] == mpiPlug->myNode) { |
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globalIndex[local_index] = i; |
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local_index++; |
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} |
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} |
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|
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return globalIndex; |
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} |
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|
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|
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void mpiSimulation::mpiRefresh( void ){ |
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|
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int isError, i; |
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int *globalIndex = new int[mpiPlug->myNlocal]; |
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|
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// Fortran indexing needs to be increased by 1 in order to get the 2 languages to |
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// not barf |
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|
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for(i=0; i<mpiPlug->myNlocal; i++) globalIndex[i] = entryPlug->atoms[i]->getGlobalIndex()+1; |
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|
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|
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isError = 0; |
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setFsimParallel( mpiPlug, &(entryPlug->n_atoms), globalIndex, &isError ); |
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if( isError ){ |
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|
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sprintf( painCave.errMsg, |
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"mpiRefresh errror: fortran didn't like something we gave it.\n" ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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delete[] globalIndex; |
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|
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sprintf( checkPointMsg, |
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" mpiRefresh successful.\n" ); |
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MPIcheckPoint(); |
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} |
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|
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|
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#endif // is_mpi |
