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#include <cstdlib> |
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#include <cstring> |
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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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|
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extern "C"{ |
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void wrapsimparallelmod_( void (*wrapFunction)(void (*fSub)( mpiSimData*, |
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int*, int*, |
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int*))); |
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} |
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|
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void wrapSimParallel(void (*fSub)(mpiSimData*, int*, int*, int*)); |
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|
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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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mpiPlug->numberProcessors = MPI::COMM_WORLD.Get_size(); |
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mpiPlug->myNode = worldRank; |
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|
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mpiSim = this; |
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wrapMe(); |
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|
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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 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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void mpiSimulation::wrapMe(){ |
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|
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wrapsimparallelmod_( wrapSimParallel ); |
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} |
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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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int* componentsNmol; |
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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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|
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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 smallDiff, bigDiff; |
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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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|
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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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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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|
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done = 0; |
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nLocal = 0; |
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molLocal = 0; |
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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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} |
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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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|
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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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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--; |
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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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|
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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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|
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numerator = (double)( entryPlug->n_atoms - atomIndex ); |
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denominator = (double)( mpiPlug->numberProcessors - (i+1) ); |
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precast = numerator / denominator; |
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nTarget = (int)( precast + 0.5 ); |
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} |
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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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|
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nLocal = 0; |
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molLocal = 0; |
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while( compIndex < nComponents ){ |
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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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|
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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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|
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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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|
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MPI_Allreduce( &nLocal, &testSum, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD ); |
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|
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if( mpiPlug->myNode == 0 ){ |
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if( testSum != entryPlug->n_atoms ){ |
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sprintf( painCave.errMsg, |
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"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; |
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simError(); |
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} |
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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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// lets create the identity array |
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|
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globalIndex = new int[mpiPlug->myNlocal]; |
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index = mpiPlug->myAtomStart; |
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for( i=0; i<mpiPlug->myNlocal; i++){ |
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globalIndex[i] = index; |
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index++; |
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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 wrapSimParallel(void (*fSub)(mpiSimData*, int*, int*, int*)){ |
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|
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mpiSim->setInternal( fSub ); |
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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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for(i=0; i<mpiPlug->myNlocal; i++) globalIndex[i] = entryPlug->atoms[i]->getGlobalIndex(); |
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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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