src/brains/mpiSimulation.cpp

#ifdef IS_MPI
#include <iostream>
#include <stdlib.h>
#include <string.h>
#include <math.h>
#include <mpi.h>

#include "brains/mpiSimulation.hpp"
#include "utils/simError.h"
#include "UseTheForce/fortranWrappers.hpp"
#include "math/randomSPRNG.hpp"

mpiSimulation* mpiSim;

mpiSimulation::mpiSimulation(SimInfo* the_entryPlug)
{
  entryPlug = the_entryPlug;
  parallelData = new mpiSimData;
  
  MPI_Comm_size(MPI_COMM_WORLD, &(parallelData->nProcessors) );
  parallelData->myNode = worldRank;

  MolToProcMap = new int[entryPlug->n_mol];
  MolComponentType = new int[entryPlug->n_mol];
  AtomToProcMap = new int[entryPlug->n_atoms];
  GroupToProcMap = new int[entryPlug->ngroup];

  mpiSim = this;
  wrapMeSimParallel( this );
}


mpiSimulation::~mpiSimulation(){
  
  delete[] MolToProcMap;
  delete[] MolComponentType;
  delete[] AtomToProcMap;
  delete[] GroupToProcMap;

  delete parallelData;
  // perhaps we should let fortran know the party is over.
  
}

void mpiSimulation::divideLabor( ){

  int nComponents;
  MoleculeStamp** compStamps;
  randomSPRNG *myRandom;
  int* componentsNmol;
  int* AtomsPerProc;
  int* GroupsPerProc;

  double numerator;
  double denominator;
  double precast;
  double x, y, a;
  int old_atoms, add_atoms, new_atoms;
  int old_groups, add_groups, new_groups;

  int nTarget;
  int molIndex, atomIndex, groupIndex;
  int done;
  int i, j, loops, which_proc;
  int nmol_global, nmol_local;
  int ngroups_global, ngroups_local;
  int natoms_global, natoms_local;
  int ncutoff_groups, nAtomsInGroups;
  int local_index;
  int baseSeed = entryPlug->getSeed();
  CutoffGroupStamp* cg;

  nComponents = entryPlug->nComponents;
  compStamps = entryPlug->compStamps;
  componentsNmol = entryPlug->componentsNmol;
  AtomsPerProc = new int[parallelData->nProcessors];
  GroupsPerProc = new int[parallelData->nProcessors];
  
  parallelData->nAtomsGlobal = entryPlug->n_atoms;
  parallelData->nBondsGlobal = entryPlug->n_bonds;
  parallelData->nBendsGlobal = entryPlug->n_bends;
  parallelData->nTorsionsGlobal = entryPlug->n_torsions;
  parallelData->nSRIGlobal = entryPlug->n_SRI;
  parallelData->nGroupsGlobal = entryPlug->ngroup;
  parallelData->nMolGlobal = entryPlug->n_mol;

  if (parallelData->nProcessors > parallelData->nMolGlobal) {
    sprintf( painCave.errMsg,
             "nProcessors (%d) > nMol (%d)\n"
             "\tThe number of processors is larger than\n"
             "\tthe number of molecules.  This will not result in a \n"
             "\tusable division of atoms for force decomposition.\n"
             "\tEither try a smaller number of processors, or run the\n"
             "\tsingle-processor version of OOPSE.\n",
             parallelData->nProcessors, parallelData->nMolGlobal );
    painCave.isFatal = 1;
    simError();
  }

  myRandom = new randomSPRNG( baseSeed );  


  a = 3.0 * (double)parallelData->nMolGlobal / (double)parallelData->nAtomsGlobal;

  // Initialize things that we'll send out later:
  for (i = 0; i < parallelData->nProcessors; i++ ) {
    AtomsPerProc[i] = 0;
    GroupsPerProc[i] = 0;
  }
  for (i = 0; i < parallelData->nMolGlobal; i++ ) {
    // default to an error condition:
    MolToProcMap[i] = -1;
    MolComponentType[i] = -1;
  }
  for (i = 0; i < parallelData->nAtomsGlobal; i++ ) {
    // default to an error condition:
    AtomToProcMap[i] = -1;
  }
  for (i = 0; i < parallelData->nGroupsGlobal; i++ ) {
    // default to an error condition:
    GroupToProcMap[i] = -1;
  }
    
  if (parallelData->myNode == 0) {
    numerator = (double) entryPlug->n_atoms;
    denominator = (double) parallelData->nProcessors;
    precast = numerator / denominator;
    nTarget = (int)( precast + 0.5 );

    // Build the array of molecule component types first
    molIndex = 0;
    for (i=0; i < nComponents; i++) {
      for (j=0; j < componentsNmol[i]; j++) {        
        MolComponentType[molIndex] = i;
        molIndex++;
      }
    }

    atomIndex = 0;
    groupIndex = 0;

    for (i = 0; i < molIndex; i++ ) {

      done = 0;
      loops = 0;

      while( !done ){
        loops++;
        
        // Pick a processor at random

        which_proc = (int) (myRandom->getRandom() * parallelData->nProcessors);

        // How many atoms does this processor have?
        
        old_atoms = AtomsPerProc[which_proc];
        add_atoms = compStamps[MolComponentType[i]]->getNAtoms();
        new_atoms = old_atoms + add_atoms;

        old_groups = GroupsPerProc[which_proc];
        ncutoff_groups = compStamps[MolComponentType[i]]->getNCutoffGroups(); 
        nAtomsInGroups = 0;
        for (j = 0; j < ncutoff_groups; j++) {
          cg = compStamps[MolComponentType[i]]->getCutoffGroup(j);
          nAtomsInGroups += cg->getNMembers();
        }
        add_groups = add_atoms - nAtomsInGroups + ncutoff_groups;        
        new_groups = old_groups + add_groups;

        // If we've been through this loop too many times, we need
        // to just give up and assign the molecule to this processor
        // and be done with it. 
        
        if (loops > 100) {          
          sprintf( painCave.errMsg,
                   "I've tried 100 times to assign molecule %d to a "
                   " processor, but can't find a good spot.\n"  
                   "I'm assigning it at random to processor %d.\n",
                   i, which_proc);
          painCave.isFatal = 0;
          simError();
          
          MolToProcMap[i] = which_proc;
          AtomsPerProc[which_proc] += add_atoms;
          for (j = 0 ; j < add_atoms; j++ ) {
            AtomToProcMap[atomIndex] = which_proc;
            atomIndex++;
          }
          GroupsPerProc[which_proc] += add_groups;
          for (j=0; j < add_groups; j++) {
            GroupToProcMap[groupIndex] = which_proc;
            groupIndex++;
          }
          done = 1;
          continue;
        }
    
        // If we can add this molecule to this processor without sending
        // it above nTarget, then go ahead and do it:
    
        if (new_atoms <= nTarget) {
          MolToProcMap[i] = which_proc;
          AtomsPerProc[which_proc] += add_atoms;
          for (j = 0 ; j < add_atoms; j++ ) {
            AtomToProcMap[atomIndex] = which_proc;
            atomIndex++;
          }
          GroupsPerProc[which_proc] += add_groups;
          for (j=0; j < add_groups; j++) {
            GroupToProcMap[groupIndex] = which_proc;
            groupIndex++;
          }
          done = 1;
          continue;
        }


        // The only situation left is when new_atoms > nTarget.  We
        // want to accept this with some probability that dies off the
        // farther we are from nTarget

        // roughly:  x = new_atoms - nTarget
        //           Pacc(x) = exp(- a * x)
        // where a = penalty / (average atoms per molecule)

        x = (double) (new_atoms - nTarget);
        y = myRandom->getRandom();
      
        if (y < exp(- a * x)) {
          MolToProcMap[i] = which_proc;
          AtomsPerProc[which_proc] += add_atoms;
          for (j = 0 ; j < add_atoms; j++ ) {
            AtomToProcMap[atomIndex] = which_proc;
            atomIndex++;
           }
          GroupsPerProc[which_proc] += add_groups;
          for (j=0; j < add_groups; j++) {
            GroupToProcMap[groupIndex] = which_proc;
            groupIndex++;
          }
          done = 1;
          continue;
        } else {
          continue;
        }       
        
      }
    }


    // Spray out this nonsense to all other processors:

    //std::cerr << "node 0 mol2proc = \n";
    //for (i = 0; i < parallelData->nMolGlobal; i++) 
    //  std::cerr << i << "\t" << MolToProcMap[i] << "\n";

    MPI_Bcast(MolToProcMap, parallelData->nMolGlobal, 
              MPI_INT, 0, MPI_COMM_WORLD);

    MPI_Bcast(AtomToProcMap, parallelData->nAtomsGlobal, 
              MPI_INT, 0, MPI_COMM_WORLD);

    MPI_Bcast(GroupToProcMap, parallelData->nGroupsGlobal, 
              MPI_INT, 0, MPI_COMM_WORLD);

    MPI_Bcast(MolComponentType, parallelData->nMolGlobal, 
              MPI_INT, 0, MPI_COMM_WORLD);

    MPI_Bcast(AtomsPerProc, parallelData->nProcessors,
              MPI_INT, 0, MPI_COMM_WORLD);    

    MPI_Bcast(GroupsPerProc, parallelData->nProcessors,
              MPI_INT, 0, MPI_COMM_WORLD);    
  } else {

    // Listen to your marching orders from processor 0:
    
    MPI_Bcast(MolToProcMap, parallelData->nMolGlobal, 
              MPI_INT, 0, MPI_COMM_WORLD);
    
    MPI_Bcast(AtomToProcMap, parallelData->nAtomsGlobal, 
              MPI_INT, 0, MPI_COMM_WORLD);

    MPI_Bcast(GroupToProcMap, parallelData->nGroupsGlobal, 
              MPI_INT, 0, MPI_COMM_WORLD);

    MPI_Bcast(MolComponentType, parallelData->nMolGlobal, 
              MPI_INT, 0, MPI_COMM_WORLD);
    
    MPI_Bcast(AtomsPerProc, parallelData->nProcessors,
              MPI_INT, 0, MPI_COMM_WORLD);

    MPI_Bcast(GroupsPerProc, parallelData->nProcessors,
              MPI_INT, 0, MPI_COMM_WORLD);


  }

  // Let's all check for sanity:

  nmol_local = 0;
  for (i = 0 ; i < parallelData->nMolGlobal; i++ ) {
    if (MolToProcMap[i] == parallelData->myNode) {
      nmol_local++;
    }
  }

  natoms_local = 0;
  for (i = 0; i < parallelData->nAtomsGlobal; i++) {
    if (AtomToProcMap[i] == parallelData->myNode) {
      natoms_local++;      
    }
  }

  ngroups_local = 0;
  for (i = 0; i < parallelData->nGroupsGlobal; i++) {
    if (GroupToProcMap[i] == parallelData->myNode) {
      ngroups_local++;      
    }
  }

  MPI_Allreduce(&nmol_local,&nmol_global,1,MPI_INT,MPI_SUM, 
                MPI_COMM_WORLD);

  MPI_Allreduce(&natoms_local,&natoms_global,1,MPI_INT,
                MPI_SUM, MPI_COMM_WORLD);

  MPI_Allreduce(&ngroups_local,&ngroups_global,1,MPI_INT,
                MPI_SUM, MPI_COMM_WORLD);
  
  if( nmol_global != entryPlug->n_mol ){
    sprintf( painCave.errMsg,
             "The sum of all nmol_local, %d, did not equal the "
             "total number of molecules, %d.\n",
             nmol_global, entryPlug->n_mol );
    painCave.isFatal = 1;
    simError();
  }
  
  if( natoms_global != entryPlug->n_atoms ){
    sprintf( painCave.errMsg,
             "The sum of all natoms_local, %d, did not equal the "
             "total number of atoms, %d.\n",
             natoms_global, entryPlug->n_atoms );
    painCave.isFatal = 1;
    simError();
  }

  if( ngroups_global != entryPlug->ngroup ){
    sprintf( painCave.errMsg,
             "The sum of all ngroups_local, %d, did not equal the "
             "total number of cutoffGroups, %d.\n",
             ngroups_global, entryPlug->ngroup );
    painCave.isFatal = 1;
    simError();
  }

  sprintf( checkPointMsg,
           "Successfully divided the molecules among the processors.\n" );
  MPIcheckPoint();

  parallelData->nMolLocal = nmol_local;
  parallelData->nAtomsLocal = natoms_local;
  parallelData->nGroupsLocal = ngroups_local;

  globalAtomIndex.resize(parallelData->nAtomsLocal);
  globalToLocalAtom.resize(parallelData->nAtomsGlobal);
  local_index = 0;
  for (i = 0; i < parallelData->nAtomsGlobal; i++) {
    if (AtomToProcMap[i] == parallelData->myNode) {
      globalAtomIndex[local_index] = i;

      globalToLocalAtom[i] = local_index;
      local_index++;
      
    }
    else
       globalToLocalAtom[i] = -1;
  }

  globalGroupIndex.resize(parallelData->nGroupsLocal);
  globalToLocalGroup.resize(parallelData->nGroupsGlobal);
  local_index = 0;
  for (i = 0; i < parallelData->nGroupsGlobal; i++) {
    if (GroupToProcMap[i] == parallelData->myNode) {
      globalGroupIndex[local_index] = i;

      globalToLocalGroup[i] = local_index;
      local_index++;
      
    }
    else
       globalToLocalGroup[i] = -1;
  }

  globalMolIndex.resize(parallelData->nMolLocal);
  globalToLocalMol.resize(parallelData->nMolGlobal);  
  local_index = 0;
  for (i = 0; i < parallelData->nMolGlobal; i++) {
    if (MolToProcMap[i] == parallelData->myNode) {
      globalMolIndex[local_index] = i;
      globalToLocalMol[i] = local_index;
      local_index++;
    }
    else
      globalToLocalMol[i] = -1;
  }
  
}


void mpiSimulation::mpiRefresh( void ){

  int isError, i;
  int *localToGlobalAtomIndex = new int[parallelData->nAtomsLocal];
  int *localToGlobalGroupIndex = new int[parallelData->nGroupsLocal];

  // Fortran indexing needs to be increased by 1 in order to get the 2
  // languages to not barf

  for(i = 0; i < parallelData->nAtomsLocal; i++) 
    localToGlobalAtomIndex[i] = globalAtomIndex[i] + 1;

  for(i = 0; i < parallelData->nGroupsLocal; i++) 
    localToGlobalGroupIndex[i] = globalGroupIndex[i] + 1;
  
  isError = 0;

  setFsimParallel( parallelData, 
                   &(parallelData->nAtomsLocal), localToGlobalAtomIndex, 
                   &(parallelData->nGroupsLocal),  localToGlobalGroupIndex, 
                   &isError );

  if( isError ){

    sprintf( painCave.errMsg,
             "mpiRefresh errror: fortran didn't like something we gave it.\n" );
    painCave.isFatal = 1;
    simError();
  }

  delete[] localToGlobalGroupIndex;
  delete[] localToGlobalAtomIndex;


  sprintf( checkPointMsg,
           " mpiRefresh successful.\n" );
  MPIcheckPoint();
}
 

#endif // is_mpi
Revision:	3
Committed:	Fri Sep 24 16:27:58 2004 UTC (20 years, 7 months ago) by tim
File size:	13058 byte(s)
Log Message:	change the #include in source files
#	User	Rev	Content
1	gezelter	2	#ifdef IS_MPI
2			#include <iostream>
3			#include <stdlib.h>
4			#include <string.h>
5			#include <math.h>
6			#include <mpi.h>
7
8	tim	3	#include "brains/mpiSimulation.hpp"
9			#include "utils/simError.h"
10			#include "UseTheForce/fortranWrappers.hpp"
11			#include "math/randomSPRNG.hpp"
12	gezelter	2
13			mpiSimulation* mpiSim;
14
15			mpiSimulation::mpiSimulation(SimInfo* the_entryPlug)
16			{
17			entryPlug = the_entryPlug;
18			parallelData = new mpiSimData;
19
20			MPI_Comm_size(MPI_COMM_WORLD, &(parallelData->nProcessors) );
21			parallelData->myNode = worldRank;
22
23			MolToProcMap = new int[entryPlug->n_mol];
24			MolComponentType = new int[entryPlug->n_mol];
25			AtomToProcMap = new int[entryPlug->n_atoms];
26			GroupToProcMap = new int[entryPlug->ngroup];
27
28			mpiSim = this;
29			wrapMeSimParallel( this );
30			}
31
32
33			mpiSimulation::~mpiSimulation(){
34
35			delete[] MolToProcMap;
36			delete[] MolComponentType;
37			delete[] AtomToProcMap;
38			delete[] GroupToProcMap;
39
40			delete parallelData;
41			// perhaps we should let fortran know the party is over.
42
43			}
44
45			void mpiSimulation::divideLabor( ){
46
47			int nComponents;
48			MoleculeStamp** compStamps;
49			randomSPRNG *myRandom;
50			int* componentsNmol;
51			int* AtomsPerProc;
52			int* GroupsPerProc;
53
54			double numerator;
55			double denominator;
56			double precast;
57			double x, y, a;
58			int old_atoms, add_atoms, new_atoms;
59			int old_groups, add_groups, new_groups;
60
61			int nTarget;
62			int molIndex, atomIndex, groupIndex;
63			int done;
64			int i, j, loops, which_proc;
65			int nmol_global, nmol_local;
66			int ngroups_global, ngroups_local;
67			int natoms_global, natoms_local;
68			int ncutoff_groups, nAtomsInGroups;
69			int local_index;
70			int baseSeed = entryPlug->getSeed();
71			CutoffGroupStamp* cg;
72
73			nComponents = entryPlug->nComponents;
74			compStamps = entryPlug->compStamps;
75			componentsNmol = entryPlug->componentsNmol;
76			AtomsPerProc = new int[parallelData->nProcessors];
77			GroupsPerProc = new int[parallelData->nProcessors];
78
79			parallelData->nAtomsGlobal = entryPlug->n_atoms;
80			parallelData->nBondsGlobal = entryPlug->n_bonds;
81			parallelData->nBendsGlobal = entryPlug->n_bends;
82			parallelData->nTorsionsGlobal = entryPlug->n_torsions;
83			parallelData->nSRIGlobal = entryPlug->n_SRI;
84			parallelData->nGroupsGlobal = entryPlug->ngroup;
85			parallelData->nMolGlobal = entryPlug->n_mol;
86
87			if (parallelData->nProcessors > parallelData->nMolGlobal) {
88			sprintf( painCave.errMsg,
89			"nProcessors (%d) > nMol (%d)\n"
90			"\tThe number of processors is larger than\n"
91			"\tthe number of molecules. This will not result in a \n"
92			"\tusable division of atoms for force decomposition.\n"
93			"\tEither try a smaller number of processors, or run the\n"
94			"\tsingle-processor version of OOPSE.\n",
95			parallelData->nProcessors, parallelData->nMolGlobal );
96			painCave.isFatal = 1;
97			simError();
98			}
99
100			myRandom = new randomSPRNG( baseSeed );
101
102
103			a = 3.0 * (double)parallelData->nMolGlobal / (double)parallelData->nAtomsGlobal;
104
105			// Initialize things that we'll send out later:
106			for (i = 0; i < parallelData->nProcessors; i++ ) {
107			AtomsPerProc[i] = 0;
108			GroupsPerProc[i] = 0;
109			}
110			for (i = 0; i < parallelData->nMolGlobal; i++ ) {
111			// default to an error condition:
112			MolToProcMap[i] = -1;
113			MolComponentType[i] = -1;
114			}
115			for (i = 0; i < parallelData->nAtomsGlobal; i++ ) {
116			// default to an error condition:
117			AtomToProcMap[i] = -1;
118			}
119			for (i = 0; i < parallelData->nGroupsGlobal; i++ ) {
120			// default to an error condition:
121			GroupToProcMap[i] = -1;
122			}
123
124			if (parallelData->myNode == 0) {
125			numerator = (double) entryPlug->n_atoms;
126			denominator = (double) parallelData->nProcessors;
127			precast = numerator / denominator;
128			nTarget = (int)( precast + 0.5 );
129
130			// Build the array of molecule component types first
131			molIndex = 0;
132			for (i=0; i < nComponents; i++) {
133			for (j=0; j < componentsNmol[i]; j++) {
134			MolComponentType[molIndex] = i;
135			molIndex++;
136			}
137			}
138
139			atomIndex = 0;
140			groupIndex = 0;
141
142			for (i = 0; i < molIndex; i++ ) {
143
144			done = 0;
145			loops = 0;
146
147			while( !done ){
148			loops++;
149
150			// Pick a processor at random
151
152			which_proc = (int) (myRandom->getRandom() * parallelData->nProcessors);
153
154			// How many atoms does this processor have?
155
156			old_atoms = AtomsPerProc[which_proc];
157			add_atoms = compStamps[MolComponentType[i]]->getNAtoms();
158			new_atoms = old_atoms + add_atoms;
159
160			old_groups = GroupsPerProc[which_proc];
161			ncutoff_groups = compStamps[MolComponentType[i]]->getNCutoffGroups();
162			nAtomsInGroups = 0;
163			for (j = 0; j < ncutoff_groups; j++) {
164			cg = compStamps[MolComponentType[i]]->getCutoffGroup(j);
165			nAtomsInGroups += cg->getNMembers();
166			}
167			add_groups = add_atoms - nAtomsInGroups + ncutoff_groups;
168			new_groups = old_groups + add_groups;
169
170			// If we've been through this loop too many times, we need
171			// to just give up and assign the molecule to this processor
172			// and be done with it.
173
174			if (loops > 100) {
175			sprintf( painCave.errMsg,
176			"I've tried 100 times to assign molecule %d to a "
177			" processor, but can't find a good spot.\n"
178			"I'm assigning it at random to processor %d.\n",
179			i, which_proc);
180			painCave.isFatal = 0;
181			simError();
182
183			MolToProcMap[i] = which_proc;
184			AtomsPerProc[which_proc] += add_atoms;
185			for (j = 0 ; j < add_atoms; j++ ) {
186			AtomToProcMap[atomIndex] = which_proc;
187			atomIndex++;
188			}
189			GroupsPerProc[which_proc] += add_groups;
190			for (j=0; j < add_groups; j++) {
191			GroupToProcMap[groupIndex] = which_proc;
192			groupIndex++;
193			}
194			done = 1;
195			continue;
196			}
197
198			// If we can add this molecule to this processor without sending
199			// it above nTarget, then go ahead and do it:
200
201			if (new_atoms <= nTarget) {
202			MolToProcMap[i] = which_proc;
203			AtomsPerProc[which_proc] += add_atoms;
204			for (j = 0 ; j < add_atoms; j++ ) {
205			AtomToProcMap[atomIndex] = which_proc;
206			atomIndex++;
207			}
208			GroupsPerProc[which_proc] += add_groups;
209			for (j=0; j < add_groups; j++) {
210			GroupToProcMap[groupIndex] = which_proc;
211			groupIndex++;
212			}
213			done = 1;
214			continue;
215			}
216
217
218			// The only situation left is when new_atoms > nTarget. We
219			// want to accept this with some probability that dies off the
220			// farther we are from nTarget
221
222			// roughly: x = new_atoms - nTarget
223			// Pacc(x) = exp(- a * x)
224			// where a = penalty / (average atoms per molecule)
225
226			x = (double) (new_atoms - nTarget);
227			y = myRandom->getRandom();
228
229			if (y < exp(- a * x)) {
230			MolToProcMap[i] = which_proc;
231			AtomsPerProc[which_proc] += add_atoms;
232			for (j = 0 ; j < add_atoms; j++ ) {
233			AtomToProcMap[atomIndex] = which_proc;
234			atomIndex++;
235			}
236			GroupsPerProc[which_proc] += add_groups;
237			for (j=0; j < add_groups; j++) {
238			GroupToProcMap[groupIndex] = which_proc;
239			groupIndex++;
240			}
241			done = 1;
242			continue;
243			} else {
244			continue;
245			}
246
247			}
248			}
249
250
251			// Spray out this nonsense to all other processors:
252
253			//std::cerr << "node 0 mol2proc = \n";
254			//for (i = 0; i < parallelData->nMolGlobal; i++)
255			// std::cerr << i << "\t" << MolToProcMap[i] << "\n";
256
257			MPI_Bcast(MolToProcMap, parallelData->nMolGlobal,
258			MPI_INT, 0, MPI_COMM_WORLD);
259
260			MPI_Bcast(AtomToProcMap, parallelData->nAtomsGlobal,
261			MPI_INT, 0, MPI_COMM_WORLD);
262
263			MPI_Bcast(GroupToProcMap, parallelData->nGroupsGlobal,
264			MPI_INT, 0, MPI_COMM_WORLD);
265
266			MPI_Bcast(MolComponentType, parallelData->nMolGlobal,
267			MPI_INT, 0, MPI_COMM_WORLD);
268
269			MPI_Bcast(AtomsPerProc, parallelData->nProcessors,
270			MPI_INT, 0, MPI_COMM_WORLD);
271
272			MPI_Bcast(GroupsPerProc, parallelData->nProcessors,
273			MPI_INT, 0, MPI_COMM_WORLD);
274			} else {
275
276			// Listen to your marching orders from processor 0:
277
278			MPI_Bcast(MolToProcMap, parallelData->nMolGlobal,
279			MPI_INT, 0, MPI_COMM_WORLD);
280
281			MPI_Bcast(AtomToProcMap, parallelData->nAtomsGlobal,
282			MPI_INT, 0, MPI_COMM_WORLD);
283
284			MPI_Bcast(GroupToProcMap, parallelData->nGroupsGlobal,
285			MPI_INT, 0, MPI_COMM_WORLD);
286
287			MPI_Bcast(MolComponentType, parallelData->nMolGlobal,
288			MPI_INT, 0, MPI_COMM_WORLD);
289
290			MPI_Bcast(AtomsPerProc, parallelData->nProcessors,
291			MPI_INT, 0, MPI_COMM_WORLD);
292
293			MPI_Bcast(GroupsPerProc, parallelData->nProcessors,
294			MPI_INT, 0, MPI_COMM_WORLD);
295
296
297			}
298
299			// Let's all check for sanity:
300
301			nmol_local = 0;
302			for (i = 0 ; i < parallelData->nMolGlobal; i++ ) {
303			if (MolToProcMap[i] == parallelData->myNode) {
304			nmol_local++;
305			}
306			}
307
308			natoms_local = 0;
309			for (i = 0; i < parallelData->nAtomsGlobal; i++) {
310			if (AtomToProcMap[i] == parallelData->myNode) {
311			natoms_local++;
312			}
313			}
314
315			ngroups_local = 0;
316			for (i = 0; i < parallelData->nGroupsGlobal; i++) {
317			if (GroupToProcMap[i] == parallelData->myNode) {
318			ngroups_local++;
319			}
320			}
321
322			MPI_Allreduce(&nmol_local,&nmol_global,1,MPI_INT,MPI_SUM,
323			MPI_COMM_WORLD);
324
325			MPI_Allreduce(&natoms_local,&natoms_global,1,MPI_INT,
326			MPI_SUM, MPI_COMM_WORLD);
327
328			MPI_Allreduce(&ngroups_local,&ngroups_global,1,MPI_INT,
329			MPI_SUM, MPI_COMM_WORLD);
330
331			if( nmol_global != entryPlug->n_mol ){
332			sprintf( painCave.errMsg,
333			"The sum of all nmol_local, %d, did not equal the "
334			"total number of molecules, %d.\n",
335			nmol_global, entryPlug->n_mol );
336			painCave.isFatal = 1;
337			simError();
338			}
339
340			if( natoms_global != entryPlug->n_atoms ){
341			sprintf( painCave.errMsg,
342			"The sum of all natoms_local, %d, did not equal the "
343			"total number of atoms, %d.\n",
344			natoms_global, entryPlug->n_atoms );
345			painCave.isFatal = 1;
346			simError();
347			}
348
349			if( ngroups_global != entryPlug->ngroup ){
350			sprintf( painCave.errMsg,
351			"The sum of all ngroups_local, %d, did not equal the "
352			"total number of cutoffGroups, %d.\n",
353			ngroups_global, entryPlug->ngroup );
354			painCave.isFatal = 1;
355			simError();
356			}
357
358			sprintf( checkPointMsg,
359			"Successfully divided the molecules among the processors.\n" );
360			MPIcheckPoint();
361
362			parallelData->nMolLocal = nmol_local;
363			parallelData->nAtomsLocal = natoms_local;
364			parallelData->nGroupsLocal = ngroups_local;
365
366			globalAtomIndex.resize(parallelData->nAtomsLocal);
367			globalToLocalAtom.resize(parallelData->nAtomsGlobal);
368			local_index = 0;
369			for (i = 0; i < parallelData->nAtomsGlobal; i++) {
370			if (AtomToProcMap[i] == parallelData->myNode) {
371			globalAtomIndex[local_index] = i;
372
373			globalToLocalAtom[i] = local_index;
374			local_index++;
375
376			}
377			else
378			globalToLocalAtom[i] = -1;
379			}
380
381			globalGroupIndex.resize(parallelData->nGroupsLocal);
382			globalToLocalGroup.resize(parallelData->nGroupsGlobal);
383			local_index = 0;
384			for (i = 0; i < parallelData->nGroupsGlobal; i++) {
385			if (GroupToProcMap[i] == parallelData->myNode) {
386			globalGroupIndex[local_index] = i;
387
388			globalToLocalGroup[i] = local_index;
389			local_index++;
390
391			}
392			else
393			globalToLocalGroup[i] = -1;
394			}
395
396			globalMolIndex.resize(parallelData->nMolLocal);
397			globalToLocalMol.resize(parallelData->nMolGlobal);
398			local_index = 0;
399			for (i = 0; i < parallelData->nMolGlobal; i++) {
400			if (MolToProcMap[i] == parallelData->myNode) {
401			globalMolIndex[local_index] = i;
402			globalToLocalMol[i] = local_index;
403			local_index++;
404			}
405			else
406			globalToLocalMol[i] = -1;
407			}
408
409			}
410
411
412			void mpiSimulation::mpiRefresh( void ){
413
414			int isError, i;
415			int *localToGlobalAtomIndex = new int[parallelData->nAtomsLocal];
416			int *localToGlobalGroupIndex = new int[parallelData->nGroupsLocal];
417
418			// Fortran indexing needs to be increased by 1 in order to get the 2
419			// languages to not barf
420
421			for(i = 0; i < parallelData->nAtomsLocal; i++)
422			localToGlobalAtomIndex[i] = globalAtomIndex[i] + 1;
423
424			for(i = 0; i < parallelData->nGroupsLocal; i++)
425			localToGlobalGroupIndex[i] = globalGroupIndex[i] + 1;
426
427			isError = 0;
428
429			setFsimParallel( parallelData,
430			&(parallelData->nAtomsLocal), localToGlobalAtomIndex,
431			&(parallelData->nGroupsLocal), localToGlobalGroupIndex,
432			&isError );
433
434			if( isError ){
435
436			sprintf( painCave.errMsg,
437			"mpiRefresh errror: fortran didn't like something we gave it.\n" );
438			painCave.isFatal = 1;
439			simError();
440			}
441
442			delete[] localToGlobalGroupIndex;
443			delete[] localToGlobalAtomIndex;
444
445
446			sprintf( checkPointMsg,
447			" mpiRefresh successful.\n" );
448			MPIcheckPoint();
449			}
450
451
452			#endif // is_mpi