OOPSE-1.0/libmdtools/mpiSimulation.cpp

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

#include "mpiSimulation.hpp"
#include "simError.h"
#include "fortranWrappers.hpp"
#include "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;

  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:	1334
Committed:	Fri Jul 16 18:58:03 2004 UTC (20 years ago) by gezelter
File size:	12444 byte(s)
Log Message:	Initial import of OOPSE-1.0 source tree
#	User	Rev	Content
1	gezelter	1334	#ifdef IS_MPI
2			#include <iostream>
3			#include <stdlib.h>
4			#include <string.h>
5			#include <math.h>
6			#include <mpi.h>
7
8			#include "mpiSimulation.hpp"
9			#include "simError.h"
10			#include "fortranWrappers.hpp"
11			#include "randomSPRNG.hpp"
12
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			myRandom = new randomSPRNG( baseSeed );
88
89			a = 3.0 * (double)parallelData->nMolGlobal / (double)parallelData->nAtomsGlobal;
90
91			// Initialize things that we'll send out later:
92			for (i = 0; i < parallelData->nProcessors; i++ ) {
93			AtomsPerProc[i] = 0;
94			GroupsPerProc[i] = 0;
95			}
96			for (i = 0; i < parallelData->nMolGlobal; i++ ) {
97			// default to an error condition:
98			MolToProcMap[i] = -1;
99			MolComponentType[i] = -1;
100			}
101			for (i = 0; i < parallelData->nAtomsGlobal; i++ ) {
102			// default to an error condition:
103			AtomToProcMap[i] = -1;
104			}
105			for (i = 0; i < parallelData->nGroupsGlobal; i++ ) {
106			// default to an error condition:
107			GroupToProcMap[i] = -1;
108			}
109
110			if (parallelData->myNode == 0) {
111			numerator = (double) entryPlug->n_atoms;
112			denominator = (double) parallelData->nProcessors;
113			precast = numerator / denominator;
114			nTarget = (int)( precast + 0.5 );
115
116			// Build the array of molecule component types first
117			molIndex = 0;
118			for (i=0; i < nComponents; i++) {
119			for (j=0; j < componentsNmol[i]; j++) {
120			MolComponentType[molIndex] = i;
121			molIndex++;
122			}
123			}
124
125			atomIndex = 0;
126			groupIndex = 0;
127
128			for (i = 0; i < molIndex; i++ ) {
129
130			done = 0;
131			loops = 0;
132
133			while( !done ){
134			loops++;
135
136			// Pick a processor at random
137
138			which_proc = (int) (myRandom->getRandom() * parallelData->nProcessors);
139
140			// How many atoms does this processor have?
141
142			old_atoms = AtomsPerProc[which_proc];
143			add_atoms = compStamps[MolComponentType[i]]->getNAtoms();
144			new_atoms = old_atoms + add_atoms;
145
146			old_groups = GroupsPerProc[which_proc];
147			ncutoff_groups = compStamps[MolComponentType[i]]->getNCutoffGroups();
148			nAtomsInGroups = 0;
149			for (j = 0; j < ncutoff_groups; j++) {
150			cg = compStamps[MolComponentType[i]]->getCutoffGroup(j);
151			nAtomsInGroups += cg->getNMembers();
152			}
153			add_groups = add_atoms - nAtomsInGroups + ncutoff_groups;
154			new_groups = old_groups + add_groups;
155
156			// If we've been through this loop too many times, we need
157			// to just give up and assign the molecule to this processor
158			// and be done with it.
159
160			if (loops > 100) {
161			sprintf( painCave.errMsg,
162			"I've tried 100 times to assign molecule %d to a "
163			" processor, but can't find a good spot.\n"
164			"I'm assigning it at random to processor %d.\n",
165			i, which_proc);
166			painCave.isFatal = 0;
167			simError();
168
169			MolToProcMap[i] = which_proc;
170			AtomsPerProc[which_proc] += add_atoms;
171			for (j = 0 ; j < add_atoms; j++ ) {
172			AtomToProcMap[atomIndex] = which_proc;
173			atomIndex++;
174			}
175			GroupsPerProc[which_proc] += add_groups;
176			for (j=0; j < add_groups; j++) {
177			GroupToProcMap[groupIndex] = which_proc;
178			groupIndex++;
179			}
180			done = 1;
181			continue;
182			}
183
184			// If we can add this molecule to this processor without sending
185			// it above nTarget, then go ahead and do it:
186
187			if (new_atoms <= nTarget) {
188			MolToProcMap[i] = which_proc;
189			AtomsPerProc[which_proc] += add_atoms;
190			for (j = 0 ; j < add_atoms; j++ ) {
191			AtomToProcMap[atomIndex] = which_proc;
192			atomIndex++;
193			}
194			GroupsPerProc[which_proc] += add_groups;
195			for (j=0; j < add_groups; j++) {
196			GroupToProcMap[groupIndex] = which_proc;
197			groupIndex++;
198			}
199			done = 1;
200			continue;
201			}
202
203
204			// The only situation left is when new_atoms > nTarget. We
205			// want to accept this with some probability that dies off the
206			// farther we are from nTarget
207
208			// roughly: x = new_atoms - nTarget
209			// Pacc(x) = exp(- a * x)
210			// where a = penalty / (average atoms per molecule)
211
212			x = (double) (new_atoms - nTarget);
213			y = myRandom->getRandom();
214
215			if (y < exp(- a * x)) {
216			MolToProcMap[i] = which_proc;
217			AtomsPerProc[which_proc] += add_atoms;
218			for (j = 0 ; j < add_atoms; j++ ) {
219			AtomToProcMap[atomIndex] = which_proc;
220			atomIndex++;
221			}
222			GroupsPerProc[which_proc] += add_groups;
223			for (j=0; j < add_groups; j++) {
224			GroupToProcMap[groupIndex] = which_proc;
225			groupIndex++;
226			}
227			done = 1;
228			continue;
229			} else {
230			continue;
231			}
232
233			}
234			}
235
236
237			// Spray out this nonsense to all other processors:
238
239			//std::cerr << "node 0 mol2proc = \n";
240			//for (i = 0; i < parallelData->nMolGlobal; i++)
241			// std::cerr << i << "\t" << MolToProcMap[i] << "\n";
242
243			MPI_Bcast(MolToProcMap, parallelData->nMolGlobal,
244			MPI_INT, 0, MPI_COMM_WORLD);
245
246			MPI_Bcast(AtomToProcMap, parallelData->nAtomsGlobal,
247			MPI_INT, 0, MPI_COMM_WORLD);
248
249			MPI_Bcast(GroupToProcMap, parallelData->nGroupsGlobal,
250			MPI_INT, 0, MPI_COMM_WORLD);
251
252			MPI_Bcast(MolComponentType, parallelData->nMolGlobal,
253			MPI_INT, 0, MPI_COMM_WORLD);
254
255			MPI_Bcast(AtomsPerProc, parallelData->nProcessors,
256			MPI_INT, 0, MPI_COMM_WORLD);
257
258			MPI_Bcast(GroupsPerProc, parallelData->nProcessors,
259			MPI_INT, 0, MPI_COMM_WORLD);
260			} else {
261
262			// Listen to your marching orders from processor 0:
263
264			MPI_Bcast(MolToProcMap, parallelData->nMolGlobal,
265			MPI_INT, 0, MPI_COMM_WORLD);
266
267			MPI_Bcast(AtomToProcMap, parallelData->nAtomsGlobal,
268			MPI_INT, 0, MPI_COMM_WORLD);
269
270			MPI_Bcast(GroupToProcMap, parallelData->nGroupsGlobal,
271			MPI_INT, 0, MPI_COMM_WORLD);
272
273			MPI_Bcast(MolComponentType, parallelData->nMolGlobal,
274			MPI_INT, 0, MPI_COMM_WORLD);
275
276			MPI_Bcast(AtomsPerProc, parallelData->nProcessors,
277			MPI_INT, 0, MPI_COMM_WORLD);
278
279			MPI_Bcast(GroupsPerProc, parallelData->nProcessors,
280			MPI_INT, 0, MPI_COMM_WORLD);
281
282
283			}
284
285			// Let's all check for sanity:
286
287			nmol_local = 0;
288			for (i = 0 ; i < parallelData->nMolGlobal; i++ ) {
289			if (MolToProcMap[i] == parallelData->myNode) {
290			nmol_local++;
291			}
292			}
293
294			natoms_local = 0;
295			for (i = 0; i < parallelData->nAtomsGlobal; i++) {
296			if (AtomToProcMap[i] == parallelData->myNode) {
297			natoms_local++;
298			}
299			}
300
301			ngroups_local = 0;
302			for (i = 0; i < parallelData->nGroupsGlobal; i++) {
303			if (GroupToProcMap[i] == parallelData->myNode) {
304			ngroups_local++;
305			}
306			}
307
308			MPI_Allreduce(&nmol_local,&nmol_global,1,MPI_INT,MPI_SUM,
309			MPI_COMM_WORLD);
310
311			MPI_Allreduce(&natoms_local,&natoms_global,1,MPI_INT,
312			MPI_SUM, MPI_COMM_WORLD);
313
314			MPI_Allreduce(&ngroups_local,&ngroups_global,1,MPI_INT,
315			MPI_SUM, MPI_COMM_WORLD);
316
317			if( nmol_global != entryPlug->n_mol ){
318			sprintf( painCave.errMsg,
319			"The sum of all nmol_local, %d, did not equal the "
320			"total number of molecules, %d.\n",
321			nmol_global, entryPlug->n_mol );
322			painCave.isFatal = 1;
323			simError();
324			}
325
326			if( natoms_global != entryPlug->n_atoms ){
327			sprintf( painCave.errMsg,
328			"The sum of all natoms_local, %d, did not equal the "
329			"total number of atoms, %d.\n",
330			natoms_global, entryPlug->n_atoms );
331			painCave.isFatal = 1;
332			simError();
333			}
334
335			if( ngroups_global != entryPlug->ngroup ){
336			sprintf( painCave.errMsg,
337			"The sum of all ngroups_local, %d, did not equal the "
338			"total number of cutoffGroups, %d.\n",
339			ngroups_global, entryPlug->ngroup );
340			painCave.isFatal = 1;
341			simError();
342			}
343
344			sprintf( checkPointMsg,
345			"Successfully divided the molecules among the processors.\n" );
346			MPIcheckPoint();
347
348			parallelData->nMolLocal = nmol_local;
349			parallelData->nAtomsLocal = natoms_local;
350			parallelData->nGroupsLocal = ngroups_local;
351
352			globalAtomIndex.resize(parallelData->nAtomsLocal);
353			globalToLocalAtom.resize(parallelData->nAtomsGlobal);
354			local_index = 0;
355			for (i = 0; i < parallelData->nAtomsGlobal; i++) {
356			if (AtomToProcMap[i] == parallelData->myNode) {
357			globalAtomIndex[local_index] = i;
358
359			globalToLocalAtom[i] = local_index;
360			local_index++;
361
362			}
363			else
364			globalToLocalAtom[i] = -1;
365			}
366
367			globalGroupIndex.resize(parallelData->nGroupsLocal);
368			globalToLocalGroup.resize(parallelData->nGroupsGlobal);
369			local_index = 0;
370			for (i = 0; i < parallelData->nGroupsGlobal; i++) {
371			if (GroupToProcMap[i] == parallelData->myNode) {
372			globalGroupIndex[local_index] = i;
373
374			globalToLocalGroup[i] = local_index;
375			local_index++;
376
377			}
378			else
379			globalToLocalGroup[i] = -1;
380			}
381
382			globalMolIndex.resize(parallelData->nMolLocal);
383			globalToLocalMol.resize(parallelData->nMolGlobal);
384			local_index = 0;
385			for (i = 0; i < parallelData->nMolGlobal; i++) {
386			if (MolToProcMap[i] == parallelData->myNode) {
387			globalMolIndex[local_index] = i;
388			globalToLocalMol[i] = local_index;
389			local_index++;
390			}
391			else
392			globalToLocalMol[i] = -1;
393			}
394
395			}
396
397
398			void mpiSimulation::mpiRefresh( void ){
399
400			int isError, i;
401			int *localToGlobalAtomIndex = new int[parallelData->nAtomsLocal];
402			int *localToGlobalGroupIndex = new int[parallelData->nGroupsLocal];
403
404			// Fortran indexing needs to be increased by 1 in order to get the 2
405			// languages to not barf
406
407			for(i = 0; i < parallelData->nAtomsLocal; i++)
408			localToGlobalAtomIndex[i] = globalAtomIndex[i] + 1;
409
410			for(i = 0; i < parallelData->nGroupsLocal; i++)
411			localToGlobalGroupIndex[i] = globalGroupIndex[i] + 1;
412
413			isError = 0;
414
415			setFsimParallel( parallelData,
416			&(parallelData->nAtomsLocal), localToGlobalAtomIndex,
417			&(parallelData->nGroupsLocal), localToGlobalGroupIndex,
418			&isError );
419
420			if( isError ){
421
422			sprintf( painCave.errMsg,
423			"mpiRefresh errror: fortran didn't like something we gave it.\n" );
424			painCave.isFatal = 1;
425			simError();
426			}
427
428			delete[] localToGlobalGroupIndex;
429			delete[] localToGlobalAtomIndex;
430
431
432			sprintf( checkPointMsg,
433			" mpiRefresh successful.\n" );
434			MPIcheckPoint();
435			}
436
437
438			#endif // is_mpi