OOPSE/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:

    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 *globalAtomIndex = new int[parallelData->nAtomsLocal];

  // 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++) globalAtomIndex[i] = entryPlug->atoms[i]->getGlobalIndex()+1;
  
  isError = 0;
  setFsimParallel( parallelData, &(entryPlug->n_atoms), globalAtomIndex, &isError );
  if( isError ){

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

  delete[] globalAtomIndex;


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

#endif // is_mpi
Revision:	1203
Committed:	Thu May 27 18:59:17 2004 UTC (20 years, 1 month ago) by gezelter
File size:	11925 byte(s)
Log Message:	Cutoff group changes under MPI
#	Content
1	#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	MPI_Bcast(MolToProcMap, parallelData->nMolGlobal,
240	MPI_INT, 0, MPI_COMM_WORLD);
241
242	MPI_Bcast(AtomToProcMap, parallelData->nAtomsGlobal,
243	MPI_INT, 0, MPI_COMM_WORLD);
244
245	MPI_Bcast(GroupToProcMap, parallelData->nGroupsGlobal,
246	MPI_INT, 0, MPI_COMM_WORLD);
247
248	MPI_Bcast(MolComponentType, parallelData->nMolGlobal,
249	MPI_INT, 0, MPI_COMM_WORLD);
250
251	MPI_Bcast(AtomsPerProc, parallelData->nProcessors,
252	MPI_INT, 0, MPI_COMM_WORLD);
253
254	MPI_Bcast(GroupsPerProc, parallelData->nProcessors,
255	MPI_INT, 0, MPI_COMM_WORLD);
256	} else {
257
258	// Listen to your marching orders from processor 0:
259
260	MPI_Bcast(MolToProcMap, parallelData->nMolGlobal,
261	MPI_INT, 0, MPI_COMM_WORLD);
262
263	MPI_Bcast(AtomToProcMap, parallelData->nAtomsGlobal,
264	MPI_INT, 0, MPI_COMM_WORLD);
265
266	MPI_Bcast(GroupToProcMap, parallelData->nGroupsGlobal,
267	MPI_INT, 0, MPI_COMM_WORLD);
268
269	MPI_Bcast(MolComponentType, parallelData->nMolGlobal,
270	MPI_INT, 0, MPI_COMM_WORLD);
271
272	MPI_Bcast(AtomsPerProc, parallelData->nProcessors,
273	MPI_INT, 0, MPI_COMM_WORLD);
274
275	MPI_Bcast(GroupsPerProc, parallelData->nProcessors,
276	MPI_INT, 0, MPI_COMM_WORLD);
277
278
279	}
280
281	// Let's all check for sanity:
282
283	nmol_local = 0;
284	for (i = 0 ; i < parallelData->nMolGlobal; i++ ) {
285	if (MolToProcMap[i] == parallelData->myNode) {
286	nmol_local++;
287	}
288	}
289
290	natoms_local = 0;
291	for (i = 0; i < parallelData->nAtomsGlobal; i++) {
292	if (AtomToProcMap[i] == parallelData->myNode) {
293	natoms_local++;
294	}
295	}
296
297	ngroups_local = 0;
298	for (i = 0; i < parallelData->nGroupsGlobal; i++) {
299	if (GroupToProcMap[i] == parallelData->myNode) {
300	ngroups_local++;
301	}
302	}
303
304	MPI_Allreduce(&nmol_local,&nmol_global,1,MPI_INT,MPI_SUM,
305	MPI_COMM_WORLD);
306
307	MPI_Allreduce(&natoms_local,&natoms_global,1,MPI_INT,
308	MPI_SUM, MPI_COMM_WORLD);
309
310	MPI_Allreduce(&ngroups_local,&ngroups_global,1,MPI_INT,
311	MPI_SUM, MPI_COMM_WORLD);
312
313	if( nmol_global != entryPlug->n_mol ){
314	sprintf( painCave.errMsg,
315	"The sum of all nmol_local, %d, did not equal the "
316	"total number of molecules, %d.\n",
317	nmol_global, entryPlug->n_mol );
318	painCave.isFatal = 1;
319	simError();
320	}
321
322	if( natoms_global != entryPlug->n_atoms ){
323	sprintf( painCave.errMsg,
324	"The sum of all natoms_local, %d, did not equal the "
325	"total number of atoms, %d.\n",
326	natoms_global, entryPlug->n_atoms );
327	painCave.isFatal = 1;
328	simError();
329	}
330
331	if( ngroups_global != entryPlug->ngroup ){
332	sprintf( painCave.errMsg,
333	"The sum of all ngroups_local, %d, did not equal the "
334	"total number of cutoffGroups, %d.\n",
335	ngroups_global, entryPlug->ngroup );
336	painCave.isFatal = 1;
337	simError();
338	}
339
340	sprintf( checkPointMsg,
341	"Successfully divided the molecules among the processors.\n" );
342	MPIcheckPoint();
343
344	parallelData->nMolLocal = nmol_local;
345	parallelData->nAtomsLocal = natoms_local;
346	parallelData->nGroupsLocal = ngroups_local;
347
348	globalAtomIndex.resize(parallelData->nAtomsLocal);
349	globalToLocalAtom.resize(parallelData->nAtomsGlobal);
350	local_index = 0;
351	for (i = 0; i < parallelData->nAtomsGlobal; i++) {
352	if (AtomToProcMap[i] == parallelData->myNode) {
353	globalAtomIndex[local_index] = i;
354
355	globalToLocalAtom[i] = local_index;
356	local_index++;
357
358	}
359	else
360	globalToLocalAtom[i] = -1;
361	}
362
363	globalGroupIndex.resize(parallelData->nGroupsLocal);
364	globalToLocalGroup.resize(parallelData->nGroupsGlobal);
365	local_index = 0;
366	for (i = 0; i < parallelData->nGroupsGlobal; i++) {
367	if (GroupToProcMap[i] == parallelData->myNode) {
368	globalGroupIndex[local_index] = i;
369
370	globalToLocalGroup[i] = local_index;
371	local_index++;
372
373	}
374	else
375	globalToLocalGroup[i] = -1;
376	}
377
378	globalMolIndex.resize(parallelData->nMolLocal);
379	globalToLocalMol.resize(parallelData->nMolGlobal);
380	local_index = 0;
381	for (i = 0; i < parallelData->nMolGlobal; i++) {
382	if (MolToProcMap[i] == parallelData->myNode) {
383	globalMolIndex[local_index] = i;
384	globalToLocalMol[i] = local_index;
385	local_index++;
386	}
387	else
388	globalToLocalMol[i] = -1;
389	}
390
391	}
392
393
394	void mpiSimulation::mpiRefresh( void ){
395
396	int isError, i;
397	int *globalAtomIndex = new int[parallelData->nAtomsLocal];
398
399	// Fortran indexing needs to be increased by 1 in order to get the 2 languages to
400	// not barf
401
402	for(i=0; i<parallelData->nAtomsLocal; i++) globalAtomIndex[i] = entryPlug->atoms[i]->getGlobalIndex()+1;
403
404	isError = 0;
405	setFsimParallel( parallelData, &(entryPlug->n_atoms), globalAtomIndex, &isError );
406	if( isError ){
407
408	sprintf( painCave.errMsg,
409	"mpiRefresh errror: fortran didn't like something we gave it.\n" );
410	painCave.isFatal = 1;
411	simError();
412	}
413
414	delete[] globalAtomIndex;
415
416
417	sprintf( checkPointMsg,
418	" mpiRefresh successful.\n" );
419	MPIcheckPoint();
420	}
421
422
423	#endif // is_mpi