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/DarkSide/simParallel_interface.h"
#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;
}


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:	1619
Committed:	Wed Oct 20 21:16:01 2004 UTC (19 years, 8 months ago) by chuckv
File size:	13042 byte(s)
Log Message:	Fortran/C++ interface de-obfuscation project appears to be complete! Woo hoo!
#	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 "brains/mpiSimulation.hpp"
9	#include "utils/simError.h"
10	#include "UseTheForce/DarkSide/simParallel_interface.h"
11	#include "math/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	}
30
31
32	mpiSimulation::~mpiSimulation(){
33
34	delete[] MolToProcMap;
35	delete[] MolComponentType;
36	delete[] AtomToProcMap;
37	delete[] GroupToProcMap;
38
39	delete parallelData;
40	// perhaps we should let fortran know the party is over.
41
42	}
43
44	void mpiSimulation::divideLabor( ){
45
46	int nComponents;
47	MoleculeStamp** compStamps;
48	randomSPRNG *myRandom;
49	int* componentsNmol;
50	int* AtomsPerProc;
51	int* GroupsPerProc;
52
53	double numerator;
54	double denominator;
55	double precast;
56	double x, y, a;
57	int old_atoms, add_atoms, new_atoms;
58	int old_groups, add_groups, new_groups;
59
60	int nTarget;
61	int molIndex, atomIndex, groupIndex;
62	int done;
63	int i, j, loops, which_proc;
64	int nmol_global, nmol_local;
65	int ngroups_global, ngroups_local;
66	int natoms_global, natoms_local;
67	int ncutoff_groups, nAtomsInGroups;
68	int local_index;
69	int baseSeed = entryPlug->getSeed();
70	CutoffGroupStamp* cg;
71
72	nComponents = entryPlug->nComponents;
73	compStamps = entryPlug->compStamps;
74	componentsNmol = entryPlug->componentsNmol;
75	AtomsPerProc = new int[parallelData->nProcessors];
76	GroupsPerProc = new int[parallelData->nProcessors];
77
78	parallelData->nAtomsGlobal = entryPlug->n_atoms;
79	parallelData->nBondsGlobal = entryPlug->n_bonds;
80	parallelData->nBendsGlobal = entryPlug->n_bends;
81	parallelData->nTorsionsGlobal = entryPlug->n_torsions;
82	parallelData->nSRIGlobal = entryPlug->n_SRI;
83	parallelData->nGroupsGlobal = entryPlug->ngroup;
84	parallelData->nMolGlobal = entryPlug->n_mol;
85
86	if (parallelData->nProcessors > parallelData->nMolGlobal) {
87	sprintf( painCave.errMsg,
88	"nProcessors (%d) > nMol (%d)\n"
89	"\tThe number of processors is larger than\n"
90	"\tthe number of molecules. This will not result in a \n"
91	"\tusable division of atoms for force decomposition.\n"
92	"\tEither try a smaller number of processors, or run the\n"
93	"\tsingle-processor version of OOPSE.\n",
94	parallelData->nProcessors, parallelData->nMolGlobal );
95	painCave.isFatal = 1;
96	simError();
97	}
98
99	myRandom = new randomSPRNG( baseSeed );
100
101
102	a = 3.0 * (double)parallelData->nMolGlobal / (double)parallelData->nAtomsGlobal;
103
104	// Initialize things that we'll send out later:
105	for (i = 0; i < parallelData->nProcessors; i++ ) {
106	AtomsPerProc[i] = 0;
107	GroupsPerProc[i] = 0;
108	}
109	for (i = 0; i < parallelData->nMolGlobal; i++ ) {
110	// default to an error condition:
111	MolToProcMap[i] = -1;
112	MolComponentType[i] = -1;
113	}
114	for (i = 0; i < parallelData->nAtomsGlobal; i++ ) {
115	// default to an error condition:
116	AtomToProcMap[i] = -1;
117	}
118	for (i = 0; i < parallelData->nGroupsGlobal; i++ ) {
119	// default to an error condition:
120	GroupToProcMap[i] = -1;
121	}
122
123	if (parallelData->myNode == 0) {
124	numerator = (double) entryPlug->n_atoms;
125	denominator = (double) parallelData->nProcessors;
126	precast = numerator / denominator;
127	nTarget = (int)( precast + 0.5 );
128
129	// Build the array of molecule component types first
130	molIndex = 0;
131	for (i=0; i < nComponents; i++) {
132	for (j=0; j < componentsNmol[i]; j++) {
133	MolComponentType[molIndex] = i;
134	molIndex++;
135	}
136	}
137
138	atomIndex = 0;
139	groupIndex = 0;
140
141	for (i = 0; i < molIndex; i++ ) {
142
143	done = 0;
144	loops = 0;
145
146	while( !done ){
147	loops++;
148
149	// Pick a processor at random
150
151	which_proc = (int) (myRandom->getRandom() * parallelData->nProcessors);
152
153	// How many atoms does this processor have?
154
155	old_atoms = AtomsPerProc[which_proc];
156	add_atoms = compStamps[MolComponentType[i]]->getNAtoms();
157	new_atoms = old_atoms + add_atoms;
158
159	old_groups = GroupsPerProc[which_proc];
160	ncutoff_groups = compStamps[MolComponentType[i]]->getNCutoffGroups();
161	nAtomsInGroups = 0;
162	for (j = 0; j < ncutoff_groups; j++) {
163	cg = compStamps[MolComponentType[i]]->getCutoffGroup(j);
164	nAtomsInGroups += cg->getNMembers();
165	}
166	add_groups = add_atoms - nAtomsInGroups + ncutoff_groups;
167	new_groups = old_groups + add_groups;
168
169	// If we've been through this loop too many times, we need
170	// to just give up and assign the molecule to this processor
171	// and be done with it.
172
173	if (loops > 100) {
174	sprintf( painCave.errMsg,
175	"I've tried 100 times to assign molecule %d to a "
176	" processor, but can't find a good spot.\n"
177	"I'm assigning it at random to processor %d.\n",
178	i, which_proc);
179	painCave.isFatal = 0;
180	simError();
181
182	MolToProcMap[i] = which_proc;
183	AtomsPerProc[which_proc] += add_atoms;
184	for (j = 0 ; j < add_atoms; j++ ) {
185	AtomToProcMap[atomIndex] = which_proc;
186	atomIndex++;
187	}
188	GroupsPerProc[which_proc] += add_groups;
189	for (j=0; j < add_groups; j++) {
190	GroupToProcMap[groupIndex] = which_proc;
191	groupIndex++;
192	}
193	done = 1;
194	continue;
195	}
196
197	// If we can add this molecule to this processor without sending
198	// it above nTarget, then go ahead and do it:
199
200	if (new_atoms <= nTarget) {
201	MolToProcMap[i] = which_proc;
202	AtomsPerProc[which_proc] += add_atoms;
203	for (j = 0 ; j < add_atoms; j++ ) {
204	AtomToProcMap[atomIndex] = which_proc;
205	atomIndex++;
206	}
207	GroupsPerProc[which_proc] += add_groups;
208	for (j=0; j < add_groups; j++) {
209	GroupToProcMap[groupIndex] = which_proc;
210	groupIndex++;
211	}
212	done = 1;
213	continue;
214	}
215
216
217	// The only situation left is when new_atoms > nTarget. We
218	// want to accept this with some probability that dies off the
219	// farther we are from nTarget
220
221	// roughly: x = new_atoms - nTarget
222	// Pacc(x) = exp(- a * x)
223	// where a = penalty / (average atoms per molecule)
224
225	x = (double) (new_atoms - nTarget);
226	y = myRandom->getRandom();
227
228	if (y < exp(- a * x)) {
229	MolToProcMap[i] = which_proc;
230	AtomsPerProc[which_proc] += add_atoms;
231	for (j = 0 ; j < add_atoms; j++ ) {
232	AtomToProcMap[atomIndex] = which_proc;
233	atomIndex++;
234	}
235	GroupsPerProc[which_proc] += add_groups;
236	for (j=0; j < add_groups; j++) {
237	GroupToProcMap[groupIndex] = which_proc;
238	groupIndex++;
239	}
240	done = 1;
241	continue;
242	} else {
243	continue;
244	}
245
246	}
247	}
248
249
250	// Spray out this nonsense to all other processors:
251
252	//std::cerr << "node 0 mol2proc = \n";
253	//for (i = 0; i < parallelData->nMolGlobal; i++)
254	// std::cerr << i << "\t" << MolToProcMap[i] << "\n";
255
256	MPI_Bcast(MolToProcMap, parallelData->nMolGlobal,
257	MPI_INT, 0, MPI_COMM_WORLD);
258
259	MPI_Bcast(AtomToProcMap, parallelData->nAtomsGlobal,
260	MPI_INT, 0, MPI_COMM_WORLD);
261
262	MPI_Bcast(GroupToProcMap, parallelData->nGroupsGlobal,
263	MPI_INT, 0, MPI_COMM_WORLD);
264
265	MPI_Bcast(MolComponentType, parallelData->nMolGlobal,
266	MPI_INT, 0, MPI_COMM_WORLD);
267
268	MPI_Bcast(AtomsPerProc, parallelData->nProcessors,
269	MPI_INT, 0, MPI_COMM_WORLD);
270
271	MPI_Bcast(GroupsPerProc, parallelData->nProcessors,
272	MPI_INT, 0, MPI_COMM_WORLD);
273	} else {
274
275	// Listen to your marching orders from processor 0:
276
277	MPI_Bcast(MolToProcMap, parallelData->nMolGlobal,
278	MPI_INT, 0, MPI_COMM_WORLD);
279
280	MPI_Bcast(AtomToProcMap, parallelData->nAtomsGlobal,
281	MPI_INT, 0, MPI_COMM_WORLD);
282
283	MPI_Bcast(GroupToProcMap, parallelData->nGroupsGlobal,
284	MPI_INT, 0, MPI_COMM_WORLD);
285
286	MPI_Bcast(MolComponentType, parallelData->nMolGlobal,
287	MPI_INT, 0, MPI_COMM_WORLD);
288
289	MPI_Bcast(AtomsPerProc, parallelData->nProcessors,
290	MPI_INT, 0, MPI_COMM_WORLD);
291
292	MPI_Bcast(GroupsPerProc, parallelData->nProcessors,
293	MPI_INT, 0, MPI_COMM_WORLD);
294
295
296	}
297
298	// Let's all check for sanity:
299
300	nmol_local = 0;
301	for (i = 0 ; i < parallelData->nMolGlobal; i++ ) {
302	if (MolToProcMap[i] == parallelData->myNode) {
303	nmol_local++;
304	}
305	}
306
307	natoms_local = 0;
308	for (i = 0; i < parallelData->nAtomsGlobal; i++) {
309	if (AtomToProcMap[i] == parallelData->myNode) {
310	natoms_local++;
311	}
312	}
313
314	ngroups_local = 0;
315	for (i = 0; i < parallelData->nGroupsGlobal; i++) {
316	if (GroupToProcMap[i] == parallelData->myNode) {
317	ngroups_local++;
318	}
319	}
320
321	MPI_Allreduce(&nmol_local,&nmol_global,1,MPI_INT,MPI_SUM,
322	MPI_COMM_WORLD);
323
324	MPI_Allreduce(&natoms_local,&natoms_global,1,MPI_INT,
325	MPI_SUM, MPI_COMM_WORLD);
326
327	MPI_Allreduce(&ngroups_local,&ngroups_global,1,MPI_INT,
328	MPI_SUM, MPI_COMM_WORLD);
329
330	if( nmol_global != entryPlug->n_mol ){
331	sprintf( painCave.errMsg,
332	"The sum of all nmol_local, %d, did not equal the "
333	"total number of molecules, %d.\n",
334	nmol_global, entryPlug->n_mol );
335	painCave.isFatal = 1;
336	simError();
337	}
338
339	if( natoms_global != entryPlug->n_atoms ){
340	sprintf( painCave.errMsg,
341	"The sum of all natoms_local, %d, did not equal the "
342	"total number of atoms, %d.\n",
343	natoms_global, entryPlug->n_atoms );
344	painCave.isFatal = 1;
345	simError();
346	}
347
348	if( ngroups_global != entryPlug->ngroup ){
349	sprintf( painCave.errMsg,
350	"The sum of all ngroups_local, %d, did not equal the "
351	"total number of cutoffGroups, %d.\n",
352	ngroups_global, entryPlug->ngroup );
353	painCave.isFatal = 1;
354	simError();
355	}
356
357	sprintf( checkPointMsg,
358	"Successfully divided the molecules among the processors.\n" );
359	MPIcheckPoint();
360
361	parallelData->nMolLocal = nmol_local;
362	parallelData->nAtomsLocal = natoms_local;
363	parallelData->nGroupsLocal = ngroups_local;
364
365	globalAtomIndex.resize(parallelData->nAtomsLocal);
366	globalToLocalAtom.resize(parallelData->nAtomsGlobal);
367	local_index = 0;
368	for (i = 0; i < parallelData->nAtomsGlobal; i++) {
369	if (AtomToProcMap[i] == parallelData->myNode) {
370	globalAtomIndex[local_index] = i;
371
372	globalToLocalAtom[i] = local_index;
373	local_index++;
374
375	}
376	else
377	globalToLocalAtom[i] = -1;
378	}
379
380	globalGroupIndex.resize(parallelData->nGroupsLocal);
381	globalToLocalGroup.resize(parallelData->nGroupsGlobal);
382	local_index = 0;
383	for (i = 0; i < parallelData->nGroupsGlobal; i++) {
384	if (GroupToProcMap[i] == parallelData->myNode) {
385	globalGroupIndex[local_index] = i;
386
387	globalToLocalGroup[i] = local_index;
388	local_index++;
389
390	}
391	else
392	globalToLocalGroup[i] = -1;
393	}
394
395	globalMolIndex.resize(parallelData->nMolLocal);
396	globalToLocalMol.resize(parallelData->nMolGlobal);
397	local_index = 0;
398	for (i = 0; i < parallelData->nMolGlobal; i++) {
399	if (MolToProcMap[i] == parallelData->myNode) {
400	globalMolIndex[local_index] = i;
401	globalToLocalMol[i] = local_index;
402	local_index++;
403	}
404	else
405	globalToLocalMol[i] = -1;
406	}
407
408	}
409
410
411	void mpiSimulation::mpiRefresh( void ){
412
413	int isError, i;
414	int *localToGlobalAtomIndex = new int[parallelData->nAtomsLocal];
415	int *localToGlobalGroupIndex = new int[parallelData->nGroupsLocal];
416
417	// Fortran indexing needs to be increased by 1 in order to get the 2
418	// languages to not barf
419
420	for(i = 0; i < parallelData->nAtomsLocal; i++)
421	localToGlobalAtomIndex[i] = globalAtomIndex[i] + 1;
422
423	for(i = 0; i < parallelData->nGroupsLocal; i++)
424	localToGlobalGroupIndex[i] = globalGroupIndex[i] + 1;
425
426	isError = 0;
427
428	setFsimParallel( parallelData,
429	&(parallelData->nAtomsLocal), localToGlobalAtomIndex,
430	&(parallelData->nGroupsLocal), localToGlobalGroupIndex,
431	&isError );
432
433	if( isError ){
434
435	sprintf( painCave.errMsg,
436	"mpiRefresh errror: fortran didn't like something we gave it.\n" );
437	painCave.isFatal = 1;
438	simError();
439	}
440
441	delete[] localToGlobalGroupIndex;
442	delete[] localToGlobalAtomIndex;
443
444
445	sprintf( checkPointMsg,
446	" mpiRefresh successful.\n" );
447	MPIcheckPoint();
448	}
449
450
451	#endif // is_mpi