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root/group/trunk/OOPSE/libmdtools/mpiSimulation.cpp
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Comparing trunk/OOPSE/libmdtools/mpiSimulation.cpp (file contents):
Revision 1198 by tim, Thu May 27 00:48:12 2004 UTC vs.
Revision 1203 by gezelter, Thu May 27 18:59:17 2004 UTC

# Line 15 | Line 15 | mpiSimulation::mpiSimulation(SimInfo* the_entryPlug)
15   mpiSimulation::mpiSimulation(SimInfo* the_entryPlug)
16   {
17    entryPlug = the_entryPlug;
18 <  mpiPlug = new mpiSimData;
18 >  parallelData = new mpiSimData;
19    
20 <  MPI_Comm_size(MPI_COMM_WORLD, &(mpiPlug->nProcessors) );
21 <  mpiPlug->myNode = worldRank;
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 );
# Line 34 | Line 35 | mpiSimulation::~mpiSimulation(){
35    delete[] MolToProcMap;
36    delete[] MolComponentType;
37    delete[] AtomToProcMap;
38 +  delete[] GroupToProcMap;
39  
40 <  delete mpiPlug;
40 >  delete parallelData;
41    // perhaps we should let fortran know the party is over.
42    
43   }
# Line 47 | Line 49 | void mpiSimulation::divideLabor( ){
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;
62 >  int molIndex, atomIndex, groupIndex;
63    int done;
64 <  int i, j, loops, which_proc, nmol_local, natoms_local;
65 <  int nmol_global, natoms_global;
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[mpiPlug->nProcessors];
76 >  AtomsPerProc = new int[parallelData->nProcessors];
77 >  GroupsPerProc = new int[parallelData->nProcessors];
78    
79 <  mpiPlug->nAtomsGlobal = entryPlug->n_atoms;
80 <  mpiPlug->nBondsGlobal = entryPlug->n_bonds;
81 <  mpiPlug->nBendsGlobal = entryPlug->n_bends;
82 <  mpiPlug->nTorsionsGlobal = entryPlug->n_torsions;
83 <  mpiPlug->nSRIGlobal = entryPlug->n_SRI;
84 <  mpiPlug->nMolGlobal = entryPlug->n_mol;
85 <  mpiPlug->nGroupsGlobal = entryPlug->ngroup;
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)mpiPlug->nMolGlobal / (double)mpiPlug->nAtomsGlobal;
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 < mpiPlug->nProcessors; i++ ) {
92 >  for (i = 0; i < parallelData->nProcessors; i++ ) {
93      AtomsPerProc[i] = 0;
94 +    GroupsPerProc[i] = 0;
95    }
96 <  for (i = 0; i < mpiPlug->nMolGlobal; i++ ) {
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 < mpiPlug->nAtomsGlobal; i++ ) {
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 (mpiPlug->myNode == 0) {
110 >  if (parallelData->myNode == 0) {
111      numerator = (double) entryPlug->n_atoms;
112 <    denominator = (double) mpiPlug->nProcessors;
112 >    denominator = (double) parallelData->nProcessors;
113      precast = numerator / denominator;
114      nTarget = (int)( precast + 0.5 );
115  
# Line 109 | Line 123 | void mpiSimulation::divideLabor( ){
123      }
124  
125      atomIndex = 0;
126 +    groupIndex = 0;
127  
128      for (i = 0; i < molIndex; i++ ) {
129  
# Line 120 | Line 135 | void mpiSimulation::divideLabor( ){
135          
136          // Pick a processor at random
137  
138 <        which_proc = (int) (myRandom->getRandom() * mpiPlug->nProcessors);
138 >        which_proc = (int) (myRandom->getRandom() * parallelData->nProcessors);
139  
140          // How many atoms does this processor have?
141          
# Line 128 | Line 143 | void mpiSimulation::divideLabor( ){
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.
# Line 147 | Line 172 | void mpiSimulation::divideLabor( ){
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          }
# Line 161 | Line 191 | void mpiSimulation::divideLabor( ){
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          }
# Line 184 | Line 219 | void mpiSimulation::divideLabor( ){
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 {
# Line 193 | Line 233 | void mpiSimulation::divideLabor( ){
233        }
234      }
235  
236 +
237      // Spray out this nonsense to all other processors:
238  
239 <    MPI_Bcast(MolToProcMap, mpiPlug->nMolGlobal,
239 >    MPI_Bcast(MolToProcMap, parallelData->nMolGlobal,
240                MPI_INT, 0, MPI_COMM_WORLD);
241  
242 <    MPI_Bcast(AtomToProcMap, mpiPlug->nAtomsGlobal,
242 >    MPI_Bcast(AtomToProcMap, parallelData->nAtomsGlobal,
243                MPI_INT, 0, MPI_COMM_WORLD);
244  
245 <    MPI_Bcast(MolComponentType, mpiPlug->nMolGlobal,
245 >    MPI_Bcast(GroupToProcMap, parallelData->nGroupsGlobal,
246                MPI_INT, 0, MPI_COMM_WORLD);
247  
248 <    MPI_Bcast(AtomsPerProc, mpiPlug->nProcessors,
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, mpiPlug->nMolGlobal,
260 >    MPI_Bcast(MolToProcMap, parallelData->nMolGlobal,
261                MPI_INT, 0, MPI_COMM_WORLD);
262      
263 <    MPI_Bcast(AtomToProcMap, mpiPlug->nAtomsGlobal,
263 >    MPI_Bcast(AtomToProcMap, parallelData->nAtomsGlobal,
264                MPI_INT, 0, MPI_COMM_WORLD);
265  
266 <    MPI_Bcast(MolComponentType, mpiPlug->nMolGlobal,
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, mpiPlug->nProcessors,
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  
228 –
281    // Let's all check for sanity:
282  
283    nmol_local = 0;
284 <  for (i = 0 ; i < mpiPlug->nMolGlobal; i++ ) {
285 <    if (MolToProcMap[i] == mpiPlug->myNode) {
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 < mpiPlug->nAtomsGlobal; i++) {
292 <    if (AtomToProcMap[i] == mpiPlug->myNode) {
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,
# Line 265 | Line 328 | void mpiSimulation::divideLabor( ){
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 <  mpiPlug->nMolLocal = nmol_local;
345 <  mpiPlug->nAtomsLocal = natoms_local;
344 >  parallelData->nMolLocal = nmol_local;
345 >  parallelData->nAtomsLocal = natoms_local;
346 >  parallelData->nGroupsLocal = ngroups_local;
347  
348 <  globalAtomIndex.resize(mpiPlug->nAtomsLocal);
349 <  globalToLocalAtom.resize(mpiPlug->nAtomsGlobal);
348 >  globalAtomIndex.resize(parallelData->nAtomsLocal);
349 >  globalToLocalAtom.resize(parallelData->nAtomsGlobal);
350    local_index = 0;
351 <  for (i = 0; i < mpiPlug->nAtomsGlobal; i++) {
352 <    if (AtomToProcMap[i] == mpiPlug->myNode) {
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;
# Line 287 | Line 360 | void mpiSimulation::divideLabor( ){
360         globalToLocalAtom[i] = -1;
361    }
362  
363 <  globalMolIndex.resize(mpiPlug->nMolLocal);
364 <  globalToLocalMol.resize(mpiPlug->nMolGlobal);
292 <  
363 >  globalGroupIndex.resize(parallelData->nGroupsLocal);
364 >  globalToLocalGroup.resize(parallelData->nGroupsGlobal);
365    local_index = 0;
366 <  for (i = 0; i < mpiPlug->nMolGlobal; i++) {
367 <    if (MolToProcMap[i] == mpiPlug->myNode) {
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++;
# Line 307 | Line 394 | void mpiSimulation::mpiRefresh( void ){
394   void mpiSimulation::mpiRefresh( void ){
395  
396    int isError, i;
397 <  int *globalIndex = new int[mpiPlug->nAtomsLocal];
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<mpiPlug->nAtomsLocal; i++) globalIndex[i] = entryPlug->atoms[i]->getGlobalIndex()+1;
316 <
402 >  for(i=0; i<parallelData->nAtomsLocal; i++) globalAtomIndex[i] = entryPlug->atoms[i]->getGlobalIndex()+1;
403    
404    isError = 0;
405 <  setFsimParallel( mpiPlug, &(entryPlug->n_atoms), globalIndex, &isError );
405 >  setFsimParallel( parallelData, &(entryPlug->n_atoms), globalAtomIndex, &isError );
406    if( isError ){
407  
408      sprintf( painCave.errMsg,
# Line 325 | Line 411 | void mpiSimulation::mpiRefresh( void ){
411      simError();
412    }
413  
414 <  delete[] globalIndex;
414 >  delete[] globalAtomIndex;
415  
416 +
417    sprintf( checkPointMsg,
418             " mpiRefresh successful.\n" );
419    MPIcheckPoint();

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