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root/group/trunk/OOPSE/libmdtools/mpiSimulation.cpp
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Comparing trunk/OOPSE/libmdtools/mpiSimulation.cpp (file contents):
Revision 404 by chuckv, Wed Mar 26 16:12:53 2003 UTC vs.
Revision 1203 by gezelter, Thu May 27 18:59:17 2004 UTC

# Line 1 | Line 1
1   #ifdef IS_MPI
2 <
3 < #include <cstdlib>
4 < #include <cstring>
2 > #include <iostream>
3 > #include <stdlib.h>
4 > #include <string.h>
5 > #include <math.h>
6   #include <mpi.h>
6 – #include <mpi++.h>
7  
8   #include "mpiSimulation.hpp"
9   #include "simError.h"
10   #include "fortranWrappers.hpp"
11 + #include "randomSPRNG.hpp"
12  
12 –
13 –
14 –
13   mpiSimulation* mpiSim;
14  
15   mpiSimulation::mpiSimulation(SimInfo* the_entryPlug)
16   {
17    entryPlug = the_entryPlug;
18 <  mpiPlug = new mpiSimData;
18 >  parallelData = new mpiSimData;
19    
20 <  mpiPlug->numberProcessors = MPI::COMM_WORLD.Get_size();
21 <  mpiPlug->myNode = worldRank;
22 <  
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   }
# Line 29 | Line 32 | mpiSimulation::~mpiSimulation(){
32  
33   mpiSimulation::~mpiSimulation(){
34    
35 <  delete mpiPlug;
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  
38 –
39 – int* mpiSimulation::divideLabor( void ){
40 –
41 –  int* globalIndex;
42 –
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, compIndex, compStart;
62 >  int molIndex, atomIndex, groupIndex;
63    int done;
64 <  int nLocal, molLocal;
65 <  int i, index;
66 <  int smallDiff, bigDiff;
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  
58 –  int testSum;
59 –
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 <  mpiPlug->nAtomsGlobal = entryPlug->n_atoms;
65 <  mpiPlug->nBondsGlobal = entryPlug->n_bonds;
66 <  mpiPlug->nBendsGlobal = entryPlug->n_bends;
67 <  mpiPlug->nTorsionsGlobal = entryPlug->n_torsions;
68 <  mpiPlug->nSRIGlobal = entryPlug->n_SRI;
69 <  mpiPlug->nMolGlobal = entryPlug->n_mol;
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 <
157 <  numerator = (double) entryPlug->n_atoms;
158 <  denominator = (double) mpiPlug->numberProcessors;
159 <  precast = numerator / denominator;
160 <  nTarget = (int)( precast + 0.5 );
161 <  
162 <  molIndex = 0;
163 <  atomIndex = 0;
164 <  compIndex = 0;
165 <  compStart = 0;
166 <  for( i=0; i<(mpiPlug->numberProcessors-1); i++){
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 <    done = 0;
185 <    nLocal = 0;
95 <    molLocal = 0;
96 <
97 <    if( i == mpiPlug->myNode ){
98 <      mpiPlug->myMolStart = molIndex;
99 <      mpiPlug->myAtomStart = atomIndex;
100 <    }
184 >        // If we can add this molecule to this processor without sending
185 >        // it above nTarget, then go ahead and do it:
186      
187 <    while( !done ){
188 <      
189 <      if( (molIndex-compStart) >= componentsNmol[compIndex] ){
190 <        compStart = molIndex;
191 <        compIndex++;
192 <        continue;
193 <      }
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 <      nLocal += compStamps[compIndex]->getNAtoms();
204 <      atomIndex += compStamps[compIndex]->getNAtoms();
205 <      molIndex++;
206 <      molLocal++;
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 ( nLocal == nTarget ) done = 1;
216 <      
217 <      else if( nLocal < nTarget ){
218 <        smallDiff = nTarget - nLocal;
219 <      }
220 <      else if( nLocal > nTarget ){
221 <        bigDiff = nLocal - nTarget;
222 <        
223 <        if( bigDiff < smallDiff ) done = 1;
224 <        else{
225 <          molIndex--;
226 <          molLocal--;
227 <          atomIndex -= compStamps[compIndex]->getNAtoms();
228 <          nLocal -= compStamps[compIndex]->getNAtoms();
229 <          done = 1;
230 <        }
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 <    if( i == mpiPlug->myNode ){
261 <      mpiPlug->myMolEnd = (molIndex - 1);
136 <      mpiPlug->myAtomEnd = (atomIndex - 1);
137 <      mpiPlug->myNlocal = nLocal;
138 <      mpiPlug->myMol = molLocal;
139 <    }
260 >    MPI_Bcast(MolToProcMap, parallelData->nMolGlobal,
261 >              MPI_INT, 0, MPI_COMM_WORLD);
262      
263 <    numerator = (double)( entryPlug->n_atoms - atomIndex );
264 <    denominator = (double)( mpiPlug->numberProcessors - (i+1) );
265 <    precast = numerator / denominator;
266 <    nTarget = (int)( precast + 0.5 );
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    }
146 –  
147 –  if( mpiPlug->myNode == mpiPlug->numberProcessors-1 ){
148 –      mpiPlug->myMolStart = molIndex;
149 –      mpiPlug->myAtomStart = atomIndex;
280  
281 <      nLocal = 0;
152 <      molLocal = 0;
153 <      while( compIndex < nComponents ){
154 <        
155 <        if( (molIndex-compStart) >= componentsNmol[compIndex] ){
156 <          compStart = molIndex;
157 <          compIndex++;
158 <          continue;
159 <        }
281 >  // Let's all check for sanity:
282  
283 <        nLocal += compStamps[compIndex]->getNAtoms();
284 <        atomIndex += compStamps[compIndex]->getNAtoms();
285 <        molIndex++;
286 <        molLocal++;
287 <      }
166 <      
167 <      mpiPlug->myMolEnd = (molIndex - 1);
168 <      mpiPlug->myAtomEnd = (atomIndex - 1);
169 <      mpiPlug->myNlocal = nLocal;  
170 <      mpiPlug->myMol = molLocal;
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 <  MPI_Allreduce( &nLocal, &testSum, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD );
298 <  
299 <  if( mpiPlug->myNode == 0 ){
300 <    if( testSum != entryPlug->n_atoms ){
178 <      sprintf( painCave.errMsg,
179 <               "The summ of all nLocals, %d, did not equal the total number of atoms, %d.\n",
180 <               testSum, entryPlug->n_atoms );
181 <      painCave.isFatal = 1;
182 <      simError();
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 <  // lets create the identity array
344 >  parallelData->nMolLocal = nmol_local;
345 >  parallelData->nAtomsLocal = natoms_local;
346 >  parallelData->nGroupsLocal = ngroups_local;
347  
348 <  globalIndex = new int[mpiPlug->myNlocal];
349 <  index = mpiPlug->myAtomStart;
350 <  for( i=0; i<mpiPlug->myNlocal; i++){
351 <    globalIndex[i] = index;
352 <    index++;
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 <  return globalIndex;
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 *globalIndex = new int[mpiPlug->myNlocal];
397 >  int *globalAtomIndex = new int[parallelData->nAtomsLocal];
398  
399 <  for(i=0; i<mpiPlug->myNlocal; i++) globalIndex[i] = entryPlug->atoms[i]->getGlobalIndex();
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( mpiPlug, &(entryPlug->n_atoms), globalIndex, &isError );
405 >  setFsimParallel( parallelData, &(entryPlug->n_atoms), globalAtomIndex, &isError );
406    if( isError ){
407  
408      sprintf( painCave.errMsg,
# Line 218 | 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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