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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 405 by gezelter, Wed Mar 26 18:02:18 2003 UTC

# Line 8 | Line 8
8   #include "mpiSimulation.hpp"
9   #include "simError.h"
10   #include "fortranWrappers.hpp"
11 + #include "randomSPRNG.hpp"
12  
13  
13 –
14 –
14   mpiSimulation* mpiSim;
15  
16   mpiSimulation::mpiSimulation(SimInfo* the_entryPlug)
# Line 21 | Line 20 | mpiSimulation::mpiSimulation(SimInfo* the_entryPlug)
20    
21    mpiPlug->numberProcessors = MPI::COMM_WORLD.Get_size();
22    mpiPlug->myNode = worldRank;
23 <  
23 >
24 >  MolToProcMap = new int[entryPlug->n_mol];
25 >  MolComponentType = new int[entryPlug->n_mol];
26 >
27 >  AtomToProcMap = new int[entryPlug->n_atoms];
28 >
29    mpiSim = this;
30    wrapMeSimParallel( this );
31   }
# Line 34 | Line 38 | mpiSimulation::~mpiSimulation(){
38    
39   }
40  
37 –
38 –
41   int* mpiSimulation::divideLabor( void ){
42  
43    int* globalIndex;
44  
45    int nComponents;
46    MoleculeStamp** compStamps;
47 +  randomSPRNG myRandom;
48    int* componentsNmol;
49 +  int* AtomsPerProc;
50  
51    double numerator;
52    double denominator;
53    double precast;
54 +  double x, y, a;
55 +  int old_atoms, add_atoms, new_atoms;
56  
57    int nTarget;
58    int molIndex, atomIndex, compIndex, compStart;
# Line 60 | Line 66 | int* mpiSimulation::divideLabor( void ){
66    nComponents = entryPlug->nComponents;
67    compStamps = entryPlug->compStamps;
68    componentsNmol = entryPlug->componentsNmol;
69 <
69 >  AtomsPerProc = new int[mpiPlug->numberProcessors];
70 >  
71    mpiPlug->nAtomsGlobal = entryPlug->n_atoms;
72    mpiPlug->nBondsGlobal = entryPlug->n_bonds;
73    mpiPlug->nBendsGlobal = entryPlug->n_bends;
# Line 68 | Line 75 | int* mpiSimulation::divideLabor( void ){
75    mpiPlug->nSRIGlobal = entryPlug->n_SRI;
76    mpiPlug->nMolGlobal = entryPlug->n_mol;
77  
78 +  myRandom = new randomSPRNG();
79  
80 +  a = (double)mpiPlug->nMolGlobal / (double)mpiPlug->nAtomsGlobal;
81  
82 +  // Initialize things that we'll send out later:
83 +  for (i = 0; i < mpiPlug->numberProcessors; i++ ) {
84 +    AtomsPerProc[i] = 0;
85 +  }
86 +  for (i = 0; i < mpiPlug->nMolGlobal; i++ ) {
87 +    // default to an error condition:
88 +    MolToProcMap[i] = -1;
89 +    MolComponentType[i] = -1;
90 +  }
91 +  for (i = 0; i < mpiPlug->nAtomsGlobal; i++ ) {
92 +    // default to an error condition:
93 +    AtomToProcMap[i] = -1;
94 +  }
95 +    
96 +  if (mpiPlug->myNode == 0) {
97 +    numerator = (double) entryPlug->n_atoms;
98 +    denominator = (double) mpiPlug->numberProcessors;
99 +    precast = numerator / denominator;
100 +    nTarget = (int)( precast + 0.5 );
101  
102 +    // Build the array of molecule component types first
103 +    molIndex = 0;
104 +    for (i=0; i < nComponents; i++) {
105 +      for (j=0; j < componentsNmol[i]; j++) {        
106 +        MolComponentType[molIndex] = i;
107 +        molIndex++;
108 +      }
109 +    }
110  
111 +    atomIndex = 0;
112  
113 +    for (i = 0; i < molIndex; i++ ) {
114  
115 +      done = 0;
116 +      loops = 0;
117  
118 +      while( !done ){
119 +        loops++;
120 +        
121 +        // Pick a processor at random
122  
123 +        which_proc = (int) (myRandom.getRandom() * mpiPlug->numberProcessors);
124  
125 +        // How many atoms does this processor have?
126 +        
127 +        old_atoms = AtomsPerProc[which_proc];
128  
129 +        // If the processor already had too many atoms, just skip this
130 +        // processor and try again.
131  
132 <  numerator = (double) entryPlug->n_atoms;
83 <  denominator = (double) mpiPlug->numberProcessors;
84 <  precast = numerator / denominator;
85 <  nTarget = (int)( precast + 0.5 );
86 <  
87 <  molIndex = 0;
88 <  atomIndex = 0;
89 <  compIndex = 0;
90 <  compStart = 0;
91 <  for( i=0; i<(mpiPlug->numberProcessors-1); i++){
92 <    
93 <    done = 0;
94 <    nLocal = 0;
95 <    molLocal = 0;
132 >        if (old_atoms >= nTarget) continue;
133  
134 <    if( i == mpiPlug->myNode ){
135 <      mpiPlug->myMolStart = molIndex;
99 <      mpiPlug->myAtomStart = atomIndex;
100 <    }
134 >        add_atoms = compStamps[MolComponentType[i]]->getNatoms();
135 >        new_atoms = old_atoms + add_atoms;
136      
137 <    while( !done ){
138 <      
139 <      if( (molIndex-compStart) >= componentsNmol[compIndex] ){
140 <        compStart = molIndex;
141 <        compIndex++;
142 <        continue;
143 <      }
137 >        // If we can add this molecule to this processor without sending
138 >        // it above nTarget, then go ahead and do it:
139 >    
140 >        if (new_atoms <= nTarget) {
141 >          MolToProcMap[i] = which_proc;
142 >          AtomsPerProc[which_proc] += add_atoms;
143 >          for (j = 0 ; j < add_atoms; j++ ) {
144 >            atomIndex++;
145 >            AtomToProcMap[atomIndex] = which_proc;
146 >          }
147 >          done = 1;
148 >          continue;
149 >        }
150  
151 <      nLocal += compStamps[compIndex]->getNAtoms();
152 <      atomIndex += compStamps[compIndex]->getNAtoms();
153 <      molIndex++;
154 <      molLocal++;
155 <      
156 <      if ( nLocal == nTarget ) done = 1;
157 <      
158 <      else if( nLocal < nTarget ){
159 <        smallDiff = nTarget - nLocal;
160 <      }
161 <      else if( nLocal > nTarget ){
162 <        bigDiff = nLocal - nTarget;
163 <        
164 <        if( bigDiff < smallDiff ) done = 1;
165 <        else{
166 <          molIndex--;
167 <          molLocal--;
168 <          atomIndex -= compStamps[compIndex]->getNAtoms();
169 <          nLocal -= compStamps[compIndex]->getNAtoms();
170 <          done = 1;
171 <        }
151 >        // If we've been through this loop too many times, we need
152 >        // to just give up and assign the molecule to this processor
153 >        // and be done with it.
154 >        
155 >        if (loops > 100) {          
156 >          sprintf( painCave.errMsg,
157 >                   "I've tried 100 times to assign molecule %d to a "
158 >                   " processor, but can't find a good spot.\n"  
159 >                   "I'm assigning it at random to processor %d.\n",
160 >                   i, which_proc);
161 >          painCave.isFatal = 0;
162 >          simError();
163 >          
164 >          MolToProcMap[i] = which_proc;
165 >          AtomsPerProc[which_proc] += add_atoms;
166 >          for (j = 0 ; j < add_atoms; j++ ) {
167 >            atomIndex++;
168 >            AtomToProcMap[atomIndex] = which_proc;
169 >          }
170 >          done = 1;
171 >          continue;
172 >        }
173 >
174 >        // The only situation left is where old_atoms < nTarget, but
175 >        // new_atoms > nTarget.   We want to accept this with some
176 >        // probability that dies off the farther we are from nTarget
177 >
178 >        // roughly:  x = new_atoms - nTarget
179 >        //           Pacc(x) = exp(- a * x)
180 >        // where a = 1 / (average atoms per molecule)
181 >
182 >        x = (double) (new_atoms - nTarget);
183 >        y = myRandom.getRandom();
184 >        
185 >        if (exp(- a * x) > y) {
186 >          MolToProcMap[i] = which_proc;
187 >          AtomsPerProc[which_proc] += add_atoms;
188 >          for (j = 0 ; j < add_atoms; j++ ) {
189 >            atomIndex++;
190 >            AtomToProcMap[atomIndex] = which_proc;
191 >          }
192 >          done = 1;
193 >          continue;
194 >        } else {
195 >          continue;
196 >        }      
197 >        
198        }
199      }
200 +
201 +    // Spray out this nonsense to all other processors:
202 +
203 +    MPI::COMM_WORLD.Bcast(&MolToProcMap, mpiPlug->nMolGlobal,
204 +                          MPI_INT, 0);
205 +
206 +    MPI::COMM_WORLD.Bcast(&AtomToProcMap, mpiPlug->nAtomsGlobal,
207 +                          MPI_INT, 0);
208 +
209 +    MPI::COMM_WORLD.Bcast(&MolComponentType, mpiPlug->nMolGlobal,
210 +                          MPI_INT, 0);
211 +
212 +    MPI::COMM_WORLD.Bcast(&AtomsPerProc, mpiPlug->numberProcessors,
213 +                          MPI_INT, 0);    
214 +  } else {
215 +
216 +    // Listen to your marching orders from processor 0:
217      
218 <    if( i == mpiPlug->myNode ){
219 <      mpiPlug->myMolEnd = (molIndex - 1);
136 <      mpiPlug->myAtomEnd = (atomIndex - 1);
137 <      mpiPlug->myNlocal = nLocal;
138 <      mpiPlug->myMol = molLocal;
139 <    }
218 >    MPI::COMM_WORLD.Bcast(&MolToProcMap, mpiPlug->nMolGlobal,
219 >                          MPI_INT, 0);
220      
221 <    numerator = (double)( entryPlug->n_atoms - atomIndex );
222 <    denominator = (double)( mpiPlug->numberProcessors - (i+1) );
223 <    precast = numerator / denominator;
224 <    nTarget = (int)( precast + 0.5 );
221 >    MPI::COMM_WORLD.Bcast(&AtomToProcMap, mpiPlug->nAtomsGlobal,
222 >                          MPI_INT, 0);
223 >
224 >    MPI::COMM_WORLD.Bcast(&MolComponentType, mpiPlug->nMolGlobal,
225 >                          MPI_INT, 0);
226 >    
227 >    MPI::COMM_WORLD.Bcast(&AtomsPerProc, mpiPlug->numberProcessors,
228 >                          MPI_INT, 0);
229    }
146 –  
147 –  if( mpiPlug->myNode == mpiPlug->numberProcessors-1 ){
148 –      mpiPlug->myMolStart = molIndex;
149 –      mpiPlug->myAtomStart = atomIndex;
230  
151 –      nLocal = 0;
152 –      molLocal = 0;
153 –      while( compIndex < nComponents ){
154 –        
155 –        if( (molIndex-compStart) >= componentsNmol[compIndex] ){
156 –          compStart = molIndex;
157 –          compIndex++;
158 –          continue;
159 –        }
231  
232 <        nLocal += compStamps[compIndex]->getNAtoms();
233 <        atomIndex += compStamps[compIndex]->getNAtoms();
234 <        molIndex++;
235 <        molLocal++;
236 <      }
237 <      
238 <      mpiPlug->myMolEnd = (molIndex - 1);
168 <      mpiPlug->myAtomEnd = (atomIndex - 1);
169 <      mpiPlug->myNlocal = nLocal;  
170 <      mpiPlug->myMol = molLocal;
232 >  // Let's all check for sanity:
233 >
234 >  nmol_local = 0;
235 >  for (i = 0 ; i < mpiPlug->nMolGlobal; i++ ) {
236 >    if (MolToProcMap[i] == mpiPlug->myNode) {
237 >      nmol_local++;
238 >    }
239    }
240  
241 +  natoms_local = 0;
242 +  for (i = 0; i < mpiPlug->nAtomsGlobal; i++) {
243 +    if (AtomToProcMap[i] == mpiPlug->myNode) {
244 +      natoms_local++;      
245 +    }
246 +  }
247  
248 <  MPI_Allreduce( &nLocal, &testSum, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD );
248 >  MPI::COMM_WORLD.Allreduce(&nmol_local,&nmol_global,1,MPI_INT,MPI_SUM);
249 >  MPI::COMM_WORLD.Allreduce(&natoms_local,&natoms_global,1,MPI_INT,MPI_SUM);
250    
251 <  if( mpiPlug->myNode == 0 ){
252 <    if( testSum != entryPlug->n_atoms ){
253 <      sprintf( painCave.errMsg,
254 <               "The summ of all nLocals, %d, did not equal the total number of atoms, %d.\n",
255 <               testSum, entryPlug->n_atoms );
256 <      painCave.isFatal = 1;
257 <      simError();
183 <    }
251 >  if( nmol_global != entryPlug->n_mol ){
252 >    sprintf( painCave.errMsg,
253 >             "The sum of all nmol_local, %d, did not equal the "
254 >             "total number of molecules, %d.\n",
255 >             nmol_global, entryPlug->n_mol );
256 >    painCave.isFatal = 1;
257 >    simError();
258    }
259 +  
260 +  if( natoms_global != entryPlug->n_atoms ){
261 +    sprintf( painCave.errMsg,
262 +             "The sum of all natoms_local, %d, did not equal the "
263 +             "total number of atoms, %d.\n",
264 +             natoms_global, entryPlug->n_atoms );
265 +    painCave.isFatal = 1;
266 +    simError();
267 +  }
268  
269    sprintf( checkPointMsg,
270             "Successfully divided the molecules among the processors.\n" );
271    MPIcheckPoint();
272  
273 <  // lets create the identity array
273 >  mpiPlug->myNMol = nmol_local;
274 >  mpiPlug->myNlocal = natoms_local;
275  
276    globalIndex = new int[mpiPlug->myNlocal];
277 <  index = mpiPlug->myAtomStart;
278 <  for( i=0; i<mpiPlug->myNlocal; i++){
279 <    globalIndex[i] = index;
280 <    index++;
277 >  local_index = 0;
278 >  for (i = 0; i < mpiPlug->nAtomsGlobal; i++) {
279 >    if (AtomToProcMap[i] == mpiPlug->myNode) {
280 >      globalIndex[local_index] =
281 >    }
282    }
283 +  
284  
285 <  return globalIndex;
285 >
286 >
287 >   index = mpiPlug->myAtomStart;
288 > //   for( i=0; i<mpiPlug->myNlocal; i++){
289 > //     globalIndex[i] = index;
290 > //     index++;
291 > //   }
292 >
293 > //   return globalIndex;
294   }
295  
296  

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