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root/group/trunk/OOPSE/libmdtools/mpiSimulation.cpp
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Comparing trunk/OOPSE/libmdtools/mpiSimulation.cpp (file contents):
Revision 378 by mmeineke, Fri Mar 21 17:42:12 2003 UTC vs.
Revision 418 by mmeineke, Thu Mar 27 14:30:24 2003 UTC

# Line 2 | Line 2
2  
3   #include <cstdlib>
4   #include <cstring>
5 + #include <cmath>
6   #include <mpi.h>
7   #include <mpi++.h>
8  
9   #include "mpiSimulation.hpp"
10   #include "simError.h"
11   #include "fortranWrappers.hpp"
12 + #include "randomSPRNG.hpp"
13  
14 + #define BASE_SEED 123456789
15  
13 –
14 –
16   mpiSimulation* mpiSim;
17  
18   mpiSimulation::mpiSimulation(SimInfo* the_entryPlug)
# Line 21 | Line 22 | mpiSimulation::mpiSimulation(SimInfo* the_entryPlug)
22    
23    mpiPlug->numberProcessors = MPI::COMM_WORLD.Get_size();
24    mpiPlug->myNode = worldRank;
25 <  
25 >
26 >  MolToProcMap = new int[entryPlug->n_mol];
27 >  MolComponentType = new int[entryPlug->n_mol];
28 >
29 >  AtomToProcMap = new int[entryPlug->n_atoms];
30 >
31    mpiSim = this;
32    wrapMeSimParallel( this );
33   }
# Line 29 | Line 35 | mpiSimulation::~mpiSimulation(){
35  
36   mpiSimulation::~mpiSimulation(){
37    
38 +  delete[] MolToProcMap;
39 +  delete[] MolComponentType;
40 +  delete[] AtomToProcMap;
41 +
42    delete mpiPlug;
43    // perhaps we should let fortran know the party is over.
44    
45   }
46  
37 –
38 –
47   int* mpiSimulation::divideLabor( void ){
48  
49    int* globalIndex;
50  
51    int nComponents;
52    MoleculeStamp** compStamps;
53 +  randomSPRNG *myRandom;
54    int* componentsNmol;
55 +  int* AtomsPerProc;
56  
57    double numerator;
58    double denominator;
59    double precast;
60 +  double x, y, a;
61 +  int old_atoms, add_atoms, new_atoms;
62  
63    int nTarget;
64    int molIndex, atomIndex, compIndex, compStart;
65    int done;
66    int nLocal, molLocal;
67 <  int i, index;
67 >  int i, j, loops, which_proc, nmol_local, natoms_local;
68 >  int nmol_global, natoms_global;
69 >  int local_index, index;
70    int smallDiff, bigDiff;
71 +  int baseSeed = BASE_SEED;
72  
73    int testSum;
74  
75    nComponents = entryPlug->nComponents;
76    compStamps = entryPlug->compStamps;
77    componentsNmol = entryPlug->componentsNmol;
78 <
78 >  AtomsPerProc = new int[mpiPlug->numberProcessors];
79 >  
80    mpiPlug->nAtomsGlobal = entryPlug->n_atoms;
81    mpiPlug->nBondsGlobal = entryPlug->n_bonds;
82    mpiPlug->nBendsGlobal = entryPlug->n_bends;
# Line 68 | Line 84 | int* mpiSimulation::divideLabor( void ){
84    mpiPlug->nSRIGlobal = entryPlug->n_SRI;
85    mpiPlug->nMolGlobal = entryPlug->n_mol;
86  
87 <  numerator = (double) entryPlug->n_atoms;
72 <  denominator = (double) mpiPlug->numberProcessors;
73 <  precast = numerator / denominator;
74 <  nTarget = (int)( precast + 0.5 );
75 <  
76 <  molIndex = 0;
77 <  atomIndex = 0;
78 <  compIndex = 0;
79 <  compStart = 0;
80 <  for( i=0; i<(mpiPlug->numberProcessors-1); i++){
81 <    
82 <    done = 0;
83 <    nLocal = 0;
84 <    molLocal = 0;
87 >  myRandom = new randomSPRNG( baseSeed );
88  
89 <    if( i == mpiPlug->myNode ){
87 <      mpiPlug->myMolStart = molIndex;
88 <      mpiPlug->myAtomStart = atomIndex;
89 <    }
90 <    
91 <    while( !done ){
92 <      
93 <      if( (molIndex-compStart) >= componentsNmol[compIndex] ){
94 <        compStart = molIndex;
95 <        compIndex++;
96 <        continue;
97 <      }
89 >  a = (double)mpiPlug->nMolGlobal / (double)mpiPlug->nAtomsGlobal;
90  
91 <      nLocal += compStamps[compIndex]->getNAtoms();
92 <      atomIndex += compStamps[compIndex]->getNAtoms();
93 <      molIndex++;
94 <      molLocal++;
95 <      
96 <      if ( nLocal == nTarget ) done = 1;
97 <      
98 <      else if( nLocal < nTarget ){
99 <        smallDiff = nTarget - nLocal;
100 <      }
101 <      else if( nLocal > nTarget ){
102 <        bigDiff = nLocal - nTarget;
103 <        
112 <        if( bigDiff < smallDiff ) done = 1;
113 <        else{
114 <          molIndex--;
115 <          molLocal--;
116 <          atomIndex -= compStamps[compIndex]->getNAtoms();
117 <          nLocal -= compStamps[compIndex]->getNAtoms();
118 <          done = 1;
119 <        }
120 <      }
121 <    }
91 >  // Initialize things that we'll send out later:
92 >  for (i = 0; i < mpiPlug->numberProcessors; i++ ) {
93 >    AtomsPerProc[i] = 0;
94 >  }
95 >  for (i = 0; i < mpiPlug->nMolGlobal; i++ ) {
96 >    // default to an error condition:
97 >    MolToProcMap[i] = -1;
98 >    MolComponentType[i] = -1;
99 >  }
100 >  for (i = 0; i < mpiPlug->nAtomsGlobal; i++ ) {
101 >    // default to an error condition:
102 >    AtomToProcMap[i] = -1;
103 >  }
104      
105 <    if( i == mpiPlug->myNode ){
106 <      mpiPlug->myMolEnd = (molIndex - 1);
107 <      mpiPlug->myAtomEnd = (atomIndex - 1);
126 <      mpiPlug->myNlocal = nLocal;
127 <      mpiPlug->myMol = molLocal;
128 <    }
129 <    
130 <    numerator = (double)( entryPlug->n_atoms - atomIndex );
131 <    denominator = (double)( mpiPlug->numberProcessors - (i+1) );
105 >  if (mpiPlug->myNode == 0) {
106 >    numerator = (double) entryPlug->n_atoms;
107 >    denominator = (double) mpiPlug->numberProcessors;
108      precast = numerator / denominator;
109      nTarget = (int)( precast + 0.5 );
134 –  }
135 –  
136 –  if( mpiPlug->myNode == mpiPlug->numberProcessors-1 ){
137 –      mpiPlug->myMolStart = molIndex;
138 –      mpiPlug->myAtomStart = atomIndex;
110  
111 <      nLocal = 0;
112 <      molLocal = 0;
113 <      while( compIndex < nComponents ){
114 <        
115 <        if( (molIndex-compStart) >= componentsNmol[compIndex] ){
116 <          compStart = molIndex;
146 <          compIndex++;
147 <          continue;
148 <        }
149 <
150 <        nLocal += compStamps[compIndex]->getNAtoms();
151 <        atomIndex += compStamps[compIndex]->getNAtoms();
152 <        molIndex++;
153 <        molLocal++;
111 >    // Build the array of molecule component types first
112 >    molIndex = 0;
113 >    for (i=0; i < nComponents; i++) {
114 >      for (j=0; j < componentsNmol[i]; j++) {        
115 >        MolComponentType[molIndex] = i;
116 >        molIndex++;
117        }
118 <      
156 <      mpiPlug->myMolEnd = (molIndex - 1);
157 <      mpiPlug->myAtomEnd = (atomIndex - 1);
158 <      mpiPlug->myNlocal = nLocal;  
159 <      mpiPlug->myMol = molLocal;
160 <  }
118 >    }
119  
120 +    atomIndex = 0;
121  
122 <  MPI_Allreduce( &nLocal, &testSum, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD );
123 <  
124 <  if( mpiPlug->myNode == 0 ){
125 <    if( testSum != entryPlug->n_atoms ){
126 <      sprintf( painCave.errMsg,
127 <               "The summ of all nLocals, %d, did not equal the total number of atoms, %d.\n",
128 <               testSum, entryPlug->n_atoms );
129 <      painCave.isFatal = 1;
130 <      simError();
122 >    for (i = 0; i < molIndex; i++ ) {
123 >
124 >      done = 0;
125 >      loops = 0;
126 >
127 >      while( !done ){
128 >        loops++;
129 >        
130 >        // Pick a processor at random
131 >
132 >        which_proc = (int) (myRandom->getRandom() * mpiPlug->numberProcessors);
133 >
134 >        // How many atoms does this processor have?
135 >        
136 >        old_atoms = AtomsPerProc[which_proc];
137 >
138 >        // If the processor already had too many atoms, just skip this
139 >        // processor and try again.
140 >
141 >        if (old_atoms >= nTarget) continue;
142 >
143 >        add_atoms = compStamps[MolComponentType[i]]->getNAtoms();
144 >        new_atoms = old_atoms + add_atoms;
145 >    
146 >        // If we can add this molecule to this processor without sending
147 >        // it above nTarget, then go ahead and do it:
148 >    
149 >        if (new_atoms <= nTarget) {
150 >          MolToProcMap[i] = which_proc;
151 >          AtomsPerProc[which_proc] += add_atoms;
152 >          for (j = 0 ; j < add_atoms; j++ ) {
153 >            atomIndex++;
154 >            AtomToProcMap[atomIndex] = which_proc;
155 >          }
156 >          done = 1;
157 >          continue;
158 >        }
159 >
160 >        // If we've been through this loop too many times, we need
161 >        // to just give up and assign the molecule to this processor
162 >        // and be done with it.
163 >        
164 >        if (loops > 100) {          
165 >          sprintf( painCave.errMsg,
166 >                   "I've tried 100 times to assign molecule %d to a "
167 >                   " processor, but can't find a good spot.\n"  
168 >                   "I'm assigning it at random to processor %d.\n",
169 >                   i, which_proc);
170 >          painCave.isFatal = 0;
171 >          simError();
172 >          
173 >          MolToProcMap[i] = which_proc;
174 >          AtomsPerProc[which_proc] += add_atoms;
175 >          for (j = 0 ; j < add_atoms; j++ ) {
176 >            atomIndex++;
177 >            AtomToProcMap[atomIndex] = which_proc;
178 >          }
179 >          done = 1;
180 >          continue;
181 >        }
182 >
183 >        // The only situation left is where old_atoms < nTarget, but
184 >        // new_atoms > nTarget.   We want to accept this with some
185 >        // probability that dies off the farther we are from nTarget
186 >
187 >        // roughly:  x = new_atoms - nTarget
188 >        //           Pacc(x) = exp(- a * x)
189 >        // where a = 1 / (average atoms per molecule)
190 >
191 >        x = (double) (new_atoms - nTarget);
192 >        y = myRandom->getRandom();
193 >        
194 >        if (exp(- a * x) > y) {
195 >          MolToProcMap[i] = which_proc;
196 >          AtomsPerProc[which_proc] += add_atoms;
197 >          for (j = 0 ; j < add_atoms; j++ ) {
198 >            atomIndex++;
199 >            AtomToProcMap[atomIndex] = which_proc;
200 >          }
201 >          done = 1;
202 >          continue;
203 >        } else {
204 >          continue;
205 >        }      
206 >        
207 >      }
208      }
209 +
210 +    // Spray out this nonsense to all other processors:
211 +
212 +    MPI::COMM_WORLD.Bcast(MolToProcMap, mpiPlug->nMolGlobal,
213 +                          MPI_INT, 0);
214 +
215 +    MPI::COMM_WORLD.Bcast(AtomToProcMap, mpiPlug->nAtomsGlobal,
216 +                          MPI_INT, 0);
217 +
218 +    MPI::COMM_WORLD.Bcast(MolComponentType, mpiPlug->nMolGlobal,
219 +                          MPI_INT, 0);
220 +
221 +    MPI::COMM_WORLD.Bcast(AtomsPerProc, mpiPlug->numberProcessors,
222 +                          MPI_INT, 0);    
223 +  } else {
224 +
225 +    // Listen to your marching orders from processor 0:
226 +    
227 +    MPI::COMM_WORLD.Bcast(MolToProcMap, mpiPlug->nMolGlobal,
228 +                          MPI_INT, 0);
229 +    
230 +    MPI::COMM_WORLD.Bcast(AtomToProcMap, mpiPlug->nAtomsGlobal,
231 +                          MPI_INT, 0);
232 +
233 +    MPI::COMM_WORLD.Bcast(MolComponentType, mpiPlug->nMolGlobal,
234 +                          MPI_INT, 0);
235 +    
236 +    MPI::COMM_WORLD.Bcast(AtomsPerProc, mpiPlug->numberProcessors,
237 +                          MPI_INT, 0);
238    }
239  
240 +
241 +  // Let's all check for sanity:
242 +
243 +  nmol_local = 0;
244 +  for (i = 0 ; i < mpiPlug->nMolGlobal; i++ ) {
245 +    if (MolToProcMap[i] == mpiPlug->myNode) {
246 +      nmol_local++;
247 +    }
248 +  }
249 +
250 +  natoms_local = 0;
251 +  for (i = 0; i < mpiPlug->nAtomsGlobal; i++) {
252 +    if (AtomToProcMap[i] == mpiPlug->myNode) {
253 +      natoms_local++;      
254 +    }
255 +  }
256 +
257 +  MPI::COMM_WORLD.Allreduce(&nmol_local,&nmol_global,1,MPI_INT,MPI_SUM);
258 +  MPI::COMM_WORLD.Allreduce(&natoms_local,&natoms_global,1,MPI_INT,MPI_SUM);
259 +  
260 +  if( nmol_global != entryPlug->n_mol ){
261 +    sprintf( painCave.errMsg,
262 +             "The sum of all nmol_local, %d, did not equal the "
263 +             "total number of molecules, %d.\n",
264 +             nmol_global, entryPlug->n_mol );
265 +    painCave.isFatal = 1;
266 +    simError();
267 +  }
268 +  
269 +  if( natoms_global != entryPlug->n_atoms ){
270 +    sprintf( painCave.errMsg,
271 +             "The sum of all natoms_local, %d, did not equal the "
272 +             "total number of atoms, %d.\n",
273 +             natoms_global, entryPlug->n_atoms );
274 +    painCave.isFatal = 1;
275 +    simError();
276 +  }
277 +
278    sprintf( checkPointMsg,
279             "Successfully divided the molecules among the processors.\n" );
280    MPIcheckPoint();
281  
282 <  // lets create the identity array
282 >  mpiPlug->myNMol = nmol_local;
283 >  mpiPlug->myNlocal = natoms_local;
284  
285    globalIndex = new int[mpiPlug->myNlocal];
286 <  index = mpiPlug->myAtomStart;
287 <  for( i=0; i<mpiPlug->myNlocal; i++){
288 <    globalIndex[i] = index;
289 <    index++;
286 >  local_index = 0;
287 >  for (i = 0; i < mpiPlug->nAtomsGlobal; i++) {
288 >    if (AtomToProcMap[i] == mpiPlug->myNode) {
289 >      local_index++;
290 >      globalIndex[local_index] = i;
291 >    }
292    }
293 <
293 >
294    return globalIndex;
295   }
296  

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