ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/group/trunk/OOPSE/libmdtools/mpiSimulation.cpp
(Generate patch)

Comparing trunk/OOPSE/libmdtools/mpiSimulation.cpp (file contents):
Revision 378 by mmeineke, Fri Mar 21 17:42:12 2003 UTC vs.
Revision 708 by tim, Wed Aug 20 22:23:34 2003 UTC

# Line 1 | Line 1
1   #ifdef IS_MPI
2 <
2 > #include <iostream>
3   #include <cstdlib>
4   #include <cstring>
5 + #include <cmath>
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  
13 + #define BASE_SEED 123456789
14  
13 –
14 –
15   mpiSimulation* mpiSim;
16  
17   mpiSimulation::mpiSimulation(SimInfo* the_entryPlug)
# Line 19 | Line 19 | mpiSimulation::mpiSimulation(SimInfo* the_entryPlug)
19    entryPlug = the_entryPlug;
20    mpiPlug = new mpiSimData;
21    
22 <  mpiPlug->numberProcessors = MPI::COMM_WORLD.Get_size();
22 >  MPI_Comm_size(MPI_COMM_WORLD, &(mpiPlug->numberProcessors) );
23    mpiPlug->myNode = worldRank;
24 <  
24 >
25 >  MolToProcMap = new int[entryPlug->n_mol];
26 >  MolComponentType = new int[entryPlug->n_mol];
27 >  AtomToProcMap = new int[entryPlug->n_atoms];
28 >
29    mpiSim = this;
30    wrapMeSimParallel( this );
31   }
# Line 29 | Line 33 | mpiSimulation::~mpiSimulation(){
33  
34   mpiSimulation::~mpiSimulation(){
35    
36 +  delete[] MolToProcMap;
37 +  delete[] MolComponentType;
38 +  delete[] AtomToProcMap;
39 +
40    delete mpiPlug;
41    // perhaps we should let fortran know the party is over.
42    
43   }
44  
37 –
38 –
45   int* mpiSimulation::divideLabor( void ){
46  
47    int* globalIndex;
48  
49    int nComponents;
50    MoleculeStamp** compStamps;
51 +  randomSPRNG *myRandom;
52    int* componentsNmol;
53 +  int* AtomsPerProc;
54  
55    double numerator;
56    double denominator;
57    double precast;
58 +  double x, y, a;
59 +  int old_atoms, add_atoms, new_atoms;
60  
61    int nTarget;
62    int molIndex, atomIndex, compIndex, compStart;
63    int done;
64    int nLocal, molLocal;
65 <  int i, index;
65 >  int i, j, loops, which_proc, nmol_local, natoms_local;
66 >  int nmol_global, natoms_global;
67 >  int local_index, index;
68    int smallDiff, bigDiff;
69 +  int baseSeed = entryPlug->getSeed();
70  
71    int testSum;
72  
73    nComponents = entryPlug->nComponents;
74    compStamps = entryPlug->compStamps;
75    componentsNmol = entryPlug->componentsNmol;
76 <
76 >  AtomsPerProc = new int[mpiPlug->numberProcessors];
77 >  
78    mpiPlug->nAtomsGlobal = entryPlug->n_atoms;
79    mpiPlug->nBondsGlobal = entryPlug->n_bonds;
80    mpiPlug->nBendsGlobal = entryPlug->n_bends;
# Line 68 | Line 82 | int* mpiSimulation::divideLabor( void ){
82    mpiPlug->nSRIGlobal = entryPlug->n_SRI;
83    mpiPlug->nMolGlobal = entryPlug->n_mol;
84  
71 –  numerator = (double) entryPlug->n_atoms;
72 –  denominator = (double) mpiPlug->numberProcessors;
73 –  precast = numerator / denominator;
74 –  nTarget = (int)( precast + 0.5 );
85    
86 <  molIndex = 0;
87 <  atomIndex = 0;
88 <  compIndex = 0;
89 <  compStart = 0;
90 <  for( i=0; i<(mpiPlug->numberProcessors-1); i++){
86 >  myRandom = new randomSPRNG( baseSeed );
87 >
88 >  a = 3.0 * (double)mpiPlug->nMolGlobal / (double)mpiPlug->nAtomsGlobal;
89 >
90 >  // Initialize things that we'll send out later:
91 >  for (i = 0; i < mpiPlug->numberProcessors; i++ ) {
92 >    AtomsPerProc[i] = 0;
93 >  }
94 >  for (i = 0; i < mpiPlug->nMolGlobal; i++ ) {
95 >    // default to an error condition:
96 >    MolToProcMap[i] = -1;
97 >    MolComponentType[i] = -1;
98 >  }
99 >  for (i = 0; i < mpiPlug->nAtomsGlobal; i++ ) {
100 >    // default to an error condition:
101 >    AtomToProcMap[i] = -1;
102 >  }
103      
104 <    done = 0;
105 <    nLocal = 0;
106 <    molLocal = 0;
104 >  if (mpiPlug->myNode == 0) {
105 >    numerator = (double) entryPlug->n_atoms;
106 >    denominator = (double) mpiPlug->numberProcessors;
107 >    precast = numerator / denominator;
108 >    nTarget = (int)( precast + 0.5 );
109  
110 <    if( i == mpiPlug->myNode ){
111 <      mpiPlug->myMolStart = molIndex;
112 <      mpiPlug->myAtomStart = atomIndex;
110 >    // Build the array of molecule component types first
111 >    molIndex = 0;
112 >    for (i=0; i < nComponents; i++) {
113 >      for (j=0; j < componentsNmol[i]; j++) {        
114 >        MolComponentType[molIndex] = i;
115 >        molIndex++;
116 >      }
117      }
118 +
119 +    atomIndex = 0;
120 +
121 +    for (i = 0; i < molIndex; i++ ) {
122 +
123 +      done = 0;
124 +      loops = 0;
125 +
126 +      while( !done ){
127 +        loops++;
128 +        
129 +        // Pick a processor at random
130 +
131 +        which_proc = (int) (myRandom->getRandom() * mpiPlug->numberProcessors);
132 +
133 +        // How many atoms does this processor have?
134 +        
135 +        old_atoms = AtomsPerProc[which_proc];
136 +        add_atoms = compStamps[MolComponentType[i]]->getNAtoms();
137 +        new_atoms = old_atoms + add_atoms;
138 +
139 +        // If we've been through this loop too many times, we need
140 +        // to just give up and assign the molecule to this processor
141 +        // and be done with it.
142 +        
143 +        if (loops > 100) {          
144 +          sprintf( painCave.errMsg,
145 +                   "I've tried 100 times to assign molecule %d to a "
146 +                   " processor, but can't find a good spot.\n"  
147 +                   "I'm assigning it at random to processor %d.\n",
148 +                   i, which_proc);
149 +          painCave.isFatal = 0;
150 +          simError();
151 +          
152 +          MolToProcMap[i] = which_proc;
153 +          AtomsPerProc[which_proc] += add_atoms;
154 +          for (j = 0 ; j < add_atoms; j++ ) {
155 +            AtomToProcMap[atomIndex] = which_proc;
156 +            atomIndex++;
157 +          }
158 +          done = 1;
159 +          continue;
160 +        }
161      
162 <    while( !done ){
163 <      
164 <      if( (molIndex-compStart) >= componentsNmol[compIndex] ){
165 <        compStart = molIndex;
166 <        compIndex++;
167 <        continue;
168 <      }
162 >        // If we can add this molecule to this processor without sending
163 >        // it above nTarget, then go ahead and do it:
164 >    
165 >        if (new_atoms <= nTarget) {
166 >          MolToProcMap[i] = which_proc;
167 >          AtomsPerProc[which_proc] += add_atoms;
168 >          for (j = 0 ; j < add_atoms; j++ ) {
169 >            AtomToProcMap[atomIndex] = which_proc;
170 >            atomIndex++;
171 >          }
172 >          done = 1;
173 >          continue;
174 >        }
175  
176 <      nLocal += compStamps[compIndex]->getNAtoms();
177 <      atomIndex += compStamps[compIndex]->getNAtoms();
178 <      molIndex++;
179 <      molLocal++;
176 >
177 >        // The only situation left is when new_atoms > nTarget.  We
178 >        // want to accept this with some probability that dies off the
179 >        // farther we are from nTarget
180 >
181 >        // roughly:  x = new_atoms - nTarget
182 >        //           Pacc(x) = exp(- a * x)
183 >        // where a = penalty / (average atoms per molecule)
184 >
185 >        x = (double) (new_atoms - nTarget);
186 >        y = myRandom->getRandom();
187        
188 <      if ( nLocal == nTarget ) done = 1;
189 <      
190 <      else if( nLocal < nTarget ){
191 <        smallDiff = nTarget - nLocal;
192 <      }
193 <      else if( nLocal > nTarget ){
194 <        bigDiff = nLocal - nTarget;
195 <        
196 <        if( bigDiff < smallDiff ) done = 1;
197 <        else{
198 <          molIndex--;
199 <          molLocal--;
200 <          atomIndex -= compStamps[compIndex]->getNAtoms();
117 <          nLocal -= compStamps[compIndex]->getNAtoms();
118 <          done = 1;
119 <        }
188 >        if (y < exp(- a * x)) {
189 >          MolToProcMap[i] = which_proc;
190 >          AtomsPerProc[which_proc] += add_atoms;
191 >          for (j = 0 ; j < add_atoms; j++ ) {
192 >            AtomToProcMap[atomIndex] = which_proc;
193 >            atomIndex++;
194 >           }
195 >          done = 1;
196 >          continue;
197 >        } else {
198 >          continue;
199 >        }      
200 >        
201        }
202      }
203 +
204 +    // Spray out this nonsense to all other processors:
205 +
206 +    MPI_Bcast(MolToProcMap, mpiPlug->nMolGlobal,
207 +              MPI_INT, 0, MPI_COMM_WORLD);
208 +
209 +    MPI_Bcast(AtomToProcMap, mpiPlug->nAtomsGlobal,
210 +              MPI_INT, 0, MPI_COMM_WORLD);
211 +
212 +    MPI_Bcast(MolComponentType, mpiPlug->nMolGlobal,
213 +              MPI_INT, 0, MPI_COMM_WORLD);
214 +
215 +    MPI_Bcast(AtomsPerProc, mpiPlug->numberProcessors,
216 +              MPI_INT, 0, MPI_COMM_WORLD);    
217 +  } else {
218 +
219 +    // Listen to your marching orders from processor 0:
220      
221 <    if( i == mpiPlug->myNode ){
222 <      mpiPlug->myMolEnd = (molIndex - 1);
125 <      mpiPlug->myAtomEnd = (atomIndex - 1);
126 <      mpiPlug->myNlocal = nLocal;
127 <      mpiPlug->myMol = molLocal;
128 <    }
221 >    MPI_Bcast(MolToProcMap, mpiPlug->nMolGlobal,
222 >              MPI_INT, 0, MPI_COMM_WORLD);
223      
224 <    numerator = (double)( entryPlug->n_atoms - atomIndex );
225 <    denominator = (double)( mpiPlug->numberProcessors - (i+1) );
226 <    precast = numerator / denominator;
227 <    nTarget = (int)( precast + 0.5 );
224 >    MPI_Bcast(AtomToProcMap, mpiPlug->nAtomsGlobal,
225 >              MPI_INT, 0, MPI_COMM_WORLD);
226 >
227 >    MPI_Bcast(MolComponentType, mpiPlug->nMolGlobal,
228 >              MPI_INT, 0, MPI_COMM_WORLD);
229 >    
230 >    MPI_Bcast(AtomsPerProc, mpiPlug->numberProcessors,
231 >              MPI_INT, 0, MPI_COMM_WORLD);
232 >
233 >
234    }
135 –  
136 –  if( mpiPlug->myNode == mpiPlug->numberProcessors-1 ){
137 –      mpiPlug->myMolStart = molIndex;
138 –      mpiPlug->myAtomStart = atomIndex;
235  
140 –      nLocal = 0;
141 –      molLocal = 0;
142 –      while( compIndex < nComponents ){
143 –        
144 –        if( (molIndex-compStart) >= componentsNmol[compIndex] ){
145 –          compStart = molIndex;
146 –          compIndex++;
147 –          continue;
148 –        }
236  
237 <        nLocal += compStamps[compIndex]->getNAtoms();
238 <        atomIndex += compStamps[compIndex]->getNAtoms();
239 <        molIndex++;
240 <        molLocal++;
241 <      }
242 <      
243 <      mpiPlug->myMolEnd = (molIndex - 1);
157 <      mpiPlug->myAtomEnd = (atomIndex - 1);
158 <      mpiPlug->myNlocal = nLocal;  
159 <      mpiPlug->myMol = molLocal;
237 >  // Let's all check for sanity:
238 >
239 >  nmol_local = 0;
240 >  for (i = 0 ; i < mpiPlug->nMolGlobal; i++ ) {
241 >    if (MolToProcMap[i] == mpiPlug->myNode) {
242 >      nmol_local++;
243 >    }
244    }
245  
246 +  natoms_local = 0;
247 +  for (i = 0; i < mpiPlug->nAtomsGlobal; i++) {
248 +    if (AtomToProcMap[i] == mpiPlug->myNode) {
249 +      natoms_local++;      
250 +    }
251 +  }
252  
253 <  MPI_Allreduce( &nLocal, &testSum, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD );
253 >  MPI_Allreduce(&nmol_local,&nmol_global,1,MPI_INT,MPI_SUM,
254 >                MPI_COMM_WORLD);
255 >  MPI_Allreduce(&natoms_local,&natoms_global,1,MPI_INT,
256 >                MPI_SUM, MPI_COMM_WORLD);
257    
258 <  if( mpiPlug->myNode == 0 ){
259 <    if( testSum != entryPlug->n_atoms ){
260 <      sprintf( painCave.errMsg,
261 <               "The summ of all nLocals, %d, did not equal the total number of atoms, %d.\n",
262 <               testSum, entryPlug->n_atoms );
263 <      painCave.isFatal = 1;
264 <      simError();
172 <    }
258 >  if( nmol_global != entryPlug->n_mol ){
259 >    sprintf( painCave.errMsg,
260 >             "The sum of all nmol_local, %d, did not equal the "
261 >             "total number of molecules, %d.\n",
262 >             nmol_global, entryPlug->n_mol );
263 >    painCave.isFatal = 1;
264 >    simError();
265    }
266 +  
267 +  if( natoms_global != entryPlug->n_atoms ){
268 +    sprintf( painCave.errMsg,
269 +             "The sum of all natoms_local, %d, did not equal the "
270 +             "total number of atoms, %d.\n",
271 +             natoms_global, entryPlug->n_atoms );
272 +    painCave.isFatal = 1;
273 +    simError();
274 +  }
275  
276    sprintf( checkPointMsg,
277             "Successfully divided the molecules among the processors.\n" );
278    MPIcheckPoint();
279  
280 <  // lets create the identity array
280 >  mpiPlug->myNMol = nmol_local;
281 >  mpiPlug->myNlocal = natoms_local;
282  
283    globalIndex = new int[mpiPlug->myNlocal];
284 <  index = mpiPlug->myAtomStart;
285 <  for( i=0; i<mpiPlug->myNlocal; i++){
286 <    globalIndex[i] = index;
287 <    index++;
284 >  local_index = 0;
285 >  for (i = 0; i < mpiPlug->nAtomsGlobal; i++) {
286 >    if (AtomToProcMap[i] == mpiPlug->myNode) {
287 >      globalIndex[local_index] = i;
288 >      local_index++;
289 >    }
290    }
291 <
291 >  
292    return globalIndex;
293   }
294  
# Line 194 | Line 298 | void mpiSimulation::mpiRefresh( void ){
298    int isError, i;
299    int *globalIndex = new int[mpiPlug->myNlocal];
300  
301 <  for(i=0; i<mpiPlug->myNlocal; i++) globalIndex[i] = entryPlug->atoms[i]->getGlobalIndex();
301 >  // Fortran indexing needs to be increased by 1 in order to get the 2 languages to
302 >  // not barf
303  
304 +  for(i=0; i<mpiPlug->myNlocal; i++) globalIndex[i] = entryPlug->atoms[i]->getGlobalIndex()+1;
305 +
306    
307    isError = 0;
308    setFsimParallel( mpiPlug, &(entryPlug->n_atoms), globalIndex, &isError );

Diff Legend

– Removed lines
+ Added lines
< Changed lines
> Changed lines