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root/group/trunk/OOPSE/libmdtools/mpiSimulation.cpp
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Comparing trunk/OOPSE/libmdtools/mpiSimulation.cpp (file contents):
Revision 406 by chuckv, Wed Mar 26 19:34:49 2003 UTC vs.
Revision 726 by tim, Tue Aug 26 20:37:30 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 –
13   mpiSimulation* mpiSim;
14  
15   mpiSimulation::mpiSimulation(SimInfo* the_entryPlug)
# Line 18 | Line 17 | mpiSimulation::mpiSimulation(SimInfo* the_entryPlug)
17    entryPlug = the_entryPlug;
18    mpiPlug = new mpiSimData;
19    
20 <  mpiPlug->numberProcessors = MPI::COMM_WORLD.Get_size();
20 >  MPI_Comm_size(MPI_COMM_WORLD, &(mpiPlug->numberProcessors) );
21    mpiPlug->myNode = worldRank;
22  
23    MolToProcMap = new int[entryPlug->n_mol];
24    MolComponentType = new int[entryPlug->n_mol];
26 –
25    AtomToProcMap = new int[entryPlug->n_atoms];
26  
27    mpiSim = this;
# Line 33 | Line 31 | mpiSimulation::~mpiSimulation(){
31  
32   mpiSimulation::~mpiSimulation(){
33    
34 +  delete[] MolToProcMap;
35 +  delete[] MolComponentType;
36 +  delete[] AtomToProcMap;
37 +
38    delete mpiPlug;
39    // perhaps we should let fortran know the party is over.
40    
# Line 44 | Line 46 | int* mpiSimulation::divideLabor( void ){
46  
47    int nComponents;
48    MoleculeStamp** compStamps;
49 <  randomSPRNG myRandom;
49 >  randomSPRNG *myRandom;
50    int* componentsNmol;
51    int* AtomsPerProc;
52  
# Line 58 | Line 60 | int* mpiSimulation::divideLabor( void ){
60    int molIndex, atomIndex, compIndex, compStart;
61    int done;
62    int nLocal, molLocal;
63 <  int i, index;
63 >  int i, j, loops, which_proc, nmol_local, natoms_local;
64 >  int nmol_global, natoms_global;
65 >  int local_index, index;
66    int smallDiff, bigDiff;
67 +  int baseSeed = entryPlug->getSeed();
68  
69    int testSum;
70  
# Line 75 | Line 80 | int* mpiSimulation::divideLabor( void ){
80    mpiPlug->nSRIGlobal = entryPlug->n_SRI;
81    mpiPlug->nMolGlobal = entryPlug->n_mol;
82  
83 <  myRandom = new randomSPRNG();
83 >  
84 >  myRandom = new randomSPRNG( baseSeed );
85  
86 <  a = (double)mpiPlug->nMolGlobal / (double)mpiPlug->nAtomsGlobal;
86 >  a = 3.0 * (double)mpiPlug->nMolGlobal / (double)mpiPlug->nAtomsGlobal;
87  
88    // Initialize things that we'll send out later:
89    for (i = 0; i < mpiPlug->numberProcessors; i++ ) {
# Line 120 | Line 126 | int* mpiSimulation::divideLabor( void ){
126          
127          // Pick a processor at random
128  
129 <        which_proc = (int) (myRandom.getRandom() * mpiPlug->numberProcessors);
129 >        which_proc = (int) (myRandom->getRandom() * mpiPlug->numberProcessors);
130  
131          // How many atoms does this processor have?
132          
133          old_atoms = AtomsPerProc[which_proc];
134 <
129 <        // If the processor already had too many atoms, just skip this
130 <        // processor and try again.
131 <
132 <        if (old_atoms >= nTarget) continue;
133 <
134 <        add_atoms = compStamps[MolComponentType[i]]->getNatoms();
134 >        add_atoms = compStamps[MolComponentType[i]]->getNAtoms();
135          new_atoms = old_atoms + add_atoms;
136 –    
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 –        }
136  
137          // If we've been through this loop too many times, we need
138          // to just give up and assign the molecule to this processor
# Line 164 | Line 150 | int* mpiSimulation::divideLabor( void ){
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;
153 >            AtomToProcMap[atomIndex] = which_proc;
154 >            atomIndex++;
155            }
156            done = 1;
157            continue;
158          }
159 +    
160 +        // If we can add this molecule to this processor without sending
161 +        // it above nTarget, then go ahead and do it:
162 +    
163 +        if (new_atoms <= nTarget) {
164 +          MolToProcMap[i] = which_proc;
165 +          AtomsPerProc[which_proc] += add_atoms;
166 +          for (j = 0 ; j < add_atoms; j++ ) {
167 +            AtomToProcMap[atomIndex] = which_proc;
168 +            atomIndex++;
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
174  
175 +        // The only situation left is when new_atoms > nTarget.  We
176 +        // want to accept this with some probability that dies off the
177 +        // farther we are from nTarget
178 +
179          // roughly:  x = new_atoms - nTarget
180          //           Pacc(x) = exp(- a * x)
181 <        // where a = 1 / (average atoms per molecule)
181 >        // where a = penalty / (average atoms per molecule)
182  
183          x = (double) (new_atoms - nTarget);
184 <        y = myRandom.getRandom();
185 <        
186 <        if (exp(- a * x) > y) {
184 >        y = myRandom->getRandom();
185 >      
186 >        if (y < exp(- a * x)) {
187            MolToProcMap[i] = which_proc;
188            AtomsPerProc[which_proc] += add_atoms;
189            for (j = 0 ; j < add_atoms; j++ ) {
190 <            atomIndex++;
191 <            AtomToProcMap[atomIndex] = which_proc;
192 <          }
190 >            AtomToProcMap[atomIndex] = which_proc;
191 >            atomIndex++;
192 >           }
193            done = 1;
194            continue;
195          } else {
# Line 200 | Line 201 | int* mpiSimulation::divideLabor( void ){
201  
202      // Spray out this nonsense to all other processors:
203  
204 <    MPI::COMM_WORLD.Bcast(&MolToProcMap, mpiPlug->nMolGlobal,
205 <                          MPI_INT, 0);
204 >    MPI_Bcast(MolToProcMap, mpiPlug->nMolGlobal,
205 >              MPI_INT, 0, MPI_COMM_WORLD);
206  
207 <    MPI::COMM_WORLD.Bcast(&AtomToProcMap, mpiPlug->nAtomsGlobal,
208 <                          MPI_INT, 0);
207 >    MPI_Bcast(AtomToProcMap, mpiPlug->nAtomsGlobal,
208 >              MPI_INT, 0, MPI_COMM_WORLD);
209  
210 <    MPI::COMM_WORLD.Bcast(&MolComponentType, mpiPlug->nMolGlobal,
211 <                          MPI_INT, 0);
210 >    MPI_Bcast(MolComponentType, mpiPlug->nMolGlobal,
211 >              MPI_INT, 0, MPI_COMM_WORLD);
212  
213 <    MPI::COMM_WORLD.Bcast(&AtomsPerProc, mpiPlug->numberProcessors,
214 <                          MPI_INT, 0);    
213 >    MPI_Bcast(AtomsPerProc, mpiPlug->numberProcessors,
214 >              MPI_INT, 0, MPI_COMM_WORLD);    
215    } else {
216  
217      // Listen to your marching orders from processor 0:
218      
219 <    MPI::COMM_WORLD.Bcast(&MolToProcMap, mpiPlug->nMolGlobal,
220 <                          MPI_INT, 0);
219 >    MPI_Bcast(MolToProcMap, mpiPlug->nMolGlobal,
220 >              MPI_INT, 0, MPI_COMM_WORLD);
221      
222 <    MPI::COMM_WORLD.Bcast(&AtomToProcMap, mpiPlug->nAtomsGlobal,
223 <                          MPI_INT, 0);
222 >    MPI_Bcast(AtomToProcMap, mpiPlug->nAtomsGlobal,
223 >              MPI_INT, 0, MPI_COMM_WORLD);
224  
225 <    MPI::COMM_WORLD.Bcast(&MolComponentType, mpiPlug->nMolGlobal,
226 <                          MPI_INT, 0);
225 >    MPI_Bcast(MolComponentType, mpiPlug->nMolGlobal,
226 >              MPI_INT, 0, MPI_COMM_WORLD);
227      
228 <    MPI::COMM_WORLD.Bcast(&AtomsPerProc, mpiPlug->numberProcessors,
229 <                          MPI_INT, 0);
228 >    MPI_Bcast(AtomsPerProc, mpiPlug->numberProcessors,
229 >              MPI_INT, 0, MPI_COMM_WORLD);
230 >
231 >
232    }
233  
234  
# Line 245 | Line 248 | int* mpiSimulation::divideLabor( void ){
248      }
249    }
250  
251 <  MPI::COMM_WORLD.Allreduce(&nmol_local,&nmol_global,1,MPI_INT,MPI_SUM);
252 <  MPI::COMM_WORLD.Allreduce(&natoms_local,&natoms_global,1,MPI_INT,MPI_SUM);
251 >  MPI_Allreduce(&nmol_local,&nmol_global,1,MPI_INT,MPI_SUM,
252 >                MPI_COMM_WORLD);
253 >  MPI_Allreduce(&natoms_local,&natoms_global,1,MPI_INT,
254 >                MPI_SUM, MPI_COMM_WORLD);
255    
256    if( nmol_global != entryPlug->n_mol ){
257      sprintf( painCave.errMsg,
# Line 277 | Line 282 | int* mpiSimulation::divideLabor( void ){
282    local_index = 0;
283    for (i = 0; i < mpiPlug->nAtomsGlobal; i++) {
284      if (AtomToProcMap[i] == mpiPlug->myNode) {
280 –      local_index++;
285        globalIndex[local_index] = i;
286 +      local_index++;
287      }
288    }
289    
290 <
286 <
287 <
288 <   index = mpiPlug->myAtomStart;
289 < //   for( i=0; i<mpiPlug->myNlocal; i++){
290 < //     globalIndex[i] = index;
291 < //     index++;
292 < //   }
293 <
294 < //   return globalIndex;
290 >  return globalIndex;
291   }
292  
293  
# Line 300 | Line 296 | void mpiSimulation::mpiRefresh( void ){
296    int isError, i;
297    int *globalIndex = new int[mpiPlug->myNlocal];
298  
299 <  for(i=0; i<mpiPlug->myNlocal; i++) globalIndex[i] = entryPlug->atoms[i]->getGlobalIndex();
299 >  // Fortran indexing needs to be increased by 1 in order to get the 2 languages to
300 >  // not barf
301  
302 +  for(i=0; i<mpiPlug->myNlocal; i++) globalIndex[i] = entryPlug->atoms[i]->getGlobalIndex()+1;
303 +
304    
305    isError = 0;
306    setFsimParallel( mpiPlug, &(entryPlug->n_atoms), globalIndex, &isError );

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