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root/group/trunk/OOPSE/libmdtools/mpiSimulation.cpp
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Comparing trunk/OOPSE/libmdtools/mpiSimulation.cpp (file contents):
Revision 419 by gezelter, Thu Mar 27 15:07:29 2003 UTC vs.
Revision 989 by gezelter, Tue Jan 27 19:38:27 2004 UTC

# Line 1 | Line 1
1   #ifdef IS_MPI
2 <
3 < #include <cstdlib>
4 < #include <cstring>
5 < #include <cmath>
2 > #include <iostream>
3 > #include <stdlib.h>
4 > #include <string.h>
5 > #include <math.h>
6   #include <mpi.h>
7 – #include <mpi++.h>
7  
8   #include "mpiSimulation.hpp"
9   #include "simError.h"
10   #include "fortranWrappers.hpp"
11   #include "randomSPRNG.hpp"
12  
14 – #define BASE_SEED 123456789
15 –
13   mpiSimulation* mpiSim;
14  
15   mpiSimulation::mpiSimulation(SimInfo* the_entryPlug)
# Line 20 | 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];
# Line 60 | Line 57 | int* mpiSimulation::divideLabor( void ){
57    int old_atoms, add_atoms, new_atoms;
58  
59    int nTarget;
60 <  int molIndex, atomIndex, compIndex, compStart;
60 >  int molIndex, atomIndex;
61    int done;
65 –  int nLocal, molLocal;
62    int i, j, loops, which_proc, nmol_local, natoms_local;
63    int nmol_global, natoms_global;
64 <  int local_index, index;
65 <  int smallDiff, bigDiff;
70 <  int baseSeed = BASE_SEED;
64 >  int local_index;
65 >  int baseSeed = entryPlug->getSeed();
66  
72 –  int testSum;
73 –
67    nComponents = entryPlug->nComponents;
68    compStamps = entryPlug->compStamps;
69    componentsNmol = entryPlug->componentsNmol;
# Line 83 | Line 76 | int* mpiSimulation::divideLabor( void ){
76    mpiPlug->nSRIGlobal = entryPlug->n_SRI;
77    mpiPlug->nMolGlobal = entryPlug->n_mol;
78  
79 +  
80    myRandom = new randomSPRNG( baseSeed );
81  
82 <  a = (double)mpiPlug->nMolGlobal / (double)mpiPlug->nAtomsGlobal;
82 >  a = 3.0 * (double)mpiPlug->nMolGlobal / (double)mpiPlug->nAtomsGlobal;
83  
84    // Initialize things that we'll send out later:
85    for (i = 0; i < mpiPlug->numberProcessors; i++ ) {
# Line 133 | Line 127 | int* mpiSimulation::divideLabor( void ){
127          // How many atoms does this processor have?
128          
129          old_atoms = AtomsPerProc[which_proc];
136 –
137 –        // If the processor already had too many atoms, just skip this
138 –        // processor and try again.
139 –
140 –        if (old_atoms >= nTarget) continue;
141 –
130          add_atoms = compStamps[MolComponentType[i]]->getNAtoms();
131          new_atoms = old_atoms + add_atoms;
144 –    
145 –        // If we can add this molecule to this processor without sending
146 –        // it above nTarget, then go ahead and do it:
147 –    
148 –        if (new_atoms <= nTarget) {
149 –          MolToProcMap[i] = which_proc;
150 –          AtomsPerProc[which_proc] += add_atoms;
151 –          for (j = 0 ; j < add_atoms; j++ ) {
152 –            atomIndex++;
153 –            AtomToProcMap[atomIndex] = which_proc;
154 –          }
155 –          done = 1;
156 –          continue;
157 –        }
132  
133          // If we've been through this loop too many times, we need
134          // to just give up and assign the molecule to this processor
# Line 172 | Line 146 | int* mpiSimulation::divideLabor( void ){
146            MolToProcMap[i] = which_proc;
147            AtomsPerProc[which_proc] += add_atoms;
148            for (j = 0 ; j < add_atoms; j++ ) {
149 <            atomIndex++;
150 <            AtomToProcMap[atomIndex] = which_proc;
149 >            AtomToProcMap[atomIndex] = which_proc;
150 >            atomIndex++;
151            }
152            done = 1;
153            continue;
154          }
155 +    
156 +        // If we can add this molecule to this processor without sending
157 +        // it above nTarget, then go ahead and do it:
158 +    
159 +        if (new_atoms <= nTarget) {
160 +          MolToProcMap[i] = which_proc;
161 +          AtomsPerProc[which_proc] += add_atoms;
162 +          for (j = 0 ; j < add_atoms; j++ ) {
163 +            AtomToProcMap[atomIndex] = which_proc;
164 +            atomIndex++;
165 +          }
166 +          done = 1;
167 +          continue;
168 +        }
169  
170 <        // The only situation left is where old_atoms < nTarget, but
171 <        // new_atoms > nTarget.   We want to accept this with some
172 <        // probability that dies off the farther we are from nTarget
170 >
171 >        // The only situation left is when new_atoms > nTarget.  We
172 >        // want to accept this with some probability that dies off the
173 >        // farther we are from nTarget
174  
175          // roughly:  x = new_atoms - nTarget
176          //           Pacc(x) = exp(- a * x)
177 <        // where a = 1 / (average atoms per molecule)
177 >        // where a = penalty / (average atoms per molecule)
178  
179          x = (double) (new_atoms - nTarget);
180          y = myRandom->getRandom();
181 <        
182 <        if (exp(- a * x) > y) {
181 >      
182 >        if (y < exp(- a * x)) {
183            MolToProcMap[i] = which_proc;
184            AtomsPerProc[which_proc] += add_atoms;
185            for (j = 0 ; j < add_atoms; j++ ) {
186 <            atomIndex++;
187 <            AtomToProcMap[atomIndex] = which_proc;
188 <          }
186 >            AtomToProcMap[atomIndex] = which_proc;
187 >            atomIndex++;
188 >           }
189            done = 1;
190            continue;
191          } else {
# Line 208 | Line 197 | int* mpiSimulation::divideLabor( void ){
197  
198      // Spray out this nonsense to all other processors:
199  
200 <    MPI::COMM_WORLD.Bcast(MolToProcMap, mpiPlug->nMolGlobal,
201 <                          MPI_INT, 0);
200 >    MPI_Bcast(MolToProcMap, mpiPlug->nMolGlobal,
201 >              MPI_INT, 0, MPI_COMM_WORLD);
202  
203 <    MPI::COMM_WORLD.Bcast(AtomToProcMap, mpiPlug->nAtomsGlobal,
204 <                          MPI_INT, 0);
203 >    MPI_Bcast(AtomToProcMap, mpiPlug->nAtomsGlobal,
204 >              MPI_INT, 0, MPI_COMM_WORLD);
205  
206 <    MPI::COMM_WORLD.Bcast(MolComponentType, mpiPlug->nMolGlobal,
207 <                          MPI_INT, 0);
206 >    MPI_Bcast(MolComponentType, mpiPlug->nMolGlobal,
207 >              MPI_INT, 0, MPI_COMM_WORLD);
208  
209 <    MPI::COMM_WORLD.Bcast(AtomsPerProc, mpiPlug->numberProcessors,
210 <                          MPI_INT, 0);    
209 >    MPI_Bcast(AtomsPerProc, mpiPlug->numberProcessors,
210 >              MPI_INT, 0, MPI_COMM_WORLD);    
211    } else {
212  
213      // Listen to your marching orders from processor 0:
214      
215 <    MPI::COMM_WORLD.Bcast(MolToProcMap, mpiPlug->nMolGlobal,
216 <                          MPI_INT, 0);
215 >    MPI_Bcast(MolToProcMap, mpiPlug->nMolGlobal,
216 >              MPI_INT, 0, MPI_COMM_WORLD);
217      
218 <    MPI::COMM_WORLD.Bcast(AtomToProcMap, mpiPlug->nAtomsGlobal,
219 <                          MPI_INT, 0);
218 >    MPI_Bcast(AtomToProcMap, mpiPlug->nAtomsGlobal,
219 >              MPI_INT, 0, MPI_COMM_WORLD);
220  
221 <    MPI::COMM_WORLD.Bcast(MolComponentType, mpiPlug->nMolGlobal,
222 <                          MPI_INT, 0);
221 >    MPI_Bcast(MolComponentType, mpiPlug->nMolGlobal,
222 >              MPI_INT, 0, MPI_COMM_WORLD);
223      
224 <    MPI::COMM_WORLD.Bcast(AtomsPerProc, mpiPlug->numberProcessors,
225 <                          MPI_INT, 0);
224 >    MPI_Bcast(AtomsPerProc, mpiPlug->numberProcessors,
225 >              MPI_INT, 0, MPI_COMM_WORLD);
226 >
227 >
228    }
229  
230  
# Line 253 | Line 244 | int* mpiSimulation::divideLabor( void ){
244      }
245    }
246  
247 <  MPI::COMM_WORLD.Allreduce(&nmol_local,&nmol_global,1,MPI_INT,MPI_SUM);
248 <  MPI::COMM_WORLD.Allreduce(&natoms_local,&natoms_global,1,MPI_INT,MPI_SUM);
247 >  MPI_Allreduce(&nmol_local,&nmol_global,1,MPI_INT,MPI_SUM,
248 >                MPI_COMM_WORLD);
249 >  MPI_Allreduce(&natoms_local,&natoms_global,1,MPI_INT,
250 >                MPI_SUM, MPI_COMM_WORLD);
251    
252    if( nmol_global != entryPlug->n_mol ){
253      sprintf( painCave.errMsg,
# Line 285 | Line 278 | int* mpiSimulation::divideLabor( void ){
278    local_index = 0;
279    for (i = 0; i < mpiPlug->nAtomsGlobal; i++) {
280      if (AtomToProcMap[i] == mpiPlug->myNode) {
288 –      local_index++;
281        globalIndex[local_index] = i;
282 +      local_index++;
283      }
284    }
285 <
285 >  
286    return globalIndex;
287   }
288  
# Line 299 | Line 292 | void mpiSimulation::mpiRefresh( void ){
292    int isError, i;
293    int *globalIndex = new int[mpiPlug->myNlocal];
294  
295 <  for(i=0; i<mpiPlug->myNlocal; i++) globalIndex[i] = entryPlug->atoms[i]->getGlobalIndex();
295 >  // Fortran indexing needs to be increased by 1 in order to get the 2 languages to
296 >  // not barf
297  
298 +  for(i=0; i<mpiPlug->myNlocal; i++) globalIndex[i] = entryPlug->atoms[i]->getGlobalIndex()+1;
299 +
300    
301    isError = 0;
302    setFsimParallel( mpiPlug, &(entryPlug->n_atoms), globalIndex, &isError );

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