OOPSE/libmdtools/mpiSimulation.cpp

#ifdef IS_MPI

#include <cstdlib>
#include <cstring>
#include <cmath>
#include <mpi.h>
#include <mpi++.h>

#include "mpiSimulation.hpp"
#include "simError.h"
#include "fortranWrappers.hpp"
#include "randomSPRNG.hpp"

#define BASE_SEED 123456789

mpiSimulation* mpiSim;

mpiSimulation::mpiSimulation(SimInfo* the_entryPlug)
{
  entryPlug = the_entryPlug;
  mpiPlug = new mpiSimData;
  
  mpiPlug->numberProcessors = MPI::COMM_WORLD.Get_size();
  mpiPlug->myNode = worldRank;

  MolToProcMap = new int[entryPlug->n_mol];
  MolComponentType = new int[entryPlug->n_mol];

  AtomToProcMap = new int[entryPlug->n_atoms];

  mpiSim = this;
  wrapMeSimParallel( this );
}


mpiSimulation::~mpiSimulation(){
  
  delete mpiPlug;
  // perhaps we should let fortran know the party is over.
  
}

int* mpiSimulation::divideLabor( void ){

  int* globalIndex;

  int nComponents;
  MoleculeStamp** compStamps;
  randomSPRNG *myRandom;
  int* componentsNmol;
  int* AtomsPerProc;

  double numerator;
  double denominator;
  double precast;
  double x, y, a;
  int old_atoms, add_atoms, new_atoms;

  int nTarget;
  int molIndex, atomIndex, compIndex, compStart;
  int done;
  int nLocal, molLocal;
  int i, j, loops, which_proc, nmol_local, natoms_local;
  int nmol_global, natoms_global;
  int local_index, index;
  int smallDiff, bigDiff;
  int baseSeed = BASE_SEED;

  int testSum;

  nComponents = entryPlug->nComponents;
  compStamps = entryPlug->compStamps;
  componentsNmol = entryPlug->componentsNmol;
  AtomsPerProc = new int[mpiPlug->numberProcessors];
  
  mpiPlug->nAtomsGlobal = entryPlug->n_atoms;
  mpiPlug->nBondsGlobal = entryPlug->n_bonds;
  mpiPlug->nBendsGlobal = entryPlug->n_bends;
  mpiPlug->nTorsionsGlobal = entryPlug->n_torsions;
  mpiPlug->nSRIGlobal = entryPlug->n_SRI;
  mpiPlug->nMolGlobal = entryPlug->n_mol;

  myRandom = new randomSPRNG( baseSeed );

  a = (double)mpiPlug->nMolGlobal / (double)mpiPlug->nAtomsGlobal;

  // Initialize things that we'll send out later:
  for (i = 0; i < mpiPlug->numberProcessors; i++ ) {
    AtomsPerProc[i] = 0;
  }
  for (i = 0; i < mpiPlug->nMolGlobal; i++ ) {
    // default to an error condition:
    MolToProcMap[i] = -1;
    MolComponentType[i] = -1;
  }
  for (i = 0; i < mpiPlug->nAtomsGlobal; i++ ) {
    // default to an error condition:
    AtomToProcMap[i] = -1;
  }
    
  if (mpiPlug->myNode == 0) {
    numerator = (double) entryPlug->n_atoms;
    denominator = (double) mpiPlug->numberProcessors;
    precast = numerator / denominator;
    nTarget = (int)( precast + 0.5 );

    // Build the array of molecule component types first
    molIndex = 0;
    for (i=0; i < nComponents; i++) {
      for (j=0; j < componentsNmol[i]; j++) {        
        MolComponentType[molIndex] = i;
        molIndex++;
      }
    }

    atomIndex = 0;

    for (i = 0; i < molIndex; i++ ) {

      done = 0;
      loops = 0;

      while( !done ){
        loops++;
        
        // Pick a processor at random

        which_proc = (int) (myRandom->getRandom() * mpiPlug->numberProcessors);

        // How many atoms does this processor have?
        
        old_atoms = AtomsPerProc[which_proc];

        // If the processor already had too many atoms, just skip this
        // processor and try again.

        if (old_atoms >= nTarget) continue;

        add_atoms = compStamps[MolComponentType[i]]->getNAtoms();
        new_atoms = old_atoms + add_atoms;
    
        // If we can add this molecule to this processor without sending
        // it above nTarget, then go ahead and do it:
    
        if (new_atoms <= nTarget) {
          MolToProcMap[i] = which_proc;
          AtomsPerProc[which_proc] += add_atoms;
          for (j = 0 ; j < add_atoms; j++ ) {
            atomIndex++;
            AtomToProcMap[atomIndex] = which_proc;
          }
          done = 1;
          continue;
        }

        // If we've been through this loop too many times, we need
        // to just give up and assign the molecule to this processor
        // and be done with it. 
        
        if (loops > 100) {          
          sprintf( painCave.errMsg,
                   "I've tried 100 times to assign molecule %d to a "
                   " processor, but can't find a good spot.\n"  
                   "I'm assigning it at random to processor %d.\n",
                   i, which_proc);
          painCave.isFatal = 0;
          simError();
          
          MolToProcMap[i] = which_proc;
          AtomsPerProc[which_proc] += add_atoms;
          for (j = 0 ; j < add_atoms; j++ ) {
            atomIndex++;
            AtomToProcMap[atomIndex] = which_proc;
          }
          done = 1;
          continue;
        }

        // The only situation left is where old_atoms < nTarget, but
        // new_atoms > nTarget.   We want to accept this with some
        // probability that dies off the farther we are from nTarget

        // roughly:  x = new_atoms - nTarget
        //           Pacc(x) = exp(- a * x)
        // where a = 1 / (average atoms per molecule)

        x = (double) (new_atoms - nTarget);
        y = myRandom->getRandom();
        
        if (exp(- a * x) > y) {
          MolToProcMap[i] = which_proc;
          AtomsPerProc[which_proc] += add_atoms;
          for (j = 0 ; j < add_atoms; j++ ) {
            atomIndex++;
            AtomToProcMap[atomIndex] = which_proc;
          }
          done = 1;
          continue;
        } else {
          continue;
        }       
        
      }
    }

    // Spray out this nonsense to all other processors:

    MPI::COMM_WORLD.Bcast(&MolToProcMap, mpiPlug->nMolGlobal, 
                          MPI_INT, 0);

    MPI::COMM_WORLD.Bcast(&AtomToProcMap, mpiPlug->nAtomsGlobal, 
                          MPI_INT, 0);

    MPI::COMM_WORLD.Bcast(&MolComponentType, mpiPlug->nMolGlobal, 
                          MPI_INT, 0);

    MPI::COMM_WORLD.Bcast(&AtomsPerProc, mpiPlug->numberProcessors,
                          MPI_INT, 0);    
  } else {

    // Listen to your marching orders from processor 0:
    
    MPI::COMM_WORLD.Bcast(&MolToProcMap, mpiPlug->nMolGlobal, 
                          MPI_INT, 0);
    
    MPI::COMM_WORLD.Bcast(&AtomToProcMap, mpiPlug->nAtomsGlobal, 
                          MPI_INT, 0);

    MPI::COMM_WORLD.Bcast(&MolComponentType, mpiPlug->nMolGlobal, 
                          MPI_INT, 0);
    
    MPI::COMM_WORLD.Bcast(&AtomsPerProc, mpiPlug->numberProcessors,
                          MPI_INT, 0);
  }


  // Let's all check for sanity:

  nmol_local = 0;
  for (i = 0 ; i < mpiPlug->nMolGlobal; i++ ) {
    if (MolToProcMap[i] == mpiPlug->myNode) {
      nmol_local++;
    }
  }

  natoms_local = 0;
  for (i = 0; i < mpiPlug->nAtomsGlobal; i++) {
    if (AtomToProcMap[i] == mpiPlug->myNode) {
      natoms_local++;      
    }
  }

  MPI::COMM_WORLD.Allreduce(&nmol_local,&nmol_global,1,MPI_INT,MPI_SUM);
  MPI::COMM_WORLD.Allreduce(&natoms_local,&natoms_global,1,MPI_INT,MPI_SUM);
  
  if( nmol_global != entryPlug->n_mol ){
    sprintf( painCave.errMsg,
             "The sum of all nmol_local, %d, did not equal the "
             "total number of molecules, %d.\n",
             nmol_global, entryPlug->n_mol );
    painCave.isFatal = 1;
    simError();
  }
  
  if( natoms_global != entryPlug->n_atoms ){
    sprintf( painCave.errMsg,
             "The sum of all natoms_local, %d, did not equal the "
             "total number of atoms, %d.\n",
             natoms_global, entryPlug->n_atoms );
    painCave.isFatal = 1;
    simError();
  }

  sprintf( checkPointMsg,
           "Successfully divided the molecules among the processors.\n" );
  MPIcheckPoint();

  mpiPlug->myNMol = nmol_local;
  mpiPlug->myNlocal = natoms_local;

  globalIndex = new int[mpiPlug->myNlocal];
  local_index = 0;
  for (i = 0; i < mpiPlug->nAtomsGlobal; i++) {
    if (AtomToProcMap[i] == mpiPlug->myNode) {
      local_index++;
      globalIndex[local_index] = i;
    }
  }
 
  return globalIndex;
}


void mpiSimulation::mpiRefresh( void ){

  int isError, i;
  int *globalIndex = new int[mpiPlug->myNlocal];

  for(i=0; i<mpiPlug->myNlocal; i++) globalIndex[i] = entryPlug->atoms[i]->getGlobalIndex();

  
  isError = 0;
  setFsimParallel( mpiPlug, &(entryPlug->n_atoms), globalIndex, &isError );
  if( isError ){

    sprintf( painCave.errMsg,
             "mpiRefresh errror: fortran didn't like something we gave it.\n" );
    painCave.isFatal = 1;
    simError();
  }

  delete[] globalIndex;

  sprintf( checkPointMsg,
           " mpiRefresh successful.\n" );
  MPIcheckPoint();
}
 

#endif // is_mpi
Revision:	416
Committed:	Wed Mar 26 23:14:02 2003 UTC (21 years, 3 months ago) by gezelter
File size:	8576 byte(s)
Log Message:	bug fixes many bug fixes
#	User	Rev	Content
1	mmeineke	377	#ifdef IS_MPI
2
3			#include <cstdlib>
4			#include <cstring>
5	gezelter	416	#include <cmath>
6	mmeineke	377	#include <mpi.h>
7			#include <mpi++.h>
8
9			#include "mpiSimulation.hpp"
10			#include "simError.h"
11			#include "fortranWrappers.hpp"
12	gezelter	405	#include "randomSPRNG.hpp"
13	mmeineke	377
14	gezelter	416	#define BASE_SEED 123456789
15	mmeineke	377
16			mpiSimulation* mpiSim;
17
18			mpiSimulation::mpiSimulation(SimInfo* the_entryPlug)
19			{
20			entryPlug = the_entryPlug;
21			mpiPlug = new mpiSimData;
22
23			mpiPlug->numberProcessors = MPI::COMM_WORLD.Get_size();
24			mpiPlug->myNode = worldRank;
25	gezelter	405
26			MolToProcMap = new int[entryPlug->n_mol];
27			MolComponentType = new int[entryPlug->n_mol];
28
29			AtomToProcMap = new int[entryPlug->n_atoms];
30
31	mmeineke	377	mpiSim = this;
32			wrapMeSimParallel( this );
33			}
34
35
36			mpiSimulation::~mpiSimulation(){
37
38			delete mpiPlug;
39			// perhaps we should let fortran know the party is over.
40
41			}
42
43			int* mpiSimulation::divideLabor( void ){
44
45			int* globalIndex;
46
47			int nComponents;
48			MoleculeStamp** compStamps;
49	gezelter	416	randomSPRNG *myRandom;
50	mmeineke	377	int* componentsNmol;
51	gezelter	405	int* AtomsPerProc;
52	mmeineke	377
53			double numerator;
54			double denominator;
55			double precast;
56	gezelter	405	double x, y, a;
57			int old_atoms, add_atoms, new_atoms;
58	mmeineke	377
59			int nTarget;
60			int molIndex, atomIndex, compIndex, compStart;
61			int done;
62			int nLocal, molLocal;
63	gezelter	416	int i, j, loops, which_proc, nmol_local, natoms_local;
64			int nmol_global, natoms_global;
65			int local_index, index;
66	mmeineke	377	int smallDiff, bigDiff;
67	gezelter	416	int baseSeed = BASE_SEED;
68	mmeineke	377
69			int testSum;
70
71			nComponents = entryPlug->nComponents;
72			compStamps = entryPlug->compStamps;
73			componentsNmol = entryPlug->componentsNmol;
74	gezelter	405	AtomsPerProc = new int[mpiPlug->numberProcessors];
75
76	mmeineke	377	mpiPlug->nAtomsGlobal = entryPlug->n_atoms;
77			mpiPlug->nBondsGlobal = entryPlug->n_bonds;
78			mpiPlug->nBendsGlobal = entryPlug->n_bends;
79			mpiPlug->nTorsionsGlobal = entryPlug->n_torsions;
80			mpiPlug->nSRIGlobal = entryPlug->n_SRI;
81			mpiPlug->nMolGlobal = entryPlug->n_mol;
82
83	gezelter	416	myRandom = new randomSPRNG( baseSeed );
84	chuckv	404
85	gezelter	405	a = (double)mpiPlug->nMolGlobal / (double)mpiPlug->nAtomsGlobal;
86	chuckv	404
87	gezelter	405	// Initialize things that we'll send out later:
88			for (i = 0; i < mpiPlug->numberProcessors; i++ ) {
89			AtomsPerProc[i] = 0;
90			}
91			for (i = 0; i < mpiPlug->nMolGlobal; i++ ) {
92			// default to an error condition:
93			MolToProcMap[i] = -1;
94			MolComponentType[i] = -1;
95			}
96			for (i = 0; i < mpiPlug->nAtomsGlobal; i++ ) {
97			// default to an error condition:
98			AtomToProcMap[i] = -1;
99			}
100
101			if (mpiPlug->myNode == 0) {
102			numerator = (double) entryPlug->n_atoms;
103			denominator = (double) mpiPlug->numberProcessors;
104			precast = numerator / denominator;
105			nTarget = (int)( precast + 0.5 );
106	chuckv	404
107	gezelter	405	// Build the array of molecule component types first
108			molIndex = 0;
109			for (i=0; i < nComponents; i++) {
110			for (j=0; j < componentsNmol[i]; j++) {
111			MolComponentType[molIndex] = i;
112			molIndex++;
113			}
114			}
115	chuckv	404
116	gezelter	405	atomIndex = 0;
117	chuckv	404
118	gezelter	405	for (i = 0; i < molIndex; i++ ) {
119	chuckv	404
120	gezelter	405	done = 0;
121			loops = 0;
122	chuckv	404
123	gezelter	405	while( !done ){
124			loops++;
125
126			// Pick a processor at random
127	chuckv	404
128	gezelter	416	which_proc = (int) (myRandom->getRandom() * mpiPlug->numberProcessors);
129	chuckv	404
130	gezelter	405	// How many atoms does this processor have?
131
132			old_atoms = AtomsPerProc[which_proc];
133	chuckv	404
134	gezelter	405	// If the processor already had too many atoms, just skip this
135			// processor and try again.
136	chuckv	404
137	gezelter	405	if (old_atoms >= nTarget) continue;
138	mmeineke	377
139	gezelter	416	add_atoms = compStamps[MolComponentType[i]]->getNAtoms();
140	gezelter	405	new_atoms = old_atoms + add_atoms;
141	mmeineke	377
142	gezelter	405	// If we can add this molecule to this processor without sending
143			// it above nTarget, then go ahead and do it:
144
145			if (new_atoms <= nTarget) {
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;
151			}
152			done = 1;
153			continue;
154			}
155	mmeineke	377
156	gezelter	405	// If we've been through this loop too many times, we need
157			// to just give up and assign the molecule to this processor
158			// and be done with it.
159
160			if (loops > 100) {
161			sprintf( painCave.errMsg,
162			"I've tried 100 times to assign molecule %d to a "
163			" processor, but can't find a good spot.\n"
164			"I'm assigning it at random to processor %d.\n",
165			i, which_proc);
166			painCave.isFatal = 0;
167			simError();
168
169			MolToProcMap[i] = which_proc;
170			AtomsPerProc[which_proc] += add_atoms;
171			for (j = 0 ; j < add_atoms; j++ ) {
172			atomIndex++;
173			AtomToProcMap[atomIndex] = which_proc;
174			}
175			done = 1;
176			continue;
177			}
178
179			// The only situation left is where old_atoms < nTarget, but
180			// new_atoms > nTarget. We want to accept this with some
181			// probability that dies off the farther we are from nTarget
182
183			// roughly: x = new_atoms - nTarget
184			// Pacc(x) = exp(- a * x)
185			// where a = 1 / (average atoms per molecule)
186
187			x = (double) (new_atoms - nTarget);
188	gezelter	416	y = myRandom->getRandom();
189	gezelter	405
190			if (exp(- a * x) > y) {
191			MolToProcMap[i] = which_proc;
192			AtomsPerProc[which_proc] += add_atoms;
193			for (j = 0 ; j < add_atoms; j++ ) {
194			atomIndex++;
195			AtomToProcMap[atomIndex] = which_proc;
196			}
197			done = 1;
198			continue;
199			} else {
200			continue;
201			}
202
203	mmeineke	377	}
204			}
205	gezelter	405
206			// Spray out this nonsense to all other processors:
207
208			MPI::COMM_WORLD.Bcast(&MolToProcMap, mpiPlug->nMolGlobal,
209			MPI_INT, 0);
210
211			MPI::COMM_WORLD.Bcast(&AtomToProcMap, mpiPlug->nAtomsGlobal,
212			MPI_INT, 0);
213
214			MPI::COMM_WORLD.Bcast(&MolComponentType, mpiPlug->nMolGlobal,
215			MPI_INT, 0);
216
217			MPI::COMM_WORLD.Bcast(&AtomsPerProc, mpiPlug->numberProcessors,
218			MPI_INT, 0);
219			} else {
220
221			// Listen to your marching orders from processor 0:
222	mmeineke	377
223	gezelter	405	MPI::COMM_WORLD.Bcast(&MolToProcMap, mpiPlug->nMolGlobal,
224			MPI_INT, 0);
225	mmeineke	377
226	gezelter	405	MPI::COMM_WORLD.Bcast(&AtomToProcMap, mpiPlug->nAtomsGlobal,
227			MPI_INT, 0);
228
229			MPI::COMM_WORLD.Bcast(&MolComponentType, mpiPlug->nMolGlobal,
230			MPI_INT, 0);
231
232			MPI::COMM_WORLD.Bcast(&AtomsPerProc, mpiPlug->numberProcessors,
233			MPI_INT, 0);
234	mmeineke	377	}
235
236
237	gezelter	405	// 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	mmeineke	377	}
245
246	gezelter	405	natoms_local = 0;
247			for (i = 0; i < mpiPlug->nAtomsGlobal; i++) {
248			if (AtomToProcMap[i] == mpiPlug->myNode) {
249			natoms_local++;
250			}
251			}
252	mmeineke	377
253	gezelter	405	MPI::COMM_WORLD.Allreduce(&nmol_local,&nmol_global,1,MPI_INT,MPI_SUM);
254			MPI::COMM_WORLD.Allreduce(&natoms_local,&natoms_global,1,MPI_INT,MPI_SUM);
255	mmeineke	377
256	gezelter	405	if( nmol_global != entryPlug->n_mol ){
257			sprintf( painCave.errMsg,
258			"The sum of all nmol_local, %d, did not equal the "
259			"total number of molecules, %d.\n",
260			nmol_global, entryPlug->n_mol );
261			painCave.isFatal = 1;
262			simError();
263	mmeineke	377	}
264	gezelter	405
265			if( natoms_global != entryPlug->n_atoms ){
266			sprintf( painCave.errMsg,
267			"The sum of all natoms_local, %d, did not equal the "
268			"total number of atoms, %d.\n",
269			natoms_global, entryPlug->n_atoms );
270			painCave.isFatal = 1;
271			simError();
272			}
273	mmeineke	377
274			sprintf( checkPointMsg,
275			"Successfully divided the molecules among the processors.\n" );
276			MPIcheckPoint();
277
278	gezelter	405	mpiPlug->myNMol = nmol_local;
279			mpiPlug->myNlocal = natoms_local;
280	mmeineke	377
281			globalIndex = new int[mpiPlug->myNlocal];
282	gezelter	405	local_index = 0;
283			for (i = 0; i < mpiPlug->nAtomsGlobal; i++) {
284			if (AtomToProcMap[i] == mpiPlug->myNode) {
285	chuckv	406	local_index++;
286			globalIndex[local_index] = i;
287	gezelter	405	}
288	mmeineke	377	}
289	gezelter	416
290			return globalIndex;
291	mmeineke	377	}
292
293
294			void mpiSimulation::mpiRefresh( void ){
295
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();
300
301
302			isError = 0;
303			setFsimParallel( mpiPlug, &(entryPlug->n_atoms), globalIndex, &isError );
304			if( isError ){
305
306			sprintf( painCave.errMsg,
307			"mpiRefresh errror: fortran didn't like something we gave it.\n" );
308			painCave.isFatal = 1;
309			simError();
310			}
311
312			delete[] globalIndex;
313
314			sprintf( checkPointMsg,
315			" mpiRefresh successful.\n" );
316			MPIcheckPoint();
317			}
318
319
320			#endif // is_mpi