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[] MolToProcMap;
  delete[] MolComponentType;
  delete[] AtomToProcMap;

  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++ ) {
            AtomToProcMap[atomIndex] = which_proc;
            atomIndex++;
          }
          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++ ) {
            AtomToProcMap[atomIndex] = which_proc;
            atomIndex++;
          }
          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++ ) {
            AtomToProcMap[atomIndex] = which_proc;
            atomIndex++;
           }
          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) {
      globalIndex[local_index] = i;
      local_index++;
    }
  }
 
  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:	422
Committed:	Thu Mar 27 19:21:42 2003 UTC (21 years, 3 months ago) by mmeineke
File size:	8607 byte(s)
Log Message:	finished updating SimSetup to initialize and use the new MPI division of labour, and Molecule class
#	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			AtomToProcMap = new int[entryPlug->n_atoms];
29
30	mmeineke	377	mpiSim = this;
31			wrapMeSimParallel( this );
32			}
33
34
35			mpiSimulation::~mpiSimulation(){
36
37	mmeineke	418	delete[] MolToProcMap;
38			delete[] MolComponentType;
39			delete[] AtomToProcMap;
40
41	mmeineke	377	delete mpiPlug;
42			// perhaps we should let fortran know the party is over.
43
44			}
45
46			int* mpiSimulation::divideLabor( void ){
47
48			int* globalIndex;
49
50			int nComponents;
51			MoleculeStamp** compStamps;
52	gezelter	416	randomSPRNG *myRandom;
53	mmeineke	377	int* componentsNmol;
54	gezelter	405	int* AtomsPerProc;
55	mmeineke	377
56			double numerator;
57			double denominator;
58			double precast;
59	gezelter	405	double x, y, a;
60			int old_atoms, add_atoms, new_atoms;
61	mmeineke	377
62			int nTarget;
63			int molIndex, atomIndex, compIndex, compStart;
64			int done;
65			int nLocal, molLocal;
66	gezelter	416	int i, j, loops, which_proc, nmol_local, natoms_local;
67			int nmol_global, natoms_global;
68			int local_index, index;
69	mmeineke	377	int smallDiff, bigDiff;
70	gezelter	416	int baseSeed = BASE_SEED;
71	mmeineke	377
72			int testSum;
73
74			nComponents = entryPlug->nComponents;
75			compStamps = entryPlug->compStamps;
76			componentsNmol = entryPlug->componentsNmol;
77	gezelter	405	AtomsPerProc = new int[mpiPlug->numberProcessors];
78
79	mmeineke	377	mpiPlug->nAtomsGlobal = entryPlug->n_atoms;
80			mpiPlug->nBondsGlobal = entryPlug->n_bonds;
81			mpiPlug->nBendsGlobal = entryPlug->n_bends;
82			mpiPlug->nTorsionsGlobal = entryPlug->n_torsions;
83			mpiPlug->nSRIGlobal = entryPlug->n_SRI;
84			mpiPlug->nMolGlobal = entryPlug->n_mol;
85
86	gezelter	416	myRandom = new randomSPRNG( baseSeed );
87	chuckv	404
88	gezelter	405	a = (double)mpiPlug->nMolGlobal / (double)mpiPlug->nAtomsGlobal;
89	chuckv	404
90	gezelter	405	// 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			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	chuckv	404
110	gezelter	405	// 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	chuckv	404
119	gezelter	405	atomIndex = 0;
120	chuckv	404
121	gezelter	405	for (i = 0; i < molIndex; i++ ) {
122	chuckv	404
123	gezelter	405	done = 0;
124			loops = 0;
125	chuckv	404
126	gezelter	405	while( !done ){
127			loops++;
128
129			// Pick a processor at random
130	chuckv	404
131	gezelter	416	which_proc = (int) (myRandom->getRandom() * mpiPlug->numberProcessors);
132	chuckv	404
133	gezelter	405	// How many atoms does this processor have?
134
135			old_atoms = AtomsPerProc[which_proc];
136	chuckv	404
137	gezelter	405	// If the processor already had too many atoms, just skip this
138			// processor and try again.
139	chuckv	404
140	gezelter	405	if (old_atoms >= nTarget) continue;
141	mmeineke	377
142	gezelter	416	add_atoms = compStamps[MolComponentType[i]]->getNAtoms();
143	gezelter	405	new_atoms = old_atoms + add_atoms;
144	mmeineke	377
145	gezelter	405	// 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	mmeineke	422	AtomToProcMap[atomIndex] = which_proc;
153			atomIndex++;
154	gezelter	405	}
155			done = 1;
156			continue;
157			}
158	mmeineke	377
159	gezelter	405	// If we've been through this loop too many times, we need
160			// to just give up and assign the molecule to this processor
161			// and be done with it.
162
163			if (loops > 100) {
164			sprintf( painCave.errMsg,
165			"I've tried 100 times to assign molecule %d to a "
166			" processor, but can't find a good spot.\n"
167			"I'm assigning it at random to processor %d.\n",
168			i, which_proc);
169			painCave.isFatal = 0;
170			simError();
171
172			MolToProcMap[i] = which_proc;
173			AtomsPerProc[which_proc] += add_atoms;
174			for (j = 0 ; j < add_atoms; j++ ) {
175	mmeineke	422	AtomToProcMap[atomIndex] = which_proc;
176			atomIndex++;
177	gezelter	405	}
178			done = 1;
179			continue;
180			}
181
182			// The only situation left is where old_atoms < nTarget, but
183			// new_atoms > nTarget. We want to accept this with some
184			// probability that dies off the farther we are from nTarget
185
186			// roughly: x = new_atoms - nTarget
187			// Pacc(x) = exp(- a * x)
188			// where a = 1 / (average atoms per molecule)
189
190			x = (double) (new_atoms - nTarget);
191	gezelter	416	y = myRandom->getRandom();
192	gezelter	405
193			if (exp(- a * x) > y) {
194			MolToProcMap[i] = which_proc;
195			AtomsPerProc[which_proc] += add_atoms;
196			for (j = 0 ; j < add_atoms; j++ ) {
197	mmeineke	422	AtomToProcMap[atomIndex] = which_proc;
198			atomIndex++;
199			}
200	gezelter	405	done = 1;
201			continue;
202			} else {
203			continue;
204			}
205
206	mmeineke	377	}
207			}
208	gezelter	405
209			// Spray out this nonsense to all other processors:
210
211	mmeineke	418	MPI::COMM_WORLD.Bcast(MolToProcMap, mpiPlug->nMolGlobal,
212	gezelter	405	MPI_INT, 0);
213
214	mmeineke	418	MPI::COMM_WORLD.Bcast(AtomToProcMap, mpiPlug->nAtomsGlobal,
215	gezelter	405	MPI_INT, 0);
216
217	mmeineke	418	MPI::COMM_WORLD.Bcast(MolComponentType, mpiPlug->nMolGlobal,
218	gezelter	405	MPI_INT, 0);
219
220	mmeineke	418	MPI::COMM_WORLD.Bcast(AtomsPerProc, mpiPlug->numberProcessors,
221	gezelter	405	MPI_INT, 0);
222			} else {
223
224			// Listen to your marching orders from processor 0:
225	mmeineke	377
226	mmeineke	418	MPI::COMM_WORLD.Bcast(MolToProcMap, mpiPlug->nMolGlobal,
227	gezelter	405	MPI_INT, 0);
228	mmeineke	377
229	mmeineke	418	MPI::COMM_WORLD.Bcast(AtomToProcMap, mpiPlug->nAtomsGlobal,
230	gezelter	405	MPI_INT, 0);
231
232	mmeineke	418	MPI::COMM_WORLD.Bcast(MolComponentType, mpiPlug->nMolGlobal,
233	gezelter	405	MPI_INT, 0);
234
235	mmeineke	418	MPI::COMM_WORLD.Bcast(AtomsPerProc, mpiPlug->numberProcessors,
236	gezelter	405	MPI_INT, 0);
237	mmeineke	377	}
238
239
240	gezelter	405	// Let's all check for sanity:
241
242			nmol_local = 0;
243			for (i = 0 ; i < mpiPlug->nMolGlobal; i++ ) {
244			if (MolToProcMap[i] == mpiPlug->myNode) {
245			nmol_local++;
246			}
247	mmeineke	377	}
248
249	gezelter	405	natoms_local = 0;
250			for (i = 0; i < mpiPlug->nAtomsGlobal; i++) {
251			if (AtomToProcMap[i] == mpiPlug->myNode) {
252			natoms_local++;
253			}
254			}
255	mmeineke	377
256	gezelter	405	MPI::COMM_WORLD.Allreduce(&nmol_local,&nmol_global,1,MPI_INT,MPI_SUM);
257			MPI::COMM_WORLD.Allreduce(&natoms_local,&natoms_global,1,MPI_INT,MPI_SUM);
258	mmeineke	377
259	gezelter	405	if( nmol_global != entryPlug->n_mol ){
260			sprintf( painCave.errMsg,
261			"The sum of all nmol_local, %d, did not equal the "
262			"total number of molecules, %d.\n",
263			nmol_global, entryPlug->n_mol );
264			painCave.isFatal = 1;
265			simError();
266	mmeineke	377	}
267	gezelter	405
268			if( natoms_global != entryPlug->n_atoms ){
269			sprintf( painCave.errMsg,
270			"The sum of all natoms_local, %d, did not equal the "
271			"total number of atoms, %d.\n",
272			natoms_global, entryPlug->n_atoms );
273			painCave.isFatal = 1;
274			simError();
275			}
276	mmeineke	377
277			sprintf( checkPointMsg,
278			"Successfully divided the molecules among the processors.\n" );
279			MPIcheckPoint();
280
281	gezelter	405	mpiPlug->myNMol = nmol_local;
282			mpiPlug->myNlocal = natoms_local;
283	mmeineke	377
284			globalIndex = new int[mpiPlug->myNlocal];
285	gezelter	405	local_index = 0;
286			for (i = 0; i < mpiPlug->nAtomsGlobal; i++) {
287			if (AtomToProcMap[i] == mpiPlug->myNode) {
288	mmeineke	422	globalIndex[local_index] = i;
289	chuckv	406	local_index++;
290	gezelter	405	}
291	mmeineke	377	}
292	gezelter	416
293			return globalIndex;
294	mmeineke	377	}
295
296
297			void mpiSimulation::mpiRefresh( void ){
298
299			int isError, i;
300			int *globalIndex = new int[mpiPlug->myNlocal];
301
302			for(i=0; i<mpiPlug->myNlocal; i++) globalIndex[i] = entryPlug->atoms[i]->getGlobalIndex();
303
304
305			isError = 0;
306			setFsimParallel( mpiPlug, &(entryPlug->n_atoms), globalIndex, &isError );
307			if( isError ){
308
309			sprintf( painCave.errMsg,
310			"mpiRefresh errror: fortran didn't like something we gave it.\n" );
311			painCave.isFatal = 1;
312			simError();
313			}
314
315			delete[] globalIndex;
316
317			sprintf( checkPointMsg,
318			" mpiRefresh successful.\n" );
319			MPIcheckPoint();
320			}
321
322
323			#endif // is_mpi