OOPSE/libmdtools/mpiSimulation.cpp

#ifdef IS_MPI
#include <iostream>
#include <cstdlib>
#include <cstring>
#include <cmath>
#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;
  
  MPI_Comm_size(MPI_COMM_WORLD, &(mpiPlug->numberProcessors) );
  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 = 3.0 * (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];
        add_atoms = compStamps[MolComponentType[i]]->getNAtoms();
        new_atoms = old_atoms + add_atoms;

        // 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;
        }
    
        // 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;
        }


        // The only situation left is when 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 = penalty / (average atoms per molecule)

        x = (double) (new_atoms - nTarget);
        y = myRandom->getRandom();
      
        if (y < exp(- a * x)) {
          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_Bcast(MolToProcMap, mpiPlug->nMolGlobal, 
              MPI_INT, 0, MPI_COMM_WORLD);

    MPI_Bcast(AtomToProcMap, mpiPlug->nAtomsGlobal, 
              MPI_INT, 0, MPI_COMM_WORLD);

    MPI_Bcast(MolComponentType, mpiPlug->nMolGlobal, 
              MPI_INT, 0, MPI_COMM_WORLD);

    MPI_Bcast(AtomsPerProc, mpiPlug->numberProcessors,
              MPI_INT, 0, MPI_COMM_WORLD);    
  } else {

    // Listen to your marching orders from processor 0:
    
    MPI_Bcast(MolToProcMap, mpiPlug->nMolGlobal, 
              MPI_INT, 0, MPI_COMM_WORLD);
    
    MPI_Bcast(AtomToProcMap, mpiPlug->nAtomsGlobal, 
              MPI_INT, 0, MPI_COMM_WORLD);

    MPI_Bcast(MolComponentType, mpiPlug->nMolGlobal, 
              MPI_INT, 0, MPI_COMM_WORLD);
    
    MPI_Bcast(AtomsPerProc, mpiPlug->numberProcessors,
              MPI_INT, 0, MPI_COMM_WORLD);


  }


  // 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_Allreduce(&nmol_local,&nmol_global,1,MPI_INT,MPI_SUM, 
                MPI_COMM_WORLD);
  MPI_Allreduce(&natoms_local,&natoms_global,1,MPI_INT,
                MPI_SUM, MPI_COMM_WORLD);
  
  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];

  // Fortran indexing needs to be increased by 1 in order to get the 2 languages to
  // not barf

  for(i=0; i<mpiPlug->myNlocal; i++) globalIndex[i] = entryPlug->atoms[i]->getGlobalIndex()+1;

  
  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:	447
Committed:	Thu Apr 3 20:21:54 2003 UTC (22 years, 6 months ago) by mmeineke
File size:	8441 byte(s)
Log Message:	fixed some small things with simError.h
#	User	Rev	Content
1	mmeineke	377	#ifdef IS_MPI
2	chuckv	432	#include <iostream>
3	mmeineke	377	#include <cstdlib>
4			#include <cstring>
5	gezelter	416	#include <cmath>
6	mmeineke	377	#include <mpi.h>
7
8			#include "mpiSimulation.hpp"
9			#include "simError.h"
10			#include "fortranWrappers.hpp"
11	gezelter	405	#include "randomSPRNG.hpp"
12	mmeineke	377
13	gezelter	416	#define BASE_SEED 123456789
14	mmeineke	377
15			mpiSimulation* mpiSim;
16
17			mpiSimulation::mpiSimulation(SimInfo* the_entryPlug)
18			{
19			entryPlug = the_entryPlug;
20			mpiPlug = new mpiSimData;
21
22	mmeineke	447	MPI_Comm_size(MPI_COMM_WORLD, &(mpiPlug->numberProcessors) );
23	mmeineke	377	mpiPlug->myNode = worldRank;
24	gezelter	405
25			MolToProcMap = new int[entryPlug->n_mol];
26			MolComponentType = new int[entryPlug->n_mol];
27			AtomToProcMap = new int[entryPlug->n_atoms];
28
29	mmeineke	377	mpiSim = this;
30			wrapMeSimParallel( this );
31			}
32
33
34			mpiSimulation::~mpiSimulation(){
35
36	mmeineke	418	delete[] MolToProcMap;
37			delete[] MolComponentType;
38			delete[] AtomToProcMap;
39
40	mmeineke	377	delete mpiPlug;
41			// perhaps we should let fortran know the party is over.
42
43			}
44
45			int* mpiSimulation::divideLabor( void ){
46
47			int* globalIndex;
48
49			int nComponents;
50			MoleculeStamp** compStamps;
51	gezelter	416	randomSPRNG *myRandom;
52	mmeineke	377	int* componentsNmol;
53	gezelter	405	int* AtomsPerProc;
54	mmeineke	377
55			double numerator;
56			double denominator;
57			double precast;
58	gezelter	405	double x, y, a;
59			int old_atoms, add_atoms, new_atoms;
60	mmeineke	377
61			int nTarget;
62			int molIndex, atomIndex, compIndex, compStart;
63			int done;
64			int nLocal, molLocal;
65	gezelter	416	int i, j, loops, which_proc, nmol_local, natoms_local;
66			int nmol_global, natoms_global;
67			int local_index, index;
68	mmeineke	377	int smallDiff, bigDiff;
69	gezelter	416	int baseSeed = BASE_SEED;
70	mmeineke	377
71			int testSum;
72
73			nComponents = entryPlug->nComponents;
74			compStamps = entryPlug->compStamps;
75			componentsNmol = entryPlug->componentsNmol;
76	gezelter	405	AtomsPerProc = new int[mpiPlug->numberProcessors];
77
78	mmeineke	377	mpiPlug->nAtomsGlobal = entryPlug->n_atoms;
79			mpiPlug->nBondsGlobal = entryPlug->n_bonds;
80			mpiPlug->nBendsGlobal = entryPlug->n_bends;
81			mpiPlug->nTorsionsGlobal = entryPlug->n_torsions;
82			mpiPlug->nSRIGlobal = entryPlug->n_SRI;
83			mpiPlug->nMolGlobal = entryPlug->n_mol;
84
85	gezelter	416	myRandom = new randomSPRNG( baseSeed );
86	chuckv	404
87	chuckv	434	a = 3.0 * (double)mpiPlug->nMolGlobal / (double)mpiPlug->nAtomsGlobal;
88	chuckv	404
89	gezelter	405	// Initialize things that we'll send out later:
90			for (i = 0; i < mpiPlug->numberProcessors; i++ ) {
91			AtomsPerProc[i] = 0;
92			}
93			for (i = 0; i < mpiPlug->nMolGlobal; i++ ) {
94			// default to an error condition:
95			MolToProcMap[i] = -1;
96			MolComponentType[i] = -1;
97			}
98			for (i = 0; i < mpiPlug->nAtomsGlobal; i++ ) {
99			// default to an error condition:
100			AtomToProcMap[i] = -1;
101			}
102
103			if (mpiPlug->myNode == 0) {
104			numerator = (double) entryPlug->n_atoms;
105			denominator = (double) mpiPlug->numberProcessors;
106			precast = numerator / denominator;
107			nTarget = (int)( precast + 0.5 );
108	chuckv	404
109	gezelter	405	// Build the array of molecule component types first
110			molIndex = 0;
111			for (i=0; i < nComponents; i++) {
112			for (j=0; j < componentsNmol[i]; j++) {
113			MolComponentType[molIndex] = i;
114			molIndex++;
115			}
116			}
117	chuckv	404
118	gezelter	405	atomIndex = 0;
119	chuckv	404
120	gezelter	405	for (i = 0; i < molIndex; i++ ) {
121	chuckv	404
122	gezelter	405	done = 0;
123			loops = 0;
124	chuckv	404
125	gezelter	405	while( !done ){
126			loops++;
127
128			// Pick a processor at random
129	chuckv	404
130	gezelter	416	which_proc = (int) (myRandom->getRandom() * mpiPlug->numberProcessors);
131	chuckv	404
132	gezelter	405	// How many atoms does this processor have?
133
134			old_atoms = AtomsPerProc[which_proc];
135	chuckv	432	add_atoms = compStamps[MolComponentType[i]]->getNAtoms();
136			new_atoms = old_atoms + add_atoms;
137	chuckv	404
138	gezelter	405	// If we've been through this loop too many times, we need
139			// to just give up and assign the molecule to this processor
140			// and be done with it.
141
142			if (loops > 100) {
143			sprintf( painCave.errMsg,
144			"I've tried 100 times to assign molecule %d to a "
145			" processor, but can't find a good spot.\n"
146			"I'm assigning it at random to processor %d.\n",
147			i, which_proc);
148			painCave.isFatal = 0;
149			simError();
150
151			MolToProcMap[i] = which_proc;
152			AtomsPerProc[which_proc] += add_atoms;
153			for (j = 0 ; j < add_atoms; j++ ) {
154	mmeineke	422	AtomToProcMap[atomIndex] = which_proc;
155			atomIndex++;
156	gezelter	405	}
157			done = 1;
158			continue;
159			}
160	chuckv	432
161			// If we can add this molecule to this processor without sending
162			// it above nTarget, then go ahead and do it:
163
164			if (new_atoms <= nTarget) {
165			MolToProcMap[i] = which_proc;
166			AtomsPerProc[which_proc] += add_atoms;
167			for (j = 0 ; j < add_atoms; j++ ) {
168			AtomToProcMap[atomIndex] = which_proc;
169			atomIndex++;
170			}
171			done = 1;
172			continue;
173			}
174
175
176	chuckv	434	// The only situation left is when new_atoms > nTarget. We
177			// want to accept this with some probability that dies off the
178			// farther we are from nTarget
179	gezelter	405
180			// roughly: x = new_atoms - nTarget
181			// Pacc(x) = exp(- a * x)
182	chuckv	434	// where a = penalty / (average atoms per molecule)
183	gezelter	405
184			x = (double) (new_atoms - nTarget);
185	gezelter	416	y = myRandom->getRandom();
186	chuckv	434
187			if (y < exp(- a * x)) {
188	gezelter	405	MolToProcMap[i] = which_proc;
189			AtomsPerProc[which_proc] += add_atoms;
190			for (j = 0 ; j < add_atoms; j++ ) {
191	mmeineke	422	AtomToProcMap[atomIndex] = which_proc;
192			atomIndex++;
193			}
194	gezelter	405	done = 1;
195			continue;
196			} else {
197			continue;
198			}
199
200	mmeineke	377	}
201			}
202	gezelter	405
203			// Spray out this nonsense to all other processors:
204
205	mmeineke	447	MPI_Bcast(MolToProcMap, mpiPlug->nMolGlobal,
206			MPI_INT, 0, MPI_COMM_WORLD);
207	gezelter	405
208	mmeineke	447	MPI_Bcast(AtomToProcMap, mpiPlug->nAtomsGlobal,
209			MPI_INT, 0, MPI_COMM_WORLD);
210	gezelter	405
211	mmeineke	447	MPI_Bcast(MolComponentType, mpiPlug->nMolGlobal,
212			MPI_INT, 0, MPI_COMM_WORLD);
213	gezelter	405
214	mmeineke	447	MPI_Bcast(AtomsPerProc, mpiPlug->numberProcessors,
215			MPI_INT, 0, MPI_COMM_WORLD);
216	gezelter	405	} else {
217
218			// Listen to your marching orders from processor 0:
219	mmeineke	377
220	mmeineke	447	MPI_Bcast(MolToProcMap, mpiPlug->nMolGlobal,
221			MPI_INT, 0, MPI_COMM_WORLD);
222	mmeineke	377
223	mmeineke	447	MPI_Bcast(AtomToProcMap, mpiPlug->nAtomsGlobal,
224			MPI_INT, 0, MPI_COMM_WORLD);
225	gezelter	405
226	mmeineke	447	MPI_Bcast(MolComponentType, mpiPlug->nMolGlobal,
227			MPI_INT, 0, MPI_COMM_WORLD);
228	gezelter	405
229	mmeineke	447	MPI_Bcast(AtomsPerProc, mpiPlug->numberProcessors,
230			MPI_INT, 0, MPI_COMM_WORLD);
231	chuckv	432
232
233	mmeineke	377	}
234
235
236	gezelter	405	// Let's all check for sanity:
237
238			nmol_local = 0;
239			for (i = 0 ; i < mpiPlug->nMolGlobal; i++ ) {
240			if (MolToProcMap[i] == mpiPlug->myNode) {
241			nmol_local++;
242			}
243	mmeineke	377	}
244
245	gezelter	405	natoms_local = 0;
246			for (i = 0; i < mpiPlug->nAtomsGlobal; i++) {
247			if (AtomToProcMap[i] == mpiPlug->myNode) {
248			natoms_local++;
249			}
250			}
251	mmeineke	377
252	mmeineke	447	MPI_Allreduce(&nmol_local,&nmol_global,1,MPI_INT,MPI_SUM,
253			MPI_COMM_WORLD);
254			MPI_Allreduce(&natoms_local,&natoms_global,1,MPI_INT,
255			MPI_SUM, MPI_COMM_WORLD);
256	mmeineke	377
257	gezelter	405	if( nmol_global != entryPlug->n_mol ){
258			sprintf( painCave.errMsg,
259			"The sum of all nmol_local, %d, did not equal the "
260			"total number of molecules, %d.\n",
261			nmol_global, entryPlug->n_mol );
262			painCave.isFatal = 1;
263			simError();
264	mmeineke	377	}
265	gezelter	405
266			if( natoms_global != entryPlug->n_atoms ){
267			sprintf( painCave.errMsg,
268			"The sum of all natoms_local, %d, did not equal the "
269			"total number of atoms, %d.\n",
270			natoms_global, entryPlug->n_atoms );
271			painCave.isFatal = 1;
272			simError();
273			}
274	mmeineke	377
275			sprintf( checkPointMsg,
276			"Successfully divided the molecules among the processors.\n" );
277			MPIcheckPoint();
278
279	gezelter	405	mpiPlug->myNMol = nmol_local;
280			mpiPlug->myNlocal = natoms_local;
281	mmeineke	377
282			globalIndex = new int[mpiPlug->myNlocal];
283	gezelter	405	local_index = 0;
284			for (i = 0; i < mpiPlug->nAtomsGlobal; i++) {
285			if (AtomToProcMap[i] == mpiPlug->myNode) {
286	mmeineke	422	globalIndex[local_index] = i;
287	chuckv	406	local_index++;
288	gezelter	405	}
289	mmeineke	377	}
290	chuckv	432
291	gezelter	416	return globalIndex;
292	mmeineke	377	}
293
294
295			void mpiSimulation::mpiRefresh( void ){
296
297			int isError, i;
298			int *globalIndex = new int[mpiPlug->myNlocal];
299
300	chuckv	441	// Fortran indexing needs to be increased by 1 in order to get the 2 languages to
301			// not barf
302	mmeineke	377
303	chuckv	441	for(i=0; i<mpiPlug->myNlocal; i++) globalIndex[i] = entryPlug->atoms[i]->getGlobalIndex()+1;
304
305	mmeineke	377
306			isError = 0;
307			setFsimParallel( mpiPlug, &(entryPlug->n_atoms), globalIndex, &isError );
308			if( isError ){
309
310			sprintf( painCave.errMsg,
311			"mpiRefresh errror: fortran didn't like something we gave it.\n" );
312			painCave.isFatal = 1;
313			simError();
314			}
315
316			delete[] globalIndex;
317
318			sprintf( checkPointMsg,
319			" mpiRefresh successful.\n" );
320			MPIcheckPoint();
321			}
322
323
324			#endif // is_mpi