OOPSE/libmdtools/mpiSimulation.cpp

#ifdef IS_MPI
#include <iostream>
#include <stdlib.h>
#include <string.h>
#include <math.h>
#include <mpi.h>

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

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.
  
}

void mpiSimulation::divideLabor( ){

  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;
  int done;
  int i, j, loops, which_proc, nmol_local, natoms_local;
  int nmol_global, natoms_global;
  int local_index;
  int baseSeed = entryPlug->getSeed();

  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;

  globalAtomIndex.resize(mpiPlug->myNlocal);
  globalToLocalAtom.resize(mpiPlug->nAtomsGlobal);
  local_index = 0;
  for (i = 0; i < mpiPlug->nAtomsGlobal; i++) {
    if (AtomToProcMap[i] == mpiPlug->myNode) {
      globalAtomIndex[local_index] = i;

      globalToLocalAtom[i] = local_index;
      local_index++;
      
    }
    else
       globalToLocalAtom[i] = -1;
  }

  globalMolIndex.resize(mpiPlug->myNMol);
  globalToLocalMol.resize(mpiPlug->nMolGlobal);
  
  local_index = 0;
  for (i = 0; i < mpiPlug->nMolGlobal; i++) {
    if (MolToProcMap[i] == mpiPlug->myNode) {
      globalMolIndex[local_index] = i;
      globalToLocalMol[i] = local_index;
      local_index++;
    }
    else
      globalToLocalMol[i] = -1;
  }
  
}


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:	1129
Committed:	Thu Apr 22 03:29:30 2004 UTC (20 years, 2 months ago) by tim
File size:	8789 byte(s)
Log Message:	fixed two bugs in MPI version of InitfromFile and one unmatch MPI command in DumpWriter
#	User	Rev	Content
1	mmeineke	377	#ifdef IS_MPI
2	chuckv	432	#include <iostream>
3	gezelter	829	#include <stdlib.h>
4			#include <string.h>
5			#include <math.h>
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			mpiSimulation* mpiSim;
14
15			mpiSimulation::mpiSimulation(SimInfo* the_entryPlug)
16			{
17			entryPlug = the_entryPlug;
18			mpiPlug = new mpiSimData;
19
20	mmeineke	447	MPI_Comm_size(MPI_COMM_WORLD, &(mpiPlug->numberProcessors) );
21	mmeineke	377	mpiPlug->myNode = worldRank;
22	gezelter	405
23			MolToProcMap = new int[entryPlug->n_mol];
24			MolComponentType = new int[entryPlug->n_mol];
25			AtomToProcMap = new int[entryPlug->n_atoms];
26
27	mmeineke	377	mpiSim = this;
28			wrapMeSimParallel( this );
29			}
30
31
32			mpiSimulation::~mpiSimulation(){
33
34	mmeineke	418	delete[] MolToProcMap;
35			delete[] MolComponentType;
36			delete[] AtomToProcMap;
37
38	mmeineke	377	delete mpiPlug;
39			// perhaps we should let fortran know the party is over.
40
41			}
42
43	tim	1108	void mpiSimulation::divideLabor( ){
44	mmeineke	377
45			int nComponents;
46			MoleculeStamp** compStamps;
47	gezelter	416	randomSPRNG *myRandom;
48	mmeineke	377	int* componentsNmol;
49	gezelter	405	int* AtomsPerProc;
50	mmeineke	377
51			double numerator;
52			double denominator;
53			double precast;
54	gezelter	405	double x, y, a;
55			int old_atoms, add_atoms, new_atoms;
56	mmeineke	377
57			int nTarget;
58	mmeineke	787	int molIndex, atomIndex;
59	mmeineke	377	int done;
60	gezelter	416	int i, j, loops, which_proc, nmol_local, natoms_local;
61			int nmol_global, natoms_global;
62	mmeineke	787	int local_index;
63	tim	708	int baseSeed = entryPlug->getSeed();
64	mmeineke	377
65			nComponents = entryPlug->nComponents;
66			compStamps = entryPlug->compStamps;
67			componentsNmol = entryPlug->componentsNmol;
68	gezelter	405	AtomsPerProc = new int[mpiPlug->numberProcessors];
69
70	mmeineke	377	mpiPlug->nAtomsGlobal = entryPlug->n_atoms;
71			mpiPlug->nBondsGlobal = entryPlug->n_bonds;
72			mpiPlug->nBendsGlobal = entryPlug->n_bends;
73			mpiPlug->nTorsionsGlobal = entryPlug->n_torsions;
74			mpiPlug->nSRIGlobal = entryPlug->n_SRI;
75			mpiPlug->nMolGlobal = entryPlug->n_mol;
76
77	gezelter	416	myRandom = new randomSPRNG( baseSeed );
78	chuckv	404
79	chuckv	434	a = 3.0 * (double)mpiPlug->nMolGlobal / (double)mpiPlug->nAtomsGlobal;
80	chuckv	404
81	gezelter	405	// Initialize things that we'll send out later:
82			for (i = 0; i < mpiPlug->numberProcessors; i++ ) {
83			AtomsPerProc[i] = 0;
84			}
85			for (i = 0; i < mpiPlug->nMolGlobal; i++ ) {
86			// default to an error condition:
87			MolToProcMap[i] = -1;
88			MolComponentType[i] = -1;
89			}
90			for (i = 0; i < mpiPlug->nAtomsGlobal; i++ ) {
91			// default to an error condition:
92			AtomToProcMap[i] = -1;
93			}
94
95			if (mpiPlug->myNode == 0) {
96			numerator = (double) entryPlug->n_atoms;
97			denominator = (double) mpiPlug->numberProcessors;
98			precast = numerator / denominator;
99			nTarget = (int)( precast + 0.5 );
100	chuckv	404
101	gezelter	405	// Build the array of molecule component types first
102			molIndex = 0;
103			for (i=0; i < nComponents; i++) {
104			for (j=0; j < componentsNmol[i]; j++) {
105			MolComponentType[molIndex] = i;
106			molIndex++;
107			}
108			}
109	chuckv	404
110	gezelter	405	atomIndex = 0;
111	chuckv	404
112	gezelter	405	for (i = 0; i < molIndex; i++ ) {
113	chuckv	404
114	gezelter	405	done = 0;
115			loops = 0;
116	chuckv	404
117	gezelter	405	while( !done ){
118			loops++;
119
120			// Pick a processor at random
121	chuckv	404
122	gezelter	416	which_proc = (int) (myRandom->getRandom() * mpiPlug->numberProcessors);
123	chuckv	404
124	gezelter	405	// How many atoms does this processor have?
125
126			old_atoms = AtomsPerProc[which_proc];
127	gezelter	989	add_atoms = compStamps[MolComponentType[i]]->getNAtoms();
128	chuckv	432	new_atoms = old_atoms + add_atoms;
129	chuckv	404
130	gezelter	405	// If we've been through this loop too many times, we need
131			// to just give up and assign the molecule to this processor
132			// and be done with it.
133
134			if (loops > 100) {
135			sprintf( painCave.errMsg,
136			"I've tried 100 times to assign molecule %d to a "
137			" processor, but can't find a good spot.\n"
138			"I'm assigning it at random to processor %d.\n",
139			i, which_proc);
140			painCave.isFatal = 0;
141			simError();
142
143			MolToProcMap[i] = which_proc;
144			AtomsPerProc[which_proc] += add_atoms;
145			for (j = 0 ; j < add_atoms; j++ ) {
146	mmeineke	422	AtomToProcMap[atomIndex] = which_proc;
147			atomIndex++;
148	gezelter	405	}
149			done = 1;
150			continue;
151			}
152	chuckv	432
153			// If we can add this molecule to this processor without sending
154			// it above nTarget, then go ahead and do it:
155
156			if (new_atoms <= nTarget) {
157			MolToProcMap[i] = which_proc;
158			AtomsPerProc[which_proc] += add_atoms;
159			for (j = 0 ; j < add_atoms; j++ ) {
160			AtomToProcMap[atomIndex] = which_proc;
161			atomIndex++;
162			}
163			done = 1;
164			continue;
165			}
166
167
168	chuckv	434	// The only situation left is when new_atoms > nTarget. We
169			// want to accept this with some probability that dies off the
170			// farther we are from nTarget
171	gezelter	405
172			// roughly: x = new_atoms - nTarget
173			// Pacc(x) = exp(- a * x)
174	chuckv	434	// where a = penalty / (average atoms per molecule)
175	gezelter	405
176			x = (double) (new_atoms - nTarget);
177	gezelter	416	y = myRandom->getRandom();
178	chuckv	434
179			if (y < exp(- a * x)) {
180	gezelter	405	MolToProcMap[i] = which_proc;
181			AtomsPerProc[which_proc] += add_atoms;
182			for (j = 0 ; j < add_atoms; j++ ) {
183	mmeineke	422	AtomToProcMap[atomIndex] = which_proc;
184			atomIndex++;
185			}
186	gezelter	405	done = 1;
187			continue;
188			} else {
189			continue;
190			}
191
192	mmeineke	377	}
193			}
194	gezelter	405
195			// Spray out this nonsense to all other processors:
196
197	mmeineke	447	MPI_Bcast(MolToProcMap, mpiPlug->nMolGlobal,
198			MPI_INT, 0, MPI_COMM_WORLD);
199	gezelter	405
200	mmeineke	447	MPI_Bcast(AtomToProcMap, mpiPlug->nAtomsGlobal,
201			MPI_INT, 0, MPI_COMM_WORLD);
202	gezelter	405
203	mmeineke	447	MPI_Bcast(MolComponentType, mpiPlug->nMolGlobal,
204			MPI_INT, 0, MPI_COMM_WORLD);
205	gezelter	405
206	mmeineke	447	MPI_Bcast(AtomsPerProc, mpiPlug->numberProcessors,
207			MPI_INT, 0, MPI_COMM_WORLD);
208	gezelter	405	} else {
209
210			// Listen to your marching orders from processor 0:
211	mmeineke	377
212	mmeineke	447	MPI_Bcast(MolToProcMap, mpiPlug->nMolGlobal,
213			MPI_INT, 0, MPI_COMM_WORLD);
214	mmeineke	377
215	mmeineke	447	MPI_Bcast(AtomToProcMap, mpiPlug->nAtomsGlobal,
216			MPI_INT, 0, MPI_COMM_WORLD);
217	gezelter	405
218	mmeineke	447	MPI_Bcast(MolComponentType, mpiPlug->nMolGlobal,
219			MPI_INT, 0, MPI_COMM_WORLD);
220	gezelter	405
221	mmeineke	447	MPI_Bcast(AtomsPerProc, mpiPlug->numberProcessors,
222			MPI_INT, 0, MPI_COMM_WORLD);
223	chuckv	432
224
225	mmeineke	377	}
226
227
228	gezelter	405	// Let's all check for sanity:
229
230			nmol_local = 0;
231			for (i = 0 ; i < mpiPlug->nMolGlobal; i++ ) {
232			if (MolToProcMap[i] == mpiPlug->myNode) {
233			nmol_local++;
234			}
235	mmeineke	377	}
236
237	gezelter	405	natoms_local = 0;
238			for (i = 0; i < mpiPlug->nAtomsGlobal; i++) {
239			if (AtomToProcMap[i] == mpiPlug->myNode) {
240			natoms_local++;
241			}
242			}
243	mmeineke	377
244	mmeineke	447	MPI_Allreduce(&nmol_local,&nmol_global,1,MPI_INT,MPI_SUM,
245			MPI_COMM_WORLD);
246			MPI_Allreduce(&natoms_local,&natoms_global,1,MPI_INT,
247			MPI_SUM, MPI_COMM_WORLD);
248	mmeineke	377
249	gezelter	405	if( nmol_global != entryPlug->n_mol ){
250			sprintf( painCave.errMsg,
251			"The sum of all nmol_local, %d, did not equal the "
252			"total number of molecules, %d.\n",
253			nmol_global, entryPlug->n_mol );
254			painCave.isFatal = 1;
255			simError();
256	mmeineke	377	}
257	gezelter	405
258			if( natoms_global != entryPlug->n_atoms ){
259			sprintf( painCave.errMsg,
260			"The sum of all natoms_local, %d, did not equal the "
261			"total number of atoms, %d.\n",
262			natoms_global, entryPlug->n_atoms );
263			painCave.isFatal = 1;
264			simError();
265			}
266	mmeineke	377
267			sprintf( checkPointMsg,
268			"Successfully divided the molecules among the processors.\n" );
269			MPIcheckPoint();
270
271	gezelter	405	mpiPlug->myNMol = nmol_local;
272			mpiPlug->myNlocal = natoms_local;
273	mmeineke	377
274	tim	1108	globalAtomIndex.resize(mpiPlug->myNlocal);
275	tim	1129	globalToLocalAtom.resize(mpiPlug->nAtomsGlobal);
276	gezelter	405	local_index = 0;
277			for (i = 0; i < mpiPlug->nAtomsGlobal; i++) {
278			if (AtomToProcMap[i] == mpiPlug->myNode) {
279	tim	1108	globalAtomIndex[local_index] = i;
280
281			globalToLocalAtom[i] = local_index;
282	chuckv	406	local_index++;
283	tim	1108
284	gezelter	405	}
285	tim	1108	else
286			globalToLocalAtom[i] = -1;
287	mmeineke	377	}
288	tim	1108
289			globalMolIndex.resize(mpiPlug->myNMol);
290	tim	1129	globalToLocalMol.resize(mpiPlug->nMolGlobal);
291
292	tim	1108	local_index = 0;
293			for (i = 0; i < mpiPlug->nMolGlobal; i++) {
294			if (MolToProcMap[i] == mpiPlug->myNode) {
295			globalMolIndex[local_index] = i;
296			globalToLocalMol[i] = local_index;
297			local_index++;
298			}
299			else
300			globalToLocalMol[i] = -1;
301			}
302	chuckv	432
303	mmeineke	377	}
304
305
306			void mpiSimulation::mpiRefresh( void ){
307
308			int isError, i;
309			int *globalIndex = new int[mpiPlug->myNlocal];
310
311	chuckv	441	// Fortran indexing needs to be increased by 1 in order to get the 2 languages to
312			// not barf
313	mmeineke	377
314	chuckv	441	for(i=0; i<mpiPlug->myNlocal; i++) globalIndex[i] = entryPlug->atoms[i]->getGlobalIndex()+1;
315
316	mmeineke	377
317			isError = 0;
318			setFsimParallel( mpiPlug, &(entryPlug->n_atoms), globalIndex, &isError );
319			if( isError ){
320
321			sprintf( painCave.errMsg,
322			"mpiRefresh errror: fortran didn't like something we gave it.\n" );
323			painCave.isFatal = 1;
324			simError();
325			}
326
327			delete[] globalIndex;
328
329			sprintf( checkPointMsg,
330			" mpiRefresh successful.\n" );
331			MPIcheckPoint();
332			}
333
334
335			#endif // is_mpi