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"

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 = entryPlug->getSeed();

  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:	726
Committed:	Tue Aug 26 20:37:30 2003 UTC (20 years, 10 months ago) by tim
File size:	8426 byte(s)
Log Message:	set default force substraction policy to PolicyByMass
#	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			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			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	tim	708	int baseSeed = entryPlug->getSeed();
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	tim	708
84	gezelter	416	myRandom = new randomSPRNG( baseSeed );
85	chuckv	404
86	chuckv	434	a = 3.0 * (double)mpiPlug->nMolGlobal / (double)mpiPlug->nAtomsGlobal;
87	chuckv	404
88	gezelter	405	// Initialize things that we'll send out later:
89			for (i = 0; i < mpiPlug->numberProcessors; i++ ) {
90			AtomsPerProc[i] = 0;
91			}
92			for (i = 0; i < mpiPlug->nMolGlobal; i++ ) {
93			// default to an error condition:
94			MolToProcMap[i] = -1;
95			MolComponentType[i] = -1;
96			}
97			for (i = 0; i < mpiPlug->nAtomsGlobal; i++ ) {
98			// default to an error condition:
99			AtomToProcMap[i] = -1;
100			}
101
102			if (mpiPlug->myNode == 0) {
103			numerator = (double) entryPlug->n_atoms;
104			denominator = (double) mpiPlug->numberProcessors;
105			precast = numerator / denominator;
106			nTarget = (int)( precast + 0.5 );
107	chuckv	404
108	gezelter	405	// Build the array of molecule component types first
109			molIndex = 0;
110			for (i=0; i < nComponents; i++) {
111			for (j=0; j < componentsNmol[i]; j++) {
112			MolComponentType[molIndex] = i;
113			molIndex++;
114			}
115			}
116	chuckv	404
117	gezelter	405	atomIndex = 0;
118	chuckv	404
119	gezelter	405	for (i = 0; i < molIndex; i++ ) {
120	chuckv	404
121	gezelter	405	done = 0;
122			loops = 0;
123	chuckv	404
124	gezelter	405	while( !done ){
125			loops++;
126
127			// Pick a processor at random
128	chuckv	404
129	gezelter	416	which_proc = (int) (myRandom->getRandom() * mpiPlug->numberProcessors);
130	chuckv	404
131	gezelter	405	// How many atoms does this processor have?
132
133			old_atoms = AtomsPerProc[which_proc];
134	chuckv	432	add_atoms = compStamps[MolComponentType[i]]->getNAtoms();
135			new_atoms = old_atoms + add_atoms;
136	chuckv	404
137	gezelter	405	// If we've been through this loop too many times, we need
138			// to just give up and assign the molecule to this processor
139			// and be done with it.
140
141			if (loops > 100) {
142			sprintf( painCave.errMsg,
143			"I've tried 100 times to assign molecule %d to a "
144			" processor, but can't find a good spot.\n"
145			"I'm assigning it at random to processor %d.\n",
146			i, which_proc);
147			painCave.isFatal = 0;
148			simError();
149
150			MolToProcMap[i] = which_proc;
151			AtomsPerProc[which_proc] += add_atoms;
152			for (j = 0 ; j < add_atoms; j++ ) {
153	mmeineke	422	AtomToProcMap[atomIndex] = which_proc;
154			atomIndex++;
155	gezelter	405	}
156			done = 1;
157			continue;
158			}
159	chuckv	432
160			// If we can add this molecule to this processor without sending
161			// it above nTarget, then go ahead and do it:
162
163			if (new_atoms <= nTarget) {
164			MolToProcMap[i] = which_proc;
165			AtomsPerProc[which_proc] += add_atoms;
166			for (j = 0 ; j < add_atoms; j++ ) {
167			AtomToProcMap[atomIndex] = which_proc;
168			atomIndex++;
169			}
170			done = 1;
171			continue;
172			}
173
174
175	chuckv	434	// The only situation left is when new_atoms > nTarget. We
176			// want to accept this with some probability that dies off the
177			// farther we are from nTarget
178	gezelter	405
179			// roughly: x = new_atoms - nTarget
180			// Pacc(x) = exp(- a * x)
181	chuckv	434	// where a = penalty / (average atoms per molecule)
182	gezelter	405
183			x = (double) (new_atoms - nTarget);
184	gezelter	416	y = myRandom->getRandom();
185	chuckv	434
186			if (y < exp(- a * x)) {
187	gezelter	405	MolToProcMap[i] = which_proc;
188			AtomsPerProc[which_proc] += add_atoms;
189			for (j = 0 ; j < add_atoms; j++ ) {
190	mmeineke	422	AtomToProcMap[atomIndex] = which_proc;
191			atomIndex++;
192			}
193	gezelter	405	done = 1;
194			continue;
195			} else {
196			continue;
197			}
198
199	mmeineke	377	}
200			}
201	gezelter	405
202			// Spray out this nonsense to all other processors:
203
204	mmeineke	447	MPI_Bcast(MolToProcMap, mpiPlug->nMolGlobal,
205			MPI_INT, 0, MPI_COMM_WORLD);
206	gezelter	405
207	mmeineke	447	MPI_Bcast(AtomToProcMap, mpiPlug->nAtomsGlobal,
208			MPI_INT, 0, MPI_COMM_WORLD);
209	gezelter	405
210	mmeineke	447	MPI_Bcast(MolComponentType, mpiPlug->nMolGlobal,
211			MPI_INT, 0, MPI_COMM_WORLD);
212	gezelter	405
213	mmeineke	447	MPI_Bcast(AtomsPerProc, mpiPlug->numberProcessors,
214			MPI_INT, 0, MPI_COMM_WORLD);
215	gezelter	405	} else {
216
217			// Listen to your marching orders from processor 0:
218	mmeineke	377
219	mmeineke	447	MPI_Bcast(MolToProcMap, mpiPlug->nMolGlobal,
220			MPI_INT, 0, MPI_COMM_WORLD);
221	mmeineke	377
222	mmeineke	447	MPI_Bcast(AtomToProcMap, mpiPlug->nAtomsGlobal,
223			MPI_INT, 0, MPI_COMM_WORLD);
224	gezelter	405
225	mmeineke	447	MPI_Bcast(MolComponentType, mpiPlug->nMolGlobal,
226			MPI_INT, 0, MPI_COMM_WORLD);
227	gezelter	405
228	mmeineke	447	MPI_Bcast(AtomsPerProc, mpiPlug->numberProcessors,
229			MPI_INT, 0, MPI_COMM_WORLD);
230	chuckv	432
231
232	mmeineke	377	}
233
234
235	gezelter	405	// Let's all check for sanity:
236
237			nmol_local = 0;
238			for (i = 0 ; i < mpiPlug->nMolGlobal; i++ ) {
239			if (MolToProcMap[i] == mpiPlug->myNode) {
240			nmol_local++;
241			}
242	mmeineke	377	}
243
244	gezelter	405	natoms_local = 0;
245			for (i = 0; i < mpiPlug->nAtomsGlobal; i++) {
246			if (AtomToProcMap[i] == mpiPlug->myNode) {
247			natoms_local++;
248			}
249			}
250	mmeineke	377
251	mmeineke	447	MPI_Allreduce(&nmol_local,&nmol_global,1,MPI_INT,MPI_SUM,
252			MPI_COMM_WORLD);
253			MPI_Allreduce(&natoms_local,&natoms_global,1,MPI_INT,
254			MPI_SUM, MPI_COMM_WORLD);
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	mmeineke	422	globalIndex[local_index] = i;
286	chuckv	406	local_index++;
287	gezelter	405	}
288	mmeineke	377	}
289	chuckv	432
290	gezelter	416	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	chuckv	441	// Fortran indexing needs to be increased by 1 in order to get the 2 languages to
300			// not barf
301	mmeineke	377
302	chuckv	441	for(i=0; i<mpiPlug->myNlocal; i++) globalIndex[i] = entryPlug->atoms[i]->getGlobalIndex()+1;
303
304	mmeineke	377
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