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 = 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:	708
Committed:	Wed Aug 20 22:23:34 2003 UTC (20 years, 10 months ago) by tim
File size:	8455 byte(s)
Log Message:	user can setup seed in bass file now, if he does not specify any value for seed, oopse will take the value of seconds of system time as seed
#	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	tim	708	int baseSeed = entryPlug->getSeed();
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	tim	708
86	gezelter	416	myRandom = new randomSPRNG( baseSeed );
87	chuckv	404
88	chuckv	434	a = 3.0 * (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	432	add_atoms = compStamps[MolComponentType[i]]->getNAtoms();
137			new_atoms = old_atoms + add_atoms;
138	chuckv	404
139	gezelter	405	// If we've been through this loop too many times, we need
140			// to just give up and assign the molecule to this processor
141			// and be done with it.
142
143			if (loops > 100) {
144			sprintf( painCave.errMsg,
145			"I've tried 100 times to assign molecule %d to a "
146			" processor, but can't find a good spot.\n"
147			"I'm assigning it at random to processor %d.\n",
148			i, which_proc);
149			painCave.isFatal = 0;
150			simError();
151
152			MolToProcMap[i] = which_proc;
153			AtomsPerProc[which_proc] += add_atoms;
154			for (j = 0 ; j < add_atoms; j++ ) {
155	mmeineke	422	AtomToProcMap[atomIndex] = which_proc;
156			atomIndex++;
157	gezelter	405	}
158			done = 1;
159			continue;
160			}
161	chuckv	432
162			// If we can add this molecule to this processor without sending
163			// it above nTarget, then go ahead and do it:
164
165			if (new_atoms <= nTarget) {
166			MolToProcMap[i] = which_proc;
167			AtomsPerProc[which_proc] += add_atoms;
168			for (j = 0 ; j < add_atoms; j++ ) {
169			AtomToProcMap[atomIndex] = which_proc;
170			atomIndex++;
171			}
172			done = 1;
173			continue;
174			}
175
176
177	chuckv	434	// The only situation left is when new_atoms > nTarget. We
178			// want to accept this with some probability that dies off the
179			// farther we are from nTarget
180	gezelter	405
181			// roughly: x = new_atoms - nTarget
182			// Pacc(x) = exp(- a * x)
183	chuckv	434	// where a = penalty / (average atoms per molecule)
184	gezelter	405
185			x = (double) (new_atoms - nTarget);
186	gezelter	416	y = myRandom->getRandom();
187	chuckv	434
188			if (y < exp(- a * x)) {
189	gezelter	405	MolToProcMap[i] = which_proc;
190			AtomsPerProc[which_proc] += add_atoms;
191			for (j = 0 ; j < add_atoms; j++ ) {
192	mmeineke	422	AtomToProcMap[atomIndex] = which_proc;
193			atomIndex++;
194			}
195	gezelter	405	done = 1;
196			continue;
197			} else {
198			continue;
199			}
200
201	mmeineke	377	}
202			}
203	gezelter	405
204			// Spray out this nonsense to all other processors:
205
206	mmeineke	447	MPI_Bcast(MolToProcMap, mpiPlug->nMolGlobal,
207			MPI_INT, 0, MPI_COMM_WORLD);
208	gezelter	405
209	mmeineke	447	MPI_Bcast(AtomToProcMap, mpiPlug->nAtomsGlobal,
210			MPI_INT, 0, MPI_COMM_WORLD);
211	gezelter	405
212	mmeineke	447	MPI_Bcast(MolComponentType, mpiPlug->nMolGlobal,
213			MPI_INT, 0, MPI_COMM_WORLD);
214	gezelter	405
215	mmeineke	447	MPI_Bcast(AtomsPerProc, mpiPlug->numberProcessors,
216			MPI_INT, 0, MPI_COMM_WORLD);
217	gezelter	405	} else {
218
219			// Listen to your marching orders from processor 0:
220	mmeineke	377
221	mmeineke	447	MPI_Bcast(MolToProcMap, mpiPlug->nMolGlobal,
222			MPI_INT, 0, MPI_COMM_WORLD);
223	mmeineke	377
224	mmeineke	447	MPI_Bcast(AtomToProcMap, mpiPlug->nAtomsGlobal,
225			MPI_INT, 0, MPI_COMM_WORLD);
226	gezelter	405
227	mmeineke	447	MPI_Bcast(MolComponentType, mpiPlug->nMolGlobal,
228			MPI_INT, 0, MPI_COMM_WORLD);
229	gezelter	405
230	mmeineke	447	MPI_Bcast(AtomsPerProc, mpiPlug->numberProcessors,
231			MPI_INT, 0, MPI_COMM_WORLD);
232	chuckv	432
233
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	mmeineke	447	MPI_Allreduce(&nmol_local,&nmol_global,1,MPI_INT,MPI_SUM,
254			MPI_COMM_WORLD);
255			MPI_Allreduce(&natoms_local,&natoms_global,1,MPI_INT,
256			MPI_SUM, MPI_COMM_WORLD);
257	mmeineke	377
258	gezelter	405	if( nmol_global != entryPlug->n_mol ){
259			sprintf( painCave.errMsg,
260			"The sum of all nmol_local, %d, did not equal the "
261			"total number of molecules, %d.\n",
262			nmol_global, entryPlug->n_mol );
263			painCave.isFatal = 1;
264			simError();
265	mmeineke	377	}
266	gezelter	405
267			if( natoms_global != entryPlug->n_atoms ){
268			sprintf( painCave.errMsg,
269			"The sum of all natoms_local, %d, did not equal the "
270			"total number of atoms, %d.\n",
271			natoms_global, entryPlug->n_atoms );
272			painCave.isFatal = 1;
273			simError();
274			}
275	mmeineke	377
276			sprintf( checkPointMsg,
277			"Successfully divided the molecules among the processors.\n" );
278			MPIcheckPoint();
279
280	gezelter	405	mpiPlug->myNMol = nmol_local;
281			mpiPlug->myNlocal = natoms_local;
282	mmeineke	377
283			globalIndex = new int[mpiPlug->myNlocal];
284	gezelter	405	local_index = 0;
285			for (i = 0; i < mpiPlug->nAtomsGlobal; i++) {
286			if (AtomToProcMap[i] == mpiPlug->myNode) {
287	mmeineke	422	globalIndex[local_index] = i;
288	chuckv	406	local_index++;
289	gezelter	405	}
290	mmeineke	377	}
291	chuckv	432
292	gezelter	416	return globalIndex;
293	mmeineke	377	}
294
295
296			void mpiSimulation::mpiRefresh( void ){
297
298			int isError, i;
299			int *globalIndex = new int[mpiPlug->myNlocal];
300
301	chuckv	441	// Fortran indexing needs to be increased by 1 in order to get the 2 languages to
302			// not barf
303	mmeineke	377
304	chuckv	441	for(i=0; i<mpiPlug->myNlocal; i++) globalIndex[i] = entryPlug->atoms[i]->getGlobalIndex()+1;
305
306	mmeineke	377
307			isError = 0;
308			setFsimParallel( mpiPlug, &(entryPlug->n_atoms), globalIndex, &isError );
309			if( isError ){
310
311			sprintf( painCave.errMsg,
312			"mpiRefresh errror: fortran didn't like something we gave it.\n" );
313			painCave.isFatal = 1;
314			simError();
315			}
316
317			delete[] globalIndex;
318
319			sprintf( checkPointMsg,
320			" mpiRefresh successful.\n" );
321			MPIcheckPoint();
322			}
323
324
325			#endif // is_mpi