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->nProcessors) );
  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->nProcessors];
  
  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;
  mpiPlug->nGroupsGlobal = entryPlug->ngroup;

  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->nProcessors; 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->nProcessors;
    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->nProcessors);

        // 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->nProcessors,
              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->nProcessors,
              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->nMolLocal = nmol_local;
  mpiPlug->nAtomsLocal = natoms_local;

  globalAtomIndex.resize(mpiPlug->nAtomsLocal);
  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->nMolLocal);
  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->nAtomsLocal];

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

  for(i=0; i<mpiPlug->nAtomsLocal; 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:	1198
Committed:	Thu May 27 00:48:12 2004 UTC (20 years, 1 month ago) by tim
File size:	8818 byte(s)
Log Message:	in the progress of fixing MPI version of cutoff group
#	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	tim	1198	MPI_Comm_size(MPI_COMM_WORLD, &(mpiPlug->nProcessors) );
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	tim	1198	AtomsPerProc = new int[mpiPlug->nProcessors];
69	gezelter	405
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	tim	1198	mpiPlug->nGroupsGlobal = entryPlug->ngroup;
77	mmeineke	377
78	gezelter	416	myRandom = new randomSPRNG( baseSeed );
79	chuckv	404
80	chuckv	434	a = 3.0 * (double)mpiPlug->nMolGlobal / (double)mpiPlug->nAtomsGlobal;
81	chuckv	404
82	gezelter	405	// Initialize things that we'll send out later:
83	tim	1198	for (i = 0; i < mpiPlug->nProcessors; i++ ) {
84	gezelter	405	AtomsPerProc[i] = 0;
85			}
86			for (i = 0; i < mpiPlug->nMolGlobal; i++ ) {
87			// default to an error condition:
88			MolToProcMap[i] = -1;
89			MolComponentType[i] = -1;
90			}
91			for (i = 0; i < mpiPlug->nAtomsGlobal; i++ ) {
92			// default to an error condition:
93			AtomToProcMap[i] = -1;
94			}
95
96			if (mpiPlug->myNode == 0) {
97			numerator = (double) entryPlug->n_atoms;
98	tim	1198	denominator = (double) mpiPlug->nProcessors;
99	gezelter	405	precast = numerator / denominator;
100			nTarget = (int)( precast + 0.5 );
101	chuckv	404
102	gezelter	405	// Build the array of molecule component types first
103			molIndex = 0;
104			for (i=0; i < nComponents; i++) {
105			for (j=0; j < componentsNmol[i]; j++) {
106			MolComponentType[molIndex] = i;
107			molIndex++;
108			}
109			}
110	chuckv	404
111	gezelter	405	atomIndex = 0;
112	chuckv	404
113	gezelter	405	for (i = 0; i < molIndex; i++ ) {
114	chuckv	404
115	gezelter	405	done = 0;
116			loops = 0;
117	chuckv	404
118	gezelter	405	while( !done ){
119			loops++;
120
121			// Pick a processor at random
122	chuckv	404
123	tim	1198	which_proc = (int) (myRandom->getRandom() * mpiPlug->nProcessors);
124	chuckv	404
125	gezelter	405	// How many atoms does this processor have?
126
127			old_atoms = AtomsPerProc[which_proc];
128	gezelter	989	add_atoms = compStamps[MolComponentType[i]]->getNAtoms();
129	chuckv	432	new_atoms = old_atoms + add_atoms;
130	chuckv	404
131	gezelter	405	// If we've been through this loop too many times, we need
132			// to just give up and assign the molecule to this processor
133			// and be done with it.
134
135			if (loops > 100) {
136			sprintf( painCave.errMsg,
137			"I've tried 100 times to assign molecule %d to a "
138			" processor, but can't find a good spot.\n"
139			"I'm assigning it at random to processor %d.\n",
140			i, which_proc);
141			painCave.isFatal = 0;
142			simError();
143
144			MolToProcMap[i] = which_proc;
145			AtomsPerProc[which_proc] += add_atoms;
146			for (j = 0 ; j < add_atoms; j++ ) {
147	mmeineke	422	AtomToProcMap[atomIndex] = which_proc;
148			atomIndex++;
149	gezelter	405	}
150			done = 1;
151			continue;
152			}
153	chuckv	432
154			// If we can add this molecule to this processor without sending
155			// it above nTarget, then go ahead and do it:
156
157			if (new_atoms <= nTarget) {
158			MolToProcMap[i] = which_proc;
159			AtomsPerProc[which_proc] += add_atoms;
160			for (j = 0 ; j < add_atoms; j++ ) {
161			AtomToProcMap[atomIndex] = which_proc;
162			atomIndex++;
163			}
164			done = 1;
165			continue;
166			}
167
168
169	chuckv	434	// The only situation left is when new_atoms > nTarget. We
170			// want to accept this with some probability that dies off the
171			// farther we are from nTarget
172	gezelter	405
173			// roughly: x = new_atoms - nTarget
174			// Pacc(x) = exp(- a * x)
175	chuckv	434	// where a = penalty / (average atoms per molecule)
176	gezelter	405
177			x = (double) (new_atoms - nTarget);
178	gezelter	416	y = myRandom->getRandom();
179	chuckv	434
180			if (y < exp(- a * x)) {
181	gezelter	405	MolToProcMap[i] = which_proc;
182			AtomsPerProc[which_proc] += add_atoms;
183			for (j = 0 ; j < add_atoms; j++ ) {
184	mmeineke	422	AtomToProcMap[atomIndex] = which_proc;
185			atomIndex++;
186			}
187	gezelter	405	done = 1;
188			continue;
189			} else {
190			continue;
191			}
192
193	mmeineke	377	}
194			}
195	gezelter	405
196			// Spray out this nonsense to all other processors:
197
198	mmeineke	447	MPI_Bcast(MolToProcMap, mpiPlug->nMolGlobal,
199			MPI_INT, 0, MPI_COMM_WORLD);
200	gezelter	405
201	mmeineke	447	MPI_Bcast(AtomToProcMap, mpiPlug->nAtomsGlobal,
202			MPI_INT, 0, MPI_COMM_WORLD);
203	gezelter	405
204	mmeineke	447	MPI_Bcast(MolComponentType, mpiPlug->nMolGlobal,
205			MPI_INT, 0, MPI_COMM_WORLD);
206	gezelter	405
207	tim	1198	MPI_Bcast(AtomsPerProc, mpiPlug->nProcessors,
208	mmeineke	447	MPI_INT, 0, MPI_COMM_WORLD);
209	gezelter	405	} else {
210
211			// Listen to your marching orders from processor 0:
212	mmeineke	377
213	mmeineke	447	MPI_Bcast(MolToProcMap, mpiPlug->nMolGlobal,
214			MPI_INT, 0, MPI_COMM_WORLD);
215	mmeineke	377
216	mmeineke	447	MPI_Bcast(AtomToProcMap, mpiPlug->nAtomsGlobal,
217			MPI_INT, 0, MPI_COMM_WORLD);
218	gezelter	405
219	mmeineke	447	MPI_Bcast(MolComponentType, mpiPlug->nMolGlobal,
220			MPI_INT, 0, MPI_COMM_WORLD);
221	gezelter	405
222	tim	1198	MPI_Bcast(AtomsPerProc, mpiPlug->nProcessors,
223	mmeineke	447	MPI_INT, 0, MPI_COMM_WORLD);
224	chuckv	432
225
226	mmeineke	377	}
227
228
229	gezelter	405	// Let's all check for sanity:
230
231			nmol_local = 0;
232			for (i = 0 ; i < mpiPlug->nMolGlobal; i++ ) {
233			if (MolToProcMap[i] == mpiPlug->myNode) {
234			nmol_local++;
235			}
236	mmeineke	377	}
237
238	gezelter	405	natoms_local = 0;
239			for (i = 0; i < mpiPlug->nAtomsGlobal; i++) {
240			if (AtomToProcMap[i] == mpiPlug->myNode) {
241			natoms_local++;
242			}
243			}
244	mmeineke	377
245	mmeineke	447	MPI_Allreduce(&nmol_local,&nmol_global,1,MPI_INT,MPI_SUM,
246			MPI_COMM_WORLD);
247			MPI_Allreduce(&natoms_local,&natoms_global,1,MPI_INT,
248			MPI_SUM, MPI_COMM_WORLD);
249	mmeineke	377
250	gezelter	405	if( nmol_global != entryPlug->n_mol ){
251			sprintf( painCave.errMsg,
252			"The sum of all nmol_local, %d, did not equal the "
253			"total number of molecules, %d.\n",
254			nmol_global, entryPlug->n_mol );
255			painCave.isFatal = 1;
256			simError();
257	mmeineke	377	}
258	gezelter	405
259			if( natoms_global != entryPlug->n_atoms ){
260			sprintf( painCave.errMsg,
261			"The sum of all natoms_local, %d, did not equal the "
262			"total number of atoms, %d.\n",
263			natoms_global, entryPlug->n_atoms );
264			painCave.isFatal = 1;
265			simError();
266			}
267	mmeineke	377
268			sprintf( checkPointMsg,
269			"Successfully divided the molecules among the processors.\n" );
270			MPIcheckPoint();
271
272	tim	1198	mpiPlug->nMolLocal = nmol_local;
273			mpiPlug->nAtomsLocal = natoms_local;
274	mmeineke	377
275	tim	1198	globalAtomIndex.resize(mpiPlug->nAtomsLocal);
276	tim	1129	globalToLocalAtom.resize(mpiPlug->nAtomsGlobal);
277	gezelter	405	local_index = 0;
278			for (i = 0; i < mpiPlug->nAtomsGlobal; i++) {
279			if (AtomToProcMap[i] == mpiPlug->myNode) {
280	tim	1108	globalAtomIndex[local_index] = i;
281
282			globalToLocalAtom[i] = local_index;
283	chuckv	406	local_index++;
284	tim	1108
285	gezelter	405	}
286	tim	1108	else
287			globalToLocalAtom[i] = -1;
288	mmeineke	377	}
289	tim	1108
290	tim	1198	globalMolIndex.resize(mpiPlug->nMolLocal);
291	tim	1129	globalToLocalMol.resize(mpiPlug->nMolGlobal);
292
293	tim	1108	local_index = 0;
294			for (i = 0; i < mpiPlug->nMolGlobal; i++) {
295			if (MolToProcMap[i] == mpiPlug->myNode) {
296			globalMolIndex[local_index] = i;
297			globalToLocalMol[i] = local_index;
298			local_index++;
299			}
300			else
301			globalToLocalMol[i] = -1;
302			}
303	chuckv	432
304	mmeineke	377	}
305
306
307			void mpiSimulation::mpiRefresh( void ){
308
309			int isError, i;
310	tim	1198	int *globalIndex = new int[mpiPlug->nAtomsLocal];
311	mmeineke	377
312	chuckv	441	// Fortran indexing needs to be increased by 1 in order to get the 2 languages to
313			// not barf
314	mmeineke	377
315	tim	1198	for(i=0; i<mpiPlug->nAtomsLocal; i++) globalIndex[i] = entryPlug->atoms[i]->getGlobalIndex()+1;
316	chuckv	441
317	mmeineke	377
318			isError = 0;
319			setFsimParallel( mpiPlug, &(entryPlug->n_atoms), globalIndex, &isError );
320			if( isError ){
321
322			sprintf( painCave.errMsg,
323			"mpiRefresh errror: fortran didn't like something we gave it.\n" );
324			painCave.isFatal = 1;
325			simError();
326			}
327
328			delete[] globalIndex;
329
330			sprintf( checkPointMsg,
331			" mpiRefresh successful.\n" );
332			MPIcheckPoint();
333			}
334
335
336			#endif // is_mpi