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);
  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);
  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:	1108
Committed:	Wed Apr 14 15:37:41 2004 UTC (20 years, 2 months ago) by tim
File size:	8687 byte(s)
Log Message:	Change DumpWriter and InitFromFile
#	Content
1	#ifdef IS_MPI
2	#include <iostream>
3	#include <stdlib.h>
4	#include <string.h>
5	#include <math.h>
6	#include <mpi.h>
7
8	#include "mpiSimulation.hpp"
9	#include "simError.h"
10	#include "fortranWrappers.hpp"
11	#include "randomSPRNG.hpp"
12
13	mpiSimulation* mpiSim;
14
15	mpiSimulation::mpiSimulation(SimInfo* the_entryPlug)
16	{
17	entryPlug = the_entryPlug;
18	mpiPlug = new mpiSimData;
19
20	MPI_Comm_size(MPI_COMM_WORLD, &(mpiPlug->numberProcessors) );
21	mpiPlug->myNode = worldRank;
22
23	MolToProcMap = new int[entryPlug->n_mol];
24	MolComponentType = new int[entryPlug->n_mol];
25	AtomToProcMap = new int[entryPlug->n_atoms];
26
27	mpiSim = this;
28	wrapMeSimParallel( this );
29	}
30
31
32	mpiSimulation::~mpiSimulation(){
33
34	delete[] MolToProcMap;
35	delete[] MolComponentType;
36	delete[] AtomToProcMap;
37
38	delete mpiPlug;
39	// perhaps we should let fortran know the party is over.
40
41	}
42
43	void mpiSimulation::divideLabor( ){
44
45	int nComponents;
46	MoleculeStamp** compStamps;
47	randomSPRNG *myRandom;
48	int* componentsNmol;
49	int* AtomsPerProc;
50
51	double numerator;
52	double denominator;
53	double precast;
54	double x, y, a;
55	int old_atoms, add_atoms, new_atoms;
56
57	int nTarget;
58	int molIndex, atomIndex;
59	int done;
60	int i, j, loops, which_proc, nmol_local, natoms_local;
61	int nmol_global, natoms_global;
62	int local_index;
63	int baseSeed = entryPlug->getSeed();
64
65	nComponents = entryPlug->nComponents;
66	compStamps = entryPlug->compStamps;
67	componentsNmol = entryPlug->componentsNmol;
68	AtomsPerProc = new int[mpiPlug->numberProcessors];
69
70	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	myRandom = new randomSPRNG( baseSeed );
78
79	a = 3.0 * (double)mpiPlug->nMolGlobal / (double)mpiPlug->nAtomsGlobal;
80
81	// 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
101	// 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
110	atomIndex = 0;
111
112	for (i = 0; i < molIndex; i++ ) {
113
114	done = 0;
115	loops = 0;
116
117	while( !done ){
118	loops++;
119
120	// Pick a processor at random
121
122	which_proc = (int) (myRandom->getRandom() * mpiPlug->numberProcessors);
123
124	// How many atoms does this processor have?
125
126	old_atoms = AtomsPerProc[which_proc];
127	add_atoms = compStamps[MolComponentType[i]]->getNAtoms();
128	new_atoms = old_atoms + add_atoms;
129
130	// 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	AtomToProcMap[atomIndex] = which_proc;
147	atomIndex++;
148	}
149	done = 1;
150	continue;
151	}
152
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	// 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
172	// roughly: x = new_atoms - nTarget
173	// Pacc(x) = exp(- a * x)
174	// where a = penalty / (average atoms per molecule)
175
176	x = (double) (new_atoms - nTarget);
177	y = myRandom->getRandom();
178
179	if (y < exp(- a * x)) {
180	MolToProcMap[i] = which_proc;
181	AtomsPerProc[which_proc] += add_atoms;
182	for (j = 0 ; j < add_atoms; j++ ) {
183	AtomToProcMap[atomIndex] = which_proc;
184	atomIndex++;
185	}
186	done = 1;
187	continue;
188	} else {
189	continue;
190	}
191
192	}
193	}
194
195	// Spray out this nonsense to all other processors:
196
197	MPI_Bcast(MolToProcMap, mpiPlug->nMolGlobal,
198	MPI_INT, 0, MPI_COMM_WORLD);
199
200	MPI_Bcast(AtomToProcMap, mpiPlug->nAtomsGlobal,
201	MPI_INT, 0, MPI_COMM_WORLD);
202
203	MPI_Bcast(MolComponentType, mpiPlug->nMolGlobal,
204	MPI_INT, 0, MPI_COMM_WORLD);
205
206	MPI_Bcast(AtomsPerProc, mpiPlug->numberProcessors,
207	MPI_INT, 0, MPI_COMM_WORLD);
208	} else {
209
210	// Listen to your marching orders from processor 0:
211
212	MPI_Bcast(MolToProcMap, mpiPlug->nMolGlobal,
213	MPI_INT, 0, MPI_COMM_WORLD);
214
215	MPI_Bcast(AtomToProcMap, mpiPlug->nAtomsGlobal,
216	MPI_INT, 0, MPI_COMM_WORLD);
217
218	MPI_Bcast(MolComponentType, mpiPlug->nMolGlobal,
219	MPI_INT, 0, MPI_COMM_WORLD);
220
221	MPI_Bcast(AtomsPerProc, mpiPlug->numberProcessors,
222	MPI_INT, 0, MPI_COMM_WORLD);
223
224
225	}
226
227
228	// 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	}
236
237	natoms_local = 0;
238	for (i = 0; i < mpiPlug->nAtomsGlobal; i++) {
239	if (AtomToProcMap[i] == mpiPlug->myNode) {
240	natoms_local++;
241	}
242	}
243
244	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
249	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	}
257
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
267	sprintf( checkPointMsg,
268	"Successfully divided the molecules among the processors.\n" );
269	MPIcheckPoint();
270
271	mpiPlug->myNMol = nmol_local;
272	mpiPlug->myNlocal = natoms_local;
273
274	globalAtomIndex.resize(mpiPlug->myNlocal);
275	local_index = 0;
276	for (i = 0; i < mpiPlug->nAtomsGlobal; i++) {
277	if (AtomToProcMap[i] == mpiPlug->myNode) {
278	globalAtomIndex[local_index] = i;
279
280	globalToLocalAtom[i] = local_index;
281	local_index++;
282
283	}
284	else
285	globalToLocalAtom[i] = -1;
286	}
287
288	globalMolIndex.resize(mpiPlug->myNMol);
289	local_index = 0;
290	for (i = 0; i < mpiPlug->nMolGlobal; i++) {
291	if (MolToProcMap[i] == mpiPlug->myNode) {
292	globalMolIndex[local_index] = i;
293	globalToLocalMol[i] = local_index;
294	local_index++;
295	}
296	else
297	globalToLocalMol[i] = -1;
298	}
299
300	}
301
302
303	void mpiSimulation::mpiRefresh( void ){
304
305	int isError, i;
306	int *globalIndex = new int[mpiPlug->myNlocal];
307
308	// Fortran indexing needs to be increased by 1 in order to get the 2 languages to
309	// not barf
310
311	for(i=0; i<mpiPlug->myNlocal; i++) globalIndex[i] = entryPlug->atoms[i]->getGlobalIndex()+1;
312
313
314	isError = 0;
315	setFsimParallel( mpiPlug, &(entryPlug->n_atoms), globalIndex, &isError );
316	if( isError ){
317
318	sprintf( painCave.errMsg,
319	"mpiRefresh errror: fortran didn't like something we gave it.\n" );
320	painCave.isFatal = 1;
321	simError();
322	}
323
324	delete[] globalIndex;
325
326	sprintf( checkPointMsg,
327	" mpiRefresh successful.\n" );
328	MPIcheckPoint();
329	}
330
331
332	#endif // is_mpi