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 = BASE_SEED;

  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:	447
Committed:	Thu Apr 3 20:21:54 2003 UTC (21 years, 3 months ago) by mmeineke
File size:	8441 byte(s)
Log Message:	fixed some small things with simError.h
#	Content
1	#ifdef IS_MPI
2	#include <iostream>
3	#include <cstdlib>
4	#include <cstring>
5	#include <cmath>
6	#include <mpi.h>
7
8	#include "mpiSimulation.hpp"
9	#include "simError.h"
10	#include "fortranWrappers.hpp"
11	#include "randomSPRNG.hpp"
12
13	#define BASE_SEED 123456789
14
15	mpiSimulation* mpiSim;
16
17	mpiSimulation::mpiSimulation(SimInfo* the_entryPlug)
18	{
19	entryPlug = the_entryPlug;
20	mpiPlug = new mpiSimData;
21
22	MPI_Comm_size(MPI_COMM_WORLD, &(mpiPlug->numberProcessors) );
23	mpiPlug->myNode = worldRank;
24
25	MolToProcMap = new int[entryPlug->n_mol];
26	MolComponentType = new int[entryPlug->n_mol];
27	AtomToProcMap = new int[entryPlug->n_atoms];
28
29	mpiSim = this;
30	wrapMeSimParallel( this );
31	}
32
33
34	mpiSimulation::~mpiSimulation(){
35
36	delete[] MolToProcMap;
37	delete[] MolComponentType;
38	delete[] AtomToProcMap;
39
40	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	randomSPRNG *myRandom;
52	int* componentsNmol;
53	int* AtomsPerProc;
54
55	double numerator;
56	double denominator;
57	double precast;
58	double x, y, a;
59	int old_atoms, add_atoms, new_atoms;
60
61	int nTarget;
62	int molIndex, atomIndex, compIndex, compStart;
63	int done;
64	int nLocal, molLocal;
65	int i, j, loops, which_proc, nmol_local, natoms_local;
66	int nmol_global, natoms_global;
67	int local_index, index;
68	int smallDiff, bigDiff;
69	int baseSeed = BASE_SEED;
70
71	int testSum;
72
73	nComponents = entryPlug->nComponents;
74	compStamps = entryPlug->compStamps;
75	componentsNmol = entryPlug->componentsNmol;
76	AtomsPerProc = new int[mpiPlug->numberProcessors];
77
78	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	myRandom = new randomSPRNG( baseSeed );
86
87	a = 3.0 * (double)mpiPlug->nMolGlobal / (double)mpiPlug->nAtomsGlobal;
88
89	// Initialize things that we'll send out later:
90	for (i = 0; i < mpiPlug->numberProcessors; i++ ) {
91	AtomsPerProc[i] = 0;
92	}
93	for (i = 0; i < mpiPlug->nMolGlobal; i++ ) {
94	// default to an error condition:
95	MolToProcMap[i] = -1;
96	MolComponentType[i] = -1;
97	}
98	for (i = 0; i < mpiPlug->nAtomsGlobal; i++ ) {
99	// default to an error condition:
100	AtomToProcMap[i] = -1;
101	}
102
103	if (mpiPlug->myNode == 0) {
104	numerator = (double) entryPlug->n_atoms;
105	denominator = (double) mpiPlug->numberProcessors;
106	precast = numerator / denominator;
107	nTarget = (int)( precast + 0.5 );
108
109	// Build the array of molecule component types first
110	molIndex = 0;
111	for (i=0; i < nComponents; i++) {
112	for (j=0; j < componentsNmol[i]; j++) {
113	MolComponentType[molIndex] = i;
114	molIndex++;
115	}
116	}
117
118	atomIndex = 0;
119
120	for (i = 0; i < molIndex; i++ ) {
121
122	done = 0;
123	loops = 0;
124
125	while( !done ){
126	loops++;
127
128	// Pick a processor at random
129
130	which_proc = (int) (myRandom->getRandom() * mpiPlug->numberProcessors);
131
132	// How many atoms does this processor have?
133
134	old_atoms = AtomsPerProc[which_proc];
135	add_atoms = compStamps[MolComponentType[i]]->getNAtoms();
136	new_atoms = old_atoms + add_atoms;
137
138	// If we've been through this loop too many times, we need
139	// to just give up and assign the molecule to this processor
140	// and be done with it.
141
142	if (loops > 100) {
143	sprintf( painCave.errMsg,
144	"I've tried 100 times to assign molecule %d to a "
145	" processor, but can't find a good spot.\n"
146	"I'm assigning it at random to processor %d.\n",
147	i, which_proc);
148	painCave.isFatal = 0;
149	simError();
150
151	MolToProcMap[i] = which_proc;
152	AtomsPerProc[which_proc] += add_atoms;
153	for (j = 0 ; j < add_atoms; j++ ) {
154	AtomToProcMap[atomIndex] = which_proc;
155	atomIndex++;
156	}
157	done = 1;
158	continue;
159	}
160
161	// If we can add this molecule to this processor without sending
162	// it above nTarget, then go ahead and do it:
163
164	if (new_atoms <= nTarget) {
165	MolToProcMap[i] = which_proc;
166	AtomsPerProc[which_proc] += add_atoms;
167	for (j = 0 ; j < add_atoms; j++ ) {
168	AtomToProcMap[atomIndex] = which_proc;
169	atomIndex++;
170	}
171	done = 1;
172	continue;
173	}
174
175
176	// The only situation left is when new_atoms > nTarget. We
177	// want to accept this with some probability that dies off the
178	// farther we are from nTarget
179
180	// roughly: x = new_atoms - nTarget
181	// Pacc(x) = exp(- a * x)
182	// where a = penalty / (average atoms per molecule)
183
184	x = (double) (new_atoms - nTarget);
185	y = myRandom->getRandom();
186
187	if (y < exp(- a * x)) {
188	MolToProcMap[i] = which_proc;
189	AtomsPerProc[which_proc] += add_atoms;
190	for (j = 0 ; j < add_atoms; j++ ) {
191	AtomToProcMap[atomIndex] = which_proc;
192	atomIndex++;
193	}
194	done = 1;
195	continue;
196	} else {
197	continue;
198	}
199
200	}
201	}
202
203	// Spray out this nonsense to all other processors:
204
205	MPI_Bcast(MolToProcMap, mpiPlug->nMolGlobal,
206	MPI_INT, 0, MPI_COMM_WORLD);
207
208	MPI_Bcast(AtomToProcMap, mpiPlug->nAtomsGlobal,
209	MPI_INT, 0, MPI_COMM_WORLD);
210
211	MPI_Bcast(MolComponentType, mpiPlug->nMolGlobal,
212	MPI_INT, 0, MPI_COMM_WORLD);
213
214	MPI_Bcast(AtomsPerProc, mpiPlug->numberProcessors,
215	MPI_INT, 0, MPI_COMM_WORLD);
216	} else {
217
218	// Listen to your marching orders from processor 0:
219
220	MPI_Bcast(MolToProcMap, mpiPlug->nMolGlobal,
221	MPI_INT, 0, MPI_COMM_WORLD);
222
223	MPI_Bcast(AtomToProcMap, mpiPlug->nAtomsGlobal,
224	MPI_INT, 0, MPI_COMM_WORLD);
225
226	MPI_Bcast(MolComponentType, mpiPlug->nMolGlobal,
227	MPI_INT, 0, MPI_COMM_WORLD);
228
229	MPI_Bcast(AtomsPerProc, mpiPlug->numberProcessors,
230	MPI_INT, 0, MPI_COMM_WORLD);
231
232
233	}
234
235
236	// Let's all check for sanity:
237
238	nmol_local = 0;
239	for (i = 0 ; i < mpiPlug->nMolGlobal; i++ ) {
240	if (MolToProcMap[i] == mpiPlug->myNode) {
241	nmol_local++;
242	}
243	}
244
245	natoms_local = 0;
246	for (i = 0; i < mpiPlug->nAtomsGlobal; i++) {
247	if (AtomToProcMap[i] == mpiPlug->myNode) {
248	natoms_local++;
249	}
250	}
251
252	MPI_Allreduce(&nmol_local,&nmol_global,1,MPI_INT,MPI_SUM,
253	MPI_COMM_WORLD);
254	MPI_Allreduce(&natoms_local,&natoms_global,1,MPI_INT,
255	MPI_SUM, MPI_COMM_WORLD);
256
257	if( nmol_global != entryPlug->n_mol ){
258	sprintf( painCave.errMsg,
259	"The sum of all nmol_local, %d, did not equal the "
260	"total number of molecules, %d.\n",
261	nmol_global, entryPlug->n_mol );
262	painCave.isFatal = 1;
263	simError();
264	}
265
266	if( natoms_global != entryPlug->n_atoms ){
267	sprintf( painCave.errMsg,
268	"The sum of all natoms_local, %d, did not equal the "
269	"total number of atoms, %d.\n",
270	natoms_global, entryPlug->n_atoms );
271	painCave.isFatal = 1;
272	simError();
273	}
274
275	sprintf( checkPointMsg,
276	"Successfully divided the molecules among the processors.\n" );
277	MPIcheckPoint();
278
279	mpiPlug->myNMol = nmol_local;
280	mpiPlug->myNlocal = natoms_local;
281
282	globalIndex = new int[mpiPlug->myNlocal];
283	local_index = 0;
284	for (i = 0; i < mpiPlug->nAtomsGlobal; i++) {
285	if (AtomToProcMap[i] == mpiPlug->myNode) {
286	globalIndex[local_index] = i;
287	local_index++;
288	}
289	}
290
291	return globalIndex;
292	}
293
294
295	void mpiSimulation::mpiRefresh( void ){
296
297	int isError, i;
298	int *globalIndex = new int[mpiPlug->myNlocal];
299
300	// Fortran indexing needs to be increased by 1 in order to get the 2 languages to
301	// not barf
302
303	for(i=0; i<mpiPlug->myNlocal; i++) globalIndex[i] = entryPlug->atoms[i]->getGlobalIndex()+1;
304
305
306	isError = 0;
307	setFsimParallel( mpiPlug, &(entryPlug->n_atoms), globalIndex, &isError );
308	if( isError ){
309
310	sprintf( painCave.errMsg,
311	"mpiRefresh errror: fortran didn't like something we gave it.\n" );
312	painCave.isFatal = 1;
313	simError();
314	}
315
316	delete[] globalIndex;
317
318	sprintf( checkPointMsg,
319	" mpiRefresh successful.\n" );
320	MPIcheckPoint();
321	}
322
323
324	#endif // is_mpi