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
#	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	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	int* mpiSimulation::divideLabor( void ){
44
45	int* globalIndex;
46
47	int nComponents;
48	MoleculeStamp** compStamps;
49	randomSPRNG *myRandom;
50	int* componentsNmol;
51	int* AtomsPerProc;
52
53	double numerator;
54	double denominator;
55	double precast;
56	double x, y, a;
57	int old_atoms, add_atoms, new_atoms;
58
59	int nTarget;
60	int molIndex, atomIndex, compIndex, compStart;
61	int done;
62	int nLocal, molLocal;
63	int i, j, loops, which_proc, nmol_local, natoms_local;
64	int nmol_global, natoms_global;
65	int local_index, index;
66	int smallDiff, bigDiff;
67	int baseSeed = entryPlug->getSeed();
68
69	int testSum;
70
71	nComponents = entryPlug->nComponents;
72	compStamps = entryPlug->compStamps;
73	componentsNmol = entryPlug->componentsNmol;
74	AtomsPerProc = new int[mpiPlug->numberProcessors];
75
76	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
84	myRandom = new randomSPRNG( baseSeed );
85
86	a = 3.0 * (double)mpiPlug->nMolGlobal / (double)mpiPlug->nAtomsGlobal;
87
88	// 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
108	// 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
117	atomIndex = 0;
118
119	for (i = 0; i < molIndex; i++ ) {
120
121	done = 0;
122	loops = 0;
123
124	while( !done ){
125	loops++;
126
127	// Pick a processor at random
128
129	which_proc = (int) (myRandom->getRandom() * mpiPlug->numberProcessors);
130
131	// How many atoms does this processor have?
132
133	old_atoms = AtomsPerProc[which_proc];
134	add_atoms = compStamps[MolComponentType[i]]->getNAtoms();
135	new_atoms = old_atoms + add_atoms;
136
137	// 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	AtomToProcMap[atomIndex] = which_proc;
154	atomIndex++;
155	}
156	done = 1;
157	continue;
158	}
159
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	// 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
179	// roughly: x = new_atoms - nTarget
180	// Pacc(x) = exp(- a * x)
181	// where a = penalty / (average atoms per molecule)
182
183	x = (double) (new_atoms - nTarget);
184	y = myRandom->getRandom();
185
186	if (y < exp(- a * x)) {
187	MolToProcMap[i] = which_proc;
188	AtomsPerProc[which_proc] += add_atoms;
189	for (j = 0 ; j < add_atoms; j++ ) {
190	AtomToProcMap[atomIndex] = which_proc;
191	atomIndex++;
192	}
193	done = 1;
194	continue;
195	} else {
196	continue;
197	}
198
199	}
200	}
201
202	// Spray out this nonsense to all other processors:
203
204	MPI_Bcast(MolToProcMap, mpiPlug->nMolGlobal,
205	MPI_INT, 0, MPI_COMM_WORLD);
206
207	MPI_Bcast(AtomToProcMap, mpiPlug->nAtomsGlobal,
208	MPI_INT, 0, MPI_COMM_WORLD);
209
210	MPI_Bcast(MolComponentType, mpiPlug->nMolGlobal,
211	MPI_INT, 0, MPI_COMM_WORLD);
212
213	MPI_Bcast(AtomsPerProc, mpiPlug->numberProcessors,
214	MPI_INT, 0, MPI_COMM_WORLD);
215	} else {
216
217	// Listen to your marching orders from processor 0:
218
219	MPI_Bcast(MolToProcMap, mpiPlug->nMolGlobal,
220	MPI_INT, 0, MPI_COMM_WORLD);
221
222	MPI_Bcast(AtomToProcMap, mpiPlug->nAtomsGlobal,
223	MPI_INT, 0, MPI_COMM_WORLD);
224
225	MPI_Bcast(MolComponentType, mpiPlug->nMolGlobal,
226	MPI_INT, 0, MPI_COMM_WORLD);
227
228	MPI_Bcast(AtomsPerProc, mpiPlug->numberProcessors,
229	MPI_INT, 0, MPI_COMM_WORLD);
230
231
232	}
233
234
235	// 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	}
243
244	natoms_local = 0;
245	for (i = 0; i < mpiPlug->nAtomsGlobal; i++) {
246	if (AtomToProcMap[i] == mpiPlug->myNode) {
247	natoms_local++;
248	}
249	}
250
251	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
256	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	}
264
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
274	sprintf( checkPointMsg,
275	"Successfully divided the molecules among the processors.\n" );
276	MPIcheckPoint();
277
278	mpiPlug->myNMol = nmol_local;
279	mpiPlug->myNlocal = natoms_local;
280
281	globalIndex = new int[mpiPlug->myNlocal];
282	local_index = 0;
283	for (i = 0; i < mpiPlug->nAtomsGlobal; i++) {
284	if (AtomToProcMap[i] == mpiPlug->myNode) {
285	globalIndex[local_index] = i;
286	local_index++;
287	}
288	}
289
290	return globalIndex;
291	}
292
293
294	void mpiSimulation::mpiRefresh( void ){
295
296	int isError, i;
297	int *globalIndex = new int[mpiPlug->myNlocal];
298
299	// Fortran indexing needs to be increased by 1 in order to get the 2 languages to
300	// not barf
301
302	for(i=0; i<mpiPlug->myNlocal; i++) globalIndex[i] = entryPlug->atoms[i]->getGlobalIndex()+1;
303
304
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