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rendevous comm option for special bonds and fix rigid/small

This commit is contained in:
Steve Plimpton 2018-11-30 11:54:48 -07:00 committed by Axel Kohlmeyer
parent 2f20581b29
commit 9912c44413
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GPG Key ID: D9B44E93BF0C375A
13 changed files with 1249 additions and 875 deletions
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487
src/RIGID/fix_rigid_small.cpp
View File

@ -34,6 +34,7 @@
#include "variable.h"
#include "random_mars.h"
#include "math_const.h"
#include "hashlittle.h"
#include "memory.h"
#include "error.h"
@ -70,8 +71,7 @@ FixRigidSmall::FixRigidSmall(LAMMPS *lmp, int narg, char **arg) :
xcmimage(NULL), displace(NULL), eflags(NULL), orient(NULL), dorient(NULL),
avec_ellipsoid(NULL), avec_line(NULL), avec_tri(NULL), counts(NULL),
itensor(NULL), mass_body(NULL), langextra(NULL), random(NULL),
id_dilate(NULL), onemols(NULL), hash(NULL), bbox(NULL), ctr(NULL),
idclose(NULL), rsqclose(NULL)
id_dilate(NULL), onemols(NULL)
{
int i;
@ -107,18 +107,18 @@ FixRigidSmall::FixRigidSmall(LAMMPS *lmp, int narg, char **arg) :
// parse args for rigid body specification
int *mask = atom->mask;
tagint *bodyid = NULL;
tagint *bodyID = NULL;
int nlocal = atom->nlocal;
if (narg < 4) error->all(FLERR,"Illegal fix rigid/small command");
if (strcmp(arg[3],"molecule") == 0) {
if (atom->molecule_flag == 0)
error->all(FLERR,"Fix rigid/small requires atom attribute molecule");
bodyid = atom->molecule;
bodyID = atom->molecule;
} else if (strcmp(arg[3],"custom") == 0) {
if (narg < 5) error->all(FLERR,"Illegal fix rigid/small command");
bodyid = new tagint[nlocal];
bodyID = new tagint[nlocal];
customflag = 1;
// determine whether atom-style variable or atom property is used.
@ -126,9 +126,11 @@ FixRigidSmall::FixRigidSmall(LAMMPS *lmp, int narg, char **arg) :
int is_double=0;
int custom_index = atom->find_custom(arg[4]+2,is_double);
if (custom_index == -1)
error->all(FLERR,"Fix rigid/small custom requires previously defined property/atom");
error->all(FLERR,"Fix rigid/small custom requires "
"previously defined property/atom");
else if (is_double)
error->all(FLERR,"Fix rigid/small custom requires integer-valued property/atom");
error->all(FLERR,"Fix rigid/small custom requires "
"integer-valued property/atom");
int minval = INT_MAX;
int *value = atom->ivector[custom_index];
@ -139,15 +141,17 @@ FixRigidSmall::FixRigidSmall(LAMMPS *lmp, int narg, char **arg) :
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
bodyid[i] = (tagint)(value[i] - minval + 1);
else bodyid[i] = 0;
bodyID[i] = (tagint)(value[i] - minval + 1);
else bodyID[i] = 0;
} else if (strstr(arg[4],"v_") == arg[4]) {
int ivariable = input->variable->find(arg[4]+2);
if (ivariable < 0)
error->all(FLERR,"Variable name for fix rigid/small custom does not exist");
error->all(FLERR,"Variable name for fix rigid/small custom "
"does not exist");
if (input->variable->atomstyle(ivariable) == 0)
error->all(FLERR,"Fix rigid/small custom variable is no atom-style variable");
error->all(FLERR,"Fix rigid/small custom variable is not "
"atom-style variable");
double *value = new double[nlocal];
input->variable->compute_atom(ivariable,0,value,1,0);
int minval = INT_MAX;
@ -158,8 +162,8 @@ FixRigidSmall::FixRigidSmall(LAMMPS *lmp, int narg, char **arg) :
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
bodyid[i] = (tagint)((tagint)value[i] - minval + 1);
else bodyid[0] = 0;
bodyID[i] = (tagint)((tagint)value[i] - minval + 1);
else bodyID[0] = 0;
delete[] value;
} else error->all(FLERR,"Unsupported fix rigid custom property");
} else error->all(FLERR,"Illegal fix rigid/small command");
@ -167,10 +171,11 @@ FixRigidSmall::FixRigidSmall(LAMMPS *lmp, int narg, char **arg) :
if (atom->map_style == 0)
error->all(FLERR,"Fix rigid/small requires an atom map, see atom_modify");
// maxmol = largest bodyid #
// maxmol = largest bodyID #
maxmol = -1;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) maxmol = MAX(maxmol,bodyid[i]);
if (mask[i] & groupbit) maxmol = MAX(maxmol,bodyID[i]);
tagint itmp;
MPI_Allreduce(&maxmol,&itmp,1,MPI_LMP_TAGINT,MPI_MAX,world);
@ -400,8 +405,19 @@ FixRigidSmall::FixRigidSmall(LAMMPS *lmp, int narg, char **arg) :
// sets bodytag for owned atoms
// body attributes are computed later by setup_bodies()
create_bodies(bodyid);
if (customflag) delete [] bodyid;
double time1 = MPI_Wtime();
create_bodies(bodyID);
if (customflag) delete [] bodyID;
double time2 = MPI_Wtime();
if (comm->me == 0) {
if (screen)
fprintf(screen," create_bodies CPU = %g secs\n",time2-time1);
if (logfile)
fprintf(logfile," create_bodies CPU = %g secs\n",time2-time1);
}
// set nlocal_body and allocate bodies I own
@ -1514,175 +1530,71 @@ void FixRigidSmall::set_v()
set bodytag for all owned atoms
------------------------------------------------------------------------- */
void FixRigidSmall::create_bodies(tagint *bodyid)
void FixRigidSmall::create_bodies(tagint *bodyID)
{
int i,m,n;
double unwrap[3];
int i,m;
// error check on image flags of atoms in rigid bodies
// allocate buffer for input to rendezvous comm
// ncount = # of my atoms in bodies
imageint *image = atom->image;
int *mask = atom->mask;
int nlocal = atom->nlocal;
int *periodicity = domain->periodicity;
int xbox,ybox,zbox;
int flag = 0;
for (i = 0; i < nlocal; i++) {
if (!(mask[i] & groupbit)) continue;
xbox = (image[i] & IMGMASK) - IMGMAX;
ybox = (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
zbox = (image[i] >> IMG2BITS) - IMGMAX;
if ((xbox && !periodicity[0]) || (ybox && !periodicity[1]) ||
(zbox && !periodicity[2])) flag = 1;
}
int flagall;
MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,world);
if (flagall) error->all(FLERR,"Fix rigid/small atom has non-zero image flag "
"in a non-periodic dimension");
// allocate buffer for passing messages around ring of procs
// percount = max number of values to put in buffer for each of ncount
int ncount = 0;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) ncount++;
int percount = 5;
double *buf;
memory->create(buf,ncount*percount,"rigid/small:buf");
int *proclist;
memory->create(proclist,ncount,"rigid/small:proclist");
InRvous *inbuf = (InRvous *)
memory->smalloc(ncount*sizeof(InRvous),"rigid/small:inbuf");
// create map hash for storing unique body IDs of my atoms
// key = body ID
// value = index into per-body data structure
// n = # of entries in hash
hash = new std::map<tagint,int>();
hash->clear();
// setup hash
// key = body ID
// value = index into N-length data structure
// n = count of unique bodies my atoms are part of
n = 0;
for (i = 0; i < nlocal; i++) {
if (!(mask[i] & groupbit)) continue;
if (hash->find(bodyid[i]) == hash->end()) (*hash)[bodyid[i]] = n++;
}
// bbox = bounding box of each rigid body my atoms are part of
memory->create(bbox,n,6,"rigid/small:bbox");
for (i = 0; i < n; i++) {
bbox[i][0] = bbox[i][2] = bbox[i][4] = BIG;
bbox[i][1] = bbox[i][3] = bbox[i][5] = -BIG;
}
// pack my atoms into buffer as body ID, unwrapped coords
// setup buf to pass to rendezvous comm
// one BodyMsg datum for each constituent atom
// datum = me, local index of atom, atomID, bodyID, unwrapped coords
// owning proc for each datum = random hash of bodyID
double **x = atom->x;
m = 0;
for (i = 0; i < nlocal; i++) {
if (!(mask[i] & groupbit)) continue;
domain->unmap(x[i],image[i],unwrap);
buf[m++] = bodyid[i];
buf[m++] = unwrap[0];
buf[m++] = unwrap[1];
buf[m++] = unwrap[2];
}
// pass buffer around ring of procs
// func = update bbox with atom coords from every proc
// when done, have full bbox for every rigid body my atoms are part of
comm->ring(m,sizeof(double),buf,1,ring_bbox,NULL,(void *)this);
// check if any bbox is size 0.0, meaning rigid body is a single particle
flag = 0;
for (i = 0; i < n; i++)
if (bbox[i][0] == bbox[i][1] && bbox[i][2] == bbox[i][3] &&
bbox[i][4] == bbox[i][5]) flag = 1;
MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,world);
if (flagall)
error->all(FLERR,"One or more rigid bodies are a single particle");
// ctr = center pt of each rigid body my atoms are part of
memory->create(ctr,n,6,"rigid/small:bbox");
for (i = 0; i < n; i++) {
ctr[i][0] = 0.5 * (bbox[i][0] + bbox[i][1]);
ctr[i][1] = 0.5 * (bbox[i][2] + bbox[i][3]);
ctr[i][2] = 0.5 * (bbox[i][4] + bbox[i][5]);
}
// idclose = ID of atom in body closest to center pt (smaller ID if tied)
// rsqclose = distance squared from idclose to center pt
memory->create(idclose,n,"rigid/small:idclose");
memory->create(rsqclose,n,"rigid/small:rsqclose");
for (i = 0; i < n; i++) rsqclose[i] = BIG;
// pack my atoms into buffer as body ID, atom ID, unwrapped coords
tagint *tag = atom->tag;
imageint *image = atom->image;
m = 0;
for (i = 0; i < nlocal; i++) {
if (!(mask[i] & groupbit)) continue;
domain->unmap(x[i],image[i],unwrap);
buf[m++] = bodyid[i];
buf[m++] = ubuf(tag[i]).d;
buf[m++] = unwrap[0];
buf[m++] = unwrap[1];
buf[m++] = unwrap[2];
proclist[m] = hashlittle(&bodyID[i],sizeof(tagint),0) % nprocs;
inbuf[m].me = me;
inbuf[m].ilocal = i;
inbuf[m].atomID = tag[i];
inbuf[m].bodyID = bodyID[i];
domain->unmap(x[i],image[i],inbuf[m].x);
m++;
}
// pass buffer around ring of procs
// func = update idclose,rsqclose with atom IDs from every proc
// when done, have idclose for every rigid body my atoms are part of
// perform rendezvous operation
// each proc owns random subset of bodies, receives all atoms in the bodies
// func = compute bbox of each body, flag atom closest to geometric center
// when done: each atom has atom ID of owning atom of its body
comm->ring(m,sizeof(double),buf,2,ring_nearest,NULL,(void *)this);
char *buf;
int nreturn = comm->rendezvous(ncount,proclist,(char *) inbuf,sizeof(InRvous),
rendezvous_body,buf,sizeof(OutRvous),
(void *) this);
OutRvous *outbuf = (OutRvous *) buf;
// set bodytag of all owned atoms, based on idclose
// find max value of rsqclose across all procs
memory->destroy(proclist);
memory->sfree(inbuf);
double rsqmax = 0.0;
for (i = 0; i < nlocal; i++) {
bodytag[i] = 0;
if (!(mask[i] & groupbit)) continue;
m = hash->find(bodyid[i])->second;
bodytag[i] = idclose[m];
rsqmax = MAX(rsqmax,rsqclose[m]);
}
// set bodytag of all owned atoms based on outbuf info for constituent atoms
// pack my atoms into buffer as bodytag of owning atom, unwrapped coords
for (i = 0; i < nlocal; i++)
if (!(mask[i] & groupbit)) bodytag[i] = 0;
m = 0;
for (i = 0; i < nlocal; i++) {
if (!(mask[i] & groupbit)) continue;
domain->unmap(x[i],image[i],unwrap);
buf[m++] = ubuf(bodytag[i]).d;
buf[m++] = unwrap[0];
buf[m++] = unwrap[1];
buf[m++] = unwrap[2];
}
for (m = 0; m < nreturn; m++)
bodytag[outbuf[m].ilocal] = outbuf[m].atomID;
// pass buffer around ring of procs
// func = update rsqfar for atoms belonging to bodies I own
// when done, have rsqfar for all atoms in bodies I own
memory->sfree(outbuf);
rsqfar = 0.0;
comm->ring(m,sizeof(double),buf,3,ring_farthest,NULL,(void *)this);
// find maxextent of rsqfar across all procs
// maxextent = max of rsqfar across all procs
// if defined, include molecule->maxextent
MPI_Allreduce(&rsqfar,&maxextent,1,MPI_DOUBLE,MPI_MAX,world);
@ -1691,125 +1603,151 @@ void FixRigidSmall::create_bodies(tagint *bodyid)
for (int i = 0; i < nmol; i++)
maxextent = MAX(maxextent,onemols[i]->maxextent);
}
}
/* ----------------------------------------------------------------------
process rigid bodies assigned to me
buf = list of N BodyMsg datums
------------------------------------------------------------------------- */
int FixRigidSmall::rendezvous_body(int n, char *inbuf,
int *&proclist, char *&outbuf,
void *ptr)
{
int i,j,m;
double delx,dely,delz,rsq;
int *iclose;
tagint *idclose;
double *x,*xown,*rsqclose;
double **bbox,**ctr;
FixRigidSmall *frsptr = (FixRigidSmall *) ptr;
Memory *memory = frsptr->memory;
Error *error = frsptr->error;
MPI_Comm world = frsptr->world;
// setup hash
// ncount = number of bodies assigned to me
// key = body ID
// value = index into Ncount-length data structure
InRvous *in = (InRvous *) inbuf;
std::map<tagint,int> hash;
tagint id;
int ncount = 0;
for (i = 0; i < n; i++) {
id = in[i].bodyID;
if (hash.find(id) == hash.end()) hash[id] = ncount++;
}
// bbox = bounding box of each rigid body
memory->create(bbox,ncount,6,"rigid/small:bbox");
for (m = 0; m < ncount; m++) {
bbox[m][0] = bbox[m][2] = bbox[m][4] = BIG;
bbox[m][1] = bbox[m][3] = bbox[m][5] = -BIG;
}
for (i = 0; i < n; i++) {
m = hash.find(in[i].bodyID)->second;
x = in[i].x;
bbox[m][0] = MIN(bbox[m][0],x[0]);
bbox[m][1] = MAX(bbox[m][1],x[0]);
bbox[m][2] = MIN(bbox[m][2],x[1]);
bbox[m][3] = MAX(bbox[m][3],x[1]);
bbox[m][4] = MIN(bbox[m][4],x[2]);
bbox[m][5] = MAX(bbox[m][5],x[2]);
}
// check if any bbox is size 0.0, meaning rigid body is a single particle
int flag = 0;
for (m = 0; m < ncount; m++)
if (bbox[m][0] == bbox[m][1] && bbox[m][2] == bbox[m][3] &&
bbox[m][4] == bbox[m][5]) flag = 1;
int flagall;
MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,world); // sync here?
if (flagall)
error->all(FLERR,"One or more rigid bodies are a single particle");
// ctr = geometric center pt of each rigid body
memory->create(ctr,ncount,3,"rigid/small:bbox");
for (m = 0; m < ncount; m++) {
ctr[m][0] = 0.5 * (bbox[m][0] + bbox[m][1]);
ctr[m][1] = 0.5 * (bbox[m][2] + bbox[m][3]);
ctr[m][2] = 0.5 * (bbox[m][4] + bbox[m][5]);
}
// idclose = atomID closest to center point of each body
memory->create(idclose,ncount,"rigid/small:idclose");
memory->create(iclose,ncount,"rigid/small:iclose");
memory->create(rsqclose,ncount,"rigid/small:rsqclose");
for (m = 0; m < ncount; m++) rsqclose[m] = BIG;
for (i = 0; i < n; i++) {
m = hash.find(in[i].bodyID)->second;
x = in[i].x;
delx = x[0] - ctr[m][0];
dely = x[1] - ctr[m][1];
delz = x[2] - ctr[m][2];
rsq = delx*delx + dely*dely + delz*delz;
if (rsq <= rsqclose[m]) {
if (rsq == rsqclose[m] && in[i].atomID > idclose[m]) continue;
iclose[m] = i;
idclose[m] = in[i].atomID;
rsqclose[m] = rsq;
}
}
// compute rsqfar for all bodies I own
// set rsqfar back in caller
double rsqfar = 0.0;
for (int i = 0; i < n; i++) {
m = hash.find(in[i].bodyID)->second;
xown = in[iclose[m]].x;
x = in[i].x;
delx = x[0] - xown[0];
dely = x[1] - xown[1];
delz = x[2] - xown[2];
rsq = delx*delx + dely*dely + delz*delz;
rsqfar = MAX(rsqfar,rsq);
}
frsptr->rsqfar = rsqfar;
// pass list of OutRvous datums back to comm->rendezvous
int nout = n;
memory->create(proclist,nout,"rigid/small:proclist");
OutRvous *out = (OutRvous *)
memory->smalloc(nout*sizeof(OutRvous),"rigid/small:out");
for (int i = 0; i < nout; i++) {
proclist[i] = in[i].me;
out[i].ilocal = in[i].ilocal;
m = hash.find(in[i].bodyID)->second;
out[i].atomID = idclose[m];
}
outbuf = (char *) out;
// clean up
// Comm::rendezvous will delete proclist and out (outbuf)
delete hash;
memory->destroy(buf);
memory->destroy(bbox);
memory->destroy(ctr);
memory->destroy(idclose);
memory->destroy(iclose);
memory->destroy(rsqclose);
}
/* ----------------------------------------------------------------------
process rigid body atoms from another proc
update bounding box for rigid bodies my atoms are part of
------------------------------------------------------------------------- */
void FixRigidSmall::ring_bbox(int n, char *cbuf, void *ptr)
{
FixRigidSmall *frsptr = (FixRigidSmall *) ptr;
std::map<tagint,int> *hash = frsptr->hash;
double **bbox = frsptr->bbox;
double *buf = (double *) cbuf;
int ndatums = n/4;
int j,imol;
double *x;
int m = 0;
for (int i = 0; i < ndatums; i++, m += 4) {
imol = static_cast<int> (buf[m]);
if (hash->find(imol) != hash->end()) {
j = hash->find(imol)->second;
x = &buf[m+1];
bbox[j][0] = MIN(bbox[j][0],x[0]);
bbox[j][1] = MAX(bbox[j][1],x[0]);
bbox[j][2] = MIN(bbox[j][2],x[1]);
bbox[j][3] = MAX(bbox[j][3],x[1]);
bbox[j][4] = MIN(bbox[j][4],x[2]);
bbox[j][5] = MAX(bbox[j][5],x[2]);
}
}
}
/* ----------------------------------------------------------------------
process rigid body atoms from another proc
update nearest atom to body center for rigid bodies my atoms are part of
------------------------------------------------------------------------- */
void FixRigidSmall::ring_nearest(int n, char *cbuf, void *ptr)
{
FixRigidSmall *frsptr = (FixRigidSmall *) ptr;
std::map<tagint,int> *hash = frsptr->hash;
double **ctr = frsptr->ctr;
tagint *idclose = frsptr->idclose;
double *rsqclose = frsptr->rsqclose;
double *buf = (double *) cbuf;
int ndatums = n/5;
int j,imol;
tagint tag;
double delx,dely,delz,rsq;
double *x;
int m = 0;
for (int i = 0; i < ndatums; i++, m += 5) {
imol = static_cast<int> (buf[m]);
if (hash->find(imol) != hash->end()) {
j = hash->find(imol)->second;
tag = (tagint) ubuf(buf[m+1]).i;
x = &buf[m+2];
delx = x[0] - ctr[j][0];
dely = x[1] - ctr[j][1];
delz = x[2] - ctr[j][2];
rsq = delx*delx + dely*dely + delz*delz;
if (rsq <= rsqclose[j]) {
if (rsq == rsqclose[j] && tag > idclose[j]) continue;
idclose[j] = tag;
rsqclose[j] = rsq;
}
}
}
}
/* ----------------------------------------------------------------------
process rigid body atoms from another proc
update rsqfar = distance from owning atom to other atom
------------------------------------------------------------------------- */
void FixRigidSmall::ring_farthest(int n, char *cbuf, void *ptr)
{
FixRigidSmall *frsptr = (FixRigidSmall *) ptr;
double **x = frsptr->atom->x;
imageint *image = frsptr->atom->image;
int nlocal = frsptr->atom->nlocal;
double *buf = (double *) cbuf;
int ndatums = n/4;
int iowner;
tagint tag;
double delx,dely,delz,rsq;
double *xx;
double unwrap[3];
int m = 0;
for (int i = 0; i < ndatums; i++, m += 4) {
tag = (tagint) ubuf(buf[m]).i;
iowner = frsptr->atom->map(tag);
if (iowner < 0 || iowner >= nlocal) continue;
frsptr->domain->unmap(x[iowner],image[iowner],unwrap);
xx = &buf[m+1];
delx = xx[0] - unwrap[0];
dely = xx[1] - unwrap[1];
delz = xx[2] - unwrap[2];
rsq = delx*delx + dely*dely + delz*delz;
frsptr->rsqfar = MAX(frsptr->rsqfar,rsq);
}
return nout;
}
/* ----------------------------------------------------------------------
@ -2472,9 +2410,9 @@ void FixRigidSmall::readfile(int which, double **array, int *inbody)
int nlocal = atom->nlocal;
hash = new std::map<tagint,int>();
std::map<tagint,int> hash;
for (i = 0; i < nlocal; i++)
if (bodyown[i] >= 0) (*hash)[atom->molecule[i]] = bodyown[i];
if (bodyown[i] >= 0) hash[atom->molecule[i]] = bodyown[i];
// open file and read header
@ -2533,11 +2471,11 @@ void FixRigidSmall::readfile(int which, double **array, int *inbody)
id = ATOTAGINT(values[0]);
if (id <= 0 || id > maxmol)
error->all(FLERR,"Invalid rigid body ID in fix rigid/small file");
if (hash->find(id) == hash->end()) {
if (hash.find(id) == hash.end()) {
buf = next + 1;
continue;
}
m = (*hash)[id];
m = hash[id];
inbody[m] = 1;
if (which == 0) {
@ -2576,7 +2514,6 @@ void FixRigidSmall::readfile(int which, double **array, int *inbody)
delete [] buffer;
delete [] values;
delete hash;
}
/* ----------------------------------------------------------------------

26
src/RIGID/fix_rigid_small.h
View File

@ -23,7 +23,7 @@ FixStyle(rigid/small,FixRigidSmall)
#include "fix.h"
// replace this later
#include <map>
//#include <map>
namespace LAMMPS_NS {
@ -180,13 +180,21 @@ class FixRigidSmall : public Fix {
// class data used by ring communication callbacks
std::map<tagint,int> *hash;
double **bbox;
double **ctr;
tagint *idclose;
double *rsqclose;
double rsqfar;
struct InRvous {
int me,ilocal;
tagint atomID,bodyID;
double x[3];
};
struct OutRvous {
int ilocal;
tagint atomID;
};
// local methods
void image_shift();
void set_xv();
void set_v();
@ -199,11 +207,9 @@ class FixRigidSmall : public Fix {
void grow_body();
void reset_atom2body();
// callback functions for ring communication
// callback function for rendezvous communication
static void ring_bbox(int, char *, void *);
static void ring_nearest(int, char *, void *);
static void ring_farthest(int, char *, void *);
static int rendezvous_body(int, char *, int *&, char *&, void *);
// debug

51
src/comm.cpp
View File

@ -28,6 +28,7 @@
#include "dump.h"
#include "group.h"
#include "procmap.h"
#include "irregular.h"
#include "accelerator_kokkos.h"
#include "memory.h"
#include "error.h"
@ -725,6 +726,56 @@ void Comm::ring(int n, int nper, void *inbuf, int messtag,
memory->destroy(bufcopy);
}
/* ----------------------------------------------------------------------
rendezvous communication operation
------------------------------------------------------------------------- */
int Comm::rendezvous(int n, int *proclist, char *inbuf, int insize,
int (*callback)(int, char *, int *&, char *&, void *),
char *&outbuf, int outsize, void *ptr)
{
// comm data from caller decomposition to rendezvous decomposition
Irregular *irregular = new Irregular(lmp);
int n_rvous = irregular->create_data(n,proclist); // add sort
char *inbuf_rvous = (char *) memory->smalloc((bigint) n_rvous*insize,
"rendezvous:inbuf_rvous");
irregular->exchange_data(inbuf,insize,inbuf_rvous);
irregular->destroy_data();
delete irregular;
// peform rendezvous computation via callback()
// callback() allocates proclist_rvous and outbuf_rvous
int *proclist_rvous;
char *outbuf_rvous;
int nout_rvous =
callback(n_rvous,inbuf_rvous,proclist_rvous,outbuf_rvous,ptr);
memory->sfree(inbuf_rvous);
// comm data from rendezvous decomposition back to caller
// caller will free outbuf
irregular = new Irregular(lmp);
int nout = irregular->create_data(nout_rvous,proclist_rvous);
outbuf = (char *) memory->smalloc((bigint) nout*outsize,"rendezvous:outbuf");
irregular->exchange_data(outbuf_rvous,outsize,outbuf);
irregular->destroy_data();
delete irregular;
memory->destroy(proclist_rvous);
memory->sfree(outbuf_rvous);
// return number of datums
return nout;
}
/* ----------------------------------------------------------------------
proc 0 reads Nlines from file into buf and bcasts buf to all procs
caller allocates buf to max size needed

4
src/comm.h
View File

@ -109,6 +109,10 @@ class Comm : protected Pointers {
void ring(int, int, void *, int, void (*)(int, char *, void *),
void *, void *, int self = 1);
int rendezvous(int, int *, char *, int,
int (*)(int, char *, int *&, char *&, void *),
char *&, int, void *);
int read_lines_from_file(FILE *, int, int, char *);
int read_lines_from_file_universe(FILE *, int, int, char *);

37
src/create_atoms.cpp
View File

@ -514,9 +514,6 @@ void CreateAtoms::command(int narg, char **arg)
if (domain->triclinic) domain->lamda2x(atom->nlocal);
}
MPI_Barrier(world);
double time2 = MPI_Wtime();
// clean up
delete ranmol;
@ -526,21 +523,6 @@ void CreateAtoms::command(int narg, char **arg)
delete [] ystr;
delete [] zstr;
// print status
if (comm->me == 0) {
if (screen) {
fprintf(screen,"Created " BIGINT_FORMAT " atoms\n",
atom->natoms-natoms_previous);
fprintf(screen," Time spent = %g secs\n",time2-time1);
}
if (logfile) {
fprintf(logfile,"Created " BIGINT_FORMAT " atoms\n",
atom->natoms-natoms_previous);
fprintf(logfile," Time spent = %g secs\n",time2-time1);
}
}
// for MOLECULE mode:
// create special bond lists for molecular systems,
// but not for atom style template
@ -550,6 +532,25 @@ void CreateAtoms::command(int narg, char **arg)
if (atom->molecular == 1 && onemol->bondflag && !onemol->specialflag) {
Special special(lmp);
special.build();
}
}
// print status
MPI_Barrier(world);
double time2 = MPI_Wtime();
if (comm->me == 0) {
if (screen) {
fprintf(screen,"Created " BIGINT_FORMAT " atoms\n",
atom->natoms-natoms_previous);
fprintf(screen," create_atoms CPU = %g secs\n",time2-time1);
}
if (logfile) {
fprintf(logfile,"Created " BIGINT_FORMAT " atoms\n",
atom->natoms-natoms_previous);
fprintf(logfile," create_atoms CPU = %g secs\n",time2-time1);
}
}
}

333
src/hashlittle.cpp Normal file
View File

@ -0,0 +1,333 @@
// Hash function hashlittle()
// from lookup3.c, by Bob Jenkins, May 2006, Public Domain
// bob_jenkins@burtleburtle.net
#include "stddef.h"
#include "stdint.h"
#define HASH_LITTLE_ENDIAN 1 // Intel and AMD are little endian
#define rot(x,k) (((x)<<(k)) | ((x)>>(32-(k))))
/*
-------------------------------------------------------------------------------
mix -- mix 3 32-bit values reversibly.
This is reversible, so any information in (a,b,c) before mix() is
still in (a,b,c) after mix().
If four pairs of (a,b,c) inputs are run through mix(), or through
mix() in reverse, there are at least 32 bits of the output that
are sometimes the same for one pair and different for another pair.
This was tested for:
* pairs that differed by one bit, by two bits, in any combination
of top bits of (a,b,c), or in any combination of bottom bits of
(a,b,c).
* "differ" is defined as +, -, ^, or ~^. For + and -, I transformed
the output delta to a Gray code (a^(a>>1)) so a string of 1's (as
is commonly produced by subtraction) look like a single 1-bit
difference.
* the base values were pseudorandom, all zero but one bit set, or
all zero plus a counter that starts at zero.
Some k values for my "a-=c; a^=rot(c,k); c+=b;" arrangement that
satisfy this are
4 6 8 16 19 4
9 15 3 18 27 15
14 9 3 7 17 3
Well, "9 15 3 18 27 15" didn't quite get 32 bits diffing
for "differ" defined as + with a one-bit base and a two-bit delta. I
used http://burtleburtle.net/bob/hash/avalanche.html to choose
the operations, constants, and arrangements of the variables.
This does not achieve avalanche. There are input bits of (a,b,c)
that fail to affect some output bits of (a,b,c), especially of a. The
most thoroughly mixed value is c, but it doesn't really even achieve
avalanche in c.
This allows some parallelism. Read-after-writes are good at doubling
the number of bits affected, so the goal of mixing pulls in the opposite
direction as the goal of parallelism. I did what I could. Rotates
seem to cost as much as shifts on every machine I could lay my hands
on, and rotates are much kinder to the top and bottom bits, so I used
rotates.
-------------------------------------------------------------------------------
*/
#define mix(a,b,c) \
{ \
a -= c; a ^= rot(c, 4); c += b; \
b -= a; b ^= rot(a, 6); a += c; \
c -= b; c ^= rot(b, 8); b += a; \
a -= c; a ^= rot(c,16); c += b; \
b -= a; b ^= rot(a,19); a += c; \
c -= b; c ^= rot(b, 4); b += a; \
}
/*
-------------------------------------------------------------------------------
final -- final mixing of 3 32-bit values (a,b,c) into c
Pairs of (a,b,c) values differing in only a few bits will usually
produce values of c that look totally different. This was tested for
* pairs that differed by one bit, by two bits, in any combination
of top bits of (a,b,c), or in any combination of bottom bits of
(a,b,c).
* "differ" is defined as +, -, ^, or ~^. For + and -, I transformed
the output delta to a Gray code (a^(a>>1)) so a string of 1's (as
is commonly produced by subtraction) look like a single 1-bit
difference.
* the base values were pseudorandom, all zero but one bit set, or
all zero plus a counter that starts at zero.
These constants passed:
14 11 25 16 4 14 24
12 14 25 16 4 14 24
and these came close:
4 8 15 26 3 22 24
10 8 15 26 3 22 24
11 8 15 26 3 22 24
-------------------------------------------------------------------------------
*/
#define final(a,b,c) \
{ \
c ^= b; c -= rot(b,14); \
a ^= c; a -= rot(c,11); \
b ^= a; b -= rot(a,25); \
c ^= b; c -= rot(b,16); \
a ^= c; a -= rot(c,4); \
b ^= a; b -= rot(a,14); \
c ^= b; c -= rot(b,24); \
}
/*
-------------------------------------------------------------------------------
hashlittle() -- hash a variable-length key into a 32-bit value
k : the key (the unaligned variable-length array of bytes)
length : the length of the key, counting by bytes
initval : can be any 4-byte value
Returns a 32-bit value. Every bit of the key affects every bit of
the return value. Two keys differing by one or two bits will have
totally different hash values.
The best hash table sizes are powers of 2. There is no need to do
mod a prime (mod is sooo slow!). If you need less than 32 bits,
use a bitmask. For example, if you need only 10 bits, do
h = (h & hashmask(10));
In which case, the hash table should have hashsize(10) elements.
If you are hashing n strings (uint8_t **)k, do it like this:
for (i=0, h=0; i<n; ++i) h = hashlittle( k[i], len[i], h);
By Bob Jenkins, 2006. bob_jenkins@burtleburtle.net. You may use this
code any way you wish, private, educational, or commercial. It's free.
Use for hash table lookup, or anything where one collision in 2^^32 is
acceptable. Do NOT use for cryptographic purposes.
-------------------------------------------------------------------------------
*/
uint32_t hashlittle( const void *key, size_t length, uint32_t initval)
{
#ifndef PURIFY_HATES_HASHLITTLE
uint32_t a,b,c; /* internal state */
union { const void *ptr; size_t i; } u; /* needed for Mac Powerbook G4 */
/* Set up the internal state */
a = b = c = 0xdeadbeef + ((uint32_t)length) + initval;
u.ptr = key;
if (HASH_LITTLE_ENDIAN && ((u.i & 0x3) == 0)) {
const uint32_t *k = (const uint32_t *)key; /* read 32-bit chunks */
const uint8_t *k8;
/*------ all but last block: aligned reads and affect 32 bits of (a,b,c) */
while (length > 12)
{
a += k[0];
b += k[1];
c += k[2];
mix(a,b,c);
length -= 12;
k += 3;
}
/*----------------------------- handle the last (probably partial) block */
/*
* "k[2]&0xffffff" actually reads beyond the end of the string, but
* then masks off the part it's not allowed to read. Because the
* string is aligned, the masked-off tail is in the same word as the
* rest of the string. Every machine with memory protection I've seen
* does it on word boundaries, so is OK with this. But VALGRIND will
* still catch it and complain. The masking trick does make the hash
* noticably faster for short strings (like English words).
*/
#ifndef VALGRIND
switch(length)
{
case 12: c+=k[2]; b+=k[1]; a+=k[0]; break;
case 11: c+=k[2]&0xffffff; b+=k[1]; a+=k[0]; break;
case 10: c+=k[2]&0xffff; b+=k[1]; a+=k[0]; break;
case 9 : c+=k[2]&0xff; b+=k[1]; a+=k[0]; break;
case 8 : b+=k[1]; a+=k[0]; break;
case 7 : b+=k[1]&0xffffff; a+=k[0]; break;
case 6 : b+=k[1]&0xffff; a+=k[0]; break;
case 5 : b+=k[1]&0xff; a+=k[0]; break;
case 4 : a+=k[0]; break;
case 3 : a+=k[0]&0xffffff; break;
case 2 : a+=k[0]&0xffff; break;
case 1 : a+=k[0]&0xff; break;
case 0 : return c; /* zero length strings require no mixing */
}
#else /* make valgrind happy */
k8 = (const uint8_t *)k;
switch(length)
{
case 12: c+=k[2]; b+=k[1]; a+=k[0]; break;
case 11: c+=((uint32_t)k8[10])<<16; /* fall through */
case 10: c+=((uint32_t)k8[9])<<8; /* fall through */
case 9 : c+=k8[8]; /* fall through */
case 8 : b+=k[1]; a+=k[0]; break;
case 7 : b+=((uint32_t)k8[6])<<16; /* fall through */
case 6 : b+=((uint32_t)k8[5])<<8; /* fall through */
case 5 : b+=k8[4]; /* fall through */
case 4 : a+=k[0]; break;
case 3 : a+=((uint32_t)k8[2])<<16; /* fall through */
case 2 : a+=((uint32_t)k8[1])<<8; /* fall through */
case 1 : a+=k8[0]; break;
case 0 : return c;
}
#endif /* !valgrind */
} else if (HASH_LITTLE_ENDIAN && ((u.i & 0x1) == 0)) {
const uint16_t *k = (const uint16_t *)key; /* read 16-bit chunks */
const uint8_t *k8;
/*--------------- all but last block: aligned reads and different mixing */
while (length > 12)
{
a += k[0] + (((uint32_t)k[1])<<16);
b += k[2] + (((uint32_t)k[3])<<16);
c += k[4] + (((uint32_t)k[5])<<16);
mix(a,b,c);
length -= 12;
k += 6;
}
/*----------------------------- handle the last (probably partial) block */
k8 = (const uint8_t *)k;
switch(length)
{
case 12: c+=k[4]+(((uint32_t)k[5])<<16);
b+=k[2]+(((uint32_t)k[3])<<16);
a+=k[0]+(((uint32_t)k[1])<<16);
break;
case 11: c+=((uint32_t)k8[10])<<16; /* fall through */
case 10: c+=k[4];
b+=k[2]+(((uint32_t)k[3])<<16);
a+=k[0]+(((uint32_t)k[1])<<16);
break;
case 9 : c+=k8[8]; /* fall through */
case 8 : b+=k[2]+(((uint32_t)k[3])<<16);
a+=k[0]+(((uint32_t)k[1])<<16);
break;
case 7 : b+=((uint32_t)k8[6])<<16; /* fall through */
case 6 : b+=k[2];
a+=k[0]+(((uint32_t)k[1])<<16);
break;
case 5 : b+=k8[4]; /* fall through */
case 4 : a+=k[0]+(((uint32_t)k[1])<<16);
break;
case 3 : a+=((uint32_t)k8[2])<<16; /* fall through */
case 2 : a+=k[0];
break;
case 1 : a+=k8[0];
break;
case 0 : return c; /* zero length requires no mixing */
}
} else { /* need to read the key one byte at a time */
const uint8_t *k = (const uint8_t *)key;
/*--------------- all but the last block: affect some 32 bits of (a,b,c) */
while (length > 12)
{
a += k[0];
a += ((uint32_t)k[1])<<8;
a += ((uint32_t)k[2])<<16;
a += ((uint32_t)k[3])<<24;
b += k[4];
b += ((uint32_t)k[5])<<8;
b += ((uint32_t)k[6])<<16;
b += ((uint32_t)k[7])<<24;
c += k[8];
c += ((uint32_t)k[9])<<8;
c += ((uint32_t)k[10])<<16;
c += ((uint32_t)k[11])<<24;
mix(a,b,c);
length -= 12;
k += 12;
}
/*-------------------------------- last block: affect all 32 bits of (c) */
switch(length) /* all the case statements fall through */
{
case 12: c+=((uint32_t)k[11])<<24;
case 11: c+=((uint32_t)k[10])<<16;
case 10: c+=((uint32_t)k[9])<<8;
case 9 : c+=k[8];
case 8 : b+=((uint32_t)k[7])<<24;
case 7 : b+=((uint32_t)k[6])<<16;
case 6 : b+=((uint32_t)k[5])<<8;
case 5 : b+=k[4];
case 4 : a+=((uint32_t)k[3])<<24;
case 3 : a+=((uint32_t)k[2])<<16;
case 2 : a+=((uint32_t)k[1])<<8;
case 1 : a+=k[0];
break;
case 0 : return c;
}
}
final(a,b,c);
return c;
#else /* PURIFY_HATES_HASHLITTLE */
/* I don't know what it is about Jenkins' hashlittle function, but
* it drives purify insane, even with VALGRIND defined. It makes
* purify unusable!! The code execution doesn't even make sense.
* Below is a (probably) weaker hash function that at least allows
* testing with purify.
*/
#define MAXINT_DIV_PHI 11400714819323198485U
uint32_t h, rest, *p, bytes, num_bytes;
char *byteptr;
num_bytes = length;
/* First hash the uint32_t-sized portions of the key */
h = 0;
for (p = (uint32_t *)key, bytes=num_bytes;
bytes >= (uint32_t) sizeof(uint32_t);
bytes-=sizeof(uint32_t), p++){
h = (h^(*p))*MAXINT_DIV_PHI;
}
/* Then take care of the remaining bytes, if any */
rest = 0;
for (byteptr = (char *)p; bytes > 0; bytes--, byteptr++){
rest = (rest<<8) | (*byteptr);
}
/* If extra bytes, merge the two parts */
if (rest)
h = (h^rest)*MAXINT_DIV_PHI;
return h;
#endif /* PURIFY_HATES_HASHLITTLE */
}

5
src/hashlittle.h Normal file
View File

@ -0,0 +1,5 @@
// Hash function hashlittle()
// from lookup3.c, by Bob Jenkins, May 2006, Public Domain
// bob_jenkins@burtleburtle.net
uint32_t hashlittle(const void *key, size_t length, uint32_t);

17
src/irregular.cpp
View File

@ -501,7 +501,8 @@ int compare_standalone(const int i, const int j, void *ptr)
void Irregular::exchange_atom(double *sendbuf, int *sizes, double *recvbuf)
{
int i,m,n,offset,count;
int i,m,n,count;
bigint offset;
// post all receives
@ -739,11 +740,13 @@ int Irregular::create_data(int n, int *proclist, int sortflag)
void Irregular::exchange_data(char *sendbuf, int nbytes, char *recvbuf)
{
int i,m,n,offset,count;
int i,n,count;
bigint m; // these 2 lines enable send/recv buf to be larger than 2 GB
char *dest;
// post all receives, starting after self copies
offset = num_self*nbytes;
bigint offset = num_self*nbytes;
for (int irecv = 0; irecv < nrecv_proc; irecv++) {
MPI_Irecv(&recvbuf[offset],num_recv[irecv]*nbytes,MPI_CHAR,
proc_recv[irecv],0,world,&request[irecv]);
@ -765,18 +768,22 @@ void Irregular::exchange_data(char *sendbuf, int nbytes, char *recvbuf)
n = 0;
for (int isend = 0; isend < nsend_proc; isend++) {
count = num_send[isend];
dest = buf;
for (i = 0; i < count; i++) {
m = index_send[n++];
memcpy(&buf[i*nbytes],&sendbuf[m*nbytes],nbytes);
memcpy(dest,&sendbuf[m*nbytes],nbytes);
dest += nbytes;
}
MPI_Send(buf,count*nbytes,MPI_CHAR,proc_send[isend],0,world);
}
// copy datums to self, put at beginning of recvbuf
dest = recvbuf;
for (i = 0; i < num_self; i++) {
m = index_self[i];
memcpy(&recvbuf[i*nbytes],&sendbuf[m*nbytes],nbytes);
memcpy(dest,&sendbuf[m*nbytes],nbytes);
dest += nbytes;
}
// wait on all incoming messages

15
src/read_data.cpp
View File

@ -120,6 +120,9 @@ void ReadData::command(int narg, char **arg)
{
if (narg < 1) error->all(FLERR,"Illegal read_data command");
MPI_Barrier(world);
double time1 = MPI_Wtime;
// optional args
addflag = NONE;
@ -906,6 +909,18 @@ void ReadData::command(int narg, char **arg)
force->kspace = saved_kspace;
}
// total time
MPI_Barrier(world);
double time2 = MPI_Wtime;
if (comm->me == 0) {
if (screen)
fprintf(screen," read_atoms CPU = %g secs\n",time2-time1);
if (logfile)
fprintf(logfile," read_atoms CPU = %g secs\n",time2-time1);
}
}
/* ----------------------------------------------------------------------

15
src/read_restart.cpp
View File

@ -81,6 +81,9 @@ void ReadRestart::command(int narg, char **arg)
if (domain->box_exist)
error->all(FLERR,"Cannot read_restart after simulation box is defined");
MPI_Barrier(world);
double time1 = MPI_Wtime;
MPI_Comm_rank(world,&me);
MPI_Comm_size(world,&nprocs);
@ -562,6 +565,18 @@ void ReadRestart::command(int narg, char **arg)
Special special(lmp);
special.build();
}
// total time
MPI_Barrier(world);
double time2 = MPI_Wtime;
if (comm->me == 0) {
if (screen)
fprintf(screen," read_restart CPU = %g secs\n",time2-time1);
if (logfile)
fprintf(logfile," read_restart CPU = %g secs\n",time2-time1);
}
}
/* ----------------------------------------------------------------------

8
src/replicate.cpp
View File

@ -76,7 +76,7 @@ void Replicate::command(int narg, char **arg)
if (atom->nextra_grow || atom->nextra_restart || atom->nextra_store)
error->all(FLERR,"Cannot replicate with fixes that store atom quantities");
// Record wall time for atom replication
// record wall time for atom replication
MPI_Barrier(world);
double time1 = MPI_Wtime();
@ -762,15 +762,15 @@ void Replicate::command(int narg, char **arg)
special.build();
}
// Wall time
// total time
MPI_Barrier(world);
double time2 = MPI_Wtime();
if (me == 0) {
if (screen)
fprintf(screen," Time spent = %g secs\n",time2-time1);
fprintf(screen," replicate CPU = %g secs\n",time2-time1);
if (logfile)
fprintf(logfile," Time spent = %g secs\n",time2-time1);
fprintf(logfile," replicate CPU = %g secs\n",time2-time1);
}
}

1099
src/special.cpp
View File

File diff suppressed because it is too large Load Diff

27
src/special.h
View File

@ -28,27 +28,30 @@ class Special : protected Pointers {
int me,nprocs;
tagint **onetwo,**onethree,**onefour;
// data used by ring callback methods
// data used by rendezvous callback methods
int *count;
int **dflag;
int max_rvous;
struct InRvous {
int me;
tagint atomID,partnerID;
};
struct OutRvous {
tagint atomID,partnerID;
};
void dedup();
void angle_trim();
void dihedral_trim();
void combine();
void fix_alteration();
void timer_output(double);
// callback functions for ring communication
// callback function for rendezvous communication
static void ring_one(int, char *, void *);
static void ring_two(int, char *, void *);
static void ring_three(int, char *, void *);
static void ring_four(int, char *, void *);
static void ring_five(int, char *, void *);
static void ring_six(int, char *, void *);
static void ring_seven(int, char *, void *);
static void ring_eight(int, char *, void *);
static int rendezvous_1234(int, char *, int *&, char *&, void *);
static int rendezvous_trim(int, char *, int *&, char *&, void *);
};
}