lijiext
/
lammps
mirror of https://github.com/lammps/lammps.git
1
0
Fork 1
Code Issues Packages Projects Releases Wiki Activity

replace STL map with atom->map in special, better code comments

This commit is contained in:
Steve Plimpton 2018-11-30 13:06:31 -07:00 committed by Axel Kohlmeyer
parent 9912c44413
commit 3f9d59294e
No known key found for this signature in database
GPG Key ID: D9B44E93BF0C375A
5 changed files with 92 additions and 37 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

8
src/RIGID/fix_rigid_small.cpp
View File

@ -1571,9 +1571,9 @@ void FixRigidSmall::create_bodies(tagint *bodyID)
}
// 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
// each proc owns random subset of bodies
// receives all atoms in those bodies
// func = compute bbox of each body, find atom closest to geometric center
char *buf;
int nreturn = comm->rendezvous(ncount,proclist,(char *) inbuf,sizeof(InRvous),
@ -1627,6 +1627,8 @@ int FixRigidSmall::rendezvous_body(int n, char *inbuf,
MPI_Comm world = frsptr->world;
// setup hash
// use STL map instead of atom->map
// b/c know nothing about body ID values specified by user
// ncount = number of bodies assigned to me
// key = body ID
// value = index into Ncount-length data structure

20
src/comm.cpp
View File

@ -728,13 +728,27 @@ void Comm::ring(int n, int nper, void *inbuf, int messtag,
/* ----------------------------------------------------------------------
rendezvous communication operation
three stages:
first Irregular converts inbuf from caller decomp to rvous decomp
callback operates on data in rendevous decomp
last Irregular converts outbuf from rvous decomp back to caller decomp
inputs:
n = # of input datums
proclist = proc that owns each input datum in rendezvous decomposition
inbuf = list of input datums
insize = size in bytes of each input datum
callback = caller function to invoke in rendezvous decomposition
outputs:
nout = # of output datums (function return)
outbuf = list of output datums
outsize = size in bytes of each output datum
------------------------------------------------------------------------- */
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
// comm inbuf from caller decomposition to rendezvous decomposition
Irregular *irregular = new Irregular(lmp);
@ -747,7 +761,7 @@ int Comm::rendezvous(int n, int *proclist, char *inbuf, int insize,
delete irregular;
// peform rendezvous computation via callback()
// callback() allocates proclist_rvous and outbuf_rvous
// callback() allocates/populates proclist_rvous and outbuf_rvous
int *proclist_rvous;
char *outbuf_rvous;
@ -757,7 +771,7 @@ int Comm::rendezvous(int n, int *proclist, char *inbuf, int insize,
memory->sfree(inbuf_rvous);
// comm data from rendezvous decomposition back to caller
// comm outbuf from rendezvous decomposition back to caller
// caller will free outbuf
irregular = new Irregular(lmp);

8
src/read_data.cpp
View File

@ -121,7 +121,7 @@ void ReadData::command(int narg, char **arg)
if (narg < 1) error->all(FLERR,"Illegal read_data command");
MPI_Barrier(world);
double time1 = MPI_Wtime;
double time1 = MPI_Wtime();
// optional args
@ -913,13 +913,13 @@ void ReadData::command(int narg, char **arg)
// total time
MPI_Barrier(world);
double time2 = MPI_Wtime;
double time2 = MPI_Wtime();
if (comm->me == 0) {
if (screen)
fprintf(screen," read_atoms CPU = %g secs\n",time2-time1);
fprintf(screen," read_data CPU = %g secs\n",time2-time1);
if (logfile)
fprintf(logfile," read_atoms CPU = %g secs\n",time2-time1);
fprintf(logfile," read_data CPU = %g secs\n",time2-time1);
}
}

4
src/read_restart.cpp
View File

@ -82,7 +82,7 @@ void ReadRestart::command(int narg, char **arg)
error->all(FLERR,"Cannot read_restart after simulation box is defined");
MPI_Barrier(world);
double time1 = MPI_Wtime;
double time1 = MPI_Wtime();
MPI_Comm_rank(world,&me);
MPI_Comm_size(world,&nprocs);
@ -569,7 +569,7 @@ void ReadRestart::command(int narg, char **arg)
// total time
MPI_Barrier(world);
double time2 = MPI_Wtime;
double time2 = MPI_Wtime();
if (comm->me == 0) {
if (screen)

89
src/special.cpp
View File

@ -108,9 +108,11 @@ void Special::build()
memory->smalloc((bigint) ncount*sizeof(InRvous),"special:inbuf");
// setup input buf to rendezvous comm
// one datum for each owned atom: datum = proc, atomID
// one datum for each bond partner: datum = atomID, bond partner ID
// input datums = pairs of bonded atoms
// owning proc for each datum = random hash of atomID
// one datum for each owned atom: datum = owning proc, atomID
// one datum for each bond partner: datum = atomID, bond partner ID
// add inverted datum when netwon_bond on
m = 0;
for (i = 0; i < nlocal; i++) {
@ -140,7 +142,8 @@ void Special::build()
}
// perform rendezvous operation
// each proc owns random subset of atoms, receives all their bond partners
// each proc owns random subset of atoms
// receives all info to form and return their onetwo lists
int nreturn = comm->rendezvous(ncount,proclist,(char *) inbuf,sizeof(InRvous),
rendezvous_1234,
@ -151,6 +154,7 @@ void Special::build()
memory->sfree(inbuf);
// set nspecial[0] and onetwo for all owned atoms based on output info
// output datums = pairs of atoms that are 1-2 neighbors
MPI_Allreduce(&max_rvous,&maxall,1,MPI_INT,MPI_MAX,world);
memory->create(onetwo,nlocal,maxall,"special:onetwo");
@ -200,9 +204,10 @@ void Special::build()
memory->smalloc((bigint) ncount*sizeof(InRvous),"special:inbuf");
// setup input buf to rendezvous comm
// one datum for each owned atom: datum = proc, atomID
// one datum for each bond partner: datum = atomID, bond partner ID
// input datums = all pairs of onetwo atoms (they are 1-3 neighbors)
// owning proc for each datum = random hash of atomID
// one datum for each owned atom: datum = owning proc, atomID
// one datum for each onetwo pair: datum = atomID1, atomID2
m = 0;
for (i = 0; i < nlocal; i++) {
@ -226,7 +231,8 @@ void Special::build()
}
// perform rendezvous operation
// each proc owns random subset of atoms, receives all their bond partners
// each proc owns random subset of atoms
// receives all info to form and return their onethree lists
nreturn = comm->rendezvous(ncount,proclist,(char *) inbuf,sizeof(InRvous),
rendezvous_1234,
@ -237,6 +243,7 @@ void Special::build()
memory->sfree(inbuf);
// set nspecial[1] and onethree for all owned atoms based on output info
// output datums = pairs of atoms that are 1-3 neighbors
MPI_Allreduce(&max_rvous,&maxall,1,MPI_INT,MPI_MAX,world);
memory->create(onethree,nlocal,maxall,"special:onethree");
@ -284,9 +291,10 @@ void Special::build()
memory->smalloc((bigint) ncount*sizeof(InRvous),"special:inbuf");
// setup input buf to rendezvous comm
// one datum for each owned atom: datum = proc, atomID
// one datum for each partner: datum = atomID, bond partner ID
// input datums = all pairs of onethree and onetwo atoms (they're 1-4 neighbors)
// owning proc for each datum = random hash of atomID
// one datum for each owned atom: datum = owning proc, atomID
// one datum for each onethree/onetwo pair: datum = atomID1, atomID2
m = 0;
for (i = 0; i < nlocal; i++) {
@ -309,9 +317,8 @@ void Special::build()
}
// 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
// each proc owns random subset of atoms
// receives all info to form and return their onefour lists
nreturn = comm->rendezvous(ncount,proclist,(char *) inbuf,sizeof(InRvous),
rendezvous_1234,
@ -322,6 +329,7 @@ void Special::build()
memory->sfree(inbuf);
// set nspecial[2] and onefour for all owned atoms based on output info
// output datums = pairs of atoms that are 1-4 neighbors
MPI_Allreduce(&max_rvous,&maxall,1,MPI_INT,MPI_MAX,world);
memory->create(onefour,nlocal,maxall,"special:onefour");
@ -934,21 +942,28 @@ int Special::rendezvous_1234(int n, char *inbuf,
int i,j,m;
Special *sptr = (Special *) ptr;
Atom *atom = sptr->atom;
Memory *memory = sptr->memory;
// setup hash
// clear atom map so it can be here as a hash table
// faster than an STL map for large atom counts
atom->map_clear();
// initialize hash
// ncount = number of atoms assigned to me
// key = atom ID
// value = index into Ncount-length data structure
InRvous *in = (InRvous *) inbuf;
std::map<tagint,int> hash;
//std::map<tagint,int> hash;
tagint id;
int ncount = 0;
for (i = 0; i < n; i++)
if (in[i].me >= 0)
hash[in[i].atomID] = ncount++;
//hash[in[i].atomID] = ncount++;
atom->map_one(in[i].atomID,ncount++);
// procowner = caller proc that owns each atom
// atomID = ID of each rendezvous atom I own
@ -961,7 +976,8 @@ int Special::rendezvous_1234(int n, char *inbuf,
for (m = 0; m < ncount; m++) npartner[m] = 0;
for (i = 0; i < n; i++) {
m = hash.find(in[i].atomID)->second;
//m = hash.find(in[i].atomID)->second;
m = atom->map(in[i].atomID);
if (in[i].me >= 0) {
procowner[m] = in[i].me;
atomID[m] = in[i].atomID;
@ -979,7 +995,8 @@ int Special::rendezvous_1234(int n, char *inbuf,
for (i = 0; i < n; i++) {
if (in[i].me >= 0) continue;
m = hash.find(in[i].atomID)->second;
//m = hash.find(in[i].atomID)->second;
m = atom->map(in[i].atomID);
partner[m][npartner[m]++] = in[i].partnerID;
}
@ -1011,6 +1028,12 @@ int Special::rendezvous_1234(int n, char *inbuf,
memory->destroy(npartner);
memory->destroy(partner);
// re-create atom map
atom->map_init(0);
atom->nghost = 0;
atom->map_set();
return nout;
}
@ -1027,21 +1050,28 @@ int Special::rendezvous_trim(int n, char *inbuf,
int i,j,m;
Special *sptr = (Special *) ptr;
Atom *atom = sptr->atom;
Memory *memory = sptr->memory;
// setup hash
// clear atom map so it can be here as a hash table
// faster than an STL map for large atom counts
atom->map_clear();
// initialize hash
// ncount = number of atoms assigned to me
// key = atom ID
// value = index into Ncount-length data structure
InRvous *in = (InRvous *) inbuf;
std::map<tagint,int> hash;
//std::map<tagint,int> hash;
tagint id;
int ncount = 0;
for (i = 0; i < n; i++)
if (in[i].me >= 0)
hash[in[i].atomID] = ncount++;
//hash[in[i].atomID] = ncount++;
atom->map_one(in[i].atomID,ncount++);
// procowner = caller proc that owns each atom
// atomID = ID of each rendezvous atom I own
@ -1055,7 +1085,8 @@ int Special::rendezvous_trim(int n, char *inbuf,
for (m = 0; m < ncount; m++) npartner[m] = 0;
for (i = 0; i < n; i++) {
m = hash.find(in[i].atomID)->second;
//m = hash.find(in[i].atomID)->second;
m = atom->map(in[i].atomID);
if (in[i].me >= 0) {
procowner[m] = in[i].me;
atomID[m] = in[i].atomID;
@ -1073,7 +1104,8 @@ int Special::rendezvous_trim(int n, char *inbuf,
for (i = 0; i < n; i++) {
if (in[i].me >= 0 || in[i].me == -2) continue;
m = hash.find(in[i].atomID)->second;
//m = hash.find(in[i].atomID)->second;
m = atom->map(in[i].atomID);
partner[m][npartner[m]++] = in[i].partnerID;
}
@ -1090,7 +1122,8 @@ int Special::rendezvous_trim(int n, char *inbuf,
for (i = 0; i < n; i++) {
if (in[i].me != -2) continue;
actual = in[i].partnerID;
m = hash.find(in[i].atomID)->second;
//m = hash.find(in[i].atomID)->second;
m = atom->map(in[i].atomID);
for (j = 0; j < npartner[m]; j++)
if (partner[m][j] == actual) {
flag[m][j] = 1;
@ -1128,6 +1161,12 @@ int Special::rendezvous_trim(int n, char *inbuf,
memory->destroy(partner);
memory->destroy(flag);
// re-create atom map
atom->map_init(0);
atom->nghost = 0;
atom->map_set();
return nout;
}
@ -1150,9 +1189,9 @@ void Special::fix_alteration()
void Special::timer_output(double time1)
{
double t2 = MPI_Wtime();
double time2 = MPI_Wtime();
if (comm->me == 0) {
if (screen) fprintf(screen," special bonds CPU = %g secs\n",t2-t1);
if (logfile) fprintf(logfile," special bonds CPU = %g secs\n",t2-t1);
if (screen) fprintf(screen," special bonds CPU = %g secs\n",time2-time1);
if (logfile) fprintf(logfile," special bonds CPU = %g secs\n",time2-time1);
}
}