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

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This commit is contained in:
Steve Plimpton
2018-11-30 13:06:31 -07:00
committed by Axel Kohlmeyer
parent 9912c44413
commit 3f9d59294e
5 changed files with 92 additions and 37 deletions
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89
src/special.cpp
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@ -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);
}
}