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Adding collection array, new user arguments, and multi communication

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This commit is contained in:
Joel Clemmer
2021-02-02 09:39:13 -07:00
parent 2c92737cd5
commit d79a2c3a02
51 changed files with 2109 additions and 697 deletions
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294
src/comm_tiled.cpp
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@ -53,6 +53,7 @@ CommTiled::CommTiled(LAMMPS *lmp) : Comm(lmp)
overlap = nullptr;
rcbinfo = nullptr;
cutghostmulti = nullptr;
cutghostmultiold = nullptr;
init_buffers();
}
@ -81,6 +82,7 @@ CommTiled::~CommTiled()
deallocate_swap(maxswap);
memory->sfree(rcbinfo);
memory->destroy(cutghostmulti);
memory->destroy(cutghostmultiold);
}
/* ----------------------------------------------------------------------
@ -98,7 +100,9 @@ void CommTiled::init_buffers()
overlap = nullptr;
rcbinfo = nullptr;
cutghostmulti = nullptr;
cutghostmultiold = nullptr;
sendbox_multi = nullptr;
sendbox_multiold = nullptr;
maxswap = 6;
allocate_swap(maxswap);
@ -115,9 +119,10 @@ void CommTiled::init()
nswap = 2*domain->dimension;
memory->destroy(cutghostmulti);
if (mode == Comm::MULTI)
memory->create(cutghostmulti,atom->ntypes+1,3,"comm:cutghostmulti");
memory->destroy(cutghostmultiold);
if (mode == Comm::MULTIOLD)
memory->create(cutghostmultiold,atom->ntypes+1,3,"comm:cutghostmultiold");
int bufextra_old = bufextra;
init_exchange();
@ -173,49 +178,62 @@ void CommTiled::setup()
// set cutoff for comm forward and comm reverse
// check that cutoff < any periodic box length
if (mode == Comm::MULTI) {
if (multi_reduce) {
// If using multi/reduce, communicate itype particles a distance equal
// to the max of itype-jtype group interaction
// only consider smaller jtype groups
int igroup, jgroup;
double **cutmultisq = neighbor->cutmultisq;
int *map_type_multi = neighbor->map_type_multi;
for (i = 1; i <= ntypes; i++) {
if (cutusermulti) {
cutghostmulti[i][0] = cutusermulti[i];
cutghostmulti[i][1] = cutusermulti[i];
cutghostmulti[i][2] = cutusermulti[i];
} else {
cutghostmulti[i][0] = 0.0;
cutghostmulti[i][1] = 0.0;
cutghostmulti[i][2] = 0.0;
}
// build collection from scratch as it is needed for atom exchange
neighbor->build_collection(0);
if(cutusermulti and ncollections != neighbor->ncollections)
error->all(FLERR, "Cannot change number of collections after defining comm_modify multi/cutoff");
ncollections = neighbor->ncollections;
// allocate memory for multi-style communication at setup as ncollections can change
if(ncollections_prior != ncollections){
memory->destroy(cutghostmulti);
if (mode == Comm::MULTI)
memory->create(cutghostmulti,ncollections,3,"comm:cutghostmulti");
igroup = map_type_multi[i];
for (j = 1; j <= ntypes; j++){
jgroup = map_type_multi[j];
if(cutmultisq[jgroup][jgroup] > cutmultisq[igroup][igroup]) continue;
cutghostmulti[i][0] = MAX(cutghostmulti[i][0],sqrt(cutmultisq[igroup][jgroup]));
cutghostmulti[i][1] = MAX(cutghostmulti[i][1],sqrt(cutmultisq[igroup][jgroup]));
cutghostmulti[i][2] = MAX(cutghostmulti[i][2],sqrt(cutmultisq[igroup][jgroup]));
}
for(i = 0; i < maxswap; i ++)
grow_swap_send_multi(i,DELTA_PROCS);
ncollections_prior = ncollections;
}
double **cutcollectionsq = neighbor->cutcollectionsq;
// If using multi/reduce, communicate particles a distance equal
// to the max cutoff with equally sized or smaller collections
// If not, communicate the maximum cutoff of the entire collection
for (i = 0; i < ncollections; i++) {
if (cutusermulti) {
cutghostmulti[i][0] = cutusermulti[i];
cutghostmulti[i][1] = cutusermulti[i];
cutghostmulti[i][2] = cutusermulti[i];
} else {
cutghostmulti[i][0] = 0.0;
cutghostmulti[i][1] = 0.0;
cutghostmulti[i][2] = 0.0;
}
} else {
// otherwise, communicate a distance equal to the maximum interaction distance for each type
double *cuttype = neighbor->cuttype;
for (i = 1; i <= ntypes; i++) {
double tmp = 0.0;
if (cutusermulti) tmp = cutusermulti[i];
cutghostmulti[i][0] = MAX(tmp,cuttype[i]);
cutghostmulti[i][1] = MAX(tmp,cuttype[i]);
cutghostmulti[i][2] = MAX(tmp,cuttype[i]);
for (j = 0; j < ncollections; j++){
if(multi_reduce and cutcollectionsq[j][j] > cutcollectionsq[i][i]) continue;
cutghostmulti[i][0] = MAX(cutghostmulti[i][0],sqrt(cutcollectionsq[i][j]));
cutghostmulti[i][1] = MAX(cutghostmulti[i][1],sqrt(cutcollectionsq[i][j]));
cutghostmulti[i][2] = MAX(cutghostmulti[i][2],sqrt(cutcollectionsq[i][j]));
}
}
}
if (mode == Comm::MULTIOLD) {
double *cuttype = neighbor->cuttype;
for (i = 1; i <= ntypes; i++) {
double tmp = 0.0;
if (cutusermultiold) tmp = cutusermultiold[i];
cutghostmultiold[i][0] = MAX(tmp,cuttype[i]);
cutghostmultiold[i][1] = MAX(tmp,cuttype[i]);
cutghostmultiold[i][2] = MAX(tmp,cuttype[i]);
}
}
double cut = get_comm_cutoff();
if ((cut == 0.0) && (me == 0))
@ -233,12 +251,20 @@ void CommTiled::setup()
length2 = h_inv[2];
cutghost[2] = cut * length2;
if (mode == Comm::MULTI) {
for (i = 1; i <= ntypes; i++) {
for (i = 0; i < ncollections; i++) {
cutghostmulti[i][0] *= length0;
cutghostmulti[i][1] *= length1;
cutghostmulti[i][2] *= length2;
}
}
if (mode == Comm::MULTIOLD) {
for (i = 1; i <= ntypes; i++) {
cutghostmultiold[i][0] *= length0;
cutghostmultiold[i][1] *= length1;
cutghostmultiold[i][2] *= length2;
}
}
}
if ((periodicity[0] && cutghost[0] > prd[0]) ||
@ -376,7 +402,7 @@ void CommTiled::setup()
// extend sbox in those lower dims to include ghost atoms
// single mode and multi mode
double oboxlo[3],oboxhi[3],sbox[6],sbox_multi[6];
double oboxlo[3],oboxhi[3],sbox[6],sbox_multi[6],sbox_multiold[6];
if (mode == Comm::SINGLE) {
for (i = 0; i < noverlap; i++) {
@ -465,7 +491,7 @@ void CommTiled::setup()
sbox[5] = MIN(oboxhi[2],hi2[2]);
}
for (int itype = 1; itype <= atom->ntypes; itype++) {
for (int icollection = 0; icollection < ncollections; icollection++) {
sbox_multi[0] = sbox[0];
sbox_multi[1] = sbox[1];
sbox_multi[2] = sbox[2];
@ -476,36 +502,112 @@ void CommTiled::setup()
sbox_multi[idim] = sublo[idim];
if (i < noverlap1)
sbox_multi[3+idim] =
MIN(sbox_multi[3+idim]+cutghostmulti[itype][idim],subhi[idim]);
MIN(sbox_multi[3+idim]+cutghostmulti[icollection][idim],subhi[idim]);
else
sbox_multi[3+idim] =
MIN(sbox_multi[3+idim]-prd[idim]+cutghostmulti[itype][idim],
MIN(sbox_multi[3+idim]-prd[idim]+cutghostmulti[icollection][idim],
subhi[idim]);
} else {
if (i < noverlap1)
sbox_multi[idim] =
MAX(sbox_multi[idim]-cutghostmulti[itype][idim],sublo[idim]);
MAX(sbox_multi[idim]-cutghostmulti[icollection][idim],sublo[idim]);
else
sbox_multi[idim] =
MAX(sbox_multi[idim]+prd[idim]-cutghostmulti[itype][idim],
MAX(sbox_multi[idim]+prd[idim]-cutghostmulti[icollection][idim],
sublo[idim]);
sbox_multi[3+idim] = subhi[idim];
}
if (idim >= 1) {
if (sbox_multi[0] == oboxlo[0])
sbox_multi[0] -= cutghostmulti[itype][idim];
sbox_multi[0] -= cutghostmulti[icollection][idim];
if (sbox_multi[3] == oboxhi[0])
sbox_multi[3] += cutghostmulti[itype][idim];
sbox_multi[3] += cutghostmulti[icollection][idim];
}
if (idim == 2) {
if (sbox_multi[1] == oboxlo[1])
sbox_multi[1] -= cutghostmulti[itype][idim];
sbox_multi[1] -= cutghostmulti[icollection][idim];
if (sbox_multi[4] == oboxhi[1])
sbox_multi[4] += cutghostmulti[itype][idim];
sbox_multi[4] += cutghostmulti[icollection][idim];
}
memcpy(sendbox_multi[iswap][i][itype],sbox_multi,6*sizeof(double));
memcpy(sendbox_multi[iswap][i][icollection],sbox_multi,6*sizeof(double));
}
}
}
if (mode == Comm::MULTIOLD) {
for (i = 0; i < noverlap; i++) {
pbc_flag[iswap][i] = 0;
pbc[iswap][i][0] = pbc[iswap][i][1] = pbc[iswap][i][2] =
pbc[iswap][i][3] = pbc[iswap][i][4] = pbc[iswap][i][5] = 0;
(this->*box_other)(idim,idir,overlap[i],oboxlo,oboxhi);
if (i < noverlap1) {
sbox[0] = MAX(oboxlo[0],lo1[0]);
sbox[1] = MAX(oboxlo[1],lo1[1]);
sbox[2] = MAX(oboxlo[2],lo1[2]);
sbox[3] = MIN(oboxhi[0],hi1[0]);
sbox[4] = MIN(oboxhi[1],hi1[1]);
sbox[5] = MIN(oboxhi[2],hi1[2]);
} else {
pbc_flag[iswap][i] = 1;
if (idir == 0) pbc[iswap][i][idim] = 1;
else pbc[iswap][i][idim] = -1;
if (triclinic) {
if (idim == 1) pbc[iswap][i][5] = pbc[iswap][i][idim];
if (idim == 2) pbc[iswap][i][4] = pbc[iswap][i][3] = pbc[iswap][i][idim];
}
sbox[0] = MAX(oboxlo[0],lo2[0]);
sbox[1] = MAX(oboxlo[1],lo2[1]);
sbox[2] = MAX(oboxlo[2],lo2[2]);
sbox[3] = MIN(oboxhi[0],hi2[0]);
sbox[4] = MIN(oboxhi[1],hi2[1]);
sbox[5] = MIN(oboxhi[2],hi2[2]);
}
for (int itype = 1; itype <= atom->ntypes; itype++) {
sbox_multiold[0] = sbox[0];
sbox_multiold[1] = sbox[1];
sbox_multiold[2] = sbox[2];
sbox_multiold[3] = sbox[3];
sbox_multiold[4] = sbox[4];
sbox_multiold[5] = sbox[5];
if (idir == 0) {
sbox_multiold[idim] = sublo[idim];
if (i < noverlap1)
sbox_multiold[3+idim] =
MIN(sbox_multiold[3+idim]+cutghostmultiold[itype][idim],subhi[idim]);
else
sbox_multiold[3+idim] =
MIN(sbox_multiold[3+idim]-prd[idim]+cutghostmultiold[itype][idim],
subhi[idim]);
} else {
if (i < noverlap1)
sbox_multiold[idim] =
MAX(sbox_multiold[idim]-cutghostmultiold[itype][idim],sublo[idim]);
else
sbox_multiold[idim] =
MAX(sbox_multiold[idim]+prd[idim]-cutghostmultiold[itype][idim],
sublo[idim]);
sbox_multiold[3+idim] = subhi[idim];
}
if (idim >= 1) {
if (sbox_multiold[0] == oboxlo[0])
sbox_multiold[0] -= cutghostmultiold[itype][idim];
if (sbox_multiold[3] == oboxhi[0])
sbox_multiold[3] += cutghostmultiold[itype][idim];
}
if (idim == 2) {
if (sbox_multiold[1] == oboxlo[1])
sbox_multiold[1] -= cutghostmultiold[itype][idim];
if (sbox_multiold[4] == oboxhi[1])
sbox_multiold[4] += cutghostmultiold[itype][idim];
}
memcpy(sendbox_multiold[iswap][i][itype],sbox_multiold,6*sizeof(double));
}
}
}
@ -937,11 +1039,14 @@ void CommTiled::exchange()
void CommTiled::borders()
{
int i,m,n,nlast,nsend,nrecv,ngroup,ncount,ncountall;
int i,m,n,nlast,nsend,nrecv,ngroup,nprior,ncount,ncountall;
double xlo,xhi,ylo,yhi,zlo,zhi;
double *bbox;
double **x;
AtomVec *avec = atom->avec;
// After exchanging, need to reconstruct collection array for border communication
if(mode == Comm::MULTI) neighbor->build_collection(0);
// send/recv max one = max # of atoms in single send/recv for any swap
// send/recv max all = max # of atoms in all sends/recvs within any swap
@ -1008,6 +1113,56 @@ void CommTiled::borders()
smaxone = MAX(smaxone,ncount);
ncountall += ncount;
} else if (mode == Comm::MULTI) {
int* collection=neighbor->collection;
int icollection;
ncount = 0;
if (!bordergroup) {
for (i = 0; i < nlast; i++) {
icollection=collection[i];
bbox = sendbox_multi[iswap][m][icollection];
xlo = bbox[0]; ylo = bbox[1]; zlo = bbox[2];
xhi = bbox[3]; yhi = bbox[4]; zhi = bbox[5];
if (x[i][0] >= xlo && x[i][0] < xhi &&
x[i][1] >= ylo && x[i][1] < yhi &&
x[i][2] >= zlo && x[i][2] < zhi) {
if (ncount == maxsendlist[iswap][m]) grow_list(iswap,m,ncount);
sendlist[iswap][m][ncount++] = i;
}
}
} else {
ngroup = atom->nfirst;
for (i = 0; i < ngroup; i++) {
icollection=collection[i];
bbox = sendbox_multi[iswap][m][icollection];
xlo = bbox[0]; ylo = bbox[1]; zlo = bbox[2];
xhi = bbox[3]; yhi = bbox[4]; zhi = bbox[5];
if (x[i][0] >= xlo && x[i][0] < xhi &&
x[i][1] >= ylo && x[i][1] < yhi &&
x[i][2] >= zlo && x[i][2] < zhi) {
if (ncount == maxsendlist[iswap][m]) grow_list(iswap,m,ncount);
sendlist[iswap][m][ncount++] = i;
}
}
for (i = atom->nlocal; i < nlast; i++) {
icollection=collection[i];
bbox = sendbox_multi[iswap][m][icollection];
xlo = bbox[0]; ylo = bbox[1]; zlo = bbox[2];
xhi = bbox[3]; yhi = bbox[4]; zhi = bbox[5];
if (x[i][0] >= xlo && x[i][0] < xhi &&
x[i][1] >= ylo && x[i][1] < yhi &&
x[i][2] >= zlo && x[i][2] < zhi) {
if (ncount == maxsendlist[iswap][m]) grow_list(iswap,m,ncount);
sendlist[iswap][m][ncount++] = i;
}
}
}
sendnum[iswap][m] = ncount;
smaxone = MAX(smaxone,ncount);
ncountall += ncount;
} else {
int* type=atom->type;
@ -1017,7 +1172,7 @@ void CommTiled::borders()
if (!bordergroup) {
for (i = 0; i < nlast; i++) {
itype=type[i];
bbox = sendbox_multi[iswap][m][itype];
bbox = sendbox_multiold[iswap][m][itype];
xlo = bbox[0]; ylo = bbox[1]; zlo = bbox[2];
xhi = bbox[3]; yhi = bbox[4]; zhi = bbox[5];
if (x[i][0] >= xlo && x[i][0] < xhi &&
@ -1031,7 +1186,7 @@ void CommTiled::borders()
ngroup = atom->nfirst;
for (i = 0; i < ngroup; i++) {
itype=type[i];
bbox = sendbox_multi[iswap][m][itype];
bbox = sendbox_multiold[iswap][m][itype];
xlo = bbox[0]; ylo = bbox[1]; zlo = bbox[2];
xhi = bbox[3]; yhi = bbox[4]; zhi = bbox[5];
if (x[i][0] >= xlo && x[i][0] < xhi &&
@ -1043,7 +1198,7 @@ void CommTiled::borders()
}
for (i = atom->nlocal; i < nlast; i++) {
itype=type[i];
bbox = sendbox_multi[iswap][m][itype];
bbox = sendbox_multiold[iswap][m][itype];
xlo = bbox[0]; ylo = bbox[1]; zlo = bbox[2];
xhi = bbox[3]; yhi = bbox[4]; zhi = bbox[5];
if (x[i][0] >= xlo && x[i][0] < xhi &&
@ -1179,8 +1334,11 @@ void CommTiled::borders()
// increment ghost atoms
n = nrecvproc[iswap];
if (n)
if (n) {
nprior = atom->nghost + atom->nlocal;
atom->nghost += forward_recv_offset[iswap][n-1] + recvnum[iswap][n-1];
if(neighbor->style == Neighbor::MULTI) neighbor->build_collection(nprior);
}
}
// For molecular systems we lose some bits for local atom indices due
@ -2120,6 +2278,7 @@ void CommTiled::allocate_swap(int n)
pbc = new int**[n];
sendbox = new double**[n];
sendbox_multi = new double***[n];
sendbox_multiold = new double***[n];
maxsendlist = new int*[n];
sendlist = new int**[n];
@ -2134,6 +2293,7 @@ void CommTiled::allocate_swap(int n)
pbc[i] = nullptr;
sendbox[i] = nullptr;
sendbox_multi[i] = nullptr;
sendbox_multiold[i] = nullptr;
maxsendlist[i] = nullptr;
sendlist[i] = nullptr;
}
@ -2182,8 +2342,9 @@ void CommTiled::grow_swap_send(int i, int n, int nold)
memory->create(pbc[i],n,6,"comm:pbc_flag");
memory->destroy(sendbox[i]);
memory->create(sendbox[i],n,6,"comm:sendbox");
memory->destroy(sendbox_multi[i]);
memory->create(sendbox_multi[i],n,atom->ntypes+1,6,"comm:sendbox_multi");
grow_swap_send_multi(i,n);
memory->destroy(sendbox_multiold[i]);
memory->create(sendbox_multiold[i],n,atom->ntypes+1,6,"comm:sendbox_multiold");
delete [] maxsendlist[i];
maxsendlist[i] = new int[n];
@ -2215,6 +2376,19 @@ void CommTiled::grow_swap_recv(int i, int n)
size_reverse_send[i] = new int[n];
}
/* ----------------------------------------------------------------------
grow info for swap I for multi as ncollections can change
------------------------------------------------------------------------- */
void CommTiled::grow_swap_send_multi(int i, int n)
{
memory->destroy(sendbox_multi[i]);
if(ncollections > 0)
memory->create(sendbox_multi[i],n,ncollections,6,"comm:sendbox_multi");
}
/* ----------------------------------------------------------------------
deallocate swap info
------------------------------------------------------------------------- */
@ -2243,6 +2417,7 @@ void CommTiled::deallocate_swap(int n)
memory->destroy(pbc[i]);
memory->destroy(sendbox[i]);
memory->destroy(sendbox_multi[i]);
memory->destroy(sendbox_multiold[i]);
delete [] maxsendlist[i];
@ -2265,6 +2440,7 @@ void CommTiled::deallocate_swap(int n)
delete [] pbc;
delete [] sendbox;
delete [] sendbox_multi;
delete [] sendbox_multiold;
delete [] maxsendlist;
delete [] sendlist;