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Made some progress with fphi_uind in the gpu pair style

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This commit is contained in:
Trung Nguyen
2022-09-09 12:14:36 -05:00
parent a0af9627e5
commit 4b8caac727
5 changed files with 114 additions and 69 deletions
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93
lib/gpu/lal_base_amoeba.cpp
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@ -555,7 +555,7 @@ void BaseAmoebaT::compute_umutual2b(int *host_amtype, int *host_amgroup, double
// Prepare for umutual1() after bspline_fill() is done on host
// - reallocate per-atom arrays, thetai1, thetai2, thetai3, and igrid if needed
// host_thetai1, host_thetai2, host_thetai3 are allocated with nmax by bsordermax by 4
// host_igrid is allocated with nmax by by 4
// host_igrid is allocated with nmax by 4
// - transfer extra data from host to device
// ---------------------------------------------------------------------------
@ -563,8 +563,9 @@ template <class numtyp, class acctyp>
void BaseAmoebaT::precompute_induce(const int inum_full, const int bsorder,
double ***host_thetai1, double ***host_thetai2,
double ***host_thetai3, int** host_igrid,
double* host_grid_brick_start, int nzlo_out,
int nzhi_out, int nylo_out, int nyhi_out,
double* host_grid_brick_start, double**** host_grid_brick,
int nzlo_out, int nzhi_out,
int nylo_out, int nyhi_out,
int nxlo_out, int nxhi_out) {
_bsorder = bsorder;
@ -599,7 +600,7 @@ void BaseAmoebaT::precompute_induce(const int inum_full, const int bsorder,
}
UCL_H_Vec<double> dview;
dview.alloc(inum_full*bsorder*4,*(this->ucl_device));
dview.alloc(_max_thetai_size*bsorder*4,*(this->ucl_device));
// pack host data to device
@ -634,7 +635,7 @@ void BaseAmoebaT::precompute_induce(const int inum_full, const int bsorder,
ucl_copy(_thetai3,dview,false);
UCL_H_Vec<int> dview_int;
dview_int.alloc(inum_full*4, *(this->ucl_device));
dview_int.alloc(_max_thetai_size*4, *(this->ucl_device));
for (int i = 0; i < inum_full; i++) {
int idx = i*4;
dview_int[idx+0] = host_igrid[i][0];
@ -643,6 +644,33 @@ void BaseAmoebaT::precompute_induce(const int inum_full, const int bsorder,
}
ucl_copy(_igrid, dview_int, false);
}
// ---------------------------------------------------------------------------
// fphi_uind = induced potential from grid
// fphi_uind extracts the induced dipole potential from the particle mesh Ewald grid
// ---------------------------------------------------------------------------
template <class numtyp, class acctyp>
void BaseAmoebaT::compute_fphi_uind(const int inum_full, const int bsorder,
double ***host_thetai1, double ***host_thetai2,
double ***host_thetai3, int** igrid,
double *host_grid_brick_start, double ****host_grid_brick,
void** host_fdip_phi1, void **host_fdip_phi2, void **host_fdip_sum_phi,
int nzlo_out, int nzhi_out, int nylo_out, int nyhi_out,
int nxlo_out, int nxhi_out, bool& first_iteration)
{
// allocation/resize and transfers before the first iteration
if (first_iteration) {
precompute_induce(inum_full, bsorder, host_thetai1, host_thetai2, host_thetai3,
igrid, host_grid_brick_start, host_grid_brick, nzlo_out, nzhi_out,
nylo_out, nyhi_out, nxlo_out, nxhi_out);
if (first_iteration) first_iteration = false;
}
// update the cgrid_brick with data host
_nzlo_out = nzlo_out;
@ -656,36 +684,27 @@ void BaseAmoebaT::precompute_induce(const int inum_full, const int bsorder,
_ngridx = nxhi_out - nxlo_out + 1;
_num_grid_points = _ngridx * _ngridy * _ngridz;
UCL_H_Vec<double> dview_cgrid;
dview_cgrid.view(host_grid_brick_start, _num_grid_points*2, *(this->ucl_device));
UCL_H_Vec<double> hview_cgrid;
hview_cgrid.alloc(_num_grid_points*2, *(this->ucl_device), UCL_READ_WRITE);
int n = 0;
for (int iz = nzlo_out; iz <= nzhi_out; iz++)
for (int iy = nylo_out; iy <= nyhi_out; iy++)
for (int ix = nxlo_out; ix <= nxhi_out; ix++) {
/*
if (iz == nzlo_out && iy == nylo_out && ix == nxlo_out) {
printf("origin = %d %d %d: grid = %f %f %f\n", iz, iy, ix, host_grid_brick[iz][iy][ix][0], host_grid_brick[iz][iy][ix][1]);
}
if (iz == -2 && iy == 4 && ix == 8) printf("ixyz = %d %d %d: grid = %f %f %f; n = %d\n", iz, iy, ix, host_grid_brick[iz][iy][ix][0], host_grid_brick[iz][iy][ix][1], n);
*/
hview_cgrid[n] = host_grid_brick[iz][iy][ix][0];
hview_cgrid[n+1] = host_grid_brick[iz][iy][ix][1];
n += 2;
}
//hview_cgrid.view(host_grid_brick_start, _num_grid_points*2, *(this->ucl_device));
_cgrid_brick.alloc(_num_grid_points*2, *(this->ucl_device), UCL_READ_ONLY);
ucl_copy(_cgrid_brick,dview_cgrid,false);
ucl_copy(_cgrid_brick,hview_cgrid,false);
}
// ---------------------------------------------------------------------------
// fphi_uind = induced potential from grid
// fphi_uind extracts the induced dipole potential from the particle mesh Ewald grid
// ---------------------------------------------------------------------------
template <class numtyp, class acctyp>
void BaseAmoebaT::compute_fphi_uind(const int inum_full, const int bsorder,
double ***host_thetai1, double ***host_thetai2,
double ***host_thetai3, int** igrid,
double *host_grid_brick_start, void** host_fdip_phi1,
void **host_fdip_phi2, void **host_fdip_sum_phi,
int nzlo_out, int nzhi_out, int nylo_out, int nyhi_out,
int nxlo_out, int nxhi_out, bool& first_iteration)
{
// allocation/resize and transfers before the first iteration
if (first_iteration) {
precompute_induce(inum_full, bsorder, host_thetai1, host_thetai2, host_thetai3,
igrid, host_grid_brick_start, nzlo_out, nzhi_out,
nylo_out, nyhi_out, nxlo_out, nxhi_out);
if (first_iteration) first_iteration = false;
}
const int red_blocks = fphi_uind();
_fdip_phi1.update_host(_max_thetai_size*10);
@ -711,16 +730,16 @@ int BaseAmoebaT::fphi_uind() {
// Compute the block size and grid size to keep all cores busy
const int BX=block_size();
int GX=static_cast<int>(ceil(static_cast<double>(ans->inum())/
(BX/_threads_per_atom)));
int GX=static_cast<int>(ceil(static_cast<double>(this->ans->inum())/BX));
time_pair.start();
int ngridyz = _ngridy * _ngridz;
int ngridxy = _ngridx * _ngridy;
k_fphi_uind.set_size(GX,BX);
k_fphi_uind.run(&atom->x, &_thetai1, &_thetai2, &_thetai3,
&_igrid, &_cgrid_brick, &_fdip_phi1, &_fdip_phi2,
&_fdip_sum_phi, &_bsorder, &ainum, &ngridyz, &_ngridy,
&_threads_per_atom);
&_fdip_sum_phi, &_bsorder, &ainum,
&_nzlo_out, &_nzhi_out, &_nylo_out, &_nyhi_out,
&_nxlo_out, &_nxhi_out, &ngridxy, &_ngridx);
time_pair.stop();
return GX;