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lammps/src/GPU/pair_table_gpu.cpp
W. Michael Brown 37f22c8627 Misc Improvements to GPU Package 
- Optimizations for molecular systems
-   Improved kernel performance and greater CPU overlap
- Reduced GPU to CPU communications for discrete devices
- Switch classic Intel makefiles to use LLVM-based compilers
- Prefetch optimizations supported for OpenCL
- Optimized data repack for quaternions
2023-03-05 21:03:12 -08:00

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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
LAMMPS development team: developers@lammps.org
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing authors: Trung Dac Nguyen (ORNL)
------------------------------------------------------------------------- */
#include "pair_table_gpu.h"
#include "atom.h"
#include "domain.h"
#include "error.h"
#include "force.h"
#include "gpu_extra.h"
#include "memory.h"
#include "neigh_list.h"
#include "neighbor.h"
#include "suffix.h"
#include <cmath>
using namespace LAMMPS_NS;
// External functions from cuda library for atom decomposition
int table_gpu_init(const int ntypes, double **cutsq, double ***host_table_coeffs,
double **host_table_data, double *special_lj, const int nlocal, const int nall,
const int max_nbors, const int maxspecial, const double cell_size, int &gpu_mode,
FILE *screen, int tabstyle, int ntables, int tablength);
void table_gpu_clear();
int **table_gpu_compute_n(const int ago, const int inum, const int nall, double **host_x,
int *host_type, double *sublo, double *subhi, tagint *tag, int **nspecial,
tagint **special, const bool eflag, const bool vflag, const bool eatom,
const bool vatom, int &host_start, int **ilist, int **jnum,
const double cpu_time, bool &success);
void table_gpu_compute(const int ago, const int inum, const int nall, double **host_x,
int *host_type, int *ilist, int *numj, int **firstneigh, const bool eflag,
const bool vflag, const bool eatom, const bool vatom, int &host_start,
const double cpu_time, bool &success);
double table_gpu_bytes();
/* ---------------------------------------------------------------------- */
PairTableGPU::PairTableGPU(LAMMPS *lmp) : PairTable(lmp), gpu_mode(GPU_FORCE)
{
respa_enable = 0;
reinitflag = 0;
cpu_time = 0.0;
suffix_flag |= Suffix::GPU;
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
}
/* ----------------------------------------------------------------------
free all arrays
------------------------------------------------------------------------- */
PairTableGPU::~PairTableGPU()
{
table_gpu_clear();
}
/* ---------------------------------------------------------------------- */
void PairTableGPU::compute(int eflag, int vflag)
{
ev_init(eflag, vflag);
int nall = atom->nlocal + atom->nghost;
int inum, host_start;
bool success = true;
int *ilist, *numneigh, **firstneigh;
if (gpu_mode != GPU_FORCE) {
double sublo[3], subhi[3];
if (domain->triclinic == 0) {
sublo[0] = domain->sublo[0];
sublo[1] = domain->sublo[1];
sublo[2] = domain->sublo[2];
subhi[0] = domain->subhi[0];
subhi[1] = domain->subhi[1];
subhi[2] = domain->subhi[2];
} else {
domain->bbox(domain->sublo_lamda, domain->subhi_lamda, sublo, subhi);
}
inum = atom->nlocal;
firstneigh =
table_gpu_compute_n(neighbor->ago, inum, nall, atom->x, atom->type, sublo, subhi, atom->tag,
atom->nspecial, atom->special, eflag, vflag, eflag_atom, vflag_atom,
host_start, &ilist, &numneigh, cpu_time, success);
} else {
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
table_gpu_compute(neighbor->ago, inum, nall, atom->x, atom->type, ilist, numneigh, firstneigh,
eflag, vflag, eflag_atom, vflag_atom, host_start, cpu_time, success);
}
if (!success) error->one(FLERR, "Insufficient memory on accelerator");
if (atom->molecular != Atom::ATOMIC && neighbor->ago == 0)
neighbor->build_topology();
if (host_start < inum) {
cpu_time = platform::walltime();
cpu_compute(host_start, inum, eflag, vflag, ilist, numneigh, firstneigh);
cpu_time = platform::walltime() - cpu_time;
}
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairTableGPU::init_style()
{
int ntypes = atom->ntypes;
// Repeat cutsq calculation because done after call to init_style
double maxcut = -1.0;
double cut;
for (int i = 1; i <= atom->ntypes; i++) {
for (int j = i; j <= atom->ntypes; j++) {
if (setflag[i][j] != 0 || (setflag[i][i] != 0 && setflag[j][j] != 0)) {
cut = init_one(i, j);
cut *= cut;
if (cut > maxcut) maxcut = cut;
cutsq[i][j] = cutsq[j][i] = cut;
} else
cutsq[i][j] = cutsq[j][i] = 0.0;
}
}
double cell_size = sqrt(maxcut) + neighbor->skin;
// pack tables and send them to device
double ***table_coeffs = nullptr;
double **table_data = nullptr;
memory->create(table_coeffs, ntypes + 1, ntypes + 1, 6, "table:coeffs");
Table *tb;
for (int i = 1; i <= atom->ntypes; i++)
for (int j = 1; j <= atom->ntypes; j++) {
int n = tabindex[i][j];
tb = &tables[n];
table_coeffs[i][j][0] = n;
table_coeffs[i][j][1] = tb->nshiftbits;
table_coeffs[i][j][2] = tb->nmask;
table_coeffs[i][j][3] = tb->innersq;
table_coeffs[i][j][4] = tb->invdelta;
table_coeffs[i][j][5] = tb->deltasq6;
}
if (tabstyle != BITMAP) {
memory->create(table_data, ntables, 6 * tablength, "table:data");
for (int n = 0; n < ntables; n++) {
tb = &tables[n];
if (tabstyle == LOOKUP) {
for (int k = 0; k < tablength - 1; k++) {
table_data[n][6 * k + 1] = tb->e[k];
table_data[n][6 * k + 2] = tb->f[k];
}
} else if (tabstyle == LINEAR) {
for (int k = 0; k < tablength; k++) {
table_data[n][6 * k + 0] = tb->rsq[k];
table_data[n][6 * k + 1] = tb->e[k];
table_data[n][6 * k + 2] = tb->f[k];
if (k < tablength - 1) {
table_data[n][6 * k + 3] = tb->de[k];
table_data[n][6 * k + 4] = tb->df[k];
}
}
} else if (tabstyle == SPLINE) {
for (int k = 0; k < tablength; k++) {
table_data[n][6 * k + 0] = tb->rsq[k];
table_data[n][6 * k + 1] = tb->e[k];
table_data[n][6 * k + 2] = tb->f[k];
table_data[n][6 * k + 3] = tb->e2[k];
table_data[n][6 * k + 4] = tb->f2[k];
}
}
}
} else {
int ntable = 1 << tablength;
memory->create(table_data, ntables, 6 * ntable, "table:data");
for (int n = 0; n < ntables; n++) {
tb = &tables[n];
for (int k = 0; k < ntable; k++) {
table_data[n][6 * k + 0] = tb->rsq[k];
table_data[n][6 * k + 1] = tb->e[k];
table_data[n][6 * k + 2] = tb->f[k];
table_data[n][6 * k + 3] = tb->de[k];
table_data[n][6 * k + 4] = tb->df[k];
table_data[n][6 * k + 5] = tb->drsq[k];
}
}
}
int maxspecial = 0;
if (atom->molecular != Atom::ATOMIC) maxspecial = atom->maxspecial;
int mnf = 5e-2 * neighbor->oneatom;
int success = table_gpu_init(atom->ntypes + 1, cutsq, table_coeffs, table_data, force->special_lj,
atom->nlocal, atom->nlocal + atom->nghost, mnf, maxspecial,
cell_size, gpu_mode, screen, tabstyle, ntables, tablength);
GPU_EXTRA::check_flag(success, error, world);
if (gpu_mode == GPU_FORCE) neighbor->add_request(this, NeighConst::REQ_FULL);
memory->destroy(table_coeffs);
memory->destroy(table_data);
}
/* ---------------------------------------------------------------------- */
double PairTableGPU::memory_usage()
{
double bytes = Pair::memory_usage();
return bytes + table_gpu_bytes();
}
/* ---------------------------------------------------------------------- */
void PairTableGPU::cpu_compute(int start, int inum, int eflag, int /* vflag */, int *ilist,
int *numneigh, int **firstneigh)
{
int i, j, ii, jj, jnum, itype, jtype, itable;
double xtmp, ytmp, ztmp, delx, dely, delz, evdwl, fpair;
double rsq, factor_lj, fraction, value, a, b;
int *jlist;
Table *tb;
union_int_float_t rsq_lookup;
int tlm1 = tablength - 1;
double **x = atom->x;
double **f = atom->f;
int *type = atom->type;
double *special_lj = force->special_lj;
// loop over neighbors of my atoms
for (ii = start; ii < inum; ii++) {
i = ilist[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
factor_lj = special_lj[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx * delx + dely * dely + delz * delz;
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
tb = &tables[tabindex[itype][jtype]];
if (rsq < tb->innersq) error->one(FLERR, "Pair distance < table inner cutoff");
if (tabstyle == LOOKUP) {
itable = static_cast<int>((rsq - tb->innersq) * tb->invdelta);
if (itable >= tlm1) error->one(FLERR, "Pair distance > table outer cutoff");
fpair = factor_lj * tb->f[itable];
} else if (tabstyle == LINEAR) {
itable = static_cast<int>((rsq - tb->innersq) * tb->invdelta);
if (itable >= tlm1) error->one(FLERR, "Pair distance > table outer cutoff");
fraction = (rsq - tb->rsq[itable]) * tb->invdelta;
value = tb->f[itable] + fraction * tb->df[itable];
fpair = factor_lj * value;
} else if (tabstyle == SPLINE) {
itable = static_cast<int>((rsq - tb->innersq) * tb->invdelta);
if (itable >= tlm1) error->one(FLERR, "Pair distance > table outer cutoff");
b = (rsq - tb->rsq[itable]) * tb->invdelta;
a = 1.0 - b;
value = a * tb->f[itable] + b * tb->f[itable + 1] +
((a * a * a - a) * tb->f2[itable] + (b * b * b - b) * tb->f2[itable + 1]) *
tb->deltasq6;
fpair = factor_lj * value;
} else {
rsq_lookup.f = rsq;
itable = rsq_lookup.i & tb->nmask;
itable >>= tb->nshiftbits;
fraction = (rsq_lookup.f - tb->rsq[itable]) * tb->drsq[itable];
value = tb->f[itable] + fraction * tb->df[itable];
fpair = factor_lj * value;
}
f[i][0] += delx * fpair;
f[i][1] += dely * fpair;
f[i][2] += delz * fpair;
if (eflag) {
if (tabstyle == LOOKUP)
evdwl = tb->e[itable];
else if (tabstyle == LINEAR || tabstyle == BITMAP)
evdwl = tb->e[itable] + fraction * tb->de[itable];
else
evdwl = a * tb->e[itable] + b * tb->e[itable + 1] +
((a * a * a - a) * tb->e2[itable] + (b * b * b - b) * tb->e2[itable + 1]) *
tb->deltasq6;
evdwl *= factor_lj;
}
if (evflag) ev_tally_full(i, evdwl, 0.0, fpair, delx, dely, delz);
}
}
}
}
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