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Added pair style sph/lj/gpu in src/GPU, removed commented codes

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This commit is contained in:
Trung Nguyen
2023-12-07 14:33:47 -06:00
parent e51a8ccfbf
commit 6fe16c7606
6 changed files with 269 additions and 30 deletions
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8
lib/gpu/lal_amoeba.cpp
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@ -281,13 +281,7 @@ int AmoebaT::polar_real(const int eflag, const int vflag) {
const int BX=this->block_size();
const int GX=static_cast<int>(ceil(static_cast<double>(ainum)/(BX/this->_threads_per_atom)));
/*
const int cus = this->device->gpu->cus();
while (GX < cus && GX > 1) {
BX /= 2;
GX=static_cast<int>(ceil(static_cast<double>(ainum)/(BX/this->_threads_per_atom)));
}
*/
this->time_pair.start();
// Build the short neighbor list if not done yet

8
lib/gpu/lal_hippo.cpp
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@ -603,13 +603,7 @@ int HippoT::polar_real(const int eflag, const int vflag) {
const int BX=this->block_size();
const int GX=static_cast<int>(ceil(static_cast<double>(ainum)/(BX/this->_threads_per_atom)));
/*
const int cus = this->device->gpu->cus();
while (GX < cus && GX > 1) {
BX /= 2;
GX=static_cast<int>(ceil(static_cast<double>(ainum)/(BX/this->_threads_per_atom)));
}
*/
this->time_pair.start();
// Build the short neighbor list if not done yet

6
lib/gpu/lal_sph_lj.cpp
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@ -107,7 +107,7 @@ int SPHLJT::init(const int ntypes,
ef_nall=2000;
_max_drhoE_size=static_cast<int>(static_cast<double>(ef_nall)*1.10);
drhoE.alloc(_max_drhoE_size,*(this->ucl_device),UCL_READ_WRITE,UCL_READ_WRITE);
drhoE.alloc(_max_drhoE_size*2,*(this->ucl_device),UCL_READ_WRITE,UCL_READ_WRITE);
_allocated=true;
this->_max_bytes=coeff.row_bytes()+drhoE.row_bytes()+sp_lj.row_bytes();
@ -134,7 +134,7 @@ double SPHLJT::host_memory_usage() const {
template <class numtyp, class acctyp>
void SPHLJT::update_drhoE(void **drhoE_ptr) {
*drhoE_ptr=drhoE.host.begin();
drhoE.update_host(_max_drhoE_size,false);
drhoE.update_host(_max_drhoE_size*2,false);
}
// ---------------------------------------------------------------------------
@ -148,7 +148,7 @@ int SPHLJT::loop(const int eflag, const int vflag) {
// Resize drhoE array if necessary
if (nall > _max_drhoE_size) {
_max_drhoE_size=static_cast<int>(static_cast<double>(nall)*1.10);
drhoE.resize(_max_drhoE_size);
drhoE.resize(_max_drhoE_size*2);
}
// signal that we need to transfer extra data from the host

30
lib/gpu/lal_sph_lj_ext.cpp
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@ -94,13 +94,15 @@ void sph_lj_gpu_clear() {
int ** sph_lj_gpu_compute_n(const int ago, const int inum_full, const int nall,
double **host_x, int *host_type, double *sublo,
double *subhi, tagint *tag, int **nspecial,
double *subhi, 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,
double **host_v, const double dtinvsqrt,
const int seed, const int timestep,
double *boxlo, double *prd) {
double **host_v, double *boxlo, double *prd) {
double dtinvsqrt = 1.0;
int seed = 0;
int timestep = 0;
tagint* tag = nullptr;
return SPHLJMF.compute(ago, inum_full, nall, host_x, host_type, sublo,
subhi, tag, nspecial, special, eflag, vflag, eatom,
vatom, host_start, ilist, jnum, cpu_time, success,
@ -108,16 +110,18 @@ int ** sph_lj_gpu_compute_n(const int ago, const int inum_full, const int nall,
}
void sph_lj_gpu_compute(const int ago, const int inum_full, 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, tagint *tag,
double **host_v, const double dtinvsqrt,
const int seed, const int timestep,
const int nlocal, double *boxlo, double *prd) {
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 **host_v, const int nlocal, double *boxlo, double *prd) {
double dtinvsqrt = 1.0;
int seed = 0;
int timestep = 0;
tagint* tag = nullptr;
SPHLJMF.compute(ago, inum_full, nall, host_x, host_type, ilist, numj,
firstneigh, eflag, vflag, eatom, vatom, host_start, cpu_time, success,
tag, host_v, dtinvsqrt, seed, timestep, nlocal, boxlo, prd);
firstneigh, eflag, vflag, eatom, vatom, host_start, cpu_time, success,
tag, host_v, dtinvsqrt, seed, timestep, nlocal, boxlo, prd);
}
void sph_lj_gpu_get_extra_data(double *host_rho, double *host_esph,

199
src/GPU/pair_sph_lj_gpu.cpp Normal file
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@ -0,0 +1,199 @@
/* ----------------------------------------------------------------------
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 author: Trung Dac Nguyen (U Chicago)
------------------------------------------------------------------------- */
#include "pair_sph_lj_gpu.h"
#include "atom.h"
#include "domain.h"
#include "error.h"
#include "force.h"
#include "gpu_extra.h"
#include "info.h"
#include "neigh_list.h"
#include "neighbor.h"
#include "suffix.h"
#include "update.h"
#include <cmath>
using namespace LAMMPS_NS;
// External functions from cuda library for atom decomposition
int sph_lj_gpu_init(const int ntypes, double **cutsq, double** host_cut,
double **host_viscosity, double *special_lj,
const int inum, const int nall,
const int max_nbors, const int maxspecial,
const double cell_size, int &gpu_mode, FILE *screen);
void sph_lj_gpu_clear();
int **sph_lj_gpu_compute_n(const int ago, const int inum_full, const int nall, double **host_x,
int *host_type, double *sublo, double *subhi, 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, double **host_v,
double *boxlo, double *prd);
void sph_lj_gpu_compute(const int ago, const int inum_full, 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 **host_v,
const int nlocal, double *boxlo, double *prd);
void sph_lj_gpu_get_extra_data(double *host_rho, double *host_esph,
double *host_cv, double *host_mass);
void sph_lj_gpu_update_drhoE(void **drhoE_ptr);
double sph_lj_gpu_bytes();
/* ---------------------------------------------------------------------- */
PairSPHLJGPU::PairSPHLJGPU(LAMMPS *lmp) : PairSPHLJ(lmp), gpu_mode(GPU_FORCE)
{
drhoE_pinned = nullptr;
respa_enable = 0;
reinitflag = 0;
cpu_time = 0.0;
suffix_flag |= Suffix::GPU;
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
}
/* ----------------------------------------------------------------------
free all arrays
------------------------------------------------------------------------- */
PairSPHLJGPU::~PairSPHLJGPU()
{
sph_lj_gpu_clear();
}
/* ---------------------------------------------------------------------- */
void PairSPHLJGPU::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;
double *rho = atom->rho;
double *esph = atom->esph;
double *cv = atom->cv;
double *mass = atom->mass;
sph_lj_gpu_get_extra_data(rho, esph, cv, mass);
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 = sph_lj_gpu_compute_n(
neighbor->ago, inum, nall, atom->x, atom->type, sublo, subhi, atom->nspecial,
atom->special, eflag, vflag, eflag_atom, vflag_atom, host_start, &ilist, &numneigh,
cpu_time, success, atom->v, domain->boxlo, domain->prd);
} else {
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
sph_lj_gpu_compute(neighbor->ago, inum, nall, atom->x, atom->type, ilist, numneigh, firstneigh,
eflag, vflag, eflag_atom, vflag_atom, host_start, cpu_time, success,
atom->v, atom->nlocal, domain->boxlo, domain->prd);
}
if (!success) error->one(FLERR, "Insufficient memory on accelerator");
// get the drho and dE from device
double *drho = atom->drho;
double *desph = atom->desph;
sph_lj_gpu_update_drhoE(&drhoE_pinned);
int nlocal = atom->nlocal;
if (acc_float) {
auto drhoE_ptr = (float *)drhoE_pinned;
int idx = 0;
for (int i = 0; i < nlocal; i++) {
drho[i] = drhoE_ptr[idx];
desph[i] = drhoE_ptr[idx+1];
idx += 2;
}
} else {
auto drhoE_ptr = (double *)drhoE_pinned;
int idx = 0;
for (int i = 0; i < nlocal; i++) {
drho[i] = drhoE_ptr[idx];
desph[i] = drhoE_ptr[idx+1];
idx += 2;
}
}
if (atom->molecular != Atom::ATOMIC && neighbor->ago == 0)
neighbor->build_topology();
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairSPHLJGPU::init_style()
{
// Repeat cutsq calculation because done after call to init_style
double maxcut = -1.0;
double mcut;
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)) {
mcut = init_one(i, j);
mcut *= mcut;
if (mcut > maxcut) maxcut = mcut;
cutsq[i][j] = cutsq[j][i] = mcut;
} else
cutsq[i][j] = cutsq[j][i] = 0.0;
}
}
double cell_size = sqrt(maxcut) + neighbor->skin;
int maxspecial = 0;
if (atom->molecular != Atom::ATOMIC) maxspecial = atom->maxspecial;
int mnf = 5e-2 * neighbor->oneatom;
int success =
sph_lj_gpu_init(atom->ntypes + 1, cutsq, cut, viscosity,
force->special_lj, atom->nlocal, atom->nlocal + atom->nghost,
mnf, maxspecial, cell_size, gpu_mode, screen);
GPU_EXTRA::check_flag(success, error, world);
acc_float = Info::has_accelerator_feature("GPU", "precision", "single");
if (gpu_mode == GPU_FORCE) neighbor->add_request(this, NeighConst::REQ_FULL);
}
/* ---------------------------------------------------------------------- */
double PairSPHLJGPU::memory_usage()
{
double bytes = Pair::memory_usage();
return bytes + sph_lj_gpu_bytes();
}

48
src/GPU/pair_sph_lj_gpu.h Normal file
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@ -0,0 +1,48 @@
/* -*- c++ -*- ----------------------------------------------------------
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.
------------------------------------------------------------------------- */
#ifdef PAIR_CLASS
// clang-format off
PairStyle(sph/lj/gpu,PairSPHLJGPU);
// clang-format on
#else
#ifndef LMP_PAIR_SPH_LJ_GPU_H
#define LMP_PAIR_SPH_LJ_GPU_H
#include "pair_sph_lj.h"
namespace LAMMPS_NS {
class PairSPHLJGPU : public PairSPHLJ {
public:
PairSPHLJGPU(LAMMPS *lmp);
~PairSPHLJGPU() override;
void cpu_compute(int, int, int, int, int *, int *, int **);
void compute(int, int) override;
void init_style() override;
double memory_usage() override;
enum { GPU_FORCE, GPU_NEIGH, GPU_HYB_NEIGH };
void *drhoE_pinned;
bool acc_float;
private:
int gpu_mode;
double cpu_time;
};
} // namespace LAMMPS_NS
#endif
#endif