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rLAMMPS lammps
lj_gpu.cu
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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
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: Mike Brown (SNL), wmbrown@sandia.gov
Peng Wang (Nvidia), penwang@nvidia.com
Paul Crozier (SNL), pscrozi@sandia.gov
------------------------------------------------------------------------- */
#include <iostream>
#include <cassert>
#include <string.h>
#include "cudatimer.h"
#include "lj_tex.h"
#include "neigh.h"
#include "cell.h"
#include "lj_gpu_kernel.h"
#ifdef WINDLL
#define EXTERN extern "C" __declspec(dllexport)
#else
#define EXTERN
#endif
static float h_boxlo[3], h_boxhi[3];
static float cell_size;
static float *energy = NULL, *d_energy = NULL;
static float3 *d_force = NULL, *f_temp = NULL, *v_temp = NULL, *d_virial = NULL;
static float4 *d_pos = NULL, *temp_pos = NULL;
static int *d_type = NULL;
static int ncellx, ncelly, ncellz;
static neigh_list_gpu d_neigh_list;
static cell_list_gpu d_cell_list;
#define TIMING(x)
// ---------------------------------------------------------------------------
// Return string with GPU info
// ---------------------------------------------------------------------------
EXTERN void lj_gpu_name(const int id, const int max_nbors, char * name)
{
struct cudaDeviceProp prop;
CUDA_SAFE_CALL( cudaGetDeviceProperties(&prop, id) );
#ifdef _WIN32
strcpy_s(name, strlen(prop.name)+1, prop.name);
#else
strncpy(name, prop.name, strlen(prop.name)+1);
#endif
}
// ---------------------------------------------------------------------------
// Allocate memory on host and device and copy constants to device
// ---------------------------------------------------------------------------
EXTERN bool lj_gpu_init(int &ij_size, const int ntypes,
double **cutsq,double **sigma,
double **epsilon, double **host_lj1, double **host_lj2,
double **host_lj3, double **host_lj4, double **offset,
double *special_lj, double *boxlo, double *boxhi,
double cellsize, double skin,
const int max_nbors, const int gpu_id)
{
int num_devices;
/* get device count */
CUDA_SAFE_CALL( cudaGetDeviceCount(&num_devices) );
if (num_devices == 0) {
printf("NO CUDA-capable GPU detected.\n");
exit(1);
}
if (gpu_id > num_devices) {
printf("gpu_id %d is larger than the number of GPUs %d\n",
gpu_id, num_devices);
exit(1);
}
/* set CUDA device to the specified GPU */
cudaThreadExit();
CUDA_SAFE_CALL( cudaSetDevice(gpu_id) );
ij_size=0;
cell_size = cellsize;
ncellx = ceil(((boxhi[0] - boxlo[0]) + 2.0*cell_size) / cell_size);
ncelly = ceil(((boxhi[1] - boxlo[1]) + 2.0*cell_size) / cell_size);
ncellz = ceil(((boxhi[2] - boxlo[2]) + 2.0*cell_size) / cell_size);
for (int i = 0; i < 3; i++) {
h_boxhi[i] = boxhi[i];
h_boxlo[i] = boxlo[i];
}
init_force_const(ntypes, cutsq, host_lj1, host_lj2, host_lj3, host_lj4, offset);
init_cell_list_const(cellsize, skin, boxlo, boxhi);
return true;
}
// ---------------------------------------------------------------------------
// Clear memory on host and device
// ---------------------------------------------------------------------------
EXTERN void lj_gpu_clear() {
free(energy);
free(v_temp);
CUDA_SAFE_CALL( cudaFreeHost(f_temp) );
if (d_force) CUDA_SAFE_CALL( cudaFree(d_force) );
if (d_energy) CUDA_SAFE_CALL( cudaFree(d_energy) );
if (d_virial) CUDA_SAFE_CALL( cudaFree(d_virial) );
if (d_pos) CUDA_SAFE_CALL( cudaFree(d_pos) );
if (d_type) CUDA_SAFE_CALL( cudaFree(d_type) );
if (temp_pos) CUDA_SAFE_CALL( cudaFreeHost(temp_pos) );
clear_neigh_list_gpu(d_neigh_list);
clear_cell_list_gpu(d_cell_list);
if (useCache) {
unbind_pos();
unbind_type();
}
//LJMF.clear();
}
template <class numtyp, class acctyp>
double _lj_gpu_neigh(double **force, double *virial,
double **host_x, int *host_type, const int inum,
const int nall, const int ago, const bool eflag, const bool vflag,
const double *boxlo, const double *boxhi)
{
double evdwl=0.0;
static int first_call = 1;
TIMING( static CUDATimer cuTimer );
TIMING( static CTimer cTimer );
TIMING( static CTimer cTimer2 );
double *atom_pos = host_x[0];
static int szTailList = inum*32;
TIMING( cTimer.Start() );
TIMING( cTimer2.Start() );
/* MPI communication just happened, reallocate space using new inum & nall
FIXME: this is costly: ~ total kernel time! Use a DIY GPU memory allocator.*/
if (first_call || ago == 0) {
if (!first_call) {
if (useCache) {
unbind_pos();
unbind_type();
}
CUDA_SAFE_CALL( cudaFree(d_force) );
CUDA_SAFE_CALL( cudaFree(d_energy) );
CUDA_SAFE_CALL( cudaFree(d_virial) );
CUDA_SAFE_CALL( cudaFree(d_pos) );
CUDA_SAFE_CALL( cudaFree(d_type) );
clear_neigh_list_gpu(d_neigh_list);
CUDA_SAFE_CALL( cudaFreeHost(f_temp) );
CUDA_SAFE_CALL( cudaFreeHost(temp_pos) );
free(energy);
free(v_temp);
}
CUDA_SAFE_CALL( cudaMalloc((void**)&d_force, inum*sizeof(float3)) );
CUDA_SAFE_CALL( cudaMalloc((void**)&d_energy, inum*sizeof(float)) );
CUDA_SAFE_CALL( cudaMalloc((void**)&d_virial, inum*3*sizeof(float3)) );
CUDA_SAFE_CALL( cudaMalloc((void**)&d_pos, nall*sizeof(float4)) );
CUDA_SAFE_CALL( cudaMalloc((void**)&d_type, nall*sizeof(int)) );
init_neigh_list_gpu(d_neigh_list, inum, NEIGH_BIN_SIZE, szTailList);
CUDA_SAFE_CALL( cudaMallocHost((void**)&temp_pos, nall*sizeof(float4)) );
CUDA_SAFE_CALL( cudaMallocHost((void**)&f_temp, inum*sizeof(float3)) );
energy = (float*) malloc(inum*sizeof(float));
v_temp = (float3*)malloc(inum*2*sizeof(float3));
if (useCache) {
bind_pos(d_pos, nall);
bind_type(d_type, nall);
}
first_call = 0;
CUDA_SAFE_CALL( cudaThreadSynchronize() );
CUDA_SAFE_CALL( cudaGetLastError() );
CUDA_SAFE_CALL( cudaMemcpy(d_type, host_type, nall*sizeof(int),
cudaMemcpyHostToDevice) );
}
TIMING( static double mallocTime = 0. );
TIMING( mallocTime += cTimer2.GetET() );
TIMING( printf("malloc time = %f ms\n", mallocTime*1e3) );
TIMING( cTimer2.Start() );
for (int i = 0; i < 3*nall; i+=3) {
temp_pos[i/3] = make_float4(atom_pos[i], atom_pos[i+1], atom_pos[i+2], 0.f);
}
TIMING( static double copyTime = 0. );
TIMING( copyTime += cTimer2.GetET() );
TIMING( printf("position copy time = %f ms\n", copyTime*1e3) );
TIMING( cTimer2.Start() );
CUDA_SAFE_CALL( cudaMemcpy(d_pos, temp_pos, nall*sizeof(float4), cudaMemcpyHostToDevice) );
TIMING( static double h2dTime = 0. );
TIMING( h2dTime += cTimer2.GetET() );
TIMING( printf("h2d copy time = %f ms\n", h2dTime*1e3) );
TIMING( cTimer2.Start() );
if (ago == 0) {
build_neigh_list_gpu(d_pos,
d_neigh_list,
h_boxlo, h_boxhi, cell_size,
inum, nall);
}
TIMING( static double neighTime = 0. );
TIMING( neighTime += cTimer2.GetET() );
TIMING( printf("Neigh List time = %f ms\n", neighTime*1e3) );
TIMING( cTimer2.Start() );
calc_lj_neigh_gpu(d_force, d_energy, d_virial,
d_pos, d_type,
d_neigh_list,
inum, nall,
eflag, vflag);
TIMING( static double forceTime = 0. );
TIMING( forceTime += cTimer2.GetET() );
TIMING( printf("Force time = %f ms\n", forceTime*1e3) );
TIMING( printf("GPU kernel time = %f ms\n", (forceTime + neighTime)*1e3) );
TIMING( cTimer2.Start() );
CUDA_SAFE_CALL( cudaMemcpy(f_temp, d_force, inum*sizeof(float3), cudaMemcpyDeviceToHost) );
TIMING( static double d2hTime = 0. );
TIMING( d2hTime += cTimer2.GetET() );
TIMING( printf("d2h copy time = %f ms\n", d2hTime*1e3) );
TIMING( printf("GPU-CPU data transfer time = %f ms\n", (h2dTime+d2hTime)*1e3) );
TIMING( cTimer2.Start() );
for (int i = 0; i < inum; i++) {
force[i][0] += f_temp[i].x;
force[i][1] += f_temp[i].y;
force[i][2] += f_temp[i].z;
}
if (eflag) {
CUDA_SAFE_CALL( cudaMemcpy(energy, d_energy,
inum*sizeof(float), cudaMemcpyDeviceToHost) );
for (int i = 0; i < inum; i++) {
evdwl += energy[i];
}
evdwl *= 0.5f;
}
if (vflag) {
CUDA_SAFE_CALL( cudaMemcpy(v_temp, d_virial, inum*2*sizeof(float3),
cudaMemcpyDeviceToHost) );
for (int i = 0; i < inum; i++) {
virial[0] += v_temp[2*i].x;
virial[1] += v_temp[2*i].y;
virial[2] += v_temp[2*i].z;
virial[3] += v_temp[2*i+1].x;
virial[4] += v_temp[2*i+1].y;
virial[5] += v_temp[2*i+1].z;
}
for (int i = 0; i < 6; i++)
virial[i] *= 0.5f;
}
TIMING( static double postTime = 0. );
TIMING( postTime += cTimer2.GetET() );
TIMING( printf("postprocess Time = %f ms\n", postTime*1e3) );
TIMING( printf("Data process time = %f ms\n", (postTime+copyTime)*1e3) );
TIMING( static double totalTime = 0. );
TIMING( totalTime += cTimer.GetET() );
TIMING( printf("lj_gpu time = %f ms\n", totalTime*1e3) );
return evdwl;
}
EXTERN double lj_gpu_neigh(double **force, double *virial,
double **host_x, int *host_type,
const int inum, const int nall,
const int ago, const bool eflag, const bool vflag,
const double *boxlo, const double *boxhi)
{
return _lj_gpu_neigh<float,float>(force, virial,
host_x, host_type, inum, nall,
ago, eflag, vflag, boxlo, boxhi);
}
template <class numtyp, class acctyp>
double _lj_gpu_cell(double **force, double *virial,
double **host_x, int *host_type, const int inum,
const int nall, const int ago,
const bool eflag, const bool vflag,
const double *boxlo, const double *boxhi)
{
double evdwl=0.0;
static int ncell = ncellx*ncelly*ncellz;
static int first_call = 1;
// allocate memory on CPU and GPU
if (first_call || ago == 0) {
if (!first_call) {
if (useCache) {
unbind_pos();
unbind_type();
}
free(energy);
free(v_temp);
CUDA_SAFE_CALL( cudaFree(d_force) );
CUDA_SAFE_CALL( cudaFree(d_energy) );
CUDA_SAFE_CALL( cudaFree(d_virial) );
CUDA_SAFE_CALL( cudaFree(d_pos) );
CUDA_SAFE_CALL( cudaFree(d_type) );
CUDA_SAFE_CALL( cudaFreeHost(f_temp) );
CUDA_SAFE_CALL( cudaFreeHost(temp_pos) );
clear_cell_list_gpu(d_cell_list);
}
energy = (float*) malloc(inum*sizeof(float));
v_temp = (float3*)malloc(inum*2*sizeof(float3));
cudaMalloc((void**)&d_force, inum*sizeof(float3));
cudaMalloc((void**)&d_energy, inum*sizeof(float));
cudaMalloc((void**)&d_virial, inum*3*sizeof(float3));
CUDA_SAFE_CALL( cudaMalloc((void**)&d_pos, nall*sizeof(float4)) );
CUDA_SAFE_CALL( cudaMalloc((void**)&d_type, nall*sizeof(int)) );
CUDA_SAFE_CALL( cudaMallocHost((void**)&f_temp, inum*sizeof(float3)) );
CUDA_SAFE_CALL( cudaMallocHost((void**)&temp_pos, nall*sizeof(float4)) );
init_cell_list_gpu(d_cell_list, nall, ncell);
CUDA_SAFE_CALL( cudaMemcpy(d_type, host_type, nall*sizeof(int),
cudaMemcpyHostToDevice) );
if (useCache) {
bind_pos(d_pos, nall);
bind_type(d_type, nall);
}
first_call = 0;
}
/* build cell-list on GPU */
double *atom_pos = host_x[0];
for (int i = 0; i < 3*nall; i+=3) {
temp_pos[i/3] = make_float4(atom_pos[i], atom_pos[i+1], atom_pos[i+2], 0.f);
}
CUDA_SAFE_CALL( cudaMemcpy(d_pos, temp_pos, nall*sizeof(float4),
cudaMemcpyHostToDevice) );
if (ago == 0) {
build_cell_list_gpu(d_pos, d_cell_list, h_boxlo, h_boxhi,
cell_size, inum, nall);
}
calc_lj_cell_gpu(d_force, d_energy, d_virial,
d_pos, d_type, d_cell_list,
inum, nall, ncellx,
ncelly, ncellz, cell_size,
eflag, vflag);
CUDA_SAFE_CALL( cudaMemcpy(f_temp, d_force, inum*sizeof(float3),
cudaMemcpyDeviceToHost) );
for (int i = 0; i < inum; i++) {
force[i][0] += f_temp[i].x;
force[i][1] += f_temp[i].y;
force[i][2] += f_temp[i].z;
}
if (eflag) {
CUDA_SAFE_CALL( cudaMemcpy(energy, d_energy,
inum*sizeof(float), cudaMemcpyDeviceToHost) );
for (int i = 0; i < inum; i++) {
evdwl += energy[i];
}
evdwl *= 0.5f;
}
if (vflag) {
CUDA_SAFE_CALL( cudaMemcpy(v_temp, d_virial, inum*2*sizeof(float3),
cudaMemcpyDeviceToHost) );
for (int i = 0; i < inum; i++) {
virial[0] += v_temp[2*i].x;
virial[1] += v_temp[2*i].y;
virial[2] += v_temp[2*i].z;
virial[3] += v_temp[2*i+1].x;
virial[4] += v_temp[2*i+1].y;
virial[5] += v_temp[2*i+1].z;
}
for (int i = 0; i < 6; i++)
virial[i] *= 0.5f;
}
return evdwl;
}
EXTERN double lj_gpu_cell(double **force, double *virial,
double **host_x, int *host_type,
const int inum, const int nall,
const int ago, const bool eflag, const bool vflag,
const double *boxlo, const double *boxhi)
{
return _lj_gpu_cell<float,float>(force, virial,
host_x, host_type, inum, nall,
ago, eflag, vflag, boxlo, boxhi);
}
EXTERN void lj_gpu_time() {
/* cout.precision(4);
cout << "Atom copy: " << LJMF.time_atom.total_seconds() << " s.\n";
cout << "Neighbor copy: " << LJMF.time_nbor.total_seconds() << " s.\n";
cout << "LJ calc: " << LJMF.time_pair.total_seconds() << " s.\n";*/
//cout << "Answer copy: " << LJMF.time_answer.total_seconds() << " s.\n";
}
EXTERN int lj_gpu_num_devices() {
int num_devices;
CUDA_SAFE_CALL( cudaGetDeviceCount(&num_devices) );
return num_devices;
}
EXTERN double lj_gpu_bytes() {
return 0.0;
}
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