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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11233 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2014-01-13 15:54:07 +00:00
parent 29af85e638
commit 94a4b3f20a
4 changed files with 373 additions and 13 deletions
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2
src/GPU/Install.sh
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@ -83,6 +83,8 @@ action pair_lj_cut_gpu.cpp
action pair_lj_cut_gpu.h
action pair_lj_expand_gpu.cpp
action pair_lj_expand_gpu.h
action pair_lj_gromacs_gpu.cpp
action pair_lj_gromacs_gpu.h
action pair_lj_sdk_coul_long_gpu.cpp pair_lj_sdk_coul_long.cpp
action pair_lj_sdk_coul_long_gpu.h pair_lj_sdk_coul_long.cpp
action pair_lj_sdk_gpu.cpp pair_lj_sdk.cpp

247
src/GPU/pair_lj_gromacs_gpu.cpp Normal file
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@ -0,0 +1,247 @@
/* ----------------------------------------------------------------------
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 author: Trung Dac Nguyen (ORNL)
------------------------------------------------------------------------- */
#include "lmptype.h"
#include "math.h"
#include "stdio.h"
#include "stdlib.h"
#include "pair_lj_gromacs_gpu.h"
#include "atom.h"
#include "atom_vec.h"
#include "comm.h"
#include "force.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "integrate.h"
#include "memory.h"
#include "error.h"
#include "neigh_request.h"
#include "universe.h"
#include "update.h"
#include "domain.h"
#include "string.h"
#include "kspace.h"
#include "gpu_extra.h"
// External functions from cuda library for atom decomposition
int ljgrm_gpu_init(const int ntypes, double **cutsq, double **host_lj1,
double **host_lj2, double **host_lj3, double **host_lj4,
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,
double **host_ljsw1, double **host_ljsw2, double **host_ljsw3,
double **host_ljsw4, double **host_ljsw5,
double **cut_inner, double **cut_innersq);
void ljgrm_gpu_clear();
int ** ljgrm_gpu_compute_n(const int ago, const int inum_full,
const int nall, double **host_x, int *host_type,
double *sublo, double *subhi, int *tag, int **nspecial,
int **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 ljgrm_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 ljgrm_gpu_bytes();
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
PairLJGromacsGPU::PairLJGromacsGPU(LAMMPS *lmp) :
PairLJGromacs(lmp), gpu_mode(GPU_FORCE)
{
respa_enable = 0;
cpu_time = 0.0;
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
}
/* ----------------------------------------------------------------------
free all arrays
------------------------------------------------------------------------- */
PairLJGromacsGPU::~PairLJGromacsGPU()
{
ljgrm_gpu_clear();
}
/* ---------------------------------------------------------------------- */
void PairLJGromacsGPU::compute(int eflag, int vflag)
{
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
int nall = atom->nlocal + atom->nghost;
int inum, host_start;
bool success = true;
int *ilist, *numneigh, **firstneigh;
if (gpu_mode != GPU_FORCE) {
inum = atom->nlocal;
firstneigh = ljgrm_gpu_compute_n(neighbor->ago, inum, nall,
atom->x, atom->type, domain->sublo,
domain->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;
ljgrm_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 (host_start<inum) {
cpu_time = MPI_Wtime();
cpu_compute(host_start, inum, eflag, vflag, ilist, numneigh, firstneigh);
cpu_time = MPI_Wtime() - cpu_time;
}
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairLJGromacsGPU::init_style()
{
if (force->newton_pair)
error->all(FLERR,"Cannot use newton pair with lj/gromacs/gpu pair 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)
maxspecial=atom->maxspecial;
int success = ljgrm_gpu_init(atom->ntypes+1, cutsq, lj1, lj2, lj3, lj4,
force->special_lj, atom->nlocal,
atom->nlocal+atom->nghost, 300, maxspecial,
cell_size, gpu_mode, screen, ljsw1, ljsw2,
ljsw3, ljsw4, ljsw5, cut_inner, cut_inner_sq);
GPU_EXTRA::check_flag(success,error,world);
if (gpu_mode == GPU_FORCE) {
int irequest = neighbor->request(this);
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->full = 1;
}
}
/* ---------------------------------------------------------------------- */
double PairLJGromacsGPU::memory_usage()
{
double bytes = Pair::memory_usage();
return bytes + ljgrm_gpu_bytes();
}
/* ---------------------------------------------------------------------- */
void PairLJGromacsGPU::cpu_compute(int start, int inum, int eflag,
int vflag, int *ilist,
int *numneigh, int **firstneigh)
{
int i,j,ii,jj,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
double rsq,r2inv,r6inv,forcelj,factor_lj;
double r,t,fswitch,eswitch;
int *jlist;
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]) {
r2inv = 1.0/rsq;
r6inv = r2inv*r2inv*r2inv;
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
if (rsq > cut_inner_sq[itype][jtype]) {
r = sqrt(rsq);
t = r - cut_inner[itype][jtype];
fswitch = r*t*t*(ljsw1[itype][jtype] + ljsw2[itype][jtype]*t);
forcelj += fswitch;
}
fpair = factor_lj*forcelj * r2inv;
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
if (eflag) {
evdwl = r6inv * (lj3[itype][jtype]*r6inv - lj4[itype][jtype]);
evdwl += ljsw5[itype][jtype];
if (rsq > cut_inner_sq[itype][jtype]) {
eswitch = t*t*t*(ljsw3[itype][jtype] + ljsw4[itype][jtype]*t);
evdwl += eswitch;
}
evdwl *= factor_lj;
}
if (evflag) ev_tally_full(i,evdwl,0.0,fpair,delx,dely,delz);
}
}
}
}

64
src/GPU/pair_lj_gromacs_gpu.h Normal file
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@ -0,0 +1,64 @@
/* ----------------------------------------------------------------------
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.
------------------------------------------------------------------------- */
#ifdef PAIR_CLASS
PairStyle(lj/gromacs/gpu,PairLJGromacsGPU)
#else
#ifndef LMP_PAIR_LJ_GROMACS_GPU_H
#define LMP_PAIR_LJ_GROMACS_GPU_H
#include "pair_lj_gromacs.h"
namespace LAMMPS_NS {
class PairLJGromacsGPU : public PairLJGromacs {
public:
PairLJGromacsGPU(LAMMPS *lmp);
~PairLJGromacsGPU();
void cpu_compute(int, int, int, int, int *, int *, int **);
void compute(int, int);
void init_style();
double memory_usage();
enum { GPU_FORCE, GPU_NEIGH, GPU_HYB_NEIGH };
private:
int gpu_mode;
double cpu_time;
int *gpulist;
};
}
#endif
#endif
/* ERROR/WARNING messages:
E: Insufficient memory on accelerator
There is insufficient memory on one of the devices specified for the gpu
package
E: Cannot use newton pair with lj/gromacs/gpu pair style
Self-explanatory.
E: Pair style is incompatible with KSpace style
If a pair style with a long-range Coulombic component is selected,
then a kspace style must also be used.
*/

73
src/GPU/pair_sw_gpu.cpp
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@ -35,11 +35,15 @@
// External functions from cuda library for atom decomposition
int sw_gpu_init(const int nlocal, const int nall, const int max_nbors,
int sw_gpu_init(const int ntypes, const int inum, const int nall, const int max_nbors,
const double cell_size, int &gpu_mode, FILE *screen,
const double, const double, const double, const double,
const double, const double, const double, const double,
const double, const double, const double);
int* host_map, const int nelements, int*** host_elem2param, const int nparams,
const double* sw_epsilon, const double* sw_sigma,
const double* sw_lambda, const double* sw_gamma,
const double* sw_costheta, const double* sw_biga,
const double* sw_bigb, const double* sw_powerp,
const double* sw_powerq, const double* sw_cut,
const double* sw_cutsq);
void sw_gpu_clear();
int ** sw_gpu_compute_n(const int ago, const int inum,
const int nall, double **host_x, int *host_type,
@ -135,21 +139,64 @@ void PairSWGPU::allocate()
void PairSWGPU::init_style()
{
double cell_size = sqrt(params[0].cutsq) + neighbor->skin;
double cell_size = cutmax + neighbor->skin;
if (atom->tag_enable == 0)
error->all(FLERR,"Pair style sw/gpu requires atom IDs");
if (force->newton_pair != 0)
error->all(FLERR,"Pair style sw/gpu requires newton pair off");
if (nparams > 1)
error->all(FLERR,"Pair style sw/gpu is currently limited to one element.");
int success = sw_gpu_init(atom->nlocal, atom->nlocal+atom->nghost, 300,
cell_size, gpu_mode, screen,params[0].epsilon,
params[0].sigma, params[0].lambda, params[0].gamma,
params[0].costheta, params[0].biga, params[0].bigb,
params[0].powerp, params[0].powerq, params[0].cut,
params[0].cutsq);
double *epsilon, *sigma, *lambda, *gamma;
double *biga, *bigb, *powerp, *powerq;
double *_cut, *_cutsq, *costheta;
epsilon = sigma = lambda = gamma = NULL;
biga = bigb = powerp = powerq = NULL;
_cut = _cutsq = costheta = NULL;
memory->create(epsilon,nparams,"pair:epsilon");
memory->create(sigma,nparams,"pair:sigma");
memory->create(lambda,nparams,"pair:lambda");
memory->create(gamma,nparams,"pair:gamma");
memory->create(biga,nparams,"pair:biga");
memory->create(bigb,nparams,"pair:bigb");
memory->create(powerp,nparams,"pair:powerp");
memory->create(powerq,nparams,"pair:powerq");
memory->create(_cut,nparams,"pair:_cut");
memory->create(_cutsq,nparams,"pair:_cutsq");
memory->create(costheta,nparams,"pair:costheta");
for (int i = 0; i < nparams; i++) {
epsilon[i] = params[i].epsilon;
sigma[i] = params[i].sigma;
lambda[i] = params[i].lambda;
gamma[i] = params[i].gamma;
biga[i] = params[i].biga;
bigb[i] = params[i].bigb;
powerp[i] = params[i].powerp;
powerq[i] = params[i].powerq;
_cut[i] = params[i].cut;
_cutsq[i] = params[i].cutsq;
costheta[i] = params[i].costheta;
}
int success = sw_gpu_init(atom->ntypes+1, atom->nlocal, atom->nlocal+atom->nghost, 300,
cell_size, gpu_mode, screen, map, nelements,
elem2param, nparams, epsilon,
sigma, lambda, gamma, costheta, biga, bigb,
powerp, powerq, _cut, _cutsq);
memory->destroy(epsilon);
memory->destroy(sigma);
memory->destroy(lambda);
memory->destroy(gamma);
memory->destroy(biga);
memory->destroy(bigb);
memory->destroy(powerp);
memory->destroy(powerq);
memory->destroy(_cut);
memory->destroy(_cutsq);
memory->destroy(costheta);
GPU_EXTRA::check_flag(success,error,world);
if (gpu_mode == GPU_FORCE) {