Homec4science
Diffusion lammps (efficient_neuronet) Browse

lammps/lib/gpu/gb_gpu.cpp
945343265e0eefficient_neuronet

Last Change
Raw File

gb_gpu.cpp
View Options

/* ----------------------------------------------------------------------
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 (ORNL), brownw@ornl.gov
------------------------------------------------------------------------- */
#include <iostream>
#include <cassert>
#include <math.h>
#include "gb_gpu_memory.h"
using namespace std;
static GB_GPU_Memory<PRECISION,ACC_PRECISION> GBMF;
#define GBMT GB_GPU_Memory<numtyp,acctyp>
template<class numtyp, class acctyp>
void gb_gpu_pack_nbors(GBMT &gbm, const int GX, const int BX, const int start,
const int inum, const int form_low, const int form_high) {
int stride=gbm.nbor->nbor_pitch();
int anall=gbm.atom->nall();
if (gbm.shared_types) {
GBMF.k_gb_nbor_fast.set_size(GX,BX);
GBMF.k_gb_nbor_fast.run(&gbm.atom->dev_x.begin(),
&gbm.cut_form.begin(), &gbm.nbor->dev_nbor.begin(), &stride,
&start, &inum, &gbm.nbor->dev_packed.begin(), &form_low,
&form_high, &anall);
} else {
GBMF.k_gb_nbor.set_size(GX,BX);
GBMF.k_gb_nbor.run(&gbm.atom->dev_x.begin(), &gbm.cut_form.begin(),
&gbm._lj_types, &gbm.nbor->dev_nbor.begin(), &stride,
&start, &inum, &gbm.nbor->dev_packed.begin(), &form_low,
&form_high, &anall);
}
}
// ---------------------------------------------------------------------------
// Allocate memory on host and device and copy constants to device
// ---------------------------------------------------------------------------
int gb_gpu_init(const int ntypes, const double gamma,
const double upsilon, const double mu, double **shape,
double **well, double **cutsq, double **sigma,
double **epsilon, double *host_lshape, int **form,
double **host_lj1, double **host_lj2, double **host_lj3,
double **host_lj4, double **offset, double *special_lj,
const int inum, const int nall, const int max_nbors,
const double cell_size, int &gpu_mode, FILE *screen) {
GBMF.clear();
gpu_mode=GBMF.device->gpu_mode();
double gpu_split=GBMF.device->particle_split();
int first_gpu=GBMF.device->first_device();
int last_gpu=GBMF.device->last_device();
int world_me=GBMF.device->world_me();
int gpu_rank=GBMF.device->gpu_rank();
int procs_per_gpu=GBMF.device->procs_per_gpu();
GBMF.device->init_message(screen,"gayberne",first_gpu,last_gpu);
bool message=false;
if (GBMF.device->replica_me()==0 && screen)
message=true;
if (message) {
fprintf(screen,"Initializing GPU and compiling on process 0...");
fflush(screen);
}
int init_ok=0;
if (world_me==0)
init_ok=GBMF.init(ntypes, gamma, upsilon, mu, shape, well, cutsq,
sigma, epsilon, host_lshape, form, host_lj1,
host_lj2, host_lj3, host_lj4, offset, special_lj,
inum, nall, max_nbors, cell_size, gpu_split, screen);
GBMF.device->world_barrier();
if (message)
fprintf(screen,"Done.\n");
for (int i=0; i<procs_per_gpu; i++) {
if (message) {
if (last_gpu-first_gpu==0)
fprintf(screen,"Initializing GPU %d on core %d...",first_gpu,i);
else
fprintf(screen,"Initializing GPUs %d-%d on core %d...",first_gpu,
last_gpu,i);
fflush(screen);
}
if (gpu_rank==i && world_me!=0)
init_ok=GBMF.init(ntypes, gamma, upsilon, mu, shape, well, cutsq, sigma,
epsilon, host_lshape, form, host_lj1, host_lj2,
host_lj3, host_lj4, offset, special_lj, inum, nall,
max_nbors, cell_size, gpu_split, screen);
GBMF.device->gpu_barrier();
if (message)
fprintf(screen,"Done.\n");
}
if (message)
fprintf(screen,"\n");
if (init_ok==0)
GBMF.estimate_gpu_overhead();
return init_ok;
}
// ---------------------------------------------------------------------------
// Clear memory on host and device
// ---------------------------------------------------------------------------
void gb_gpu_clear() {
GBMF.clear();
}
// ---------------------------------------------------------------------------
// Build neighbor list on device
// ---------------------------------------------------------------------------
template <class gbmtyp>
inline void _gb_gpu_build_nbor_list(gbmtyp &gbm, const int inum,
const int host_inum, const int nall,
double **host_x, double **host_quat,
int *host_type, double *sublo,
double *subhi, bool &success) {
gbm.nbor_time_avail=true;
success=true;
gbm.resize_atom(inum,nall,success);
gbm.resize_local(inum,host_inum,gbm.nbor->max_nbors(),0,success);
if (!success)
return;
gbm.atom->cast_copy_x(host_x,host_type);
int mn;
gbm.nbor->build_nbor_list(inum, host_inum, nall, *gbm.atom,
sublo, subhi, NULL, NULL, NULL, success, mn);
gbm.nbor->copy_unpacked(inum,mn);
gbm.last_ellipse=inum;
gbm.max_last_ellipse=inum;
}
// ---------------------------------------------------------------------------
// Copy neighbor list from host and (if spheres) reorder so ellipses first
// ---------------------------------------------------------------------------
template <class gbmtyp>
void _gb_gpu_reset_nbors(gbmtyp &gbm, const int nall,
const int inum, const int osize,
int *ilist, int *numj,
int *type, int **firstneigh,
bool &success) {
success=true;
gbm.nbor_time_avail=true;
int mn=gbm.nbor->max_nbor_loop(inum,numj,ilist);
gbm.resize_atom(inum,nall,success);
gbm.resize_local(inum,0,mn,osize,success);
if (!success)
return;
if (gbm.multiple_forms) {
int p=0;
for (int i=0; i<osize; i++) {
int itype=type[ilist[i]];
if (gbm.host_form[itype][itype]==ELLIPSE_ELLIPSE) {
gbm.host_olist[p]=ilist[i];
p++;
}
}
gbm.max_last_ellipse=p;
gbm.last_ellipse=std::min(inum,gbm.max_last_ellipse);
for (int i=0; i<osize; i++) {
int itype=type[ilist[i]];
if (gbm.host_form[itype][itype]!=ELLIPSE_ELLIPSE) {
gbm.host_olist[p]=ilist[i];
p++;
}
}
gbm.nbor->get_host(inum,gbm.host_olist.begin(),numj,firstneigh,
gbm.block_size());
gbm.nbor->copy_unpacked(inum,mn);
return;
}
gbm.last_ellipse=inum;
gbm.max_last_ellipse=inum;
gbm.nbor->get_host(inum,ilist,numj,firstneigh,gbm.block_size());
gbm.nbor->copy_unpacked(inum,mn);
}
// ---------------------------------------------------------------------------
// Calculate energies, forces, and torques
// ---------------------------------------------------------------------------
template <class numtyp, class acctyp>
void _gb_gpu_gayberne(GBMT &gbm, const bool _eflag, const bool _vflag) {
// Compute the block size and grid size to keep all cores busy
const int BX=gbm.block_size();
int eflag, vflag;
if (_eflag)
eflag=1;
else
eflag=0;
if (_vflag)
vflag=1;
else
vflag=0;
int GX=static_cast<int>(ceil(static_cast<double>(gbm.ans->inum())/
(BX/gbm._threads_per_atom)));
int stride=gbm.nbor->nbor_pitch();
int ainum=gbm.ans->inum();
int anall=gbm.atom->nall();
if (gbm.multiple_forms) {
gbm.time_kernel.start();
if (gbm.last_ellipse>0) {
// ------------ ELLIPSE_ELLIPSE and ELLIPSE_SPHERE ---------------
GX=static_cast<int>(ceil(static_cast<double>(gbm.last_ellipse)/
(BX/gbm._threads_per_atom)));
gb_gpu_pack_nbors(gbm,GX,BX, 0, gbm.last_ellipse,ELLIPSE_SPHERE,
ELLIPSE_ELLIPSE);
gbm.time_kernel.stop();
gbm.time_gayberne.start();
GBMF.k_gayberne.set_size(GX,BX);
GBMF.k_gayberne.run(&gbm.atom->dev_x.begin(),
&gbm.atom->dev_quat.begin(), &gbm.shape.begin(), &gbm.well.begin(),
&gbm.gamma_upsilon_mu.begin(), &gbm.sigma_epsilon.begin(),
&gbm._lj_types, &gbm.lshape.begin(), &gbm.nbor->dev_nbor.begin(),
&stride, &gbm.ans->dev_ans.begin(),&ainum,&gbm.ans->dev_engv.begin(),
&gbm.dev_error.begin(), &eflag, &vflag, &gbm.last_ellipse, &anall,
&gbm._threads_per_atom);
gbm.time_gayberne.stop();
if (gbm.last_ellipse==gbm.ans->inum()) {
gbm.time_kernel2.start();
gbm.time_kernel2.stop();
gbm.time_gayberne2.start();
gbm.time_gayberne2.stop();
gbm.time_pair.start();
gbm.time_pair.stop();
return;
}
// ------------ SPHERE_ELLIPSE ---------------
gbm.time_kernel2.start();
GX=static_cast<int>(ceil(static_cast<double>(gbm.ans->inum()-
gbm.last_ellipse)/
(BX/gbm._threads_per_atom)));
gb_gpu_pack_nbors(gbm,GX,BX,gbm.last_ellipse,gbm.ans->inum(),
SPHERE_ELLIPSE,SPHERE_ELLIPSE);
gbm.time_kernel2.stop();
gbm.time_gayberne2.start();
GBMF.k_sphere_gb.set_size(GX,BX);
GBMF.k_sphere_gb.run(&gbm.atom->dev_x.begin(),&gbm.atom->dev_quat.begin(),
&gbm.shape.begin(), &gbm.well.begin(),
&gbm.gamma_upsilon_mu.begin(), &gbm.sigma_epsilon.begin(),
&gbm._lj_types, &gbm.lshape.begin(),
&gbm.nbor->dev_nbor.begin(), &stride, &gbm.ans->dev_ans.begin(),
&gbm.ans->dev_engv.begin(), &gbm.dev_error.begin(), &eflag,
&vflag, &gbm.last_ellipse, &ainum, &anall,
&gbm._threads_per_atom);
gbm.time_gayberne2.stop();
} else {
gbm.ans->dev_ans.zero();
gbm.ans->dev_engv.zero();
gbm.time_kernel.stop();
gbm.time_gayberne.start();
gbm.time_gayberne.stop();
gbm.time_kernel2.start();
gbm.time_kernel2.stop();
gbm.time_gayberne2.start();
gbm.time_gayberne2.stop();
}
// ------------ LJ ---------------
gbm.time_pair.start();
if (gbm.last_ellipse<gbm.ans->inum()) {
if (gbm.shared_types) {
GBMF.k_lj_fast.set_size(GX,BX);
GBMF.k_lj_fast.run(&gbm.atom->dev_x.begin(), &gbm.lj1.begin(),
&gbm.lj3.begin(), &gbm.gamma_upsilon_mu.begin(),
&stride, &gbm.nbor->dev_packed.begin(),
&gbm.ans->dev_ans.begin(),
&gbm.ans->dev_engv.begin(), &gbm.dev_error.begin(),
&eflag, &vflag, &gbm.last_ellipse, &ainum, &anall,
&gbm._threads_per_atom);
} else {
GBMF.k_lj.set_size(GX,BX);
GBMF.k_lj.run(&gbm.atom->dev_x.begin(), &gbm.lj1.begin(),
&gbm.lj3.begin(), &gbm._lj_types,
&gbm.gamma_upsilon_mu.begin(), &stride,
&gbm.nbor->dev_packed.begin(), &gbm.ans->dev_ans.begin(),
&gbm.ans->dev_engv.begin(), &gbm.dev_error.begin(),
&eflag, &vflag, &gbm.last_ellipse, &ainum, &anall,
&gbm._threads_per_atom);
}
}
gbm.time_pair.stop();
} else {
gbm.time_kernel.start();
gb_gpu_pack_nbors(gbm, GX, BX, 0, gbm.ans->inum(),SPHERE_SPHERE,
ELLIPSE_ELLIPSE);
gbm.time_kernel.stop();
gbm.time_gayberne.start();
GBMF.k_gayberne.set_size(GX,BX);
GBMF.k_gayberne.run(&gbm.atom->dev_x.begin(), &gbm.atom->dev_quat.begin(),
&gbm.shape.begin(), &gbm.well.begin(),
&gbm.gamma_upsilon_mu.begin(), &gbm.sigma_epsilon.begin(),
&gbm._lj_types, &gbm.lshape.begin(), &gbm.nbor->dev_nbor.begin(),
&stride, &gbm.ans->dev_ans.begin(), &ainum,
&gbm.ans->dev_engv.begin(), &gbm.dev_error.begin(),
&eflag, &vflag, &ainum, &anall, &gbm._threads_per_atom);
gbm.time_gayberne.stop();
}
}
// ---------------------------------------------------------------------------
// Reneighbor on GPU if necessary and then compute forces, torques, energies
// ---------------------------------------------------------------------------
template <class gbmtyp>
inline int** _gb_gpu_compute_n(gbmtyp &gbm, const int ago,
const int inum_full, const int nall,
double **host_x, int *host_type,
double *sublo, double *subhi, 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_quat) {
gbm.acc_timers();
if (inum_full==0) {
host_start=0;
gbm.zero_timers();
return NULL;
}
gbm.hd_balancer.balance(cpu_time);
int inum=gbm.hd_balancer.get_gpu_count(ago,inum_full);
gbm.ans->inum(inum);
gbm.last_ellipse=std::min(inum,gbm.max_last_ellipse);
host_start=inum;
// Build neighbor list on GPU if necessary
if (ago==0) {
_gb_gpu_build_nbor_list(gbm, inum, inum_full-inum, nall, host_x,
host_quat, host_type, sublo, subhi, success);
if (!success)
return NULL;
gbm.atom->cast_quat_data(host_quat[0]);
gbm.hd_balancer.start_timer();
} else {
gbm.atom->cast_x_data(host_x,host_type);
gbm.atom->cast_quat_data(host_quat[0]);
gbm.hd_balancer.start_timer();
gbm.atom->add_x_data(host_x,host_type);
}
gbm.atom->add_quat_data();
*ilist=gbm.nbor->host_ilist.begin();
*jnum=gbm.nbor->host_acc.begin();
_gb_gpu_gayberne<PRECISION,ACC_PRECISION>(gbm,eflag,vflag);
gbm.ans->copy_answers(eflag,vflag,eatom,vatom);
gbm.device->add_ans_object(gbm.ans);
gbm.hd_balancer.stop_timer();
return gbm.nbor->host_jlist.begin()-host_start;
}
int** gb_gpu_compute_n(const int ago, const int inum_full, const int nall,
double **host_x, int *host_type, double *sublo,
double *subhi, 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_quat) {
return _gb_gpu_compute_n(GBMF, ago, inum_full, nall, host_x, host_type, sublo,
subhi, eflag, vflag, eatom, vatom, host_start, ilist,
jnum, cpu_time, success, host_quat);
}
// ---------------------------------------------------------------------------
// Copy nbor list from host if necessary and then calculate forces, torques,..
// ---------------------------------------------------------------------------
template <class gbmtyp>
inline int * _gb_gpu_compute(gbmtyp &gbm, const int f_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_quat) {
gbm.acc_timers();
if (inum_full==0) {
host_start=0;
gbm.zero_timers();
return NULL;
}
int ago=gbm.hd_balancer.ago_first(f_ago);
int inum=gbm.hd_balancer.balance(ago,inum_full,cpu_time);
gbm.ans->inum(inum);
gbm.last_ellipse=std::min(inum,gbm.max_last_ellipse);
host_start=inum;
if (ago==0) {
_gb_gpu_reset_nbors(gbm, nall, inum, inum_full, ilist, numj, host_type,
firstneigh, success);
if (!success)
return NULL;
}
int *list;
if (gbm.multiple_forms)
list=gbm.host_olist.begin();
else
list=ilist;
gbm.atom->cast_x_data(host_x,host_type);
gbm.atom->cast_quat_data(host_quat[0]);
gbm.hd_balancer.start_timer();
gbm.atom->add_x_data(host_x,host_type);
gbm.atom->add_quat_data();
_gb_gpu_gayberne<PRECISION,ACC_PRECISION>(gbm,eflag,vflag);
gbm.ans->copy_answers(eflag,vflag,eatom,vatom,list);
gbm.device->add_ans_object(gbm.ans);
gbm.hd_balancer.stop_timer();
return list;
}
int * gb_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_quat) {
return _gb_gpu_compute(GBMF, ago, inum_full, nall, host_x,
host_type, ilist, numj, firstneigh, eflag, vflag,
eatom, vatom, host_start, cpu_time, success,
host_quat);
}
// ---------------------------------------------------------------------------
// Return memory usage
// ---------------------------------------------------------------------------
double gb_gpu_bytes() {
return GBMF.host_memory_usage();
}
c4science · Help