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lammps/lib/gpu/gb_gpu.cpp
W. Michael Brown 71ff7b8096 Updating all code to use full neighbor lists for all host forces 
computations. Changed the load balancing scheme. Added timing estimates
for GPU and driver overhead, cpu idle time.
2011-03-28 13:18:39 -04:00

454 lines
17 KiB
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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 (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
// ---------------------------------------------------------------------------
bool 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);
}
if (world_me==0) {
bool 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);
if (!init_ok)
return false;
}
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) {
bool 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);
if (!init_ok)
return false;
}
GBMF.device->gpu_barrier();
if (message)
fprintf(screen,"Done.\n");
}
if (message)
fprintf(screen,"\n");
GBMF.estimate_gpu_overhead();
return true;
}
// ---------------------------------------------------------------------------
// 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 *boxlo,
double *boxhi, 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,
boxlo, boxhi, 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));
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)/
static_cast<double>(BX)));
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.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));
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.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);
} 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.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.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 *boxlo, double *boxhi, 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, boxlo, boxhi, 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 *boxlo,
double *boxhi, 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, boxlo,
boxhi, 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();
}
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