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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@6053 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2011-05-02 15:02:52 +00:00
parent 2be078632d
commit 5f799182b3
70 changed files with 4489 additions and 2253 deletions
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203
lib/gpu/gb_gpu.cpp
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@ -49,14 +49,14 @@ void gb_gpu_pack_nbors(GBMT &gbm, const int GX, const int BX, const int start,
// ---------------------------------------------------------------------------
// 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) {
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();
@ -77,14 +77,12 @@ bool gb_gpu_init(const int ntypes, const double gamma,
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;
}
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)
@ -99,22 +97,22 @@ bool gb_gpu_init(const int ntypes, const double gamma,
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;
}
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");
return true;
if (init_ok==0)
GBMF.estimate_gpu_overhead();
return init_ok;
}
// ---------------------------------------------------------------------------
@ -131,8 +129,8 @@ 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) {
int *host_type, double *sublo,
double *subhi, bool &success) {
gbm.nbor_time_avail=true;
success=true;
@ -144,7 +142,7 @@ inline void _gb_gpu_build_nbor_list(gbmtyp &gbm, const int inum,
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);
sublo, subhi, NULL, NULL, NULL, success, mn);
gbm.nbor->copy_unpacked(inum,mn);
gbm.last_ellipse=inum;
gbm.max_last_ellipse=inum;
@ -163,7 +161,7 @@ void _gb_gpu_reset_nbors(gbmtyp &gbm, const int nall,
gbm.nbor_time_avail=true;
int mn=gbm.nbor->max_nbor_loop(inum,numj);
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)
@ -216,9 +214,10 @@ void _gb_gpu_gayberne(GBMT &gbm, const bool _eflag, const bool _vflag) {
else
vflag=0;
int GX=static_cast<int>(ceil(static_cast<double>(gbm.atom->inum())/BX));
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.atom->inum();
int ainum=gbm.ans->inum();
int anall=gbm.atom->nall();
if (gbm.multiple_forms) {
@ -226,7 +225,7 @@ void _gb_gpu_gayberne(GBMT &gbm, const bool _eflag, const bool _vflag) {
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)));
(BX/gbm._threads_per_atom)));
gb_gpu_pack_nbors(gbm,GX,BX, 0, gbm.last_ellipse,ELLIPSE_SPHERE,
ELLIPSE_ELLIPSE);
gbm.time_kernel.stop();
@ -237,11 +236,12 @@ void _gb_gpu_gayberne(GBMT &gbm, const bool _eflag, const bool _vflag) {
&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.atom->dev_ans.begin(),&ainum,&gbm.atom->dev_engv.begin(),
&gbm.dev_error.begin(), &eflag, &vflag, &gbm.last_ellipse, &anall);
&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.atom->inum()) {
if (gbm.last_ellipse==gbm.ans->inum()) {
gbm.time_kernel2.start();
gbm.time_kernel2.stop();
gbm.time_gayberne2.start();
@ -254,9 +254,10 @@ void _gb_gpu_gayberne(GBMT &gbm, const bool _eflag, const bool _vflag) {
// ------------ SPHERE_ELLIPSE ---------------
gbm.time_kernel2.start();
GX=static_cast<int>(ceil(static_cast<double>(gbm.atom->inum()-
gbm.last_ellipse)/BX));
gb_gpu_pack_nbors(gbm,GX,BX,gbm.last_ellipse,gbm.atom->inum(),
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();
@ -266,13 +267,14 @@ void _gb_gpu_gayberne(GBMT &gbm, const bool _eflag, const bool _vflag) {
&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.atom->dev_ans.begin(),
&gbm.atom->dev_engv.begin(), &gbm.dev_error.begin(), &eflag,
&vflag, &gbm.last_ellipse, &ainum, &anall);
&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.atom->dev_ans.zero();
gbm.atom->dev_engv.zero();
gbm.ans->dev_ans.zero();
gbm.ans->dev_engv.zero();
gbm.time_kernel.stop();
gbm.time_gayberne.start();
gbm.time_gayberne.stop();
@ -284,29 +286,31 @@ void _gb_gpu_gayberne(GBMT &gbm, const bool _eflag, const bool _vflag) {
// ------------ LJ ---------------
gbm.time_pair.start();
if (gbm.last_ellipse<gbm.atom->inum()) {
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.atom->dev_ans.begin(),
&gbm.atom->dev_engv.begin(), &gbm.dev_error.begin(),
&eflag, &vflag, &gbm.last_ellipse, &ainum, &anall);
&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.atom->dev_ans.begin(),
&gbm.atom->dev_engv.begin(), &gbm.dev_error.begin(),
&eflag, &vflag, &gbm.last_ellipse, &ainum, &anall);
&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.atom->inum(),SPHERE_SPHERE,
gb_gpu_pack_nbors(gbm, GX, BX, 0, gbm.ans->inum(),SPHERE_SPHERE,
ELLIPSE_ELLIPSE);
gbm.time_kernel.stop();
gbm.time_gayberne.start();
@ -315,9 +319,9 @@ void _gb_gpu_gayberne(GBMT &gbm, const bool _eflag, const bool _vflag) {
&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.atom->dev_ans.begin(), &ainum,
&gbm.atom->dev_engv.begin(), &gbm.dev_error.begin(),
&eflag, &vflag, &ainum, &anall);
&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();
}
}
@ -326,30 +330,31 @@ void _gb_gpu_gayberne(GBMT &gbm, const bool _eflag, const bool _vflag) {
// Reneighbor on GPU if necessary and then compute forces, torques, energies
// ---------------------------------------------------------------------------
template <class gbmtyp>
inline int * _gb_gpu_compute_n(gbmtyp &gbm, const int timestep, 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,
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,
const double cpu_time, bool &success,
double **host_quat) {
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,gbm.nbor->gpu_nbor());
int inum=gbm.hd_balancer.get_gpu_count(timestep,ago,inum_full);
gbm.atom->inum(inum);
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);
host_quat, host_type, sublo, subhi, success);
if (!success)
return NULL;
gbm.atom->cast_quat_data(host_quat[0]);
@ -361,47 +366,49 @@ inline int * _gb_gpu_compute_n(gbmtyp &gbm, const int timestep, const int ago,
gbm.atom->add_x_data(host_x,host_type);
}
gbm.atom->add_other_data();
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.atom->copy_answers(eflag,vflag,eatom,vatom);
gbm.ans->copy_answers(eflag,vflag,eatom,vatom);
gbm.device->add_ans_object(gbm.ans);
gbm.hd_balancer.stop_timer();
return gbm.device->nbor.host_nbor.begin();
return gbm.nbor->host_jlist.begin()-host_start;
}
int * gb_gpu_compute_n(const int timestep, 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, const double cpu_time, bool &success,
double **host_quat) {
return _gb_gpu_compute_n(GBMF, timestep, ago, inum_full, nall, host_x,
host_type, boxlo, boxhi, eflag, vflag, eatom, vatom,
host_start, cpu_time, success, host_quat);
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 timestep, 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) {
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(timestep,ago,inum_full,cpu_time,
gbm.nbor->gpu_nbor());
gbm.atom->inum(inum);
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;
@ -421,21 +428,21 @@ inline int * _gb_gpu_compute(gbmtyp &gbm, const int timestep, const int f_ago,
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_other_data();
gbm.atom->add_quat_data();
_gb_gpu_gayberne<PRECISION,ACC_PRECISION>(gbm,eflag,vflag);
gbm.atom->copy_answers(eflag,vflag,eatom,vatom,list);
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 timestep, 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, timestep, ago, inum_full, nall, host_x,
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);