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Refactored neighbor list builds and per-atom reallocation parts

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This commit is contained in:
Trung Nguyen
2021-09-07 13:05:57 -05:00
parent be5aa46df8
commit 4e346c2de6
4 changed files with 107 additions and 78 deletions
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5
lib/gpu/lal_amoeba_ext.cpp
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@ -127,6 +127,7 @@ int** amoeba_gpu_compute_polar_real(const int ago, const int inum_full,
int** amoeba_gpu_compute_udirect2b(const int ago, const int inum_full,
const int nall, double **host_x, int *host_type,
int *host_amtype, int *host_amgroup, double **host_rpole,
double **host_uind, double **host_uinp,
double *sublo, double *subhi, tagint *tag, int **nspecial,
tagint **special, int *nspecial15, tagint** special15,
const bool eflag, const bool vflag,
@ -135,8 +136,8 @@ int** amoeba_gpu_compute_udirect2b(const int ago, const int inum_full,
bool &success, double *host_q, double *boxlo,
double *prd, void **fieldp_ptr) {
return AMOEBAMF.compute_udirect2b(ago, inum_full, nall, host_x, host_type,
host_amtype, host_amgroup, host_rpole, sublo, subhi,
tag, nspecial, special, nspecial15, special15,
host_amtype, host_amgroup, host_rpole, host_uind, host_uinp,
sublo, subhi, tag, nspecial, special, nspecial15, special15,
eflag, vflag, eatom, vatom, host_start, ilist, jnum,
cpu_time, success, host_q, boxlo, prd, fieldp_ptr);
}

139
lib/gpu/lal_base_amoeba.cpp
View File

@ -121,9 +121,12 @@ int BaseAmoebaT::init_atomic(const int nlocal, const int nall,
ef_nall=2000;
_max_tep_size=static_cast<int>(static_cast<double>(ef_nall)*1.10);
_tep.alloc(_max_tep_size*4,*(this->ucl_device),UCL_READ_WRITE,UCL_READ_WRITE);
_max_fieldp_size = _max_tep_size;
_fieldp.alloc(_max_fieldp_size*8,*(this->ucl_device),UCL_READ_WRITE,UCL_READ_WRITE);
_tep.alloc(_max_tep_size*4,*(this->ucl_device),UCL_READ_WRITE,UCL_READ_WRITE);
_nmax = nall;
dev_nspecial15.alloc(nall,*(this->ucl_device),UCL_READ_ONLY);
dev_special15.alloc(_maxspecial15*nall,*(this->ucl_device),UCL_READ_ONLY);
dev_special15_t.alloc(nall*_maxspecial15,*(this->ucl_device),UCL_READ_ONLY);
@ -312,10 +315,12 @@ void BaseAmoebaT::compute_polar_real(const int f_ago, const int inum_full, const
}
// ---------------------------------------------------------------------------
// Reneighbor on GPU if necessary, and then compute polar real-space
// Prepare for multiple kernel calls in a time step:
// - reallocate per-atom arrays, if needed
// - build the full neighbor lists for use by different kernels
// ---------------------------------------------------------------------------
template <class numtyp, class acctyp>
int** BaseAmoebaT::compute_polar_real(const int ago, const int inum_full, const int nall,
int** BaseAmoebaT::precompute(const int ago, const int inum_full, const int nall,
double **host_x, int *host_type, int *host_amtype,
int *host_amgroup, double **host_rpole,
double **host_uind, double **host_uinp,
@ -324,9 +329,9 @@ int** BaseAmoebaT::compute_polar_real(const int ago, const int inum_full, const
int *nspecial15, tagint **special15,
const bool eflag_in, const bool vflag_in,
const bool eatom, const bool vatom, int &host_start,
int **ilist, int **jnum, const double cpu_time,
int **&ilist, int **&jnum, const double cpu_time,
bool &success, double *host_q, double *boxlo,
double *prd, void **tep_ptr) {
double *prd) {
acc_timers();
int eflag, vflag;
if (eatom) eflag=2;
@ -343,12 +348,10 @@ int** BaseAmoebaT::compute_polar_real(const int ago, const int inum_full, const
set_kernel(eflag,vflag);
// ------------------- Resize _tep array ------------------------
if (nall>_max_tep_size) {
_max_tep_size=static_cast<int>(static_cast<double>(nall)*1.10);
_tep.resize(_max_tep_size*4);
// ------------------- Resize 1-5 neighbor arrays ------------------------
if (nall>_nmax) {
_nmax = nall;
dev_nspecial15.clear();
dev_special15.clear();
dev_special15_t.clear();
@ -356,7 +359,6 @@ int** BaseAmoebaT::compute_polar_real(const int ago, const int inum_full, const
dev_special15.alloc(_maxspecial15*nall,*(this->ucl_device),UCL_READ_ONLY);
dev_special15_t.alloc(nall*_maxspecial15,*(this->ucl_device),UCL_READ_ONLY);
}
*tep_ptr=_tep.host.begin();
if (inum_full==0) {
host_start=0;
@ -397,6 +399,60 @@ int** BaseAmoebaT::compute_polar_real(const int ago, const int inum_full, const
device->precompute(ago,inum_full,nall,host_x,host_type,success,host_q,
boxlo, prd);
return nbor->host_jlist.begin()-host_start;
}
// ---------------------------------------------------------------------------
// Reneighbor on GPU if necessary, and then compute polar real-space
// ---------------------------------------------------------------------------
template <class numtyp, class acctyp>
int** BaseAmoebaT::compute_polar_real(const int ago, const int inum_full, const int nall,
double **host_x, int *host_type, int *host_amtype,
int *host_amgroup, double **host_rpole,
double **host_uind, double **host_uinp,
double *sublo, double *subhi, tagint *tag,
int **nspecial, tagint **special,
int *nspecial15, tagint **special15,
const bool eflag_in, const bool vflag_in,
const bool eatom, const bool vatom, int &host_start,
int **ilist, int **jnum, const double cpu_time,
bool &success, double *host_q, double *boxlo,
double *prd, void **tep_ptr) {
acc_timers();
int eflag, vflag;
if (eatom) eflag=2;
else if (eflag_in) eflag=1;
else eflag=0;
if (vatom) vflag=2;
else if (vflag_in) vflag=1;
else vflag=0;
#ifdef LAL_NO_BLOCK_REDUCE
if (eflag) eflag=2;
if (vflag) vflag=2;
#endif
set_kernel(eflag,vflag);
// reallocate per-atom arrays and build the neighbor lists if needed
int** firstneigh = nullptr;
firstneigh = precompute(ago, inum_full, nall, host_x, host_type,
host_amtype, host_amgroup, host_rpole,
host_uind, host_uinp, sublo, subhi, tag,
nspecial, special, nspecial15, special15,
eflag_in, vflag_in, eatom, vatom,
host_start, ilist, jnum, cpu_time,
success, host_q, boxlo, prd);
// ------------------- Resize _tep array ------------------------
if (nall>_max_tep_size) {
_max_tep_size=static_cast<int>(static_cast<double>(nall)*1.10);
_tep.resize(_max_tep_size*4);
}
*tep_ptr=_tep.host.begin();
const int red_blocks=polar_real(eflag,vflag);
ans->copy_answers(eflag_in,vflag_in,eatom,vatom,red_blocks);
device->add_ans_object(ans);
@ -412,7 +468,7 @@ int** BaseAmoebaT::compute_polar_real(const int ago, const int inum_full, const
printf("i = %d; tep = %f %f %f\n", i, p->x, p->y, p->z);
}
*/
return nbor->host_jlist.begin()-host_start;
return firstneigh; // nbor->host_jlist.begin()-host_start;
}
// ---------------------------------------------------------------------------
@ -423,6 +479,7 @@ template <class numtyp, class acctyp>
int** BaseAmoebaT::compute_udirect2b(const int ago, const int inum_full, const int nall,
double **host_x, int *host_type, int *host_amtype,
int *host_amgroup, double **host_rpole,
double **host_uind, double **host_uinp,
double *sublo, double *subhi, tagint *tag,
int **nspecial, tagint **special,
int *nspecial15, tagint **special15,
@ -447,59 +504,26 @@ int** BaseAmoebaT::compute_udirect2b(const int ago, const int inum_full, const i
set_kernel(eflag,vflag);
// reallocate per-atom arrays and build the neighbor lists if needed
int** firstneigh = nullptr;
firstneigh = precompute(ago, inum_full, nall, host_x, host_type,
host_amtype, host_amgroup, host_rpole,
host_uind, host_uinp, sublo, subhi, tag,
nspecial, special, nspecial15, special15,
eflag_in, vflag_in, eatom, vatom,
host_start, ilist, jnum, cpu_time,
success, host_q, boxlo, prd);
// ------------------- Resize _fieldp array ------------------------
if (nall>_max_fieldp_size) {
_max_fieldp_size=static_cast<int>(static_cast<double>(nall)*1.10);
_fieldp.resize(_max_fieldp_size*8);
dev_nspecial15.clear();
dev_special15.clear();
dev_special15_t.clear();
dev_nspecial15.alloc(nall,*(this->ucl_device),UCL_READ_ONLY);
dev_special15.alloc(_maxspecial15*nall,*(this->ucl_device),UCL_READ_ONLY);
dev_special15_t.alloc(nall*_maxspecial15,*(this->ucl_device),UCL_READ_ONLY);
}
*fieldp_ptr=_fieldp.host.begin();
if (inum_full==0) {
host_start=0;
// Make sure textures are correct if realloc by a different hybrid style
resize_atom(0,nall,success);
zero_timers();
return nullptr;
}
hd_balancer.balance(cpu_time);
int inum=hd_balancer.get_gpu_count(ago,inum_full);
ans->inum(inum);
host_start=inum;
// Build neighbor list on GPU if necessary
if (ago==0) {
build_nbor_list(inum, inum_full-inum, nall, host_x, host_type,
sublo, subhi, tag, nspecial, special, nspecial15, special15,
success);
if (!success)
return nullptr;
atom->cast_q_data(host_q);
cast_extra_data(host_amtype, host_amgroup, host_rpole, nullptr, nullptr);
hd_balancer.start_timer();
} else {
atom->cast_x_data(host_x,host_type);
atom->cast_q_data(host_q);
cast_extra_data(host_amtype, host_amgroup, host_rpole, nullptr, nullptr);
hd_balancer.start_timer();
atom->add_x_data(host_x,host_type);
}
atom->add_q_data();
atom->add_extra_data();
*ilist=nbor->host_ilist.begin();
*jnum=nbor->host_acc.begin();
const int red_blocks=udirect2b(eflag,vflag);
hd_balancer.stop_timer();
// copy field and fieldp from device to host (_fieldp store both arrays, one after another)
@ -511,8 +535,7 @@ int** BaseAmoebaT::compute_udirect2b(const int ago, const int inum_full, const i
printf("i = %d; field = %f %f %f\n", i, p->x, p->y, p->z);
}
*/
return nbor->host_jlist.begin()-host_start;
return firstneigh; //nbor->host_jlist.begin()-host_start;
}
template <class numtyp, class acctyp>

18
lib/gpu/lal_base_amoeba.h
View File

@ -128,6 +128,18 @@ class BaseAmoeba {
tagint **special, int *nspecial15, tagint **special15,
bool &success);
/// Reallocate per-atom arrays if needed, and build neighbor lists once, if needed
int** precompute(const int ago, const int inum_full, const int nall,
double **host_x, int *host_type, int *host_amtype,
int *host_amgroup, double **host_rpole, double **host_uind,
double **host_uinp, double *sublo, double *subhi,
tagint *tag, int **nspecial, tagint **special,
int *nspecial15, tagint **special15,
const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
int **&ilist, int **&numj, const double cpu_time, bool &success,
double *charge, double *boxlo, double *prd);
/// Compute polar real-space with host neighboring (not active for now)
void compute_polar_real(const int f_ago, const int inum_full, const int nall,
double **host_x, int *host_type, int *host_amtype,
@ -153,7 +165,9 @@ class BaseAmoeba {
/// Compute the direct real space part of the permanent field (udirect2b) with device neighboring
int** compute_udirect2b(const int ago, const int inum_full, const int nall,
double **host_x, int *host_type, int *host_amtype,
int *host_amgroup, double **host_rpole, double *sublo, double *subhi,
int *host_amgroup, double **host_rpole,
double **host_uind, double **host_uinp,
double *sublo, double *subhi,
tagint *tag, int **nspecial, tagint **special,
int *nspecial15, tagint **special15,
const bool eflag, const bool vflag,
@ -191,7 +205,7 @@ class BaseAmoeba {
/// Per-atom arrays
UCL_Vector<numtyp,numtyp> _tep, _fieldp;
int _max_tep_size, _max_fieldp_size;
int _nmax, _max_tep_size, _max_fieldp_size;
// ------------------------ FORCE/ENERGY DATA -----------------------

17
src/GPU/pair_amoeba_gpu.cpp
View File

@ -66,7 +66,8 @@ void amoeba_gpu_clear();
int ** amoeba_gpu_compute_udirect2b(const int ago, const int inum, const int nall,
double **host_x, int *host_type, int *host_amtype, int *host_amgroup,
double **host_rpole, double *sublo, double *subhi, tagint *tag, int **nspecial,
double **host_rpole, double **host_uind, double **host_uinp,
double *sublo, double *subhi, tagint *tag, int **nspecial,
tagint **special, int* nspecial15, tagint** special15,
const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
@ -370,16 +371,6 @@ void PairAmoebaGPU::induce()
crstyle = FIELD;
comm->reverse_comm_pair(this);
// DEBUG statements
/*
for (i = 0; i < nlocal; i++)
if (atom->tag[i] == 1)
printf("AAA FIELD atom %d: field %g %g %g: fieldp %g %g %g\n",
atom->tag[i],
field[i][0],field[i][1],field[i][2],
fieldp[i][0],fieldp[i][1],fieldp[i][2]);
*/
// set induced dipoles to polarizability times direct field
@ -814,8 +805,8 @@ void PairAmoebaGPU::udirect2b(double **field, double **fieldp)
inum = atom->nlocal;
firstneigh = amoeba_gpu_compute_udirect2b(neighbor->ago, inum, nall, atom->x,
atom->type, amtype, amgroup, rpole, sublo,
subhi, atom->tag, atom->nspecial, atom->special,
atom->type, amtype, amgroup, rpole, uind, uinp,
sublo, subhi, atom->tag, atom->nspecial, atom->special,
atom->nspecial15, atom->special15,
eflag, vflag, eflag_atom, vflag_atom,
host_start, &ilist, &numneigh, cpu_time,