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Moved precompute() out of the terms in amoeba and hippo, to be involed in the first term in a time step: multipole for amoeba and repulsion for hippo

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This commit is contained in:
Trung Nguyen
2022-09-30 16:31:13 -05:00
parent e6d2582642
commit 1d75ca3b20
9 changed files with 140 additions and 57 deletions
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2
lib/gpu/lal_amoeba.cpp
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@ -162,7 +162,7 @@ int AmoebaT::multipole_real(const int eflag, const int vflag) {
this->time_pair.start();
// Build the short neighbor list for the cutoff off2_mpole,
// at this point mpole is the first kernel in a time step
// at this point mpole is the first kernel in a time step for AMOEBA
this->k_short_nbor.set_size(GX,BX);
this->k_short_nbor.run(&this->atom->x, &this->nbor->dev_nbor,

25
lib/gpu/lal_amoeba_ext.cpp
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@ -117,7 +117,28 @@ void amoeba_gpu_clear() {
AMOEBAMF.clear();
}
int** amoeba_gpu_compute_multipole_real(const int ago, const int inum_full,
int** amoeba_gpu_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 *host_pval,
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) {
return AMOEBAMF.precompute(ago, inum_full, nall, host_x, host_type,
host_amtype, host_amgroup, host_rpole,
nullptr, nullptr, nullptr, sublo, subhi, tag,
nspecial, special, nspecial15, special15,
eflag_in, vflag_in, eatom, vatom,
host_start, ilist, jnum, cpu_time,
success, host_q, boxlo, prd);
}
void amoeba_gpu_compute_multipole_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 *sublo, double *subhi, tagint *tag, int **nspecial,
@ -127,7 +148,7 @@ int** amoeba_gpu_compute_multipole_real(const int ago, const int inum_full,
int **ilist, int **jnum, const double cpu_time,
bool &success, const double aewald, const double felec, const double off2,
double *host_q, double *boxlo, double *prd, void **tep_ptr) {
return AMOEBAMF.compute_multipole_real(ago, inum_full, nall, host_x, host_type,
AMOEBAMF.compute_multipole_real(ago, inum_full, nall, host_x, host_type,
host_amtype, host_amgroup, host_rpole, nullptr, sublo, subhi,
tag, nspecial, special, nspecial15, special15,
eflag, vflag, eatom, vatom, host_start, ilist, jnum,

21
lib/gpu/lal_base_amoeba.cpp
View File

@ -226,12 +226,12 @@ int * BaseAmoebaT::reset_nbors(const int nall, const int inum, int *ilist,
// ---------------------------------------------------------------------------
template <class numtyp, class acctyp>
inline int BaseAmoebaT::build_nbor_list(const int inum, const int host_inum,
const int nall, double **host_x,
int *host_type, double *sublo,
double *subhi, tagint *tag,
int **nspecial, tagint **special,
int *nspecial15, tagint **special15,
bool &success) {
const int nall, double **host_x,
int *host_type, double *sublo,
double *subhi, tagint *tag,
int **nspecial, tagint **special,
int *nspecial15, tagint **special15,
bool &success) {
success=true;
resize_atom(inum,nall,success);
resize_local(inum,host_inum,nbor->max_nbors(),success);
@ -450,7 +450,7 @@ int** BaseAmoebaT::precompute(const int ago, const int inum_full, const int nall
// Reneighbor on GPU if necessary, and then compute multipole real-space
// ---------------------------------------------------------------------------
template <class numtyp, class acctyp>
int** BaseAmoebaT::compute_multipole_real(const int ago, const int inum_full,
void BaseAmoebaT::compute_multipole_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_pval,
@ -469,7 +469,7 @@ int** BaseAmoebaT::compute_multipole_real(const int ago, const int inum_full,
// NOTE:
// Once all the kernels are ready, precompute() is needed only once
// in the first kernel in a time step.
/*
int** firstneigh = nullptr;
firstneigh = precompute(ago, inum_full, nall, host_x, host_type,
host_amtype, host_amgroup, host_rpole,
@ -478,7 +478,7 @@ int** BaseAmoebaT::compute_multipole_real(const int ago, const int inum_full,
eflag_in, vflag_in, eatom, vatom,
host_start, ilist, jnum, cpu_time,
success, host_q, boxlo, prd);
*/
// ------------------- Resize _tep array ------------------------
if (inum_full>_max_tep_size) {
@ -503,7 +503,7 @@ int** BaseAmoebaT::compute_multipole_real(const int ago, const int inum_full,
_tep.update_host(_max_tep_size*4,false);
return firstneigh; // nbor->host_jlist.begin()-host_start;
// return firstneigh; // nbor->host_jlist.begin()-host_start;
}
// ---------------------------------------------------------------------------
@ -782,7 +782,6 @@ int BaseAmoebaT::fphi_mpole() {
// Compute the block size and grid size to keep all cores busy
const int BX=block_size();
//printf("BX = %d; pppm block size = %d\n", BX, PPPM_BLOCK_1D);
int GX=static_cast<int>(ceil(static_cast<double>(this->ans->inum())/BX));
time_pair.start();

2
lib/gpu/lal_base_amoeba.h
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@ -152,7 +152,7 @@ class BaseAmoeba {
double *charge, double *boxlo, double *prd);
/// Compute multipole real-space with device neighboring
virtual int** compute_multipole_real(const int ago, const int inum_full, const int nall,
virtual void compute_multipole_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_pval,
double *sublo, double *subhi, tagint *tag,

18
lib/gpu/lal_hippo.cpp
View File

@ -172,7 +172,7 @@ double HippoT::host_memory_usage() const {
// Reneighbor on GPU if necessary, and then compute repulsion
// ---------------------------------------------------------------------------
template <class numtyp, class acctyp>
int** HippoT::compute_repulsion(const int ago, const int inum_full,
void HippoT::compute_repulsion(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,
@ -213,7 +213,7 @@ int** HippoT::compute_repulsion(const int ago, const int inum_full,
// We only need to cast the necessary from host to device here
// if the neighbor lists are rebuilt and other per-atom arrays
// (x, type, amtype, amgroup, rpole) are ready on the device.
/*
int** firstneigh = nullptr;
firstneigh = this->precompute(ago, inum_full, nall, host_x, host_type,
host_amtype, host_amgroup, host_rpole,
@ -222,7 +222,7 @@ int** HippoT::compute_repulsion(const int ago, const int inum_full,
eflag_in, vflag_in, eatom, vatom,
host_start, ilist, jnum, cpu_time,
success, host_q, boxlo, prd);
*/
// ------------------- Resize _tep array ------------------------
if (inum_full>this->_max_tep_size) {
@ -253,7 +253,7 @@ int** HippoT::compute_repulsion(const int ago, const int inum_full,
this->_tep.update_host(this->_max_tep_size*4,false);
return firstneigh; // nbor->host_jlist.begin()-host_start;
// return firstneigh; // nbor->host_jlist.begin()-host_start;
}
// ---------------------------------------------------------------------------
@ -275,7 +275,7 @@ int HippoT::repulsion(const int eflag, const int vflag) {
this->time_pair.start();
// Build the short neighbor list for the cutoff off2_disp,
// at this point mpole is the first kernel in a time step
// at this point repuslion is the first kernel in a time step for HIPPO
this->k_short_nbor.set_size(GX,BX);
this->k_short_nbor.run(&this->atom->x, &this->nbor->dev_nbor,
@ -302,7 +302,7 @@ int HippoT::repulsion(const int eflag, const int vflag) {
// Reneighbor on GPU if necessary, and then compute dispersion real-space
// ---------------------------------------------------------------------------
template <class numtyp, class acctyp>
int** HippoT::compute_dispersion_real(int *host_amtype, int *host_amgroup,
void HippoT::compute_dispersion_real(int *host_amtype, int *host_amgroup,
double **host_rpole, const double aewald,
const double off2_disp) {
@ -324,7 +324,7 @@ int** HippoT::compute_dispersion_real(int *host_amtype, int *host_amgroup,
this->hd_balancer.stop_timer();
return nullptr; // nbor->host_jlist.begin()-host_start;
// return nullptr; // nbor->host_jlist.begin()-host_start;
}
// ---------------------------------------------------------------------------
@ -372,7 +372,7 @@ int HippoT::dispersion_real(const int eflag, const int vflag) {
// Reneighbor on GPU if necessary, and then compute multipole real-space
// ---------------------------------------------------------------------------
template <class numtyp, class acctyp>
int** HippoT::compute_multipole_real(const int ago, const int inum_full,
void HippoT::compute_multipole_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,
@ -417,7 +417,7 @@ int** HippoT::compute_multipole_real(const int ago, const int inum_full,
this->_tep.update_host(this->_max_tep_size*4,false);
return nullptr; // nbor->host_jlist.begin()-host_start;
//return nullptr; // nbor->host_jlist.begin()-host_start;
}
// ---------------------------------------------------------------------------

6
lib/gpu/lal_hippo.h
View File

@ -55,7 +55,7 @@ class Hippo : public BaseAmoeba<numtyp, acctyp> {
const double polar_dscale, const double polar_uscale);
/// Compute repulsion with device neighboring
int** compute_repulsion(const int ago, const int inum_full,
virtual void compute_repulsion(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,
@ -72,12 +72,12 @@ class Hippo : public BaseAmoeba<numtyp, acctyp> {
double c3, double c4, double c5,void** tep_ptr);
/// Compute dispersion real-space with device neighboring
int** compute_dispersion_real(int *host_amtype, int *host_amgroup,
virtual void compute_dispersion_real(int *host_amtype, int *host_amgroup,
double **host_rpole, const double aewald,
const double off2_disp);
/// Compute multipole real-space with device neighboring
virtual int** compute_multipole_real(const int ago, const int inum_full, const int nall,
virtual void compute_multipole_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_pval,
double *sublo, double *subhi, tagint *tag, int **nspecial, tagint **special,

28
lib/gpu/lal_hippo_ext.cpp
View File

@ -120,7 +120,27 @@ void hippo_gpu_clear() {
HIPPOMF.clear();
}
int** hippo_gpu_compute_repulsion(const int ago, const int inum_full,
int** hippo_gpu_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 *host_pval,
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) {
return HIPPOMF.precompute(ago, inum_full, nall, host_x, host_type,
host_amtype, host_amgroup, host_rpole,
nullptr, nullptr, nullptr, sublo, subhi, tag,
nspecial, special, nspecial15, special15,
eflag_in, vflag_in, eatom, vatom,
host_start, ilist, jnum, cpu_time,
success, host_q, boxlo, prd);
}
void hippo_gpu_compute_repulsion(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, tagint *tag, int **nspecial,
@ -132,7 +152,7 @@ int** hippo_gpu_compute_repulsion(const int ago, const int inum_full,
double *host_q, double *boxlo, double *prd,
double cut2, double c0, double c1, double c2,
double c3, double c4, double c5, void **tep_ptr) {
return HIPPOMF.compute_repulsion(ago, inum_full, nall, host_x, host_type,
HIPPOMF.compute_repulsion(ago, inum_full, nall, host_x, host_type,
host_amtype, host_amgroup, host_rpole, sublo, subhi,
tag, nspecial, special, nspecial15, special15,
eflag, vflag, eatom, vatom, host_start, ilist, jnum,
@ -147,7 +167,7 @@ void hippo_gpu_compute_dispersion_real(int *host_amtype, int *host_amgroup,
aewald, off2);
}
int** hippo_gpu_compute_multipole_real(const int ago, const int inum_full,
void hippo_gpu_compute_multipole_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_pval, double *sublo, double *subhi, tagint *tag, int **nspecial,
@ -157,7 +177,7 @@ int** hippo_gpu_compute_multipole_real(const int ago, const int inum_full,
int **ilist, int **jnum, const double cpu_time,
bool &success, const double aewald, const double felec, const double off2,
double *host_q, double *boxlo, double *prd, void **tep_ptr) {
return HIPPOMF.compute_multipole_real(ago, inum_full, nall, host_x, host_type,
HIPPOMF.compute_multipole_real(ago, inum_full, nall, host_x, host_type,
host_amtype, host_amgroup, host_rpole, host_pval, sublo, subhi,
tag, nspecial, special, nspecial15, special15,
eflag, vflag, eatom, vatom, host_start, ilist, jnum,

47
src/GPU/pair_amoeba_gpu.cpp
View File

@ -69,7 +69,19 @@ int amoeba_gpu_init(const int ntypes, const int max_amtype, const int max_amclas
const double polar_dscale, const double polar_uscale, int& tq_size);
void amoeba_gpu_clear();
int ** amoeba_gpu_compute_multipole_real(const int ago, const int inum, const int nall,
int** amoeba_gpu_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 *host_pval,
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 amoeba_gpu_compute_multipole_real(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, tagint **special, int* nspecial15, tagint** special15,
@ -240,6 +252,18 @@ void PairAmoebaGPU::multipole_real()
}
inum = atom->nlocal;
firstneigh = amoeba_gpu_precompute(neighbor->ago, inum, nall, atom->x,
atom->type, amtype, amgroup, rpole,
nullptr, nullptr, nullptr,
sublo, subhi, atom->tag,
atom->nspecial, atom->special,
atom->nspecial15, atom->special15,
eflag, vflag, eflag_atom, vflag_atom,
host_start, &ilist, &numneigh, cpu_time,
success, atom->q, domain->boxlo, domain->prd);
if (!success)
error->one(FLERR,"Insufficient memory on accelerator");
// select the correct cutoff for the term
if (use_ewald) choose(MPOLE_LONG);
@ -249,18 +273,17 @@ void PairAmoebaGPU::multipole_real()
double felec = electric / am_dielectric;
firstneigh = amoeba_gpu_compute_multipole_real(neighbor->ago, inum, nall, atom->x,
atom->type, amtype, amgroup, rpole,
sublo, subhi, atom->tag,
atom->nspecial, atom->special,
atom->nspecial15, atom->special15,
eflag, vflag, eflag_atom, vflag_atom,
host_start, &ilist, &numneigh, cpu_time,
success, aewald, felec, off2, atom->q,
domain->boxlo, domain->prd, &tq_pinned);
amoeba_gpu_compute_multipole_real(neighbor->ago, inum, nall, atom->x,
atom->type, amtype, amgroup, rpole,
sublo, subhi, atom->tag,
atom->nspecial, atom->special,
atom->nspecial15, atom->special15,
eflag, vflag, eflag_atom, vflag_atom,
host_start, &ilist, &numneigh, cpu_time,
success, aewald, felec, off2, atom->q,
domain->boxlo, domain->prd, &tq_pinned);
if (!success)
error->one(FLERR,"Insufficient memory on accelerator");
// reference to the tep array from GPU lib

48
src/GPU/pair_hippo_gpu.cpp
View File

@ -70,7 +70,19 @@ int hippo_gpu_init(const int ntypes, const int max_amtype, const int max_amclass
const double polar_dscale, const double polar_uscale, int& tq_size);
void hippo_gpu_clear();
int** hippo_gpu_compute_repulsion(const int ago, const int inum_full,
int** hippo_gpu_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 *host_pval,
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 hippo_gpu_compute_repulsion(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, tagint *tag, int **nspecial,
@ -86,7 +98,7 @@ int** hippo_gpu_compute_repulsion(const int ago, const int inum_full,
void hippo_gpu_compute_dispersion_real(int *host_amtype, int *host_amgroup, double **host_rpole,
const double aewald, const double off2);
int ** hippo_gpu_compute_multipole_real(const int ago, const int inum, const int nall,
void hippo_gpu_compute_multipole_real(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 *host_pval, double *sublo, double *subhi, tagint *tag,
int **nspecial, tagint **special, int* nspecial15, tagint** special15,
@ -258,22 +270,30 @@ void PairHippoGPU::repulsion()
}
inum = atom->nlocal;
firstneigh = hippo_gpu_precompute(neighbor->ago, inum, nall, atom->x,
atom->type, amtype, amgroup, rpole,
nullptr, nullptr, nullptr,
sublo, subhi, atom->tag,
atom->nspecial, atom->special,
atom->nspecial15, atom->special15,
eflag, vflag, eflag_atom, vflag_atom,
host_start, &ilist, &numneigh, cpu_time,
success, atom->q, domain->boxlo, domain->prd);
// select the correct cutoff for the term
choose(REPULSE);
// set the energy unit conversion factor for multipolar real-space calculation
firstneigh = hippo_gpu_compute_repulsion(neighbor->ago, inum, nall, atom->x,
atom->type, amtype, amgroup, rpole,
sublo, subhi, atom->tag,
atom->nspecial, atom->special,
atom->nspecial15, atom->special15,
eflag, vflag, eflag_atom, vflag_atom,
host_start, &ilist, &numneigh, cpu_time,
success, aewald, off2, atom->q,
domain->boxlo, domain->prd, cut2,
c0, c1, c2, c3, c4, c5, &tq_pinned);
hippo_gpu_compute_repulsion(neighbor->ago, inum, nall, atom->x,
atom->type, amtype, amgroup, rpole,
sublo, subhi, atom->tag,
atom->nspecial, atom->special,
atom->nspecial15, atom->special15,
eflag, vflag, eflag_atom, vflag_atom,
host_start, &ilist, &numneigh, cpu_time,
success, aewald, off2, atom->q,
domain->boxlo, domain->prd, cut2,
c0, c1, c2, c3, c4, c5, &tq_pinned);
if (!success)
error->one(FLERR,"Insufficient memory on accelerator");