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Gradually cleaned up and removed redundancy in amoeba and hippo

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This commit is contained in:
Trung Nguyen
2021-10-02 00:09:53 -05:00
parent f126f785a4
commit f4d3d3a2b5
7 changed files with 61 additions and 309 deletions
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156
lib/gpu/lal_base_amoeba.cpp
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@ -245,8 +245,8 @@ inline int BaseAmoebaT::build_nbor_list(const int inum, const int host_inum,
// ---------------------------------------------------------------------------
template <class numtyp, class acctyp>
void BaseAmoebaT::compute_polar_real_host_nbor(const int f_ago, const int inum_full,
const int nall, double **host_x, int *host_type, int *host_amtype,
int *host_amgroup, double **host_rpole,
const int nall, double **host_x, int *host_type,
int *host_amtype, int *host_amgroup, double **host_rpole,
double **host_uind, double **host_uinp,
int *ilist, int *numj, int **firstneigh,
const bool eflag_in, const bool vflag_in,
@ -353,7 +353,6 @@ int** BaseAmoebaT::precompute(const int ago, const int inum_full, const int nall
bool &success, double *host_q, double *boxlo,
double *prd) {
acc_timers();
//int eflag, vflag;
if (eatom) _eflag=2;
else if (eflag_in) _eflag=1;
else _eflag=0;
@ -401,12 +400,10 @@ int** BaseAmoebaT::precompute(const int ago, const int inum_full, const int nall
if (!success)
return nullptr;
atom->cast_q_data(host_q);
//cast_extra_data(host_amtype, host_amgroup, host_rpole, host_uind, host_uinp, host_pval);
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, host_uind, host_uinp, host_pval);
hd_balancer.start_timer();
atom->add_x_data(host_x,host_type);
}
@ -444,23 +441,6 @@ int** BaseAmoebaT::compute_multipole_real(const int ago, const int inum_full,
const double aewald, const double felec,
const double off2_mpole, 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, transfer data from the host
// and build the neighbor lists if needed
// NOTE:
@ -499,13 +479,7 @@ int** BaseAmoebaT::compute_multipole_real(const int ago, const int inum_full,
// copy tep from device to host
_tep.update_host(_max_tep_size*4,false);
/*
printf("GPU lib: tep size = %d: max tep size = %d\n", this->_tep.cols(), _max_tep_size);
for (int i = 0; i < 10; i++) {
numtyp4* p = (numtyp4*)(&this->_tep[4*i]);
printf("i = %d; tep = %f %f %f\n", i, p->x, p->y, p->z);
}
*/
return firstneigh; // nbor->host_jlist.begin()-host_start;
}
@ -529,36 +503,11 @@ int** BaseAmoebaT::compute_udirect2b(const int ago, const int inum_full,
const double aewald, const double off2_polar,
double *host_q, double *boxlo, double *prd,
void** fieldp_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, transfer data from the host
// 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, 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);
*/
cast_extra_data(host_amtype, host_amgroup, host_rpole, host_uind, host_uinp, host_pval);
atom->add_extra_data();
@ -577,14 +526,7 @@ int** BaseAmoebaT::compute_udirect2b(const int ago, const int inum_full,
// copy field and fieldp from device to host (_fieldp store both arrays, one after another)
_fieldp.update_host(_max_fieldp_size*8,false);
/*
printf("GPU lib: _fieldp size = %d: max fieldp size = %d\n",
this->_fieldp.cols(), _max_fieldp_size);
for (int i = 0; i < 10; i++) {
numtyp4* p = (numtyp4*)(&this->_fieldp[4*i]);
printf("i = %d; field = %f %f %f\n", i, p->x, p->y, p->z);
}
*/
return firstneigh; //nbor->host_jlist.begin()-host_start;
}
@ -608,36 +550,11 @@ int** BaseAmoebaT::compute_umutual2b(const int ago, const int inum_full,
const double aewald, const double off2_polar,
double *host_q, double *boxlo, double *prd,
void** fieldp_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, transfer extra data from the host
// 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, 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);
*/
cast_extra_data(host_amtype, host_amgroup, host_rpole, host_uind, host_uinp, host_pval);
atom->add_extra_data();
@ -656,14 +573,7 @@ int** BaseAmoebaT::compute_umutual2b(const int ago, const int inum_full,
// copy field and fieldp from device to host (_fieldp store both arrays, one after another)
_fieldp.update_host(_max_fieldp_size*8,false);
/*
printf("GPU lib: _fieldp size = %d: max fieldp size = %d\n",
this->_fieldp.cols(), _max_fieldp_size);
for (int i = 0; i < 10; i++) {
numtyp4* p = (numtyp4*)(&this->_fieldp[4*i]);
printf("i = %d; field = %f %f %f\n", i, p->x, p->y, p->z);
}
*/
return firstneigh; //nbor->host_jlist.begin()-host_start;
}
@ -686,44 +596,9 @@ int** BaseAmoebaT::compute_polar_real(const int ago, const int inum_full,
const double aewald, const double felec,
const double off2_polar, 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, transfer data from the host
// and build the neighbor lists if needed
// NOTE:
// For now we invoke precompute() again here,
// to be able to turn on/off the udirect2b kernel (which comes before this)
// Once all the kernels are ready, precompute() is needed only once
// in the first kernel in a time step.
// We only need to cast uind and uinp 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 = precompute(ago, inum_full, nall, host_x, host_type,
host_amtype, host_amgroup, host_rpole,
host_uind, host_uinp, 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);
*/
cast_extra_data(host_amtype, host_amgroup, host_rpole, host_uind, host_uinp, host_pval);
atom->add_extra_data();
@ -750,13 +625,7 @@ int** BaseAmoebaT::compute_polar_real(const int ago, const int inum_full,
// copy tep from device to host
_tep.update_host(_max_tep_size*4,false);
/*
printf("GPU lib: tep size = %d: max tep size = %d\n", this->_tep.cols(), _max_tep_size);
for (int i = 0; i < 10; i++) {
numtyp4* p = (numtyp4*)(&this->_tep[4*i]);
printf("i = %d; tep = %f %f %f\n", i, p->x, p->y, p->z);
}
*/
return firstneigh; // nbor->host_jlist.begin()-host_start;
}
@ -826,7 +695,6 @@ void BaseAmoebaT::cast_extra_data(int* amtype, int* amgroup, double** rpole,
n += nstride*_nall;
if (pval) {
for (int i = 0; i < _nall; i++) {
int idx = n+i*nstride;
pextra[idx] = pval[i];
@ -889,9 +757,9 @@ int BaseAmoebaT::add_onefive_neighbors() {
k_special15.set_size(GX,BX);
k_special15.run(&nbor->dev_nbor, &_nbor_data->begin(),
&atom->dev_tag, &dev_nspecial15, &dev_special15,
&ainum, &_nall, &nbor_pitch,
&_threads_per_atom);
&atom->dev_tag, &dev_nspecial15, &dev_special15,
&ainum, &_nall, &nbor_pitch,
&_threads_per_atom);
return GX;
}