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Switched to the short neighbor list implementation in the pre-10Feb21 version (the recent version enforces tpa = 1 for short nbor)

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This commit is contained in:
Trung Nguyen
2021-09-11 00:34:43 -05:00
parent 4ebe5833d3
commit 7f5a82dc54
5 changed files with 103 additions and 54 deletions
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39
lib/gpu/lal_amoeba.cpp
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@ -141,14 +141,31 @@ int AmoebaT::polar_real(const int eflag, const int vflag) {
int nbor_pitch=this->nbor->nbor_pitch();
this->time_pair.start();
// Build the short neighbor list if needed
if (!this->short_nbor_avail) {
this->k_short_nbor.set_size(GX,BX);
this->k_short_nbor.run(&this->atom->x, &this->nbor->dev_nbor,
&this->_nbor_data->begin(),
&this->dev_short_nbor, &_off2, &ainum,
&nbor_pitch, &this->_threads_per_atom);
this->short_nbor_avail = true;
}
this->k_polar.set_size(GX,BX);
this->k_polar.run(&this->atom->x, &this->atom->extra, &damping, &sp_polar,
&this->nbor->dev_nbor, &this->_nbor_data->begin(),
&this->dev_short_nbor,
&this->ans->force, &this->ans->engv, &this->_tep,
&eflag, &vflag, &ainum, &_nall, &nbor_pitch,
&this->_threads_per_atom,
&_aewald, &_felec, &_off2, &_polar_dscale, &_polar_uscale);
this->time_pair.stop();
// Signal that short nbor list is not avail for the next time step
// do it here because polar_real() is the last kernel in a time step at this point
this->short_nbor_avail = false;
return GX;
}
@ -163,20 +180,22 @@ int AmoebaT::udirect2b(const int eflag, const int vflag) {
// Compute the block size and grid size to keep all cores busy
const int BX=this->block_size();
int GX;
int GX=static_cast<int>(ceil(static_cast<double>(this->ans->inum())/(BX/this->_threads_per_atom)));
// Build the short neighbor list if needed
if (!this->short_nbor_avail) {
this->k_short_nbor.set_size(GX,BX);
this->k_short_nbor.run(&this->atom->x, &this->nbor->dev_nbor,
&this->_nbor_data->begin(),
&this->dev_short_nbor, &_off2, &ainum,
&nbor_pitch, &this->_threads_per_atom);
this->short_nbor_avail = true;
}
GX=static_cast<int>(ceil(static_cast<double>(ainum)/BX));
this->k_short_nbor.set_size(GX,BX);
// NOTE: this->nbor->dev_packed is not allocated!!
/*
this->k_short_nbor.run(&this->atom->x, &_off2,
&this->nbor->dev_nbor, &this->nbor->dev_packed,
&ainum, &nbor_pitch, &this->_threads_per_atom);
*/
GX=static_cast<int>(ceil(static_cast<double>(this->ans->inum())/(BX/this->_threads_per_atom)));
this->k_udirect2b.set_size(GX,BX);
this->k_udirect2b.run(&this->atom->x, &this->atom->extra, &damping, &sp_polar,
&this->nbor->dev_nbor, &this->_nbor_data->begin(),
&this->dev_short_nbor,
&this->_fieldp, &ainum, &_nall, &nbor_pitch,
&this->_threads_per_atom, &_aewald, &_off2,
&_polar_dscale, &_polar_uscale);