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Working on short neighbor list for tersoff/gpu

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This commit is contained in:
Trung Nguyen
2017-07-08 14:15:26 -05:00
parent 68206079da
commit 1c6533e53d
3 changed files with 178 additions and 71 deletions
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81
lib/gpu/lal_tersoff.cpp
View File

@ -55,7 +55,8 @@ int TersoffT::init(const int ntypes, const int nlocal, const int nall, const int
int success;
success=this->init_three(nlocal,nall,max_nbors,0,cell_size,gpu_split,
_screen,tersoff,"k_tersoff_repulsive",
"k_tersoff_three_center", "k_tersoff_three_end");
"k_tersoff_three_center", "k_tersoff_three_end",
"k_tersoff_short_nbor");
if (success!=0)
return success;
@ -157,8 +158,12 @@ int TersoffT::init(const int ntypes, const int nlocal, const int nall, const int
UCL_H_Vec<numtyp> cutsq_view(nparams,*(this->ucl_device),
UCL_WRITE_ONLY);
for (int i=0; i<nparams; i++)
double cutsqmax = 0.0;
for (int i=0; i<nparams; i++) {
cutsq_view[i]=static_cast<numtyp>(host_cutsq[i]);
if (cutsqmax < host_cutsq[i]) cutsqmax = host_cutsq[i];
}
_cutshortsq = static_cast<numtyp>(cutsqmax);
cutsq.alloc(nparams,*(this->ucl_device),UCL_READ_ONLY);
ucl_copy(cutsq,cutsq_view,false);
@ -250,7 +255,7 @@ void TersoffT::compute(const int f_ago, const int inum_full, const int nall,
this->reset_nbors(nall, inum, nlist, ilist, numj, firstneigh, success);
if (!success)
return;
_max_nbors = this->nbor->max_nbor_loop(nlist,numj,ilist);
this->_max_nbors = this->nbor->max_nbor_loop(nlist,numj,ilist);
}
this->atom->cast_x_data(host_x,host_type);
@ -258,29 +263,19 @@ void TersoffT::compute(const int f_ago, const int inum_full, const int nall,
this->atom->add_x_data(host_x,host_type);
// re-allocate zetaij if necessary
if (nall*_max_nbors > _zetaij.cols()) {
if (nall*this->_max_nbors > _zetaij.cols()) {
int _nmax=static_cast<int>(static_cast<double>(nall)*1.10);
_zetaij.resize(_max_nbors*_nmax);
_zetaij.resize(this->_max_nbors*_nmax);
}
this->_ainum=nlist;
int _eflag;
if (eflag)
_eflag=1;
else
_eflag=0;
int ainum=nlist;
int nbor_pitch=this->nbor->nbor_pitch();
int BX=this->block_pair();
int GX=static_cast<int>(ceil(static_cast<double>(ainum)/
(BX/(JTHREADS*KTHREADS))));
this->k_zeta.set_size(GX,BX);
this->k_zeta.run(&this->atom->x, &ts1, &ts2, &ts3, &ts4, &ts5, &cutsq,
&map, &elem2param, &_nelements, &_nparams, &_zetaij,
&this->nbor->dev_nbor, &this->_nbor_data->begin(),
&_eflag, &ainum, &nbor_pitch, &this->_threads_per_atom);
int evatom=0;
if (eatom || vatom)
evatom=1;
@ -329,7 +324,7 @@ int ** TersoffT::compute(const int ago, const int inum_full,
// Build neighbor list on GPU if necessary
if (ago==0) {
_max_nbors = this->build_nbor_list(inum, inum_full-inum, nall, host_x, host_type,
this->_max_nbors = this->build_nbor_list(inum, inum_full-inum, nall, host_x, host_type,
sublo, subhi, tag, nspecial, special, success);
if (!success)
return NULL;
@ -343,29 +338,19 @@ int ** TersoffT::compute(const int ago, const int inum_full,
*jnum=this->nbor->host_acc.begin();
// re-allocate zetaij if necessary
if (nall*_max_nbors > _zetaij.cols()) {
if (nall*this->_max_nbors > _zetaij.cols()) {
int _nmax=static_cast<int>(static_cast<double>(nall)*1.10);
_zetaij.resize(_max_nbors*_nmax);
_zetaij.resize(this->_max_nbors*_nmax);
}
this->_ainum=nall;
int _eflag;
if (eflag)
_eflag=1;
else
_eflag=0;
int ainum=nall;
int nbor_pitch=this->nbor->nbor_pitch();
int BX=this->block_pair();
int GX=static_cast<int>(ceil(static_cast<double>(ainum)/
(BX/(JTHREADS*KTHREADS))));
this->k_zeta.set_size(GX,BX);
this->k_zeta.run(&this->atom->x, &ts1, &ts2, &ts3, &ts4, &ts5, &cutsq,
&map, &elem2param, &_nelements, &_nparams, &_zetaij,
&this->nbor->dev_nbor, &this->_nbor_data->begin(),
&_eflag, &ainum, &nbor_pitch, &this->_threads_per_atom);
int evatom=0;
if (eatom || vatom)
evatom=1;
@ -402,9 +387,32 @@ void TersoffT::loop(const bool _eflag, const bool _vflag, const int evatom) {
else
vflag=0;
int ainum=this->ans->inum();
// build the short neighbor list
int ainum=this->_ainum;
int nbor_pitch=this->nbor->nbor_pitch();
int GX=static_cast<int>(ceil(static_cast<double>(this->ans->inum())/
int GX=static_cast<int>(ceil(static_cast<double>(ainum)/
(BX/this->_threads_per_atom)));
this->k_short_nbor.set_size(GX,BX);
this->k_short_nbor.run(&this->atom->x, &_cutshortsq,
&this->nbor->dev_nbor, &this->_nbor_data->begin(),
&this->dev_short_nbor, &ainum,
&nbor_pitch, &this->_threads_per_atom);
nbor_pitch=this->nbor->nbor_pitch();
GX=static_cast<int>(ceil(static_cast<double>(this->_ainum)/
(BX/(JTHREADS*KTHREADS))));
this->k_zeta.set_size(GX,BX);
this->k_zeta.run(&this->atom->x, &ts1, &ts2, &ts3, &ts4, &ts5, &cutsq,
&map, &elem2param, &_nelements, &_nparams, &_zetaij,
&this->nbor->dev_nbor, &this->_nbor_data->begin(),
&this->dev_short_nbor,
&_eflag, &this->_ainum, &nbor_pitch, &this->_threads_per_atom);
ainum=this->ans->inum();
nbor_pitch=this->nbor->nbor_pitch();
GX=static_cast<int>(ceil(static_cast<double>(this->ans->inum())/
(BX/this->_threads_per_atom)));
this->time_pair.start();
@ -423,6 +431,7 @@ void TersoffT::loop(const bool _eflag, const bool _vflag, const int evatom) {
this->k_three_center.run(&this->atom->x, &ts1, &ts2, &ts4, &cutsq,
&map, &elem2param, &_nelements, &_nparams, &_zetaij,
&this->nbor->dev_nbor, &this->_nbor_data->begin(),
&this->dev_short_nbor,
&this->ans->force, &this->ans->engv, &eflag, &vflag, &ainum,
&nbor_pitch, &this->_threads_per_atom, &evatom);
@ -437,7 +446,7 @@ void TersoffT::loop(const bool _eflag, const bool _vflag, const int evatom) {
this->k_three_end_vatom.run(&this->atom->x, &ts1, &ts2, &ts4, &cutsq,
&map, &elem2param, &_nelements, &_nparams, &_zetaij,
&this->nbor->dev_nbor, &this->_nbor_data->begin(),
&this->nbor->dev_acc,
&this->nbor->dev_acc, &this->dev_short_nbor,
&end_ans->force, &end_ans->engv, &eflag, &vflag, &ainum,
&nbor_pitch, &this->_threads_per_atom, &this->_gpu_nbor);
@ -446,7 +455,7 @@ void TersoffT::loop(const bool _eflag, const bool _vflag, const int evatom) {
this->k_three_end.run(&this->atom->x, &ts1, &ts2, &ts4, &cutsq,
&map, &elem2param, &_nelements, &_nparams, &_zetaij,
&this->nbor->dev_nbor, &this->_nbor_data->begin(),
&this->nbor->dev_acc,
&this->nbor->dev_acc, &this->dev_short_nbor,
&end_ans->force, &end_ans->engv, &eflag, &vflag, &ainum,
&nbor_pitch, &this->_threads_per_atom, &this->_gpu_nbor);
}

165
lib/gpu/lal_tersoff.cu
View File

@ -164,6 +164,57 @@ texture<int4> ts5_tex;
#endif
__kernel void k_tersoff_short_nbor(const __global numtyp4 *restrict x_,
const numtyp cutshortsq,
const __global int * dev_nbor,
const __global int * dev_packed,
__global int * dev_short_nbor,
const int inum, const int nbor_pitch,
const int t_per_atom) {
__local int n_stride;
int tid, ii, offset;
atom_info(t_per_atom,ii,tid,offset);
if (ii<inum) {
int nbor, nbor_end;
int i, numj;
nbor_info(dev_nbor,dev_packed,nbor_pitch,t_per_atom,ii,offset,i,numj,
n_stride,nbor_end,nbor);
numtyp4 ix; fetch4(ix,i,pos_tex); //x_[i];
int ncount = 0;
int m = nbor;
dev_short_nbor[m] = 0;
int nbor_short = nbor+n_stride;
for ( ; nbor<nbor_end; nbor+=n_stride) {
int j=dev_packed[nbor];
int nj = j;
j &= NEIGHMASK;
numtyp4 jx; fetch4(jx,j,pos_tex); //x_[j];
// Compute r12
numtyp delx = ix.x-jx.x;
numtyp dely = ix.y-jx.y;
numtyp delz = ix.z-jx.z;
numtyp rsq = delx*delx+dely*dely+delz*delz;
if (rsq<cutshortsq) {
dev_short_nbor[nbor_short] = nj;
nbor_short += n_stride;
ncount++;
}
} // for nbor
// store the number of neighbors for each thread
dev_short_nbor[m] = ncount;
} // if ii
}
// Tersoff is currently used for 3 elements at most: 3*3*3 = 27 entries
// while the block size should never be less than 32.
// SHARED_SIZE = 32 for now to reduce the pressure on the shared memory per block
@ -184,6 +235,7 @@ __kernel void k_tersoff_zeta(const __global numtyp4 *restrict x_,
__global acctyp4 * zetaij,
const __global int * dev_nbor,
const __global int * dev_packed,
const __global int * dev_short_nbor,
const int eflag, const int inum,
const int nbor_pitch, const int t_per_atom) {
__local int tpa_sq,n_stride;
@ -218,15 +270,20 @@ __kernel void k_tersoff_zeta(const __global numtyp4 *restrict x_,
nbor_info(dev_nbor,dev_packed,nbor_pitch,t_per_atom,ii,offset_j,i,numj,
n_stride,nbor_end,nbor_j);
int offset_k=tid & (t_per_atom-1);
int nborj_start = nbor_j;
numtyp4 ix; fetch4(ix,i,pos_tex); //x_[i];
int itype=ix.w;
itype=map[itype];
// recalculate numj and nbor_end for use of the short nbor list
numj = dev_short_nbor[nbor_j];
nbor_j += n_stride;
int nborj_start = nbor_j;
nbor_end = nbor_j+fast_mul(numj,n_stride);
for ( ; nbor_j<nbor_end; nbor_j+=n_stride) {
int j=dev_packed[nbor_j];
int j=dev_short_nbor[nbor_j];
j &= NEIGHMASK;
numtyp4 jx; fetch4(jx,j,pos_tex); //x_[j];
@ -247,8 +304,11 @@ __kernel void k_tersoff_zeta(const __global numtyp4 *restrict x_,
z = (acctyp)0;
int nbor_k = nborj_start-offset_j+offset_k;
for ( ; nbor_k < nbor_end; nbor_k+=n_stride) {
int k=dev_packed[nbor_k];
int numk = dev_short_nbor[nbor_k-n_stride];
int k_end = nbor_k+fast_mul(numk,n_stride);
for ( ; nbor_k < k_end; nbor_k+=n_stride) {
int k=dev_short_nbor[nbor_k];
k &= NEIGHMASK;
if (k == j) continue;
@ -284,9 +344,10 @@ __kernel void k_tersoff_zeta(const __global numtyp4 *restrict x_,
//int jj = (nbor_j-offset_j-2*nbor_pitch)/n_stride;
//int idx = jj*n_stride + i*t_per_atom + offset_j;
int idx;
zeta_idx(dev_nbor,dev_packed, nbor_pitch, n_stride, t_per_atom,
i, nbor_j, offset_j, idx);
//idx to zetaij is shifted by n_stride relative to nbor_j in dev_short_nbor
int idx = nbor_j - n_stride;
// zeta_idx(dev_nbor,dev_packed, nbor_pitch, n_stride, t_per_atom,
// i, nbor_j, offset_j, idx);
store_zeta(z, tid, t_per_atom, offset_k);
numtyp4 ts1_ijparam = ts1[ijparam]; //fetch4(ts1_ijparam,ijparam,ts1_tex);
@ -428,6 +489,7 @@ __kernel void k_tersoff_three_center(const __global numtyp4 *restrict x_,
const __global acctyp4 *restrict zetaij,
const __global int * dev_nbor,
const __global int * dev_packed,
const __global int * dev_short_nbor,
__global acctyp4 *restrict ans,
__global acctyp *restrict engv,
const int eflag, const int vflag,
@ -466,15 +528,20 @@ __kernel void k_tersoff_three_center(const __global numtyp4 *restrict x_,
nbor_info(dev_nbor,dev_packed,nbor_pitch,t_per_atom,ii,offset_j,i,numj,
n_stride,nbor_end,nbor_j);
int offset_k=tid & (t_per_atom-1);
int nborj_start = nbor_j;
numtyp4 ix; fetch4(ix,i,pos_tex); //x_[i];
int itype=ix.w;
itype=map[itype];
// recalculate numj and nbor_end for use of the short nbor list
numj = dev_short_nbor[nbor_j];
nbor_j += n_stride;
int nborj_start = nbor_j;
nbor_end = nbor_j+fast_mul(numj,n_stride);
for ( ; nbor_j<nbor_end; nbor_j+=n_stride) {
int j=dev_packed[nbor_j];
int j=dev_short_nbor[nbor_j];
j &= NEIGHMASK;
numtyp4 jx; fetch4(jx,j,pos_tex); //x_[j];
@ -497,9 +564,10 @@ __kernel void k_tersoff_three_center(const __global numtyp4 *restrict x_,
//int jj = (nbor_j-offset_j-2*nbor_pitch) / n_stride;
//int idx = jj*n_stride + i*t_per_atom + offset_j;
int idx;
zeta_idx(dev_nbor,dev_packed, nbor_pitch, n_stride, t_per_atom,
i, nbor_j, offset_j, idx);
//idx to zetaij is shifted by n_stride relative to nbor_j in dev_short_nbor
int idx = nbor_j - n_stride;
// zeta_idx(dev_nbor,dev_packed, nbor_pitch, n_stride, t_per_atom,
// i, nbor_j, offset_j, idx);
acctyp4 zeta_ij = zetaij[idx]; // fetch(zeta_ij,idx,zeta_tex);
numtyp force = zeta_ij.x*tpainv;
numtyp prefactor = zeta_ij.y;
@ -520,9 +588,12 @@ __kernel void k_tersoff_three_center(const __global numtyp4 *restrict x_,
virial[5] += delr1[1]*delr1[2]*mforce;
}
int nbor_k=nborj_start-offset_j+offset_k;
for ( ; nbor_k<nbor_end; nbor_k+=n_stride) {
int k=dev_packed[nbor_k];
int nbor_k = nborj_start-offset_j+offset_k;
int numk = dev_short_nbor[nbor_k-n_stride];
int k_end = nbor_k+fast_mul(numk,n_stride);
for ( ; nbor_k<k_end; nbor_k+=n_stride) {
int k=dev_short_nbor[nbor_k];
k &= NEIGHMASK;
if (j == k) continue;
@ -598,6 +669,7 @@ __kernel void k_tersoff_three_end(const __global numtyp4 *restrict x_,
const __global int * dev_nbor,
const __global int * dev_packed,
const __global int * dev_acc,
const __global int * dev_short_nbor,
__global acctyp4 *restrict ans,
__global acctyp *restrict engv,
const int eflag, const int vflag,
@ -643,9 +715,15 @@ __kernel void k_tersoff_three_end(const __global numtyp4 *restrict x_,
itype=map[itype];
numtyp tpainv = ucl_recip((numtyp)t_per_atom);
// recalculate numj and nbor_end for use of the short nbor list
numj = dev_short_nbor[nbor_j];
nbor_j += n_stride;
nbor_end = nbor_j+fast_mul(numj,n_stride);
for ( ; nbor_j<nbor_end; nbor_j+=n_stride) {
int j=dev_packed[nbor_j];
int j=dev_short_nbor[nbor_j];
j &= NEIGHMASK;
numtyp4 jx; fetch4(jx,j,pos_tex); //x_[j];
@ -683,13 +761,18 @@ __kernel void k_tersoff_three_end(const __global numtyp4 *restrict x_,
k_end=nbor_k+numk;
nbor_k+=offset_k;
}
// recalculate numk and k_end for the use of short neighbor list
numk = dev_short_nbor[nbor_k];
nbor_k += n_stride;
k_end = nbor_k+fast_mul(numk,n_stride);
int nbork_start = nbor_k;
// look up for zeta_ji: find i in the j's neighbor list
int m = tid / t_per_atom;
int ijnum = -1;
for ( ; nbor_k<k_end; nbor_k+=n_stride) {
int k=dev_packed[nbor_k];
int k=dev_short_nbor[nbor_k];
k &= NEIGHMASK;
if (k == i) {
ijnum = nbor_k;
@ -711,9 +794,10 @@ __kernel void k_tersoff_three_end(const __global numtyp4 *restrict x_,
//int iix = (ijnum - offset_kf - 2*nbor_pitch) / n_stride;
//int idx = iix*n_stride + j*t_per_atom + offset_kf;
int idx;
zeta_idx(dev_nbor,dev_packed, nbor_pitch, n_stride, t_per_atom,
j, ijnum, offset_kf, idx);
//idx to zetaij is shifted by n_stride relative to ijnum in dev_short_nbor
int idx = ijnum - n_stride;
// zeta_idx(dev_nbor,dev_packed, nbor_pitch, n_stride, t_per_atom,
// j, ijnum, offset_kf, idx);
acctyp4 zeta_ji = zetaij[idx]; // fetch(zeta_ji,idx,zeta_tex);
numtyp force = zeta_ji.x*tpainv;
numtyp prefactor_ji = zeta_ji.y;
@ -736,7 +820,7 @@ __kernel void k_tersoff_three_end(const __global numtyp4 *restrict x_,
// attractive forces
for (nbor_k = nbork_start ; nbor_k<k_end; nbor_k+=n_stride) {
int k=dev_packed[nbor_k];
int k=dev_short_nbor[nbor_k];
k &= NEIGHMASK;
if (k == i) continue;
@ -777,9 +861,10 @@ __kernel void k_tersoff_three_end(const __global numtyp4 *restrict x_,
//int kk = (nbor_k - offset_k - 2*nbor_pitch) / n_stride;
//int idx = kk*n_stride + j*t_per_atom + offset_k;
int idx;
zeta_idx(dev_nbor,dev_packed, nbor_pitch, n_stride, t_per_atom,
j, nbor_k, offset_k, idx);
//idx to zetaij is shifted by n_stride relative to nbor_k in dev_short_nbor
int idx = nbor_k - n_stride;
// zeta_idx(dev_nbor,dev_packed, nbor_pitch, n_stride, t_per_atom,
// j, nbor_k, offset_k, idx);
acctyp4 zeta_jk = zetaij[idx]; // fetch(zeta_jk,idx,zeta_tex);
numtyp prefactor_jk = zeta_jk.y;
int jkiparam=elem2param[jtype*nelements*nelements+ktype*nelements+itype];
@ -824,6 +909,7 @@ __kernel void k_tersoff_three_end_vatom(const __global numtyp4 *restrict x_,
const __global int * dev_nbor,
const __global int * dev_packed,
const __global int * dev_acc,
const __global int * dev_short_nbor,
__global acctyp4 *restrict ans,
__global acctyp *restrict engv,
const int eflag, const int vflag,
@ -869,9 +955,15 @@ __kernel void k_tersoff_three_end_vatom(const __global numtyp4 *restrict x_,
itype=map[itype];
numtyp tpainv = ucl_recip((numtyp)t_per_atom);
// recalculate numj and nbor_end for use of the short nbor list
numj = dev_short_nbor[nbor_j];
nbor_j += n_stride;
nbor_end = nbor_j+fast_mul(numj,n_stride);
for ( ; nbor_j<nbor_end; nbor_j+=n_stride) {
int j=dev_packed[nbor_j];
int j=dev_short_nbor[nbor_j];
j &= NEIGHMASK;
numtyp4 jx; fetch4(jx,j,pos_tex); //x_[j];
@ -909,13 +1001,18 @@ __kernel void k_tersoff_three_end_vatom(const __global numtyp4 *restrict x_,
k_end=nbor_k+numk;
nbor_k+=offset_k;
}
// recalculate numk and k_end for the use of short neighbor list
numk = dev_short_nbor[nbor_k];
nbor_k += n_stride;
k_end = nbor_k+fast_mul(numk,n_stride);
int nbork_start = nbor_k;
// look up for zeta_ji
int m = tid / t_per_atom;
int ijnum = -1;
for ( ; nbor_k<k_end; nbor_k+=n_stride) {
int k=dev_packed[nbor_k];
int k=dev_short_nbor[nbor_k];
k &= NEIGHMASK;
if (k == i) {
ijnum = nbor_k;
@ -937,9 +1034,10 @@ __kernel void k_tersoff_three_end_vatom(const __global numtyp4 *restrict x_,
//int iix = (ijnum - offset_kf - 2*nbor_pitch) / n_stride;
//int idx = iix*n_stride + j*t_per_atom + offset_kf;
int idx;
zeta_idx(dev_nbor,dev_packed, nbor_pitch, n_stride, t_per_atom,
j, ijnum, offset_kf, idx);
//idx to zetaij is shifted by n_stride relative to ijnum in dev_short_nbor
int idx = ijnum - n_stride;
// zeta_idx(dev_nbor,dev_packed, nbor_pitch, n_stride, t_per_atom,
// j, ijnum, offset_kf, idx);
acctyp4 zeta_ji = zetaij[idx]; // fetch(zeta_ji,idx,zeta_tex);
numtyp force = zeta_ji.x*tpainv;
numtyp prefactor_ji = zeta_ji.y;
@ -962,7 +1060,7 @@ __kernel void k_tersoff_three_end_vatom(const __global numtyp4 *restrict x_,
// attractive forces
for (nbor_k = nbork_start; nbor_k<k_end; nbor_k+=n_stride) {
int k=dev_packed[nbor_k];
int k=dev_short_nbor[nbor_k];
k &= NEIGHMASK;
if (k == i) continue;
@ -1010,9 +1108,10 @@ __kernel void k_tersoff_three_end_vatom(const __global numtyp4 *restrict x_,
//int kk = (nbor_k - offset_k - 2*nbor_pitch) / n_stride;
//int idx = kk*n_stride + j*t_per_atom + offset_k;
int idx;
zeta_idx(dev_nbor,dev_packed, nbor_pitch, n_stride, t_per_atom,
j, nbor_k, offset_k, idx);
//idx to zetaij is shifted by n_stride relative to nbor_k in dev_short_nbor
int idx = nbor_k - n_stride;
// zeta_idx(dev_nbor,dev_packed, nbor_pitch, n_stride, t_per_atom,
// j, nbor_k, offset_k, idx);
acctyp4 zeta_jk = zetaij[idx]; // fetch(zeta_jk,idx,zeta_tex);
numtyp prefactor_jk = zeta_jk.y;

3
lib/gpu/lal_tersoff.h
View File

@ -104,8 +104,7 @@ class Tersoff : public BaseThree<numtyp, acctyp> {
UCL_Kernel k_zeta;
UCL_Texture ts1_tex, ts2_tex, ts3_tex, ts4_tex, ts5_tex;
int _max_nbors;
numtyp _cutshortsq;
private:
bool _allocated;