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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10667 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2013-08-23 14:41:20 +00:00
parent 4047288238
commit 402d1a8605
105 changed files with 2003 additions and 954 deletions
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135
lib/gpu/lal_neighbor.cpp
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@ -38,7 +38,8 @@ bool Neighbor::init(NeighborShared *shared, const int inum,
const bool pre_cut, const int block_cell_2d,
const int block_cell_id, const int block_nbor_build,
const int threads_per_atom, const int warp_size,
const bool time_device) {
const bool time_device,
const std::string compile_flags) {
clear();
_threads_per_atom=threads_per_atom;
@ -92,13 +93,13 @@ bool Neighbor::init(NeighborShared *shared, const int inum,
if (gpu_nbor==0)
success=success && (host_packed.alloc(2*IJ_SIZE,*dev,
UCL_WRITE_OPTIMIZED)==UCL_SUCCESS);
UCL_WRITE_ONLY)==UCL_SUCCESS);
alloc(success);
if (!success)
return false;
if (_use_packing==false)
_shared->compile_kernels(devi,gpu_nbor);
_shared->compile_kernels(devi,gpu_nbor,compile_flags);
return success;
}
@ -114,7 +115,7 @@ void Neighbor::alloc(bool &success) {
success=success && (dev_nbor.alloc(3*_max_atoms,*dev,
UCL_READ_ONLY)==UCL_SUCCESS);
success=success && (host_acc.alloc(nt*2,*dev,
UCL_WRITE_OPTIMIZED)==UCL_SUCCESS);
UCL_READ_WRITE)==UCL_SUCCESS);
_c_bytes=dev_nbor.row_bytes();
if (_alloc_packed) {
@ -129,10 +130,10 @@ void Neighbor::alloc(bool &success) {
host_ilist.clear();
host_jlist.clear();
success=(nbor_host.alloc(_max_nbors*_max_host,*dev,UCL_RW_OPTIMIZED,
UCL_WRITE_ONLY)==UCL_SUCCESS) && success;
success=(nbor_host.alloc(_max_nbors*_max_host,*dev,UCL_READ_WRITE,
UCL_READ_WRITE)==UCL_SUCCESS) && success;
success=success && (dev_numj_host.alloc(_max_host,*dev,
UCL_WRITE_ONLY)==UCL_SUCCESS);
UCL_READ_WRITE)==UCL_SUCCESS);
success=success && (host_ilist.alloc(nt,*dev,UCL_NOT_PINNED)==UCL_SUCCESS);
if (!success)
return;
@ -161,7 +162,7 @@ void Neighbor::alloc(bool &success) {
success=success && (dev_nspecial.alloc(3*at,*dev,
UCL_READ_ONLY)==UCL_SUCCESS);
success=success && (dev_special.alloc(_maxspecial*at,*dev,
UCL_READ_ONLY)==UCL_SUCCESS);
UCL_READ_WRITE)==UCL_SUCCESS);
success=success && (dev_special_t.alloc(_maxspecial*at,*dev,
UCL_READ_ONLY)==UCL_SUCCESS);
_gpu_bytes+=dev_nspecial.row_bytes()+dev_special.row_bytes()+
@ -178,11 +179,9 @@ void Neighbor::clear() {
_bin_time=0.0;
if (_ncells>0) {
_ncells=0;
dev_cell_counts.clear();
if (_gpu_nbor==2) {
host_cell_counts.clear();
cell_counts.clear();
if (_gpu_nbor==2)
delete [] cell_iter;
}
}
if (_allocated) {
_allocated=false;
@ -286,6 +285,80 @@ void Neighbor::get_host(const int inum, int *ilist, int *numj,
}
}
// This is the same as get host, but the requirement that ilist[i]=i and
// inum=nlocal is forced to be true to allow direct indexing of neighbors of
// neighbors
void Neighbor::get_host3(const int inum, const int nlist, int *ilist, int *numj,
int **firstneigh, const int block_size) {
_nbor_time_avail=true;
time_nbor.start();
UCL_H_Vec<int> ilist_view;
ilist_view.view(ilist,inum,*dev);
ucl_copy(dev_nbor,ilist_view,false);
UCL_D_Vec<int> nbor_offset;
UCL_H_Vec<int> host_offset;
int copy_count=0;
int ij_count=0;
int acc_count=0;
int dev_count=0;
int *h_ptr=host_packed.begin();
_nbor_pitch=inum;
if (nlist!=inum)
host_acc.zero(inum);
for (int ii=0; ii<nlist; ii++) {
int i=ilist[ii];
int nj=numj[i];
host_acc[i]=nj;
host_acc[i+inum]=acc_count;
acc_count+=nj;
}
for (int i=0; i<inum; i++) {
int nj=host_acc[i];
int *jlist=firstneigh[i];
for (int jj=0; jj<nj; jj++) {
*h_ptr=jlist[jj];
h_ptr++;
ij_count++;
if (ij_count==IJ_SIZE) {
dev_nbor.sync();
host_offset.view_offset(IJ_SIZE*(copy_count%2),host_packed,IJ_SIZE);
nbor_offset.view_offset(dev_count,dev_packed,IJ_SIZE);
ucl_copy(nbor_offset,host_offset,true);
copy_count++;
ij_count=0;
dev_count+=IJ_SIZE;
h_ptr=host_packed.begin()+(IJ_SIZE*(copy_count%2));
}
}
}
if (ij_count!=0) {
dev_nbor.sync();
host_offset.view_offset(IJ_SIZE*(copy_count%2),host_packed,ij_count);
nbor_offset.view_offset(dev_count,dev_packed,ij_count);
ucl_copy(nbor_offset,host_offset,true);
}
UCL_D_Vec<int> acc_view;
acc_view.view_offset(inum,dev_nbor,inum*2);
ucl_copy(acc_view,host_acc,true);
time_nbor.stop();
if (_use_packing==false) {
time_kernel.start();
int GX=static_cast<int>(ceil(static_cast<double>(inum)*_threads_per_atom/
block_size));
_shared->k_nbor.set_size(GX,block_size);
_shared->k_nbor.run(&dev_nbor, &dev_packed, &inum, &_threads_per_atom);
time_kernel.stop();
}
}
template <class numtyp, class acctyp>
void Neighbor::resize_max_neighbors(const int maxn, bool &success) {
if (maxn>_max_nbors) {
@ -330,24 +403,20 @@ void Neighbor::build_nbor_list(double **x, const int inum, const int host_inum,
ncellz = static_cast<int>(ceil((subhi[2]-sublo[2])/_cell_size))+ghost_cells;
ncell_3d = ncellx * ncelly * ncellz;
if (ncell_3d+1>_ncells) {
cell_counts.clear();
if (_gpu_nbor==2) {
if (_ncells>0) {
host_cell_counts.clear();
if (_ncells>0)
delete [] cell_iter;
}
cell_iter = new int[ncell_3d+1];
host_cell_counts.alloc(ncell_3d+1,dev_nbor);
}
if (_gpu_nbor==2 && atom.host_view())
dev_cell_counts.view(host_cell_counts);
else {
dev_cell_counts.clear();
dev_cell_counts.alloc(ncell_3d+1,dev_nbor);
cell_counts.alloc(ncell_3d+1,dev_nbor,UCL_READ_WRITE,UCL_READ_ONLY);
} else {
cell_counts.device.clear();
cell_counts.device.alloc(ncell_3d+1,dev_nbor);
}
_ncells=ncell_3d+1;
_cell_bytes=dev_cell_counts.row_bytes();
_cell_bytes=cell_counts.device.row_bytes();
}
const numtyp cutoff_cast=static_cast<numtyp>(_cutoff);
@ -381,7 +450,7 @@ void Neighbor::build_nbor_list(double **x, const int inum, const int host_inum,
int *particle_id=atom.host_particle_id.begin();
// Build cell list on CPU
host_cell_counts.zero();
cell_counts.host.zero();
double i_cell_size=1.0/_cell_size;
int offset_hi=_cells_in_cutoff+1;
@ -403,7 +472,7 @@ void Neighbor::build_nbor_list(double **x, const int inum, const int host_inum,
int id = ix+iy*ncellx+iz*ncellx*ncelly;
cell_id[i] = id;
host_cell_counts[id+1]++;
cell_counts[id+1]++;
}
for (int i=nt; i<nall; i++) {
@ -424,12 +493,12 @@ void Neighbor::build_nbor_list(double **x, const int inum, const int host_inum,
int id = ix+iy*ncellx+iz*ncellx*ncelly;
cell_id[i] = id;
host_cell_counts[id+1]++;
cell_counts[id+1]++;
}
mn=0;
for (int i=0; i<_ncells; i++)
mn=std::max(mn,host_cell_counts[i]);
mn=std::max(mn,cell_counts[i]);
mn*=8;
set_nbor_block_size(mn/2);
@ -440,11 +509,11 @@ void Neighbor::build_nbor_list(double **x, const int inum, const int host_inum,
cell_iter[0]=0;
for (int i=1; i<_ncells; i++) {
host_cell_counts[i]+=host_cell_counts[i-1];
cell_iter[i]=host_cell_counts[i];
cell_counts[i]+=cell_counts[i-1];
cell_iter[i]=cell_counts[i];
}
time_hybrid1.start();
ucl_copy(dev_cell_counts,host_cell_counts,true);
cell_counts.update_device(true);
time_hybrid1.stop();
for (int i=0; i<nall; i++) {
int celli=cell_id[i];
@ -481,7 +550,7 @@ void Neighbor::build_nbor_list(double **x, const int inum, const int host_inum,
/* calculate cell count */
_shared->k_cell_counts.set_size(GX,neigh_block);
_shared->k_cell_counts.run(&atom.dev_cell_id, &dev_cell_counts, &nall,
_shared->k_cell_counts.run(&atom.dev_cell_id, &cell_counts, &nall,
&ncell_3d);
}
@ -490,7 +559,7 @@ void Neighbor::build_nbor_list(double **x, const int inum, const int host_inum,
_shared->k_build_nbor.set_size(ncellx-ghost_cells,(ncelly-ghost_cells)*
(ncellz-ghost_cells),cell_block,1);
_shared->k_build_nbor.run(&atom.x, &atom.dev_particle_id,
&dev_cell_counts, &dev_nbor, &nbor_host,
&cell_counts, &dev_nbor, &nbor_host,
&dev_numj_host, &_max_nbors, &cutoff_cast, &ncellx,
&ncelly, &ncellz, &inum, &nt, &nall,
&_threads_per_atom, &_cells_in_cutoff);