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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@7885 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2012-03-02 15:57:05 +00:00
parent 17091c755e
commit d30ba2d7eb
9 changed files with 193 additions and 122 deletions
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160
lib/gpu/lal_neighbor.cpp
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@ -69,10 +69,12 @@ bool Neighbor::init(NeighborShared *shared, const int inum,
time_kernel.init(*dev);
time_hybrid1.init(*dev);
time_hybrid2.init(*dev);
time_transpose.init(*dev);
time_nbor.zero();
time_kernel.zero();
time_hybrid1.zero();
time_hybrid2.zero();
time_transpose.zero();
_max_atoms=static_cast<int>(static_cast<double>(inum)*1.10);
if (_max_atoms==0)
@ -203,6 +205,7 @@ void Neighbor::clear() {
time_nbor.clear();
time_hybrid1.clear();
time_hybrid2.clear();
time_transpose.clear();
}
}
@ -285,6 +288,41 @@ void Neighbor::get_host(const int inum, int *ilist, int *numj,
}
}
template <class numtyp, class acctyp>
void Neighbor::resize_max_neighbors(const int maxn, bool &success) {
if (maxn>_max_nbors) {
int mn=static_cast<int>(static_cast<double>(maxn)*1.10);
dev_nbor.clear();
success=success &&
(dev_nbor.alloc((mn+1)*_max_atoms,*dev)==UCL_SUCCESS);
_gpu_bytes=dev_nbor.row_bytes();
if (_max_host>0) {
host_nbor.clear();
dev_host_nbor.clear();
success=success && (host_nbor.alloc(mn*_max_host,*dev,
UCL_RW_OPTIMIZED)==UCL_SUCCESS);
success=success && (dev_host_nbor.alloc(mn*_max_host,
*dev,UCL_WRITE_ONLY)==UCL_SUCCESS);
int *ptr=host_nbor.begin();
for (int i=0; i<_max_host; i++) {
host_jlist[i]=ptr;
ptr+=mn;
}
_gpu_bytes+=dev_host_nbor.row_bytes();
} else {
dev_host_nbor.view(dev_nbor);
dev_host_numj.view(dev_nbor);
}
if (_alloc_packed) {
dev_packed.clear();
success=success && (dev_packed.alloc((mn+2)*_max_atoms,*dev,
UCL_READ_ONLY)==UCL_SUCCESS);
_gpu_bytes+=dev_packed.row_bytes();
}
_max_nbors=mn;
}
}
template <class numtyp, class acctyp>
void Neighbor::build_nbor_list(double **x, const int inum, const int host_inum,
const int nall, Atom<numtyp,acctyp> &atom,
@ -320,6 +358,29 @@ void Neighbor::build_nbor_list(double **x, const int inum, const int host_inum,
const numtyp cell_size_cast=static_cast<numtyp>(_cell_size);
if (_maxspecial>0) {
time_nbor.start();
UCL_H_Vec<int> view_nspecial, view_special, view_tag;
view_nspecial.view(nspecial[0],nt*3,*dev);
view_special.view(special[0],nt*_maxspecial,*dev);
view_tag.view(tag,nall,*dev);
ucl_copy(dev_nspecial,view_nspecial,nt*3,false);
ucl_copy(dev_special_t,view_special,nt*_maxspecial,false);
ucl_copy(atom.dev_tag,view_tag,nall,false);
time_nbor.stop();
if (_time_device)
time_nbor.add_to_total();
time_transpose.start();
const int b2x=_block_cell_2d;
const int b2y=_block_cell_2d;
const int g2x=static_cast<int>(ceil(static_cast<double>(_maxspecial)/b2x));
const int g2y=static_cast<int>(ceil(static_cast<double>(nt)/b2y));
_shared->k_transpose.set_size(g2x,g2y,b2x,b2y);
_shared->k_transpose.run(&dev_special.begin(),&dev_special_t.begin(),
&_maxspecial,&nt);
time_transpose.stop();
}
// If binning on CPU, do this now
if (_gpu_nbor==2) {
double stime = MPI_Wtime();
@ -352,6 +413,16 @@ void Neighbor::build_nbor_list(double **x, const int inum, const int host_inum,
cell_id[i]=id;
host_cell_counts[id+1]++;
}
mn=0;
for (int i=0; i<_ncells; i++)
mn=std::max(mn,host_cell_counts[i]);
mn*=8;
resize_max_neighbors<numtyp,acctyp>(mn,success);
if (!success)
return;
_total_atoms=nt;
cell_iter[0]=0;
for (int i=1; i<_ncells; i++) {
host_cell_counts[i]+=host_cell_counts[i-1];
@ -372,28 +443,7 @@ void Neighbor::build_nbor_list(double **x, const int inum, const int host_inum,
_bin_time+=MPI_Wtime()-stime;
}
if (_maxspecial>0) {
time_nbor.start();
UCL_H_Vec<int> view_nspecial, view_special, view_tag;
view_nspecial.view(nspecial[0],nt*3,*dev);
view_special.view(special[0],nt*_maxspecial,*dev);
view_tag.view(tag,nall,*dev);
ucl_copy(dev_nspecial,view_nspecial,nt*3,false);
ucl_copy(dev_special_t,view_special,nt*_maxspecial,false);
ucl_copy(atom.dev_tag,view_tag,nall,false);
time_nbor.stop();
if (_time_device)
time_nbor.add_to_total();
time_kernel.start();
const int b2x=_block_cell_2d;
const int b2y=_block_cell_2d;
const int g2x=static_cast<int>(ceil(static_cast<double>(_maxspecial)/b2x));
const int g2y=static_cast<int>(ceil(static_cast<double>(nt)/b2y));
_shared->k_transpose.set_size(g2x,g2y,b2x,b2y);
_shared->k_transpose.run(&dev_special.begin(),&dev_special_t.begin(),
&_maxspecial,&nt);
} else
time_kernel.start();
time_kernel.start();
_nbor_pitch=inum;
_shared->neigh_tex.bind_float(atom.dev_x,4);
@ -435,54 +485,30 @@ void Neighbor::build_nbor_list(double **x, const int inum, const int host_inum,
/* Get the maximum number of nbors and realloc if necessary */
UCL_D_Vec<int> numj;
numj.view_offset(inum,dev_nbor,inum);
ucl_copy(host_acc,numj,inum,false);
ucl_copy(host_acc,numj,inum,true);
if (nt>inum) {
UCL_H_Vec<int> host_offset;
host_offset.view_offset(inum,host_acc,nt-inum);
ucl_copy(host_offset,dev_host_numj,nt-inum,false);
ucl_copy(host_offset,dev_host_numj,nt-inum,true);
}
mn=host_acc[0];
for (int i=1; i<nt; i++)
mn=std::max(mn,host_acc[i]);
if (_gpu_nbor!=2) {
host_acc.sync();
mn=host_acc[0];
for (int i=1; i<nt; i++)
mn=std::max(mn,host_acc[i]);
if (mn>_max_nbors) {
mn=static_cast<int>(static_cast<double>(mn)*1.10);
dev_nbor.clear();
success=success &&
(dev_nbor.alloc((mn+1)*_max_atoms,atom.dev_x)==UCL_SUCCESS);
_gpu_bytes=dev_nbor.row_bytes();
if (_max_host>0) {
host_nbor.clear();
dev_host_nbor.clear();
success=success && (host_nbor.alloc(mn*_max_host,dev_nbor,
UCL_RW_OPTIMIZED)==UCL_SUCCESS);
success=success && (dev_host_nbor.alloc(mn*_max_host,
dev_nbor,UCL_WRITE_ONLY)==UCL_SUCCESS);
int *ptr=host_nbor.begin();
for (int i=0; i<_max_host; i++) {
host_jlist[i]=ptr;
ptr+=mn;
}
_gpu_bytes+=dev_host_nbor.row_bytes();
} else {
dev_host_nbor.view(dev_nbor);
dev_host_numj.view(dev_nbor);
}
if (_alloc_packed) {
dev_packed.clear();
success=success && (dev_packed.alloc((mn+2)*_max_atoms,*dev,
UCL_READ_ONLY)==UCL_SUCCESS);
_gpu_bytes+=dev_packed.row_bytes();
}
if (!success)
if (mn>_max_nbors) {
resize_max_neighbors<numtyp,acctyp>(mn,success);
if (!success)
return;
time_kernel.stop();
if (_time_device)
time_kernel.add_to_total();
build_nbor_list(x, inum, host_inum, nall, atom, sublo, subhi, tag,
nspecial, special, success, mn);
return;
_max_nbors=mn;
time_kernel.stop();
if (_time_device)
time_kernel.add_to_total();
build_nbor_list(x, inum, host_inum, nall, atom, sublo, subhi, tag, nspecial,
special, success, mn);
return;
}
}
if (_maxspecial>0) {
@ -497,8 +523,10 @@ void Neighbor::build_nbor_list(double **x, const int inum, const int host_inum,
time_kernel.stop();
time_nbor.start();
if (inum<nt)
ucl_copy(host_nbor,dev_host_nbor,false);
if (inum<nt) {
ucl_copy(host_nbor,dev_host_nbor,true);
host_nbor.sync();
}
time_nbor.stop();
}