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new neighbor list changes

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This commit is contained in:
Steve Plimpton
2016-09-07 13:42:58 -06:00
parent 0252347d43
commit c9c2ae6c61
259 changed files with 23076 additions and 14650 deletions
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107
src/USER-INTEL/intel_buffers.cpp
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@ -26,18 +26,17 @@ IntelBuffers<flt_t, acc_t>::IntelBuffers(class LAMMPS *lmp_in) :
_buf_size(0), _buf_local_size(0) {
_list_alloc_atoms = 0;
_ntypes = 0;
_off_map_maxlocal = 0;
_off_map_listlocal = 0;
_ccachex = 0;
_host_nmax = 0;
#ifdef _LMP_INTEL_OFFLOAD
_separate_buffers = 0;
_off_f = 0;
_off_map_ilist = 0;
_off_map_nmax = 0;
_off_map_maxhead = 0;
_off_list_alloc = false;
_off_threads = 0;
_off_ccache = 0;
_host_nmax = 0;
#endif
}
@ -173,21 +172,15 @@ void IntelBuffers<flt_t, acc_t>::free_nmax()
const int * tag = _off_map_tag;
const int * special = _off_map_special;
const int * nspecial = _off_map_nspecial;
const int * bins = _off_map_bins;
const int * binpacked = _binpacked;
if (tag != 0 && special != 0 && nspecial !=0 && bins != 0) {
if (tag != 0 && special != 0 && nspecial !=0) {
#pragma offload_transfer target(mic:_cop) \
nocopy(tag:alloc_if(0) free_if(1)) \
nocopy(special,nspecial:alloc_if(0) free_if(1)) \
nocopy(bins,binpacked:alloc_if(0) free_if(1))
nocopy(special,nspecial:alloc_if(0) free_if(1))
}
_off_map_nmax = 0;
}
#endif
if (_host_nmax > 0) {
lmp->memory->destroy(_binpacked);
_host_nmax = 0;
}
#endif
}
/* ---------------------------------------------------------------------- */
@ -195,12 +188,11 @@ void IntelBuffers<flt_t, acc_t>::free_nmax()
template <class flt_t, class acc_t>
void IntelBuffers<flt_t, acc_t>::_grow_nmax(const int offload_end)
{
#ifdef _LMP_INTEL_OFFLOAD
free_nmax();
int size = lmp->atom->nmax;
_host_nmax = size;
lmp->memory->create(_binpacked, _host_nmax, "_binpacked");
#ifdef _LMP_INTEL_OFFLOAD
if (!offload_end) return;
int *special, *nspecial;
int tag_length, special_length, nspecial_length;
@ -220,10 +212,7 @@ void IntelBuffers<flt_t, acc_t>::_grow_nmax(const int offload_end)
else
tag_length = 1;
int *tag = lmp->atom->tag;
int *bins = lmp->neighbor->bins;
int * binpacked = _binpacked;
#pragma offload_transfer target(mic:_cop) \
nocopy(bins,binpacked:length(size) alloc_if(1) free_if(0)) \
nocopy(tag:length(tag_length) alloc_if(1) free_if(0)) \
nocopy(special:length(special_length) alloc_if(1) free_if(0)) \
nocopy(nspecial:length(nspecial_length) alloc_if(1) free_if(0))
@ -231,18 +220,16 @@ void IntelBuffers<flt_t, acc_t>::_grow_nmax(const int offload_end)
_off_map_special = special;
_off_map_nspecial = nspecial;
_off_map_nmax = size;
_off_map_bins = bins;
#endif
}
/* ---------------------------------------------------------------------- */
template <class flt_t, class acc_t>
void IntelBuffers<flt_t, acc_t>::free_local()
void IntelBuffers<flt_t, acc_t>::free_list_local()
{
if (_off_map_maxlocal > 0) {
if (_off_map_listlocal > 0) {
int * cnumneigh = _cnumneigh;
int * atombin = _atombin;
#ifdef _LMP_INTEL_OFFLOAD
if (_off_map_ilist != NULL) {
const int * ilist = _off_map_ilist;
@ -250,40 +237,36 @@ void IntelBuffers<flt_t, acc_t>::free_local()
_off_map_ilist = NULL;
if (numneigh != 0 && ilist != 0) {
#pragma offload_transfer target(mic:_cop) \
nocopy(ilist,numneigh,cnumneigh,atombin:alloc_if(0) free_if(1))
nocopy(ilist,numneigh,cnumneigh:alloc_if(0) free_if(1))
}
}
#endif
lmp->memory->destroy(cnumneigh);
lmp->memory->destroy(atombin);
_off_map_maxlocal = 0;
_off_map_listlocal = 0;
}
}
/* ---------------------------------------------------------------------- */
template <class flt_t, class acc_t>
void IntelBuffers<flt_t, acc_t>::_grow_local(NeighList *list,
const int offload_end)
void IntelBuffers<flt_t, acc_t>::_grow_list_local(NeighList *list,
const int offload_end)
{
free_local();
free_list_local();
int size = list->get_maxlocal();
lmp->memory->create(_cnumneigh, size, "_cnumneigh");
lmp->memory->create(_atombin, size, "_atombin");
_off_map_maxlocal = size;
_off_map_listlocal = size;
#ifdef _LMP_INTEL_OFFLOAD
if (offload_end > 0) {
int * numneigh = list->numneigh;
int * ilist = list->ilist;
int * cnumneigh = _cnumneigh;
int * atombin = _atombin;
if (cnumneigh != 0 && atombin != 0) {
if (cnumneigh != 0) {
#pragma offload_transfer target(mic:_cop) \
nocopy(ilist:length(size) alloc_if(1) free_if(0)) \
nocopy(numneigh:length(size) alloc_if(1) free_if(0)) \
nocopy(cnumneigh:length(size) alloc_if(1) free_if(0)) \
nocopy(atombin:length(size) alloc_if(1) free_if(0))
nocopy(cnumneigh:length(size) alloc_if(1) free_if(0))
}
_off_map_ilist = ilist;
_off_map_numneigh = numneigh;
@ -293,39 +276,6 @@ void IntelBuffers<flt_t, acc_t>::_grow_local(NeighList *list,
/* ---------------------------------------------------------------------- */
template <class flt_t, class acc_t>
void IntelBuffers<flt_t, acc_t>::free_binhead()
{
#ifdef _LMP_INTEL_OFFLOAD
if (_off_map_maxhead > 0) {
const int * binhead = _off_map_binhead;
if (binhead !=0) {
#pragma offload_transfer target(mic:_cop) \
nocopy(binhead:alloc_if(0) free_if(1))
}
_off_map_maxhead = 0;
}
#endif
}
/* ---------------------------------------------------------------------- */
template <class flt_t, class acc_t>
void IntelBuffers<flt_t, acc_t>::_grow_binhead()
{
#ifdef _LMP_INTEL_OFFLOAD
free_binhead();
int * binhead = lmp->neighbor->binhead;
const int maxhead = lmp->neighbor->maxhead;
#pragma offload_transfer target(mic:_cop) \
nocopy(binhead:length(maxhead+1) alloc_if(1) free_if(0))
_off_map_binhead = binhead;
_off_map_maxhead = maxhead;
#endif
}
/* ---------------------------------------------------------------------- */
template <class flt_t, class acc_t>
void IntelBuffers<flt_t, acc_t>::free_nbor_list()
{
@ -333,11 +283,8 @@ void IntelBuffers<flt_t, acc_t>::free_nbor_list()
#ifdef _LMP_INTEL_OFFLOAD
if (_off_list_alloc) {
int * list_alloc = _list_alloc;
int * stencil = _off_map_stencil;
if (list_alloc != 0 && stencil != 0) {
#pragma offload_transfer target(mic:_cop) \
nocopy(list_alloc:alloc_if(0) free_if(1))
}
#pragma offload_transfer target(mic:_cop) \
nocopy(list_alloc:alloc_if(0) free_if(1))
_off_list_alloc = false;
}
#endif
@ -364,33 +311,16 @@ void IntelBuffers<flt_t, acc_t>::_grow_nbor_list(NeighList *list,
#ifdef _LMP_INTEL_OFFLOAD
if (offload_end > 0) {
int * list_alloc =_list_alloc;
int * stencil = list->stencil;
if (list_alloc != NULL) {
#pragma offload_transfer target(mic:_cop) \
in(stencil:length(list->maxstencil) alloc_if(1) free_if(0)) \
nocopy(list_alloc:length(list_alloc_size) alloc_if(1) free_if(0))
_off_map_stencil = stencil;
_off_list_alloc = true;
}
}
#endif
}
template <class flt_t, class acc_t>
void IntelBuffers<flt_t, acc_t>::_grow_stencil(NeighList *list)
{
#ifdef _LMP_INTEL_OFFLOAD
int * stencil = _off_map_stencil;
#pragma offload_transfer target(mic:_cop) \
nocopy(stencil:alloc_if(0) free_if(1))
stencil = list->stencil;
#pragma offload_transfer target(mic:_cop) \
in(stencil:length(list->maxstencil) alloc_if(1) free_if(0))
_off_map_stencil = stencil;
#endif
}
/* ---------------------------------------------------------------------- */
template <class flt_t, class acc_t>
@ -544,7 +474,6 @@ double IntelBuffers<flt_t, acc_t>::memory_usage(const int nthreads)
if (_off_f) tmem += fstride*_off_threads * sizeof(vec3_acc_t);
#endif
tmem += _off_map_maxlocal * sizeof(int) * 2;
tmem += (_list_alloc_atoms + _off_threads) * get_max_nbors() * sizeof(int);
tmem += _ntypes * _ntypes * sizeof(int);