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nbin_intel.cpp
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Sat, Jun 29, 13:50

nbin_intel.cpp
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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: W. Michael Brown (Intel)
------------------------------------------------------------------------- */
#include "nbin_intel.h"
#include "atom.h"
#include "group.h"
#include "domain.h"
#include "comm.h"
#include "update.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
NBinIntel::NBinIntel(LAMMPS *lmp) : NBinStandard(lmp) {
int ifix = modify->find_fix("package_intel");
if (ifix < 0)
error->all(FLERR,
"The 'package intel' command is required for /intel styles");
_fix = static_cast<FixIntel *>(modify->fix[ifix]);
_precision_mode = _fix->precision();
_atombin = NULL;
_binpacked = NULL;
#ifdef _LMP_INTEL_OFFLOAD
_cop = _fix->coprocessor_number();
_offload_alloc = 0;
#endif
}
/* ---------------------------------------------------------------------- */
NBinIntel::~NBinIntel() {
#ifdef _LMP_INTEL_OFFLOAD
if (_offload_alloc) {
const int * binhead = this->binhead;
const int * bins = this->bins;
const int * _atombin = this->_atombin;
const int * _binpacked = this->_binpacked;
#pragma offload_transfer target(mic:_cop) \
nocopy(binhead,bins,_atombin,_binpacked:alloc_if(0) free_if(1))
}
#endif
}
/* ----------------------------------------------------------------------
setup for bin_atoms()
------------------------------------------------------------------------- */
void NBinIntel::bin_atoms_setup(int nall)
{
// binhead = per-bin vector, mbins in length
// add 1 bin for USER-INTEL package
if (mbins > maxbin) {
#ifdef _LMP_INTEL_OFFLOAD
if (_offload_alloc) {
const int * binhead = this->binhead;
#pragma offload_transfer target(mic:_cop) \
nocopy(binhead:alloc_if(0) free_if(1))
}
#endif
maxbin = mbins;
memory->destroy(binhead);
memory->create(binhead,maxbin+1,"neigh:binhead");
#ifdef _LMP_INTEL_OFFLOAD
if (_fix->offload_balance() != 0) {
int * binhead = this->binhead;
#pragma offload_transfer target(mic:_cop) \
nocopy(binhead:length(maxbin+1) alloc_if(1) free_if(0))
}
#endif
}
// bins = per-atom vector
if (nall > maxatom) {
maxatom = nall;
#ifdef _LMP_INTEL_OFFLOAD
if (_offload_alloc) {
const int * bins = this->bins;
const int * _atombin = this->_atombin;
const int * _binpacked = this->_binpacked;
#pragma offload_transfer target(mic:_cop) \
nocopy(bins,_atombin,_binpacked:alloc_if(0) free_if(1))
}
#endif
memory->destroy(bins);
memory->destroy(_atombin);
memory->destroy(_binpacked);
memory->create(bins,maxatom,"neigh:bins");
memory->create(_atombin,maxatom,"neigh:bins");
memory->create(_binpacked,maxatom,"neigh:bins");
#ifdef _LMP_INTEL_OFFLOAD
if (_fix->offload_balance() != 0) {
const int * bins = this->bins;
const int * _atombin = this->_atombin;
const int * _binpacked = this->_binpacked;
#pragma offload_transfer target(mic:_cop) \
nocopy(bins,_atombin,_binpacked:length(maxatom) alloc_if(1) free_if(0))
_offload_alloc=1;
}
#endif
if (_precision_mode == FixIntel::PREC_MODE_MIXED)
_fix->get_mixed_buffers()->set_bininfo(_atombin,_binpacked);
else if (_precision_mode == FixIntel::PREC_MODE_SINGLE)
_fix->get_single_buffers()->set_bininfo(_atombin,_binpacked);
else
_fix->get_double_buffers()->set_bininfo(_atombin,_binpacked);
}
}
/* ----------------------------------------------------------------------
bin owned and ghost atoms
------------------------------------------------------------------------- */
void NBinIntel::bin_atoms()
{
last_bin = update->ntimestep;
if (_precision_mode == FixIntel::PREC_MODE_MIXED)
bin_atoms(_fix->get_mixed_buffers());
else if (_precision_mode == FixIntel::PREC_MODE_SINGLE)
bin_atoms(_fix->get_single_buffers());
else
bin_atoms(_fix->get_double_buffers());
}
template <class flt_t, class acc_t>
void NBinIntel::bin_atoms(IntelBuffers<flt_t,acc_t> * buffers) {
const int nlocal = atom->nlocal;
const int nall = nlocal + atom->nghost;
const int aend = _fix->offload_end_neighbor();
// ---------- Sanity check for padding --------------
{
const flt_t dx = (INTEL_BIGP - bboxhi[0]);
const flt_t dy = (INTEL_BIGP - bboxhi[1]);
const flt_t dz = (INTEL_BIGP - bboxhi[2]);
if (dx * dx + dy * dy + dz * dz <
static_cast<flt_t>(neighbor->cutneighmaxsq))
error->one(FLERR,
"Intel package expects no atoms within cutoff of {1e15,1e15,1e15}.");
}
// ---------- Grow and cast/pack buffers -------------
_fix->start_watch(TIME_PACK);
buffers->grow(nall, atom->nlocal, comm->nthreads, aend);
ATOM_T biga;
biga.x = INTEL_BIGP;
biga.y = INTEL_BIGP;
biga.z = INTEL_BIGP;
biga.w = 1;
buffers->get_x()[nall] = biga;
int nthreads;
if (comm->nthreads > INTEL_HTHREADS) nthreads = comm->nthreads;
else nthreads = 1;
#if defined(_OPENMP)
#pragma omp parallel if(nthreads > INTEL_HTHREADS)
#endif
{
int ifrom, ito, tid;
IP_PRE_omp_range_id_align(ifrom, ito, tid, nall, nthreads,
sizeof(ATOM_T));
buffers->thr_pack(ifrom, ito, 0);
}
_fix->stop_watch(TIME_PACK);
// ---------- Bin Atoms -------------
_fix->start_watch(TIME_HOST_NEIGHBOR);
const ATOM_T * _noalias const x = buffers->get_x();
int * _noalias const atombin = this->_atombin;
int * _noalias const binpacked = this->_binpacked;
const double sboxlo0 = bboxlo[0] + mbinxlo/bininvx;
const double sboxlo1 = bboxlo[1] + mbinylo/bininvy;
const double sboxlo2 = bboxlo[2] + mbinzlo/bininvz;
int i, ibin;
for (i = 0; i < mbins; i++) binhead[i] = -1;
int *mask = atom->mask;
if (includegroup) {
int bitmask = group->bitmask[includegroup];
for (i = nall-1; i >= nlocal; i--) {
if (mask[i] & bitmask) {
ibin = coord2bin(atom->x[i]);
bins[i] = binhead[ibin];
binhead[ibin] = i;
}
}
for (i = atom->nfirst-1; i >= 0; i--) {
ibin = coord2bin(atom->x[i]);
atombin[i] = ibin;
bins[i] = binhead[ibin];
binhead[ibin] = i;
}
} else {
for (i = nall-1; i >= nlocal; i--) {
ibin = coord2bin(atom->x[i]);
bins[i] = binhead[ibin];
binhead[ibin] = i;
}
for (i = nlocal-1; i >= 0; i--) {
ibin = coord2bin(atom->x[i]);
atombin[i]=ibin;
bins[i] = binhead[ibin];
binhead[ibin] = i;
}
}
int newhead = 0;
for (i = 0; i < mbins; i++) {
int j = binhead[i];
binhead[i] = newhead;
for ( ; j >= 0; j = bins[j])
binpacked[newhead++] = j;
}
binhead[mbins] = newhead;
}
/* ---------------------------------------------------------------------- */
bigint NBinIntel::memory_usage()
{
return NBinStandard::memory_usage() + maxatom*2*sizeof(int);
}

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