npair_full_bin_ghost_intel.cpp
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Created: Mon, May 20, 17:15

npair_full_bin_ghost_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 authors: W. Michael Brown (Intel)
	------------------------------------------------------------------------- */

	#include "npair_full_bin_ghost_intel.h"
	#include "neighbor.h"
	#include "nstencil.h"
	#include "neigh_list.h"
	#include "atom.h"
	#include "atom_vec.h"
	#include "molecule.h"
	#include "error.h"

	using namespace LAMMPS_NS;

	/* ---------------------------------------------------------------------- */

	NPairFullBinGhostIntel::NPairFullBinGhostIntel(LAMMPS *lmp) : NPairIntel(lmp) {}

	/* ----------------------------------------------------------------------
	binned neighbor list construction for all neighbors
	include neighbors of ghost atoms, but no "special neighbors" for ghosts
	every neighbor pair appears in list of both atoms i and j
	------------------------------------------------------------------------- */

	void NPairFullBinGhostIntel::build(NeighList *list)
	{
	#ifdef _LMP_INTEL_OFFLOAD
	if (_fix->offload_noghost())
	error->all(FLERR,
	"The 'ghost no' option cannot be used with this USER-INTEL pair style.");
	#endif

	if (nstencil > INTEL_MAX_STENCIL_CHECK)
	error->all(FLERR, "Too many neighbor bins for USER-INTEL package.");

	#ifdef _LMP_INTEL_OFFLOAD
	if (exclude)
	error->all(FLERR, "Exclusion lists not yet supported for Intel offload");
	#endif

	if (_fix->precision() == FixIntel::PREC_MODE_MIXED)
	fbi(list, _fix->get_mixed_buffers());
	else if (_fix->precision() == FixIntel::PREC_MODE_DOUBLE)
	fbi(list, _fix->get_double_buffers());
	else
	fbi(list, _fix->get_single_buffers());

	_fix->stop_watch(TIME_HOST_NEIGHBOR);
	}

	/* ---------------------------------------------------------------------- */

	template<class flt_t, class acc_t>
	void NPairFullBinGhostIntel::fbi(NeighList * list,
	IntelBuffers<flt_t,acc_t> * buffers)
	{
	const int nlocal = atom->nlocal;
	const int nall = atom->nlocal + atom->nghost;
	list->inum = atom->nlocal;
	list->gnum = atom->nghost;

	int host_start = _fix->host_start_neighbor();
	const int off_end = _fix->offload_end_neighbor();

	#ifdef _LMP_INTEL_OFFLOAD
	if (off_end) grow_stencil();
	if (_fix->full_host_list()) host_start = 0;
	int offload_noghost = _fix->offload_noghost();
	#endif

	// only uses offload_end_neighbor to check whether we are doing offloading
	// at all, no need to correct this later
	buffers->grow_list(list, nall, comm->nthreads, off_end,
	_fix->nbor_pack_width());

	int need_ic = 0;
	if (atom->molecular)
	dminimum_image_check(need_ic, neighbor->cutneighmax, neighbor->cutneighmax,
	neighbor->cutneighmax);

	if (need_ic) {
	fbi<flt_t,acc_t,1>(1, list, buffers, 0, off_end);
	fbi<flt_t,acc_t,1>(0, list, buffers, host_start, nlocal);
	} else {
	fbi<flt_t,acc_t,0>(1, list, buffers, 0, off_end);
	fbi<flt_t,acc_t,0>(0, list, buffers, host_start, nlocal);
	}
	}

	/* ---------------------------------------------------------------------- */

	template<class flt_t, class acc_t, int need_ic>
	void NPairFullBinGhostIntel::fbi(const int offload, NeighList * list,
	IntelBuffers<flt_t,acc_t> * buffers,
	const int pstart, const int pend) {
	if (pend-pstart == 0) return;

	const int nall = atom->nlocal + atom->nghost;
	int pad = 1;
	int nall_t = nall;
	const int aend = nall;

	const int pack_width = _fix->nbor_pack_width();
	const ATOM_T * _noalias const x = buffers->get_x();
	int * _noalias const firstneigh = buffers->firstneigh(list);
	const int e_nall = nall_t;

	const int molecular = atom->molecular;
	int *ns = NULL;
	tagint *s = NULL;
	int tag_size = 0, special_size;
	if (buffers->need_tag()) tag_size = e_nall;
	if (molecular) {
	s = atom->special[0];
	ns = atom->nspecial[0];
	special_size = aend;
	} else {
	s = &buffers->_special_holder;
	ns = &buffers->_nspecial_holder;
	special_size = 0;
	}
	const tagint * _noalias const special = s;
	const int * _noalias const nspecial = ns;
	const int maxspecial = atom->maxspecial;
	const tagint * _noalias const tag = atom->tag;

	int * _noalias const ilist = list->ilist;
	int * _noalias numneigh = list->numneigh;
	int * _noalias const cnumneigh = buffers->cnumneigh(list);
	const int nstencil = this->nstencil;
	const int * _noalias const stencil = this->stencil;
	const flt_t * _noalias const cutneighsq = buffers->get_cutneighsq()[0];
	const flt_t * _noalias const cutneighghostsq =
	buffers->get_cutneighghostsq()[0];
	const int ntypes = atom->ntypes + 1;
	const int nlocal = atom->nlocal;

	#ifndef _LMP_INTEL_OFFLOAD
	int * const mask = atom->mask;
	tagint * const molecule = atom->molecule;
	#endif

	int *molindex = atom->molindex;
	int *molatom = atom->molatom;
	Molecule **onemols = atom->avec->onemols;
	int moltemplate;
	if (molecular == 2) moltemplate = 1;
	else moltemplate = 0;
	if (moltemplate)
	error->all(FLERR,
	"Can't use moltemplate with npair style full/bin/ghost/intel.");

	int tnum;
	int *overflow;
	double *timer_compute;
	#ifdef _LMP_INTEL_OFFLOAD
	if (offload) {
	timer_compute = _fix->off_watch_neighbor();
	tnum = buffers->get_off_threads();
	overflow = _fix->get_off_overflow_flag();
	_fix->stop_watch(TIME_HOST_NEIGHBOR);
	_fix->start_watch(TIME_OFFLOAD_LATENCY);
	} else
	#endif
	{
	tnum = comm->nthreads;
	overflow = _fix->get_overflow_flag();
	}
	const int nthreads = tnum;
	const int maxnbors = buffers->get_max_nbors();
	int * _noalias const atombin = buffers->get_atombin();
	const int * _noalias const binpacked = buffers->get_binpacked();

	const int xperiodic = domain->xperiodic;
	const int yperiodic = domain->yperiodic;
	const int zperiodic = domain->zperiodic;
	const flt_t xprd_half = domain->xprd_half;
	const flt_t yprd_half = domain->yprd_half;
	const flt_t zprd_half = domain->zprd_half;

	flt_t * _noalias const ncachex = buffers->get_ncachex();
	flt_t * _noalias const ncachey = buffers->get_ncachey();
	flt_t * _noalias const ncachez = buffers->get_ncachez();
	int * _noalias const ncachej = buffers->get_ncachej();
	int * _noalias const ncachejtype = buffers->get_ncachejtype();
	int * _noalias const ncachetag = buffers->get_ncachetag();
	const int ncache_stride = buffers->ncache_stride();

	const int mbinx = this->mbinx;
	const int mbiny = this->mbiny;
	const int mbinz = this->mbinz;
	const int * const stencilxyz = &this->stencilxyz[0][0];

	#ifdef _LMP_INTEL_OFFLOAD
	const int * _noalias const binhead = this->binhead;
	const int * _noalias const bins = this->bins;
	const int cop = _fix->coprocessor_number();
	const int separate_buffers = _fix->separate_buffers();
	#pragma offload target(mic:cop) if(offload) \
	in(x:length(e_nall+1) alloc_if(0) free_if(0)) \
	in(tag:length(tag_size) alloc_if(0) free_if(0)) \
	in(special:length(special_size*maxspecial) alloc_if(0) free_if(0)) \
	in(nspecial:length(special_size*3) alloc_if(0) free_if(0)) \
	in(bins,binpacked:length(nall) alloc_if(0) free_if(0)) \
	in(binhead:length(mbins+1) alloc_if(0) free_if(0)) \
	in(cutneighsq:length(0) alloc_if(0) free_if(0)) \
	in(cutneighghostsq:length(0) alloc_if(0) free_if(0)) \
	in(firstneigh:length(0) alloc_if(0) free_if(0)) \
	in(cnumneigh:length(0) alloc_if(0) free_if(0)) \
	in(numneigh:length(0) alloc_if(0) free_if(0)) \
	in(ilist:length(0) alloc_if(0) free_if(0)) \
	in(atombin:length(aend) alloc_if(0) free_if(0)) \
	in(stencil:length(nstencil) alloc_if(0) free_if(0)) \
	in(ncachex,ncachey,ncachez,ncachej:length(0) alloc_if(0) free_if(0)) \
	in(ncachejtype,ncachetag:length(0) alloc_if(0) free_if(0)) \
	in(ncache_stride,maxnbors,nthreads,maxspecial,nstencil,e_nall,offload) \
	in(separate_buffers,aend,nlocal,molecular,ntypes,mbinx,mbiny) \
	in(mbinz,xperiodic,yperiodic,zperiodic,xprd_half,yprd_half,zprd_half) \
	in(stencilxyz:length(3*nstencil)) \
	out(overflow:length(5) alloc_if(0) free_if(0)) \
	out(timer_compute:length(1) alloc_if(0) free_if(0)) \
	signal(tag)
	#endif
	{
	#if defined(__MIC__) && defined(_LMP_INTEL_OFFLOAD)
	*timer_compute = MIC_Wtime();
	#endif

	#ifdef _LMP_INTEL_OFFLOAD
	overflow[LMP_LOCAL_MIN] = 0;
	overflow[LMP_LOCAL_MAX] = aend - 1;
	overflow[LMP_GHOST_MIN] = e_nall;
	overflow[LMP_GHOST_MAX] = -1;
	#endif

	int nstencilp = 0;
	int binstart[INTEL_MAX_STENCIL], binend[INTEL_MAX_STENCIL];
	for (int k = 0; k < nstencil; k++) {
	binstart[nstencilp] = stencil[k];
	int end = stencil[k] + 1;
	for (int kk = k + 1; kk < nstencil; kk++) {
	if (stencil[kk-1]+1 == stencil[kk]) {
	end++;
	k++;
	} else break;
	}
	binend[nstencilp] = end;
	nstencilp++;
	}

	const int mbinyx = mbiny * mbinx;

	#if defined(_OPENMP)
	#pragma omp parallel
	#endif
	{
	const int num = aend;
	int tid, ifrom, ito;

	const double balance_factor = 2.0;
	const double ibalance_factor = 1.0 / balance_factor;
	const int gnum = num - nlocal;
	const int wlocal = static_cast<int>(ceil(balance_factor * nlocal));
	const int snum = wlocal + gnum;
	IP_PRE_omp_range_id(ifrom, ito, tid, snum, nthreads);
	if (ifrom < wlocal) ifrom = static_cast<int>(ibalance_factor * ifrom);
	else ifrom -= wlocal - nlocal;
	if (ito < wlocal) ito = static_cast<int>(ibalance_factor * ito);
	else ito -= wlocal - nlocal;

	int e_ito = ito;
	const int list_size = (e_ito + tid * 2 + 2) * maxnbors;

	int which;

	int pack_offset = maxnbors;
	int ct = (ifrom + tid * 2) * maxnbors;
	int *neighptr = firstneigh + ct;
	const int obound = pack_offset + maxnbors * 2;

	const int toffs = tid * ncache_stride;
	flt_t * _noalias const tx = ncachex + toffs;
	flt_t * _noalias const ty = ncachey + toffs;
	flt_t * _noalias const tz = ncachez + toffs;
	int * _noalias const tj = ncachej + toffs;
	int * _noalias const tjtype = ncachejtype + toffs;
	int * _noalias const ttag = ncachetag + toffs;

	// loop over all atoms in other bins in stencil, store every pair
	int istart, icount, ncount, oldbin = -9999999, lane, max_chunk;
	for (int i = ifrom; i < ito; i++) {
	const flt_t xtmp = x[i].x;
	const flt_t ytmp = x[i].y;
	const flt_t ztmp = x[i].z;
	const int itype = x[i].w;
	const tagint itag = tag[i];
	const int ioffset = ntypes * itype;

	const int ibin = atombin[i];
	if (ibin != oldbin) {
	oldbin = ibin;
	ncount = 0;
	if (i < nlocal) {
	for (int k = 0; k < nstencilp; k++) {
	const int bstart = binhead[ibin + binstart[k]];
	const int bend = binhead[ibin + binend[k]];
	#if defined(LMP_SIMD_COMPILER)
	#pragma simd
	#endif
	for (int jj = bstart; jj < bend; jj++)
	tj[ncount++] = binpacked[jj];
	}
	} else {
	const int zbin = ibin / mbinyx;
	const int zrem = ibin % mbinyx;
	const int ybin = zrem / mbinx;
	const int xbin = zrem % mbinx;
	for (int k = 0; k < nstencil; k++) {
	const int xbin2 = xbin + stencilxyz[3 * k + 0];
	const int ybin2 = ybin + stencilxyz[3 * k + 1];
	const int zbin2 = zbin + stencilxyz[3 * k + 2];
	if (xbin2 < 0 \|\| xbin2 >= mbinx \|\|
	ybin2 < 0 \|\| ybin2 >= mbiny \|\|
	zbin2 < 0 \|\| zbin2 >= mbinz) continue;

	const int bstart = binhead[ibin + stencil[k]];
	const int bend = binhead[ibin + stencil[k] + 1];
	#if defined(LMP_SIMD_COMPILER)
	#pragma simd
	#endif
	for (int jj = bstart; jj < bend; jj++)
	tj[ncount++] = binpacked[jj];
	}
	} // if i < nlocal
	#if defined(LMP_SIMD_COMPILER)
	#pragma vector aligned
	#pragma simd
	#endif
	for (int u = 0; u < ncount; u++) {
	const int j = tj[u];
	tx[u] = x[j].x;
	ty[u] = x[j].y;
	tz[u] = x[j].z;
	tjtype[u] = x[j].w;
	ttag[u] = tag[j];
	}
	} // if ibin != oldbin

	// ---------------------- Loop over other bins

	int n = maxnbors;
	int n2 = n * 2;
	int *neighptr2 = neighptr;
	const flt_t * _noalias cutsq;
	if (i < nlocal) cutsq = cutneighsq;
	else cutsq = cutneighghostsq;

	const int icp = i;

	#if defined(LMP_SIMD_COMPILER)
	#pragma vector aligned
	#pragma ivdep
	#endif
	for (int u = 0; u < ncount; u++) {
	int addme = 1;
	int j = tj[u];

	if (i == j) addme = 0;

	// Cutoff Check
	const flt_t delx = xtmp - tx[u];
	const flt_t dely = ytmp - ty[u];
	const flt_t delz = ztmp - tz[u];
	const int jtype = tjtype[u];
	const int jtag = ttag[u];
	const flt_t rsq = delx * delx + dely * dely + delz * delz;
	if (rsq > cutsq[ioffset + jtype]) addme = 0;

	if (need_ic && icp < nlocal) {
	int no_special;
	ominimum_image_check(no_special, delx, dely, delz);
	if (no_special)
	j = -j - 1;
	}

	int flist = 0;
	if (itag > jtag) {
	if (((itag+jtag) & 1) == 0) flist = 1;
	} else if (itag < jtag) {
	if (((itag+jtag) & 1) == 1) flist = 1;
	} else {
	if (tz[u] < ztmp) flist = 1;
	else if (tz[u] == ztmp && ty[u] < ytmp) flist = 1;
	else if (tz[u] == ztmp && ty[u] == ytmp && tx[u] < xtmp)
	flist = 1;
	}
	if (addme) {
	if (flist)
	neighptr2[n2++] = j;
	else
	neighptr[n++] = j;
	}
	} // for u

	#ifndef _LMP_INTEL_OFFLOAD
	if (exclude) {
	int alln = n;
	n = maxnbors;
	for (int u = pack_offset; u < alln; u++) {
	const int j = neighptr[u];
	int pj = j;
	if (need_ic)
	if (pj < 0) pj = -j - 1;
	const int jtype = x[pj].w;
	if (exclusion(i,pj,itype,jtype,mask,molecule)) continue;
	neighptr[n++] = j;
	}
	alln = n2;
	n2 = maxnbors * 2;
	for (int u = n2; u < alln; u++) {
	const int j = neighptr[u];
	int pj = j;
	if (need_ic)
	if (pj < 0) pj = -j - 1;
	const int jtype = x[pj].w;
	if (exclusion(i,pj,itype,jtype,mask,molecule)) continue;
	neighptr[n2++] = j;
	}
	}
	#endif
	int ns = n - maxnbors;
	int alln = n;
	atombin[i] = ns;
	n = 0;
	for (int u = maxnbors; u < alln; u++)
	neighptr[n++] = neighptr[u];
	ns += n2 - maxnbors * 2;
	for (int u = maxnbors * 2; u < n2; u++)
	neighptr[n++] = neighptr[u];
	if (ns > maxnbors) *overflow = 1;

	ilist[i] = i;
	cnumneigh[i] = ct;
	numneigh[i] = ns;

	ct += ns;
	const int alignb = (INTEL_DATA_ALIGN / sizeof(int));
	const int edge = ct & (alignb - 1);
	if (edge) ct += alignb - edge;
	neighptr = firstneigh + ct;
	if (ct + obound > list_size) {
	if (i < ito - 1) {
	*overflow = 1;
	ct = (ifrom + tid * 2) * maxnbors;
	}
	}
	}

	if (*overflow == 1)
	for (int i = ifrom; i < ito; i++)
	numneigh[i] = 0;

	#ifdef _LMP_INTEL_OFFLOAD
	int ghost_offset = 0, nall_offset = e_nall;
	if (separate_buffers) {
	for (int i = ifrom; i < ito; ++i) {
	int * _noalias jlist = firstneigh + cnumneigh[i];
	const int jnum = numneigh[i];
	#if __INTEL_COMPILER+0 > 1499
	#pragma vector aligned
	#pragma simd
	#endif
	for (int jj = 0; jj < jnum; jj++) {
	int j = jlist[jj];
	if (need_ic && j < 0) j = -j - 1;
	}
	}

	overflow[LMP_LOCAL_MIN] = 0;
	overflow[LMP_LOCAL_MAX] = nlocal - 1;
	overflow[LMP_GHOST_MIN] = nlocal;
	overflow[LMP_GHOST_MAX] = e_nall - 1;

	int nghost = overflow[LMP_GHOST_MAX] + 1 - overflow[LMP_GHOST_MIN];
	if (nghost < 0) nghost = 0;
	if (offload) {
	ghost_offset = overflow[LMP_GHOST_MIN] - overflow[LMP_LOCAL_MAX] - 1;
	nall_offset = overflow[LMP_LOCAL_MAX] + 1 + nghost;
	} else {
	ghost_offset = overflow[LMP_GHOST_MIN] - nlocal;
	nall_offset = nlocal + nghost;
	}
	} // if separate_buffers
	#endif

	if (molecular) {
	int ito_m = ito;
	if (ito >= nlocal) ito_m = nlocal;
	for (int i = ifrom; i < ito_m; ++i) {
	int * _noalias jlist = firstneigh + cnumneigh[i];
	const int jnum = numneigh[i];

	#if defined(LMP_SIMD_COMPILER)
	#pragma vector aligned
	#pragma simd
	#endif
	for (int jj = 0; jj < jnum; jj++) {
	const int j = jlist[jj];
	if (need_ic && j < 0) {
	which = 0;
	jlist[jj] = -j - 1;
	} else
	ofind_special(which, special, nspecial, i, tag[j]);
	#ifdef _LMP_INTEL_OFFLOAD
	if (j >= nlocal) {
	if (j == e_nall)
	jlist[jj] = nall_offset;
	else if (which)
	jlist[jj] = (j-ghost_offset) ^ (which << SBBITS);
	else jlist[jj]-=ghost_offset;
	} else
	#endif
	if (which) jlist[jj] = j ^ (which << SBBITS);
	}
	} // for i
	} // if molecular
	#ifdef _LMP_INTEL_OFFLOAD
	else if (separate_buffers) {
	for (int i = ifrom; i < ito; ++i) {
	int * _noalias jlist = firstneigh + cnumneigh[i];
	const int jnum = numneigh[i];
	int jj = 0;
	#pragma vector aligned
	#pragma simd
	for (jj = 0; jj < jnum; jj++) {
	if (jlist[jj] >= nlocal) {
	if (jlist[jj] == e_nall) jlist[jj] = nall_offset;
	else jlist[jj] -= ghost_offset;
	}
	}
	}
	}
	#endif
	} // end omp
	#if defined(__MIC__) && defined(_LMP_INTEL_OFFLOAD)
	timer_compute = MIC_Wtime() - timer_compute;
	#endif
	} // end offload

	#ifdef _LMP_INTEL_OFFLOAD
	if (offload) {
	_fix->stop_watch(TIME_OFFLOAD_LATENCY);
	_fix->start_watch(TIME_HOST_NEIGHBOR);
	for (int n = 0; n < aend; n++) {
	ilist[n] = n;
	numneigh[n] = 0;
	}
	} else {
	for (int i = 0; i < aend; i++)
	list->firstneigh[i] = firstneigh + cnumneigh[i];
	if (separate_buffers) {
	_fix->start_watch(TIME_PACK);
	_fix->set_neighbor_host_sizes();
	buffers->pack_sep_from_single(_fix->host_min_local(),
	_fix->host_used_local(),
	_fix->host_min_ghost(),
	_fix->host_used_ghost());
	_fix->stop_watch(TIME_PACK);
	}
	}
	#else
	#pragma vector aligned
	#pragma simd
	for (int i = 0; i < aend; i++)
	list->firstneigh[i] = firstneigh + cnumneigh[i];
	#endif
	}

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