Port changes to OPENMP and INTEL packages
This commit is contained in:
Stan Gerald Moore
271
src/INTEL/npair_skip_trim_intel.cpp
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271
src/INTEL/npair_skip_trim_intel.cpp
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@ -0,0 +1,271 @@
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// clang-format off
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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https://www.lammps.org/, Sandia National Laboratories
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LAMMPS development team: developers@lammps.org
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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/* ----------------------------------------------------------------------
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Contributing author: Stan Moore (SNL)
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------------------------------------------------------------------------- */
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#include "npair_skip_trim_intel.h"
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#include "atom.h"
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#include "comm.h"
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#include "error.h"
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#include "modify.h"
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#include "my_page.h"
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#include "neigh_list.h"
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#include "neigh_request.h"
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#include "neighbor.h"
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using namespace LAMMPS_NS;
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/* ---------------------------------------------------------------------- */
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NPairSkipTrimIntel::NPairSkipTrimIntel(LAMMPS *lmp) : NPair(lmp) {
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_fix = static_cast<FixIntel *>(modify->get_fix_by_id("package_intel"));
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if (!_fix) error->all(FLERR, "The 'package intel' command is required for /intel styles");
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_inum_starts = new int[comm->nthreads];
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_inum_counts = new int[comm->nthreads];
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_full_props = nullptr;
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}
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/* ---------------------------------------------------------------------- */
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NPairSkipTrimIntel::~NPairSkipTrimIntel() {
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delete []_inum_starts;
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delete []_inum_counts;
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delete[] _full_props;
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}
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/* ---------------------------------------------------------------------- */
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void NPairSkipTrimIntel::copy_neighbor_info()
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{
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NPair::copy_neighbor_info();
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// Only need to set _full_props once; npair object deleted for changes
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if (_full_props) return;
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_full_props = new int[neighbor->nrequest];
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for (int i = 0; i < neighbor->nrequest; i++)
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_full_props[i] = neighbor->requests[i]->full;
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}
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/* ----------------------------------------------------------------------
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build skip list for subset of types from parent list
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works for half and full lists
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works for owned (non-ghost) list, also for ghost list
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iskip and ijskip flag which atom types and type pairs to skip
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if ghost, also store neighbors of ghost atoms & set inum,gnum correctly
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------------------------------------------------------------------------- */
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template<class flt_t, class acc_t, int THREE>
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void NPairSkipTrimIntel::build_t(NeighList *list, int *numhalf, int *cnumneigh,
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int *numhalf_skip, IntelBuffers<flt_t,acc_t> *buffers)
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{
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const int nlocal = atom->nlocal;
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const int e_nall = nlocal + atom->nghost;
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const ATOM_T * _noalias const x = buffers->get_x();
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const int * _noalias const type = atom->type;
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int * _noalias const ilist = list->ilist;
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int * _noalias const numneigh = list->numneigh;
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int ** _noalias const firstneigh = (int ** const)list->firstneigh; // NOLINT
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const int * _noalias const ilist_skip = list->listskip->ilist;
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const int * _noalias const numneigh_skip = list->listskip->numneigh;
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const int ** _noalias const firstneigh_skip = (const int ** const)list->listskip->firstneigh; // NOLINT
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const int * _noalias const iskip = list->iskip;
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const int ** _noalias const ijskip = (const int ** const)list->ijskip; // NOLINT
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const flt_t cutsq_custom = cutoff_custom * cutoff_custom;
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int num_skip = list->listskip->inum;
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if (list->ghost) num_skip += list->listskip->gnum;
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int packthreads;
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if (comm->nthreads > INTEL_HTHREADS && THREE==0)
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packthreads = comm->nthreads;
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else
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packthreads = 1;
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#if defined(_OPENMP)
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#pragma omp parallel if (packthreads > 1)
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#endif
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{
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int tid, ifrom, ito;
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IP_PRE_omp_range_id(ifrom, ito, tid, num_skip, packthreads);
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// each thread has its own page allocator
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MyPage<int> &ipage = list->ipage[tid];
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ipage.reset();
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int my_inum = ifrom;
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_inum_starts[tid] = ifrom;
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// loop over parent full list
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for (int ii = ifrom; ii < ito; ii++) {
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const int i = ilist_skip[ii];
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const int itype = type[i];
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if (iskip[itype]) continue;
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const flt_t xtmp = x[i].x;
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const flt_t ytmp = x[i].y;
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const flt_t ztmp = x[i].z;
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int n = 0;
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int *neighptr = ipage.vget();
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// loop over parent non-skip list
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const int * _noalias const jlist = firstneigh_skip[i];
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const int jnum = numneigh_skip[i];
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if (THREE) {
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const int jnumhalf = numhalf_skip[ii];
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for (int jj = 0; jj < jnumhalf; jj++) {
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const int joriginal = jlist[jj];
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const int j = joriginal & NEIGHMASK;
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int addme = 1;
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if (ijskip[itype][type[j]]) addme = 0;
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// trim to shorter cutoff
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const flt_t delx = xtmp - x[j].x;
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const flt_t dely = ytmp - x[j].y;
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const flt_t delz = ztmp - x[j].z;
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const flt_t rsq = delx * delx + dely * dely + delz * delz;
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if (rsq > cutsq_custom) addme = 0;
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if (addme)
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neighptr[n++] = joriginal;
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}
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numhalf[my_inum] = n;
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for (int jj = jnumhalf; jj < jnum; jj++) {
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const int joriginal = jlist[jj];
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const int j = joriginal & NEIGHMASK;
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int addme = 1;
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if (ijskip[itype][type[j]]) addme = 0;
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// trim to shorter cutoff
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const flt_t delx = xtmp - x[j].x;
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const flt_t dely = ytmp - x[j].y;
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const flt_t delz = ztmp - x[j].z;
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const flt_t rsq = delx * delx + dely * dely + delz * delz;
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if (rsq > cutsq_custom) addme = 0;
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if (addme)
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neighptr[n++] = joriginal;
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}
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} else {
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#if defined(LMP_SIMD_COMPILER)
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#pragma vector aligned
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#pragma ivdep
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#endif
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for (int jj = 0; jj < jnum; jj++) {
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const int joriginal = jlist[jj];
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const int j = joriginal & NEIGHMASK;
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int addme = 1;
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if (ijskip[itype][type[j]]) addme = 0;
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// trim to shorter cutoff
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const flt_t delx = xtmp - x[j].x;
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const flt_t dely = ytmp - x[j].y;
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const flt_t delz = ztmp - x[j].z;
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const flt_t rsq = delx * delx + dely * dely + delz * delz;
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if (rsq > cutsq_custom) addme = 0;
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if (addme)
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neighptr[n++] = joriginal;
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}
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}
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ilist[my_inum++] = i;
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firstneigh[i] = neighptr;
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numneigh[i] = n;
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int pad_end = n;
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IP_PRE_neighbor_pad(pad_end, 0);
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#if defined(LMP_SIMD_COMPILER)
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#pragma vector aligned
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#pragma loop_count min=1, max=INTEL_COMPILE_WIDTH-1, \
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avg=INTEL_COMPILE_WIDTH/2
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#endif
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for ( ; n < pad_end; n++)
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neighptr[n] = e_nall;
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ipage.vgot(n);
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if (ipage.status())
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error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
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}
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int last_inum = 0, loop_end;
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_inum_counts[tid] = my_inum;
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}
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int inum = _inum_counts[0];
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for (int tid = 1; tid < packthreads; tid++) {
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for (int i = _inum_starts[tid]; i < _inum_counts[tid]; i++) {
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if (THREE) numhalf[inum] = numhalf[i];
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ilist[inum++] = ilist[i];
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}
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}
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list->inum = inum;
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if (THREE && num_skip > 0) {
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int * const list_start = firstneigh[ilist[0]];
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for (int ii = 0; ii < inum; ii++) {
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int i = ilist[ii];
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cnumneigh[ii] = static_cast<int>(firstneigh[i] - list_start);
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}
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}
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if (list->ghost) {
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int num = 0;
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int my_inum = list->inum;
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for (int i = 0; i < my_inum; i++)
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if (ilist[i] < nlocal) num++;
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else break;
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list->inum = num;
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list->gnum = my_inum - num;
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}
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}
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/* ---------------------------------------------------------------------- */
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void NPairSkipTrimIntel::build(NeighList *list)
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{
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if (_fix->three_body_neighbor()==0 ||
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_full_props[list->listskip->index] == 0) {
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if (_fix->precision() == FixIntel::PREC_MODE_MIXED)
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build_t<float,double,0>(list, nullptr, nullptr, nullptr, _fix->get_mixed_buffers());
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else if (_fix->precision() == FixIntel::PREC_MODE_DOUBLE)
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build_t<double,double,0>(list, nullptr, nullptr, nullptr, _fix->get_double_buffers());
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else
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build_t<float,float,0>(list, nullptr, nullptr, nullptr, _fix->get_single_buffers());
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} else {
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int *nhalf, *cnumneigh, *nhalf_skip, *u;
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if (_fix->precision() == FixIntel::PREC_MODE_MIXED) {
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_fix->get_mixed_buffers()->get_list_data3(list->listskip,nhalf_skip,u);
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_fix->get_mixed_buffers()->grow_data3(list, nhalf, cnumneigh);
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build_t<float,double,1>(list, nhalf, cnumneigh, nhalf_skip, _fix->get_mixed_buffers());
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} else if (_fix->precision() == FixIntel::PREC_MODE_DOUBLE) {
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_fix->get_double_buffers()->get_list_data3(list->listskip,nhalf_skip,u);
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_fix->get_double_buffers()->grow_data3(list, nhalf, cnumneigh);
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build_t<double,double,1>(list, nhalf, cnumneigh, nhalf_skip, _fix->get_double_buffers());
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} else {
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_fix->get_single_buffers()->get_list_data3(list->listskip,nhalf_skip,u);
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_fix->get_single_buffers()->grow_data3(list,nhalf,cnumneigh);
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build_t<float,float,1>(list, nhalf, cnumneigh, nhalf_skip, _fix->get_single_buffers());
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}
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}
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}
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62
src/INTEL/npair_skip_trim_intel.h
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62
src/INTEL/npair_skip_trim_intel.h
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@ -0,0 +1,62 @@
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// clang-format off
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/* -*- c++ -*- ----------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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https://www.lammps.org/, Sandia National Laboratories
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LAMMPS development team: developers@lammps.org
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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#ifdef NPAIR_CLASS
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// clang-format off
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NPairStyle(skip/trim/intel,
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NPairSkipTrimIntel,
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NP_SKIP | NP_HALF | NP_FULL |
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NP_NSQ | NP_BIN | NP_MULTI |
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NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_TRIM | NP_INTEL);
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NPairStyle(skip/trim/ghost/intel,
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NPairSkipTrimIntel,
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NP_SKIP | NP_HALF | NP_FULL |
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NP_NSQ | NP_BIN | NP_MULTI |
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NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_TRIM | NP_GHOST | NP_INTEL);
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// clang-format on
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#else
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#ifndef LMP_NPAIR_SKIP_TRIM_INTEL_H
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#define LMP_NPAIR_SKIP_TRIM_INTEL_H
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#include "fix_intel.h"
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#include "npair.h"
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#if defined(_OPENMP)
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#include <omp.h>
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#endif
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namespace LAMMPS_NS {
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class NPairSkipTrimIntel : public NPair {
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public:
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NPairSkipTrimIntel(class LAMMPS *);
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~NPairSkipTrimIntel() override;
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void copy_neighbor_info() override;
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void build(class NeighList *) override;
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protected:
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FixIntel *_fix;
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int *_inum_starts, *_inum_counts, *_full_props;
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template <class flt_t, class acc_t, int THREE>
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void build_t(NeighList *, int *numhalf, int *cnumneigh, int *numhalf_skip,
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IntelBuffers<flt_t, acc_t> *);
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};
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} // namespace LAMMPS_NS
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#endif
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#endif
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@ -88,7 +88,6 @@ void NPairTrimIntel::build_t(NeighList *list,
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for (int jj = 0; jj < jnum; jj++) {
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const int joriginal = jlist[jj];
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const int j = joriginal & NEIGHMASK;
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int addme = 1;
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// trim to shorter cutoff
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@ -97,9 +96,7 @@ void NPairTrimIntel::build_t(NeighList *list,
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const flt_t delz = ztmp - x[j].z;
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const flt_t rsq = delx * delx + dely * dely + delz * delz;
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if (rsq > cutsq_custom) addme = 0;
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if (addme)
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if (rsq <= cutsq_custom)
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neighptr[n++] = joriginal;
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}
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@ -20,36 +20,36 @@ NPairStyle(skip/omp,
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NPairSkip,
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NP_SKIP | NP_HALF | NP_FULL |
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NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD |
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NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_OMP);
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NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_TRIM | NP_OMP);
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NPairStyle(skip/half/respa/omp,
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NPairSkipRespa,
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NP_SKIP | NP_RESPA | NP_HALF | NP_FULL |
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NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD |
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NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_OMP);
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NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_TRIM | NP_OMP);
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NPairStyle(skip/half/size/omp,
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NPairSkipSize,
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NP_SKIP | NP_SIZE | NP_HALF | NP_FULL | NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD |
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NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_OMP);
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NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_TRIM | NP_OMP);
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NPairStyle(skip/size/off2on/omp,
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NPairSkipSizeOff2on,
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NP_SKIP | NP_SIZE | NP_OFF2ON | NP_HALF |
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NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_MULTI_OLD |
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NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_OMP);
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NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_TRIM | NP_OMP);
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NPairStyle(skip/size/off2on/oneside/omp,
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NPairSkipSizeOff2onOneside,
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NP_SKIP | NP_SIZE | NP_OFF2ON | NP_ONESIDE | NP_HALF |
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NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_NEWTON | NP_NEWTOFF |
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NP_ORTHO | NP_TRI | NP_OMP);
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NP_ORTHO | NP_TRI | NP_TRIM | NP_OMP);
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NPairStyle(skip/ghost/omp,
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NPairSkip,
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NP_SKIP | NP_HALF | NP_FULL |
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NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD |
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NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_OMP | NP_GHOST);
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NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_TRIM | NP_OMP | NP_GHOST);
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// clang-format off
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#endif
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@ -26,6 +26,7 @@ class NeighRequest : protected Pointers {
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friend class NStencil;
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friend class NeighborKokkos;
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friend class NPairSkipIntel;
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friend class NPairSkipTrimIntel;
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friend class FixIntel;
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protected:
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