--- /dev/null
- * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
- if (nsp_cj4 > 0 && nsp + nsp_cj4 > nsp_max)
++ * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+#include <string.h>
+#include <assert.h>
+
+#include "sysstuff.h"
+#include "gromacs/utility/smalloc.h"
+#include "types/commrec.h"
+#include "macros.h"
+#include "gromacs/math/utilities.h"
+#include "vec.h"
+#include "pbc.h"
+#include "nbnxn_consts.h"
+/* nbnxn_internal.h included gromacs/simd/macros.h */
+#include "nbnxn_internal.h"
+#ifdef GMX_NBNXN_SIMD
+#include "gromacs/simd/vector_operations.h"
+#endif
+#include "nbnxn_atomdata.h"
+#include "nbnxn_search.h"
+#include "gmx_omp_nthreads.h"
+#include "nrnb.h"
+#include "ns.h"
+
+#include "gromacs/fileio/gmxfio.h"
+
+#ifdef NBNXN_SEARCH_BB_SIMD4
+/* Always use 4-wide SIMD for bounding box calculations */
+
+# ifndef GMX_DOUBLE
+/* Single precision BBs + coordinates, we can also load coordinates with SIMD */
+# define NBNXN_SEARCH_SIMD4_FLOAT_X_BB
+# endif
+
+# if defined NBNXN_SEARCH_SIMD4_FLOAT_X_BB && (GPU_NSUBCELL == 4 || GPU_NSUBCELL == 8)
+/* Store bounding boxes with x, y and z coordinates in packs of 4 */
+# define NBNXN_PBB_SIMD4
+# endif
+
+/* The packed bounding box coordinate stride is always set to 4.
+ * With AVX we could use 8, but that turns out not to be faster.
+ */
+# define STRIDE_PBB 4
+# define STRIDE_PBB_2LOG 2
+
+#endif /* NBNXN_SEARCH_BB_SIMD4 */
+
+#ifdef GMX_NBNXN_SIMD
+
+/* The functions below are macros as they are performance sensitive */
+
+/* 4x4 list, pack=4: no complex conversion required */
+/* i-cluster to j-cluster conversion */
+#define CI_TO_CJ_J4(ci) (ci)
+/* cluster index to coordinate array index conversion */
+#define X_IND_CI_J4(ci) ((ci)*STRIDE_P4)
+#define X_IND_CJ_J4(cj) ((cj)*STRIDE_P4)
+
+/* 4x2 list, pack=4: j-cluster size is half the packing width */
+/* i-cluster to j-cluster conversion */
+#define CI_TO_CJ_J2(ci) ((ci)<<1)
+/* cluster index to coordinate array index conversion */
+#define X_IND_CI_J2(ci) ((ci)*STRIDE_P4)
+#define X_IND_CJ_J2(cj) (((cj)>>1)*STRIDE_P4 + ((cj) & 1)*(PACK_X4>>1))
+
+/* 4x8 list, pack=8: i-cluster size is half the packing width */
+/* i-cluster to j-cluster conversion */
+#define CI_TO_CJ_J8(ci) ((ci)>>1)
+/* cluster index to coordinate array index conversion */
+#define X_IND_CI_J8(ci) (((ci)>>1)*STRIDE_P8 + ((ci) & 1)*(PACK_X8>>1))
+#define X_IND_CJ_J8(cj) ((cj)*STRIDE_P8)
+
+/* The j-cluster size is matched to the SIMD width */
+#if GMX_SIMD_REAL_WIDTH == 2
+#define CI_TO_CJ_SIMD_4XN(ci) CI_TO_CJ_J2(ci)
+#define X_IND_CI_SIMD_4XN(ci) X_IND_CI_J2(ci)
+#define X_IND_CJ_SIMD_4XN(cj) X_IND_CJ_J2(cj)
+#else
+#if GMX_SIMD_REAL_WIDTH == 4
+#define CI_TO_CJ_SIMD_4XN(ci) CI_TO_CJ_J4(ci)
+#define X_IND_CI_SIMD_4XN(ci) X_IND_CI_J4(ci)
+#define X_IND_CJ_SIMD_4XN(cj) X_IND_CJ_J4(cj)
+#else
+#if GMX_SIMD_REAL_WIDTH == 8
+#define CI_TO_CJ_SIMD_4XN(ci) CI_TO_CJ_J8(ci)
+#define X_IND_CI_SIMD_4XN(ci) X_IND_CI_J8(ci)
+#define X_IND_CJ_SIMD_4XN(cj) X_IND_CJ_J8(cj)
+/* Half SIMD with j-cluster size */
+#define CI_TO_CJ_SIMD_2XNN(ci) CI_TO_CJ_J4(ci)
+#define X_IND_CI_SIMD_2XNN(ci) X_IND_CI_J4(ci)
+#define X_IND_CJ_SIMD_2XNN(cj) X_IND_CJ_J4(cj)
+#else
+#if GMX_SIMD_REAL_WIDTH == 16
+#define CI_TO_CJ_SIMD_2XNN(ci) CI_TO_CJ_J8(ci)
+#define X_IND_CI_SIMD_2XNN(ci) X_IND_CI_J8(ci)
+#define X_IND_CJ_SIMD_2XNN(cj) X_IND_CJ_J8(cj)
+#else
+#error "unsupported GMX_SIMD_REAL_WIDTH"
+#endif
+#endif
+#endif
+#endif
+
+#endif /* GMX_NBNXN_SIMD */
+
+
+#ifdef NBNXN_SEARCH_BB_SIMD4
+/* Store bounding boxes corners as quadruplets: xxxxyyyyzzzz */
+#define NBNXN_BBXXXX
+/* Size of bounding box corners quadruplet */
+#define NNBSBB_XXXX (NNBSBB_D*DIM*STRIDE_PBB)
+#endif
+
+/* We shift the i-particles backward for PBC.
+ * This leads to more conditionals than shifting forward.
+ * We do this to get more balanced pair lists.
+ */
+#define NBNXN_SHIFT_BACKWARD
+
+
+/* This define is a lazy way to avoid interdependence of the grid
+ * and searching data structures.
+ */
+#define NBNXN_NA_SC_MAX (GPU_NSUBCELL*NBNXN_GPU_CLUSTER_SIZE)
+
+
+static void nbs_cycle_clear(nbnxn_cycle_t *cc)
+{
+ int i;
+
+ for (i = 0; i < enbsCCnr; i++)
+ {
+ cc[i].count = 0;
+ cc[i].c = 0;
+ }
+}
+
+static double Mcyc_av(const nbnxn_cycle_t *cc)
+{
+ return (double)cc->c*1e-6/cc->count;
+}
+
+static void nbs_cycle_print(FILE *fp, const nbnxn_search_t nbs)
+{
+ int n;
+ int t;
+
+ fprintf(fp, "\n");
+ fprintf(fp, "ns %4d grid %4.1f search %4.1f red.f %5.3f",
+ nbs->cc[enbsCCgrid].count,
+ Mcyc_av(&nbs->cc[enbsCCgrid]),
+ Mcyc_av(&nbs->cc[enbsCCsearch]),
+ Mcyc_av(&nbs->cc[enbsCCreducef]));
+
+ if (nbs->nthread_max > 1)
+ {
+ if (nbs->cc[enbsCCcombine].count > 0)
+ {
+ fprintf(fp, " comb %5.2f",
+ Mcyc_av(&nbs->cc[enbsCCcombine]));
+ }
+ fprintf(fp, " s. th");
+ for (t = 0; t < nbs->nthread_max; t++)
+ {
+ fprintf(fp, " %4.1f",
+ Mcyc_av(&nbs->work[t].cc[enbsCCsearch]));
+ }
+ }
+ fprintf(fp, "\n");
+}
+
+static void nbnxn_grid_init(nbnxn_grid_t * grid)
+{
+ grid->cxy_na = NULL;
+ grid->cxy_ind = NULL;
+ grid->cxy_nalloc = 0;
+ grid->bb = NULL;
+ grid->bbj = NULL;
+ grid->nc_nalloc = 0;
+}
+
+static int get_2log(int n)
+{
+ int log2;
+
+ log2 = 0;
+ while ((1<<log2) < n)
+ {
+ log2++;
+ }
+ if ((1<<log2) != n)
+ {
+ gmx_fatal(FARGS, "nbnxn na_c (%d) is not a power of 2", n);
+ }
+
+ return log2;
+}
+
+static int nbnxn_kernel_to_ci_size(int nb_kernel_type)
+{
+ switch (nb_kernel_type)
+ {
+ case nbnxnk4x4_PlainC:
+ case nbnxnk4xN_SIMD_4xN:
+ case nbnxnk4xN_SIMD_2xNN:
+ return NBNXN_CPU_CLUSTER_I_SIZE;
+ case nbnxnk8x8x8_CUDA:
+ case nbnxnk8x8x8_PlainC:
+ /* The cluster size for super/sub lists is only set here.
+ * Any value should work for the pair-search and atomdata code.
+ * The kernels, of course, might require a particular value.
+ */
+ return NBNXN_GPU_CLUSTER_SIZE;
+ default:
+ gmx_incons("unknown kernel type");
+ }
+
+ return 0;
+}
+
+int nbnxn_kernel_to_cj_size(int nb_kernel_type)
+{
+ int nbnxn_simd_width = 0;
+ int cj_size = 0;
+
+#ifdef GMX_NBNXN_SIMD
+ nbnxn_simd_width = GMX_SIMD_REAL_WIDTH;
+#endif
+
+ switch (nb_kernel_type)
+ {
+ case nbnxnk4x4_PlainC:
+ cj_size = NBNXN_CPU_CLUSTER_I_SIZE;
+ break;
+ case nbnxnk4xN_SIMD_4xN:
+ cj_size = nbnxn_simd_width;
+ break;
+ case nbnxnk4xN_SIMD_2xNN:
+ cj_size = nbnxn_simd_width/2;
+ break;
+ case nbnxnk8x8x8_CUDA:
+ case nbnxnk8x8x8_PlainC:
+ cj_size = nbnxn_kernel_to_ci_size(nb_kernel_type);
+ break;
+ default:
+ gmx_incons("unknown kernel type");
+ }
+
+ return cj_size;
+}
+
+static int ci_to_cj(int na_cj_2log, int ci)
+{
+ switch (na_cj_2log)
+ {
+ case 2: return ci; break;
+ case 1: return (ci<<1); break;
+ case 3: return (ci>>1); break;
+ }
+
+ return 0;
+}
+
+gmx_bool nbnxn_kernel_pairlist_simple(int nb_kernel_type)
+{
+ if (nb_kernel_type == nbnxnkNotSet)
+ {
+ gmx_fatal(FARGS, "Non-bonded kernel type not set for Verlet-style pair-list.");
+ }
+
+ switch (nb_kernel_type)
+ {
+ case nbnxnk8x8x8_CUDA:
+ case nbnxnk8x8x8_PlainC:
+ return FALSE;
+
+ case nbnxnk4x4_PlainC:
+ case nbnxnk4xN_SIMD_4xN:
+ case nbnxnk4xN_SIMD_2xNN:
+ return TRUE;
+
+ default:
+ gmx_incons("Invalid nonbonded kernel type passed!");
+ return FALSE;
+ }
+}
+
+/* Initializes a single nbnxn_pairlist_t data structure */
+static void nbnxn_init_pairlist_fep(t_nblist *nl)
+{
+ nl->type = GMX_NBLIST_INTERACTION_FREE_ENERGY;
+ nl->igeometry = GMX_NBLIST_GEOMETRY_PARTICLE_PARTICLE;
+ /* The interaction functions are set in the free energy kernel fuction */
+ nl->ivdw = -1;
+ nl->ivdwmod = -1;
+ nl->ielec = -1;
+ nl->ielecmod = -1;
+
+ nl->maxnri = 0;
+ nl->maxnrj = 0;
+ nl->nri = 0;
+ nl->nrj = 0;
+ nl->iinr = NULL;
+ nl->gid = NULL;
+ nl->shift = NULL;
+ nl->jindex = NULL;
+ nl->jjnr = NULL;
+ nl->excl_fep = NULL;
+
+}
+
+void nbnxn_init_search(nbnxn_search_t * nbs_ptr,
+ ivec *n_dd_cells,
+ gmx_domdec_zones_t *zones,
+ gmx_bool bFEP,
+ int nthread_max)
+{
+ nbnxn_search_t nbs;
+ int d, g, t;
+
+ snew(nbs, 1);
+ *nbs_ptr = nbs;
+
+ nbs->bFEP = bFEP;
+
+ nbs->DomDec = (n_dd_cells != NULL);
+
+ clear_ivec(nbs->dd_dim);
+ nbs->ngrid = 1;
+ if (nbs->DomDec)
+ {
+ nbs->zones = zones;
+
+ for (d = 0; d < DIM; d++)
+ {
+ if ((*n_dd_cells)[d] > 1)
+ {
+ nbs->dd_dim[d] = 1;
+ /* Each grid matches a DD zone */
+ nbs->ngrid *= 2;
+ }
+ }
+ }
+
+ snew(nbs->grid, nbs->ngrid);
+ for (g = 0; g < nbs->ngrid; g++)
+ {
+ nbnxn_grid_init(&nbs->grid[g]);
+ }
+ nbs->cell = NULL;
+ nbs->cell_nalloc = 0;
+ nbs->a = NULL;
+ nbs->a_nalloc = 0;
+
+ nbs->nthread_max = nthread_max;
+
+ /* Initialize the work data structures for each thread */
+ snew(nbs->work, nbs->nthread_max);
+ for (t = 0; t < nbs->nthread_max; t++)
+ {
+ nbs->work[t].cxy_na = NULL;
+ nbs->work[t].cxy_na_nalloc = 0;
+ nbs->work[t].sort_work = NULL;
+ nbs->work[t].sort_work_nalloc = 0;
+
+ snew(nbs->work[t].nbl_fep, 1);
+ nbnxn_init_pairlist_fep(nbs->work[t].nbl_fep);
+ }
+
+ /* Initialize detailed nbsearch cycle counting */
+ nbs->print_cycles = (getenv("GMX_NBNXN_CYCLE") != 0);
+ nbs->search_count = 0;
+ nbs_cycle_clear(nbs->cc);
+ for (t = 0; t < nbs->nthread_max; t++)
+ {
+ nbs_cycle_clear(nbs->work[t].cc);
+ }
+}
+
+static real grid_atom_density(int n, rvec corner0, rvec corner1)
+{
+ rvec size;
+
+ if (n == 0)
+ {
+ /* To avoid zero density we use a minimum of 1 atom */
+ n = 1;
+ }
+
+ rvec_sub(corner1, corner0, size);
+
+ return n/(size[XX]*size[YY]*size[ZZ]);
+}
+
+static int set_grid_size_xy(const nbnxn_search_t nbs,
+ nbnxn_grid_t *grid,
+ int dd_zone,
+ int n, rvec corner0, rvec corner1,
+ real atom_density)
+{
+ rvec size;
+ int na_c;
+ real adens, tlen, tlen_x, tlen_y, nc_max;
+ int t;
+
+ rvec_sub(corner1, corner0, size);
+
+ if (n > grid->na_sc)
+ {
+ assert(atom_density > 0);
+
+ /* target cell length */
+ if (grid->bSimple)
+ {
+ /* To minimize the zero interactions, we should make
+ * the largest of the i/j cell cubic.
+ */
+ na_c = max(grid->na_c, grid->na_cj);
+
+ /* Approximately cubic cells */
+ tlen = pow(na_c/atom_density, 1.0/3.0);
+ tlen_x = tlen;
+ tlen_y = tlen;
+ }
+ else
+ {
+ /* Approximately cubic sub cells */
+ tlen = pow(grid->na_c/atom_density, 1.0/3.0);
+ tlen_x = tlen*GPU_NSUBCELL_X;
+ tlen_y = tlen*GPU_NSUBCELL_Y;
+ }
+ /* We round ncx and ncy down, because we get less cell pairs
+ * in the nbsist when the fixed cell dimensions (x,y) are
+ * larger than the variable one (z) than the other way around.
+ */
+ grid->ncx = max(1, (int)(size[XX]/tlen_x));
+ grid->ncy = max(1, (int)(size[YY]/tlen_y));
+ }
+ else
+ {
+ grid->ncx = 1;
+ grid->ncy = 1;
+ }
+
+ grid->sx = size[XX]/grid->ncx;
+ grid->sy = size[YY]/grid->ncy;
+ grid->inv_sx = 1/grid->sx;
+ grid->inv_sy = 1/grid->sy;
+
+ if (dd_zone > 0)
+ {
+ /* This is a non-home zone, add an extra row of cells
+ * for particles communicated for bonded interactions.
+ * These can be beyond the cut-off. It doesn't matter where
+ * they end up on the grid, but for performance it's better
+ * if they don't end up in cells that can be within cut-off range.
+ */
+ grid->ncx++;
+ grid->ncy++;
+ }
+
+ /* We need one additional cell entry for particles moved by DD */
+ if (grid->ncx*grid->ncy+1 > grid->cxy_nalloc)
+ {
+ grid->cxy_nalloc = over_alloc_large(grid->ncx*grid->ncy+1);
+ srenew(grid->cxy_na, grid->cxy_nalloc);
+ srenew(grid->cxy_ind, grid->cxy_nalloc+1);
+ }
+ for (t = 0; t < nbs->nthread_max; t++)
+ {
+ if (grid->ncx*grid->ncy+1 > nbs->work[t].cxy_na_nalloc)
+ {
+ nbs->work[t].cxy_na_nalloc = over_alloc_large(grid->ncx*grid->ncy+1);
+ srenew(nbs->work[t].cxy_na, nbs->work[t].cxy_na_nalloc);
+ }
+ }
+
+ /* Worst case scenario of 1 atom in each last cell */
+ if (grid->na_cj <= grid->na_c)
+ {
+ nc_max = n/grid->na_sc + grid->ncx*grid->ncy;
+ }
+ else
+ {
+ nc_max = n/grid->na_sc + grid->ncx*grid->ncy*grid->na_cj/grid->na_c;
+ }
+
+ if (nc_max > grid->nc_nalloc)
+ {
+ grid->nc_nalloc = over_alloc_large(nc_max);
+ srenew(grid->nsubc, grid->nc_nalloc);
+ srenew(grid->bbcz, grid->nc_nalloc*NNBSBB_D);
+
+ sfree_aligned(grid->bb);
+ /* This snew also zeros the contents, this avoid possible
+ * floating exceptions in SIMD with the unused bb elements.
+ */
+ if (grid->bSimple)
+ {
+ snew_aligned(grid->bb, grid->nc_nalloc, 16);
+ }
+ else
+ {
+#ifdef NBNXN_BBXXXX
+ int pbb_nalloc;
+
+ pbb_nalloc = grid->nc_nalloc*GPU_NSUBCELL/STRIDE_PBB*NNBSBB_XXXX;
+ snew_aligned(grid->pbb, pbb_nalloc, 16);
+#else
+ snew_aligned(grid->bb, grid->nc_nalloc*GPU_NSUBCELL, 16);
+#endif
+ }
+
+ if (grid->bSimple)
+ {
+ if (grid->na_cj == grid->na_c)
+ {
+ grid->bbj = grid->bb;
+ }
+ else
+ {
+ sfree_aligned(grid->bbj);
+ snew_aligned(grid->bbj, grid->nc_nalloc*grid->na_c/grid->na_cj, 16);
+ }
+ }
+
+ srenew(grid->flags, grid->nc_nalloc);
+ if (nbs->bFEP)
+ {
+ srenew(grid->fep, grid->nc_nalloc*grid->na_sc/grid->na_c);
+ }
+ }
+
+ copy_rvec(corner0, grid->c0);
+ copy_rvec(corner1, grid->c1);
+ copy_rvec(size, grid->size);
+
+ return nc_max;
+}
+
+/* We need to sort paricles in grid columns on z-coordinate.
+ * As particle are very often distributed homogeneously, we a sorting
+ * algorithm similar to pigeonhole sort. We multiply the z-coordinate
+ * by a factor, cast to an int and try to store in that hole. If the hole
+ * is full, we move this or another particle. A second pass is needed to make
+ * contiguous elements. SORT_GRID_OVERSIZE is the ratio of holes to particles.
+ * 4 is the optimal value for homogeneous particle distribution and allows
+ * for an O(#particles) sort up till distributions were all particles are
+ * concentrated in 1/4 of the space. No NlogN fallback is implemented,
+ * as it can be expensive to detect imhomogeneous particle distributions.
+ * SGSF is the maximum ratio of holes used, in the worst case all particles
+ * end up in the last hole and we need #particles extra holes at the end.
+ */
+#define SORT_GRID_OVERSIZE 4
+#define SGSF (SORT_GRID_OVERSIZE + 1)
+
+/* Sort particle index a on coordinates x along dim.
+ * Backwards tells if we want decreasing iso increasing coordinates.
+ * h0 is the minimum of the coordinate range.
+ * invh is the 1/length of the sorting range.
+ * n_per_h (>=n) is the expected average number of particles per 1/invh
+ * sort is the sorting work array.
+ * sort should have a size of at least n_per_h*SORT_GRID_OVERSIZE + n,
+ * or easier, allocate at least n*SGSF elements.
+ */
+static void sort_atoms(int dim, gmx_bool Backwards,
+ int gmx_unused dd_zone,
+ int *a, int n, rvec *x,
+ real h0, real invh, int n_per_h,
+ int *sort)
+{
+ int nsort, i, c;
+ int zi, zim, zi_min, zi_max;
+ int cp, tmp;
+
+ if (n <= 1)
+ {
+ /* Nothing to do */
+ return;
+ }
+
+#ifndef NDEBUG
+ if (n > n_per_h)
+ {
+ gmx_incons("n > n_per_h");
+ }
+#endif
+
+ /* Transform the inverse range height into the inverse hole height */
+ invh *= n_per_h*SORT_GRID_OVERSIZE;
+
+ /* Set nsort to the maximum possible number of holes used.
+ * In worst case all n elements end up in the last bin.
+ */
+ nsort = n_per_h*SORT_GRID_OVERSIZE + n;
+
+ /* Determine the index range used, so we can limit it for the second pass */
+ zi_min = INT_MAX;
+ zi_max = -1;
+
+ /* Sort the particles using a simple index sort */
+ for (i = 0; i < n; i++)
+ {
+ /* The cast takes care of float-point rounding effects below zero.
+ * This code assumes particles are less than 1/SORT_GRID_OVERSIZE
+ * times the box height out of the box.
+ */
+ zi = (int)((x[a[i]][dim] - h0)*invh);
+
+#ifndef NDEBUG
+ /* As we can have rounding effect, we use > iso >= here */
+ if (zi < 0 || (dd_zone == 0 && zi > n_per_h*SORT_GRID_OVERSIZE))
+ {
+ gmx_fatal(FARGS, "(int)((x[%d][%c]=%f - %f)*%f) = %d, not in 0 - %d*%d\n",
+ a[i], 'x'+dim, x[a[i]][dim], h0, invh, zi,
+ n_per_h, SORT_GRID_OVERSIZE);
+ }
+#endif
+
+ /* In a non-local domain, particles communcated for bonded interactions
+ * can be far beyond the grid size, which is set by the non-bonded
+ * cut-off distance. We sort such particles into the last cell.
+ */
+ if (zi > n_per_h*SORT_GRID_OVERSIZE)
+ {
+ zi = n_per_h*SORT_GRID_OVERSIZE;
+ }
+
+ /* Ideally this particle should go in sort cell zi,
+ * but that might already be in use,
+ * in that case find the first empty cell higher up
+ */
+ if (sort[zi] < 0)
+ {
+ sort[zi] = a[i];
+ zi_min = min(zi_min, zi);
+ zi_max = max(zi_max, zi);
+ }
+ else
+ {
+ /* We have multiple atoms in the same sorting slot.
+ * Sort on real z for minimal bounding box size.
+ * There is an extra check for identical z to ensure
+ * well-defined output order, independent of input order
+ * to ensure binary reproducibility after restarts.
+ */
+ while (sort[zi] >= 0 && ( x[a[i]][dim] > x[sort[zi]][dim] ||
+ (x[a[i]][dim] == x[sort[zi]][dim] &&
+ a[i] > sort[zi])))
+ {
+ zi++;
+ }
+
+ if (sort[zi] >= 0)
+ {
+ /* Shift all elements by one slot until we find an empty slot */
+ cp = sort[zi];
+ zim = zi + 1;
+ while (sort[zim] >= 0)
+ {
+ tmp = sort[zim];
+ sort[zim] = cp;
+ cp = tmp;
+ zim++;
+ }
+ sort[zim] = cp;
+ zi_max = max(zi_max, zim);
+ }
+ sort[zi] = a[i];
+ zi_max = max(zi_max, zi);
+ }
+ }
+
+ c = 0;
+ if (!Backwards)
+ {
+ for (zi = 0; zi < nsort; zi++)
+ {
+ if (sort[zi] >= 0)
+ {
+ a[c++] = sort[zi];
+ sort[zi] = -1;
+ }
+ }
+ }
+ else
+ {
+ for (zi = zi_max; zi >= zi_min; zi--)
+ {
+ if (sort[zi] >= 0)
+ {
+ a[c++] = sort[zi];
+ sort[zi] = -1;
+ }
+ }
+ }
+ if (c < n)
+ {
+ gmx_incons("Lost particles while sorting");
+ }
+}
+
+#ifdef GMX_DOUBLE
+#define R2F_D(x) ((float)((x) >= 0 ? ((1-GMX_FLOAT_EPS)*(x)) : ((1+GMX_FLOAT_EPS)*(x))))
+#define R2F_U(x) ((float)((x) >= 0 ? ((1+GMX_FLOAT_EPS)*(x)) : ((1-GMX_FLOAT_EPS)*(x))))
+#else
+#define R2F_D(x) (x)
+#define R2F_U(x) (x)
+#endif
+
+/* Coordinate order x,y,z, bb order xyz0 */
+static void calc_bounding_box(int na, int stride, const real *x, nbnxn_bb_t *bb)
+{
+ int i, j;
+ real xl, xh, yl, yh, zl, zh;
+
+ i = 0;
+ xl = x[i+XX];
+ xh = x[i+XX];
+ yl = x[i+YY];
+ yh = x[i+YY];
+ zl = x[i+ZZ];
+ zh = x[i+ZZ];
+ i += stride;
+ for (j = 1; j < na; j++)
+ {
+ xl = min(xl, x[i+XX]);
+ xh = max(xh, x[i+XX]);
+ yl = min(yl, x[i+YY]);
+ yh = max(yh, x[i+YY]);
+ zl = min(zl, x[i+ZZ]);
+ zh = max(zh, x[i+ZZ]);
+ i += stride;
+ }
+ /* Note: possible double to float conversion here */
+ bb->lower[BB_X] = R2F_D(xl);
+ bb->lower[BB_Y] = R2F_D(yl);
+ bb->lower[BB_Z] = R2F_D(zl);
+ bb->upper[BB_X] = R2F_U(xh);
+ bb->upper[BB_Y] = R2F_U(yh);
+ bb->upper[BB_Z] = R2F_U(zh);
+}
+
+/* Packed coordinates, bb order xyz0 */
+static void calc_bounding_box_x_x4(int na, const real *x, nbnxn_bb_t *bb)
+{
+ int j;
+ real xl, xh, yl, yh, zl, zh;
+
+ xl = x[XX*PACK_X4];
+ xh = x[XX*PACK_X4];
+ yl = x[YY*PACK_X4];
+ yh = x[YY*PACK_X4];
+ zl = x[ZZ*PACK_X4];
+ zh = x[ZZ*PACK_X4];
+ for (j = 1; j < na; j++)
+ {
+ xl = min(xl, x[j+XX*PACK_X4]);
+ xh = max(xh, x[j+XX*PACK_X4]);
+ yl = min(yl, x[j+YY*PACK_X4]);
+ yh = max(yh, x[j+YY*PACK_X4]);
+ zl = min(zl, x[j+ZZ*PACK_X4]);
+ zh = max(zh, x[j+ZZ*PACK_X4]);
+ }
+ /* Note: possible double to float conversion here */
+ bb->lower[BB_X] = R2F_D(xl);
+ bb->lower[BB_Y] = R2F_D(yl);
+ bb->lower[BB_Z] = R2F_D(zl);
+ bb->upper[BB_X] = R2F_U(xh);
+ bb->upper[BB_Y] = R2F_U(yh);
+ bb->upper[BB_Z] = R2F_U(zh);
+}
+
+/* Packed coordinates, bb order xyz0 */
+static void calc_bounding_box_x_x8(int na, const real *x, nbnxn_bb_t *bb)
+{
+ int j;
+ real xl, xh, yl, yh, zl, zh;
+
+ xl = x[XX*PACK_X8];
+ xh = x[XX*PACK_X8];
+ yl = x[YY*PACK_X8];
+ yh = x[YY*PACK_X8];
+ zl = x[ZZ*PACK_X8];
+ zh = x[ZZ*PACK_X8];
+ for (j = 1; j < na; j++)
+ {
+ xl = min(xl, x[j+XX*PACK_X8]);
+ xh = max(xh, x[j+XX*PACK_X8]);
+ yl = min(yl, x[j+YY*PACK_X8]);
+ yh = max(yh, x[j+YY*PACK_X8]);
+ zl = min(zl, x[j+ZZ*PACK_X8]);
+ zh = max(zh, x[j+ZZ*PACK_X8]);
+ }
+ /* Note: possible double to float conversion here */
+ bb->lower[BB_X] = R2F_D(xl);
+ bb->lower[BB_Y] = R2F_D(yl);
+ bb->lower[BB_Z] = R2F_D(zl);
+ bb->upper[BB_X] = R2F_U(xh);
+ bb->upper[BB_Y] = R2F_U(yh);
+ bb->upper[BB_Z] = R2F_U(zh);
+}
+
+/* Packed coordinates, bb order xyz0 */
+static void calc_bounding_box_x_x4_halves(int na, const real *x,
+ nbnxn_bb_t *bb, nbnxn_bb_t *bbj)
+{
+ calc_bounding_box_x_x4(min(na, 2), x, bbj);
+
+ if (na > 2)
+ {
+ calc_bounding_box_x_x4(min(na-2, 2), x+(PACK_X4>>1), bbj+1);
+ }
+ else
+ {
+ /* Set the "empty" bounding box to the same as the first one,
+ * so we don't need to treat special cases in the rest of the code.
+ */
+#ifdef NBNXN_SEARCH_BB_SIMD4
+ gmx_simd4_store_f(&bbj[1].lower[0], gmx_simd4_load_f(&bbj[0].lower[0]));
+ gmx_simd4_store_f(&bbj[1].upper[0], gmx_simd4_load_f(&bbj[0].upper[0]));
+#else
+ bbj[1] = bbj[0];
+#endif
+ }
+
+#ifdef NBNXN_SEARCH_BB_SIMD4
+ gmx_simd4_store_f(&bb->lower[0],
+ gmx_simd4_min_f(gmx_simd4_load_f(&bbj[0].lower[0]),
+ gmx_simd4_load_f(&bbj[1].lower[0])));
+ gmx_simd4_store_f(&bb->upper[0],
+ gmx_simd4_max_f(gmx_simd4_load_f(&bbj[0].upper[0]),
+ gmx_simd4_load_f(&bbj[1].upper[0])));
+#else
+ {
+ int i;
+
+ for (i = 0; i < NNBSBB_C; i++)
+ {
+ bb->lower[i] = min(bbj[0].lower[i], bbj[1].lower[i]);
+ bb->upper[i] = max(bbj[0].upper[i], bbj[1].upper[i]);
+ }
+ }
+#endif
+}
+
+#ifdef NBNXN_SEARCH_BB_SIMD4
+
+/* Coordinate order xyz, bb order xxxxyyyyzzzz */
+static void calc_bounding_box_xxxx(int na, int stride, const real *x, float *bb)
+{
+ int i, j;
+ real xl, xh, yl, yh, zl, zh;
+
+ i = 0;
+ xl = x[i+XX];
+ xh = x[i+XX];
+ yl = x[i+YY];
+ yh = x[i+YY];
+ zl = x[i+ZZ];
+ zh = x[i+ZZ];
+ i += stride;
+ for (j = 1; j < na; j++)
+ {
+ xl = min(xl, x[i+XX]);
+ xh = max(xh, x[i+XX]);
+ yl = min(yl, x[i+YY]);
+ yh = max(yh, x[i+YY]);
+ zl = min(zl, x[i+ZZ]);
+ zh = max(zh, x[i+ZZ]);
+ i += stride;
+ }
+ /* Note: possible double to float conversion here */
+ bb[0*STRIDE_PBB] = R2F_D(xl);
+ bb[1*STRIDE_PBB] = R2F_D(yl);
+ bb[2*STRIDE_PBB] = R2F_D(zl);
+ bb[3*STRIDE_PBB] = R2F_U(xh);
+ bb[4*STRIDE_PBB] = R2F_U(yh);
+ bb[5*STRIDE_PBB] = R2F_U(zh);
+}
+
+#endif /* NBNXN_SEARCH_BB_SIMD4 */
+
+#ifdef NBNXN_SEARCH_SIMD4_FLOAT_X_BB
+
+/* Coordinate order xyz?, bb order xyz0 */
+static void calc_bounding_box_simd4(int na, const float *x, nbnxn_bb_t *bb)
+{
+ gmx_simd4_float_t bb_0_S, bb_1_S;
+ gmx_simd4_float_t x_S;
+
+ int i;
+
+ bb_0_S = gmx_simd4_load_f(x);
+ bb_1_S = bb_0_S;
+
+ for (i = 1; i < na; i++)
+ {
+ x_S = gmx_simd4_load_f(x+i*NNBSBB_C);
+ bb_0_S = gmx_simd4_min_f(bb_0_S, x_S);
+ bb_1_S = gmx_simd4_max_f(bb_1_S, x_S);
+ }
+
+ gmx_simd4_store_f(&bb->lower[0], bb_0_S);
+ gmx_simd4_store_f(&bb->upper[0], bb_1_S);
+}
+
+/* Coordinate order xyz?, bb order xxxxyyyyzzzz */
+static void calc_bounding_box_xxxx_simd4(int na, const float *x,
+ nbnxn_bb_t *bb_work_aligned,
+ real *bb)
+{
+ calc_bounding_box_simd4(na, x, bb_work_aligned);
+
+ bb[0*STRIDE_PBB] = bb_work_aligned->lower[BB_X];
+ bb[1*STRIDE_PBB] = bb_work_aligned->lower[BB_Y];
+ bb[2*STRIDE_PBB] = bb_work_aligned->lower[BB_Z];
+ bb[3*STRIDE_PBB] = bb_work_aligned->upper[BB_X];
+ bb[4*STRIDE_PBB] = bb_work_aligned->upper[BB_Y];
+ bb[5*STRIDE_PBB] = bb_work_aligned->upper[BB_Z];
+}
+
+#endif /* NBNXN_SEARCH_SIMD4_FLOAT_X_BB */
+
+
+/* Combines pairs of consecutive bounding boxes */
+static void combine_bounding_box_pairs(nbnxn_grid_t *grid, const nbnxn_bb_t *bb)
+{
+ int i, j, sc2, nc2, c2;
+
+ for (i = 0; i < grid->ncx*grid->ncy; i++)
+ {
+ /* Starting bb in a column is expected to be 2-aligned */
+ sc2 = grid->cxy_ind[i]>>1;
+ /* For odd numbers skip the last bb here */
+ nc2 = (grid->cxy_na[i]+3)>>(2+1);
+ for (c2 = sc2; c2 < sc2+nc2; c2++)
+ {
+#ifdef NBNXN_SEARCH_BB_SIMD4
+ gmx_simd4_float_t min_S, max_S;
+
+ min_S = gmx_simd4_min_f(gmx_simd4_load_f(&bb[c2*2+0].lower[0]),
+ gmx_simd4_load_f(&bb[c2*2+1].lower[0]));
+ max_S = gmx_simd4_max_f(gmx_simd4_load_f(&bb[c2*2+0].upper[0]),
+ gmx_simd4_load_f(&bb[c2*2+1].upper[0]));
+ gmx_simd4_store_f(&grid->bbj[c2].lower[0], min_S);
+ gmx_simd4_store_f(&grid->bbj[c2].upper[0], max_S);
+#else
+ for (j = 0; j < NNBSBB_C; j++)
+ {
+ grid->bbj[c2].lower[j] = min(bb[c2*2+0].lower[j],
+ bb[c2*2+1].lower[j]);
+ grid->bbj[c2].upper[j] = max(bb[c2*2+0].upper[j],
+ bb[c2*2+1].upper[j]);
+ }
+#endif
+ }
+ if (((grid->cxy_na[i]+3)>>2) & 1)
+ {
+ /* The bb count in this column is odd: duplicate the last bb */
+ for (j = 0; j < NNBSBB_C; j++)
+ {
+ grid->bbj[c2].lower[j] = bb[c2*2].lower[j];
+ grid->bbj[c2].upper[j] = bb[c2*2].upper[j];
+ }
+ }
+ }
+}
+
+
+/* Prints the average bb size, used for debug output */
+static void print_bbsizes_simple(FILE *fp,
+ const nbnxn_grid_t *grid)
+{
+ int c, d;
+ dvec ba;
+
+ clear_dvec(ba);
+ for (c = 0; c < grid->nc; c++)
+ {
+ for (d = 0; d < DIM; d++)
+ {
+ ba[d] += grid->bb[c].upper[d] - grid->bb[c].lower[d];
+ }
+ }
+ dsvmul(1.0/grid->nc, ba, ba);
+
+ fprintf(fp, "ns bb: grid %4.2f %4.2f %4.2f abs %4.2f %4.2f %4.2f rel %4.2f %4.2f %4.2f\n",
+ grid->sx,
+ grid->sy,
+ grid->na_c/(grid->atom_density*grid->sx*grid->sy),
+ ba[XX], ba[YY], ba[ZZ],
+ ba[XX]/grid->sx,
+ ba[YY]/grid->sy,
+ ba[ZZ]/(grid->na_c/(grid->atom_density*grid->sx*grid->sy)));
+}
+
+/* Prints the average bb size, used for debug output */
+static void print_bbsizes_supersub(FILE *fp,
+ const nbnxn_grid_t *grid)
+{
+ int ns, c, s;
+ dvec ba;
+
+ clear_dvec(ba);
+ ns = 0;
+ for (c = 0; c < grid->nc; c++)
+ {
+#ifdef NBNXN_BBXXXX
+ for (s = 0; s < grid->nsubc[c]; s += STRIDE_PBB)
+ {
+ int cs_w, i, d;
+
+ cs_w = (c*GPU_NSUBCELL + s)/STRIDE_PBB;
+ for (i = 0; i < STRIDE_PBB; i++)
+ {
+ for (d = 0; d < DIM; d++)
+ {
+ ba[d] +=
+ grid->pbb[cs_w*NNBSBB_XXXX+(DIM+d)*STRIDE_PBB+i] -
+ grid->pbb[cs_w*NNBSBB_XXXX+ d *STRIDE_PBB+i];
+ }
+ }
+ }
+#else
+ for (s = 0; s < grid->nsubc[c]; s++)
+ {
+ int cs, d;
+
+ cs = c*GPU_NSUBCELL + s;
+ for (d = 0; d < DIM; d++)
+ {
+ ba[d] += grid->bb[cs].upper[d] - grid->bb[cs].lower[d];
+ }
+ }
+#endif
+ ns += grid->nsubc[c];
+ }
+ dsvmul(1.0/ns, ba, ba);
+
+ fprintf(fp, "ns bb: grid %4.2f %4.2f %4.2f abs %4.2f %4.2f %4.2f rel %4.2f %4.2f %4.2f\n",
+ grid->sx/GPU_NSUBCELL_X,
+ grid->sy/GPU_NSUBCELL_Y,
+ grid->na_sc/(grid->atom_density*grid->sx*grid->sy*GPU_NSUBCELL_Z),
+ ba[XX], ba[YY], ba[ZZ],
+ ba[XX]*GPU_NSUBCELL_X/grid->sx,
+ ba[YY]*GPU_NSUBCELL_Y/grid->sy,
+ ba[ZZ]/(grid->na_sc/(grid->atom_density*grid->sx*grid->sy*GPU_NSUBCELL_Z)));
+}
+
+/* Potentially sorts atoms on LJ coefficients !=0 and ==0.
+ * Also sets interaction flags.
+ */
+void sort_on_lj(int na_c,
+ int a0, int a1, const int *atinfo,
+ int *order,
+ int *flags)
+{
+ int subc, s, a, n1, n2, a_lj_max, i, j;
+ int sort1[NBNXN_NA_SC_MAX/GPU_NSUBCELL];
+ int sort2[NBNXN_NA_SC_MAX/GPU_NSUBCELL];
+ gmx_bool haveQ, bFEP;
+
+ *flags = 0;
+
+ subc = 0;
+ for (s = a0; s < a1; s += na_c)
+ {
+ /* Make lists for this (sub-)cell on atoms with and without LJ */
+ n1 = 0;
+ n2 = 0;
+ haveQ = FALSE;
+ a_lj_max = -1;
+ for (a = s; a < min(s+na_c, a1); a++)
+ {
+ haveQ = haveQ || GET_CGINFO_HAS_Q(atinfo[order[a]]);
+
+ if (GET_CGINFO_HAS_VDW(atinfo[order[a]]))
+ {
+ sort1[n1++] = order[a];
+ a_lj_max = a;
+ }
+ else
+ {
+ sort2[n2++] = order[a];
+ }
+ }
+
+ /* If we don't have atoms with LJ, there's nothing to sort */
+ if (n1 > 0)
+ {
+ *flags |= NBNXN_CI_DO_LJ(subc);
+
+ if (2*n1 <= na_c)
+ {
+ /* Only sort when strictly necessary. Ordering particles
+ * Ordering particles can lead to less accurate summation
+ * due to rounding, both for LJ and Coulomb interactions.
+ */
+ if (2*(a_lj_max - s) >= na_c)
+ {
+ for (i = 0; i < n1; i++)
+ {
+ order[a0+i] = sort1[i];
+ }
+ for (j = 0; j < n2; j++)
+ {
+ order[a0+n1+j] = sort2[j];
+ }
+ }
+
+ *flags |= NBNXN_CI_HALF_LJ(subc);
+ }
+ }
+ if (haveQ)
+ {
+ *flags |= NBNXN_CI_DO_COUL(subc);
+ }
+ subc++;
+ }
+}
+
+/* Fill a pair search cell with atoms.
+ * Potentially sorts atoms and sets the interaction flags.
+ */
+void fill_cell(const nbnxn_search_t nbs,
+ nbnxn_grid_t *grid,
+ nbnxn_atomdata_t *nbat,
+ int a0, int a1,
+ const int *atinfo,
+ rvec *x,
+ int sx, int sy, int sz,
+ nbnxn_bb_t gmx_unused *bb_work_aligned)
+{
+ int na, a;
+ size_t offset;
+ nbnxn_bb_t *bb_ptr;
+#ifdef NBNXN_BBXXXX
+ float *pbb_ptr;
+#endif
+
+ na = a1 - a0;
+
+ if (grid->bSimple)
+ {
+ sort_on_lj(grid->na_c, a0, a1, atinfo, nbs->a,
+ grid->flags+(a0>>grid->na_c_2log)-grid->cell0);
+ }
+
+ if (nbs->bFEP)
+ {
+ /* Set the fep flag for perturbed atoms in this (sub-)cell */
+ int c, at;
+
+ /* The grid-local cluster/(sub-)cell index */
+ c = (a0 >> grid->na_c_2log) - grid->cell0*(grid->bSimple ? 1 : GPU_NSUBCELL);
+ grid->fep[c] = 0;
+ for (at = a0; at < a1; at++)
+ {
+ if (nbs->a[at] >= 0 && GET_CGINFO_FEP(atinfo[nbs->a[at]]))
+ {
+ grid->fep[c] |= (1 << (at - a0));
+ }
+ }
+ }
+
+ /* Now we have sorted the atoms, set the cell indices */
+ for (a = a0; a < a1; a++)
+ {
+ nbs->cell[nbs->a[a]] = a;
+ }
+
+ copy_rvec_to_nbat_real(nbs->a+a0, a1-a0, grid->na_c, x,
+ nbat->XFormat, nbat->x, a0,
+ sx, sy, sz);
+
+ if (nbat->XFormat == nbatX4)
+ {
+ /* Store the bounding boxes as xyz.xyz. */
+ offset = (a0 - grid->cell0*grid->na_sc) >> grid->na_c_2log;
+ bb_ptr = grid->bb + offset;
+
+#if defined GMX_NBNXN_SIMD && GMX_SIMD_REAL_WIDTH == 2
+ if (2*grid->na_cj == grid->na_c)
+ {
+ calc_bounding_box_x_x4_halves(na, nbat->x+X4_IND_A(a0), bb_ptr,
+ grid->bbj+offset*2);
+ }
+ else
+#endif
+ {
+ calc_bounding_box_x_x4(na, nbat->x+X4_IND_A(a0), bb_ptr);
+ }
+ }
+ else if (nbat->XFormat == nbatX8)
+ {
+ /* Store the bounding boxes as xyz.xyz. */
+ offset = (a0 - grid->cell0*grid->na_sc) >> grid->na_c_2log;
+ bb_ptr = grid->bb + offset;
+
+ calc_bounding_box_x_x8(na, nbat->x+X8_IND_A(a0), bb_ptr);
+ }
+#ifdef NBNXN_BBXXXX
+ else if (!grid->bSimple)
+ {
+ /* Store the bounding boxes in a format convenient
+ * for SIMD4 calculations: xxxxyyyyzzzz...
+ */
+ pbb_ptr =
+ grid->pbb +
+ ((a0-grid->cell0*grid->na_sc)>>(grid->na_c_2log+STRIDE_PBB_2LOG))*NNBSBB_XXXX +
+ (((a0-grid->cell0*grid->na_sc)>>grid->na_c_2log) & (STRIDE_PBB-1));
+
+#ifdef NBNXN_SEARCH_SIMD4_FLOAT_X_BB
+ if (nbat->XFormat == nbatXYZQ)
+ {
+ calc_bounding_box_xxxx_simd4(na, nbat->x+a0*nbat->xstride,
+ bb_work_aligned, pbb_ptr);
+ }
+ else
+#endif
+ {
+ calc_bounding_box_xxxx(na, nbat->xstride, nbat->x+a0*nbat->xstride,
+ pbb_ptr);
+ }
+ if (gmx_debug_at)
+ {
+ fprintf(debug, "%2d %2d %2d bb %5.2f %5.2f %5.2f %5.2f %5.2f %5.2f\n",
+ sx, sy, sz,
+ pbb_ptr[0*STRIDE_PBB], pbb_ptr[3*STRIDE_PBB],
+ pbb_ptr[1*STRIDE_PBB], pbb_ptr[4*STRIDE_PBB],
+ pbb_ptr[2*STRIDE_PBB], pbb_ptr[5*STRIDE_PBB]);
+ }
+ }
+#endif
+ else
+ {
+ /* Store the bounding boxes as xyz.xyz. */
+ bb_ptr = grid->bb+((a0-grid->cell0*grid->na_sc)>>grid->na_c_2log);
+
+ calc_bounding_box(na, nbat->xstride, nbat->x+a0*nbat->xstride,
+ bb_ptr);
+
+ if (gmx_debug_at)
+ {
+ int bbo;
+ bbo = (a0 - grid->cell0*grid->na_sc)/grid->na_c;
+ fprintf(debug, "%2d %2d %2d bb %5.2f %5.2f %5.2f %5.2f %5.2f %5.2f\n",
+ sx, sy, sz,
+ grid->bb[bbo].lower[BB_X],
+ grid->bb[bbo].lower[BB_Y],
+ grid->bb[bbo].lower[BB_Z],
+ grid->bb[bbo].upper[BB_X],
+ grid->bb[bbo].upper[BB_Y],
+ grid->bb[bbo].upper[BB_Z]);
+ }
+ }
+}
+
+/* Spatially sort the atoms within one grid column */
+static void sort_columns_simple(const nbnxn_search_t nbs,
+ int dd_zone,
+ nbnxn_grid_t *grid,
+ int a0, int a1,
+ const int *atinfo,
+ rvec *x,
+ nbnxn_atomdata_t *nbat,
+ int cxy_start, int cxy_end,
+ int *sort_work)
+{
+ int cxy;
+ int cx, cy, cz, ncz, cfilled, c;
+ int na, ash, ind, a;
+ int na_c, ash_c;
+
+ if (debug)
+ {
+ fprintf(debug, "cell0 %d sorting columns %d - %d, atoms %d - %d\n",
+ grid->cell0, cxy_start, cxy_end, a0, a1);
+ }
+
+ /* Sort the atoms within each x,y column in 3 dimensions */
+ for (cxy = cxy_start; cxy < cxy_end; cxy++)
+ {
+ cx = cxy/grid->ncy;
+ cy = cxy - cx*grid->ncy;
+
+ na = grid->cxy_na[cxy];
+ ncz = grid->cxy_ind[cxy+1] - grid->cxy_ind[cxy];
+ ash = (grid->cell0 + grid->cxy_ind[cxy])*grid->na_sc;
+
+ /* Sort the atoms within each x,y column on z coordinate */
+ sort_atoms(ZZ, FALSE, dd_zone,
+ nbs->a+ash, na, x,
+ grid->c0[ZZ],
+ 1.0/grid->size[ZZ], ncz*grid->na_sc,
+ sort_work);
+
+ /* Fill the ncz cells in this column */
+ cfilled = grid->cxy_ind[cxy];
+ for (cz = 0; cz < ncz; cz++)
+ {
+ c = grid->cxy_ind[cxy] + cz;
+
+ ash_c = ash + cz*grid->na_sc;
+ na_c = min(grid->na_sc, na-(ash_c-ash));
+
+ fill_cell(nbs, grid, nbat,
+ ash_c, ash_c+na_c, atinfo, x,
+ grid->na_sc*cx + (dd_zone >> 2),
+ grid->na_sc*cy + (dd_zone & 3),
+ grid->na_sc*cz,
+ NULL);
+
+ /* This copy to bbcz is not really necessary.
+ * But it allows to use the same grid search code
+ * for the simple and supersub cell setups.
+ */
+ if (na_c > 0)
+ {
+ cfilled = c;
+ }
+ grid->bbcz[c*NNBSBB_D ] = grid->bb[cfilled].lower[BB_Z];
+ grid->bbcz[c*NNBSBB_D+1] = grid->bb[cfilled].upper[BB_Z];
+ }
+
+ /* Set the unused atom indices to -1 */
+ for (ind = na; ind < ncz*grid->na_sc; ind++)
+ {
+ nbs->a[ash+ind] = -1;
+ }
+ }
+}
+
+/* Spatially sort the atoms within one grid column */
+static void sort_columns_supersub(const nbnxn_search_t nbs,
+ int dd_zone,
+ nbnxn_grid_t *grid,
+ int a0, int a1,
+ const int *atinfo,
+ rvec *x,
+ nbnxn_atomdata_t *nbat,
+ int cxy_start, int cxy_end,
+ int *sort_work)
+{
+ int cxy;
+ int cx, cy, cz = -1, c = -1, ncz;
+ int na, ash, na_c, ind, a;
+ int subdiv_z, sub_z, na_z, ash_z;
+ int subdiv_y, sub_y, na_y, ash_y;
+ int subdiv_x, sub_x, na_x, ash_x;
+
+ /* cppcheck-suppress unassignedVariable */
+ nbnxn_bb_t bb_work_array[2], *bb_work_aligned;
+
+ bb_work_aligned = (nbnxn_bb_t *)(((size_t)(bb_work_array+1)) & (~((size_t)15)));
+
+ if (debug)
+ {
+ fprintf(debug, "cell0 %d sorting columns %d - %d, atoms %d - %d\n",
+ grid->cell0, cxy_start, cxy_end, a0, a1);
+ }
+
+ subdiv_x = grid->na_c;
+ subdiv_y = GPU_NSUBCELL_X*subdiv_x;
+ subdiv_z = GPU_NSUBCELL_Y*subdiv_y;
+
+ /* Sort the atoms within each x,y column in 3 dimensions */
+ for (cxy = cxy_start; cxy < cxy_end; cxy++)
+ {
+ cx = cxy/grid->ncy;
+ cy = cxy - cx*grid->ncy;
+
+ na = grid->cxy_na[cxy];
+ ncz = grid->cxy_ind[cxy+1] - grid->cxy_ind[cxy];
+ ash = (grid->cell0 + grid->cxy_ind[cxy])*grid->na_sc;
+
+ /* Sort the atoms within each x,y column on z coordinate */
+ sort_atoms(ZZ, FALSE, dd_zone,
+ nbs->a+ash, na, x,
+ grid->c0[ZZ],
+ 1.0/grid->size[ZZ], ncz*grid->na_sc,
+ sort_work);
+
+ /* This loop goes over the supercells and subcells along z at once */
+ for (sub_z = 0; sub_z < ncz*GPU_NSUBCELL_Z; sub_z++)
+ {
+ ash_z = ash + sub_z*subdiv_z;
+ na_z = min(subdiv_z, na-(ash_z-ash));
+
+ /* We have already sorted on z */
+
+ if (sub_z % GPU_NSUBCELL_Z == 0)
+ {
+ cz = sub_z/GPU_NSUBCELL_Z;
+ c = grid->cxy_ind[cxy] + cz;
+
+ /* The number of atoms in this supercell */
+ na_c = min(grid->na_sc, na-(ash_z-ash));
+
+ grid->nsubc[c] = min(GPU_NSUBCELL, (na_c+grid->na_c-1)/grid->na_c);
+
+ /* Store the z-boundaries of the super cell */
+ grid->bbcz[c*NNBSBB_D ] = x[nbs->a[ash_z]][ZZ];
+ grid->bbcz[c*NNBSBB_D+1] = x[nbs->a[ash_z+na_c-1]][ZZ];
+ }
+
+#if GPU_NSUBCELL_Y > 1
+ /* Sort the atoms along y */
+ sort_atoms(YY, (sub_z & 1), dd_zone,
+ nbs->a+ash_z, na_z, x,
+ grid->c0[YY]+cy*grid->sy,
+ grid->inv_sy, subdiv_z,
+ sort_work);
+#endif
+
+ for (sub_y = 0; sub_y < GPU_NSUBCELL_Y; sub_y++)
+ {
+ ash_y = ash_z + sub_y*subdiv_y;
+ na_y = min(subdiv_y, na-(ash_y-ash));
+
+#if GPU_NSUBCELL_X > 1
+ /* Sort the atoms along x */
+ sort_atoms(XX, ((cz*GPU_NSUBCELL_Y + sub_y) & 1), dd_zone,
+ nbs->a+ash_y, na_y, x,
+ grid->c0[XX]+cx*grid->sx,
+ grid->inv_sx, subdiv_y,
+ sort_work);
+#endif
+
+ for (sub_x = 0; sub_x < GPU_NSUBCELL_X; sub_x++)
+ {
+ ash_x = ash_y + sub_x*subdiv_x;
+ na_x = min(subdiv_x, na-(ash_x-ash));
+
+ fill_cell(nbs, grid, nbat,
+ ash_x, ash_x+na_x, atinfo, x,
+ grid->na_c*(cx*GPU_NSUBCELL_X+sub_x) + (dd_zone >> 2),
+ grid->na_c*(cy*GPU_NSUBCELL_Y+sub_y) + (dd_zone & 3),
+ grid->na_c*sub_z,
+ bb_work_aligned);
+ }
+ }
+ }
+
+ /* Set the unused atom indices to -1 */
+ for (ind = na; ind < ncz*grid->na_sc; ind++)
+ {
+ nbs->a[ash+ind] = -1;
+ }
+ }
+}
+
+/* Determine in which grid column atoms should go */
+static void calc_column_indices(nbnxn_grid_t *grid,
+ int a0, int a1,
+ rvec *x,
+ int dd_zone, const int *move,
+ int thread, int nthread,
+ int *cell,
+ int *cxy_na)
+{
+ int n0, n1, i;
+ int cx, cy;
+
+ /* We add one extra cell for particles which moved during DD */
+ for (i = 0; i < grid->ncx*grid->ncy+1; i++)
+ {
+ cxy_na[i] = 0;
+ }
+
+ n0 = a0 + (int)((thread+0)*(a1 - a0))/nthread;
+ n1 = a0 + (int)((thread+1)*(a1 - a0))/nthread;
+ if (dd_zone == 0)
+ {
+ /* Home zone */
+ for (i = n0; i < n1; i++)
+ {
+ if (move == NULL || move[i] >= 0)
+ {
+ /* We need to be careful with rounding,
+ * particles might be a few bits outside the local zone.
+ * The int cast takes care of the lower bound,
+ * we will explicitly take care of the upper bound.
+ */
+ cx = (int)((x[i][XX] - grid->c0[XX])*grid->inv_sx);
+ cy = (int)((x[i][YY] - grid->c0[YY])*grid->inv_sy);
+
+#ifndef NDEBUG
+ if (cx < 0 || cx > grid->ncx ||
+ cy < 0 || cy > grid->ncy)
+ {
+ gmx_fatal(FARGS,
+ "grid cell cx %d cy %d out of range (max %d %d)\n"
+ "atom %f %f %f, grid->c0 %f %f",
+ cx, cy, grid->ncx, grid->ncy,
+ x[i][XX], x[i][YY], x[i][ZZ], grid->c0[XX], grid->c0[YY]);
+ }
+#endif
+ /* Take care of potential rouding issues */
+ cx = min(cx, grid->ncx - 1);
+ cy = min(cy, grid->ncy - 1);
+
+ /* For the moment cell will contain only the, grid local,
+ * x and y indices, not z.
+ */
+ cell[i] = cx*grid->ncy + cy;
+ }
+ else
+ {
+ /* Put this moved particle after the end of the grid,
+ * so we can process it later without using conditionals.
+ */
+ cell[i] = grid->ncx*grid->ncy;
+ }
+
+ cxy_na[cell[i]]++;
+ }
+ }
+ else
+ {
+ /* Non-home zone */
+ for (i = n0; i < n1; i++)
+ {
+ cx = (int)((x[i][XX] - grid->c0[XX])*grid->inv_sx);
+ cy = (int)((x[i][YY] - grid->c0[YY])*grid->inv_sy);
+
+ /* For non-home zones there could be particles outside
+ * the non-bonded cut-off range, which have been communicated
+ * for bonded interactions only. For the result it doesn't
+ * matter where these end up on the grid. For performance
+ * we put them in an extra row at the border.
+ */
+ cx = max(cx, 0);
+ cx = min(cx, grid->ncx - 1);
+ cy = max(cy, 0);
+ cy = min(cy, grid->ncy - 1);
+
+ /* For the moment cell will contain only the, grid local,
+ * x and y indices, not z.
+ */
+ cell[i] = cx*grid->ncy + cy;
+
+ cxy_na[cell[i]]++;
+ }
+ }
+}
+
+/* Determine in which grid cells the atoms should go */
+static void calc_cell_indices(const nbnxn_search_t nbs,
+ int dd_zone,
+ nbnxn_grid_t *grid,
+ int a0, int a1,
+ const int *atinfo,
+ rvec *x,
+ const int *move,
+ nbnxn_atomdata_t *nbat)
+{
+ int n0, n1, i;
+ int cx, cy, cxy, ncz_max, ncz;
+ int nthread, thread;
+ int *cxy_na, cxy_na_i;
+
+ nthread = gmx_omp_nthreads_get(emntPairsearch);
+
+#pragma omp parallel for num_threads(nthread) schedule(static)
+ for (thread = 0; thread < nthread; thread++)
+ {
+ calc_column_indices(grid, a0, a1, x, dd_zone, move, thread, nthread,
+ nbs->cell, nbs->work[thread].cxy_na);
+ }
+
+ /* Make the cell index as a function of x and y */
+ ncz_max = 0;
+ ncz = 0;
+ grid->cxy_ind[0] = 0;
+ for (i = 0; i < grid->ncx*grid->ncy+1; i++)
+ {
+ /* We set ncz_max at the beginning of the loop iso at the end
+ * to skip i=grid->ncx*grid->ncy which are moved particles
+ * that do not need to be ordered on the grid.
+ */
+ if (ncz > ncz_max)
+ {
+ ncz_max = ncz;
+ }
+ cxy_na_i = nbs->work[0].cxy_na[i];
+ for (thread = 1; thread < nthread; thread++)
+ {
+ cxy_na_i += nbs->work[thread].cxy_na[i];
+ }
+ ncz = (cxy_na_i + grid->na_sc - 1)/grid->na_sc;
+ if (nbat->XFormat == nbatX8)
+ {
+ /* Make the number of cell a multiple of 2 */
+ ncz = (ncz + 1) & ~1;
+ }
+ grid->cxy_ind[i+1] = grid->cxy_ind[i] + ncz;
+ /* Clear cxy_na, so we can reuse the array below */
+ grid->cxy_na[i] = 0;
+ }
+ grid->nc = grid->cxy_ind[grid->ncx*grid->ncy] - grid->cxy_ind[0];
+
+ nbat->natoms = (grid->cell0 + grid->nc)*grid->na_sc;
+
+ if (debug)
+ {
+ fprintf(debug, "ns na_sc %d na_c %d super-cells: %d x %d y %d z %.1f maxz %d\n",
+ grid->na_sc, grid->na_c, grid->nc,
+ grid->ncx, grid->ncy, grid->nc/((double)(grid->ncx*grid->ncy)),
+ ncz_max);
+ if (gmx_debug_at)
+ {
+ i = 0;
+ for (cy = 0; cy < grid->ncy; cy++)
+ {
+ for (cx = 0; cx < grid->ncx; cx++)
+ {
+ fprintf(debug, " %2d", grid->cxy_ind[i+1]-grid->cxy_ind[i]);
+ i++;
+ }
+ fprintf(debug, "\n");
+ }
+ }
+ }
+
+ /* Make sure the work array for sorting is large enough */
+ if (ncz_max*grid->na_sc*SGSF > nbs->work[0].sort_work_nalloc)
+ {
+ for (thread = 0; thread < nbs->nthread_max; thread++)
+ {
+ nbs->work[thread].sort_work_nalloc =
+ over_alloc_large(ncz_max*grid->na_sc*SGSF);
+ srenew(nbs->work[thread].sort_work,
+ nbs->work[thread].sort_work_nalloc);
+ /* When not in use, all elements should be -1 */
+ for (i = 0; i < nbs->work[thread].sort_work_nalloc; i++)
+ {
+ nbs->work[thread].sort_work[i] = -1;
+ }
+ }
+ }
+
+ /* Now we know the dimensions we can fill the grid.
+ * This is the first, unsorted fill. We sort the columns after this.
+ */
+ for (i = a0; i < a1; i++)
+ {
+ /* At this point nbs->cell contains the local grid x,y indices */
+ cxy = nbs->cell[i];
+ nbs->a[(grid->cell0 + grid->cxy_ind[cxy])*grid->na_sc + grid->cxy_na[cxy]++] = i;
+ }
+
+ if (dd_zone == 0)
+ {
+ /* Set the cell indices for the moved particles */
+ n0 = grid->nc*grid->na_sc;
+ n1 = grid->nc*grid->na_sc+grid->cxy_na[grid->ncx*grid->ncy];
+ if (dd_zone == 0)
+ {
+ for (i = n0; i < n1; i++)
+ {
+ nbs->cell[nbs->a[i]] = i;
+ }
+ }
+ }
+
+ /* Sort the super-cell columns along z into the sub-cells. */
+#pragma omp parallel for num_threads(nthread) schedule(static)
+ for (thread = 0; thread < nthread; thread++)
+ {
+ if (grid->bSimple)
+ {
+ sort_columns_simple(nbs, dd_zone, grid, a0, a1, atinfo, x, nbat,
+ ((thread+0)*grid->ncx*grid->ncy)/nthread,
+ ((thread+1)*grid->ncx*grid->ncy)/nthread,
+ nbs->work[thread].sort_work);
+ }
+ else
+ {
+ sort_columns_supersub(nbs, dd_zone, grid, a0, a1, atinfo, x, nbat,
+ ((thread+0)*grid->ncx*grid->ncy)/nthread,
+ ((thread+1)*grid->ncx*grid->ncy)/nthread,
+ nbs->work[thread].sort_work);
+ }
+ }
+
+ if (grid->bSimple && nbat->XFormat == nbatX8)
+ {
+ combine_bounding_box_pairs(grid, grid->bb);
+ }
+
+ if (!grid->bSimple)
+ {
+ grid->nsubc_tot = 0;
+ for (i = 0; i < grid->nc; i++)
+ {
+ grid->nsubc_tot += grid->nsubc[i];
+ }
+ }
+
+ if (debug)
+ {
+ if (grid->bSimple)
+ {
+ print_bbsizes_simple(debug, grid);
+ }
+ else
+ {
+ fprintf(debug, "ns non-zero sub-cells: %d average atoms %.2f\n",
+ grid->nsubc_tot, (a1-a0)/(double)grid->nsubc_tot);
+
+ print_bbsizes_supersub(debug, grid);
+ }
+ }
+}
+
+static void init_buffer_flags(nbnxn_buffer_flags_t *flags,
+ int natoms)
+{
+ int b;
+
+ flags->nflag = (natoms + NBNXN_BUFFERFLAG_SIZE - 1)/NBNXN_BUFFERFLAG_SIZE;
+ if (flags->nflag > flags->flag_nalloc)
+ {
+ flags->flag_nalloc = over_alloc_large(flags->nflag);
+ srenew(flags->flag, flags->flag_nalloc);
+ }
+ for (b = 0; b < flags->nflag; b++)
+ {
+ flags->flag[b] = 0;
+ }
+}
+
+/* Sets up a grid and puts the atoms on the grid.
+ * This function only operates on one domain of the domain decompostion.
+ * Note that without domain decomposition there is only one domain.
+ */
+void nbnxn_put_on_grid(nbnxn_search_t nbs,
+ int ePBC, matrix box,
+ int dd_zone,
+ rvec corner0, rvec corner1,
+ int a0, int a1,
+ real atom_density,
+ const int *atinfo,
+ rvec *x,
+ int nmoved, int *move,
+ int nb_kernel_type,
+ nbnxn_atomdata_t *nbat)
+{
+ nbnxn_grid_t *grid;
+ int n;
+ int nc_max_grid, nc_max;
+
+ grid = &nbs->grid[dd_zone];
+
+ nbs_cycle_start(&nbs->cc[enbsCCgrid]);
+
+ grid->bSimple = nbnxn_kernel_pairlist_simple(nb_kernel_type);
+
+ grid->na_c = nbnxn_kernel_to_ci_size(nb_kernel_type);
+ grid->na_cj = nbnxn_kernel_to_cj_size(nb_kernel_type);
+ grid->na_sc = (grid->bSimple ? 1 : GPU_NSUBCELL)*grid->na_c;
+ grid->na_c_2log = get_2log(grid->na_c);
+
+ nbat->na_c = grid->na_c;
+
+ if (dd_zone == 0)
+ {
+ grid->cell0 = 0;
+ }
+ else
+ {
+ grid->cell0 =
+ (nbs->grid[dd_zone-1].cell0 + nbs->grid[dd_zone-1].nc)*
+ nbs->grid[dd_zone-1].na_sc/grid->na_sc;
+ }
+
+ n = a1 - a0;
+
+ if (dd_zone == 0)
+ {
+ nbs->ePBC = ePBC;
+ copy_mat(box, nbs->box);
+
+ /* Avoid zero density */
+ if (atom_density > 0)
+ {
+ grid->atom_density = atom_density;
+ }
+ else
+ {
+ grid->atom_density = grid_atom_density(n-nmoved, corner0, corner1);
+ }
+
+ grid->cell0 = 0;
+
+ nbs->natoms_local = a1 - nmoved;
+ /* We assume that nbnxn_put_on_grid is called first
+ * for the local atoms (dd_zone=0).
+ */
+ nbs->natoms_nonlocal = a1 - nmoved;
+
+ if (debug)
+ {
+ fprintf(debug, "natoms_local = %5d atom_density = %5.1f\n",
+ nbs->natoms_local, grid->atom_density);
+ }
+ }
+ else
+ {
+ nbs->natoms_nonlocal = max(nbs->natoms_nonlocal, a1);
+ }
+
+ /* We always use the home zone (grid[0]) for setting the cell size,
+ * since determining densities for non-local zones is difficult.
+ */
+ nc_max_grid = set_grid_size_xy(nbs, grid,
+ dd_zone, n-nmoved, corner0, corner1,
+ nbs->grid[0].atom_density);
+
+ nc_max = grid->cell0 + nc_max_grid;
+
+ if (a1 > nbs->cell_nalloc)
+ {
+ nbs->cell_nalloc = over_alloc_large(a1);
+ srenew(nbs->cell, nbs->cell_nalloc);
+ }
+
+ /* To avoid conditionals we store the moved particles at the end of a,
+ * make sure we have enough space.
+ */
+ if (nc_max*grid->na_sc + nmoved > nbs->a_nalloc)
+ {
+ nbs->a_nalloc = over_alloc_large(nc_max*grid->na_sc + nmoved);
+ srenew(nbs->a, nbs->a_nalloc);
+ }
+
+ /* We need padding up to a multiple of the buffer flag size: simply add */
+ if (nc_max*grid->na_sc + NBNXN_BUFFERFLAG_SIZE > nbat->nalloc)
+ {
+ nbnxn_atomdata_realloc(nbat, nc_max*grid->na_sc+NBNXN_BUFFERFLAG_SIZE);
+ }
+
+ calc_cell_indices(nbs, dd_zone, grid, a0, a1, atinfo, x, move, nbat);
+
+ if (dd_zone == 0)
+ {
+ nbat->natoms_local = nbat->natoms;
+ }
+
+ nbs_cycle_stop(&nbs->cc[enbsCCgrid]);
+}
+
+/* Calls nbnxn_put_on_grid for all non-local domains */
+void nbnxn_put_on_grid_nonlocal(nbnxn_search_t nbs,
+ const gmx_domdec_zones_t *zones,
+ const int *atinfo,
+ rvec *x,
+ int nb_kernel_type,
+ nbnxn_atomdata_t *nbat)
+{
+ int zone, d;
+ rvec c0, c1;
+
+ for (zone = 1; zone < zones->n; zone++)
+ {
+ for (d = 0; d < DIM; d++)
+ {
+ c0[d] = zones->size[zone].bb_x0[d];
+ c1[d] = zones->size[zone].bb_x1[d];
+ }
+
+ nbnxn_put_on_grid(nbs, nbs->ePBC, NULL,
+ zone, c0, c1,
+ zones->cg_range[zone],
+ zones->cg_range[zone+1],
+ -1,
+ atinfo,
+ x,
+ 0, NULL,
+ nb_kernel_type,
+ nbat);
+ }
+}
+
+/* Add simple grid type information to the local super/sub grid */
+void nbnxn_grid_add_simple(nbnxn_search_t nbs,
+ nbnxn_atomdata_t *nbat)
+{
+ nbnxn_grid_t *grid;
+ float *bbcz;
+ nbnxn_bb_t *bb;
+ int ncd, sc;
+ int nthreads gmx_unused;
+
+ grid = &nbs->grid[0];
+
+ if (grid->bSimple)
+ {
+ gmx_incons("nbnxn_grid_simple called with a simple grid");
+ }
+
+ ncd = grid->na_sc/NBNXN_CPU_CLUSTER_I_SIZE;
+
+ if (grid->nc*ncd > grid->nc_nalloc_simple)
+ {
+ grid->nc_nalloc_simple = over_alloc_large(grid->nc*ncd);
+ srenew(grid->bbcz_simple, grid->nc_nalloc_simple*NNBSBB_D);
+ srenew(grid->bb_simple, grid->nc_nalloc_simple);
+ srenew(grid->flags_simple, grid->nc_nalloc_simple);
+ if (nbat->XFormat)
+ {
+ sfree_aligned(grid->bbj);
+ snew_aligned(grid->bbj, grid->nc_nalloc_simple/2, 16);
+ }
+ }
+
+ bbcz = grid->bbcz_simple;
+ bb = grid->bb_simple;
+
+ nthreads = gmx_omp_nthreads_get(emntPairsearch);
+#pragma omp parallel for num_threads(nthreads) schedule(static)
+ for (sc = 0; sc < grid->nc; sc++)
+ {
+ int c, tx, na;
+
+ for (c = 0; c < ncd; c++)
+ {
+ tx = sc*ncd + c;
+
+ na = NBNXN_CPU_CLUSTER_I_SIZE;
+ while (na > 0 &&
+ nbat->type[tx*NBNXN_CPU_CLUSTER_I_SIZE+na-1] == nbat->ntype-1)
+ {
+ na--;
+ }
+
+ if (na > 0)
+ {
+ switch (nbat->XFormat)
+ {
+ case nbatX4:
+ /* PACK_X4==NBNXN_CPU_CLUSTER_I_SIZE, so this is simple */
+ calc_bounding_box_x_x4(na, nbat->x+tx*STRIDE_P4,
+ bb+tx);
+ break;
+ case nbatX8:
+ /* PACK_X8>NBNXN_CPU_CLUSTER_I_SIZE, more complicated */
+ calc_bounding_box_x_x8(na, nbat->x+X8_IND_A(tx*NBNXN_CPU_CLUSTER_I_SIZE),
+ bb+tx);
+ break;
+ default:
+ calc_bounding_box(na, nbat->xstride,
+ nbat->x+tx*NBNXN_CPU_CLUSTER_I_SIZE*nbat->xstride,
+ bb+tx);
+ break;
+ }
+ bbcz[tx*NNBSBB_D+0] = bb[tx].lower[BB_Z];
+ bbcz[tx*NNBSBB_D+1] = bb[tx].upper[BB_Z];
+
+ /* No interaction optimization yet here */
+ grid->flags_simple[tx] = NBNXN_CI_DO_LJ(0) | NBNXN_CI_DO_COUL(0);
+ }
+ else
+ {
+ grid->flags_simple[tx] = 0;
+ }
+ }
+ }
+
+ if (grid->bSimple && nbat->XFormat == nbatX8)
+ {
+ combine_bounding_box_pairs(grid, grid->bb_simple);
+ }
+}
+
+void nbnxn_get_ncells(nbnxn_search_t nbs, int *ncx, int *ncy)
+{
+ *ncx = nbs->grid[0].ncx;
+ *ncy = nbs->grid[0].ncy;
+}
+
+void nbnxn_get_atomorder(nbnxn_search_t nbs, int **a, int *n)
+{
+ const nbnxn_grid_t *grid;
+
+ grid = &nbs->grid[0];
+
+ /* Return the atom order for the home cell (index 0) */
+ *a = nbs->a;
+
+ *n = grid->cxy_ind[grid->ncx*grid->ncy]*grid->na_sc;
+}
+
+void nbnxn_set_atomorder(nbnxn_search_t nbs)
+{
+ nbnxn_grid_t *grid;
+ int ao, cx, cy, cxy, cz, j;
+
+ /* Set the atom order for the home cell (index 0) */
+ grid = &nbs->grid[0];
+
+ ao = 0;
+ for (cx = 0; cx < grid->ncx; cx++)
+ {
+ for (cy = 0; cy < grid->ncy; cy++)
+ {
+ cxy = cx*grid->ncy + cy;
+ j = grid->cxy_ind[cxy]*grid->na_sc;
+ for (cz = 0; cz < grid->cxy_na[cxy]; cz++)
+ {
+ nbs->a[j] = ao;
+ nbs->cell[ao] = j;
+ ao++;
+ j++;
+ }
+ }
+ }
+}
+
+/* Determines the cell range along one dimension that
+ * the bounding box b0 - b1 sees.
+ */
+static void get_cell_range(real b0, real b1,
+ int nc, real c0, real s, real invs,
+ real d2, real r2, int *cf, int *cl)
+{
+ *cf = max((int)((b0 - c0)*invs), 0);
+
+ while (*cf > 0 && d2 + sqr((b0 - c0) - (*cf-1+1)*s) < r2)
+ {
+ (*cf)--;
+ }
+
+ *cl = min((int)((b1 - c0)*invs), nc-1);
+ while (*cl < nc-1 && d2 + sqr((*cl+1)*s - (b1 - c0)) < r2)
+ {
+ (*cl)++;
+ }
+}
+
+/* Reference code calculating the distance^2 between two bounding boxes */
+static float box_dist2(float bx0, float bx1, float by0,
+ float by1, float bz0, float bz1,
+ const nbnxn_bb_t *bb)
+{
+ float d2;
+ float dl, dh, dm, dm0;
+
+ d2 = 0;
+
+ dl = bx0 - bb->upper[BB_X];
+ dh = bb->lower[BB_X] - bx1;
+ dm = max(dl, dh);
+ dm0 = max(dm, 0);
+ d2 += dm0*dm0;
+
+ dl = by0 - bb->upper[BB_Y];
+ dh = bb->lower[BB_Y] - by1;
+ dm = max(dl, dh);
+ dm0 = max(dm, 0);
+ d2 += dm0*dm0;
+
+ dl = bz0 - bb->upper[BB_Z];
+ dh = bb->lower[BB_Z] - bz1;
+ dm = max(dl, dh);
+ dm0 = max(dm, 0);
+ d2 += dm0*dm0;
+
+ return d2;
+}
+
+/* Plain C code calculating the distance^2 between two bounding boxes */
+static float subc_bb_dist2(int si, const nbnxn_bb_t *bb_i_ci,
+ int csj, const nbnxn_bb_t *bb_j_all)
+{
+ const nbnxn_bb_t *bb_i, *bb_j;
+ float d2;
+ float dl, dh, dm, dm0;
+
+ bb_i = bb_i_ci + si;
+ bb_j = bb_j_all + csj;
+
+ d2 = 0;
+
+ dl = bb_i->lower[BB_X] - bb_j->upper[BB_X];
+ dh = bb_j->lower[BB_X] - bb_i->upper[BB_X];
+ dm = max(dl, dh);
+ dm0 = max(dm, 0);
+ d2 += dm0*dm0;
+
+ dl = bb_i->lower[BB_Y] - bb_j->upper[BB_Y];
+ dh = bb_j->lower[BB_Y] - bb_i->upper[BB_Y];
+ dm = max(dl, dh);
+ dm0 = max(dm, 0);
+ d2 += dm0*dm0;
+
+ dl = bb_i->lower[BB_Z] - bb_j->upper[BB_Z];
+ dh = bb_j->lower[BB_Z] - bb_i->upper[BB_Z];
+ dm = max(dl, dh);
+ dm0 = max(dm, 0);
+ d2 += dm0*dm0;
+
+ return d2;
+}
+
+#ifdef NBNXN_SEARCH_BB_SIMD4
+
+/* 4-wide SIMD code for bb distance for bb format xyz0 */
+static float subc_bb_dist2_simd4(int si, const nbnxn_bb_t *bb_i_ci,
+ int csj, const nbnxn_bb_t *bb_j_all)
+{
+ gmx_simd4_float_t bb_i_S0, bb_i_S1;
+ gmx_simd4_float_t bb_j_S0, bb_j_S1;
+ gmx_simd4_float_t dl_S;
+ gmx_simd4_float_t dh_S;
+ gmx_simd4_float_t dm_S;
+ gmx_simd4_float_t dm0_S;
+
+ bb_i_S0 = gmx_simd4_load_f(&bb_i_ci[si].lower[0]);
+ bb_i_S1 = gmx_simd4_load_f(&bb_i_ci[si].upper[0]);
+ bb_j_S0 = gmx_simd4_load_f(&bb_j_all[csj].lower[0]);
+ bb_j_S1 = gmx_simd4_load_f(&bb_j_all[csj].upper[0]);
+
+ dl_S = gmx_simd4_sub_f(bb_i_S0, bb_j_S1);
+ dh_S = gmx_simd4_sub_f(bb_j_S0, bb_i_S1);
+
+ dm_S = gmx_simd4_max_f(dl_S, dh_S);
+ dm0_S = gmx_simd4_max_f(dm_S, gmx_simd4_setzero_f());
+
+ return gmx_simd4_dotproduct3_f(dm0_S, dm0_S);
+}
+
+/* Calculate bb bounding distances of bb_i[si,...,si+3] and store them in d2 */
+#define SUBC_BB_DIST2_SIMD4_XXXX_INNER(si, bb_i, d2) \
+ { \
+ int shi; \
+ \
+ gmx_simd4_float_t dx_0, dy_0, dz_0; \
+ gmx_simd4_float_t dx_1, dy_1, dz_1; \
+ \
+ gmx_simd4_float_t mx, my, mz; \
+ gmx_simd4_float_t m0x, m0y, m0z; \
+ \
+ gmx_simd4_float_t d2x, d2y, d2z; \
+ gmx_simd4_float_t d2s, d2t; \
+ \
+ shi = si*NNBSBB_D*DIM; \
+ \
+ xi_l = gmx_simd4_load_f(bb_i+shi+0*STRIDE_PBB); \
+ yi_l = gmx_simd4_load_f(bb_i+shi+1*STRIDE_PBB); \
+ zi_l = gmx_simd4_load_f(bb_i+shi+2*STRIDE_PBB); \
+ xi_h = gmx_simd4_load_f(bb_i+shi+3*STRIDE_PBB); \
+ yi_h = gmx_simd4_load_f(bb_i+shi+4*STRIDE_PBB); \
+ zi_h = gmx_simd4_load_f(bb_i+shi+5*STRIDE_PBB); \
+ \
+ dx_0 = gmx_simd4_sub_f(xi_l, xj_h); \
+ dy_0 = gmx_simd4_sub_f(yi_l, yj_h); \
+ dz_0 = gmx_simd4_sub_f(zi_l, zj_h); \
+ \
+ dx_1 = gmx_simd4_sub_f(xj_l, xi_h); \
+ dy_1 = gmx_simd4_sub_f(yj_l, yi_h); \
+ dz_1 = gmx_simd4_sub_f(zj_l, zi_h); \
+ \
+ mx = gmx_simd4_max_f(dx_0, dx_1); \
+ my = gmx_simd4_max_f(dy_0, dy_1); \
+ mz = gmx_simd4_max_f(dz_0, dz_1); \
+ \
+ m0x = gmx_simd4_max_f(mx, zero); \
+ m0y = gmx_simd4_max_f(my, zero); \
+ m0z = gmx_simd4_max_f(mz, zero); \
+ \
+ d2x = gmx_simd4_mul_f(m0x, m0x); \
+ d2y = gmx_simd4_mul_f(m0y, m0y); \
+ d2z = gmx_simd4_mul_f(m0z, m0z); \
+ \
+ d2s = gmx_simd4_add_f(d2x, d2y); \
+ d2t = gmx_simd4_add_f(d2s, d2z); \
+ \
+ gmx_simd4_store_f(d2+si, d2t); \
+ }
+
+/* 4-wide SIMD code for nsi bb distances for bb format xxxxyyyyzzzz */
+static void subc_bb_dist2_simd4_xxxx(const float *bb_j,
+ int nsi, const float *bb_i,
+ float *d2)
+{
+ gmx_simd4_float_t xj_l, yj_l, zj_l;
+ gmx_simd4_float_t xj_h, yj_h, zj_h;
+ gmx_simd4_float_t xi_l, yi_l, zi_l;
+ gmx_simd4_float_t xi_h, yi_h, zi_h;
+
+ gmx_simd4_float_t zero;
+
+ zero = gmx_simd4_setzero_f();
+
+ xj_l = gmx_simd4_set1_f(bb_j[0*STRIDE_PBB]);
+ yj_l = gmx_simd4_set1_f(bb_j[1*STRIDE_PBB]);
+ zj_l = gmx_simd4_set1_f(bb_j[2*STRIDE_PBB]);
+ xj_h = gmx_simd4_set1_f(bb_j[3*STRIDE_PBB]);
+ yj_h = gmx_simd4_set1_f(bb_j[4*STRIDE_PBB]);
+ zj_h = gmx_simd4_set1_f(bb_j[5*STRIDE_PBB]);
+
+ /* Here we "loop" over si (0,STRIDE_PBB) from 0 to nsi with step STRIDE_PBB.
+ * But as we know the number of iterations is 1 or 2, we unroll manually.
+ */
+ SUBC_BB_DIST2_SIMD4_XXXX_INNER(0, bb_i, d2);
+ if (STRIDE_PBB < nsi)
+ {
+ SUBC_BB_DIST2_SIMD4_XXXX_INNER(STRIDE_PBB, bb_i, d2);
+ }
+}
+
+#endif /* NBNXN_SEARCH_BB_SIMD4 */
+
+/* Plain C function which determines if any atom pair between two cells
+ * is within distance sqrt(rl2).
+ */
+static gmx_bool subc_in_range_x(int na_c,
+ int si, const real *x_i,
+ int csj, int stride, const real *x_j,
+ real rl2)
+{
+ int i, j, i0, j0;
+ real d2;
+
+ for (i = 0; i < na_c; i++)
+ {
+ i0 = (si*na_c + i)*DIM;
+ for (j = 0; j < na_c; j++)
+ {
+ j0 = (csj*na_c + j)*stride;
+
+ d2 = sqr(x_i[i0 ] - x_j[j0 ]) +
+ sqr(x_i[i0+1] - x_j[j0+1]) +
+ sqr(x_i[i0+2] - x_j[j0+2]);
+
+ if (d2 < rl2)
+ {
+ return TRUE;
+ }
+ }
+ }
+
+ return FALSE;
+}
+
+#ifdef NBNXN_SEARCH_SIMD4_FLOAT_X_BB
+
+/* 4-wide SIMD function which determines if any atom pair between two cells,
+ * both with 8 atoms, is within distance sqrt(rl2).
+ * Using 8-wide AVX is not faster on Intel Sandy Bridge.
+ */
+static gmx_bool subc_in_range_simd4(int na_c,
+ int si, const real *x_i,
+ int csj, int stride, const real *x_j,
+ real rl2)
+{
+ gmx_simd4_real_t ix_S0, iy_S0, iz_S0;
+ gmx_simd4_real_t ix_S1, iy_S1, iz_S1;
+
+ gmx_simd4_real_t rc2_S;
+
+ int dim_stride;
+ int j0, j1;
+
+ rc2_S = gmx_simd4_set1_r(rl2);
+
+ dim_stride = NBNXN_GPU_CLUSTER_SIZE/STRIDE_PBB*DIM;
+ ix_S0 = gmx_simd4_load_r(x_i+(si*dim_stride+0)*STRIDE_PBB);
+ iy_S0 = gmx_simd4_load_r(x_i+(si*dim_stride+1)*STRIDE_PBB);
+ iz_S0 = gmx_simd4_load_r(x_i+(si*dim_stride+2)*STRIDE_PBB);
+ ix_S1 = gmx_simd4_load_r(x_i+(si*dim_stride+3)*STRIDE_PBB);
+ iy_S1 = gmx_simd4_load_r(x_i+(si*dim_stride+4)*STRIDE_PBB);
+ iz_S1 = gmx_simd4_load_r(x_i+(si*dim_stride+5)*STRIDE_PBB);
+
+ /* We loop from the outer to the inner particles to maximize
+ * the chance that we find a pair in range quickly and return.
+ */
+ j0 = csj*na_c;
+ j1 = j0 + na_c - 1;
+ while (j0 < j1)
+ {
+ gmx_simd4_real_t jx0_S, jy0_S, jz0_S;
+ gmx_simd4_real_t jx1_S, jy1_S, jz1_S;
+
+ gmx_simd4_real_t dx_S0, dy_S0, dz_S0;
+ gmx_simd4_real_t dx_S1, dy_S1, dz_S1;
+ gmx_simd4_real_t dx_S2, dy_S2, dz_S2;
+ gmx_simd4_real_t dx_S3, dy_S3, dz_S3;
+
+ gmx_simd4_real_t rsq_S0;
+ gmx_simd4_real_t rsq_S1;
+ gmx_simd4_real_t rsq_S2;
+ gmx_simd4_real_t rsq_S3;
+
+ gmx_simd4_bool_t wco_S0;
+ gmx_simd4_bool_t wco_S1;
+ gmx_simd4_bool_t wco_S2;
+ gmx_simd4_bool_t wco_S3;
+ gmx_simd4_bool_t wco_any_S01, wco_any_S23, wco_any_S;
+
+ jx0_S = gmx_simd4_set1_r(x_j[j0*stride+0]);
+ jy0_S = gmx_simd4_set1_r(x_j[j0*stride+1]);
+ jz0_S = gmx_simd4_set1_r(x_j[j0*stride+2]);
+
+ jx1_S = gmx_simd4_set1_r(x_j[j1*stride+0]);
+ jy1_S = gmx_simd4_set1_r(x_j[j1*stride+1]);
+ jz1_S = gmx_simd4_set1_r(x_j[j1*stride+2]);
+
+ /* Calculate distance */
+ dx_S0 = gmx_simd4_sub_r(ix_S0, jx0_S);
+ dy_S0 = gmx_simd4_sub_r(iy_S0, jy0_S);
+ dz_S0 = gmx_simd4_sub_r(iz_S0, jz0_S);
+ dx_S1 = gmx_simd4_sub_r(ix_S1, jx0_S);
+ dy_S1 = gmx_simd4_sub_r(iy_S1, jy0_S);
+ dz_S1 = gmx_simd4_sub_r(iz_S1, jz0_S);
+ dx_S2 = gmx_simd4_sub_r(ix_S0, jx1_S);
+ dy_S2 = gmx_simd4_sub_r(iy_S0, jy1_S);
+ dz_S2 = gmx_simd4_sub_r(iz_S0, jz1_S);
+ dx_S3 = gmx_simd4_sub_r(ix_S1, jx1_S);
+ dy_S3 = gmx_simd4_sub_r(iy_S1, jy1_S);
+ dz_S3 = gmx_simd4_sub_r(iz_S1, jz1_S);
+
+ /* rsq = dx*dx+dy*dy+dz*dz */
+ rsq_S0 = gmx_simd4_calc_rsq_r(dx_S0, dy_S0, dz_S0);
+ rsq_S1 = gmx_simd4_calc_rsq_r(dx_S1, dy_S1, dz_S1);
+ rsq_S2 = gmx_simd4_calc_rsq_r(dx_S2, dy_S2, dz_S2);
+ rsq_S3 = gmx_simd4_calc_rsq_r(dx_S3, dy_S3, dz_S3);
+
+ wco_S0 = gmx_simd4_cmplt_r(rsq_S0, rc2_S);
+ wco_S1 = gmx_simd4_cmplt_r(rsq_S1, rc2_S);
+ wco_S2 = gmx_simd4_cmplt_r(rsq_S2, rc2_S);
+ wco_S3 = gmx_simd4_cmplt_r(rsq_S3, rc2_S);
+
+ wco_any_S01 = gmx_simd4_or_b(wco_S0, wco_S1);
+ wco_any_S23 = gmx_simd4_or_b(wco_S2, wco_S3);
+ wco_any_S = gmx_simd4_or_b(wco_any_S01, wco_any_S23);
+
+ if (gmx_simd4_anytrue_b(wco_any_S))
+ {
+ return TRUE;
+ }
+
+ j0++;
+ j1--;
+ }
+ return FALSE;
+
+}
+#endif
+
+
+/* Returns the j sub-cell for index cj_ind */
+static int nbl_cj(const nbnxn_pairlist_t *nbl, int cj_ind)
+{
+ return nbl->cj4[cj_ind >> NBNXN_GPU_JGROUP_SIZE_2LOG].cj[cj_ind & (NBNXN_GPU_JGROUP_SIZE - 1)];
+}
+
+/* Returns the i-interaction mask of the j sub-cell for index cj_ind */
+static unsigned int nbl_imask0(const nbnxn_pairlist_t *nbl, int cj_ind)
+{
+ return nbl->cj4[cj_ind >> NBNXN_GPU_JGROUP_SIZE_2LOG].imei[0].imask;
+}
+
+/* Ensures there is enough space for extra extra exclusion masks */
+static void check_excl_space(nbnxn_pairlist_t *nbl, int extra)
+{
+ if (nbl->nexcl+extra > nbl->excl_nalloc)
+ {
+ nbl->excl_nalloc = over_alloc_small(nbl->nexcl+extra);
+ nbnxn_realloc_void((void **)&nbl->excl,
+ nbl->nexcl*sizeof(*nbl->excl),
+ nbl->excl_nalloc*sizeof(*nbl->excl),
+ nbl->alloc, nbl->free);
+ }
+}
+
+/* Ensures there is enough space for ncell extra j-cells in the list */
+static void check_subcell_list_space_simple(nbnxn_pairlist_t *nbl,
+ int ncell)
+{
+ int cj_max;
+
+ cj_max = nbl->ncj + ncell;
+
+ if (cj_max > nbl->cj_nalloc)
+ {
+ nbl->cj_nalloc = over_alloc_small(cj_max);
+ nbnxn_realloc_void((void **)&nbl->cj,
+ nbl->ncj*sizeof(*nbl->cj),
+ nbl->cj_nalloc*sizeof(*nbl->cj),
+ nbl->alloc, nbl->free);
+ }
+}
+
+/* Ensures there is enough space for ncell extra j-subcells in the list */
+static void check_subcell_list_space_supersub(nbnxn_pairlist_t *nbl,
+ int nsupercell)
+{
+ int ncj4_max, j4, j, w, t;
+
+#define NWARP 2
+#define WARP_SIZE 32
+
+ /* We can have maximally nsupercell*GPU_NSUBCELL sj lists */
+ /* We can store 4 j-subcell - i-supercell pairs in one struct.
+ * since we round down, we need one extra entry.
+ */
+ ncj4_max = ((nbl->work->cj_ind + nsupercell*GPU_NSUBCELL + NBNXN_GPU_JGROUP_SIZE - 1) >> NBNXN_GPU_JGROUP_SIZE_2LOG);
+
+ if (ncj4_max > nbl->cj4_nalloc)
+ {
+ nbl->cj4_nalloc = over_alloc_small(ncj4_max);
+ nbnxn_realloc_void((void **)&nbl->cj4,
+ nbl->work->cj4_init*sizeof(*nbl->cj4),
+ nbl->cj4_nalloc*sizeof(*nbl->cj4),
+ nbl->alloc, nbl->free);
+ }
+
+ if (ncj4_max > nbl->work->cj4_init)
+ {
+ for (j4 = nbl->work->cj4_init; j4 < ncj4_max; j4++)
+ {
+ /* No i-subcells and no excl's in the list initially */
+ for (w = 0; w < NWARP; w++)
+ {
+ nbl->cj4[j4].imei[w].imask = 0U;
+ nbl->cj4[j4].imei[w].excl_ind = 0;
+
+ }
+ }
+ nbl->work->cj4_init = ncj4_max;
+ }
+}
+
+/* Set all excl masks for one GPU warp no exclusions */
+static void set_no_excls(nbnxn_excl_t *excl)
+{
+ int t;
+
+ for (t = 0; t < WARP_SIZE; t++)
+ {
+ /* Turn all interaction bits on */
+ excl->pair[t] = NBNXN_INTERACTION_MASK_ALL;
+ }
+}
+
+/* Initializes a single nbnxn_pairlist_t data structure */
+static void nbnxn_init_pairlist(nbnxn_pairlist_t *nbl,
+ gmx_bool bSimple,
+ nbnxn_alloc_t *alloc,
+ nbnxn_free_t *free)
+{
+ if (alloc == NULL)
+ {
+ nbl->alloc = nbnxn_alloc_aligned;
+ }
+ else
+ {
+ nbl->alloc = alloc;
+ }
+ if (free == NULL)
+ {
+ nbl->free = nbnxn_free_aligned;
+ }
+ else
+ {
+ nbl->free = free;
+ }
+
+ nbl->bSimple = bSimple;
+ nbl->na_sc = 0;
+ nbl->na_ci = 0;
+ nbl->na_cj = 0;
+ nbl->nci = 0;
+ nbl->ci = NULL;
+ nbl->ci_nalloc = 0;
+ nbl->ncj = 0;
+ nbl->cj = NULL;
+ nbl->cj_nalloc = 0;
+ nbl->ncj4 = 0;
+ /* We need one element extra in sj, so alloc initially with 1 */
+ nbl->cj4_nalloc = 0;
+ nbl->cj4 = NULL;
+ nbl->nci_tot = 0;
+
+ if (!nbl->bSimple)
+ {
+ nbl->excl = NULL;
+ nbl->excl_nalloc = 0;
+ nbl->nexcl = 0;
+ check_excl_space(nbl, 1);
+ nbl->nexcl = 1;
+ set_no_excls(&nbl->excl[0]);
+ }
+
+ snew(nbl->work, 1);
+ if (nbl->bSimple)
+ {
+ snew_aligned(nbl->work->bb_ci, 1, NBNXN_SEARCH_BB_MEM_ALIGN);
+ }
+ else
+ {
+#ifdef NBNXN_BBXXXX
+ snew_aligned(nbl->work->pbb_ci, GPU_NSUBCELL/STRIDE_PBB*NNBSBB_XXXX, NBNXN_SEARCH_BB_MEM_ALIGN);
+#else
+ snew_aligned(nbl->work->bb_ci, GPU_NSUBCELL, NBNXN_SEARCH_BB_MEM_ALIGN);
+#endif
+ }
+ snew_aligned(nbl->work->x_ci, NBNXN_NA_SC_MAX*DIM, NBNXN_SEARCH_BB_MEM_ALIGN);
+#ifdef GMX_NBNXN_SIMD
+ snew_aligned(nbl->work->x_ci_simd_4xn, 1, NBNXN_MEM_ALIGN);
+ snew_aligned(nbl->work->x_ci_simd_2xnn, 1, NBNXN_MEM_ALIGN);
+#endif
+ snew_aligned(nbl->work->d2, GPU_NSUBCELL, NBNXN_SEARCH_BB_MEM_ALIGN);
+
+ nbl->work->sort = NULL;
+ nbl->work->sort_nalloc = 0;
+ nbl->work->sci_sort = NULL;
+ nbl->work->sci_sort_nalloc = 0;
+}
+
+void nbnxn_init_pairlist_set(nbnxn_pairlist_set_t *nbl_list,
+ gmx_bool bSimple, gmx_bool bCombined,
+ nbnxn_alloc_t *alloc,
+ nbnxn_free_t *free)
+{
+ int i;
+
+ nbl_list->bSimple = bSimple;
+ nbl_list->bCombined = bCombined;
+
+ nbl_list->nnbl = gmx_omp_nthreads_get(emntNonbonded);
+
+ if (!nbl_list->bCombined &&
+ nbl_list->nnbl > NBNXN_BUFFERFLAG_MAX_THREADS)
+ {
+ gmx_fatal(FARGS, "%d OpenMP threads were requested. Since the non-bonded force buffer reduction is prohibitively slow with more than %d threads, we do not allow this. Use %d or less OpenMP threads.",
+ nbl_list->nnbl, NBNXN_BUFFERFLAG_MAX_THREADS, NBNXN_BUFFERFLAG_MAX_THREADS);
+ }
+
+ snew(nbl_list->nbl, nbl_list->nnbl);
+ snew(nbl_list->nbl_fep, nbl_list->nnbl);
+ /* Execute in order to avoid memory interleaving between threads */
+#pragma omp parallel for num_threads(nbl_list->nnbl) schedule(static)
+ for (i = 0; i < nbl_list->nnbl; i++)
+ {
+ /* Allocate the nblist data structure locally on each thread
+ * to optimize memory access for NUMA architectures.
+ */
+ snew(nbl_list->nbl[i], 1);
+
+ /* Only list 0 is used on the GPU, use normal allocation for i>0 */
+ if (i == 0)
+ {
+ nbnxn_init_pairlist(nbl_list->nbl[i], nbl_list->bSimple, alloc, free);
+ }
+ else
+ {
+ nbnxn_init_pairlist(nbl_list->nbl[i], nbl_list->bSimple, NULL, NULL);
+ }
+
+ snew(nbl_list->nbl_fep[i], 1);
+ nbnxn_init_pairlist_fep(nbl_list->nbl_fep[i]);
+ }
+}
+
+/* Print statistics of a pair list, used for debug output */
+static void print_nblist_statistics_simple(FILE *fp, const nbnxn_pairlist_t *nbl,
+ const nbnxn_search_t nbs, real rl)
+{
+ const nbnxn_grid_t *grid;
+ int cs[SHIFTS];
+ int s, i, j;
+ int npexcl;
+
+ /* This code only produces correct statistics with domain decomposition */
+ grid = &nbs->grid[0];
+
+ fprintf(fp, "nbl nci %d ncj %d\n",
+ nbl->nci, nbl->ncj);
+ fprintf(fp, "nbl na_sc %d rl %g ncp %d per cell %.1f atoms %.1f ratio %.2f\n",
+ nbl->na_sc, rl, nbl->ncj, nbl->ncj/(double)grid->nc,
+ nbl->ncj/(double)grid->nc*grid->na_sc,
+ nbl->ncj/(double)grid->nc*grid->na_sc/(0.5*4.0/3.0*M_PI*rl*rl*rl*grid->nc*grid->na_sc/(grid->size[XX]*grid->size[YY]*grid->size[ZZ])));
+
+ fprintf(fp, "nbl average j cell list length %.1f\n",
+ 0.25*nbl->ncj/(double)nbl->nci);
+
+ for (s = 0; s < SHIFTS; s++)
+ {
+ cs[s] = 0;
+ }
+ npexcl = 0;
+ for (i = 0; i < nbl->nci; i++)
+ {
+ cs[nbl->ci[i].shift & NBNXN_CI_SHIFT] +=
+ nbl->ci[i].cj_ind_end - nbl->ci[i].cj_ind_start;
+
+ j = nbl->ci[i].cj_ind_start;
+ while (j < nbl->ci[i].cj_ind_end &&
+ nbl->cj[j].excl != NBNXN_INTERACTION_MASK_ALL)
+ {
+ npexcl++;
+ j++;
+ }
+ }
+ fprintf(fp, "nbl cell pairs, total: %d excl: %d %.1f%%\n",
+ nbl->ncj, npexcl, 100*npexcl/(double)nbl->ncj);
+ for (s = 0; s < SHIFTS; s++)
+ {
+ if (cs[s] > 0)
+ {
+ fprintf(fp, "nbl shift %2d ncj %3d\n", s, cs[s]);
+ }
+ }
+}
+
+/* Print statistics of a pair lists, used for debug output */
+static void print_nblist_statistics_supersub(FILE *fp, const nbnxn_pairlist_t *nbl,
+ const nbnxn_search_t nbs, real rl)
+{
+ const nbnxn_grid_t *grid;
+ int i, j4, j, si, b;
+ int c[GPU_NSUBCELL+1];
+
+ /* This code only produces correct statistics with domain decomposition */
+ grid = &nbs->grid[0];
+
+ fprintf(fp, "nbl nsci %d ncj4 %d nsi %d excl4 %d\n",
+ nbl->nsci, nbl->ncj4, nbl->nci_tot, nbl->nexcl);
+ fprintf(fp, "nbl na_c %d rl %g ncp %d per cell %.1f atoms %.1f ratio %.2f\n",
+ nbl->na_ci, rl, nbl->nci_tot, nbl->nci_tot/(double)grid->nsubc_tot,
+ nbl->nci_tot/(double)grid->nsubc_tot*grid->na_c,
+ nbl->nci_tot/(double)grid->nsubc_tot*grid->na_c/(0.5*4.0/3.0*M_PI*rl*rl*rl*grid->nsubc_tot*grid->na_c/(grid->size[XX]*grid->size[YY]*grid->size[ZZ])));
+
+ fprintf(fp, "nbl average j super cell list length %.1f\n",
+ 0.25*nbl->ncj4/(double)nbl->nsci);
+ fprintf(fp, "nbl average i sub cell list length %.1f\n",
+ nbl->nci_tot/((double)nbl->ncj4));
+
+ for (si = 0; si <= GPU_NSUBCELL; si++)
+ {
+ c[si] = 0;
+ }
+ for (i = 0; i < nbl->nsci; i++)
+ {
+ for (j4 = nbl->sci[i].cj4_ind_start; j4 < nbl->sci[i].cj4_ind_end; j4++)
+ {
+ for (j = 0; j < NBNXN_GPU_JGROUP_SIZE; j++)
+ {
+ b = 0;
+ for (si = 0; si < GPU_NSUBCELL; si++)
+ {
+ if (nbl->cj4[j4].imei[0].imask & (1U << (j*GPU_NSUBCELL + si)))
+ {
+ b++;
+ }
+ }
+ c[b]++;
+ }
+ }
+ }
+ for (b = 0; b <= GPU_NSUBCELL; b++)
+ {
+ fprintf(fp, "nbl j-list #i-subcell %d %7d %4.1f\n",
+ b, c[b], 100.0*c[b]/(double)(nbl->ncj4*NBNXN_GPU_JGROUP_SIZE));
+ }
+}
+
+/* Returns a pointer to the exclusion mask for cj4-unit cj4, warp warp */
+static void low_get_nbl_exclusions(nbnxn_pairlist_t *nbl, int cj4,
+ int warp, nbnxn_excl_t **excl)
+{
+ if (nbl->cj4[cj4].imei[warp].excl_ind == 0)
+ {
+ /* No exclusions set, make a new list entry */
+ nbl->cj4[cj4].imei[warp].excl_ind = nbl->nexcl;
+ nbl->nexcl++;
+ *excl = &nbl->excl[nbl->cj4[cj4].imei[warp].excl_ind];
+ set_no_excls(*excl);
+ }
+ else
+ {
+ /* We already have some exclusions, new ones can be added to the list */
+ *excl = &nbl->excl[nbl->cj4[cj4].imei[warp].excl_ind];
+ }
+}
+
+/* Returns a pointer to the exclusion mask for cj4-unit cj4, warp warp,
+ * generates a new element and allocates extra memory, if necessary.
+ */
+static void get_nbl_exclusions_1(nbnxn_pairlist_t *nbl, int cj4,
+ int warp, nbnxn_excl_t **excl)
+{
+ if (nbl->cj4[cj4].imei[warp].excl_ind == 0)
+ {
+ /* We need to make a new list entry, check if we have space */
+ check_excl_space(nbl, 1);
+ }
+ low_get_nbl_exclusions(nbl, cj4, warp, excl);
+}
+
+/* Returns pointers to the exclusion mask for cj4-unit cj4 for both warps,
+ * generates a new element and allocates extra memory, if necessary.
+ */
+static void get_nbl_exclusions_2(nbnxn_pairlist_t *nbl, int cj4,
+ nbnxn_excl_t **excl_w0,
+ nbnxn_excl_t **excl_w1)
+{
+ /* Check for space we might need */
+ check_excl_space(nbl, 2);
+
+ low_get_nbl_exclusions(nbl, cj4, 0, excl_w0);
+ low_get_nbl_exclusions(nbl, cj4, 1, excl_w1);
+}
+
+/* Sets the self exclusions i=j and pair exclusions i>j */
+static void set_self_and_newton_excls_supersub(nbnxn_pairlist_t *nbl,
+ int cj4_ind, int sj_offset,
+ int si)
+{
+ nbnxn_excl_t *excl[2];
+ int ei, ej, w;
+
+ /* Here we only set the set self and double pair exclusions */
+
+ get_nbl_exclusions_2(nbl, cj4_ind, &excl[0], &excl[1]);
+
+ /* Only minor < major bits set */
+ for (ej = 0; ej < nbl->na_ci; ej++)
+ {
+ w = (ej>>2);
+ for (ei = ej; ei < nbl->na_ci; ei++)
+ {
+ excl[w]->pair[(ej & (NBNXN_GPU_JGROUP_SIZE-1))*nbl->na_ci + ei] &=
+ ~(1U << (sj_offset*GPU_NSUBCELL + si));
+ }
+ }
+}
+
+/* Returns a diagonal or off-diagonal interaction mask for plain C lists */
+static unsigned int get_imask(gmx_bool rdiag, int ci, int cj)
+{
+ return (rdiag && ci == cj ? NBNXN_INTERACTION_MASK_DIAG : NBNXN_INTERACTION_MASK_ALL);
+}
+
+/* Returns a diagonal or off-diagonal interaction mask for cj-size=2 */
+static unsigned int get_imask_simd_j2(gmx_bool rdiag, int ci, int cj)
+{
+ return (rdiag && ci*2 == cj ? NBNXN_INTERACTION_MASK_DIAG_J2_0 :
+ (rdiag && ci*2+1 == cj ? NBNXN_INTERACTION_MASK_DIAG_J2_1 :
+ NBNXN_INTERACTION_MASK_ALL));
+}
+
+/* Returns a diagonal or off-diagonal interaction mask for cj-size=4 */
+static unsigned int get_imask_simd_j4(gmx_bool rdiag, int ci, int cj)
+{
+ return (rdiag && ci == cj ? NBNXN_INTERACTION_MASK_DIAG : NBNXN_INTERACTION_MASK_ALL);
+}
+
+/* Returns a diagonal or off-diagonal interaction mask for cj-size=8 */
+static unsigned int get_imask_simd_j8(gmx_bool rdiag, int ci, int cj)
+{
+ return (rdiag && ci == cj*2 ? NBNXN_INTERACTION_MASK_DIAG_J8_0 :
+ (rdiag && ci == cj*2+1 ? NBNXN_INTERACTION_MASK_DIAG_J8_1 :
+ NBNXN_INTERACTION_MASK_ALL));
+}
+
+#ifdef GMX_NBNXN_SIMD
+#if GMX_SIMD_REAL_WIDTH == 2
+#define get_imask_simd_4xn get_imask_simd_j2
+#endif
+#if GMX_SIMD_REAL_WIDTH == 4
+#define get_imask_simd_4xn get_imask_simd_j4
+#endif
+#if GMX_SIMD_REAL_WIDTH == 8
+#define get_imask_simd_4xn get_imask_simd_j8
+#define get_imask_simd_2xnn get_imask_simd_j4
+#endif
+#if GMX_SIMD_REAL_WIDTH == 16
+#define get_imask_simd_2xnn get_imask_simd_j8
+#endif
+#endif
+
+/* Plain C code for making a pair list of cell ci vs cell cjf-cjl.
+ * Checks bounding box distances and possibly atom pair distances.
+ */
+static void make_cluster_list_simple(const nbnxn_grid_t *gridj,
+ nbnxn_pairlist_t *nbl,
+ int ci, int cjf, int cjl,
+ gmx_bool remove_sub_diag,
+ const real *x_j,
+ real rl2, float rbb2,
+ int *ndistc)
+{
+ const nbnxn_list_work_t *work;
+
+ const nbnxn_bb_t *bb_ci;
+ const real *x_ci;
+
+ gmx_bool InRange;
+ real d2;
+ int cjf_gl, cjl_gl, cj;
+
+ work = nbl->work;
+
+ bb_ci = nbl->work->bb_ci;
+ x_ci = nbl->work->x_ci;
+
+ InRange = FALSE;
+ while (!InRange && cjf <= cjl)
+ {
+ d2 = subc_bb_dist2(0, bb_ci, cjf, gridj->bb);
+ *ndistc += 2;
+
+ /* Check if the distance is within the distance where
+ * we use only the bounding box distance rbb,
+ * or within the cut-off and there is at least one atom pair
+ * within the cut-off.
+ */
+ if (d2 < rbb2)
+ {
+ InRange = TRUE;
+ }
+ else if (d2 < rl2)
+ {
+ int i, j;
+
+ cjf_gl = gridj->cell0 + cjf;
+ for (i = 0; i < NBNXN_CPU_CLUSTER_I_SIZE && !InRange; i++)
+ {
+ for (j = 0; j < NBNXN_CPU_CLUSTER_I_SIZE; j++)
+ {
+ InRange = InRange ||
+ (sqr(x_ci[i*STRIDE_XYZ+XX] - x_j[(cjf_gl*NBNXN_CPU_CLUSTER_I_SIZE+j)*STRIDE_XYZ+XX]) +
+ sqr(x_ci[i*STRIDE_XYZ+YY] - x_j[(cjf_gl*NBNXN_CPU_CLUSTER_I_SIZE+j)*STRIDE_XYZ+YY]) +
+ sqr(x_ci[i*STRIDE_XYZ+ZZ] - x_j[(cjf_gl*NBNXN_CPU_CLUSTER_I_SIZE+j)*STRIDE_XYZ+ZZ]) < rl2);
+ }
+ }
+ *ndistc += NBNXN_CPU_CLUSTER_I_SIZE*NBNXN_CPU_CLUSTER_I_SIZE;
+ }
+ if (!InRange)
+ {
+ cjf++;
+ }
+ }
+ if (!InRange)
+ {
+ return;
+ }
+
+ InRange = FALSE;
+ while (!InRange && cjl > cjf)
+ {
+ d2 = subc_bb_dist2(0, bb_ci, cjl, gridj->bb);
+ *ndistc += 2;
+
+ /* Check if the distance is within the distance where
+ * we use only the bounding box distance rbb,
+ * or within the cut-off and there is at least one atom pair
+ * within the cut-off.
+ */
+ if (d2 < rbb2)
+ {
+ InRange = TRUE;
+ }
+ else if (d2 < rl2)
+ {
+ int i, j;
+
+ cjl_gl = gridj->cell0 + cjl;
+ for (i = 0; i < NBNXN_CPU_CLUSTER_I_SIZE && !InRange; i++)
+ {
+ for (j = 0; j < NBNXN_CPU_CLUSTER_I_SIZE; j++)
+ {
+ InRange = InRange ||
+ (sqr(x_ci[i*STRIDE_XYZ+XX] - x_j[(cjl_gl*NBNXN_CPU_CLUSTER_I_SIZE+j)*STRIDE_XYZ+XX]) +
+ sqr(x_ci[i*STRIDE_XYZ+YY] - x_j[(cjl_gl*NBNXN_CPU_CLUSTER_I_SIZE+j)*STRIDE_XYZ+YY]) +
+ sqr(x_ci[i*STRIDE_XYZ+ZZ] - x_j[(cjl_gl*NBNXN_CPU_CLUSTER_I_SIZE+j)*STRIDE_XYZ+ZZ]) < rl2);
+ }
+ }
+ *ndistc += NBNXN_CPU_CLUSTER_I_SIZE*NBNXN_CPU_CLUSTER_I_SIZE;
+ }
+ if (!InRange)
+ {
+ cjl--;
+ }
+ }
+
+ if (cjf <= cjl)
+ {
+ for (cj = cjf; cj <= cjl; cj++)
+ {
+ /* Store cj and the interaction mask */
+ nbl->cj[nbl->ncj].cj = gridj->cell0 + cj;
+ nbl->cj[nbl->ncj].excl = get_imask(remove_sub_diag, ci, cj);
+ nbl->ncj++;
+ }
+ /* Increase the closing index in i super-cell list */
+ nbl->ci[nbl->nci].cj_ind_end = nbl->ncj;
+ }
+}
+
+#ifdef GMX_NBNXN_SIMD_4XN
+#include "nbnxn_search_simd_4xn.h"
+#endif
+#ifdef GMX_NBNXN_SIMD_2XNN
+#include "nbnxn_search_simd_2xnn.h"
+#endif
+
+/* Plain C or SIMD4 code for making a pair list of super-cell sci vs scj.
+ * Checks bounding box distances and possibly atom pair distances.
+ */
+static void make_cluster_list_supersub(const nbnxn_grid_t *gridi,
+ const nbnxn_grid_t *gridj,
+ nbnxn_pairlist_t *nbl,
+ int sci, int scj,
+ gmx_bool sci_equals_scj,
+ int stride, const real *x,
+ real rl2, float rbb2,
+ int *ndistc)
+{
+ int na_c;
+ int npair;
+ int cjo, ci1, ci, cj, cj_gl;
+ int cj4_ind, cj_offset;
+ unsigned int imask;
+ nbnxn_cj4_t *cj4;
+#ifdef NBNXN_BBXXXX
+ const float *pbb_ci;
+#else
+ const nbnxn_bb_t *bb_ci;
+#endif
+ const real *x_ci;
+ float *d2l, d2;
+ int w;
+#define PRUNE_LIST_CPU_ONE
+#ifdef PRUNE_LIST_CPU_ONE
+ int ci_last = -1;
+#endif
+
+ d2l = nbl->work->d2;
+
+#ifdef NBNXN_BBXXXX
+ pbb_ci = nbl->work->pbb_ci;
+#else
+ bb_ci = nbl->work->bb_ci;
+#endif
+ x_ci = nbl->work->x_ci;
+
+ na_c = gridj->na_c;
+
+ for (cjo = 0; cjo < gridj->nsubc[scj]; cjo++)
+ {
+ cj4_ind = (nbl->work->cj_ind >> NBNXN_GPU_JGROUP_SIZE_2LOG);
+ cj_offset = nbl->work->cj_ind - cj4_ind*NBNXN_GPU_JGROUP_SIZE;
+ cj4 = &nbl->cj4[cj4_ind];
+
+ cj = scj*GPU_NSUBCELL + cjo;
+
+ cj_gl = gridj->cell0*GPU_NSUBCELL + cj;
+
+ /* Initialize this j-subcell i-subcell list */
+ cj4->cj[cj_offset] = cj_gl;
+ imask = 0;
+
+ if (sci_equals_scj)
+ {
+ ci1 = cjo + 1;
+ }
+ else
+ {
+ ci1 = gridi->nsubc[sci];
+ }
+
+#ifdef NBNXN_BBXXXX
+ /* Determine all ci1 bb distances in one call with SIMD4 */
+ subc_bb_dist2_simd4_xxxx(gridj->pbb+(cj>>STRIDE_PBB_2LOG)*NNBSBB_XXXX+(cj & (STRIDE_PBB-1)),
+ ci1, pbb_ci, d2l);
+ *ndistc += na_c*2;
+#endif
+
+ npair = 0;
+ /* We use a fixed upper-bound instead of ci1 to help optimization */
+ for (ci = 0; ci < GPU_NSUBCELL; ci++)
+ {
+ if (ci == ci1)
+ {
+ break;
+ }
+
+#ifndef NBNXN_BBXXXX
+ /* Determine the bb distance between ci and cj */
+ d2l[ci] = subc_bb_dist2(ci, bb_ci, cj, gridj->bb);
+ *ndistc += 2;
+#endif
+ d2 = d2l[ci];
+
+#ifdef PRUNE_LIST_CPU_ALL
+ /* Check if the distance is within the distance where
+ * we use only the bounding box distance rbb,
+ * or within the cut-off and there is at least one atom pair
+ * within the cut-off. This check is very costly.
+ */
+ *ndistc += na_c*na_c;
+ if (d2 < rbb2 ||
+ (d2 < rl2 &&
+#ifdef NBNXN_PBB_SIMD4
+ subc_in_range_simd4
+#else
+ subc_in_range_x
+#endif
+ (na_c, ci, x_ci, cj_gl, stride, x, rl2)))
+#else
+ /* Check if the distance between the two bounding boxes
+ * in within the pair-list cut-off.
+ */
+ if (d2 < rl2)
+#endif
+ {
+ /* Flag this i-subcell to be taken into account */
+ imask |= (1U << (cj_offset*GPU_NSUBCELL+ci));
+
+#ifdef PRUNE_LIST_CPU_ONE
+ ci_last = ci;
+#endif
+
+ npair++;
+ }
+ }
+
+#ifdef PRUNE_LIST_CPU_ONE
+ /* If we only found 1 pair, check if any atoms are actually
+ * within the cut-off, so we could get rid of it.
+ */
+ if (npair == 1 && d2l[ci_last] >= rbb2)
+ {
+ /* Avoid using function pointers here, as it's slower */
+ if (
+#ifdef NBNXN_PBB_SIMD4
+ !subc_in_range_simd4
+#else
+ !subc_in_range_x
+#endif
+ (na_c, ci_last, x_ci, cj_gl, stride, x, rl2))
+ {
+ imask &= ~(1U << (cj_offset*GPU_NSUBCELL+ci_last));
+ npair--;
+ }
+ }
+#endif
+
+ if (npair > 0)
+ {
+ /* We have a useful sj entry, close it now */
+
+ /* Set the exclucions for the ci== sj entry.
+ * Here we don't bother to check if this entry is actually flagged,
+ * as it will nearly always be in the list.
+ */
+ if (sci_equals_scj)
+ {
+ set_self_and_newton_excls_supersub(nbl, cj4_ind, cj_offset, cjo);
+ }
+
+ /* Copy the cluster interaction mask to the list */
+ for (w = 0; w < NWARP; w++)
+ {
+ cj4->imei[w].imask |= imask;
+ }
+
+ nbl->work->cj_ind++;
+
+ /* Keep the count */
+ nbl->nci_tot += npair;
+
+ /* Increase the closing index in i super-cell list */
+ nbl->sci[nbl->nsci].cj4_ind_end =
+ ((nbl->work->cj_ind+NBNXN_GPU_JGROUP_SIZE-1) >> NBNXN_GPU_JGROUP_SIZE_2LOG);
+ }
+ }
+}
+
+/* Set all atom-pair exclusions from the topology stored in excl
+ * as masks in the pair-list for simple list i-entry nbl_ci
+ */
+static void set_ci_top_excls(const nbnxn_search_t nbs,
+ nbnxn_pairlist_t *nbl,
+ gmx_bool diagRemoved,
+ int na_ci_2log,
+ int na_cj_2log,
+ const nbnxn_ci_t *nbl_ci,
+ const t_blocka *excl)
+{
+ const int *cell;
+ int ci;
+ int cj_ind_first, cj_ind_last;
+ int cj_first, cj_last;
+ int ndirect;
+ int i, ai, aj, si, eind, ge, se;
+ int found, cj_ind_0, cj_ind_1, cj_ind_m;
+ int cj_m;
+ gmx_bool Found_si;
+ int si_ind;
+ nbnxn_excl_t *nbl_excl;
+ int inner_i, inner_e;
+
+ cell = nbs->cell;
+
+ if (nbl_ci->cj_ind_end == nbl_ci->cj_ind_start)
+ {
+ /* Empty list */
+ return;
+ }
+
+ ci = nbl_ci->ci;
+
+ cj_ind_first = nbl_ci->cj_ind_start;
+ cj_ind_last = nbl->ncj - 1;
+
+ cj_first = nbl->cj[cj_ind_first].cj;
+ cj_last = nbl->cj[cj_ind_last].cj;
+
+ /* Determine how many contiguous j-cells we have starting
+ * from the first i-cell. This number can be used to directly
+ * calculate j-cell indices for excluded atoms.
+ */
+ ndirect = 0;
+ if (na_ci_2log == na_cj_2log)
+ {
+ while (cj_ind_first + ndirect <= cj_ind_last &&
+ nbl->cj[cj_ind_first+ndirect].cj == ci + ndirect)
+ {
+ ndirect++;
+ }
+ }
+#ifdef NBNXN_SEARCH_BB_SIMD4
+ else
+ {
+ while (cj_ind_first + ndirect <= cj_ind_last &&
+ nbl->cj[cj_ind_first+ndirect].cj == ci_to_cj(na_cj_2log, ci) + ndirect)
+ {
+ ndirect++;
+ }
+ }
+#endif
+
+ /* Loop over the atoms in the i super-cell */
+ for (i = 0; i < nbl->na_sc; i++)
+ {
+ ai = nbs->a[ci*nbl->na_sc+i];
+ if (ai >= 0)
+ {
+ si = (i>>na_ci_2log);
+
+ /* Loop over the topology-based exclusions for this i-atom */
+ for (eind = excl->index[ai]; eind < excl->index[ai+1]; eind++)
+ {
+ aj = excl->a[eind];
+
+ if (aj == ai)
+ {
+ /* The self exclusion are already set, save some time */
+ continue;
+ }
+
+ ge = cell[aj];
+
+ /* Without shifts we only calculate interactions j>i
+ * for one-way pair-lists.
+ */
+ if (diagRemoved && ge <= ci*nbl->na_sc + i)
+ {
+ continue;
+ }
+
+ se = (ge >> na_cj_2log);
+
+ /* Could the cluster se be in our list? */
+ if (se >= cj_first && se <= cj_last)
+ {
+ if (se < cj_first + ndirect)
+ {
+ /* We can calculate cj_ind directly from se */
+ found = cj_ind_first + se - cj_first;
+ }
+ else
+ {
+ /* Search for se using bisection */
+ found = -1;
+ cj_ind_0 = cj_ind_first + ndirect;
+ cj_ind_1 = cj_ind_last + 1;
+ while (found == -1 && cj_ind_0 < cj_ind_1)
+ {
+ cj_ind_m = (cj_ind_0 + cj_ind_1)>>1;
+
+ cj_m = nbl->cj[cj_ind_m].cj;
+
+ if (se == cj_m)
+ {
+ found = cj_ind_m;
+ }
+ else if (se < cj_m)
+ {
+ cj_ind_1 = cj_ind_m;
+ }
+ else
+ {
+ cj_ind_0 = cj_ind_m + 1;
+ }
+ }
+ }
+
+ if (found >= 0)
+ {
+ inner_i = i - (si << na_ci_2log);
+ inner_e = ge - (se << na_cj_2log);
+
+ nbl->cj[found].excl &= ~(1U<<((inner_i<<na_cj_2log) + inner_e));
+ }
+ }
+ }
+ }
+ }
+}
+
+/* Add a new i-entry to the FEP list and copy the i-properties */
+static gmx_inline void fep_list_new_nri_copy(t_nblist *nlist)
+{
+ /* Add a new i-entry */
+ nlist->nri++;
+
+ assert(nlist->nri < nlist->maxnri);
+
+ /* Duplicate the last i-entry, except for jindex, which continues */
+ nlist->iinr[nlist->nri] = nlist->iinr[nlist->nri-1];
+ nlist->shift[nlist->nri] = nlist->shift[nlist->nri-1];
+ nlist->gid[nlist->nri] = nlist->gid[nlist->nri-1];
+ nlist->jindex[nlist->nri] = nlist->nrj;
+}
+
+/* For load balancing of the free-energy lists over threads, we set
+ * the maximum nrj size of an i-entry to 40. This leads to good
+ * load balancing in the worst case scenario of a single perturbed
+ * particle on 16 threads, while not introducing significant overhead.
+ * Note that half of the perturbed pairs will anyhow end up in very small lists,
+ * since non perturbed i-particles will see few perturbed j-particles).
+ */
+const int max_nrj_fep = 40;
+
+/* Exclude the perturbed pairs from the Verlet list. This is only done to avoid
+ * singularities for overlapping particles (0/0), since the charges and
+ * LJ parameters have been zeroed in the nbnxn data structure.
+ * Simultaneously make a group pair list for the perturbed pairs.
+ */
+static void make_fep_list(const nbnxn_search_t nbs,
+ const nbnxn_atomdata_t *nbat,
+ nbnxn_pairlist_t *nbl,
+ gmx_bool bDiagRemoved,
+ nbnxn_ci_t *nbl_ci,
+ const nbnxn_grid_t *gridi,
+ const nbnxn_grid_t *gridj,
+ t_nblist *nlist)
+{
+ int ci, cj_ind_start, cj_ind_end, cj_ind, cja, cjr;
+ int nri_max;
+ int ngid, gid_i = 0, gid_j, gid;
+ int egp_shift, egp_mask;
+ int gid_cj = 0;
+ int i, j, ind_i, ind_j, ai, aj;
+ int nri;
+ gmx_bool bFEP_i, bFEP_i_all;
+
+ if (nbl_ci->cj_ind_end == nbl_ci->cj_ind_start)
+ {
+ /* Empty list */
+ return;
+ }
+
+ ci = nbl_ci->ci;
+
+ cj_ind_start = nbl_ci->cj_ind_start;
+ cj_ind_end = nbl_ci->cj_ind_end;
+
+ /* In worst case we have alternating energy groups
+ * and create #atom-pair lists, which means we need the size
+ * of a cluster pair (na_ci*na_cj) times the number of cj's.
+ */
+ nri_max = nbl->na_ci*nbl->na_cj*(cj_ind_end - cj_ind_start);
+ if (nlist->nri + nri_max > nlist->maxnri)
+ {
+ nlist->maxnri = over_alloc_large(nlist->nri + nri_max);
+ reallocate_nblist(nlist);
+ }
+
+ ngid = nbat->nenergrp;
+
+ if (ngid*gridj->na_cj > sizeof(gid_cj)*8)
+ {
+ gmx_fatal(FARGS, "The Verlet scheme with %dx%d kernels and free-energy only supports up to %d energy groups",
+ gridi->na_c, gridj->na_cj, (sizeof(gid_cj)*8)/gridj->na_cj);
+ }
+
+ egp_shift = nbat->neg_2log;
+ egp_mask = (1<<nbat->neg_2log) - 1;
+
+ /* Loop over the atoms in the i sub-cell */
+ bFEP_i_all = TRUE;
+ for (i = 0; i < nbl->na_ci; i++)
+ {
+ ind_i = ci*nbl->na_ci + i;
+ ai = nbs->a[ind_i];
+ if (ai >= 0)
+ {
+ nri = nlist->nri;
+ nlist->jindex[nri+1] = nlist->jindex[nri];
+ nlist->iinr[nri] = ai;
+ /* The actual energy group pair index is set later */
+ nlist->gid[nri] = 0;
+ nlist->shift[nri] = nbl_ci->shift & NBNXN_CI_SHIFT;
+
+ bFEP_i = gridi->fep[ci - gridi->cell0] & (1 << i);
+
+ bFEP_i_all = bFEP_i_all && bFEP_i;
+
+ if ((nlist->nrj + cj_ind_end - cj_ind_start)*nbl->na_cj > nlist->maxnrj)
+ {
+ nlist->maxnrj = over_alloc_small((nlist->nrj + cj_ind_end - cj_ind_start)*nbl->na_cj);
+ srenew(nlist->jjnr, nlist->maxnrj);
+ srenew(nlist->excl_fep, nlist->maxnrj);
+ }
+
+ if (ngid > 1)
+ {
+ gid_i = (nbat->energrp[ci] >> (egp_shift*i)) & egp_mask;
+ }
+
+ for (cj_ind = cj_ind_start; cj_ind < cj_ind_end; cj_ind++)
+ {
+ unsigned int fep_cj;
+
+ cja = nbl->cj[cj_ind].cj;
+
+ if (gridj->na_cj == gridj->na_c)
+ {
+ cjr = cja - gridj->cell0;
+ fep_cj = gridj->fep[cjr];
+ if (ngid > 1)
+ {
+ gid_cj = nbat->energrp[cja];
+ }
+ }
+ else if (2*gridj->na_cj == gridj->na_c)
+ {
+ cjr = cja - gridj->cell0*2;
+ /* Extract half of the ci fep/energrp mask */
+ fep_cj = (gridj->fep[cjr>>1] >> ((cjr&1)*gridj->na_cj)) & ((1<<gridj->na_cj) - 1);
+ if (ngid > 1)
+ {
+ gid_cj = nbat->energrp[cja>>1] >> ((cja&1)*gridj->na_cj*egp_shift) & ((1<<(gridj->na_cj*egp_shift)) - 1);
+ }
+ }
+ else
+ {
+ cjr = cja - (gridj->cell0>>1);
+ /* Combine two ci fep masks/energrp */
+ fep_cj = gridj->fep[cjr*2] + (gridj->fep[cjr*2+1] << gridj->na_c);
+ if (ngid > 1)
+ {
+ gid_cj = nbat->energrp[cja*2] + (nbat->energrp[cja*2+1] << (gridj->na_c*egp_shift));
+ }
+ }
+
+ if (bFEP_i || fep_cj != 0)
+ {
+ for (j = 0; j < nbl->na_cj; j++)
+ {
+ /* Is this interaction perturbed and not excluded? */
+ ind_j = cja*nbl->na_cj + j;
+ aj = nbs->a[ind_j];
+ if (aj >= 0 &&
+ (bFEP_i || (fep_cj & (1 << j))) &&
+ (!bDiagRemoved || ind_j >= ind_i))
+ {
+ if (ngid > 1)
+ {
+ gid_j = (gid_cj >> (j*egp_shift)) & egp_mask;
+ gid = GID(gid_i, gid_j, ngid);
+
+ if (nlist->nrj > nlist->jindex[nri] &&
+ nlist->gid[nri] != gid)
+ {
+ /* Energy group pair changed: new list */
+ fep_list_new_nri_copy(nlist);
+ nri = nlist->nri;
+ }
+ nlist->gid[nri] = gid;
+ }
+
+ if (nlist->nrj - nlist->jindex[nri] >= max_nrj_fep)
+ {
+ fep_list_new_nri_copy(nlist);
+ nri = nlist->nri;
+ }
+
+ /* Add it to the FEP list */
+ nlist->jjnr[nlist->nrj] = aj;
+ nlist->excl_fep[nlist->nrj] = (nbl->cj[cj_ind].excl >> (i*nbl->na_cj + j)) & 1;
+ nlist->nrj++;
+
+ /* Exclude it from the normal list.
+ * Note that the charge has been set to zero,
+ * but we need to avoid 0/0, as perturbed atoms
+ * can be on top of each other.
+ */
+ nbl->cj[cj_ind].excl &= ~(1U << (i*nbl->na_cj + j));
+ }
+ }
+ }
+ }
+
+ if (nlist->nrj > nlist->jindex[nri])
+ {
+ /* Actually add this new, non-empty, list */
+ nlist->nri++;
+ nlist->jindex[nlist->nri] = nlist->nrj;
+ }
+ }
+ }
+
+ if (bFEP_i_all)
+ {
+ /* All interactions are perturbed, we can skip this entry */
+ nbl_ci->cj_ind_end = cj_ind_start;
+ }
+}
+
+/* Return the index of atom a within a cluster */
+static gmx_inline int cj_mod_cj4(int cj)
+{
+ return cj & (NBNXN_GPU_JGROUP_SIZE - 1);
+}
+
+/* Convert a j-cluster to a cj4 group */
+static gmx_inline int cj_to_cj4(int cj)
+{
+ return cj >> NBNXN_GPU_JGROUP_SIZE_2LOG;
+}
+
+/* Return the index of an j-atom within a warp */
+static gmx_inline int a_mod_wj(int a)
+{
+ return a & (NBNXN_GPU_CLUSTER_SIZE/2 - 1);
+}
+
+/* As make_fep_list above, but for super/sub lists. */
+static void make_fep_list_supersub(const nbnxn_search_t nbs,
+ const nbnxn_atomdata_t *nbat,
+ nbnxn_pairlist_t *nbl,
+ gmx_bool bDiagRemoved,
+ const nbnxn_sci_t *nbl_sci,
+ real shx,
+ real shy,
+ real shz,
+ real rlist_fep2,
+ const nbnxn_grid_t *gridi,
+ const nbnxn_grid_t *gridj,
+ t_nblist *nlist)
+{
+ int sci, cj4_ind_start, cj4_ind_end, cj4_ind, gcj, cjr;
+ int nri_max;
+ int c, c_abs;
+ int i, j, ind_i, ind_j, ai, aj;
+ int nri;
+ gmx_bool bFEP_i;
+ real xi, yi, zi;
+ const nbnxn_cj4_t *cj4;
+
+ if (nbl_sci->cj4_ind_end == nbl_sci->cj4_ind_start)
+ {
+ /* Empty list */
+ return;
+ }
+
+ sci = nbl_sci->sci;
+
+ cj4_ind_start = nbl_sci->cj4_ind_start;
+ cj4_ind_end = nbl_sci->cj4_ind_end;
+
+ /* Here we process one super-cell, max #atoms na_sc, versus a list
+ * cj4 entries, each with max NBNXN_GPU_JGROUP_SIZE cj's, each
+ * of size na_cj atoms.
+ * On the GPU we don't support energy groups (yet).
+ * So for each of the na_sc i-atoms, we need max one FEP list
+ * for each max_nrj_fep j-atoms.
+ */
+ nri_max = nbl->na_sc*nbl->na_cj*(1 + ((cj4_ind_end - cj4_ind_start)*NBNXN_GPU_JGROUP_SIZE)/max_nrj_fep);
+ if (nlist->nri + nri_max > nlist->maxnri)
+ {
+ nlist->maxnri = over_alloc_large(nlist->nri + nri_max);
+ reallocate_nblist(nlist);
+ }
+
+ /* Loop over the atoms in the i super-cluster */
+ for (c = 0; c < GPU_NSUBCELL; c++)
+ {
+ c_abs = sci*GPU_NSUBCELL + c;
+
+ for (i = 0; i < nbl->na_ci; i++)
+ {
+ ind_i = c_abs*nbl->na_ci + i;
+ ai = nbs->a[ind_i];
+ if (ai >= 0)
+ {
+ nri = nlist->nri;
+ nlist->jindex[nri+1] = nlist->jindex[nri];
+ nlist->iinr[nri] = ai;
+ /* With GPUs, energy groups are not supported */
+ nlist->gid[nri] = 0;
+ nlist->shift[nri] = nbl_sci->shift & NBNXN_CI_SHIFT;
+
+ bFEP_i = (gridi->fep[c_abs - gridi->cell0*GPU_NSUBCELL] & (1 << i));
+
+ xi = nbat->x[ind_i*nbat->xstride+XX] + shx;
+ yi = nbat->x[ind_i*nbat->xstride+YY] + shy;
+ zi = nbat->x[ind_i*nbat->xstride+ZZ] + shz;
+
+ if ((nlist->nrj + cj4_ind_end - cj4_ind_start)*NBNXN_GPU_JGROUP_SIZE*nbl->na_cj > nlist->maxnrj)
+ {
+ nlist->maxnrj = over_alloc_small((nlist->nrj + cj4_ind_end - cj4_ind_start)*NBNXN_GPU_JGROUP_SIZE*nbl->na_cj);
+ srenew(nlist->jjnr, nlist->maxnrj);
+ srenew(nlist->excl_fep, nlist->maxnrj);
+ }
+
+ for (cj4_ind = cj4_ind_start; cj4_ind < cj4_ind_end; cj4_ind++)
+ {
+ cj4 = &nbl->cj4[cj4_ind];
+
+ for (gcj = 0; gcj < NBNXN_GPU_JGROUP_SIZE; gcj++)
+ {
+ unsigned int fep_cj;
+
+ if ((cj4->imei[0].imask & (1U << (gcj*GPU_NSUBCELL + c))) == 0)
+ {
+ /* Skip this ci for this cj */
+ continue;
+ }
+
+ cjr = cj4->cj[gcj] - gridj->cell0*GPU_NSUBCELL;
+
+ fep_cj = gridj->fep[cjr];
+
+ if (bFEP_i || fep_cj != 0)
+ {
+ for (j = 0; j < nbl->na_cj; j++)
+ {
+ /* Is this interaction perturbed and not excluded? */
+ ind_j = (gridj->cell0*GPU_NSUBCELL + cjr)*nbl->na_cj + j;
+ aj = nbs->a[ind_j];
+ if (aj >= 0 &&
+ (bFEP_i || (fep_cj & (1 << j))) &&
+ (!bDiagRemoved || ind_j >= ind_i))
+ {
+ nbnxn_excl_t *excl;
+ int excl_pair;
+ unsigned int excl_bit;
+ real dx, dy, dz;
+
+ get_nbl_exclusions_1(nbl, cj4_ind, j>>2, &excl);
+
+ excl_pair = a_mod_wj(j)*nbl->na_ci + i;
+ excl_bit = (1U << (gcj*GPU_NSUBCELL + c));
+
+ dx = nbat->x[ind_j*nbat->xstride+XX] - xi;
+ dy = nbat->x[ind_j*nbat->xstride+YY] - yi;
+ dz = nbat->x[ind_j*nbat->xstride+ZZ] - zi;
+
+ /* The unpruned GPU list has more than 2/3
+ * of the atom pairs beyond rlist. Using
+ * this list will cause a lot of overhead
+ * in the CPU FEP kernels, especially
+ * relative to the fast GPU kernels.
+ * So we prune the FEP list here.
+ */
+ if (dx*dx + dy*dy + dz*dz < rlist_fep2)
+ {
+ if (nlist->nrj - nlist->jindex[nri] >= max_nrj_fep)
+ {
+ fep_list_new_nri_copy(nlist);
+ nri = nlist->nri;
+ }
+
+ /* Add it to the FEP list */
+ nlist->jjnr[nlist->nrj] = aj;
+ nlist->excl_fep[nlist->nrj] = (excl->pair[excl_pair] & excl_bit) ? 1 : 0;
+ nlist->nrj++;
+ }
+
+ /* Exclude it from the normal list.
+ * Note that the charge and LJ parameters have
+ * been set to zero, but we need to avoid 0/0,
+ * as perturbed atoms can be on top of each other.
+ */
+ excl->pair[excl_pair] &= ~excl_bit;
+ }
+ }
+
+ /* Note that we could mask out this pair in imask
+ * if all i- and/or all j-particles are perturbed.
+ * But since the perturbed pairs on the CPU will
+ * take an order of magnitude more time, the GPU
+ * will finish before the CPU and there is no gain.
+ */
+ }
+ }
+ }
+
+ if (nlist->nrj > nlist->jindex[nri])
+ {
+ /* Actually add this new, non-empty, list */
+ nlist->nri++;
+ nlist->jindex[nlist->nri] = nlist->nrj;
+ }
+ }
+ }
+ }
+}
+
+/* Set all atom-pair exclusions from the topology stored in excl
+ * as masks in the pair-list for i-super-cell entry nbl_sci
+ */
+static void set_sci_top_excls(const nbnxn_search_t nbs,
+ nbnxn_pairlist_t *nbl,
+ gmx_bool diagRemoved,
+ int na_c_2log,
+ const nbnxn_sci_t *nbl_sci,
+ const t_blocka *excl)
+{
+ const int *cell;
+ int na_c;
+ int sci;
+ int cj_ind_first, cj_ind_last;
+ int cj_first, cj_last;
+ int ndirect;
+ int i, ai, aj, si, eind, ge, se;
+ int found, cj_ind_0, cj_ind_1, cj_ind_m;
+ int cj_m;
+ gmx_bool Found_si;
+ int si_ind;
+ nbnxn_excl_t *nbl_excl;
+ int inner_i, inner_e, w;
+
+ cell = nbs->cell;
+
+ na_c = nbl->na_ci;
+
+ if (nbl_sci->cj4_ind_end == nbl_sci->cj4_ind_start)
+ {
+ /* Empty list */
+ return;
+ }
+
+ sci = nbl_sci->sci;
+
+ cj_ind_first = nbl_sci->cj4_ind_start*NBNXN_GPU_JGROUP_SIZE;
+ cj_ind_last = nbl->work->cj_ind - 1;
+
+ cj_first = nbl->cj4[nbl_sci->cj4_ind_start].cj[0];
+ cj_last = nbl_cj(nbl, cj_ind_last);
+
+ /* Determine how many contiguous j-clusters we have starting
+ * from the first i-cluster. This number can be used to directly
+ * calculate j-cluster indices for excluded atoms.
+ */
+ ndirect = 0;
+ while (cj_ind_first + ndirect <= cj_ind_last &&
+ nbl_cj(nbl, cj_ind_first+ndirect) == sci*GPU_NSUBCELL + ndirect)
+ {
+ ndirect++;
+ }
+
+ /* Loop over the atoms in the i super-cell */
+ for (i = 0; i < nbl->na_sc; i++)
+ {
+ ai = nbs->a[sci*nbl->na_sc+i];
+ if (ai >= 0)
+ {
+ si = (i>>na_c_2log);
+
+ /* Loop over the topology-based exclusions for this i-atom */
+ for (eind = excl->index[ai]; eind < excl->index[ai+1]; eind++)
+ {
+ aj = excl->a[eind];
+
+ if (aj == ai)
+ {
+ /* The self exclusion are already set, save some time */
+ continue;
+ }
+
+ ge = cell[aj];
+
+ /* Without shifts we only calculate interactions j>i
+ * for one-way pair-lists.
+ */
+ if (diagRemoved && ge <= sci*nbl->na_sc + i)
+ {
+ continue;
+ }
+
+ se = ge>>na_c_2log;
+ /* Could the cluster se be in our list? */
+ if (se >= cj_first && se <= cj_last)
+ {
+ if (se < cj_first + ndirect)
+ {
+ /* We can calculate cj_ind directly from se */
+ found = cj_ind_first + se - cj_first;
+ }
+ else
+ {
+ /* Search for se using bisection */
+ found = -1;
+ cj_ind_0 = cj_ind_first + ndirect;
+ cj_ind_1 = cj_ind_last + 1;
+ while (found == -1 && cj_ind_0 < cj_ind_1)
+ {
+ cj_ind_m = (cj_ind_0 + cj_ind_1)>>1;
+
+ cj_m = nbl_cj(nbl, cj_ind_m);
+
+ if (se == cj_m)
+ {
+ found = cj_ind_m;
+ }
+ else if (se < cj_m)
+ {
+ cj_ind_1 = cj_ind_m;
+ }
+ else
+ {
+ cj_ind_0 = cj_ind_m + 1;
+ }
+ }
+ }
+
+ if (found >= 0)
+ {
+ inner_i = i - si*na_c;
+ inner_e = ge - se*na_c;
+
+ if (nbl_imask0(nbl, found) & (1U << (cj_mod_cj4(found)*GPU_NSUBCELL + si)))
+ {
+ w = (inner_e >> 2);
+
+ get_nbl_exclusions_1(nbl, cj_to_cj4(found), w, &nbl_excl);
+
+ nbl_excl->pair[a_mod_wj(inner_e)*nbl->na_ci+inner_i] &=
+ ~(1U << (cj_mod_cj4(found)*GPU_NSUBCELL + si));
+ }
+ }
+ }
+ }
+ }
+ }
+}
+
+/* Reallocate the simple ci list for at least n entries */
+static void nb_realloc_ci(nbnxn_pairlist_t *nbl, int n)
+{
+ nbl->ci_nalloc = over_alloc_small(n);
+ nbnxn_realloc_void((void **)&nbl->ci,
+ nbl->nci*sizeof(*nbl->ci),
+ nbl->ci_nalloc*sizeof(*nbl->ci),
+ nbl->alloc, nbl->free);
+}
+
+/* Reallocate the super-cell sci list for at least n entries */
+static void nb_realloc_sci(nbnxn_pairlist_t *nbl, int n)
+{
+ nbl->sci_nalloc = over_alloc_small(n);
+ nbnxn_realloc_void((void **)&nbl->sci,
+ nbl->nsci*sizeof(*nbl->sci),
+ nbl->sci_nalloc*sizeof(*nbl->sci),
+ nbl->alloc, nbl->free);
+}
+
+/* Make a new ci entry at index nbl->nci */
+static void new_ci_entry(nbnxn_pairlist_t *nbl, int ci, int shift, int flags)
+{
+ if (nbl->nci + 1 > nbl->ci_nalloc)
+ {
+ nb_realloc_ci(nbl, nbl->nci+1);
+ }
+ nbl->ci[nbl->nci].ci = ci;
+ nbl->ci[nbl->nci].shift = shift;
+ /* Store the interaction flags along with the shift */
+ nbl->ci[nbl->nci].shift |= flags;
+ nbl->ci[nbl->nci].cj_ind_start = nbl->ncj;
+ nbl->ci[nbl->nci].cj_ind_end = nbl->ncj;
+}
+
+/* Make a new sci entry at index nbl->nsci */
+static void new_sci_entry(nbnxn_pairlist_t *nbl, int sci, int shift)
+{
+ if (nbl->nsci + 1 > nbl->sci_nalloc)
+ {
+ nb_realloc_sci(nbl, nbl->nsci+1);
+ }
+ nbl->sci[nbl->nsci].sci = sci;
+ nbl->sci[nbl->nsci].shift = shift;
+ nbl->sci[nbl->nsci].cj4_ind_start = nbl->ncj4;
+ nbl->sci[nbl->nsci].cj4_ind_end = nbl->ncj4;
+}
+
+/* Sort the simple j-list cj on exclusions.
+ * Entries with exclusions will all be sorted to the beginning of the list.
+ */
+static void sort_cj_excl(nbnxn_cj_t *cj, int ncj,
+ nbnxn_list_work_t *work)
+{
+ int jnew, j;
+
+ if (ncj > work->cj_nalloc)
+ {
+ work->cj_nalloc = over_alloc_large(ncj);
+ srenew(work->cj, work->cj_nalloc);
+ }
+
+ /* Make a list of the j-cells involving exclusions */
+ jnew = 0;
+ for (j = 0; j < ncj; j++)
+ {
+ if (cj[j].excl != NBNXN_INTERACTION_MASK_ALL)
+ {
+ work->cj[jnew++] = cj[j];
+ }
+ }
+ /* Check if there are exclusions at all or not just the first entry */
+ if (!((jnew == 0) ||
+ (jnew == 1 && cj[0].excl != NBNXN_INTERACTION_MASK_ALL)))
+ {
+ for (j = 0; j < ncj; j++)
+ {
+ if (cj[j].excl == NBNXN_INTERACTION_MASK_ALL)
+ {
+ work->cj[jnew++] = cj[j];
+ }
+ }
+ for (j = 0; j < ncj; j++)
+ {
+ cj[j] = work->cj[j];
+ }
+ }
+}
+
+/* Close this simple list i entry */
+static void close_ci_entry_simple(nbnxn_pairlist_t *nbl)
+{
+ int jlen;
+
+ /* All content of the new ci entry have already been filled correctly,
+ * we only need to increase the count here (for non empty lists).
+ */
+ jlen = nbl->ci[nbl->nci].cj_ind_end - nbl->ci[nbl->nci].cj_ind_start;
+ if (jlen > 0)
+ {
+ sort_cj_excl(nbl->cj+nbl->ci[nbl->nci].cj_ind_start, jlen, nbl->work);
+
+ /* The counts below are used for non-bonded pair/flop counts
+ * and should therefore match the available kernel setups.
+ */
+ if (!(nbl->ci[nbl->nci].shift & NBNXN_CI_DO_COUL(0)))
+ {
+ nbl->work->ncj_noq += jlen;
+ }
+ else if ((nbl->ci[nbl->nci].shift & NBNXN_CI_HALF_LJ(0)) ||
+ !(nbl->ci[nbl->nci].shift & NBNXN_CI_DO_LJ(0)))
+ {
+ nbl->work->ncj_hlj += jlen;
+ }
+
+ nbl->nci++;
+ }
+}
+
+/* Split sci entry for load balancing on the GPU.
+ * Splitting ensures we have enough lists to fully utilize the whole GPU.
+ * With progBal we generate progressively smaller lists, which improves
+ * load balancing. As we only know the current count on our own thread,
+ * we will need to estimate the current total amount of i-entries.
+ * As the lists get concatenated later, this estimate depends
+ * both on nthread and our own thread index.
+ */
+static void split_sci_entry(nbnxn_pairlist_t *nbl,
+ int nsp_max_av, gmx_bool progBal, int nc_bal,
+ int thread, int nthread)
+{
+ int nsci_est;
+ int nsp_max;
+ int cj4_start, cj4_end, j4len, cj4;
+ int sci;
+ int nsp, nsp_sci, nsp_cj4, nsp_cj4_e, nsp_cj4_p;
+ int p;
+
+ if (progBal)
+ {
+ /* Estimate the total numbers of ci's of the nblist combined
+ * over all threads using the target number of ci's.
+ */
+ nsci_est = nc_bal*thread/nthread + nbl->nsci;
+
+ /* The first ci blocks should be larger, to avoid overhead.
+ * The last ci blocks should be smaller, to improve load balancing.
+ */
+ nsp_max = max(1,
+ nsp_max_av*nc_bal*3/(2*(nsci_est - 1 + nc_bal)));
+ }
+ else
+ {
+ nsp_max = nsp_max_av;
+ }
+
+ cj4_start = nbl->sci[nbl->nsci-1].cj4_ind_start;
+ cj4_end = nbl->sci[nbl->nsci-1].cj4_ind_end;
+ j4len = cj4_end - cj4_start;
+
+ if (j4len > 1 && j4len*GPU_NSUBCELL*NBNXN_GPU_JGROUP_SIZE > nsp_max)
+ {
+ /* Remove the last ci entry and process the cj4's again */
+ nbl->nsci -= 1;
+
+ sci = nbl->nsci;
+ nsp = 0;
+ nsp_sci = 0;
+ nsp_cj4_e = 0;
+ nsp_cj4 = 0;
+ for (cj4 = cj4_start; cj4 < cj4_end; cj4++)
+ {
+ nsp_cj4_p = nsp_cj4;
+ /* Count the number of cluster pairs in this cj4 group */
+ nsp_cj4 = 0;
+ for (p = 0; p < GPU_NSUBCELL*NBNXN_GPU_JGROUP_SIZE; p++)
+ {
+ nsp_cj4 += (nbl->cj4[cj4].imei[0].imask >> p) & 1;
+ }
+
++ /* Check if we should split at this cj4 to get a list of size nsp */
++ if (nsp > 0 && nsp + nsp_cj4 > nsp_max)
+ {
+ /* Split the list at cj4 */
+ nbl->sci[sci].cj4_ind_end = cj4;
+ /* Create a new sci entry */
+ sci++;
+ nbl->nsci++;
+ if (nbl->nsci+1 > nbl->sci_nalloc)
+ {
+ nb_realloc_sci(nbl, nbl->nsci+1);
+ }
+ nbl->sci[sci].sci = nbl->sci[nbl->nsci-1].sci;
+ nbl->sci[sci].shift = nbl->sci[nbl->nsci-1].shift;
+ nbl->sci[sci].cj4_ind_start = cj4;
+ nsp_sci = nsp;
+ nsp_cj4_e = nsp_cj4_p;
+ nsp = 0;
+ }
+ nsp += nsp_cj4;
+ }
+
+ /* Put the remaining cj4's in the last sci entry */
+ nbl->sci[sci].cj4_ind_end = cj4_end;
+
+ /* Possibly balance out the last two sci's
+ * by moving the last cj4 of the second last sci.
+ */
+ if (nsp_sci - nsp_cj4_e >= nsp + nsp_cj4_e)
+ {
+ nbl->sci[sci-1].cj4_ind_end--;
+ nbl->sci[sci].cj4_ind_start--;
+ }
+
+ nbl->nsci++;
+ }
+}
+
+/* Clost this super/sub list i entry */
+static void close_ci_entry_supersub(nbnxn_pairlist_t *nbl,
+ int nsp_max_av,
+ gmx_bool progBal, int nc_bal,
+ int thread, int nthread)
+{
+ int j4len, tlen;
+ int nb, b;
+
+ /* All content of the new ci entry have already been filled correctly,
+ * we only need to increase the count here (for non empty lists).
+ */
+ j4len = nbl->sci[nbl->nsci].cj4_ind_end - nbl->sci[nbl->nsci].cj4_ind_start;
+ if (j4len > 0)
+ {
+ /* We can only have complete blocks of 4 j-entries in a list,
+ * so round the count up before closing.
+ */
+ nbl->ncj4 = ((nbl->work->cj_ind + NBNXN_GPU_JGROUP_SIZE - 1) >> NBNXN_GPU_JGROUP_SIZE_2LOG);
+ nbl->work->cj_ind = nbl->ncj4*NBNXN_GPU_JGROUP_SIZE;
+
+ nbl->nsci++;
+
+ if (nsp_max_av > 0)
+ {
+ /* Measure the size of the new entry and potentially split it */
+ split_sci_entry(nbl, nsp_max_av, progBal, nc_bal, thread, nthread);
+ }
+ }
+}
+
+/* Syncs the working array before adding another grid pair to the list */
+static void sync_work(nbnxn_pairlist_t *nbl)
+{
+ if (!nbl->bSimple)
+ {
+ nbl->work->cj_ind = nbl->ncj4*NBNXN_GPU_JGROUP_SIZE;
+ nbl->work->cj4_init = nbl->ncj4;
+ }
+}
+
+/* Clears an nbnxn_pairlist_t data structure */
+static void clear_pairlist(nbnxn_pairlist_t *nbl)
+{
+ nbl->nci = 0;
+ nbl->nsci = 0;
+ nbl->ncj = 0;
+ nbl->ncj4 = 0;
+ nbl->nci_tot = 0;
+ nbl->nexcl = 1;
+
+ nbl->work->ncj_noq = 0;
+ nbl->work->ncj_hlj = 0;
+}
+
+/* Clears a group scheme pair list */
+static void clear_pairlist_fep(t_nblist *nl)
+{
+ nl->nri = 0;
+ nl->nrj = 0;
+ if (nl->jindex == NULL)
+ {
+ snew(nl->jindex, 1);
+ }
+ nl->jindex[0] = 0;
+}
+
+/* Sets a simple list i-cell bounding box, including PBC shift */
+static gmx_inline void set_icell_bb_simple(const nbnxn_bb_t *bb, int ci,
+ real shx, real shy, real shz,
+ nbnxn_bb_t *bb_ci)
+{
+ bb_ci->lower[BB_X] = bb[ci].lower[BB_X] + shx;
+ bb_ci->lower[BB_Y] = bb[ci].lower[BB_Y] + shy;
+ bb_ci->lower[BB_Z] = bb[ci].lower[BB_Z] + shz;
+ bb_ci->upper[BB_X] = bb[ci].upper[BB_X] + shx;
+ bb_ci->upper[BB_Y] = bb[ci].upper[BB_Y] + shy;
+ bb_ci->upper[BB_Z] = bb[ci].upper[BB_Z] + shz;
+}
+
+#ifdef NBNXN_BBXXXX
+/* Sets a super-cell and sub cell bounding boxes, including PBC shift */
+static void set_icell_bbxxxx_supersub(const float *bb, int ci,
+ real shx, real shy, real shz,
+ float *bb_ci)
+{
+ int ia, m, i;
+
+ ia = ci*(GPU_NSUBCELL>>STRIDE_PBB_2LOG)*NNBSBB_XXXX;
+ for (m = 0; m < (GPU_NSUBCELL>>STRIDE_PBB_2LOG)*NNBSBB_XXXX; m += NNBSBB_XXXX)
+ {
+ for (i = 0; i < STRIDE_PBB; i++)
+ {
+ bb_ci[m+0*STRIDE_PBB+i] = bb[ia+m+0*STRIDE_PBB+i] + shx;
+ bb_ci[m+1*STRIDE_PBB+i] = bb[ia+m+1*STRIDE_PBB+i] + shy;
+ bb_ci[m+2*STRIDE_PBB+i] = bb[ia+m+2*STRIDE_PBB+i] + shz;
+ bb_ci[m+3*STRIDE_PBB+i] = bb[ia+m+3*STRIDE_PBB+i] + shx;
+ bb_ci[m+4*STRIDE_PBB+i] = bb[ia+m+4*STRIDE_PBB+i] + shy;
+ bb_ci[m+5*STRIDE_PBB+i] = bb[ia+m+5*STRIDE_PBB+i] + shz;
+ }
+ }
+}
+#endif
+
+/* Sets a super-cell and sub cell bounding boxes, including PBC shift */
+static void set_icell_bb_supersub(const nbnxn_bb_t *bb, int ci,
+ real shx, real shy, real shz,
+ nbnxn_bb_t *bb_ci)
+{
+ int i;
+
+ for (i = 0; i < GPU_NSUBCELL; i++)
+ {
+ set_icell_bb_simple(bb, ci*GPU_NSUBCELL+i,
+ shx, shy, shz,
+ &bb_ci[i]);
+ }
+}
+
+/* Copies PBC shifted i-cell atom coordinates x,y,z to working array */
+static void icell_set_x_simple(int ci,
+ real shx, real shy, real shz,
+ int gmx_unused na_c,
+ int stride, const real *x,
+ nbnxn_list_work_t *work)
+{
+ int ia, i;
+
+ ia = ci*NBNXN_CPU_CLUSTER_I_SIZE;
+
+ for (i = 0; i < NBNXN_CPU_CLUSTER_I_SIZE; i++)
+ {
+ work->x_ci[i*STRIDE_XYZ+XX] = x[(ia+i)*stride+XX] + shx;
+ work->x_ci[i*STRIDE_XYZ+YY] = x[(ia+i)*stride+YY] + shy;
+ work->x_ci[i*STRIDE_XYZ+ZZ] = x[(ia+i)*stride+ZZ] + shz;
+ }
+}
+
+/* Copies PBC shifted super-cell atom coordinates x,y,z to working array */
+static void icell_set_x_supersub(int ci,
+ real shx, real shy, real shz,
+ int na_c,
+ int stride, const real *x,
+ nbnxn_list_work_t *work)
+{
+ int ia, i;
+ real *x_ci;
+
+ x_ci = work->x_ci;
+
+ ia = ci*GPU_NSUBCELL*na_c;
+ for (i = 0; i < GPU_NSUBCELL*na_c; i++)
+ {
+ x_ci[i*DIM + XX] = x[(ia+i)*stride + XX] + shx;
+ x_ci[i*DIM + YY] = x[(ia+i)*stride + YY] + shy;
+ x_ci[i*DIM + ZZ] = x[(ia+i)*stride + ZZ] + shz;
+ }
+}
+
+#ifdef NBNXN_SEARCH_BB_SIMD4
+/* Copies PBC shifted super-cell packed atom coordinates to working array */
+static void icell_set_x_supersub_simd4(int ci,
+ real shx, real shy, real shz,
+ int na_c,
+ int stride, const real *x,
+ nbnxn_list_work_t *work)
+{
+ int si, io, ia, i, j;
+ real *x_ci;
+
+ x_ci = work->x_ci;
+
+ for (si = 0; si < GPU_NSUBCELL; si++)
+ {
+ for (i = 0; i < na_c; i += STRIDE_PBB)
+ {
+ io = si*na_c + i;
+ ia = ci*GPU_NSUBCELL*na_c + io;
+ for (j = 0; j < STRIDE_PBB; j++)
+ {
+ x_ci[io*DIM + j + XX*STRIDE_PBB] = x[(ia+j)*stride+XX] + shx;
+ x_ci[io*DIM + j + YY*STRIDE_PBB] = x[(ia+j)*stride+YY] + shy;
+ x_ci[io*DIM + j + ZZ*STRIDE_PBB] = x[(ia+j)*stride+ZZ] + shz;
+ }
+ }
+ }
+}
+#endif
+
+static real minimum_subgrid_size_xy(const nbnxn_grid_t *grid)
+{
+ if (grid->bSimple)
+ {
+ return min(grid->sx, grid->sy);
+ }
+ else
+ {
+ return min(grid->sx/GPU_NSUBCELL_X, grid->sy/GPU_NSUBCELL_Y);
+ }
+}
+
+static real effective_buffer_1x1_vs_MxN(const nbnxn_grid_t *gridi,
+ const nbnxn_grid_t *gridj)
+{
+ const real eff_1x1_buffer_fac_overest = 0.1;
+
+ /* Determine an atom-pair list cut-off buffer size for atom pairs,
+ * to be added to rlist (including buffer) used for MxN.
+ * This is for converting an MxN list to a 1x1 list. This means we can't
+ * use the normal buffer estimate, as we have an MxN list in which
+ * some atom pairs beyond rlist are missing. We want to capture
+ * the beneficial effect of buffering by extra pairs just outside rlist,
+ * while removing the useless pairs that are further away from rlist.
+ * (Also the buffer could have been set manually not using the estimate.)
+ * This buffer size is an overestimate.
+ * We add 10% of the smallest grid sub-cell dimensions.
+ * Note that the z-size differs per cell and we don't use this,
+ * so we overestimate.
+ * With PME, the 10% value gives a buffer that is somewhat larger
+ * than the effective buffer with a tolerance of 0.005 kJ/mol/ps.
+ * Smaller tolerances or using RF lead to a smaller effective buffer,
+ * so 10% gives a safe overestimate.
+ */
+ return eff_1x1_buffer_fac_overest*(minimum_subgrid_size_xy(gridi) +
+ minimum_subgrid_size_xy(gridj));
+}
+
+/* Clusters at the cut-off only increase rlist by 60% of their size */
+static real nbnxn_rlist_inc_outside_fac = 0.6;
+
+/* Due to the cluster size the effective pair-list is longer than
+ * that of a simple atom pair-list. This function gives the extra distance.
+ */
+real nbnxn_get_rlist_effective_inc(int cluster_size_j, real atom_density)
+{
+ int cluster_size_i;
+ real vol_inc_i, vol_inc_j;
+
+ /* We should get this from the setup, but currently it's the same for
+ * all setups, including GPUs.
+ */
+ cluster_size_i = NBNXN_CPU_CLUSTER_I_SIZE;
+
+ vol_inc_i = (cluster_size_i - 1)/atom_density;
+ vol_inc_j = (cluster_size_j - 1)/atom_density;
+
+ return nbnxn_rlist_inc_outside_fac*pow(vol_inc_i + vol_inc_j, 1.0/3.0);
+}
+
+/* Estimates the interaction volume^2 for non-local interactions */
+static real nonlocal_vol2(const gmx_domdec_zones_t *zones, rvec ls, real r)
+{
+ int z, d;
+ real cl, ca, za;
+ real vold_est;
+ real vol2_est_tot;
+
+ vol2_est_tot = 0;
+
+ /* Here we simply add up the volumes of 1, 2 or 3 1D decomposition
+ * not home interaction volume^2. As these volumes are not additive,
+ * this is an overestimate, but it would only be significant in the limit
+ * of small cells, where we anyhow need to split the lists into
+ * as small parts as possible.
+ */
+
+ for (z = 0; z < zones->n; z++)
+ {
+ if (zones->shift[z][XX] + zones->shift[z][YY] + zones->shift[z][ZZ] == 1)
+ {
+ cl = 0;
+ ca = 1;
+ za = 1;
+ for (d = 0; d < DIM; d++)
+ {
+ if (zones->shift[z][d] == 0)
+ {
+ cl += 0.5*ls[d];
+ ca *= ls[d];
+ za *= zones->size[z].x1[d] - zones->size[z].x0[d];
+ }
+ }
+
+ /* 4 octants of a sphere */
+ vold_est = 0.25*M_PI*r*r*r*r;
+ /* 4 quarter pie slices on the edges */
+ vold_est += 4*cl*M_PI/6.0*r*r*r;
+ /* One rectangular volume on a face */
+ vold_est += ca*0.5*r*r;
+
+ vol2_est_tot += vold_est*za;
+ }
+ }
+
+ return vol2_est_tot;
+}
+
+/* Estimates the average size of a full j-list for super/sub setup */
+static int get_nsubpair_max(const nbnxn_search_t nbs,
+ int iloc,
+ real rlist,
+ int min_ci_balanced)
+{
+ const nbnxn_grid_t *grid;
+ rvec ls;
+ real xy_diag2, r_eff_sup, vol_est, nsp_est, nsp_est_nl;
+ int nsubpair_max;
+
+ grid = &nbs->grid[0];
+
+ ls[XX] = (grid->c1[XX] - grid->c0[XX])/(grid->ncx*GPU_NSUBCELL_X);
+ ls[YY] = (grid->c1[YY] - grid->c0[YY])/(grid->ncy*GPU_NSUBCELL_Y);
+ ls[ZZ] = (grid->c1[ZZ] - grid->c0[ZZ])*grid->ncx*grid->ncy/(grid->nc*GPU_NSUBCELL_Z);
+
+ /* The average squared length of the diagonal of a sub cell */
+ xy_diag2 = ls[XX]*ls[XX] + ls[YY]*ls[YY] + ls[ZZ]*ls[ZZ];
+
+ /* The formulas below are a heuristic estimate of the average nsj per si*/
+ r_eff_sup = rlist + nbnxn_rlist_inc_outside_fac*sqr((grid->na_c - 1.0)/grid->na_c)*sqrt(xy_diag2/3);
+
+ if (!nbs->DomDec || nbs->zones->n == 1)
+ {
+ nsp_est_nl = 0;
+ }
+ else
+ {
+ nsp_est_nl =
+ sqr(grid->atom_density/grid->na_c)*
+ nonlocal_vol2(nbs->zones, ls, r_eff_sup);
+ }
+
+ if (LOCAL_I(iloc))
+ {
+ /* Sub-cell interacts with itself */
+ vol_est = ls[XX]*ls[YY]*ls[ZZ];
+ /* 6/2 rectangular volume on the faces */
+ vol_est += (ls[XX]*ls[YY] + ls[XX]*ls[ZZ] + ls[YY]*ls[ZZ])*r_eff_sup;
+ /* 12/2 quarter pie slices on the edges */
+ vol_est += 2*(ls[XX] + ls[YY] + ls[ZZ])*0.25*M_PI*sqr(r_eff_sup);
+ /* 4 octants of a sphere */
+ vol_est += 0.5*4.0/3.0*M_PI*pow(r_eff_sup, 3);
+
+ nsp_est = grid->nsubc_tot*vol_est*grid->atom_density/grid->na_c;
+
+ /* Subtract the non-local pair count */
+ nsp_est -= nsp_est_nl;
+
+ if (debug)
+ {
+ fprintf(debug, "nsp_est local %5.1f non-local %5.1f\n",
+ nsp_est, nsp_est_nl);
+ }
+ }
+ else
+ {
+ nsp_est = nsp_est_nl;
+ }
+
+ if (min_ci_balanced <= 0 || grid->nc >= min_ci_balanced || grid->nc == 0)
+ {
+ /* We don't need to worry */
+ nsubpair_max = -1;
+ }
+ else
+ {
+ /* Thus the (average) maximum j-list size should be as follows */
+ nsubpair_max = max(1, (int)(nsp_est/min_ci_balanced+0.5));
+
+ /* Since the target value is a maximum (this avoids high outliers,
+ * which lead to load imbalance), not average, we add half the
+ * number of pairs in a cj4 block to get the average about right.
+ */
+ nsubpair_max += GPU_NSUBCELL*NBNXN_GPU_JGROUP_SIZE/2;
+ }
+
+ if (debug)
+ {
+ fprintf(debug, "nbl nsp estimate %.1f, nsubpair_max %d\n",
+ nsp_est, nsubpair_max);
+ }
+
+ return nsubpair_max;
+}
+
+/* Debug list print function */
+static void print_nblist_ci_cj(FILE *fp, const nbnxn_pairlist_t *nbl)
+{
+ int i, j;
+
+ for (i = 0; i < nbl->nci; i++)
+ {
+ fprintf(fp, "ci %4d shift %2d ncj %3d\n",
+ nbl->ci[i].ci, nbl->ci[i].shift,
+ nbl->ci[i].cj_ind_end - nbl->ci[i].cj_ind_start);
+
+ for (j = nbl->ci[i].cj_ind_start; j < nbl->ci[i].cj_ind_end; j++)
+ {
+ fprintf(fp, " cj %5d imask %x\n",
+ nbl->cj[j].cj,
+ nbl->cj[j].excl);
+ }
+ }
+}
+
+/* Debug list print function */
+static void print_nblist_sci_cj(FILE *fp, const nbnxn_pairlist_t *nbl)
+{
+ int i, j4, j, ncp, si;
+
+ for (i = 0; i < nbl->nsci; i++)
+ {
+ fprintf(fp, "ci %4d shift %2d ncj4 %2d\n",
+ nbl->sci[i].sci, nbl->sci[i].shift,
+ nbl->sci[i].cj4_ind_end - nbl->sci[i].cj4_ind_start);
+
+ ncp = 0;
+ for (j4 = nbl->sci[i].cj4_ind_start; j4 < nbl->sci[i].cj4_ind_end; j4++)
+ {
+ for (j = 0; j < NBNXN_GPU_JGROUP_SIZE; j++)
+ {
+ fprintf(fp, " sj %5d imask %x\n",
+ nbl->cj4[j4].cj[j],
+ nbl->cj4[j4].imei[0].imask);
+ for (si = 0; si < GPU_NSUBCELL; si++)
+ {
+ if (nbl->cj4[j4].imei[0].imask & (1U << (j*GPU_NSUBCELL + si)))
+ {
+ ncp++;
+ }
+ }
+ }
+ }
+ fprintf(fp, "ci %4d shift %2d ncj4 %2d ncp %3d\n",
+ nbl->sci[i].sci, nbl->sci[i].shift,
+ nbl->sci[i].cj4_ind_end - nbl->sci[i].cj4_ind_start,
+ ncp);
+ }
+}
+
+/* Combine pair lists *nbl generated on multiple threads nblc */
+static void combine_nblists(int nnbl, nbnxn_pairlist_t **nbl,
+ nbnxn_pairlist_t *nblc)
+{
+ int nsci, ncj4, nexcl;
+ int n, i;
+ int nthreads gmx_unused;
+
+ if (nblc->bSimple)
+ {
+ gmx_incons("combine_nblists does not support simple lists");
+ }
+
+ nsci = nblc->nsci;
+ ncj4 = nblc->ncj4;
+ nexcl = nblc->nexcl;
+ for (i = 0; i < nnbl; i++)
+ {
+ nsci += nbl[i]->nsci;
+ ncj4 += nbl[i]->ncj4;
+ nexcl += nbl[i]->nexcl;
+ }
+
+ if (nsci > nblc->sci_nalloc)
+ {
+ nb_realloc_sci(nblc, nsci);
+ }
+ if (ncj4 > nblc->cj4_nalloc)
+ {
+ nblc->cj4_nalloc = over_alloc_small(ncj4);
+ nbnxn_realloc_void((void **)&nblc->cj4,
+ nblc->ncj4*sizeof(*nblc->cj4),
+ nblc->cj4_nalloc*sizeof(*nblc->cj4),
+ nblc->alloc, nblc->free);
+ }
+ if (nexcl > nblc->excl_nalloc)
+ {
+ nblc->excl_nalloc = over_alloc_small(nexcl);
+ nbnxn_realloc_void((void **)&nblc->excl,
+ nblc->nexcl*sizeof(*nblc->excl),
+ nblc->excl_nalloc*sizeof(*nblc->excl),
+ nblc->alloc, nblc->free);
+ }
+
+ /* Each thread should copy its own data to the combined arrays,
+ * as otherwise data will go back and forth between different caches.
+ */
+ nthreads = gmx_omp_nthreads_get(emntPairsearch);
+#pragma omp parallel for num_threads(nthreads) schedule(static)
+ for (n = 0; n < nnbl; n++)
+ {
+ int sci_offset;
+ int cj4_offset;
+ int ci_offset;
+ int excl_offset;
+ int i, j4;
+ const nbnxn_pairlist_t *nbli;
+
+ /* Determine the offset in the combined data for our thread */
+ sci_offset = nblc->nsci;
+ cj4_offset = nblc->ncj4;
+ ci_offset = nblc->nci_tot;
+ excl_offset = nblc->nexcl;
+
+ for (i = 0; i < n; i++)
+ {
+ sci_offset += nbl[i]->nsci;
+ cj4_offset += nbl[i]->ncj4;
+ ci_offset += nbl[i]->nci_tot;
+ excl_offset += nbl[i]->nexcl;
+ }
+
+ nbli = nbl[n];
+
+ for (i = 0; i < nbli->nsci; i++)
+ {
+ nblc->sci[sci_offset+i] = nbli->sci[i];
+ nblc->sci[sci_offset+i].cj4_ind_start += cj4_offset;
+ nblc->sci[sci_offset+i].cj4_ind_end += cj4_offset;
+ }
+
+ for (j4 = 0; j4 < nbli->ncj4; j4++)
+ {
+ nblc->cj4[cj4_offset+j4] = nbli->cj4[j4];
+ nblc->cj4[cj4_offset+j4].imei[0].excl_ind += excl_offset;
+ nblc->cj4[cj4_offset+j4].imei[1].excl_ind += excl_offset;
+ }
+
+ for (j4 = 0; j4 < nbli->nexcl; j4++)
+ {
+ nblc->excl[excl_offset+j4] = nbli->excl[j4];
+ }
+ }
+
+ for (n = 0; n < nnbl; n++)
+ {
+ nblc->nsci += nbl[n]->nsci;
+ nblc->ncj4 += nbl[n]->ncj4;
+ nblc->nci_tot += nbl[n]->nci_tot;
+ nblc->nexcl += nbl[n]->nexcl;
+ }
+}
+
+static void balance_fep_lists(const nbnxn_search_t nbs,
+ nbnxn_pairlist_set_t *nbl_lists)
+{
+ int nnbl, th;
+ int nri_tot, nrj_tot, nrj_target;
+ int th_dest;
+ t_nblist *nbld;
+
+ nnbl = nbl_lists->nnbl;
+
+ if (nnbl == 1)
+ {
+ /* Nothing to balance */
+ return;
+ }
+
+ /* Count the total i-lists and pairs */
+ nri_tot = 0;
+ nrj_tot = 0;
+ for (th = 0; th < nnbl; th++)
+ {
+ nri_tot += nbl_lists->nbl_fep[th]->nri;
+ nrj_tot += nbl_lists->nbl_fep[th]->nrj;
+ }
+
+ nrj_target = (nrj_tot + nnbl - 1)/nnbl;
+
+ assert(gmx_omp_nthreads_get(emntNonbonded) == nnbl);
+
+#pragma omp parallel for schedule(static) num_threads(nnbl)
+ for (th = 0; th < nnbl; th++)
+ {
+ t_nblist *nbl;
+
+ nbl = nbs->work[th].nbl_fep;
+
+ /* Note that here we allocate for the total size, instead of
+ * a per-thread esimate (which is hard to obtain).
+ */
+ if (nri_tot > nbl->maxnri)
+ {
+ nbl->maxnri = over_alloc_large(nri_tot);
+ reallocate_nblist(nbl);
+ }
+ if (nri_tot > nbl->maxnri || nrj_tot > nbl->maxnrj)
+ {
+ nbl->maxnrj = over_alloc_small(nrj_tot);
+ srenew(nbl->jjnr, nbl->maxnrj);
+ srenew(nbl->excl_fep, nbl->maxnrj);
+ }
+
+ clear_pairlist_fep(nbl);
+ }
+
+ /* Loop over the source lists and assign and copy i-entries */
+ th_dest = 0;
+ nbld = nbs->work[th_dest].nbl_fep;
+ for (th = 0; th < nnbl; th++)
+ {
+ t_nblist *nbls;
+ int i, j;
+
+ nbls = nbl_lists->nbl_fep[th];
+
+ for (i = 0; i < nbls->nri; i++)
+ {
+ int nrj;
+
+ /* The number of pairs in this i-entry */
+ nrj = nbls->jindex[i+1] - nbls->jindex[i];
+
+ /* Decide if list th_dest is too large and we should procede
+ * to the next destination list.
+ */
+ if (th_dest+1 < nnbl && nbld->nrj > 0 &&
+ nbld->nrj + nrj - nrj_target > nrj_target - nbld->nrj)
+ {
+ th_dest++;
+ nbld = nbs->work[th_dest].nbl_fep;
+ }
+
+ nbld->iinr[nbld->nri] = nbls->iinr[i];
+ nbld->gid[nbld->nri] = nbls->gid[i];
+ nbld->shift[nbld->nri] = nbls->shift[i];
+
+ for (j = nbls->jindex[i]; j < nbls->jindex[i+1]; j++)
+ {
+ nbld->jjnr[nbld->nrj] = nbls->jjnr[j];
+ nbld->excl_fep[nbld->nrj] = nbls->excl_fep[j];
+ nbld->nrj++;
+ }
+ nbld->nri++;
+ nbld->jindex[nbld->nri] = nbld->nrj;
+ }
+ }
+
+ /* Swap the list pointers */
+ for (th = 0; th < nnbl; th++)
+ {
+ t_nblist *nbl_tmp;
+
+ nbl_tmp = nbl_lists->nbl_fep[th];
+ nbl_lists->nbl_fep[th] = nbs->work[th].nbl_fep;
+ nbs->work[th].nbl_fep = nbl_tmp;
+
+ if (debug)
+ {
+ fprintf(debug, "nbl_fep[%d] nri %4d nrj %4d\n",
+ th,
+ nbl_lists->nbl_fep[th]->nri,
+ nbl_lists->nbl_fep[th]->nrj);
+ }
+ }
+}
+
+/* Returns the next ci to be processes by our thread */
+static gmx_bool next_ci(const nbnxn_grid_t *grid,
+ int conv,
+ int nth, int ci_block,
+ int *ci_x, int *ci_y,
+ int *ci_b, int *ci)
+{
+ (*ci_b)++;
+ (*ci)++;
+
+ if (*ci_b == ci_block)
+ {
+ /* Jump to the next block assigned to this task */
+ *ci += (nth - 1)*ci_block;
+ *ci_b = 0;
+ }
+
+ if (*ci >= grid->nc*conv)
+ {
+ return FALSE;
+ }
+
+ while (*ci >= grid->cxy_ind[*ci_x*grid->ncy + *ci_y + 1]*conv)
+ {
+ *ci_y += 1;
+ if (*ci_y == grid->ncy)
+ {
+ *ci_x += 1;
+ *ci_y = 0;
+ }
+ }
+
+ return TRUE;
+}
+
+/* Returns the distance^2 for which we put cell pairs in the list
+ * without checking atom pair distances. This is usually < rlist^2.
+ */
+static float boundingbox_only_distance2(const nbnxn_grid_t *gridi,
+ const nbnxn_grid_t *gridj,
+ real rlist,
+ gmx_bool simple)
+{
+ /* If the distance between two sub-cell bounding boxes is less
+ * than this distance, do not check the distance between
+ * all particle pairs in the sub-cell, since then it is likely
+ * that the box pair has atom pairs within the cut-off.
+ * We use the nblist cut-off minus 0.5 times the average x/y diagonal
+ * spacing of the sub-cells. Around 40% of the checked pairs are pruned.
+ * Using more than 0.5 gains at most 0.5%.
+ * If forces are calculated more than twice, the performance gain
+ * in the force calculation outweighs the cost of checking.
+ * Note that with subcell lists, the atom-pair distance check
+ * is only performed when only 1 out of 8 sub-cells in within range,
+ * this is because the GPU is much faster than the cpu.
+ */
+ real bbx, bby;
+ real rbb2;
+
+ bbx = 0.5*(gridi->sx + gridj->sx);
+ bby = 0.5*(gridi->sy + gridj->sy);
+ if (!simple)
+ {
+ bbx /= GPU_NSUBCELL_X;
+ bby /= GPU_NSUBCELL_Y;
+ }
+
+ rbb2 = sqr(max(0, rlist - 0.5*sqrt(bbx*bbx + bby*bby)));
+
+#ifndef GMX_DOUBLE
+ return rbb2;
+#else
+ return (float)((1+GMX_FLOAT_EPS)*rbb2);
+#endif
+}
+
+static int get_ci_block_size(const nbnxn_grid_t *gridi,
+ gmx_bool bDomDec, int nth)
+{
+ const int ci_block_enum = 5;
+ const int ci_block_denom = 11;
+ const int ci_block_min_atoms = 16;
+ int ci_block;
+
+ /* Here we decide how to distribute the blocks over the threads.
+ * We use prime numbers to try to avoid that the grid size becomes
+ * a multiple of the number of threads, which would lead to some
+ * threads getting "inner" pairs and others getting boundary pairs,
+ * which in turns will lead to load imbalance between threads.
+ * Set the block size as 5/11/ntask times the average number of cells
+ * in a y,z slab. This should ensure a quite uniform distribution
+ * of the grid parts of the different thread along all three grid
+ * zone boundaries with 3D domain decomposition. At the same time
+ * the blocks will not become too small.
+ */
+ ci_block = (gridi->nc*ci_block_enum)/(ci_block_denom*gridi->ncx*nth);
+
+ /* Ensure the blocks are not too small: avoids cache invalidation */
+ if (ci_block*gridi->na_sc < ci_block_min_atoms)
+ {
+ ci_block = (ci_block_min_atoms + gridi->na_sc - 1)/gridi->na_sc;
+ }
+
+ /* Without domain decomposition
+ * or with less than 3 blocks per task, divide in nth blocks.
+ */
+ if (!bDomDec || ci_block*3*nth > gridi->nc)
+ {
+ ci_block = (gridi->nc + nth - 1)/nth;
+ }
+
+ return ci_block;
+}
+
+/* Generates the part of pair-list nbl assigned to our thread */
+static void nbnxn_make_pairlist_part(const nbnxn_search_t nbs,
+ const nbnxn_grid_t *gridi,
+ const nbnxn_grid_t *gridj,
+ nbnxn_search_work_t *work,
+ const nbnxn_atomdata_t *nbat,
+ const t_blocka *excl,
+ real rlist,
+ int nb_kernel_type,
+ int ci_block,
+ gmx_bool bFBufferFlag,
+ int nsubpair_max,
+ gmx_bool progBal,
+ int min_ci_balanced,
+ int th, int nth,
+ nbnxn_pairlist_t *nbl,
+ t_nblist *nbl_fep)
+{
+ int na_cj_2log;
+ matrix box;
+ real rl2, rl_fep2 = 0;
+ float rbb2;
+ int d;
+ int ci_b, ci, ci_x, ci_y, ci_xy, cj;
+ ivec shp;
+ int tx, ty, tz;
+ int shift;
+ gmx_bool bMakeList;
+ real shx, shy, shz;
+ int conv_i, cell0_i;
+ const nbnxn_bb_t *bb_i = NULL;
+#ifdef NBNXN_BBXXXX
+ const float *pbb_i = NULL;
+#endif
+ const float *bbcz_i, *bbcz_j;
+ const int *flags_i;
+ real bx0, bx1, by0, by1, bz0, bz1;
+ real bz1_frac;
+ real d2cx, d2z, d2z_cx, d2z_cy, d2zx, d2zxy, d2xy;
+ int cxf, cxl, cyf, cyf_x, cyl;
+ int cx, cy;
+ int c0, c1, cs, cf, cl;
+ int ndistc;
+ int ncpcheck;
+ int gridi_flag_shift = 0, gridj_flag_shift = 0;
+ unsigned int *gridj_flag = NULL;
+ int ncj_old_i, ncj_old_j;
+
+ nbs_cycle_start(&work->cc[enbsCCsearch]);
+
+ if (gridj->bSimple != nbl->bSimple)
+ {
+ gmx_incons("Grid incompatible with pair-list");
+ }
+
+ sync_work(nbl);
+ nbl->na_sc = gridj->na_sc;
+ nbl->na_ci = gridj->na_c;
+ nbl->na_cj = nbnxn_kernel_to_cj_size(nb_kernel_type);
+ na_cj_2log = get_2log(nbl->na_cj);
+
+ nbl->rlist = rlist;
+
+ if (bFBufferFlag)
+ {
+ /* Determine conversion of clusters to flag blocks */
+ gridi_flag_shift = 0;
+ while ((nbl->na_ci<<gridi_flag_shift) < NBNXN_BUFFERFLAG_SIZE)
+ {
+ gridi_flag_shift++;
+ }
+ gridj_flag_shift = 0;
+ while ((nbl->na_cj<<gridj_flag_shift) < NBNXN_BUFFERFLAG_SIZE)
+ {
+ gridj_flag_shift++;
+ }
+
+ gridj_flag = work->buffer_flags.flag;
+ }
+
+ copy_mat(nbs->box, box);
+
+ rl2 = nbl->rlist*nbl->rlist;
+
+ if (nbs->bFEP && !nbl->bSimple)
+ {
+ /* Determine an atom-pair list cut-off distance for FEP atom pairs.
+ * We should not simply use rlist, since then we would not have
+ * the small, effective buffering of the NxN lists.
+ * The buffer is on overestimate, but the resulting cost for pairs
+ * beyond rlist is neglible compared to the FEP pairs within rlist.
+ */
+ rl_fep2 = nbl->rlist + effective_buffer_1x1_vs_MxN(gridi, gridj);
+
+ if (debug)
+ {
+ fprintf(debug, "nbl_fep atom-pair rlist %f\n", rl_fep2);
+ }
+ rl_fep2 = rl_fep2*rl_fep2;
+ }
+
+ rbb2 = boundingbox_only_distance2(gridi, gridj, nbl->rlist, nbl->bSimple);
+
+ if (debug)
+ {
+ fprintf(debug, "nbl bounding box only distance %f\n", sqrt(rbb2));
+ }
+
+ /* Set the shift range */
+ for (d = 0; d < DIM; d++)
+ {
+ /* Check if we need periodicity shifts.
+ * Without PBC or with domain decomposition we don't need them.
+ */
+ if (d >= ePBC2npbcdim(nbs->ePBC) || nbs->dd_dim[d])
+ {
+ shp[d] = 0;
+ }
+ else
+ {
+ if (d == XX &&
+ box[XX][XX] - fabs(box[YY][XX]) - fabs(box[ZZ][XX]) < sqrt(rl2))
+ {
+ shp[d] = 2;
+ }
+ else
+ {
+ shp[d] = 1;
+ }
+ }
+ }
+
+ if (nbl->bSimple && !gridi->bSimple)
+ {
+ conv_i = gridi->na_sc/gridj->na_sc;
+ bb_i = gridi->bb_simple;
+ bbcz_i = gridi->bbcz_simple;
+ flags_i = gridi->flags_simple;
+ }
+ else
+ {
+ conv_i = 1;
+#ifdef NBNXN_BBXXXX
+ if (gridi->bSimple)
+ {
+ bb_i = gridi->bb;
+ }
+ else
+ {
+ pbb_i = gridi->pbb;
+ }
+#else
+ /* We use the normal bounding box format for both grid types */
+ bb_i = gridi->bb;
+#endif
+ bbcz_i = gridi->bbcz;
+ flags_i = gridi->flags;
+ }
+ cell0_i = gridi->cell0*conv_i;
+
+ bbcz_j = gridj->bbcz;
+
+ if (conv_i != 1)
+ {
+ /* Blocks of the conversion factor - 1 give a large repeat count
+ * combined with a small block size. This should result in good
+ * load balancing for both small and large domains.
+ */
+ ci_block = conv_i - 1;
+ }
+ if (debug)
+ {
+ fprintf(debug, "nbl nc_i %d col.av. %.1f ci_block %d\n",
+ gridi->nc, gridi->nc/(double)(gridi->ncx*gridi->ncy), ci_block);
+ }
+
+ ndistc = 0;
+ ncpcheck = 0;
+
+ /* Initially ci_b and ci to 1 before where we want them to start,
+ * as they will both be incremented in next_ci.
+ */
+ ci_b = -1;
+ ci = th*ci_block - 1;
+ ci_x = 0;
+ ci_y = 0;
+ while (next_ci(gridi, conv_i, nth, ci_block, &ci_x, &ci_y, &ci_b, &ci))
+ {
+ if (nbl->bSimple && flags_i[ci] == 0)
+ {
+ continue;
+ }
+
+ ncj_old_i = nbl->ncj;
+
+ d2cx = 0;
+ if (gridj != gridi && shp[XX] == 0)
+ {
+ if (nbl->bSimple)
+ {
+ bx1 = bb_i[ci].upper[BB_X];
+ }
+ else
+ {
+ bx1 = gridi->c0[XX] + (ci_x+1)*gridi->sx;
+ }
+ if (bx1 < gridj->c0[XX])
+ {
+ d2cx = sqr(gridj->c0[XX] - bx1);
+
+ if (d2cx >= rl2)
+ {
+ continue;
+ }
+ }
+ }
+
+ ci_xy = ci_x*gridi->ncy + ci_y;
+
+ /* Loop over shift vectors in three dimensions */
+ for (tz = -shp[ZZ]; tz <= shp[ZZ]; tz++)
+ {
+ shz = tz*box[ZZ][ZZ];
+
+ bz0 = bbcz_i[ci*NNBSBB_D ] + shz;
+ bz1 = bbcz_i[ci*NNBSBB_D+1] + shz;
+
+ if (tz == 0)
+ {
+ d2z = 0;
+ }
+ else if (tz < 0)
+ {
+ d2z = sqr(bz1);
+ }
+ else
+ {
+ d2z = sqr(bz0 - box[ZZ][ZZ]);
+ }
+
+ d2z_cx = d2z + d2cx;
+
+ if (d2z_cx >= rl2)
+ {
+ continue;
+ }
+
+ bz1_frac =
+ bz1/((real)(gridi->cxy_ind[ci_xy+1] - gridi->cxy_ind[ci_xy]));
+ if (bz1_frac < 0)
+ {
+ bz1_frac = 0;
+ }
+ /* The check with bz1_frac close to or larger than 1 comes later */
+
+ for (ty = -shp[YY]; ty <= shp[YY]; ty++)
+ {
+ shy = ty*box[YY][YY] + tz*box[ZZ][YY];
+
+ if (nbl->bSimple)
+ {
+ by0 = bb_i[ci].lower[BB_Y] + shy;
+ by1 = bb_i[ci].upper[BB_Y] + shy;
+ }
+ else
+ {
+ by0 = gridi->c0[YY] + (ci_y )*gridi->sy + shy;
+ by1 = gridi->c0[YY] + (ci_y+1)*gridi->sy + shy;
+ }
+
+ get_cell_range(by0, by1,
+ gridj->ncy, gridj->c0[YY], gridj->sy, gridj->inv_sy,
+ d2z_cx, rl2,
+ &cyf, &cyl);
+
+ if (cyf > cyl)
+ {
+ continue;
+ }
+
+ d2z_cy = d2z;
+ if (by1 < gridj->c0[YY])
+ {
+ d2z_cy += sqr(gridj->c0[YY] - by1);
+ }
+ else if (by0 > gridj->c1[YY])
+ {
+ d2z_cy += sqr(by0 - gridj->c1[YY]);
+ }
+
+ for (tx = -shp[XX]; tx <= shp[XX]; tx++)
+ {
+ shift = XYZ2IS(tx, ty, tz);
+
+#ifdef NBNXN_SHIFT_BACKWARD
+ if (gridi == gridj && shift > CENTRAL)
+ {
+ continue;
+ }
+#endif
+
+ shx = tx*box[XX][XX] + ty*box[YY][XX] + tz*box[ZZ][XX];
+
+ if (nbl->bSimple)
+ {
+ bx0 = bb_i[ci].lower[BB_X] + shx;
+ bx1 = bb_i[ci].upper[BB_X] + shx;
+ }
+ else
+ {
+ bx0 = gridi->c0[XX] + (ci_x )*gridi->sx + shx;
+ bx1 = gridi->c0[XX] + (ci_x+1)*gridi->sx + shx;
+ }
+
+ get_cell_range(bx0, bx1,
+ gridj->ncx, gridj->c0[XX], gridj->sx, gridj->inv_sx,
+ d2z_cy, rl2,
+ &cxf, &cxl);
+
+ if (cxf > cxl)
+ {
+ continue;
+ }
+
+ if (nbl->bSimple)
+ {
+ new_ci_entry(nbl, cell0_i+ci, shift, flags_i[ci]);
+ }
+ else
+ {
+ new_sci_entry(nbl, cell0_i+ci, shift);
+ }
+
+#ifndef NBNXN_SHIFT_BACKWARD
+ if (cxf < ci_x)
+#else
+ if (shift == CENTRAL && gridi == gridj &&
+ cxf < ci_x)
+#endif
+ {
+ /* Leave the pairs with i > j.
+ * x is the major index, so skip half of it.
+ */
+ cxf = ci_x;
+ }
+
+ if (nbl->bSimple)
+ {
+ set_icell_bb_simple(bb_i, ci, shx, shy, shz,
+ nbl->work->bb_ci);
+ }
+ else
+ {
+#ifdef NBNXN_BBXXXX
+ set_icell_bbxxxx_supersub(pbb_i, ci, shx, shy, shz,
+ nbl->work->pbb_ci);
+#else
+ set_icell_bb_supersub(bb_i, ci, shx, shy, shz,
+ nbl->work->bb_ci);
+#endif
+ }
+
+ nbs->icell_set_x(cell0_i+ci, shx, shy, shz,
+ gridi->na_c, nbat->xstride, nbat->x,
+ nbl->work);
+
+ for (cx = cxf; cx <= cxl; cx++)
+ {
+ d2zx = d2z;
+ if (gridj->c0[XX] + cx*gridj->sx > bx1)
+ {
+ d2zx += sqr(gridj->c0[XX] + cx*gridj->sx - bx1);
+ }
+ else if (gridj->c0[XX] + (cx+1)*gridj->sx < bx0)
+ {
+ d2zx += sqr(gridj->c0[XX] + (cx+1)*gridj->sx - bx0);
+ }
+
+#ifndef NBNXN_SHIFT_BACKWARD
+ if (gridi == gridj &&
+ cx == 0 && cyf < ci_y)
+#else
+ if (gridi == gridj &&
+ cx == 0 && shift == CENTRAL && cyf < ci_y)
+#endif
+ {
+ /* Leave the pairs with i > j.
+ * Skip half of y when i and j have the same x.
+ */
+ cyf_x = ci_y;
+ }
+ else
+ {
+ cyf_x = cyf;
+ }
+
+ for (cy = cyf_x; cy <= cyl; cy++)
+ {
+ c0 = gridj->cxy_ind[cx*gridj->ncy+cy];
+ c1 = gridj->cxy_ind[cx*gridj->ncy+cy+1];
+#ifdef NBNXN_SHIFT_BACKWARD
+ if (gridi == gridj &&
+ shift == CENTRAL && c0 < ci)
+ {
+ c0 = ci;
+ }
+#endif
+
+ d2zxy = d2zx;
+ if (gridj->c0[YY] + cy*gridj->sy > by1)
+ {
+ d2zxy += sqr(gridj->c0[YY] + cy*gridj->sy - by1);
+ }
+ else if (gridj->c0[YY] + (cy+1)*gridj->sy < by0)
+ {
+ d2zxy += sqr(gridj->c0[YY] + (cy+1)*gridj->sy - by0);
+ }
+ if (c1 > c0 && d2zxy < rl2)
+ {
+ cs = c0 + (int)(bz1_frac*(c1 - c0));
+ if (cs >= c1)
+ {
+ cs = c1 - 1;
+ }
+
+ d2xy = d2zxy - d2z;
+
+ /* Find the lowest cell that can possibly
+ * be within range.
+ */
+ cf = cs;
+ while (cf > c0 &&
+ (bbcz_j[cf*NNBSBB_D+1] >= bz0 ||
+ d2xy + sqr(bbcz_j[cf*NNBSBB_D+1] - bz0) < rl2))
+ {
+ cf--;
+ }
+
+ /* Find the highest cell that can possibly
+ * be within range.
+ */
+ cl = cs;
+ while (cl < c1-1 &&
+ (bbcz_j[cl*NNBSBB_D] <= bz1 ||
+ d2xy + sqr(bbcz_j[cl*NNBSBB_D] - bz1) < rl2))
+ {
+ cl++;
+ }
+
+#ifdef NBNXN_REFCODE
+ {
+ /* Simple reference code, for debugging,
+ * overrides the more complex code above.
+ */
+ int k;
+ cf = c1;
+ cl = -1;
+ for (k = c0; k < c1; k++)
+ {
+ if (box_dist2(bx0, bx1, by0, by1, bz0, bz1, bb+k) < rl2 &&
+ k < cf)
+ {
+ cf = k;
+ }
+ if (box_dist2(bx0, bx1, by0, by1, bz0, bz1, bb+k) < rl2 &&
+ k > cl)
+ {
+ cl = k;
+ }
+ }
+ }
+#endif
+
+ if (gridi == gridj)
+ {
+ /* We want each atom/cell pair only once,
+ * only use cj >= ci.
+ */
+#ifndef NBNXN_SHIFT_BACKWARD
+ cf = max(cf, ci);
+#else
+ if (shift == CENTRAL)
+ {
+ cf = max(cf, ci);
+ }
+#endif
+ }
+
+ if (cf <= cl)
+ {
+ /* For f buffer flags with simple lists */
+ ncj_old_j = nbl->ncj;
+
+ switch (nb_kernel_type)
+ {
+ case nbnxnk4x4_PlainC:
+ check_subcell_list_space_simple(nbl, cl-cf+1);
+
+ make_cluster_list_simple(gridj,
+ nbl, ci, cf, cl,
+ (gridi == gridj && shift == CENTRAL),
+ nbat->x,
+ rl2, rbb2,
+ &ndistc);
+ break;
+#ifdef GMX_NBNXN_SIMD_4XN
+ case nbnxnk4xN_SIMD_4xN:
+ check_subcell_list_space_simple(nbl, ci_to_cj(na_cj_2log, cl-cf)+2);
+ make_cluster_list_simd_4xn(gridj,
+ nbl, ci, cf, cl,
+ (gridi == gridj && shift == CENTRAL),
+ nbat->x,
+ rl2, rbb2,
+ &ndistc);
+ break;
+#endif
+#ifdef GMX_NBNXN_SIMD_2XNN
+ case nbnxnk4xN_SIMD_2xNN:
+ check_subcell_list_space_simple(nbl, ci_to_cj(na_cj_2log, cl-cf)+2);
+ make_cluster_list_simd_2xnn(gridj,
+ nbl, ci, cf, cl,
+ (gridi == gridj && shift == CENTRAL),
+ nbat->x,
+ rl2, rbb2,
+ &ndistc);
+ break;
+#endif
+ case nbnxnk8x8x8_PlainC:
+ case nbnxnk8x8x8_CUDA:
+ check_subcell_list_space_supersub(nbl, cl-cf+1);
+ for (cj = cf; cj <= cl; cj++)
+ {
+ make_cluster_list_supersub(gridi, gridj,
+ nbl, ci, cj,
+ (gridi == gridj && shift == CENTRAL && ci == cj),
+ nbat->xstride, nbat->x,
+ rl2, rbb2,
+ &ndistc);
+ }
+ break;
+ }
+ ncpcheck += cl - cf + 1;
+
+ if (bFBufferFlag && nbl->ncj > ncj_old_j)
+ {
+ int cbf, cbl, cb;
+
+ cbf = nbl->cj[ncj_old_j].cj >> gridj_flag_shift;
+ cbl = nbl->cj[nbl->ncj-1].cj >> gridj_flag_shift;
+ for (cb = cbf; cb <= cbl; cb++)
+ {
+ gridj_flag[cb] = 1U<<th;
+ }
+ }
+ }
+ }
+ }
+ }
+
+ /* Set the exclusions for this ci list */
+ if (nbl->bSimple)
+ {
+ set_ci_top_excls(nbs,
+ nbl,
+ shift == CENTRAL && gridi == gridj,
+ gridj->na_c_2log,
+ na_cj_2log,
+ &(nbl->ci[nbl->nci]),
+ excl);
+
+ if (nbs->bFEP)
+ {
+ make_fep_list(nbs, nbat, nbl,
+ shift == CENTRAL && gridi == gridj,
+ &(nbl->ci[nbl->nci]),
+ gridi, gridj, nbl_fep);
+ }
+ }
+ else
+ {
+ set_sci_top_excls(nbs,
+ nbl,
+ shift == CENTRAL && gridi == gridj,
+ gridj->na_c_2log,
+ &(nbl->sci[nbl->nsci]),
+ excl);
+
+ if (nbs->bFEP)
+ {
+ make_fep_list_supersub(nbs, nbat, nbl,
+ shift == CENTRAL && gridi == gridj,
+ &(nbl->sci[nbl->nsci]),
+ shx, shy, shz,
+ rl_fep2,
+ gridi, gridj, nbl_fep);
+ }
+ }
+
+ /* Close this ci list */
+ if (nbl->bSimple)
+ {
+ close_ci_entry_simple(nbl);
+ }
+ else
+ {
+ close_ci_entry_supersub(nbl,
+ nsubpair_max,
+ progBal, min_ci_balanced,
+ th, nth);
+ }
+ }
+ }
+ }
+
+ if (bFBufferFlag && nbl->ncj > ncj_old_i)
+ {
+ work->buffer_flags.flag[(gridi->cell0+ci)>>gridi_flag_shift] = 1U<<th;
+ }
+ }
+
+ work->ndistc = ndistc;
+
+ nbs_cycle_stop(&work->cc[enbsCCsearch]);
+
+ if (debug)
+ {
+ fprintf(debug, "number of distance checks %d\n", ndistc);
+ fprintf(debug, "ncpcheck %s %d\n", gridi == gridj ? "local" : "non-local",
+ ncpcheck);
+
+ if (nbl->bSimple)
+ {
+ print_nblist_statistics_simple(debug, nbl, nbs, rlist);
+ }
+ else
+ {
+ print_nblist_statistics_supersub(debug, nbl, nbs, rlist);
+ }
+
+ if (nbs->bFEP)
+ {
+ fprintf(debug, "nbl FEP list pairs: %d\n", nbl_fep->nrj);
+ }
+ }
+}
+
+static void reduce_buffer_flags(const nbnxn_search_t nbs,
+ int nsrc,
+ const nbnxn_buffer_flags_t *dest)
+{
+ int s, b;
+ const unsigned int *flag;
+
+ for (s = 0; s < nsrc; s++)
+ {
+ flag = nbs->work[s].buffer_flags.flag;
+
+ for (b = 0; b < dest->nflag; b++)
+ {
+ dest->flag[b] |= flag[b];
+ }
+ }
+}
+
+static void print_reduction_cost(const nbnxn_buffer_flags_t *flags, int nout)
+{
+ int nelem, nkeep, ncopy, nred, b, c, out;
+
+ nelem = 0;
+ nkeep = 0;
+ ncopy = 0;
+ nred = 0;
+ for (b = 0; b < flags->nflag; b++)
+ {
+ if (flags->flag[b] == 1)
+ {
+ /* Only flag 0 is set, no copy of reduction required */
+ nelem++;
+ nkeep++;
+ }
+ else if (flags->flag[b] > 0)
+ {
+ c = 0;
+ for (out = 0; out < nout; out++)
+ {
+ if (flags->flag[b] & (1U<<out))
+ {
+ c++;
+ }
+ }
+ nelem += c;
+ if (c == 1)
+ {
+ ncopy++;
+ }
+ else
+ {
+ nred += c;
+ }
+ }
+ }
+
+ fprintf(debug, "nbnxn reduction: #flag %d #list %d elem %4.2f, keep %4.2f copy %4.2f red %4.2f\n",
+ flags->nflag, nout,
+ nelem/(double)(flags->nflag),
+ nkeep/(double)(flags->nflag),
+ ncopy/(double)(flags->nflag),
+ nred/(double)(flags->nflag));
+}
+
+/* Perform a count (linear) sort to sort the smaller lists to the end.
+ * This avoids load imbalance on the GPU, as large lists will be
+ * scheduled and executed first and the smaller lists later.
+ * Load balancing between multi-processors only happens at the end
+ * and there smaller lists lead to more effective load balancing.
+ * The sorting is done on the cj4 count, not on the actual pair counts.
+ * Not only does this make the sort faster, but it also results in
+ * better load balancing than using a list sorted on exact load.
+ * This function swaps the pointer in the pair list to avoid a copy operation.
+ */
+static void sort_sci(nbnxn_pairlist_t *nbl)
+{
+ nbnxn_list_work_t *work;
+ int m, i, s, s0, s1;
+ nbnxn_sci_t *sci_sort;
+
+ if (nbl->ncj4 <= nbl->nsci)
+ {
+ /* nsci = 0 or all sci have size 1, sorting won't change the order */
+ return;
+ }
+
+ work = nbl->work;
+
+ /* We will distinguish differences up to double the average */
+ m = (2*nbl->ncj4)/nbl->nsci;
+
+ if (m + 1 > work->sort_nalloc)
+ {
+ work->sort_nalloc = over_alloc_large(m + 1);
+ srenew(work->sort, work->sort_nalloc);
+ }
+
+ if (work->sci_sort_nalloc != nbl->sci_nalloc)
+ {
+ work->sci_sort_nalloc = nbl->sci_nalloc;
+ nbnxn_realloc_void((void **)&work->sci_sort,
+ 0,
+ work->sci_sort_nalloc*sizeof(*work->sci_sort),
+ nbl->alloc, nbl->free);
+ }
+
+ /* Count the entries of each size */
+ for (i = 0; i <= m; i++)
+ {
+ work->sort[i] = 0;
+ }
+ for (s = 0; s < nbl->nsci; s++)
+ {
+ i = min(m, nbl->sci[s].cj4_ind_end - nbl->sci[s].cj4_ind_start);
+ work->sort[i]++;
+ }
+ /* Calculate the offset for each count */
+ s0 = work->sort[m];
+ work->sort[m] = 0;
+ for (i = m - 1; i >= 0; i--)
+ {
+ s1 = work->sort[i];
+ work->sort[i] = work->sort[i + 1] + s0;
+ s0 = s1;
+ }
+
+ /* Sort entries directly into place */
+ sci_sort = work->sci_sort;
+ for (s = 0; s < nbl->nsci; s++)
+ {
+ i = min(m, nbl->sci[s].cj4_ind_end - nbl->sci[s].cj4_ind_start);
+ sci_sort[work->sort[i]++] = nbl->sci[s];
+ }
+
+ /* Swap the sci pointers so we use the new, sorted list */
+ work->sci_sort = nbl->sci;
+ nbl->sci = sci_sort;
+}
+
+/* Make a local or non-local pair-list, depending on iloc */
+void nbnxn_make_pairlist(const nbnxn_search_t nbs,
+ nbnxn_atomdata_t *nbat,
+ const t_blocka *excl,
+ real rlist,
+ int min_ci_balanced,
+ nbnxn_pairlist_set_t *nbl_list,
+ int iloc,
+ int nb_kernel_type,
+ t_nrnb *nrnb)
+{
+ nbnxn_grid_t *gridi, *gridj;
+ gmx_bool bGPUCPU;
+ int nzi, zi, zj0, zj1, zj;
+ int nsubpair_max;
+ int th;
+ int nnbl;
+ nbnxn_pairlist_t **nbl;
+ int ci_block;
+ gmx_bool CombineNBLists;
+ gmx_bool progBal;
+ int np_tot, np_noq, np_hlj, nap;
+
+ /* Check if we are running hybrid GPU + CPU nbnxn mode */
+ bGPUCPU = (!nbs->grid[0].bSimple && nbl_list->bSimple);
+
+ nnbl = nbl_list->nnbl;
+ nbl = nbl_list->nbl;
+ CombineNBLists = nbl_list->bCombined;
+
+ if (debug)
+ {
+ fprintf(debug, "ns making %d nblists\n", nnbl);
+ }
+
+ nbat->bUseBufferFlags = (nbat->nout > 1);
+ /* We should re-init the flags before making the first list */
+ if (nbat->bUseBufferFlags && (LOCAL_I(iloc) || bGPUCPU))
+ {
+ init_buffer_flags(&nbat->buffer_flags, nbat->natoms);
+ }
+
+ if (nbl_list->bSimple)
+ {
+ switch (nb_kernel_type)
+ {
+#ifdef GMX_NBNXN_SIMD_4XN
+ case nbnxnk4xN_SIMD_4xN:
+ nbs->icell_set_x = icell_set_x_simd_4xn;
+ break;
+#endif
+#ifdef GMX_NBNXN_SIMD_2XNN
+ case nbnxnk4xN_SIMD_2xNN:
+ nbs->icell_set_x = icell_set_x_simd_2xnn;
+ break;
+#endif
+ default:
+ nbs->icell_set_x = icell_set_x_simple;
+ break;
+ }
+ }
+ else
+ {
+#ifdef NBNXN_SEARCH_BB_SIMD4
+ nbs->icell_set_x = icell_set_x_supersub_simd4;
+#else
+ nbs->icell_set_x = icell_set_x_supersub;
+#endif
+ }
+
+ if (LOCAL_I(iloc))
+ {
+ /* Only zone (grid) 0 vs 0 */
+ nzi = 1;
+ zj0 = 0;
+ zj1 = 1;
+ }
+ else
+ {
+ nzi = nbs->zones->nizone;
+ }
+
+ if (!nbl_list->bSimple && min_ci_balanced > 0)
+ {
+ nsubpair_max = get_nsubpair_max(nbs, iloc, rlist, min_ci_balanced);
+ }
+ else
+ {
+ nsubpair_max = 0;
+ }
+
+ /* Clear all pair-lists */
+ for (th = 0; th < nnbl; th++)
+ {
+ clear_pairlist(nbl[th]);
+
+ if (nbs->bFEP)
+ {
+ clear_pairlist_fep(nbl_list->nbl_fep[th]);
+ }
+ }
+
+ for (zi = 0; zi < nzi; zi++)
+ {
+ gridi = &nbs->grid[zi];
+
+ if (NONLOCAL_I(iloc))
+ {
+ zj0 = nbs->zones->izone[zi].j0;
+ zj1 = nbs->zones->izone[zi].j1;
+ if (zi == 0)
+ {
+ zj0++;
+ }
+ }
+ for (zj = zj0; zj < zj1; zj++)
+ {
+ gridj = &nbs->grid[zj];
+
+ if (debug)
+ {
+ fprintf(debug, "ns search grid %d vs %d\n", zi, zj);
+ }
+
+ nbs_cycle_start(&nbs->cc[enbsCCsearch]);
+
+ if (nbl[0]->bSimple && !gridi->bSimple)
+ {
+ /* Hybrid list, determine blocking later */
+ ci_block = 0;
+ }
+ else
+ {
+ ci_block = get_ci_block_size(gridi, nbs->DomDec, nnbl);
+ }
+
+ /* With GPU: generate progressively smaller lists for
+ * load balancing for local only or non-local with 2 zones.
+ */
+ progBal = (LOCAL_I(iloc) || nbs->zones->n <= 2);
+
+#pragma omp parallel for num_threads(nnbl) schedule(static)
+ for (th = 0; th < nnbl; th++)
+ {
+ /* Re-init the thread-local work flag data before making
+ * the first list (not an elegant conditional).
+ */
+ if (nbat->bUseBufferFlags && ((zi == 0 && zj == 0) ||
+ (bGPUCPU && zi == 0 && zj == 1)))
+ {
+ init_buffer_flags(&nbs->work[th].buffer_flags, nbat->natoms);
+ }
+
+ if (CombineNBLists && th > 0)
+ {
+ clear_pairlist(nbl[th]);
+ }
+
+ /* Divide the i super cell equally over the nblists */
+ nbnxn_make_pairlist_part(nbs, gridi, gridj,
+ &nbs->work[th], nbat, excl,
+ rlist,
+ nb_kernel_type,
+ ci_block,
+ nbat->bUseBufferFlags,
+ nsubpair_max,
+ progBal, min_ci_balanced,
+ th, nnbl,
+ nbl[th],
+ nbl_list->nbl_fep[th]);
+ }
+ nbs_cycle_stop(&nbs->cc[enbsCCsearch]);
+
+ np_tot = 0;
+ np_noq = 0;
+ np_hlj = 0;
+ for (th = 0; th < nnbl; th++)
+ {
+ inc_nrnb(nrnb, eNR_NBNXN_DIST2, nbs->work[th].ndistc);
+
+ if (nbl_list->bSimple)
+ {
+ np_tot += nbl[th]->ncj;
+ np_noq += nbl[th]->work->ncj_noq;
+ np_hlj += nbl[th]->work->ncj_hlj;
+ }
+ else
+ {
+ /* This count ignores potential subsequent pair pruning */
+ np_tot += nbl[th]->nci_tot;
+ }
+ }
+ nap = nbl[0]->na_ci*nbl[0]->na_cj;
+ nbl_list->natpair_ljq = (np_tot - np_noq)*nap - np_hlj*nap/2;
+ nbl_list->natpair_lj = np_noq*nap;
+ nbl_list->natpair_q = np_hlj*nap/2;
+
+ if (CombineNBLists && nnbl > 1)
+ {
+ nbs_cycle_start(&nbs->cc[enbsCCcombine]);
+
+ combine_nblists(nnbl-1, nbl+1, nbl[0]);
+
+ nbs_cycle_stop(&nbs->cc[enbsCCcombine]);
+ }
+ }
+ }
+
+ if (!nbl_list->bSimple)
+ {
+ /* Sort the entries on size, large ones first */
+ if (CombineNBLists || nnbl == 1)
+ {
+ sort_sci(nbl[0]);
+ }
+ else
+ {
+#pragma omp parallel for num_threads(nnbl) schedule(static)
+ for (th = 0; th < nnbl; th++)
+ {
+ sort_sci(nbl[th]);
+ }
+ }
+ }
+
+ if (nbat->bUseBufferFlags)
+ {
+ reduce_buffer_flags(nbs, nnbl, &nbat->buffer_flags);
+ }
+
+ if (nbs->bFEP)
+ {
+ /* Balance the free-energy lists over all the threads */
+ balance_fep_lists(nbs, nbl_list);
+ }
+
+ /* Special performance logging stuff (env.var. GMX_NBNXN_CYCLE) */
+ if (LOCAL_I(iloc))
+ {
+ nbs->search_count++;
+ }
+ if (nbs->print_cycles &&
+ (!nbs->DomDec || (nbs->DomDec && !LOCAL_I(iloc))) &&
+ nbs->search_count % 100 == 0)
+ {
+ nbs_cycle_print(stderr, nbs);
+ }
+
+ if (debug && (CombineNBLists && nnbl > 1))
+ {
+ if (nbl[0]->bSimple)
+ {
+ print_nblist_statistics_simple(debug, nbl[0], nbs, rlist);
+ }
+ else
+ {
+ print_nblist_statistics_supersub(debug, nbl[0], nbs, rlist);
+ }
+ }
+
+ if (debug)
+ {
+ if (gmx_debug_at)
+ {
+ if (nbl[0]->bSimple)
+ {
+ print_nblist_ci_cj(debug, nbl[0]);
+ }
+ else
+ {
+ print_nblist_sci_cj(debug, nbl[0]);
+ }
+ }
+
+ if (nbat->bUseBufferFlags)
+ {
+ print_reduction_cost(&nbat->buffer_flags, nnbl);
+ }
+ }
+}
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff