Corrected parameter for sorting on search grid

The nbnxn grid search sorting range parameter used the whole box
height instead of the local DD cell height with domain decomposition
along z. This could not cause errors, but the search used O(N^2) time
with more than 4 domains along z, instead of O(N).

Change-Id: I324df6b15635a5ecff7c8bfeb124fdb933e5f845

diff --git a/src/gromacs/mdlib/nbnxn_internal.h b/src/gromacs/mdlib/nbnxn_internal.h
index fc42e6093566bca679cda924585feaff2fece613..e8e94fdfdedde8797668401b9a68b3062d17063f 100644 (file)
--- a/src/gromacs/mdlib/nbnxn_internal.h
+++ b/src/gromacs/mdlib/nbnxn_internal.h
@@ -97,6 +97,7 @@ typedef struct {
 typedef struct {
     rvec          c0;               /* The lower corner of the (local) grid        */
     rvec          c1;               /* The upper corner of the (local) grid        */
+    rvec          size;             /* c1 - c0                                     */
     real          atom_density;     /* The atom number density for the local grid  */
 
     gmx_bool      bSimple;          /* Is this grid simple or super/sub            */

diff --git a/src/gromacs/mdlib/nbnxn_search.c b/src/gromacs/mdlib/nbnxn_search.c
index 3114bebc22b048559369dede69c9774cf4d8f21a..5d182ee11c15a1202243e9bc3f3e4428cffbf2df 100644 (file)
--- a/src/gromacs/mdlib/nbnxn_search.c
+++ b/src/gromacs/mdlib/nbnxn_search.c
@@ -571,6 +571,7 @@ static int set_grid_size_xy(const nbnxn_search_t nbs,
 
     copy_rvec(corner0, grid->c0);
     copy_rvec(corner1, grid->c1);
+    copy_rvec(size,    grid->size);
 
     return nc_max;
 }
@@ -1007,7 +1008,6 @@ static void combine_bounding_box_pairs(nbnxn_grid_t *grid, const nbnxn_bb_t *bb)
 
 /* Prints the average bb size, used for debug output */
 static void print_bbsizes_simple(FILE                *fp,
-                                 const nbnxn_search_t nbs,
                                  const nbnxn_grid_t  *grid)
 {
     int  c, d;
@@ -1023,19 +1023,18 @@ static void print_bbsizes_simple(FILE                *fp,
     }
     dsvmul(1.0/grid->nc, ba, ba);
 
-    fprintf(fp, "ns bb: %4.2f %4.2f %4.2f  %4.2f %4.2f %4.2f rel %4.2f %4.2f %4.2f\n",
-            nbs->box[XX][XX]/grid->ncx,
-            nbs->box[YY][YY]/grid->ncy,
-            nbs->box[ZZ][ZZ]*grid->ncx*grid->ncy/grid->nc,
+    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->ncx/nbs->box[XX][XX],
-            ba[YY]*grid->ncy/nbs->box[YY][YY],
-            ba[ZZ]*grid->nc/(grid->ncx*grid->ncy*nbs->box[ZZ][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_search_t nbs,
                                    const nbnxn_grid_t  *grid)
 {
     int  ns, c, s;
@@ -1077,14 +1076,14 @@ static void print_bbsizes_supersub(FILE                *fp,
     }
     dsvmul(1.0/ns, ba, ba);
 
-    fprintf(fp, "ns bb: %4.2f %4.2f %4.2f  %4.2f %4.2f %4.2f rel %4.2f %4.2f %4.2f\n",
-            nbs->box[XX][XX]/(grid->ncx*GPU_NSUBCELL_X),
-            nbs->box[YY][YY]/(grid->ncy*GPU_NSUBCELL_Y),
-            nbs->box[ZZ][ZZ]*grid->ncx*grid->ncy/(grid->nc*GPU_NSUBCELL_Z),
+    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]*grid->ncx*GPU_NSUBCELL_X/nbs->box[XX][XX],
-            ba[YY]*grid->ncy*GPU_NSUBCELL_Y/nbs->box[YY][YY],
-            ba[ZZ]*grid->nc*GPU_NSUBCELL_Z/(grid->ncx*grid->ncy*nbs->box[ZZ][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.
@@ -1332,7 +1331,7 @@ static void sort_columns_simple(const nbnxn_search_t nbs,
         sort_atoms(ZZ, FALSE, dd_zone,
                    nbs->a+ash, na, x,
                    grid->c0[ZZ],
-                   1.0/nbs->box[ZZ][ZZ], ncz*grid->na_sc,
+                   1.0/grid->size[ZZ], ncz*grid->na_sc,
                    sort_work);
 
         /* Fill the ncz cells in this column */
@@ -1418,7 +1417,7 @@ static void sort_columns_supersub(const nbnxn_search_t nbs,
         sort_atoms(ZZ, FALSE, dd_zone,
                    nbs->a+ash, na, x,
                    grid->c0[ZZ],
-                   1.0/nbs->box[ZZ][ZZ], ncz*grid->na_sc,
+                   1.0/grid->size[ZZ], ncz*grid->na_sc,
                    sort_work);
 
         /* This loop goes over the supercells and subcells along z at once */
@@ -1742,14 +1741,14 @@ static void calc_cell_indices(const nbnxn_search_t nbs,
     {
         if (grid->bSimple)
         {
-            print_bbsizes_simple(debug, nbs, grid);
+            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, nbs, grid);
+            print_bbsizes_supersub(debug, grid);
         }
     }
 }
@@ -2623,7 +2622,7 @@ static void print_nblist_statistics_simple(FILE *fp, const nbnxn_pairlist_t *nbl
     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/det(nbs->box)));
+            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);
@@ -2673,7 +2672,7 @@ static void print_nblist_statistics_supersub(FILE *fp, const nbnxn_pairlist_t *n
     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/det(nbs->box)));
+            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);