Merge branch 'release-4-6' into release-5-0

Change-Id: Icd1eafab98512328523a3ea788626b3fb415b0a8

diff --git a/src/gromacs/gmxana/gmx_tune_pme.c b/src/gromacs/gmxana/gmx_tune_pme.c
index 3dbda71d479041b6d544af01fcf82be779beb277..e76d32518e287bfa7ab09d4ef908358f4429aa4b 100644 (file)
--- a/src/gromacs/gmxana/gmx_tune_pme.c
+++ b/src/gromacs/gmxana/gmx_tune_pme.c
@@ -708,7 +708,7 @@ static void check_mdrun_works(gmx_bool    bThreads,
             gmx_fatal(FARGS, "Need a threaded version of mdrun. This one\n"
                       "(%s)\n"
                       "seems to have been compiled with MPI instead.",
-                      *cmd_mdrun);
+                      cmd_mdrun);
         }
     }
     else
@@ -718,7 +718,7 @@ static void check_mdrun_works(gmx_bool    bThreads,
             gmx_fatal(FARGS, "Need an MPI-enabled version of mdrun. This one\n"
                       "(%s)\n"
                       "seems to have been compiled without MPI support.",
-                      *cmd_mdrun);
+                      cmd_mdrun);
         }
     }
 

diff --git a/src/gromacs/gmxlib/nonbonded/nonbonded.c b/src/gromacs/gmxlib/nonbonded/nonbonded.c
index 6a93fff21614f4fd6697213b86561b6a0184886b..3c0880c8c3547743675ce5f6675871051ed6adc4 100644 (file)
--- a/src/gromacs/gmxlib/nonbonded/nonbonded.c
+++ b/src/gromacs/gmxlib/nonbonded/nonbonded.c
@@ -285,8 +285,11 @@ gmx_nonbonded_set_kernel_pointers(FILE *log, t_nblist *nl)
             }
         }
 
-        /* Give up, pick a generic one instead */
-        if (nl->kernelptr_vf == NULL)
+        /* Give up. If this was a water kernel, leave the pointer as NULL, which
+         * will disable water optimization in NS. If it is a particle kernel, set
+         * the pointer to the generic NB kernel.
+         */
+        if (nl->kernelptr_vf == NULL && !gmx_strcasecmp_min(geom,"Particle-Particle"))
         {
             nl->kernelptr_vf       = (void *) gmx_nb_generic_kernel;
             nl->kernelptr_f        = (void *) gmx_nb_generic_kernel;
@@ -410,7 +413,11 @@ void do_nonbonded(t_forcerec *fr,
                         /* We don't need the non-perturbed interactions */
                         continue;
                     }
-                    (*kernelptr)(&(nlist[i]), x, f, fr, mdatoms, &kernel_data, nrnb);
+                    /* Neighborlists whose kernelptr==NULL will always be empty */
+                    if(kernelptr != NULL)
+                    {
+                        (*kernelptr)(&(nlist[i]), x, f, fr, mdatoms, &kernel_data, nrnb);
+                    }
                 }
             }
         }

diff --git a/src/gromacs/mdlib/domdec.c b/src/gromacs/mdlib/domdec.c
index fc82a2d455ba1a7e9ec7e49cf7e08f658a221404..185e9c3ab1bdab605c97e7e426714f37fee16059 100644 (file)
--- a/src/gromacs/mdlib/domdec.c
+++ b/src/gromacs/mdlib/domdec.c
@@ -3080,8 +3080,15 @@ static void check_box_size(gmx_domdec_t *dd, gmx_ddbox_t *ddbox)
     }
 }
 
+enum { setcellsizeslbLOCAL, setcellsizeslbMASTER, setcellsizeslbPULSE_ONLY };
+
+/* Set the domain boundaries. Use for static (or no) load balancing,
+ * and also for the starting state for dynamic load balancing.
+ * setmode determine if and where the boundaries are stored, use enum above.
+ * Returns the number communication pulses in npulse.
+ */
 static void set_dd_cell_sizes_slb(gmx_domdec_t *dd, gmx_ddbox_t *ddbox,
-                                  gmx_bool bMaster, ivec npulse)
+                                  int setmode, ivec npulse)
 {
     gmx_domdec_comm_t *comm;
     int                d, j;
@@ -3098,20 +3105,23 @@ static void set_dd_cell_sizes_slb(gmx_domdec_t *dd, gmx_ddbox_t *ddbox,
         {
             /* Uniform grid */
             cell_dx = ddbox->box_size[d]/dd->nc[d];
-            if (bMaster)
-            {
-                for (j = 0; j < dd->nc[d]+1; j++)
-                {
-                    dd->ma->cell_x[d][j] = ddbox->box0[d] + j*cell_dx;
-                }
-            }
-            else
+            switch (setmode)
             {
-                comm->cell_x0[d] = ddbox->box0[d] + (dd->ci[d]  )*cell_dx;
-                comm->cell_x1[d] = ddbox->box0[d] + (dd->ci[d]+1)*cell_dx;
+                case setcellsizeslbMASTER:
+                    for (j = 0; j < dd->nc[d]+1; j++)
+                    {
+                        dd->ma->cell_x[d][j] = ddbox->box0[d] + j*cell_dx;
+                    }
+                    break;
+                case setcellsizeslbLOCAL:
+                    comm->cell_x0[d] = ddbox->box0[d] + (dd->ci[d]  )*cell_dx;
+                    comm->cell_x1[d] = ddbox->box0[d] + (dd->ci[d]+1)*cell_dx;
+                    break;
+                default:
+                    break;
             }
             cellsize = cell_dx*ddbox->skew_fac[d];
-            while (cellsize*npulse[d] < comm->cutoff && npulse[d] < dd->nc[d]-1)
+            while (cellsize*npulse[d] < comm->cutoff)
             {
                 npulse[d]++;
             }
@@ -3124,7 +3134,7 @@ static void set_dd_cell_sizes_slb(gmx_domdec_t *dd, gmx_ddbox_t *ddbox,
              * all cell borders in a loop to obtain identical values
              * to the master distribution case and to determine npulse.
              */
-            if (bMaster)
+            if (setmode == setcellsizeslbMASTER)
             {
                 cell_x = dd->ma->cell_x[d];
             }
@@ -3145,10 +3155,13 @@ static void set_dd_cell_sizes_slb(gmx_domdec_t *dd, gmx_ddbox_t *ddbox,
                 }
                 cellsize_min[d] = min(cellsize_min[d], cellsize);
             }
-            if (!bMaster)
+            if (setmode == setcellsizeslbLOCAL)
             {
                 comm->cell_x0[d] = cell_x[dd->ci[d]];
                 comm->cell_x1[d] = cell_x[dd->ci[d]+1];
+            }
+            if (setmode != setcellsizeslbMASTER)
+            {
                 sfree(cell_x);
             }
         }
@@ -3159,12 +3172,23 @@ static void set_dd_cell_sizes_slb(gmx_domdec_t *dd, gmx_ddbox_t *ddbox,
         if (d < ddbox->npbcdim &&
             dd->nc[d] > 1 && npulse[d] >= dd->nc[d])
         {
-            gmx_fatal_collective(FARGS, NULL, dd,
-                                 "The box size in direction %c (%f) times the triclinic skew factor (%f) is too small for a cut-off of %f with %d domain decomposition cells, use 1 or more than %d %s or increase the box size in this direction",
-                                 dim2char(d), ddbox->box_size[d], ddbox->skew_fac[d],
-                                 comm->cutoff,
-                                 dd->nc[d], dd->nc[d],
-                                 dd->nnodes > dd->nc[d] ? "cells" : "processors");
+            char error_string[STRLEN];
+
+            sprintf(error_string,
+                     "The box size in direction %c (%f) times the triclinic skew factor (%f) is too small for a cut-off of %f with %d domain decomposition cells, use 1 or more than %d %s or increase the box size in this direction",
+                    dim2char(d), ddbox->box_size[d], ddbox->skew_fac[d],
+                    comm->cutoff,
+                    dd->nc[d], dd->nc[d],
+                    dd->nnodes > dd->nc[d] ? "cells" : "processors");
+
+            if (setmode == setcellsizeslbLOCAL)
+            {
+                gmx_fatal_collective(FARGS, NULL, dd, error_string);
+            }
+            else
+            {
+                gmx_fatal(FARGS, error_string);
+            }
         }
     }
 
@@ -3774,7 +3798,7 @@ static void set_dd_cell_sizes(gmx_domdec_t *dd,
     }
     else
     {
-        set_dd_cell_sizes_slb(dd, ddbox, FALSE, npulse);
+        set_dd_cell_sizes_slb(dd, ddbox, setcellsizeslbLOCAL, npulse);
         realloc_comm_ind(dd, npulse);
     }
 
@@ -4041,6 +4065,7 @@ static void get_cg_distribution(FILE *fplog, gmx_int64_t step, gmx_domdec_t *dd,
     int                  i, cg_gl;
     int                 *ibuf, buf2[2] = { 0, 0 };
     gmx_bool             bMaster = DDMASTER(dd);
+
     if (bMaster)
     {
         ma = dd->ma;
@@ -4050,7 +4075,7 @@ static void get_cg_distribution(FILE *fplog, gmx_int64_t step, gmx_domdec_t *dd,
             check_screw_box(box);
         }
 
-        set_dd_cell_sizes_slb(dd, ddbox, TRUE, npulse);
+        set_dd_cell_sizes_slb(dd, ddbox, setcellsizeslbMASTER, npulse);
 
         distribute_cg(fplog, step, box, ddbox->tric_dir, cgs, pos, dd);
         for (i = 0; i < dd->nnodes; i++)
@@ -7182,7 +7207,7 @@ static void print_dd_settings(FILE *fplog, gmx_domdec_t *dd,
     }
     else
     {
-        set_dd_cell_sizes_slb(dd, ddbox, FALSE, np);
+        set_dd_cell_sizes_slb(dd, ddbox, setcellsizeslbPULSE_ONLY, np);
         fprintf(fplog, "The initial number of communication pulses is:");
         for (d = 0; d < dd->ndim; d++)
         {

diff --git a/src/gromacs/mdlib/domdec_setup.c b/src/gromacs/mdlib/domdec_setup.c
index d8001ea9dabaaa52c91f565e5daecc8c73a5628e..5da2d3a58ee71a39beec0880a9a561e06af0348a 100644 (file)
--- a/src/gromacs/mdlib/domdec_setup.c
+++ b/src/gromacs/mdlib/domdec_setup.c
@@ -359,11 +359,16 @@ static float comm_cost_est(real limit, real cutoff,
     {
         bt[i] = ddbox->box_size[i]*ddbox->skew_fac[i];
 
-        /* Without PBC there are no cell size limits with 2 cells */
+        /* Without PBC and with 2 cells, there are no lower limits on the cell size */
         if (!(i >= ddbox->npbcdim && nc[i] <= 2) && bt[i] < nc[i]*limit)
         {
             return -1;
         }
+        /* With PBC, check if the cut-off fits in nc[i]-1 cells */
+        if (i < ddbox->npbcdim && nc[i] > 1 && (nc[i] - 1)*bt[i] < nc[i]*cutoff)
+        {
+            return -1;
+        }
     }
 
     if (npme_tot > 1)

diff --git a/src/gromacs/mdlib/ns.c b/src/gromacs/mdlib/ns.c
index 6558e2be9cfe51e3347fb4c7b8f180169c34144f..5208983deccab7cc9b8e44c25ab7ba293a59f4cb 100644 (file)
--- a/src/gromacs/mdlib/ns.c
+++ b/src/gromacs/mdlib/ns.c
@@ -291,7 +291,10 @@ void init_neighbor_list(FILE *log, t_forcerec *fr, int homenr)
             )
         {
             fr->solvent_opt = esolNO;
-            fprintf(log, "Note: The available nonbonded kernels do not support water optimization - disabling.\n");
+            if (log != NULL)
+            {
+                fprintf(log, "Note: The available nonbonded kernels do not support water optimization - disabling.\n");
+            }
         }
 
         if (fr->efep != efepNO)