Merge branch 'release-4-6'

Conflicts:
	src/gromacs/legacyheaders/topsort.h
Resolved in favour of comment change in release-4-6

Change-Id: Ib930277635cdd260c136ab9b3e02809682587252

diff --git a/admin/installguide/installguide.tex b/admin/installguide/installguide.tex
index ebac30512233d004dd2baf602adf928f1a82335c..91d4b1dd8a170c76a002fd6c9c80b12e1ba28be7 100644 (file)
--- a/admin/installguide/installguide.tex
+++ b/admin/installguide/installguide.tex
@@ -535,7 +535,7 @@ will generally speed things up by quite a bit.
 \subsection{Installing \gromacs{}}
 
 Finally, \verb+make install+ will install \gromacs{} in the
-directory given in \verb+GMX_INSTALL_PREFIX+. If this is an system
+directory given in \verb+CMAKE_INSTALL_PREFIX+. If this is an system
 directory, then you will need permission to write there, and you
 should use super-user privileges only for \verb+make install+ and
 not the whole procedure.

diff --git a/src/gromacs/gmxlib/gpu_utils/gpu_utils.cu b/src/gromacs/gmxlib/gpu_utils/gpu_utils.cu
index dcb701f4ac31731c8bd25e33e0fca3441ca56049..eb3e7dd7813f227af57b597337265613e43edf23 100644 (file)
--- a/src/gromacs/gmxlib/gpu_utils/gpu_utils.cu
+++ b/src/gromacs/gmxlib/gpu_utils/gpu_utils.cu
@@ -857,10 +857,7 @@ int get_gpu_device_id(const gmx_gpu_info_t *gpu_info,
 {
     assert(gpu_info);
     assert(gpu_opt);
-    if (idx < 0 && idx >= gpu_opt->ncuda_dev_use)
-    {
-        return -1;
-    }
+    assert(idx >= 0 && idx < gpu_opt->ncuda_dev_use);
 
     return gpu_info->cuda_dev[gpu_opt->cuda_dev_use[idx]].id;
 }

diff --git a/src/gromacs/gmxlib/topsort.c b/src/gromacs/gmxlib/topsort.c
index 07858aaafbf6259427fc5ddce5c2353a45e5fcd6..c6c976ed5d74242bbeddb172f57beb63cd0f8d1f 100644 (file)
--- a/src/gromacs/gmxlib/topsort.c
+++ b/src/gromacs/gmxlib/topsort.c
@@ -189,7 +189,7 @@ gmx_bool gmx_mtop_bondeds_free_energy(const gmx_mtop_t *mtop)
         }
     }
 
-    return (bPert ? ilsortFE_UNSORTED : ilsortNO_FE);
+    return bPert;
 }
 
 void gmx_sort_ilist_fe(t_idef *idef, const real *qA, const real *qB)

diff --git a/src/gromacs/legacyheaders/topsort.h b/src/gromacs/legacyheaders/topsort.h
index 6179b34150193f7200c9cfc3359e798f1c4ddd4d..649e4b7b14ec91c2f8a00530ce593d673987edd6 100644 (file)
--- a/src/gromacs/legacyheaders/topsort.h
+++ b/src/gromacs/legacyheaders/topsort.h
@@ -43,7 +43,7 @@ extern "C" {
 #endif
 
 
-/* Returns if the are bonded interactions for free energy calculations */
+/* Returns if there are perturbed bonded interactions */
 gmx_bool gmx_mtop_bondeds_free_energy(const gmx_mtop_t *mtop);
 
 /* Sort all the bonded ilists in idef to have the perturbed ones at the end

diff --git a/src/gromacs/mdlib/domdec.c b/src/gromacs/mdlib/domdec.c
index 0e58da49b30a2bd92b53aed199f876352733b2fb..886bbcf813d3be36a9f4d7a36f95f68b014a22db 100644 (file)
--- a/src/gromacs/mdlib/domdec.c
+++ b/src/gromacs/mdlib/domdec.c
@@ -5676,7 +5676,7 @@ void dd_setup_dlb_resource_sharing(t_commrec           gmx_unused *cr,
 
     physicalnode_id_hash = gmx_physicalnode_id_hash();
 
-    gpu_id = get_gpu_device_id(&hwinfo->gpu_info, &hw_opt->gpu_opt, cr->nodeid);
+    gpu_id = get_gpu_device_id(&hwinfo->gpu_info, &hw_opt->gpu_opt, cr->rank_pp_intranode);
 
     dd = cr->dd;
 

diff --git a/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_outer.h b/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_outer.h
index b7e6ac8786444c1f2ebd84a20b56c403f15b02d5..9e22d6c653a30ef462f69325f5ab917f80f13d04 100644 (file)
--- a/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_outer.h
+++ b/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_outer.h
@@ -110,12 +110,12 @@
     const real *tab_coul_V;
 #endif
     /* Thread-local working buffers for force and potential lookups */
-    int        ti0_array[2*GMX_SIMD_WIDTH_HERE-1], *ti0 = NULL;
-    int        ti1_array[2*GMX_SIMD_WIDTH_HERE-1], *ti1 = NULL;
-    int        ti2_array[2*GMX_SIMD_WIDTH_HERE-1], *ti2 = NULL;
-    int        ti3_array[2*GMX_SIMD_WIDTH_HERE-1], *ti3 = NULL;
+    int         ti0_array[2*GMX_SIMD_WIDTH_HERE], *ti0 = NULL;
+    int         ti1_array[2*GMX_SIMD_WIDTH_HERE], *ti1 = NULL;
+    int         ti2_array[2*GMX_SIMD_WIDTH_HERE], *ti2 = NULL;
+    int         ti3_array[2*GMX_SIMD_WIDTH_HERE], *ti3 = NULL;
 #ifdef CALC_ENERGIES
-    gmx_mm_pr  mhalfsp_S;
+    gmx_mm_pr   mhalfsp_S;
 #endif
 #endif
 

diff --git a/src/programs/mdrun/runner.c b/src/programs/mdrun/runner.c
index f43fa0fb34cbb8ed8f304aa0190fdb53f1909190..6d0e85df592da48876de61975e5affb18f6dc79e 100644 (file)
--- a/src/programs/mdrun/runner.c
+++ b/src/programs/mdrun/runner.c
@@ -1473,6 +1473,11 @@ int mdrunner(gmx_hw_opt_t *hw_opt,
         gmx_select_gpu_ids(fplog, cr, &hwinfo->gpu_info, bForceUseGPU,
                            &hw_opt->gpu_opt);
     }
+    else
+    {
+        /* Ignore (potentially) manually selected GPUs */
+        hw_opt->gpu_opt.ncuda_dev_use = 0;
+    }
 
     /* check consistency of CPU acceleration and number of GPUs selected */
     gmx_check_hw_runconf_consistency(fplog, hwinfo, cr, hw_opt, bUseGPU);