Merge "Merge release-5-0 into master"

diff --git a/src/gromacs/commandline/cmdlineinit.cpp b/src/gromacs/commandline/cmdlineinit.cpp
index 017f2b31c87fd52a690088281b8092b6b5f34143..853901386c8bc495de91d6a608ec38b749633515 100644 (file)
--- a/src/gromacs/commandline/cmdlineinit.cpp
+++ b/src/gromacs/commandline/cmdlineinit.cpp
@@ -58,6 +58,8 @@
 #include "gromacs/utility/programcontext.h"
 #include "gromacs/utility/smalloc.h"
 
+#include "config.h"
+
 namespace gmx
 {
 

diff --git a/src/gromacs/gmxana/gmx_pme_error.cpp b/src/gromacs/gmxana/gmx_pme_error.cpp
index 0d33fa3d702ada433c85a0e16b7d6b0de42c0117..b132b6b2b16ad4641a4d06492e91f8dda5d75f25 100644 (file)
--- a/src/gromacs/gmxana/gmx_pme_error.cpp
+++ b/src/gromacs/gmxana/gmx_pme_error.cpp
@@ -58,6 +58,8 @@
 
 #include "gromacs/utility/fatalerror.h"
 
+#include "config.h"
+
 /* We use the same defines as in mvdata.c here */
 #define  block_bc(cr,   d) gmx_bcast(     sizeof(d),     &(d), (cr))
 #define nblock_bc(cr, nr, d) gmx_bcast((nr)*sizeof((d)[0]), (d), (cr))

diff --git a/src/gromacs/gmxlib/nonbonded/nb_kernel_avx_128_fma_single/kernelutil_x86_avx_128_fma_single.h b/src/gromacs/gmxlib/nonbonded/nb_kernel_avx_128_fma_single/kernelutil_x86_avx_128_fma_single.h
index 319ad63efa49a51665eaa0aaf9037bd2dd918fbe..1715f97cbc0d28939b0109262860937bfcb25bb7 100644 (file)
--- a/src/gromacs/gmxlib/nonbonded/nb_kernel_avx_128_fma_single/kernelutil_x86_avx_128_fma_single.h
+++ b/src/gromacs/gmxlib/nonbonded/nb_kernel_avx_128_fma_single/kernelutil_x86_avx_128_fma_single.h
@@ -35,6 +35,7 @@
 #ifndef _kernelutil_x86_avx_128_fma_single_h_
 #define _kernelutil_x86_avx_128_fma_single_h_
 
+#include "config.h"
 
 #include <math.h>
 #include <immintrin.h>

diff --git a/src/gromacs/gmxlib/nonbonded/nb_kernel_avx_256_single/kernelutil_x86_avx_256_single.h b/src/gromacs/gmxlib/nonbonded/nb_kernel_avx_256_single/kernelutil_x86_avx_256_single.h
index 171e1653ecbc0c36e4857d3d394d316bc66614e9..eacf202462a7a6d4dd1fe1cd63ee3bb170ce35e7 100644 (file)
--- a/src/gromacs/gmxlib/nonbonded/nb_kernel_avx_256_single/kernelutil_x86_avx_256_single.h
+++ b/src/gromacs/gmxlib/nonbonded/nb_kernel_avx_256_single/kernelutil_x86_avx_256_single.h
@@ -35,6 +35,8 @@
 #ifndef _kernelutil_x86_avx_256_single_h_
 #define _kernelutil_x86_avx_256_single_h_
 
+#include "config.h"
+
 #define gmx_mm_castsi128_ps(a) _mm_castsi128_ps(a)
 
 static gmx_inline __m256 gmx_simdcall

diff --git a/src/gromacs/imd/imd.h b/src/gromacs/imd/imd.h
index 212ea954bfd4e590df9a9d403bcdb387ff347fa1..f6f26f2c3bd15404dd46e7575b40a568c2982103 100644 (file)
--- a/src/gromacs/imd/imd.h
+++ b/src/gromacs/imd/imd.h
@@ -64,6 +64,8 @@
 #include "../fileio/filenm.h"
 #include "../timing/wallcycle.h"
 
+#include "config.h"
+
 #ifdef GMX_NATIVE_WINDOWS
 #include <Windows.h>
 #define NOFLAGS 0

diff --git a/src/gromacs/imd/imdsocket.h b/src/gromacs/imd/imdsocket.h
index 5903db3cacecf627f22335f66029412f0b2a821e..d7f0ce95482b4d4ba3f0938a8f56b0adc2d6dcfc 100644 (file)
--- a/src/gromacs/imd/imdsocket.h
+++ b/src/gromacs/imd/imdsocket.h
@@ -51,6 +51,8 @@
 #ifndef GMX_IMD_IMDSOCKET_H
 #define GMX_IMD_IMDSOCKET_H
 
+#include "config.h"
+
 /* Check if we can/should use winsock or standard UNIX sockets. */
 #ifdef GMX_NATIVE_WINDOWS
   #ifdef GMX_HAVE_WINSOCK

diff --git a/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_data_mgmt.h b/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_data_mgmt.h
index a600fdf1bbe80642ac5acd714cfa3a195a39dea8..b3c34e9a446f10ab32cc6e823d4653d0f130faad 100644 (file)
--- a/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_data_mgmt.h
+++ b/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_data_mgmt.h
@@ -41,6 +41,8 @@
 #include "gromacs/legacyheaders/types/nbnxn_cuda_types_ext.h"
 #include "gromacs/legacyheaders/types/hw_info.h"
 
+#include "config.h"
+
 #ifdef GMX_GPU
 #define FUNC_TERM ;
 #define FUNC_QUALIFIER

diff --git a/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_simd_utils.h b/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_simd_utils.h
index 6eb97445b02e3fb40632135e91b18c0de54b7181..5d081738f85d0359fa21ece0c35ce7eb69a8b11c 100644 (file)
--- a/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_simd_utils.h
+++ b/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_simd_utils.h
@@ -37,6 +37,8 @@
 
 #include "gromacs/legacyheaders/types/simple.h"
 
+#include "config.h"
+
 /*! \brief Provides hardware-specific utility routines for the SIMD kernels.
  *
  * Defines all functions, typedefs, constants and macros that have

diff --git a/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h b/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h
index 228fa8b25831d5e5b85e4d46644c2c1b6fe00fe0..a87ca0eb169f9d344beb90311960b78106c8026c 100644 (file)
--- a/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h
+++ b/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h
@@ -49,7 +49,7 @@
 #define UNROLLJ    (GMX_SIMD_REAL_WIDTH/GMX_SIMD_J_UNROLL_SIZE)
 
 /* The stride of all the atom data arrays is equal to half the SIMD width */
-#define STRIDE     (GMX_SIMD_REAL_WIDTH/GMX_SIMD_J_UNROLL_SIZE)
+#define STRIDE     UNROLLJ
 
 #include "../nbnxn_kernel_simd_utils.h"
 

diff --git a/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_inner.h b/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_inner.h
index c051d7e763696668fbdea0f26f390ae12752875e..2f45b53bafe0acd349b949ad2bf60e603a0e1220 100644 (file)
--- a/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_inner.h
+++ b/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_inner.h
@@ -247,17 +247,9 @@
     /* Atom indices (of the first atom in the cluster) */
     aj            = cj*UNROLLJ;
 #if defined CALC_LJ && (defined LJ_COMB_GEOM || defined LJ_COMB_LB || defined LJ_EWALD_GEOM)
-#if UNROLLJ == STRIDE
     aj2           = aj*2;
-#else
-    aj2           = (cj>>1)*2*STRIDE + (cj & 1)*UNROLLJ;
-#endif
 #endif
-#if UNROLLJ == STRIDE
     ajx           = aj*DIM;
-#else
-    ajx           = (cj>>1)*DIM*STRIDE + (cj & 1)*UNROLLJ;
-#endif
     ajy           = ajx + STRIDE;
     ajz           = ajy + STRIDE;
 

diff --git a/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h b/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h
index 32d5554e87bbe797bb616f63c03c08f2c31dd1eb..9216457430e57b278fdd7818fc5202fa2cd03bda 100644 (file)
--- a/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h
+++ b/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h
@@ -41,6 +41,8 @@
 #include "gromacs/math/utilities.h"
 #endif
 
+#include "config.h"
+
 #ifndef GMX_SIMD_J_UNROLL_SIZE
 #error "Need to define GMX_SIMD_J_UNROLL_SIZE before including the 4xn kernel common header file"
 #endif

diff --git a/src/gromacs/mdlib/nbnxn_search_simd_4xn.h b/src/gromacs/mdlib/nbnxn_search_simd_4xn.h
index ab98088ae48860fee506f734ddce0a6b70ba5a57..33a307b58456ab8080b37e6c0309915d0f148217 100644 (file)
--- a/src/gromacs/mdlib/nbnxn_search_simd_4xn.h
+++ b/src/gromacs/mdlib/nbnxn_search_simd_4xn.h
@@ -33,6 +33,7 @@
  * the research papers on the package. Check out http://www.gromacs.org.
  */
 
+#include "config.h"
 
 #if GMX_SIMD_REAL_WIDTH >= NBNXN_CPU_CLUSTER_I_SIZE
 #define STRIDE_S  (GMX_SIMD_REAL_WIDTH)

diff --git a/src/gromacs/selection/parser_internal.h b/src/gromacs/selection/parser_internal.h
index a9482fa856b07d40abf2b3fdb8e5a9d8873d069d..b74ce1a313c3e07be49b2d1298c1694003b9b515 100644 (file)
--- a/src/gromacs/selection/parser_internal.h
+++ b/src/gromacs/selection/parser_internal.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2012, by the GROMACS development team, led by
+ * Copyright (c) 2012,2014, 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.
@@ -57,6 +57,8 @@
 
 #include "scanner.h"
 
+#include "config.h"
+
 //! Error handler needed by Bison.
 static void
 yyerror(yyscan_t scanner, char const *s)

diff --git a/src/programs/mdrun/tests/replicaexchange.cpp b/src/programs/mdrun/tests/replicaexchange.cpp
index d972b859da38df2a9c5eac0fbc79c04ad1a214e4..ea8a7b20c64e4b2f7ac1f6a8768c702b8f2797ea 100644 (file)
--- a/src/programs/mdrun/tests/replicaexchange.cpp
+++ b/src/programs/mdrun/tests/replicaexchange.cpp
@@ -59,6 +59,8 @@
 
 #include "testutils/cmdlinetest.h"
 
+#include "config.h"
+
 namespace
 {