Merge branch release-5-1

Change-Id: Iefe28408022b6964e7b1cbab07032f5d110c5f6b

diff --git a/cmake/gmxFindFlagsForSource.cmake b/cmake/gmxFindFlagsForSource.cmake
index d2533e72e40090e29bc336504bd7acb20f42c091..68673f69d0145d0c27c0ec2f2a48e48e342c027c 100644 (file)
--- a/cmake/gmxFindFlagsForSource.cmake
+++ b/cmake/gmxFindFlagsForSource.cmake
@@ -1,7 +1,7 @@
 #
 # This file is part of the GROMACS molecular simulation package.
 #
-# Copyright (c) 2013,2014, by the GROMACS development team, led by
+# Copyright (c) 2013,2014,2016, 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.
@@ -39,6 +39,10 @@
 #                     The compiler is chosen based on the extension of this file
 # FLAGSVAR            Variable (string) to which we should add the correct flag
 # Args 5 through N    Multiple strings with optimization flags to test
+#
+# If a compile flag is found, but the project in check_c_source_compiles
+# fails to build, sets SUGGEST_BINUTILS_UPDATE in parent scope to suggest
+# that the calling code tell the user about this issue if needed.
 FUNCTION(GMX_FIND_CFLAG_FOR_SOURCE VARIABLE DESCRIPTION SOURCE CFLAGSVAR)
     IF(NOT DEFINED ${VARIABLE})
         # Insert a blank element last in the list (try without any flags too)
@@ -55,9 +59,13 @@ FUNCTION(GMX_FIND_CFLAG_FOR_SOURCE VARIABLE DESCRIPTION SOURCE CFLAGSVAR)
             check_c_compiler_flag("${_testflag}" ${COMPILE_FLAG_VARIABLE})
 
             if(${COMPILE_FLAG_VARIABLE})
-                # Check that we can compile SIMD source (this does not catch warnings)
+                # Check that we can compile SIMD source (this does not catch compiler warnings)
                 check_c_source_compiles("${SOURCE}" ${COMPILE_SIMD_VARIABLE})
-            endif(${COMPILE_FLAG_VARIABLE})
+                if(NOT ${COMPILE_SIMD_VARIABLE})
+                    message(STATUS "Compiler flag was valid, but executable did not build - perhaps update the binutils package")
+                    set(SUGGEST_BINUTILS_UPDATE 1 PARENT_SCOPE)
+                endif()
+            endif()
 
             if(${COMPILE_FLAG_VARIABLE} AND ${COMPILE_SIMD_VARIABLE})
                 set(${VARIABLE}_FLAG "${_testflag}" CACHE INTERNAL "${DESCRIPTION}")
@@ -82,6 +90,10 @@ ENDFUNCTION(GMX_FIND_CFLAG_FOR_SOURCE VARIABLE DESCRIPTION SOURCE CFLAGSVAR)
 #                     The compiler is chosen based on the extension of this file
 # FLAGSVAR            Variable (string) to which we should add the correct flag
 # Args 5 through N    Multiple strings with optimization flags to test
+#
+# If a compile flag is found, but the project in check_cxx_source_compiles
+# fails to build, sets SUGGEST_BINUTILS_UPDATE in parent scope to suggest
+# that the calling code tell the user about this issue if needed.
 FUNCTION(GMX_FIND_CXXFLAG_FOR_SOURCE VARIABLE DESCRIPTION SOURCE CXXFLAGSVAR)
 
     IF(NOT DEFINED ${VARIABLE})
@@ -99,9 +111,13 @@ FUNCTION(GMX_FIND_CXXFLAG_FOR_SOURCE VARIABLE DESCRIPTION SOURCE CXXFLAGSVAR)
             check_cxx_compiler_flag("${_testflag}" ${COMPILE_FLAG_VARIABLE})
 
             if(${COMPILE_FLAG_VARIABLE})
-                # Check that we can compile SIMD source (this does not catch warnings)
+                # Check that we can compile SIMD source (this does not catch compiler warnings)
                 check_cxx_source_compiles("${SOURCE}" ${COMPILE_SIMD_VARIABLE})
-            endif(${COMPILE_FLAG_VARIABLE})
+                if(NOT ${COMPILE_SIMD_VARIABLE})
+                    message(STATUS "Compiler flag was valid, but executable did not build - perhaps update the binutils package")
+                    set(SUGGEST_BINUTILS_UPDATE 1 PARENT_SCOPE)
+                endif()
+            endif()
 
             if(${COMPILE_FLAG_VARIABLE} AND ${COMPILE_SIMD_VARIABLE})
                 set(${VARIABLE}_FLAG "${_testflag}" CACHE INTERNAL "${DESCRIPTION}")

diff --git a/cmake/gmxManageGPU.cmake b/cmake/gmxManageGPU.cmake
index eb889d9e471870185c8c2412c231cd08de596366..9b4f328ce71be9b7e6fd847d637ca8560f6ea570 100644 (file)
--- a/cmake/gmxManageGPU.cmake
+++ b/cmake/gmxManageGPU.cmake
@@ -158,7 +158,7 @@ if (GMX_GPU)
         set(NVML_FIND_QUIETLY TRUE)
     endif()
     find_package(NVML)
-    option(GMX_USE_NVML "Use NVML support for better CUDA performance" ${HAVE_NVML})
+    option(GMX_USE_NVML "Use NVML support for better CUDA performance" ${NVML_FOUND})
     mark_as_advanced(GMX_USE_NVML)
     if(GMX_USE_NVML)
         if(NVML_FOUND)

diff --git a/cmake/gmxManageSimd.cmake b/cmake/gmxManageSimd.cmake
index 66fe788f5f1b084fcb4aa2ccf8a1287ad38fae0d..959ac77fc0c09834a64b29506b63ec4abec42e16 100644 (file)
--- a/cmake/gmxManageSimd.cmake
+++ b/cmake/gmxManageSimd.cmake
@@ -1,7 +1,7 @@
 #
 # This file is part of the GROMACS molecular simulation package.
 #
-# Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+# Copyright (c) 2012,2013,2014,2015,2016, 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.
@@ -51,6 +51,21 @@ macro(gmx_use_clang_as_with_gnu_compilers_on_osx)
     endif()
 endmacro()
 
+# Issue a fatal error with an appropriate message, when the toolchain
+# was not able to compile code for SIMD support.
+#
+# Inputs:
+#  SIMD_STRING              A string describing the kind of SIMD support that didn't work.
+#  ALTERNATIVE_SUGGESTION   A string describing anything the user could try other than getting a new compiler.
+#  SUGGEST_BINUTILS_UPDATE  True when there's information that the compiler was OK, but something else was not.
+function(gmx_give_fatal_error_when_simd_support_not_found SIMD_STRING ALTERNATIVE_SUGGESTION SUGGEST_BINUTILS_UPDATE)
+    if(SUGGEST_BINUTILS_UPDATE)
+        set(_msg "Found a compiler flag for ${SIMD_STRING} support, but some other problem exists. Update your assembler and/or linker, e.g. in the binutils package of your distribution.")
+    else()
+        set(_msg "Cannot find ${SIMD_STRING} compiler flag. Use a newer compiler, or ${ALTERNATIVE_SUGGESTION}.")
+    endif()
+    message(FATAL_ERROR ${_msg})
+endfunction()
 
 macro(gmx_manage_simd)
 
@@ -103,7 +118,7 @@ elseif(GMX_SIMD STREQUAL "SSE2")
                                 "-msse2" "/arch:SSE2" "-hgnu")
 
     if(NOT CFLAGS_SSE2 OR NOT CXXFLAGS_SSE2)
-        message(FATAL_ERROR "Cannot find SSE2 compiler flag. Use a newer compiler, or disable SIMD (slower).")
+        gmx_give_fatal_error_when_simd_support_not_found("SSE2" "disable SIMD support (slow)" "${SUGGEST_BINUTILS_UPDATE}")
     endif()
 
     set(GMX_SIMD_X86_SSE2 1)
@@ -124,8 +139,7 @@ elseif(GMX_SIMD STREQUAL "SSE4.1")
                                 "-msse4.1" "/arch:SSE4.1" "/arch:SSE2" "-hgnu")
 
     if(NOT CFLAGS_SSE4_1 OR NOT CXXFLAGS_SSE4_1)
-        message(FATAL_ERROR "Cannot find SSE4.1 compiler flag. "
-                            "Use a newer compiler, or choose SSE2 SIMD (slower).")
+        gmx_give_fatal_error_when_simd_support_not_found("SSE4.1" "choose SSE2 SIMD (slower)" "${SUGGEST_BINUTILS_UPDATE}")
     endif()
 
     if(CMAKE_C_COMPILER_ID MATCHES "Intel" AND CMAKE_C_COMPILER_VERSION VERSION_EQUAL "11.1")
@@ -184,7 +198,7 @@ int main(){__m128 x=_mm_set1_ps(0.5);x=_mm_macc_ps(x,x,x);return _mm_movemask_ps
 
     # We only need to check the last (FMA) test; that will always fail if the basic AVX128 test failed
     if(NOT CFLAGS_AVX_128_FMA OR NOT CXXFLAGS_AVX_128_FMA)
-        message(FATAL_ERROR "Cannot find compiler flags for 128 bit AVX with FMA support. Use a newer compiler, or choose SSE4.1 SIMD (slower).")
+        gmx_give_fatal_error_when_simd_support_not_found("128-bit AVX with FMA support" "choose SSE4.1 SIMD (slower)" "${SUGGEST_BINUTILS_UPDATE}")
     endif()
 
     ### STAGE 3: Optional: Find the XOP instruction flag (No point in yelling if this does not work)
@@ -244,7 +258,7 @@ elseif(GMX_SIMD STREQUAL "AVX_256")
                                 "-mavx" "/arch:AVX" "-hgnu")
 
     if(NOT CFLAGS_AVX OR NOT CXXFLAGS_AVX)
-        message(FATAL_ERROR "Cannot find AVX compiler flag. Use a newer compiler, or choose SSE4.1 SIMD (slower).")
+        gmx_give_fatal_error_when_simd_support_not_found("AVX" "choose SSE4.1 SIMD (slower)" "${SUGGEST_BINUTILS_UPDATE}")
     endif()
 
     gmx_test_avx_gcc_maskload_bug(GMX_SIMD_X86_AVX_GCC_MASKLOAD_BUG "${SIMD_C_FLAGS}")
@@ -268,7 +282,7 @@ elseif(GMX_SIMD STREQUAL "AVX2_256")
                                 "-march=core-avx2" "-mavx2" "/arch:AVX" "-hgnu") # no AVX2-specific flag for MSVC yet
 
     if(NOT CFLAGS_AVX2 OR NOT CXXFLAGS_AVX2)
-        message(FATAL_ERROR "Cannot find AVX2 compiler flag. Use a newer compiler, or choose AVX SIMD (slower).")
+        gmx_give_fatal_error_when_simd_support_not_found("AVX2" "choose AVX SIMD (slower)" "${SUGGEST_BINUTILS_UPDATE}")
     endif()
 
     # No need to test for Maskload bug - it was fixed before gcc added AVX2 support
@@ -298,7 +312,7 @@ elseif(GMX_SIMD STREQUAL "AVX_512F")
                                 "-xMIC-AVX512" "-mavx512f" "/arch:AVX" "-hgnu") # no AVX_512F flags known for MSVC yet
 
     if(NOT CFLAGS_AVX_512F OR NOT CXXFLAGS_AVX_512F)
-        message(FATAL_ERROR "Cannot find AVX 512F compiler flag. Use a newer compiler, or choose a lower level of SIMD")
+        gmx_give_fatal_error_when_simd_support_not_found("AVX 512F" "choose a lower level of SIMD (slower)" "${SUGGEST_BINUTILS_UPDATE}")
     endif()
 
     set(GMX_SIMD_X86_AVX_512F 1)
@@ -320,7 +334,7 @@ elseif(GMX_SIMD STREQUAL "AVX_512ER")
                                 "-xMIC-AVX512" "-mavx512er" "/arch:AVX" "-hgnu") # no AVX_512ER flags known for MSVC yet
 
     if(NOT CFLAGS_AVX_512ER OR NOT CXXFLAGS_AVX_512ER)
-        message(FATAL_ERROR "Cannot find AVX 512ER compiler flag. Use a newer compiler, or choose a lower level of SIMD")
+        gmx_give_fatal_error_when_simd_support_not_found("AVX 512ER" "choose a lower level of SIMD (slower)" "${SUGGEST_BINUTILS_UPDATE}")
     endif()
 
     set(GMX_SIMD_X86_AVX_512ER 1)
@@ -340,7 +354,7 @@ elseif(GMX_SIMD STREQUAL "ARM_NEON")
                                 "-mfpu=neon-vfpv4" "-mfpu=neon" "-D__STDC_CONSTANT_MACROS" "")
 
     if(NOT CFLAGS_ARM_NEON OR NOT CXXFLAGS_ARM_NEON)
-        message(FATAL_ERROR "Cannot find ARM NEON compiler flag. Use a newer compiler, or disable NEON SIMD.")
+        gmx_give_fatal_error_when_simd_support_not_found("ARM NEON" "disable SIMD support (slower)" "${SUGGEST_BINUTILS_UPDATE}")
     endif()
 
     set(GMX_SIMD_ARM_NEON 1)
@@ -360,7 +374,7 @@ elseif(GMX_SIMD STREQUAL "ARM_NEON_ASIMD")
                                 "")
 
     if(NOT CFLAGS_ARM_NEON_ASIMD OR NOT CXXFLAGS_ARM_NEON_ASIMD)
-        message(FATAL_ERROR "Compiler does not fully support ARM (AArch64) NEON Advanced SIMD. Use a newer compiler (gcc version 4.9 or later), or disable SIMD.")
+        gmx_give_fatal_error_when_simd_support_not_found("ARM (AArch64) NEON Advanced SIMD" "particularly gcc version 4.9 or later, or disable SIMD support (slower)" "${SUGGEST_BINUTILS_UPDATE}")
     endif()
 
     if(CMAKE_C_COMPILER_ID MATCHES "Clang" AND CMAKE_C_COMPILER_VERSION VERSION_LESS "3.4")
@@ -381,7 +395,7 @@ elseif(GMX_SIMD STREQUAL "IBM_QPX")
         set(SIMD_STATUS_MESSAGE "Enabling IBM QPX SIMD instructions")
 
     else()
-        message(FATAL_ERROR "Cannot compile the requested IBM QPX intrinsics. If you are compiling for BlueGene/Q with the XL compilers, use 'cmake .. -DCMAKE_TOOLCHAIN_FILE=Platform/BlueGeneQ-static-XL-C' to set up the tool chain.")
+        gmx_give_fatal_error_when_simd_support_not_found("IBM QPX" "or 'cmake .. -DCMAKE_TOOLCHAIN_FILE=Platform/BlueGeneQ-static-XL-CXX' to set up the tool chain" "${SUGGEST_BINUTILS_UPDATE}")
     endif()
 
 elseif(GMX_SIMD STREQUAL "IBM_VMX")
@@ -398,7 +412,7 @@ elseif(GMX_SIMD STREQUAL "IBM_VMX")
                                 "-maltivec -mabi=altivec" "-qarch=auto -qaltivec")
 
     if(NOT CFLAGS_IBM_VMX OR NOT CXXFLAGS_IBM_VMX)
-        message(FATAL_ERROR "Cannot find IBM VMX SIMD compiler flag. Use a newer compiler, or disable VMX SIMD.")
+        gmx_give_fatal_error_when_simd_support_not_found("IBM VMX" "disable SIMD support (slower)" "${SUGGEST_BINUTILS_UPDATE}")
     endif()
 
     set(GMX_SIMD_IBM_VMX 1)
@@ -437,7 +451,7 @@ elseif(GMX_SIMD STREQUAL "IBM_VSX")
                                 "-mvsx" "-maltivec -mabi=altivec" "-qarch=auto -qaltivec")
 
     if(NOT CFLAGS_IBM_VSX OR NOT CXXFLAGS_IBM_VSX)
-        message(FATAL_ERROR "Cannot find IBM VSX SIMD compiler flag. Use a newer compiler, or disable VSX SIMD.")
+        gmx_give_fatal_error_when_simd_support_not_found("IBM VSX" "disable SIMD support (slower)" "${SUGGEST_BINUTILS_UPDATE}")
     endif()
 
     set(GMX_SIMD_IBM_VSX 1)

diff --git a/docs/install-guide/index.rst b/docs/install-guide/index.rst
index 21cb69d763653dc66e5ddbe5c7958ffb931cbd46..ecda804883ce30b871b1554e80ac48584ae858e8 100644 (file)
--- a/docs/install-guide/index.rst
+++ b/docs/install-guide/index.rst
@@ -118,7 +118,10 @@ most recent version of your preferred compiler for your platform.
 There is a large amount of |Gromacs| code that depends on effective
 compiler optimization to get high performance. This makes |Gromacs|
 performance sensitive to the compiler used, and the binary will often
-only work on the hardware for which it is compiled.
+only work on the hardware for which it is compiled. You may also need
+the most recent version compiler toolchain components beside the
+compiler itself (e.g. assembler or linker); these are often shipped by
+the distribution's binutils package.
 
 * In particular, |Gromacs| includes a lot of explicit SIMD (single
   instruction, multiple data) optimization that suits

diff --git a/docs/manual/analyse.tex b/docs/manual/analyse.tex
index 2acd1acdc954e90d6e9c84a5319805f918d3f359..ca3e5344a8a2650b43a21b455701b3d54f42d8f0 100644 (file)
--- a/docs/manual/analyse.tex
+++ b/docs/manual/analyse.tex
@@ -1,7 +1,7 @@
 %
 % This file is part of the GROMACS molecular simulation package.
 %
-% Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+% Copyright (c) 2013,2014,2015,2016, 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.
@@ -731,7 +731,7 @@ provide the radius of gyration around the coordinate axis (or, optionally, princ
 by only summing the radii components orthogonal to each axis, for instance
 \beq
 R_{g,x} ~=~ \left({\frac{\sum_i \left( r_{i,y}^2 + r_{i,z}^2 \right) m_i}{\sum_i m_i}}\right)^{\half}
-\label{eqn:rg}
+\label{eqn:rgaxis}
 \eeq
 
 Sometimes it is interesting to plot the {\em distance} between two atoms,