Merge release-4-5-patches into release-4-6

Change-Id: I420226d869a1d755c731b9f65b66a29c233e9b6e

diff --combined src/gmxlib/CMakeLists.txt
index 708ede1f7e099e60d745005437b3df82efdaa520,8be047595a02d3931652e0ce158a41e26a37f241..c8ce87dfdf066bb3ac780e896cb04589e1f2b23d
--- 1/src/gmxlib/CMakeLists.txt
--- 2/src/gmxlib/CMakeLists.txt
+++ b/src/gmxlib/CMakeLists.txt
@@@ -6,8 -6,8 +6,8 @@@ include_directories(${CMAKE_CURRENT_SOU
  if(USE_VERSION_H)
      add_custom_target(gmx_version ALL
              COMMAND ${CMAKE_COMMAND} 
 -                -D Git_EXECUTABLE="${Git_EXECUTABLE}"
 -                -D Git_VERSION="${Git_VERSION}"
 +                -D GIT_EXECUTABLE="${GIT_EXECUTABLE}"
 +                -D GIT_VERSION="${GIT_VERSION}"
                  -D PROJECT_VERSION="${PROJECT_VERSION}"
                  -D PROJECT_SOURCE_DIR="${PROJECT_SOURCE_DIR}"
                  -D VERSION_C_CMAKEIN="${CMAKE_SOURCE_DIR}/src/gmxlib/version.c.cmakein"
@@@ -22,12 -22,7 +22,12 @@@ endif(
  # conditionally built, so we cannot use a GLOB_RECURSE here.
  file(GLOB GMXLIB_SOURCES *.c 
       selection/*.c trajana/*.c
 -     statistics/*.c nonbonded/*.c nonbonded/nb_kernel_c/*.c)
 +     statistics/*.c nonbonded/*.c nonbonded/nb_kernel_c/*.c
 +     nonbonded/nb_kernel_adress_c/*.c)
 +
 +if(NOT GMX_USE_PLUGINS)
 +  list(REMOVE_ITEM GMXLIB_SOURCES vmdio.c vmddlopen.c)
 +endif()
  
  # This source file is generated
  file(GLOB VERSION_SOURCE version.c)
@@@ -97,9 -92,9 +97,9 @@@ endif(NOT GMX_EXTERNAL_LAPACK
  
  # This would be the standard way to include thread_mpi, but we want libgmx
  # to link the functions directly
 -#if(GMX_THREADS)
 +#if(GMX_THREAD_MPI)
  #    add_subdirectory(thread_mpi)
 -#endif(GMX_THREADS)
 +#endif(GMX_THREAD_MPI)
  #target_link_libraries(gmx ${GMX_EXTRA_LIBRARIES} ${THREAD_MPI_LIB})
  
  # Files called xxx_test.c are test drivers with a main() function for module xxx.c,
@@@ -111,7 -106,7 +111,7 @@@ file(GLOB SELECTION_TEST selection/test
  list(REMOVE_ITEM GMXLIB_SOURCES ${SELECTION_TEST})
  
  # only fiddle with assembly kernels if we're not doing OpenMM build
- if(NOT GMX_OPENMM) 
+ if(GMX_SSEKERNEL_ASM_SRC AND NOT GMX_OPENMM)
  if(GMX_ASM_USEASM_NASM)
    enable_language(ASM_NASM)
  
@@@ -139,7 -134,7 +139,7 @@@ else(GMX_ASM_USEASM_NASM
    endif()
  
  endif(GMX_ASM_USEASM_NASM)
- endif(NOT GMX_OPENMM)
+ endif(GMX_SSEKERNEL_ASM_SRC AND NOT GMX_OPENMM)
  
  add_library(gmx ${GMXLIB_SOURCES} ${BLAS_SOURCES} ${LAPACK_SOURCES} ${GMX_SSEKERNEL_C_SRC} ${GMX_SSEKERNEL_ASM_SRC} ${FORTRAN_SOURCES} ${GMX_BLUEGENE_C_SRC} ${GMX_PPC_ALTIVEC_SRC} ${THREAD_MPI_SRC})
  target_link_libraries(gmx ${GMX_EXTRA_LIBRARIES}  ${THREAD_LIB})