Merge remote-tracking branch 'gerrit/release-4-5-patches' into release-4-6

Change-Id: I825d441cf0d13d53ea8b460cb97e2e7775f2e8ce

diff --cc cmake/gmxCFlags.cmake
index 855c19a0b1e6be5718c044d9abd40826bdc7e916,8e41dfd0226ac7ab28b79e472ac0ae49a5de2000..6dc46b8ca36ee8d9d77471b203cd2f99426069f9
--- 1/cmake/gmxCFlags.cmake
--- 2/cmake/gmxCFlags.cmake
+++ b/cmake/gmxCFlags.cmake
@@@ -58,16 -51,13 +58,16 @@@ MACRO(gmx_c_flags
      # icc
      if (CMAKE_C_COMPILER_ID MATCHES "Intel")
          if (NOT WIN32) 
-             GMX_TEST_CFLAG(CFLAGS_OPT "-ip -funroll-all-loops -std=gnu99" 
-                             GMXC_CFLAGS)
-             GMX_TEST_CFLAG(CFLAGS_SSE2 "-msse2" GMXC_CFLAGS)
+             GMX_TEST_CFLAG(CFLAGS_OPT "-std=gnu99" GMXC_CFLAGS)
+             GMX_TEST_CFLAG(CFLAGS_OPT "-ip -funroll-all-loops" GMXC_CFLAGS_RELEASE)
+             GMX_TEST_CFLAG(CFLAGS_SSE2 "-msse2" GMXC_CFLAGS_RELEASE)
              GMX_TEST_CFLAG(CFLAGS_X86 "-mtune=core2" GMXC_CFLAGS_RELEASE)
              GMX_TEST_CFLAG(CFLAGS_IA64 "-mtune=itanium2" GMXC_CFLAGS_RELEASE)
 +            if(NOT GMX_OPENMP)
 +                GMX_TEST_CFLAG(CFLAGS_PRAGMA "-Wno-unknown-pragmas" GMXC_CFLAGS)
 +            endif()
          else()
-             GMX_TEST_CFLAG(CFLAGS_SSE2 "/arch:SSE2" GMXC_CFLAGS)
+             GMX_TEST_CFLAG(CFLAGS_SSE2 "/arch:SSE2" GMXC_CFLAGS_RELEASE)
              GMX_TEST_CFLAG(CFLAGS_X86 "/Qip" GMXC_CFLAGS_RELEASE)
          endif()
      endif()
@@@ -81,11 -70,8 +80,11 @@@
              GMX_TEST_CXXFLAG(CXXFLAGS_X86 "-mtune=core2" GMXC_CXXFLAGS_RELEASE)
              GMX_TEST_CXXFLAG(CXXFLAGS_IA64 "-mtune=itanium2" 
                                GMXC_CXXFLAGS_RELEASE)
 +            if(NOT GMX_OPENMP)
 +                GMX_TEST_CFLAG(CXXFLAGS_PRAGMA "-Wno-unknown-pragmas" GMXC_CXXFLAGS)
 +            endif()
          else()
-             GMX_TEST_CXXFLAG(CXXFLAGS_SSE2 "/arch:SSE2" GMXC_CXXFLAGS)
+             GMX_TEST_CXXFLAG(CXXFLAGS_SSE2 "/arch:SSE2" GMXC_CXXFLAGS_RELEASE)
              GMX_TEST_CXXFLAG(CXXFLAGS_X86 "/Qip" GMXC_CXXFLAGS_RELEASE)
          endif()
      endif()

diff --cc src/kernel/readir.c
Simple merge

diff --cc src/kernel/tpbcmp.c
Simple merge