Bump oldest cmake, compiler and CUDA versions required

Bump oldest cmake, compiler and CUDA versions required

For release 2017 we now require gcc-4.8.1, clang-3.3 and icc-15, so we
can rely on full C++11 support. We now also require CUDA-6.5 and
CMake-3.4.3. This in turn means we can remove some older cmake tests,
and since many users won't read the install guide there are now
version tests that produce fatal errors during CMake configuration for
compiler versions we know are too old.

Various hacks and workarounds in source and build system can
now be removed.

Fixed error in previous definition of GMX_ALIGNED

Updated C++11 compatibility tests in line with code we are now using.

Fixed that hwloc includes were not treated as system headers.

Treated including thread-MPI and TNG header files as system paths, to
be consistent with how we'd treat them if we were using external
versions of these.

Fixed icc 16 warnings in lapack routines.

Fixes #2012.

Change-Id: I36e02379a985b22c72f0f06481c65cae6e780c02