Hack compiler flags to silence warnings on gcc 4.8

GCC changed its default behaviour when reporting a number of different
kinds of warnings. We don't want to fix these in the bugfix branch
because even where it is possible it looks too invasive. We plan to
address these issues in a less heavy-handed manner in master branch.

Note when merging to master, do not include this patch.

Change-Id: I14f00357195424dd538aca4b319e5c2c120c691d
New version of thread_mpi with many minor enhancements

- Fixed issues with collective calls with 1 thread
- Fixed deadlocks with copy buffer turned on
- Turned off copy buffers by default for Gromacs
- Fixed error handling on low-level calls
- Low-level errors are now propagated correctly through MPI
- Simplified the atomics
- Compiles for platforms for which atomics are not supported.
- Added Fujitsu Sparc64 support

Change-Id: I3553906d6630cea8b1efe59fca293fe3c066c8d9
Fujitsu Sparc64 acceleration and general fixes for non-x86 builds

Fixes configurations not to assume x86 and avoid warnings, in
particular if a non-x86 acceleration is used.
The cpu detection code has been extended to parse /proc/cpuinfo on
Linux in cases where the x86 CPUID instruction (or the inline
assembly to execute it) is not available.
Finally, there are new group kernels accelerated for use on the
K computer, which uses the Sparc64 HPC-ACE instruction set. These
kernels are roughly ~35% faster than the compiled C version, which
means Gromacs-4.6 is now ~70% faster on K than Gromacs-4.5.

Change-Id: I92559f0ac6159b504f100447a41a03e4b33fec19
Fixed problem with bond constraint dhdl being left out

At some point, the dhdl from the holonomic bond constraints got left out,
because the term got zeroed before being added to the bonded energy.

Also, I made some of the variable names involved more descriptive to
clarify the logic.

Removed velocity constraint calls, as don't contribute to dhdl.

Fixes redmine #1255

Change-Id: I2eebf357d1a922b7636dc015b09f286827283dd0
Fix -neutral option in genion

The help for -neutral says that it "will add enough ions to neutralize
the system", but this option can only be used in combination with -conc.
This commit makes -neutral independent.

Change-Id: I08b019b05cf3d8511757c4665c24dcaa37968ceb
Updated grompp cut-off and PME-Switch checks

Added a warning with PME-Switch when switching over more than 5%.
Charge-group size rlist notes/warnings now also appear when
potential modifiers are used.
Documented effect of potential-modifiers on the group scheme cut-off
treatment in mdp_opt.html.

Fixes #1179

Change-Id: Ide00caf5ae378104f99611bf197e896d1b53d7d7
Fix genion -nq and -pq when using -neutral

Currently genion can't neutralize (-neutral) systems when -nq/-pq
differs from -1/+1. This commit fixes the problem.

Change-Id: If2a82ace079555d8a684ea876daa947677d5e442
Merge branch 'release-4-6'

Omitted the patch with the hacks for silencing warnings with gcc-4.8,
since we plan to do a proper job of that in master branch.

Some minor conflicts resolved.

Conflicts:
	CMakeLists.txt
	cmake/ThreadMPI.cmake
	src/config.h.cmakein
	src/programs/mdrun/md.c

Change-Id: I2c1f1b9b40100c269eea6b06b7b073491b5e17d6
Merge "Merge branch 'release-4-6'"