Made mdrun more verbose about PME split

Change-Id: Ieda0ba5dcf08260cf94ad9aefd8937e067f2c6e2
Added more suggested strategies to error message

Change-Id: I4a68ea06697890175bb03e900664dd9bb886305c
Fix endian test functionality

Code for big-endian systems was silently failing with CMake. This
patch brings CMake and autotools into agreement.

Partial fix of #944
Change-Id: I1f14938fd23e926e05397977963fbf968f0406e0
Work around failure of endianness testing on BlueGene

Refs #944

Change-Id: I4bbfe9865800bbe4e407a88cdecec6678d56f3b4
Merge "Added more suggested strategies to error message" into release-4-5-patches
Small fix for g_tune_pme

Change-Id: I12fd2e48dc409f87b270f1ddaaaf2d1a83683fd1
Merge "Made mdrun more verbose about PME split" into release-4-5-patches
Merge "Work around failure of endianness testing on BlueGene" into release-4-5-patches
Fix g_lie counting last frame twice

Change-Id: Ia1c37e79843cd0e10d5e8444d004c7aca9cce87a
Makes g_hbond -contact work

Fixes #955

Change-Id: I5d421d5f2e25d3801497efccb291425f90480a8c
Quiet linker on BlueGene

Change-Id: Ib105a93ca233c763d3b6caf3c3c636a673078986
Simple patch for openmm_wrapper.cpp

The naming of several variables is changed to be consistent with the
latest free energy changes.  Allows mdrun-gpu to be compiled, which
otherwise fails (as reported on gmx-developers).

Change-Id: I497ba07ee6883ef78d23022450f6c3d971b2127e
Fixes #882 -  looping bug in trxio.c

This led to infinite output files in the case of a corrupt
input file.

Change-Id: I25d61752d901012e9ce5e6adae1679c2ef99467a
New CPU detection & AVX/SSE code, removed raw assembly files.

Removed all raw assembly files and deprecated altivec support.
Removed support for NASM and other assemblers, and replaced
previous SSE detection code with a new module using CPUID instead.
Added detection for SSE2, SSE4.1, AVX 128-bit with FMA, and AVX 256-bit.
Added Cmake detection of build platform based on CPUID, and output this
to the log file. The executables now compare the compile-time platform
and selected acceleration with the run-time platform and most suitable
acceleration and warns the user if they do not match. The compiler
detection code has also been reordered slightly to produce more readable
warnings when OpenMP is not available, and correctly disable pragma
warnings.

Added intrinsics code and math functions for SSE2, SSE4.1, AVX128/256
both in single and double precision. All math functions and permutation
code have been tested & verified. Single precision math functions are
correct apart from the least significant bit, and double precision has
roughly twice the accuracy.

This has forced me to temporarily disable the SSE & Fortran acceleration.
SSE will be added back soon based on new intrinsics-only kernels currently
in testing, and we will test if Fortran still makes sense then.

Finally, the patch includes a modification to gmx_rmsdist where
a regression issue was introduced recently by using sqrtf() for
the norm function. This caused the intel compiler to produce slightly
different results at high optimization leves, which got evident here.

Closes #926 - Raw assembly code has been removed.
Refs #923 - Old kernels removed, new will be added shortly.
Fixes #914 - Cmake now does architecture-speficic optimization.
Fixes #912, #913
Fixes #857 - We detect rdtscp support with CPUID and use it if possible.
Fixes #750
Closes #537, #574 - Altivec is now deprecated.

Change-Id: Icfca5a940762f8d82ae67b59c65b2d2ac683256d
gmx_dyecoupl: check selected groups from user

check if the user accidentally selected the same group twice. Abort
with error, since this will not produce any meaningful results.

Change-Id: Iace69c473e5f1b815e35d20a39845533297ad208
Merge "Fix g_lie counting last frame twice" into release-4-5-patches
Merge "Quiet linker on BlueGene" into release-4-5-patches
Merge "Fixes #882 -  looping bug in trxio.c" into release-4-5-patches
Correct normalization for HB-contact c-correlation.

Fixes #960

Change-Id: I391dd84fd38e784ac6c311dd913284de47d6a93d
Fix gmx_fatal for serial compilation

With neither GMX_MPI nor GMX_THREAD_MPI gmx_fatal
called gmx_abort which called gmx_fatal.

Change-Id: Id18c3bc94f19a8008fa2aaa8335c221f115fcd8b