Merge branch release-2016

Change-Id: Idb888bea9e78a9979468ff0c2bc2c02443e02026

diff --cc admin/builds/post-submit-matrix.txt
index 52f77725293434d9f3283cb06de146faf46a5697,fc2f6a19afe03b73a63b8949e3eb80530250dfbc..c839021f815ae4d676d7a56d8a38a3323280e655
--- 1/admin/builds/post-submit-matrix.txt
--- 2/admin/builds/post-submit-matrix.txt
+++ b/admin/builds/post-submit-matrix.txt
@@@ -1,15 -1,14 +1,22 @@@
  # Comment line(s) preceding each configuration document the main
  # intent behind that configuration, so that we can correctly judge
  # whether to preserve that during maintenance decisions.
+ #
+ # Other configurations might coincidentally test such configurations
+ # (e.g. because they are the current default), but it is appropriate
+ # to intend to teach each feature (or a feature combination) exactly
+ # once, and for the intent to be reflected precisely in the
+ # configuration syntax, so that the configurations are stable even
+ # if the defaults change in future.
  
 +# Test on ARM v7
 +# Test ARM_NEON SIMD
 +gcc-4.8 simd=ARM_NEON release
 +
 +# Test on ARM v8
 +# Test ARM_NEON_ASIMD SIMD
 +gcc-5 simd=ARM_NEON_ASIMD release
 +
  # Test the mdrun-only build
  # TODO In combination with gmx from another build, arrange to run regressiontests
  clang-3.7 double mpi no-openmp fftpack mdrun-only

diff --cc admin/builds/pre-submit-matrix.txt
index 1dd25a6eebfa46510314a05c96a9a6e3a0f04347,124f966871d1ca3f004af8fdd0bd29dcf8435ebd..d3500728f3e32425cdfaa9fd1584166b05c2eb31
--- 1/admin/builds/pre-submit-matrix.txt
--- 2/admin/builds/pre-submit-matrix.txt
+++ b/admin/builds/pre-submit-matrix.txt
@@@ -2,11 -2,12 +2,18 @@@
  # intent behind that configuration, so that we can correctly judge
  # whether to preserve that during maintenance decisions.
  #
+ # Other configurations might coincidentally test such configurations
+ # (e.g. because they are the current default), but it is appropriate
+ # to intend to teach each feature (or a feature combination) exactly
+ # once, and for the intent to be reflected precisely in the
+ # configuration syntax, so that the configurations are stable even
+ # if the defaults change in future.
++#
 +# The phrase "at time of release" refers to either the initial
 +# GROMACS release from that branch, or the next expected release
 +# from that branch. (We will tend not to retroactively support
 +# newer infrastructure in CI, unless it's either easy or of
 +# high impact.)
  
  # Test older gcc
  # Test oldest supported CUDA
@@@ -18,26 -24,23 +25,27 @@@ gcc-4.8 gpu cuda-6.5 mpi npme=1 nranks=
  
  # Test newest gcc supported by newest CUDA at time of release
  # Test thread-MPI with CUDA
- # Test SIMD (AVX2_256) GPU code-path
- gcc-5 gpu cuda-8.0 openmp release simd=avx2_256
 -gcc-4.8 gpu thread-mpi cuda-7.5 openmp release
++# Test SIMD implementation of pair search for GPU code-path
++gcc-5 gpu cuda-8.0 thread-mpi openmp release simd=avx2_256
  
 -# Test with ThreadSanitizer
 +# Test with ThreadSanitizer (without OpenMP, because of Redmine #1850)
  # Test AVX2_256 SIMD
  # Test fftpack fallback
  gcc-4.9 tsan fftpack simd=avx2_256
  
  # Test newest gcc at time of release
- # Test on MacOS
 -# Test on MacOS (because gcc-6.1 is only available there)
 -gcc-6.1 double
++# Test on MacOS (because gcc-6 is only available there)
 +gcc-6 double
  
  # Test older clang
  # Test double precision
 -# Test with AddressSanitizer
  # Test without OpenMP
- clang-3.4 double no-openmp fftpack
+ # Test thread-MPI
 -clang-3.4 double thread-mpi no-openmp fftpack asan
++clang-3.4 double thread-mpi no-openmp fftpack
 +
 +# Test newest clang at time of release
 +# Test with AddressSanitizer (without OpenMP, see below)
 +clang-4 no-openmp asan
  
  # Test oldest supported MSVC on Windows
  # Test newest supported MSVC on Windows
@@@ -50,12 -53,11 +58,12 @@@ icc-16.0 msvc-2015 fftpac
  # Test newest cmake at time of release
  # Test MKL
  # Test without any MPI
- # Test on CentOS
+ # Test on CentOS (because icc-16.0 is only available there)
 -icc-16.0 no-thread-mpi openmp mkl cmake-3.3.2 simd=avx_256
 +icc-16.0 no-thread-mpi openmp mkl cmake-3.6.1 simd=avx_256
  
 +# Test oldest supported cmake
  # Test AVX_128_FMA SIMD
 -gcc-5 mpi openmp simd=avx_128_fma
 +gcc-5 mpi openmp simd=avx_128_fma cmake-3.4.3
  
  # Test NVIDIA OpenCL
  # Test MPI + OpenCL

diff --cc src/gromacs/imd/imd.cpp
Simple merge

diff --cc src/gromacs/imd/imdsocket.cpp
Simple merge