Merge branch release-2016

Change-Id: I14f7cd22447b8a76110d8b41487666eb49835835

diff --cc cmake/gmxManageSimd.cmake
Simple merge

diff --cc docs/install-guide/index.rst
index 9fc01b432e03b38570d5663cf36777408a9f0f88,eab5e872849fc70d256a7ccd21fe1288eec69675..09950835793bd507346058a0194a5fd7e608f8eb
--- 1/docs/install-guide/index.rst
--- 2/docs/install-guide/index.rst
+++ b/docs/install-guide/index.rst
@@@ -100,12 -100,13 +100,14 @@@ compiler. We recommend gcc, because it 
  frequently provides the best performance.
  
  You should strive to use the most recent version of your
 -compiler. Minimum supported compiler versions are
 +compiler. Since we require full C++11 support the minimum supported
 +compiler versions are
+ 
 -* GNU (gcc) 4.6
 -* Intel (icc) 14
 -* LLVM (clang) 3.4
 +* GNU (gcc) 4.8.1
 +* Intel (icc) 15.0
 +* LLVM (clang) 3.3
  * Microsoft (MSVC) 2015
+ 
  Other compilers may work (Cray, Pathscale, older clang) but do
  not offer competitive performance. We recommend against PGI because
  the performance with C++ is very bad.

diff --cc src/gromacs/gmxana/gmx_do_dssp.cpp
Simple merge

diff --cc src/gromacs/gmxana/gmx_mindist.cpp
Simple merge

diff --cc src/gromacs/gmxana/gmx_traj.cpp
Simple merge

diff --cc src/gromacs/gmxana/gmx_trjconv.cpp
Simple merge

diff --cc src/gromacs/gmxana/gmx_tune_pme.cpp
Simple merge

diff --cc src/gromacs/gmxpreprocess/readir.cpp
Simple merge

diff --cc src/gromacs/gmxpreprocess/solvate.cpp
Simple merge

diff --cc src/gromacs/listed-forces/pairs.cpp
Simple merge

diff --cc src/gromacs/mdlib/sim_util.cpp
index 38dbbd4a67cd99ade440e11a71ca4665151e2389,4973896b2c3efd2d5eada84210a6b2b444b12a5a..f0bbde93e52d96c12ad3ad79cd3e124d9566ebc8
--- 1/src/gromacs/mdlib/sim_util.cpp
--- 2/src/gromacs/mdlib/sim_util.cpp
+++ b/src/gromacs/mdlib/sim_util.cpp
@@@ -2487,8 -2587,9 +2497,8 @@@ void finish_run(FILE *fplog, const gmx:
  
      if (!walltime_accounting_get_valid_finish(walltime_accounting))
      {
 -        md_print_warn(cr, fplog,
 -                      "Simulation ended prematurely, no performance report will be written.");
 +        GMX_LOG(mdlog.warning).asParagraph().appendText("Simulation ended prematurely, no performance report will be written.");
-         return;
+         printReport = false;
      }
  
      if (cr->nnodes > 1)
@@@ -2549,11 -2650,11 +2559,11 @@@
      wallcycle_scale_by_num_threads(wcycle, cr->duty == DUTY_PME, nthreads_pp, nthreads_pme);
      auto cycle_sum(wallcycle_sum(cr, wcycle));
  
-     if (SIMMASTER(cr))
+     if (printReport)
      {
 -        struct gmx_wallclock_gpu_t* gputimes = use_GPU(nbv) ? nbnxn_gpu_get_timings(nbv->gpu_nbv) : NULL;
 +        struct gmx_wallclock_gpu_t* gputimes = use_GPU(nbv) ? nbnxn_gpu_get_timings(nbv->gpu_nbv) : nullptr;
  
 -        wallcycle_print(fplog, cr->nnodes, cr->npmenodes, nthreads_pp, nthreads_pme,
 +        wallcycle_print(fplog, mdlog, cr->nnodes, cr->npmenodes, nthreads_pp, nthreads_pme,
                          elapsed_time_over_all_ranks,
                          wcycle, cycle_sum, gputimes);
  

diff --cc src/gromacs/utility/binaryinformation.cpp
Simple merge

diff --cc src/programs/mdrun/md.cpp
index 2e58d0a7660190baa6d93f4e3a8281c31a03290f,8cf13863611a9927aea73f5f5e7d6303901a20da..0a52bbe3017c56414e301ec61a1d36d5d6ee39b8
--- 1/src/programs/mdrun/md.cpp
--- 2/src/programs/mdrun/md.cpp
+++ b/src/programs/mdrun/md.cpp
@@@ -1268,10 -1276,10 +1275,10 @@@ double gmx::do_md(FILE *fplog, t_commre
                                   bCPT, bRerunMD, bLastStep, (Flags & MD_CONFOUT),
                                   bSumEkinhOld);
          /* Check if IMD step and do IMD communication, if bIMD is TRUE. */
 -        bIMDstep = do_IMD(ir->bIMD, step, cr, bNS, state->box, state->x, ir, t, wcycle);
 +        bIMDstep = do_IMD(ir->bIMD, step, cr, bNS, state->box, as_rvec_array(state->x.data()), ir, t, wcycle);
  
          /* kludge -- virial is lost with restart for MTTK NPT control. Must reload (saved earlier). */
-         if (startingFromCheckpoint && bTrotter)
+         if (startingFromCheckpoint && (inputrecNptTrotter(ir) || inputrecNphTrotter(ir)))
          {
              copy_mat(state->svir_prev, shake_vir);
              copy_mat(state->fvir_prev, force_vir);

diff --cc src/testutils/CMakeLists.txt
index 0b3dc645eed307cd51dd40afde6f009baa64fe1c,da1fc6a6603530da8b06e35fd1c8540abc21220d..0f1afabcebae4ec4b9d9835c97eca874ef83e15a
--- 1/src/testutils/CMakeLists.txt
--- 2/src/testutils/CMakeLists.txt
+++ b/src/testutils/CMakeLists.txt
@@@ -40,11 -35,10 +40,12 @@@ endif(
  include_directories(BEFORE SYSTEM ${GMOCK_INCLUDE_DIRS})
  set(TESTUTILS_SOURCES
      cmdlinetest.cpp
+     conftest.cpp
      integrationtests.cpp
      interactivetest.cpp
 +    loggertest.cpp
      mpi-printer.cpp
 +    mpitest.cpp
      refdata.cpp
      refdata-xml.cpp
      stringtest.cpp