Version 2018

Removed "-rc1" per policy. Bumped regressiontests hash.

Updated release notes for final release, including release date, and
removing beta-phase fix content. Sorted tools page by tool name/topic.
Fixed some text to refer to changes in the past tense. Updated
some line wrapping.

Change-Id: Ia82a1cef3270dbdddd173c58248fc9bf6ea420c5

cmake/gmxVersionInfo.cmake

@@ -191,7 +191,7 @@ set(GMX_VERSION_PATCH 0)
 # candidates, where it signifies the most recent such release from
 # this branch; it will be empty before the first such release, as well
 # as after the final release is out.
-set(GMX_VERSION_SUFFIX "-rc1")
+set(GMX_VERSION_SUFFIX "")
 
 # Conventionally with libtool, any ABI change must change the major
 # version number, the minor version number should change if it's just
@@ -226,7 +226,7 @@ endif()
 
 set(REGRESSIONTEST_VERSION "${GMX_VERSION_STRING}")
 set(REGRESSIONTEST_BRANCH "refs/heads/release-2018")
-set(REGRESSIONTEST_MD5SUM "d4c535a06fd8f34c9fd21e7ee5a30808" CACHE INTERNAL "MD5 sum of the regressiontests tarball")
+set(REGRESSIONTEST_MD5SUM "5a609bea6b6777072063be9e665121ef" CACHE INTERNAL "MD5 sum of the regressiontests tarball")
 
 math(EXPR GMX_VERSION_NUMERIC
      "${GMX_VERSION_MAJOR}*10000 + ${GMX_VERSION_PATCH}")

docs/release-notes/bugs-fixed.rst

@@ -1,5 +1,3 @@
-.. TODO Remove beta-phase fixes below before final release
-
 Bugs fixed
 ^^^^^^^^^^
 
@@ -19,25 +17,25 @@ nstpcouple steps. Note that this change prevents continuation from old
 checkpoint files for Berendsen pressuring-coupling runs, since the
 previous-step pressure is no longer stored.
 
-Add missing Ewald correction for PME-User
+Added missing Ewald correction for PME-User
 """"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 With :mdp-value:`coulombtype=PME-User`, the Ewald mesh energy was not subtracted
 leading to (very) incorrect Coulomb energies and forces.
 
 Fixes :issue:`2286`
 
-Fix incorrect dV/dlambda for walls
+Fixed incorrect dV/dlambda for walls
 """"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
-The free-energy derivative dV/dlambda for walls, which can
-be perturbed by changing atom types of non-wall atoms, only
-contained the B-state contribution.
+The free-energy derivative dV/dlambda for walls, which can be
+perturbed by changing atom types of non-wall atoms, only contained the
+B-state contribution.
 
 Fixes :issue:`2267`
 
 Supported OpenMP for orientation restraints
 """"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
-Previously this was broken, but has been fixed and is now tested
-and supported.
+Previously this was broken, but has been fixed and is now tested and
+supported.
 
 Fixed orientation restraint reference
 """"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
@@ -58,7 +56,7 @@ restraints.
 
 Fixes :issue:`2228`
 
-Fix Ekin at step 0 with COM removal
+Fixed Ekin at step 0 with COM removal
 """"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 The kinetic energy at step 0 was computed from the velocities without
 the center of mass velocity removed. This could cause a relatively
@@ -125,7 +123,7 @@ the intention of ``mdrun -reprod``, and is now fixed.
 
 Refs Fixes :issue:`2318`
 
-Now mdrun only stops at nstlist steps with mdrun -reprod
+Made mdrun only stop at nstlist steps with mdrun -reprod
 """"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 Stopping mdrun with two INT or TERM signals (e.g. from Ctrl-C from the
 terminal shell) would always happen right after the first global
@@ -146,8 +144,7 @@ Fixes :issue:`2322`
 
 Removed duplicated lines from OPLS ffbonded.itp
 """"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
-Identical lines have been removed, as identified
-with uniq.
+Identical lines have been removed, as identified with uniq.
 
 Fixes :issue:`1678`.
 
@@ -254,206 +251,3 @@ number of ranks, but it's safer to ask the user to explicity set
 always worked correctly.
 
 Fixes :issue:`2348`
-
-``mdrun -pme cpu -pmefft gpu`` now gives a fatal error  - beta-phase fix
-""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
-Previously was silently ignored.
-
-Fixed mdrun -nb auto -pme auto when GPUs are absent - beta-phase fix
-""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
-The logic was flawed such that GPUs were "selected" for use even
-though none had been detected. That led to the GPU behaviour of
-avoiding using separate PME ranks.
-
-Also made a minor fix to the logic for emulation. The new
-interpretation of ``mdrun -gpu_id`` does not need to trigger an error
-when GPU IDs have been supplied along with the emulation environmnet
-variable.
-
-Fixes :issue:`2315`
-
-Fixed ArrayRef<SimdDInt32> for SSE/AVX128 - beta-phase fix
-""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
-Fixes :issue:`2326`
-
-Fixed PME gather in double with AVX(2)_128 - beta-phase fix
-""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
-The 4NSIMD PME gather change did not change the conditional
-for grid alignment. This is made consistent here.
-Note that the 4NSIMD change lowered the performance of PME gather
-on AVX_128_FMA and AVX2_128 in double precision. We should consider
-using 256-bit AVX for double precision instead.
-
-Fixes :issue:`2326`
-
-Reformulated PME and SHAKE test tolerances - beta-phase fix
-""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
-Fixes :issue:`2306`
-Fixes :issue:`2337`
-Fixes :issue:`2338`
-
-Fixed freeing of GPU context - beta-phase fix
-""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
-If a device context was not used, CUDA gives an error if we attempt to
-clear it, so we must avoid clearing it.
-
-:issue:`2322`
-
-Fixed initial temperature reporting - beta-phase fix
-""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
-Fixes :issue:`2314`
-
-Fixed compilation issues for AVX-512 - beta-phase fix
-""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
-- gcc-5.4.0 incorrectly requires the second argument of
-  _mm512_i32gather_pd() to be a double pointer instead
-  of void, but this should fix compilation for both
-  cases.
-- Work around double precision permute instruction
-  only available with AVX512VL instructions.
-
-Fixes :issue:`2312`
-
-Cleared vsite velocities for simple integrators - beta-phase fix
-""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
-The simple integrator loops did not clear
-the velocities of virtual sites. This allows velocities of virtual
-sites to slowly increase over time. To prevent this, velocities
-of virtual sites are now cleared in a separate loop.
-
-Fixes :issue:`2316`
-
-Fixed fft5d pinning - beta-phase fix
-""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
-A CUDA build on a node with no driver installed can never have
-selected a CUDA pinning policy, and erroneously unpinning leads to a
-fatal error. Instead, FFT5D now remembers whether it made pinning
-possible, which can only occur when there was a driver and a valid
-device, so that it can unpin only when appropriate.
-
-Fixes :issue:`2322`
-
-Avoided assertion failure in AWH - beta-phase fix
-""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
-With an unstable reaction coordinate or unequilibrated system, AWH
-could cause an assertion to fail. Now AWH checks for valid coordinate
-input and throws an exception with a clear message.
-
-Corrected AWH input file name in documentation - beta-phase fix
-""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
-Mdrun was expecting user input data file 'awhinit.xvg' while the
-mdp-option documentation has 'awh-init.xvg'.
-
-Changed the GPU SMT cut-off to quadratic - beta-phase fix
-""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
-The advantage of SMT diminishes rapidly with the number of cores.
-So the system sizes should be compares to the square of the number
-of cores.
-
-Fixed AVX-512 SIMD test for C compilation - beta-phase fix
-""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
-Avoid using C++ features in the test, since it should test both the C
-and C++ compilers.
-
-Leave NVML use off by default - beta-phase fix
-""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
-Even if NVML is found, leave the default off because the
-linking is unreliable for reasons that are currently unclear,
-and only in some cases is linking with NVML advantageous.
-
-Fixes :issue:`2311`
-
-Fixes for compiler support - beta-phase fix
-""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
-Double precision, debug mode, proper release mode and some quirky
-cases were all improved in multiple ways to compile and pass tests
-reliably.
-
-Consume any error produced during GPU detection - beta-phase fix
-""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
-Having reported it, we should clear the CUDA error status so that
-future calls do not continue to return it.
-
-Fixes :issue:`2321`
-
-Replace intrinsic with inline asm for AVX512 unit test - beta-phase fix
-""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
-Using inline assembly avoids compilers at low optimization
-levels not generating efficient code for the timing routines, and
-also avoids needing an assembler.
-
-Fixes :issue:`2340`
-
-Fixed table tests and improve table construction - beta phase fix
-""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
-Since compilers are allowed to use different FMA constructs, we
-now allow the consistency check to deviate a few ulps.
-
-For sinc and other extreme functions that oscillate, the
-scan over the definition range to locate the minimum quotient
-between the 1st and 4th derivative to set the table spacing
-exposes some delicate errors. Basically, it is not possible
-to have arbitrarily low relative errors for the derivative
-for a function that has large magnitude in the same place.
-For now we reduce the test interval for sinc(); this should
-anyway not be relevant for normal well-behaved MD functional
-forms.
-
-Fixes :issue:`2336`.
-
-Supported Simd4N for SimdRealWidth<4 - beta-phase fix
-""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
-If the SIMD with is smaller 4 but Simd4N is supported
-then use Simd4 for Simd4N.
-
-Fixes :issue:`2327`
-
-Made AVX-512 CMake detection work - beta phase fix
-""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
-Both inline assembly and the support flag have to be set for the
-timing code to be compiled.
-
-Fixed shift usage for KNC - beta phase fix
-""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
-9437181eacb removed the shift operator without replacing the usage for
-KNC.
-
-Made acceleration correction VCM mode work - beta phase fix
-""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
-The new acceleration correction VCM mode did not actually correct
-the coordinate for the acceleration, since a null pointer was passed.
-Introduced an extra CGLO flag to allow for correction of the
-coordinates, but leave the initial coordinates unaffected.
-
-Fix builds on ARM & clarify (ARM) GPU support - beta phase fix
-""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
-Fixed a typo in architecture.h that prevented
-the Neon Asimd instructions from being selected,
-and updated the CPU brand detection to also look
-for a new label with Tegra X1 on Ubuntu 16.04
-
-Fixes :issue:`2287`
-
-Improved documentation and code for physical validation - beta phase fix
-""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
-Adds documentation for the physical validation suite in
-docs/dev-manual/physical_validation.rst
-
-As this was misunderstandable, changed the default behavior of
-`make check-phys` and `make check-all` to actually run the simulations.
-This might take very long, but since the physical validation tests need to
-be turned on explicitly via cmake option, the chances of somebody using the
-tests by mistake are low. The `check` targets are:
-
-* `make check`: Run unit and regression tests (unchanged)
-* `make check-phys`: Run simulations needed for physical validation, then
-  run physical validation tests
-* `make check-phys-analyze`: Only run physical validation tests, assuming
-  that simulations were run previously and are available.
-* `make check-all`: Combination of `make check` and `make check-phys`
-
-Additionally, `make check-phys-prepare` can be used to prepare |Gromacs|
-input files and a script to run the simulations needed for the physical
-validation tests.
-
-Fixes :issue:`2349`

docs/release-notes/index.rst

@@ -1,9 +1,9 @@
 Release notes
 =============
 
-This version was released on TODO. These release notes document the
-functionality changes in |Gromacs| |version| that have taken place in
-|Gromacs| since version 2016.
+This version was released on January 10, 2018. These release notes
+document the functionality changes in |Gromacs| |version| that have
+taken place in |Gromacs| since version 2016.
 
 Some bug fixes are mentioned here, but those fixed in 5.1 or 2016
 branches are (or will be) documented there. If the same functionality
@@ -45,19 +45,6 @@ There are some new features available also:
 * Conserved quantities are computed and reported for more integration
   schemes - now including all Berendsen and Parrinello-Rahman schemes.
 
-.. TODO remove before final release
-
-Beta phase
-----------
-
-During the beta phase, numerous fixes will occur, many of which will
-be fixes of fixes, or fixes of new features. Those will be temporarily
-documented in the release notes, but will not appear in the final 2018
-release notes because they were never bugs that formally affected
-users. If you want to find whether a beta-phase issue has been fixed,
-you can find them by searching for the text "beta-phase fix" in the
-relevant subsection.
-
 Details
 -------
 

docs/release-notes/miscellaneous.rst

@@ -23,13 +23,14 @@ with domain decomposition. This allows for internal checks on valid
 commrec, which have now been added, and would have prevented :issue:`2257`.
 
 Added partial support for writing masses and partial charges with TNG files
-""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""^
+"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
 :issue:`2188`
 
 Updated TNG to version 1.8.1
 """"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 Added data block for atom masses.
+
 Fixes :issue:`2187` and :issue:`2250` and other bugs and warnings.
 
 Added load balance fraction to DLB print
@@ -43,10 +44,11 @@ The OPLS four-term dihedral function was not described in the
 reference listed earlier, so this was updated. Also updated
 the reference to the three term dihedral to an older paper.
 
-Updated developer guide
+Updated many aspects of the documentation
 """"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
-Imported and updated more material from the wiki. Included coverage of
-some recent discussion points on C++11 and preprocessor use.
+Imported and updated more material from the wiki. Incorporated
+suggestions arising from many Redmine issues. Updated user guide,
+developer guide, install guide, and reference manual.
 
 Updated mdrun signal help text
 """"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
@@ -55,3 +57,41 @@ to the behavior.
 
 Fixes :issue:`2324`
 
+Changed to handle erroneous command line args better
+""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+Some gmx modules need to be able to accept non-option arguments, and
+some should not. Introduced enough functionality to support such
+behaviour, while giving useful error messages in cases where the
+command line is merely missing hyphens (which can happen e.g. when
+people copy-paste from inconveniently built PDF files for tutorials).
+Increased test coverage of relevant cases.
+
+Removed some useless command-line argument strings from test cases
+that never needed them.
+
+Also tested some behaviours of handling string options, and renamed
+some test input strings to reflect the intent.
+
+:issue:`2153`
+
+Changed to no longer allow multiple energy groups for GPU runs
+""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+Exit with a fatal error instead of only warning, since the latter
+leads to writing data for energy groups that is incorrect to the
+energy file.
+
+:issue:`1822`
+
+Removed duplications in GMXLIB search paths
+""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+Remove entries that are duplicated, or identical to the default search
+path, to avoid e.g.  listing identical force fields multiple times.
+
+:issue:`1928`
+
+Changed to no longer write reference pull group 0 to log
+""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+This is an internal group used for absolute references, which cannot
+be set by users, so printing it just leads to confusion.
+
+:issue:`2143`