Berk Hess [Fri, 16 Sep 2016 11:40:25 +0000 (13:40 +0200)]
Merge branch release-2016
Change-Id: I0c8c02d4fbd56042ad77e7b646323b2570d06c7c
Berk Hess [Wed, 10 Aug 2016 10:23:03 +0000 (12:23 +0200)]
Made distance restraints work with threads and DD
The NMR distance restraints use several buffers for summing distances
that were indexed based on the index of the thread+domain local ilist
force atoms. This gives incorrect results with OpenMP and/or domain
decomposition. Using the type index for the restraint and a domain-
local, but not thread-local index for the pair resolves these issues.
The are now only two limitations left:
* Time-averaged restraint don't work with DD.
* Multiple copies of molecules in the same system without ensemble
averaging does not work with DD.
Fixes #1117.
Fixes #1989.
Fixes #2029.
Change-Id: Ic51230aa19a4640caca29a7d7ff471e30a3d9f09
Aleksei Iupinov [Tue, 13 Sep 2016 12:50:11 +0000 (14:50 +0200)]
Move the PME Ewald coefficients to the PME structure
Ewald coefficients no longer get passed every step to gmx_pme_do().
Instead, they are passed to gmx_pme_(re)init,
as they only change together with the grid size, not every MD step.
Change-Id: Iea75063cf060317e3f0fcfd147431520b6c83a90
Berk Hess [Thu, 8 Sep 2016 14:24:40 +0000 (16:24 +0200)]
Moved expanded ensemble history to pointer in t_state
Data of special modules such as expanded ensemble should be stored
in pointers in t_state. This is also needed for converting t_state
to C++ without converting all special modules at the same time.
Change-Id: I22e5a939638ac318eb8167fee5f1097c1f1981e0
Roland Schulz [Thu, 1 Sep 2016 21:15:42 +0000 (14:15 -0700)]
Tidy: modernize-use-emplace
run-clang-tidy.py -checks=modernize-use-emplace -header-filter=.* -fix -j80
http://llvm.org/releases/3.9.0/tools/clang/tools/extra/docs/clang-tidy/checks/modernize-use-emplace.html
Change-Id: I57a17487837f7afacc915d1c3cbf13c802c2a83c
Berk Hess [Thu, 8 Sep 2016 13:27:05 +0000 (15:27 +0200)]
Change ED and swapstate to pointers in t_state
Data of special modules such as ED and swapstate should be stored in
pointers in t_state.
This is also needed for converting t_state to C++ without converting
all special modules at the same time.
Change-Id: If8c7cb197f325ccf113aeebd807491ebd5a7b169
Mark Abraham [Wed, 31 Aug 2016 21:42:34 +0000 (23:42 +0200)]
Preliminary clean up of NVML code
Restructured logic so that it's simpler - there's multiple reasons why
we might not be able to change clocks, so now we just return after any
check that fails. No functionality changes here.
nvml_initialized does not need to persist.
Reading driver and runtime version is not needed.
Fixed some spelling.
Noted TODOs for subsequent cleanup.
Change-Id: I5e4cf73a470e60f53f098f7d28742403111f7da0
Berk Hess [Wed, 7 Sep 2016 07:58:57 +0000 (09:58 +0200)]
Add const to thread-MPI functions
Added const qualifiers to send buffer pointers for Several thread-MPI
functions. This is required by the MPI 2 standard and allows us to
use more const qualifiers in the GROMACS communication code.
Note that internally thread-MPI does not distinguish send and receive
buffers, so we need cast away the const.
Change-Id: I0fe03fd92325b9030c8584349c958deb20b30bfd
Vedran Miletić [Wed, 31 Aug 2016 18:52:46 +0000 (20:52 +0200)]
Document wallcycle counters and subcounters
List the available counters and explain how they are used. For subcounters,
explain the difference to counters and mention how to enable them.
Change-Id: Id5ce0e99b37a899f84d10b799840abad27d15c9c
Teemu Murtola [Sun, 11 Sep 2016 06:04:03 +0000 (09:04 +0300)]
Fix various memory leaks
These leaks are reported when building and running the tests with
LeakSanitizer (ignoring regression tests and tests marked as integration
tests).
- Free memory on 'gmx help -export completion' paths, which also fixes
all 'gmx help <module>' paths.
- Free all memory in genconf on exit to make the gmxpreprocess tests not
leak memory.
- Add settle_free() to free memory properly in mdlib tests.
- Add missing sfree in done_state() (fixes leaks in read_tps_conf() for
tpr files).
- Add missing virtual destructor in IOptionValueStore (various leaks
from correct destructors not getting called).
- Free the final symbol in selection parser in case the parsing ends
after the maximum number of selections has already been provided.
- Add missing frees in selection test helper for atom type strings.
Change-Id: I0d796033ce3b30cda0a18743a28f4d3133fd477f
Vedran Miletić [Tue, 30 Aug 2016 18:18:13 +0000 (20:18 +0200)]
Print OpenCL error string instead of error code
Change-Id: I00871b7f295373d8497a13d0bc3cbd0c0ff99668
Berk Hess [Wed, 7 Sep 2016 08:53:29 +0000 (10:53 +0200)]
Remove continuation from convert_tpr
Removed the obsolote option of convert_tpr to write a tpr file for
continuation using a trajectory and energy file. This is superseded
by checkpointing.
Change-Id: I46c49621a8cca247d5a9429961d85e6028fefb14
Aleksei Iupinov [Fri, 15 Apr 2016 14:34:12 +0000 (16:34 +0200)]
Fix PME data destructor not being called
The existing function gmx_pme_destroy is now being called at MD run end.
Erroneous memory freeing has been fixed.
Added freeing of pme_atomcomm_t.
Change-Id: I8761d2dbc168ec9d4e0e042fec788e39fb3e3ae5
Mark Abraham [Thu, 8 Sep 2016 10:40:51 +0000 (12:40 +0200)]
Merge branch release-5-1 into release-2016
Trivial conflicts in minimize.cpp from bug fix in same region that now
has exceptions caught within an OpenMP region.
Change-Id: I8b3c269a2afd7d4967e0f7310c96af6022533ddd
Mark Abraham [Thu, 8 Sep 2016 08:07:13 +0000 (10:07 +0200)]
Bumped patch number to prepare for future 5.1.5 release
Change-Id: I37e3120ec8ab257f0aeb1cf137dff27391e0689f
Mark Abraham [Wed, 7 Sep 2016 12:39:33 +0000 (14:39 +0200)]
Version 5.1.4
Bumped SOVERSION_MINOR and REGRESSIONTEST_HASH
Change-Id: Ib8404367c7ac15e0de567bf103f5ceb5d4dd5091
Mark Abraham [Mon, 5 Sep 2016 15:49:22 +0000 (17:49 +0200)]
Removed HIS1 from oplsaa and charmm definitions
HIS1 is intended for linking with heme, which oplsaa doesn't
define. charmm converts HIS1 to HSD in its .r2b.
This makes the recent fix for oplsaa HISD "consistent" with HIS1.
Fixes #2047
Refs #2049
Change-Id: Ibc0463c779e76689dc7ef65e48aedc716de9e032
Mark Abraham [Mon, 5 Sep 2016 15:32:19 +0000 (17:32 +0200)]
Fix LYN charges in amber03
These charges now match those found in AMBER 14 and 16. The
validation of the AMBER ports was done with AMBER 8.0, and
this fix was made afterwards in
http://ambermd.org/bugfixes/8.0/bugfix.19 (and perhaps LYN wasn't
in the validation set).
Fixes #2046.
Change-Id: Ibcaab337b527a44e42d5a7c68f71ef4fde2acf66
Mark Abraham [Tue, 6 Sep 2016 13:57:00 +0000 (15:57 +0200)]
Fix amber03 HIP charges
These were changed in Nov 2005, and now match AmberTools 16
Fixes #2050
Change-Id: I191b60c6acd2f521b3481578114ff48fca0979e5
Teemu Murtola [Mon, 30 May 2016 19:56:22 +0000 (22:56 +0300)]
Clean up CTest test management
- Add explicit timeouts to CTest tests. These should work better than
the current Jenkins timeout: it should produce better JUnit test
reports, and should catch also tests that end up in an infinite loop
printing stuff. The timeouts are still quite generous, since at least
the coverage run can take a while.
- Use a more easily extensible and better encapsulated mechanism for
producing the messages about missing tests with 'make check'.
- Abort if running a non-MPI test binary with MPI instead of trying to
run it on the master rank, since it might deadlock.
- Clean up the macros used to register CTest tests and use a clearer set
of test labels, and move more logic into src/testutils/CMakeLists.txt.
- Resolve various TODOs.
Change-Id: Ia1370d99eabd5839682832e8c3c60668a667cdde
Erik Lindahl [Fri, 5 Aug 2016 10:05:26 +0000 (12:05 +0200)]
Bump oldest cmake, compiler and CUDA versions required
For release 2017 we now require gcc-4.8.1, clang-3.3 and icc-15, so we
can rely on full C++11 support. We now also require CUDA-6.5 and
CMake-3.4.3. This in turn means we can remove some older cmake tests,
and since many users won't read the install guide there are now
version tests that produce fatal errors during CMake configuration for
compiler versions we know are too old.
Various hacks and workarounds in source and build system can
now be removed.
Fixed error in previous definition of GMX_ALIGNED
Updated C++11 compatibility tests in line with code we are now using.
Fixed that hwloc includes were not treated as system headers.
Treated including thread-MPI and TNG header files as system paths, to
be consistent with how we'd treat them if we were using external
versions of these.
Fixed icc 16 warnings in lapack routines.
Fixes #2012.
Change-Id: I36e02379a985b22c72f0f06481c65cae6e780c02
Mark Abraham [Mon, 27 Jun 2016 17:18:12 +0000 (19:18 +0200)]
Work around glibc 2.23 with CUDA
Note: Cherry-pick of
e2cd2e2e from the 2016 branch.
Fixes #2022
Change-Id: Id9881efb3f26af341b9c89b4bd1f983a2149c9e4
Berk Hess [Tue, 6 Sep 2016 13:14:17 +0000 (15:14 +0200)]
Fix bug with conjugate-gradient and OpenMP
The conjugate-gradient update routine re-used the pointer variable for
x for cg_p. This pointer was shared over threads and no barrier was
present before the pointer modification.
Fixes #1941.
Change-Id: I5f635fc3054147543820c4e5e74f3519637d541d
Berk Hess [Mon, 5 Sep 2016 09:27:43 +0000 (11:27 +0200)]
Consolidate MD algorithm atom setup
The setup of atom data for several MD algorithms that was called in
do_md, init_em and dd_partition_system has been moved to a single
routine called mdAlgorithmsSetupAtomData.
We should also move algorithm initialization cals to a single routine.
Change-Id: I3c87394e793e92d66555dc60388a47cedf6eeac9
David van der Spoel [Mon, 5 Sep 2016 13:49:10 +0000 (15:49 +0200)]
Merge "Merge branch release-2016"
Berk Hess [Mon, 5 Sep 2016 08:58:45 +0000 (10:58 +0200)]
Re-enable flexible constraints with DD
Commit
409edb80 added a fatal error in init_shell_flexcon() with DD.
But flexible constraints without shells work correctly with DD.
Change-Id: Ic3c5028a7aa6d956cf85f779347df16329d817bb
Berk Hess [Sun, 4 Sep 2016 16:29:34 +0000 (18:29 +0200)]
Merge branch release-2016
Change-Id: I11339f3f6ce583827af85fc8187c4f42ae5a8e52
Berk Hess [Fri, 2 Sep 2016 12:59:28 +0000 (14:59 +0200)]
Clean up PME flags variable use
PME flag bits for triggering Coulomb and/or LJ calculations were mixed
between different flags variables. These flag bits are now removed,
because they passed constant values based on inputrec.
Similarly, the free-energy calculation flags were never changed during
a run and have also been removed.
Note that these calculations probably could/can actually be run
selectively, but that should be tested.
Change-Id: Ib8e121fd08f2dd8776d29b0f896b3df2322ecf6d
Berk Hess [Fri, 2 Sep 2016 15:28:25 +0000 (17:28 +0200)]
Merge branch release-5-1 into release-2016
Change-Id: Ia1a7fad67f0ff11175ea24c46f813a445cd49ed6
Berk Hess [Mon, 15 Aug 2016 19:03:13 +0000 (21:03 +0200)]
Fix Parrinello-Rahman with nstpcouple>1
Fixes #2031.
Change-Id: I37cf18c40c6cf5e301d7981c9f10bbf963d8cda8
Teemu Murtola [Tue, 26 Jul 2016 13:05:13 +0000 (16:05 +0300)]
Basic support for transforming KeyValueTrees
Add support for writing transforms from one KeyValueTree to another.
For now, only a small subset of simple transforms is supported, but this
should be mostly sufficient for a proof-of-concept for MDP processing on
the electric field code, and new cases can be relatively easily added.
These transforms can support two use cases: specifying how a legacy MDP
file maps to a more structured format, and for supporting changes from
version to version in the structured format. However, versioning for
the structured format (in particular, if/when it will be necessary to
recognize the version from input) likely still needs some work.
There is not much in terms of consistency checks, error handling, or
documentation, but that is better to add once using code exists.
Change-Id: Ie2570eee8a62c2d64b79e00925bbf1e40b62b261
Berk Hess [Wed, 17 Aug 2016 13:27:49 +0000 (15:27 +0200)]
Make virial reproducible
OpenMP reduction was used to reduce virial contributions over threads,
which does not have a defined order. This leads to different rounding,
which makes runs non-reproducible (but still fully correct).
Now thread local buffers are used.
Also removed OpenMP parallezation for small count (e.g. shift forces).
Change-Id: I8d80def602337cc12ab601916bf40d7f66bf9bbc
Szilárd Páll [Wed, 24 Aug 2016 15:49:14 +0000 (17:49 +0200)]
Make ASAN/TSAN/MSAN build types easier to discover
While these build types are indeed aimed at developers, realistically
not many will be interested in changing the build type from the default
"Release" except in rare cases. Therefore, along Debug or RelWithAssert,
it makes sense to list the other developer-oriented build types
ASAN, TSAN, and MSAN if nothing else for the benefit having docs in the
ccmake gui.
Change-Id: Ie54fc57a06aee3be996c9a8ff62e54a3ac284065
Mark Abraham [Tue, 23 Aug 2016 22:40:04 +0000 (00:40 +0200)]
Stop using gmx_fatal in grompp
Added warning_error_and_exit to issue an error that describes the
location in the input file, and then halt processing (because data
structures would not be safe to use) while also describing where in
the code that occured. Either set of metadata can be useful to users
or developers diagnosing issues.
Refactored implementation of check_warning_error() so that
warning_error_and_exit() can have the gmx_noreturn qualifier, so that
analyzers understand the behaviour of the calling code, and compilers
can understand the implementation of warning_error_and_exit().
This permits more effective diagnostics in various places, and
eliminates some existing hacks.
Bumped all declarations of errbuf to have size STRLEN, since some of
the new uses might be safer that way.
Also made a minor fix to output to avoid redundant output from
done_warning when an error has occured.
Change-Id: I29f8afeb70d0da3598c6443c15090bca9bf5c639
Teemu Murtola [Fri, 29 Jul 2016 04:45:33 +0000 (07:45 +0300)]
Support KeyValueTree objects in refdata
Make it possible to check KeyValueTreeObject-rooted trees through
TestReferenceData. This is the simplest way to actually verify the
contents of such a data structure. For now, the contents can be
inspected through the XML output.
Change-Id: Ic6fc87c4934166acad4e9b5068c6d39c02866a73
Berk Hess [Wed, 24 Aug 2016 09:00:19 +0000 (11:00 +0200)]
Reduce rounding errors in SETTLE
The parameters for SETTLE are now computed in double precision.
This lowers the systematic error in settle.
Change-Id: I537a618830ab149d5f33251d9edca3aa9c43404c
Roland Schulz [Wed, 24 Aug 2016 20:57:28 +0000 (13:57 -0700)]
Fix build with GMX_USE_TNG=off
Change-Id: I305edfafbe87f0ad1e8ff410f419e5d32b23e1a7
Jochen Hub [Wed, 24 Aug 2016 15:50:08 +0000 (17:50 +0200)]
Fixed bug in gmx insert-molecules.
With option -ip, and if all trials were unsuccessful, a molecule was
eventually incorrectly placed at 0/0/0 due to a memory error
when referencing to rpos[XX][mol].
Change-Id: I367727210b893652af39217925906cc2dc703465
Roland Schulz [Fri, 5 Jun 2015 09:23:46 +0000 (05:23 -0400)]
Remove unnecessary ICC warning suppression
Change-Id: Icdb24d0fed40608a11a884fe5181778180bcc5e2
Berk Hess [Wed, 24 Aug 2016 11:00:14 +0000 (13:00 +0200)]
Fix Ewald surface+3DC corrections
Ewald surface and 3DC correction forces were only applied up to,
but not including, the last atom with exclusions. With water at
the end of the system only the last H would not be corrected.
With ions at the end all ions would be missing.
In addition, with the Verlet scheme and domain decomposition
no force correction was applied at all.
Fixes #2040.
Change-Id: I064bf01fab561dca40451763b75283b6f59e0fbd
Mark Abraham [Tue, 16 Aug 2016 09:42:00 +0000 (11:42 +0200)]
Remove hacks for outdated BlueGene support
GMX_BLUEGENE hasn't been a thing for a while now.
XL compiler is no longer supported on BG/Q (no C++11 support will ever
exist), so a bunch of accommodations for it can go away. bgclang
is still supported however.
Some BG/L workarounds can also go away.
Change-Id: I5b76c02b4fc421889d7ca60f41574c491af05f2f
David van der Spoel [Wed, 17 Aug 2016 07:05:15 +0000 (09:05 +0200)]
Added documentation for shell potentials.
Added documentation for simple and anharmonic shell potentials.
Added two references.
Change-Id: Ica2b694b9b57bcf52bfe8434cfb3f8fe4dc7b9a2
Berk Hess [Wed, 24 Aug 2016 11:12:21 +0000 (13:12 +0200)]
Merge branch release-5-1 into release-2016
Also applied the merged fix to nbnxn_cuda_kernel_fermi.cuh.
Change-Id: I79d0cb59214290097d6f356e35dd13c4eadaed75
Berk Hess [Tue, 23 Aug 2016 10:13:35 +0000 (12:13 +0200)]
Remove variable precision gro writing
The gro precision is now fixed to 3, 4 and 5 decimal places for
x, v and box respectively to ensure compatibility with other software.
Variable precision reading is still supported.
Fixes #2037.
Change-Id: I0e593622ee0380c3934a7b7b6826ae29aed00a59
Teemu Murtola [Mon, 1 Aug 2016 05:16:12 +0000 (08:16 +0300)]
Check for unused refdata values
Make a test using refdata fail if it does not produce some reference
values at all. Use this instead of checkPresent() for some cases where
the new functionality is a clearer fit for the purpose. It is possible
to trigger the check explicitly for a subtree, but if not done
otherwise, it is always done for all values at the end of the test.
Change-Id: I722abd978f0c8fa9dc279264ff90cdad02e02b9d
Teemu Murtola [Sat, 23 Jul 2016 18:23:25 +0000 (21:23 +0300)]
Generic structured key-value tree for options
Add classes KeyValueTree* for representing a JSON-like data structure
that allows mapping a hierarchical set of string keys to values with
dynamic types. Make it possible to assign options from such a
structure.
The tree objects only provide read-only accessors that are currently
used. To construct such trees, a separate set of builders is used.
Better error handling will be added once this is actually used somewhere
and the best way to construct the messages can be determined.
Change-Id: I08c2536f4b2eb4678c11a179e31f6a85693fc4ec
Teemu Murtola [Fri, 8 Jul 2016 15:10:12 +0000 (18:10 +0300)]
Support for non-string option value assignment
Make it possible to assign non-string values to options through
OptionsAssigner. For now, the only thing that actually works is
assigning std::string values, and assigning the exact type stored for
the option. Also, the list of supported conversions is initialized
separately for every instance of each option, but in practice that might
not matter that much.
This adds the infrastructure that allows assigning option values from
something like a JSON structure that already does data type conversions
during parsing. The same infrastructure can also support #653.
Change-Id: I8f81d57da1b6eeac06a6ac9a8ab68bfa8ed0c148
Teemu Murtola [Tue, 5 Jul 2016 18:24:27 +0000 (21:24 +0300)]
Basic support for array-of-structs in options
This makes it possible to parse structured data that has
arrays-of-struct type of constructs (as long as the structure for the
array elements is reasonably uniform). Iteration over the sections does
not work reasonably for these types of sections yet, and there are other
things that might not work. For complicated nested data structures,
there is also some unnecessary copying. But the tests show that basic
stuff does work.
Change-Id: Ib485248a5adabecc3ed126dfa3736a5e71577bfd
Teemu Murtola [Mon, 4 Jul 2016 18:52:02 +0000 (21:52 +0300)]
Generalize and simplify option value storage
Move responsibility of managing the final storage of parsed option
values out of OptionStorageTemplate to a separate OptionValueStore
interface. Reduce complexity by removing support for some unused cases
(like storing the values in more than one place), which allows complete
removal of refreshValues().
This turned out to be not strictly necessary for supporting repeating
sections in options, but it is a useful simplification nonetheless.
It also provides some reusable elements that are also used in later
changes.
Change-Id: Ib367ae987cd265a08777c2fe054b43fdd5310762
Teemu Murtola [Sat, 2 Jul 2016 18:14:13 +0000 (21:14 +0300)]
Generalize option section internals
Use a similar mechanism as for options to allow multiple different
section types to be handled through addSection(). Prerequisite for
adding support for repeating sections. Support for iterating over
option sections is not of particular focus at this point; the initial
focus is to get the API for declaring sections and options working.
Also change the approach in IOptionsContainer to remove the need for
using directives in classes implementing it, and make the build system
list the source files explicitly.
Change-Id: I3f70f6937cb6b594c5bff120d5f2f87e42841ac4
Teemu Murtola [Fri, 10 Jun 2016 19:54:56 +0000 (22:54 +0300)]
Reimplement subsections in Options
Now the support for sections in Options provides an API similar to
other option types. The main thing missing (both in the old and the new
implementation) is support for an "array of structs"-kind of options,
where multiple instances of the same section could create multiple
instances of some object in the code. That should also be possible to
add following a similar public API, but the internals need quite a bit
of generalization to make that possible. That will be done in
subsequent changes to keep the changes smaller.
Remove now-unused name and title for an Options object.
Change-Id: Ie76e31aae2de0816b4d294ff6869606d4a2bef49
Berk Hess [Wed, 17 Aug 2016 13:35:05 +0000 (15:35 +0200)]
Fixed opening of wall table files
Fixes #2033.
Change-Id: Ie5092476f021d0578bbcbd84c7e4f895959fd06e
Mark Abraham [Mon, 15 Aug 2016 19:09:04 +0000 (21:09 +0200)]
Merge branch release-2016
Change-Id: I39dd5524c70707d1784f2814876930c3905a52ba
Mark Abraham [Fri, 12 Aug 2016 08:19:34 +0000 (10:19 +0200)]
Fixes for BG/Q platform files and install guide
Renamed the platform file to reflect normal practice
and the install guide.
Change-Id: Icffde855789f561faa0249d095838fea9f97ce1d
Berk Hess [Mon, 8 Aug 2016 13:24:14 +0000 (15:24 +0200)]
Reduce FE pair-list memory usage
Refs #2014.
Change-Id: Ia8bbc55eed7e3590e6944127ab94dd41f475e6a7
Mark Abraham [Fri, 12 Aug 2016 08:11:49 +0000 (10:11 +0200)]
Bump number to prepare for first patch release
Change-Id: I1cdfd715d2681677460945ed6670adb2a35f9839
Berk Hess [Tue, 9 Aug 2016 20:26:04 +0000 (22:26 +0200)]
Fix deadlock with thread-MPI
With thread-MPI mdrun could deadlock while pinning threads.
Fixes #2025.
Change-Id: Ib42e9625134531b1e2f910b11339aa0f78b80624
Berk Hess [Tue, 9 Aug 2016 11:24:49 +0000 (13:24 +0200)]
Fix twin-cutoff for GPU LJ pot-switch
With rcoulomb>rvdw, as used with PME tuning, the GPU kernels performed
the LJ cut-off check before applying the potential-switch to the LJ
forces and energies.
Fixes #2007.
Change-Id: Ie2f6fdfec10bdb8800123e6fa299839a31bc0f93
Erik Lindahl [Sun, 31 Jul 2016 16:34:36 +0000 (18:34 +0200)]
Fix proper relative tolerance checking in testutils
The previous relative tolerances were convereted to ULP
checks, but since the relative difference for 1 ULP
depends on whether the exponent changes there is no strict
1-to-1 correspondence between ULP and relative differences.
Fixed by storing the original magnitude of the numbers
in FloatingPointDifference and using a traditional relative
tolerance check for the case when a relative tolerance is
set from floating point values; other checks still use ULP.
Change-Id: I95331b46da00cd0b4e369f087991c553cd05f18f
Mark Abraham [Wed, 3 Aug 2016 13:13:10 +0000 (15:13 +0200)]
Version 2016
Removed "-rc1" per policy. Bumped regressiontests hash.
Change-Id: If94c03e280fce13143d238fa3e7f2df3b8b659cf
Teemu Murtola [Thu, 4 Aug 2016 04:23:46 +0000 (07:23 +0300)]
Fix/improve doc links in template/README
For installations from a tarball, put a link to an appropriate version
at manual.gromacs.org instead of Jenkins-generated documentation which
might be for a newer version. For builds from the repository, the links
still point to the nightly Jenkins job.
The first link was also pointing to an obsolete Jenkins job.
Change-Id: Ib56c62cd572879c8dadde6881507e54f6d22a784
David van der Spoel [Tue, 2 Aug 2016 21:23:55 +0000 (23:23 +0200)]
Three new quotes.
Change-Id: I9a7ed8343a0133a68bf7790e85bff9d331dd6294
Vedran Miletić [Tue, 12 Jul 2016 17:07:30 +0000 (19:07 +0200)]
Use only legal characters in OpenCL cache filename
The device name from the vendor could contain anything, and we need to
avoid dot and slash when we try to make a filename from it. To help
keep it valid for all possible users, we permit only alphanumeric
characters from the current locale.
Change-Id: Ie55959a9a2161d0cfc7effa6ab57fffc8160f4e2
Teemu Murtola [Fri, 29 Jul 2016 04:15:43 +0000 (07:15 +0300)]
Function to split delimited strings
Add a function to split a string at given non-whitespace delimiters, and
tests for it. Will be used for subsequent work on KeyValueTree.
Change-Id: I28f2658e7c9b32565c02b16600b2e09b444415f4
James Graham [Tue, 26 Jul 2016 11:11:47 +0000 (12:11 +0100)]
Avoid blank line in writing index file
Removes extra newline added in index file when an index group
contains a multiple of 15 atoms. This broke some analysis scripts
that were not expecting blank lines e.g. MARTINI fluxer.py. Also
removed from duplicate index file.
Change-Id: I6058799fbfb71096e47db02c4dc7a5ebd060425a
David van der Spoel [Sun, 31 Jul 2016 07:18:27 +0000 (09:18 +0200)]
Merge "Merge branch release-5-1 into release-2016" into release-2016
Roland Schulz [Mon, 18 Jul 2016 19:17:15 +0000 (12:17 -0700)]
Update GCC version for reference build
4.7 isn't available anymore with recent Linux distributions.
Change-Id: I27b9d1af386b4891f648a033872b876230247b67
Vedran Miletić [Wed, 27 Jul 2016 15:01:25 +0000 (17:01 +0200)]
Document gmx_cgsort_t and gmx_domdec_sort_t structs
Add descriptions to fields of gmx_cgsort_t and gmx_domdec_sort_t
structs used in domain decomposition code.
Change-Id: Ie64664ed46413e51ba22504270ab11350c39b84a
Mark Abraham [Fri, 29 Jul 2016 11:56:19 +0000 (13:56 +0200)]
Improve handling of gmock and gcc6
This patch reverts commit
d6e35c96 that used gcc
-fno-delete-null-pointer-checks to work around implementation errors
in gmock 1.7. There's been no new release of gmock for several years,
but a patch is now available to address this issue.
This commit applies that patch, found at
https://github.com/google/googletest/issues/705#issuecomment-
235067917. Updated
our README describing modifications GROMACS has found it necessary to
make.
Fixes #1911
Change-Id: I0d5abe9bf8172f6749bcad97a13765edaa3d4c80
Mark Abraham [Fri, 29 Jul 2016 12:32:44 +0000 (14:32 +0200)]
Merge branch release-5-1 into release-2016
Change-Id: Id782b78da4b2080fec208d29b9b4afc363f1418c
David van der Spoel [Fri, 22 Jul 2016 07:43:02 +0000 (09:43 +0200)]
Fixes incorrect charges in OPLS/AA-L for HISD and HISE
With the present charges results from Michael Shirts et al.
J. Chem. Phys. 119 (2003) 5740 can be reproduced.
Fixes #2013
Change-Id: Ifb037961499633210d26ff32ec6bf3bebc505461
Mark Abraham [Thu, 28 Jul 2016 17:53:50 +0000 (19:53 +0200)]
Add toolchain flags for SSE2 compilation
This is how the code should be, though my testing didn't need it.
Also fixed function documentation.
Fixes #2008
Change-Id: Ic1e1c16d22e054e9f741d91c667305de7398cd30
Roland Schulz [Sat, 23 Jul 2016 00:06:56 +0000 (17:06 -0700)]
Merge release-2016 into master
Conflicts:
src/programs/mdrun/resource-division.cpp
src/programs/mdrun/resource-division.h
src/programs/mdrun/runner.cpp
Change-Id: I02a0af8295df0fa271e6e236daf035ea442cb73a
Mark Abraham [Thu, 21 Jul 2016 18:40:39 +0000 (20:40 +0200)]
Bumped patch number to prepare for future 5.1.4 release
Change-Id: I813e0d8c976d0afca316f5cfe095c5647b8fd66c
Roland Schulz [Fri, 15 Jul 2016 22:21:29 +0000 (15:21 -0700)]
Fix non-parallel build
Change-Id: Iba9bd4b51172df5157359fc79a5b50f3954784ce
Mark Abraham [Thu, 14 Jul 2016 15:31:49 +0000 (17:31 +0200)]
Fix issues with using int for number of steps
Mostly we use a 64-bit integer, but we messed up a few
things.
During mdrun -rerun, edr writing complained about the negative step
number, implied it might be working around it, and threatened to
crash, which it can't do. Silenced the complaint during writing,
and reduced the scope of the message when reading.
Fixed TNG wrapper routines to pass a 64-bit integer like they should.
Made various infrastructure use gmx_int64_t for consistency, and noted
where in a few places the practical range of the value stored in such
a type is likely to be smaller. We can't extend the definition of XTC
or TRR, so we're stuck. TNG is already good, though.
Fixes #2006
Change-Id: If485d9d92cb4b99a3bbe25e8e9fa082fc3fccd5f
Teemu Murtola [Thu, 14 Jul 2016 13:49:56 +0000 (16:49 +0300)]
Use newer gcc for coverage
The coverage build no longer works with gcc-4.6 on bs_mac because of too
old stdlib. With changes in releng and on bs_mac, it is now possible to
update the compiler and gcov used for the build.
Change-Id: Ib6cb6589c53d0a56a7d04a32367d84fcf91cfecf
Mark Abraham [Wed, 13 Jul 2016 10:27:17 +0000 (12:27 +0200)]
Version 5.1.3
Bumped minor soversion and regressiontest hash
Change-Id: I55f1cc4f1154f053512c8cc3509fd0be8e3c347b
Mark Abraham [Mon, 11 Jul 2016 15:36:33 +0000 (17:36 +0200)]
Merge branch release-2016
Many conflicts from modified warnings and the introduction of
the new logging module, but straightforward to resolve by
using the new infrastructure to deliver the old message.
Change-Id: I15bdee3aa6dd19d55ff46b737e0abd3f76153494
Mark Abraham [Tue, 12 Jul 2016 13:55:46 +0000 (15:55 +0200)]
Fix trr magic number reading
The trr header-reading routine returned an "OK" value if the magic
number was wrong, which might lead to chaotic results everywhere,
because checking of return values tends not to happen (even when
they're right). Other GROMACS magic-number reading routines tend to
give a fatal error if the the number is wrong, e.g. by reading a file
written in wrong endianness. (This should never be a thing for XDR
files, which are defined to be big endian, but such code has existed.)
This change adds/restores that behaviour to trr reading, along
with separating the behaviour of failing to read a magic integer
from reading one that doesn't match.
Fixes #1926
Change-Id: I3cdd8ae9172e3b95fc232d8fa31a442d239233db
Mark Abraham [Mon, 11 Jul 2016 14:43:44 +0000 (16:43 +0200)]
Fix gmx mdrun -membed -ntmpi -1
This used to give a fatal error if we'd chosen more than one rank, but
instead we should choose to use a single rank. Now that we have
several kinds of things that want to trigger such handling, build some
infrastructure to handle it. This allows us to separate the trigger
logic from how we report back to the user.
Change-Id: If01177b590c1a817113c642c30fd30d6d4bc3eab
Erik Lindahl [Sat, 9 Jul 2016 21:32:58 +0000 (23:32 +0200)]
Fix membed with partial revert of 29943f
The membrane embedding algorithm must be initialized before
we call init_forcerec(), so it cannot trivially be moved into
do_md(). This has to be cleaned up anyway for release-2017
since we will remove the group scheme be then, but for now
this fix will allow us have the method working in release-2016.
Fixes #1998.
Change-Id: I8e16a67b8df16999793649d79eebca051b8b474f
Michael Shirts [Mon, 27 Jun 2016 04:19:26 +0000 (22:19 -0600)]
Fix for incorrectly setting expanded ensemble when fep_state = 0
Expanded ensemble lambda values were not being copied over when the
proposed fep_state was 0. This commit fixes that by removing a
a conditonal that was incorrectly added.
Fixes #1995
Change-Id: I3d49b0936d973fb70a9a79799743f5069ba4fff4
Mark Abraham [Mon, 11 Jul 2016 12:24:52 +0000 (14:24 +0200)]
Fix regressiontest download md5sum
I forgot that the md5sum changes with the decision to
name it rc1 rather than beta3, because the directory
name within the tarball changes.
Change-Id: I5b5f5b9de43ee5771fbdfb53842609f1635f3f38
Mark Abraham [Thu, 23 Jun 2016 14:12:06 +0000 (16:12 +0200)]
First 2016 release candidate
Change-Id: I54a3e3c33015eb42ba5c18994ef76ce1bb2888c5
Erik Lindahl [Thu, 7 Jul 2016 14:01:13 +0000 (16:01 +0200)]
Hardware detection clean-up and pre/post-processing
This change cleans up the various tests and hacks we have
had in different places to remove a number of false warnings
and errors. It also unifies all this processing to two
small routines that are called just before/after the
hardware is detected, so the user can choose whether it
should be done or not in other places.
- Rather than trying to guess when we should or shouldn't
override the number of cores online, the preprocessing
uses a piece of code that allows sleeping cores to come
online automatically by running a small C++11 thread loop before
doing the hardware topology detection. This way we can
remove all ARM-specific paths. To avoid wasting a second
on systems where SMT is disabled, we avoid calling it on x86.
- All SMT warnings are handled in the post-processing call,
but only as notes in the log file to avoid writing
warnings on stderr.
- The check for OpenMP thread mismatch has been removed
since it caused incorrect warnings by comparing the number
or threads configured for each OpenMP process with the
total number of cores in the entire system. We will have
to rewrite this later as a test in the MPI/OpenMP
parallelization setup instead.
By sticking with the hwloc/sysconf-online detection, we should
now also handle all special cases where cores have been taken
offline manually in a correct way without using hardware-specific
paths.
Change-Id: I37edb3eada3f4c8c0906c641c7041cc0270985e8
Erik Lindahl [Tue, 24 May 2016 23:04:50 +0000 (01:04 +0200)]
Prevent fragile use cases of checkpoint appending
There are way too many ways we allow runs to be continued
and extended. We still allow the checkpoint file to be
missing (so -cpi can be used for all command lines), but
we warn if it is not found. To avoid mistakes with file
appending when restarting from checkpoints, we now require
that all previous output files must be present
(unless -noappend is used), and that the file names must
match the ones used in the previous run.
Fixes #1777.
Change-Id: Id9e89773a4a9214be6dbb76676c526e98e12bd37
Erik Lindahl [Thu, 7 Jul 2016 18:29:33 +0000 (20:29 +0200)]
Update affinity checking for Intel compiler
Since release 2013, the Intel compiler no longer sets
OpenMP affinity by default according to intel docs. This
means the code that tried to disable it by setting
environment variables no longer had any effect (and we
likely have not checked it the last few years). In
addition, it is not ideal behaviour in a library either to
assume that no other code has executed OpenMP prior to a call
or to set environment variables that influence other code
execution too. However, we will still disable Gromacs' own
thread affinity if it has been set by the user or calling code.
Change-Id: I57a952766e87a35483f1960b349f7c30d5b85f24
Vedran Miletić [Wed, 6 Jul 2016 14:49:31 +0000 (16:49 +0200)]
Print working dir before command line
When running GROMACS via a batch script, it is useful to know which
working dir is being used for relative paths (file names) in the
command line.
Change-Id: Iab6701e09ad3b0386b59c2bdda2c4f908fdc2d0a
David van der Spoel [Fri, 8 Jul 2016 14:24:25 +0000 (16:24 +0200)]
Merge "Merge branch release-5-1 into release-2016" into release-2016
Jochen Hub [Thu, 11 Dec 2014 11:19:58 +0000 (12:19 +0100)]
Updated g_wham for the new pull setup
This bring g_wham up to date with the new pull setup where the pull
type and geometry can now be set per coordinate and the pull
coordinate has changed and is more configurable.
Change-Id: I629fee9dfea9715e2bd54685cd1c203c66d05089
Mark Abraham [Fri, 8 Jul 2016 13:41:00 +0000 (15:41 +0200)]
Merge branch release-5-1 into release-2016
Change-Id: I976ad584d1c8757c6464aae482cb5a4c245beacb
David van der Spoel [Fri, 8 Jul 2016 12:12:27 +0000 (14:12 +0200)]
Introduce fatal error for too few frames in gmx dos.
To prevent gmx dos from crashing with an incomprehensible error
message when there are too few frames, test for this.
Part of #1813
Change-Id: Ie2f23d68cb3d4570944c4ade5ced49873dc98a29
Mark Abraham [Wed, 25 May 2016 13:56:33 +0000 (15:56 +0200)]
Simplify SIMD compiler flag construction
Lots of code duplication for handling both C and C++ is removed. Some
new helper functions handle the language-specific aspects separately
from the main logic. Introduced the notion of preparing the toolchain.
Removed one lot of status messages now that the try_compile status
message is more descriptive that it is checking for flags for SIMD
support.
Moved checking code that caters for ancient clang for AVX_128_FMA to a
common point, eliminating some variables. Moved that point to before
the AVX_128_FMA compiler flag tests, which seems more likely to work
in this case. This unlikely combination is of little significance,
however.
Change-Id: I5377a7951f5414ee52c4960fe63c999f55ff5109
Erik Lindahl [Thu, 7 Jul 2016 11:45:47 +0000 (13:45 +0200)]
Add detection for ARMv7 cycle counter support
ARMv7 requires special kernel settings to allow cycle
counters to be read. This change adds a cmake setting
to enable/disable counters. On all architectures but ARMv7
it is enabled by default, and on ARMv7 we run a small test
program to see if the can be executed successfully. When
cross-compiling to ARMv7 counters will be disabled, but
either choice can be overridden by setting a value for
GMX_CYCLECOUNTERS in cmake.
Fixes #1933.
Change-Id: I1e217d7a09f84a6bcf4eb5bf4a656d430465c915
Erik Lindahl [Thu, 7 Jul 2016 23:05:17 +0000 (01:05 +0200)]
Work around compiler issue with random test
gcc-4.8.4 running on 32-bit Linux fails a few
tests for random distributions. This seems
to be caused by the compiler doing something
strange (that can lead to differences in the lsb)
when we do not use the result as floating-point
values, but rather do exact binary comparisions.
This is valid C++, and bad behaviour of the
compiler (IMHO), but technically it is not required
to produce bitwise identical results at high
optimization. However, by using floating-point
tests with zero ULP tolerance the problem
appears to go away.
Fixes #1986.
Change-Id: I252f37b46605424c02435af0fbf7a4f81b493eb8
Szilárd Páll [Fri, 1 Apr 2016 21:46:46 +0000 (23:46 +0200)]
Add PDF metadata to the manual
Not only nice, but should also help search engines.
Also make sure that the PDF is UTF8 (and is tagged as unicode too).
Replaced in the bib a Unicode minus sign (U+2212) that was causing
trouble with the standard hyphen-minus.
Change-Id: I4708084282cad24b62369101e6155d99dc236981
Szilárd Páll [Tue, 5 Jul 2016 18:10:13 +0000 (20:10 +0200)]
User guide clarifications
Clarified OpenCL and CUDA as well as pinning in the glossary.
Change-Id: Ib3b74805812e8c02545819873e077f9d7ec9bab4
Erik Lindahl [Mon, 4 Jul 2016 22:45:45 +0000 (00:45 +0200)]
Reduce hwloc & cpuid test requirements
On some non-x86 linux platforms hwloc does not report
caches, which means it will fail our strict test
requirements of full topology support. There is no
problem whatsoever with this, so we reduce the
test to only require basic support from hwloc - this
is still better than anything we can get ourselves.
Similarly for CPUID, it is not an error for an
architecture to not provide any of the specific flags
we have defined, so avoid marking it as such.
Fixes #1987.
Change-Id: I0a065296bc647b7f7f5d3cb178e88df80fac81a7
Mark Abraham [Mon, 4 Jul 2016 13:42:40 +0000 (15:42 +0200)]
Move consistency check for number of threads
Recent refactoring meant that the count of threads known to OpenMP was
only used to provide a consistency check in the fallback case of
sysconf detection.
Note that no version of the HardwareTopology code ever used
information from OpenMP as an input.
Parameters for implementing warnings currently remain in
HardwareTopology::detect(), so that the sysconf case can continue to
handle cases where we think we know how to advise the user. This
will go away in master branch with the new logging module.
Change-Id: Iaf383abc420d2f04b6514e8856c9f1414cbba55c