Szilárd Páll [Mon, 23 Apr 2018 18:10:59 +0000 (20:10 +0200)]
Bump required CUDA version to 7.0
This simplifies cmake-time requirements as we can now require the same
CUDA version for all cases except MSVC. It also allows us to
unconditionally compile with the cudaLaunchKernel API and remove the
alternative chevron-notation at least in the nonbonded module.
Change-Id: I199f17151cb227fda9d76c1bf0d7fd73f1d31275
Aleksei Iupinov [Wed, 18 Apr 2018 11:32:56 +0000 (13:32 +0200)]
Separate PME GPU host-only and host/device data structures
This distinction will be necessary with OpenCL.
Change-Id: I042624233e31264acb64f0bbc28c4ff736e50ebd
Paul Bauer [Thu, 26 Apr 2018 08:34:09 +0000 (10:34 +0200)]
Split up special topics section in manual
Change-Id: I80cc67a076e7a42022028f05c2c7611c5c8c2768
Aleksei Iupinov [Mon, 23 Apr 2018 10:22:35 +0000 (12:22 +0200)]
Add copyFromDeviceBuffer() CUDA/OpenCL implementations
Change-Id: Ib74f0bc65e97d74e09bdac312a90135251f72b60
Mark Abraham [Sat, 21 Apr 2018 16:51:16 +0000 (18:51 +0200)]
Revert "Tweak PME run mode checks"
This reverts commit
49ca05c7a05209845609c62f122ab7313b19dd39.
Change-Id: I412172df6832eeb0d9c7e03cc0e7e26a7c10439e
Paul Bauer [Thu, 26 Apr 2018 08:20:11 +0000 (10:20 +0200)]
Split up topology section in manual
Change-Id: Ie7773d15aabe6fdedabacebe5203224028fc4219
Paul Bauer [Thu, 26 Apr 2018 07:53:01 +0000 (09:53 +0200)]
Split up algorithms manual page
Change-Id: I47c76d4aa6d6280237d76723604e5b9a1d024c6b
Paul Bauer [Wed, 25 Apr 2018 08:28:30 +0000 (10:28 +0200)]
Add page breaks in reference manual
Added manual page breaks between the different sections of the reference
manual in the LaTeX pdf build.
Change-Id: I6a9f1ae3608867ff683845dfdae16f6f1d795401
Paul Bauer [Tue, 24 Apr 2018 16:02:12 +0000 (18:02 +0200)]
Split up Interaction functions manual page
First set of patches that split up the individual sections
of the reference manual into smaller pieces.
Also adding comments in CMake which chapters files belong to.
Starting with Interaction function and force fields.
Change-Id: Ia0175f548ef91fe9f39457490cd4087ccbd75f02
Mark Abraham [Fri, 13 Apr 2018 11:39:31 +0000 (12:39 +0100)]
Refactor SD update
The former use of multiple boolean control variables made the logic
hard to follow. Without constraints, the two parts of the integrator
are fused, which is now expressed explicitly.
This means it is now clear that the second half of the sd update does
not compute anything from the foreces.
Removed some of the vestiges of the way we once had two SD
integrators.
Refs #2423, #1793
Change-Id: I39d4cd0b8568859220b3a592b138f3f4405f8991
Paul Bauer [Mon, 23 Apr 2018 15:48:58 +0000 (17:48 +0200)]
Change image conversion to only be build once
Change to CMake so that the image conversion needed for the web version
of the reference manual is only done once.
Also added some comments to specify the changes to USeLatex.cmake
and corrected the usuage of variable names in the cmake scripts.
Change-Id: I1caf09e899467e4de7451892536db967a35814fa
Aleksei Iupinov [Fri, 16 Feb 2018 15:12:51 +0000 (16:12 +0100)]
Removed cu_realloc_buffered() in favor of reallocateDeviceBuffer()
Change-Id: I5f0d374f8e7e22505265f3cebc60fe29948ab6e9
Aleksei Iupinov [Tue, 13 Feb 2018 12:08:13 +0000 (13:08 +0100)]
DeviceBuffer headers are added
For now they contain templated versions of GPU memory (re-)allocation
and host-to-device copy routines. The DeviceBuffer declarations
and the freeDeviceBuffer() implementations are moved there as well.
Using those, the GPU pairlist allocation code is made look
mostly the same in CUDA and OpenCL. ocl_realloc_buffered() is
removed; cu_realloc_buffered() is to go next.
Change-Id: Ic724113d7d0ed6b4707d094010e11ccbcd5da3c5
Szilárd Páll [Thu, 19 Apr 2018 13:50:25 +0000 (15:50 +0200)]
Fix icc warning in post-submit
icc refuses to understand GMX_UNUSED_VALUE.
Change-Id: Ieca8ad781e6f3bb7908f346a14367dc86ae8b15f
Szilárd Páll [Fri, 13 Apr 2018 16:25:57 +0000 (18:25 +0200)]
Add post-submit with ARM HPC Toolchain
Using gcc-7 and armclang-18.2.
Change-Id: I0cd310786598b7c980af970849ba0de95b91d2ad
Szilárd Páll [Tue, 17 Apr 2018 17:51:59 +0000 (19:51 +0200)]
Tweak PME run mode checks
These should allow compile-time evaluation when mdrun is compiled with
GMX_GPU=OFF.
As the CPU-only build can now optimize out quite some code, this also
fixes a gcc 7 warning that an argument of pme_gpu_reduce_outputs()
may be used uninitialized.
Change-Id: I2397e0dc7e4e2f6587d01d94db27072938e85e7d
Paul Bauer [Thu, 26 Oct 2017 13:47:03 +0000 (15:47 +0200)]
Convert manual from LaTeX to Markup
Manual has been automatically converted from *.tex to *.rst using
pandoc (after passing through the conversion script and some manual
hacking of the tex input files).
New rst formatted manual replaces the old one, with the pdf version
now also being generated from the information in the rst files.
Additionally, the eps image files have been converted to pdf and svg file
types to make it easier to automatically include them in the created
manual.
Proper change tracking depends on change
I3986740ab42a4054c4d0f9f67923ebf7a51320d9
and
Ice29bde4d9aa2ec99b416c668c21bef13fdd9d3e
Change-Id: I6702dde7be9cdd4199db2e6a8470698203449e31
Paul Bauer [Tue, 21 Nov 2017 07:22:18 +0000 (08:22 +0100)]
Second change tracking commit
Another intermediate commit to ensure proper change tracking for the work on the reference manual
This commit changes the file names and paths.
It as well changes the image files to svg and pdf, to make the automatic
conversion work better for the child change.
Change-Id: Ice29bde4d9aa2ec99b416c668c21bef13fdd9d3e
Paul Bauer [Mon, 6 Nov 2017 15:03:46 +0000 (16:03 +0100)]
Intermediate commit to track changes to manual
This is just an intermediate commit to make sure git properly tracks the
changes to the files for the manual, and is not expected to compile
the manual at all.
This change does the conversion from tex to rst, while keeping the file
names.
The original LaTex inputs are included in a pandoc conversion friendly
format in the orignal-conversion-friendly subfolder, together with the
output from the automatic conversion.
Change-Id: I3986740ab42a4054c4d0f9f67923ebf7a51320d9
Szilárd Páll [Thu, 13 Jul 2017 15:48:14 +0000 (17:48 +0200)]
Minor fix for pre-submit matrix docs
Fixed comment to avoid confusion as CMake 3.8 did not introduce any new
CUDA feature that we actually do use (and can test).
Change-Id: I9d559a8bc606c14060fb6abbc93465d4d97e838a
Szilárd Páll [Wed, 18 Apr 2018 15:59:39 +0000 (17:59 +0200)]
Move the PME GPU clearing to the end of the step
This places the call to the end of the force-compute next to the nbnxn
output clearing also fixing the cycle counting that previously
incorrectly assigned the cost of launching the clearing to the wait for
gather cycle counter.
Change-Id: I63b27a91d88a54d701831edda592b5d6277e3fb9
Mark Abraham [Tue, 10 Apr 2018 11:37:48 +0000 (13:37 +0200)]
Introduce gmx_used_in_debug
Sometimes variables are only used to support assertions or other debug
code. This alternative annotation makes clear that the variable is
used as intended, so that if the value becomes truly unused then we
will be prompted to remove it by a warning from a suitable debug
build, thereby simplifying the code.
Deprecated GMX_UNUSED_VALUE following review discussion.
Change-Id: I39fe11d8062e599ef3e78b80320fe31fb2a503c0
Viveca Lindahl [Tue, 27 Mar 2018 10:37:33 +0000 (12:37 +0200)]
Disallow -skip values <= 0 for gmx trjconv.
Fixes #2467
Change-Id: Ic8b1892c454100bf4d5668b1c55b33ec6fbff4a2
Paul Bauer [Mon, 16 Apr 2018 14:16:23 +0000 (16:16 +0200)]
Fix legacy topology memory error
The change to port mtop to c++ has exposed a number of issues in the
legacy topology data structure, where pointers would be copied from a
temporary mtop object to the local topology, and subsequently
invalidated when mtop was correctly free'd.
This change is a bit of wooden mallet applied to the problem, by brute
forcing the assignment of the values that were previously copied by
pointer.
Fixes #2479
Change-Id: I7d702666fa48cb3840f914ee3bd28787d3caeec8
Mark Abraham [Fri, 13 Apr 2018 11:34:36 +0000 (12:34 +0100)]
Shift per-step control logic to do_md
There are multiple reasons why do_md can decide this is the last step,
so we should be consistent about it.
Refs #1793
Change-Id: I46f377630fa12be482ccb532c05d96cfe0537523
Mark Abraham [Fri, 2 Mar 2018 21:42:06 +0000 (22:42 +0100)]
Break apart update_constraints
There are four distinct kinds of work being done, and never was any
call to update_constraints doing all of them, so it's better to have a
group of functions, each of which do one thing, and the relevant ones
called. This also makes it simpler to express by returning fast that
when we don't have constraints, we do nothing.
Made the logic for whether this is a log or energy step match that of
the main MD loop. The old implementation may not have prepared for the
last step correctly when it was triggered by something other than the
nsteps inputrec value.
Removed a commment mentioning iteration, which is a feature
that was removed a while ago.
Removed some ancient debug dump output.
Refs #2423, #1793
Change-Id: I21c10826721ddc9a79a33b1dc75971a20d0855d9
Szilárd Páll [Mon, 9 Apr 2018 18:17:11 +0000 (20:17 +0200)]
Add post-submit test with hwloc off
This tests exercises the internal CPU topology detection code-path.
Change-Id: I2444b95c53b678ae88a66d95dbc93a55f7ed2725
Berk Hess [Wed, 7 Mar 2018 11:53:39 +0000 (12:53 +0100)]
Move natoms_mol out of gmx_molblock_t
natoms_mol is derived information, so moved to MolecluleBlockIndices.
Change-Id: I10080dc8fd43bac1f1976551d66218fcc1d2c53c
Mark Abraham [Tue, 29 Dec 2015 17:39:44 +0000 (18:39 +0100)]
Updated mdrun comparison infrastructure
The functionality for running grompp to produce a .tpr file useful for
comparing two mdrun calculations works better as free functions than a
base class. This patch is essentially a rewrite of the interface,
though the core functionality is roughly the same.
Used raw string literals for nicer looking embedded strings.
Refs #1868
Change-Id: I4b5137b34c3da286e344809b71afd985d9c7bfab
Szilárd Páll [Tue, 10 Apr 2018 13:28:11 +0000 (15:28 +0200)]
Use trivalue option for GMX_HWLOC
Don't run hwloc detection if GMX_HWLOC=OFF. Separated the value of the
variable set by the user from the specification of the default
behaviour and the selected behaviour.
Change-Id: I70dbe9e40857680dc3987eb8b6820c5ccac96b63
Mark Abraham [Fri, 13 Apr 2018 10:09:09 +0000 (11:09 +0100)]
Merge branch release-2018
Minor conflicts documenting gpuregiontimer_ocl.h, resolved
with a suitable mix from both branches.
Change-Id: I5bb417acaff941f18730f0417c5e46c8f4c2fc1e
Mark Abraham [Wed, 28 Feb 2018 18:08:14 +0000 (19:08 +0100)]
Clean up constraints code
Moved constraint code into gmx namespace.
Used more forward declarations in both the old and new headers.
Removed typedef from type declarations.
Removed gmx_ prefix from some names, since it is no longer required
and we may as well avoid verbiage.
Renamed some types more consistently with newer coding styles, and
called them class now where they will be one shortly.
Added some const correctness.
Apparently this inspires uncrustify to change positions of some
comments. Go figure.
Replaced all gmx_bool in constraints code with bool.
Maths functions from vec.h (which are not in the top-level namespace)
now need namespace qualifications.
Added and fixed various Doxygen, which is primitive in some cases
where the code was particularly cryptic.
Noted policy on multiple authors within Doxygen comments.
Refs #2423
Change-Id: I41bf3a4b9a4fbbcb3a3a7a27dc922d563abedbcb
Aleksei Iupinov [Thu, 12 Apr 2018 14:31:43 +0000 (16:31 +0200)]
Make in-source OpenCL kernel path a per-module parameter
Change-Id: I19cd66b441fec6ceba74eb648bea3409b6521917
Mark Abraham [Fri, 2 Mar 2018 21:08:23 +0000 (22:08 +0100)]
Remove use of where(), if DEBUG etc.
The where() debugging function causes run-time branches in
release-mode builds, and replaces functionality for which one should
use a debugger.
Other such preprocessing clutter should also go away. Since we don't
check whether any of it compiles or produces useful data, we may as
well delete it.
This coincidentally simplifies the call sigatures of some
functionality, too.
Retained some useful essentialdynamics debug code, which is now always
compiled, and written from setup code only at debug level 2.
Refs #2423
Fixes #2122
Change-Id: I2c60c162734f4c2ec1d56153853a36d28e6a66ff
Aleksei Iupinov [Thu, 12 Apr 2018 12:42:48 +0000 (14:42 +0200)]
Remove CUDA_FUNC macros from many functions in PME GPU
As pme-gpu*.cpp files are not compiled during CPU builds anymore,
PME GPU functions that are not exposed to mdrun/tests do not need
to be hidden.
Change-Id: Id39c0bb6e586b508f5bbe8c7501ffd560d3cf14c
Aleksei Iupinov [Tue, 27 Mar 2018 11:18:51 +0000 (13:18 +0200)]
Stop PME GPU code from compiling on non-CUDA builds
On non-CUDA builds: all entrypoints into PME GPU code are
marked as stubs; pme-gpu.cpp and pme-gpu-internal.cpp are
excluded from compiling. Several common functions (such as
check for GPU support at the end of PME initialization)
are moved to pme.cpp, to still work with non-GPU builds.
Change-Id: Iaa9ea7b3e42665c60b788e76510a810457a69f20
Mark Abraham [Mon, 26 Feb 2018 16:47:24 +0000 (17:47 +0100)]
Reorganize energy evaluation for EM
Used aggregate initialized structs to simplify future refactoring.
Refs #1793, #2423
Change-Id: Iedb8bf3b4cb2d7f238c4b674ce459564a3f76a20
Aleksei Iupinov [Tue, 27 Mar 2018 20:30:43 +0000 (22:30 +0200)]
Prevent OpenCL timing memory leak
Fixes #2470
Change-Id: I4917de697bee7df98da0037e9165e52e660f83a0
Viveca Lindahl [Tue, 10 Apr 2018 13:52:25 +0000 (15:52 +0200)]
Minor text edits and fix of broken link in user guide.
Link to domain decomposition section was broken. Also:
* removed a TODO that was already done
* reordered words in SIMD to make it a definition
Change-Id: I7943e4f59e2de82c2c6e94d15a6089a92f196132
Berk Hess [Wed, 14 Feb 2018 08:46:59 +0000 (09:46 +0100)]
Convert gmx_molblock_t to C++
Changed posres pointers in molblock to std vector.
Also moved the derived helper index data into a separate struct.
That is merged into this change to keep MPI broadcasting simple.
natoms_mol will be moved into the new struct in a child change.
Change-Id: I131fd14ab53cec98800c7e0731d3a92df3f93422
Mark Abraham [Wed, 28 Feb 2018 15:20:03 +0000 (16:20 +0100)]
Simplified handling of simulation runners
Argments to runners are now passed via struct members. That struct is
expected to change over the medium term, as most of its contents
should either be in a container of modules, or data with such a
module. As such, it does not make sense to do a lot of coding to
manage its contents in a sound way. The practical effects of using
this struct are almost the same as the old approach of passing a
forest of arguments - some variables are declared in a scope,
initialized with values, then used once.
The form is chosen so that
* the do_md() etc. functions do not need a large number of useless
textual changes now
* future changes to names and types of the former parameters do not
need to be edited in matching way in multiple places of code and
their doxygen
* we don't need to mark things gmx_unused anywhere
Useless unchecked return values have been removed.
Some excessive includes in integrator.h were removed, which
generates a few minor fixes elsewhere.
Refs #1793
Change-Id: I678598175192c9c68113fdd79fcee17f8e5c504e
Mark Abraham [Wed, 28 Feb 2018 14:54:26 +0000 (15:54 +0100)]
Create gromacs/mdrun module and move code there
Improving how we dispatch the work for do_md and friends requires that
they all compile as part of libgromacs (or all outside of it). The
code currently in src/programs/mdrun is there simply because it hasn't
been moved from the old src/kernel layout, rather than through any
clear design, so we should move it now that we have a reason.
Other code from src/programs/mdrun now needs to move into libgromacs
also, but we currently don't have a module for miscellanous mdrun
features, so we're adding to the abuse of mdlib for now.
Refs #1793
Refs #2423
Change-Id: I4f9ad5d0bf6585675472b49b2d5654f588b7214e
Szilárd Páll [Tue, 29 Mar 2016 20:20:22 +0000 (22:20 +0200)]
Refactor cj preload in the nonbonded OpenCL kernels
This change hides the implementation detail of preload/load operation in
inline functions configured based on the source flavor.
One of the main benefits is that this corrects the "nowarp" force and
pruning kernels removing a warp assumption (that was violated on
hardware with <32 wide wavefronts).
A step towards correctness on alternative GPU hardware, so
Refs #2030
Change-Id: If88d11df6613eadc9b59e5f03c34bac52df3514b
Mark Abraham [Fri, 26 Jan 2018 16:28:01 +0000 (17:28 +0100)]
Quiet checkpoint reading
If reading succeeds, it should write anything of interest to the log
file. If it does not, it should make a fatal error. Code here might
be run as part of mdrun (possibly in a multi-simulation), or grompp,
or compare, or dump, or eventually from an API caller, so we can't
make assumptions about what should be reported to a terminal.
Removed support for issuing a warning about restarting from very old
checkpoint formats, instead issuing a fatal error. Elsewhere, we
anyway observe that checkpoint restarts across major version
differences are not supported.
Change-Id: Id2b084bf0792a6992931609fb78d4a38a5f255fe
Pascal Merz [Mon, 19 Mar 2018 18:59:57 +0000 (12:59 -0600)]
Move checkNumberOfBondedInteractions
In task #1868, we will move the rerun functionality from do_md to
a separate function in a new file. As both do_md and the new
do_rerun need access to checkNumberOfBondedInteractions(), it needs
to be moved to a more central location.
Change-Id: Iae0ace11db2f83e5034fdfae21ccac3e7b9e34d1
Berk Hess [Tue, 13 Feb 2018 13:30:22 +0000 (14:30 +0100)]
Convert gmx_mtop_t to C++
gmx_mtop_t now uses std vectors for moltype and molblock.
gmx_mtop_t, gmx_moltype_t and gmx_molblock_t now have constructors
and destructors.
Changed declarations of gmx_mtop_t* to not use a pointer or to use
std::unique_ptr.
Several sub-structs still use C style pointers and will be converted
later.
Change-Id: Iee802e4382a0a389496bb9395389e5926918d0f8
Mark Abraham [Thu, 29 Mar 2018 12:22:26 +0000 (14:22 +0200)]
Remove leftover mention of twin-range scheme
Also fixed a broken symref to a version number that should
never have been a symref
Change-Id: Id1b10614106748de6ff114ade4b542ac7581f4cf
Mark Abraham [Tue, 3 Apr 2018 09:44:09 +0000 (11:44 +0200)]
Merge "Merge branch release-2018"
Berk Hess [Tue, 3 Apr 2018 08:00:15 +0000 (10:00 +0200)]
Change warninp filenm to std::string
This prevent buffer overflows with long filenames.
Fixes #2465
Change-Id: Ifcd264a6b33929f6b369d543c83c16d5378db937
Berk Hess [Fri, 23 Mar 2018 10:10:56 +0000 (11:10 +0100)]
Do not calculate COM for pull group 0
Pull group 0 is an absolute reference with coordinates 0,0,0,
so it is clearer to never compute its center of mass.
Refs #2143
Change-Id: Ifa974ab84afe303594c3b65e9567e0568bb151a9
Berk Hess [Fri, 23 Mar 2018 11:14:23 +0000 (12:14 +0100)]
Move file opening out of init_pull()
This is a step towards making a constructor for t_pull.
Change-Id: I24583fa32066503ccfbe0abaef6a412241974b12
Szilárd Páll [Mon, 26 Mar 2018 20:18:07 +0000 (22:18 +0200)]
Tweak/enable icc 18 post-submit tests
SIMD was disabled due to #2335
Change-Id: Ia55742958cfbdfb75e96c8d2b0ba5620a57a6f56
Magnus Lundborg [Thu, 1 Mar 2018 07:39:18 +0000 (08:39 +0100)]
Improved check of if only forces are computed in do_pairs()
Use the check introduced in I67bdb0cba9c6ec20b to see if the
SIMD version can be used.
Change-Id: I3dfd401aa1dc421757bf243809ac85e17a9062b6
Paul Bauer [Wed, 28 Mar 2018 11:33:02 +0000 (13:33 +0200)]
Fix cmake Sphinx detection for versions >1.6.4
The output from sphinx-build --version changed between version 1.6.4 and
1.7.x, leading to the cmake detection script to fail and reporting no
version at all. This fixes detection for both before and after the
change to the output format.
Change-Id: I34e50067f52f8127d137db28e9411420559d44cf
Szilárd Páll [Fri, 2 Mar 2018 21:23:06 +0000 (22:23 +0100)]
Switch CUDA 9.0/gcc 5 test to CUDA 9.1/gcc 6
Change-Id: If3e7277243c986ce96bf31de314edb1a255a44a6
Berk Hess [Tue, 13 Mar 2018 20:00:00 +0000 (21:00 +0100)]
Modularize pull_coord_work_t
Organized the 19 members of pull_coord_work_t into 5 sub-groups
and moved some into a new external PullCoordVectorForces struct.
Added a constructor and changed the pointer to coord in pull_t
to std::vector.
Also fixes #2446
Change-Id: I48d176ddbf3f5649f9072aacfb6bcb2d69785f91
Mark Abraham [Sun, 11 Mar 2018 18:11:31 +0000 (19:11 +0100)]
Free more memory in grompp and mdrun
This will be increasingly useful as we start adding more GoogleTest
cases that call grompp and mdrun repeatedly.
Refs #1793, #1868
Change-Id: Ic0faaa4c3dec2891d0cdc6166561f8ccd4391f44
Berk Hess [Wed, 14 Feb 2018 14:36:49 +0000 (15:36 +0100)]
Remove mols from gmx_mtop_t
The molecule atom begin/end information in gmx_mtop_t was derived
information. Now the mols struct is removed and the information is
derived when necessary.
Introduced BlockRanges, a C++ verion of t_block.
This is preparation for converison of gmx_mtop_t to C++.
Change-Id: I1717a101de82354a7f9cf14fd7f43c7227e554ef
Mark Abraham [Wed, 28 Mar 2018 11:19:26 +0000 (13:19 +0200)]
Merge branch release-2018
Some meaningful conflicts in init_multisim associated with multisim
fixes and clarifications in release-2018 combining with reorganization
in master branch.
Preserved the master-branch pre-submit matrix, since all branches have
separate changes that cope with gpu_id=2 no longer being valid.
Change-Id: Idefe4f1ec3bbbc76dfedf03a81abef8233328de2
Mark Abraham [Tue, 27 Mar 2018 19:39:34 +0000 (21:39 +0200)]
Clarified mdp options relating to bonds
Change-Id: Iffcaaaf1fc6c707c8f644da18cf03e28d2137557
Mark Abraham [Tue, 20 Mar 2018 07:39:37 +0000 (08:39 +0100)]
More gcc-8 fixes for POWER
Fixes #2421
Change-Id: I43c13df3a217d0f2154dca0ef215efd9cd27474a
Joe Jordan [Thu, 22 Mar 2018 08:59:25 +0000 (09:59 +0100)]
minor fix to flag strings for gmx potential
Change-Id: I2dadc8d74888dc2ebcd4fcf71e275c21fdd23cd6
Mark Abraham [Wed, 21 Mar 2018 15:04:44 +0000 (16:04 +0100)]
Updated to prepare for 2018.2 release
Change-Id: I1c72e8a3ac1b6b2e29b39c2d52bad5b87a884912
Viveca Lindahl [Thu, 22 Mar 2018 09:36:31 +0000 (10:36 +0100)]
Added cool quote.
Change-Id: I89d86d788f45f0d9124f5d00133709de83a73f38
David van der Spoel [Tue, 20 Mar 2018 21:04:42 +0000 (22:04 +0100)]
Renamed entropy.* to thermochemistry.*
This is a content-less patch to get the renaming history
correct in git.
Change-Id: I34f1d15f2e9136962b1718a60863b3b20a66fda5
Mark Abraham [Fri, 23 Feb 2018 13:20:17 +0000 (14:20 +0100)]
Version 2018.1
Change-Id: I3285c77fc557c1a6f34796c4bfb4843846b0d8a5
Mark Abraham [Wed, 21 Mar 2018 11:07:16 +0000 (12:07 +0100)]
Merge "Merge branch release-2016 into release-2018" into release-2018
Mark Abraham [Tue, 27 Feb 2018 16:10:15 +0000 (17:10 +0100)]
Update release notes for 2018.1
Change-Id: Ia60d523647e1915856ae3b00a0cb9eacd939fc56
Mark Abraham [Tue, 20 Mar 2018 22:17:51 +0000 (23:17 +0100)]
Merge branch release-2016 into release-2018
Conflict in pre-submit matrix, kept 2018 content that already
has the same logical change made.
Change-Id: I40b2db8d149388bed07471fcdb8082b0fc92b9b5
Vedran Miletić [Tue, 20 Mar 2018 11:27:45 +0000 (12:27 +0100)]
Document matrix_convert function in PBC
The brief documentation was in place, but the documentation of the
function parameters was missing. This patch adds it and also fixes
incorrect Doxygen syntax at pbc_dx_d.
Change-Id: Ic897911bf4b8866bb7c4dc3aea982493cc03874c
Berk Hess [Tue, 20 Mar 2018 12:19:01 +0000 (13:19 +0100)]
Fix gmx dump AWH formatting issue
A comma was missing in the list of AWH checkpoint entry string
which caused the naming to be messed up in the gmx dump output.
Change-Id: I85d0722236f3f9559c1117fdcee39766d04b424d
Mark Abraham [Tue, 20 Mar 2018 11:50:17 +0000 (12:50 +0100)]
Update use of gpu_id in Jenkins
We plan to remove one of the GPUs from the slave that had three, so we
need to update the testing configurations. The new configuration might
balance load a little better.
Refs #2408, #2410
Change-Id: I3b5d9c8702c021f0676ea3ca12f9e7f1d3317ed1
Berk Hess [Mon, 19 Mar 2018 13:33:47 +0000 (14:33 +0100)]
Disallow single simulation with multisim
To avoid many untested code paths, we, at least temporarily,
disable a single simulation with mdrun -multisim and -multidir.
Refs #2448
Change-Id: I9befdb677f3c77bcc6dc0c77abc3478f0b83ba8d
Mark Abraham [Tue, 20 Mar 2018 11:51:56 +0000 (12:51 +0100)]
Update use of gpu_id in Jenkins
We plan to remove one of the GPUs from the slave that had three, so we
need to update the testing configurations. The new configuration might
balance load a little better.
Refs #2408, #2410
Change-Id: Ie253ef07998cf45c5fc2e118a5394f0817e66f75
Mark Abraham [Sun, 18 Mar 2018 19:34:53 +0000 (20:34 +0100)]
Update use of gpu_id in Jenkins
We plan to remove one of the GPUs from the slave that had three, so we
need to update the testing configurations. The new configuration might
balance load a little better.
Refs #2408, #2410
Change-Id: Ia63cb701049a02ad86fdd9f9c03388cd11a14bcc
Aleksei Iupinov [Thu, 1 Mar 2018 22:32:03 +0000 (23:32 +0100)]
Clarify the mdrun GPU options docs
Refs #2359
Change-Id: If112077a59f875ffb1c689b2ac67dad7cdf2adb9
Mark Abraham [Tue, 6 Mar 2018 09:53:19 +0000 (10:53 +0100)]
Add helper function to make a vector from an ArrayRef
This syntactic sugar makes it easy to make a vector with a copy of the
contents.
Change-Id: Ib51c8a1d88aee7ca35fe1715d6f094b60e90e0b2
Mark Abraham [Fri, 16 Mar 2018 21:21:48 +0000 (22:21 +0100)]
Fix VSX SIMD with gcc 8
gcc 8 apparently generates different code for the former GROMACS
code, which seems buggy. See
https://bugzilla.redhat.com/show_bug.cgi?id=
1556989#c3
and https://gcc.gnu.org/bugzilla/show_bug.cgi?id=84907
Fixes #2421
Change-Id: I31492cd582b785cdfb42e8b999a165a7339ce4be
Paul Bauer [Wed, 14 Mar 2018 09:15:42 +0000 (10:15 +0100)]
Only free topology when allocated
Fix trjconv so that the topology only gets free'd when it has been
previously allocated.
Fixes #2430
Change-Id: Idc9a4219d988e1794ef86f7cc79f0d00750394ca
Aleksei Iupinov [Thu, 1 Feb 2018 16:16:52 +0000 (17:16 +0100)]
Add a basic TPI sanity test
The floating point exceptions are for now toggled off
in the test body instead of mdrun itself.
Refs #2391
Change-Id: I41b584f4753b9b0e126256a94c1304f0a870aa73
Aleksei Iupinov [Fri, 16 Mar 2018 10:18:47 +0000 (11:18 +0100)]
Stop gmx_feenableexcept() from returning previous exception settings on Apple
This makes the function return value unambiguous.
Change-Id: I3e64e769b27fb0fa59b650d18b2fd099a9181025
David van der Spoel [Fri, 29 Dec 2017 20:56:09 +0000 (21:56 +0100)]
Split off entropy calculation to separate file.
The calculation of the quasiharmonic entropy or the one
through the Schlitter formula has some popularity. In
order to allow computation from a normal mode analysis
as well as from a PCA (essential dynamics analysis) the
code was split off into a separate file. Proper documentation
and five tests are provided as well. Minor cleanups
were done as well.
Change-Id: Ic5e4feab6a304946947d6e69be75c06b46aff75c
Berk Hess [Fri, 16 Mar 2018 10:00:41 +0000 (11:00 +0100)]
Correct PMF sign error in AWH bias sharing
Recent commit
229c8f63 was though to fix a sign error in
the calculation of the deconvolution of the AWH PMF when sharing
the bias over multiple simulations, but this sign was misplaced.
Fixes #2439
Change-Id: I67ec06ff4d832a857467b58b362f9f6f88671aa8
Berk Hess [Thu, 15 Mar 2018 17:09:55 +0000 (18:09 +0100)]
Fix recent mdrun signaling bug
Recent commit
e4deba12 accidentally negated the locality condition
for signaling checkpoint and termination in mdrun.
Fixes #2457
Change-Id: I1b7a4c26637766a44cad2581c9c9ec420aa4ab6e
Aleksei Iupinov [Tue, 23 Jan 2018 11:45:04 +0000 (12:45 +0100)]
Restore the lost mc_temp check in grompp
The expression for checking whether the reference temperature
is defined is moved into a helper function.
Change-Id: Ib331f52e8031a5e5d7c32234cfe936024c49ac28
Berk Hess [Thu, 15 Mar 2018 10:25:50 +0000 (11:25 +0100)]
Fix virial with external pull potential and MPI
When using an external pull potential with domain decomposition,
currently this is only used by AWH, the virial contribution would
be multiplied with the number of MPI ranks.
Fixes #2455
Change-Id: I61452fb9eca6e68fea3256cc25b39033a9c5d8e7
Berk Hess [Wed, 14 Mar 2018 10:59:53 +0000 (11:59 +0100)]
Improve inter-simulation signaling
Use a single boolean for controlling inter-simulation signaling.
This would have prevented issue #2447.
Introduce an inter-simulating signaling frequency. This both
simplifies the code and significantly reduces communiation overhead
for many simulations and/or many ranks per simulation.
Correct the terminimation step print with replica exchange.
Refs #2440 and #2447
Change-Id: I8ed50c5b11564d9a967bcacb15c4fcd3be05caea
Mark Abraham [Thu, 25 Jan 2018 14:47:35 +0000 (15:47 +0100)]
Make a persistent physical node communicator
Rather than make and re-make this communicator multiple times for for
almost all common run configurations, build one, and keep it in a
place distinct from commrec (which has too many responsibilities
already).
Note that the master thread-MPI rank builds a fake one initially,
because MPI is not yet initialized, then coordinates to build the real
one with the newly launched threads. However that communicator is not
actually used until after the execution paths have re-joined.
Simplifies IThreadAffinityAccess while retaining the ability to test
the affinity-setting logic without requiring specific attributes of
the node. Note that some of the tests already required that a
particular MPI environment exists.
Change-Id: Ie0800b07a65f9579ddc8af8f418cd14b85671de7
Berk Hess [Wed, 14 Mar 2018 08:32:23 +0000 (09:32 +0100)]
Fix mdrun signalling with AWH bias sharing
The recent commit
717fd5b8, which should have fixed issue #2440,
disabled checkpointing and termination by disabled signalling
between AWH runs that share a bias.
Fixes #2447
Refs #2440
Change-Id: Ic80ea07cfa1bde1b31fa9d660f00492b794b000f
Berk Hess [Mon, 12 Mar 2018 15:54:04 +0000 (16:54 +0100)]
Fix COM pulling with external potential with #ranks>32
With more than 32 PP-ranks, the pull code could use only a subset
of the PP-ranks. This change forces all ranks to do pulling when
external potentials are present (currently only used by AWH).
Fixes #2441
Change-Id: I8501024b7961600ec79f3707e239ddf25525aa79
Berk Hess [Tue, 13 Mar 2018 13:59:19 +0000 (14:59 +0100)]
Fix pull bug with geometry=direction-periodic
When doing COM pulling with geometry direction-periodic,
the reference location needs to be used to compute the current
distance. This reference was taken from the previous step instead
of the current. In practice this only caused issues at restarts
when the distance was more than half the box length.
Fixes #2446
Change-Id: Ie0c0341ad8c6ce1e78951270cab27ecaf95d65eb
Berk Hess [Tue, 13 Mar 2018 13:18:45 +0000 (14:18 +0100)]
Add AWH fixes to release notes
Change-Id: I17531da77495367b0e62b4e0b0e912bbd16659f9
Mark Abraham [Mon, 26 Feb 2018 16:47:02 +0000 (17:47 +0100)]
Add more const to uses of t_commrec and t_inputrec
Also removed some pointless struct keywords.
Refs #2423
Change-Id: Iacc008fb11a31646e798364e253de322c16ccaee
Szilárd Páll [Tue, 13 Mar 2018 02:24:58 +0000 (03:24 +0100)]
Require OpenCL 1.2
This commit bumps the requirement and removes OpenCL 1.1 API
compatibility support.
Refs #2438
Change-Id: Iaedf5fbdfd24a2d020983847815c2c21bac0f74c
Berk Hess [Mon, 12 Mar 2018 15:43:53 +0000 (16:43 +0100)]
Fix AWH ensemble checkpointing
AWH multi-runs with shared bias could terminate at different steps
leading to checkpointing from which continuation was impossible.
Fixes #2440.
Change-Id: I728c6aea9d030fcfad04efc6082309dafe3408bd
Berk Hess [Mon, 12 Mar 2018 20:36:07 +0000 (21:36 +0100)]
Fix AWH deconvolution when sharing a bias
When sharing an AWH bias over multiple simulations, the PMF output
was garbage due to a missing minus sign in the reduction.
Note that this only affected the PMF output, not the sampling.
Fixes #2439
Change-Id: I688cda045f5e757e58b392d64384705b3ac73a17
Mark Abraham [Wed, 21 Feb 2018 15:02:46 +0000 (16:02 +0100)]
Introduce constrain_shake
Also move various functions and fields of general constraint code and
data to the SHAKE code and data structures. Made some use of inputrec
const, to suit later changes.
Change-Id: I09b7a719b58f8f8192762431edc139674eaf23ae
Szilárd Páll [Mon, 12 Mar 2018 23:23:07 +0000 (00:23 +0100)]
Fix clang 6.0 with CUDA 9.0
This enables clang 6.0 CUDA build for sm_70 and works around an issue
which seems to affect sm_37 support.
Fixes #2443
Change-Id: Ib9c52e4a3a8ac1e05e851c8166eec4a6b5df4825
Mark Abraham [Tue, 13 Mar 2018 08:52:50 +0000 (09:52 +0100)]
Merge "Merge branch release-2018"
Szilárd Páll [Wed, 15 Nov 2017 19:48:50 +0000 (20:48 +0100)]
Avoid icc-specific -march=core-avx2 flag with gcc/clang
This change makes sure that the -march=core-avx2 icc-specific
optimization flag is only used for Intel compilers. It is not only
unnecessary for gcc/clang but also undocumented (and not proven to be
useful, actually potentually harmful with gcc <=6, measured 1-3% lower
perf.).
Change-Id: Ic2f05554ea6e460c53fa307fc1da3de1b6868e2f