Paul Bauer [Wed, 21 Nov 2018 09:46:29 +0000 (10:46 +0100)]
Merge branch release-2018 into release-2019
Several changes addressing known issues have not
been brought forward, either because they are
inappropriate or the bug is already fixed in
release-2019 branch.
Resolved Conflicts:
admin/builds/gromacs.py
admin/builds/post-submit-matrix.txt
cmake/gmxVersionInfo.cmake
docs/CMakeLists.txt
src/gromacs/mdlib/minimize.cpp
src/gromacs/mdlib/shellfc.cpp
src/gromacs/topology/mtop_util.cpp
src/programs/mdrun/md.cpp
src/programs/mdrun/mdrun.cpp
src/programs/mdrun/runner.cpp
src/testutils/testinit.cpp
Change-Id: Ia18b43854925fb2c6e1bf4256b99bd8f42359f68
Mark Abraham [Tue, 20 Nov 2018 11:51:43 +0000 (12:51 +0100)]
Partial revert of "Fix inefficient shell minimization"
This reverts the minimize.cpp part of commit
5749eb1c9934c3597f140b793c7b374610a56335. That would likely affect
large systems instead, and those are likely more common targets for
normal mode analysis.
Change-Id: Ia586beb7b47480499907352a96175bd1dda29684
Joe Jordan [Mon, 19 Nov 2018 08:46:30 +0000 (09:46 +0100)]
fix unused variable warning from gmxapi compilation
Fixes #2768
Change-Id: I8c77dd19f15df6f365122e25680e9d0a553cb36c
Mark Abraham [Fri, 9 Nov 2018 07:12:26 +0000 (08:12 +0100)]
Fix inefficient shell minimization
In
5268b73d6cd, a bug was introduced when a shallow copy was used
instead of the former deep copy. However, in the original code some
pointers were used as "short-cuts", which is not neccessary. Those
pointers have been removed, and now the shell-code position vectors
are fully initialized at allocation time.
In order to get reproducible normal modes the delta x used for
computing derivatives was reduced.
Fixes #2705
Change-Id: Iad8a0b0793304e2c10d9abf3a180cfe9bdc85c4c
David van der Spoel [Sun, 18 Nov 2018 13:55:16 +0000 (14:55 +0100)]
Added citation for new analysis functionality.
Change-Id: I91e90c5b00db740cfc072cd65ada2c5f9c70941c
M. Eric Irrgang [Fri, 16 Nov 2018 13:40:31 +0000 (16:40 +0300)]
Expand gmxapi testing to include thread-MPI.
Some tests were disabled when GMX_THREAD_MPI was set because they were
not able to handle the GROMACS testing framework. These exclusions are
no longer necessary because the tests have been ported to use the mdrun
test fixtures.
Change-Id: I2a91d992031605ab4144eed774a2af55367565d8
M. Eric Irrgang [Fri, 16 Nov 2018 13:27:14 +0000 (16:27 +0300)]
Remove extraneous CMake config.
The generated gmxapi-config.cmake package config file had an unused
variable definition due to an extraneous option to
`configure_package_config_file()`
Change-Id: I67a70fa21cea92fa0de6ed7ebb49877aaf11cc89
Berk Hess [Fri, 16 Nov 2018 09:47:37 +0000 (10:47 +0100)]
grompp now checks tau-p>=2*tau-t with NH+PR
Added check to avoid resonances when combining Nose-Hoover and
Parrinello-Rahman coupling algorithms.
Fixes #2749
Change-Id: I061d5021ba5f9c3a68336d623c06843be9addbde
Paul Bauer [Thu, 15 Nov 2018 13:29:44 +0000 (14:29 +0100)]
Refine FindSphinx
The FindSphinx function would not work on older versions of sphinx,
because the output from the program changed between versions. Modified
the detection logic to cover both cases.
Fixes #2751
Change-Id: I84525c5b9237d369fd78ac59b763e063456571e2
M. Eric Irrgang [Tue, 13 Nov 2018 12:43:32 +0000 (15:43 +0300)]
Note GMX_ENABLE_CCACHE in build system docs.
Added to the list in "Variables affecting compilation/linking".
Fixes #2743
Change-Id: I1a3184fbda1d879db60fea2333bc4f7db95b0277
Mark Abraham [Thu, 15 Nov 2018 16:37:21 +0000 (10:37 -0600)]
Fix checkpoint restart of tpr with infinite step count
The recent fix of #2717 did not account for the way a user's .tpr file
can require an infinite number of steps by using the special value
-1. Such special values are difficult to remember when maintaining the
code, so we should tend to avoid introducing them.
Fixes #2757
Change-Id: I6570c4f4e7d63b2375dbb595a514c9e709f18856
Paul Bauer [Thu, 4 Oct 2018 09:52:48 +0000 (11:52 +0200)]
Rework GMXAPI tests
Changed the tests to use a test fixture and only generate the tpr files
during the actual tests.
Fixes #2664
Change-Id: Ic8a0c1c5eed2189abb9006cb45097d1acd41d175
Mark Abraham [Thu, 15 Nov 2018 05:17:30 +0000 (23:17 -0600)]
Relax arbitrary tolerance on rerun test
Fixes #2759
Change-Id: Iaff0893d495d198b55f0d3fb27484005cb2a9b6b
Mark Abraham [Mon, 5 Nov 2018 22:28:44 +0000 (23:28 +0100)]
Fix OpenCL mdrun from installed path
Previously we could dump all the headers and source files in the
share/gromacs/opencl directory, because they all came from the NB
module. Now that we have code in the gpu_utils module used by both
Ewald and NB modules, that is not an option. So we may as well use the
same approach for the pbcutil and high-level NBNXN headers also.
Change-Id: I894e6a8032547077bb5198cc6c40f65916d1b17f
Alan Gray [Wed, 14 Nov 2018 15:19:36 +0000 (07:19 -0800)]
Added Alan and Jon to List of Contributers
Change-Id: I7609963e4d124056beab69546f1402bf60e967cd
Mark Abraham [Fri, 9 Nov 2018 04:06:12 +0000 (05:06 +0100)]
More warning suppressions for QMMM code
These are typically not configured, and the resulting dead code and
possible noreturn attributes are more trouble than they are worth,
particularly when other compilers then get confused.
Change-Id: I2b374aa66feef55b518517d1c752f2b65b7a9d2b
M. Eric Irrgang [Tue, 13 Nov 2018 13:07:00 +0000 (16:07 +0300)]
Note GMXAPI CMake variables and build targets.
`build-system.rst` is a good place to note CMake variables and targets,
but the `GMXAPI` option, and the `Gromacs::gmxapi`, `gmxapi-cppdocs`,
and `gmxapi-cppdocs-dev` CMake targets, were not mentioned there.
Also, changes the names of the targets to use hyphens instead of
underscores for word separators.
Fixes #2744
Change-Id: I19db4a4124b125a4a0678c90b946d5fe3bc2e21c
Paul Bauer [Wed, 7 Nov 2018 09:23:16 +0000 (10:23 +0100)]
Update to prepare for 2018.5 point release
Change-Id: If5d058821024fe3e0110b7501b154e508a12149c
Joe Jordan [Mon, 12 Nov 2018 15:48:27 +0000 (16:48 +0100)]
Add coolquotes
Change-Id: Ifcbbb45f531612454bd080f91b247817530f78e0
Paul Bauer [Wed, 7 Nov 2018 09:16:41 +0000 (10:16 +0100)]
Version 2018.4
Add release notes for change that was missing them.
Change-Id: I56d76f87d967221d037869ca5b93400b67fcd42d
Viacheslav Bolnykh [Fri, 9 Nov 2018 16:33:45 +0000 (17:33 +0100)]
Fixing segfault in parallel MiMiC QM/MM runs
Removed unnecessary copy of coordinate array from global state to
the local one that was causing memory corruption.
Fixes #2753
Change-Id: I6d0bc6edfabc1444d7d24eb2d5401b6ff174a57d
David van der Spoel [Sat, 10 Nov 2018 06:00:24 +0000 (07:00 +0100)]
Fix entropy calculation in gmx anaeig
gmx anaeig reads eigenvectors produced by gmx covar and
can compute entropy according to Schlitter's formula or
based on the quasiharmonic method. If the number of
eigenvectors is not consistent with the number of atoms
the entropy calculation could use uninitialized variables.
Added a warning when this happens.
Fixes #2668
Change-Id: I4f265212ce0a7bf82e25e1aa6f9cbb544c45db3f
Mark Abraham [Thu, 8 Nov 2018 16:13:25 +0000 (17:13 +0100)]
Disabled FPE checking for non-release builds
This means that Jenkins will no longer give any reports, false or
true, from floating-point exceptions. Test binaries can still have FPE
checking enabled manually, however.
The content of this change should not be merged into the release-2019
branch.
Fixes #2750
Change-Id: I12c5e1a08e43e48cb7012edb6d5e8aea08baddc8
David van der Spoel [Wed, 31 Oct 2018 12:06:06 +0000 (13:06 +0100)]
Change get_atom_index to allow multiple molecules.
Make gromacs take into account atoms in all molecules.
This allows Hessian matrix creation to work over all
molecules in a simulation. An update to the regression
tests has been submitted as well.
During fixing of the problem, another problem surfaced in
the normal mode calculations to do with ordering of atoms
which is fixed here as well.
Fixes #2720
Change-Id: I9fc2dd05cb1c67d46b6d4c3d9139e6b3bed72f17
Paul Bauer [Thu, 8 Nov 2018 15:18:25 +0000 (16:18 +0100)]
Give error when rerun with identical file names
Fixes #2634
Change-Id: If3985274b3e74910c9ddefbddcfb52d1b01a3fba
Paul Bauer [Mon, 29 Oct 2018 11:24:06 +0000 (12:24 +0100)]
Issue fatal error if checkpoint does not suit the .tpr
If the step number in the checkpoint is out of range for that
described in the .tpr, then the user has provided mismatching
inputs. We do not intend then to be able to address this with the
mdrun -nsteps option.
Fixes #2717
Change-Id: I827bdc1b92ee69bf6287e2fd552ace7583b62028
Paul Bauer [Wed, 31 Oct 2018 15:32:00 +0000 (16:32 +0100)]
Actually fix gmx helix segmentation fault
The residue indexing in hxprops was wrong because the residue indices
used for residue name lookup were wrong.
Added some documentation to clarify what this code does.
Fixes #2701
Change-Id: Ie6c002be6ff2139f6af27c7b891a180338ae5b20
Berk Hess [Tue, 6 Nov 2018 14:03:32 +0000 (15:03 +0100)]
Fix bug with DD for dims without PBC
When using DD along dimensions without PBC, many pair forces could
be missing. This would not cause silent errors, except when only
running a few steps.
Fixes #2736
Change-Id: Ia256b907e25eef811e1c8f348dc0a78aaddb5610
Mark Abraham [Thu, 8 Nov 2018 09:45:14 +0000 (10:45 +0100)]
Pragma warning suppressins for icc+windows
Recent use of a pragma didn't cover this case relevant to post-submit
testing.
Change-Id: I3740548c22590688a5872474941151df8e536021
Szilárd Páll [Mon, 5 Nov 2018 18:28:32 +0000 (19:28 +0100)]
Re-enable the armclang post-submit build
bs_overdrive_1000 has been fixed and upgraded to ARM HPC toolkit 18.4.
The gcc build stays disabled as it still emits a warning.
Change-Id: I384a8ca083b5252988c1a48a63111f27f681c753
Mark Abraham [Wed, 7 Nov 2018 12:37:14 +0000 (13:37 +0100)]
Suppress clang warnings about QMMM code
These are typically not configured, and the resulting dead code and
possible noreturn attributes are more trouble than they are worth,
particularly when other compilers then get confused.
Change-Id: Idf51ee7c0a8c34d71d204db405f18704002acb58
Paul Bauer [Tue, 6 Nov 2018 12:28:10 +0000 (13:28 +0100)]
Mark new cmake variables advanced
Fixes #2738
Change-Id: I481a2e8f06055e8b1b69ab60e75bbbeaabad8355
Szilárd Páll [Thu, 1 Nov 2018 15:59:30 +0000 (16:59 +0100)]
Eliminate macro that expands to variable in PME GPU
The PME_SPREADGATHER_THREADS_PER_ATOM expanded to a statement containing
variables that needed to be declared. This has been eliminated and the
order constant is used through a constexpr.
Added consistency checks to make sure that the PME order stored in the
data structures matches the constant in question.
Also converted a few more macros to constexpr.
Change-Id: I73efea25c2da7cbde40df961f8bfae7e364bd74d
Szilárd Páll [Wed, 31 Oct 2018 20:04:02 +0000 (21:04 +0100)]
Ensure minimum exec width of the PME OpenCL kernels
This change adds checks to make sure that we don't execute incorrect
kernels in the case of the rare event if the Intel OpenCL compiler
decides to generate spread or gather kernels for 8-wide execution.
Refs #2516 #2520
Change-Id: I7ab33accebe908a56eb194e8245dfcfa6f817324
Paul Bauer [Tue, 6 Nov 2018 16:06:24 +0000 (17:06 +0100)]
Add global directory for simulation test inputs
Adds the ability to testfilemanager to use input files from a global
defined directory that is set at CMake time and contains the input files
for tpr file generation in the tests.
When a file is not found in the current directory, the code searches
the global archive for it and finally falls back to the current
directory if no file extension was given.
Example case is given for the tool test that needs a pdb and a top file.
Change-Id: Ic94f4a4d0d451024b435bf2900360aa60cd01b11
Paul Bauer [Tue, 6 Nov 2018 15:49:55 +0000 (16:49 +0100)]
Fix wrong branch for regressiontests
Change-Id: Ibcc447ceafa9e861c4db264d2a49cb2b5a659da0
Paul Bauer [Tue, 6 Nov 2018 11:28:26 +0000 (12:28 +0100)]
Prepare for beta3
Change-Id: I8d9b574f2a513154decd294a3c8ffd011ef1ab16
Paul Bauer [Thu, 1 Nov 2018 08:56:11 +0000 (09:56 +0100)]
GROMACS 2019 second beta release
Updated regressiontest hash to build release tarballs.
Change-Id: I0e2f2aadd0490e4481ffbf07691e4962b93647e1
Mark Abraham [Mon, 5 Nov 2018 17:53:03 +0000 (18:53 +0100)]
Make PME OpenCL enabled only for AMD devices
Other vendor devices have known issues, but fixes
are not yet complete.
Refs #2702, #2719
Change-Id: I0d443229ffe4cee3bb4029f57502f9c7fba2574d
Mark Abraham [Mon, 5 Nov 2018 13:41:32 +0000 (14:41 +0100)]
Remove source file with no content
Visual Studio + icc warns that nothing can link to anything in this
source file.
Also updated the CMake for this module to use our newer idioms.
Fixes #2732
Change-Id: I5cfe81aabc6ee80a6c0044cc219b1a121293aded
Paul Bauer [Mon, 5 Nov 2018 13:18:36 +0000 (14:18 +0100)]
Fix non ascii characters in manual references
Change-Id: I1c50b58df39a1ffca4b4782482da6642ad129556
Paul Bauer [Wed, 24 Oct 2018 07:20:15 +0000 (09:20 +0200)]
Make QM/MM code always compile
Brought all the old interfaces back to a state where they can always
compile regardless of the build configuration, and give fatal errors
if used from a configuration that didn't support the method.
When configured, this should work as before, but we have no ability to
test that in Jenkins.
Added some necessary const correctness.
Did QM/MM preparation all in the same place, to simplify runner.cpp
Added deprecation status to release notes.
Refs #2706, #2569
Change-Id: I4a6566c60bfbf27a7b1916be1874b36987fb7da5
Alexey Shvetsov [Mon, 22 Oct 2018 19:22:30 +0000 (22:22 +0300)]
Disable -Wno-missing-prototypes
The warning is valid for C++
The -Wno-missing-prototypes flag is valid for C++ files with clang,
but not with other compilers.
Change-Id: I85aecc92129b6db482ccff3ef5f6af5a8551ace7
Signed-off-by: Alexey Shvetsov <alexxy@omrb.pnpi.spb.ru>
Paul Bauer [Tue, 23 Oct 2018 15:12:37 +0000 (17:12 +0200)]
Give more info when trying to build manual
The manual build would fail with cryptic reasons when Sphinx was not
available because the include was not properly set.
Also set up Sphinx detection to be verbose so that users will have it
easier to see whether they can build the docs or not.
Building the docs will not work now when using Python3.
Add test script to check if ImageMagick convert actually works or not.
Refs #2709
Change-Id: I1c49d683d971a5bf0b0ce217f7e9ecd60603e6e6
Paul Bauer [Mon, 5 Nov 2018 12:25:04 +0000 (13:25 +0100)]
Fix formatting issue
Clang static analyser complained about extra semi-colons that are fixed
here.
Change-Id: I1e39a0db64aaba88293cb26c87d8d55293797694
Mark Abraham [Thu, 1 Nov 2018 14:06:53 +0000 (15:06 +0100)]
Quiet unused variable warnings
gcc 4.8 in debug mode warns about unused manager variables
Change-Id: I84b9729036c929a14550357d82321f7122462e04
Berk Hess [Sat, 27 Oct 2018 21:19:17 +0000 (23:19 +0200)]
Fix broken update groups
With 2D/3D domain decomposition, atoms in an update group could end
up in different DD cells due to different rounding.
Also added an assertion on atoms in constraint being in the same
cell when atoms are in the reverse top, as that was violated with
this bug.
Fixes #2712
Change-Id: Ic9ea10d6a20c46b89d1fa9e0aacfcc5037903428
Mark Abraham [Wed, 31 Oct 2018 17:17:14 +0000 (18:17 +0100)]
Stop using hwloc on old ARM slave
We're not sure what the problem is, but it will never be
a priority to fix it.
Fixes #2284
Change-Id: I20d7662004baeba36c4b89294457da4c36128c50
M. Eric Irrgang [Thu, 1 Nov 2018 10:40:41 +0000 (13:40 +0300)]
Fully define symbols in restraintpotential.h
External client code (i.e. an MD plugin) is expected to link against
libgmxapi, but not against libgromacs directly. This change allows
client code to implement gmx::IRestraintPotential using only GROMACS
installed headers, without relying on libgromacs to define methods in
gmx::PotentialPointData or gmx::IRestraintPotential.
Fixes #2725
Change-Id: I530c8b74d490645de25c722036be5387a4fc0a61
M. Eric Irrgang [Thu, 1 Nov 2018 10:14:18 +0000 (13:14 +0300)]
Add missing blame for restraint module files.
Several files in gromacs/restraint were missing the suggested doxygen
`\author` tag.
Change-Id: I4ad1d86a5a31082fde3346bcb89cd0bbc5bc2e4f
Mark Abraham [Sat, 27 Oct 2018 13:10:01 +0000 (15:10 +0200)]
Disable ccache by default
There are too many use cases where build trees might be used on
different nodes where ccache might not be available, or with compilers
that it cannot support to continue to enable it by default. If the
user opts in, then the build system searches for ccache and gives a
fatal error if it is not found, or if the compiler is not supported.
The wrappers used by clang-tidy and clang-analyzer do not work
with ccache, so those configurations issue a fatal error if
ccache is enabled.
Made various minor aspects conform to style for naming cache
variables, use of endif(), etc.
Refs #2688
Change-Id: I55c8d4a8a07ada704c49d4f99c1557a7ab97f353
Paul Bauer [Wed, 31 Oct 2018 08:54:43 +0000 (09:54 +0100)]
Properly define Bromine in amber forcefields
Added the proper values for Bromine to the amber forcefield definitions
in share/top/amber*/ffnonbonded.itp from the corresponding parm99.dat
file in amber itself.
Also removed the Iron parameters as they were not fully defined
and also not available in amber itself.
Fixes #2711
Change-Id: I8adb5dc1124ba39ab4a30568bd679a204dc83fc8
Berk Hess [Fri, 19 Oct 2018 19:20:40 +0000 (21:20 +0200)]
Limit auto assignment of bondeds to GPUs
When the CPU has no forces to calculatie, we should not assign
bondeds to the GPU. Here we only assign bondeds to the GPU when
the CPU does PME for electrostatics and/or LJ.
Change-Id: I82f3047311bde45c026c78e44adc4985eb07b0e7
Berk Hess [Tue, 16 Oct 2018 08:50:20 +0000 (10:50 +0200)]
Pin important buffers in CUDA bondeds
This allows for asynchronous transfers.
Change-Id: I0f251c17bdd44856bf773641633e8fa78e6be894
Jonathan Vincent [Mon, 1 Oct 2018 09:59:40 +0000 (02:59 -0700)]
Add CUDA bonded kernels
CUDA bonded kernels are added for the most common bonded and LJ-14
interactions.
The default auto settings of mdrun offloads these interactions
to the GPU when possible.
Currently these interactions are computed in the local or non-local
nbnxn non-bonded streams. We should consider using a separate stream.
This change uses synchronous transfers. A child change will change
these to asynchronous.
Updated release notes and performance guide.
Fixes #2678
Refs #2675
Change-Id: Ifc6d97854cc7afa8526602942ec3b1712ba45bac
Berk Hess [Tue, 30 Oct 2018 08:46:53 +0000 (09:46 +0100)]
Work around expanded ensemble issues
Two bugs could cause expanded ensemble sampling to use
outdated or zero energies. In these cases mdrun now modifies
nstcalcenergy to 1 to avoid these bugs.
Note: This change should not be merged upstream, since there
is a proper fix for release-2019.
Refs #2714
Refs #2718
Change-Id: I79be9c5da55eaebb857bac6a98e6671720532e0e
Berk Hess [Sat, 27 Oct 2018 21:23:54 +0000 (23:23 +0200)]
Fix FP exception in energy reduction
Energies are now only reduced over ranks when energy are requested.
This avoid FP exceptions due to uninitialized energy buffers.
Change-Id: Ib4130074c5890064446c9f38c10d5caf5622ee70
Berk Hess [Mon, 29 Oct 2018 16:12:46 +0000 (17:12 +0100)]
Correct VV integrator nstcalcenergy use
With velocity Verlet integrators, mdrun would compute energies
which contribute to averages in the energy output and might be
used for expanded ensemble calculcations one step too late.
Fixes #2718
Refs #2714
Change-Id: I67e4d00f7151ec9eb5dab6ca4e87b81ca12236e2
Berk Hess [Sun, 28 Oct 2018 19:38:21 +0000 (20:38 +0100)]
Correct grompp nstexpanded/nstcalcenergy check
With expanded ensemble, but without free-energy perturbation, grompp
would not check if nstexpanded was a multiple of nstcalcenergy.
If the latter was not the case, results might have been incorrect.
Also added a check in mdrun to catch old, incorrect tpr files.
Fixes #2714
Change-Id: I554351e2c9873a71efbc6e803134eb744e229f1d
Paul Bauer [Sat, 27 Oct 2018 14:25:32 +0000 (16:25 +0200)]
Add equation numbers in reference manual
Went through the reference manual and added equation numbers to all
equations, as Sphinx only numbers those with a label.
Also performed some formatting fixes.
Change-Id: If37b3a0a9b9def9b7428bdbd01c13b0b685933a1
Mark Abraham [Sat, 27 Oct 2018 13:24:24 +0000 (15:24 +0200)]
Improve ccache implementation
Renamed the launch-c* scripts to make clear that they are supporting
infrastructure for ccache, so maintainers know what the script is for
without having to read it.
Moved them into the admin directory, which contains other
development-time resources. This also means that these scripts are no
longer in the top-level directory of the unpacked tarball, where they
might confuse users. ccache will still work for builds from the
tarball, however.
Eliminated temporary helper variables that didn't add value to
how we use configure_file().
Renamed GMX_CACHE_.*_COMPILER variables to use CCACHE rather
than CACHE, for consistency.
This change would have broken build trees that used to work with
ccache, because the wrapper scripts may not be regenerated
because the old GMX_CACHE_* variables are defined. But
changing to GMX_CCACHE_* has the side effect of fixing this
because the new variables will be undefined in such build trees.
Change-Id: I3b449251ee06adc8023ac1a58cb98a7b0be9bba5
Paul Bauer [Mon, 29 Oct 2018 10:57:43 +0000 (11:57 +0100)]
Change Table of contents depth
Changes the table of contents depth on the main
GROMACS documentation to only show the headers by default, to reduce
clutter on the main page.
This also addresses the issue in #2716, but I'll keep this up for
discussion as it is a major change to what kind of information is
available at the main documentation page.
Fixes #2716
Change-Id: I699de47c09a9c2ef52de2b29a04c6c7f57759820
Mark Abraham [Sat, 27 Oct 2018 08:26:17 +0000 (10:26 +0200)]
Rename to GMX_OPENCL_NB_CLUSTER_SIZE
The Intel iGPU OpenCL support for NB kernels needs a different cluster
size from the support for AMD and NVIDIA devices. We do use GMX_OCL as
a prefix for various developer-facing aspects of the OpenCL support,
but we shouldn't expose the use of OCL as an abbreviation to users,
given that we use GMX_USE_OPENCL fully written out to control the use
of the OpenCL build configuration.
Change-Id: I9d9b43e2888d77575fc0a781e6c9577c73551b8a
Mark Abraham [Thu, 11 Oct 2018 05:20:20 +0000 (07:20 +0200)]
Updates to docs for OpenCL support
Improved recognition of support for Intel devices, and some
organization.
Change-Id: Ia788e3c96fd495c47f7900001a1cac5d9405881e
Mark Abraham [Fri, 26 Oct 2018 18:47:22 +0000 (20:47 +0200)]
Merge "Merge branch release-2018 into release-2019" into release-2019
Mark Abraham [Fri, 26 Oct 2018 13:47:06 +0000 (15:47 +0200)]
Merge branch release-2018 into release-2019
Restored some text about gmx_enerdata_t fields that got list when
master branch moved some content from forcerec.h into the new
enerdata.h.
Change-Id: I45b956e02d6713190fca456ad0a5948db5001737
Paul Bauer [Fri, 26 Oct 2018 12:01:38 +0000 (14:01 +0200)]
Fix link formatting in developer manual
Example used during code development and contribution session.
Change-Id: I636f5947ae6bb149b6510cff23dbc346c7f19775
Berk Hess [Wed, 24 Oct 2018 06:37:35 +0000 (08:37 +0200)]
Add missing mass term to deltaH
The mass contribution was missing from foreign Hamiltonian difference
output from mdrun used for BAR.
Refs #2703
Change-Id: I415c835e9e1a8473243041be004013af7141a1cc
Paul Bauer [Fri, 26 Oct 2018 07:17:47 +0000 (09:17 +0200)]
Update user documentation overview
Change-Id: I433c28907d92b9c722772a0e0cb6f227bcfcc9f3
Mark Abraham [Thu, 18 Oct 2018 08:33:16 +0000 (10:33 +0200)]
Introduce ArrayRefWithPadding
Modules need to access views of memory with and without padding. This
class can be constructed from a PaddedVector, and provides the
capacity to hide the underlying padded container (and allocator),
while being able to obtain ArrayRef with and without padding.
Also updated wording of docs for ArrayRef, and attribution
Fixed issue with shell code using the same pointer for trial and
minimum configuration.
Fixes #2642
Fixes #2705
Change-Id: I45197215342ae011298abc310b877c34f8fab88b
Paul Bauer [Fri, 19 Oct 2018 08:25:13 +0000 (10:25 +0200)]
Change doc build without image conversion
Changed logic to use selective inclusion so that the manual gets build
without pages with images when images cannot be converted.
Cherry picked from master.
Refs #2692
Change-Id: Id112b2b8f20eb5de3b704bc2b27ab7ce55f035ff
Paul Bauer [Tue, 23 Oct 2018 10:20:00 +0000 (12:20 +0200)]
Update QM gaussian interface
The files had not been touched due to being hidden beneath
the QMMM flag and have thus started to rot.
Updated files and changed functions to reflect current status of the
rest of the code.
Fixes #2706
Change-Id: I2ecd24f3f85f36f704bbd5ba5df3c5faa6a7d6e5
Paul Bauer [Tue, 23 Oct 2018 13:47:30 +0000 (15:47 +0200)]
Fix MPI w/o MPI_IN_PLACE
Fixes #2708
Change-Id: Ib251797c11cb5aa344bbc2d7083eee18487c4062
Berk Hess [Tue, 23 Oct 2018 15:13:58 +0000 (17:13 +0200)]
Add missing constraint term to deltaH
The constraint contribution was missing from foreign Hamiltonian
difference output from mdrun used for BAR.
Refs #2703
Change-Id: I00fb88bed76f9ff03faed7543e90adf163b99f08
Joe Jordan [Mon, 22 Oct 2018 16:21:31 +0000 (18:21 +0200)]
Properly attribute work and use correct dates for binaryinformation
Several people contributed over the past year and it seems
their work should be attributed.
Is there anyone else we are forgetting?
Change-Id: I0837815bf0375827822f58291c1a97e332dbea4e
Paul Bauer [Mon, 22 Oct 2018 15:27:24 +0000 (17:27 +0200)]
Prepare for beta 2
Change-Id: I4aa103b3bee382fd9cc0d46f3afbcd21c29020c0
Paul Bauer [Wed, 10 Oct 2018 09:20:18 +0000 (11:20 +0200)]
GROMACS 2019 first beta release
Change-Id: I50c584c4cc36f0f73ccffdc30ed299b81393a591
Berk Hess [Fri, 19 Oct 2018 19:50:33 +0000 (21:50 +0200)]
Fix mdrun start/end time print
Fixes #2704
Change-Id: I2dc4f19edceee718e581369f0b93a81522c1de34
M. Eric Irrgang [Fri, 19 Oct 2018 07:05:14 +0000 (09:05 +0200)]
Documentation bug in gmxapi/context.h
Documentation for launch() refers to old behavior. Removed mentioned of
a persistent Status object.
Change-Id: I40ba7bd5fc7fb4896de9be4ce3dd817b1a0467d4
Paul Bauer [Thu, 18 Oct 2018 12:59:40 +0000 (14:59 +0200)]
Remove unused files in docs/manual
Refs #2692
Change-Id: Ib9f0a7079397cb638bc2d7f67b9d450c004a612e
Paul Bauer [Wed, 17 Oct 2018 12:47:33 +0000 (14:47 +0200)]
Fix segmentation fault in gmx helix
Changed the logic in tpxio to only try to access the mtop
datastructure if it is actually present.
Fixes #2701
Change-Id: I268af10dc125a57758f5f3e79e4b14a25050b3b3
Berk Hess [Wed, 17 Oct 2018 20:37:58 +0000 (22:37 +0200)]
Add env.var. to disable update groups
Change-Id: Iba4d9636f2da01fa1bc9e003446621c743fb9114
Mark Abraham [Mon, 15 Oct 2018 16:27:12 +0000 (18:27 +0200)]
Eliminated t_ifunc from t_interaction_function
Declared an equivalent function type within the listed-forces module,
because it is local there.
This eliminates the inappropriate dependency on listed-forces by the
topology module, and also the recently discovered inappropriate
transitive dependency on gmxlib by topology.
Change-Id: I0f818767711cdf3fac88c06e01fac7564e9ccc65
Magnus Lundborg [Mon, 15 Oct 2018 12:55:59 +0000 (14:55 +0200)]
Move gmx_ffparams_t to forcefieldparameters
Change-Id: I4639211f419724bcf3282140c8291e0b1272abe5
Mark Abraham [Thu, 11 Oct 2018 19:53:38 +0000 (21:53 +0200)]
Task assignment for bonded interactions on CUDA GPUs
Made a query function to find whether any interactions of supported
times exist in the global topology, so that we can make efficient
high-level decisions.
Added free for gpuBondedLists pointer.
Minor cleanup in manage-threading.h
Fixes #2679
Change-Id: I0ebbbd33c2cba5808561111b0ec6160bfd2f840d
Mark Abraham [Tue, 16 Oct 2018 07:08:34 +0000 (09:08 +0200)]
Fix compiler issues
We recently added some extern template declarations to a function
whose argument list was then modified, but gerrit didn't flag the
change as requiring a rebase.
Also fixed mdrun-only build
Change-Id: Ib7aa0d685e881faa2abce628f06aef3d666d260c
Mark Abraham [Sun, 14 Oct 2018 09:16:39 +0000 (11:16 +0200)]
Removed support for NVIDIA CC 2.x devices (codename Fermi)
These are no longer tested or supported, but it is possible that the
OpenCL version of GROMACS will still run on such old devices.
Various code for configuration, the use of texture objects, the use
of shared memory, and the kernel dispatch is now simpler.
Fixes #2408
Fixes #2410
Fixes #2665
Change-Id: Ia7a00e5d6a97f93cd2768beb7ad56b2cce628a6f
Mark Abraham [Tue, 9 Oct 2018 23:20:36 +0000 (01:20 +0200)]
Improve robustness of end-to-end testing
Previously one could choose the number of ranks to run the test binary
with, but e.g. DD errors could exit the binary if an unsuitable number
could be chosen.
Fixes #2680
Change-Id: I5ca165c6a80763083f2db9beec61ad3b4bfbe00d
M. Eric Irrgang [Sun, 14 Oct 2018 17:51:16 +0000 (20:51 +0300)]
Release notes for restraint module and gmxapi.
Describe new features supporting gmxapi client code and runtime binding
of restraint code. Add "gmxapi external API" section to install guide.
Refs #2585
Change-Id: I3da0d130b07862abc90387ade781d111ccbcd740
Mark Abraham [Mon, 15 Oct 2018 07:49:00 +0000 (09:49 +0200)]
Create ExclusionBlocks
Moves exclusion modification functionality to the topology module, as
it is not functionality unique to preproceessing.
Renamed t_block2 to ExclusionBlocks, since that is the only use we
currently have for it, and any new use should be using std::vectors
anyway.
Used an assertion for an error that can only triggered by coding bug.
This fixes the broken mdrun-only configuration, found in post-submit
Jenkins testing.
Fixes #2690
Change-Id: I2d0916bc3be1c20d44e1c4e07b53488f2b6971a3
Mark Abraham [Mon, 8 Oct 2018 23:47:59 +0000 (01:47 +0200)]
De-duplicating mdrun setup
Made the API context setup use LegacyMdrunOptions to keep the two
client setup procedures in step and avoid duplicating code.
Refs #2585
Change-Id: I9909e26a41fd2015667c2f86335c09b6f9708e99
Magnus Lundborg [Thu, 17 Nov 2016 15:48:57 +0000 (16:48 +0100)]
Enable output of average pull force and positions.
Write pull data to checkpoints to keep a proper average.
Add option whether to write instantaneous or average pull
coordinates and forces, respectively.
Fixes #2626
Change-Id: Id0268e00486028f497463dc13ae8d65a6c5df325
M. Eric Irrgang [Mon, 15 Oct 2018 07:57:11 +0000 (10:57 +0300)]
Ignore pyenv config file.
Among other possibilities, [pyenv](https://github.com/pyenv/pyenv)
allows directory-scoped Python installation choices, which can be handy
when developing on the same system for projects with different Python
version requirements. For this, it uses a "hidden" `.python-version`.
Such files should not clutter up `git status` messages or be easily
accidentally included in a commit. This change adds `.python-version`
files to `.gitignore`
Change-Id: I88bbe813966282755097da674cb53d1f88a8e031
M. Eric Irrgang [Sun, 14 Oct 2018 12:33:48 +0000 (15:33 +0300)]
Preparation for de-duplicating mdrun setup
Recent work introducing the API extracted MdFilenames and then
essentially duplicated everything else. This commit expands
MdFilenames into LegacyMdrunOptions, and clarified the plan that all
such code needs to become either module-based option handling, or
aspects of SimulationContext suitable for both CLI and API.
This commit introduces the Legacy MdrunOptions struct, so that a
future commit can make it available to the API setup for an mdrun
session. The layout of the changes is intended to minimize the textual
diff for the CLI. Code motion for clarity and also use by the API will
follow.
Removed MdFilenames, made its data a std::vector in
LegacyMdrunOptions, and used it via an ArrayRef. This clarifies that
it is read-only input data supplied by the client.
Change-Id: I3438cfe1ab52eeb2fffbd16f4bd5254b2a74f03f
M. Eric Irrgang [Mon, 8 Oct 2018 13:46:19 +0000 (16:46 +0300)]
Add some "to do"s for MDModules and Impl.
The intention for the modules_ member in MDModules::Impl was not very
clear. Made some notes about forward directions, given the inconsistent
way we handle the electric field library MDModule and externally
provided modules.
Also, improve readability/formatting of data member declaration.
Change-Id: If3a83209c128dc52bab90cbc322565bc81416871
Mark Abraham [Sun, 14 Oct 2018 08:10:46 +0000 (10:10 +0200)]
Fix compiler warnings
clang 6 warned about these.
Change-Id: I4692d1c0e76e8cbe984e22028980956e1bd628d5
M. Eric Irrgang [Sun, 14 Oct 2018 13:41:42 +0000 (16:41 +0300)]
Resolve some linter warnings.
Local linting (not Jenkins builds) discovered some warnings that are
easily resolved.
* Remove unused variable from gmxapi session resources factory.
* Provide stronger hinting that a pointer is not null
Change-Id: I56f6758884b7f77d5091d273a93ac6bd1495a973
Szilárd Páll [Mon, 8 Oct 2018 22:49:16 +0000 (00:49 +0200)]
Fix more clang-6 warnings in CUDA code
Fixes #2681
Change-Id: Ic1e096328687e53ca814034c4c3eb8db40db46df
M. Eric Irrgang [Sat, 13 Oct 2018 11:44:21 +0000 (14:44 +0300)]
Test signaling facility through session resources.
Build a simple MD extension that can optionally issue MD stop signals
when called in the MD loop. Use gmxapi session resources to access the
session signal manager. If initialized to do so, issues the signal when
called to evaluate restraint forces. Tracks the steps on which it is
called.
A toy simulation expects the restraint to be called `nsteps` times if
default constructed or `nstlist` times if initialized to issue signals.
Change-Id: I885cfeb207fd587b7ddd946203bd16ea4713dbf2
Szilárd Páll [Tue, 9 Oct 2018 19:00:12 +0000 (21:00 +0200)]
Modernize OpenCL memory allocation flags
This change correct the memory allocation flags in the nonbonded module
so that these reflect the R/W use on both host- and device-side; the
former is made possible by requiring OpenCL 1.2.
Also improve some lacking error handling.
Refs #2193
Change-Id: Icef4890aa412b811bf189b78ff42ee8ca8c50113