Joe Jordan [Mon, 25 Jan 2021 12:48:56 +0000 (12:48 +0000)]
Check availability of compile flags at cmake time
Fixes #3821
Ensures that compile flag can be used before using it. Gives a
message if flag cannot be used.
ejjordan [Mon, 25 Jan 2021 09:53:33 +0000 (10:53 +0100)]
Rename DefaultAngle to HarmonicAngleType in nblib listed forces
This change renames the type corresponding to harmonic angles
in nblib from DefaultAngle to HarmonicAngleType. This is both
more descriptive, and more similar to other listed forces
types in nblib.
Additionaly, one failing test is disabled. This disabling
is needed so that all tests can pass to allow this MR to
be merged. A subsequent MR fixes the test issues.
Berk Hess [Mon, 25 Jan 2021 08:29:03 +0000 (08:29 +0000)]
MTS release note
M. Eric Irrgang [Sun, 24 Jan 2021 17:01:21 +0000 (20:01 +0300)]
Update Dockerfiles for Python subpackages.
Some appropriate adjustments were discovered while
investigating computing environments for an upcoming workshop.
* Bump the base Linux distribution.
* Refine the inline documentation.
* Adjust the package list and build options.
M. Eric Irrgang [Sun, 24 Jan 2021 16:57:36 +0000 (19:57 +0300)]
Finalize gmxapi Python package version 0.2.
Szilárd Páll [Fri, 22 Jan 2021 15:11:30 +0000 (16:11 +0100)]
Disable CUDA textures also on NVIDIA Ampere A100
The same benefits have been shown as those observed with V100.
Partially addresses #3845
Mark Abraham [Thu, 21 Jan 2021 12:11:36 +0000 (12:11 +0000)]
Ensure residue name used by pdb2gmx matches rtp name
The default for GLU/GLUH and ASP/ASPH is the unprotonated form. The
help text pdb2gmx specifically states this, and there is no attempt to
use the residue name to infer the protonation.
The old code set the rtp name to the unprotonated form without
changing the residue name read from the configuration file. The
original residue name was then used in the output configuration and
topology file. That name indicated the wrong protonation if the user
input tried to specify the protonated form via the residue name. Now
it changes the residue name to match the rtp name.
This has been surprising, so whenever pdb2gmx implements its default by
changing the residue name, it now reports that.
The same problem occurs when using pdb2gmx -asp if the input
configuration had the name of the protonated form and the interactive
choice was for the unprotonated form. However, in that case there is
no need to inform the user that the input residue naming is being
overridden. Tested manually.
Updated the tests to handle this case.
Added some release notes, Doxygen, added some comments, and updated some code style
so the review is easier.
Fixes #2480
Andrey Alekseenko [Thu, 21 Jan 2021 09:39:13 +0000 (09:39 +0000)]
Keep the number of tMPI ranks consistent with the number of GPUs
When the number of atoms in a system is small, and the automatic resource
assignment is used (i.e., a user just runs gmx mdrun), the number of ranks
chosen by get_nthreads_mpi might be incompatible with the expectations of
GpuTaskAssignmentsBuilder, namely that the number of ranks must be
divisible by the number of threads.
If the user did not supply the -ntmpi value, and we have to limit the
number of ranks due to small system size, we round it down down to the
nearest value divisible by the number of GPUs to use (or 1, whichever is
greater).
Fixes #3874
Mark Abraham [Wed, 20 Jan 2021 10:56:38 +0000 (11:56 +0100)]
Suggest a workaround for pulling with -deffnm
Also fixed use of settings, use settings to do the line wrapping,
and wrote some newlines to make the output more readable.
Refs #3875
Fixes #3442
Paul Bauer [Wed, 20 Jan 2021 10:39:02 +0000 (10:39 +0000)]
Use correct python interpreter cmake check
Still needed to complete address checksumming issue.
Fixes #3862
Mark Abraham [Tue, 19 Jan 2021 10:46:01 +0000 (11:46 +0100)]
Describe the configured precision correctly for mdrun
We adopted the build configuration naming scheme for GMX_DOUBLE
"mixed" vs "double" some years ago so that people knew we don't reduce
forces in mdrun solely in single. This change improves consistency in
this regard in the cases that are important to users, ie. log files
and messages about checkpoint restarts.
Various file-reading tools still refer to "single" in contexts where
they are reading floats, which is fine.
Paul Bauer [Wed, 13 Jan 2021 11:23:02 +0000 (12:23 +0100)]
NBLIB: Remove preprocessor macros
Macros used to implement part of the listed forces calculation have been
removed and replaced with a pure C++ template implementation.
Also addresses review comments not fully resolved from previous merge
requests.
Paul Bauer [Wed, 20 Jan 2021 06:10:40 +0000 (06:10 +0000)]
Fix TPR handling for older versions.
Reading in a newer TPR file in a pre-2021 version would fail hard with
symtab errors due to us forgetting to increment the tpr generation when
adding the VSite1 type to ftupd.
This fixes the omission an makes the tpr generation an enum similar to
the tpr version.
Fixes #3867
Paul Bauer [Tue, 19 Jan 2021 09:17:49 +0000 (10:17 +0100)]
Fix checksumming code
Recent additions to the code to avoid errors with certain IDEs
caused issues by never trying to validate the checksums.
Fixed by properly passing the necessary variables to the script.
Fixes #3862
Mark Abraham [Wed, 20 Jan 2021 04:57:46 +0000 (04:57 +0000)]
Fix PaddedVector move constructor
This could leave the moved-from vector in a state unfit to destruct.
Expanded test coverage, including improving the tests and their
infrastructure, so I could understand my own code.
Fixes #2832
Mark Abraham [Tue, 19 Jan 2021 11:06:38 +0000 (12:06 +0100)]
Report hwloc 1.x deprecation only when found
Refs #3818
Berk Hess [Tue, 19 Jan 2021 16:38:19 +0000 (16:38 +0000)]
Change default MTS force group selection
Because of instabilities of aliphatic protons with the Amber
force fields, the default force group selection for multiple
time stepping has been changed to include longrange-nonbonded only.
Refs #3804
Szilárd Páll [Tue, 19 Jan 2021 12:09:15 +0000 (12:09 +0000)]
Disable CUDA textures on NVIDIA Volta
This has significant performance benefit for the nbnxm kernels with
tabulated Ewald correction and it has negligible impact on the PME kernels.
Partially addresses #3845
Mark Abraham [Wed, 13 Jan 2021 14:49:39 +0000 (15:49 +0100)]
Deprecate mdrun -deffnm
This functionality is more trouble to implement and test well than
we expected. Even though it is convenient in some cases, on balance
we should remove it and encourage users to use standard approaches
for grouping their files.
Refs #3442, #942, #2205, #2154.
Fixes #3818
Pascal Merz [Tue, 19 Jan 2021 09:39:34 +0000 (09:39 +0000)]
Fix modular simulator log writing in fresh simulation starts with nstlog == 0
With nstlog = 0, legacy simulator writes log on the initial step, while
modular simulator wasn't. This adapts modular simulator to the legacy
approach.
Szilárd Páll [Tue, 19 Jan 2021 09:02:55 +0000 (09:02 +0000)]
Add G. Gouaillardet to the list of contributors
Berk Hess [Tue, 12 Jan 2021 07:38:38 +0000 (07:38 +0000)]
Avoid NMR restraints calls for MTS levels > 0
Distance and orientation restraint code was called for MTS levels > 0
whereas this should not happen.
Fixes #3863
Andrey Alekseenko [Sat, 9 Jan 2021 19:57:42 +0000 (22:57 +0300)]
densityfit: Fix typo in use of iterators
... and some typos in comments.
While both referenceDensity_ and referenceDensity are views into the same data,
it's clearer to use the same variable for both begin() and end().
This is a remake of MR !740. That MR was reverted (in !748) due to
failed tests. The test failures, however, were caused by an unrelated bug
(issue #3791, fix !827). So, this change is brought back.
Gilles Gouaillardet [Fri, 8 Jan 2021 07:47:46 +0000 (16:47 +0900)]
ARM_SVE: misc fixes
- fix a typo
- remove debug assert()
Paul Bauer [Wed, 6 Jan 2021 07:55:14 +0000 (08:55 +0100)]
Add new GROMACS logo
Replaces previous logo with new vector graphics one.
Logo (C) by Cathrine Bergh.
Gilles Gouaillardet [Thu, 7 Jan 2021 15:24:13 +0000 (15:24 +0000)]
arm_sve: fix GMX_SIMD_HAVE_4NSIMD_UTIL_{FLOAT,DOUBLE} macro definitions
only define these macros in impl_arm_sve_definitions.h when the number of
elements per vector greater than 4
Paul Bauer [Thu, 7 Jan 2021 14:11:04 +0000 (15:11 +0100)]
Merge branch release-2020 into merge-2020-into-2021
Resolved Conflicts:
cmake/gmxVersionInfo.cmake
docs/CMakeLists.txt
docs/conf.cmakein.py
src/gromacs/gmxpreprocess/readir.cpp
src/gromacs/mdlib/expanded.cpp
src/gromacs/mdlib/tests/CMakeLists.txt
Paul Bauer [Thu, 7 Jan 2021 13:08:41 +0000 (13:08 +0000)]
Write copyright output files as utf8
The script could fail otherwise when encodings didn't match.
Christian Blau [Thu, 7 Jan 2021 07:51:56 +0000 (07:51 +0000)]
Prepare for GROMACS 2020.6
Reset DOI strings.
Prepare release note stubs.
Set patch number in build infrastructure.
Christian Blau [Wed, 6 Jan 2021 12:45:31 +0000 (12:45 +0000)]
GROMACS version 2020.5
Set DOI strings.
Szilárd Páll [Tue, 5 Jan 2021 20:58:23 +0000 (20:58 +0000)]
Update src/regressiontests URLs to https
With the recent server migration we support https downloads and we
should offer those over http.
Also updated the regressiontests URL to point to the ftp server.
Kevin Boyd [Wed, 30 Dec 2020 17:51:25 +0000 (09:51 -0800)]
Fix broken random seed generation.
On Ryzen 3k CPUs with the RDRAND microcode bug, the
std::mt19937_64 alternate path yields the same seed
on multiple calls that fall within the same second. Changed
the "seed" of the random seed to rescramble each time the
makeRandomSeed() function is called.
Fixes #3859
Kevin Boyd [Tue, 5 Jan 2021 13:28:26 +0000 (13:28 +0000)]
Fix broken random seed generation.
On Ryzen 3k CPUs with the RDRAND microcode bug, the
std::mt19937_64 alternate path yields the same seed
on multiple calls that fall within the same second. Changed
the "seed" of the random seed to rescramble each time the
makeRandomSeed() function is called.
Fixes #3859
Christian Blau [Tue, 5 Jan 2021 12:29:37 +0000 (13:29 +0100)]
Fix copyright year
Merging !423 on January 1st 2021 causes the pipeline to fail
due to a missed copyright year update.
The copyright year is updated with this patch.
Michael Shirts [Fri, 1 Jan 2021 10:30:38 +0000 (10:30 +0000)]
Expanded ensemble changes.
Fix the numerical stability issues encountered with simulated tempering (also, would have occurred with any alchemical problem with large energy differences between states). In most cases, we simply flip the form around and compute an alternate form that always gives a 0 instead of infinity when the energy difference between states is too far in any direction. Also added a citation. Fixes https://gitlab.com/gromacs/gromacs/-/issues/3304
Note that there is no way to get good estimates for free energy differences between states with the very large differences between examples. One of the numerical stability fixes is not expected to be great, but it's not really relevant since nothing would work in this case; using Wang-Landau (i.e. visitation based approaches) rather than metropolis style methods (energy difference analysis methods) is the only thing that works.
Szilárd Páll [Wed, 30 Dec 2020 12:27:34 +0000 (13:27 +0100)]
Bump version post-release to rc2
Szilárd Páll [Wed, 30 Dec 2020 16:28:34 +0000 (16:28 +0000)]
GROMACS 2021-rc1 release candidate
First release candidate.
Mark Abraham [Wed, 23 Dec 2020 13:44:37 +0000 (13:44 +0000)]
Deprecate .pdo file reading
Analysing such files is likely not relevant a decade later, and such
needs can be met by using an older version of GROMACS that did still
support reading these formats.
Fixes #3818
Alan Gray [Fri, 18 Dec 2020 07:45:10 +0000 (23:45 -0800)]
Stage bonded kernel atomics through shared memory
Fixes performance bug introduced in
01b2f20bd5 by staging energy step
atomics through shared memory rather than have all threads write
atomically directly to global memory.
Fixes #3443
Mark Abraham [Thu, 17 Dec 2020 11:10:35 +0000 (11:10 +0000)]
Update CI image to OneAPI 2021.1.1, add ICC tests.
Also, backport a change from MR !796 that silences the false-positive ICC
compiler warning.
Mark Abraham [Tue, 15 Dec 2020 17:01:19 +0000 (17:01 +0000)]
Update deprecation statuses
Various functionality has been agreed as deprecated at #3818 and
elsewhere. Those are now noted in the release notes, documentation,
and CMake status messages. The changes are all minor so there is
little need to make mdrun report when such configurations are used.
The deprecation content for release 2020 (and 2021) series is updated
to include the relevant content from release 2019 series. Comments
have been added to help us to this better in future.
Fixes #3818
Paul Bauer [Mon, 14 Dec 2020 12:44:02 +0000 (12:44 +0000)]
Fix pull group index handling
The pull code never validated its own index groups, leading to the
possibility of an invalid group either hanging the process or triggering
an assertion, depending on the build type.
Fixed by introducing the check for other index groups also to pull
groups.
Fixes #3810
Magnus Lundborg [Mon, 14 Dec 2020 11:22:48 +0000 (11:22 +0000)]
Fix incorrect AWH free-energy output with multiple walkers
The free-energy was averaged exponentially over walkers using the wrong
sign for the exponent. The meant that the free-energy output was off
for large update sizes. This error was quadratic in the update interval
and the number of walkers. This likely has no measurable effects with
the default AWH free-energy update interval. But the effect is noticeable
with the not uncommon update interval of 1000 steps.
Fixes: #3828
Simon Christ [Mon, 30 Nov 2020 10:37:00 +0000 (10:37 +0000)]
Correct signs of lj and coulomb forces
Pascal Merz [Fri, 11 Dec 2020 13:07:23 +0000 (13:07 +0000)]
Restrict force frame comparison for FEP tests
Closes #3741.
Pascal Merz [Fri, 11 Dec 2020 12:22:44 +0000 (12:22 +0000)]
Fix trx frame reading from modular simulator checkpoint files
trx frames from checkpoints written by modular simulator could be
slightly off depending on the algorithms used (always up-to-date with
domain decomposition only). The global state is still written to
modular checkpoints (as there is a significant amount of setup work at
runner time that needs to be refactored before modular simulator can
get spawned completely without a global state). It is, however, not
guaranteed to be absolutely up to date, as it's not used in the
simulation continuation.
The trx frame reading is now handled by modular simulator if the
checkpoint was written by modular simulator. A test was added to
ensure that the final frame of the simulation is equivalent to the
checkpointed configuration.
Note that this was not affecting simulation restart (exact
continuation is tested also for modular simulator). It would, however,
affect other tools accessing the configuration from the checkpoint
file. The error was only present in master and 2021 beta, so it was
never in a released version.
trx frame reading by modular simulator required some refactoring of
the StatePropagatorData and FreeEnergyPerturbationData
checkpointing. The main read and write function was moved to the data
object itself rather than being owned by its element. This is likely a
better design decision anyway: The element orchestrates the
checkpointing during the simulations, but the data object is handling
the actual data reading / writing. This allows to create a dummy data
object, restore it from checkpoint, and read out the quantities
relevant for the trx frame.
Closes #3838
Berk Hess [Thu, 10 Dec 2020 13:34:59 +0000 (13:34 +0000)]
A check for perturbed listed pairs beyond rlist
Excluded atoms pairs should be within the pairlist cut-off, as
otherwise long-range corrections are not applied. This is problematic
for free-energy calculations where intra-molecular interactions are
not coupled and replaced by pair interactions. Now a fatal error
is generated when perturbed pair interactions are beyond rlist.
Also added PME grid correction for LJ excluded pairs beyond rvdw,
which was missing from #3403.
Added missing release note for the fix of #3403.
Fixes #3403
Fixes #3809
Paul Bauer [Wed, 9 Dec 2020 14:45:51 +0000 (14:45 +0000)]
Fix indexing bug in electric field module
Improper refactoring in
c8eca5d1f27cc34903718ade7d44527c22ec3d93 lead to
the module using the wrong maximum atom index for applying the electric
field forces to atoms.
Fixes #3800
Andrey Alekseenko [Wed, 9 Dec 2020 11:24:13 +0000 (11:24 +0000)]
Fix defining of EXCLUSION_FORCES in CUDA/OpenCL kernels
For the case of cut-off electrostatics + Ewald LJ + no energy calculation,
the EXCLUSION_FORCES macro should be active.
However, LJ_EWALD macro is (conditionally) set only later, and so is
always undefined when it is being checked for EXCLUSION_FORCES.
Mark Abraham [Wed, 9 Dec 2020 10:14:01 +0000 (10:14 +0000)]
Fix compilation and tests with icc 19.1.2
Closes #3822
Pascal Merz [Wed, 9 Dec 2020 09:51:32 +0000 (09:51 +0000)]
Fix and activate tests for kv-tree checkpoint functions
The tests in src/gromacs/fileio/tests/checkpoint.cpp were introduced
in
64bee06aa, but the file was never added to the CMakeLists.txt,
meaning they were never executed (or even compiled).
Added the file to the CMake target and fixed a few compilation
errors and warning to activate the tests.
Pascal Merz [Wed, 9 Dec 2020 09:23:13 +0000 (09:23 +0000)]
Fix dump of checkpoint files
With the addition of the MdModules and the modular checkpointing,
`gmx dump -cp` would end with an error when either of the two was
written to checkpoint. Reason was that the function dumping
checkpoint files was not aware of the additional blocks present.
As the new functionality checkpoints at the end of the files, the
remainder of the information was printed anyway, but the call ended
with an error.
This adds the two new checkpointing blocks to the function used
by gmx dump, and prints the kv-tree they are based on. To achieve
this, the kv-tree printing functionality had to be expanded to
allow for arrays of objects.
Finally, this change also fixes a wrong comment in the modular
simulator checkpoint helper - checkpointing happens on top of the
integration step, so _before_ the last step.
Pascal Merz [Mon, 7 Dec 2020 08:42:44 +0000 (08:42 +0000)]
Fix Nose-Hoover conserved energy
Closes #3831
Pascal Merz [Sat, 5 Dec 2020 01:07:13 +0000 (18:07 -0700)]
Clarify checkpoint mismatch error, and enable in release
As of GROMACS 2021, checkpoint files written with the modular and the
legacy codepath need to be continued with the same code path. The
respective check was not executed in release mode, which would lead
to less descriptive errors.
Also reworded the error to guide users how they can solve the problem.
Pascal Merz [Fri, 4 Dec 2020 05:29:12 +0000 (22:29 -0700)]
Relax simulator comparison tests
The simulator comparison tests have proven to be too strict when running
them on more diverse hardware / compiler / parallelization combinations.
This doubles the tolerances for the energies of tests containing
constraints. Note that at 160 double precision ULPs, these are still
very tight for end-to-end tests, so the danger of relaxing them a bit
is low.
Closes #3836
Pascal Merz [Wed, 2 Dec 2020 21:38:48 +0000 (14:38 -0700)]
Print energy conservation in modular simulator
Paul Bauer [Wed, 2 Dec 2020 14:39:57 +0000 (14:39 +0000)]
Third GROMACS 2021 beta release
All features should now be stable before the release.
Pascal Merz [Wed, 2 Dec 2020 08:52:40 +0000 (01:52 -0700)]
Fixes post submit broken by
05f02ab82
Pascal Merz [Wed, 2 Dec 2020 00:30:34 +0000 (17:30 -0700)]
Separate simulator comparison tests
The simulator comparison tests ensure that legacy and modular
simulator code paths don't diverge while both exist. They are
currently part of the mdrun tests. Separating them has two
advantages:
* As the feature set of modular simulator grew, the run time
of these tests became the largest contributor to the run time of
mdrun-test. Keeping it separate makes it easy to keep the
run time in check and to disable the tests if necessary.
* It is useful to run the simulator comparison tests on
multiple ranks (at least locally). Not all other tests
in mdrun-test support more than one rank. Having a separate
binary simplifies running it with different parallelization schemes.
Pascal Merz [Wed, 11 Nov 2020 23:38:46 +0000 (16:38 -0700)]
Fix error when using simulator test with pre-defined environment variable
The simulator test compares the results of functionality implemented in
both the legacy and the modular simulator by running two simulations using
the environment variables GMX_DISABLE_MODULAR_SIMULATOR and
GMX_USE_MODULAR_SIMULATOR to cover both code paths. If one of these
variables was already present in the test sytem, the tests would fail with
an error.
This change backs up the current state of both variables, disables them,
runs the tests, and resets them to their previous state (if any).
Pascal Merz [Wed, 2 Dec 2020 07:37:43 +0000 (00:37 -0700)]
Fix kinetic energy and temperatures reporting
Fixes the reporting of kinetic energy and temperatures, which is
(very slightly) off in md-vv with Trotter NPT (Nose-Hoover & MTTK)
in the legacy code path.
Closes #3832
Pascal Merz [Wed, 11 Nov 2020 22:52:22 +0000 (15:52 -0700)]
Modular simulator: Disable invalid code paths
This explicitly disables two invalid code paths for modular simulator:
* The new MTS is not implemented for modular simulator. It is only
implemented for integrator = md, which by default uses the legacy
code path. This default can however be overwritten by setting
the environment variable GMX_USE_MODULAR_SIMULATOR=ON, which would
result in errors due to the MTS data structures not being properly
initialized.
* The non-MTTK Parrinello-Rahman barostat is available in modular
simulator, but not in the legacy simulator. The case that this
barostat is chosen in combination with other options not compatible
with modular simulator needs to be caught explicitly.
Paul Bauer [Mon, 30 Nov 2020 16:07:42 +0000 (16:07 +0000)]
Add tests for newer GCC versions
Added gcc-9 + OpenCL (in release builds) and gcc-10 + OpenCL
during merge pipelines to replace previous gcc-7 + OpenCL builds.
Shuffled around previous gcc-8 + CUDA builds to now have
gcc-7 + CUDA 10.2 and gcc-8 + CUDA 11.0 instead.
Test OpenCL with internal clFFT during release builds.
M. Eric Irrgang [Fri, 27 Nov 2020 14:12:07 +0000 (17:12 +0300)]
Explicitly use xunit2 schema for pytest output.
Resolves #3717
M. Eric Irrgang [Sun, 29 Nov 2020 19:54:39 +0000 (19:54 +0000)]
Improve accessibility of pytest documentation.
* Update gmxapi install.rst.
* Consolidate (and prune) some README.md content in
python_packaging subdirectory.
Also ref #3706
Fixes #3702
Paul Bauer [Fri, 27 Nov 2020 14:37:28 +0000 (15:37 +0100)]
Fix build on CentOS 7
The compiler toolset coming with devtoolset-7 on CentOS still suffers
from https://gcc.gnu.org/bugzilla/show_bug.cgi?id=58265. The workaround
for this has been removed before because other gcc-7 compilers are not
affected by this, but it is obviously still needed for CentOS.
Fixes #3826
M. Eric Irrgang [Fri, 27 Nov 2020 14:24:01 +0000 (17:24 +0300)]
Import setuptools early to suppress distutils warning.
Also apply PEP-8 formatting corrections.
Fixes #3715
Berk Hess [Thu, 26 Nov 2020 08:33:36 +0000 (09:33 +0100)]
Fix pull fatal error message
Fix pull group indices in fatal error message for geometries with
more than two groups.
Refs #3613
Paul Bauer [Wed, 25 Nov 2020 10:30:08 +0000 (11:30 +0100)]
Fix cyclecounters on x32
A missing check meant that the code wouldn't compile due to an asm block
that is not compatible with 32 bit datatype ABI and x86_64 registers.
Fix provided by Nicholas Breen.
Fixes #3816
Paul Bauer [Wed, 25 Nov 2020 08:30:08 +0000 (09:30 +0100)]
Fix error with links in docs
Linkchecker complained about issues that I didn't fix correctly during
the latest merge.
Gilles Gouaillardet [Wed, 25 Nov 2020 07:06:46 +0000 (16:06 +0900)]
Fix frexp() for ARM SVE SIMD
Mark Abraham [Tue, 24 Nov 2020 15:26:49 +0000 (16:26 +0100)]
Stop GoogleTest requiring ancient CMake minimum versions
In practice the version is always new enough, and avoiding the
redundant minimum specifications means GROMACS developers will not be
spammed with useless warnings.
Erik Lindahl [Tue, 24 Nov 2020 11:48:54 +0000 (12:48 +0100)]
Fix frexp() for ARM neon SIMD.
Implements the same fix for arguments +-0 as previously done
for x86 and power implementations. After this, the only
remaining architecture is ARM SVE.
Refs #3773.
Paul Bauer [Tue, 24 Nov 2020 13:38:39 +0000 (14:38 +0100)]
Merge branch 'origin/release-2020' into merge-2020-into-2021
Resolved Conflicts:
admin/containers/scripted_gmx_docker_builds.py
docs/conf.cmakein.py
docs/dev-manual/change-management.rst
docs/dev-manual/contribute.rst
docs/dev-manual/releng/index.rst
docs/dev-manual/tools.rst
docs/install-guide/index.rst
docs/reference-manual/preface.rst
docs/release-notes/index.rst
scripts/GMXRC.bash.cmakein
src/gromacs/gmxana/gmx_covar.cpp
src/gromacs/gmxana/gmx_do_dssp.cpp
src/gromacs/gmxana/gmx_h2order.cpp
src/gromacs/gmxana/nsfactor.cpp
src/gromacs/hardware/detecthardware.cpp
src/gromacs/mdlib/coupling.cpp
src/gromacs/mdrun/md.cpp
src/gromacs/mdtypes/state.h
src/gromacs/trajectoryanalysis/modules/pairdist.cpp
src/gromacs/utility/basedefinitions.h
Paul Bauer [Tue, 24 Nov 2020 10:22:47 +0000 (11:22 +0100)]
Fix gmx h2order -d option
The code to implement this was never added.
Fixes #3820
Erik Lindahl [Tue, 24 Nov 2020 08:23:37 +0000 (08:23 +0000)]
Make sure frexp() returns correct for argument 0.0
Previous functions in gromacs have never called frexp
with argument 0.0, but cbrt() needs this. This will not
have caused any bugs, but since it results in FP
exceptions in debug builds we want to have it fixed
so our unit tests work.
This change adds the correct behavior for all x86
SIMD instruction sets, and it has also been tested
on all of them in both single and double, with the
exception for MIC (which should be correct, but we
cannot test it).
The ARM SIMD flavors have not yet been fixed yet
since the ARM build fails due to an apparent nblib
error. Once that is fixed, I will add it in a separate
change and close the issue.
Refs #3773.
Artem Zhmurov [Tue, 24 Nov 2020 08:02:48 +0000 (08:02 +0000)]
Improve handling of CUDA API errors
Consolidate the construction of the printed error message in one
place and make sure that the CUDA API information on error is
printed when the error is detected.
Paul Bauer [Mon, 23 Nov 2020 20:51:28 +0000 (20:51 +0000)]
Fixes for Intel and container build fixes
Generalizes the TSAN build stage to a compiler build stage, and uses
it for containing the installation process for the free Intel tools
Fixed or worked around several bugs
Updated install guide section on tested platforms to describe
what we actually do
Refs #3459, #3620
Change-Id: I28e4b816923395edead9d425cec5d85581e22b5e
Magnus Lundborg [Mon, 23 Nov 2020 06:55:13 +0000 (07:55 +0100)]
Properly check if there are perturbed constraints or masses
Instead of just checking, when running updates on GPU, if
there are lambda states that involve constraints or masses
(e.g. if using fep-lambdas) check if any constraints or masses
are actually perturbed.
Artem Zhmurov [Tue, 17 Nov 2020 14:22:41 +0000 (17:22 +0300)]
Make corresponding device active before each TestDevice is created
When populating the list of GPU devices for tests, the DeviceContext and
DeviceStream objects are created for each TestDevice. In CUDA, the
active device has to be explicitly set by the API since the DeviceStream
is created for the active device. Otherwise, all the streams are created
for the first device. When these streams are later used for the devices
other than first, CUDA API returns an invalid argument error. The bug only
affects unit tests in CUDA builds for systems with more than one GPU.
Does not affect OpenCL/SYCL builds, because they use DeviceContext to
attach the device to the stream (queue).
Fixes #3781, #3782 and #3805.
M. Eric Irrgang [Thu, 29 Oct 2020 21:07:19 +0000 (22:07 +0100)]
Look for the various possible names of the gromacs package.
Refs #3777
Artem Zhmurov [Mon, 23 Nov 2020 13:52:57 +0000 (16:52 +0300)]
Remove coolquote that sounds offensive without context
Joe Jordan [Tue, 17 Nov 2020 13:53:46 +0000 (13:53 +0000)]
Remove some extraneous compiler flags from nblib
Closes #3798
Gilles Gouaillardet [Fri, 13 Nov 2020 09:14:37 +0000 (09:14 +0000)]
Detect ARM SVE Vector length if possible
arm_sve: unless the SVE vector length is explicitly set via the
GMX_SIMD_ARM_SVE_LENGTH macro, detect the default vector length
and aborts if it cannot be found.
Thanks Olly Perks for the pointer.
Paul Bauer [Thu, 12 Nov 2020 10:45:27 +0000 (11:45 +0100)]
Fix thread mpi linking for mdrun only build
The linking would fail because the library include directory was not
added properly.
Fixes #3807
Paul Bauer [Thu, 12 Nov 2020 08:56:08 +0000 (09:56 +0100)]
Restore correct dynamics linking behaviour
Recent changes to the way shared libraries are managed introduced a bug
in setting up static linking by default when building mdrun only.
Fixes #3806
Paul Bauer [Wed, 11 Nov 2020 14:36:20 +0000 (15:36 +0100)]
Fix gmx do_dssp CHARMM support
The tool would not work correctly due to issues with detecting some
oxygen molecules.
Fixes #3568
Szilárd Páll [Wed, 11 Nov 2020 14:28:14 +0000 (14:28 +0000)]
Fix gcc 9 "warning: ‘unused’ attribute ignored"
gcc 9 seems to not like the unused because it would never warn anyway
about members, but clang does require it.
Paul Bauer [Wed, 11 Nov 2020 13:56:29 +0000 (13:56 +0000)]
Fix segmentation fault in gmx pairdist
When using the pairdist tool with a coordinate in space as selection,
the tool would overwrite the selection group of the selection by default
to implement reference grouping. This would change the selection type of
the coordinate from INDEX_UNKNOWN to INDEX_ALL by default (or to any
other user supplied reference grouping). The change of the selection
type would then later cause a segmentation fault, as the underlying
machinery would try to access the non-existing atoms belonging to the
selection.
This changes the mechanism to no longer overwrite the selection group
type if the current one is INDEX_UNKNOWN.
Introduces test case with command line selection that would crash
without the fix.
Fixes #3762
Paul Bauer [Wed, 11 Nov 2020 10:30:50 +0000 (10:30 +0000)]
Second GROMACS 2021 beta release
Feature freeze for 2021 branch.
Berk Hess [Wed, 11 Nov 2020 07:42:53 +0000 (08:42 +0100)]
Update gmx msd documentation
Removed comment on weighted fitting for determining the diffusion
coefficients. This weighting had been removed at some point, but
the documentation had not been updated.
Andrey Alekseenko [Tue, 10 Nov 2020 15:21:45 +0000 (16:21 +0100)]
Fix "GMX_CUDA|OCL_NB_EWALD_TWINCUT is disabling twin cut-off"
Paul Bauer [Tue, 10 Nov 2020 16:45:03 +0000 (17:45 +0100)]
Disable failing NB-LIB listed forces tests
Tests are not stable enough to be run in all configurations and need
some more digging into for a proper solution.
Refs #3795
kanduri [Tue, 10 Nov 2020 16:54:53 +0000 (16:54 +0000)]
NBLIB: Fix build warning from uninitialized array
Szilárd Páll [Tue, 10 Nov 2020 12:33:23 +0000 (12:33 +0000)]
GPU codepath cycle counting fixes
* eliminated double-counting in bonded module initialization
* moved the bonded kernel launch counting into the gpuBoned module
* avoid counting ~0 CPU update work on the GPU path by conditionally
starting the ewcUPDATE counter
* also added some minimal improvements to the wallcycle debugging
tooling which should facilitate finding invalid nesting and missing
stop calls.
Refs #3764
Mark Abraham [Mon, 9 Nov 2020 15:16:01 +0000 (16:16 +0100)]
Add move operations to GpuHaloExchange
This avoids needing to put the objects in a unique_ptr to put them in
a container. Also made a collection of them use std::array for
clarity.
Berk Hess [Mon, 9 Nov 2020 20:37:31 +0000 (21:37 +0100)]
Fix dHdl and foreign energy clearing at checkpointing
The code copying dH/dl and foreign lambda energies to the checkpoint
data structures copied the wrong way around leading to zero values
being written to energy file for steps in between the last energy
frame and the checkpoint.
Fixes #3763
Pascal Merz [Tue, 10 Nov 2020 03:01:39 +0000 (20:01 -0700)]
Fix MTTK constant energy bugs
Fixes #3796
This also fixes an unclear comment relating to the barostat
Nose-Hoover chain variables in t_state.
Andrey Alekseenko [Mon, 9 Nov 2020 17:57:21 +0000 (17:57 +0000)]
Add SYCL implementation of LeapFrogGpu
An implementation of LeapFrogGpu integrator using SYCL. Also, some additions to SYCL's DeviceBuffer.
Code pretty much follows CUDA version.
For float3, I had to use gmx::RVec instead of SYCL's built-in cl::sycl::float3, since latter is 16 bytes.
Joe Jordan [Mon, 9 Nov 2020 14:55:16 +0000 (14:55 +0000)]
Add backend for nblib listed forces API
This adds the back-end for the nblib API defined in
listed_forces/bondtypes.h and listed_forces/definitions.h.
Additionally, header and source are added for the private
implementations of these files. These are implementation details,
and are not visible to or interactable with by the user, so they
are not part of the public API. This backend is a ground up refactoring
of gromacs, copying the force and energy kernels but rewriting the disipatch.
There are tests that compare forces and energies to gromacs.
Each function in this commit has at least one test for correctness,
though in most cases there are many more since the functionality is
cumulative. All of this functionality has undergone extensive design
review and code review already, so it should not be necessary to go
through the whole change with a fine-tooth comb. Suggestions on how
implementations could be improved are welcome. However, they will
likely need to be addressed as follow-up issues unless they are
trivial to fix.