Artem Zhmurov [Mon, 30 Dec 2019 11:17:20 +0000 (12:17 +0100)]
Fix gpuupdate matrix
1. Set GPU direct communications environment variables in update
matrix to allow for multi-rank testing.
2. Fall back to the CPU update if PME is not fully offloaded
in DD case and with PME-only rank (requred for GPU direct
communications).
Change-Id: I66283a446b0cc58fd0165226b01bf58ce9ec90f1
Mark Abraham [Mon, 30 Dec 2019 12:44:17 +0000 (12:44 +0000)]
Tests that verify serializer behaviours
xdr_vector serializing char uses four bytes per char, which is
wasteful when that char buffer is just a binary dump such as with the
tpr file body. This test ensures that our assumption when writing tpr
files is that we can reinterpret as a wider data type and avoid excess
padding.
It also tests that xdr_opaque does not introduce such padding.
Refs #3269
Refs #3276
Change-Id: I9c40b8ab7b9dabe461cb4dd146bb132d8f5a9681
Mark Abraham [Sun, 29 Dec 2019 23:08:15 +0000 (00:08 +0100)]
Remove use of tuple in LINCS code for GPU implementation
GCC 6.4 for POWER9 couldn't compile any form of increasing the size of
a vector of tuples that I could think of, so got rid of the tuple.
Used some range-based for, rather than explicit indexing plus the (slow)
at() function. There's no need to check indices are in range if there
are no indices!
Change-Id: Ie36a7a6fafe8f6613ec449778cfe2fbf97e02007
Paul Bauer [Mon, 23 Dec 2019 12:11:02 +0000 (13:11 +0100)]
Fix build error with wrong name from cached cmake file
The CMakeCache files could go out of sync when the name of the source
directory changes, leading to an unrecoverable build error.
To avoid this, CMakeCache files are no longer preserved between build.
Change-Id: Ifa1d808c05bd2f40132b9a721348b1bddb86fc02
Erik Lindahl [Sun, 29 Dec 2019 13:43:35 +0000 (14:43 +0100)]
Write TPR body as opaque XDR data in big-endian format
This implements support for opaque data in our serializers,
as well as a few missing XDR support opaque routines,
including support for data objects larger than 2GB.
By using this for the new serialization of the TPR body
we avoid the unintended 4x growth of the file size, and
avoid introducing extra endian swapping or padding.
We also adjust the endian so the InMemorySerializer
swaps to big endian (i.e., swap if host is little endian)
such that the body of the TPR file is compatible with
the header that is already written as big-endian by
the XDR routines.
Fixes #3276.
Change-Id: I99011dffe190155e671bd656127c2a33459923e2
Artem Zhmurov [Fri, 27 Dec 2019 11:15:23 +0000 (12:15 +0100)]
Change the behavior of the GPU update UI
1. By default, update will now run on the CPU
2. The "-update cpu" will override the GMX_FORCE_UPDATE_DEFAULT_GPU
environment variable.
Change-Id: I08efb6a594fb062fe145baa7cc00ba5c8ec63374
M. Eric Irrgang [Fri, 27 Dec 2019 13:54:44 +0000 (16:54 +0300)]
Resolve CMake ambiguities for gmxapi Python package build.
* Fix inconsistency in documented package dependencies.
* Update version of the required `cmake` Python package.
* Simplify setup.py since we can assume CMake >= 3.12 at build time. Avoids
having the CMake dependency too early in the Python package build.
Fixes #3270
Change-Id: I6d4a4b838f05985741f4560a05a3d9f257b2ec3d
Paul Bauer [Sat, 28 Dec 2019 11:20:23 +0000 (12:20 +0100)]
Change releng to give information about Gitlab
Started with converting the information for releng into information for
Gitlab when build can not find the releng repository.
Refs #3272
Change-Id: I027dd8eb3d01435cb06fba093fb2c64f381d47f3
Paul Bauer [Sat, 28 Dec 2019 11:10:25 +0000 (12:10 +0100)]
Extend information for GPU update
Refs #3167
Change-Id: I0df45487839c46ac98e99865c0d61637230ddc1a
Paul Bauer [Mon, 23 Dec 2019 09:07:06 +0000 (10:07 +0100)]
Exclude build-system files from CPack
Found that during Gitlab CI builds both ccache and build directory
where included in the final archive. Added exclusions to make sure
they do not propagate there.
Change-Id: I79717914c1d91a548ff295ff479b84ae19640e5d
Mark Abraham [Sat, 28 Dec 2019 12:26:27 +0000 (13:26 +0100)]
Merge "Merge origin/release-2019 into release-2020" into release-2020
Paul Bauer [Sat, 28 Dec 2019 10:59:13 +0000 (11:59 +0100)]
Remove membed from features
gmx membed currently does not work because the group scheme has been
removed.
Change-Id: I775ee8d2268e44610fa04ca15a1f3ff92b18f574
Paul Bauer [Fri, 27 Dec 2019 15:37:12 +0000 (16:37 +0100)]
Deprecate support for Armv7
Fixes #2990
Change-Id: Ia9dbfc9ea6cf23782e812ef2929e4851b264bc82
Artem Zhmurov [Fri, 20 Dec 2019 13:08:36 +0000 (14:08 +0100)]
Add a note to the log file when -update gpu was set with DD
GPU update with DD is not enabled with DD even if '-update gpu'
is requested. The only way to enable it is to set
GMX_FORCE_UPDATE_DEFAULT_GPU environment variable. This patch
adds a note to the output, expaining that. Also, extra warning
note is added when the environment variable is set.
Fixes #3259.
Change-Id: I480dd8e734ff60156e117cc80b1cd9af6a161791
Paul Bauer [Mon, 23 Dec 2019 09:19:16 +0000 (10:19 +0100)]
Add copyright check and improve cache usage
Changed the way jobs are using the runner cache, so that each subsequent
build can benefit from the cache.
Also removed caching from jobs that don't benefit from it.
Change-Id: Ic4505cc034ddf83dc2a7e8dc07ed1dfa9558633d
Paul Bauer [Fri, 27 Dec 2019 12:58:41 +0000 (13:58 +0100)]
Merge origin/release-2019 into release-2020
Resolved Conflicts:
cmake/FindHwloc.cmake
cmake/gmxVersionInfo.cmake
docs/CMakeLists.txt
src/gromacs/gmxana/anadih.cpp
src/gromacs/gmxana/gmx_angle.cpp
src/gromacs/mdlib/forcerec.cpp
Change-Id: Ie4408c932a712d4f9d1f42117a512e0474535df5
Artem Zhmurov [Fri, 27 Dec 2019 10:19:52 +0000 (11:19 +0100)]
Clean bad auto-format in decidegpuusage doxygen comments
Change-Id: Ia2ca1dcc138c920d54ce928889cfcad63fc3784b
M. Eric Irrgang [Thu, 12 Dec 2019 13:08:28 +0000 (16:08 +0300)]
Update intersphinx configuration.
Disable intersphinx cache expiration and set a finite timeout to play
more nicely in non-networked environments.
Change-Id: I5802f7dbba43897e27a77366013e254f868357e7
M. Eric Irrgang [Thu, 12 Dec 2019 13:06:41 +0000 (16:06 +0300)]
Set Sphinx default role.
Set default_role config value to 'any' for better automatic handling of
interpreted text in the default role. Allows improved readability for
documentation that may not always be processed by Sphinx, such as
Python docstrings.
Change-Id: I5bf37111d6870117810ac308cfaa8c5f1ae9bb5c
M. Eric Irrgang [Thu, 26 Dec 2019 16:18:55 +0000 (19:18 +0300)]
Fix external web link.
Ineffective syntax was used to try to make a link from the text "Conda"
to the Conda website. Instead, make a properly defined link target and
use "Conda_" for hyperlinked text throughout the document.
Change-Id: Iee77f8b28c9ee2e621da1fb9c8e46832a95e5e5e
M. Eric Irrgang [Thu, 12 Dec 2019 12:58:40 +0000 (15:58 +0300)]
Clean up Sphinx interpreted text in the default role.
* Fix typos or syntax for several text literals that Sphinx tries to
process as interpreted text (in the default role).
* Use Google docstring conventions to guide adjustment of gmxapi
docstrings.
Change-Id: If6eeede8dcc782c04fc4363005c38c746a8664ea
Paul Bauer [Fri, 20 Dec 2019 14:00:02 +0000 (15:00 +0100)]
Add files for Gitlab CI
Change-Id: I2508b6ba4a551a0768b1d5dfd742d97ebec37c7c
Paul Bauer [Mon, 16 Dec 2019 11:39:33 +0000 (12:39 +0100)]
Prepare for GROMACS 2019.6
Reset doi strings
Change-Id: I38fa39c52cde5d967525770ec2a6381b7fcee33a
Paul Bauer [Mon, 16 Dec 2019 11:36:38 +0000 (12:36 +0100)]
GROMACS version 2019.5
Added doi strings
Updated regressiontest hash.
Change-Id: If6c34638caf40f562fd8a744af767be4941ff73b
Paul Bauer [Sun, 22 Dec 2019 16:04:37 +0000 (17:04 +0100)]
Revert "Fix that tests intended for multiple ranks run that way"
This reverts commit
1ebc7b0bff4a32ce957fd79a1d1bd20b535ea518.
Reason for revert: The parallel running of tests doesn't work the way we want here and the effort for fixing things in a soon to be critical fixes only branch is not worth it in my opinion
Change-Id: I59fb6f9daf7019592de7e8db202ccd050c133610
Alan Gray [Thu, 12 Dec 2019 11:06:36 +0000 (03:06 -0800)]
Add user guide doc for GPU buffer ops and comms env variables
Change-Id: Ib6701adbf6f4909a804394606a362fa209716497
Paul Bauer [Fri, 20 Dec 2019 13:28:10 +0000 (14:28 +0100)]
Fix wrong header in release notes
Fixes #3261
Change-Id: Icc31b7a273670e99c21c9bb60343e1ce5d532653
Christian Blau [Mon, 25 Nov 2019 15:42:25 +0000 (16:42 +0100)]
Remove problematic output of gmx angle
It could happen that the calculation of the standard deviation
for angles caused a divide by zero error for empty populations.
Because this standard deviation of per frame averages over all
frames was anyhow meaningless, it has been removed.
Refs #3206
Change-Id: Icf541a8b3bef502da9a22b55a8e8154b2d4fc8f8
Paul Bauer [Tue, 17 Dec 2019 14:21:38 +0000 (15:21 +0100)]
GROMACS 2020 release candidate
Adjusted regresstiontest hash
Change-Id: I37cec8154843b8f8a2a9136051b50bce7eba5888
Szilárd Páll [Thu, 19 Dec 2019 19:44:35 +0000 (20:44 +0100)]
Enable buffer ops when GMX_GPU_DD_COMMS is set
Buffer ops is always a hard dependency for DD with GPU direct comm, so
enable it instead of requiring an extra env var to be set on mdrun
invocation.
Change-Id: Iea354f8ce636a115e0ed866228746e91f34df228
Paul Bauer [Thu, 19 Dec 2019 16:42:15 +0000 (17:42 +0100)]
Fix regressiontests failing with ctest
Setting the -ntomp variable and not -nt at the same time causes errors
when running the regressiontests through ctest.
This was introduced in I78925951dcb59a11af01bc64f0dea373fe172cbb while
updating things for Gitlab CI.
Fixes #3257
Change-Id: I19afd7817b5c637d6653fda8533f23720b45cc41
Alan Gray [Thu, 19 Dec 2019 13:32:53 +0000 (05:32 -0800)]
Release note for GPU direct communications
Change-Id: I4487f2ed6bc789e6cfb3e68d802ccedda0c51962
Alan Gray [Thu, 19 Dec 2019 09:45:58 +0000 (01:45 -0800)]
Fix PME tuning issue when PME-PP communications are active
If PME-PP direct GPU communication is active, the CPU-GPU
asynchronicity in the codepath causes the timing load balance ratio
used to trigger PME tuning to be unreliable. This change
unconditionally starts PME tuning when the PME-PP communication
feature is active (unless PME tuning has been de-activated with
the -notunepme option).
Partially addresses #3208
Change-Id: Iea173d19062dbd11d57ca9ceb4e52b9f20d4ff15
Szilárd Páll [Fri, 29 Nov 2019 00:10:10 +0000 (01:10 +0100)]
PP-PME load balancing improvements
Add a minimum number of nstlist tuning intervals and minimum time delay
at the beginning of the run before the load balancing starts. This allow
hardware clocks to ramp up and avoids having early measurements
overestimate rendering subsequent ones with different grid setups only
faster due to hardware warmup.
Also use global variables to adjust the number of measurements to be
skipped after switching configs.
Refs #3208
Fixes #2203
Change-Id: If835d2482e127caa51d50f45f25c19144d35efaa
M. Eric Irrgang [Thu, 19 Dec 2019 11:09:18 +0000 (14:09 +0300)]
Add issue tracking for deprecations.
Provide links in release notes to issue tracking for announced
deprecations.
Fixes #3251
Change-Id: I246651f8cb868eb1deecac86c2e7d6f0ec81b3f1
Berk Hess [Wed, 18 Dec 2019 18:23:43 +0000 (19:23 +0100)]
Fix mdrun appending invalidating energy files
When appending at mdrun restarts, energy files would become
unreadable at the appending point.
Fixes #3250
Change-Id: I7683e1a954fb8865acb5e77aae028ae717ae0ab3
Alan Gray [Wed, 18 Dec 2019 15:41:45 +0000 (07:41 -0800)]
Fix conditional on assertion for combining GPU Update and GPU coordinate send
Fixes a problem introduced in
9a3c2ce312c1e04634d636655388a8aaad53c8d1
which unintentionally blocks any use of GPU update with PME-PP
Communication because !stepWork.doNeighborSearch is missing from the
condition on the assertion.
Related to #3159 and #3160 which, when implemented, will remove the
restriction on coordinate send originating from the GPU (on non search steps).
Change-Id: Ie9b1102386b2c1bc927c09e4d8ead2bd2321320d
Szilárd Páll [Tue, 10 Dec 2019 11:24:32 +0000 (12:24 +0100)]
Allow x D2H to overlap with GPU force compute
With GPU update coordinates are transferred back to the CPU every step
if there are forces to compute on the CPU. Originally this was
implemented with a back-to-back transfer launch and wait at the
beginning of do_force().
This change moves the CPU wait for the completion of the coordinate
transfer closer to the consumer tasks in order to avoid blocking GPU
force tasks' launch and allowing compute and transfer to overlap.
Fixes #3221
Change-Id: Ia6641147bbec1186b54c1445d36dc31000eae9c4
M. Eric Irrgang [Fri, 13 Dec 2019 16:41:48 +0000 (19:41 +0300)]
Update reference to uncrustify and clang-format.
Correct some copy-paste errors. Consolidate some references to
formatting tools and continue to transition away from uncrustify.
uncrustify references and infrastructure remain, along with Jenkins
documentation. These can be removed after transitioning from Jenkins to
GitLab Runner, pending clarification on how to distinguish between
documentation for all supported versions versus the current version.
There are also various references and workarounds related to uncrustify
in the source code. These can be updated in separate changes against the
post-release-2020 master branch.
Refs #3248
Change-Id: I3331f73921812a918d32dd6a045eabc4da4a6a6d
Berk Hess [Fri, 6 Dec 2019 13:39:28 +0000 (14:39 +0100)]
Change grompp decoupling SD warning to note
The warning that grompp issues when decoupling a molecule
without the use of the SD integrator has been changed to a note,
since there are valid use cases for using normal MD when not
running in the completely decoupled state.
Note that checking for actual decoupled VdW states requires a lot of
code and would still not be 100% correct.
Fixes #2767
Change-Id: I55c84afcbcb7b19bdb8a7a8bc586a65c50f8d0c1
Paul Bauer [Tue, 17 Dec 2019 17:22:16 +0000 (18:22 +0100)]
Add ability to set OMP and tMPI thread for ctest
For Gitlab CI we need at some points to be able to set the threads used
for running the regressiontests through ctest.
(cherry picked from commit
4e6b4134e62f17d64520a46e0aad7cbd60f778f3)
Change-Id: I78925951dcb59a11af01bc64f0dea373fe172cbb
Paul Bauer [Fri, 13 Dec 2019 15:51:44 +0000 (16:51 +0100)]
Ignore build host for CI builds
When moving the CMake build directory between hosts a warning was
generated. This does not integrate well with containerized CI.
(cherry picked from commit
33079aa495e7e3b7da78bd58de9c6f30edff51d4)
Change-Id: If0a775ab86d25a7d5646e824243892320d4ddbe3
Berk Hess [Mon, 16 Dec 2019 09:50:06 +0000 (10:50 +0100)]
Add note for COM removal with position restraints
Center of mass motion removal in combination with position restraints
will often cause artifacts. We should (automatically) disable this,
but this will disrupt workflows, so for now grompp will issue a note.
Refs #3244
Change-Id: If983e918d26f0af2fab96d44d0f2b1fc3cedb901
Artem Zhmurov [Mon, 16 Dec 2019 21:17:47 +0000 (22:17 +0100)]
Clean-up buffer-ops CUDA kernels
1. Adjust naming according to conventions.
2. Reduce number of type casting.
3. Use native CUDA types.
Fixes #3237.
Change-Id: I79da0dd1edf6c302661ba0954e4191fde1ebf2e8
Paul Bauer [Tue, 10 Dec 2019 10:11:26 +0000 (11:11 +0100)]
Test parallel mpi only with openmp
Can time out in other conditions
Found while working on Gitlab CI
Refs #3232
Change-Id: I7cf62ed913d2bc8c88317a674b0594dbe54ba394
Szilárd Páll [Tue, 17 Dec 2019 12:43:00 +0000 (13:43 +0100)]
Comment the use of waitCoordinatesCopiedToDevice
Tthis is to note that we are only using a barrier a mechanism to sync
with GPU tasks rather than to preventing a race between the copy and
other CPU tasks.
Change-Id: I8d432f7ef3e87e56beffa7f58230e50bcd59a666
Paul Bauer [Fri, 13 Dec 2019 15:50:21 +0000 (16:50 +0100)]
Set correct dependency for doc build on gmxapi
When building the documentation with the python package, we need to know
about the symbols in the package when building docs for e.g. the pdf
manual.
Change-Id: Ia9a248da5746a5d90736cd3f3aa345fe8ffd0c79
(cherry picked from commit
0aa283c6b578b1b6bf6673169697865142014368)
Paul Bauer [Fri, 13 Dec 2019 15:50:01 +0000 (16:50 +0100)]
Fix compiler warning about extra ;
Change-Id: I9718ab9d9772dfc7251bc1eb175be59544b2c2cb
(cherry picked from commit
6ef70b67bb06f03da97315170a44f76679d92a23)
Szilárd Páll [Fri, 6 Dec 2019 18:57:24 +0000 (19:57 +0100)]
Add wallcycle counting to StatePropagatorDataGpu
Launch overheads are counted in the main GPU launch overhead counter and
a separate subcounter is used for the launch and a main counter for the
CPU blocking wait timing.
Note that this chnge introduces mdtypes->timing->mdtypes cyclic dependency,
the warning on which is suppressed.
Fixes #3207
Change-Id: I3b69df9e4888800b43712a42b863958db80f5caa
M. Eric Irrgang [Fri, 13 Dec 2019 16:14:43 +0000 (19:14 +0300)]
Be more specific with clang-format suggestions.
Refs #3238
Change-Id: If71687cbab9a9aa1c10e3501849932a0ea0f3112
Paul Bauer [Mon, 16 Dec 2019 12:51:02 +0000 (13:51 +0100)]
Fix formatting error
Fix originally proposed by Boris Timofeev.
Refs #3225
Change-Id: Ie742f2c751473d17fc8f69e9ed79faacdd6fc56c
Mark Abraham [Sat, 28 Sep 2019 08:25:41 +0000 (10:25 +0200)]
Fix that tests intended for multiple ranks run that way
Added the flag that triggers ctest to use the flags that will produce
multiple ranks in both thread-MPI and real MPI cases.
Change-Id: I4ef3af4fd1750ab7cc231a29191fc4042385c309
Pascal Merz [Tue, 17 Dec 2019 04:24:40 +0000 (21:24 -0700)]
Fix exact continuation modular simulator
With modular simulator, the center of mass motion was mistakenly
removed also when continuing from checkpoint, breaking exact
continuation.
Change-Id: I4db837a1b11f1b44cfae4970230a51a2c05d84aa
Szilárd Páll [Sat, 14 Dec 2019 22:15:44 +0000 (23:15 +0100)]
Fix the GPU bonded stream with 1 PP + 1 PME rank
WIth 1 PP + 1 PME rank the GpuBonded constructor gets passed the
non-local nonbonded stream which is nullptr and as a result the bonded
kernel launch happens in the default stream blocking concurrent
kernel execution.
This change makes sure that only when there is PP domain decomposition
is the GpuBonded constructor passed the nonlocal stream.
Fixes #3241
Change-Id: I858401b78c620adc3bea176e40e6fa179e583483
Paul Bauer [Fri, 6 Dec 2019 11:18:23 +0000 (12:18 +0100)]
Fix torsion angle calculation
Fix originally contributed by Boris Timofeev.
Fixes #3225
Change-Id: I4862679e4aeae514736df53f0eff44bf3b85f928
Christian Blau [Mon, 9 Dec 2019 18:42:20 +0000 (19:42 +0100)]
Fix densityfitting stalling and energies
Density guided simulations would stall when there were no atoms on a
node. Further, the energy contributions were added for every
participating node, resulting in wrong energies.
Both issues are fixed with this patch.
fixes: #3230
refs: #3235
Change-Id: Iab773993fb3f98bd154acaa1d3971e655182a2b2
Mark Abraham [Wed, 31 Oct 2018 13:44:55 +0000 (14:44 +0100)]
Simplify gmxapi RPATH handling
Fixes #2722
Change-Id: Ic697f596285acdb5c7728b7ebc995ea44c82f3ac
Paul Bauer [Wed, 27 Nov 2019 15:35:16 +0000 (16:35 +0100)]
Check for using correct hwloc headers and runtime
Also add assertion in the code to prevent errors from linking
against the wrong library while running.
Fixes #3200
Change-Id: Ib2f2861702e111f67c38b0c9d65ccbe4c81a0ccd
Artem Zhmurov [Thu, 12 Dec 2019 16:30:27 +0000 (17:30 +0100)]
Clean up outdated comments in md.cpp
Some of the comments were left unattended as the code evolved.
Change-Id: I12c2e313645fcbb1a112f3f0c9f4c72e7943d9d6
Pascal Merz [Wed, 11 Dec 2019 01:49:24 +0000 (18:49 -0700)]
Test for expected output files
Ie7f03f5b fixes a bug where modular simulator would not write
final coordinates to file. This test checks whether some basic
output files are present (edr, trr, log, gro, cpt).
Change-Id: I02299d342667104ccc19f0af6d557bb8aa916494
Pascal Merz [Wed, 4 Dec 2019 06:55:36 +0000 (23:55 -0700)]
Fix final configuration writing for modular simulator
Modular simulator was not writing final configuration (.gro) file.
This commit fixes this, and removes an outdated sentence in the
documentation of ITrajectoryWriterClient.
I02299d34 introduces a test to avoid similar errors in the future.
Note that the complexity required to introduce this feature implies that
trajectory writing in the modular simulator needs some work for
GROMACS 2021.
Change-Id: Ie7f03f5beea2d78411c7a0cdfa85f71deeb622fa
Szilárd Páll [Mon, 2 Dec 2019 18:29:28 +0000 (19:29 +0100)]
Allow overlapping CPU force H2D with compute
The reduction orchestration code already uses explicit sync event
in all cases and StateGpu implements the ability to schedule force
H2D in a separate stream for the "All" locality.
Hence, this change switches for non-DD runs the CPU force H2D to be done
in the update stream to allow overlap with force work in the local
stream.
Refs #3170 #3029
Change-Id: Iceb9aac395335c062109d552d3f0289688a9c75f
Christian Blau [Tue, 22 Oct 2019 08:55:59 +0000 (10:55 +0200)]
Densityfitting - enforce similarity increase with adaptive force scaling
Previous to this patch, the force constant for density guided
simulations with adaptive force constant scaling was scaled up the same
amount that it was scaled down, not resulting in the announced enforced
increase in similarity. Now, the force constant is increased more strongly
than decreased, resulting in the desired enforced increase in similarity.
Change-Id: I5b149c79d91ea9e5ceeb5b0e7dce854bd6f34711
Artem Zhmurov [Thu, 5 Dec 2019 13:49:25 +0000 (14:49 +0100)]
Allow using GPU update with DD and update groups
The GPU update is now can be enabled for the supported DD cases
with the GMX_FORCE_UPDATE_DEFAULT_GPU environment variable. Also
added the checks on whether the SHAKE algorithm was requested,
since SHAKE is not supported by the GPU update.
Refs. #3226, #3163.
Change-Id: I57e3ad3b8a571ec244989e888afd5cfcbaf9b75e
Artem Zhmurov [Wed, 11 Dec 2019 15:19:15 +0000 (16:19 +0100)]
Enable most of the pulling flavors with GPU update
Only constraints pulling is not supported, since it is not implemented
in GPU version of LINCS. There is no reason to disallow other flavors
of pulling.
Change-Id: Iceca52bba5e040bd241a156f9cf58ab3556acdac
Mark Abraham [Wed, 11 Dec 2019 14:46:51 +0000 (15:46 +0100)]
Document DOMAINDECOMP(cr) correctly
It is likely there are numerous cases where this is used mistakenly
when havePPDomainDecomposition expresses the real intent. If so,
runs with 1 PP and 1 PME rank may have buggy behaviour.
Refs #2395
Change-Id: I07be73a6c690887b3043140a2a78ae6fe6bb17f1
Artem Zhmurov [Wed, 11 Dec 2019 10:53:31 +0000 (11:53 +0100)]
Clarify what setting zero to some output mdp options does
Change-Id: I36dc059e982c3358cbfa55596e71093ce3208446
M. Eric Irrgang [Wed, 11 Dec 2019 13:50:33 +0000 (16:50 +0300)]
gmxapi landing page update.
In response to user feedback, replace some content that was confusing
instead of informative.
Change-Id: Ida8c12ba2caf4ef224b9276570bc719c9000e2bd
M. Eric Irrgang [Wed, 11 Dec 2019 13:45:36 +0000 (16:45 +0300)]
gmxapi documentation readability improvements.
In response to user feedback, provide a "quick install" overview section.
Rearrange and update some content.
Change-Id: I2a1bbf1a1efbda769e330b85925ed01dbcdae29e
M. Eric Irrgang [Wed, 11 Dec 2019 13:39:56 +0000 (16:39 +0300)]
gmxapi documentation formatting improvements.
Improve some formatting mark-up. Use normative Sphinx roles for
commands, Python modules, environment variables, and file paths.
Change-Id: Iff1d4b09da13c421da809f882e73c8404eb70f38
Mark Abraham [Wed, 31 Oct 2018 13:44:55 +0000 (14:44 +0100)]
Simplify gmxapi RPATH handling
Fixes #2722
Change-Id: Ic697f596285acdb5c7728b7ebc995ea44c82f3ac
Artem Zhmurov [Mon, 9 Dec 2019 18:20:03 +0000 (19:20 +0100)]
Set GPU update to false in case of a rerun
Rerun does not require the numerical integration of equation of
motion, hence the useGpuUpdate should be false.
Fixes #3231.
Change-Id: I9027641e9dc32fb464ebbb6148c11c530c0eb2cd
M. Eric Irrgang [Fri, 6 Dec 2019 12:29:57 +0000 (15:29 +0300)]
Finalize gmxapi 0.1
Set 0.1 release metadata for Python package and C++ library.
Note that 0.1 is API identical to 0.0.8, but we are
taking the next step to the targeted semantic versioning,
and patch releases should no longer affect the APIs.
However, we are not yet at a point where we can have
clear stability guarantees between minor versions.
Change-Id: I4f4a6ba84353730e2962b730cd1e656bae4e377a
Mark Abraham [Fri, 6 Dec 2019 09:45:21 +0000 (10:45 +0100)]
Avoid 386 O3 codegen bug
Refs #3205
Change-Id: I2aa5018bde089b11497892dd68a7f9715e69e20e
M. Eric Irrgang [Thu, 5 Dec 2019 10:48:18 +0000 (13:48 +0300)]
Add notes on MPI with gmxapi Python package.
Change-Id: I7ecd33fcea482b8f300873fc7fdcea2c3958215e
Artem Zhmurov [Fri, 6 Dec 2019 09:35:17 +0000 (10:35 +0100)]
Pass array ref instead of casting to basic array in PME redistribute
Change-Id: I98b3c211b2669266f8bc6b37580b8f48087e3645
Christian Blau [Fri, 29 Nov 2019 16:31:00 +0000 (17:31 +0100)]
Change arbitrary units to counts in RMSD distance distribution output
Users were confused by the "a.u." label in the RMSD distance
distribution output. This patch changes the label to "counts"
to better state that this is the number of events captured in the
histogram column.
Change-Id: I6c082147ae9f1647ec743275af6b72564401de8d
Mark Abraham [Wed, 4 Dec 2019 16:07:59 +0000 (17:07 +0100)]
Provide more feedback when listed forces tests fail
Refs #3205
Change-Id: Ic012aeaf8b35af88b78e109acabb6048d593cab3
M. Eric Irrgang [Thu, 5 Dec 2019 10:46:50 +0000 (13:46 +0300)]
gmxapi Python package usage prose.
* Provide a walk through of basic gmxapi Python usage.
* Update one of the helper functions in test_subgraph.py to
make sure that a documented example is tested.
Change-Id: I2ad3368fe8a39307bcd7e676dc36627e30ab7ac1
M. Eric Irrgang [Thu, 5 Dec 2019 14:47:07 +0000 (17:47 +0300)]
Improve pytest fixtures for directory management.
* Add a pytest command line option to control whether to remove
temporary directories always, never, or conditionally upon test success.
* Encapsulate context managers and test fixtures for tempdir removal,
temporary changes of working directory, and access to the new pytest
command line argument.
* Use a context manager to use the temporary testing directories
for working directory, as well. Works around potential issues
with GROMACS creating temporary files in different directories
(or filesystems) from where they are relevant.
This change makes identical changes to 3 different conftest.py files.
Consolidation into the gmxapi.testsupport module is deferred to a
separate change.
Refs #3227
Change-Id: I703d1e3806f7b4d8f2ae3b80c39ec64acd9cf3b4
Christian Blau [Wed, 4 Dec 2019 15:52:01 +0000 (16:52 +0100)]
Relax cross-correlation test precision
Relase the floating point precision in cross-correlation evaluations on
large data arrays further. i386 fails here with debian experimental build.
Refs #3205
Change-Id: I86c9ad1804da5be98671ac14a5bc37ea5636aad0
Mark Abraham [Mon, 5 Nov 2018 18:07:20 +0000 (19:07 +0100)]
Added OpenCL build to release matrix
Added missing information for one build.
Change-Id: I30da8ce4e19e104182ee082cc18a83e318069b3c
Mark Abraham [Wed, 4 Dec 2019 15:25:35 +0000 (16:25 +0100)]
Removed unnecessary link_directories command for gtest
This warns at link time on MacOS Catalina with macports
clang-9 and cmake 3.15.5
Change-Id: If493f72133c0388e6119ea7a30aa1dc5c5830c7a
Christian Blau [Wed, 4 Dec 2019 12:08:10 +0000 (13:08 +0100)]
Remove cutoff-scheme group from default mdout.mdp output
The .mdp default output file had a reference to the group scheme in it,
which might prove confusing to users that assume that this is still
available.
Change-Id: I434f15e46dfc0a8ebffe8d826855dc8e67168fba
Paul Bauer [Tue, 26 Nov 2019 09:37:15 +0000 (10:37 +0100)]
Third beta release of GROMACS 2020
Updated regressiontest hash
Change-Id: I96be9b7b9f3f94f6eddf1fd4603cc829fd3e1848
Paul Bauer [Tue, 3 Dec 2019 10:21:47 +0000 (11:21 +0100)]
Revert "Enable GPU update with DD when GPU comm features are enabled"
This reverts commit
b88f3eadf90261555508f6a4df64ce184141a66a.
Reason for revert: Mark found the code segfaulting under some conditions with domain decomposition and update enabled, so this is not ready to be used yet.
Refs #3226
Change-Id: I45cf9564a87595d445057da071a8fca5c60f9d9a
Paul Bauer [Tue, 3 Dec 2019 11:25:54 +0000 (12:25 +0100)]
Fix nightly build by correctly defining several
variables as bool instead of int.
Change-Id: Ia22fe3acdc55131ea40c80b104293273cafb1017
Alan Gray [Tue, 5 Nov 2019 12:52:21 +0000 (04:52 -0800)]
Enable GPU update with DD when GPU comm features are enabled
Changes assertions to allow GPU update to run with domain
decomposition, only when GPU PME-PP communication and GPU halo
exchange features are enabled through their respective environment
variables.
Added test coverage to the gpuupdate matrix
Change-Id: Ie05dac64eada8f704c3a33d0eb6e5bc74dfcc61e
Paul Bauer [Fri, 29 Nov 2019 15:00:52 +0000 (16:00 +0100)]
Set update to run on GPU by default if possible
Change-Id: I1a2052968c8d8dd8020744bf15f974bc0d92a6ef
Jonathan Vincent [Wed, 6 Nov 2019 14:55:10 +0000 (06:55 -0800)]
Heuristics for switching between CUDA spread/gather kernels
The various CUDA spread/gather kernels perform better in different circumstances,
so heuristics are used to control which one is selected.
Refs #3189
Change-Id: I32c0726021a48dc8721e337f8f41e9c9d334e05c
Berk Hess [Mon, 2 Dec 2019 13:15:08 +0000 (14:15 +0100)]
Add check for coupled constraints for CUDA update
The CUDA LINCS code has a limit on the number of coupled constraints.
This is now checked during in the GPU update decision function.
Change-Id: I5eee96b82f3f5196b64a5e815eae78d4ed367a80
Berk Hess [Mon, 2 Dec 2019 10:43:16 +0000 (11:43 +0100)]
Extract LINCS CUDA helper functions
Change-Id: I00fb311053aa9c13036b401107399409f9a01599
Christian Blau [Mon, 2 Dec 2019 13:52:27 +0000 (14:52 +0100)]
Relax test tolerance for cross correlation measure for densities
Some compilers do not perform the optimisations that are necessary to
reach default real tolerance when calculating the cross correlation of
larger three dimensional densities (100x100x100 voxels)
This patch loosens the requirement on the precision of cross correlation
evaluations.
refs #3205
Change-Id: Iad1bb1b17bb6935b2ce2537bcbb6c3902172a6bc
Paul Bauer [Fri, 29 Nov 2019 15:10:05 +0000 (16:10 +0100)]
Use DOI for citing in reference manual section
Change-Id: I84ee722345669afbca972697ebcc76d874af1b46
Mark Abraham [Thu, 28 Nov 2019 16:49:26 +0000 (17:49 +0100)]
Further improve taskassignment exception handling
It was still posssible that the exit() from one thread-MPI rank would
cut off another rank while the latter's error output before it
finished being written to the terminal stream.
This solution is still deficient in some aspects, but it will
always work on single-node testing (ie. including Jenkins) and
often work usefully in multi-node testing.
Change-Id: Ib41e012b9f56591c80046b44891dd77af5a2f938
Berk Hess [Fri, 29 Nov 2019 16:22:15 +0000 (17:22 +0100)]
Merge "Merge branch release-2019 into release-2020" into release-2020
Paul Bauer [Fri, 29 Nov 2019 13:21:44 +0000 (14:21 +0100)]
Fix unaligned access with AVX512
Found and debugged by Gilles Gouaillardet
Change-Id: I9203593c94eb745020274b126601d30e49d7aac2
Paul Bauer [Fri, 29 Nov 2019 10:32:17 +0000 (11:32 +0100)]
Fix build error without thread or regular mpi
Some more unused variable warnings that I haven't fixed yet.
Fixes #3218
Change-Id: Id47718bb0af97d3a494afa133af8b54ba71b9d5d
Artem Zhmurov [Thu, 28 Nov 2019 18:59:36 +0000 (19:59 +0100)]
Print OpenCL error info in case of failed assertion in device buffer management
Having error code availible is helpful for debugging.
Change-Id: I71c808c9171eae3f87b72253f3e81f0e2e2c22a2
Mark Abraham [Fri, 29 Nov 2019 12:52:13 +0000 (13:52 +0100)]
Merge branch release-2019 into release-2020
Change-Id: I138d910b0d5cb8555460f87345c4e312e528a3ce