Kevin Boyd [Fri, 12 Jul 2019 15:50:02 +0000 (11:50 -0400)]
Modernize syntax of enable_if and traits to use _t helpers
From c++ 14, "typename std::enable_if<something>::type"
can be reduced to
"std::enable_if_t<something>"
as can traits with ::type
Note that when we switch to C++ 17, a number of traits with
::value can be similarly shorthanded with _v
Change-Id: I92d4502c51ac613fa81f130ed3127c812c4e0a6f
Szilárd Páll [Mon, 15 Jul 2019 11:26:36 +0000 (13:26 +0200)]
Conditionally pin GPU-related grid data
Data that is transferred to the GPU when the buffer ops is offloaded is
now only pinned when the nonbonded module uses GPU offload avoidign the
runtime errors encountered when a GPU-enabled build does not detect a
GPU and therefore the CUDA runtime refuses to register the memory.
Refs #2817 #2934
Change-Id: Iabbc0d9f37fad0e88cd39a078af1346e8f713ec1
Alan Gray [Fri, 8 Mar 2019 09:05:47 +0000 (01:05 -0800)]
F buffer operations in CUDA
This patch performs GPU buffer ops for force buffers.
Enable with GMX_USE_GPU_BUFFER_OPS env variable.
Currently, the H2D transfer of the force buffer is switched on with
haveSpecialForces || haveCpuBondedWork || haveCpuPmeWork,
where haveCpuPmeWork is true even when useGpuPme == true
until on-GPU PME-nonbonded reduction is added in follow-up.
TODO: enable PME reduction in GPU buffer ops and remove associated H2D
transfer
Implements part of #2817
Change-Id: Ice984425301d24bac1340e883698244489cd686e
M. Eric Irrgang [Tue, 16 Jul 2019 15:09:07 +0000 (18:09 +0300)]
Improve some documentation formatting and spelling.
Change-Id: Ic59eb3407fda2dbd341fb4ce6235d7c5c99c7630
M. Eric Irrgang [Thu, 11 Jul 2019 16:59:53 +0000 (19:59 +0300)]
Remove extraneous file.
A file was overlooked in Change-Id: I0d847bc2490935e0ddc3170b674d7460a5a08506
Refs #3033
Change-Id: I4fb6af0b6d51b477091c6305872c0c7124e754d6
Paul Bauer [Thu, 27 Jun 2019 15:13:39 +0000 (17:13 +0200)]
Extend MDLogger levels
Added logging levels for errors and debug information.
Extended tests to check those.
Refs #2999
Change-Id: I8b23de7baf3555ffc89896e68c1998608b7b71cf
Paul Bauer [Wed, 10 Jul 2019 14:07:20 +0000 (16:07 +0200)]
Move methods out from trjconv
Moves some functions out of trjconv to allow access in other tools as
well. This change is just code movement.
Change-Id: I37e9f8d87862e6ad6666704dc85d74b09b144f49
Mark Abraham [Wed, 10 Jul 2019 18:33:05 +0000 (20:33 +0200)]
Add gpubufferops test matrix
This commit teaches Jenkins to understand how to enable the GPU buffer
ops environment variable that is the feature flag for a developmental
feature. The new capability is used in a releng build configuration
matrix that releng can be taught to trigger on demand with
[JENKINS] gpubufferops
comments in gerrit
Change-Id: I30ca4a5d84fe136a657be7a134829f4c696c5d85
Szilárd Páll [Wed, 24 Apr 2019 12:03:39 +0000 (14:03 +0200)]
Use HostVector for Grid/GridSet data need on-GPU
Grid.cxy_na_, Grid.cxy_ind_, GridSet.cells and GridSet.atomIndices
have been converted from std::vector to gmx::HostVector. This allow
the code to pin the HostVector when X buffer ops is used and to
eliminate the hacky pin/unpin in CUDA buffer ops functions.
Part of #2934
Refs #2817
Change-Id: Icca21dd076128ec582f805ed96e253dfab461270
Mark Abraham [Tue, 2 Jul 2019 07:46:13 +0000 (09:46 +0200)]
Fix pre-submit build matrix and description
Pre-submit should not fail because the ftp server is not reachable, so
moved it to nightly matrix. Also recorded the intent to test
such a build.
Also fixed that the intent to test AVX_128_FMA in mixed precision was
broken in Ib2c5e14e5d89665130ae8d6c749c3230ccfe72a9. There's no
ability to test this SIMD in pre-submit without wider changes, and their
is neither large risk nor consequence of breaking it, so nightly is OK.
Refs #2809, #2629
Change-Id: I9cd41a359ba662a8a9529540c50c9a7ef546cd29
Kevin Boyd [Wed, 10 Jul 2019 22:01:59 +0000 (18:01 -0400)]
Use const views in matrix determinant calculation
Reduces scope of the matrix.h implementation to just reals
Change-Id: Ide66967b35ffc58b3e61c403d3ce1862b5f5b8ca
Kevin Boyd [Tue, 2 Jul 2019 03:31:02 +0000 (23:31 -0400)]
Add trace functionality to 3x3 matrices
Replacement for vec.h trace
Change-Id: I5c452cb36bab277ffcb3f2f9645d3d025a1805a8
Pascal Merz [Mon, 1 Jul 2019 05:45:18 +0000 (23:45 -0600)]
Get rid of clang-tidy warning in do_md/rerun/mimic
This change silences most of the clang-tidy warnings
"Clang-Tidy: Use of a signed integer operand with a binary
bitwise operator" in do_md, do_rerun and do_mimic. This warning
is triggered when using a signed integer with a binary bitwise
operator, as we do all over the code when encoding / decoding
flags. Such warnings are popping up in other parts of the code,
but this change takes only care of the ones which can be
silenced by changes in the simulator functions and the bit shift
definitions.
Change-Id: I7345e987e91051c9688cb2e8a96026682f025b6b
Pascal Merz [Mon, 1 Jul 2019 00:10:42 +0000 (18:10 -0600)]
Remove dependence of compute_globals on t_state
This change makes the different function related to compute_globals
request the fields of t_state explicitly, instead of simply taking
a pointer to the full t_state object. This simplifies refactoring
the t_state object in future commits. This change also clarifies why
both state->box and an additional parameter `matrix box` is required -
the latter one is the box at the last complete timestep in do_md and
has been renamed accordingly.
Note that in the documentation to checkNumberOfBondedInteractions(),
which was changed in a similar way, the argument `state` was
described as being the global state. Throughout the code, the local
state was used, however. This part of the documentation is now
changed, but if that was intended, then a follow-up change fixing
this might be necessary.
Change-Id: If913656fe9bf07567a29f68592402bb5ff17fc52
Pascal Merz [Tue, 9 Jul 2019 13:14:27 +0000 (07:14 -0600)]
Make relax_shell_flexcon independent of t_state
This change writes out the fields of t_state needed as explicit
arguments of relax_shell_flexcon instead of taking a pointer to
the full t_state object. This simplifies refactoring the t_state
object in future commits.
Change-Id: Iec3d0aea7462325963341b1d192cff697b764a7c
Kevin Boyd [Thu, 27 Jun 2019 02:38:22 +0000 (22:38 -0400)]
Clean up gmx solvate
Changed c-style struct to C++ with defaults, and changed a char*
field to a string.
Used vector instead of pointer array, and associated changes
to appending.
Moved a number of incrementing variables to local scope
Removed some unused variables and renamed confusing increment variables
Change-Id: I4a8def5621e133d48dc3dfb82efa916cbffabce6
Kevin Boyd [Fri, 5 Jul 2019 00:30:34 +0000 (20:30 -0400)]
Add implicit conversion of mdspan-containing types to mdspan.
Analagous to arrayRef function args taking vectors, arrays as input
Change-Id: I701f6373592cdf4d30649041ffe8dee76423433b
M. Eric Irrgang [Wed, 26 Jun 2019 18:25:20 +0000 (21:25 +0300)]
gmxapi Python package documentation layout.
Refs #2698
Change-Id: Id7fb8c6c91640660566394c37e63b5acb8bd9e3d
Pascal Merz [Tue, 2 Jul 2019 03:06:48 +0000 (21:06 -0600)]
Added trivial const qualifier to relax_shell_flexcon()
Change-Id: Id9e93c1254634e45fd0ef4f951a74670deae8607
Pascal Merz [Tue, 25 Jun 2019 19:34:44 +0000 (13:34 -0600)]
Const qualifier for forces in update_coords
Reflect the fact that forces are not changed in the coordinate
update routines.
Change-Id: I3c168bf185c6bb746c07d2bb10ff0bf6782c05cf
M. Eric Irrgang [Tue, 4 Jun 2019 21:12:58 +0000 (16:12 -0500)]
Incorporate sample_restraint repository.
This commit transfers development of the sample MD plug-in
code from an external repository to the GROMACS repository.
It should not be considered to add or change functionality,
but serves as a base for future integrated development.
The sample_restraint subtree serves as the root of a
template repository that a researcher could start from
to develop gmxapi MD extension code. It is meant to be
self-contained and built against an existing GROMACS
installation. Moving it to a GROMACS repo subdirectory
makes it less accessible to extension developers, but
easier to test and maintain for GROMACS developers. Near
term follow-up should include the creation of an external
skeleton repository, downstream subtree repository, or
"cookie cutter" repository drawing core content from the
GROMACS subtree.
* Import project from GitHub
- https://github.com/kassonlab/sample_restraint/releases/tag/v0.0.7.3
- Bundled sources for external projects are omitted.
- Bundled test data files are omitted.
* Updates for compatibility with the gmxapi Python package are deferred
to future changes.
Refs #3027
Change-Id: I1033a4a74dbce1bf1f9220a31cc9c15055c5dbaf
M. Eric Irrgang [Thu, 23 May 2019 21:44:00 +0000 (16:44 -0500)]
Begin CMake front-end for Python packaging machinery.
Allow gmxapi Python package sources to be discovered in the main GROMACS
CMake configuration step. During build, a functioning package will
appear in the build tree in
${CMAKE_BINARY_DIR}/python_packaging/src/gmxapi_staging that can be used
for tests and auto-generated documentation builds.
A Python 'sdist' can be built from this location in the build tree, or
the package can be built and installed directly from the source tree
with setup.py in python_packaging/src/
Refs: #2896
Change-Id: I225dd890c93405880ef057465eb7c159cd097665
Paul Bauer [Mon, 8 Jul 2019 09:20:13 +0000 (11:20 +0200)]
Fix postsubmit
Fix unstable post submit matrix by removing unused member functions in
constraint tests.
Change-Id: I156e8b1e6b1689afaa4269e2e4bb505768eea5c9
Szilárd Páll [Fri, 5 Jul 2019 21:09:36 +0000 (23:09 +0200)]
Eliminate a use of double precision in the GPU bonded kernels
The usual degree-to-radian conversion macro pulled in a double
literal.
Change-Id: I0d401427a2649e02dd81f603bf12979d7b15c583
Berk Hess [Thu, 14 Mar 2019 15:20:22 +0000 (16:20 +0100)]
Store nbnxm gridSet data in GridSetData
Change-Id: Ib018c59de965195c3093a0092eb711ff3d1ef41b
Mark Abraham [Sat, 6 Jul 2019 19:06:33 +0000 (21:06 +0200)]
Fix hwloc and sphinx detection
These were too noisy and were not implemented efficiently (e.g. not
caching the result of execute process). If an environment change is
needed to detect something (like loading a module) then we expect
developers to be able to unset a cache variable (or just regenerate a
new cache).
Refs #3024, #3011, #2998
Change-Id: I84dfb03856b9f900fb21004bc676e4ff2647a4b4
Mark Abraham [Tue, 2 Jul 2019 22:12:28 +0000 (00:12 +0200)]
Test specific hwloc versions
Now that releng understands the installed hwloc versions, we can
specify those in the matrix configurations. We can also specify that a
test configuration requires hwloc, but don't have to specify the
version. And we can leave it auto and provide a specific version of
the library to get detected automatically.
Refs #2899
Change-Id: I7f72b79746e77d04d9e2657b75821a8e3d62d83b
Kevin Boyd [Thu, 4 Jul 2019 22:17:27 +0000 (18:17 -0400)]
Change error message when attempting to offload to nonexistent GPUs
A user could interpret the error as no interactions detected rather
than no GPUs
Change-Id: Iedcc4555313edbb84a504bf01afc99c15eb4fdcb
Berk Hess [Mon, 24 Jun 2019 20:03:55 +0000 (22:03 +0200)]
Change affinity enum to enum class
Change-Id: I6accea15d82d2e2e911ce1e6f0735b7859b25021
Artem Zhmurov [Fri, 17 May 2019 14:08:24 +0000 (16:08 +0200)]
Remove PImpl scaffolding from CUDA version of LINCS
The CUDA implementation of LINCS was initially introduced as a
stand-alone feature. This required hiding CUDA-specific variables
and subroutines into the private implementation subclass. Since the
LINCS is not a part of Update and Constraints module, this is no
longer required and can be removed.
Refs #2816, #2888
Change-Id: I9698224d4702dfb8d99106999335c62e83a511df
Mark Abraham [Wed, 29 May 2019 13:37:21 +0000 (15:37 +0200)]
Improve tests of index block construction
Only trivial topologies were tested, and bugs have been
identified. Some test code is commented out until the fix lands.
Added missing Doxygen
Improved some assertions hit while investigating the issue.
Refs #2951
Change-Id: Ia03e38aca42be43efa1fd548c32e522d97e13e94
Mark Abraham [Wed, 3 Jul 2019 10:53:16 +0000 (12:53 +0200)]
Modernize FindHwloc.cmake
Users (and Jenkins) need the ability to direct finding a particular
hwloc version, e.g. from a module. This is particularly important now
that two API versions exist and are supported in GROMACS. Imported the
find module from Inria, which adds several useful capababilities,
including the ability to specify where to look for a specific version
of this library.
Removed the pkgconfig support from the imported FindHwloc.cmake
because it seems the hwloc.pc file from libhwloc does not lead to the
CMake idiomatic behaviour of HWLOC_LIBRARIES being the full path to
the library.
Refs #2539, #3011
Change-Id: I6837144a556f1c61a0f13406fb31fe1d527b65f4
M. Eric Irrgang [Thu, 23 May 2019 21:44:00 +0000 (16:44 -0500)]
Python bindings for mdrun.
This change makes a near-exact copy of the mdrun Python
bindings from gmxapi 0.0.7.
Reference https://github.com/kassonlab/gmxapi/releases/tag/v0.0.7.3
This establishes a base from which to transition Python bindings
development from GitHub to the GROMACS repository, so Python wrappers,
interface updates, and other changes are deferred to separate commits.
The provided interface largely opaque except for arguments passed the
same way as mdrun command line flags.
GROMACS must be built with GMXAPI=ON.
Fixes #2912
Change-Id: I2f51ae8f2369334d06a7ceaa8a4abf3ed9fc444a
Mark Abraham [Thu, 4 Jul 2019 08:58:38 +0000 (10:58 +0200)]
Further clang-tidy-7 fix
Change-Id: Ic2915148e6822f10fec6288f29aee55cddacf0f7
Szilárd Páll [Wed, 3 Jul 2019 12:33:24 +0000 (14:33 +0200)]
Bump latest CUDA + gcc in the pre-submit matrix
CUDA 10.1 and gcc 8 is the latest combination supported.
Change-Id: I4c7a5cc7817de1120e1d4d60783f00db70fb6e70
Szilárd Páll [Thu, 4 Jul 2019 10:01:19 +0000 (12:01 +0200)]
Fix a -Wformat-truncation warning in tng
Change-Id: Ib0cc008ad50957dededc857adf6bf921f98118b5
Artem Zhmurov [Thu, 27 Jun 2019 11:35:07 +0000 (13:35 +0200)]
Use reallocateDeviceBuffer(...) in CUDA version of SETTLE
Refs #2886 and #2888
Change-Id: Ia45254a24eda8e6ad151b1f4c6583b1a2c926004
Mark Abraham [Tue, 2 Jul 2019 21:24:18 +0000 (23:24 +0200)]
Fix clang-tidy-7 issues
These are detected on the mac build agent, but weren't on a Linux one,
e.g. because there is a system xdr library found on Linux.
Refs #2899
Change-Id: I591fda21c718b3a76f1fe17962150421f85fce22
Magnus Lundborg [Wed, 19 Jun 2019 11:28:42 +0000 (13:28 +0200)]
Vectorize GPU bonded data.
Loads data for bonds, angles, UB angles and pairs in blocks
of 3, 4, 4 and 3 ints respectively.
Refs: #2983
Change-Id: I37605395bd0c375b2eb4b94e76f9b30f6cb15e8d
Artem Zhmurov [Fri, 28 Jun 2019 14:52:17 +0000 (16:52 +0200)]
Early exit for CUDA versions of SETTLE and LINCS
Change-Id: Ia3c56a1be6b8ceaa8e1b7be956c1f1f3628c9139
Artem Zhmurov [Thu, 27 Jun 2019 10:04:23 +0000 (12:04 +0200)]
Memory management fixes in CUDA version of LINCS
This fix is to prepare LINCS to run with DD.
1. The masses array size depends on the current number of atoms
rather than on the number of constraints.
2. The size of other arrays should be based on the number of
threads launched on the GPU, which include padding added to
align coupled constraints with the thread blocks. Also
renamed variable according to conventions.
Refs #2885 and #2888
Change-Id: I20cb53ebc6da6a1ff2ee1e385613b27c4a01d11f
Mark Abraham [Tue, 2 Jul 2019 21:39:11 +0000 (23:39 +0200)]
Reorder options
If these are in alphabetical order, inserting new ones is less likely
to clash than if we always insert at the end of the list.
Change-Id: I3262959dc02deeaa628874028b10b9948f177842
Artem Zhmurov [Fri, 22 Mar 2019 15:47:54 +0000 (16:47 +0100)]
Combine CUDA Leap-Frog, LINCS and SETTLE. II.
Stand-alone CUDA implementations of Leap-Frog, LINCS
and SETTLE required additional scaffolding for integration
and testing. The most prominent part of this is the
management of coordinates, velocities and forces, which
is removed in this commit. Management of periodic boundary
conditions and virial reduction will be removed in
following commits.
Refs #2816, #2888
Change-Id: I4c65a6c7088fd8059f4e7fa3cb4637cb2af79ebc
Kevin Boyd [Tue, 2 Jul 2019 02:45:11 +0000 (22:45 -0400)]
Updates to math/vec.h
Removed unused functions
Added some file-level documentation indicating that the file
is deprecated and will be replaced in future
Change-Id: I2d6045884a4e14fa4278ef7a0606ccfbe2db7b63
Kevin Boyd [Fri, 18 Jan 2019 14:11:47 +0000 (09:11 -0500)]
Move more tools out of gmxana
Moved some files to simulationdatabase and updated references to them
refs #2727
Change-Id: Idf8375b672fbb6e4676fa22b9eb9c33d1b347166
M. Eric Irrgang [Thu, 16 May 2019 11:51:24 +0000 (14:51 +0300)]
Python detection consolidation.
* Move Python discovery up one level to the project root.
* Remove a TODO and clean up comments for validation test.
* Allow Sphinx discovery to appear in CMake output on first config.
Refs #2998
Change-Id: I16a406b2f21c517042729f3d970e0b5a79d40f33
M. Eric Irrgang [Wed, 19 Jun 2019 17:43:37 +0000 (20:43 +0300)]
Rearrange some definitions.
Reduce diff noise in related changes.
Change-Id: Ia1e30507918a3d2ecea7cc6d63b60312576077e9
Berk Hess [Mon, 24 Jun 2019 14:19:12 +0000 (16:19 +0200)]
Refactor thread affinity checking
Extracted the function detectDefaultAffinityMask() from
gmx_check_thread_affinity_set(). Now the affinity query check and
CPU count results are also reduced over MPI, so we avoid potential
deadlocks when results differ between ranks.
Change-Id: Ib382f47d63695357f8517b2657c3eb414e5afeef
Berk Hess [Mon, 24 Jun 2019 13:57:50 +0000 (15:57 +0200)]
Re-enable affinity diagonostics with MPI
Without thread-MPI, printing diagnostics of detected external
affinity settings when requesting affinities through GROMACS
got lost during refactoring. Now this is enabled again, which
also unifies code paths with and without thread-MPI.
Change-Id: I7a7e43ac4dc45713bda72d62b877d0c7108f1df7
Kevin Boyd [Tue, 18 Jun 2019 01:27:30 +0000 (21:27 -0400)]
Add mdspan basic elementwise math
BasicMatrix3x3 provides a replacement for the c-style tensors, but
has yet to replicate the tensor operations in math/vec.h. This provides
a subset of that functionality for msdpan in general, which can be used
for MultiDimArray trivially
Refs #2976
Change-Id: I17b77df032dbbfde0ff87108215edcec07fef6c4
M. Eric Irrgang [Wed, 26 Jun 2019 13:55:16 +0000 (16:55 +0300)]
Update gmxapi test fixtures.
* Rename spc216 to spc_water_box to be more clear and correct. Actual
solvent number depends on the results of 'solvate'.
* Improve error messaging (fix typo).
* Fix error in mdp parameter writing (surprised this didn't cause an
error previously...)
* Make spc_water_box fixture and other facilities from unit tests
available to integration tests.
* Use 2 instead of 1000 nsteps in test fixture TPR
Change-Id: I62eadeb5133d88ee11082755b1c33ae047d8f4dd
Kevin Boyd [Fri, 21 Jun 2019 01:25:42 +0000 (21:25 -0400)]
Add function for calculating 3x3 matrix determinant
C++ matrix compatible version of the det() function in math/vec.h
Change-Id: Iaa2749dc8059fb6c3c112c4798f8e8cc8eae993c
Kevin Boyd [Thu, 17 Jan 2019 03:54:11 +0000 (22:54 -0500)]
Remove references to ecutsGROUP
Changed warning that group scheme was deprecated to fatal error that
group scheme no longer exists
Modified warning when no cutoff scheme is specified
Change-Id: If971f88003af46c9ccedb98bb2d33987848509ed
Pascal Merz [Mon, 24 Jun 2019 22:37:35 +0000 (16:37 -0600)]
Fix module detection for physical validation
In I2edbe213, an implicit include() command was deleted, leading to
the module detection for physical validation not working anymore.
This change fixes the problem.
Refs #2615
Change-Id: If865227c2050f5739cd855261f6229f902fa0346
Szilárd Páll [Thu, 27 Jun 2019 17:53:08 +0000 (19:53 +0200)]
Refactor tracking of GPU short-range work/skipping
This change introduces a set of flags that, for each interaction
locality, whether there are short-range interactions computed and
exposes a query in the nonbonded module's API.
This allows consistent checks for both when work has been done
and whether results need to be reduced.
Refs #2986
Change-Id: I15020d83f73a132d9b8e93d7339529176396089a
Alan Gray [Wed, 12 Jun 2019 15:03:27 +0000 (08:03 -0700)]
Bug fix and simplification for CUDA X Buffer Ops
Fixes bug when there are more than two grids (ie they don't naively
map to local/nonlocal), by using a separate GPU memory space for
cxy_na and cxy_ind data for each grid (it previously only had one
local and one nonlocal space with overwriting). Also simpifies by now
only calling init fn once per NS step to set up data for all grids
(previously called for both local and nonlocal).
Change-Id: Ia2b97d22324aa97dca34b05da2eca2e2090372af
Berk Hess [Mon, 24 Jun 2019 09:50:35 +0000 (11:50 +0200)]
Fix MPI deadlock in affinity setting
Commit
96d28d6b introduced the possiblity for deadlocks when
the affinity masks changed over time.
Fixes #2989
Change-Id: I454b38deb9ff11c90cdf4a19aaa80e79e8898df5
Berk Hess [Wed, 19 Jun 2019 10:44:51 +0000 (12:44 +0200)]
Template free-energy kernel on differing coul/vdw soft-core
The power function used for the soft-core potential is expensive.
When using the same lambda and alpha parameters for Coulomb and VdW,
we can skip one power core, giving a 10% performance improvement.
Change-Id: I8733838c6c32ef2b6fee5a6fb97657679f9bd3b3
M. Eric Irrgang [Sat, 29 Jun 2019 06:08:43 +0000 (09:08 +0300)]
gmxapi Python package documentation infrastructure.
* Begin a documentation tree in python_packaging/documentation.
* Create a docker image for quick rebuild and review of Sphinx docs.
Refs #2698
Change-Id: Ib05e0309e60bfdadf52dadc7af0942c25c89f1e4
Szilárd Páll [Thu, 27 Jun 2019 15:26:50 +0000 (17:26 +0200)]
Create dedicated subcounter for nonbonded FEP
Now all nonbonded work has their own separate subcoutners which allows
measuring the performance of each task separately.
Refs #2997
Change-Id: I601445364592923d08087a858da4629b0b58ae76
Kevin Boyd [Sat, 12 Jan 2019 14:47:54 +0000 (09:47 -0500)]
Remove group scheme checks from runner
refs #1852
Change-Id: I906ffc7c063694fbbd17128ee0d1e62259040306
Magnus Lundborg [Tue, 18 Jun 2019 12:22:10 +0000 (14:22 +0200)]
Cleaning up the GPU bonded kernel
Improved variable names
Removed unnecessary includes
Refs #2988
Change-Id: Ife5f50e68f27994203305e376f2781a076052b64
Szilárd Páll [Mon, 13 Nov 2017 22:54:21 +0000 (23:54 +0100)]
Separate CPU NB kernel and buffer clearing subcounters
This is aimed to allow comparing the performance of the pair-interaction
kernels separately from the force buffer clearing.
Change-Id: Ifb2b4b3e5a43ac2ee547da651f9432a22fe58421
Christian Blau [Wed, 19 Jun 2019 11:35:18 +0000 (13:35 +0200)]
Add copy and move operations to density similarity
Enable copying and moving for DensitySimilarityMeasure.
Change-Id: Ie4250f67ae42b5cea227b7c17b0a932b04a42a63
Magnus Lundborg [Thu, 23 May 2019 14:39:50 +0000 (16:39 +0200)]
Fused GPU bonded kernels
To reduce the GPU kernel launch times the
GPU bonded kernels have been fused to a single kernel.
Refs #2818
Change-Id: I2299e1857df5db469739e3aefbc0f771968a6bd5
Christian Blau [Fri, 31 May 2019 06:30:39 +0000 (08:30 +0200)]
Add class to look up density fitting amplitudes
Adds a look-up for the weight used for spreading atoms on a grid and
calculate forces on them.
refs #2282
Change-Id: Iadd26f04265aa85ad30a827c92f2c5d5fc48ef85
Szilárd Páll [Thu, 27 Jun 2019 12:35:53 +0000 (14:35 +0200)]
Remove already resolved post-submit matrix TODO
Change-Id: I4b4f8c81376ac36c141e27fd6a3301f550968d1a
Kevin Boyd [Thu, 27 Jun 2019 01:57:48 +0000 (21:57 -0400)]
Use random water removal in gmx solvate
Given a number of solvent molecules to remove, gmx solvate
previously used a striding selection. This patch addresses a
TODO to use random selection
Change-Id: Icb065d61349a55b816337fa49470050eac194aa9
M. Eric Irrgang [Mon, 24 Jun 2019 10:11:15 +0000 (13:11 +0300)]
Add helpful note about gmxpai docker notebook server.
Per Joe's comment on https://gerrit.gromacs.org/c/gromacs/+/11502, it
was not clear where the notebook files live or how they may / may not
change. An extra snippet in the README.md may be helpful.
Change-Id: Ifd7b68ebf58fb3f2c3bed50f3267980358ffc047
Berk Hess [Wed, 26 Jun 2019 15:44:21 +0000 (17:44 +0200)]
Remove tabulation from free-energy kernel
The recent group scheme removal cleanup forgot to remove the cubic
spline tabulated Coulomb and VdW interaction. This is done now.
Also removed the switches in the inner loops, as now there are only
two types of Coulomb and LJ interaction functional forms left.
Change-Id: Ia4aa8917077a3e48c7f1f055f171698a4fede8d0
Szilárd Páll [Thu, 20 Jun 2019 17:18:23 +0000 (19:18 +0200)]
Only use AVX512 in own-FFTW if GROMACS also uses it
Building the own FFTW with AVX512 enabled for all AVX-flavors means that
an AVX2 build can end up loosing a significant amount of performance due
to clock throttle if the FFTW auto-tuner inadvertently picks and AVX512
kernel. This is not unlikely as measurements at startup are very noisy
and often lead to inconsistent kernel choice (observed in practice).
Change-Id: I857326a13a7c4dd1a6f5ab44360211301b05d3ac
Pascal Merz [Wed, 12 Jun 2019 17:22:12 +0000 (11:22 -0600)]
Make global topology constant in trajectory writing
Added a few trivial const qualifiers to make the global topology
const in the call to do_md_trajectory_writing(...).
Change-Id: Id9a501a37bafb4ac25ef6157429d6fb5cb1ff098
M. Eric Irrgang [Wed, 12 Jun 2019 10:47:28 +0000 (13:47 +0300)]
Add a docker layer with a jupyter notebook server.
Provide a docker image based on the gmxapi/ci-mpich image that runs a
Jupyter notebook server for easier browsing of the gmxapi Python package
artifacts.
Change-Id: I245bccb0522bd7c1e4e7467e10e2e91f09976f25
Paul Bauer [Wed, 5 Jun 2019 13:18:34 +0000 (15:18 +0200)]
Use ISerializer for TPR file IO
Change all the function calls in do_tpx and friends to use the
ISerializer instead of the previous t_fileio pointer.
This is intended to prepare for the change where the datastructures
get populated from a byte buffer instead of reading them from disk one
by one.
Refs #2971
Change-Id: I9c2d51c4af0cad5a14da7026d58ecbe053e8efb7
Christian Blau [Fri, 31 May 2019 06:25:03 +0000 (08:25 +0200)]
Add coordinate scaling class and extend TranslateAndScale
- Make TranslateAndScale copyable and movable.
- Make coordinate transformation application const on the
TranslateAndScale object itself
- Add a function that returns the scale operation only without translation.
- Add a coordinate scaling class that also allows to inverse the scaling, ignoring zero input.
refs #2282
Change-Id: I73f9bd892f1f81692e05ac6b2fece2e7be9e8e69
Christian Blau [Fri, 31 May 2019 06:19:52 +0000 (08:19 +0200)]
Allow non-uniform Gaussians
For three-dimensional Gaussian spreading, as well as density guided force
evaluation, allow spreading with different widths along x, y, and z-direction.
This required to account for the common, slightly non-uniform grid
spacing in input densities.
Added some simplifactions for the vector operations based on newly
implemented functions in for BasicVector in a previous patch.
refs #2282
Change-Id: I730897fe672d2444a04ea68fea83e2273b359b27
Berk Hess [Wed, 19 Jun 2019 07:46:19 +0000 (09:46 +0200)]
Remove unnecessary #if GMX_MPI in pme code
Change-Id: I1c645c84b229258527d4c40edb055a706189c2bf
Berk Hess [Wed, 19 Jun 2019 09:33:05 +0000 (11:33 +0200)]
Template free-energy kernel on soft-core
Templated the free-energy kernel on the presence of soft-core
and the soft-core r-power.
Not doing the soft-core math when not using soft-core doubles
the speed of the free-energy kernel.
Templating for the soft-core power gives 15% performance improvement
with soft-core power 6.
Double precision r variables are only needed with r-power 48.
Change-Id: I5a37307b2a83304a40343a0708afce46f4bdcf75
Christian Blau [Wed, 19 Jun 2019 13:00:12 +0000 (15:00 +0200)]
Add BasicVector scaling, max, min and toIvec
Allows element-wise multiplication, maximum, minimum evaluation
as well as conversion to IVec.
Change-Id: I49ba61aff72b197dbe3a67a9516ae0924d28c786
Berk Hess [Wed, 15 May 2019 11:04:44 +0000 (13:04 +0200)]
Refactor PME atom handling
Converted pme_atomcomm_t to PmeAtomComm class.
The PME atom count on CPU without separate PME ranks is now set by
gmx_pme_reinit_atoms(), as for PME on GPU.
Made all coordinates in PME const and use arrayref where possible.
Change-Id: Iaeb59f8cee910e4c52f2f59016af85662b2109fb
Paul Bauer [Tue, 11 Jun 2019 09:20:28 +0000 (11:20 +0200)]
Split tpr header reading reading from tpr body
Split the low level functions for TPR file header and file body reading
into fully separate parts to allow reading the main part of the file
without having to read the header again.
Also gave the header datastructure a new name in line with naming
conventions and default initialized all fields.
Refs #2971
Change-Id: I110fb80cf19d9d2e59df1576e50c64806f532e00
Berk Hess [Wed, 19 Jun 2019 08:29:55 +0000 (10:29 +0200)]
Removed unused code paths in the NB FE kernel
Code paths that were only used with the group scheme were removed.
Change-Id: I27175abfad5da9948f0626af90d16e7801eaf19d
M. Eric Irrgang [Tue, 2 Apr 2019 16:41:50 +0000 (19:41 +0300)]
Updates to gmxapi docker entry points.
* Read GMXRC in gmxapi docker test environment. Allows `gmx` binary to
be easily discovered by Python wrappers. Supports expected behavior
for gmxapi/ci-... docker containers and ensures that GROMACS
components available during image build are available when running.
* Allow more granular testing. Rename and reorganize entry points for
the docker test containers.
Ref: #2756
Change-Id: I5e781fae4709e4ccb718a8295c3fbe68dd59de44
Paul Bauer [Wed, 12 Jun 2019 09:39:33 +0000 (11:39 +0200)]
Fix gmx dump
The program would fail because the filename for writing the output mdp
file was passed as valid empty string that could not be opened as an
output file.
Now only passes the string when it is not empty.
Added test and fixed possible floating point exception found by the
test.
Change-Id: I8b18fbc0dfc5642399935f32fb0b1999fad44c98
Mark Abraham [Mon, 20 May 2019 08:28:28 +0000 (10:28 +0200)]
Move code handling mdrun -gpu_id to taskassignment module
Also made the error message report all incompatible GPU IDs, not just
the first, and do so by throwing an exception.
Change-Id: I4e1f26a59903077b5ab6cc671486fb059cb78964
Berk Hess [Tue, 18 Jun 2019 08:28:19 +0000 (10:28 +0200)]
Make forcerec const in dispatchNonbondedKernel()
Changed forcrecin Nbnxm::dispatchNonbondedKernel() from a pointer
to a const reference. The GPU emulation kernel now writes the shift
forces to nbnxn_atomdata_t.
Change-Id: I170165529ba447db9b5d1824eea10675ae1bef7d
Christian Blau [Fri, 3 May 2019 10:21:32 +0000 (12:21 +0200)]
Mrc format header to lattice coordinate transform
Extracts a coordinate transformation into lattice coordinates from the mrc density
header, as well as the three dimensional grid extents.
refs #2282
Change-Id: I8c01a370e3010add29b8810e2f3320b9ab428c02
Christian Blau [Wed, 17 Apr 2019 11:43:52 +0000 (13:43 +0200)]
Density similarity measure and gradient
Adding a class that allows evaluating the similarity of three dimensional
densities and their gradient given a comparison method, along with a
concrete implementation of the inner-product as a comparison method.
refs #2282
Change-Id: Id73f237e123bed14241227b84cbf83970a09ff49
Paul Bauer [Mon, 10 Jun 2019 07:54:06 +0000 (09:54 +0200)]
Extend ISerializer functionality
Add datatypes to ISerializer that are needed to read TPR files but were
missing.
Refs #2971
Change-Id: I5d5e7f1f91c533a079cb287b018fa1d579c4f3f9
Artem Zhmurov [Mon, 18 Mar 2019 18:03:59 +0000 (19:03 +0100)]
Combine CUDA Leap-Frog, LINCS and SETTLE. I.
This is the first step in combining constraints and integrator
into "UpdateAndConstraints" module. The initial merge does not
imply any performance optimisation or code clean-up. Hence, this
patch keeps all the temporary infrastructure that was built
around SETTLE, LINCS and Leap-Frog to allow them to function as
a separate units. In the following commits, this infrastructure
will be removed and these three implementations will be more closely
integrated. To enable, set GMX_UPDATE_CONSTRAIN_GPU environment
variable. Note, that environment variables GMX_LINCS_GPU,
GMX_SETTLE_GPU and GMX_INTEGRATE_GPU will no longer work.
Refs #2816, #2888
Change-Id: I8730aad0ecaa0230686fe89d1157b0da2f01f7bc
M. Eric Irrgang [Wed, 12 Jun 2019 10:40:07 +0000 (13:40 +0300)]
Reduce docker image size for gmxapi CI.
Use ``--no-cache-dir`` option to ``pip install``.
Change-Id: I4c1794cc020096c3cee377ff2d79c6c599542bc1
Artem Zhmurov [Thu, 16 May 2019 08:06:06 +0000 (10:06 +0200)]
Bug fix: Constraints tests are not instantiated with CUDA
If the tests initialization macros is called with ValuesIn
function, the container provided should be filled. In the
current version, it is filled in the test SetUp function,
after the macros is processed. As a result, the empty
container is used in instantiation and no test are run.
Only CUDA-enabled builds are affected.
Change-Id: Ia2f38c9908d4b7d4277d282c01781b278eeeead0
Berk Hess [Fri, 7 Jun 2019 07:37:25 +0000 (09:37 +0200)]
Simplify GPU nbnxm x conversion
The GPU nbnxm x conversion change
42b343b9 lead to data being transferred
multiple times and introduced several ugly hacks. This change simplifies
the code and transfers each coordinate only once.
Change-Id: I430496251ae40ee4c604e3920b789b3ae2b297dd
Berk Hess [Mon, 17 Jun 2019 07:54:26 +0000 (09:54 +0200)]
Remove unused nbnxm include files
Change-Id: I04ca522139dfa7f1b809a2db9dd494ed9f0f0b23
Mark Abraham [Wed, 12 Jun 2019 15:39:08 +0000 (17:39 +0200)]
Fix pygments detection for sphinx for docs build
Got broken in
29616660 but somehow wasn't a problem in the docs build
on the dedicated slave for that.
Refs #2615
Change-Id: I407383bd0342decae56e4c60202ffbf190e8bb1b
Mark Abraham [Tue, 21 May 2019 20:59:26 +0000 (22:59 +0200)]
Use RAII approaches for hardware information detection
Eliminated gmx_hardware_info_free. The lifetime of the hardware info
should be from the first time it is needed until the end of the
process, and in particular its ownership should not be related to the
lifetime of any threads implementing mdrun.
The implementation of gmx_detect_hardware now uses a simple mutex and
file static smart pointer to hold the data, lazily create it, and leave
it to process cleanup to call the destructor to free resources. Helper
functions no longer refer to the static smart pointer directly.
Internal data structures of gmx_hw_info_t are now held by smart pointer rather
than needing manual memory cleanup.
Extended not_null to be able to be created from smart pointers, and
tested the new behaviours.
Reduced the header dependencies of detecthardware.cpp, now that it
doesn't do all the string handling of printhardware.cpp
Change-Id: I9d5cd838dc6e214163cf2e3104e0f7aaa356fcf8
Mark Abraham [Sun, 26 May 2019 22:00:46 +0000 (00:00 +0200)]
Clean up multisim, communication, and REMD code
Moved multisim declarations and code to one place.
Moved mpi_in_place_buf_t to its own files in a low-level module, and
made sure we tested a build that needed it. Removed duplicate tng
option declaration while I was there.
Moved a check for REMD to its code, removed another that was redundant
with that for multisim requiring more than one simulation.
Added some t_commrec and gmx_multisim_t cleanup code, but not all
of it can work before some more cleanup takes place.
Change-Id: Ie591f50a2162dce2e83552102f8633c8d49553a7
Erik Lindahl [Sun, 9 Jun 2019 11:51:36 +0000 (13:51 +0200)]
More quotes
Having to prepare slides for a Gromacs workshop is
a great motivation for procrastination in the form
of adding more quotes :-)
Change-Id: Ieed151881f5eecdc552726f8d95541a2ab9b5eb7
Szilárd Páll [Mon, 29 Apr 2019 10:02:32 +0000 (12:02 +0200)]
Template x buffer ops call on whether GPU is used
This allows the code to get optimized to avoid the overhead of merged
CPU and GPU codepaths.
Change-Id: If98c5eff327f5f9ecb81f278ca27b6d139bc19ab
Pascal Merz [Mon, 27 May 2019 04:42:47 +0000 (22:42 -0600)]
Clean up renamed simulator.h file
This change is a follow-up to I9bc31588, in which the Integrator class
was renamed to Simulator, and integrator.{h,cpp} was accordingly
renamed to simulator.{h,cpp}. The former change did, however, miss
the include guard, a typedef, and two mentions of "integrator" in
comments. The current change addresses this.
Change-Id: I14d55eeb35c18f198d4123a7132fbee2366713df