Andrey Alekseenko [Wed, 9 Jun 2021 16:05:57 +0000 (16:05 +0000)]
Bump hipSYCL version in the CI container
Artem Zhmurov [Wed, 9 Jun 2021 13:26:45 +0000 (16:26 +0300)]
Use [..] instead of at(..) in LINCS GPU data management code
The .at(..) was used to make sure that the indices are within bonds
while the code is not thoroughly tested. Now it can be replaced with
direct access [..] for performance reasons.
Joe Jordan [Wed, 9 Jun 2021 14:04:20 +0000 (14:04 +0000)]
Move nbnxm setup responsibility to its own files and add tests
Artem Zhmurov [Tue, 8 Jun 2021 11:48:22 +0000 (14:48 +0300)]
Compute reference indices in GPU LINCS upon data preparation
The reference indices are used to map into shared memory location.
The start of the block is then subtracted from the index in map
to get the location in shared memory that should be used. This can
be done when the structure is populated to reduce the amount of
computations in the GPU kernel.
Refs #3350
Joe Jordan [Wed, 9 Jun 2021 11:19:25 +0000 (11:19 +0000)]
Expose and test getVdwKernelType
Paul Bauer [Wed, 9 Jun 2021 08:22:49 +0000 (08:22 +0000)]
Add .clang-tidy file for nbnxn tests
Joe Jordan [Wed, 9 Jun 2021 07:56:18 +0000 (07:56 +0000)]
Extend nblib listed pbc holder and template kernels
Pascal Merz [Tue, 8 Jun 2021 16:59:02 +0000 (10:59 -0600)]
Prepare simulated annealing refactoring
Prepare simulated annealing refactoring by moving variable declarations
to where they are first used, rename a non-descriptive integer `i`, use
a const reference to the inputrec where possible, replace a gmx_fatal
by an assert, and replace a switch / case construct by an if / else.
This is pure refactoring, no change in functionality, but will make
follow-up changes significantly easier to review.
Joe Jordan [Tue, 8 Jun 2021 17:36:18 +0000 (17:36 +0000)]
CoulombKernelType enum, lookup function, and tests
Pascal Merz [Tue, 8 Jun 2021 15:31:59 +0000 (15:31 +0000)]
Unify FEP period setting
Szilárd Páll [Tue, 8 Jun 2021 14:40:14 +0000 (14:40 +0000)]
Work around hipSYCL buffer reinterpret error
M. Eric Irrgang [Tue, 8 Jun 2021 11:29:02 +0000 (14:29 +0300)]
Remove gmxapi roadmap.rst and acceptance tests.
This document and the supporting tests are out-of-date and unused for
project planning, as far as I can tell.
Resolves #3706
Andrey Alekseenko [Tue, 8 Jun 2021 12:19:05 +0000 (15:19 +0300)]
Fix clang-tidy complaints
Introduced in
6cd214d6 (MR !1591)
Paul Bauer [Tue, 8 Jun 2021 09:38:34 +0000 (09:38 +0000)]
Allow selection of rocm version to install
Mark Abraham [Mon, 7 Jun 2021 13:35:19 +0000 (15:35 +0200)]
Unite the post-DD-partition update of the local topology
Also simplify and clarify the implementation of doSorting
Removed ilsortFE_UNSORTED now that it is unused
Refs #4004
Mark Abraham [Mon, 7 Jun 2021 23:37:24 +0000 (23:37 +0000)]
Add hasPerturbedChargeIn14Interaction to atomInfo bits
Pascal Merz [Mon, 7 Jun 2021 21:07:27 +0000 (21:07 +0000)]
Introduce Trotter decomposition / MTTK for modular simulator
Paul Bauer [Mon, 7 Jun 2021 19:06:42 +0000 (19:06 +0000)]
Use enum class for checkpoint version
Mark Abraham [Tue, 1 Jun 2021 09:51:58 +0000 (11:51 +0200)]
Make LocalTopologyChecker class and hide implementation details
This allows capturing useful state that is only used when writing the
error output, without leaking dependencies for implementation details
to high-level code.
Some minor improvements to const correctness of the error output. Also
moved it into gmx namespace.
Minor improvement to include order
Removed unused forward declaration in domdec.h
Refs #3887
ejjordan [Mon, 7 Jun 2021 10:39:41 +0000 (12:39 +0200)]
Rename some paramters in nblib listed forces
This is pure refactoring.
HarmonicAngleType -> HarmonicAngle
EquilDistance -> EquilConstant
Mark Abraham [Mon, 7 Jun 2021 12:43:00 +0000 (12:43 +0000)]
Add unit tests for topology sorting
Artem Zhmurov [Mon, 7 Jun 2021 10:53:30 +0000 (13:53 +0300)]
Remove duplicating pointers to device buffers in GPU listed forces
XYZQ, forces and shift forces are saved in both ListedForces class and
in BondedCudaKernelParameters class. This removes the later and
make it so the buffers are passed directly to the kernel.
Alan Gray [Mon, 7 Jun 2021 11:54:56 +0000 (11:54 +0000)]
Push GPU PME-PP force from PME task instead of pull from PP task
Andrey Alekseenko [Mon, 7 Jun 2021 11:22:11 +0000 (11:22 +0000)]
Add SYCL-related information to the mdrun version header
Dmitry Morozov [Mon, 7 Jun 2021 11:00:13 +0000 (11:00 +0000)]
Added EnergyOutputRequestChecker notification for MDModules
Joe Jordan [Mon, 7 Jun 2021 09:16:35 +0000 (09:16 +0000)]
Miscellaneous updates from nblib
Mark Abraham [Mon, 7 Jun 2021 08:57:19 +0000 (08:57 +0000)]
Update to Ubuntu 20.04 in CI
Artem Zhmurov [Mon, 7 Jun 2021 06:51:12 +0000 (09:51 +0300)]
Joe Jordan [Sun, 6 Jun 2021 20:50:28 +0000 (20:50 +0000)]
Updates to nblib test infra and tests
Pascal Merz [Fri, 4 Jun 2021 16:57:54 +0000 (16:57 +0000)]
AWH data structures modular checkpointing
Pascal Merz [Fri, 4 Jun 2021 15:47:20 +0000 (15:47 +0000)]
Pull and AWH exact continuation tests
Mark Abraham [Thu, 3 Jun 2021 08:26:22 +0000 (10:26 +0200)]
Convert atomInfo to int64_t
This ensures we can use bits from a 64-bit range if we ever need
that. Or easily switch to 32-bit range if that's advantageous.
Refs #4004
Szilárd Páll [Fri, 4 Jun 2021 10:15:32 +0000 (10:15 +0000)]
Require CUDA 11.0
Also remove some cmake code that aided support for version <11.0.
Refs #3708
Szilárd Páll [Fri, 4 Jun 2021 06:46:49 +0000 (06:46 +0000)]
Move useMts flag from forcerec to simulationWorkload
Artem Zhmurov [Thu, 3 Jun 2021 20:23:35 +0000 (20:23 +0000)]
Make constraints and SETTLE tests backend-agnostic
Mark Abraham [Thu, 3 Jun 2021 17:35:14 +0000 (17:35 +0000)]
Remove useless charge-group work during repartitioning
Mark Abraham [Thu, 3 Jun 2021 16:03:23 +0000 (16:03 +0000)]
Update tested CUDA versions
Mark Abraham [Thu, 3 Jun 2021 14:58:26 +0000 (14:58 +0000)]
Remove preprocessor usage for atomInfo
Dmitry Morozov [Thu, 3 Jun 2021 14:33:14 +0000 (14:33 +0000)]
Added QM input file name as command-line parameter for grompp
Part of #3172
Szilárd Páll [Thu, 3 Jun 2021 13:26:20 +0000 (15:26 +0200)]
Fix getLocalAtomCount()
Pass dd as pointer to avoid nullptr dereferencing introduced in
ba71b7526c22715aceb36586e76f2ae58c4a2461.
Refs #3915
Berk Hess [Thu, 3 Jun 2021 09:54:55 +0000 (11:54 +0200)]
Minor pull code cleanup
Replaced some pointer by references, removed some unnecessary struct,
converted a loop to range and converted some documentation to doxygen.
Szilárd Páll [Thu, 3 Jun 2021 07:36:24 +0000 (09:36 +0200)]
Add domainWorkload flags for CPU local force contributions
Part of #3913
Pascal Merz [Tue, 17 Nov 2020 01:14:32 +0000 (18:14 -0700)]
Free energy history modular checkpointing
This introduces a function that allows df_history_t objects to save to
and reset from modular simulator checkpoints. This allows elements
owning such an object to easily checkpoint it.
This also introduces a helper function to create CheckpointDataOperation
dependent ArrayRefs from C arrays.
Szilárd Páll [Thu, 3 Jun 2021 08:18:40 +0000 (10:18 +0200)]
Add a getter function for the local atom count
Refs #3915
Pascal Merz [Thu, 3 Jun 2021 01:32:19 +0000 (19:32 -0600)]
Remove unneeded template keyword which trips up MSVC
Solves part 1 of #4065
Andrey Alekseenko [Wed, 2 Jun 2021 09:06:18 +0000 (12:06 +0300)]
SYCL: Update env. vars to select GPUs
SYCL_DEVICE_FILTER is supported in OneAPI releases, so we can safely
recommend it. Also added the ROCm string when compiled with hipSYCL.
Dmitry Morozov [Wed, 2 Jun 2021 09:41:44 +0000 (09:41 +0000)]
Add notifications for MDModules that will be used in QMMM
Mark Abraham [Wed, 2 Jun 2021 06:44:51 +0000 (08:44 +0200)]
Removed GMX_CLANG_CUDA build using old versions
Clarified that a release job was targetting clang as host-only
compiler, ie. not GMX_CLANG_CUDA.
Refs #3708
Andrey Alekseenko [Tue, 1 Jun 2021 14:13:32 +0000 (17:13 +0300)]
Mark a variable as unused in non-MPI build
Eliane Briand [Mon, 31 May 2021 14:46:31 +0000 (16:46 +0200)]
Fix gmx nmr -viol option
Ref #4060
Mark Abraham [Mon, 31 May 2021 15:32:14 +0000 (15:32 +0000)]
Finish breaking up domdec_topology.cpp
ejjordan [Mon, 31 May 2021 09:36:09 +0000 (11:36 +0200)]
Increase const correctness in gmx_pme_send_parameters
Also switched to ArrayRef<const RVec> from pointer in one function
and removed an unused header.
Mark Abraham [Mon, 31 May 2021 10:14:22 +0000 (10:14 +0000)]
Move total bonded count to LocalTopologyChecker
Mark Abraham [Mon, 31 May 2021 09:05:50 +0000 (11:05 +0200)]
Split localtopology from domdec_topology
This is a separable responsibility and can go in its own
translation unit.
Refs #3887
Mark Abraham [Mon, 31 May 2021 08:14:35 +0000 (08:14 +0000)]
Partial renaming of cginfo to atom info
Andrey Alekseenko [Sun, 30 May 2021 15:54:10 +0000 (18:54 +0300)]
Fix one more missing template declaration
Continuation of the work started in
bf9b81c4 (MR !1652)
Pascal Merz [Mon, 31 May 2021 00:10:49 +0000 (18:10 -0600)]
Introduce Andersen temperature coupling for modular simulator
This introduces the `andersen` and `andersen-massive` temperature coupling
for modular simulator. Since reshuffeling the velocities does require a
constraining step, the Andersen temperature coupling uses the composite
element to combine the Andersen element with a constraining element.
Refs #3423, refs #3417
Andrey Alekseenko [Mon, 31 May 2021 06:26:32 +0000 (06:26 +0000)]
Add nightly CI test on OneAPI + Intel GPU
Andrey Alekseenko [Fri, 28 May 2021 22:51:33 +0000 (01:51 +0300)]
Disable false-positive warnings for ICPX 2021.2.0
Not happening in open-source intel/llvm compiler.
While originally it was enough to disable them at include stage, in
2021.2 the warning is issued in the kernel itself, so we had to expand
its usage beyond gmxsycl.h.
Paul Bauer [Fri, 28 May 2021 08:55:23 +0000 (08:55 +0000)]
Fix missing template declaration
Mark Abraham [Fri, 28 May 2021 07:32:08 +0000 (07:32 +0000)]
Compute global bonded interaction count from system topology
Eliane Briand [Fri, 28 May 2021 07:11:10 +0000 (07:11 +0000)]
Reworked convert-tpr runtime extension
Mark Abraham [Thu, 27 May 2021 12:41:24 +0000 (14:41 +0200)]
Remove orphaned code
This should have been removed in
c17939744a88e but somehow it
survived long enough to move location. This should have failed
testing because optional std header is not included here, but
it somehow passed.
Now it is removed
Refs #3887
Mark Abraham [Thu, 27 May 2021 09:48:39 +0000 (09:48 +0000)]
Move reverse topology code to its own translation unit
Artem Zhmurov [Wed, 26 May 2021 11:48:01 +0000 (14:48 +0300)]
Add release notes about REMD with GPU update
REMD is now possible with GPU update, which should be noted in
release notes.
Feature enabled in
29c336cd0a518507c86094b08a447ec388afaad2
Refs #3997
Pascal Merz [Thu, 27 May 2021 08:55:14 +0000 (08:55 +0000)]
Clean up simulator algorithm
Artem Zhmurov [Wed, 26 May 2021 09:05:03 +0000 (12:05 +0300)]
Rename GpuBonded into ListedForcesGpu
The listed forces name describes better what the class is
doing and also follows the naming for other modules.
Paul Bauer [Thu, 27 May 2021 07:41:49 +0000 (09:41 +0200)]
Disable CUDA clang-tidy test
This is failing for some reason and needs proper fixing later.
Mark Abraham [Wed, 5 May 2021 06:53:36 +0000 (08:53 +0200)]
Move the code of what will later implement LocalTopologyChecker
Some common implementation functionality used in making
the reverse topology also needs to be exposed. Otherwise,
this is pure code movement with no functionality changes.
Refs #3887
Dmitry Morozov [Wed, 26 May 2021 15:01:42 +0000 (15:01 +0000)]
Moved PME-only ranks check to domain decomposition setup
Szilárd Páll [Wed, 26 May 2021 14:06:24 +0000 (14:06 +0000)]
Eliminate redundant GPU force reduction event dependency
CPU force transfers happen on the same strem as GPU reduction, so no explicit dependency is needed.
Additionally, due to a StatePropagatorDataGpu bug, whenever the force readiness event queried is not AtomLocality::All, an incorrect event is returned leading to circular dependency on force reduction, as described in #4032.
This change however does not fix the StatePropagatorDataGpu bug, but it should help avoiding workarounds for the new SYCL backend (#3932).
Refs #4032 #3988
Mark Abraham [Wed, 26 May 2021 08:39:19 +0000 (10:39 +0200)]
Fix clang-format
ejjordan [Mon, 24 May 2021 15:38:49 +0000 (17:38 +0200)]
Remove foreign energy groups from gmx_enerdata_t
These members are only used for local storage and can be eliminated.
Added function to zero the energy group pair terms.
This will aid in further refactoring of the nonboded FEP kernels.
Joe Jordan [Wed, 26 May 2021 09:14:47 +0000 (09:14 +0000)]
Move t_forcetable and table enums to forcetable header
Szilárd Páll [Tue, 30 Mar 2021 13:24:08 +0000 (15:24 +0200)]
Implement generic j-reduction in the nbnxm SYCL kernels
This commit implements the generic j-reduction identical to the OpenCL
version of the same.
Also added a subGroupBarrier() helper which is needed for
correctness on the CUDA backend when targetting NVIDIA
architectures.
Refs #3934
Paul Bauer [Wed, 26 May 2021 07:39:06 +0000 (07:39 +0000)]
Fix clang tidy version for CUDA
Pascal Merz [Wed, 26 May 2021 07:05:54 +0000 (07:05 +0000)]
Introduce domain decomposition notifications
Pascal Merz [Fri, 21 May 2021 21:33:37 +0000 (15:33 -0600)]
Split expanded ensemble function
The expanded ensemble function was split into a part chosing a new
lambda state, and a second part updating the reference temperature
in the case of simulated tempering. To leave legacy paths unchanged,
the original function name has been maintained, which calls the two
parts. The function chosing a new lambda state is declared in the
header to allow modular simulator to call it separately.
This is pure refactoring (with the exception of moving a few variable
declarations to their initialization sites). Expanded ensemble is
covered by the new FEP tests.
This prepares introducing the expanded ensemble in modular simulator,
and is a first step towards #3848.
Refs #3417
Joe Jordan [Tue, 25 May 2021 09:41:58 +0000 (09:41 +0000)]
Only Pass needed data to nonbonded param setup in forcerec
Paul Bauer [Fri, 21 May 2021 09:07:07 +0000 (11:07 +0200)]
Add CUDA clang tidy build to CI
Runs test script for pre-submit and full build nightly.
Paul Bauer [Mon, 24 May 2021 12:58:44 +0000 (12:58 +0000)]
Apply clang-tidy-11 fixes to CUDA files
Joe Jordan [Mon, 24 May 2021 12:34:55 +0000 (12:34 +0000)]
Remove dead members from gmx_pme_t
Joe Jordan [Mon, 24 May 2021 11:53:02 +0000 (11:53 +0000)]
Remove forcerec from dispatchFreeEnergyKernel signature
M. Eric Irrgang [Fri, 21 May 2021 15:02:15 +0000 (10:02 -0500)]
Let installed library options default to BUILD_SHARED_LIBS.
Fixes #4053
Mark Abraham [Mon, 24 May 2021 03:58:19 +0000 (05:58 +0200)]
Remove GMX_CONSTRVIR
Simplifies handling of energy output by removing a feature that was
likely useful only during debugging yet incurred function-call
overhead every MD step even when not used.
Resolves previous TODO
Updates tests to no longer check such output while not changing
the numerical output previously written.
Pascal Merz [Tue, 17 Nov 2020 01:19:08 +0000 (18:19 -0700)]
Add a const getter for the enerd struct to EnergyData
This is not currently used, but will allow for more const-correctness
in upcoming changes.
Pascal Merz [Mon, 24 May 2021 04:27:50 +0000 (04:27 +0000)]
Implement Berendsen and c-rescale pressure coupling for modular simulator
Pascal Merz [Tue, 17 Nov 2020 01:13:37 +0000 (18:13 -0700)]
Expose DD distribution of free energy history
To implement expanded ensemble, modular simulator needs to be able
to distribute the free energy history without initiating a full
t_state object. This exposes the required function to make it
available to the expanded ensemble modular simulator element.
Refs #3417, #3419
Pascal Merz [Mon, 7 Sep 2020 16:28:37 +0000 (10:28 -0600)]
Introduce frequency for CompositeSimulatorElement
This adds functionality to run a composite simulator element at a
prescribed frequency. This prepares the introduction of Andersen
thermostatting.
Szilárd Páll [Fri, 21 May 2021 10:16:51 +0000 (10:16 +0000)]
Workaround for a hipSYCL assertion error
Joe Jordan [Thu, 20 May 2021 23:29:01 +0000 (23:29 +0000)]
Localize variables in gmx_pme_do
Alan Gray [Tue, 18 May 2021 14:33:42 +0000 (07:33 -0700)]
Remove GPU update restriction for replica exchange
Ensures that the end-of-step D2H coordinate copy is active for replica
exchange steps, to allow the GPU update restriction to be relaxed.
Artem Zhmurov [Thu, 20 May 2021 14:01:15 +0000 (14:01 +0000)]
Use MessageStringCollector class to construct error messages
Paul Bauer [Thu, 20 May 2021 07:57:58 +0000 (09:57 +0200)]
Disable ArrayRefDeathTests when building without assertions
Would otherwise lead to spurious failures.
ejjordan [Wed, 19 May 2021 16:28:07 +0000 (18:28 +0200)]
Remove inputrec from do_ewald
Also rename some parameters more verbosely and remove a dead code
block.
Joe Jordan [Thu, 20 May 2021 06:25:18 +0000 (06:25 +0000)]
Localize variables in ewald_LRcorrection
Artem Zhmurov [Wed, 19 May 2021 15:46:59 +0000 (18:46 +0300)]
Andrey Alekseenko [Wed, 19 May 2021 16:15:08 +0000 (16:15 +0000)]
Support GPU update without constraints
ejjordan [Mon, 17 May 2021 13:54:03 +0000 (15:54 +0200)]
Make TrotterSequence enum class
A subesquent MR can make an extended Trotter enum class, removing
dependence of coupling and update_vv headers on md_enums header.
Joe Jordan [Wed, 19 May 2021 15:09:16 +0000 (15:09 +0000)]
Clean up some headers in mdlib