Szilárd Páll [Fri, 19 Mar 2021 19:04:42 +0000 (20:04 +0100)]
Remove a misplaced update cycle closing
This was removed in
b80b7a327b1 but got added back later presumably
during a merge.
Refs #3764
Szilárd Páll [Wed, 10 Mar 2021 10:50:47 +0000 (11:50 +0100)]
Rename sendFToPpCudaDirect
sendFSynchronizerToPpCudaDirect expresses what the method actually does.
Artem Zhmurov [Thu, 18 Mar 2021 06:49:18 +0000 (09:49 +0300)]
Move the atomToInteractionLocality(...) into locality.h
The atomToInteractionLocality(...) does not depend on NBNXM
and can naturally reside alongside the definitions of localitiy
enumerations. This allows to combine haveGpuShortRangeWork(...)
functions in NBNXM, avoding confuciton of having two very similar
functions with different signatures.
Andrey Alekseenko [Wed, 10 Mar 2021 11:53:49 +0000 (14:53 +0300)]
Store buffer without offset in GpuForceReduction::Impl::baseForce_
- Store the pointer to the beginning of the array and apply offset to
it when invoking the kernel. Offsets to other arrays are applied at
the invocation time, so it makes sense to do the same with baseForce_.
- This also avoid storing pointers to the middle of the device buffer,
which is not a good fit for OpenCL and SYCL.
This change is preparation for adding a SYCL implementation of GPU
update (Issue #3932).
Artem Zhmurov [Fri, 19 Mar 2021 16:48:38 +0000 (16:48 +0000)]
Unify init_gpu function in NBNXM
Refs. #2608
Andrey Alekseenko [Tue, 16 Mar 2021 10:03:24 +0000 (11:03 +0100)]
Use DeviceBuffer<RVec> in GPU force reduction and PME code
... instead of raw device pointers.
Preparation for #3932. PME change is incidental, the main focus is
GpuForceReduction.
Andrey Alekseenko [Tue, 16 Mar 2021 11:21:51 +0000 (12:21 +0100)]
Enable compiling LeapFrog with hipSYCL
No testing yet. Trivial change after !1268.
Closes #3941.
Paul Bauer [Fri, 19 Mar 2021 11:45:06 +0000 (12:45 +0100)]
Bulk change to const ref for mtop
Change function signatures in mtop_lookup.h and mtop_util.h to be const
ref only for mtop. Also change signatures in other files as I went
along.
This change is only refactoring.
Paul Bauer [Fri, 19 Mar 2021 07:59:47 +0000 (08:59 +0100)]
Make wallcycle comments proper doxygen
Should reduce noise in other refactoring commits.
Berk Hess [Fri, 19 Mar 2021 12:42:49 +0000 (12:42 +0000)]
Remove const cast in update code
Joe Jordan [Fri, 19 Mar 2021 11:45:23 +0000 (11:45 +0000)]
Use more arrayref in listed forces sigatures
Pass members of t_mdatoms directly in many places in listed_forces.
Part of work on making refactor of t_mdatoms easier.
Paul Bauer [Fri, 19 Mar 2021 11:11:49 +0000 (11:11 +0000)]
Remove mdatoms from forceprovider call signature
This makes it possible to test the forceprovider without having to build
a partial mdatoms datastructure first. Needed for future refactoring of
mdatoms.
Joe Jordan [Fri, 19 Mar 2021 10:50:48 +0000 (10:50 +0000)]
Use ArrayRef in ewald_LRcorrection
This will make refactoring t_mdatoms easier. Also changed
signatures of calculateLongRangeNonbondeds to use more
ArrayRef.
Joe Jordan [Fri, 19 Mar 2021 09:54:58 +0000 (09:54 +0000)]
Make non bonded energy terms enum class
Also renamed some of the enum values.
Andrey Alekseenko [Fri, 19 Mar 2021 08:13:39 +0000 (11:13 +0300)]
Fix a warning from CUDA 10.1
Discovered during nightly build:
warning: static_assert with no message is a C++17 extension [-Wc++17-extensions]
ejjordan [Thu, 18 Mar 2021 15:42:02 +0000 (16:42 +0100)]
Use ArrayRef in gmx_pme_send_parameters
This will make refactoring t_mdatoms easier.
ejjordan [Thu, 18 Mar 2021 16:05:02 +0000 (17:05 +0100)]
Use const refs in atoms2md signature
Const refs are now used for mtop and inputrec in atoms2md. Doxygen
is also added and inputrec renamed from ir.
Paul Bauer [Thu, 18 Mar 2021 17:12:34 +0000 (17:12 +0000)]
Add wallcycle counting tests
Basic tests for running main and sub counters, and to check overhead.
Andrey Alekseenko [Thu, 11 Mar 2021 10:48:06 +0000 (13:48 +0300)]
Use DeviceBuffer in GPU update and NBNXM code
... instead of raw device pointers and DeviceBuffer<float3>.
We try to use DeviceBuffer<Float3>, but in some places we have to use
DeviceVector<gmx::RVec>, until we can define FloatN types without
including any backend-specific headers. Currently, Float3 is defined as
gmx::RVec, so this should not cause any issues.
Also added some helper functions to convert RVec ̌<-> Float3 <-> float3.
Preparation for #3932 and #3941.
ejjordan [Wed, 17 Mar 2021 09:31:48 +0000 (10:31 +0100)]
Use ArrayRef<const real> in gmx_pme_do
Also changed some static functions to use ArrayRef. Some local
variables need to be vectors because they use operator[]. This
is part of preliminary work to make refactoring t_mdatoms
easier.
Paul Bauer [Wed, 17 Mar 2021 05:59:56 +0000 (05:59 +0000)]
Fix errors overlooked in gmx msd changes
Made some NOLINT sections more broad.
Fixed documentation.
Joe Jordan [Tue, 16 Mar 2021 18:03:19 +0000 (18:03 +0000)]
Use RVec and std::array in gmx_domdec_comm_t
Where possible, rvecs have been changed to RVecs and pointers
changed to std::arrays.
Kevin Boyd [Tue, 16 Mar 2021 17:28:24 +0000 (17:28 +0000)]
Migrate gmx msd to the trajectoryanalysis framework
Features to still be added
-tensor, for the MSD tensor
-pdb, for per molecule B-factors
-rmcomm, for system COM removal
-mw, for tuning mass-weighting options
-maxtau, for limiting resource usage and unneccessary computation (refs #3870)
-improvements to documentation and maybe some flag behavior changes (refs #3869)
Refs #2368
Artem Zhmurov [Tue, 16 Mar 2021 12:53:21 +0000 (15:53 +0300)]
Unify gpu_init_atomdata(...) function
Refs #2608
Artem Zhmurov [Tue, 16 Mar 2021 13:26:37 +0000 (16:26 +0300)]
Unify gpu_launch_cpyback(...) function in NBNXM
Refs #2608
Joe Jordan [Tue, 16 Mar 2021 11:21:10 +0000 (11:21 +0000)]
Remove conditional assignemnt of cell sizes from domdec partition
The variable cellsizesWithDlb is always initiallized since it is a
std::vector, so there is no reason to set it to nullptr in
domdec/partition.
Artem Zhmurov [Sat, 13 Mar 2021 13:13:14 +0000 (16:13 +0300)]
Unify gpu_init_atomdata(...) function
Refs #2608
Artem Zhmurov [Mon, 15 Mar 2021 16:57:02 +0000 (19:57 +0300)]
Move pmalloc(..)/pfree(...) to separate source files in CUDA/OpenCL/SYCL
Having pmalloc(..) and pfree(..) functions in unrelated files in CUDA,
OpenCL and SYCL makes it hard to use these functions in platform-agnostic
code. This creates common header and moves these functions to separate
source files.
Paul Bauer [Mon, 15 Mar 2021 13:56:18 +0000 (14:56 +0100)]
Add subcycle counting to MPI build
This code path has not been tested in CI and should be added.
Paul Bauer [Mon, 15 Mar 2021 14:59:03 +0000 (14:59 +0000)]
Move M_PI definition to math/units.h
This makes more sense to have the definition there with the other
constants.
Resolves build issues with MSVC not finding M_PI definition.
Needed some minor header fixes.
Paul Bauer [Mon, 15 Mar 2021 10:06:16 +0000 (11:06 +0100)]
Add another cool quote.
Recently seen on Twitter ...
Artem Zhmurov [Mon, 15 Mar 2021 09:12:04 +0000 (12:12 +0300)]
Do not overallocate shiftVec and fshifts buffers in OpenCL
When changing buffers from flat float format to Float3,
the sizes of the shiftVec and fshift buffers were not updated
in OpenCL NBNXM data management, which lead to the buffers being
overallocated. This fixes the issue.
Introduced in
c66827166fc9099ecd1a4a2f7080558df70bf529
Artem Zhmurov [Mon, 15 Mar 2021 10:16:45 +0000 (10:16 +0000)]
Add a cool quote from Elvis Presley's song
Artem Zhmurov [Mon, 15 Mar 2021 09:09:49 +0000 (12:09 +0300)]
Fix clang-format in topio.cpp
Introduced in
0dab36f99294056b33f4ee58383587a82447b9e6
Kevin Boyd [Sun, 14 Mar 2021 19:53:15 +0000 (12:53 -0700)]
Fix leak in cpp_opts
Refs #3984
Szilárd Páll [Fri, 5 Mar 2021 19:29:38 +0000 (20:29 +0100)]
Use existing PME f ready event in PmeForceSenderGpu
Instead of recording internally into the PME stream and sending that
event to the PP rank to sycn on from the separate PME rank, use the
already existing event recorded in PME.
This also eliminates the unnecessary use of multiple events, one for
each PP rank.
Refs #2891 #2915
Szilárd Páll [Sat, 13 Mar 2021 11:05:43 +0000 (11:05 +0000)]
Rename launchReceiveCoordinatesFromPpCudaDirect
The receiveCoordinatesSynchronizerFromPpCudaDirect() method name better
reflects what the code it actually does.
Refs #2891
Paul Bauer [Sat, 13 Mar 2021 08:31:24 +0000 (08:31 +0000)]
Remove cyclic dependency check from check-source
This hasn't been properly checked for a while now and we are planning to
move this to a CMake check anyway.
Andrey Alekseenko [Fri, 12 Mar 2021 15:46:48 +0000 (15:46 +0000)]
Add DeviceAccessor<T,read> ctor from const DeviceBuffer<T>
A bit hacky, but better preserves the intent behind declaring
DeviceBuffer const.
Part of preparatory work for #3932.
Paul Bauer [Fri, 12 Mar 2021 11:44:11 +0000 (11:44 +0000)]
Modernize PME GPU timing enums
Part of general modernization of enums to enum classes.
Used enumerationarray in places where it made sense.
Alan Gray [Fri, 12 Mar 2021 06:52:02 +0000 (06:52 +0000)]
Move responsibility for GPU force clearing to state propagator
Force was previously cleared within GPU force halo exchange which was
quite opaque. Now moved into do_force() and done by state propagator,
to make schedule clearer.
Fixes #3971 and partly addresses #3970
Artem Zhmurov [Thu, 11 Mar 2021 20:04:05 +0000 (20:04 +0000)]
Unify insertNonLocalDependency(...) function in NBNXM
Refs #2608
Szilárd Páll [Thu, 11 Mar 2021 10:54:19 +0000 (10:54 +0000)]
Simplify gmx_pme_send_force_vir_ener()
sendFToPP() provided no benfit, so code is merged back into the caller.
Also removed unused send bufer pointers.
Alan Gray [Thu, 11 Mar 2021 09:26:58 +0000 (09:26 +0000)]
Fix unit test error due to GPU peer access already enabled
Fixes #3980
Artem Zhmurov [Thu, 11 Mar 2021 04:40:32 +0000 (07:40 +0300)]
Fix clang-tidy failures in AWH tests
Commit
d4610e91e7815756f728e68785b58b884aead153 introduced a
clang-tidy warning in AWH tests with integer used in place of
bool argument (modernize-use-bool-literals,-warnings-as-errors).
This removes these warnings.
Andrey Alekseenko [Thu, 11 Mar 2021 05:33:39 +0000 (05:33 +0000)]
Properly check for frozen atoms when disabling GPU update
Follow-up of !1241 (
9550c3e8564068c86a0f34baee0f578e8ce6d5a9)
Initially, the check was overly relaxed, and was triggered even when
there were no frozen atoms.
Thanks to @alangray3 for noticing!
Paul Bauer [Wed, 10 Mar 2021 20:06:31 +0000 (20:06 +0000)]
Make AWH parameters proper C++
All structs have been converted to classes with RAII constructors.
Parameter objects can only be constructed from input data or
serializers.
Tests are adapted to use the new constructors, this means some code got
a bit ugly there.
This change is only refactoring, plus adding tests for the
serialization.
Artem Zhmurov [Wed, 10 Mar 2021 18:34:49 +0000 (18:34 +0000)]
Rename some variables in GPU task assignment and fix their usage
Some variables are oddly named which causes a confusion. This changes
the naming so that it reflects the meaning of the variables. Also,
fixes a miss0use of one of such variables cause by the bad naming.
Fixes #3980
Fixes #3981
Artem Zhmurov [Wed, 10 Mar 2021 09:43:52 +0000 (12:43 +0300)]
Rework atom locality validity checks
The function that checks the validity of atom locality partly
duplicates its callers logic. The chacks are done naturally in
the callers and the function is used to construct and print
an error message.
Andrey Alekseenko [Wed, 10 Mar 2021 10:37:52 +0000 (13:37 +0300)]
Convert PmeGpu->kernelParams->atoms.d_forces to RVec
In most other places, forces are in RVec format, while it was float
here. While it is used as float in gather kernels, it is more consistent
to keep the buffer type as RVec.
This change is preparation for adding a SYCL implementation of GPU
update (Issue #3932).
Joe Jordan [Wed, 10 Mar 2021 12:37:49 +0000 (12:37 +0000)]
Remove param fillLocal, which was always false, from nbnxm call stack
Several functions in nbnxm took a bool to determine whether to fill
local atoms with zeros, but the parameter was always set to false.
This is now removed from the function signatures, and some code is
slightly simplified.
Paul Bauer [Wed, 10 Mar 2021 09:39:18 +0000 (10:39 +0100)]
Change vector references to Arrayref in AWH
Preparation for further refactoring.
Andrey Alekseenko [Wed, 10 Mar 2021 09:06:41 +0000 (09:06 +0000)]
Revert "Wrap more device pointers in DeviceBuffer" (!1244)
This reverts commit
850429f3ebe34d27dabed6d8c31c08968befd1f5,
which broke some MPI functionality, as revealed in post-merge tests.
Pascal Merz [Wed, 10 Mar 2021 05:58:07 +0000 (22:58 -0700)]
Don't test for pressure in replica exchange regression
Pressure is not reproducible enough to have reliable regression tests.
The failures described in #3976 happen on step 0, so are independent
of replica exchange.
This change replaces testing for the pressure by testing for the
volume, where possible.
Fixes #3976
Andrey Alekseenko [Wed, 10 Mar 2021 05:55:30 +0000 (05:55 +0000)]
Disable GPU update in the presence of frozen atoms
There is a known bug (Issue #3920) affecting GPU update when frozen
atoms are present. While the bug is being resolved, we mark such
configuration as not allowed.
Refs #3920
Andrey Alekseenko [Wed, 10 Mar 2021 05:28:27 +0000 (05:28 +0000)]
Wrap more device pointers in DeviceBuffer
Store and pass around more device pointers as DeviceBuffer<T>
instead of as a raw or even void pointer.
Related changes:
- PmeGpu->kernelParams->atoms.d_forces is now RVec, not float. Forces in
most other places are RVec, so it seems more logical.
- GpuForceReduction::Impl::baseForce_ now stores pointer to the
beginning of the array, without shift.
Artem Zhmurov [Tue, 9 Mar 2021 16:17:15 +0000 (19:17 +0300)]
Unify gpu_copy_xq_to_gpu(...) function
Refs. #2608
ejjordan [Tue, 9 Mar 2021 15:16:05 +0000 (16:16 +0100)]
Move radian-angle conversions to math/utility
The constant M_PI is always defined there, and conversion is more
properly a utility than a unit.
Joe Jordan [Tue, 9 Mar 2021 14:33:55 +0000 (14:33 +0000)]
Use constexpr for physical constants and move them into gmx namespace
The physical constants that are part of the public API are converted from
defines to constexprs and are moved into the gmx namespace. This means
that many files are touched with tirvial changes. The benefit is that
now the risk of symbol collision is reduced in cases where a library
might depend on these constants.
Additionally, in the same vein of library cleanup, the math/utility
header is removed from units header and included only in the sources
that actually need it.
Paul Bauer [Tue, 9 Mar 2021 13:37:55 +0000 (13:37 +0000)]
Fix missing stdint.h
MSVC complained about missing definitions for int64_t because stdint.h was
not included.
Mark Abraham [Mon, 8 Mar 2021 09:24:30 +0000 (10:24 +0100)]
Revert "Use std::aligned_alloc"
This C++17 library capability is not yet available on Windows or Mac.
This reverts most of commit
768894fb93bb03a6972b10a8c930b1d1f64221c3.
Incidental aspects of that commit have not been reverted,
specifically, where unused header inclusions and unused functions were
removed.
Fixes #3968
Andrey Alekseenko [Mon, 8 Mar 2021 16:38:32 +0000 (16:38 +0000)]
Use map to speed up PreprocessingAtomTypes::atomTypeFromName
Previously, we were doing O(numExistingTypes) string comparisons in
PreprocessingAtomTypes::atomTypeFromName.
This significantly slowed down print_bonded function from toputil.cpp,
and, consequently, the pdb2top.
Here, we add an unordered map to store the mapping from type name to
type number, making the whole search O(log(numExistingTypes)), and
avoiding constantly constructing new std::string's from char*'s.
On my machine, this change reduced run time of Pdb2gmx3Test test from ~8
seconds to ~2 seconds.
Closes #3974
ejjordan [Mon, 8 Mar 2021 08:15:05 +0000 (09:15 +0100)]
Remove includes from math/utilities that are not needed there
Neither of the include statements in math/utilities were actually needed there.
Andrey Alekseenko [Fri, 5 Mar 2021 15:37:51 +0000 (18:37 +0300)]
Fix "wait before marking" synchronization bug
We did not initiate a D2H copy of coordinates when doing a neighbor
search but were anyway waiting on the associated event.
Unlikely that it had any negative consequences, but that's still a logic
bug.
Andrey Alekseenko [Sat, 6 Mar 2021 14:01:57 +0000 (17:01 +0300)]
Fix clang-tidy complaint failing our CI lint test
The complaint was about non-const reference, but I also changed an
uninitialized variable nearby.
Andrey Alekseenko [Fri, 5 Mar 2021 17:45:18 +0000 (20:45 +0300)]
Fix typo introduced during nbfp_comb refactoring
d440c46ef06c3a4c1695e3ec37e7e108ab7a2817 introduced a bug in OpenCL
NBXNM kernel.
Refs 3973
Szilárd Páll [Fri, 5 Mar 2021 16:18:45 +0000 (16:18 +0000)]
Clarify the SYCL subgroup size on different targets
Also added some doxygen.
Refs #3934
Paul Bauer [Fri, 5 Mar 2021 15:01:47 +0000 (15:01 +0000)]
Remove physical constant enums
Those have not been used anywhere.
Removed unused conversion functions.
Noted change in release notes API section.
Mark Abraham [Fri, 5 Mar 2021 11:46:51 +0000 (11:46 +0000)]
Fix clang-format and naming of static variable
Mark Abraham [Fri, 5 Mar 2021 08:02:59 +0000 (08:02 +0000)]
Introduce StringToEnumValue
This helper functor seems useful in a few places. Adds tests and
improves documentation.
Fixes #3963
Paul Bauer [Thu, 4 Mar 2021 08:39:30 +0000 (09:39 +0100)]
Modernize AWH enumerations
Changed enums to enum classes.
Use EnumerationArray for strings.
Szilárd Páll [Thu, 4 Mar 2021 08:08:51 +0000 (08:08 +0000)]
Simplify LJ parameter lookup
- Unify the CUDA per-pair scaled C6/C12 LJ parameter
loading codepaths so both texture and LDG paths do
8-byte float2 loads.
- Unify the CUDA per-atom LJ parameter loading codepaths
so both texture and LDG paths do 8-byte float2 loads.
- Simplify the LJ self interaction energy term calculation
by only using the non-texture loads path to simplify code.
As this is outside the main loop, its impact is negligible.
- Use float2 loads for the above in OpenCL as well.
Paul Bauer [Wed, 3 Mar 2021 18:52:43 +0000 (18:52 +0000)]
Check version names to be correct for release
Adds a check during release verification that the version names coming
from CMake and the actual name in the binary match.
Prevents issues with calculation of verified checksum.
Refs #3862
M. Eric Irrgang [Wed, 3 Mar 2021 14:05:32 +0000 (14:05 +0000)]
Create a documentation section for GitLab Label guidelines.
Also rename `gitlab.rst` to `gitlab-ci.rst` since we are starting
to document non-CI GitLab-related information in various places,
making `gitlab.rst` a misleading name.
Fixes #3949
Mark Abraham [Wed, 3 Mar 2021 08:56:19 +0000 (08:56 +0000)]
Remove PDO reading from gmx wham
These files were written by gmx 3.x, so likely nobody has any left
that they care about. Subsequent versons of GROMACS can still read
them if anybody does still have them. Meanwhile, we can simplify gmx
wham by removing this support, which was deprecated in GROMACS 2021.
Paul Bauer [Tue, 2 Mar 2021 15:34:21 +0000 (15:34 +0000)]
Modernize atom enums
Use enum classes and enumeration array for particle and PDB record
types.
Paul Bauer [Tue, 2 Mar 2021 13:01:28 +0000 (14:01 +0100)]
Fix nightly clang-tidy build
Function signatures had not been correctly updated.
Paul Bauer [Tue, 2 Mar 2021 13:13:38 +0000 (13:13 +0000)]
Use optional instead of magic numbers in preprocessing
Replaced the NOTUSED magic numbers in the atom type preprocessing
functions with optionals to indicate that an entry was found or not.
Needed for modernizing the particle type and pdb record type enums
further along.
Mark Abraham [Tue, 2 Mar 2021 08:18:02 +0000 (08:18 +0000)]
Use std::aligned_alloc
There is no longer any need to write our own code to allocate aligned
memory, as the C++ standard library provides a function to do that.
Relaxed some comments on our allocators as it is now technically
possible to free such memory with std::free.
Removed related configuration infrastructure that is no longer
required.
Also removed the unused gmx_pause, which shared some of that
infrastructure, and so was able to reduce the include requirements of
gmxomp.h header file.
Andrey Alekseenko [Tue, 2 Mar 2021 07:30:21 +0000 (07:30 +0000)]
Set up build with hipSYCL
The kernel code is currently non-functional on NVIDIA/AMD hardware, but
the build itself is useful to ensure code portability.
- Disabled LeapFrog for hipSYCL. With `float3` being used in the host
code, it is easiest to just disable the integrator until #3312 is
resolved. This will have to be resolved in order to run full MD loop
on GPU with hipSYCL. See #3941.
- Some warnings from the compiler and include headers silenced.
- Workarounds for features not supported by hipSYCL are introduced.
- - Shuffles. Should work, but not tested. Hopefully, they will be
introduced in the mainline hipSYCL soon.
- - Barrier synchronization. Intel-specific extension to SYCL which can
be imitated fairly well with native OpenCL/CUDA calls, but is
stubbed very stupidly now. Proper solution will be done after #2527
and #3924 are resolved.
- CI jobs are added. The set of target device architectures is chosen
semi-arbitrarily, since the code is not being run yet anyway. Main
concern was to have both HIP and CUDA there.
Refs #3923.
Joe Jordan [Mon, 1 Mar 2021 08:14:16 +0000 (08:14 +0000)]
Use const ref for mtop and inputrec in EnergyOutput initialization
Some renaming for ir to inputrec is also done.
Joe Jordan [Sun, 28 Feb 2021 14:10:06 +0000 (14:10 +0000)]
Use more const ref in domdec API
Several places that were using const pointers are changed to use
const refs. A few gmx_bool are replaced with bool as well.
Paul Bauer [Fri, 26 Feb 2021 14:36:45 +0000 (14:36 +0000)]
Add coverage build to post merge
Every merged commit will be checked for changes to code coverage with
this addition.
Small change to flags added when building for coverage.
Build can be extended for other metrics later as well.
Joe Jordan [Fri, 26 Feb 2021 14:02:54 +0000 (14:02 +0000)]
Only use const ref for mtop and inputrec in domdec
All const pointers of mtop and inputrec in domdec module are
converted to const refs. Additionally, since inputrec lines need
to change anyway, renaming from ir to inputrec is performed.
Artem Zhmurov [Wed, 24 Feb 2021 21:44:28 +0000 (00:44 +0300)]
Add device-to-device copy function wrapper with tests in CUDA
The D2D copy is currently only used in CUDA, so only stubs are added for OpenCL and SYCL.
Closes #3321
Refs #3318
Mark Abraham [Thu, 25 Feb 2021 10:49:13 +0000 (11:49 +0100)]
Deprecate gmx::Any
Refs #3951
Pascal Merz [Fri, 26 Feb 2021 12:31:41 +0000 (12:31 +0000)]
Introduce GTest regression tests for replica exchange
This introduces regression tests within the GTest framework for
replica exchange simulations. These tests are restricted to 4
MPI ranks, used as either 2 replicas with 2 ranks each (using
the DD code path), or 4 replicas with 1 rank each (using code
paths used by multiple replicas). As the reference data would
be different for each combination of number of ranks / number
of simulations, this is restricted to a few setups to keep the
reference data manageable.
The tests are run with integrator `md` using v-rescale and
Nose-Hoover thermostats and c-rescale and parrinello-rahman
barostats, covering the thermodynamically correct temperature
and pressure control algorithms. The tests are also run with
integrator `md-vv`, Nose-Hoover thermostat and no barostat
to cover the Trotter decomposition code path (MTTK barostat
would require a different system because it doesn't work
with constraints, and it's not obvious that it would actually
increase code coverage significantly).
Refs #3918
Pascal Merz [Thu, 25 Feb 2021 20:08:52 +0000 (20:08 +0000)]
Increase multsim test flexibility, test multisim + DD
This increases the flexibility of the multisim testing infrastructure
by allowing to parametrize it for number of ranks per simulation,
integrator algorithm, and temperature and pressure coupling.
The multisim tests are also extracted into a separate test binary,
allowing to use a different MPI setup than the remaining MPI tests.
Finally, the flexibility is used to introduce multisim tests which
use domain decomposition in the respective single simulations.
Refs #3918
Pascal Merz [Tue, 23 Feb 2021 02:15:43 +0000 (19:15 -0700)]
Fix testing of positions against reference data
When applying PBC to positions before comparing them to reference
data, a returned std::vector was assigned to an ArrayRef. This lead
to undefined values being compared. Position comparison against reference
data is currently unused, so this did not lead to any failing tests.
Artem Zhmurov [Wed, 24 Feb 2021 19:24:01 +0000 (19:24 +0000)]
Add tests on asynchronous host-to-device copy and back
The copy routines take different paths depending on transfer kind,
hence both sync and async copy should be tested. This adds tests
for async calls.
Paul Bauer [Wed, 24 Feb 2021 17:05:57 +0000 (17:05 +0000)]
Rework state checkpoint enum handling
The state enumerations have been changed to enum classes and enumeration
arrays. This was required by clang-tidy to remove the global available char
arrays.
Added templated function to convert enum to underlying int.
Was able to simplify quite a lot of the checkpoint handling that had to
work around the pure ints used before the enumerations to get the
correct names for the entries.
Artem Zhmurov [Wed, 24 Feb 2021 13:42:23 +0000 (16:42 +0300)]
Use GpuTimers in CUDA and OpenCL versions of NBNXM directly
The GpuTimers are used through proxy objects in OpenCL and CUDA
versions of NBNXM, which complicates the unification of the code.
This change eliminates the proxy object by using the underlying
object directly.
Refs #2608
Pascal Merz [Fri, 19 Feb 2021 06:10:54 +0000 (23:10 -0700)]
Fix multi-sim checkpoint writing bug
In rare cases (when a checkpoint file existed on at least one multisim
rank but not on all), checkpoint writing with multiple simulation could
cause the ranks to get out of sync. This fixes the problem by moving
the barrier outside of the relevant if clause, making sure that it
is hit by all ranks.
Fixes #3919
Joe Jordan [Tue, 23 Feb 2021 13:10:31 +0000 (13:10 +0000)]
Use verbose names in init_forcerec
Artem Zhmurov [Tue, 23 Feb 2021 11:09:57 +0000 (14:09 +0300)]
Fix doxygen in domdec
e2adf21a8c2ed0f6a8e1e590e3a12a099a6ebe24 was merged before all
Doxygen warnings got fixed. This fixes them.
Artem Zhmurov [Mon, 22 Feb 2021 18:27:08 +0000 (21:27 +0300)]
Use getAtomRanges(...) function in NBNXM more
Make getAtomRanges(...) function to return gmx::Range and
use it more.
Refs #2608
Mark Abraham [Mon, 22 Feb 2021 12:54:38 +0000 (13:54 +0100)]
Hide newly exposed domdec internals
By declaring the top-level destructor, we avoid needing to expose
details so the compiler has to generate the destructor everywhere.
Fixes #3926
Joe Jordan [Mon, 22 Feb 2021 19:00:38 +0000 (19:00 +0000)]
Hold unique_ptr to gmx_ewald_tab_t in forcerec
Proper constructor and destructor are added. The field eir, which
was anyway recomputed with every call to do_ewald, is removed from
the struct and made local to do_ewald. Since the type cvec is only
used by eir, it is moved to reside in ewald.cpp.
Joe Jordan [Mon, 22 Feb 2021 17:35:53 +0000 (17:35 +0000)]
Hold unique_ptr for interaction_const in forcerec
Also renamed ic->interactionConst in init_interactionConst.
Mark Abraham [Mon, 22 Feb 2021 12:29:43 +0000 (13:29 +0100)]
Fix code so clang-tidy no longer complains