Andrey Alekseenko [Mon, 28 Sep 2020 15:35:39 +0000 (15:35 +0000)]
Fix error in ensureReferenceCount
We were overwriting input value and comparing it to itself.
Joe Jordan [Mon, 28 Sep 2020 10:35:59 +0000 (10:35 +0000)]
Add initial nblib public API
Giovanni Bussi [Mon, 28 Sep 2020 07:46:02 +0000 (07:46 +0000)]
Fixed incorrect enum
Harmless, since both have value 1, but confusing
Artem Zhmurov [Mon, 28 Sep 2020 06:00:40 +0000 (06:00 +0000)]
add detection of CPX 5300 w/ 2FMAs
Signed-off-by: Hammond, Jeff R <jeff.r.hammond@intel.com>
Pascal Merz [Sun, 27 Sep 2020 11:23:20 +0000 (11:23 +0000)]
Compare trajectories to reference data
This introduces functionality to compare trajectories (x/v/f/box)
to reference data. It also allows to define the maximum number of
frames which should be checked. The latter allows to have a single
reference data, but decide based on the simulation setup (e.g.
parallelization scheme) how many frames are expected to match
before numerical divergence gets too large. To allow this, the
reference data functionality needs to give the option to ignore
unused reference frames.
Pascal Merz [Sun, 27 Sep 2020 06:55:11 +0000 (00:55 -0600)]
Roll back "Ensure the modular simulator runs only when it should"
The fact that GMX_USE_MODULAR_SIMULATOR does not lead to an error
when the run is not supported is a feature, not a bug. It allows
to run the entire test set using modular simulator wherever is is
implemented by using "export GMX_USE_MODULAR_SIMULATOR=ON; make check",
even if modular simulator is disabled by default. It is the only way
to make sure that modular simulator is a valid replacement for the
legacy code path.
Similarly, using "export GMX_DISABLE_MODULAR_SIMULATOR=OFF; make check"
allows to check the legacy code path, even if modular simulator is used
by default.
Andrey Alekseenko [Fri, 25 Sep 2020 20:41:08 +0000 (20:41 +0000)]
Fix #3668
Following the implementation in Google's cpu_features tool made by an
Intel engineer used for original implementation, we only check for the
presence of the second AVX-512 FMA unit if the CPU supports AVX-512F
(foundation), which should be present for all AVX-512 implementations.
That's distinct from the way cpu_features tool does AVX detection, but
should be no less reliable.
Pascal Merz [Fri, 25 Sep 2020 16:37:48 +0000 (16:37 +0000)]
Replace FramesToCompare enum by MaxNumFrames
This allows to explicitly chose a maximum number of frames to be
tested, rather than only chosing to compare the first frame or
all frames. It also implements to chose the number of frames for
tests comparing to reference data rather than only when comparing
simulation results.
Mark Abraham [Fri, 25 Sep 2020 15:21:43 +0000 (17:21 +0200)]
Ensure the modular simulator runs only when it should
Previous checks were ineffective if an unsupported inputrec
was accompanied by GMX_USE_MODULAR_SIMULATOR.
Change-Id: I74e4c177b6b4d7dc25bb3ca32a7dff5a6027276e
Paul Bauer [Fri, 25 Sep 2020 13:15:44 +0000 (15:15 +0200)]
Fix bad logic in regressiontest branch selection
Change-Id: I1eed8a5228362d34af9426a73c2a9d06eae7a714
Paul Bauer [Thu, 24 Sep 2020 14:46:18 +0000 (14:46 +0000)]
Allow deployment of nightly webpage to server
Still needs to have variables defined on Gitlab.
Change-Id: Id7378942555b69df19cbe377d7c90851d6cf56ba
Szilárd Páll [Thu, 24 Sep 2020 12:44:09 +0000 (12:44 +0000)]
Improve OpenCL log/error reporting
Improve reporting by making messages more specific; also added logging of binary caching also for the case where a cache files is found in addition to the case where no cache file is present
Andrey Alekseenko [Wed, 23 Sep 2020 16:34:29 +0000 (18:34 +0200)]
Fix false-positives in checkDeviceBuffer for OpenCL
The function takes required number of elements as its argument, but then
compares it with the buffer size measured in bytes.
Mark Abraham [Wed, 23 Sep 2020 15:26:35 +0000 (17:26 +0200)]
Report name of missing OpenCL kernels
Refs #3686
Pascal Merz [Wed, 23 Sep 2020 16:59:06 +0000 (16:59 +0000)]
Access write checkpoint functionality directly
Pascal Merz [Tue, 8 Sep 2020 03:03:50 +0000 (21:03 -0600)]
Implement Berendsen thermostat for modular simulator
Refs #3423
Mark Abraham [Wed, 23 Sep 2020 14:56:57 +0000 (14:56 +0000)]
Permit comparison of only first frames
Integration tests of mdrun sometimes want to compare only the
quantities from the first frame of a trajectory. This is now
permitted.
Alan Gray [Wed, 23 Sep 2020 07:02:47 +0000 (07:02 +0000)]
Add regression tests for gpucomm paths
Adds regression test runs with GPU communication codepaths enabled for
both thread-MPI and MPI builds.
Mark Abraham [Tue, 22 Sep 2020 13:18:17 +0000 (13:18 +0000)]
Split mdrun-test
The PME tests are the most time-consuming part, so have been split off.
Andrey Alekseenko [Tue, 22 Sep 2020 12:50:41 +0000 (12:50 +0000)]
Draft: Fix compilation
Also, make ctor etc always defined for DeviceInformation. Otherwise it's
just ugly.
Paul Bauer [Tue, 22 Sep 2020 10:04:35 +0000 (10:04 +0000)]
Make Oneapi use CCache again
The custom before_script meant that builds are not using the cache.
Change-Id: Iaf0546e2dd48cf2a6438c2aa0d6461977ee6b2dd
Christian Blau [Tue, 22 Sep 2020 07:30:09 +0000 (07:30 +0000)]
Nelder-Mead downhill simplex optimisation
Nelder-Mead simplex optimiser, according to Saša Singer and
John Nelder (2009), Scholarpedia, 4(7):2928. doi:10.4249/scholarpedia.2928
Implementation for functions returning real values from
vectors of reals.
Pascal Merz [Mon, 21 Sep 2020 16:34:37 +0000 (16:34 +0000)]
Checkpointdata DD followup
Mark Abraham [Mon, 21 Sep 2020 14:21:14 +0000 (16:21 +0200)]
Wrong logic was used
Log files in gitlab gave the warning message for twin-cutoff, but we
are not setting these env variables.
Gilles Gouaillardet [Mon, 21 Sep 2020 15:01:19 +0000 (15:01 +0000)]
simd/impl_none: add missing macros
add macros for GMX_SIMD_HAVE_HSIMD_UTIL_{FLOAT,DOUBLE}
Paul Bauer [Mon, 21 Sep 2020 13:33:09 +0000 (13:33 +0000)]
Fix script building all CI containers and add gcovr
Additions in
48f9056c196fda338b83e74212d4f9bc5ab3474e broke the script
by changing the default values, while
e9cb08d17b06bc5649d316ee06159b633db9b3d8 inadvertently made all images
use the oneapi images as base.
Also add gcovr tool to documentation images, preparing for coverage
builds.
Change-Id: I0eb9a3bf1e8b45dd4b4a3a41fd214678c4c1c4c2
Paul Bauer [Mon, 21 Sep 2020 08:44:58 +0000 (10:44 +0200)]
Add OpenSSH to docs build images
Change-Id: I9b1994a78ef869f3147aa45b5893645ce74f5e04
Magnus Lundborg [Mon, 21 Sep 2020 09:07:13 +0000 (09:07 +0000)]
AWH avoid constructors only differing in parameter types
Also clarified a function name in the tests.
Tests had to be updated since the force constant (now removed)
should not have been used before at all.
Artem Zhmurov [Mon, 21 Sep 2020 08:26:52 +0000 (08:26 +0000)]
Do not run PinnedMemoryCheckerTest when there are no CUDA-capable devices
If there are no CUDA devices in the system, cudaPointerGetAttributes(...)
CUDA API call returns an error. This causes the GPU Utils tests to fail
with fatal error.
Fixes #3679
Artem Zhmurov [Mon, 21 Sep 2020 07:59:07 +0000 (07:59 +0000)]
Move the message to the deprEcation-policy file
Also update the message according to the move
Andrey Alekseenko [Sun, 20 Sep 2020 09:39:41 +0000 (09:39 +0000)]
Add NVIDIA GPU compatibility check, following issue #3125
The incompatibility is documented, but better to verify.
Artem Zhmurov [Sun, 20 Sep 2020 09:18:16 +0000 (09:18 +0000)]
Set active device when the device stream manager is initialized
Replace the direct CUDA API call in PME by the wrapper called
when the device context and streams are created.
Artem Zhmurov [Sun, 20 Sep 2020 08:56:29 +0000 (08:56 +0000)]
Allow using old environment variables, but print deprecation message
The following environment variables were unified in
2c644d3b5ebb64f6c89a5db36160c9dc30329888:
GMX_CUDA_NB_ANA_EWALD and GMX_OCL_NB_ANA_EWALD into GMX_GPU_NB_ANA_EWALD
GMX_CUDA_NB_TAB_EWALD and GMX_OCL_NB_TAB_EWALD into GMX_GPU_NB_TAB_EWALD
GMX_CUDA_NB_EWALD_TWINCUT and GMX_OCL_NB_EWALD_TWINCUT into GMX_GPU_NB_EWALD_TWINCUT
This allows user to use old environment variables, but prints deprecation message.
Pascal Merz [Tue, 8 Sep 2020 02:40:22 +0000 (20:40 -0600)]
Refactor v-rescale thermostat to allow for other algorithms
This is pure refactoring, splitting the element class (interfaces with
the simulator and other objects) from the actual implementation of the
thermostat. This will allow to implement other thermostat algorithms
using the same infrastructure.
Refs #3423
M. Eric Irrgang [Tue, 15 Sep 2020 19:18:22 +0000 (22:18 +0300)]
Improve naming and docs.
Follow up from https://gitlab.com/gromacs/gromacs/-/merge_requests/541
Fixes #3673
Berk Hess [Fri, 18 Sep 2020 09:01:21 +0000 (09:01 +0000)]
Remove cutoff_scheme from t_forcerec and interaction_const_t
M. Eric Irrgang [Mon, 14 Sep 2020 16:15:04 +0000 (19:15 +0300)]
Document a Mdrunner::BuilderImplementation member.
Fixes #3665.
Berk Hess [Thu, 17 Sep 2020 12:13:57 +0000 (14:13 +0200)]
Move bNonbonded flag from t_forcerec to SimulationWorkload
The flag to store whether nonbonded calculations are requested to be
skipped (set by env.var.) is move from t_forcerec to
SimulationWorkload. A minor side-effect of this change is that the
nbnxn module logs kernels choices when this option is set.
Pascal Merz [Thu, 3 Sep 2020 03:56:11 +0000 (21:56 -0600)]
Rename VRescaleThermostat to VelocityScalingTemperatureCoupling
Also moves vrescalethermostat.h/cpp to
velocityscalingtemperaturecoupling.h/cpp.
This reflects upcoming changes making the thermostat more general.
As these changes touch a lot of lines in the implementation file,
renaming the file at the same time throws git diff off. Doing the
renaming in a separate commit should therefore make for easier reviewing.
Refs #3423
Artem Zhmurov [Thu, 17 Sep 2020 12:49:10 +0000 (12:49 +0000)]
Remove the CPU hardware context from the general list of test hardware contexts
Having CPU code path in the general hardware context list leads to having
many if (CPU) clauses. This complicates things in places, where there are
several CPU runners. Since in most cases (i.e. everywhere apart from Ewald
tests) the runners know the hardware they should use, the selection of CPU
or GPU is now done when the runners are created. TestHardwareContext is
to become TestDeviceContext and will only hold GPU devices.
Berk Hess [Wed, 16 Sep 2020 13:33:12 +0000 (15:33 +0200)]
Remove unnecessary condition in DD force buffer resizing
Removed a condition that was no longer necessary, as exactly
the same condition is checked inside the resize() method of
ForceHelperBuffers.
Mark Abraham [Wed, 16 Sep 2020 15:41:05 +0000 (15:41 +0000)]
Activate AMD OpenCL build in release matrix
This had never been turned on.
Fixed missing file for OpenCL installation.
Also reordered the install list in alphabetical order, per style.
Refs #3272
Sebastian Keller [Tue, 15 Sep 2020 09:09:45 +0000 (11:09 +0200)]
Reduce transitive dependencies in arrayref.h
Reduce transitive dependencies on other GROMACS headers.
* Replace `GMX_ASSERT` with `assert`
* Replace `index` with `difference_type`
Refs #3674
Christian Blau [Tue, 15 Sep 2020 14:55:31 +0000 (16:55 +0200)]
Extend user docs on affine transformations for densities
Add more extensive information to the reference manual and .mdp option description
in the user-guide.
Fix one documentation typo.
Pascal Merz [Wed, 16 Sep 2020 07:34:44 +0000 (07:34 +0000)]
Implement modular checkpointing
Using the CheckpointData format introduced in a parent commit, this
rewrites checkpointing for the modular simulator to completely use
the new format.
The CheckpointHelper is now passing a CheckpointData object to its
clients (instead of a legacy t_state object). Clients are now stored
in a map, as they are identified by their unique key to be able to
assign the correct CheckpointData sub-objects at reading and writing.
If checkpoint reading occured, the newly introduced
CheckpointHelperBuilder receives the CheckpointData object read at the
runner level from the ModularSimulator. It then initializes its clients
with their respective, read-only CheckpointData subobjects.
The ICheckpointHelperClient interface is adapted to reflect above
changes.
The ModularSimulatorAlgorithmBuilder is slightly simplified thanks to
to the introduction of a proper builder for the CheckpointHelper.
The ComputeGlobalsElement is simplified, as it is not required to know
about the needs of communication of the EnergyData object which
depends on checkpoint reading.
Finally, all elements which are checkpoint clients are updated to
implement the new design. Note that they all introduce their own
checkpoint versioning, as the data being checkpointed is opaque to the
checkpointing infrastructure.
Closes #3517
Closes #3422
In partial fulfillment of #3419
Artem Zhmurov [Tue, 15 Sep 2020 16:43:43 +0000 (16:43 +0000)]
Use common device context header for OpenCL
This moves the OpenCL specific definition into under macro in the main header.
Makes device stream and context definitions more consistent.
Paul Bauer [Tue, 15 Sep 2020 14:17:42 +0000 (14:17 +0000)]
Break off some tests from mdrun tests
Done to not hit the time limit in CI with OpenCL.
Change-Id: Ic2e2686530aef51475ab7f49c1bfd29442c3fc0a
M. Eric Irrgang [Fri, 11 Sep 2020 13:52:31 +0000 (16:52 +0300)]
Remove outdated workaround.
Remove a workaround left over from before issue #2689 was closed.
Refs #2689
Berk Hess [Tue, 15 Sep 2020 09:40:23 +0000 (11:40 +0200)]
Only extend Ewald table when necessary
The Ewald correction table for non-bonded interactions was always
extended by change
24595dbb. No this is limited to free-energy
runs only.
Erik Lindahl [Tue, 15 Sep 2020 12:38:19 +0000 (12:38 +0000)]
Enable GMX_GPU=SYCL compiles
Update CMake config to properly apply -fsycl, but only to files
including actual SYCL code, and get linking working. Tested
with both dpcpp and icpx, and added trivial SYCL code to a
dimmy device context, just to ensure compiles and linking works
both with and without SYCL support enabled.
Also fixes a number of new warnings about unused variables now
detected with dpcpp and icpx.
Paul Bauer [Tue, 15 Sep 2020 11:31:21 +0000 (13:31 +0200)]
Fix missing installed files for OpenCL PME
Change
fa6862b510acd7b0225580b661446c278dbb0039 forgot to modify
the CMake files to install the renamed OpenCL header files.
Refs #3664
Christian Blau [Tue, 15 Sep 2020 11:21:14 +0000 (11:21 +0000)]
All coordinates in the density-guided-simulation group undergo an affine transformation before density-fitting forces on them are evaluated, which allows rotation, transformation and scaling of coordinates.
Resolves part of #3581.
Berk Hess [Tue, 15 Sep 2020 10:17:46 +0000 (10:17 +0000)]
Fix task assignment with multiruns
Change
e0f481ae broke the physical node hardware detection and task
assignment by passing the simulation instead of the world communicator
to the creation of the physical node communicator. Now the world
communicator is stored and passed.
Fixes #3666
Erik Lindahl [Tue, 15 Sep 2020 07:59:04 +0000 (09:59 +0200)]
Fix minor warnings noticed by Intel compilers
New things found by dpcpp & ipcx compilers.
Alan Gray [Fri, 11 Sep 2020 11:51:58 +0000 (04:51 -0700)]
Pass devFlags into createSimulationWorkload replacing bools
Artem Zhmurov [Tue, 15 Sep 2020 05:46:44 +0000 (08:46 +0300)]
Fix VSite out of range error message
M. Eric Irrgang [Mon, 14 Sep 2020 15:37:40 +0000 (15:37 +0000)]
Create and use SimulationInput module.
Allow Mdrunner to accept a handle to SimulationInput from the client.
This change adds an input method to the MdRunner builder to provide
access to resources provided through the new SimulationInput module.
Refs #3374
Artem Zhmurov [Mon, 14 Sep 2020 09:46:19 +0000 (09:46 +0000)]
Use common device context header for OpenCL
This moves the OpenCL specific definition into under macro in the main header.
Makes device stream and context definitions more consistent.
M. Eric Irrgang [Fri, 11 Sep 2020 13:47:56 +0000 (16:47 +0300)]
Refine the CMakeLists.txt for MPI gmxapi tests.
Exclude tests when GMX_MPI is not set. Normalize test working directory.
Berk Hess [Sun, 13 Sep 2020 09:30:20 +0000 (09:30 +0000)]
Decouple nsttcouple and nstpcouple from nstlist
The default values of nsttcouple and nstpcouple of -1 would cause
nstlist to be used as the coupling interval. But coupling intervals
should not be linked to nstlist. The default is now set to 10, which
will not change settings for mdp files where nstlist was not specified
as the default nstlist value is also 10.
Mark Abraham [Sat, 12 Sep 2020 11:42:42 +0000 (13:42 +0200)]
Fix GPU device info broadcast with MPI
ejjordan [Fri, 11 Sep 2020 12:34:27 +0000 (14:34 +0200)]
Move src/api cmake logic into src/api cmake file
Paul Bauer [Fri, 11 Sep 2020 06:26:02 +0000 (08:26 +0200)]
Remove leftover data after refactoring
The modular simulator still hat the old datastructure for initial
lambdas, causing a complaint in the CI.
Change-Id: Ic97ee36ebea8cd40d7c513f44f767751f5c271cc
Paul Bauer [Fri, 11 Sep 2020 10:11:17 +0000 (10:11 +0000)]
Fix doxygen for unused parameters.
Recent addition to the code didn't use the parameters for the SYCL
stubs, leading to errors from doxygen.
Change-Id: I61666e4e76cfdcfa5c618c7bc6f58cf24ea2b4f8
Artem Zhmurov [Fri, 11 Sep 2020 09:06:16 +0000 (09:06 +0000)]
Define stubs for GPU data structures in SYCL to make SYCL compilation possible
Paul Bauer [Fri, 11 Sep 2020 07:58:35 +0000 (07:58 +0000)]
Force use of Python3 in Doxygen CMakeFiles
Change-Id: Ia7d430fef243d6b3236de903907dbf8e9ba92222
Christian Blau [Thu, 10 Sep 2020 19:04:49 +0000 (19:04 +0000)]
Simplify and fix how lambda values are set
Simplified setCurrentLambdasLocal method to return an array of
current lambda points. Removed the faulty use of lam0 as initial
lambdas.
Roland Schulz [Thu, 10 Sep 2020 04:51:17 +0000 (21:51 -0700)]
Fix Visual Studio build
- Add /permissive- flag to disable MSVC extension. Fixes
ternary operator.
- Fix usage of %l for size_t
- Disable non-wroking FFTW SIMD check
- Missing imports
- Compiler warning fix
Roland Schulz [Wed, 9 Sep 2020 20:06:04 +0000 (13:06 -0700)]
Simpify CheckpointData
Paul Bauer [Thu, 10 Sep 2020 12:37:44 +0000 (14:37 +0200)]
Minor fix to the printout for regtest builds
Was not printing the branch it is building the archive from.
Change-Id: I597e68a3780d3f300b5a4be447ecac7834126408
Artem Zhmurov [Thu, 10 Sep 2020 13:49:23 +0000 (13:49 +0000)]
Use common device context header for OpenCL
This moves the OpenCL specific definition into under macro in the main header.
Makes device stream and context definitions more consistent.
Berk Hess [Thu, 10 Sep 2020 11:37:55 +0000 (13:37 +0200)]
Add angles to ListedForces selections
Artem Zhmurov [Thu, 10 Sep 2020 10:27:03 +0000 (10:27 +0000)]
Use device information object instead of id when performing device checks
Initializing plain object is dangerous, since it then can be used to set
active device, with default id. This change ensures that proper device
will be used, even if the high level device management is used in the
checks.
Berk Hess [Thu, 10 Sep 2020 09:00:52 +0000 (11:00 +0200)]
Fix memory corruption with strings in grompp
Using a string of more than 31 characters as a default value for
a string entry in the mdp file would lead to memory corruption.
Joe Jordan [Thu, 10 Sep 2020 06:42:13 +0000 (06:42 +0000)]
Replace GMX_ASSERT with assert in vectypes.h
It is inappropriate to have a wrapper around assert in a public API.
This change removes dependence on GMX_ASSERT in one component of the
installed API. Transient dependencies related to inclusion of
gmxassert.h in vectypes.h are also removed.
Artem Zhmurov [Thu, 10 Sep 2020 05:39:44 +0000 (05:39 +0000)]
Unify more functions in CUDA and OpenCL implementations of NBNXM
M. Eric Irrgang [Wed, 9 Sep 2020 17:34:13 +0000 (17:34 +0000)]
Explicitly include STL headers used in test.
Include `array` and `optional` in strconvert.cpp test.
Fixes #3657
Artem Zhmurov [Wed, 9 Sep 2020 06:29:11 +0000 (09:29 +0300)]
Restore GMX_FORCE_UPDATE_DEFAULT_GPU environment varible check
This line was accidently removed during unrelated refactoring
in
75c17a76b69c1ade1f29fdce9fe2f6dd78221c1d .
Alan Gray [Tue, 8 Sep 2020 16:34:25 +0000 (16:34 +0000)]
Bug fix in call to deviceStreamManager constructor
DeviceStreamManager construction expects
(deviceInfo,useGpuForPme,havePpDomainDecomposition,
doGpuPmePpTransfer,useGpuForUpdate,useTiming) but was being passed
(deviceInfo,useGpuForPme,useGpuForNonbonded,
havePPDomainDecomposition,useGpuForUpdate,useTiming) Now passing
correct arguments through simulationWork. Also ensures update stream
is correctly set up when gpu buffer ops are enabled.
Fixes #3639 and #3641
Andrey Alekseenko [Tue, 8 Sep 2020 12:51:19 +0000 (14:51 +0200)]
Fix clang-tidy warning
Andrey Alekseenko [Tue, 8 Sep 2020 12:29:08 +0000 (14:29 +0200)]
Fix "GPU detection deactivated" message when it in fact failed
Also remove duplicate GPU detection check, and raise log level on failure from GPU detection API.
Pascal Merz [Tue, 8 Sep 2020 13:20:07 +0000 (13:20 +0000)]
Make legacy energy elements use CheckpointData
This enables some legacy energy elements to write to CheckpointData,
namely
* energyhistory_t
* delta_h_history_t
* ekinstate_t
Refs #3517
Refs #3422
Refs #3419
Christian Blau [Tue, 8 Sep 2020 12:49:24 +0000 (12:49 +0000)]
Allow density-guided simulations to translate structure
Density-guided simulations acquire a new feature that allows a
user-defined shift on the structure before forces are calculated.
First step to address #3581
Pascal Merz [Tue, 8 Sep 2020 10:56:09 +0000 (10:56 +0000)]
Remove dependency of EnergyData on t_state
EnergyData used a t_state object to calculate the conserved energy.
This responsibility is now given to the respective temperature /
pressure control algorithms. This allows to remove the dependency
of EnergyData on t_state.
This also introduces the conserved energy as a test quantity in the
tests comparing legacy and modular simulator code paths.
Refs #3419
Paul Bauer [Tue, 8 Sep 2020 07:29:07 +0000 (07:29 +0000)]
Move densityfitting to its own directory
Preparing for adding more applied_forces modules
Change-Id: Ieec20d1f0752a369d26352ec6b0997812decd21e
Paul Bauer [Mon, 7 Sep 2020 22:47:17 +0000 (22:47 +0000)]
Fix output string for GPU support
This used to print only disabled or CUDA because the variable was only 0
or 1.
Change-Id: Ie406a36e61617c29629f97d811eb93244b5a2e3a
Christian Blau [Mon, 7 Sep 2020 16:12:52 +0000 (18:12 +0200)]
Fix clang-format failure in coordinatetransformation.h
Fixes formatting clang format error.
Pascal Merz [Mon, 7 Sep 2020 20:23:36 +0000 (20:23 +0000)]
Make EnergyOutput::addDataAtEnergyStep independent of t_state
EnergyOutput::addDataAtEnergyStep took a pointer to a full t_state,
although it only uses a small part of the object. This makes the
dependencies explicit. This is a necessary step to make EnergyData
independent of t_state.
Refs #3419
Artem Zhmurov [Mon, 7 Sep 2020 10:58:02 +0000 (13:58 +0300)]
Remove in-body comment from init_forcerec(...) function
Fixes doxygen warning
Artem Zhmurov [Mon, 7 Sep 2020 17:44:03 +0000 (20:44 +0300)]
Fix clang-format
M. Eric Irrgang [Mon, 7 Sep 2020 16:13:31 +0000 (16:13 +0000)]
Replace filename-based initialization functions.
Decouple Mdrunner from the details of `-s` and `-cpi`
filename arguments when establishing initial simulation state.
Declare gmx::SimulationInput and the library utilities needed to
replace direct reference to TPR and CPT files in Mdrunner.
Use SimulationInput and accompanying utilities to remove read_tpx_state
and load_checkpoint from Mdrunner.
Allows TPR and checkpoint file handling to be considered separately
from Mdrunner initialization in future development.
Refs #3374
Christian Blau [Mon, 7 Sep 2020 13:46:40 +0000 (13:46 +0000)]
Implement affine coordinate transformation
Introduce a new class and tests for affine coordinate transformations.
Allows to perform a matrix multiplication and shift to coordinates of the form A*x+t with a 3x3 real valued matrix A and a translation vector t.
Artem Zhmurov [Mon, 7 Sep 2020 06:09:04 +0000 (06:09 +0000)]
Access the device status directly, remove the getter
DeviceInformation is a basic contained and does not need the getters.
Pascal Merz [Sun, 6 Sep 2020 18:15:55 +0000 (18:15 +0000)]
Prepare legacy checkpoint for modular simulator checkpointing
* Extend legacy checkpointing functionality to accept a CheckpointDataHolder
for reading and writing
* Bump checkpoint version to reflect above change
* Turn off some checkpoint sanity checks when using modular simulator
* Pass CheckpointDataHolder object into checkpoint reading in runner, and
move this object in SimulatorBuilder and then ModularSimulator for element
setup
Refs #3517
Refs #3422
Refs #3419
Pascal Merz [Sun, 6 Sep 2020 12:01:42 +0000 (12:01 +0000)]
Modular simulator: Simplify velocity update dispatch
This simplifies the velocity update dispatch of the modular simulator
propagator. This is pure rebasing reducing the number of branches
required to dispatch the right templated version of the velocity
update.
Christian Blau [Fri, 4 Sep 2020 11:59:43 +0000 (11:59 +0000)]
String to array conversion functions
Introduce and test a function that allows to convert a string into
a fixed-size array of arbitrary ElementType.
Pascal Merz [Thu, 30 Apr 2020 02:25:41 +0000 (20:25 -0600)]
Introduce CheckpointData
CheckpointData exposes methods to read and write scalar values,
ArrayRefs, and tensors. It also allows to create a "sub-object" of
type CheckpointData which allows to have more complex members
implement their own checkpointing routines. All methods are templated
on the chosen operation, CheckpointDataOperation::Read or
CheckpointDataOperation::Write, allowing clients to use the same code
to read and write to checkpoint. Type traits and constness are used to
catch as many errors as possible at compile time. CheckpointData uses
a KV-tree to store the data internally. This is however never exposed
to the client. Having this abstraction layer gives freedom to change
the internal implementation in the future.
All CheckpointData objects are owned by a ReadCheckpointDataHolder or
WriteCheckpointDataHolder. These holder classes own the internal
KV-tree, and offer deserialize(ISerializer*) and
serialize(ISerializer*) functions, respectively, which allow to read
from / write to file. This separation clearly defines ownership and
separates the interface aimed at file IO from the interface aimed at
objects reading/writing checkpoints.
Refs #3517
Refs #3422
Refs #3419
Pascal Merz [Thu, 3 Sep 2020 15:28:59 +0000 (09:28 -0600)]
Remove unnecessary friend declaration
Magnus Lundborg [Tue, 1 Sep 2020 11:24:20 +0000 (13:24 +0200)]
Print lambda state to log file if using AWH for FEP.
Change-Id: I08c7e6d51a299eb53556d5bde63c29f7c7640f6e
Alan Gray [Sun, 23 Aug 2020 13:05:51 +0000 (06:05 -0700)]
Fix bug it GPU halo exchange initialization for continuation runs
Fixes a bug introduced in
fdf8c9064e2289bb01b1536a06f83755450caee8
where, due to the presence of !(bFirstStep && ir->bContinuation) in
the if statement predicate of the block in which the init call was
located. In the case of continuation runs the halo exchange would not
be initialized until the second search step, causing the code to
crash. This change moves the init call to a separate block with the
correct logic in the if statement.