GROMACS

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

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

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

Use reallocateDeviceBuffer(...) in CUDA version of SETTLE

Refs #2886 and #2888

Change-Id: Ia45254a24eda8e6ad151b1f4c6583b1a2c926004

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

Remove PImpl scaffolding from CUDA version of SETTLE

GPU version of SETTLE was implemented as a class with private
implementation so it will be possible to initialize on
non-CUDA hosts. Now, the implementation can be hidden
inside the Update and Constraints PImpl so that the CUDA
specific types and calls can be exposed in SETTLE and
private implementation is no longer needed there.

Refs #2816, #2888

Change-Id: I4c78f2629be34b42bb5f4f7d34970c3e41515691

Remove PImpl scaffolding from CUDA version of Leap-Frog

Private implementation in CUDA version of Leap-Frog was
used to introduce this integrator as a stand-alone unit.
Now it is merged with constraints, PImpl is no longer
needed.

Refs #2816, #2888

Change-Id: Iea82abef016b7e15b9be44a0e1b446e12e582d3c

Refactor Leap-Frog tests and connect them to CPU version

This introduces test data object and runners to the Leap-Frog
tests, which are now connected to the CPU version of Leap-Frog.
This also makes possible to include tests based on the reference
values, which are needed to make sure that the temperature and(or)
pressure control works fine in new implementations.

Refs. #2816, #2888.

Change-Id: Id2d934c43138889ad178a94126cab4da2895bb5a

Refactoring of the SETTLE tests

Current version of tests for CUDA version of SETTLE was a quick
addition to the old tests, with direct comparison of the GPU
implementation with the old original CPU-based implementation.
This commit rearranges the test structure, making it possible
to apply the same set of tests to both implementations. There
is no changes to the tests themselves. Currently, comparison tests
will run twice and will dry-run on CUDA builds without CUDA-
capable devices.

TODO: Add comparison with pre-computed values for coordinates,
velocities and virial. Remove the CPU vs GPU comparison
tests.

Refs #2886, #2888.

Change-Id: Ifcb6af9af6c93787b919b785348f9f4547b6c267

Prepare Update and Constraints for Domain Decomposition

Initial GPU-based version of the update and constraints was not
designed to run with the Domain decomposition. This introduces a
couple of fixes to the memory management that should alow the
module to work with the DD enabled. The memory buffers are now
re-allocated at the set(...) stage, if so needed.

Refs. #2816, #2888.

Change-Id: I155884f5797252cf048a6400a2dd7b042d355b7e

Make use of reference data in SETTLE tests

As a temporary measure, the CPU and GPU versions of SETTLE
were tested agains each other. Making use of the reference
data framework allows to test them against precomputed values.
Now, the final positions, velocities and virial are properly
tested in CPU and, if available, in GPU versions.

Refs. #2886, #2888.

Change-Id: I8e54e1a741263b8bf9774a21141c527f58130fa9

Remove PImpl scaffolding from CUDA version of SETTLE

GPU version of SETTLE was implemented as a class with private
implementation so it will be possible to initialize on
non-CUDA hosts. Now, the implementation can be hidden
inside the Update and Constraints PImpl so that the CUDA
specific types and calls can be exposed in SETTLE and
private implementation is no longer needed there.

Refs #2816, #2888

Change-Id: I4c78f2629be34b42bb5f4f7d34970c3e41515691

Remove PImpl scaffolding from CUDA version of Leap-Frog

Private implementation in CUDA version of Leap-Frog was
used to introduce this integrator as a stand-alone unit.
Now it is merged with constraints, PImpl is no longer
needed.

Refs #2816, #2888

Change-Id: Iea82abef016b7e15b9be44a0e1b446e12e582d3c

Prepare Update and Constraints for Domain Decomposition

Initial GPU-based version of the update and constraints was not
designed to run with the Domain decomposition. This introduces a
couple of fixes to the memory management that should alow the
module to work with the DD enabled. The memory buffers are now
re-allocated at the set(...) stage, if so needed.

Refs. #2816, #2888.

Change-Id: I155884f5797252cf048a6400a2dd7b042d355b7e

Add temperature coupling to CUDA Leap-Frog integrator

Velocity rescaling added to the integrator. None, one,
or multiple rescaling groups are supported. Tests that
include temperature coupling are added.

NoseHoover temperature control is not implemented.

Refs. #2887, #2888.

Change-Id: I1e6850eeb74de829554260fba6a6e6c1c63ceb46

Add Parrinello-Rahman pressure coupling to CUDA Leap-Frog integrator

Parrinello-Rahman isotropic pressure coupling scheme is now
added to CUDA version of the Leap-Frog integrator. The
Leap-Frog tests are updated to check the new addition.

Refs. #2887, #2888.

Change-Id: Icf42667621c16a994e68baf5158ea4abac387928