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Feature #2816

Device-side update&constraits, buffer ops and multi-gpu comms

Added by Alan Gray 8 months ago. Updated 24 days ago.

Status:
New
Priority:
Normal
Assignee:
Category:
mdrun
Target version:
Difficulty:
hard
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Description

Gromacs is sub-optimal on modern GPU Servers.

When running on a single GPU, all force calculations are now done on the device, but the buffer operations plus update & constraints are done on the host, and repeated PCI-e transfers are required. Such CPU computation and PCI-e communication comprise an increasingly significant overhead as the performance of the GPU continues to increase with each subsequent generation.

On multi-GPU the situation is ever worse because the required multi-GPU communications are routed through the CPU.

NVIDIA have developed prototype code with all compute and communication parts now device-side, with coordinate and force PCIe transfers removed for regular timesteps. Gerrit patch 8506 introduces device-side buffer ops, and patch 8859 (based on the buffer ops patch) demonstrates the remainder of the new developments:

  • GPU Update and Constraints
  • Device MPI: PME/PP Gather and Scatter
    - Relatively straightforward solution using CUDA-Aware MPI
  • Device MPI: PP local/nonlocal exchanges
    - New functionality to pack device-buffers and exchange using CUDA-aware MPI
    - Similar D2D exchanges also for Constraints Lincs part

See the attached slides for more info.

These developments show major performance improvements, but are still in prototype form, and the purpose of this issue is to track the work required to integrate properly into the master branch.

TODOs common across multiple tasks:
  • Add assertions when converting between rvec types on CPU to float3 types on GPU
NVDevUpdate21Dec18.pdf (1.21 MB) NVDevUpdate21Dec18.pdf Slides describing NVIDIA developments Alan Gray, 12/21/2018 11:15 AM

Subtasks

Feature #2817: GPU X/F buffer opsIn Progress
Feature #2934: GPU X Buffer opsNew
Task #3026: add flags for GPU force buffer op / reduction activationNew
Feature #3029: GPU force buffer ops + reduction In Progress
Feature #3052: GPU virial reduction/calculationNew
Task #3037: add missing cylcle counters related to buffer ops/reduction launchesNew
Feature #2885: CUDA version of LINCSNewArtem Zhmurov
Feature #2886: CUDA version of SETTLENewArtem Zhmurov
Feature #2887: CUDA version of Leap Frog algorithmNewArtem Zhmurov
Feature #2888: CUDA Update and Constraints moduleNewArtem Zhmurov
Feature #2890: GPU Halo ExchangeNew
Feature #2891: PME/PP GPU communications New
Feature #2915: GPU direct communicationsNew
Task #2965: Performance of GPU direct communicationsNew
Feature #3021: Completion of docs for GPU developmentsNew
Feature #3022: modernized naming for new GPU developmentsNew

Associated revisions

Revision bec0fa7b (diff)
Added by Artem Zhmurov 6 months ago

Test for LINCS and SHAKE constraints.

This version updates the tests making the selection of the
constraining algorithm more abstract. Makes it possible
to use the same test routines for new implementations (e.g.
CPU- or GPU-based) or (and) algorithms (e.g. LINCS or SHAKE).
Partly this is preparation for the GPU-based version of
the constraints (Refs #2816).

Change-Id: Ice7dfdcc6d86c04656b0a1dd4e328c5afdb8a263

Revision 0a1aae78 (diff)
Added by Artem Zhmurov 4 months ago

CUDA version of LINCS constraints.

Implementation of the LINCS constraints for NVIDIA GPUs.
Currently works isolated from the other parts of the code:
coordinates and velocities are copied to and from GPU on
every integration timestep. Part of the GPU-only loop.
Loosely based on change 9162 by Alan Gray. To enable,
set the environmental variable GMX_LINCS_GPU.

Limitations:
1. Works only if the constraints can be split in short
uncoupled groups (currently < 256, designed for H-bonds
constraints).
2. Does not change the matrix inversion order for costraints
triangles.
3. Does not support free energy computations.
4. Assumes no communications between domains (i.e. assumes that
there is no constraints connecting atoms from two different
domains).
5. Number of thread per blocks should be a power of 2 for
reduction of virial to work.

TODOs:
1. Move more data from the global memory to local.
2. Change .at() to []
3. Add sorting by the number of coupled constraints to decrease
warp divergencies.
4. numAtoms should be changeable (for multi-GPU case).

Refs #2816, #2885

Change-Id: I3c975cf898053b7467bcd30459e60ce2c8852be6

Revision 02a92f23 (diff)
Added by Artem Zhmurov 4 months ago

CUDA version of SETTLE algorithm with basic tests

CUDA-based GPU implementation of SETTLE. This is a part of
all-GPU loop. Can work isolated from other parts of the code
since coordinates are copied to (from) device before (after)
SETTLE kernel call. The velocity update as well as virial
evaluations can be enabled.

To enable, set GMX_SETTLE_GPU environment variable.

Limitations:
1. Does not work when domain decomposition is enabled.
2. Projection of the derivative is not implemented.
3. Not fully integrated/unified with the CPU version.

TODOs:
1. Multi-GPU case.
2. Better virial reduction. This is a more general feature,
not only related to constraints.
5. More cleanup in constr.cpp needed.
6. Better unit tests.

Refs #2816, #2886

Change-Id: I218e1bf1f86a2351e189e3c27f950f45c06135a4

Revision d061dec5 (diff)
Added by Artem Zhmurov 3 months ago

CUDA version of Leap-Frog integrator with basic tests

Part of the GPU-only loop. Curent version is as a stand-alone module,
with its own coordinate, velocities and forces data management.
To activate, set environment variable GMX_INTEGRATE_GPU.

Limitations:

-- Only basic Leap-Frog is implemented.
-- No temperature control.
-- No pressure control.

Refs #2816, #2887

Change-Id: I439d7f5fd4f69a17ca7aaa412e242ce5e3aa5dbd

Revision 1c8eb7c5 (diff)
Added by Artem Zhmurov 2 months ago

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

Revision fb7a59cd (diff)
Added by Artem Zhmurov about 2 months ago

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

Revision 6385f296 (diff)
Added by Artem Zhmurov about 2 months ago

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

Revision b1150eee (diff)
Added by Artem Zhmurov 30 days ago

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

Revision 1bfc9ba5 (diff)
Added by Artem Zhmurov 19 days ago

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

Revision b1be1e72 (diff)
Added by Artem Zhmurov 17 days ago

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

Revision 0cd72f2b (diff)
Added by Artem Zhmurov 15 days ago

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

Revision a80b9cef (diff)
Added by Artem Zhmurov 12 days ago

Make use of reference data in integrator tests

Current version of tests is based on exactly solvable model,
which does not allow for testing more sophisticated cases,
including when temperature or pressure control is enabled.
This commit adds the tests that are based on the reference
data, which can be generated for any existing use-case.

Refs. #2816, #2887.

Change-Id: I64bb2326b0adf44be8b48449ef09cd26939ea467

Revision 1fbaf8ff (diff)
Added by Artem Zhmurov 9 days ago

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

Revision 3d35e919 (diff)
Added by Artem Zhmurov 9 days ago

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

Revision 039709b7 (diff)
Added by Artem Zhmurov 9 days ago

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

History

#1 Updated by Gerrit Code Review Bot 6 months ago

Gerrit received a related patchset '26' for Issue #2816.
Uploader: Artem Zhmurov ()
Change-Id: gromacs~master~Ice7dfdcc6d86c04656b0a1dd4e328c5afdb8a263
Gerrit URL: https://gerrit.gromacs.org/8982

#2 Updated by Gerrit Code Review Bot 6 months ago

Gerrit received a related DRAFT patchset '1' for Issue #2816.
Uploader: Artem Zhmurov ()
Change-Id: gromacs~master~I3c975cf898053b7467bcd30459e60ce2c8852be6
Gerrit URL: https://gerrit.gromacs.org/9193

#3 Updated by Alan Gray 6 months ago

I want to add a subtask here for "GPU Halo exchange", but can't see a way to do it. Are special permissions required?

#4 Updated by Gerrit Code Review Bot 6 months ago

Gerrit received a related patchset '2' for Issue #2816.
Uploader: Alan Gray ()
Change-Id: gromacs~master~I8e6473481ad4d943df78d7019681bfa821bd5798
Gerrit URL: https://gerrit.gromacs.org/9225

#5 Updated by Gerrit Code Review Bot 6 months ago

Gerrit received a related DRAFT patchset '1' for Issue #2816.
Uploader: Artem Zhmurov ()
Change-Id: gromacs~master~I218e1bf1f86a2351e189e3c27f950f45c06135a4
Gerrit URL: https://gerrit.gromacs.org/9244

#6 Updated by Gerrit Code Review Bot 6 months ago

Gerrit received a related DRAFT patchset '4' for Issue #2816.
Uploader: Artem Zhmurov ()
Change-Id: gromacs~master~I439d7f5fd4f69a17ca7aaa412e242ce5e3aa5dbd
Gerrit URL: https://gerrit.gromacs.org/9272

#7 Updated by Szilárd Páll 6 months ago

We need to decouple these changes; there are several distinct features that are proposed here, so we need redmine issues for those. I would also prefer to organize trees of issues around a certain target feature-set, e.g. single-GPU no-DD all offloaded, or multi-GPU with-DD, most offloaded, etc. While feature sets may overlap, the higher-level features are these parallelization functionalities that will depend/be related to both common and individual tasks.
Consequently, at least a separate LINCS, SETTLE, Update, halo exchange, and PP-PME comm issues would be desirable, possibly even separate ones for with/without communication (when this makes sense).

#8 Updated by Alan Gray 6 months ago

Yes. I already tried to create a sub-task here for halo exchange, but couldn't see how to do it. Could you let me know how you did it for the "GPU X/F Buffer Ops" task? It may be a permissions thing.

#9 Updated by Artem Zhmurov 6 months ago

I've created blank features for the GPU-only loop. Will start filling them up .

#10 Updated by Gerrit Code Review Bot 5 months ago

Gerrit received a related patchset '4' for Issue #2816.
Uploader: Artem Zhmurov ()
Change-Id: gromacs~master~I8730aad0ecaa0230686fe89d1157b0da2f01f7bc
Gerrit URL: https://gerrit.gromacs.org/9329

#11 Updated by Gerrit Code Review Bot 5 months ago

Gerrit received a related DRAFT patchset '2' for Issue #2816.
Uploader: Artem Zhmurov ()
Change-Id: gromacs~master~I4c65a6c7088fd8059f4e7fa3cb4637cb2af79ebc
Gerrit URL: https://gerrit.gromacs.org/9349

#12 Updated by Alan Gray 3 months ago

  • Description updated (diff)

#13 Updated by Alan Gray 3 months ago

  • Description updated (diff)

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