GROMACS

I'd suggest creating subtasks to tack progress of what needs to be done.

There are a couple of PME CPU unit test patches sitting idle in Gerrit.
These are https://gerrit.gromacs.org/6251/ and https://gerrit.gromacs.org/6337.
I would like to get these in sooner rather than later,
as the GPU spline computation/spreading patch involves the unit test which builds both on those and on the main PME GPU patch https://gerrit.gromacs.org/6212 as well.
Don't be discouraged by their sizes - most of that is just generated reference data, the actual code is ~500 lines in each.

Gerrit received a related patchset '10' for Issue #2054.
Uploader: Aleksei Iupinov (a.yupinov@gmail.com)
Change-Id: gromacs~master~If5ec49f030b9b94395db28fa454ea25c3efb05d1
Gerrit URL: https://gerrit.gromacs.org/6357

Gerrit received a related DRAFT patchset '2' for Issue #2054.
Uploader: Aleksei Iupinov (a.yupinov@gmail.com)
Change-Id: gromacs~master~I162e3a14cb9aa8ddeac17c5ad1ca709df72b8986
Gerrit URL: https://gerrit.gromacs.org/6437

Gerrit received a related patchset '4' for Issue #2054.
Uploader: Aleksei Iupinov (a.yupinov@gmail.com)
Change-Id: gromacs~master~Ic610e7f077f39a64089dd9b80df9905094b10459
Gerrit URL: https://gerrit.gromacs.org/6459

Gerrit received a related DRAFT patchset '16' for Issue #2054.
Uploader: Aleksei Iupinov (a.yupinov@gmail.com)
Change-Id: gromacs~master~I9e705b86d5aa07d59544de68234cdd6242ad1194
Gerrit URL: https://gerrit.gromacs.org/6472

I would like to urge everyone to review the low-level PME GPU building blocks:

https://gerrit.gromacs.org/#/c/6357/ (spreading kernel)
https://gerrit.gromacs.org/#/c/6459/ (solving kernel)
https://gerrit.gromacs.org/#/c/6437/ (gathering kernel)
https://gerrit.gromacs.org/#/c/6212/ (the data structures, their management, cuFFT calls) - this one is large and already has some renaming/cleanup TODOs, which would be much easier to resolve when all these 4 changes are merged in.

There is more work to do if you look at https://gerrit.gromacs.org/#/q/topic:pme, so I suggest that these components are reviewed first - they have been sitting there for a while, and I think they would do more good being tested by users of the master branch with included unit-tests.

Note that there is a GPU-task assignment change https://gerrit.gromacs.org/#/c/6205/ which sits at the bottom of the PME GPU branch (and in hindsight probably should have started higher), so I would appreciate more reviews on that as well. Otherwise, rebasing the core PME GPU changes once they're reviewed to skip it should be trivial.

Gerrit received a related DRAFT patchset '2' for Issue #2054.
Uploader: Aleksei Iupinov (a.yupinov@gmail.com)
Change-Id: gromacs~master~I5af2ab95cedff422c39592255f01205d42fc7eb7
Gerrit URL: https://gerrit.gromacs.org/6670

Mark Abraham wrote:

This is now implemented as intended

Yeah, suggest closing.

OK, I'm just not familiar with issue tracking logic - if we implement e.g. coordinate conversion kernel, or PME GPU decomposition, and make an issue for that, is it alright for it to have a closed parent?

Aleksei Iupinov wrote:

OK, I'm just not familiar with issue tracking logic - if we implement e.g. coordinate conversion kernel, or PME GPU decomposition, and make an issue for that, is it alright for it to have a closed parent?

We targeted this feature for the next release. While some of the subtask did not materialize (but overall the feature was implemented), it might be cleaner to close this issue and continue with the few smaller remaining tasks. #2208 and #2240 should be possible to resolve on way or another.

yeah we'll make new tasks (that can refer to this one) when we decide to do future work to add mroe functionality.

Does anyone have any rough suggestions where to start implementing PME with free energy on GPU?

Gerrit received a related patchset '1' for Issue #2054.
Uploader: Magnus Lundborg (magnus.lundborg@scilifelab.se)
Change-Id: gromacs~master~Ibc610cb63afaadf4aa97608b8e03b6906fe2d026
Gerrit URL: https://gerrit.gromacs.org/8305