[gmx-developers] time to make 5.1 happen

[Erik Marklund]

Dear all,

I’ve had a patch for review for a couple of weeks, being one +1 from being accepted. It concerns a periodicity issue with gmx hbond that causes problems for non-periodic systems. May I ask you to consider reviewing https://gerrit.gromacs.org/#/c/4350/ so that it can make it for 5.1? Although most simulations use periodic boxes there is a growing number of gas-phase studies and it would be a shame to keep users waiting for a fully functioning analysis tool when there is a committed bug fix.

Kind regards,
Erik


Erik Marklund, PhD
Postdoctoral Research Fellow, Fulford JRF

Department of Chemistry
Physical & Theoretical Chemistry Laboratory
University of Oxford
South Parks Road
Oxford
OX1 3QZ

On 10 Feb 2015, at 15:30, Magnus Lundborg <magnus.lundborg at scilifelab.se<mailto:magnus.lundborg at scilifelab.se>> wrote:

Hi,

Sounds good. It would be nice to get my latest TNG version patch in there, but it's on master, so perhaps it's already planned.

Cheers,

Magnus

On 02/10/2015 04:00 PM, Mark Abraham wrote:
Hi,

Sorry for quietness on the management front, I've had a bunch of non-code tasks lately. We're a few weeks behind on my original timeline for 5.1-beta1. Various people had expressed hopes of putting code on gerrit, but few things have actually appeared, so I think we should pretty much regard the feature stuff on gerrit now as the maximum extent of 5.1. There's still a bunch of dead / experimental patches on gerrit that won't make the 5.1 cut, of course. Please speak up super-fast if that's a problem - you should have had code in gerrit a month and more ago!

So I plan to roll 5.1-beta1 from master HEAD on Friday, and branch release-5-1 and Jenkins infrastructure at that time. Per my original suggestion, release-5-1 will be open for "feature"-type content for a few weeks while we deal with remaining code review of things currently on master. Once we release 5.1-rc1 (perhaps after another beta if appropriate) then features are frozen. The gerrit cherry-pick feature should be good for people to make clear that they are proposing a "feature" patch for release-5-1.

I'd like to see a couple more of the new Sphinx-based docs commits at https://gerrit.gromacs.org/#/q/status:open+project:gromacs+branch:master+topic:docs get merged, so that we can invite users to give feedback or contribute docs.

It would be great for our colleagues at StreamComputing if we get their OpenCL work out to the world in the first beta; I know Berk has given some feedback but is basically OK with the commit. Szilard has a few outstanding questions we can probably resolve quickly. I have a reservation about whether using more than one Nvidia GPU works, but since that is in any case not a useful configuration for performance, we can hack a temporary fatal error in front of that and ship something usable.

Szilard's CUDA work needs to get in, but the remaining issues there are minor, I think.

Berk's halo-decomposition is not yet clearly useful (right, Berk?) so perhaps we will leave that on the shelf for now.

Erik's SIMD support patches need one more reviewer. It would be nice to be able to say to hardware devs that we already have preliminary support in released code when early-phase testing is on the cards.

Happy hacking!

Mark



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