[gmx-developers] time to make 5.1 happen

David van der Spoel spoel at xray.bmc.uu.se
Sat Feb 14 12:50:12 CET 2015


On 2015-02-14 11:55, Erik Marklund wrote:
> Hi,
>
> Thank you. Now merged.
Pleasure.

Now I have somewhat problematic patch
https://gerrit.gromacs.org/#/c/4354/
that is ready to merge, but in the previous patch to this I broke 
performing fitting to a function with fixed parameters. Upon working 
with the present improvements I found out that fitting with fixed 
parameters is used regularly in g_analyze -ee, so this needs to be fixed 
before 5.1!


>
> Kind regards,
> Erik
>
>> On 13 Feb 2015, at 18:57, Mark Abraham <mark.j.abraham at gmail.com
>> <mailto:mark.j.abraham at gmail.com>> wrote:
>>
>> Hi Erik,
>>
>> Yes, that should be fine.
>>
>> On a wider note, I'm out of time to do 5.1-beta1 today, so I'll try
>> again Monday afternoon.
>>
>> Cheers,
>>
>> Mark
>>
>> On Fri, Feb 13, 2015 at 3:46 PM, Erik Marklund
>> <erik.marklund at chem.ox.ac.uk <mailto:erik.marklund at chem.ox.ac.uk>> wrote:
>>
>>     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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>>
>>
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>
>
>


-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se


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