[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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>
>
--
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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