[gmx-developers] last days for 5.1

[Anton Feenstra]

Congrats all!

On 14-08-15 15:28, Mark Abraham wrote:
> Hi all,
>
> As you may have seen, 5.1 is now live. Thanks all very much for the hard
> work - we hope the new version meets your simulation needs better than ever!
>
> Naturally there's a bunch of things we have been planning for the next
> GROMACS release, so watch this space!
>
> Mark
>
> On Thu, Aug 13, 2015 at 2:24 PM Mark Abraham <mark.j.abraham at gmail.com
> <mailto:mark.j.abraham at gmail.com>> wrote:
>
>     Hi,
>
>     Update - everything is looking pretty good. Iplan to release 5.1
>     tomorrow. Thanks, all, for all the help!
>
>     I haven't done as much work on the docs as I would like, but c'est
>     la vie.
>
>     We've got a new FTP server set up and DNS transfer is underway. I'll
>     put the files on old and new servers so there should be no problems
>     while DNS changes propagate.
>
>     Mark
>
>     On Sat, Aug 8, 2015 at 1:47 AM Mark Abraham
>     <mark.j.abraham at gmail.com <mailto:mark.j.abraham at gmail.com>> wrote:
>
>         Hi,
>
>         On Thu, Aug 6, 2015 at 1:21 PM Kutzner, Carsten <ckutzne at gwdg.de
>         <mailto:ckutzne at gwdg.de>> wrote:
>
>             Hi,
>
>             I wanted to quickly report back on tune_pme for 5.1, what
>             are the issues
>             so we could discuss on how best to proceed.
>
>
>         Many thanks!
>
>             In principle, tune_pme works, however as a user one may have
>             to set extra
>             options so that actually tuning can be done.
>
>             The issues are:
>
>             a) A valid mdrun executable needs to be specified first, see:
>             https://gerrit.gromacs.org/#/c/4771/
>
>
>         OK. I think we need to make this a first-class property of
>         tune_pme, and have proposed such at https://gerrit.gromacs.org/4963
>
>             b) On GPU nodes, mdrun typically segfaults, due to timers
>             not being reset
>             at a neighborsearching step, see:
>             and http://redmine.gromacs.org/issues/1781
>
>
>         Fixed at https://gerrit.gromacs.org/4964
>
>             c) One needs to specify -ntomp somevalue, otherwise it is 1
>             by default
>             and mdrun refuses to run.
>
>
>         Can you provide an example here? I'm not sure what's the
>         problem, to assign blame or to fix! :-)
>
>             Issue b) is probably the most important one to address,
>             which could be either
>             done in mdrun or in tune_pme.
>             Tune_pme would have to determine from the .tpr what the
>             actual neighborsearching
>             frequency will be and adjust the counter resetting
>             appropriately.
>
>
>         Not very workable - nstlist varies according to what hardware is
>         available, and one can't really know that without running mdrun.
>         (e.g. you could run gmx tune_pme from a non-CUDA install and it
>         has no idea that mdrun can use a GPU).
>
>         Mark
>


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | IBIVU/Bioinformatics - Vrije Universiteit Amsterdam   |
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|             | Feenstra at few.vu.nl - www.few.vu.nl/~feenstra/         |
|             | "She's a Good Sheila Bruce" (Monty Python)            |
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