[gmx-developers] last days for 5.1

[Mark Abraham]

Hi,

Update - everything is looking pretty good. I plan 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>
wrote:

> Hi,
>
> On Thu, Aug 6, 2015 at 1:21 PM Kutzner, Carsten <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
>
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