[gmx-users] segfault when running the alchemistry.org ethanol solvation free energy tutorial

[Michael Shirts]

Sounds like we've resolved all the confusion.  Thanks for prompt help
in making this clearer and better.

On Thu, Sep 26, 2013 at 7:01 PM, Christopher Neale
<chris.neale at mail.utoronto.ca> wrote:
> Agreed, the following parameters do not segfault in single or double precision:
> sc-alpha                 = 0.5
> sc-power                 = 1
> sc-r-power               = 6
> Same goes for http://bugzilla.gromacs.org/issues/1306
>
> The following parameters give a segfault in single precision but are ok in double precision
> sc-alpha                 = 0.001
> sc-power                 = 1
> sc-r-power               = 48
> Same goes for http://bugzilla.gromacs.org/issues/1306
>
> Sorry for the confusion earlier. I was using a compilation that I thought was double precision
> but it was actually single. Recompiling in double precision gave me the stability outlined above.
>
> Thank you for your assitance Mark and Michael.
>
> Chris.
>
> -- original message --
>
> Michael Shirts mrshirts at gmail.com
> Fri Sep 27 00:41:17 CEST 2013
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> And with this change, single is running fine as well.
>
> This was a known issue, but was only documented in the expanded.mdp
> files, which was an oversight.  After this, I switched so the default
> is less likely to cause problems.  Because of some theory improvements
> developed in the group in free energy calculation pathways, the
> sc-r-power=48 pathway will now be phased out anyway by 5.1.
>
> On Thu, Sep 26, 2013 at 6:37 PM, Michael Shirts <mrshirts at gmail.com> wrote:
>> I thought I had just managed to solve the issue :)
>>
>> If you look at the soft core parameters, there are two types listed --
>> one with sc-r-power = 48, and one with sc-r-power = 6.  The sc-r-power
>> are more stable with single precision calculations.
>>
>> I have changed the files on the website to make the single precision
>> ones the default.  Expanded.mdp warned about the issues with
>> precision, but left the sc-r-power in place; the Ethanol.mdp did not
>> warn about the potential issue.  Now both include the more efficient
>> path commented out.
>>
>> NOTE that this means the exact numbers of the tutorials are not quite
>> right anymore; the process is unchanged, as is the final answer, but
>> the intermediate dG's will be slightly different.
>>
>> However, I need to redo them anyway to make them easier in the next
>> 1-2 weeks, so I will update them then.
>>
>> If it still fails with double, that's a different issue -- because I'm
>> running them fine with double.
>>
>>
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