[Dock-fans] Parallel processing resource allocation question

Phan, Jason jason.phan at Vanderbilt.Edu
Wed Apr 18 16:40:03 PDT 2012


Hi John,

I meant the heterocyclic ring subset on the Zinc.docking.org site. I can use filters to pick them out but if there's a clean subset, it'd be nice to be able to download.

http://zinc.docking.org/browse/rings/?page=1&type=simple

Jason

On Apr 18, 2012, at 6:31 PM, John Irwin wrote:

> Hi Jason
> 
> What do you mean by the ring subset?
> 
> John
> 
> 
> On Wed, Apr 18, 2012 at 9:08 AM, Phan, Jason <jason.phan at vanderbilt.edu> wrote:
>> Got you! Thanks.
>> 
>> Is it possible to download the ring subset from ZINC for docking?
>> 
>> Jason
>> 
>> On Apr 18, 2012, at 10:53 AM, John Irwin wrote:
>> 
>>> Jason
>>> 
>>> My advice to you and anyone using DOCK 5.X or 6.X is to upgrade to
>>> DOCK 6.5. It contains many significant changes and bug fixes. It is
>>> not worth spending another minute of your life on DOCK5.4.
>>> 
>>> John
>>> 
>>> 
>>> On Wed, Apr 18, 2012 at 8:46 AM, Phan, Jason <jason.phan at vanderbilt.edu> wrote:
>>>> Dear All,
>>>> 
>>>> Sorry if this has been addressed already and if so please point me to those threads. I'll move to dock6.5 soon but right now, I'm stuck with dock5.4. Using mpiexec -n 12 dock5mpi -i etc..., it only lets me use 12 processors (e.g. nodes=4:ppn=3 or nodes=6:ppn=2 or any of the combinations that add up to 12 processors total). If I go over 12, it got bumped out with this error: "Error: Missing parameter/value pair" and eventually, "Parameterization Failed. 16 missing parameters". If I stay at 12 or lower, no problem. Also, while this is running, I cannot start another dock run... same error. It looks like these processes are competing for some parameter files. I did copy them to a local directory but did not help. Any suggestions?
>>>> 
>>>> Thanks,
>>>> Jason
>>>> _______________________________________________
>>>> Dock-fans mailing list
>>>> Dock-fans at docking.org
>>>> http://mailman.docking.org/mailman/listinfo/dock-fans
>>> 
>> 
>> 
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> 




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