[Dock-fans] Parallel processing resource allocation question

John Irwin jir322 at gmail.com
Wed Apr 18 16:31:28 PDT 2012


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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