[Dock-fans] Parallel processing resource allocation question
jason.phan at Vanderbilt.Edu
Wed Apr 18 16:40:03 PDT 2012
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.
On Apr 18, 2012, at 6:31 PM, John Irwin wrote:
> Hi Jason
> What do you mean by the ring subset?
> 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?
>> On Apr 18, 2012, at 10:53 AM, John Irwin wrote:
>>> 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.
>>> 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?
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>>>> Dock-fans at docking.org
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