[Dock-fans] Parallel processing resource allocation question

Phan, Jason jason.phan at Vanderbilt.Edu
Wed Apr 18 09:08:27 PDT 2012

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:

> 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
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