ADL: compute cluster

Daniel Jana dfjana at gmail.com
Wed Aug 22 10:30:43 PDT 2007


On 16/08/07, Miguel Quiliano Meza <qilime at yahoo.es> wrote:
> Dear  Autodock community
>
>  I have heard that is possible run autodock on compute cluster,  well..
> now I have a question: how can I parallelize my computer with autodock4?
> I have a little cluster of 6 computers with LINUX  so I was surprised
> because the tutorial does not mentione nothing about that.

I have not search deep enough about this but...

This paper:
http://scripts.iucr.org/cgi-bin/paper?kk5006
(of this year) talks about the parallelization of Autodock. I do not
have access to that journal so I cannot read the entire content of the
paper but it seems to me that it is not an official modification.

On the other hand:
http://www.hpcvl.org/faqs/autodock/autodock.html#4
says that version 3 of Autodock is serial only. When I installed
version 4 I did not see any info on it working in parallel so I'd say
that it is still a serial only program.

So, to the best of my knowledge (and unlike you heard) Autodock is not
available in a parallel form.
However, this does not stop you from using it in a computer cluster
(and perhaps that's what someone tried to tell you). We have Autodock
running on a small cluster of 20 computers (with a total of 40
processors). We use Autodock in one of the serial queues. If you need
some more details I can give you, but it isn't anything out of the
ordinary.

Once again, I may be wrong.

Daniel Jana


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