ADL: Best modern hardware for autodock vina use

Witold Witkowski wwitkowski at bostonbiomedical.com
Tue Apr 29 08:39:54 PDT 2014


Just to add my own experience, after about 16 threads on a AMD multicore
machine, it seems that you saturate the memory bus bandwidth, so you get
diminishing returns. After about  24 cores, cores 16-24 are at about
60%-80% utilization, and it drops fast from there. (I tried it across 128
procs in one run for fun, cores 64+ were fairly idle)

My Vina machines are all 8-12 core machines with about 32 gigs of memory.
Vina never seems to hit the memory hard, so I¹ve never even touched swap
on them. I think 32 Gigs was the standard config when I bought them
though. 

If you can, I would spin up a few virtual instances at your friendly
neighborhood IaaS provider and try it out. Its a cheap way to see what
your needs will be.

Cheers

-W2



On 4/28/14, 4:40 PM, "Brian Moldover" <moldoverb at gmail.com> wrote:

>If you're into building your own, you can put together a quad processor
>server pretty easily and populate it with multicore processors. Vina won't
>necessarily need to use all the processors per docking, but you can write
>some scripts and run multiple jobs at once.
>
>I build a 32-core test server last year for about $2k. Supermicro
>motherboard and  8-core Opteron 6100 processors. Put in in a 4u server
>case.
>The newer boards allow up to the 16-core chips, but those are expensive.
> 
>-----Original Message-----
>From: autodock-bounces at scripps.edu [mailto:autodock-bounces at scripps.edu]
>On
>Behalf Of Aiden Aceves
>Sent: Monday, April 28, 2014 3:44 PM
>To: autodock at scripps.edu
>Subject: ADL: Best modern hardware for autodock vina use
>
>Hi All,
>I am in the process of writing a grant to purchase hardware for running
>Vina. If my budget is $3000 or so, what is recommended? I know number of
>cores and clock speed are important, but what about RAM? I have been
>looking
>at dell power edge servers, with xeon processors, and also desktop
>octa-core
>chip sets. I will be preforming 10's of thousands of dockings.
>Thoughts?
>
>--
>Aiden J. Aceves
>860903101
>Undergraduate Student
>BS, Chemistry
>University of California Riverside
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