See below for some considerations when buying a computing cluster to run 
relion on.
S


-------- Original Message --------
Subject: 	Re: Optimal cluster for Relion
Date: 	Mon, 2 Jun 2014 15:48:48 -0400
From: 	Brad Battey <[log in to unmask]>
To: 	[log in to unmask]



Thank you Sjors!  This is very helpful.

Do feel free to forward this on.

-Brad

On Jun 2, 2014, at 6:20 AM, Sjors Scheres <[log in to unmask]> wrote:

> Hi Brad,
>
> Relion uses hybrid parallelisation, so one can scale using MPI and make
> use of shared memory using pthreads. Therefore, as long as each node has
> in total sufficient memory, one can always run multiple threads (and only
> one MPI job) on each node. Therefore, RAM/core isn't that important:
> RAM/node is more relevant. The bigger the box, the higher the RAM usage.
> Our own nodes are 12-cores with 60Gb of RAM in total. For our
> high-resolution ribosome refinements (in ~400x400 boxes) we use up to 32Gb
> of RAM per node. I wouldn't recommend buying anything less than 32Gb per
> node.
>
> HTH,
> S
>
> PS: would you mind if I forward this message to the ccp-em list?
>
>
>> Hi Sjors,
>> 	My name is Brad Battey and I am the IT Manager of the University of
>> Michigan’s Life Sciences Institute.  We are in the process of spec’ing
>> out a local cluster specifically for CryoEM use.  I’ve been asked to make
>> sure we optimize for the two most heavily used computational apps used
>> our small Cryo cluster today (EMAN2 and Relion) but also the parameters
>> required to take best advantage of our high resolution direct detectors
>> (7k x 7k).  It seems that EMAN2 is happy with 10gigabit ethernet networks
>> and just a few GB of RAM per core, but I’m having trouble locating
>> anything concrete about Relion’s preferred compute environment. A recent
>> thread in the CCPEM list (Re: Cluster Survey) asked after compute and
>> cluster specs for a specific box size and particle count, but it did not
>> garner any useful responses.
>>
>> 	If you have a couple moments, can you share some info on what Relion
>> likes in terms of RAM per core and connectivity?  If you have some sort
>> of roadmap, can you give some guidance how planned future features may
>> affect both?
>>
>> 	Many thanks in advance for any help you can provide!
>>
>> 	Sincerely,
>> 		Brad Battey
>> 		IT Manager
>> 		University of Michigan Life Sciences Institute
>
>
> --
> Sjors Scheres
> MRC Laboratory of Molecular Biology
> Francis Crick Avenue, Cambridge Biomedical Campus
> Cambridge CB2 0QH, U.K.
> tel: +44 (0)1223 267061
> http://www2.mrc-lmb.cam.ac.uk/groups/scheres
>