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Subject:

Re: Relion on Cluster

From:

Wolfgang Lugmayr <[log in to unmask]>

Reply-To:

Wolfgang Lugmayr <[log in to unmask]>

Date:

Thu, 21 Apr 2016 11:33:28 +0200

Content-Type:

text/plain

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Parts/Attachments

text/plain (1 lines)

hi huy,

your question are not exact to answer, since relion has a lot of 
different options to use it (mpi, threaded, 2D, 3D, movies, ...).

i don't know your budget, so some things to think of:
- in general prefer high throuput:
-- in the nodes a recent motherboard and bus system (it makes no sense 
if some cores run idle or lower their speed, because they are waiting 
for data)
-- good network connection between the nodes (the big relion jobs depend 
on mpi communication between the nodes)
-- good access to the storage (good network connection and/or parallel 
filesystem)
-- storage accellerator disks can never be wrong

other things:
- put in as much main memory into your nodes as you can
-- most relion jobs run with 6gb/core, but the current movie processing 
step runs sometimes with 16gb/core+

- if you don't have many users with different needs (especially 
single-core jobs):
-- relion runs best if a job gets whole nodes, so if you do not have 
many users and mostly use relion or mpi-based programs consider slurm as 
cluster manager

- consider buying the intel compiler and build optimised executables for 
your hardware

best regards,
wolfgang


On 04/20/2016 08:59 PM, Huy Bui wrote:
> Dear Sjor and list,
>
> I am now thinking to buy a small local cluster for data processing. I 
> want to config an HPC entry cluster manager with RAID storage 
> (64-96TB) and a 4-nodes (8 CPUs).
>
> One question that I got from the salesperson is that whether 
> Relion will write a lot temporarily on the local HDD of the nodes or 
> it will write directly to the central storage, so that they will get a 
> SSD suitable for that. Anyone can tell me the answer?
>
> By the way, is 8 x 10 cores E5-2650 v3 2.3GHz much better than 8 x 8 
> cores E5-2640 v3 2.6Ghz in Relion?
>
> Best regards,
> Huy


-- 
Universitätsklinikum Hamburg-Eppendorf (UKE)
@ Centre for Structral Systems Biology (CSSB)
@ Institute of Molecular Biotechnology (IMBA)
Dr. Bohr-Gasse 3-7 (Room 6.14)
1030 Vienna, Austria
Tel.: +43 (1) 790 44-4649
Email: [log in to unmask]
http://www.cssb-hamburg.de/

-- 
 
_____________________________________________________________________ 
 
Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg | www.uke.de 
Vorstandsmitglieder: Prof. Dr. Burkhard Göke (Vorsitzender), Prof. Dr. Dr. Uwe Koch-Gromus, Joachim Prölß, Rainer Schoppik 
_____________________________________________________________________ 
 
SAVE PAPER - THINK BEFORE PRINTING

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