I am trying to put together a funding request for a cluster and I would be interested to know what people’s thoughts and experiences are regarding optimal cluster configuration for Relion. In particular I am wondering whether lots of 8-core nodes (with ~64 GB RAM) or fewer higher core-density nodes would be preferable for example with 4x E7-8420 cores and ~512 GB RAM? Is 8-12 GB/core an appropriate amount of memory (considering we sometimes work with quite large viruses)? It seems to me that most of the heavy lifting in terms of memory use is done by the MPI master - is this true, and if so is it possible to configure SGE to address MPI jobs to designated high-memory nodes?
Also any comments on where bottlenecks are would be helpful - what is the best networking option (10Gb?), is parallel disk access beneficial?
I would be most grateful for any guidance or recent experience. Finally, should I just forget local hardware and go for a cloud computing option? (What worries me about this is that we then pay for data processing from our grants for ever after rather than a one-off capital equipment award to cover several years of number crunching.)
Many thanks,
D.
Dr David Bhella
MRC-University of Glasgow Centre for Virus Research
Sir Michael Stoker Building
Garscube Campus
464 Bearsden Road
Glasgow G61 1QH
Scotland (UK)
Telephone: 0141-330-3685
Skype: d.bhella
Virus structure group on Facebook: https://www.facebook.com/CVRstructure
Molecular Machines - Images from Virus Research: http://www.molecularmachines.org.uk
CVR website: http://www.cvr.ac.uk
CVR on Facebook: https://www.facebook.com/centreforvirusresearch
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