Optimal hardware for large networks

[Mat]

Hi all,

I want to analyze RNAseq data (100.000+ nodes) which means I need a lot of power.

So I'm looking to replace the current system, which is:

12 Gb Ram

Intel XEON X5650 @ 2.67 GHz

ATI FireMV 2260

But I'm wondering what the best system for Cytoscape would be.

For example can Cytoscape work with two different processors and how much will a high-end graphics card contribute to performing analyses in Cytoscape? 

So should I invest in processors or in the graphics card or both?

I have two potential systems here:

Intel Core i7-5960X Boxed

MSI X99S SLI PLUS

HP NVIDIA Quadro K4200

4x 32Gb DDR4 2,4GHz

2x Intel Xeon E5-2630 v3 Boxed

Asus Z10PE-D16 WS

HP NVIDIA Quadro K4200

4x 32Gb DDR4 2,4GHz

So one with a single processor and one with two. What would you preference be based on how Cytoscape works and performs its analyses?

Regards,

Matthias

[Scooter Morris]

Hi Mat,
    The critical thing for managing large networks is the amount of memory.  You certainly don't need the power of a workstation graphics card (the Quadro line) for this generation of Cytoscape (although that might change in the future).  You would be better off with 64Gb of RAM and a less expensive graphics card.  You get 8 cores with the Core i7 and 12 with the two Xeon's, but the Xeon chips run at a much lower clock rate, so I would sort of guess that balances out.  The Asus motherboard with the Xeon's will support a lot more memory (1,024GB vs. 64GB/16 DIM slots vs 4).  On balance, I think I would go with the Core i7/MSI motherboard and max out the memory.   I don't think you're going to get that much extra performance from the extra cores in the Xeon machine.

-- scooter

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[Mat]

Hi Scooter,

Thanks for your swift reaction.

So I'm currently thinking about the following setup:

Intel Core i7-5960X Boxed

MSI X99S SLI PLUS

MSI GeForce GTX 970 GAMING 4G

4x16Gb (64Gb) DDR4 2,1GHz

I think this should work pretty fast. A decent graphics card for when it can be used (for example allegro layout which is a GPU plugin) and still a lot of processor power in case when the graphics card can't be used.

Matthias