desktop bioinformatics platform specs
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7.6 years ago
rob234king ▴ 610

I've had an enquiry about an individual that works in an institute without any supercomputer/cluster facilities. They want to setup their own desktop bioinformatics computer. They are only going to be doing fungal genome assembly/annotation and trinity jobs so 64 gb ram should be ok for fungal transcriptomes etc. I was thinking something like below but not big on hardware. Any ideas on spec recommendations for say £2000-4000 British pounds? Looking for an idea on specs to suggest to them to source quotes on

How about? only mention those above just getting the cheapest item i.e. no need to get anything but the basic graphics card

intel core i7 Eight core processor extreme i7-5960X (3.0GHz) 20MB cache

Gigabyte X99 Gaming 5P: E-ATX, LG2011-3 USB 3.0 SATA 6GBs

64 GB Kingston HYPER-X predator Quad-DDR4 3000MHz (8 x 8 GB)

2 TB 1st hard drive

6 TB 2nd hard drive

RAID 1

Corsair 650W series VS-650 Power supply

Corsair H100i GTX Hydro series high performance CPU cooler

no windows

hardware desktop • 4.1k views
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I suggest throwing in a 250Gb SSD for the root partition (faster boot time and excution); also,if you have to handle lots of small files they can be quite nice. 64Gb RAM is a very good idea. Trinity and lots of similar software can always use more CPU cores for faster execution. As for GPUs, well they are not often used in bioinformatics at the moment.

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Maybe things have improved since I last made a RAID1, but i don't think you can have your hard drives different sizes. I mean you can, but the second drive will be limited to the size of the first. Perhaps you can put a second, non-backed up partition on it... hmm... i dont know.
Also, looking at your price range, you might want to consider a Xeon rather than some premium gamer CPU. You'll save money, and it will actually be a better chip in my humble opinion.

http://ark.intel.com/compare/83359,82930

Although they are essentially the same chip in many aspects, the Xeon supports much larger amounts of total RAM if for whatever reason you one day wanted to add more than 64Gb.
Also this particular xeon CPU can be paired with another in a dual-cpu setup if you buy the right mother board.
This might sound like overkill now (although such a system would still be less than 4000 GPB), but in 2 years time when a second identical Xeon can be had for under 500 GBP, it will be much cheaper to buy another one than a modern 16-core CPU after throwing your i7 away.
Dont be fooled by the baseline difference in processing power - its basically nil since the Xeon powers down when not used to save energy and lifespan. When you do any mapping/etc, you'll get the same speed as the i7. The main difference really is that it runs a lot cooler when idle, is cheaper, and can utilize more than 10x as much total RAM. Just stick to Intel-accredited RAM and not aftermarkets as the Xeons dont play nicely with heat-sink-encrusted RAM.

One final word - lots of RAM and an SSD almost always means DONT make a swap partition! Unnecessary swapping ruins the SSD life, and actually hurts (somewhat) performance. In fact, don't buy an SSD at all, because in the next few weeks the entire market is going to change:
http://www.tomshardware.com/reviews/ssd-recommendation-benchmark,3269.html
and very low-cost SSDs will become much more prevalent.
I found this out just a week ago having just bought three 250Gb Samsungs on my stipend (-_-')

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They should buy ECC memory. In my opinion, I think they should buy "server" hardware instead of "gaming" hardware: even if performance is worst, it should be more durable and reliable.

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For things I can't be bothered to move to the cluster, I have a workstation from Broadberry. I actually have more cores than the individual cluster nodes, so increasingly it's simply replacing it completely for me. You can configure them in every respect and a) it's server hardware b) comes with a warranty c) is an awful lot better than that for the money. You can configure a 32-core Opteron system with 128G RAM and SSD scratch for £4k! http://www.broadberry.co.uk/amd-opteron-6000-workstations

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Your specs seem reasonable, and +1 on Cyril's suggestion for the SSD root/boot drive.

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The Mac Pro tends to be cheaper than equivalent Dell, HP, etc. options, especially at the higher ends (more cores, etc.). You could get better processors (Xeon E5) for around the same money, while trading hard drives for an SSD. Might be worth investigating.

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This is what I use when I am not on cluster. Have linux and added 2x ram and 3x4tb drives(costs you like 150$ per piece) in addition to base specs.

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