Question: In my institution, there is a lot of talent available, but for computing we only have a handful of rather old servers available.
My expectation is that many institutions do have the budget to buy 128GB(+) RAM servers priced far north of the 10K pricing mark. Servers that are likely using the Xeon Intel technology, which might be very good processors, but perhaps
not optimal, when one aims to squeeze the most out of the budget (bang for the buck).

The aim is to build a 128(+)GB RAM Computing server for less then 10K.
I was wondering if anyone has any experience/tips regarding buying/building such a 'budget' server. Also, I can say that I am open to any 'hack' or 'trick' that might get the job done. Examples of this could be:

**1.) Use AMD processors**, instead of Intel processors. I find it hard to find out how much this can be a (cost saving)
option. Pricing for servers is not very transparent.

**2.) Use consumer hardware** instead of server hardware. In the link, it is shown how one can get 128GB of RAM
onto a normal PC motherboard: http://www.pcworld.com/article/2938855/hardcore-hardware-we-stuffed-this-pc-with-128gb-of-cutting-edge-ddr4-ram.html .. As far as I can see, using the new DDR4 RAM 8 slots motherboards plus 8x16 ECC RAM kits, this machine could be well under 3K and perhaps it is even possible to put 8 * 32GB RAM kits into such
a motherboard and have a 256GB RAM Computing Server for ~3K (2 x http://tinyurl.com/h3e8om5). I also heard that Xeon processors have some advantages (e.g. larger cache), but is this really worth the extra money in our case? Also, I generally find that the servers are not running on full speed because there are too many large jobs using only one core at certain times, which might influence the overall picture. Assuming it is even a workable solution: ~3K is quite a different number then the 20K+ one might need to pay for a Xeon computing server.

**3.) Cloud services:** Although some of the data we would like to analyse might perhaps be best kept behind a firewall,
it seems that there is a trend of using such services. It seems that people are even analyzing dbGAP data on AWS, these
days, but perhaps these approaches are immature/expensive (if you take: equipment depreciation/power usage, etc. into consideration).

Also, one of this issues is that most vendors that sell server hardware do not put prices on their websites making it
difficult to estimate the cost. I understand that these systems might require some service, but since all these things have to be included in the price, this will likely make it more expensive.

Thanks!

Answer: As soon as you want something to fit in a 1 or 2U space, the cost of everything doubles and the quality doesn't improve a whole bunch more. Yes "server-grade" components tend to be better, but is it worth it? No, not at all. The hard drives fail, capacitors pop, and RAM suddenly stops working with more-or-less the same frequency as consumer hardware. A lot of what you pay for with server-grade hardware is the peace of mind that comes with a warranty - everyone knows that "brush-less titanium-coated metorite graphite" or whatever the sales pitch is, is not going to make a more durable hard drive. The only reason these overly-priced products exist is that some contractors will get paid a % of the cost of the machine they build, and other people have sunk-cost-fallacy issues.

If you're paying for high-performance rather than high-durability, then this is even more obvious -- although to Intel/AMD's credit they're a lot more up-front about it. The difference between a [2.4Ghz octacore chip][1] and a [2.6Ghz octacore chip][2] is a 50% price jump. So as long as you aim for the middle-ground and aren't tempted to "upgrade", you should get a fair deal.

At the end of last year I built myself a compute PC, mainly because I was really struggling to get the software I needed installed on my institute's servers (this was before Devon and a new OPs guy joined my institute - now stuff gets updated before I even know its out of date!). Before then however, the institute servers ran a really ancient version of Red Hat Enterprise Linux with a kernel so ancient I couldn't install some modern tools like Kallisto. Other userland software that couldn't be installed as a user was 8 years + out of date, and the guy responsible for maintaining the servers at the time was very uncommunicative. It was also riddled with security holes and other uncomfortable issues. So I decided to build my own, and this is what I went for:

Motherboard: [ASUS Z10PE-D8][3]

CPUs: 2x [Xeon E5-2640 v3 Octa-core @2.60 GHz ][4] (in hindsight, i wish i got the 2.4Ghz)

RAM: 8x [16Gb Samsung M393A2G40DB0-CPB][5]

Scratch space: A few [Samsung SSD 850 PRO 256GB][6] in RAID0 (I would not buy these now, new SSD prices are crashing).

Long-term storage: x3 4Tb cheap external USB drives from the local supermarket in RAID5

Graphics Card: Some garbage i found at the bottom of a box in my cupboard

Chassis: [Cooler Master Cosmos II][7]

The whole thing cost me €3974, has 32 virtual cores @ 2.6Ghz, 128Gb of RAM

My experience so far in using it has been that it's impossible to make a good all-round compute server for Bioinformatics. Far better to make one for YOUR bioinformatics. For example, mapping reads with Bismark was totally memory-bound, using up all 128Gb of RAM, and utilizing only a handful of cores. Meanwhile, bwa-meth used up all my cores, and only 1/2 the RAM. The GATK pipeline however, really pushed that SSD RAID0 array to its limits - I was constantly having to move data around so I didn't run out of space in /tmp.

But then Devon came and the servers got totally upgraded :P hahahaha - Not that i'm complaining! This is how it should be :D

EDIT: Sorry I wrote this in the time it took Micheal to close it -- and he was right to do so in my opinion because server design/maintenance is not a bioinformatician's job.

[1]: http://www.amazon.com/gp/product/B00N0W3N54/ref=pd_lpo_sbs_dp_ss_2?pf_rd_p=1944687602&pf_rd_s=lpo-top-stripe-1&pf_rd_t=201&pf_rd_i=B00NBP04YI&pf_rd_m=ATVPDKIKX0DER&pf_rd_r=0QQ8C33131ERAVE90Q5Z
[2]: http://www.amazon.com/Intel-Xeon-E5-2640-Octa-core-Processor/dp/B00NBP04YI
[3]: http://www.amazon.com/Memory-2011-3-Motherboard-Z10PE-D8-WS/dp/B00O1AXIHM/ref=sr_1_1?ie=UTF8&qid=1461584937&sr=8-1&keywords=Z10PE-D8%20WS
[4]: http://www.amazon.com/Intel-Xeon-E5-2640-Octa-core-Processor/dp/B00NBP04YI
[5]: http://www.newegg.com/Product/Product.aspx?Item=N82E16820147382
[6]: http://www.amazon.de/Samsung-Basic-MZ-7KE256BW-interne-schwarz/dp/B00LMXBOP4
[7]: http://www.techspot.com/review/541-cooler-master-cosmos-2/