Forum:Construct a small computing server for GWAS Analysis

Question

[mkh]

Hi All,

I would like to build up a small private server for high-throughput sequence analysis purposes. Unfortunately, I have no experience with building up such a computing server. I would appreciate if you can make a comment on this. What type of criteria do I need to consider? I know the high RAM (like 250 GB) or 16TB storage with 32 core, are good for such a server but I need to have more information in order to order a server.

Do I need to consider the IT structure of the university? What type of criteria do I need to consider in order to be able to connect to the server remotely?

Thank you,

[steve]

you should consider just using AWS or GCP

[Ram]

This is the route I'd go. For a considerably lower price than purchasing a computer, you'd get to try out various hardware configurations and settle on one, while spending not more than $1000 in a year. Once you have a configuration picked, you should be able to lease it yearly/3 years for quite a bit of discount. If you make a miscalculation purchasing a computer part, it might not be easy/inexpensive to undo it so be careful.

[ATpoint]

Do I need to consider the IT structure of the university

If there is a relevant installation at your institution use it. I would check if they provide a HPC that you can access. That would save you the installation- and maintenance work given you build something yourself which only distracts you from your actual scientific work.

What type of criteria do I need to consider in order to be able to connect to the server remotely?

Well I guess nothing special beyond a stable internet connection and a terminal (at least I have nothing special beyond this to connect to our HPC).

[mkh]

thank you for reply. the problem is that i am going to use this server to prepare md simulation as well. the hpc at my university is very expensive and it would be more cheaper for me to have my own server for my primary computation and only use hpc of ut for only heavy analysis. somebody suggest me to use thinkmate website to build and order server (or microsuper computer however i dont have skill to order hardwares.

[GenoMax]

i dont have skill to order hardwares

While fun if you have never done this before then you should practically think about this idea again.

Have you actually priced out components that you list above? 32-core threadripper (AMD) CPU alone is ~$550. Motherboard may be ~$250 and at the most may support 128 GB DDR4 RAM (which itself would be ~$700-$1000+). Going Intel xeon route would add hundreds more to the cost. You would be easily looking at spending $3-5K. Then you would have to deal with individual manufacturers if something breaks and requires warranty service.

If you insist on having your own machine then buy something pre-assembled from a reputable vendor (you may be able to get academic discounts). This would be more expensive but the machine will come with one source of warranty and peace of mind. You can pull the computer out of box, plug it in and have it work without any hassle.

[mkh]

thank you. Any suggestions for vendor?

[GenoMax]

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