Optimal hardware for TPP server?

[Will Comstock]

Hi all,

Kind of a naive tech question, but my lab is going to purchase a Linux server to run the TPP and we're trying to decide on a hardware configuration that would let us run Comet, PeptideProphet, PTM Prophet, XPRESS, Libra, and a few other modules at robust speeds.

We currently run the TPP locally on a Windows PC with 64 cores (AMD Threadripper 3990X) and 128gb of RAM running on an SSD. Would a stronger CPU or more RAM (or even a GPU) give us any significant boost in search speeds if we're running a Docker image of the TPP on a Linux server?

Thank you!

-Will

[Eric Deutsch]

Hi Will, thanks for the question. There no easy answer. An SSD is good because there’s a lot of disk I/O processing data. Comet itself is pretty thrifty with memory, so you won’t need lots of memory for Comet. The Prophets can use a lot of memory if you process huge experiments at once, although they can often be broken up into pieces. Many of our cluster nodes have only 96 GB of RAM and do fine for most datasets. I would probably spend more on cores than on RAM. The machine you list there with 64 cores and 128 GB is a good choice. If you can spend more than that, I think I would increase the core count over more than 128 GB. A GPU won’t help for Comet and the Prophets, so I would save money and go without the GPU.

 

Regards,

Eric

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[Will Comstock]

Thank you Eric, this is very good to know! We'll probably stick with something similar to our current specifications in this case.

Best,

-Will