[AMBER] Simple Amber GPU simulations on GridMarkets Cloud

From: Ross Walker via AMBER <amber.ambermd.org>
Date: Mon, 22 May 2023 09:16:13 -0400

Dear Fellow Amberites,

I wanted to bring your attention to a project I have been working on recently which is to offer easy, cost effective access to GPUs (A4500, A5500 etc rather than the crazy expensive A100/H100s) for running MD simulations. Working with Gridmarkets <https://www.pharma.gridmarkets.com/?utm_source=community_email&utm_medium=amber&utm_campaign=home> we now have the first version of a simple GUI based system for running Amber calculations on cloud based GPUs without the complexity of dealing with marketplace images, S3 buckets, upload and download of files, egress costs etc. There is also a command line interface for those interested in scripting calculations. The available hardware is simply bucketed into "Low", "Medium" and "High" instances so you can select based on required performance and budget.

JAC Production NVE 4fs
    Low . . . . . . (A4000) 808.51 ns/day
    Medium . . . (A5000) 1020.60 ns/day
    High . . . . . .(A6000) 1087.85 ns/day

STMV Production NPT
    Low . . . . . . (A4000) 19.99 ns/day
    Medium . . . (A5000) 29.80 ns/day
    High . . . . . .(A6000) 35.85 ns/day​

This is a great resource if you only need to run MD simulations occasionally and so cannot justify buying onprem GPU hardware or alternatively if you have a lot of calculations you need to run in a short period of time and don't have access to enough GPUs locally.

The idea is to make it as simple as possible to run calculations on remote hardware. For those interested in learning more here is a link to the Gridmarks Amber specific instructions <https://www.pharma.gridmarkets.com/amber?utm_source=community_email&utm_medium=amber&utm_campaign=home> which includes information on getting started. Everyone who signs up gets 10 free credits to try things out, there are no recurring costs or contract, you simply pay for the simulations you using credits that you can purchase on an as needed basis - no surprise AWS EC2 bills!

Amber 22 + AmberTools 23 is precompiled and tested on the hardware. All you need to do is point the GUI at your input files and click submit. There is also a step by step tutorial for running Amber on GridMarkets <https://support.gridmarkets.com/portal/en/kb/articles/submitting-an-amber-job?utm_source=community_email&utm_medium=amber&utm_campaign=home>.

NAMD and Gromacs <https://www.pharma.gridmarkets.com/?utm_source=community_email&utm_medium=amber&utm_campaign=home> are also available and the plan is to add additional life sciences related software over the coming month.

I'd be very interested in your feedback and any suggestions for improvements.

All the best
Ross


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Received on Mon May 22 2023 - 06:30:03 PDT
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