Re: [AMBER] Amazon Cloud services and Amber

From: Luca Codutti <>
Date: Wed, 12 Aug 2020 14:58:40 +0200

I include an old email from my experience from 22/08/18

Dear all,

I want to share my experience, especially with academic colleagues, of
running Amber18 in Amazon AWS, to give you a rough idea of the iter,
costs and performance of the system.

1. Customer activation and setup of EC2 machine

Activation of the account was straightforward, but after selecting the
server zone I had to wait a couple of days to get a P3.2xlarge instance
activated. The default limit is 0 and you need to send a customer
support request to activate it.

I selected an ubuntu 16.4 server image and 64GB of space in a EBS space.
You must  select an EBS volume if you want to keep the virtual machine
once switched off. Installation of cuda and amber was straight forward
following the manual of Amber and CUDA 9.2 ubuntu installaation
istructions. I also installed intel MKL libraries.

2. Run

I did an aMD test on a system which has ~180K atoms, in TIP3P water.
AMber18 patch 9 on the Nvidia Volta V100 GPU (single card) performed an
average of 96.5 ns per day.

3. Costs

On this system 25 Hrs of usage and including data transfer accounted
with taxes for about 140 $ . The price does not include storage which is
however quite cheap.

2. Issues

Most of the issues I had to face were related to the too fast data
accumulation on the HD, with hindsight I would have selected a bigger
storage space. To overcome the problem I had to prepare a script which
rsyncs and deletes the trajectories as soon as they are done to keep the
hard drive free.

All the best

On 8/12/2020 2:24 PM, Debarati DasGupta wrote:
> Hello everyone,
> I was wondering has anyone used AWS for Amber18 simulations and can guide me to some resources wherein I can see the compute costs and details about Amazon cloud services?
> At the lab we currently have 20 Nvidia RTX 2080 TI machines, but because of an influx of new rotation students/postdocs we were thinking whether we could transition to AWS...
> Any ideas on expensive or not-expensive it will be ?
> Thanks
> Debarati
> _______________________________________________
> AMBER mailing list

Dr Luca Codutti
Carlomagno Group
Universität hannover - BMWZ
Schneiderberg 38, PLZ30167
Tel.  +49 511 762 16353
AMBER mailing list
Received on Wed Aug 12 2020 - 06:00:06 PDT
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