[gmx-users] A favor question: experience running Gromacs in the cloud

Szilárd Páll szilard.pall at cbr.su.se
Fri Oct 19 18:31:39 CEST 2012


When it comes to hardware, pretty much the only thing that matters is
processors (CPUs and maybe GPUs) , memory will always be more than enough
-- unless you plan to run massive analysis in the cloud. In general, if
your simulation system runs fast enough on a single compute node (1-2
CPUs), the could could very well be worth it. When it comes to running over
a network, I'm not sure what the cloud-based options are, but I think it is
not not worth bothering with anything slower than 10G Ethernet or

If you are not after a few long trajectories, but you're doing
some ensemble-simulations and need lots of independent trajectories, the
could will be quite well suited, especially if you can manage the
simulations in an elegant manner, e.g. see http://copernicus-computing.org.

I have no first hand concrete experience, but I know that some GROMACS
developers have been testing Amazon EC2 instances with pretty positive
results. You can get really low prices and good performance with the
"High-CPU Spot Instances".

Just to make it clear, I do not mean to advertise Amazon EC2, just that
I've only heard about first-hand experiences on this resource. There are
quite a few other cloud providers, so you might want compare and try before


On Fri, Oct 19, 2012 at 1:59 AM, Andrew DeYoung <adeyoung at andrew.cmu.edu>wrote:

> Hi, Gromacs users,
> If you have time, I am wondering if you have any advice, as a favor.
> I'm a graduate student in computational chemistry in the U.S.  My
> department
> has an EXCELLENT "in-house" cluster, on which I routinely run Gromacs jobs
> on 8 to 24 cores.  However, it occasionally happens that I run into a
> "crunch time" need for some more computational resources.  For example, I
> recently found a mistake (an incorrect parameter) that I made in an .itp
> file that I wrote.  This means that I need to rerun a whole slew of
> simulations as quickly as possible so that I can continue on with the
> project.
> I am interested in purchasing temporary computational resources for using
> Gromacs.  Do any of you have experience running Gromacs "in the cloud" --
> on
> a service such as Amazon EC2 (http://aws.amazon.com/ec2/)?  For my quick
> need for computational resources, some sort of cloud solution looks
> interesting to me.  On the other hand, I could apply for time on XSEDE
> (https://www.xsede.org/), but that would probably be a lengthier process,
> and probably more suitable for a longterm solution.
> The problem with the cloud idea is that I am not an expert on computers and
> networking, so I am worried that actually successfully using cluster time
> might be difficult (whereas I have heard that, in contrast, Gromacs is
> sometimes more or less pre-installed on university/national lab-based
> supercomputer resources available through XSEDE grants).  Have you ever
> used
> Gromacs on a cloud service?
> Thank you for your time!
> Andrew DeYoung
> Carnegie Mellon University
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