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

[Joris Poort]

At Rescale (www.rescale.com) we have cloud-based options for 10Gb/s
I/O to run mpi versions of Gromacs.  The performance for these has
been very good and can scale to hundreds of simulation dynos
(computing nodes).

Regardless of which service you use, I would highly recommend trying
some of the cloud options.  Cloud-based computing is a very cost
effective way to get your results fast without any upfront investment
and you only pay for what you use.

Cheers,
Joris

Joris Poort
Rescale
joris at rescale.com

On Fri, Oct 19, 2012 at 9:31 AM, Szilárd Páll <szilard.pall at cbr.su.se> wrote:
> Hi,
>
> 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
> Infiniband.
>
> 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
> buying!
>
> Cheers,
> --
> Szilárd
>
>
> 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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