[gmx-users] A favor question: experience running Gromacs in the cloud
joris at rescale.com
Fri Oct 19 20:25:30 CEST 2012
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
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.
joris at rescale.com
On Fri, Oct 19, 2012 at 9:31 AM, Szilárd Páll <szilard.pall at cbr.su.se> wrote:
> 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
>> 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
>> I am interested in purchasing temporary computational resources for using
>> Gromacs. Do any of you have experience running Gromacs "in the cloud" --
>> 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
>> Gromacs on a cloud service?
>> Thank you for your time!
>> Andrew DeYoung
>> Carnegie Mellon University
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