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 <[email protected]>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 > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
