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 [email protected] On Fri, Oct 19, 2012 at 9:31 AM, Szilárd Páll <[email protected]> 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 > <[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 -- 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
