Re: [gmx-users] OpenMosix and Gromacs

Thanks for your comments (and sorry for the late answer) Actually, I was not primarily thinking about using OpenMosix to run simulation (that would be stupid considering the size of our cluster). But it could be valuable to have a tool like OpenMosix when you quickly want to setup a system (i.

Re: [gmx-users] OpenMosix and Gromacs

Hi, On Jul 2, 2007, at 11:15 AM, Ansgar Esztermann wrote: On Fri, Jun 29, 2007 at 03:49:01PM -0600, Nicolas Sapay wrote: I wonder if someone has some experience with Gromacs and OpenMosix. Has someone tried recently to run Gromacs in parallel with an OpenMosix cluster? I have read some mes

Re: [gmx-users] OpenMosix and Gromacs

On Fri, Jun 29, 2007 at 03:49:01PM -0600, Nicolas Sapay wrote: > > I wonder if someone has some experience with Gromacs and OpenMosix. Has > someone tried recently to run Gromacs in parallel with an OpenMosix > cluster? I have read some messages about that on the mailing-list but I have not tr

Re: [gmx-users] OpenMosix and Gromacs

OpenMosix indeed provides a second model for clustering besides beuwolf model, which uses MPI, PVM-based communication. You may run thousands of processes and get good scaling. I tried it with normal network, 100M Ethernet, two processes, quite bad efficiency, 1.1-1.3x speed-up. To get OpenMos

Re: [gmx-users] OpenMosix and Gromacs

Nicolas Sapay wrote: Actually, I have used OpenMosix some time ago in a another life :) All I remember is that NAMD was performing reasonably well as far as you didn't ask it to write coordinates every frames. It was handy to minimize/equilibrate a system or do some small computation like press

Re: [gmx-users] OpenMosix and Gromacs

Actually, I have used OpenMosix some time ago in a another life :) All I remember is that NAMD was performing reasonably well as far as you didn't ask it to write coordinates every frames. It was handy to minimize/equilibrate a system or do some small computation like pressure profile. As far a

Re: [gmx-users] OpenMosix and Gromacs

My 0.02. Based on one of Moshe Bar's OpenMosix papers, Mosix increases the performance of MPI processes by load balancing. However I would have to say that this only works for compute bound processes. If there's going to be lots of I/O between nodes Mosix won't do so well and may very well degrade

[gmx-users] OpenMosix and Gromacs

Hi everybody, I wonder if someone has some experience with Gromacs and OpenMosix. Has someone tried recently to run Gromacs in parallel with an OpenMosix cluster? I have read some messages about that on the mailing-list but they have been posted several years ago... Things may have changed now