[gmx-users] Number of nodes

[Mark Abraham]

On 31/10/2011 11:29 PM, Kavyashree M wrote:
> Hello,
>
> System Admin said that the Job fails on 32 and 128 because memory
> is insufficient for each task, so upon increasing the nodes, data gets
> distributed across more number of nodes and each node gets less
> memory occupancy and he also mentioned that he was able to run
> on 512 nodes but it was giving error for not having sufficient data for
> 512 nodes.

That combination of observations is inconceivable. 60K atom simulations 
run just fine on 32 nodes in coprocessor or virtual-node mode, and I'd 
bet 600K atoms is also fine.

>
> I have run the same job on 8 nodes in i7 machine.

A very rough rule of thumb is that at least about a thousand atoms per 
processor is enough to make that number of processors worth using.

Mark

>
> Thank you
> With Regards
> Kavya
>
> On Mon, Oct 31, 2011 at 5:47 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
>     Kavyashree M wrote:
>
>         Dear Users,
>
>         I was trying to run a simulation (gromacs4.5.3)
>         on a Bluegene/L machine. But I was unable to run.
>         System admin say that I need to change the input
>         file. I am not sure what needs to be changed in the
>         input file which specifies no. of nodes usage.
>
>
>     Sounds like your system admin should be offering you some more
>     help, since they know the specifics of the hardware, queuing
>     software, etc.
>
>
>         I am not familiar with the bluegene machines. Kindly
>         suggest the possible solutions.
>
>
>     Without seeing your input file(s), there's nothing anyone can do.
>      Be mindful that this list pertains to Gromacs-specific problems,
>     which do not seem to be present here.
>
>     -Justin
>
>     -- 
>     ========================================
>
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
>     ========================================
>     -- 
>     gmx-users mailing list gmx-users at gromacs.org
>     <mailto:gmx-users at gromacs.org>
>     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 gmx-users-request at gromacs.org
>     <mailto:gmx-users-request at gromacs.org>.
>     Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
>
>

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20111031/8575d156/attachment.html>