[gmx-users] Number of nodes

Kavyashree M hmkvsri at gmail.com
Mon Oct 31 13:29:17 CET 2011


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.

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

Thank you
With Regards

On Mon, Oct 31, 2011 at 5:47 PM, Justin A. Lemkul <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
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> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
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