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 <jalem...@vt.edu
<mailto:jalem...@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
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