Hi Anthony,
Good choice, your admins should be able to help. Do emphasize when talking
to them that you need your job to be placed as compact as possible, on
the closest possible set of cores with the tightest possible affinity
settings.
Cheers,
--
Szilárd
On Thu, Aug 20, 2015 at 6:12 PM,
Hi all,
I appear to have a very high load imbalance on some of my runs. Values
starting from approx. 7% up to 31.8% with reported vol min/aver of around
0.6 (I haven¹t found one under half yet).
When I look through the .log file at the start of the run I see:
Initializing Domain Decomposition
Hi,
In cases like this, it's good to describe what's in your simulation, and
share the full .log file on a file-sharing service, so we can see both the
things mdrun reports early and late.
Mark
On Thu, Aug 20, 2015 at 8:22 AM Nash, Anthony a.n...@ucl.ac.uk wrote:
Hi all,
I appear to have a
Hi Mark,
Many thanks for looking into this.
One of the log files (the job hasn’t finished running) is here:
https://www.dropbox.com/s/zwrro54yni2uxtn/umb_3_umb.log?dl=0
The system is a soluble collagenase in water with a collagen substrate and
two zinc co-factors. There are 287562 atoms in the
Hi,
You're not pinning threads and it seems that you're running on a large SMP
machine! Assuming that the 512 threads reported (line 91) is correct that's
a 32 socket SMP machine, perhaps an SGI UV? In any case Xeon E5-4xxx is
typically deployed in 4-8 socket installations, so your 8 threads will
On Thu, Aug 20, 2015 at 5:52 PM, Szilárd Páll pall.szil...@gmail.com
wrote:
Hi,
You're not pinning threads and it seems that you're running on a large SMP
machine! Assuming that the 512 threads reported (line 91) is correct that's
a 32 socket SMP machine, perhaps an SGI UV? In any case Xeon
Hi Szilárd
Thanks for all of that advice. I’m going to have to take a lot of this up
with the Cluster Service Staff. This is a new cluster service I won a
grant for, thus not my usual platform which would typically yield an
imbalance of somewhere around 0.8% to 2%.
Thanks again
Anthony
On
