[gmx-users] Simulation runs on iMac but explodes on cluster

Mark Abraham Mark.Abraham at anu.edu.au
Wed Jul 13 11:38:20 CEST 2011

On 13/07/2011 7:32 PM, Luke Goodsell wrote:
> Hi Per,
> I did as you suggested and it's just reached step 15000 and is still 
> going. Many thanks indeed!

I'd still be skeptical. 15000 steps is a long time for the trajectories 
to diverge. If you can run to 14550 with SSE and stop, and then show 
that continuing with SSE explodes and unoptimized kernels do not, then 
you have serious evidence of a bug. Diagnosing the cause of such a bug 
will need such a test case, anyway.


> Is there something I can do to extract useful debugging information to 
> submit to redmine?
> Luke
> On Wed, Jul 13, 2011 at 10:00, Per Larsson <per.larsson at sbc.su.se 
> <mailto:per.larsson at sbc.su.se>> wrote:
>     Hi!
>     Could you try running with GMX_NOOPTIMIZEDKERNELS=1, to see if
>     this could potentially be a bug in the sse code (I noticed
>     nb_kernel410_x86_64_sse in your error message.
>     Thanks
>     /Per
>     13 jul 2011 kl. 09.35 skrev Luke Goodsell:
>     > As the subject suggests, I have a simulation that runs correctly
>     on my iMac, but fails when I try to run it on a cluster, and I am
>     hoping someone may be able to suggest which things to try first to
>     resolve the issue.
>     >
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