Hi Chris,
I mentioned that PS would have helped! I am sorry about the confusion. I should
have been more clear. I guess you have not followed the particle decomposition
threads lately :))
The PD option has been associated some serious issues lately … notably I
noticed it does not work well i
Thanks for the hint XAvier.
Unfortunately, I get crashes with particle decomposition (see below). If I use
either DD or PD, I can run on up to 2 threads
without adjusting -rdd or -dds. I can only use >2 thread with DD if I set -rdd
2.8. If I try to use more than 2 threads with PD,
I get lincs
Yes it is a pity!
But particle decomposition helps :)) well helped!
>
> It's a shame that long distance restraints limit the parallalization so much,
> but it is understandable. Thanks for helping me with this.
>
> Chris.
>
> -- original message --
>
> Initializing Domain Decomposition on
Indeed, sorry that I didn't notice that, Mark. Looks as if the two-body bonded
interaction gets multiplied by 1.1/0.8 so I suppose that this is working as it
should.
It's a shame that long distance restraints limit the parallalization so much,
but it is understandable. Thanks for helping me wit
Hi,
The log file gives a breakdown of how the minimum cell size was computed.
What does it say?
Mark
On Oct 17, 2013 5:17 AM, "Christopher Neale"
wrote:
> I have a system that also uses a set of distance restraints
>
> The box size is:
>7.12792 7.12792 10.25212
>
> When running mdrun -nt
I have a system that also uses a set of distance restraints
The box size is:
7.12792 7.12792 10.25212
When running mdrun -nt 8, I get:
Fatal error:
There is no domain decomposition for 8 nodes that is compatible with the given
box and a minimum cell size of 3.62419 nm
However, the larges
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