Also, have you tried optimising the bandwidth of the sparse system by 
renumbering 
the DoFs 
<https://www.dealii.org/8.4.0/doxygen/deal.II/namespaceDoFRenumbering.html>?

On Friday, July 22, 2016 at 12:30:01 PM UTC+2, Matthias Maier wrote:
>
> > I have the feeling, that my setup is the root cause of poor performance 
> > of both solve and assemble (3s for assemble in release mode for 2000 
> dofs 
> > is according to my opinion slow [17s in debug mode]). 
>
> Have you run your computations against the debug library, or against the 
> optimized release library? More precisely, does 
>
>   $ make release 
>   $ make run 
>
> improve the timings? 
>

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