> The task generally contain  on the order of 50M to 100M DOFs and are 
> transient DNS problems.

With this you are likely at a point where factorizations (even ILU)
not work very well. Even if you can afford a Block ILU, you likely run
on 100+ cores, which means the quality of the preconditioner will
deteriorate quite a lot just based on the number of processors. You
likely need something that puts more effort into the parallel aspect.

> Our solver : Either GMRES or BiCGStab. In our case it seems GMRES is a bit 
> faster (around 20%) because the iterations are cheaper. I have tried all of 
> the solvers in the TrilinosWrappers except FGMRES actually.

My general advice is to work on the preconditioner to have a method in
the 10-40 iterations range. Then, it doesn't really matter which
Krylov method you use. Just use FGMRES (if you need flexibility), CG
(for SPD), MINRES (for symmetric), or GMRES (for everything else).
Switching between different Krylov methods is unlikely to make a big
difference unless you are in the 100k+ core range or need too many
iterations.

> Our current preconditioner : ILU(0)
> Element order : Q2-Q2, Q3-Q3 or Q4-Q4.

Are you just applying ILU to the whole system? My general advice is to
exploit the block structure of your PDE first and then apply ILU or
AMG to individual blocks. Time dependent Navier-Stokes with small time
steps is a relatively easy case. Let me know if you want more details.


-- 
Timo Heister
http://www.math.clemson.edu/~heister/

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