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Is there any solution to the warning that xml-flie is very large and is not scalable for parallel simulations?

0 votes
asked Dec 28, 2015 by mptashnyk FEniCS Novice (300 points)

1 Answer

0 votes

Yes, stop using xml and use the xdmf format.

answered Dec 28, 2015 by chris_richardson FEniCS Expert (31,740 points)

Thanks for the answer. I was tried to change to xdmf format, but getting run time error when convert xml into xdmf format, since xml is really large. Is it possible to refine the grid in xdmf format directly?

commented Dec 28, 2015 by mptashnyk FEniCS Novice (300 points)

If you can open the xml in dolfin in serial, then save as XDMF, that might be easier.

mesh=Mesh('a.xml')
xdmf=File('b.xdmf')
xdmf << mesh
commented Dec 28, 2015 by chris_richardson FEniCS Expert (31,740 points)

Thanks. For a 3D mesh it works, however for 2D mesh it does not work and I am getting RuntimeError.

I have also a general question to FeniCs: Could it be that some of FeniCs (dolfin) functions (commands) have limitation on how much RAM they can use? I have 90GB RAM and in some cases the RuntimeError is a bit surprising (from rough estimations it should be more than enough memory to perform the computations). And if yes, are the possibilities to change this restrictions and allow more RAM to be used.

Thanks

commented Dec 28, 2015 by mptashnyk FEniCS Novice (300 points)

I am sure it does work for 2D meshes. If you want more help, you will have to post the actual error and possibly the mesh file.

As for RAM limitations, it is usually the (third party) solver which takes most memory. You need to say which commands are causing you problems. Post a minimum example.

commented Dec 28, 2015 by chris_richardson FEniCS Expert (31,740 points)

Thank you very much. Will try once more with the 2D mesh and if it still not works - will post the mesh file (but not sure how to post a mesh file of 7GB).

commented Dec 30, 2015 by mptashnyk FEniCS Novice (300 points)
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