Ok - MeshCommunication::assign_global_indices() is beyond my
comprehension... BUT there are a couple of "#if 0" error checks in there
that if un-#if'd they do trigger these things with my test case:
Error: nodes with duplicate Hilbert keys!
node 7, (x,y,z)=( 0.5, 0.5, 0) has HilbertIndices
3758096384_0_0
node 9, (x,y,z)=( 0.5, 0.5, 0) has HilbertIndices
3758096384_0_0
So I do suspect that to be the issue...
So what to do? We basically shouldn't be relying on Hilbert indices for
this part of libMesh.
Is it time for a new IO type for EquationSystems? Should I do an
EquationSystemsCheckpointIO class like I did for the mesh? If you don't
care about m->n restart then it should be unbelievably simple (each
processor just writes it's local data) and it should scale better in
parallel than the current stuff (which ultimately serializes through
processor 0).
Thoughts?
Derek
On Fri, Jan 3, 2014 at 8:17 AM, Roy Stogner <royst...@ices.utexas.edu>wrote:
>
> On Thu, 2 Jan 2014, Derek Gaston wrote:
>
> One of my users brought an issue to my attention: libMesh is not properly
>> handling multiple nodes occupying the same
>> position when writing out xda/xdr files for the solution vector.
>> I am attaching a mesh and main.C that show the issue. If you look at the
>> resulting eq_sys.xda file you will see that it
>> has two zeros at the end of the solution vector. Those two zeros should
>> be "4.0".
>>
>> The mesh has 2 pairs of nodes that are "duplicated". They are at (0,
>> 0.5, 0) and (0.5, 0.5, 0). What I mean by
>> duplicated is that there are two nodes in the same physical position (so
>> there is a "slit" in the mesh). Think of it
>> like a "crack" in the mesh...
>>
>> Solving on a mesh like this works just fine... but something about the
>> XDA/R output routines doesn't like it (I suspect
>> it's the Hilbert space reorder... but that's just a guess). Note that
>> the Exodus output looks perfectly fine - as does
>> the print of the solution vector. It really is an issue just with XDA/R
>>
>> I would really appreciate help on this one!
>>
>
> IIRC there was a problem with find_neighbors() that was causing meshes
> with slits to fail at AMR, and so I've never really investigated the
> compatibility of the rest of the library with those cases. I'd
> definitely also suspect the Hilbert reordering as the culprit here.
> ---
> Roy
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