Arbitrary grid updates

[kubagalecki]

Some updates to the arbitrary grid formulation:

• Edges between bulk nodes removed from the connectivity graph. This reduces the communication volume and associated costs.
• The local permutation strategy can now be set via the (optional) "permutation" attribute of the "ArbitraryLattice" xml node. Valid values are:
  • "none" - use default ordering, not recommended, only for debugging/benchmarking purposes
  • "coords" - sort only by coordinates, this was the previous behavior. This is still the default.
  • "type" - sort only by node type, not recommended, only for debugging/benchmarking purposes
  • "both" - sort by node type, subsort by coordinates. Somewhat surprisingly, for the fontaine benchmark (on a single GPU), this resulted in a ~8.5% performance penalty, meaning less coalesced memory access outweighed the gains from more efficient warp utilization. I still think for some cases this might be more efficient than the "coords" strategy (maybe for very low porosity, or when the geometry is more structured?)
• Added some missing handlers

Outstanding items:

• Symmetry conditions
• Some handlers are still missing
  • Mostly related to things like particles, so implementing them is outside the scope of this project
  • RunR is definitely still broken
  • Failcheck semantics make little sense for arbitrary grid, see Failcheck always triggers for arbitrary grid #476
  • You can check which handlers still need implementing by grepping for getCartLattice
• Adjoint functionality is definitely broken, the main iteration is missing as well as saving/loading components. There are probably also a bunch of other places where I screwed something up, but I don't really have the bandwidth to go hunting for them.

[codecov-commenter]

Codecov Report

Attention: 421 lines in your changes are missing coverage. Please review.

Comparison is base (b38b8dd) 38.09% compared to head (e02f071) 37.72%.

Files	Patch %	Lines
src/ArbLattice.cpp	0.00%	146 Missing ⚠️
src/vtkLattice.cpp	13.33%	65 Missing ⚠️
src/Handlers/cbFailcheck.cpp	0.00%	54 Missing ⚠️
src/toArb.cpp	0.00%	44 Missing ⚠️
src/Handlers/cbSaveCheckpoint.cpp	0.00%	40 Missing ⚠️
src/Handlers/cbSaveBinary.cpp	0.00%	16 Missing ⚠️
src/Handlers/cbSaveMemoryDump.cpp	0.00%	15 Missing ⚠️
src/Handlers/cbTXT.cpp	0.00%	13 Missing ⚠️
src/Handlers/acLoadMemoryDump.cpp	0.00%	11 Missing ⚠️
src/Handlers/cbBIN.cpp	0.00%	9 Missing ⚠️
... and 2 more

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Additional details and impacted files

@@             Coverage Diff              @@
##           unstable     #477      +/-   ##
============================================
- Coverage     38.09%   37.72%   -0.38%     
============================================
  Files           185      185              
  Lines          8355     8461     +106     
============================================
+ Hits           3183     3192       +9     
- Misses         5172     5269      +97     

Flag	Coverage Δ
d2q9	26.38% <2.32%> (-0.26%)	⬇️
d2q9_bc	23.20% <2.32%> (-0.22%)	⬇️
d2q9_kuper	23.97% <2.32%> (-0.23%)	⬇️
d3q27_PSM_NEBB	31.46% <2.32%> (-0.32%)	⬇️

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[llaniewski]

Before Christmas I started some refactoring, and these things are in a bit of a conflict, so there will be some weird merge-magic going on soon :-)

@kubagalecki If I see a single commit after Jan 1 in your TCLB fork, I'll start harassing you about things you are supposed to be doing.