Refactor Capstone support

[bobpaw]

Refactor Capstone support

apf_cap

• move MeshCAP implementation into apfCAP.cc.
• document functions and add documentation group.
• remove unused/obsolete capMesh and capEntity forward declarations.
• forward declare function arguments to reduce translation unit dependencies.
• add functions to create a Capstone apf::Mesh2 from an existing gmi_model, load by mesh name, generate a mesh with Capstone meshing, and create empty meshes.
• add model ownership like with MDS.
• remove fake castEntity function
• add hasCAP to query support programmatically.
• always setup full adjacencies when loading Capstone meshes.
• only destroy the associated model if it exists and is owned.

gmi_cap

• remove using namespace declarations from the global scope
• remove most #includes in favor of forward declaration.
  • left in CreateMG_Framework_Geometry.h because I don't think I can forward declare toGmiEntity/fromGmiEntity arguments (i.e. CreateMG::M_GTopo).
• document all functions and add documentation group.
• add functions to probe, write, or load specific associated meshes from CRE files.
• gmi_cap is now the preferred way to interact (load/write) with CRE files.
• gmi_cap_start and gmi_cap_stop actually do things now (previously they were no-ops).
  • they load/unload an internal CapstoneModule for interaction with Capstone APIs
• if models are owned (loaded with gmi_cap) they will call the Capstone API to delete the underlying model when destroyed.
• base APIs (start, stop, register, load, write) are still C interfaces, but the extended ones (probe, load_selective, export, import) are C++ only.

test cases

• Add capProbe and capLoadSome cases to test new APIs
• Rewrite capVol to use new APIs, support parallel adaptation with intermediate MDS object, rework argument parsing, and change the names of output VTKs.
• update the capVolSizeFields to work in parallel (namely CylBoundaryLayer).
• add a new cube shock size field for capVol and make it the default given option 3.
• Rewrite cap2vtk, capGeomTest, capCheckParam, cap_closestPoint, cap_inClosureOf tests to use new APIs.

[bobpaw]

Running into problem with empty parts after --fixLargeAngles. Likely related to #198.

[bobpaw]

This occurred with the capVol wing case with METIS on 4 procs.

Log for mpirun -np 4 ./capVol -gm 3 wing_surf_only.cre out.cre

Initalization of MetricInterpolation ...
Initalization of MetricInterpolation ...
Threads : 1
Threads : 1
Initalization of MetricInterpolation ...
Initalization of MetricInterpolation ...
Threads : 1Threads : 1
Expiration Date = 2025-8-26
Expiration Date = 2025-8-26
Expiration Date = 2025-8-26
Expiration Date = 2025-8-26
Number of Breps = 1
Number of Breps = 1
Number of Breps = 1
Number of Breps = 1
Loading Data Timer : cpu = 5.924e-03s  wall = 7.67e-02s
Loading Data Timer : cpu = 5.807e-03s  wall = 7.67e-02s
Loading Data Timer : cpu = 6.076e-03s  wall = 7.67e-02s
Loading Data Timer : cpu = 8.435e-03s  wall = 7.68e-02s
GenerateNMesh  : Num Threads = 1
Number of sources : 12
Generating isotropic proxy
For iteration:0 marked cells:0 out of:1331
Max source number:12
Average source number:2.7408
Sizing Field Timing : cpu = 1.133e-02s  wall = 3.69e-01s
Meshing edge 1
Meshing edge 2
Meshing edge 3
Meshing edge 4
Meshing edge 5
Meshing edge 6
Meshing edge 7
Meshing edge 8
Meshing edge 9
Meshing edge 10
Meshing edge 11
Meshing edge 12
Meshing face 1
Meshing face 2
Meshing face 3
Meshing face 4
Meshing face 5
Meshing face 6
Faces Mesher : cpu = 2.343e-02s  wall = 2.84e-02s
Meshing region 1
Missing edges:0 over:2010
Iter=0 npoin=672 nelem=2037
Iter=1 npoin=673 nelem=2314
Iter=2 npoin=673 nelem=2314
Iter=0 npoin=673 nelem=2314 nface=1340
Iter=1 npoin=1119 nelem=4466 nface=2356
Iter=2 npoin=1121 nelem=4479 nface=1982
Iter=3 npoin=1153 nelem=4686 nface=1004
Iter=4 npoin=1409 nelem=6245 nface=1472
Iter=5 npoin=1413 nelem=6283 nface=1200
Iter=6 npoin=1449 nelem=6499 nface=636
Iter=7 npoin=1583 nelem=7305 nface=844
Iter=8 npoin=1590 nelem=7348 nface=644
Iter=9 npoin=1615 nelem=7497 nface=374
Iter=10 npoin=1664 nelem=7801 nface=396
Iter=11 npoin=1671 nelem=7847 nface=280
Iter=12 npoin=1682 nelem=7915 nface=188
Iter=13 npoin=1695 nelem=7996 nface=142
Iter=14 npoin=1696 nelem=8014 nface=96
Iter=15 npoin=1697 nelem=8025 nface=44
Iter=16 npoin=1697 nelem=8025 nface=14
Worst quality before optim:2900.75
Average quality before optim:2.46743
Iter=0
Edges swapped:480 over:10376 tried:8366
Elements swapped:0 over:8025 tried:30372
Points optimized:592 over:1025 tried:1023
Iter=1
Edges swapped:53 over:10376 tried:6144
Elements swapped:0 over:8025 tried:25745
Points optimized:233 over:1025 tried:922
Iter=2
Edges swapped:6 over:10376 tried:2891
Elements swapped:0 over:8025 tried:15572
Points optimized:97 over:1025 tried:711
Average quality after optim:1.37659
Worst quality after optim:1.91675
Regions Mesher : cpu = 6.954e-01s  wall = 7.30e-01s
Timing(GenerateNMesh) : cpu = 7.310e-01s  wall = 1.13e+00s
mesh verified in 0.036884 seconds
METIS: weights are not supported
METIS: partitioned in 0.003553 seconds
METIS: planned in 0.000735 seconds
METIS: split in 0.011952 seconds
mesh expanded from 1 to 4 parts in 0.003679 seconds
mesh migrated from 1 to 4 in 0.051315 seconds
writeVtuFile into buffers: 0.001556 seconds
writeVtuFile buffers to disk: 0.144549 seconds
vtk files before.vtk written in 0.167789 seconds
MeshAdapt: ma::configure:  Based on requested sizefield, MeshAdapt requires at least 5 iterations.
Setting the number of iteration to 6!
MeshAdapt: version 2.0 !
METIS: weights are not supported
METIS: localized graph in 0.000232 seconds
METIS: partitioned in 0.004619 seconds
METIS: remapped in 0.000094 seconds
METIS: scattered in 0.000051 seconds
METIS: planned in 0.000422 seconds
METIS: migrated in 0.026521 seconds
METIS: balanced in 0.037136 seconds
MeshAdapt: iteration 0
MeshAdapt: coarsened 538 edges in 0.230906 seconds
METIS: weights are not supported
METIS: localized graph in 0.000538 seconds
METIS: partitioned in 0.002582 seconds
METIS: remapped in 0.000074 seconds
METIS: scattered in 0.000027 seconds
METIS: planned in 0.000142 seconds
METIS: migrated in 0.011190 seconds
METIS: balanced in 0.017814 seconds
MeshAdapt: refined 1603 edges in 0.032561 seconds
MeshAdapt: snapped in 0.000494 seconds: 0 targets, 0 non-layer snaps
MeshAdapt: iteration 1
MeshAdapt: coarsened 458 edges in 0.401182 seconds
METIS: weights are not supported
METIS: localized graph in 0.002649 seconds
METIS: partitioned in 0.005030 seconds
METIS: remapped in 0.000161 seconds
METIS: scattered in 0.000039 seconds
METIS: planned in 0.000228 seconds
METIS: migrated in 0.025560 seconds
METIS: balanced in 0.041595 seconds
MeshAdapt: refined 4695 edges in 0.089507 seconds
MeshAdapt: snapped in 0.000980 seconds: 0 targets, 0 non-layer snaps
MeshAdapt: iteration 2
MeshAdapt: coarsened 1175 edges in 1.189498 seconds
METIS: weights are not supported
METIS: localized graph in 0.009365 seconds
METIS: partitioned in 0.011108 seconds
METIS: remapped in 0.000358 seconds
METIS: scattered in 0.000066 seconds
METIS: planned in 0.000405 seconds
METIS: migrated in 0.083376 seconds
METIS: balanced in 0.138617 seconds
MeshAdapt: refined 10097 edges in 0.209393 seconds
MeshAdapt: snapped in 0.002037 seconds: 0 targets, 0 non-layer snaps
MeshAdapt: iteration 3
MeshAdapt: coarsened 3976 edges in 2.870489 seconds
METIS: weights are not supported
METIS: localized graph in 0.021831 seconds
METIS: partitioned in 0.021483 seconds
METIS: remapped in 0.000682 seconds
METIS: scattered in 0.000094 seconds
METIS: planned in 0.000864 seconds
METIS: migrated in 0.184952 seconds
METIS: balanced in 0.306471 seconds
MeshAdapt: refined 14780 edges in 0.388254 seconds
MeshAdapt: snapped in 0.003598 seconds: 0 targets, 0 non-layer snaps
MeshAdapt: iteration 4
MeshAdapt: coarsened 7300 edges in 4.476811 seconds
METIS: weights are not supported
METIS: localized graph in 0.025776 seconds
METIS: partitioned in 0.036831 seconds
METIS: remapped in 0.001051 seconds
METIS: scattered in 0.000134 seconds
METIS: planned in 0.001526 seconds
METIS: migrated in 0.236706 seconds
METIS: balanced in 0.409361 seconds
MeshAdapt: refined 15780 edges in 0.435036 seconds
MeshAdapt: snapped in 0.004559 seconds: 0 targets, 0 non-layer snaps
MeshAdapt: iteration 5
MeshAdapt: coarsened 10152 edges in 6.280703 seconds
METIS: weights are not supported
METIS: localized graph in 0.029699 seconds
METIS: partitioned in 0.043759 seconds
METIS: remapped in 0.001136 seconds
METIS: scattered in 0.000149 seconds
METIS: planned in 0.002603 seconds
METIS: migrated in 0.268942 seconds
METIS: balanced in 0.477790 seconds
MeshAdapt: refined 8500 edges in 0.299709 seconds
MeshAdapt: snapped in 0.004292 seconds: 0 targets, 0 non-layer snaps
MeshAdapt: --iter 0 of shape correction loop: #bad elements 166453
MeshAdapt: snapped in 0.005070 seconds: 0 targets, 0 non-layer snaps
MeshAdapt: --fixLargeAngles       in 9.376438 seconds: #bad elements 174251
MeshAdapt: --fixShortEdgeElements in 217.924783 seconds: #bad elements 78956
METIS: weights are not supported
METIS: localized graph in 0.071383 seconds
METIS: partitioned in 0.025649 seconds
METIS: remapped in 0.001230 seconds
METIS: scattered in 0.000119 seconds
METIS: planned in 0.000415 seconds
METIS: migrated in 0.592544 seconds
METIS: balanced in 0.900624 seconds
MeshAdapt: --percent change in number of bad elements 0.525656
MeshAdapt: --iter 1 of shape correction loop: #bad elements 78956
MeshAdapt: snapped in 0.003536 seconds: 0 targets, 0 non-layer snaps
MeshAdapt: --fixLargeAngles       in 4.660544 seconds: #bad elements 78143
MeshAdapt: --fixShortEdgeElements in 123.399546 seconds: #bad elements 37207
METIS: weights are not supported
METIS: localized graph in 0.041078 seconds
METIS: partitioned in 0.014809 seconds
METIS: remapped in 0.000719 seconds
METIS: scattered in 0.000078 seconds
METIS: planned in 0.000419 seconds
METIS: migrated in 0.358449 seconds
METIS: balanced in 0.537830 seconds
MeshAdapt: --percent change in number of bad elements 0.528763
MeshAdapt: --iter 2 of shape correction loop: #bad elements 37207
MeshAdapt: snapped in 0.002259 seconds: 0 targets, 0 non-layer snaps
MeshAdapt: --fixLargeAngles       in 2.428371 seconds: #bad elements 35320
APF warning: 1 empty parts
APF warning: 1 empty parts
APF warning: 1 empty parts
MeshAdapt: --fixShortEdgeElements in 71.502453 seconds: #bad elements 16995
METIS: weights are not supported
owned_xadj.size() > 1 failed at /users/woodra/lore/projects/capstone/core-capstone/metis/apfMETISbalancer.cc + 37
===================================================================================
=   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
=   PID 2952076 RUNNING AT trouble.scorec.rpi.edu
=   EXIT CODE: 134
=   CLEANING UP REMAINING PROCESSES
=   YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Aborted (signal 6)
This typically refers to a problem with your application.
Please see the FAQ page for debugging suggestions

[bobpaw]

Metis balancing for meshes with empty parts is fixed in #499

[bobpaw]

@cwsmith please review when you get a chance.

[bobpaw]

Also might be good to get Jacob's eyes on this since there are substantial API changes and he might have inputs.

[cwsmith]

/runtests

[github-actions[bot]]

Build Log Simmetrix Test Result: success Simmetrix + CGNS Test Result: success