su2gmf error in branch feat_adap_dev

[criki1498]

Hello,

I recently tried the SU2-feature_adap branch, and it worked correctly. The only issue was that this branch is based on an outdated version of SU2, so I installed the SU2-feat_adap_dev branch.

When I run the Python script mesh_adaption.py, the first part, where the CFD run is executed, goes smoothly. However, as soon as the program attempts to perform mesh adaptation, I receive an error:

 > py378 $SU2_RUN/mesh_adaptation.py -f config.cfg
SU2-AMG Anisotropic Mesh Adaptation

Mesh adaptation options:
ADAP_SIZES              : (2000, 4000, 8000)
ADAP_SUBITER            : (2, 2, 2)
ADAP_RESIDUAL_REDUCTION : (3, 3, 3)
ADAP_SENSOR             : DENSITY
ADAP_HMAX               : 200
ADAP_HMIN               : 1e-8
ADAP_HGRAD              : 1.3
ADAP_NORM               : 1

Preprocessing background surface mesh.
  ## WARNING: MISSING SU2 MESH FILE KEYWORD: NCORNERS=.
Preprocessing initial mesh.
  ## WARNING: MISSING SU2 MESH FILE KEYWORD: NCORNERS=.

Running initial CFD solution.

Starting mesh adaptation process.

  ## WARNING: MISSING SU2 MESH FILE KEYWORD: NCORNERS=.
SystemError: Objects/longobject.c:415: bad argument to internal function

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/u1/cafr792/.SU2/bin/mesh_adaptation.py", line 87, in <module>
    main()
  File "/u1/cafr792/.SU2/bin/mesh_adaptation.py", line 51, in main
    options.partitions )
  File "/u1/cafr792/.SU2/bin/mesh_adaptation.py", line 77, in mesh_adaptation
    SU2.run.amg(config)
  File "/u1/cafr792/.SU2/bin/SU2/run/amg.py", line 247, in amg
    su2amg.write_mesh_and_sol('flo.meshb', 'flo.solb', mesh)
  File "/u1/cafr792/.SU2/bin/SU2/amginria/interface.py", line 253, in write_mesh_and_sol
    su2gmf.WriteMeshAndSol(mesh_name, solution_name, Ver, Cor, Tri, Tet, Edg, Hex, Qua, Pyr, Pri, Sol, SolTag, Markers, Dim)
  File "/u1/cafr792/.pyenv/versions/3.7.8/lib/python3.7/site-packages/su2gmf.py", line 343, in WriteMeshAndSol
    return _su2gmf.WriteMeshAndSol(MshNam, SolNam, pyVer, pyCor, pyTri, pyTet, pyEdg, pyHex, pyQua, pyPyr, pyPri, pySol, pySolHeader, pyMarkers, Dim)
SystemError: <built-in function WriteMeshAndSol> returned a result with an error set

The mesh is the ONERA M6 used for official tutorial.
I have tried this branch on some different Linux computers, with Python 3.7.7 and 3.7.8, but I encounter the same error everywhere.

Can anyone help me?

[criki1498]

I have just attempted the SU2 tutorial at:

In this tutorial (files here), there are two different meshes:

• mesh_ONERAM6_100k.su2
• mesh_ONERAM6_turb_hexa_43008.su2

In this tutorial, two meshes are provided:

With one mesh (mesh_ONERAM6_100k.su2), I encounter the same error of the previous message.

With the other mesh (mesh_ONERAM6_turb_hexa_43008.su2), the program completes all the iterations specified in the ITER setting, and then performs mesh adaptation once before terminating without any error showed in the terminal.
In truth, from the configuration parameters, it can be seen that it should have performed several mesh adaptation steps.
These are the parameters for the mesh:

% ------------- MESH ADAPTATION PARAMETER ------------%
ADAP_COMPLEXITY= (20000, 60000, 120000)
ADAP_SIZES= (3000, 600000, 600000)
ADAP_SUBITER= (3, 3, 3)

ADAP_FLOW_ITER= (2, 2, 2)
%ADAP_RESIDUAL_REDUCTION= (3, 3, 3)

ADAP_SENSOR=  PRESSURE

%ADAP_BACK= SBW_baseline10_back
%ADAP_SOURCE= adap_coarse.source

ADAP_HMAX=  40
ADAP_HMIN=  1
ADAP_HGRAD= 1.5
ADAP_NORM = 1

However, in this last case, there is an amg.out output file in the ite0 folder. Its contents are as follows:

 fefloa_Python2Mesh : 3d mesh on input 
 fefloa_Python2Mesh : msh->NbrVer 46417 
 fefloa_Python2Mesh : leaving with 46417 ver. 0 tri. 0 edg. 
  -- Maximal memory 
  Maximum number of Points                  26800000 
  Maximun number of Bnd Points               5360000
  Maximum number of Triangles               10720000 
  Maximum number of Tetrahedra             147400000 
  Allocated Memory 24.959 Gb 
  Physical Memory  31.258 Gb
  ## WARNING: NO TETRAHEDRON
  ## WARNING: NO BOUNDARY FACES.
  bounding box x: -6.4472 5.6413 y: 0 7.64342 z: -6.4472 6.4472 
   0 FACES CREATED  
       46417 Vertex 
           0 Boundary Vertices   
           0 Tetrahedra   
           0 Triangles  
           0 Edges  
           0 Surface(s) 
   ## WARNING: NO BOUNDARY FACE: NORMALS COMPUTATION SKIPPED 
  ## WARNING: GEOMETRY ENRICHMENT (CORNERS) DEACTIVATED 
  ## WARNING: GEOMETRY ENRICHMENT (RIDGES)  DEACTIVATED 
           0 Points inside surfaces 
           0 Points along  lines 
           0 Points corners  
  Metric set to size 12.8944 
  -- Time for IOs :  real 0.018s 	 user 0.017s 	 sys  0.000s
  Reading back mesh /home/casco/Downloads/mesh2/adap/ite0/../../adap/ite0/mesh_back.meshb

  ## WARNING: FEFLO.A: NO BOUNDARY FACES IGNORED
    NUMBER OF FACES = 0
  number of edges 0 number of points 0 
           0 Points inside surfaces 
           0 Points along  lines 
           0 Points corners  
  ## WARNING: FEFLO.A: SUB-DOMAIN DETECTION RESTARTED 
   ## WARNING: NO BOUNDARY FACE: NORMALS COMPUTATION SKIPPED 
  ## ERROR: UTIF_NEWHYBRIDHASHTABLE FAILS SIZE = 0  NBROBJ = 0
  % Output meshp3_smoo.meshb Mesh ndimn=3, mpoin=46417, mface=0  
  % Output back.meshb Mesh ndimn=3, mpoin=46417, melem=0, mface=0
 Corners 0 Required 0 
  Reading background mesh     real 0.023s 	 user 0.023s 	 sys  0.000s
    
   Surface metric estimate 
   Metric-growth factor      1.00000000000000     
   no surface flagged for surface approximation 
     
   Recovering surface metric 
   Metric-growth factor      1.00000000000000     
   Minimal size on normal direction 
   no surface flagged for surface metric recovery  
   am_surf: end of module 
  
  Computing surface density 
  total air   0.000000000000000E+000  0.000000000000000E+000
  nedge            0
   Mesh-Gradation    1.50000000000000       law            3  iter. max. 
          50  fac.   5.000000000000000E-002
   * Mixed-Space  law gradation 
   # proc =            1
           0  corrections done, size grad    1.50000000000000     
   Mesh gradation cpu time   real 0.000s	 user 0.000s	 sys  0.000s
  Computing surface density 
  total air   0.000000000000000E+000  0.000000000000000E+000
   ## ERROR: MIN SIZE IS NULL IN METRIC FIELD 
   1/Size**2   0.000000000000000E+000

1. Why do I get that error with the first mesh?
2. What is the problem with the second mesh, and how to solve?

[tbellosta]

Hi, not sure about the status of the branches you mention. The mesh adaptation library (pyAMG) used by that branch of SU2 only works with tetra/triangle meshes . The same is true for other mesh adaptation libraries i.e. MMG, Omega_h or refine (although it has some limited capabilities to work with mixed element meshes).
If you have a mixed mesh (i.e. HEXA boundary layer and tetra everywhere else), you could try freezing the structured part and adapt only the tetra region. I guess you wold need to implement that yourself, I don't remember it being an option in the SU2 implementation.