[Simnibs-discuss] "Gmsh failed meshing one or more surfaces. Trying Delaunay meshing"

[Ben Hatton]

Hi,

I am using the ernie data set to try out headreco, and have found that there is gmsh error when meshing. I ran the file on a compute cluster using linux, and have installed simnibs with anaconda.

Here is the error message:

GENERATING VOLUME MESH
========================================================================
Creating .geo file
Creating volume mesh using Gmsh
========================================================================
Gmsh exit code: 127
Gmsh failed meshing one or more surfaces. Doing uniform remeshing and retrying
Remeshing wm.stl
Remeshing gm.stl
Remeshing csf.stl
Remeshing bone.stl
Remeshing skin.stl
Remeshing eyes.stl
Remeshing cavities.stl
Remeshing air_outer_decoupled.stl
Remeshing ventricles.stl
Decoupling
Decoupling ventricles from GM
Decoupling WM from ventricles
Decoupling GM from WM
Gmsh exit code: 127
Gmsh failed meshing one or more surfaces. Trying Delaunay meshing
Gmsh exit code: 127

Traceback (most recent call last):
  File "/gpfs01/home/msabh6/.conda/envs/simnibs_env/bin/headreco", line 8, in <module>
    sys.exit(main())
  File "/gpfs01/home/msabh6/.conda/envs/simnibs_env/lib/python3.7/site-packages/simnibs/cli/headreco.py", line 10, in main
    headmodel(sys.argv)
 File "/gpfs01/home/msabh6/.conda/envs/simnibs_env/lib/python3.7/site-packages/simnibs/msh/headreco.py", line 693, in headmodel
    vmsh = make_volume_mesh(args.subject_id, surfaces, subject_dir, args.keep_air)
  File "/gpfs01/home/msabh6/.conda/envs/simnibs_env/lib/python3.7/site-packages/simnibs/msh/headreco.py", line 1941, in make_volume_mesh
    raise RuntimeError("Gmsh failed meshing one or more surfaces in {} attempts.".format(attempts))
RuntimeError: Gmsh failed meshing one or more surfaces in 3 attempts.



And the log is here:

2022-04-25 13:04:55 [DEBUG] Running "/gpfs01/home/msabh6/.conda/envs/simnibs_env/lib/python3.7/site-packages/simnibs/bin/linux/meshfix" "/gpfs01/home/msabh6/SIMNIBS/simnibs_examples/ernie/m2m_ernie/ventricles.stl" "/gpfs01/home/msabh6/SIMNIBS/simnibs_examples/ernie/m2m_ernie/wm.stl" --shells 2 --no-clean -q --intersect
2022-04-25 13:04:55 [DEBUG] meshfix /gpfs01/home/msabh6/SIMNIBS/simnibs_examples/ernie/m2m_ernie/ventricles.stl
2022-04-25 13:04:55 [DEBUG] Running "/gpfs01/home/msabh6/.conda/envs/simnibs_env/lib/python3.7/site-packages/simnibs/bin/linux/meshfix" "/gpfs01/home/msabh6/SIMNIBS/simnibs_examples/ernie/m2m_ernie/ventricles.stl" "/gpfs01/home/msabh6/SIMNIBS/simnibs_examples/ernie/m2m_ernie/gm.stl" --shells 2 --no-clean -q --intersect
2022-04-25 13:04:55 [DEBUG] meshfix /gpfs01/home/msabh6/SIMNIBS/simnibs_examples/ernie/m2m_ernie/ventricles.stl
2022-04-25 13:04:55 [DEBUG] Running "/gpfs01/home/msabh6/.conda/envs/simnibs_env/lib/python3.7/site-packages/simnibs/bin/linux/meshfix" "/gpfs01/home/msabh6/SIMNIBS/simnibs_examples/ernie/m2m_ernie/wm.stl" "/gpfs01/home/msabh6/SIMNIBS/simnibs_examples/ernie/m2m_ernie/gm.stl" --shells 2 --no-clean -q --intersect
2022-04-25 13:05:31 [DEBUG] meshfix /gpfs01/home/msabh6/SIMNIBS/simnibs_examples/ernie/m2m_ernie/wm.stl
2022-04-25 13:05:31 [DEBUG] Testing for intersections ...
2022-04-25 13:05:31 [DEBUG] Running "/gpfs01/home/msabh6/.conda/envs/simnibs_env/lib/python3.7/site-packages/simnibs/bin/linux/meshfix" "/gpfs01/home/msabh6/SIMNIBS/simnibs_examples/ernie/m2m_ernie/ventricles.stl" "/gpfs01/home/msabh6/SIMNIBS/simnibs_examples/ernie/m2m_ernie/wm.stl" --shells 2 --no-clean -q --intersect
2022-04-25 13:05:31 [DEBUG] meshfix /gpfs01/home/msabh6/SIMNIBS/simnibs_examples/ernie/m2m_ernie/ventricles.stl
2022-04-25 13:05:31 [DEBUG] Running "/gpfs01/home/msabh6/.conda/envs/simnibs_env/lib/python3.7/site-packages/simnibs/bin/linux/meshfix" "/gpfs01/home/msabh6/SIMNIBS/simnibs_examples/ernie/m2m_ernie/ventricles.stl" "/gpfs01/home/msabh6/SIMNIBS/simnibs_examples/ernie/m2m_ernie/gm.stl" --shells 2 --no-clean -q --intersect
2022-04-25 13:05:31 [DEBUG] meshfix /gpfs01/home/msabh6/SIMNIBS/simnibs_examples/ernie/m2m_ernie/ventricles.stl
2022-04-25 13:05:31 [DEBUG] Running "/gpfs01/home/msabh6/.conda/envs/simnibs_env/lib/python3.7/site-packages/simnibs/bin/linux/meshfix" "/gpfs01/home/msabh6/SIMNIBS/simnibs_examples/ernie/m2m_ernie/wm.stl" "/gpfs01/home/msabh6/SIMNIBS/simnibs_examples/ernie/m2m_ernie/gm.stl" --shells 2 --no-clean -q --intersect
2022-04-25 13:06:07 [DEBUG] meshfix /gpfs01/home/msabh6/SIMNIBS/simnibs_examples/ernie/m2m_ernie/wm.stl
2022-04-25 13:06:07 [DEBUG] Testing for intersections ...
2022-04-25 13:06:07 [DEBUG] Running "/gpfs01/home/msabh6/.conda/envs/simnibs_env/lib/python3.7/site-packages/simnibs/bin/linux/gmsh" -3 -bin -o "/gpfs01/home/msabh6/SIMNIBS/simnibs_examples/ernie/m2m_ernie/ernie.msh" "/gpfs01/home/msabh6/SIMNIBS/simnibs_examples/ernie/m2m_ernie/ernie.geo" >> gmsh_log.txt
2022-04-25 13:06:07 [INFO ] Gmsh exit code: 127
2022-04-25 13:06:07 [INFO ] Gmsh failed meshing one or more surfaces. Trying Delaunay meshing
2022-04-25 13:06:07 [DEBUG] Running "/gpfs01/home/msabh6/.conda/envs/simnibs_env/lib/python3.7/site-packages/simnibs/bin/linux/gmsh" -3 -bin -o "/gpfs01/home/msabh6/SIMNIBS/simnibs_examples/ernie/m2m_ernie/ernie.msh" "/gpfs01/home/msabh6/SIMNIBS/simnibs_examples/ernie/m2m_ernie/ernie.geo" >> gmsh_log.txt
2022-04-25 13:06:07 [INFO ] Gmsh exit code: 127
2022-04-25 13:06:07 [ERROR] Traceback (most recent call last):
  File "/gpfs01/home/msabh6/.conda/envs/simnibs_env/bin/headreco", line 8, in <module>
    sys.exit(main())
  File "/gpfs01/home/msabh6/.conda/envs/simnibs_env/lib/python3.7/site-packages/simnibs/cli/headreco.py", line 10, in main
    headmodel(sys.argv)
  File "/gpfs01/home/msabh6/.conda/envs/simnibs_env/lib/python3.7/site-packages/simnibs/msh/headreco.py", line 693, in headmodel
    vmsh = make_volume_mesh(args.subject_id, surfaces, subject_dir, args.keep_air)
  File "/gpfs01/home/msabh6/.conda/envs/simnibs_env/lib/python3.7/site-packages/simnibs/msh/headreco.py", line 1941, in make_volume_mesh
    raise RuntimeError("Gmsh failed meshing one or more surfaces in {} attempts.".format(attempts))
RuntimeError: Gmsh failed meshing one or more surfaces in 3 attempts.


Thanks for your help,
Ben



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