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<p class="MsoNormal">Hi,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">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.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Here is the error message:<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">GENERATING VOLUME MESH<o:p></o:p></p>
<p class="MsoNormal">========================================================================<o:p></o:p></p>
<p class="MsoNormal">Creating .geo file<o:p></o:p></p>
<p class="MsoNormal">Creating volume mesh using Gmsh<o:p></o:p></p>
<p class="MsoNormal">========================================================================<o:p></o:p></p>
<p class="MsoNormal">Gmsh exit code: 127<o:p></o:p></p>
<p class="MsoNormal">Gmsh failed meshing one or more surfaces. Doing uniform remeshing and retrying<o:p></o:p></p>
<p class="MsoNormal">Remeshing wm.stl<o:p></o:p></p>
<p class="MsoNormal">Remeshing gm.stl<o:p></o:p></p>
<p class="MsoNormal">Remeshing csf.stl<o:p></o:p></p>
<p class="MsoNormal">Remeshing bone.stl<o:p></o:p></p>
<p class="MsoNormal">Remeshing skin.stl<o:p></o:p></p>
<p class="MsoNormal">Remeshing eyes.stl<o:p></o:p></p>
<p class="MsoNormal">Remeshing cavities.stl<o:p></o:p></p>
<p class="MsoNormal">Remeshing air_outer_decoupled.stl<o:p></o:p></p>
<p class="MsoNormal">Remeshing ventricles.stl<o:p></o:p></p>
<p class="MsoNormal">Decoupling<o:p></o:p></p>
<p class="MsoNormal">Decoupling ventricles from GM<o:p></o:p></p>
<p class="MsoNormal">Decoupling WM from ventricles<o:p></o:p></p>
<p class="MsoNormal">Decoupling GM from WM<o:p></o:p></p>
<p class="MsoNormal">Gmsh exit code: 127<o:p></o:p></p>
<p class="MsoNormal">Gmsh failed meshing one or more surfaces. Trying Delaunay meshing<o:p></o:p></p>
<p class="MsoNormal">Gmsh exit code: 127<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Traceback (most recent call last):<o:p></o:p></p>
<p class="MsoNormal"> File "/gpfs01/home/msabh6/.conda/envs/simnibs_env/bin/headreco", line 8, in <module><o:p></o:p></p>
<p class="MsoNormal"> sys.exit(main())<o:p></o:p></p>
<p class="MsoNormal"> File "/gpfs01/home/msabh6/.conda/envs/simnibs_env/lib/python3.7/site-packages/simnibs/cli/headreco.py", line 10, in main<o:p></o:p></p>
<p class="MsoNormal"> headmodel(sys.argv)<o:p></o:p></p>
<p class="MsoNormal"> File "/gpfs01/home/msabh6/.conda/envs/simnibs_env/lib/python3.7/site-packages/simnibs/msh/headreco.py", line 693, in headmodel<o:p></o:p></p>
<p class="MsoNormal"> vmsh = make_volume_mesh(args.subject_id, surfaces, subject_dir, args.keep_air)<o:p></o:p></p>
<p class="MsoNormal"> File "/gpfs01/home/msabh6/.conda/envs/simnibs_env/lib/python3.7/site-packages/simnibs/msh/headreco.py", line 1941, in make_volume_mesh<o:p></o:p></p>
<p class="MsoNormal"> raise RuntimeError("Gmsh failed meshing one or more surfaces in {} attempts.".format(attempts))<o:p></o:p></p>
<p class="MsoNormal">RuntimeError: Gmsh failed meshing one or more surfaces in 3 attempts.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">And the log is here:<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">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<o:p></o:p></p>
<p class="MsoNormal">2022-04-25 13:04:55 [DEBUG] meshfix /gpfs01/home/msabh6/SIMNIBS/simnibs_examples/ernie/m2m_ernie/ventricles.stl<o:p></o:p></p>
<p class="MsoNormal">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<o:p></o:p></p>
<p class="MsoNormal">2022-04-25 13:04:55 [DEBUG] meshfix /gpfs01/home/msabh6/SIMNIBS/simnibs_examples/ernie/m2m_ernie/ventricles.stl<o:p></o:p></p>
<p class="MsoNormal">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<o:p></o:p></p>
<p class="MsoNormal">2022-04-25 13:05:31 [DEBUG] meshfix /gpfs01/home/msabh6/SIMNIBS/simnibs_examples/ernie/m2m_ernie/wm.stl<o:p></o:p></p>
<p class="MsoNormal">2022-04-25 13:05:31 [DEBUG] Testing for intersections ...<o:p></o:p></p>
<p class="MsoNormal">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<o:p></o:p></p>
<p class="MsoNormal">2022-04-25 13:05:31 [DEBUG] meshfix /gpfs01/home/msabh6/SIMNIBS/simnibs_examples/ernie/m2m_ernie/ventricles.stl<o:p></o:p></p>
<p class="MsoNormal">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<o:p></o:p></p>
<p class="MsoNormal">2022-04-25 13:05:31 [DEBUG] meshfix /gpfs01/home/msabh6/SIMNIBS/simnibs_examples/ernie/m2m_ernie/ventricles.stl<o:p></o:p></p>
<p class="MsoNormal">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<o:p></o:p></p>
<p class="MsoNormal">2022-04-25 13:06:07 [DEBUG] meshfix /gpfs01/home/msabh6/SIMNIBS/simnibs_examples/ernie/m2m_ernie/wm.stl<o:p></o:p></p>
<p class="MsoNormal">2022-04-25 13:06:07 [DEBUG] Testing for intersections ...<o:p></o:p></p>
<p class="MsoNormal">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<o:p></o:p></p>
<p class="MsoNormal">2022-04-25 13:06:07 [INFO ] Gmsh exit code: 127<o:p></o:p></p>
<p class="MsoNormal">2022-04-25 13:06:07 [INFO ] Gmsh failed meshing one or more surfaces. Trying Delaunay meshing<o:p></o:p></p>
<p class="MsoNormal">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<o:p></o:p></p>
<p class="MsoNormal">2022-04-25 13:06:07 [INFO ] Gmsh exit code: 127<o:p></o:p></p>
<p class="MsoNormal">2022-04-25 13:06:07 [ERROR] Traceback (most recent call last):<o:p></o:p></p>
<p class="MsoNormal"> File "/gpfs01/home/msabh6/.conda/envs/simnibs_env/bin/headreco", line 8, in <module><o:p></o:p></p>
<p class="MsoNormal"> sys.exit(main())<o:p></o:p></p>
<p class="MsoNormal"> File "/gpfs01/home/msabh6/.conda/envs/simnibs_env/lib/python3.7/site-packages/simnibs/cli/headreco.py", line 10, in main<o:p></o:p></p>
<p class="MsoNormal"> headmodel(sys.argv)<o:p></o:p></p>
<p class="MsoNormal"> File "/gpfs01/home/msabh6/.conda/envs/simnibs_env/lib/python3.7/site-packages/simnibs/msh/headreco.py", line 693, in headmodel<o:p></o:p></p>
<p class="MsoNormal"> vmsh = make_volume_mesh(args.subject_id, surfaces, subject_dir, args.keep_air)<o:p></o:p></p>
<p class="MsoNormal"> File "/gpfs01/home/msabh6/.conda/envs/simnibs_env/lib/python3.7/site-packages/simnibs/msh/headreco.py", line 1941, in make_volume_mesh<o:p></o:p></p>
<p class="MsoNormal"> raise RuntimeError("Gmsh failed meshing one or more surfaces in {} attempts.".format(attempts))<o:p></o:p></p>
<p class="MsoNormal">RuntimeError: Gmsh failed meshing one or more surfaces in 3 attempts.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Thanks for your help,<o:p></o:p></p>
<p class="MsoNormal">Ben<o:p></o:p></p>
</div>
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