# When trying to create mesh using gmsh I am getting PETSC ERROR

**URL:** <https://fenicsproject.discourse.group/t/when-trying-to-create-mesh-using-gmsh-i-am-getting-petsc-error/16039>\
**Category:** General\
**Tags:** dolfinx, gmsh\
**Created:** [October 13, 2024, 12:07pm UTC](https://fenicsproject.discourse.group/t/when-trying-to-create-mesh-using-gmsh-i-am-getting-petsc-error/16039 "2024-10-13T12:07:07Z")\
**Posts on this page:** 3\
**Page:** 1

<div class="post-metadata">

**Author:** ![vishalkr](https://yyz2.discourse-cdn.com/free1/user_avatar/fenicsproject.discourse.group/vishalkr/32/6589_2.png) [@vishalkr](https://fenicsproject.discourse.group/u/vishalkr)\
**Post date:** [October 13, 2024, 12:07pm UTC](https://fenicsproject.discourse.group/t/when-trying-to-create-mesh-using-gmsh-i-am-getting-petsc-error/16039/1 "2024-10-13T12:07:07Z")

</div>

```auto
from mpi4py import MPI
import numpy as np
import ufl
import gmsh
import dolfinx
from mpi4py import MPI
from dolfinx.io import (VTXWriter, distribute_entity_data, gmshio)
from dolfinx.fem.petsc import LinearProblem
from basix.ufl import element, mixed_element
from dolfinx import default_scalar_type, plot
from dolfinx.fem import (functionspace, dirichletbc)

# Physical parameters
D = 1
Ht = 1.62 # height till top
Hb = 1.9 # height till bottom

L = 6
H = Ht+Hb
c_x = 0
c_y = 0
r = D/2

# Numerical parameters
resolution = 0.1 # Target characteristic length factor #0.05

# EPS = np.finfo(float).eps # Machine epsilon for float

model_rank = 0
mesh_comm = MPI.COMM_WORLD

gdim=2

# Create gmsh geometry
gmsh.initialize()

# Create channel
rectangle = gmsh.model.occ.addRectangle(-L/2, -Hb, 0, L, H)

# Create circle
obstacle = gmsh.model.occ.addDisk(c_x, c_y, 0, r, r)

gmsh.model.occ.cut([(gdim, rectangle)], [(gdim, obstacle)])
gmsh.model.occ.synchronize()

# # Set mesh resolution
gmsh.option.setNumber("Mesh.CharacteristicLengthFactor", resolution)
gmsh.option.setNumber("Mesh.Algorithm", 8)
gmsh.option.setNumber("Mesh.RecombinationAlgorithm", 2)
gmsh.option.setNumber("Mesh.RecombineAll", 1)
gmsh.option.setNumber("Mesh.SubdivisionAlgorithm", 1)
gmsh.model.mesh.generate(gdim)
gmsh.model.mesh.setOrder(2)
gmsh.model.mesh.optimize("Netgen")
# 
# 
gmsh.write("mesh2.msh")
# 
# # gmsh.fltk().run()
# # Convert gmsh mesh to dolfinx mesh
mesh_obj, _, _ = gmshio.model_to_mesh(gmsh.model, mesh_comm, model_rank, gdim=gdim)
gmsh.finalize()

```

Getting this error

```auto
Info : Meshing 1D...
Info : [0%] Meshing curve 5 (Ellipse)
Info : [20%] Meshing curve 6 (Line)
Info : [40%] Meshing curve 7 (Line)
Info : [60%] Meshing curve 8 (Line)
Info : [80%] Meshing curve 9 (Line)
Info : Done meshing 1D (Wall 0.000345293s, CPU 9e-05s)
Info : Meshing 2D...
Info : Meshing surface 1 (Plane, Frontal-Delaunay for Quads)
[0]PETSC ERROR: ------------------------------------------------------------------------
[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range
[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[0]PETSC ERROR: or see https://petsc.org/release/faq/#valgrind
[0]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to find memory corruption errors
[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run 
[0]PETSC ERROR: to get more information on the crash.
[0]PETSC ERROR: Run with -malloc_debug to check if memory corruption is causing the crash.
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode 59.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------

Process ended with exit code 59.

```

---

<div class="post-metadata">

**Author:** ![francesco-ballarin](https://avatars.discourse-cdn.com/v4/letter/f/f05b48/32.png) [@francesco-ballarin](https://fenicsproject.discourse.group/u/francesco-ballarin)\
**Post date:** [October 13, 2024, 1:52pm UTC](https://fenicsproject.discourse.group/t/when-trying-to-create-mesh-using-gmsh-i-am-getting-petsc-error/16039/2 "2024-10-13T13:52:20Z")

</div>

Drop every FEniCSx related import and command to confirm that the error is still there.

```auto
from mpi4py import MPI
import numpy as np
import gmsh

# Physical parameters
D = 1
Ht = 1.62 # height till top
Hb = 1.9 # height till bottom

L = 6
H = Ht+Hb
c_x = 0
c_y = 0
r = D/2

# Numerical parameters
resolution = 0.1 # Target characteristic length factor #0.05

# EPS = np.finfo(float).eps # Machine epsilon for float

model_rank = 0
mesh_comm = MPI.COMM_WORLD

gdim=2

# Create gmsh geometry
gmsh.initialize()

# Create channel
rectangle = gmsh.model.occ.addRectangle(-L/2, -Hb, 0, L, H)

# Create circle
obstacle = gmsh.model.occ.addDisk(c_x, c_y, 0, r, r)

gmsh.model.occ.cut([(gdim, rectangle)], [(gdim, obstacle)])
gmsh.model.occ.synchronize()

# # Set mesh resolution
gmsh.option.setNumber("Mesh.CharacteristicLengthFactor", resolution)
gmsh.option.setNumber("Mesh.Algorithm", 8)
gmsh.option.setNumber("Mesh.RecombinationAlgorithm", 2)
gmsh.option.setNumber("Mesh.RecombineAll", 1)
gmsh.option.setNumber("Mesh.SubdivisionAlgorithm", 1)
gmsh.model.mesh.generate(gdim)
gmsh.model.mesh.setOrder(2)
gmsh.model.mesh.optimize("Netgen")

gmsh.finalize()

```

and get

```auto
[0] /lib/x86_64-linux-gnu/libc.so.6(+0x3f5d0) [0x7f54bc5b85d0]
[1] /lib/x86_64-linux-gnu/libgmsh.so.4.12(_ZNK14MElementOctree4findEdddib+0x1e) [0x7f54b2cb720e]
[2] /lib/x86_64-linux-gnu/libgmsh.so.4.12(_ZNK14backgroundMesh8getAngleEddd+0x5a) [0x7f54b2e1939a]
[3] /lib/x86_64-linux-gnu/libgmsh.so.4.12(_ZN5MTri3C2EP9MTriangledP8SMetric3P13bidimMeshDataP5GFace+0xa7b) [0x7f54b2d646cb]
[4] /lib/x86_64-linux-gnu/libgmsh.so.4.12(_Z33buildMeshGenerationDataStructuresP5GFaceRSt3setIP5MTri314compareTri3PtrSaIS3_EER13bidimMeshData+0x1333) [0x7f54b2d76633]
[5] /lib/x86_64-linux-gnu/libgmsh.so.4.12(_Z25bowyerWatsonFrontalLayersP5GFacebPSt3mapIP7MVertexS3_St4lessIS3_ESaISt4pairIKS3_S3_EEEPS1_IS3_7SPoint2S5_SaIS6_IS7_SC_EEE+0x1ba) [0x7f54b2d6a23a]
[6] /lib/x86_64-linux-gnu/libgmsh.so.4.12(+0x737077) [0x7f54b2d37077]
[7] /lib/x86_64-linux-gnu/libgmsh.so.4.12(_ZN9meshGFaceclEP5GFaceb+0x3d3) [0x7f54b2d40e53]
[8] /lib/x86_64-linux-gnu/libgmsh.so.4.12(_ZN5GFace4meshEb+0x67) [0x7f54b2b0cad7]
[9] /lib/x86_64-linux-gnu/libgmsh.so.4.12(+0x716c8b) [0x7f54b2d16c8b]
[10] /lib/x86_64-linux-gnu/libgomp.so.1(GOMP_parallel+0x46) [0x7f54b8021866]
[11] /lib/x86_64-linux-gnu/libgmsh.so.4.12(_Z12GenerateMeshP6GModeli+0xa6f) [0x7f54b2d1ed5f]
[12] /lib/x86_64-linux-gnu/libgmsh.so.4.12(_ZN6GModel4meshEi+0x29) [0x7f54b2b5f2d9]
[13] /lib/x86_64-linux-gnu/libgmsh.so.4.12(_ZN4gmsh5model4mesh8generateEi+0x34) [0x7f54b29993b4]
[14] /lib/x86_64-linux-gnu/libgmsh.so.4.12(gmshModelMeshGenerate+0x18) [0x7f54b34cc328]

```

Therefore, this is an error in gmsh, and not in dolfinx. Hence support must be asked on the gmsh support channel [Issues · gmsh / gmsh · GitLab](https://gitlab.onelab.info/gmsh/gmsh/-/issues) and not here.

---

<div class="post-metadata">

**Author:** ![francesco-ballarin](https://avatars.discourse-cdn.com/v4/letter/f/f05b48/32.png) [@francesco-ballarin](https://fenicsproject.discourse.group/u/francesco-ballarin)\
**Post date:** [October 13, 2024, 1:52pm UTC](https://fenicsproject.discourse.group/t/when-trying-to-create-mesh-using-gmsh-i-am-getting-petsc-error/16039/3 "2024-10-13T13:52:24Z")

</div>