### Author:  [@French\_fries](https://fenicsproject.discourse.group/u/French_fries)
#### Post date: [July 29, 2024, 1:29pm UTC](https://fenicsproject.discourse.group/t/when-using-gmshio-to-read-hexahedral-mesh-an-error-occurs/15376/1 "2024-07-29T13:29:34Z")
As per the title, I have confirmed that there is only one type of mesh (hexahedral), but I still encounter an error when reading the .msh file:
```auto
from dolfinx.io import gmshio
proc = MPI.COMM_WORLD.rank
mesh, cell_markers, facet_markers = gmshio.read_from_msh("test.msh", MPI.COMM_WORLD, gdim=3)
```
```auto
Traceback (most recent call last):
File "/home/dyfluid/Desktop/data_3D/convert.py", line 10, in
mesh, cell_markers, facet_markers = gmshio.read_from_msh("test.msh", MPI.COMM_WORLD, gdim=3)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/dyfluid/anaconda3/envs/fenicsx-env/lib/python3.11/site-packages/dolfinx/io/gmshio.py", line 373, in read_from_msh
msh = model_to_mesh(gmsh.model, comm, rank, gdim=gdim, partitioner=partitioner)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/dyfluid/anaconda3/envs/fenicsx-env/lib/python3.11/site-packages/dolfinx/io/gmshio.py", line 244, in model_to_mesh
topologies = extract_topology_and_markers(model)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/dyfluid/anaconda3/envs/fenicsx-env/lib/python3.11/site-packages/dolfinx/io/gmshio.py", line 138, in extract_topology_and_markers
assert len(entity_types) == 1
^^^^^^^^^^^^^^^^^^^^^^
AssertionError
```
Here is my .geo file:
```auto
Circle(1) = {0, 0, 0, 0.5, 0, 2*Pi};
Curve Loop(1) = {1};
Plane Surface(1) = {1};
Extrude {0, 0, 0.3} {Surface{1};Layers {3};Recombine;}
Physical Surface("top_bottom", 4) = {1,3};
Physical Surface("cylinder", 5) = {2};
Physical Volume("v", 6) = {1};
Mesh 2;
RecombineMesh;
Mesh.SubdivisionAlgorithm = 1;
```
and the visualization results from the Gmsh interface are shown below. According to the log message, it’s evident that all the face meshes are quadrilateral:
I hope to receive guidance, thank you!
---
### Author:  [@francesco-ballarin](https://fenicsproject.discourse.group/u/francesco-ballarin)
#### Post date: [July 29, 2024, 3:45pm UTC](https://fenicsproject.discourse.group/t/when-using-gmshio-to-read-hexahedral-mesh-an-error-occurs/15376/2 "2024-07-29T15:45:57Z")
Very first step could be to edit `/home/dyfluid/anaconda3/envs/fenicsx-env/lib/python3.11/site-packages/dolfinx/io/gmshio.py`, adding a new line before line 138 with a `print(entity_types)` to see what `entity_types` contains.
---
### Author:  [@French\_fries](https://fenicsproject.discourse.group/u/French_fries)
#### Post date: [July 30, 2024, 12:50am UTC](https://fenicsproject.discourse.group/t/when-using-gmshio-to-read-hexahedral-mesh-an-error-occurs/15376/3 "2024-07-30T00:50:43Z")
According to your suggestion, I got the output below, and I’m not quite sure what it means. Could you help me analyze it.
```auto
[3]
[3]
[3]
[]
```
---
### Author:  [@francesco-ballarin](https://fenicsproject.discourse.group/u/francesco-ballarin)
#### Post date: [July 30, 2024, 7:22am UTC](https://fenicsproject.discourse.group/t/when-using-gmshio-to-read-hexahedral-mesh-an-error-occurs/15376/4 "2024-07-30T07:22:56Z")
Which version of gmsh are you using? The file you provided does not seem to be a valid `geo` file for my version (4.12.2).
```auto
$ gmsh mesh.geo -2 -o mesh.msh
Info : Running 'gmsh mesh.geo -2 -o mesh.msh' [Gmsh 4.12.2, 1 node, max. 1 thread]
Info : Started on Tue Jul 30 09:20:53 2024
Info : Reading 'mesh.geo'...
Error : 'mesh.geo', line 1: Circle requires 3 points
Error : Unknown curve 1
Error : 'mesh.geo', line 4: Could not add plane surface
Warning : Skipping unknown surface 2 in physical surface 5
Info : Meshing 1D...
Info : Done meshing 1D (Wall 1.489e-05s, CPU 1.6e-05s)
Info : Meshing 2D...
Info : [0%] Meshing surface 1 (Plane, Frontal-Delaunay)
Warning : Mesh generation of surface 1 skipped: only 0 nodes on the boundary
Warning : Surface 1 consists of no elements
Info : [50%] Meshing surface 3 (Extruded)
Info : Done meshing 2D (Wall 0.000101788s, CPU 9.7e-05s)
Info : 0 nodes 0 elements
Warning : ------------------------------
Warning : Mesh generation error summary
Warning : 2 warnings
Warning : 0 errors
Warning : Check the full log for details
Warning : ------------------------------
Info : Recombining 2D mesh...
Info : Blossom recombination completed (Wall 1.8739e-05s, CPU 1.8e-05s): 0 quads, 0 triangles, 0 invalid quads, 0 quads with Q < 0.1, avg Q = -nan, min Q = 1
Info : Blossom recombination completed (Wall 1.529e-06s, CPU 1e-06s): 0 quads, 0 triangles, 0 invalid quads, 0 quads with Q < 0.1, avg Q = -nan, min Q = 1
Info : Done recombining 2D mesh (Wall 4.3256e-05s, CPU 4.1e-05s)
Warning : Skipping unknown surface 2 in physical surface 5
Info : Done reading 'mesh.geo'
Info : Meshing 1D...
Info : Done meshing 1D (Wall 3.665e-06s, CPU 4e-06s)
Info : Meshing 2D...
Info : [0%] Meshing surface 1 (Plane, Frontal-Delaunay)
Warning : Mesh generation of surface 1 skipped: only 0 nodes on the boundary
Warning : Surface 1 consists of no elements
Info : [50%] Meshing surface 3 (Extruded)
Info : Done meshing 2D (Wall 2.6817e-05s, CPU 2.5e-05s)
Info : 0 nodes 0 elements
Warning : ------------------------------
Warning : Mesh generation error summary
Warning : 2 warnings
Warning : 0 errors
Warning : Check the full log for details
Warning : ------------------------------
Info : Writing 'mesh.msh'...
Info : Done writing 'mesh.msh'
Info : Stopped on Tue Jul 30 09:20:53 2024 (From start: Wall 0.0534747s, CPU 0.076493s)
```
```auto
$ gmsh mesh.geo -3 -o mesh.msh
Info : Running 'gmsh mesh.geo -3 -o mesh.msh' [Gmsh 4.12.2, 1 node, max. 1 thread]
Info : Started on Tue Jul 30 09:21:34 2024
Info : Reading 'mesh.geo'...
Error : 'mesh.geo', line 1: Circle requires 3 points
Error : Unknown curve 1
Error : 'mesh.geo', line 4: Could not add plane surface
Warning : Skipping unknown surface 2 in physical surface 5
Info : Meshing 1D...
Info : Done meshing 1D (Wall 5.503e-06s, CPU 6e-06s)
Info : Meshing 2D...
Info : [0%] Meshing surface 1 (Plane, Frontal-Delaunay)
Warning : Mesh generation of surface 1 skipped: only 0 nodes on the boundary
Warning : Surface 1 consists of no elements
Info : [50%] Meshing surface 3 (Extruded)
Info : Done meshing 2D (Wall 4.4268e-05s, CPU 4.2e-05s)
Info : 0 nodes 0 elements
Warning : ------------------------------
Warning : Mesh generation error summary
Warning : 2 warnings
Warning : 0 errors
Warning : Check the full log for details
Warning : ------------------------------
Info : Recombining 2D mesh...
Info : Blossom recombination completed (Wall 1.1907e-05s, CPU 1.1e-05s): 0 quads, 0 triangles, 0 invalid quads, 0 quads with Q < 0.1, avg Q = -nan, min Q = 1
Info : Blossom recombination completed (Wall 6.78e-07s, CPU 1e-06s): 0 quads, 0 triangles, 0 invalid quads, 0 quads with Q < 0.1, avg Q = -nan, min Q = 1
Info : Done recombining 2D mesh (Wall 2.446e-05s, CPU 2.3e-05s)
Warning : Skipping unknown surface 2 in physical surface 5
Info : Done reading 'mesh.geo'
Info : Meshing 1D...
Info : Done meshing 1D (Wall 1.694e-06s, CPU 2e-06s)
Info : Meshing 2D...
Info : [0%] Meshing surface 1 (Plane, Frontal-Delaunay)
Warning : Mesh generation of surface 1 skipped: only 0 nodes on the boundary
Warning : Surface 1 consists of no elements
Info : [50%] Meshing surface 3 (Extruded)
Info : Done meshing 2D (Wall 1.2938e-05s, CPU 1.2e-05s)
Info : Meshing 3D...
Info : Meshing volume 1 (Extruded)
Error : No elements in volume 1
Info : Done meshing 3D (Wall 3.6784e-05s, CPU 3.5e-05s)
Info : 0 nodes 0 elements
Error : ------------------------------
Error : Mesh generation error summary
Error : 2 warnings
Error : 1 error
Error : Check the full log for details
Error : ------------------------------
Info : Writing 'mesh.msh'...
Info : Done writing 'mesh.msh'
Info : Stopped on Tue Jul 30 09:21:34 2024 (From start: Wall 0.00126867s, CPU 0.078055s)
```
---
### Author:  [@French\_fries](https://fenicsproject.discourse.group/u/French_fries)
#### Post date: [July 30, 2024, 12:43pm UTC](https://fenicsproject.discourse.group/t/when-using-gmshio-to-read-hexahedral-mesh-an-error-occurs/15376/7 "2024-07-30T12:43:06Z")
I am using version 4.10.5. I modified the msh file to eliminate the previous error. However, when I tried to read it again, MPI-related errors occurred:
```auto
from mpi4py import MPI
from dolfinx.io import gmshio
mesh, cell_markers, facet_markers = gmshio.read_from_msh("test.msh", MPI.COMM_WORLD, gdim=3)
```
```auto
Invalid rank, error stack:
internal_Issend(60788): MPI_Issend(buf=0x25f3e61, count=1, MPI_BYTE, 1, 1, comm=0x84000005, request=0x25f3e84) failed
internal_Issend(60749): Invalid rank has value 1 but must be nonnegative and less than 1
Abort(674890502) on node 0 (rank 0 in comm 416): application called MPI_Abort(comm=0x84000005, 674890502) - process 0
```
Below is my current .geo file:
```auto
// Gmsh project created on Tue Jul 30 10:39:54 2024
SetFactory("OpenCASCADE");
Circle(1) = {0, 0, 0, 0.5, 0, 2*Pi};
Curve Loop(1) = {1};
Plane Surface(1) = {1};
Extrude {0, 0, 0.3} {Surface{1};Layers {3};Recombine;}
Physical Surface("top_bottom", 4) = {1,3};
Physical Surface("cylinder", 5) = {2};
Physical Volume("v", 6) = {1};
Mesh.SubdivisionAlgorithm = 1;
```
Here is the visualization result in ParaView:
---
### Author:  [@francesco-ballarin](https://fenicsproject.discourse.group/u/francesco-ballarin)
#### Post date: [July 30, 2024, 12:50pm UTC](https://fenicsproject.discourse.group/t/when-using-gmshio-to-read-hexahedral-mesh-an-error-occurs/15376/8 "2024-07-30T12:50:52Z")
When I run this, I get
```auto
Info : Reading 'mesh.msh'...
Info : 9 entities
Info : 260 nodes
Info : 596 elements
Info : Done reading 'mesh.msh'
Unknown cell type 6.
Traceback (most recent call last):
File "/tmp/test.py", line 4, in
mesh, cell_markers, facet_markers = gmshio.read_from_msh("mesh.msh", MPI.COMM_WORLD, gdim=3)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/lib/python3.12/site-packages/dolfinx/io/gmshio.py", line 374, in read_from_msh
msh = model_to_mesh(gmsh.model, comm, rank, gdim=gdim, partitioner=partitioner)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/lib/python3.12/site-packages/dolfinx/io/gmshio.py", line 291, in model_to_mesh
ufl_domain = ufl_mesh(cell_id, gdim, dtype=dtype)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/lib/python3.12/site-packages/dolfinx/io/gmshio.py", line 75, in ufl_mesh
raise e
File "/lib/python3.12/site-packages/dolfinx/io/gmshio.py", line 72, in ufl_mesh
shape, degree = _gmsh_to_cells[gmsh_cell]
~~~~~~~~~~~~~~ ^^^^^^^^^^^
KeyError: 6
```
From [Gmsh 4.13.1](https://gmsh.info/doc/texinfo/gmsh.html#MSH-file-format) you can see that 6 means `6-node prism`, which not in the list at [dolfinx/python/dolfinx/io/gmshio.py at 5d15d263f20a9d8ada051dd2ece0f35894d38d4a · FEniCS/dolfinx · GitHub](https://github.com/FEniCS/dolfinx/blob/5d15d263f20a9d8ada051dd2ece0f35894d38d4a/python/dolfinx/io/gmshio.py#L37)
Please ask at [Issues · gmsh / gmsh · GitLab](https://gitlab.onelab.info/gmsh/gmsh/-/issues) how to change your `geo` file so that it uses one of the supported cell types (hex, I guess), and then report back the answer.
---
### Author:  [@French\_fries](https://fenicsproject.discourse.group/u/French_fries)
#### Post date: [July 30, 2024, 2:01pm UTC](https://fenicsproject.discourse.group/t/when-using-gmshio-to-read-hexahedral-mesh-an-error-occurs/15376/9 "2024-07-30T14:01:09Z")
Sorry, this is my mistake: I just found that the .msh files generated from the same .geo file are different in different versions of Gmsh. When you use the new software to convert the .geo file I provided into a .msh file, the surface mesh shape is triangular, corresponding to the 3D mesh that you mentioned earlier with six vertices forming a prism. However, in the old version of the software, the same .geo file gave me the result as in my previous reply, which is a hexahedral mesh, but it produced an MPI error. Perhaps I should directly provide you with the .msh file (I tried just now, but I don’t know which cloud storage I should upload the file to), so we wouldn’t get different results due to the different versions of Gmsh.
So, my question is regarding the MPI-related error mentioned in my previous reply. Do you have any suggestions for this error? (I have searched for related posts, but there isn’t much content about this error, so I can’t find help)
---
### Author:  [@francesco-ballarin](https://fenicsproject.discourse.group/u/francesco-ballarin)
#### Post date: [July 30, 2024, 4:56pm UTC](https://fenicsproject.discourse.group/t/when-using-gmshio-to-read-hexahedral-mesh-an-error-occurs/15376/10 "2024-07-30T16:56:35Z")
Please sort out the gmsh part first with them. It’s unlikely that a version upgrade changes so dramatically (different cell types) the final mesh.
---
### Author:  [@French\_fries](https://fenicsproject.discourse.group/u/French_fries)
#### Post date: [July 31, 2024, 12:35am UTC](https://fenicsproject.discourse.group/t/when-using-gmshio-to-read-hexahedral-mesh-an-error-occurs/15376/11 "2024-07-31T00:35:17Z")
Sure, I will do my best to resolve the Gmsh issue. However, the same MPI problem still exists and has not been resolved, as mentioned in this post.
[https://fenicsproject.discourse.group/t/read-meshtags-causing-invalid-rank-issues/14349?u=french\_fries](https://fenicsproject.discourse.group/t/read-meshtags-causing-invalid-rank-issues/14349)
I hope you can take a look at it.
---
### Author:  [@francesco-ballarin](https://fenicsproject.discourse.group/u/francesco-ballarin)
#### Post date: [July 31, 2024, 7:27am UTC](https://fenicsproject.discourse.group/t/when-using-gmshio-to-read-hexahedral-mesh-an-error-occurs/15376/12 "2024-07-31T07:27:56Z")
As I said, please ask at [Sign in · GitLab](https://gitlab.onelab.info/gmsh/gmsh/-/issues:) a relevant question could be why with a certain version you get a hex mesh, and with another a prism mesh. That is the gmsh support channel, which is surely more qualified than me to help in that respect. I won’t be replying any further until that part has been sorted.
The MPI error you link in that post is not necessarily related: `MPI_Issend` is a very low level function, which may be called in several places in the code, hence there is no guarantee that the two failures occur at exactly the same place.
---
### Author:  [@French\_fries](https://fenicsproject.discourse.group/u/French_fries)
#### Post date: [July 31, 2024, 7:41am UTC](https://fenicsproject.discourse.group/t/when-using-gmshio-to-read-hexahedral-mesh-an-error-occurs/15376/13 "2024-07-31T07:41:14Z")
I see, it looks like I indeed need to address the issue with the grid first. Thank you for your explanation.
---
### Author:  [@French\_fries](https://fenicsproject.discourse.group/u/French_fries)
#### Post date: [August 16, 2024, 3:03am UTC](https://fenicsproject.discourse.group/t/when-using-gmshio-to-read-hexahedral-mesh-an-error-occurs/15376/15 "2024-08-16T03:03:51Z")
Dear, I found that it is not a Gmsh version issue. In fact, the same geo file produces different results depending on how it is opened: for the mesh below, if I use `gmsh test.geo -format msh2 -3` to convert it to an msh file, the result is as shown in Figure 1; however, if I open the geo file in the UI interface and save it as an msh file (which may require opening it twice), the result is as shown in Figure 2 (These are two different shapes of hexahedral meshes, perhaps you can reproduce this based on my description).
```auto
// Gmsh project created on Tue Jul 30 10:39:54 2024
SetFactory("OpenCASCADE");
Circle(1) = {0, 0, 0, 0.5, 0, 2*Pi};
Curve Loop(1) = {1};
Plane Surface(1) = {1};
Extrude {0, 0, 0.3} {Surface{1};Layers {3};Recombine;}
Physical Surface("top_bottom", 4) = {1,3};
Physical Surface("cylinder", 5) = {2};
Physical Volume("v", 6) = {1};
Mesh 2;
RecombineMesh;
Mesh.SubdivisionAlgorithm = 1;
```
The msh file generated in the latter case produces the following error when reading with `gmshio.read_from_msh` :
```auto
Traceback (most recent call last):
File "/home/dyfluid/Desktop/data_3Dunit/convert.py", line 10, in
mesh, cell_markers, facet_markers = gmshio.read_from_msh("test.msh", MPI.COMM_WORLD, gdim=3)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/dyfluid/anaconda3/envs/fenicsx-env/lib/python3.11/site-packages/dolfinx/io/gmshio.py", line 374, in read_from_msh
msh = model_to_mesh(gmsh.model, comm, rank, gdim=gdim, partitioner=partitioner)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/dyfluid/anaconda3/envs/fenicsx-env/lib/python3.11/site-packages/dolfinx/io/gmshio.py", line 245, in model_to_mesh
topologies = extract_topology_and_markers(model)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/dyfluid/anaconda3/envs/fenicsx-env/lib/python3.11/site-packages/dolfinx/io/gmshio.py", line 139, in extract_topology_and_markers
assert len(entity_types) == 1
^^^^^^^^^^^^^^^^^^^^^^
AssertionError
```
---
### Author:  [@francesco-ballarin](https://fenicsproject.discourse.group/u/francesco-ballarin)
#### Post date: [August 16, 2024, 6:38am UTC](https://fenicsproject.discourse.group/t/when-using-gmshio-to-read-hexahedral-mesh-an-error-occurs/15376/16 "2024-08-16T06:38:21Z")
As I’ve already stated, you must ask at the gmsh forum, since this is a gmsh issue. I am closing this.
---
### Author:  [@francesco-ballarin](https://fenicsproject.discourse.group/u/francesco-ballarin)
#### Post date: [August 16, 2024, 6:38am UTC](https://fenicsproject.discourse.group/t/when-using-gmshio-to-read-hexahedral-mesh-an-error-occurs/15376/17 "2024-08-16T06:38:23Z")