Error in Meshing on Ubuntu 22.04

[danishTUE]

Hi,

I have installed Neper on a new machine with Ubuntu 22.04. I have a script that works completely fine on a different machine with Ubuntu 18.04 and 20.04 but on Ubntu 22.04 it gives the following error when the meshing module goes from 2D meshing to 3d meshing.

Info : - Fixing 2D-mesh pinches...
Info : - 3d meshing... Error : Wrong mesh dimension: -1!
Error : Wrong mesh dimension: -1!
Aborted (core dumped)

I am not sure if its because of incorrect installation. However, I had installed almost all the required dependencies via the following commands:

sudo apt-get install gsl-bin
sudo apt install libomp-dev
sudo apt install libgsl-dev
sudo apt-get install libpthread-stubs0-dev
sudo apt install gmsh
sudo apt-install povray
sudo apt-get install povray
sudo apt-get install libnlopt0
git clone https://github.com/neperfepx/neper.git
cd neper/
cd src/
mkdir build
cd build
cmake ..
make
sudo make install
make test

Tests resulted in some failed tests as well. Most of the failed tests were from M and V module.

Can you please help me in figuring out what may be missing?

Many thanks

[danishTUE]

I am attaching the log file for the test. The log file shows that most of these test resulted in the same error
LastTest.log
.

[xshang93]

Did you test if the dependant, in particular gmsh, is working properly?

[danishTUE]

How can I test that? When I type gmsh in the command window, the GUI of gmsh gets opened up. So i presume its working fine?

[rquey]

Try to run the following:

export OMP_NUM_THREADS=1
gmsh --version
neper -T -n 2
neper -M n2-id1.tess -tmp .

After Neper crashes, there should be a file named tmp...-1.geo and a file named tmp...-1.msh in the working directory. Please provide your terminal output and the tmp files.

[ngrilli]

Answering myself: I compiled gmsh from source and it works
I did:

1. download gmsh source code here: https://gmsh.info/
2. Move to project folder
3. Follow instructions in ~/projects/gmsh-4.10.5-source/README.txt
   that is:
   cd ~/projects/gmsh-4.10.5-source/
   mkdir build
   cd build
   cmake ..
   make
   sudo make install
   This will create the executable gmsh and you can launch gmsh from terminal.
   Then redo the procedure explained by @danishTUE but skip "sudo apt install gmsh"
   redo neper installation, now it works.
   The only thing I don't understand is that by compiling gmsh from source,
   when I launch gmsh from terminal, that does not open the graphical interface.
   Best Regards,
   Nicolò

[rquey]

The only thing I don't understand is that by compiling gmsh from source,
when I launch gmsh from terminal, that does not open the graphical interface.

You probably did not install FLTK (listed as dependency when you do cmake .. in Gmsh).

Once I download the gmsh binaries, how do I link it to neper?

Neper uses the binary, there is no need to link (or reinstall Neper, after you install Gmsh).

[danishTUE]

Thanks Nicolo for giving out the procedure for compiling gmsh from source. I was not able to do that and hence I had used binary. I just downloaded the binary and exported its bin path in the bashrc. After that the call to gmsh was always made to the gmsh binary i downloaded which made the neper work.

[liu373994209]

Dear danish TUE, I have encountered the same problem as you. Can you provide me with detailed guidance on how to proceed

[rquey]

https://neper.info/doc/tutorials/install_ubuntu22.html#installing-gmsh