Bug report-can't

[Yinzhanqing]

At first, I write 'neper -T -n 121 -dim 2 -domain 'square("330,330")' -morpho 'gg' -o n121-id1' and visualized successful. Then I shot down the Ubuntu. Then I do some work in virtual machines.(I mean these operations should not affect my host?) Then I came back to Tessellation again, using 'neper -T -n 121 -dim 2 -domain 'square("330,330")' -morpho 'gg' -reg 1 -o n121-id1', things went wrong here. After running this code, it shows "No initialization file found (`/home/yin/.neperrc')." and "> Aborted (core dumped)" in the end. So I run some test:

1. Look neper's version

yin@Yin:~$ neper -V

========================    N   e   p   e   r    =======================
Info   : A software package for polycrystal generation and meshing.
Info   : Version 4.10.1
Info   : Built with: gsl|muparser|opengjk|openmp|nlopt|libscotch (full)
Info   : Running on 22 threads.
Info   : <https://neper.info>
Info   : Copyright (C) 2003-2024, and GNU GPL'd, by Romain Quey.
Info   : No initialization file found (`/home/yin/.neperrc').
Info   : ---------------------------------------------------------------
Info   : MODULE  -V loaded with arguments:
Info   : [ini file] (none)
Info   : [com line] (none)
Info   : ---------------------------------------------------------------
Info   :   - Reading arguments...
Info   : Elapsed time: 0.050 secs.
========================================================================

also says No initialization file found (`/home/yin/.neperrc').

3. After ask GPT, I write a file

yin@Yin:~$ echo -e "# Neper configuration file\nverbosity = 3\noutputdir = ." > /home/yin/.neperrc

4. Look version again

yin@Yin:~$ neper -V

========================    N   e   p   e   r    =======================
Info   : A software package for polycrystal generation and meshing.
Info   : Version 4.10.1
Info   : Built with: gsl|muparser|opengjk|openmp|nlopt|libscotch (full)
Info   : Running on 22 threads.
Info   : <https://neper.info>
Info   : Copyright (C) 2003-2024, and GNU GPL'd, by Romain Quey.
Info   : Loading initialization file `/home/yin/.neperrc'...
Info   : ---------------------------------------------------------------
Info   : MODULE  -V loaded with arguments:
Info   : [ini file] (none)
Info   : [com line] (none)
Info   : ---------------------------------------------------------------
Info   :   - Reading arguments...
Info   : Elapsed time: 0.041 secs.
========================================================================

seems like finding the initialization file.

5. cd to the work file and try Tessellation again

========================    N   e   p   e   r    =======================
Info   : A software package for polycrystal generation and meshing.
Info   : Version 4.10.1
Info   : Built with: gsl|muparser|opengjk|openmp|nlopt|libscotch (full)
Info   : Running on 8 threads.
Info   : <https://neper.info>
Info   : Copyright (C) 2003-2024, and GNU GPL'd, by Romain Quey.
Info   : Loading initialization file `/home/yin/.neperrc'...
Info   : ---------------------------------------------------------------
Info   : MODULE  -T loaded with arguments:
Info   : [ini file] (none)
Info   : [com line] -n 121 -dim 2 -domain square("330,330") -morpho gg
         -reg 1 -o n121-id1
Info   : ---------------------------------------------------------------
Info   : Reading input data...
Info   : Creating domain...
Info   : Creating tessellation...
Info   :   - Setting seeds... 100%
Info   :   - Running tessellation...
Info   :     >  Aborted (core dumped)

6. Try a basic code

yin@Yin:/mnt/e/Python/CPFEM/Test-Neper2cae+PyCiGen$ neper -T -n 121

========================    N   e   p   e   r    =======================
Info   : A software package for polycrystal generation and meshing.
Info   : Version 4.10.1
Info   : Built with: gsl|muparser|opengjk|openmp|nlopt|libscotch (full)
Info   : Running on 8 threads.
Info   : <https://neper.info>
Info   : Copyright (C) 2003-2024, and GNU GPL'd, by Romain Quey.
Info   : Loading initialization file `/home/yin/.neperrc'...
Info   : ---------------------------------------------------------------
Info   : MODULE  -T loaded with arguments:
Info   : [ini file] (none)
Info   : [com line] -n 121
Info   : ---------------------------------------------------------------
Info   : Reading input data...
Info   : Creating domain...
Info   : Creating tessellation...
Info   :   - Setting seeds...
Info   :   - Running tessellation...
Info   : Generating crystal orientations...
Info   : Writing results...
Info   :     [o] Writing file `n121-id1.tess'...
Info   :     [o] Wrote file `n121-id1.tess'.
Info   : Elapsed time: 0.018 secs.
========================================================================

succeed

7. Try again

yin@Yin:/mnt/e/Python/CPFEM/Test-Neper2cae+PyCiGen$ neper -T -n 121 -dim 2 -domain 'square("330,330")' -morpho 'gg' -o n121-id1

========================    N   e   p   e   r    =======================
Info   : A software package for polycrystal generation and meshing.
Info   : Version 4.10.1
Info   : Built with: gsl|muparser|opengjk|openmp|nlopt|libscotch (full)
Info   : Running on 8 threads.
Info   : <https://neper.info>
Info   : Copyright (C) 2003-2024, and GNU GPL'd, by Romain Quey.
Info   : Loading initialization file `/home/yin/.neperrc'...
Info   : ---------------------------------------------------------------
Info   : MODULE  -T loaded with arguments:
Info   : [ini file] (none)
Info   : [com line] -n 121 -dim 2 -domain square("330,330") -morpho gg -o
         n121-id1
Info   : ---------------------------------------------------------------
Info   : Reading input data...
Info   : Creating domain...
Info   : Creating tessellation...
Info   :   - Setting seeds... 100%
Info   :   - Running tessellation...
Info   :     >  Aborted (core dumped)

failed

8. delate '-morpho 'gg'' in the code

yin@Yin:/mnt/e/Python/CPFEM/Test-Neper2cae+PyCiGen$ neper -T -n 121 -dim 2 -domain 'square("330,330")'

========================    N   e   p   e   r    =======================
Info   : A software package for polycrystal generation and meshing.
Info   : Version 4.10.1
Info   : Built with: gsl|muparser|opengjk|openmp|nlopt|libscotch (full)
Info   : Running on 8 threads.
Info   : <https://neper.info>
Info   : Copyright (C) 2003-2024, and GNU GPL'd, by Romain Quey.
Info   : Loading initialization file `/home/yin/.neperrc'...
Info   : ---------------------------------------------------------------
Info   : MODULE  -T loaded with arguments:
Info   : [ini file] (none)
Info   : [com line] -n 121 -dim 2 -domain square("330,330")
Info   : ---------------------------------------------------------------
Info   : Reading input data...
Info   : Creating domain...
Info   : Creating tessellation...
Info   :   - Setting seeds...
Info   :   - Running tessellation...
Info   : Generating crystal orientations...
Info   : Writing results...
Info   :     [o] Writing file `n121-id1.tess'...
Info   :     [o] Wrote file `n121-id1.tess'.
Info   : Elapsed time: 0.036 secs.
========================================================================

succeed

9. Try another code

yin@Yin:/mnt/e/Python/CPFEM/Test-Neper2cae+PyCiGen/test1$ neper -T -n 121 -dim 2 -domain 'square("330,330")' -reg 1 -o n
121-id1

========================    N   e   p   e   r    =======================
Info   : A software package for polycrystal generation and meshing.
Info   : Version 4.10.1
Info   : Built with: gsl|muparser|opengjk|openmp|nlopt|libscotch (full)
Info   : Running on 8 threads.
Info   : <https://neper.info>
Info   : Copyright (C) 2003-2024, and GNU GPL'd, by Romain Quey.
Info   : Loading initialization file `/home/yin/.neperrc'...
Info   : ---------------------------------------------------------------
Info   : MODULE  -T loaded with arguments:
Info   : [ini file] (none)
Info   : [com line] -n 121 -dim 2 -domain square("330,330") -reg 1 -o
         n121-id1
Info   : ---------------------------------------------------------------
Info   : Reading input data...
Info   : Creating domain...
Info   : Creating tessellation...
Info   :   - Setting seeds...
Info   :   - Running tessellation...
Info   : Generating crystal orientations...
Info   : Regularizing tessellation...
Info   :   -
Info   : Writing results...
Info   :     [o] Writing file `n121-id1.tess'...
Info   :     [o] Wrote file `n121-id1.tess'.
Info   : Elapsed time: 0.015 secs.
========================================================================

succeed

10. Try to visualized

yin@Yin:/mnt/e/Python/CPFEM/Test-Neper2cae+PyCiGen/test1$ neper -V n121-id1.tess -datacellcol id -datacelltrs 0.5 -imagesize 1200:1200 -print n121-id1_image

========================    N   e   p   e   r    =======================
Info   : A software package for polycrystal generation and meshing.
Info   : Version 4.10.1
Info   : Built with: gsl|muparser|opengjk|openmp|nlopt|libscotch (full)
Info   : Running on 8 threads.
Info   : <https://neper.info>
Info   : Copyright (C) 2003-2024, and GNU GPL'd, by Romain Quey.
Info   : Loading initialization file `/home/yin/.neperrc'...
Info   : ---------------------------------------------------------------
Info   : MODULE  -V loaded with arguments:
Info   : [ini file] (none)
Info   : [com line] n121-id1.tess -datacellcol id -datacelltrs 0.5
         -imagesize 1200:1200 -print n121-id1_image
Info   : ---------------------------------------------------------------
Info   :   - Reading arguments...
Info   : Loading tessellation...
Info   :     [i] Parsing file `n121-id1.tess'...
Info   :     [i] Parsed file `n121-id1.tess'.
Info   : Reading data (cell, col)...
Info   : Reading data (cell, trs)...
Info   : Printing image...
Info   :   - Printing tessellation...
Info   :   - Generating png file (1200x1200 pixels)...
Info   :     [o] Writing file `n121-id1_image.png'...
Error  :     > File `n121-id1_image.png' could not be generated!
Aborted (core dumped)

failed!

11. I don't know why, after ask GPT, I run ''yin@Yin:/$ sudo apt-get install libcairo2-dev libpng-dev", after that, also visualized failed and

yin@Yin:/mnt/e/Python/CPFEM/Test-Neper2cae+PyCiGen/test1$ neper -V n121-id1.tess -datacellcol id -datacelltrs 0.5 -imagesize 1200:1200 -print n121-id1_image

========================    N   e   p   e   r    =======================
Info   : A software package for polycrystal generation and meshing.
Info   : Version 4.10.1
Info   : Built with: gsl|muparser|opengjk|openmp|nlopt|libscotch (full)
Info   : Running on 8 threads.
Info   : <https://neper.info>
Info   : Copyright (C) 2003-2024, and GNU GPL'd, by Romain Quey.
Info   : Loading initialization file `/home/yin/.neperrc'...
Info   : ---------------------------------------------------------------
Info   : MODULE  -V loaded with arguments:
Info   : [ini file] (none)
Info   : [com line] n121-id1.tess -datacellcol id -datacelltrs 0.5
         -imagesize 1200:1200 -print n121-id1_image
Info   : ---------------------------------------------------------------
Info   :   - Reading arguments...
Info   : Loading tessellation...
Info   :     [i] Parsing file `n121-id1.tess'...
Info   :     [i] Parsed file `n121-id1.tess'.
Info   : Reading data (cell, col)...
Info   : Reading data (cell, trs)...
Info   : Printing image...
Info   :   - Printing tessellation...
Info   :   - Generating png file (1200x1200 pixels)...
Info   :     [o] Writing file `n121-id1_image.png'...
Error  :     > File `n121-id1_image.png' could not be generated!
Aborted (core dumped)

[rquey]

1-4. The configuration file is optional. You don't need it (and the chatgpt-generated is wrongly formatted anyway).

Otherwise, -domain 'square("330,330")' should be written -domain 'square(330,330)'...

I'm not sure about running Neper on a Virtual machine and don't know if this might be the cause of your errors.

10-11 suggest that Povray is not installed properly.