Closed NotRealEngineering closed 4 years ago
It looks like it does not find Gmsh or Gmsh is broken.
gmsh
from the command line?-gmsh
? Does it point to a valid Gmsh binary?cmake ..
stage) when compiling Gmsh?Thank you for your response.
Thank you for your help.
On Fri, Oct 2, 2020 at 8:59 AM Romain Quey notifications@github.com wrote:
It looks like it does not find Gmsh or Gmsh is broken.
- Is Gmsh available as gmsh from the command line?
- Are you using option -gmsh? Does it point to a valid Gmsh binary?
- Did you resolve all dependencies (cmake .. stage) when compiling Gmsh?
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-- Regards, Not Real Engineering
When you run cmake .., there are messages about whether the dependencies are found or not.
Thank you. Indeed some dependencies were missing for Gmsh. I installed them all and now while running cmake .. for gmsh all dependencies are found. I installed the gmsh and neper again after this but still the same issue is there. When I run make test for neper. The following tests fail.
90% tests passed, 29 tests failed out of 282
Total Test time (real) = 160.77 sec
The following tests FAILED: 142 - M_mesh2dalgo_netg (Child aborted) 151 - M_remesh3 (Child aborted) 154 - M_nset3 (Child aborted) 170 - M_interface2 (Child aborted) 175 - V_pretest3 (Child aborted) 177 - V_pretest5 (Child aborted) 242 - V_nodecol (Child aborted) 243 - V_nodecol_real (Child aborted) 244 - V_nodecolscheme (Child aborted) 245 - V_nodescale (Child aborted) 246 - V_nodescale2 (Child aborted) 247 - V_elsetcol (Child aborted) 248 - V_elsetcol_real (Child aborted) 249 - V_elsetcolscheme (Child aborted) 250 - V_elsetscale (Child aborted) 251 - V_elsetscale2 (Child aborted) 252 - V_elsetscaletitle (Child aborted) 253 - V_elsetcol_ori (Child aborted) 254 - V_nodecoo (Child aborted) 255 - V_nodecoo_disp (Child aborted) 256 - V_nodecoofact (Child aborted) 257 - V_slicemesh (Child aborted) 258 - V_slicemesh2 (Child aborted) 267 - V_showelt (Child aborted) 268 - V_dataelt3d (Child aborted) 270 - V_cameracoo2 (Child aborted) 271 - V_cameracoo3 (Child aborted) 273 - V_cameralookat2 (Child aborted) 282 - V_loop (Child aborted) Errors while running CTest make: *** [Makefile:107: test] Error 8
Any help is appreciated.
If I run the make test again, this time only 9 tests failed.
97% tests passed, 9 tests failed out of 282
Total Test time (real) = 195.79 sec
The following tests FAILED: 139 - M_mesh2dalgo_mead (Child aborted) 140 - M_mesh2dalgo_dela (Child aborted) 144 - M_mesh3dalgo_netggmsh (Child aborted) 145 - M_mesh3dalgo_netggmne (Child aborted) 150 - M_remesh2 (Child aborted) 151 - M_remesh3 (Child aborted) 154 - M_nset3 (Child aborted) 155 - M_faset (Child aborted) 177 - V_pretest5 (Child aborted) Errors while running CTest make: *** [Makefile:107: test] Error 8
@NotRealEngineering: Please provide the terminal output for this:
neper --rcfile none -T -n 2 -id 1 -reg 1
neper --rcfile none -M n2-id1.tess -mesh3dclreps 1 -mesh2dalgo mead
Terminal output for 1st line:
======================== N e p e r =======================
Info : A software package for polycrystal generation and meshing.
Info : Version 4.0.2
Info : Built with: gsl|muparser|opengjk|openmp|nlopt
Info : Running on 12 threads.
Info : <http://neper.info>
Info : Copyright (C) 2003-2020, and GNU GPL'd, by Romain Quey.
Info : Ignoring initialization file.
Info : ---------------------------------------------------------------
Info : MODULE -T loaded with arguments:
Info : [ini file] (none)
Info : [com line] -n 2 -id 1 -reg 1
Info : ---------------------------------------------------------------
Info : Reading input data...
Info : Creating domain...
Info : Creating tessellation...
Info : - Setting seeds...
Info : - Generating crystal orientations...
Info : - Running tessellation...
Info : Regularizing tessellation...
Info : - loop 1/2: 100% del=3
Info : Writing results...
Info : [o] Writing file `n2-id1.tess'...
Info : [o] Wrote file `n2-id1.tess'.
Info : Elapsed time: 0.016 secs.
========================================================================
Terminal output for the second line:
======================== N e p e r =======================
Info : A software package for polycrystal generation and meshing.
Info : Version 4.0.2
Info : Built with: gsl|muparser|opengjk|openmp|nlopt
Info : Running on 12 threads.
Info : <http://neper.info>
Info : Copyright (C) 2003-2020, and GNU GPL'd, by Romain Quey.
Info : Ignoring initialization file.
Info : ---------------------------------------------------------------
Info : MODULE -M loaded with arguments:
Info : [ini file] (none)
Info : [com line] n2-id1.tess -mesh3dclreps 1 -mesh2dalgo mead
Info : ---------------------------------------------------------------
Info : Reading input data...
Info : - Reading arguments...
Info : Loading input data...
Info : - Loading tessellation...
Info : [i] Parsing file `n2-id1.tess'...
Info : [i] Parsed file `n2-id1.tess'.
Info : Meshing...
Info : - Preparing... (cl = 0.3969) 100%
Info : - 0D meshing... 100%
Info : - 1D meshing... 100%
Info : - 2D meshing... 100% (0.85|0.89/100%)
Info : - Fixing 2D-mesh pinches...
Info : - 3D meshing... 100% (0.91|0.91/100%| 0%| 0%)
Info : Searching nsets and fasets...
Info : Writing mesh results...
Info : - Preparing mesh...
Info : - Mesh properties:
Info : > Node number: 79
Info : > Elt number: 209
Info : > Mesh volume: 1.000
Info : - Writing mesh...
Info : [o] Writing file `n2-id1.msh'...
Info : [o] Wrote file `n2-id1.msh'.
Info : Elapsed time: 0.481 secs.
========================================================================
Thank you.
Also would like to mention that meshing works fine for Hex elements. The problem happens only in the case of tet elements.
And can you run
ctest -R M_mesh2dalgo_mead
The commands I made you run previously correspond to this test; so, it should pass.
I think this is a problem with the tests rather than with Neper itself...
As for hex vs tet elements, this is expected, since Gmsh is used only for tet meshing.
But still, I am not able to get mesh with tet elements. Following commands still fails
neper -T -n 100 -id 1 neper -M n100-id1.tess -order 2 -meshqualexpr Odis -meshqualmin 1
Output for running:
Test project /mnt/c/Ubuntu_onWin/neper-4.0.2/src/build Start 139: M_mesh2dalgo_mead 1/1 Test #139: M_mesh2dalgo_mead ................Child aborted***Exception: 0.46 sec
0% tests passed, 1 tests failed out of 1
Total Test time (real) = 0.48 sec
The following tests FAILED: 139 - M_mesh2dalgo_mead (Child aborted) Errors while running CTest
So, please provide the terminal output for this one:
neper -T -n 100 -id 1
neper -M n100-id1.tess -order 2 -meshqualexpr Odis -meshqualmin 1
The output of the first line:
======================== N e p e r =======================
Info : A software package for polycrystal generation and meshing.
Info : Version 4.0.2
Info : Built with: gsl|muparser|opengjk|openmp|nlopt
Info : Running on 12 threads.
Info : <http://neper.info>
Info : Copyright (C) 2003-2020, and GNU GPL'd, by Romain Quey.
Info : No initialization file found (`/home/kulk969/.neperrc').
Info : ---------------------------------------------------------------
Info : MODULE -T loaded with arguments:
Info : [ini file] (none)
Info : [com line] -n 100 -id 1
Info : ---------------------------------------------------------------
Info : Reading input data...
Info : Creating domain...
Info : Creating tessellation...
Info : - Setting seeds...
Info : - Generating crystal orientations...
Info : - Running tessellation...
Info : Writing results...
Info : [o] Writing file `n100-id1.tess'...
Info : [o] Wrote file `n100-id1.tess'.
Info : Elapsed time: 0.041 secs.
========================================================================
The output of the second line:
======================== N e p e r =======================
Info : A software package for polycrystal generation and meshing.
Info : Version 4.0.2
Info : Built with: gsl|muparser|opengjk|openmp|nlopt
Info : Running on 12 threads.
Info : <http://neper.info>
Info : Copyright (C) 2003-2020, and GNU GPL'd, by Romain Quey.
Info : No initialization file found (`/home/kulk969/.neperrc').
Info : ---------------------------------------------------------------
Info : MODULE -M loaded with arguments:
Info : [ini file] (none)
Info : [com line] n100-id1.tess -order 2 -meshqualexpr Odis
-meshqualmin 1
Info : ---------------------------------------------------------------
Info : Reading input data...
Info : - Reading arguments...
Info : Loading input data...
Info : - Loading tessellation...
Info : [i] Parsing file `n100-id1.tess'...
Info : [i] Parsed file `n100-id1.tess'.
Info : Meshing...
Info : - Preparing... (cl = 0.1077) 100%
Info : - 0D meshing... 100%
Info : - 1D meshing... 100%
Info : - 2D meshing... 5% (0|0.97/36%|25%|39%)Error : > Meshing of face 34 failed
Aborted (core dumped)
Let's try this:
neper -T -n 10 -dim 2 -o test
neper -M test.tess
If it works, switch dim
to 3 and/or n
to 100; if it does not, switch n
to 1.
Works for 2D only. If I switch dim to 3 I get the following error again.
======================== N e p e r =======================
Info : A software package for polycrystal generation and meshing.
Info : Version 4.0.2
Info : Built with: gsl|muparser|opengjk|openmp|nlopt
Info : Running on 12 threads.
Info : <http://neper.info>
Info : Copyright (C) 2003-2020, and GNU GPL'd, by Romain Quey.
Info : No initialization file found (`/home/kulk969/.neperrc').
Info : ---------------------------------------------------------------
Info : MODULE -M loaded with arguments:
Info : [ini file] (none)
Info : [com line] test.tess
Info : ---------------------------------------------------------------
Info : Reading input data...
Info : - Reading arguments...
Info : Loading input data...
Info : - Loading tessellation...
Info : [i] Parsing file `test.tess'...
Info : [i] Parsed file `test.tess'.
Info : Meshing...
Info : - Preparing... (cl = 0.2321) 100%
Info : - 0D meshing... 100%
Info : - 1D meshing... 100%
Info : - 2D meshing... 23% (0.38|0.68/100%| 0%| 0%)Error : > Meshing of face 17 failed
Aborted (core dumped)
Can you run export OMP_NUM_THREADS=1
and run again Neper. Does it fail always for the same face?
(Enclose your code by ```s when you paste.)
Now it works! No error with more number of grains as well.
Can you please explain what was wrong? so that I will keep the note for the future.
Thanks a lot.
export OMP_NUM_THREADS=1
makes Neper run on 1 core only (no multithreading)...
So, it seems that multithreading does not work properly on Windows 10 / Ubuntu App. Good to know...
You can also compile Neper without openMP support, so that Neper won't try to multithread. To do so, use cmake -DHAVE_OPENMP=OFF ..
(instead of cmake ..
) before running make
. You will then not need to run export OMP_NUM_THREADS=1
.
Sure. I will do that.
Just wanted to share with you, I make educational YouTube videos on many topics related to modeling and did a few about software Neper.
You can find them here:
Thank you very much for your help. Keep up the good work.
Yes, I saw that. Nice!
Thank you again.
Hi sir : i have another problem if you can help me plaese becouse it take along time from me and i cant solve it i use ubuntu on win 10 and i do the same instructions that ( Not Real Engineering) do in the channel on youtube and i install all dependancies as he do. i will send you the running terminal .
export OMP_NUM_THREADS=1
sameer@DESKTOP-JSN2KJA:/mnt/e/neper$ neper -T -n 100 -id 1
======================== N e p e r =======================
Info : A software package for polycrystal generation and meshing.
Info : Version 4.8.0
Info : Built with: gsl|muparser|opengjk|openmp|nlopt|libscotch (full)
Info : Running on 1 threads.
Info : <https://neper.info>
Info : Copyright (C) 2003-2022, and GNU GPL'd, by Romain Quey.
Info : No initialization file found (`/home/sameer/.neperrc').
Info : ---------------------------------------------------------------
Info : MODULE -T loaded with arguments:
Info : [ini file] (none)
Info : [com line] -n 100 -id 1
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 `n100-id1.tess'...
Info : [o] Wrote file `n100-id1.tess'.
Info : Elapsed time: 0.033 secs.
========================================================================
sameer@DESKTOP-JSN2KJA:/mnt/e/neper$ neper -V n100-id1.tess -datacellcol id -print Image_1
======================== N e p e r =======================
Info : A software package for polycrystal generation and meshing.
Info : Version 4.8.0
Info : Built with: gsl|muparser|opengjk|openmp|nlopt|libscotch (full)
Info : Running on 1 threads.
Info : <https://neper.info>
Info : Copyright (C) 2003-2022, and GNU GPL'd, by Romain Quey.
Info : No initialization file found (`/home/sameer/.neperrc').
Info : ---------------------------------------------------------------
Info : MODULE -V loaded with arguments:
Info : [ini file] (none)
Info : [com line] n100-id1.tess -datacellcol id -print Image_1
Info : ---------------------------------------------------------------
Info : - Reading arguments...
Info : Loading tessellation...
Info : [i] Parsing file `n100-id1.tess'...
Info : [i] Parsed file `n100-id1.tess'.
Info : Reading data (cell, col)...
Info : Printing image...
Info : - Printing tessellation...
Info : - Generating png file (1200x900 pixels)...
Info : [o] Writing file `Image_1.png'...
Info : [o] Wrote file `Image_1.png'.
Info : Printing scale...
Info : Elapsed time: 1.594 secs.
========================================================================
sameer@DESKTOP-JSN2KJA:/mnt/e/neper$ neper -M n100-id1.tess -meshqualmin 1
======================== N e p e r =======================
Info : A software package for polycrystal generation and meshing.
Info : Version 4.8.0
Info : Built with: gsl|muparser|opengjk|openmp|nlopt|libscotch (full)
Info : Running on 1 threads.
Info : <https://neper.info>
Info : Copyright (C) 2003-2022, and GNU GPL'd, by Romain Quey.
Info : No initialization file found (`/home/sameer/.neperrc').
Info : ---------------------------------------------------------------
Info : MODULE -M loaded with arguments:
Info : [ini file] (none)
Info : [com line] n100-id1.tess -meshqualmin 1
Info : ---------------------------------------------------------------
Info : Reading input data...
Info : - Reading arguments...
Info : Loading input data...
Info : - Loading tessellation...
Info : [i] Parsing file `n100-id1.tess'...
Info : [i] Parsed file `n100-id1.tess'.
Info : Meshing...
Info : - Preparing... (cl = 0.1077) 100%
Info : - 0D meshing... 100%
Info : - 1D meshing... 100%
Info : - 2D meshing... 100% (0.045|0.64/95%| 4%| 1%)
Info : - Fixing 2D-mesh pinches...
Info : - 3D meshing... Error : - Failed to read msh file
Aborted (core dumped)
that the error . plaese if you can help me . thank you
Update to version 4.8.1.
@rquey its solved thank you very much ... neper now worked without any problems after update.
I am using neper 4.0.2 along with Gmsh 4.6.0 (compiled from source) on a windows machine using the Ubuntu app.
I installed the following dependencies:
$ sudo apt-get install libgsl-dev $ sudo apt-get install libnlopt-dev $ sudo apt-get install libomp-dev $ sudo apt-get install libscotch-dev $ sudo apt-get install libpthread-stubs0-dev $ sudo apt-get install povray
Now I am facing a strange error. Meshing works fine for Hex elements but for tet elements, the core gets dumped. Also it gives different errors every time. Please see the errors below:
1. Info : Meshing... Info : - Preparing... (cl = 0.1077) 100% Info : - 0D meshing... 100% Info : - 1D meshing... 100% Info : - 2D meshing... 0% (0|0/ 0%| 0%| 0%)bnodeqty = 17 (*pN).NodeQty = 3 Error : You have discovered a bug in Neper! Please file an issue at https://github.com/rquey/neper/issues. Thank you.
Aborted (core dumped)
Info : Meshing... Info : - Preparing... (cl = 0.1077) 100% Info : - 0D meshing... 100% Info : - 1D meshing... 100% Info : - 2D meshing... 3% (0|0.63/96%| 4%| 0%)Error : > Meshing of face 19 failed Aborted (core dumped)
Info : Meshing... Info : - Preparing... (cl = 0.1077) 100% Info : - 0D meshing... 100% Info : - 1D meshing... 100% Info : - 2D meshing... 2% (0.39|0.62/100%| 0%| 0%)Error : Bad msh file format version detected! 6/100%| 0%| 0%)Aborted (core dumped)
Please let me know if you have a solution for this. Thank you.