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neperfepx / neper

Polycrystal generation and meshing
http://neper.info
GNU General Public License v3.0
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Aborted (core dumped) During 2D Meshing #254

Closed VarmaNarendra closed 3 years ago

VarmaNarendra commented 3 years ago

Hi,

I got this aborted (core dumped) error for the following.

please help

Thanks, Narendra Varma.

nvdan@LAPTOP-421FLP5E:~$ neper

========================    N   e   p   e   r    =======================
Info   : A software package for polycrystal generation and meshing.
Info   : Version 4.2.0
Info   : Built with: gsl|muparser|opengjk|openmp|nlopt|libscotch (full)
Info   : Running on 4 threads.
Info   : <https://neper.info>
Info   : Copyright (C) 2003-2021, and GNU GPL'd, by Romain Quey.
========================================================================

nvdan@LAPTOP-421FLP5E:~$ cd /mnt/c
nvdan@LAPTOP-421FLP5E:/mnt/c$ cd FEPX_Example/
nvdan@LAPTOP-421FLP5E:/mnt/c/FEPX_Example$ neper -T -n 50 -reg 1 -morpho gg -o simulation

========================    N   e   p   e   r    =======================
Info   : A software package for polycrystal generation and meshing.
Info   : Version 4.2.0
Info   : Built with: gsl|muparser|opengjk|openmp|nlopt|libscotch (full)
Info   : Running on 4 threads.
Info   : <https://neper.info>
Info   : Copyright (C) 2003-2021, and GNU GPL'd, by Romain Quey.
Info   : No initialization file found (`/home/nvdan/.neperrc').
Info   : ---------------------------------------------------------------
Info   : MODULE  -T loaded with arguments:
Info   : [ini file] (none)
Info   : [com line] -n 50 -reg 1 -morpho gg -o simulation
Info   : ---------------------------------------------------------------
Info   : Reading input data...
Info   : Creating domain...
Info   : Creating tessellation...
Info   :   - Setting seeds... 100%
Info   :   - Generating crystal orientations...
Info   :   - Running tessellation...
Info   :     > Initial solution: f   =1.952240136
Info   :     > Iteration  51992: fmin=0.011713355 f=0.011713356
Info   :     > Final solution  : f   =0.011713355
Info   :     > Reached `eps' criterion.
Info   : Regularizing tessellation...
Info   :   - loop 2/2: 100% del=14
Info   : Writing results...
Info   :     [o] Writing file `simulation.tess'...
Info   :     [o] Wrote file `simulation.tess'.
Info   : Elapsed time: 85.404 secs.
========================================================================

nvdan@LAPTOP-421FLP5E:/mnt/c/FEPX_Example$ neper -V simulation.tess -datacellcol id -print Image_Polycrystal

========================    N   e   p   e   r    =======================
Info   : A software package for polycrystal generation and meshing.
Info   : Version 4.2.0
Info   : Built with: gsl|muparser|opengjk|openmp|nlopt|libscotch (full)
Info   : Running on 4 threads.
Info   : <https://neper.info>
Info   : Copyright (C) 2003-2021, and GNU GPL'd, by Romain Quey.
Info   : No initialization file found (`/home/nvdan/.neperrc').
Info   : ---------------------------------------------------------------
Info   : MODULE  -V loaded with arguments:
Info   : [ini file] (none)
Info   : [com line] simulation.tess -datacellcol id -print
         Image_Polycrystal
Info   : ---------------------------------------------------------------
Info   : Loading tessellation...
Info   :     [i] Parsing file `simulation.tess'...
Info   :     [i] Parsed file `simulation.tess'.
Info   : Reading data (poly, col)...
Info   : Printing image...
Info   :     [o] Writing file `Image_Polycrystal.pov'...
Info   :   - Printing tessellation...
Info   :     [o] Wrote file `Image_Polycrystal.pov'.
Info   :   - Generating png file (1200x900 pixels)...
Info   :     [o] Writing file `Image_Polycrystal.png'...
Info   :     [o] Wrote file `Image_Polycrystal.png'.
Info   : Printing scale...
Info   : Elapsed time: 2.077 secs.
========================================================================

nvdan@LAPTOP-421FLP5E:/mnt/c/FEPX_Example$ neper -M simulation.tess -order 2 -part 4

========================    N   e   p   e   r    =======================
Info   : A software package for polycrystal generation and meshing.
Info   : Version 4.2.0
Info   : Built with: gsl|muparser|opengjk|openmp|nlopt|libscotch (full)
Info   : Running on 4 threads.
Info   : <https://neper.info>
Info   : Copyright (C) 2003-2021, and GNU GPL'd, by Romain Quey.
Info   : No initialization file found (`/home/nvdan/.neperrc').
Info   : ---------------------------------------------------------------
Info   : MODULE  -M loaded with arguments:
Info   : [ini file] (none)
Info   : [com line] simulation.tess -order 2 -part 4
Info   : ---------------------------------------------------------------
Info   : Reading input data...
Info   :   - Reading arguments...
Info   : Loading input data...
Info   :   - Loading tessellation...
Info   :     [i] Parsing file `simulation.tess'...
Info   :     [i] Parsed file `simulation.tess'.
Info   : Meshing...
Info   :   - Preparing... (cl = 0.1357) 100%
Info   :   - 0D meshing... 100%
Info   :   - 1D meshing... 100%
Info   :   - 2D meshing...   6% (0|0.76/70%|18%|12%)Error  :     > Meshing of face 16 failed
Aborted (core dumped)
rquey commented 3 years ago

Is Gmsh installed? Did you run ctest after compiling?

VarmaNarendra commented 3 years ago

Yes,

Gmsh is installed.

Is this the CTest?

i'm using ubuntu app in windows.

i got the below result syntax errors.

nvdan@LAPTOP-421FLP5E:/mnt/c/FEPX_Example$ # CTEST
nvdan@LAPTOP-421FLP5E:/mnt/c/FEPX_Example$ enable_testing()
> include(CTest)
-bash: syntax error near unexpected token `include'
nvdan@LAPTOP-421FLP5E:/mnt/c/FEPX_Example$
nvdan@LAPTOP-421FLP5E:/mnt/c/FEPX_Example$ # Module -T
nvdan@LAPTOP-421FLP5E:/mnt/c/FEPX_Example$
nvdan@LAPTOP-421FLP5E:/mnt/c/FEPX_Example$ add_test(T_n                      ./neper --rcfile none -T -n 2)
-bash: syntax error near unexpected token `T_n'
nvdan@LAPTOP-421FLP5E:/mnt/c/FEPX_Example$ add_test(T_id                     ./neper --rcfile none -T -n 2 -id 2)
-bash: syntax error near unexpected token `T_id'
nvdan@LAPTOP-421FLP5E:/mnt/c/FEPX_Example$ add_test(T_dim                    ./neper --rcfile none -T -n 2 -dim 2)
-bash: syntax error near unexpected token `T_dim'
nvdan@LAPTOP-421FLP5E:/mnt/c/FEPX_Example$ add_test(T_domain_cube            ./neper --rcfile none -T -n 2 -domain "cube(1,2,4)")
-bash: syntax error near unexpected token `T_domain_cube'
nvdan@LAPTOP-421FLP5E:/mnt/c/FEPX_Example$ add_test(T_domain_cylinder        ./neper --rcfile none -T -n 2 -domain "cylinder(1,2,100)")
-bash: syntax error near unexpected token `T_domain_cylinder'
nvdan@LAPTOP-421FLP5E:/mnt/c/FEPX_Example$ add_test(T_domain_sphere          ./neper --rcfile none -T -n 2 -domain "sphere(2,100)")
-bash: syntax error near unexpected token `T_domain_sphere'
nvdan@LAPTOP-421FLP5E:/mnt/c/FEPX_Example$ add_test(T_domain_square          ./neper --rcfile none -T -n 2 -dim 2 -domain "square(1,2)")
-bash: syntax error near unexpected token `T_domain_square'
nvdan@LAPTOP-421FLP5E:/mnt/c/FEPX_Example$ add_test(T_domain_rotate          ./neper --rcfile none -T -n 2 -domain "cube(1,1,1):rotate(1,1,1,10)")
-bash: syntax error near unexpected token `T_domain_rotate'
nvdan@LAPTOP-421FLP5E:/mnt/c/FEPX_Example$ add_test(T_domain_translate       ./neper --rcfile none -T -n 2 -domain "cube(1,1,1):translate(1,2,3)")
-bash: syntax error near unexpected token `T_domain_translate'
nvdan@LAPTOP-421FLP5E:/mnt/c/FEPX_Example$ add_test(T_domain_scale           ./neper --rcfile none -T -n 2 -domain "cube(1,1,1):scale(1,2,3)")
-bash: syntax error near unexpected token `T_domain_scale'
nvdan@LAPTOP-421FLP5E:/mnt/c/FEPX_Example$ add_test(T_domain_split           ./neper --rcfile none -T -n 2 -domain "cube(1,1,1):split(z)")
tinistep-bash: syntax error near unexpected token `T_domain_split'
       .nvdan@LAPTOP-421FLP5E:/mnt/c/FEPX_Example$ add_test(T_domain_rotate2         ./neper --rcfile none -T -n 2 -dim 2 -domain "square(1,1):rotate(10)")
-bash: syntax error near unexpected token `T_domain_rotate2'
nvdan@LAPTOP-421FLP5E:/mnt/c/FEPX_Example$ add_test(T_domain_translate2      ./neper --rcfile none -T -n 2 -dim 2 -domain "square(1,1):translate(1,2)")
-bash: syntax error near unexpected token `T_domain_translate2'
nvdan@LAPTOP-421FLP5E:/mnt/c/FEPX_Example$ add_test(T_domain_scale2          ./neper --rcfile none -T -n 2 -dim 2 -domain "square(1,1):scale(1,2)")
-bash: syntax error near unexpected token `T_domain_scale2'
nvdan@LAPTOP-421FLP5E:/mnt/c/FEPX_Example$ add_test(T_periodic               ./neper --rcfile none -T -n 2 -periodic 1)
-bash: syntax error near unexpected token `T_periodic'
nvdan@LAPTOP-421FLP5E:/mnt/c/FEPX_Example$ add_test(T_periodic_x             ./neper --rcfile none -T -n 2 -periodic x)
-bash: syntax error near unexpected token `T_periodic_x'
nvdan@LAPTOP-421FLP5E:/mnt/c/FEPX_Example$ add_test(T_morpho_voronoi         ./neper --rcfile none -T -n 2 -morpho voronoi)
-bash: syntax error near unexpected token `T_morpho_voronoi'
nvdan@LAPTOP-421FLP5E:/mnt/c/FEPX_Example$ add_test(T_morpho_centroidal      ./neper --rcfile none -T -n 2 -morpho centroidal -morphooptistop "itermax=100")
-bash: syntax error near unexpected token `T_morpho_centroidal'
nvdan@LAPTOP-421FLP5E:/mnt/c/FEPX_Example$ add_test(T_morpho_cube            ./neper --rcfile none -T -n from_morpho -morpho "cube(2)")
-bash: syntax error near unexpected token `T_morpho_cube'
nvdan@LAPTOP-421FLP5E:/mnt/c/FEPX_Example$ add_test(T_morpho_cube3           ./neper --rcfile none -T -n from_morpho -morpho "cube(2,3,4)")
-bash: syntax error near unexpected token `T_morpho_cube3'
nvdan@LAPTOP-421FLP5E:/mnt/c/FEPX_Example$ add_test(T_morpho_square          ./neper --rcfile none -T -n from_morpho -dim 2 -morpho "square(2)")
-bash: syntax error near unexpected token `T_morpho_square'
nvdan@LAPTOP-421FLP5E:/mnt/c/FEPX_Example$ add_test(T_morpho_square2         ./neper --rcfile none -T -n from_morpho -dim 2 -morpho "square(2,3)")
-bash: syntax error near unexpected token `T_morpho_square2'
nvdan@LAPTOP-421FLP5E:/mnt/c/FEPX_Example$ add_test(T_morpho_tocta           ./neper --rcfile none -T -n from_morpho -morpho "tocta(2)")
-bash: syntax error near unexpected token `T_morpho_tocta'
[...]
rquey commented 3 years ago

For testing, just type ctest at the command line (inside the build directory).

There are known issues with multithreading on Windows. Either recompile Neper using

cmake -DHAVE_OPENMP=OFF` ..
make

or run export OMP_NUM_THREADS=1 before running Neper.

VarmaNarendra commented 3 years ago

I did ctest there are some failed.

nvdan@LAPTOP-421FLP5E:/mnt/c/ubuntu_app/gmsh-4.8.3-source/build$ ctest Test project /mnt/c/ubuntu_app/gmsh-4.8.3-source/build Start 1: ../demos/boolean/hybrid_occ_builtin.geo 1/39 Test #1: ../demos/boolean/hybrid_occ_builtin.geo ....***Failed 0.65 sec Start 2: ../demos/post_processing/lowmem-anim.geo 2/39 Test #2: ../demos/post_processing/lowmem-anim.geo ... Passed 0.43 sec Start 3: ../demos/post_processing/plot2d.geo 3/39 Test #3: ../demos/post_processing/plot2d.geo ........ Passed 0.31 sec Start 4: ../demos/post_processing/view_groups.geo 4/39 Test #4: ../demos/post_processing/view_groups.geo ... Passed 0.43 sec Start 5: ../demos/simple_geo/antenna.geo 5/39 Test #5: ../demos/simple_geo/antenna.geo ............ Passed 1.33 sec Start 6: ../demos/simple_geo/cone.geo 6/39 Test #6: ../demos/simple_geo/cone.geo ............... Passed 0.33 sec Start 7: ../demos/simple_geo/cube.geo 7/39 Test #7: ../demos/simple_geo/cube.geo ............... Passed 0.30 sec Start 8: ../demos/simple_geo/filter.geo 8/39 Test #8: ../demos/simple_geo/filter.geo ............. Passed 0.75 sec Start 9: ../demos/simple_geo/hex.geo 9/39 Test #9: ../demos/simple_geo/hex.geo ................ Passed 0.41 sec Start 10: ../demos/simple_geo/homology.geo 10/39 Test #10: ../demos/simple_geo/homology.geo ........... Passed 1.30 sec Start 11: ../demos/simple_geo/indheat.geo 11/39 Test #11: ../demos/simple_geo/indheat.geo ............ Passed 1.41 sec Start 12: ../demos/simple_geo/machine.geo 12/39 Test #12: ../demos/simple_geo/machine.geo ............ Passed 0.60 sec Start 13: ../demos/simple_geo/piece-extr-rec.geo 13/39 Test #13: ../demos/simple_geo/piece-extr-rec.geo ..... Passed 0.54 sec Start 14: ../demos/simple_geo/piece-extr.geo 14/39 Test #14: ../demos/simple_geo/piece-extr.geo ......... Passed 0.97 sec Start 15: ../demos/simple_geo/piece.geo 15/39 Test #15: ../demos/simple_geo/piece.geo .............. Passed 0.85 sec Start 16: ../demos/simple_geo/pripyrtet.geo 16/39 Test #16: ../demos/simple_geo/pripyrtet.geo .......... Passed 0.30 sec Start 17: ../demos/simple_geo/sphere-discrete.geo 17/39 Test #17: ../demos/simple_geo/sphere-discrete.geo .... Passed 0.48 sec Start 18: ../demos/simple_geo/sphere.geo 18/39 Test #18: ../demos/simple_geo/sphere.geo ............. Passed 0.38 sec Start 19: ../demos/simple_geo/splines.geo 19/39 Test #19: ../demos/simple_geo/splines.geo ............ Passed 0.73 sec Start 20: ../demos/simple_geo/square_regular.geo 20/39 Test #20: ../demos/simple_geo/square_regular.geo ..... Passed 0.40 sec Start 21: ../demos/simple_geo/tower.geo 21/39 Test #21: ../demos/simple_geo/tower.geo .............. Passed 0.67 sec Start 22: ../demos/simple_geo/transfinite.geo 22/39 Test #22: ../demos/simple_geo/transfinite.geo ........ Passed 0.43 sec Start 23: ../demos/struct/Exists_GetForced.geo 23/39 Test #23: ../demos/struct/Exists_GetForced.geo ....... Passed 0.39 sec Start 24: ../demos/struct/struct.geo 24/39 Test #24: ../demos/struct/struct.geo ................. Passed 0.40 sec Start 25: ../tutorial/t1.geo 25/39 Test #25: ../tutorial/t1.geo ......................... Passed 0.42 sec Start 26: ../tutorial/t10.geo 26/39 Test #26: ../tutorial/t10.geo ........................ Passed 1.43 sec Start 27: ../tutorial/t11.geo 27/39 Test #27: ../tutorial/t11.geo ........................ Passed 0.57 sec Start 28: ../tutorial/t12.geo 28/39 Test #28: ../tutorial/t12.geo ........................ Passed 0.33 sec Start 29: ../tutorial/t13.geo 29/39 Test #29: ../tutorial/t13.geo ........................ Passed 1.13 sec Start 30: ../tutorial/t14.geo 30/39 Test #30: ../tutorial/t14.geo ........................ Passed 1.21 sec Start 31: ../tutorial/t15.geo 31/39 Test #31: ../tutorial/t15.geo ........................ Passed 0.32 sec Start 32: ../tutorial/t2.geo 32/39 Test #32: ../tutorial/t2.geo ......................... Passed 0.51 sec Start 33: ../tutorial/t3.geo 33/39 Test #33: ../tutorial/t3.geo ......................... Passed 0.66 sec Start 34: ../tutorial/t4.geo 34/39 Test #34: ../tutorial/t4.geo ......................... Passed 0.44 sec Start 35: ../tutorial/t5.geo 35/39 Test #35: ../tutorial/t5.geo ......................... Passed 0.72 sec Start 36: ../tutorial/t6.geo 36/39 Test #36: ../tutorial/t6.geo ......................... Passed 0.35 sec Start 37: ../tutorial/t7.geo 37/39 Test #37: ../tutorial/t7.geo ......................... Passed 0.56 sec Start 38: ../tutorial/t8.geo 38/39 Test #38: ../tutorial/t8.geo ......................... Passed 2.12 sec Start 39: ../tutorial/t9.geo 39/39 Test #39: ../tutorial/t9.geo ......................... Passed 0.25 sec

97% tests passed, 1 tests failed out of 39

Total Test time (real) = 26.19 sec

The following tests FAILED: 1 - ../demos/boolean/hybrid_occ_builtin.geo (Failed) Errors while running CTest Output from these tests are in: /mnt/c/ubuntu_app/gmsh-4.8.3-source/build/Testing/Temporary/LastTest.log Use "--rerun-failed --output-on-failure" to re-run the failed cases verbosely.

rquey commented 3 years ago

I was talking about running ctest for Neper, not for Gmsh...

VarmaNarendra commented 3 years ago

For Neper 

92% tests passed, 22 tests failed out of 285

Total Test time (real) = 434.68 sec

The following tests FAILED:
        118 - M_cl (Subprocess aborted)
        124 - M_cl_expr (Subprocess aborted)
        127 - M_dim2 (Subprocess aborted)
        128 - M_dim_expr (Subprocess aborted)
        129 - M_order (Subprocess aborted)
        135 - M_clmin (Subprocess aborted)
        137 - M_meshqualexpr (Subprocess aborted)
        139 - M_mesh2dalgo_mead (Subprocess aborted)
        140 - M_mesh2dalgo_dela (Subprocess aborted)
        141 - M_mesh2dalgo_fron (Subprocess aborted)
        143 - M_mesh3dalgo_netgnetg (Subprocess aborted)
        145 - M_mesh3dalgo_netggmne (Subprocess aborted)
        155 - M_nset1 (Subprocess aborted)
        156 - M_nset2 (Subprocess aborted)
        172 - M_interface (Subprocess aborted)
        257 - V_nodecoo (Subprocess aborted)
        258 - V_nodecoo_disp (Subprocess aborted)
        259 - V_nodecoofact (Subprocess aborted)
        261 - V_slicemesh2 (Subprocess aborted)
        273 - V_cameracoo2 (Subprocess aborted)
        274 - V_cameracoo3 (Subprocess aborted)
        285 - V_loop (Subprocess aborted)
Errors while running CTest
Output from these tests are in: /mnt/c/ubuntu_app/neper-4.2.0/src/build/Testing/Temporary/LastTest.log
Use "--rerun-failed --output-on-failure" to re-run the failed cases verbosely.

nvdan@LAPTOP-421FLP5E:/mnt/c/ubuntu_app/neper-4.2.0/src/build$ ctest --rerun-failed --output-on-failure
Test project /mnt/c/ubuntu_app/neper-4.2.0/src/build
      Start 118: M_cl
 1/22 Test #118: M_cl .............................Subprocess aborted***Exception:   0.91 sec

========================    N   e   p   e   r    =======================
Info   : A software package for polycrystal generation and meshing.
Info   : Version 4.2.0
Info   : Built with: gsl|muparser|opengjk|openmp|nlopt|libscotch (full)
Info   : Running on 4 threads.
Info   : <https://neper.info>
Info   : Copyright (C) 2003-2021, 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 -cl 0.5
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 = 0.5)
  0%
  9%
 18%
 27%
 36%
 45%
 55%
 64%
 73%
 82%
 91%
100%Info   :   - 0D meshing...
  0%
 10%
 20%
 30%
 40%
 50%
 60%
 70%
 80%
 90%
100%
Info   :   - 1D meshing...
  0%
  6%
 11%
 17%
 22%
 28%
 33%
 39%
 44%
 50%
 56%
 61%
 67%
 72%
 78%
 83%
 89%
 94%
100%Info   :   - 2D meshing...
  0% (0|0/ 0%| 0%| 0%)
  9% (0|0/100%| 0%| 0%)Error  : Input file is not a msh file!
[...]
rquey commented 3 years ago

You are still using multithreading. Please compile as described above.

VarmaNarendra commented 3 years ago

For testing, just type ctest at the command line (inside the build directory).

There are known issues with multithreading on Windows. Either recompile Neper using

cmake -DHAVE_OPENMP=OFF` ..
make

or run export OMP_NUM_THREADS=1 before running Neper.

Thanks a lot export OMP_NUM_THREADS=1

this worked ..