Comments (9)
Did gmsh -3 n2-id1.geo
provide a meaningful mesh? Try opening it with gmsh n2-id1.msh
or visualizing it with neper -V n2-id1.tess,n2-id1.msh -dataelsetcol id -print n2-id1
. (You may also post it here.)
If meshing did not work properly, I think you did not compile Gmsh properly (typically with missing dependencies - blas and/or lapack).
from neper.
Hi Romain,
Thanks for the reply
AFAIK gmsh was compiled with all necessary dependencies.
$ gmsh --info
Version : 4.5.3
License : GNU General Public License
Build OS : Linux64-sdk
Build date : 20200302
Build host : node700.pri.csf3.alces.network
Build options : 64Bit ALGLIB Ann Bamg Blas[openblas] Blossom DIntegration Dlopen DomHex GMP Gmm Hxt Hxt3D Kbipack Lapack[openblas] LinuxJoystick MathEx Mesh Metis Mmg3d Netgen ONELAB ONELABMetamodel OptHom Parser Plugins Post QuadTri Solver TetGen/BR Voro++
Packaged by :
Web site : http://gmsh.info
Issue tracker : https://gitlab.onelab.info/gmsh/gmsh/issues
$ gmsh -3 n2-id1.geo
Info : 0.90 < quality < 1.00 : 90 elements
Info : Done optimizing mesh (0.002288 s)
Info : 404 nodes 2263 elements
Info : Writing 'n2-id1.msh'...
Info : Done writing 'n2-id1.msh'
Info : Stopped on Mon Mar 2 11:49:46 2020
Info : No current model available: creating one
$ ./neper -V n2-id1.tess,n2-id1.msh -dataelsetcol id -print n2-id1
======================== N e p e r =======================
Info : A software package for polycrystal generation and meshing.
Info : Version 3.5.1
Info : Built with: gsl|muparser|opengjk|openmp|nlopt
Info : Running on 28 threads.
Info : <http://neper.info>
Info : Copyright (C) 2003-2019, and GNU GPL'd, by Romain Quey.
Info : No initialization file found (`/mnt/iusers01/support/mzysscg3/.neperrc').
Info : ---------------------------------------------------------------
Info : MODULE -V loaded with arguments:
Info : [ini file] (none)
Info : [com line] n2-id1.tess,n2-id1.msh -dataelsetcol id -print
n2-id1
Info : ---------------------------------------------------------------
Info : Loading tessellation...
Info : [i] Parsing file `n2-id1.tess'...
Info : [i] Parsed file `n2-id1.tess'.
Info : Loading mesh...
Info : [i] Parsing file `n2-id1.msh'...
Error : Bad msh file format version detected!
Aborted
However, if I run specifying the older gmsh format I have some success.
$ gmsh -format msh2 -3 n2-id1.geo
Then
$ ./neper -V n2-id1.tess,n2-id1.msh -dataelsetcol id -print n2-id1
======================== N e p e r =======================
Info : A software package for polycrystal generation and meshing.
Info : Version 3.5.1
Info : Built with: gsl|muparser|opengjk|openmp|nlopt
Info : Running on 28 threads.
Info : <http://neper.info>
Info : Copyright (C) 2003-2019, and GNU GPL'd, by Romain Quey.
Info : No initialization file found (`/mnt/iusers01/support/mzysscg3/.neperrc').
Info : ---------------------------------------------------------------
Info : MODULE -V loaded with arguments:
Info : [ini file] (none)
Info : [com line] n2-id1.tess,n2-id1.msh -dataelsetcol id -print
n2-id1
Info : ---------------------------------------------------------------
Info : Loading tessellation...
Info : [i] Parsing file `n2-id1.tess'...
Info : [i] Parsed file `n2-id1.tess'.
Info : Loading mesh...
Info : [i] Parsing file `n2-id1.msh'...
Info : [i] Parsed file `n2-id1.msh'.
Info : Reading data (elset2d, col)...
Info : Printing image...
Info : [o] Writing file `n2-id1.pov'...
Info : - Printing mesh...
Info : [o] Wrote file `n2-id1.pov'.
Info : - Generating png file (1200x900 pixels)...
Info : [o] Writing file `n2-id1.png'...
Info : [o] Wrote file `n2-id1.png'.
Info : Printing scale...
Info : Elapsed time: 1.786 secs.
========================================================================
Is this still indicative of a problem with gmsh?
from neper.
Indeed, -format msh2
should be used in the gmsh command (for the newer versions). Let's consider your Gmsh is working...
While neper --rcfile none -M n2-id1.tess -mesh3dclreps 1
is running (and hanging indefinitely), what does top
tell you? Do you see any instance of neper
or gmsh
taking cpu?
from neper.
$ ./neper --rcfile none -M n2-id1.tess -mesh3dclreps 1
top produces the following. Neper process is running but not gmsh
Tasks: 607 total, 1 running, 606 sleeping, 0 stopped, 0 zombie
%Cpu(s): 38.6 us, 2.0 sy, 0.0 ni, 54.2 id, 5.1 wa, 0.0 hi, 0.0 si, 0.0 st
KiB Mem : 13174428+total, 3280516 free, 2290984 used, 12617279+buff/cache
KiB Swap: 16777212 total, 16624448 free, 152764 used. 44100632 avail Mem
PID USER PR NI VIRT RES SHR S %CPU %MEM TIME+ COMMAND
61776 username 20 0 1966692 7344 4872 S 1099 0.0 25:41.68 neper
61812 username 20 0 168560 2880 1612 R 0.7 0.0 0:00.55 top
26981 username 20 0 175032 2980 1400 S 0.0 0.0 0:01.08 sshd
26982 username 20 0 127144 3728 1824 S 0.0 0.0 0:00.40 bash
38962 username 20 0 175032 2956 1416 S 0.0 0.0 0:00.51 sshd
38963 username 20 0 127184 3720 1836 S 0.0 0.0 0:00.28 bash
from neper.
Can you recompile Neper in debugging mode:
cmake -DDEVEL_DEBUGGING_FLAG=ON -DDEVEL_OPTIMIZATION=OFF ..
make
then run the Neper command from within gdb:
gdb ./neper
run --rcfile none -M n2-id1.tess -mesh3dclreps 1
and stop it with Ctrl+C, then hit where
, and report the output.
from neper.
Hi Romain,
When I add those options it fails to compile.
$ cmake neper-3.5.1/src/ -DCMAKE_INSTALL_PREFIX=$APPDIR -DCMAKE_CXX_FLAGS="$FLAGS" -DCMAKE_C_FLAGS="$FLAGS" -DNLOPT_LIBRARY="/opt/apps/libs/intel-18.0/nlopt/2.6.1/lib64/libnlopt.so" -DNLOPT_INCLUDE_DIR="/opt/apps/libs/intel-18.0/nlopt/2.6.1/include" -DDEVEL_DEBUGGING_FLAG=ON -DDEVEL_OPTIMIZATION=OFF
$ make
...omitted for clarity....
[ 49%] Building C object neper_v/CMakeFiles/neper_v.dir/nev_print/nev_print_mesh/nev_print_mesh_nodes/nev_print_mesh_nodes1.c.o
/opt/apps/apps/intel-18.0/neper/build/neper-3.5.1/src/neper_v/nev_print/nev_print_mesh/nev_print_mesh_nodes/nev_print_mesh_nodes1.c(49): error #192: unrecognized character escape sequence
"Number of nodes reduced by %3.0f\%% (to %d).\n",
^
compilation aborted for /opt/apps/apps/intel-18.0/neper/build/neper-3.5.1/src/neper_v/nev_print/nev_print_mesh/nev_print_mesh_nodes/nev_print_mesh_nodes1.c (code 2)
make[2]: *** [neper_v/CMakeFiles/neper_v.dir/nev_print/nev_print_mesh/nev_print_mesh_nodes/nev_print_mesh_nodes1.c.o] Error 2
make[1]: *** [neper_v/CMakeFiles/neper_v.dir/all] Error 2
make: *** [all] Error 2
from neper.
Did you give it a try with the new version? It should compile.
from neper.
Hi,
Firstly apologies, with all the turmoil this has slipped down the pile.
Thank you for the updated release it has successfully compiled see below for the resulting output from where. I hope it helps.
(gdb) where
#0 0x00002aaaac3b9c72 in load (this=<optimized out>, _O=<optimized out>)
at /nfs/site/proj/openmp/compilers/intel/16.0/Linux/install/update4/compilers_and_libraries_2016.4.258/linux/compiler/include/atomicint.h:42
#1 __kmp_release_ticket_lock (lck=0x2aaaac6c00c0 <__kmp_initz_lock>, gtid=-2) at ../../src/kmp_lock.cpp:740
#2 0x00002aaaac4010d6 in __kmp_release_bootstrap_lock (lck=<optimized out>) at ../../src/kmp_lock.h:528
#3 _INTERNAL_26_______src_z_Linux_util_cpp_ea62c7c0::__kmp_atfork_prepare () at ../../src/z_Linux_util.cpp:1533
#4 0x00002aaaacbe6232 in fork () from /lib64/libc.so.6
#5 0x000000000070dc0c in ut_sys_runwtime (exec=0x2aaaac6c00c0 <__kmp_initz_lock> "\300", command=0xfffffffe <Address 0xfffffffe out of bounds>,
tmax=1.2648951612337956e-306, pctrlc_t=0x2aaaac6c00d4 <__kmp_initz_lock+20>)
at /opt/apps/apps/intel-18.0/neper/build/neper-3.5.2/src/contrib/ut/src/ut_sys/ut_sys.c:89
#6 0x000000000052a603 in nem_meshing_2D_face_mesh_gmsh (Tess=..., RNodes=..., RMesh=0x2aaaac6c00c0 <__kmp_initz_lock>, face=-2, MeshPara=...,
Nodes=..., Mesh=0x2aaaac6c00d4 <__kmp_initz_lock+20>, cl=1.2648951612337956e-306, gmsh=0x1 <Address 0x1 out of bounds>,
tmp=0x1c <Address 0x1c out of bounds>, algo=0x1c <Address 0x1c out of bounds>, rnd=1009, allowed_t=0, pN=0x7fffffff9680, pM=0x7fffffff9710,
pbnodes=0x7fffffff9708, plbnodes=0x7fffffff9768, pbnodeqty=0x7fffffff97a0, pacl=0x7fffffff9770, pctrlc_t=0x7fffffffa6b0,
pelapsed_t=0x7fffffff9778)
at /opt/apps/apps/intel-18.0/neper/build/neper-3.5.2/src/neper_m/nem_meshing/nem_meshing_2D/nem_meshing_2D_face_mesh_gmsh/nem_meshing_2D_face_mesh_gmsh1.c:87
#7 0x0000000000528ff6 in nem_meshing_2D_face_mesh (In=..., MeshPara=..., pMultim=0x2aaaac6c00c0 <__kmp_initz_lock>, algo=-2,
pctrlc_t=0x2aaaac6c00d4 <__kmp_initz_lock+20>, pallowed_t=0x1, pmax_elapsed_t=0x1c, Tess=..., RNodes=..., RMesh=0x1c, Nodes=..., Mesh=0xae3c50,
face=11420624, pN=0xae4760, pM=0xae4300, pbnodes=0x0, plbnodes=0xadf0f0, pbnodeqty=0xadf160, pmOsize=0x0, pelapsed_t=0x74)
at /opt/apps/apps/intel-18.0/neper/build/neper-3.5.2/src/neper_m/nem_meshing/nem_meshing_2D/nem_meshing_2D3.c:37
#8 0x000000000052853d in nem_meshing_2D_face (In=..., MeshPara=..., pMultim=0x2aaaac6c00c0 <__kmp_initz_lock>, pctrlc_t=0xfffffffe,
pallowed_t=0x2aaaac6c00d4 <__kmp_initz_lock+20>, pmax_elapsed_t=0x1, Tess=..., RNodes=..., RMesh=0x1c, Nodes=..., Mesh=0x1c, pN=0x7fffffffa6b0,
pM=0xc, pbnodes=0x7fffffffb560, plbnodes=0xa, pbnodeqty=0x7fffffffa770, face=-21944)
at /opt/apps/apps/intel-18.0/neper/build/neper-3.5.2/src/neper_m/nem_meshing/nem_meshing_2D/nem_meshing_2D2.c:67
#9 0x0000000000527ede in L_nem_meshing_2D_46__par_loop0_2_0 ()
at /opt/apps/apps/intel-18.0/neper/build/neper-3.5.2/src/neper_m/nem_meshing/nem_meshing_2D/nem_meshing_2D1.c:54
#10 0x00002aaaac3fd7d3 in __kmp_invoke_microtask ()
from /opt/apps/compilers/intel/18.0.3/compilers_and_libraries_2018.3.222/linux/compiler/lib/intel64/libiomp5.so
#11 0x00002aaaac3c454a in __kmp_invoke_task_func (gtid=-1402208064) at ../../src/kmp_runtime.cpp:7277
#12 0x00002aaaac3c5d47 in __kmp_fork_call (loc=0x2aaaac6c00c0 <__kmp_initz_lock>, gtid=-2, call_context=(unknown: 2892759252), argc=1,
microtask=0x1c, invoker=0x1c, ap=0x7fffffffa4f0) at ../../src/kmp_runtime.cpp:2463
#13 0x00002aaaac385100 in __kmpc_fork_call (loc=0x2aaaac6c00c0 <__kmp_initz_lock>, argc=-2, microtask=0x2aaaac6c00d4 <__kmp_initz_lock+20>)
at ../../src/kmp_csupport.cpp:349
---Type <return> to continue, or q <return> to quit---
#14 0x0000000000527101 in nem_meshing_2D (In=..., MeshPara=..., Tess=..., RNodes=..., RMesh=0x0, pNodes=0x3, Mesh=0x0)
at /opt/apps/apps/intel-18.0/neper/build/neper-3.5.2/src/neper_m/nem_meshing/nem_meshing_2D/nem_meshing_2D1.c:46
#15 0x000000000051b8cc in nem_meshing (In=..., pMeshPara=0x2aaaac6c00c0 <__kmp_initz_lock>, pTess=0xfffffffe, RNodes=...,
RMesh=0x2aaaac6c00d4 <__kmp_initz_lock+20>, pNodes=0x1, Mesh=0x1c)
at /opt/apps/apps/intel-18.0/neper/build/neper-3.5.2/src/neper_m/nem_meshing/nem_meshing1.c:50
#16 0x00000000005168dd in neper_m (fargc=-1402208064, fargv=0xfffffffe, argc=-1402208044, argv=0x1)
at /opt/apps/apps/intel-18.0/neper/build/neper-3.5.2/src/neper_m/neper_m.c:164
#17 0x00000000004386ed in main (argc=-1402208064, argv=0xfffffffe) at /opt/apps/apps/intel-18.0/neper/build/neper-3.5.2/src/neper.c:111
from neper.
So, there must be a problem with fork
.
You are using an Intel compiler, right? I've never done that. Can you try with a GNU compiler instead? (If it helps, you can disable openmp).
from neper.
Related Issues (20)
- Model visualization is returning an error HOT 5
- Segmentation fault (core dumped)
- CMAKE_INSTALL_PREFIX_COMPLETION completion path. HOT 1
- Problem with -transform "cut()" in multiscale tesselation HOT 1
- Missing Parenthesis Error in File - net_mtess_flatten_cell1.c:41:89: HOT 1
- initial 2d tesselation iteration segfaults with large number of cells HOT 2
- Is it possible to control the area fraction and distribution of grains ? HOT 1
- Bug when prescribing initial centroid coords HOT 3
- incorrect msh4 format generated from neper HOT 8
- missing physical tags description in the Entities section in msh4 file HOT 3
- A bug occurred when generating tessellation using coordinate files. HOT 2
- all $PhysicalNames not reflected in $Entities
- error:Cannot convert to ".inp" format.
- Quiery about the Error: - simulation.tess and simulation.msh do not match (2D).
- Query about the error "simulation.tess and simulation.msh do not match (2D)."
- Undeclared Function HOT 1
- Meshing Tests Fail (Mac M1) HOT 2
- Error slicing tessellation HOT 1
- Build failures on 32 bit systems HOT 2
- Can't read .msh file in -M module
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from neper.