Converts a mesh written with gmsh to the exodus II format to use it with Peridigm
Home Page: https://iapcs.github.io/gmsh-exodus-converter/
License: GNU General Public License v2.0
Hi, I'm interested in your convert script. However, when I run:
python convert.py -i plate_test_element2.msh -o output.g -t 2
I get a segmentation fault. Here is the stack trace:
#0 0x00007fffe5fa4a1b in vtkMultiProcessController::GetNumberOfProcesses() ()
from /usr/lib/x86_64-linux-gnu/libvtkParallelCore-6.0.so.6.0
#1 0x00007fffc0cf33df in vtkPExodusIIWriter::CheckParameters() ()
from /usr/lib/x86_64-linux-gnu/libvtkIOParallelExodus-6.0.so.6.0
#2 0x00007fffd9b571ee in vtkExodusIIWriter::WriteData() ()
from /usr/lib/x86_64-linux-gnu/libvtkIOExodus-6.0.so.6.0
#3 0x00007fffd9b4aafa in vtkExodusIIWriter::RequestData(vtkInformation*, vtkInformationVector**, vtkInformationVector*) () from /usr/lib/x86_64-linux-gnu/libvtkIOExodus-6.0.so.6.0
#4 0x00007ffff2ba7b80 in vtkExecutive::CallAlgorithm(vtkInformation*, int, vtkInformationVector**, vtkInformationVector*) () from /usr/lib/x86_64-linux-gnu/libvtkCommonExecutionModel-6.0.so.6.0
#5 0x00007ffff2b9df37 in vtkDemandDrivenPipeline::ExecuteData(vtkInformation*, vtkInformationVector**, vtkInformationVector*) () from /usr/lib/x86_64-linux-gnu/libvtkCommonExecutionModel-6.0.so.6.0
#6 0x00007ffff2b99fa6 in vtkCompositeDataPipeline::ExecuteData(vtkInformation*, vtkInformationVector**, vtkInformationVector*) () from /usr/lib/x86_64-linux-gnu/libvtkCommonExecutionModel-6.0.so.6.0
#7 0x00007ffff2ba0d51 in vtkDemandDrivenPipeline::ProcessRequest(vtkInformation*, vtkInformationVector**, vtkInformationVector*) () from /usr/lib/x86_64-linux-gnu/libvtkCommonExecutionModel-6.0.so.6.0
#8 0x00007ffff2bbf4b1 in vtkStreamingDemandDrivenPipeline::ProcessRequest(vtkInformation*, vtkInformationVector**, vtkInformationVector*) ()
from /usr/lib/x86_64-linux-gnu/libvtkCommonExecutionModel-6.0.so.6.0
#9 0x00007ffff2b9f74d in vtkDemandDrivenPipeline::UpdateData(int) ()
from /usr/lib/x86_64-linux-gnu/libvtkCommonExecutionModel-6.0.so.6.0
#10 0x00007ffff2bbc955 in vtkStreamingDemandDrivenPipeline::Update(int) ()
from /usr/lib/x86_64-linux-gnu/libvtkCommonExecutionModel-6.0.so.6.0
#11 0x00007fffeec43f4e in vtkWriter::Write() ()
from /usr/lib/x86_64-linux-gnu/libvtkIOCore-6.0.so.6.0
#12 0x00007fffeee7be35 in ?? () from /usr/lib/python2.7/dist-packages/vtk/vtkIOCorePython.so
#13 0x000000000049968d in PyEval_EvalFrameEx ()
#14 0x0000000000499ef2 in PyEval_EvalFrameEx ()
#15 0x0000000000499ef2 in PyEval_EvalFrameEx ()
#16 0x00000000004a1634 in ?? ()
#17 0x000000000044e4a5 in PyRun_FileExFlags ()
#18 0x000000000044ec9f in PyRun_SimpleFileExFlags ()
#19 0x000000000044f904 in Py_Main ()
#20 0x00007ffff7818ec5 in __libc_start_main (main=0x44f9c2 , argc=8, argv=0x7fffffffd188,
init=, fini=, rtld_fini=, stack_end=0x7fffffffd178)
at libc-start.c:287
#21 0x0000000000578c4e in _start ()
Does that help identify what my problem might be?
I converted the file 2D fie plate_test_element2.msh as a .g file using the script.
Then, I tried using Peridigm to load this file with a dummy.peridigm input deck.
I get the following error:
adminu@a4217-03:/mnt/hgfs/Peridigm_shared/Gmsh_to_Exodus2$ Peridigm specimen.peridigm
-- Peridigm
-- version 1.4.1
/root/install/Peridigm/src/io/discretization/Peridigm_ExodusDiscretization.cpp:409:
Throw number = 1
Throw test that evaluated to true: true
**** Error in loadData(), unknown element type TRIANGLE.
Wallclock Time (seconds):
Total 0.021
@diehlpk , any ideas ?
I have installed libvtk6.2 and python-vtk6. When I run
python /home/yudan/Downloads/gmsh-exodus-converter-master/convert.py -i /home/yudan/Desktop/test.msh -o test.g -t 4
I have:
Traceback (most recent call last):
File "/home/yudan/Downloads/gmsh-exodus-converter-master/convert.py", line 10, in
from vtk import vtkExodusIIWriter
File "/usr/lib/python2.7/dist-packages/vtk/init.py", line 113, in
from vtkIOGDAL import *
File "/usr/lib/python2.7/dist-packages/vtk/vtkIOGDAL.py", line 1, in
from vtkIOGDALPython import *
ImportError: /usr/lib/libgdal.so.1: undefined symbol: nc_def_var_deflate
Hello. Me again.
I found that after I run the command of convert.py, it worked, but it lost the points internal.
before
after
The code in this repo is probably obsoleted by meshio:
meshio-convert input.msh output.e(Btw, I'd used vtk in meshio once, but found it too large (and unreliable) as a dependency. meshio handles VTK files (and Exodus) manually now.)
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
An Open Source Machine Learning Framework for Everyone
Django
The Web framework for perfectionists with deadlines.
Laravel
A PHP framework for web artisans
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
Some thing interesting about web. New door for the world.
A server is a program made to process requests and deliver data to clients.
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Some thing interesting about visualization, use data art
Some thing interesting about game, make everyone happy.
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
Microsoft
Open source projects and samples from Microsoft.
Google
Google ❤️ Open Source for everyone.
Alibaba
Alibaba Open Source for everyone
D3
Data-Driven Documents codes.
Tencent
China tencent open source team.