Genius is not compiled with XML VTK support, skip VTK export... #18
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Please see my install note: This version still uses waf. Later version use cmake instead on my fork. |
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Oh, I figured it out. It was to do with specifying the VTK_DATA_ROOT while configuring vtk. |
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Sounds good. With my instructions, it is possible to avoid compiling vtk. |
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Great, I'll surely have a look at it. /usr/bin/ld: /usr/local/lib/vtk-5.4/libvtkIO.a(vtkXMLUnstructuredGridWriter.o): relocation R_X86_64_32 against `.rodata' can not be used when making a shared object; recompile with -fPIC Hoping to hear from you soon. |
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Look at setting CMAKE_CXX_FLAGS and CMAKE_C_FLAGS in your CMakeCache.txt. According to this: http://vtk.1045678.n5.nabble.com/Compile-and-build-VTK-with-shared-libraries-enabled-td5721521.html |
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Thanks buddy. My first day on Git and issues have started to solve faster. |
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You're welcome. Sounds like you are well on your way. Any issues with cmake or vtk are best handled on their mailing lists. |
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Another error now, /usr/bin/ld: warning: libvtkNetCDF.so.5.4, needed by /usr/local/lib/vtk-5.4/libvtkIO.so, not found (try using -rpath or -rpath-link) I am really having a hard time now. Hoping to hear from you soon. |
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Hi, These are missing: It looks like you need to add the missing libraries to the linker line You'd have to look through the wscript file and add them: def config_vtk(): |
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Hi, src/solution/vtk_io.cc.2.o: In function ... and this continues. Too long to be fully pasted. |
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The 20 or so lines before the first "undefined reference" will help. shenchen On 2014-02-15 16:06, Ashish Kumar wrote:
Links:[1] |
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There were none. It just starts with these undefined references. |
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What I understand is that all these issues are related to vtk. If possible can you please provide me with a step by step guide to build vtk? I am using version 5.4.2. |
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Below is the options I used for VTK, using static library '-DCMAKE_BUILD_TYPE:STRING=RELEASE' '-DCMAKE_INSTALL_PREFIX:PATH=${TGTDIR}' '-DCMAKE_INCLUDE_PATH:PATH=${TGTDIR}/include' '-DCMAKE_LIBRARY_PATH:PATH=${TGTDIR}/lib' '-DBUILD_DOCUMENTATION:BOOL=OFF' '-DBUILD_TESTING:BOOL=OFF' '-DVTK_USE_RPATH:BOOL=OFF' '-DVTK_USE_GUISUPPORT:BOOL=ON' '-DVTK_USE_PARALLEL:BOOL=OFF' '-DVTK_USE_VIEWS:BOOL=ON' '-DVTK_USE_N_WAY_ARRAYS:BOOL=ON' '-DVTK_WRAP_JAVA:BOOL=OFF' '-DVTK_WRAP_TCL:BOOL=OFF' '-DCMAKE_C_FLAGS:STRING=-O3 -DNDEBUG -fPIC' '-DCMAKE_CXX_FLAGS:STRING=-O3 -DNDEBUG -fPIC' As you see, a lot of VTK We may switch to cmake at some regards, On 2014-02-15 20:29, Ashish
Links:[1] |
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I get the same error again. Have built vtk as directged but still. Setting top to : /home/pinkchalk/Downloads/Genius-TCAD-Open-master Hoping to hear from you soon. |
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It seems to me that genius is not able to check for libraries of VTK as indicated by, Checking for header vtkConfigure.h : yes thereby leading to these undefined references. Any ideas on how to correct this. |
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The detailed error message is in the config.log file in the It will try to link vtk libs from a few where is your vtk's shenchen On 2014-02-15 23:20, Ashish Kumar
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/usr/local/lib |
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Corrected the issue, edited the wscript file appropriately to include vtkNetCDF, vtkmetaio, vtksqlite instead of libvtkNetCDF, libvtkmetaio, libvtksqlite Genius builds successfully. pinkchalk@pinklet:~/Test/examples/PN_Diode/1D$ $GENIUS_DIR/bin/genius.LINUX -i pn1d.inp |
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Please check that the head/lib files are actually in /usr/local/vtk/include/vtk-5.4 and /usr/local/vtk/lib/vtk-5.4 respectively. If not, please change your VTK configure scripts as I If this still doesn't work, please shenchen On
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do export LD_LIBRARY_PATH=/usr/local/lib/vtk-5.4 before you run shenchen On 2014-02-15 23:46,
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Thanks a lot. Regards |
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My fork of the software, https://github.com/lutherthecat/Genius-TCAD-Open builds using cmake using the instructions in myinstall.txt. I recommend used the vtk packages in that file so that the program will run on any ubuntu system with those libraries preinstalled. |
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I will definitely read your cmake code. Thank you for your shenchen On
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Anyone! Please Help! I have a very similar problem, Genius is installed and built but the first time I tried to run the diode example on Genius with:
The following error is reported:
I deterred this by using Cogenda's suggestion:
This allowed Genius to compile/iterate successfully, however this prompted PinkChalk's error:
Disallowing the VTK file to pop up I am relatively new to Linux, maybe my cgnslib files are in the wrong directory? Should they be in /usr/lib as well? Does me having to declare the LD_LIBRARY_PATH for the cgnslib location prevent the use of VTK? Again I can't compile Genius LD_LIBRARY_PATH set to VTK due to the above error "cannot open shared object file: No such file or directory". Also, my BUILD_SHARED_LIBS is ON for VTK config VTK is located in my /usr/local/lib Thank you, I'm so close to get this running! |
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This is to do with incorrect vtk installation. Did you specify VTK_DATA_ROOT while installation? Were the -fPIC flags set correctly? This might come in handy. http://thilinasameera.wordpress.com/2013/02/09/setting-up-vtk-and-itk-environments-for-ubuntu/ CMAKE_CXX_FLAGS and CMAKE_C_FLAGS need to be set to -fPIC while installation. Regards |
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Thank you for your helpful response, I reconfigured VTK with the correct -fPIC flags, Shared Libraries ON, and VTK_DATA_ROOT set to my VTKData, reconfigured Genius then received this error again:
after performing:
I can get Genius to compile after this error only by:
Which renders VTK useless, any suggestions regarding this inability to find cngslib.so, because it seems I need to reserve the export LD_LIBRARY_PATH for finding VTK? Is there an easy way to use gnuplot or paraview instead of VTK? Here is my VTK ccmake config window:
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you can use a ":" to separate the paths: |
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I appreciate the support. I tried that as well, still would compile Genius but not export anything to VTK (mentioning I need xml support). Does cgnslib need to be located in /usr/local/lib or /usr/lib like VTK is? |
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Are you sure that you have VTK enabled? You need a command line like this: |
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I ran that command but I guess I'm confused about where each of these sub-directories should be stored. petsc, cgns, vtk, and Genius-TCAD-Open-master are all folders under my Genius directory. When I point petsc to anywhere other than $PETSC_DIR it gives me "Could not find petscversion.h, or it can not be parsed." An above user had VTK in /usr/local/lib/vtk-5.4 where mine is also stored, but do I set the path to that, or to /home/me/Genius/VTK? Thank you |
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What happens when you start building genius? Do you see something like this? Checking for header cgnslib.h : yes If no, then you have to specify the location where genius can find cgns. |
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Genius is installed but still won't run due libcgns.so not being found. Checking for header nglib.h : no after commanding
then I export GENIUS_DIR to Genius-TCAD-Open-master and run the example after cd'ing:
Thank you again for your assistance! |
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It looks like you would just need to set LD_LIBRARY_PATH to where the libcgns.so would be found. If you run "ldd", you can see which shared libraries that genius found and did not find. Then set LD_LIBRARY_PATH to the ":" delimited list of paths to find the libraries. |
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Thank you, the ldd on libcgns.so then setting LD_LIBRARY_PATH to this location as well as the /usr/local/lib/vtk did the trick. Now when I run the 2D PN Diode example it writes system to .vtu XML files which can only be accessed through a .dat text file, and to a Legacy VTK file pn2d.vtk which is a Dataset Unstructured Grid big text file. Is this the extent of the simulation, having to manually move and plot this text output? |
I have installed Genius open source on my Ubuntu 13.10.
While compiling any input test file genius gives an error
"Genius is not compiled with XML VTK support, skip VTK export..."
and hence no vtk files are generated. I have vtk 5.4.2 installed on my system and I am pretty sure that I had specified the correct paths while building Genius.
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