VTK linking not working

[david.t...@utsouthwestern.edu]

Hi,

We are trying to get icy up and running on our HPC cluster here, which is using RedHat Enterprise Linux 6.7. The included VTK libs require GLIBC 2.14, newer than RHEL provides, so we build our own VTK.

I've verified VTK is in the LD_LIBRARY_PATH and VTK_WRAP_JAVA was set on build, so it does have java bindings and the vtk.jar present. LD_LIBRARY_PATH is as below: 

02:54 PM $ echo $LD_LIBRARY_PATH

/cm/shared/apps/java/oracle/jdk1.7.0_51/lib:/cm/shared/apps/vtk/6.3.0-intel/lib:/cm/shared/apps/slurm/2.5.7/lib64/slurm:/cm/shared/apps/slurm/2.5.7/lib64

As soon as I try to use a VTK plugin I get linking errors, e.g. if I open a TIFF stack and the try Other Plugins -> tutorial -> vtk -> VTKPainterExample:

java.lang.UnsatisfiedLinkError: vtk.vtkEarthSource.VTKInit()J

at vtk.vtkEarthSource.VTKInit(Native Method)

at vtk.vtkObjectBase.<init>(vtkObjectBase.java:43)

at vtk.vtkObject.<init>(vtkObject.java:94)

at vtk.vtkAlgorithm.<init>(vtkAlgorithm.java:510)

at vtk.vtkPolyDataAlgorithm.<init>(vtkPolyDataAlgorithm.java:78)

at vtk.vtkEarthSource.<init>(vtkEarthSource.java:66)

</snip>

VTK was built with the relevant module (geovis) that supplies vtkEarthSource it's trying to get here.

Any hints for debugging this - or are there additional requirements of the VTK build?

Many Thanks,

Dave Trudgian

[david.t...@utsouthwestern.edu]

Sorry - should mention this is latest icy 1.8.1.0 and VTK 6.3.0

[Stephane]

Hi David,

I was about to ask for the VTK version ;) It's true that provided VTK library in Icy is certified for Ubuntu (and derived) distributions and may not work on other distribs (we just can't compile for each possible distribution).
Icy is also using VTK 6.3 internally so it should work... Something you can try is to replace directly the VTK library inside the Icy "lib/linux64/vtk" folder with the ones you compiled (make a backup before). Files should have the same name so you may need to remove the version extension or at least have symbolic link with original name, note that if you use the INSTALL_FOR_JAVA build switch it should remove the version extension for you.

Best,

- Stephane

[david.t...@utsouthwestern.edu]

Hi Stephane,

Thanks for the info. I built VTK again with the INSTALL_FOR_JAVA oprtion ON, so it does version-less .so files as suggested. Then copied these into the lib/unix64/vtk folder in the icy distribution.

Trying the VTKPainterExamples I now have success.

However - the default icy.sh seems to call an updater.jar that updated vtk, wiping the libs out at some point. I guess I'll just change icy.sh to call icy.jar directly and all will be good.

Thanks,

DT

[Stephane]

Hi David,

Oh indeed the auto update can replace you own lib files. I guess it detects the files has been modified and try to fix "corrupted" files by updating them with the last available version. In the meantime you can just disable the auto update in Icy Preferences (you can still update by using manual update) :)

Best,

- Stephane