[Docker image] [register] error while loading shared libraries: libMIRTKPointSet.so.0 annot open shared object file: No such file or directory

[tmspvn]

Hi,
After pulling the official image updated 25 days ago register returns the following error:

/usr/local/lib/mirtk/tools/register: error while loading shared libraries: libMIRTKPointSet.so.0: cannot open shared object file: No such file or directory
Error: register command returned non-zero exit status 127

[schuhschuh]

Thanks for reporting this! It seems the python/mirtk/__init__.py module is not setting the LD_LIBRARY_PATH correctly.

This works:

docker run --rm -it -e LD_LIBRARY_PATH=/usr/local/lib/mirtk biomedia/mirtk register -h

[schuhschuh]

I made this change to the Dockerfile to fix this by setting the dynamic library search path in the Docker image. This is easier than fixing the generation of the __init__.py module for now. Keeping issue open, though, to address this later.

[karllandheer]

Hello, I have run into this same error. I am not calling MIRTK through Docker (I am actually running a package which uses MIRTK that I did not write so I cannot really modify it). Do you know how I could resolve this issue? Because you said it has something to do with LD_LIBRARY_PATH here is it for my system:

/usr/lib64/openmpi/lib/:/usr/local/cuda/lib64:/usr/local/lib:/usr/lib:/usr/local/cuda/extras/CUPTI/lib64:/usr/local/mpi/lib:/lib/:/usr/local/cuda/lib64:/usr/local/lib:/usr/lib:/usr/local/cuda/extras/CUPTI/lib64:/opt/amazon/openmpi/lib:/usr/local/cuda/lib:/opt/amazon/efa/lib:/usr/local/mpi/lib:/usr/lib64/openmpi/lib/:/usr/local/cuda/lib64:/usr/local/lib:/usr/lib:/usr/local/cuda/extras/CUPTI/lib64:/usr/local/mpi/lib:/lib/:/usr/local/cuda/lib64:/usr/local/lib:/usr/lib:/usr/local/cuda/extras/CUPTI/lib64:/opt/amazon/openmpi/lib:/usr/local/cuda/lib:/opt/amazon/efa/lib:/usr/local/mpi/lib:/usr/lib64/openmpi/lib/:/usr/local/cuda/lib64:/usr/local/lib:/usr/lib:/usr/local/cuda/extras/CUPTI/lib64:/usr/local/mpi/lib:/lib/:

I was able to locate the file libMIRTKPointSet.so.0, it was located in /opt/mirtk/lib on my system. Any help regarding this would be greatly appreciated, thank you very much.

[schuhschuh]

@karllandheer Have you tried

export LD_LIBRARY_PATH=/opt/mirtk/lib:${LD_LIBRARY_PATH}

in your shell before executing the command? Specifically, I am assuming you are using Bash shell. This may be different if you use a different shell.

[karllandheer]

Yes that fixed the issue. Thank you very much!