GLIBC version not found

[Nimrod Bernat]

Hi Elastix,

I'm calling elastix from python using

cmd = ElastixBinary + ' -threads 16 -m ' + movingImage + ' -f ' + fixedImage + ' -p ' + affineParameterFile + ' -p ' + bSplineParameterFile + ' -out ' + resultDirectory

res = os.system(cmd);
    
    if res != 0:
        raise RuntimeError('alignData: failed executing: ' + cmd)

And I get an error that the command was not executed. I don't have much experience with python but I assume the error has something to do with GLIBC version, that before the error message python console says are required by this file elastix-5.0.1-linux/bin/elastix.

I updated the libc6 version through my ubuntu 16.04 terminal and the terminal responds: libc6 is already the newest version (2.23-0ubuntu11.2)

Can you help with this?

Thanks!

Nimrod

[Stuart Rowland]

The RuntimeError output includes the command that it was executing. Copy that command to the clipboard and paste it in a terminal window. This should tell you exactly what the problem is.

[Stuart Rowland]

Sorry. That output should have been in the python window. What is the exact error message?

[Nimrod Bernat]

Hi Stuart,

I upgraded my Ubuntu from 16.04 to 18.04, and it didn't show any 'GLIBC version not found' messages, but the command still doesn't work. I copied the command to the terminal, in the terminal shows the following error:

/home/kupchiklab/ClearMap/elastix-5.0.1-linux/bin/elastix: error while loading shared libraries: libANNlib-5.0.so.1: cannot open shared object file: No such file or directory

Now, the file does exist in the dirstory mentioned error. I think it might have something to do with bash. file setups, but when I run the file locating the PATHs in the LD_LIBRARY_PATH, the output is that everything was found.

Maybe it has something to do with shared  object settings?

Thanks

Nimrod

‫בתאריך יום א׳, 15 בנוב׳ 2020 ב-0:36 מאת ‪Stuart Rowland‬‏ <‪swr.j...@gmail.com‬‏>:‬

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[Stuart Rowland]

The problem seems to be with libANNlib. Run the following command and post the output.

$ ldd /home/kupchiklab/ClearMap/elastix-5.0.1-linux/bin/elastix

[M.St...@lumc.nl]

Dear Nimrod,

Could it also mean that elastix was not found? Which means it should be placed in your PATH variable. I would consult a local linux guru for further help and looking over you shoulder.

Best regards,

Marius Staring

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From: elastix-imag...@googlegroups.com <elastix-imag...@googlegroups.com> on behalf of Nimrod Bernat <nimrod...@mail.huji.ac.il>
Sent: 09 November 2020 10:20 AM
To: elastix-imageregistration
Subject: [elastix-imageregistration] GLIBC version not found

 

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