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undefined symbol: ZN9CifString12UnknownValueE error meaning?

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undefined symbol: ZN9CifString12UnknownValueE error meaning?


I am trying to run mp_domain_assembly protocol via the cluster and getting this error:

/truba/home/aniyaz/softs/rosetta/main/source/bin/mp_domain_assembly.mpi.linuxgccrelease: symbol lookup error: /truba/home/aniyaz/softs/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/mpi/ undefined symbol: _ZN9CifString12UnknownValueE

After several same rows it ended up with the Exit code: 127

Could anyone please say what's the problem with that? I couldn't figure out what does it mean..

slurm-498899.err_.txt7.82 KB
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Wed, 2023-01-04 08:37

Typically symbol errors mean there's something wrong with your compilation/build of Rosetta. You may want to try doing a fresh compile of Rosetta and see if that helps.

However, one issue you may be running into with that symbol is the "external" libraries which are compiled as part of Rosetta. They're stored in a separate directory, and while the compliation should be done in a manner which allows Rosetta to normally find them, if you've moved Rosetta or are running Rosetta on a network drive which is mounted in a different location on the running machine than the compilation machine, you can have issues with that. (Though normally you get a different error.) -- You may want to try first adding the path to that external library directory to your LD_LIBRARY_PATH environment variable. It's probably going to be something like /truba/home/aniyaz/softs/rosetta/main/source/build/external/release/linux/3.10/64/x86/gcc/4.8/mpi/, though depending on the details of compliation it might be in a slightly different location (but under the main/source/build/external directory)

Wed, 2023-01-04 08:50

Thank you very much rmoretti, appreciate your time! 

Tried first adding the path of the external library to LD_LIBRARY_PATH in the SLURM file (Not sure if it should be done in a different way. I'm not authorized to change .bash_profile in the cluster). Got the same error.

Then, remove all the files, wget and install rosetta again. After running, got the same error.

Wed, 2023-01-11 01:21

I had installed miniconda + AmberTools alongside rosetta. It somehow interferes with previously installed rosetta.

First, I deactivated miniconda (conda config --set auto_activate_base false) and then, remove the AmberTools installation. After that, I did a fresh compile of Rosetta (removed the old one and downloaded&installed it again). And now it works normally.

Thank you very much again!

Wed, 2023-01-11 01:23