ERROR: libpython3.7m.so from LD_PRELOAD cannot be preloaded:

Troubleshooting
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I updated cyrosparc and got the following error:
ERROR: ld.so: object ‘/home/mckn_csparc/cryosparc2/cryosparc2_master/deps/anaconda/envs/cryosparc_master_env/lib/libpython3.7m.so’ from LD_PRELOAD cannot be preloaded: ignored.

What is your advice to fix this? Thank you very much!

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@chenzhao A few questions to get more information about this:

  • Where exactly did you see this message? While updating CryoSPARC or when running a job?
  • What version of CryoSPARC did you have prior to the update?
  • Could you share the full update log from /home/mckn_csparc/cryosparc2/cryosparc2_master/run/update.log (you may DM it directly to me)

Once you’ve sent me that information, try running the following command:

/home/mckn_csparc/cryosparc2/cryosparc2_master/bin/cryosparcm update --override

If that doesn’t fix the issue, please send me the full output.

1 Like
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Hi @nfrasser, thank you so much for your help! The error message appeared when I typed any command, such as nvidia-smi. However, for some reason the error disappeared now without me doing anything obvious. The only things I did were:

  1. restarted cryosparc (I restarted before and this didn’t clear this error message)
  2. installed Anaconda and topaz
    I agree this is really strange but I am glad that I don’t see this any more. Again thank you for your help!
1 Like
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Ah I see, it looks like there was a component of the previous CryoSPARC installation still active in your environment after the update. In the future, restart your command line or SSH session to fix similar errors. Glad everything is working now!

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Ah, this this interesting. Thank you very much for the explanation!

Best,
Chen