This is an experiment. Is a GitHub Gist comment a good way to log publically how I fixed an installation or similar issue?
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October 2, 2024 15:07
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Save matteoferla/2001c5578c24651bb04ef910004c7d52 to your computer and use it in GitHub Desktop.
I am going to write a comment for every damn IT issue/fix I get...
APBS does not work out of the box on Rocky Linux 8.10
https://github.com/Electrostatics/apbs/releases/download/v3.4.1/APBS-3.4.1.Linux.zip
$ unzip APBS-3.4.1.Linux.zip
...REDACTED...
$ ./APBS-3.4.1.Linux/bin/apbs pentakaihemimer.relax.pdb
./APBS-3.4.1.Linux/bin/apbs: /lib64/libm.so.6: version `GLIBC_2.29' not found (required by ./APBS-3.4.1.Linux/bin/apbs)
./APBS-3.4.1.Linux/bin/apbs: /lib64/libpthread.so.0: version `GLIBC_2.30' not found (required by ./APBS-3.4.1.Linux/bin/apbs)
$ ldd --version
ldd (GNU libc) 2.28
Copyright (C) 2018 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
Written by Roland McGrath and Ulrich Drepper.
$ source /etc/os-release
$ echo $PRETTY_NAME
Rocky Linux 8.10 (Green Obsidian)
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Jupyter decided to stop starting kernels after a pip install in conda base env. Cause:
prompt-toolkit-3.0.42giving errorModuleNotFoundError: No module named 'prompt_toolkit.output'—ipython run, but import raised error. Fix was simply topip install prompt-toolkit -Uto version 3.0.47.Oddly, this applied to all conda envs.
One environment's kernel was still effe'ed, but fixed when disinstalled and reinstalled possibly due to lack of
conda env config vars set PYTHONUSERBASE=$CONDA_PREFIX