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E4S-Project / e4s-cl

Container manager for E4S
https://e4s-cl.readthedocs.io
MIT License
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Singularity: error with PATH commands #72

Closed spoutn1k closed 2 years ago

spoutn1k commented 2 years ago

Running a command in e4s-cl with no path (e.g. e4s-cl ls) fails when the guest glibc is being overrun by the host's. The error message is the following:

ls: error while loading shared libraries: ls: cannot open shared object file

This does not happen when using a relative or absolute path, and may be due to a process parsing the PATH loading the container's glibc and thus creating conflict when the host glibc is loaded.

spoutn1k commented 2 years ago 
[jskutnik@spoutnik e4s_cl]$ e4s-cl ls
Using selected profile MPICH_3.4.2-2
Process 126742 failed with code 127:
WARNING: /etc/singularity/ exists, migration to apptainer by system administrator is not complete
WARNING: DEPRECATED USAGE: Environment variable SINGULARITY_BIND will not be supported in the future, use APPTAINER_BIND instead
WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_LD_PRELOAD as environment variable will not be supported in the future, use APPTAINERENV_LD_PRELOAD instead
WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_LD_LIBRARY_PATH as environment variable will not be supported in the future, use APPTAINERENV_LD_LIBRARY_PATH instead
ls: error while loading shared libraries: ls: cannot open shared object file
See /home/jskutnik/.local/e4s_cl/logs/faa0a4688be22205d5d7ada6740e9ff7f622c061928aa7149ac58317a6ec875d/process.126742 for details.
Container command failed with error code 127
[jskutnik@spoutnik e4s_cl]$ e4s-cl /usr/bin/ls
Using selected profile MPICH_3.4.2-2
cf  cli  error.py  __init__.py  logger.py  model  mvc  __pycache__  sample.py  util.py  variables.py  version.py