Analysis3 dask_jobqueue storage flags query

Technical
, ,
21

Okay, last thing to try before I’m out of ideas:

At the end of your .bash_rc, you have:

# >>> conda initialize >>>
# !! Contents within this block are managed by 'conda init' !!
__conda_setup="$('/g/data/w42/dr6273/apps/conda/bin/conda' 'shell.bash' 'hook' 2> /dev/null)"
if [ $? -eq 0 ]; then
    eval "$__conda_setup"
else
    if [ -f "/g/data/w42/dr6273/apps/conda/etc/profile.d/conda.sh" ]; then
        . "/g/data/w42/dr6273/apps/conda/etc/profile.d/conda.sh"
    else
        export PATH="/g/data/w42/dr6273/apps/conda/bin:$PATH"
    fi
fi
unset __conda_setup

Can you change this to:


# >>> conda initialize >>>
# !! Contents within this block are managed by 'conda init' !!
__conda_setup="$('/opt/conda/bin/conda' 'shell.bash' 'hook' 2> /dev/null)"
if [ $? -eq 0 ]; then
    eval "$__conda_setup"
else
    if [ -f "/opt/conda/etc/profile.d/conda.sh" ]; then
        . "/opt/conda/etc/profile.d/conda.sh"
    else
        export PATH="/opt/conda/bin:$PATH"
    fi
fi
unset __conda_setup
# <<< conda initialize <<<

It looks like this could also be mangling your conda path. I would keep all the aliases commented out when trying this, just to be safe.

If that doesn’t work, I’ll see if I can find someone else who might have debugged something similar before.

1 Like
22

I don’t believe I’m writing this but that seems to have worked :smiley: Thank you so much for your help and persistence! I can slowly go back and uncomment those aliases and stuff in case they break it again, but I suspect the problem is resolved?

1 Like
23

Yeah, I don’t think that they’re the issue, so you should be safe to add them back in now.

The offending block of code in your .bashrc is autogenerated by conda, I think when you first create a conda environment.

Glad got it fixed! :sweat_smile:

For anyone else that comes across this in future:

  • .bash_rc is sourced on every shell invocation, so can be a source of subtle & persistent configuration bugs.
  • Anything like eg. module load generally should not live in .bashrc, but instead in .bash_profile - module load pbs is an exception.
  • Unfortunately, conda generates the offending block of code when conda init is run.
  • If you have previously run conda init on Gadi, you might potentially experience this bug.
2 Likes