run a crontab job using an anaconda env
After MUCH fiddling I got crontab
to activate my conda environment with conda activate my_env
and run the Python interpreter within that environment.
Note I'm using Ubuntu 18.04.
Background
When the Anaconda installer initializes conda, it appends a snippet at the end of the
~/.bashrc
file. This file is executed each time the user opensbash
interactively. The snippet allows the user to runconda
commands (ieconda activate my_env
) frombash
.Anaconda installer v2020.02 appended the following
conda
snippet in~/.bashrc
:
# >>> conda initialize >>>
# !! Contents within this block are managed by 'conda init' !!
__conda_setup="$('/opt/anaconda3/bin/conda' 'shell.bash' 'hook' 2> /dev/null)"
if [ $? -eq 0 ]; then
eval "$__conda_setup"
else
if [ -f "/opt/anaconda3/etc/profile.d/conda.sh" ]; then
. "/opt/anaconda3/etc/profile.d/conda.sh"
else
export PATH="/opt/anaconda3/bin:$PATH"
fi
fi
unset __conda_setup
# <<< conda initialize <<<
- The path
/opt/anaconda3/
to be replaced with the correct reference: usually/home/USERNAME/anaconda3/
.
The problem
Sourcing ~/.bashrc
in crontab -e
won't work (at least not on Ubuntu).
Explanation:
- On Ubuntu,
~/.bashrc
has the following (or similar) line at the beginning of the file:
# If not running interactively, don't do anything
[ -z "$PS1" ] && return
- This means that if we try to source the
~/.bashrc
file incrontab
, the rest of the.bashrc
file will not execute becausecrontab
is not running interactively (see another post on this topic). Which means that theconda
snippet mentioned above will never get executed bycrontab
even if we source~/.bashrc
.
_________ Working solution _________
The solution I have found is to copy the conda
snippet to a separate file.
1. Copying the conda
snippet from ~/.bashrc
to ~/.bashrc_conda
Copy the snippet mentioned above to another file, for example ~/.bashrc_conda
.
Ensure that:
- The user running the cronjob has permission to read this file.
- Other users cannot write to this file (security risk).
2. In crontab -e
insert 2 lines to run bash
instead of sh
and to source ~/.bashrc_conda
Run crontab -e
and add the following 2 lines before the cronjob:
SHELL=/bin/bash
BASH_ENV=~/.bashrc_conda
Explanation:
SHELL=/bin/bash
means thatcrontab
will run the cronjobs viabash
instead ofsh
(default). See post.BASH_ENV=~/.bashrc_conda
sources theconda
snippet tobash
run bychrontab
. See post and post.
3. In crontab -e
insert in the cronjob line conda activate my_env;
before the desired .py
script execution
Example of entry for a script that would execute at noon 12:30 each day within the desired conda environment:
30 12 * * * conda activate my_env; python /path/to/script.py
Notice conda activate my_env;
before the command to run the Python interpreter.
_______________
And voilà, it worked.
Any downsides?If the conda
snippet in .bashrc
gets updated by a conda
update, it will of course not be reflected in the separate .bashrc_conda
file. One may need to check for updates from time to time.
One could also to append ; conda deactivate
at the end of that cronjob, but this may be redundant.
I recently switched from canopy to Anaconda precisely to get away from having to activate an env in cron jobs. Anaconda makes this very simple, based on the PATH enviornment variable. (I'm using miniconda not the full Anaconds install but I believe anaconda should work the same way)
There are two different approaches, I've tested;
Add a shebang in your python script, main.py
#!/home/users/user_name/miniconda2/envs/my_env/bin/python
Add PATH to the top of your crontab
PATH=/home/users/user_name/miniconda2/envs/my_env/bin
Update:
Jérôme's answer and cbarrick's comments are correct. I just got burned using the above approach in a Conda env which needed pynco,
which needs the full conda environment to find proper the nco
commands, such as ncks, ncrcat.
Solved by running a bash script from cron which calls conda activate first.
Don't call sh
but bash
. source
is a bash command.
- sh scripts/my_script.bash
+ bash scripts/my_script.bash
Or just
chmod +x scripts/my_script.bash
./scripts/my_script.bash
since you added the bash shebang.