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I want to have a cron job execute a python script using an already existing anaconda python environment called my_env. The only thing I can think to do is have the cron job run a script called my_script.bash which in turn activates the env and then runs the python script.

#!/bin/bash
source activate my_env
python ~/my_project/main.py

Trying to execute this script from the command lines doesn't work:

$ sh scripts/my_script.bash
scripts/my_script.bash: 9: scripts/my_script.bash: source: not found

What do I need to do to make sure the proper environment is activated. Its ok to explain it to me like I'm 5.

Anders_K
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stoebelj
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9 Answers9

23

I recently switched from 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 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.

Eric Bridger
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  • I implemented your solution in Ubuntu 16 and successfully got Anaconda to run. However, when trying to import PANDAS package in the python script that is run, I get an [Errno 2] No such file or directory. Any thoughts as to why? My bash command setup is pretty straightforward. `PATH=/home/dev/anaconda3/bin` `python /home/dev/AUTOSIFT/script.sh` – Adestin Apr 13 '17 at 17:36
  • Don't really understand your question. script.sh is not a python script. Is this a cron job? Perhaps you need to first do a conda install pandas. – Eric Bridger Apr 15 '17 at 03:09
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    A shell command triggers a python script. I figured this out though. The problem was that the .sh needed a PATH variable set when it runs. – Adestin Apr 16 '17 at 04:21
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    Some packages may register scripts to be run upon activation. Activation also sets environment variables that some packages may depend on. Therefore you should always activate your env with `source activate`. Following this answer may cause problems when using packages like `proj4` or `cartopy`. – cbarrick Sep 30 '17 at 21:04
  • @cbarrick, what would you suggest then? – rwb Mar 08 '18 at 11:05
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    Within the cron job, you should `source activate` (or `conda activate` in the new 4.4 release). This will setup the path _and_ run the activation scripts at once. – cbarrick Mar 09 '18 at 22:33
  • @Adestin perhaps you need to add `:/usr/bin:/bin` to the end of your `PATH` to ensure access to system utilities and libraries (note that `$PATH` doesn't work in a crontab file!). I guess pandas will look for other OS commands/libraries than python, and with the PATH truncated as you have, it won't find them. (**this is an edit to a previous erroneous comment, now deleted**) – drevicko Jul 10 '18 at 14:40
20

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 opens bash interactively. The snippet allows the user to run conda commands (ie conda activate my_env) from bash.

  • 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 in crontab, the rest of the .bashrc file will not execute because crontab is not running interactively (see another post on this topic). Which means that the conda snippet mentioned above will never get executed by crontab 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 that crontab will run the cronjobs via bash instead of sh (default). See post.

  • BASH_ENV=~/.bashrc_conda sources the conda snippet to bash run by chrontab. 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.

Jean Monet
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17

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.

Jérôme
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  • Is there an update to this, now that `conda activate my_env` is preferred over `source activate my_env`? I'm having trouble... – Dustin Michels Mar 14 '19 at 22:56
  • I don't use conda. I suppose you can use either sh or bash, then. – Jérôme Mar 15 '19 at 08:51
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    Figured it out. In my bash script, I run `source /home/ubuntu/miniconda3/bin/activate` then `conda activate my_env`, vs. the `source activate my_env` in the original script. – Dustin Michels Mar 15 '19 at 16:47
8

In my case, I got this error when I ran this line of shell script: source activate my_env

activate: No such file or directory

So I changed source activate my_env to source /path/to/conda/bin/activate my_env. Then it starts working.

Youngmin Kim
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2

Use a full path to conda

A simple solution that worked for me was to specify a full path to conda in the crontab entry, and to use the conda run -n <env> option to execute the command in the required environment. In my case I wanted to launch a command on start up, so my crontab entry looked like this:

@reboot ~/miniconda3/bin/conda run -n <env> <command>

where <env> and <command> are substituted according to your own requirements.

James
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As of May 2022, I just use a .bat in Windows 10 to activate myenv and then start my localhost or whatever script you need:

@echo off
set CONDAPATH=C:\Users\MyName\anaconda3
set ENVNAME=myenv
if %ENVNAME%==base (set ENVPATH=%CONDAPATH%) else (set ENVPATH=%CONDAPATH%\envs\%ENVNAME%)
call %CONDAPATH%\Scripts\activate.bat %ENVPATH%

call cd /d d:/mysite
python manage.py runserver 0.0.0.0:8000
Alfred Wallace
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0

This approach could be a bit simpler and more concise in some cases:

  1. find the path of your conda environment

    conda env list

  2. add this as "PATH" on top of the crontab file:

    PATH=/Users/your_user_name/opt/anaconda3/envs/your_env/bin

For more details check this tutorial (Source)

sivi
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0

I think conda has changed, and so none of these solutions work for me anymore, other than the one posted by @James to specify the full path to conda within crontab.

However, sometimes I want to run a full bash script from crontab, and activate a conda environment throughout that script. For that, the solution which worked was to source conda.sh, as posted by @effecor here: https://stackoverflow.com/a/65183109/1676378.

For me, this means adding the following line to the top of my bash script that is called by cron:

source /home/chris/miniconda3/etc/profile.d/conda.sh

Your conda.sh may be located somewhere else.

The underlying issue is explained here: https://github.com/conda/conda/issues/7980 As nehaljwani writes: "Functions are not exported by default to be made available in subshells."

cxrodgers
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0

U just need to add PATH and use conda run -n command

PATH=/root/miniconda3/envs/my_env/bin:/root/miniconda3/bin:/root/miniconda3/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin

5 0 * * * conda run -n my_env python ~/my_project/main.py

easy solution

Олег Кирьянов
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