Using conda activate or specifying python path in bash script?

Question

I'm running some python scripts on some Linux clusters using SGE or SLURM. I already have my conda environment set up properly using the login node. I have been writing something like

source ~/.bashrc
module purge #Kill all active modules
conda init bash
conda deactivate
conda deactivate
conda activate my_env

python my_script.py

to activate the environment properly. (I have done a lot of work to figure this out) However, I just found some example codes like

/anaconda3/envs/my_env/bin/python my_script.py

seems to do the same thing without the need for tedious deactivation and activation. Are they actually doing the same thing? If so, which would be the better practice?

Answer 1

Programmatic execution with an environment is usually better done through the conda run subcommand. E.g.,

my_slurm_script.sh

#!/bin/bash -l
conda run -n my_env python my_script.py

Read the conda run --help for details.