'Using conda activate or specifying python path in bash script?
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?
Solution 1:[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.
Solution 2:[2]
When you activate an env, it just changes the python executable to /anaconda3/envs/my_env/bin/python instead of the system's python executable /usr/bin/python in layman terms.
A bertter approach will be to use conda's built in method conda run -n env_name script.py.
Sources
This article follows the attribution requirements of Stack Overflow and is licensed under CC BY-SA 3.0.
Source: Stack Overflow
| Solution | Source |
|---|---|
| Solution 1 | merv |
| Solution 2 |