0

I am trying to run a python script in a virtual environment in a server using oarsub :

So firstly I run this command in a server name "a" : 

oarsub -l /host=1/gpu=1,walltime=2:00:00 './training_corpus1.sh'

training_corpus1.sh looks like this at the beguinning :

#!/bin/bash

cd /home/ge/ke/anaconda3/envs

source activate env

cd ~/eXP/bert

CUDA_VISIBLE_DEVICES=0,1 python training.py \
    --exp_name bert \ ...

At the beguinning, I am suppose to open my virtual environment and then run the script but I am always getting this error in the OAR.18651.stderr file :


./training_corpus1.sh: line 5: activate: No such file or directory
Traceback (most recent call last):
  File "training.py", line 18, in <module>
    from xlm.slurm import init_signal_handler, init_distributed_mode
  File "/home/ge/ke/eXP/bert/xlm/slurm.py", line 11, in <module>
    import torch
ImportError: No module named torch

Torch is located in my virtual environment , it seems that It did not open.Whenusing "conda " a thte place of "source" I get:

./training_corpus1.sh: line 5: conda: command not found
talonmies
  • 70,661
  • 34
  • 192
  • 269
kely789456123
  • 605
  • 1
  • 6
  • 21
  • Does this answer your question? [calling conda source activate from bash script](https://stackoverflow.com/questions/34534513/calling-conda-source-activate-from-bash-script) – AMC Mar 10 '20 at 22:29

1 Answers1

0

For a virtual environment and bash the activation command is

source env/bin/activate

where env is the directory of the virtual environment to activate.

PS. Let me advice you to start any script with set -e to allow fast failing on any error:

#!/usr/bin/env bash
set -e
…
phd
  • 82,685
  • 13
  • 120
  • 165
  • So I should write source /home/ge/ke/anaconda3/envs/env/bin/activate ? – kely789456123 Mar 10 '20 at 11:09
  • After `cd /home/ge/ke/anaconda3/envs` you can use relative path: `source env/bin/activate`. `env` is now a subdirectory of the current directory. – phd Mar 10 '20 at 11:10
  • it gices this : ./training_corpus1.sh: line 8: env/bin/activate: No such file or directory it seems activate does not exist in env/bin like : (env) ke@dere2:~/anaconda3/envs/env/bin$ cd activate -bash: cd: activate: Aucun fichier ou dossier de ce type – kely789456123 Mar 10 '20 at 13:28
  • `activate` must be present in a virtual environment and must be a bash script. Not sure about `conda` though. – phd Mar 10 '20 at 16:34