Blogs (Useful commands)

Linux OS Useful Commands

List all directories with size:

du -sh *

Find all files containg a string ‘pathlib” and ending with “.py”, for example:

find . -name '*.py' -exec grep -H 'pathlib' {} +

Join two files vertically:

awk 'NF' file1 file > result

Move some particular files from one directory to another using AWK:

ll | awk -F' ' '{if($5<=20 && NF>=9) {cmd="mv "$9" ../backup/"$9; system(cmd) } }'

Choose the first row and then print the parts (sed and AWK):

sed -n '1p' /*/*/COVID21_Expansion_all.mat | awk -F ' ' '{for(i=1;i<=NF;i++) print i":"$i; }'

ln -s source_file new_file

Split a files into parts:

split -l 50000 fused-run/combsum_runs fused-run/

Install softwares in a folder:

easy_install --prefix=$HOME/local package_name

Install a software package in linux (Configure, Make, and Make Install):

./configure --prefix=<instalation directory>


make install

Install with a configuration file but cmake list

mkdir build

cd build

cmake .. --DCMAKE_INSTALL_PREFIX=<instalation director>

Show the permission mode of a file

stat -c %a

Change permission as (full permissions for the owner, read-only for the group, and nothing for the other users)

chmod 740

Slurm cluster commands

Slurm control a job:

scontrol show job jobid(#xxxxx)

Show the available resources:

sinfo --Node -o %N:%C

Working with Git

Initiate a git project:

git init

Add file(s) to staging for committing:

git add <filename>

git add --all #all files and folder


git commit -m "message"

Push to a remote repository:

git remote add origin

git push -u origin master

Pull from a remote repository:

git pull

Useful R commands

Update all R package:

update.packages(checkBuilt = TRUE, ask = FALSE)

Virtual environment for Python

Create a virtual environment:

python3 -m venv env_name

Add a virtual environment to the jupyter:

pip install ipykernel

python -m ipykernel install --user --name env_name --display-name "env_name"

List all packages installed in the virtual environment to requirements.txt file:

pip freeze requirements.txt

Create a virtual environment using Conda:

conda create -y --name py37 python==3.7

Activate a virtual environment using Conda:

conda activate py37

Install packages in a virtual environment using Conda:

conda install --force-reinstall -y -q --name py37 -c conda-forge --file requirements.txt

Deactivating a virtual environment using Conda:

conda deactivate

Working with Singularity

Create a singularity image from a recipe file:

sudo singularity build growl-llo-world.sif recipe_file

Executing a Singularity image:

singularity shell /logiciels/containerCollections/CUDA11/pytorch-NGC-20-06-py3.sif

conda create -n env36tc11 python=3.6

source activate env36tc11

Docker container

A few useful commands

To list existing Jupyter virtual environments

jupyter kernelspec list

To list existing conda environments

conda env list

To remove conda environment

conda env remove -n ‘environment_name’

To remove the environment from Jupyter

jupyter kernelspec uninstall ‘environment_name’