Gekko / Unix

CommonUnixCmd.md

Files and folder management

Size of a folder

du -sh folder

Find text in files

grep "Dio" . -R

Count the number of files recursively

find runs/ -type f -name '*_VEI4_*.tif' | wc -l

Cluster

Delete all jobs from a given user

qselect -u sbiasse | xargs qdel

GekkoGPU.md

Setting up GPU on Gekko

Setup

• qsub interactive mode

qsub -q gpu8 -P eos_susanna.jenkins -l select=1:ngpus=1 -I

• Check if GPU access

nvidia-smi

• Load conda

module load anaconda2020/python3
eval "$(/usr/local/anaconda3-2020/bin/conda shell.bash hook)"
conda activate ML

Check usage

ssh hostname
top
nvidia-smi

Bashrc

alias get1gpu='qsub -q gpu8 -P eos_susanna.jenkins -l select=1:ngpus=1 -I'

Find host

qstat -f 655465 | grep hpc-

Rsync.md

The parameters in detail:

-h: human readable numbers -v: verbose -r: recurse into directories -P: --partial (keep partially transferred files) + --progress (show progress during transfer) -t: preserve modification times