HPC-Job-Scripts

HPC Job Scripts for Particle-in-Cell codes

General Naming Convention

<HPC name>_<CODE name>.sh

e.g. saga_ptetra.sh, a job script for PTetra code on SAGA HPC

Special Example

1. pbs_script.sh, a job script for generic code on PBS system
2. bashrc, a Bash shell script with configuration specially designed for HPC systems with proxy configuration

Steps to prepare you machine seamlessly work with HPC systems

STEP:1 Configure you SSH

Edit .ssh/config and the following lines for HPC SAGA

Host saga
    HostName saga.sigma2.no
    Port 22
    User username
    ForwardAgent yes
    ForwardX11Trusted yes
    ForwardX11 yes
    ServerAliveInterval 240
    ServerAliveCountMax 100

NOTE: Replace username with your own and add many configuration as you need just copying it. Remember to change the HostName.

WARNING: If you are doing this for the first time, you may need to manually create this .ssh/config file.

STEP:2 Passwordless SSH

ssh-copy-id installs an SSH key on a server as an authorized key.

ssh-copy-id saga

NOTE: It will ask you to enter the login password for the first time.

WARNING: If you are doing this for the first time, you may need to generate an SSH key. Use the ssh-keygen tool that comes as a part of OpenSSH. This tool generates public and private key files stored in the ~/.ssh directory. Check more details here.

HPC commands (SAGA/FRAM)

General

dusage: File quota for current user and the project

cost --project=<projectnumber> -d: File quota for current user and the project. Make sure to replace the with your own.

JOB Management

sbatch <jobscript>.sh: Submit a job. Make sure to replace the with your own.

squeue -u <username>: View the job queue of a specific user. Make sure to replace the with your own.

scancel <jobID>: Cancel a job with its JOBID. Make sure to replace the with your own.

All about Modules

Module represents the avialable softwares/libraries pre-installed in the system. Instead of installing them locally, it is advised to load them while running or compiling a code.

module avail: List of all possible softwares/libraries in the system.

module spider <keyword of specific software/lib>: List all possible version of that module. e.g. module spider anaconda

module load <software/library name>: Load a specific software/library. e.g. module load Anaconda3/2019.07

module list <software/library name>: List of loaded modules.

module purge: Unload all the modules from your current session.