HPC Job Scripts for Particle-in-Cell codes
<HPC name>_<CODE name>.sh
e.g. saga_ptetra.sh
, a job script for PTetra code on SAGA HPC
pbs_script.sh
, a job script for generic code on PBS systembashrc
, a Bash shell script with configuration specially designed for HPC systems with proxy configuration
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.
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.
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.
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.
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.