Accessing NCI resources
Welcome to the NCI workshop for Flinders researchers wanting to access NCI resources!
Getting started
You should first create an account at https://my.nci.org.au. Then you can request an allocation for your own project or join and existing project.
Once you have an account on NCI, you can login to NCI using ssh as follows. You can also use PuTTY on Windows or the Australian Research Environment. You have to replace <username> with your username.
ssh <username>@gadi.nci.org.au
Once you are logged in, you can check the path on the login node using pwd or echo $HOME.
You can check your default project using echo $PROJECT and your default shell using echo $SHELL. $PROJECT and $SHELL are set in the file $HOME/.config/gadi-login.conf.
You can move to your scratch directory using the following command. You have to replace <project_code> with your own project code and <username> with your username.
cd /scratch/<project_code>/<username>
Similarly, you can move to your gdata directory using the following command.
cd /d/data/<project_code>/<username>
Sample job script
You can create a job script (e.g., job.sh) using any text editor such as nano or vi. A sample job script is provided below. The lines starting with #PBS are known as PBS directives. More details about PBS directives can be found here.
#!/bin/bash
#PBS -P <project_code>
#PBS -q normal
#PBS -l ncpus=16
#PBS -l mem=1GB
#PBS -l jobfs=64GB
#PBS -l walltime=01:00:00
#PBS -l wd
#PBS -l other=hyperthread
#PBS -l storage=scratch/<project_code>+gdata/<project_code>
# Your code/commands
echo "Hello World!"
Gadi commands cheatsheet
Storage allocation and usage
Check home quota
quota –s
Check the grant/usage of the project on gdata
nci_account -P <project_code>
Check how much storage you have access to on scratch and gdata through which projects
lquota
Files created by user/project
nci-files-report
nci-files-report --project <project_code>
Transferring files to/from Gadi
Upload data to Gadi from local PC
scp –r <file/folder> <username>@gadi-dm.nci.org.au:<destination>
rsync -ravPS <file/folder> <username>@gadi-dm.nci.org.au:<destination>
Download data from Gadi to local PC
scp –r <username>@gadi-dm.nci.org.au:<file/folder> <destination>
rsync -ravPS <username>@gadi-dm.nci.org.au:<file/folder> <destination>
Software
List out software applications centrally available on Gadi
module avail <software>
Load the module into your current shell environment and check
module load <software>/<version>
which <software>
List currently loaded modules
module list
Remove a module from your environment
module unload <software>
Jobs
Submit a job script.
qsub job.sh
Delete a job from the queue
qdel <job_id>
Check status of your jobs
qstat
qstat -u <username>
Check status of your jobs
qstat
qstat -u <username>
Check status of a particular job in the queue
qstat -sw <job_id>
Check CPU and memory usage the job
nqstat_anu <job_id>
Useful NCI links
Gadi Quick Reference Guide - https://opus.nci.org.au/display/Help/Gadi+Quick+Reference+Guide
PBS Directives Explained - https://opus.nci.org.au/display/Help/PBS+Directives+Explained
Compute Grant and Job Debiting - https://opus.nci.org.au/display/Help/2.+Compute+Grant+and+Job+Debiting
Queue Limits - https://opus.nci.org.au/display/Help/Queue+Limits
NCI helpdesk - https://nci.org.au/users/nci-helpdesk