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| Filesystems | |
|---|---|
/home | Backed up. 10 GiB fixed quota per user. |
/scratch | Not backed up, temporary files, auto purge policy applied. |
/g/data | Not backed up, long-term large data files. |
/apps | Read only, centrally installed software applications and their module files. |
$PBS_JOBFS | Not backed up, local to the node, I/O intensive data. |
massdata | Backed up, archiving large data files. |
○ man mdss | Read manual of all `mdss` commands |
○ mdss dmls -l | List files with status: online/in disk cache(REG), on tape(OFF), or both (DUL) |
○ mdss put/get | Put or retrieve files from mdss |
| Accounting | |
nci_account | Display compute grant and usage |
quota -s | Display storage grant and usage on /home |
lquota | Display storage grant and usage on /scratch and /g/data by project |
nci-files-report -f <fs> -g <grp> | Report data usage on filesystem <fs> owned by the project <grp> by (project folder, user) |
| Module command | |
module avail | List all available modules |
module load <app>/<ver> | Load the module for application <app> version <ver> |
module unload <app> | Remove the module for application <app> from the current shell |
module show <app>/<ver> | Show what the module <app>/<version> does |
module list | List all modules loaded in the current shell |
| PBSPro command | Run commands in this section with the frequency < 0.2 Hz |
qsub job.sh | Submit job defined in the submission script job.sh |
qdel <jobid> | Delete the job with jobID <jobid> |
qstat -swx <jobid> | Display the job status in the queue with comment |
qstat -fx <jobid> | Display full job status information |
qps <jobid> | Take a snapshot of the process status of all current processes in the running job |
qcat [-s/-o/-e] <jobid> | Display [submission script/STDOUT/STDERR] of the running job |
qls <jobid> | List contents in the folder $PBS_JOBFS |
qcp <jobid> <dst> | Copy files and directories from the folder $PBS_JOBFS to the destination folder <dst> |
| PBSPro Directives | |
#PBS -P <prj> | Project for job debiting, /scratch project folder access and data ownership |
#PBS -q <queue> | Submit the job to the queue <queue> |
#PBS -l ncpus=<xx> | Request <xx> CPU cores |
#PBS -l ncpusstorage=<scratch/prj1+gdata/prj2+massdata/prj3> | Storage needed to be available inside the job. massdata is only available in copyq jobs. |
#PBS -l ngpus=<yy> | Number of GPUs, ncpus has to be 12 x ngpus and the job has to be submitted to `gpuvolta`. |
#PBS -l walltime=<hh:mm:ss> | Max walltime the job would run |
#PBS -l mem=<10GB> | Memory allocation |
#PBS -l jobfs=<40GB> | Disk allocation on compute/copyq node(s) |
#PBS -l software=<app1,app2> | Licenses required |
#PBS -l wd | Start the job from the directory in which it was submitted |
#PBS -W depend=beforeok:<jobid1,jobid2> | Set dependencies between this and other jobs. |
#PBS -a <YYMMhhmm> | Time after which the job is eligible for execution |
#PBS -M <email@example.com,email2@anu.edu.au> | List of receivers to whom email about the job is sent |
#PBS -m <aben> | Email events. `a` for abortioin, `b` for begin, `e` for end, `n` for none |
| Useful URLs | |
| User & Project Management | my.nci.org.au |
| Knowledge Base | opus.nci.org.au |
| Training Course | learning.hpc-australia.org.au |
| Service Desk Portal | help.nci.org.au |
| License Live Status | usersupport.nci.org.au/license-status.html |
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