Frequently Asked Questions

If there are any questions cannot reslove,please don't hesitate to let us know by sending your questions to centralcluster@cuhk.edu.hk

  1. How can I check status of my jobs?
  2. Can I remote login to compute node?
  3. When will my job start to run?
  4. Can I submit multiple jobs?
  5. How can I check my disk usage and quota?
  6. How to check the reason why my job not running?
  7. How to access my file contents when using Singularity?
  8. How to pull image from 3rd party Docker repositories require login using Singularity?

How can I check status of my jobs?

In order to check status of your jobs, issue command squeue.

Can I remote login to compute node?

While you have no job running on a particular node, you are restricted from logging in the compute node. However, if your job is running on particular compute nodes.

When will my job start to run?

The Central Cluster implements the fair share policy. While the system is full occupied by jobs, user jobs with high share portion will given priority for running. But if the system is not fully utilized, jobs submitted will be dispatched free node for execution.

Can I submit multiple jobs?

Yes, you can submit and run more than one job simultaneously.

How can I check my disk usage and quota?

In order to check disk usage and disk quota of your PI group, issue command 

% lfs quota -hu your_username [/users/your_username|/project/your_pi_group|/scratch/s1/your_pi_group]

How to check the reason why my job not running?

You can check the details of status of your job by command scontrol. Below is the command line: 

% scontrol show job job_number

How to access my file contents when using Singularity?

By default, singularity will bind serval directories to the container. Those resources locate in the following directories, the container wil able to access them:

$HOME
/project
/scratch/s1
/tmp
If the resource locate on other directories or you want to bind the directories into different path, you may use -B option or environment variable SINGULARITY_BINDPATH. These options are supported by singularity run, singularity exec and singularity shell as follow: 
#/tmp will bind to /temp , /opt will bind to /opt inside container
#By -B option
singularity shell -B /tmp:/temp,/opt singularity_container.simg
          
#By environment variable SINGULARITY_BINDPATH
export SINGULARITY_BINDPATH="/tmp:/temp,/opt"
singularity shell singularity_container.simg

How to access image from 3rd party Docker repositories require login using Singularity?

All Docker repositories are support by Singularity. Just use singularity pull like docker pull command. But singularity pull command does not have login option. So you need to pass your login information by environment variables like the following: 

export SINGULARITY_DOCKER_USERNAME='username'
export SINGULARITY_DOCKER_PASSWORD='password_or_API_Key'
After that, you can run the singularity pull or singularity build command as normal.