Utilities

MetaCentrum offers various utilities on frontends and compute nodes.

Usage of these utilities is not necessary to get full-featured MetaCentrum services. However, it may make the work on the CLI and with the infrastructure easier.

Go to scratch

• Command go_to_scratch automatically changes (redirects) the directory from a frontend server to the scratch of the used compute node
• Usage is go_to_scratch [job_ID]

  user_name@frontend:~$ go_to_scratch 12345
  user_name@compute_node:/scratch/user_name/job_12345.pbs-m1$

• See more on how to get job ID

• go_to_scratch command works only 24 hours after the calculation is done or terminated. After this period, the user needs to use an ssh to log in to the compute node and the cd command for navigation to the scratch directory.

  user_name@frontend:~$ ssh compute_node
  user_name@compute_node:~$ cd /scratch/user_name/job_ID.pbs-m1

Check local quota

• If you encounter the message “exhausted root filesystem quota” on a specific node, use the check-local-quota command to diagnose the issue. This error typically occurs when your jobs generate large output (.OU), error (.ER), or temporary files in directories like /var/spool or /tmp.
• Usage: Access the node via SSH

  $ ssh novak@turin28.metacentrum.cz

  Run the following command to view files consuming your tmp filesystem quota:

  $ check-local-quota

  Inspect and manage files: If the listed files contain valuable data, copy them to /storage. Once copied, remove the unnecessary files or directories to free up space:

  $ rm file_XX
  $ rm -rf directory_XX

• See more on FAQ/No space left on device