Helix/Filesystems

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1 Overview

The cluster storage system provides a large parallel file system based on IBM Spectrum Scale for $HOME, for workspaces, and for temporary storage via the $TMPDIR environment variable.

$HOME Workspaces $TMPDIR
Visibility global global local
Lifetime permanent workspace lifetime batch job walltime
Quotas 200 GB 10 TB none
Backup no no no
  • global: all nodes access the same file system.
  • local: each node has its own temporary file space.
  • permanent: files are stored permanently.
  • workspace lifetime: files are removed at end of workspace lifetime.
  • batch job walltime: files are removed at end of the batch job.

2 $HOME

Home directories are meant for permanent storage of files that are kept being used like source codes, configuration files, executable programs. There is currently no backup for the home directory. The disk space per user is limited to 200 GB. The used disk space is displayed with the command:

homequotainfo

3 Workspaces

Workspace tools can be used to get temporary space for larger amounts of data necessary for or produced by running jobs. To create a workspace you need to supply a name for the workspace and a lifetime in days. The maximum lifetime is 30 days. It is possible to extend the lifetime 10 times.

Command Action
ws_allocate -r 7 -m <email> foo 10 Allocate a workspace named foo for 10 days and set a email reminder 7 days before expiring.

Important: You should add your email address and a relative date for notification!

ws_list -a List all your workspaces.
ws_find foo Get absolute path of workspace foo.
ws_extend foo 5 Extend lifetime of workspace foo by 5 days from now.
ws_release foo Manually erase your workspace foo.
ws_send_ical -m <email> foo sending a .ical calendar entry for reminding workspace expiring

If you plan to produce or copy large amounts of data in workspaces, please check the availability. The used and free disk space on the workspace filesystem is displayed with the command:

workquotainfo

3.1 Restoring expired Workspaces

At expiration time your workspace will be moved to a special, hidden directory. For a short period of time you can still restore your data into a valid workspace. For that, use

ws_restore -l

to get a list of your expired workspaces, and then restore them into an existing, active workspace restored_ws:

ws_restore <deleted_workspacename> restored_ws

NOTE: the expired workspace has to be specified using the full name as listed by ws_restore -l, including username prefix and timestamp suffix (otherwise, it cannot be uniquely identified). The target workspace, on the other hand, must be given with just its short name as listed by ws_list, without the username prefix.

NOTE: ws_restore can only work on the same filesystem! So you have to ensure that the new workspace allocated with ws_allocate is placed on the same filesystem as the expired workspace. Therefor you can use -F <filesystem> flag if needed.

3.2 Linking workspaces in Home

It might be valuable to have links to personal workspaces within a certain directory, e.g., the user home directory. The command

ws_register <DIR>

will create and manage links to all personal workspaces within in the directory <DIR>. Calling this command will do the following:

  • The directory <DIR> will be created if necessary
  • Links to all personal workspaces will be managed:
    • Creates links to all available workspaces if not already present
    • Removes links to released workspaces

3.3 Troubleshooting

If you are getting the error:

Error: could not create workspace directory!

you should check the localesetting of your ssh client. Some clients (e.g. the one from MacOSX) set values that are not valid. You should overwrite LC_CTYPE and set it to a valid locale value like:

export LC_CTYPE=de_DE.UTF-8

To make this change persistent you can add this line also to your .bashrc file.

A list of valid locales can be retrieved via

locale -a

4 $TMPDIR

The variable $TMPDIR provides file space for temporary data of running jobs. Each node has its own $TMPDIR. The data in $TMPDIR become unavailable as soon as the job has finished.

5 Access to SDS@hd

It is possible to access your storage space on SDS@hd directly on the bwForCluster Helix in /mnt/sds-hd/ on all login and compute nodes.