Unix filesystem

As a user of the NBI UNIX system you could possibly access as much as 4 different file systems.

1. Home directory.

This is where you start after a successful login. The path to your home directory is /home/<group>/<userid> . On two machines, alf.nbi.dk and afs.nbi.dk, it may be displayed differently for some diffuse historical and technical reasons. The name you type or refer to should always be the one written above.
  The usage is limited by a quota that is adjusted according to your needs. Store only important files here, not data or temporary downloads for which we have two large scratch disks (see below). Non-physics multimedia and music files are absolutely forbidden and may be removed without notice.
  Your home directory is backed up every night. The process starts at 7 pm. Lost files can normally be restored to a version from the day before or earlier. Files created the same day you lost them are obviously not backed up and can consequently not be restored.
  Requests for files to be restored from backup should be sent by email to it-support@nbi.ku.dk. Carefully state the full directory path(s) and name(s). Also give as precise as possible an indication of when the file was changed the last time.

2. Scratch disks

You should use the scratch disks for everything that does not need to be backed up. Examples are data files, verbose output files, debugging output, temporary downloads etc.
  The present 2 scratch disks have a capacity of 2 TB and 1.5 TB resp. Hardware-wise they are on a RAID 5 disk system, thus providing reasonable but not full physical security. There are no disk quotas. However, the usage is checked from time to time. The owners of files that have not been accessed recently are notified and asked to remove them. If there is no reaction such files may be deleted by the management.
  The scratch disks are mounted at /scr and /scrx resp. They contain one subdirectory for each computer group. You should create and use a subdirectory in your group directory with the same name as your userid. You can use the following procedure to start:
This will display your home directory in the form /home/group/userid . Your scratch directories will therefore normally be /scr/group/userid and/or /scrx/group/userid . Exceptions from this rule are groups of the form fys-* or gfy-* which should use fys and gfy resp. as the group below. If necessary you can create these directories with
mkdir /scr/group/userid
mkdir /scrx/group/userid
Note: The scratch disks are automounted. This means that you have to access something on the disk before you can "see" it. Thus, often
ls -al /scr
displays an empty directory, while e.g.
ls -al /scr/biophys
forces the disk to be mounted and then displays the contents of the directory.

3. Local disks

On most Linux machines there is free capacity on the local disk. This is sometimes used for private or group data. It seems often attractive to use surplus disk space this way, but it is not recommended. Instead you should strive at using the scratch disks, which provides easier administration and a better structure.

4. /tmp file system

All UNIX machines have a file system or directory named /tmp . This is used by compilers, editors, mail programs etc. to store temporary files. You should never use this file system on your own initiative. If it is filled up, crucial programs may stop to work.
Last modified: Thu Feb 21 16:17:32 MET 2013
Björn S. Nilsson