iRefIndex Maintenance

When building iRefIndex there can be a need to manage the database system and to assess whether enough disk space is available. The use of MySQL's single tablespace can lead to a very large single file in the filesystem that can appear to use most of the available space (as reported by df -h):

Filesystem            Size  Used Avail Use% Mounted on
/dev/sda1             996M  575M  370M  61% /
/dev/sda3              24G  885M   22G   4% /biotek/cn1/programs
/dev/sda8             475G  443G  8.0G  99% /biotek/cn1/storage
tmpfs                 7.9G     0  7.9G   0% /dev/shm
/dev/sda5             9.5G  151M  8.9G   2% /tmp
/dev/sda6             7.6G  3.2G  4.1G  44% /usr
/dev/sda7             1.5G  437M  941M  32% /var

The file itself will look like this (as reported by ls -lh):

-rwxr-xr-x 1 nobody nobody 440G Feb 17 13:39 /biotek/cn1/storage/mysql/var/ibdata1

The following resources describe the situation and potential solutions:

• MySQL Forums :: Database Administration :: how to shrink a MySQL database
• MySQL: Reducing ibdata1
• MySQL 5.0 Reference Manual :: 13 Storage Engines :: 13.2 The InnoDB Storage Engine :: 13.2.2 InnoDB Configuration

Unfortunately, reducing the database footprint on the disk requires substantial administrative work in single tablespace mode.