iRefIndex Maintenance
From irefindex
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.