Turning off Spotlight indexing Mac OSX 10.6

[ChrisL]

For those of you doing NextGen bioinformatics on a Mac, you may have noticed a process called "mds" that chews up RAM (sometimes 2 GB or more), especially when working with large files. This is the Spotlight indexer and it tries to index text characters, including the bases in analysis files. While I was performing a large TopHat run, mds was using over 2 GB RAM, which was needed by TopHat, to avoid having to use virtual memory (32 GB Mac Pro).

The following command successfully turned mds off, as I don't need it on a machine used just for analysis:

sudo mdutil -a -i off

You will need an administrator level password to execute this command. The following command should turn the indexer back on, but I have not tried it:

sudo mdutil -a -i on

[drio]

Many thanks to sharing this. This was a huge problem for me too.
The global performance of the machine was severely degraded due this indexing.

[Cole Trapnell]

I just wanted to make 2 comments:

1) You probably don't need to globally turn off Spotlight indexing. Spotlight preferences includes a place where you can add folders within which mds won't do any indexing. That way, you can keep your alignments in subdirectories of the one you specify in the preferences, without losing Spotlight for the whole machine.

2) This problem is not specific to TopHat - any program that generates large text files (e.g. aligners that report SAM) will probably cause problems with Spotlight.

[ChrisL]

Correct, all files with text content get indexed by mds, SAM being but one example. I think for dedicated analysis computers turning off the indexer is the way to go as Spotlight is unlikely to be used. For Macs that act as both general purpose workstations as well as doing analysis Cole's suggestion would be the better option.