Can I clear BioFormatsCache to manage memory?

Hello OMERO team,

We are hosting OMERO on a cloud server with 5TB of space. We have encountered the issue of running out of storage space as a result of importing a large dataset a few weeks ago. The dataset was imported in-place so as to minimize duplication and conserve resources, but it appears that a large chunk of it is being stored in a cache or that temp file generation is using a lot of space.

After digging around a bit, it looks like the folder omero/data/BioFormatsCache is using a lot of storage. Is this where images are cached (or general temp files are stored)? If so, can I clear its contents to free up space?

Lastly, is there a way to limit the size of the cache to prevent this issue in the future?

Many thanks in advance,

Ashley

Hi Ashley,

BioFormatsCache is used to cache the metadata in files to speed up accessing the image data. You can delete the directory, but it’ll be re-generated overtime. How large are the largest files in your cache? And what file format do they represent? Would you mind running the command from Question on OMERO's "BioFormatsCache" directory - #3 by ehrenfeu to get a histogram of all the file sizes?

Cheers,
~Josh

2 Likes

Hi Josh,

Sorry for the delayed response, I must’ve missed the notification of your reply.

Our files are TIFF and SVS, the largest of which are up to 8GB each (I’m unsure if these ones are cached though). The histogram of file sizes is as follows:

     32768 132
    131072 883
    262144 1110
    524288  89
   1048576 256
   2097152  54
   4194304   1

We also noticed that the Pixels directory was taking up the bulk of the space (significantly more than the BioFormatsCache directory) and cleared these files in an effort to free up storage. Will these be regenerated as well?

Cheers,
Ashley