Filesystem full System Data at 950GB

My M1 MacBook Pro is the household backup server. It has a batch of spinning disks attached to it.

From time to time it makes me regret running MacOS. Today is one of those days. I’ve rebooted the machine several times today and forced Spotlight to reindex once.

The SSD is 1TB, the file system reports that there is ~2GB free with another 70MB purgeable.

Looking from the root of the harddrive none of /Applications /Library /Users or /System has more than handful of GBs.

I really wish this thing was set and forget.

IMO, you need a minimum of 10% free space on your internal drive for normal operations. YMMV

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Agreed - however this is a backup computer only. This “used” space is phantom. I can’t find it.

What happens if you try make a large file? E.g. mkfile 10g in Terminal.

I assume you’re using a tool to look at the whole disk like Daisydisk?

Any other users logged into the the system or with a login to the system which may be taking space up (I know it’s a backup server, but historically it may not be)

If it was a cacheing issue, a reboot would provide a lot of space?

I cannot but recommend DaisyDisk or GrandPerspective, well worth their money. Sometimes ~/Library/Application Support, ~/Library/Caches or similar places can be left with a lot of cruft even after uninstalling the application. Tried Docker or VMWare fusion? You might have big disk images lying around. Used an AI based transcription tool? You might have downloaded models. Also, servers with long uptimes may have consumed swap space (no idea how to recover that without rebooting). And finally, machine longevity means logs, caches, diagnostic reports, whatever can be kept around not in your user folder but in the system partition. Onyx or similar tools are your friends to clean up this kind of stuff. For everything else, Grand Perspective or Daisy Disk.

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If you’re comfortable on the command line, you can try the free (and open source) mole to clean up your drive:

If you’re not, they also have a paid ($19 lifetime) desktop app with a free trial:

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Tagging @geoffaire as well. Both GrandPerspective and command line tools run into insane problem prompting me for permission to look at other apps files. I might have clicked allow 50 times.

I ran the command line tool under sudo and still got bombarded with permissions. Worse when you get Grand Perspective to finish it reports on the external drives as well. Making it impossible to what is true.

Two things that seem interesting:

  • Spotlight decided to index one of the backup volumes. Having disabled that and done ‘sudo mdutil -E’ - 100 times nothing has changed.
  • Looking at the root level of with the four folders (Applications; Library; System; Users) there isn’t even 50GB used across all of them.

Tomorrow I will try detaching the external disks, Safe Mode, @rob command line utility and possible sacrificing a rubber chicken. In who knows what order.

I appreciate the support I get from my friends on this forum. (Thanks to @cornchip and @WayneG as well. Too tired to do individual reponses.)

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Please also check in disk utility whether you have some local Time Machine backups piling up. I had this issue once with deprecated back up containers. after I deleted them I didn’t have any disc space issues anymore. If your MacBook is used for backup only anyway, I suspect that Time Machine on that system wouldn’t be necessary for you?

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No Time Machine running.

In the end I’m doing a repave which seems silly, but likely easier.

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Yes, that’s the sorry state of macOS security grants. As the file scanning tool tries to traverse some special directories, it triggers the macOS security policies. You can give it Full Disk Access permission, but when it tries to access, for example, ~/Library/MobileDocs then it will trigger iCloud Drive access, which is a different grant.

The only good news here is that it only happens once, next runs should not request the million permissions again.

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Even better news. I repaved the whole machine.

The only strangeness was the CCC couldn’t speak to it at first. I tried ssh to get to the machine, was told it was untrustworthy. I said trust the remote Mac. Boom it worked.

So in the end I have no idea what happened. I worked around and didn’t solve.

I genuinely appreciate the efforts of everyone here to make it work.

Danke

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That’s usually the best move :stuck_out_tongue: