File system very slow; applications appear normal

Consider downloading and running this little "discovery" utility, Etrecheck. It changes NOTHING. Etrecheck was developed by senior contributor here, and uses system calls to collect often-needed information.

it contains little tests for speeds of devices, CPU utilization, memory usage, energy usage and a digest of recent problems, in one easy to use package. it does not even need to be Installed. Because less can be learned when your Mac is running great, best time to run is when your problems are actually occurring, if possible.

if you follow the directions faithfully, its report (pre-laundered of all personally-identifiable information) can be "Shared" to the system ClipBoard, then Pasted into an ‘Additional Text’ window in a reply on the forums.

How to use Etrecheck pro for free

http://etrecheck.com

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Are you moving files from the system disk to the HDD? What file system is on this HDD, and HDD model, and what types of files do you usually move (large ones in gigabytes or thousands of small ones)? If your external drive is exFAT, this could be a big problem. In any case, I recommend checking the SMART status of your disk, as it may be degrading (smartmontools, Disk Drill, DriveDX, etc.).

By far the easiest way to cause poor performance, instability, overheating and crashing is to install ANY third-party speeder-uppers, Cleaners, Optimizers, or Virus scanners, or a VPN that you installed yourself. The main reason is that they are relentless in scanning your files, non-stop, looking for virus-like patterns in Everything, or looking for files that have changed. When completed, they do it all again.

¿are you running anything like that?

you also have. a lot of stuff "phoning home" while scanning all your files for any changes. Any third-party file sync-er will be much slower and much more resource intensive than iCloud sync-ing, because it ignores the Mac File System Event store and feels obligated to look at every file to see if it has changed.

You show OneDrive and DropBox launching at login and running continuously. the preferred method is launch when needed, and quit when sync is completed.

also, it appears Day One is constantly 'on the phone' sending stuff to/from the web. That slows everything down.

If rebuilding the Spotlight Index does not resolve the problem, go to  > System Settings > Siri & Spotlight, and uncheck PDF Documents.

It does take some time to complete the index and sometimes syncing with another source such as OneDrive will compound the problem if the files are constantly changing. If you can stop OneDrive from syncing then that may be another troubleshooting step.

I am guessing you have quite a bit of PDF's and it appears that there is trouble indexing them which the OS will do after an update. I suggest reindexing spotlight by following this support article:

Rebuild the Spotlight index on your Mac - Apple Support

How much room is left on the startup drive? If you have completely filled the drive, that could cause problems.

Without providing the free EtreCheck report as already been suggested, there is no way anyone will be able to tell what is installed on your computer that is causing the slowdown. The report also includes information about your drive speed and processes that are consuming too many resources. To avoid just throwing out guesses of any possible cause or software conflict, post the report and you are more likely to get the answer quickly.

Get and run the free version of EtreCheckPro on your Mac Studio, from > https://etrecheck.com/en/index.html

Then post your EtreCheckPro Report, as per > How to use the Add Text Feature When Post… - Apple Community

you said no VPNs, but Etrecheck says this one:

  VPNs:

        NetworkProtectionAppExtension - /Applications/DuckDuckGo.app/Contents/Library/LoginItems/DuckDuckGo VPN.app

Grant Bennet-Alder wrote:

I am very surprised to see TWO processes with the same name, one from Apple, one Unsigned:

Top Processes Snapshot by Energy Use:

    Process (count) Energy (0-100) (Source - Location)

    CGPDFService (10) 15 (Not signed)

    CGPDFService (21) 11 (Apple)

    mdworker_shared (28) 6 (Not signed)

Yes, I also saw that mdworker_shared shows up as Not Signed and it is usually signed by Apple for Spotlight indexing.

1. Run Apple Diagnostics for your Mac.

2. Check the system disk for file file-system errors.

No need to create a PDF. Just click the Share Report button on the top of that page and Copy to Clipboard. Once that is done create a post here and choose the Additional Text (looks like a page icon) option to post.

I am very surprised to see TWO processes with the same name, one from Apple, one Unsigned:

Top Processes Snapshot by Energy Use:

    Process (count) Energy (0-100) (Source - Location)

    CGPDFService (10) 15 (Not signed)

    CGPDFService (21) 11 (Apple)

    mdworker_shared (28) 6 (Not signed)

    WindowServer 6 (Apple)

    mds_stores 4 (Apple)