Level 2 Clean Install of Ventura Solves Deep-Rooted Problems

Originally published at: Level 2 Clean Install of Ventura Solves Deep-Rooted Problems - TidBITS

Faced with recurrent kernel panics and an inexplicable problem on the first boot after installing a minor macOS update, Adam Engst opts for a Level 2 clean install when upgrading to macOS 13 Ventura. What’s a Level 2 clean install? And did it work?

Your story sounded awfully familiar. I too have been plagued by kernel panics for some time now. They come seemingly random and in waves, sometimes a few a week, sometimes several per hour.

I first installed the OS over the drive, hoping this would straighten out the assumed bugs. This had no effect.

Then I did a level 3 clean Install. Took a long time to get back up and running, but getting rid of dead wood was worth it. The kernel panics didn’t go away though. Was I looking at a hardware defect?

I then resorted to an old utility, Onyx. This has reduced the kernel panic rate to just one or two a week, suggestive of a software cause. I now run Onyx once a week.

But the problem is not gone; Still a hardware fault? I’m not ready yet to bring my M1 MBP in for analysis and/or repair.

At least I’m not the only one having kernel panics…


Update: I just had two kernel panics in quick succession. Ran Onyx. Let’s see how long the current session lasts…

Thank you for clarifying that. I had suspected it, but I appreciate the confirmation, especially before I actually attempted it.

Panic reports are here:

Sellotape:Desktop mnewman$ cd /library/logs/diagnosticreports/
Sellotape:diagnosticreports mnewman$ ls *.panic

Older ones get moved here:



On the other hand I started out with a 2008 INTEL iMac and have installed every version of macOS right over the top of the current one, then moved from that 2008 iMac to a 2013 iMac and now a Mac Studio Max using Migration Assistant to Ventura 13.3.1. No clean installs of any level and things are rock solid.

So is it luck or just karma? Am I typical or are you the outlier?

Thankfully, I’ve never had any of these problems. How much of your article is covered in any of the Take Control books? If not all, I hope it all will be soon - just in case!

I did not have the specific problems you describe, but I wanted to restore my M1 MacBook Air and start from scratch. I followed the instructions here, Erase your Mac and reset it to factory settings - Apple Support to erase my Mac and reset it to factory settings. Then I signed in with my Apple ID. I had previously saved the files that were not in iCloud so I copied them and then reinstalled all the third party applications. It took awhile, but I am retired. Anyway it all works and some funny little things that were annoying me are gone.

I was not aware of the feature mentioned in the linked Apple article. I think it must be something new.

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Yes it is very powerful, and much easier and safer than going into Disk Utility and deleting volumes. It basically erases your -Data volume, restoring the Mac to factory state with just the SSV installed. Setup Assistant launches to enable the setup of the Data volume.
As Adam’s article says there is no need to erase a working SSV because if one byte has changed it will fail verification (which happens on every boot) and will not boot.

My first Mac was a 2006 White MacBook. After using Setup Assistant from Mac to Mac to my present 2018 Mac mini, a lot of cruft had accumulated and things got slightly quirky. About 6 months ago, after multiple backups on different drives, I did a level 3 clean install and manually copied the data files from a Home directory backup, leaving Library behind. I reinstalled apps as I needed them, which spread out the pain and left behind many old, unused apps. I keep current downloads of paid apps with registration details on a separate drive, separately backed up, so reinstalling was not much trouble.

Imported mail wound in a folder named Import under On My Mac, but the extensive subfolder structure was preserved. I forget now how I got the music over.

The only moment of panic was seeing that the new Photos library was empty. Option-starting Photos allowed me to open the old library and then to select it as the system library.

Smooth sailing ever since.

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Just to clarify, “level N clean install” is as defined in this article, right? It’s not referred to by Apple as that in any of their documentation, is it?

Have you done a RAM check? Mine passed Apple diagnostics, but I never got to the point of doing the USB stick with MemTest86.


Drat! It appears that Time Machine doesn’t back up the ~/Library/Logs folder, so I can’t go back to see what’s there.

Again, I install a vast amount more software than most people. It’s certainly uncommon for people to have these sort of problems, but if they do happen, a clean install of some level can help.

I don’t know, sorry—that would be up to Joe Kissell and the current authors. (Tonya and I haven’t had much to do with Take Control since we sold it in 2017.)

Erase All Content and Settings is a relatively new option in macOS, so I honestly didn’t even think of using it. On reflection, it would probably provide the same level erasure as reformatting the boot drive, and since macOS can’t run if there’s any drive corruption rendering the seal invalid, I think it’s safe to assume that a reformat wasn’t necessary to eliminate lurking corruption.

However you erase the current drive, the important bit is not restoring everything from backup, but bringing apps and their components back selectively. It sounds like you did that successfully as well.

Yes, these are terms I’ve coined. “Clean install” is bandied about a lot, but it really makes a difference as to whether you restore everything, just data and settings, or just data.

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I’m curious. You said you had 236 items in your Application folder and thought it a large number because your job calls for trying lots of software. My business doesn’t, but the current count in my 2018 MacMini running 12.6.5 is 268 items (from the Info box). Only four of them are 2018 or earlier – three years of TurboTax and a now-defunct web page app called Sandbox. Am I a digital pack rat, or is the count inflated by the contents of some folders in the App folder. For example, it contains the EasyDraw Folder which contains 50 items. Are they being counted as items? If I just count the number of visible apps or folders in the list, it looks there are really about 120 items.

It is the 120 you have to compare with. After a clean install you will have 35-40 Apple Applications. The rest is installed by you afterwards. I have 180. 236 is a lot!

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It’s not ~/Library/Logs but /Library/Logs.

One of the benefits of using Carbon Copy Cloner is that it backs up that sort of stuff. That saved me when I needed things like /etc/hosts and /etc/fstab.

That leaves the final ‘Nuclear’ Level Zero Option.

Performing a full restore using a second Mac and Apple Configurator which is the only truly clean installation for Apple Silicon based Macs. It also works with Intel and especially those with the T2 Security Chip. The only requirements are a second working Mac with Apple Configurator installed and a Thunderbolt3/4 USB-C data cable. Charge cables may work in some cases but would be very slow if they do work.

Revive or restore a Mac with Apple silicon using Apple Configurator

# Revive or restore an Intel-based Mac using Apple Configurator

By default Apple Configurator will grab the latest macOS release. However you can obtain a specific IPSW installer for an older macOS version. You just need to download it from the Apple CDN manually. Here is a site to help you do just that without needing to reverse engineer the CDN and read XML / JSON data to do so. This site will grab any and all IPSW images for any Apple product. You add the IPSW to Apple Configurator.

IPSW Downloads (Apple Silicon Only)

The steps to entering DFU mode effectively require very specific steps and very specific USB-C ports and will likely take multiple attempts to achieve.

Once re-installed you now have a super clean macOS factory reload in perfect condition. Create the first user account which is very special as it has the systems first secure token. All other accounts should be created with this initial account to ensure they can boot the Mac. It’s recommended you consider this account an emergency admin account. Using this account to create your primary accounts which you can make as administrators or standard users. You should never remove the initial first account. Of course, the first account can be your only account, but it’s smart to add your primary accounts and leave this one alone. It can be useful for trouble-shooting, etc.

At this point you can decide to restore from backup either with Migration Assistant or another manual method. Then decide if you wish to restore your Apps or user settings or not.

The key is to ensure you have a super clean System volume and the DFU Restore does just that. The next most important thing about restoring your data and applications is to not reintroduce the problem by restoring the problem from backup. So copying only data and not the user settings and applications might be an essential although time consuming step. You’ll need to re-install, license, activate and configure all the software.

Many people have things installed that are old and out of date. Any advanced software that uses kernel or system extensions will have compatibility issues with newer macOS releases as Apple has been making changes for years. One needs to ensure that those applications are compatible and up-to-date. It is very likely such software would require an upgrade.

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Can an older mac like my MacBook Pro (Retina, 15-inch, Mid 2015) run Configurator to restore my MacBook Pro M1? Do not need it now and hope never to, but nice to know.

Yep, @paalb is right. I was just counting the apps, not the contents of folders. Other than the /Applications/Utilities folder, pretty much all of my apps are loose in the /Applications folder. To be clear, I’m not recommending what I do! It’s generally better to keep things clean, but it’s just too hard for me. (Don’t ask what my iPhone App Library looks like, either.)

Oops, thanks! Although Time Machine seems to back up that folder, I suspect what it’s actually showing are just available snapshots, since they only go back 24 hours.

I do have a duplicate made with Super Duper that would have the files, but after a week or so of Ventura working fine, I started those duplicates again, thus overwriting the old logs.

Good to know for the future, thanks!

Good suggestion! I’d forgotten about this approach, and it’s probably overkill unless the Mac is entirely unresponsive, but it’s certainly good to know about.

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I actually have no idea how many apps are in my Applications folder because I never open it…about 99.9% of my app launches are either double clicking a doc or selecting either the doc or app in LaunchBar and hitting Return…all of my repeatedly opened apps or docs have abbreviations in LB to make it easier to type. Back many versions of macOS ago…some apps got installed in Utilities subfolder but later installers sometimes put them there, sometimes in Apps or their own folder, or sometimes are just a .dmg and you drag it wherever you want it…and sometimes they get put into user’s Application folder depending on authentication. I’ve found that some installers recently put it in some place but if you move it the app breaks which never used to happen…Topaz is an offender here as some apps are in Apps and some in Apps/Topaz…and if you move the former into the latter it won’t launch.

@paalb - Older Mac’s that do not have a T2 Security Chip nor Apple Silicon SoC CPU can just be re-installed via a bootable thumb drive installer.

Here’s how you download macOS (including older versions):

Here’s how to create a bootable installer on a flash drive:

Then on older Intel Macs you hold down the Option key when powering on and you can choose to boot from the flash drive. At that point you can go to the Utilities menu and Disk Utility and completely erase the internal storage. Then you install macOS cleanly on the disk.

Apple Configurator is more for supervising Mac’s. It’s a poor-mans MDM (Mobile Device Manager). There are unlikely to be IPSW installers for older Macs. Only the new ones and mostly Apple Silicon and supposedly any Intel w/T2 models.

Any MacBook Pro from 2018+ with Intel will have the T2 Security Chip unless it is an Apple Silicon M1/M2 in which case the security is built-in to the SoC. This hardware makes it more difficult to reload an OS from scratch. You can’t even boot external if the internal disk is missing specialized partitions. In that case the only option is using an Apple Configurator full Restore to fix it.

The question was the opposite of your reply. Can the old mac be used to restore the new?