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While reviewing the Sitecore logs I'm seeing the following:

ManagedPoolThread #13 15:25:29 INFO Trace: Warning: Counter 'Sitecore.Caching\Cache Clearings / sec' does not exist on this server. Using temporary internal counter instead. ManagedPoolThread #2 15:25:29 INFO Trace: Warning: Counter 'Sitecore.Caching\Cache Hits / sec' does not exist on this server. Using temporary internal counter instead. ManagedPoolThread #3 15:25:29 INFO Trace: Warning: Counter 'Sitecore.Caching\Cache Misses / sec' does not exist on this server. Using temporary internal counter instead. [...] ManagedPoolThread #12 15:25:38 INFO Trace: Warning: Counter 'Sitecore.Security\Access Denied / sec' does not exist on this server. Using temporary internal counter instead. ManagedPoolThread #12 15:25:38 INFO Trace: Warning: Counter 'Sitecore.Security\Access Granted / sec' does not exist on this server. Using temporary internal counter instead. ManagedPoolThread #12 15:25:38 INFO Trace: Warning: Counter 'Sitecore.Security\Access Resolved / sec' does not exist on this server. Using temporary internal counter instead. ManagedPoolThread #12 15:25:38 INFO Trace: Warning: Counter 'Sitecore.Security\Modify Requests / sec' does not exist on this server. Using temporary internal counter instead. ManagedPoolThread #12 15:25:38 INFO Trace: Warning: Counter 'Sitecore.Security\Programmatic Disabling / sec' does not exist on this server. Using temporary internal counter instead. [...]

The application pool user is within the Performance Log Users group, so that doesn't seem to be the issue.

It appears that there is information on how to install performance counters manually for Sitecore 7.5+, but looking at the files it doesn't appear the new Sitecore 8/9 counters are present. (These instances were all upgraded from 7.x and lower.)

What is the best way to create the missing performance counters?

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You can easily create all the missing performance counters using the old skool sitecorecounters tool which you can find in the SDN archive. https://doc.sitecore.com/SdnArchive/Products/Sitecore%20V5/Sitecore%20CMS%206/Update/6_2_0_rev_100104.html You can find a list of all the necessary counters in the config files of Sitecore but there are lots of ways to get to that list.

Best regards, Alex

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Based upon testing, it appears using the Errors when accessing performance counters KB article referenced in the question is still the current solution, even for 9.x.

Using Solution 1's link to Sitecore log filling up with warnings includes a download for Sitecore 7.5 or later that is still current.

Running that version of the zip file's executable as an administrator appears to have installed all of the necessary counters, after it purged all of the older versions.

Note that since it deletes the previous performance counters you may want to make sure you have the data that you need before running the executable.

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