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My entry level MBP has a similar sequential read speed as my MP 6,1, which is about 1,350 MB/s. Its write speed is actually much worse at only 450MB/s. However, when starting Anaconda Navigator app, this MBP takes 10 seconds while MP 6,1 takes 21 seconds.

I am wondering if I need to tune/clean up my Mac Pro? Or if it can be done at all?
It's difficult to find a problem with an install without having a clean starting point for comparison. You have to compare your Mac Pro, taking a base point from your MBP don't make much sense since it's a very different Mac.

Make a clone of your Mac Pro disk, fully erase your SSD removing the containers then the partition/etc, then do a clean install and check if you have better opening times.
 
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Make a clone of your Mac Pro disk, fully erase your SSD removing the containers then the partition/etc, then do a clean install and check if you have better opening times.

The new (1 month old) 2TB Samsung SSD on my Mac Pro was formatted and Catalina OS installed from scratch. Then apps and files were restored from the Time Machine backup. Are you suggesting re-installing each app one by one? Thanks.
 
The new (1 month old) 2TB Samsung SSD on my Mac Pro was formatted and Catalina OS installed from scratch. Then apps and files were restored from the Time Machine backup. Are you suggesting re-installing each app one by one? Thanks.
For getting a baseline comparison, don't use a TimeMachine restore, a lot of old gunk is restored too. You need to do a fully clean install to get your reference.
 
Late with input, but hopefully will help someone.
Photoshop CS6 (non CC) runs better on my MP 6 core, 64ram, 512gb Apple ssd. Then on other multi-core 8,10 and 12 I have tried it with.
I use it for digital painting and illustration and design work.
I have a 12 core cpu waiting, but until El Capitan (last MacOS CS6 works on without issues) is no longer supported I will stick with the current set-up.

Because people will ask.
I do not plan on moving to Adobe CC rental. I am transitioning to the three Affinity software apps (which if you have not tried, I highly recommend).
I also have an external 20TB RAID connected via Thunderbolt.
 
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