The best exercise to learn the notes on the fretboard is right here!
View the full lesson at The "Find-A-Note" Exercise | JustinGuitar
I’m glad you mention leaving out the open strings. That has the nice benefit of making clean breaks between the octaves as you move up and down the strings. I’ve combined this exercise with a visual technique to get a picture of how the octave ranges cover the fretboard. I drew a 22 fret fretboard and colored the four octave ranges with four different colored pencils. I found this very helpful for me to look at and get a different perspective on the range of the guitar.
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Hello @mindsounds and welcome to the Community.
That sounds like a good way of helping yourself to digest and absorb the learning.
Cheers 
| Richard_close2u | JustinGuitar Official Guide
When it comes to putting this exercise to a metronome I did find even 60bpm very challenging at one note per click. My answer to this problem is to allow more clicks between notes. I started at 4 clicks, then down to 2 until I was ready for the 1.
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What has helped more than anything else when it comes to memorizing the fretboard is Justin’s Guitar Note Trainer. The app is a must. It makes learning the fretboard fun.
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Thanks for the recommendation @JamesSuntres
Cheers
| Richard_close2u | JustinGuitar Official Guide & Approved Teacher
I played around on this exercise for the first time yesterday and I totally discovered something that made me very excited. I’m not going to spoil it for others by describing it here, because it feels awesome to have discovered it on my own, and I’m sure others will feel the same way too if they USE THIS APP AND THIS EXERCISE. It is way cool!
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I’m curious on guidance around how long to keep doing the exercises. I’m able to play each note, for all notes, up and down the fretboard at 80bpm and, using the Note Trainer app, can quickly name all notes either by sight or using the fretboard in the mind. Like anyone, I’ve invested a lot of time memorizing the notes across the fretboard and I fret (see what I did there) that if I don’t keep it up, I’ll start to forget the notes. I guess what I’m asking is, based on other’s experience, is learning the fretboard like riding a bike - once done, never forgotten?
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There’s no right or wrong here. Finding any note within one or two seconds is what I’m aiming for.
Most people will find it pretty easy to name any note right away on the low E, the A and the high E string, because we (should) know the root notes for our barre/power chords.
The other strings are a bit more difficult, that’s where the octave shapes are really helpful.
I stopped doing this exercise exercise once I started transcribing and analyzing songs, melodies and solos. It became part of the bigger picture.
Many songs I like use the E and A minor pentatonic scale. By now, I know where those notes are (E, G, A, B, C and D). So any other note is just one fret next to a note I know.
The more you learn and analyze stuff, the easier it gets. I don’t think you forget it once it’s under your fingers.
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As you utilise triads, arpeggios, scales, etc,etc …all these are reinforcing and continually developing fretboard knowkedge, so it will be neverending…
Cheers, Shane
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Hello @summacube and welcome to the community.
From what you describe you’re fine to move on. You may occasionally reach a point where you need to think again but as Jeff says, in practice, the notes will all pop out and be there for you.
I hope that helps.
Cheers 
| Richard | JustinGuitar Approved Teacher, Official Guide & Moderator
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Thanks so much for the helpful feedback and taking the time to respond. 
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Thank you!
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Great. Thanks so much!
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I want to know what your record in 3 minutes is with the notetrainer app in all four learning methods. I want to see what my goal could be or what should I reach?
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This is an awesome and really helpful exercise.
added to my daily until I know the fret board 
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Just found out about this from the video, I’ll try it out, from the looks of it it seems to be pretty good…