I am doing "spider exercise" from JOHN PATITUCCI Bass Workshop 1 3 Left Hand Dexterity Builders chunk 1, After a couple of minutes I start feeling increasing left thumb tension, in 10 minutes it becomes almost painful. Is it inevitable for guitar beginners or my left hand position is wrong? Should I find a teacher to place my hands correctly? Or are there any useful video guides on the subject?
As with any dexterity exercise, slow it down!
Your hands are likely hurting because you're trying to push them too hard to either:
as with the answer above me, give it a rest when your hands start to hurt, but frankly, anyone's hands should be able to play for about 10 minutes without major pain if they're playing to their skill level. Working your hands out is good, but you should NEVER walk away in pain, cramps are common, some soreness is to be expected if you push, but if you're actually in pain, you're doing something wrong.
Try slowing down the exercise, or working on your fretting. The biggest detriment to a player's speed (and their hands!) that I've found is that they're just fretting too hard.
Once you find the 'Sweet Spot' for fretting (the place where you can hold the note without much effort beyond that), your speed will increase dramatically. The way I used to work on this is by fretting a note, and slowly releasing pressure from my finger and striking the string. Do this until you start hearing your string buzz against the frets, then add a little more pressure until it stops buzzing. This area where its not buzzing is the 'Sweet Spot'.
Try working on that in tandem with the exercise you're doing now, and you should start noticing some real progress, and you should start noticing your playing beginning to sound similar to the exercise.
Golden rule: When you hurt, stop! You don't want to damage your hand. It might make you stop playing music for ever!
The spider as you said is for building dexterity. Hence, at first it will hurt if you are a beginner.
But think of it as this: When you start running to build dexterity (and you are out of shape), you won't be able to run for a long time at first. You will run for 5-10 minutes and when you get tired, you will stop for 2-3 minutes. Then you will start again and do the same thing.
You should do the same thing with the spider exercise. Work it for 5 minutes and when you start to hurt, stop and do some stretching exercises for your hand for a a couple of minutes. Then play the spider again for 5 minutes then stop again etc...
It's really important to stop when you are painfully hurt, because it could some serious damage to your hand.
It would be good to get a teacher if you could afford one, cos he'll be able to tell you some technical mistakes you might be making that would result in false techniques.