<p>I cannot generate the upper part of the solid properly which contain a hole (as in the picture).  The solid part (bottom section) printed well. </p>

<p><a href="https://i.stack.imgur.com/QpBfR.jpg" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/QpBfRm.jpg" alt="enter image description here"></a></p>

<p>What should I change to print the part with hole properly?<br>
Is it a problem with machine or the design?<br>
I am using Hydra 3D printer. </p>

It appears that the upper part of your print contains less plastic than the lower. This would mean that as the printer begins to operate in that area, the previously deposited plastic has less time to cool.
The distortions are difficult to see from the distortions of the photograph, but I've experienced similar upper, smaller section failures.
You could consider to print more than one copy of the item on the bed, which will require the nozzle to move away from each layer, allowing more cooling time, or add a throw-away model.
I've also added an ooze shield using Simplify3D to create a single wall around the part, providing the same cooling time concept.
If you try these options and still experience a problem, please consider editing your post with material used (PLA, ABS, PETG, etc) as well as temperatures and speeds used for this print.
Your slicer is not likely the problem, but is often useful information. Printer name is sometimes helpful, but I think it's not critical in this circumstance.
It's also useful to orient the part in the photograph to match that of the print. It's apparent in this case that the top of the print is to the right and bottom is to the left. If that is not correct, please advise in edit.