I am facing a performance issue when I open some of the pages Taking too long time.. after checking the queries and the time for each query I found that those too functions are taking the long time

DrupalDatabaseCache::clear DrupalDatabaseCache::set

Comments

Is that a question or statement?

Since it is phrased as a statement, I can only agree that the cache set queries can be a bit slow. It is probably not a bug. I have found that with Drupal one does need to spend time and effort and money on hosting, unless you are happy with a slow site. Probably you need to look at your server setup if want non-cached pages to be faster.

Sorry John, it's a question.. I need to solve this issue..
cache queries are taking a long time and my site is slow because of that

The site is on an excellent dedicated server
I am trying to track the reason for that but I could not

By the way I am installing commons on that server with my customization

Cache set queries are usually slow in my experience. So I would suggest trying a clean install of Commons, with a little sample content and comparing it. If the speed is similar (as I expect) you will know that this is just the way Drupal is, rather than a bug specific to your site, and your options for fixing it lie in work on the server. Assuming, since the server is excellent, you already use very fast hard disks on your server (do you? I regard this as essential for Drupal), and you still need better performance, you could look into using Drupal's pluggable cache system to store the cache tables other than in Mysql.

If, contrary to my guess, your clean install has significantly faster cache set queries, then of course you will be looking around for bugs on the site.