I'm pulling my hair out trying to solve this issue, maybe someone has an idea.
I'm hosting on a WiredTree Managed VPS768 using WordPress 3.0.3, PHP 5.2.6 and MySQL 5.0.91-community.
I'm experiencing intermittent delays of anywhere from 10 to 35 seconds when loading my site http://mightyfinemacapps.com/ . The delays do not occur on each load. In fact, once the site has loaded, subsequent loads are quite fast. But after a while (say, 10 or 20 minutes, sometimes several hours) I get the delay again.
I used Firebug to log the whole process and the delay occurs between the initial GET and the first response from the server. Once the server starts sending data the transfer is fast.
So the delay is occurring on the server itself. This could, as far as I understand it, involve Apache, PHP or MySQL or a combination of them. I'm ruling out Apache because other sites on the same server that don't run WordPress don't have any issues. That leaves PHP and/or MySQL.
One other thing to take into account is that I have another site on the same server that is running a seriously out-of-date version of WordPress (I know, I know, I should update) and I've never had any issues whatsoever with that site. So the newer version of WordPress itself might be the culprit.
I've also tried disabling all plugins and reverting to the standard Twenty Ten theme, but the issue subsists. I'm also using W3 Total Cache on another site on the same server, but that site has the same issues.
Support from WiredTree so far hasn't been very helpful. It took several back-and-forth emails to get the support rep to acknowledge that the issue is server-side and has nothing to do with large page elements or remote servers not being reachable. Nonetheless, the support rep suggested installing memcache, memcached and a caching plugin. I told him that I didn't think randomly installing caching was a good idea since the site isn't getting a lot of traffic and that, if the caching indeed did improve performance, that would prove that there was something else going on that the caching would merely cover up. In my mind, if a site with low traffic is experiencing performance issues on load and caching solves those issues, there has to be an issue with either PHP or the database. Anyway, he insisted on the caching, so he installed the memcache stuff and I installed W3 Total Cache. The next day, the issues resurfaced.
So, at this point, I can't think of anything else I could try. The support rep is probably going to continue on his trial and error quest and will eventually blame WordPress or something outside of his responsibility.
My approach would be to check Apache, PHP and MySQL log files for big gaps between time stamps which would indicate where the delay is occurring. Only problem is I'm not too familiar with WiredTree's implementation of CentOS, the log files aren't where they usually are. And the support rep isn't being very helpful in this regard either.
Is anyone experiencing similar issues or does anyone have an idea what could be causing this? I've found some threads on these forums where users are experiencing delays, but they were mostly related to specific plugins or older WordPress versions.