I've been struggling with this for what feels like months. On a project, we're using a third party hosting provider, who offers us space on a managed server, complete with everything we need to run Drupal in a shared hosting environment. We're running a copy of Provisionator on the server to help us deploy lots of Drupal sites easily.
Here's where it gets messy. We can create new databases just fine, but importing a .sql file takes for freaking ever. Imports that take 3 seconds on my Powerbook can take 90 - 300 seconds on this server. Running the import on a dual G5 XServe with the same version of MySQL finishes the job in about a second.
I've tried removing variables from the equation. Using full-on Provisionator. Using a separate custom .php script. Using phpMyAdmin. Each take so long that browsers often time out before completing the import (leaving partially imported databases). I've tried command line mysql directly on the server, with the same range of very slow times.
I can't seem to find anything that might make imports of a smallish .sql (~400K) file take so long. Unfortunately, it's making the process of deploying new sites essentially useless for now.
The curious thing is that once a database has (eventually) been populated, the select queries seem to run at normalish speed.
Any ideas on how to get the server back up to speed? It's running MySQL 4.1.20 with MyISAM tables on a RedHat Linux box. I don't have access to tools like top, ps, netstat, or even env, so exact details of the box's config are shrouded in a veil of mystery and obscurity.