Some things coming to my mind:
1) Are you using a lot of indices and/or compound indices? Sometimes when you have large tables, loading those indices the first time, takes a while. So there is a fine balance between too many and not enough indices; we have noticed with FB. As such, after every server restart, we "warm up" the database to get it going.
2) If your DB is too fragmented, consider writing it to a flat-file, and restoring it; as shown in the FB docs.
3) How is your underlying storage medium doing? Enough free disk space? Consider deploying on SSDs.
With Kind Regards,
Dennis Gaastra, Chief Technology Officer, WEBAPPZ® Systems, Inc.
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