WordPress MU

I'm trying to backup the database so I can upgrade, but ran into a problem.

root@host [~]# mysqldump -uuser -ppass mu_database > /path/to/backup.sql
mysqldump: Got error: 1105: File './mu_database/wp_1234_links.MYD' not found (Errcode: 24) when using LOCK TABLES
root@host [~]# mysqldump -uuser -ppass mu_database > /path/to/backup.sql
mysqldump: Got error: 1017: Can't find file: './mu_database/wp_1234_options.frm' (errno: 24) when using LOCK TABLES

I can't seem to get past that. I ran mysqlcheck but didn't turn up any errors.

Is anyone familiar with this sort of problem that might be able to offer advice?

thanks :)

try repairing those tables with myisamchk -r .
If you have thousands of blogs, mysqldump won't be viable for long anyway, unless you have hours to make your backups. You may want to have a look into mysqlhotcopy, or even (that's what I'm doing) shutting down your DB for good and going the rsync route. Just my 2c.