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Alright, so a power outage occurred while my computer running Xubuntu 13.04 was on. Has happened before, just restart and make sure nothing broke. Well, it has been a long and arduous journey, and I am still stuck. First, my filesystem was mounted read-only, so I couldn't boot. Used a liveCD to run fdisk and fix some things on the drive, then my computer would boot.

Then I was in a really weird place: I have a second internal hard drive and an external hard drive, but neither of these show up once I have booted. Both drives show up perfectly fine when using the liveCD. Upon further inspection, even though the drive is not read-only as a whole, the /root folder and /media/{user} folders are both read-only (I assume, since they just read "permission denied". I have cleared my CROM, done fdisk repairs on both the other drives. Fdisk shows clean on everything. Furthermore, boot and running anything is incredibly slow - much slower than it was before. I thought maybe this was a symptom of the filesystem being full (even though it wasn't before the crash), but it is not, still has a hundred or so MB free (which is also suspicious, because it had several gigs before crashing...). That shouldn't prevent me from mounting other drives or running updates (because root is read-only).

What is wrong with my system? I am not even sure where to continue looking at this point - any and all suggestions are appreciated.

UPDATE: So of course the second I finally post this question, things change. I tried turning off the computer and it asked if I wanted to, since other people were logged in. Who else was logged in? There was only one account! So I logged out and logged back in, and suddenly I could see the two external drives! The folders are still read-only, and everything is still very slow. Also, when trying to mount the external drive, I get an error saying "Error opening /dev/sdc1: No such file or address". Which is odd, since ast I checked this drive was usually done as sdg1. But that may or may not be related.caused by the read-only media/{user} folder.

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Okay, first of all, "permission-denied" is different than "read-only". A whole partition can be set to "read-only" when mounting it. "Permission-denied" means that the user trying to execute the command does not have permission to do so, but other users might. If you want to know if your partitions are mounted as read-only or read/write, execute the command mount | grep '^/'. This will show you all the mounted partitions, with their options in brackets (); if there's an rw in the brackets, then the partition is read/write; if there's an ro, it's read-only. –  Alaa Ali Aug 22 '13 at 12:53
Anyways, after your last edit, can you please clarify your question? What is it that you're looking for? Mounting the second HDD and external HDD as "read-write"? What's the output of these three commands: sudo fdisk -l, mount | grep '^/' and cat /etc/fstab? –  Alaa Ali Aug 22 '13 at 12:56
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