Broken /boot partition: input/output error

Question

The Problem

The issue I am facing is that I get the following error on boot, after I select Ubuntu in GRUB:

Error: File "/vmlinuz-3.13.0-24-generic.efi.signed" not found.  
unaligned pointer 0xd0a26c68
Aborted. Press any key to exit.

I already posted a question regarding this issue here, but as a lot of things changed, I set up this question.

My Setup

I had some different troubles to play around if during installation, as I have a setup with a fully encrypted root. Plus, there were issues with the UEFI and GPT, especially to get everything work with Windows. As the install was a long time ago, I don't remember any details.

On my Ubuntu harddrive, I have three main partitions:

• /dev/sda1: fat32, boot flag.
  This should be the EFI partition (/boot/efi, isn't it?)
• /dev/sda2: ext2
  Should be /boot
• /dev/sda3: crypt-luks
  The encrypted container, contains root and swap

Troubleshooting

In a live system I started from a USB, I found the following issues:

Error in nautilus

Clicking on the mounted boot-Partition (/dev/sda2) in nautilus gives the following error:

Sorry, could not display all the contents of “boot”: Error when getting information for file '/media/ujosh/root/boot/System.map-3.11.0-17-generic': Input/output error

Error updating initramfs

Nevertheless, I could mount all three partitions and bring them together via mount --bind in the right constellation so I could chroot into my system. There, I ran

apt-get update
apt-get dist-upgrade

Everything worked as expected until

update-initramfs: Generating /boot/initrd.img-3.13.0-24-generic
cat: /proc/cmdline: No such file or directory

gzip: stdout: No space left on device
E: mkinitramfs failure cpio 141 gzip 1
update-initramfs: failed for /boot/initrd.img-3.13.0-24-generic with 1.
dpkg: error processing package initramfs-tools (--configure):
subprocess installed post-installation script returned error exit status 1
No apport report written because MaxReports is reached already
Errors were encountered while processing:
linux-image-3.13.0-24-generic
grub-efi-amd64
grub-efi-amd64-signed
linux-image-extra-3.13.0-24-generic
linux-signed-image-3.13.0-24-generic
linux-signed-image-generic
linux-signed-generic
initramfs-tools
E: Sub-process /usr/bin/dpkg returned an error code (1)

boot-repair doesn't help

I as well ran boot-repair on the setup, which eventually triggered the same errors while updating the initramfs as above.

Running file system checks

By the help of @zoid, I used the following tests on my /boot-partition:enter code here

sudo fsck.ext2 -p -f -C0 /dev/sda2
/dev/sda2: Inode 29 has illegal block(s).  

/dev/sda2: UNEXPECTED INCONSISTENCY; RUN fsck MANUALLY.
    (i.e., without -a or -p options)

---

sudo fsck.ext2 -f -C0 /dev/sda2

results pasted here

---

sudo smartctl -H /dev/sda 
smartctl 6.2 2013-07-26 r3841 [x86_64-linux-3.13.0-24-generic] (local build)
Copyright (C) 2002-13, Bruce Allen, Christian Franke, www.smartmontools.org

=== START OF READ SMART DATA SECTION ===
SMART overall-health self-assessment test result: PASSED

---

sudo smartctl -A /dev/sda 
smartctl 6.2 2013-07-26 r3841 [x86_64-linux-3.13.0-24-generic] (local build)
Copyright (C) 2002-13, Bruce Allen, Christian Franke, www.smartmontools.org

=== START OF READ SMART DATA SECTION ===
SMART Attributes Data Structure revision number: 1
Vendor Specific SMART Attributes with Thresholds:
ID# ATTRIBUTE_NAME          FLAG     VALUE WORST THRESH TYPE      UPDATED              WHEN_FAILED RAW_VALUE
5 Reallocated_Sector_Ct   0x0033   100   100   010    Pre-fail  Always       -       0
9 Power_On_Hours          0x0032   099   099   000    Old_age   Always       -       2869
12 Power_Cycle_Count       0x0032   098   098   000    Old_age   Always       -       1836
177 Wear_Leveling_Count     0x0013   098   098   000    Pre-fail  Always       -       48
179 Used_Rsvd_Blk_Cnt_Tot   0x0013   100   100   010    Pre-fail  Always       -       0
181 Program_Fail_Cnt_Total  0x0032   100   100   010    Old_age   Always       -       0
182 Erase_Fail_Count_Total  0x0032   100   100   010    Old_age   Always       -       0
183 Runtime_Bad_Block       0x0013   100   100   010    Pre-fail  Always       -       0
187 Uncorrectable_Error_Cnt 0x0032   100   100   000    Old_age   Always       -       0
190 Airflow_Temperature_Cel 0x0032   062   050   000    Old_age   Always       -       38
195 ECC_Error_Rate          0x001a   200   200   000    Old_age   Always       -       0
199 CRC_Error_Count         0x003e   253   253   000    Old_age   Always       -       0
235 POR_Recovery_Count      0x0012   099   099   000    Old_age   Always       -       128
241 Total_LBAs_Written      0x0032   099   099   000    Old_age   Always       -       6450810314

My question

How to recover my /boot-partition? I think that it's broken is causing the whole issue.
What is wrong with my /boot-partition and how could this happen? My whole productive OS is broken and I would like to know how to avoid this in the future.

Any help is highly appreciated!

Answer 1

"Input/output error" indicates a reading/writing error, possibly caused by a disk defect. It seems not being able to read/write blocks, and so it can't modify the partition.

I recommend backing up all your personal data on the disk and checking the filesystem with a tool of your choice.

-- Update --

for filesystem-check you could use

fsck.ext2 -p -f -C0 /dev/sda2

It will check the filesystem (-f), give you some information what's going on, show a progress bar (-C0) and ask you, whether it should try to fix major problems (-p).

If you got a lot of problems, I'd advise to install

smartmontools

and run

sudo smartctl -H /dev/sda 

for a fast test

sudo smartctl -t long /dev/sda 

check the hard disk thoroughly

sudo smartctl -a /dev/sda 

to show hard disk state

sudo smartctl -A /dev/sda 

to show hard disk attributes.

Answer 2

I'm back in!

Using fsck.ext2 really made the deal. After sudo fsck.ext2 -f -C0 /dev/sda2 and answering everything with "yes" (see in the question) the filesystem was fixed.

After that I unlocked my encrypted partition, mounted everything and chrooted into my system. There, I ran apt-get dist-upgrade. After that, grub went into the grub command line on startup.

I went back into the live system and ran boot-repair afterwards. After that I had to reconfigure my encryption setup, see EncryptedFilesystemsViaUbiquity.

Now, I am able to use my system again. The network is somehow broken, it connects nicely but I cannot use the internet in programs. sudo dhclient wlan0 fixes this for one session.