Corrupted filesystem after resizing

[Andrés Torti]

Hi! I'm trying to get my old Pandaboard ES working again. I did some projects with it some years ago and I will be using it again. I got the Ubuntu 12.04 Server image from here and followed all the steps using dd to write to the SD Card. The board boots and starts resizing the partition but after rebooting it just fails in everything, the log is below. I'm using an 8Gb Kingston SD Card with serial port connected to my PC, no monitor, no keyboard, no mouse attached to the board. I tried Ubuntu Server 12.04 and Ubuntu Desktop 12.04, both fails, I couldn't find where to download previous versions.

U-Boot SPL 2011.12 (Apr 02 2012 - 18:13:04)

Texas Instruments OMAP4460 ES1.1

OMAP SD/MMC: 0

reading u-boot.img

reading u-boot.bin

mkimage signature not found - ih_magic = ea000014

Assuming u-boot.bin ..

reading u-boot.bin

U-Boot 2011.12 (Apr 02 2012 - 18:13:04)

CPU  : OMAP4460 ES1.1

Board: OMAP4 Panda

I2C:   ready

DRAM:  1 GiB

WARNING: Caches not enabled

MMC:   OMAP SD/MMC: 0

Using default environment

In:    serial

Out:   serial

Err:   serial

Net:   No ethernet found.

checking for preEnv.txt

reading preEnv.txt

** Unable to read "preEnv.txt" from mmc 0:1 **

Hit any key to stop autoboot:  3 ... 2 ... 1 ... 0 

reading uEnv.txt

** Unable to read "uEnv.txt" from mmc 0:1 **

reading boot.scr

350 bytes read

Loaded script from boot.scr

Running bootscript from mmc0 ...

## Executing script at 82000000

reading uImage

4434784 bytes read

reading uInitrd

4314202 bytes read

## Booting kernel from Legacy Image at 80000000 ...

   Image Name:   Ubuntu Kernel

   Image Type:   ARM Linux Kernel Image (uncompressed)

   Data Size:    4434720 Bytes = 4.2 MiB

   Load Address: 80008000

   Entry Point:  80008000

   Verifying Checksum ... OK

## Loading init Ramdisk from Legacy Image at 81600000 ...

   Image Name:   Ubuntu Initrd

   Image Type:   ARM Linux RAMDisk Image (gzip compressed)

   Data Size:    4314138 Bytes = 4.1 MiB

   Load Address: 00000000

   Entry Point:  00000000

   Verifying Checksum ... OK

   Loading Kernel Image ... OK

OK

Starting kernel ...

Uncompressing Linux... done, booting the kernel.

Resizing root partition ...

Disk /dev/mmcblk0: 3768 cylinders, 128 heads, 32 sectors/track

Old situation:

Units = sectors of 512 bytes, counting from 0

   Device Boot    Start       End   #sectors  Id  System

/dev/mmcblk0p1   *        32    147455     147424   c  W95 FAT32 (LBA)

/dev/mmcblk0p2        147456   3104767    2957312  83  Linux

/dev/mmcblk0p3             0         -          0   0  Empty

/dev/mmcblk0p4             0         -          0   0  Empty

New situation:

Units = sectors of 512 bytes, counting from 0

   Device Boot    Start       End   #sectors  Id  System

/dev/mmcblk0p1   *        32    147455     147424   c  W95 FAT32 (LBA)

/dev/mmcblk0p2        147456  15433727   15286272  83  Linux

/dev/mmcblk0p3             0         -          0   0  Empty

/dev/mmcblk0p4             0         -          0   0  Empty

Successfully wrote the new partition table

Re-reading the partition table ...

If you created or changed a DOS partition, /dev/foo7, say, then use dd(1)

to zero the first 512 bytes:  dd if=/dev/zero of=/dev/foo7 bs=512 count=1

(See fdisk(8).)

Resizing root filesystem. Please wait, this will take a moment ...

Checking filesystem before resizing...

Resizing, please wait...

Resizing, pass: 1 [  2/100]

Resizing, pass: 1 [  5/100]

Resizing, pass: 1 [  8/100]

Resizing, pass: 1 [ 10/100]

Resizing, pass: 1 [ 12/100]

Resizing, pass: 1 [ 15/100]

Resizing, pass: 1 [ 18/100]

Resizing, pass: 1 [ 20/100]

Resizing, pass: 1 [ 22/100]

Resizing, pass: 1 [ 25/100]

Resizing, pass: 1 [ 28/100]

Resizing, pass: 1 [ 30/100]

Resizing, pass: 1 [ 32/100]

Resizing, pass: 1 [ 35/100]

Resizing, pass: 1 [ 38/100]

Resizing, pass: 1 [ 40/100]

Resizing, pass: 1 [ 42/100]

Resizing, pass: 1 [ 45/100]

Resizing, pass: 1 [ 48/100]

Resizing, pass: 1 [ 50/100]

Resizing, pass: 1 [ 52/100]

Resizing, pass: 1 [ 55/100]

Resizing, pass: 1 [ 58/100]

Resizing, pass: 1 [ 60/100]

Resizing, pass: 1 [ 62/100]

Resizing, pass: 1 [ 65/100]

Resizing, pass: 1 [ 68/100]

Resizing, pass: 1 [ 70/100]

Resizing, pass: 1 [ 72/100]

Resizing, pass: 1 [ 75/100]

Resizing, pass: 1 [ 78/100]

Resizing, pass: 1 [ 80/100]

Resizing, pass: 1 [ 82/100]

Resizing, pass: 1 [ 85/100]

Resizing, pass: 1 [ 88/100]

Resizing, pass: 1 [ 90/100]

Resizing, pass: 1 [ 92/100]

Resizing, pass: 1 [ 95/100]

Resizing, pass: 1 [ 98/100]

Resizing, pass: 1 [100/100]Enabling serial console login

cp: can't stat '/root/usr/share/jasper-initramfs/init/serial.conf': Input/output error

mountall: Event failed

mountall: Event failed

[  135.852935] EXT4-fs error (device mmcblk0p2): ext4_mb_generate_buddy:739: group 176, 4670 clusters in bitmap, 1832 in gd

[  135.861145] EXT4-fs (mmcblk0p2): previous I/O error to superblock detected

 * Starting Uncomplicated firewall.[74G[ OK ]

 * Stopping cold plug devices.[74G[ OK ]

 * Stopping log initial device creation.[74G[ OK ]

 * Starting enable remaining boot-time encrypted block devices.[74G[ OK ]

 * Starting save udev log and update rules.[74G[ OK ]

 * Stopping save udev log and update rules.[74G[ OK ]

 * Stopping enable remaining boot-time encrypted block devices.[74G[ OK ]

 * Starting configure network device security.[74G[ OK ]

 * Starting configure network device.[74G[ OK ]

 * Starting configure network device security.[74G[ OK ]

 * Starting Mount network filesystems.[74G[ OK ]

 * Starting Failsafe Boot Delay.[74G[ OK ]

 * Stopping Mount network filesystems.[74G[ OK ]

 * Starting configure network device.[74G[ OK ]

 * Stopping Failsafe Boot Delay.[74G[ OK ]

 * Starting System V initialisation compatibility.[74G[ OK ]

 * Starting set sysctls from /etc/sysctl.conf.[74G[ OK ]

 * Stopping set sysctls from /etc/sysctl.conf.[74G[ OK ]

 * Starting Bridge socket events into upstart.[74G[ OK ]

 * Starting configure network device security.[74G[ OK ]

 * Starting configure network device.[74G[ OK ]

 * Starting configure network device security.[74G[ OK ]

 * Starting configure virtual network devices.[74G[ OK ]

 * Stopping configure virtual network devices.[74G[ OK ]

Skipping profile in /etc/apparmor.d/disable: usr.sbin.rsyslogd

 * Starting AppArmor profiles       .[80G 

.[74G[ OK ]

 * Stopping System V initialisation compatibility.[74G[ OK ]

 * Starting System V runlevel compatibility.[74G[ OK ]

 * Starting save kernel messages.[74G[ OK ]

 * Starting deferred execution scheduler.[74G[ OK ]

 * Starting regular background program processing daemon.[74G[ OK ]

 * Starting End-user configuration after initial OEM installation.[74G[ OK ]

 * Stopping End-user configuration after initial OEM installation.[74G[ OK ]

 * Starting End-user configuration after initial OEM installation (debconf).[74G[ OK ]

 * Starting save kernel messages.[74G[.[31mfail.[39;49m]

 * Starting CPU interrupts balancing daemon.[74G[ OK ]

 * Stopping End-user configuration after initial OEM installation (debconf).[74G[ OK ]

 * Stopping System V runlevel compatibility.[74G[ OK ]

[  200.516510] mmcblk0: error -110 transferring data, sector 2859000, nr 10, cmd response 0x900, card status 0xc00

[  200.527496] end_request: I/O error, dev mmcblk0, sector 2859000

[  200.533782] end_request: I/O error, dev mmcblk0, sector 2859008

[  200.533782] Buffer I/O error on device mmcblk0p2, logical block 1355772

[  200.547058] Buffer I/O error on device mmcblk0p2, logical block 1355773

[  200.554077] Buffer I/O error on device mmcblk0p2, logical block 1355774

[  200.554077] Buffer I/O error on device mmcblk0p2, logical block 1355775

[  200.554077] Buffer I/O error on device mmcblk0p2, logical block 1355776

[  201.393341] mmcblk0: error -110 transferring data, sector 2867184, nr 18, cmd response 0x900, card status 0xc00

[  201.404357] end_request: I/O error, dev mmcblk0, sector 2867184

[  201.410644] end_request: I/O error, dev mmcblk0, sector 2867192

[  201.410644] Buffer I/O error on device mmcblk0p2, logical block 1359864

[  201.423919] Buffer I/O error on device mmcblk0p2, logical block 1359865

[  201.423919] Buffer I/O error on device mmcblk0p2, logical block 1359866

[  201.430938] Buffer I/O error on device mmcblk0p2, logical block 1359867

[  201.444946] Buffer I/O error on device mmcblk0p2, logical block 1359868

[  201.444946] end_request: I/O error, dev mmcblk0, sector 2867194

[  201.451995] Buffer I/O error on device mmcblk0p2, logical block 1359869

[  201.465270] Buffer I/O error on device mmcblk0p2, logical block 1359870

[  201.465270] Buffer I/O error on device mmcblk0p2, logical block 1359871

[  201.479278] Buffer I/O error on device mmcblk0p2, logical block 1359872

[  208.872192] mmcblk0: error -110 transferring data, sector 1445878, nr 2, cmd response 0x900, card status 0xc00

[  208.883148] end_request: I/O error, dev mmcblk0, sector 1445878

[  208.883148] Buffer I/O error on device mmcblk0p2, logical block 649211

[  209.708709] mmcblk0: error -110 transferring data, sector 1722590, nr 6, cmd response 0x900, card status 0xc00

[  209.720184] end_request: I/O error, dev mmcblk0, sector 1722590

[  209.720184] Buffer I/O error on device mmcblk0p2, logical block 787567

[  209.733520] end_request: I/O error, dev mmcblk0, sector 1722592

[  209.733520] Buffer I/O error on device mmcblk0p2, logical block 787568

[  209.746826] end_request: I/O error, dev mmcblk0, sector 1722594

[  209.753173] Buffer I/O error on device mmcblk0p2, logical block 787569

[  210.459533] mmcblk0: timed out sending r/w cmd command, card status 0xe00

[  210.459533] end_request: I/O error, dev mmcblk0, sector 147468

[  210.459533] Buffer I/O error on device mmcblk0p2, logical block 6

[  210.480590] mmcblk0: timed out sending r/w cmd command, card status 0x400e00

[  210.488098] mmcblk0: timed out sending r/w cmd command, card status 0x400e00

[  210.495605] mmcblk0: timed out sending r/w cmd command, card status 0x400e00

[  210.503112] mmcblk0: timed out sending r/w cmd command, card status 0x400e00

[  210.510620] mmcblk0: timed out sending r/w cmd command, card status 0x400e00

[  210.518127] mmcblk0: timed out sending r/w cmd command, card status 0x400e00

[  210.525573] end_request: I/O error, dev mmcblk0, sector 1476376

[  210.531829] Aborting journal on device mmcblk0p2-8.

[  210.537445] mmcblk0: timed out sending r/w cmd command, card status 0x400e00

[  210.544952] mmcblk0: timed out sending r/w cmd command, card status 0x400e00

[  210.552459] mmcblk0: timed out sending r/w cmd command, card status 0x400e00

[  210.559936] mmcblk0: timed out sending r/w cmd command, card status 0x400e00

[  211.266540] mmcblk0: timed out sending r/w cmd command, card status 0xe00

[  211.275054] end_request: I/O error, dev mmcblk0, sector 1475088

[  211.275054] Buffer I/O error on device mmcblk0p2, logical block 663816

[  211.288482] JBD2: I/O error detected when updating journal superblock for mmcblk0p2-8.

[  212.900512] journal commit I/O error

[  212.908233] mmcblk0: timed out sending r/w cmd command, card status 0x400900

[  214.884399] mmcblk0: error -110 transferring data, sector 2506784, nr 2, cmd response 0x900, card status 0xc00

[  214.895416] end_request: I/O error, dev mmcblk0, sector 2506784

[  214.895477] Buffer I/O error on device mmcblk0p2, logical block 1179664

[  215.859771] mmcblk0: error -110 transferring data, sector 2768898, nr 2, cmd response 0x900, card status 0xc00

[  215.870697] end_request: I/O error, dev mmcblk0, sector 2768898

[  215.877044] Buffer I/O error on device mmcblk0p2, logical block 1310721

[  216.204315] EXT4-fs error (device mmcblk0p2): ext4_journal_start_sb:327: Detected aborted journal

[  216.211944] EXT4-fs (mmcblk0p2): Remounting filesystem read-only

[  216.836791] EXT4-fs error (device mmcblk0p2): ext4_journal_start_sb:327: Detected aborted journal

 * Stopping Read required files in advance.[74G[ OK ]

[Tom Mitchell]

Do you have a Linux machine or live USB linux machine so you can 

examine and if needed run fsck  and friends on the media?  
Double check the connector and look for bent pins... my Panda board's

SD card is a bit fragile and I try to do most stuff on an external powered

USB device but getting there is a bit of work.
I have found that resizing and repartitioning my filesystems on a spare old Linux laptop 

is the way to go.   To this end I have some old old laptops just for this purpose.

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  T o m    M i t c h e l l

[Andrés Torti]

I'm on a Mac, I will run a virtual machine with linux to try to repair the filesystem

[Andrés Torti]

Ok, I dd Ubuntu Server again on the SD Card and used Gparted to expand the partition to take all the available space. When I boot it detects a corrupt filesystem and asks me to fix it, I press F to fix it automatically. After a really long wait repairing the filesystem it boots again but the same happens. Liner builds works fine, i guess because they don't expand the partition but I can't find a Linaro Ubuntu Server. Any ideas?

[Tom Mitchell]

If you can boot your panda and ignore the filesystem resize you

have a system to work from.

Boot the panda and enable ssh and friends then with a USB SD card reader 

you can mount a second SD card and repair or expand it as a server 

with a ssh connection.

I do recommend a powered hub for any USB device.  Many keyboards

and mice together will tax the system regulator.   Bad power results

in all sort of errors.

[Andrés Torti]

Great, how do I stop it from resizing the filesystem?

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Torti Andrés Fernando

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[Tom Mitchell]

Nevermind   I thought you had something that booted.   Do you have any USB devices connected?
If you do disconnect them and try again.

[Andrés Torti]

I don't have anything connected, just the power and the serial cable to my computer. I booted a Linaro Ubuntu successfully but the problem is wifi is not working, iwconfig reports wlan0     no wireless extensions. I don't know why so I can't use it, I just need a wifi connection. Do you know how I can solve that or how to stop Ubuntu from resizing the partition? 

[Tom Mitchell]

Lack of wireless -- can you connect to a wired ethernet long enough to update?
It really does help to have a Linux machine to do a lot of stuff.
For some this is sufficient to use a live USB or CDROM boot.... 
If you have never run a live USB linux on a machine with data you care about

take some time to explore options and do some homework.   It is easy 

for those that know how..  Errors are trouble so make a list check it twice...

[Andrés Torti]

Yes, I have a machine running Ubuntu. I know how to run a live CD too, I'm not a Linux expert but I know some things :) What do you recommend? Do you have any Ubuntu image that you have used and you knows it works? I also tried changing the SD Card but it's exactly the same. Will try to connect to an ethernet cable now to update the packages and see what happens.

[Tom Mitchell]

Since you have a Ubuntu machine you can mount the SD card directly (many laptops) of via a USB media reader.
Then you can resize the partition and resize the filesystem.  You can also look at the startup scripts and comment out

the parts that auto resize.  

Linux on the pandaboard and on any other machine are very much alike.
The solution for many is a second system even a Raspberry-Pi.   A lot

of this is like working on a care engine.  You need a second car or truck to 

go and get parts.

[Andrés Torti]

Great, do you know where is the script that resizes the partition? I've been looking in /etc/init but couldn't find anything. Thank you very much for all the help! :)