Pandaboard (Rev A2) ARM/OMAP4 upgrade to 12.10 from 12.04 fails

[Winston Smith]

Tried to upgrade a 12.04 (Precise) Ubuntu-Server install running on an OMAP4 Pandaboard (rev A2) to 12.10 (Quantal) using:

do-release-upgrade -d

Upgrade appeared to proceed normally, but once the system had rebooted, I found a number of problems that were not present in the previous releases.

NOTE: This particular system was installed on a 8GB SDHC card 6 months ago using the following 12.04 omap4-armhf image:

http://cdimage.ubuntu.com/releases/12.04/release/ubuntu-12.04-preinstalled-server-armhf+omap4.img.gz

And that prior to upgrading the system was completely up-to-date (i.e. apt-get update ; apt-get dist-upgrade ; reboot).

NOTE2: I notice that in dmesg, the board is being detected as a OMAP4430 ES2.2, but the A2 revision actually has the ES2.1 silicon, I don't know if this perhaps is a contributing factor (see http://omappedia.org/wiki/PandaBoard_Revisions).

NOTE3: I should point out that the root filesystem (ext4) has been [force] checked with fsck and there are no issues; also there is no encryption in use.

1) mongod now fails to start with:

[ 1147.582946] Alignment trap: not handling instruction ed900a00 at [<00156400>]
[ 1147.591156] Unhandled fault: alignment exception (0x011) at 0x01b69f63

...

Thu Nov 8 10:57:22 Backtrace:
0x180b9c 0x34d95e 0x34dae4 0xb6c1e9f0
 mongod(_ZN5mongo15printStackTraceERSo+0xf) [0x180b9c]
 mongod(_ZN5mongo10abruptQuitEi+0x99) [0x34d95e]
 mongod(_ZN5mongo24abruptQuitWithAddrSignalEiP7siginfoPv+0x6b) [0x34dae4]
 /lib/arm-linux-gnueabihf/libc.so.6(__default_rt_sa_restorer_v2+0) [0xb6c1e9f0]

2) Serial console is now broken after upgrade:

The flash-kernel utility seemed to add the following preEnv.txt:

bootargs=ro quiet splash root=UUID=...

But this overrides the proper bootargs in boot.scr:

setenv bootargs ro elevator=noop vram=40M mem=456M@0x80000000 mem=512M@0xA0000000 root=UUID=... fixrtc quiet splash console=ttyO2,115200n8

Which causes /etc/init/serial.conf to fail to start a getty for the console as it inspects /proc/cmdline looking for "console=", which it no longer finds because /proc/cmdline now contains the contents of preEnv.txt.

Because preEnv.txt uses 'quiet', the last thing you see at the console while booting is:

## Booting kernel from Legacy Image at 80000000 ...
   Image Name: kernel 3.5.0-213-omap4
   Image Type: ARM Linux Kernel Image (uncompressed)
   Data Size: 4276896 Bytes = 4.1 MiB
   Load Address: 80008000
   Entry Point: 80008000
   Verifying Checksum ... OK
## Loading init Ramdisk from Legacy Image at 81600000 ...
   Image Name: ramdisk 3.5.0-213-omap4
   Image Type: ARM Linux RAMDisk Image (gzip compressed)
   Data Size: 5903851 Bytes = 5.6 MiB
   Load Address: 00000000
   Entry Point: 00000000
   Verifying Checksum ... OK
   Loading Kernel Image ... OK
OK

Starting kernel ...

Uncompressing Linux... done, booting the kernel.

There is no more output after this! The workaround for this was to mount the boot partition mmcblk0p1 and rename preEnv.txt (although now u-boot complains that preEnv.txt is missing).

3) System will no longer reboot

Running the command /sbin/reboot causes the system to shutdown but then hang (and NOT restart), power must be removed, or the reset button pressed to get a restart.

Once the system "stops" the status LEDs (STATUS1 and STATUS2) are both lit, as are both of the ethernet link/activity LEDs.

4) Previously unseen "abnormal" messages in dmesg output:

I'm now seeing "abnormal" messages in the dmesg output that I didn't see with previous releases (I don't know if these are significant issues or not!).

[ 10.550048] init: plymouth main process (246) killed by ABRT signal
[ 10.553527] init: plymouth-splash main process (449) terminated with status 2
...
[ 13.749603] init: failsafe main process (514) killed by TERM signal
...
[ 14.306884] init: plymouth-stop pre-start process (827) terminated with statu
...
error: unexpectedly disconnected from boot status daemon

[Ubuntu Foundations Team Bug Bot (crichton)]

Thank you for taking the time to report this bug and helping to make Ubuntu better. It seems that your bug report is not filed about a specific source package though, rather it is just filed against Ubuntu in general. It is important that bug reports be filed about source packages so that people interested in the package can find the bugs about it. You can find some hints about determining what package your bug might be about at https://wiki.ubuntu.com/Bugs/FindRightPackage. You might also ask for help in the #ubuntu-bugs irc channel on Freenode.

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[Winston Smith (smith-winston-101)]

Running mongod under gdb, I get more detail on the SIGBUS:

Program received signal SIGBUS, Bus error.
0x00156404 in mongo::BSONElement::numberDouble() const ()
(gdb) bt
#0 0x00156404 in mongo::BSONElement::numberDouble() const ()
#1 0x0015fc14 in mongo::compareElementValues(mongo::BSONElement const&, mongo::BSONElement const&) ()
#2 0x0015b32e in mongo::BSONObj::woCompare(mongo::BSONObj const&, mongo::BSONObj const&, bool) const ()
#3 0x00161796 in mongo::BsonUnitTest::run() ()
#4 0x003507da in mongo::UnitTest::runTests() ()
#5 0x00153ad6 in main ()

Seems that Quantal is shipping with a rather old version of mongo, 2.0.6, it looks like this was fixed a while ago but only on the 2.2.x versions (the latest 2.0.8rc0 does not have an equivalent fix).

https://github.com/mongodb/mongo/commit/0575d874318ceb33b42b526d1076c659af0aaca5

Given that Precise shipped with 2.0.4, which also does not have this change, I can only guess that it was a compiler change that has caused this issue to suddenly appear. None-the-less, it appears mongodb is completely broken in Quantal for ARMv7 systems.

Additional information can be found in this thread:

https://jira.mongodb.org/browse/SERVER-1811

[Winston Smith (smith-winston-101)]

Issue #3 appears to have been resolved since I updated to today's newer kernel:

linux-meta-ti-omap4_3.5.0.214.13

[Winston Smith (smith-winston-101)]

Looks like issue #3 (not rebooting) is back after updating today to:

3.5.0-216-omap4 #23-Ubuntu

[Fabio Marconi (fabiomarconi)]

reassigned as it seems a kernel issue
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[Brad Figg (brad-figg)]

This bug is missing log files that will aid in diagnosing the problem. From a terminal window please run:

apport-collect 1076447

and then change the status of the bug to 'Confirmed'.

If, due to the nature of the issue you have encountered, you are unable to run this command, please add a comment stating that fact and change the bug status to 'Confirmed'.

This change has been made by an automated script, maintained by the Ubuntu Kernel Team.

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