pacman -Syu stucks at the step "synchronizing filesystem..."

[ahmetuludag]

Hi,

I installed ArchLinux ARM (os.archlinuxarm.org/os/ArchLinuxARM-am33x-latest.tar.gz) to my beaglebone black (rev. A6A). After installation, it booted and started successfully. Then, I executed the followings to update package db & upgrade:

$this->bbcode_second_pass_code('', '
pacman -Syy
pacman -Syu --debug
')

But it stuck at the step "synchronizing filesystem...". Here is the end of related log file:

$this->bbcode_second_pass_code('', '
debug: updating database
debug: adding database entry 'shadow'
debug: writing shadow-4.2.1-1 DESC information back to db
debug: writing shadow-4.2.1-1 FILES information back to db
debug: adding entry 'shadow' in 'local' cache
debug: executing ". /tmp/alpm_MznVta/.INSTALL; post_upgrade 4.2.1-1 4.1.5.1-9"
debug: executing "/usr/bin/bash" under chroot "/"
debug: call to waitpid succeeded
debug: running ldconfig
debug: executing "/usr/bin/ldconfig" under chroot "/"
debug: call to waitpid succeeded
synchronizing filesystem...
')

Also, USR2 led remains lit and the others are OFF. After restarting, pacman started to give no reaction (seems broken). For instance:
$this->bbcode_second_pass_code('', '
[root@alarm ~]# pacman
[root@alarm ~]# pacman -h
[root@alarm ~]# pacman -Syy
[root@alarm ~]# pacman -Syu
[root@alarm ~]#
')

Re-installing the arch didn't help, it exactly repeated in the same way.

Do you have any idea why it may get stuck and broke pacman ?

Thanks

[PLyttle]

three threads down http://archlinuxarm.org/forum/viewtopic.php?f=48&t=7094 "Can't boot Beagleboard-XM zImage not found " gives your answer

[ahmetuludag]

I found that zImage seems normal in my system. It's about ~3.2MB in size after both update and upgrade. In spite of this, I tried to do same thing ignoring kernel packages. I used these commands:

$this->bbcode_second_pass_code('', '
pacman -Syy --ignore linux-am33x-legacy
pacman -Syu --ignore linux-am33x-legacy
')

Again, it stuck at the same step but pacman is working after reboot (and zImage isn't zero length)

[ahmetuludag]

An update,
Even if stuck, I was able to do update & upgrade after reboot since pacman is not broken. And it didn't stuck and upgraded successfully without ignoring the kernel package

Thank you for your helps.

[PLyttle]

The problem is that when you upgrade after an new install a lot of data is transferred. Particularly on a slow disk the synching of the filesystem chokes and the system crashes when it times out, without all files being written correctly, leaving you with a broken system. The new pacman should work better, but I found that it is better to upgrade in steps.
first update pacman, then the rest without the new kernel and finally the kernel. last, making sure filesync has completed in between.
It is quite frustrating, particular for new users, that the system crashes on just following instructions.
on the bright side, once you're done, you won't have this problem again.

success, LP

[WarheadsSE]

I did a completely fresh install to both SD and eMMC on two BBB's, one Rev B3, one Rev C. Neither of these systems say this behavior you speak of, where it "stucks".

[PLyttle]

Mine did, without fail. Maybe there is some variance in hardware, or in the cards used.

Made a new install, and this is what it looks like on the debug interface:

everything looks normal until:

$this->bbcode_second_pass_code('', 'synchronizing filesystem...
[ 300.502621] INFO: task pacman:272 blocked for more than 60 seconds.
[ 300.509278] "echo 0 > /proc/sys/kernel/hung_task_timeout_secs" disables this message.
[ 300.517711] Kernel panic - not syncing: hung_task: blocked tasks
[ 300.524002] [<c00132d8>] (unwind_backtrace+0x0/0xe0) from [<c05f32f0>] (panic+0x84/0x1d4)
[ 300.532559] [<c05f32f0>] (panic+0x84/0x1d4) from [<c0093058>] (watchdog+0x210/0x248)
[ 300.540669] [<c0093058>] (watchdog+0x210/0x248) from [<c00599b0>] (kthread+0xa0/0xac)
[ 300.548860] [<c00599b0>] (kthread+0xa0/0xac) from [<c000d6f8>] (ret_from_fork+0x14/0x3c)
[ 300.557322] drm_kms_helper: panic occurred, switching back to text console
')

Happens every time, but only on fresh installs. A large update later happens without problems

would the suggestion:
$this->bbcode_second_pass_code('', 'echo 0 > /proc/sys/kernel/hung_task_timeout_secs')
help?

LP

[PLyttle]

The timeout is normally set at 120 secs. Maybe that is why the problem never occurs again. It looks like this value is initially set at 60?

LP

[PLyttle]

When the timeout is initially set at 120 instead of 60 the update works fine
$this->bbcode_second_pass_code('', '[root@alarm ~]# cat /proc/sys/kernel/hung_task_timeout_secs
60
[root@alarm ~]# echo 120 > /proc/sys/kernel/hung_task_timeout_secs
[root@alarm ~]# cat /proc/sys/kernel/hung_task_timeout_secs
120
pacman -Syu
:: Synchronizing package databases...
...')

Problem solved.
PS. I've got a rev A5A

LP