Possible to fix os on beaglebone black emmc?

[inkydinky]

I was updating the OS last night on the sd card that is on a Beagle Bone Black and the update crapped out with the following output:

$this->bbcode_second_pass_code('', '[puffjay@archd820 ~]$ bbb
beagleboneblack@192.168.1.102's password:
Last login: Mon Nov 9 03:58:31 2015 from 192.168.1.106
[beagleboneblack@alarm ~]$ sudo pacman -Syu
:: Synchronizing package databases...
core 210.4 KiB 1315K/s 00:00 [######################] 100%
extra 2.3 MiB 2.10M/s 00:01 [######################] 100%
community 3.2 MiB 2.10M/s 00:02 [######################] 100%
alarm 104.6 KiB 581K/s 00:00 [######################] 100%
aur 31.2 KiB 0.00B/s 00:00 [######################] 100%
:: Starting full system upgrade...
resolving dependencies...
looking for conflicting packages...

Packages (53) bash-4.3.042-4 ca-certificates-mozilla-3.21-1
cryptsetup-1.7.0-1 curl-7.46.0-1 db-5.3.28-3 dbus-1.10.6-1
device-mapper-2.02.137-1 dhcpcd-6.9.4-1 gcc-libs-5.3.0-3
gettext-0.19.6-2 git-2.6.4-1 glib2-2.46.2-2 gmp-6.1.0-2
gnupg-2.1.10-3 gnutls-3.4.7-2 groff-1.22.3-5 kmod-22-1
libassuan-2.4.2-1 libdbus-1.10.6-1 libelf-0.164-2
libgpg-error-1.21-1 libldap-2.4.43-1 libsigc++-2.6.2-1
libsystemd-228-3 libtirpc-1.0.1-2 libtorrent-0.13.6-2
libutil-linux-2.27.1-1 libxml2-2.9.3-1 linux-am33x-4.3.3-1
lvm2-2.02.137-1 man-db-2.7.5-1 man-pages-4.03-1 nano-2.5.0-1
ncurses-6.0-4 nfs-utils-1.3.3-3 openresolv-3.7.2-1
openssl-1.0.2.e-1 p11-kit-0.23.2-1 pacman-mirrorlist-20151228-1
pam-1.2.1-3 pciutils-3.4.0-1 pcre-8.38-2 perl-5.22.1-1
pinentry-0.9.7-1 rpcbind-0.2.3-3 rtorrent-0.9.6-3
sqlite-3.9.2-1 systemd-228-3 systemd-sysvcompat-228-3
thin-provisioning-tools-0.5.6-2 util-linux-2.27.1-1
xfsprogs-4.3.0-1 xmlrpc-c-1:1.41.01-2

Total Download Size: 86.93 MiB
Total Installed Size: 291.97 MiB
Net Upgrade Size: 29.14 MiB

:: Proceed with installation? [Y/n]
:: Retrieving packages ...
gcc-libs-5.3.0-3-armv7h 8.7 MiB 1348K/s 00:07 [######################] 100%
curses-6.0-4-armv7h 977.6 KiB 1746K/s 00:01 [######################] 100%
bash-4.3.042-4-armv7h 1175.3 KiB 1367K/s 00:01 [######################] 100%
db-5.3.28-3-armv7h 893.0 KiB 2.13M/s 00:00 [######################] 100%
perl-5.22.1-1-armv7h 12.2 MiB 2.04M/s 00:06 [######################] 100%
pcre-8.38-2-armv7h 840.1 KiB 1024K/s 00:01 [######################] 100%
p11-kit-0.23.2-1-armv7h 222.7 KiB 2024K/s 00:00 [######################] 100%
openssl-1.0.2.e-1-a... 2.3 MiB 2.12M/s 00:01 [######################] 100%
gmp-6.1.0-2-armv7h 328.0 KiB 2.00M/s 00:00 [######################] 100%
ca-certificates-moz... 362.7 KiB 2.21M/s 00:00 [######################] 100%
libgpg-error-1.21-1... 127.5 KiB 2.49M/s 00:00 [######################] 100%
libsystemd-228-3-armv7h 276.1 KiB 2.25M/s 00:00 [######################] 100%
libdbus-1.10.6-1-armv7h 115.4 KiB 2.82M/s 00:00 [######################] 100%
dbus-1.10.6-1-armv7h 290.3 KiB 2.18M/s 00:00 [######################] 100%
glib2-2.46.2-2-armv7h 1956.3 KiB 2.10M/s 00:01 [######################] 100%
kmod-22-1-armv7h 95.8 KiB 2.34M/s 00:00 [######################] 100%
libutil-linux-2.27.... 246.9 KiB 2.19M/s 00:00 [######################] 100%
libldap-2.4.43-1-armv7h 247.8 KiB 2.42M/s 00:00 [######################] 100%
libtirpc-1.0.1-2-armv7h 157.6 KiB 2.57M/s 00:00 [######################] 100%
pam-1.2.1-3-armv7h 583.0 KiB 2.19M/s 00:00 [######################] 100%
libelf-0.164-2-armv7h 322.3 KiB 2.25M/s 00:00 [######################] 100%
util-linux-2.27.1-1... 1615.9 KiB 2.10M/s 00:01 [######################] 100%
systemd-228-3-armv7h 4.1 MiB 1634K/s 00:03 [######################] 100%
device-mapper-2.02.... 252.5 KiB 2.47M/s 00:00 [######################] 100%
cryptsetup-1.7.0-1-... 211.1 KiB 1320K/s 00:00 [######################] 100%
curl-7.46.0-1-armv7h 760.0 KiB 2.12M/s 00:00 [######################] 100%
dhcpcd-6.9.4-1-armv7h 128.1 KiB 2.09M/s 00:00 [######################] 100%
gettext-0.19.6-2-armv7h 1789.8 KiB 2.13M/s 00:01 [######################] 100%
libassuan-2.4.2-1-a... 76.9 KiB 3.75M/s 00:00 [######################] 100%
pinentry-0.9.7-1-armv7h 76.7 KiB 3.75M/s 00:00 [######################] 100%
gnutls-3.4.7-2-armv7h 2.0 MiB 2.12M/s 00:01 [######################] 100%
sqlite-3.9.2-1-armv7h 621.1 KiB 2.17M/s 00:00 [######################] 100%
gnupg-2.1.10-3-armv7h 1565.8 KiB 2.09M/s 00:01 [######################] 100%
groff-1.22.3-5-armv7h 1707.8 KiB 773K/s 00:02 [######################] 100%
linux-am33x-4.3.3-1... 25.9 MiB 2010K/s 00:13 [######################] 100%
hin-provisioning-t... 294.4 KiB 2.21M/s 00:00 [######################] 100%
lvm2-2.02.137-1-armv7h 875.9 KiB 2.14M/s 00:00 [######################] 100%
man-db-2.7.5-1-armv7h 353.8 KiB 283K/s 00:01 [######################] 100%
man-pages-4.03-1-any 5.4 MiB 2.10M/s 00:03 [######################] 100%
ano-2.5.0-1-armv7h 376.6 KiB 1506K/s 00:00 [######################] 100%
rpcbind-0.2.3-3-armv7h 29.0 KiB 2.83M/s 00:00 [######################] 100%
fs-utils-1.3.3-3-a... 222.4 KiB 2.41M/s 00:00 [######################] 100%
openresolv-3.7.2-1-any 18.4 KiB 0.00B/s 00:00 [######################] 100%
pacman-mirrorlist-2... 1408.0 B 0.00B/s 00:00 [######################] 100%
pciutils-3.4.0-1-armv7h 66.8 KiB 3.26M/s 00:00 [######################] 100%
systemd-sysvcompat-... 6.0 KiB 0.00B/s 00:00 [######################] 100%
xfsprogs-4.3.0-1-armv7h 642.4 KiB 2.16M/s 00:00 [######################] 100%
git-2.6.4-1-armv7h 3.9 MiB 2.10M/s 00:02 [######################] 100%
libsigc++-2.6.2-1-a... 60.7 KiB 867K/s 00:00 [######################] 100%
libxml2-2.9.3-1-armv7h 1104.7 KiB 1139K/s 00:01 [######################] 100%
libtorrent-0.13.6-2... 345.8 KiB 2.25M/s 00:00 [######################] 100%
xmlrpc-c-1:1.41.01-... 236.7 KiB 2.31M/s 00:00 [######################] 100%
rtorrent-0.9.6-3-armv7h 357.2 KiB 2.33M/s 00:00 [######################] 100%
(53/53) checking keys in keyring [######################] 100%
(53/53) checking package integrity [######################] 100%
(53/53) loading package files [######################] 100%
(53/53) checking for file conflicts [######################] 100%
(53/53) checking available disk space [######################] 100%
( 1/53) upgrading gcc-libs [######################] 100%
( 2/53) upgrading ncurses [######################] 100%
( 3/53) upgrading bash [######################] 100%
( 4/53) upgrading db [######################] 100%
( 5/53) upgrading perl [######################] 100%
( 6/53) upgrading pcre [######################] 100%
( 7/53) upgrading p11-kit [######################] 100%
( 8/53) upgrading openssl [######################] 100%
( 9/53) upgrading gmp [######################] 100%
(10/53) upgrading ca-certificates-mozilla [######################] 100%
(11/53) upgrading libgpg-error [######################] 100%
(12/53) upgrading libsystemd [######################] 100%
(13/53) upgrading libdbus [######################] 100%
(14/53) upgrading dbus [######################] 100%
(15/53) upgrading glib2 [######################] 100%
(16/53) upgrading kmod [######################] 100%
(17/53) upgrading libutil-linux [######################] 100%
(18/53) upgrading libldap [######################] 100%
(19/53) upgrading libtirpc [######################] 100%
(20/53) upgrading pam [######################] 100%
(21/53) installing libelf [######################] 100%
(22/53) upgrading util-linux [######################] 100%
(23/53) upgrading systemd [----------------------] 1%
error: failed to commit transaction (transaction aborted)################-] 99%
Errors occurred, no packages were upgraded.
Bus error
[beagleboneblack@alarm ~]$
[beagleboneblack@alarm ~]$ sudo pacman -Syu
Segmentation fault
[beagleboneblack@alarm ~]$ tmux
-bash: /usr/bin/tmux: Input/output error
[beagleboneblack@alarm ~]$ sudo reboot
Segmentation fault
[beagleboneblack@alarm ~]$ packet_write_wait: Connection to 192.168.1.102: Broken pipe
')
Sadly this is all I have currently. Just the output from my ssh session.

At this point the device doesn't appear to be booting at all which leads me to think the failed upgrade did something really unpleasant.

If I was on a pc/laptop, I'd pop in a CD/USB with the distro on it to debug after editing the BIOS to boot from whichever media I was using.
Is there such a way to do that with the OS residing on the emmc?

At this point is my best option to simply re-image and move on?

I'm curious what my options are to debug and fix the issues encountered here.

Is there an easy way to keep any configs etc and to simply reinstall the OS on the emmc? IIRC, installing on the SD cards typically involves wiping the card, formatting and using `dd` to burn the image (at least that is how I think I've done it in the past) and then copying that over to the emmc.

EDITED:I thought the OS was on an SD card when in fact it was on the eMMC.

[kleykenb]

I confirm that BeagleBone Black becomes unbootable after upgrade (pacman -Syu).

The next boot craps out like this :
[ 4.972623] omap_i2c 44e0b000.i2c: bus 0 rev0.11 at 400 kHz
[ 4.979705] at24 2-0054: 32768 byte 24c256 EEPROM, writable, 1 bytes/write
[ 4.987044] at24 2-0055: 32768 byte 24c256 EEPROM, writable, 1 bytes/write
[ 4.994258] at24 2-0056: 32768 byte 24c256 EEPROM, writable, 1 bytes/write
[ 5.001531] at24 2-0057: 32768 byte 24c256 EEPROM, writable, 1 bytes/write
[ 5.008489] omap_i2c 4819c000.i2c: bus 2 rev0.11 at 100 kHz
[ 5.020552] bone_capemgr bone_capemgr: Baseboard: 'A335BNLT,00C0,3614BBBK273'
[ 5.027851] bone_capemgr bone_capemgr: compatible-baseboard=ti,beaglebone-bl4
[ 5.094752] bone_capemgr bone_capemgr: slot #0: No cape found
[ 5.154743] bone_capemgr bone_capemgr: slot #1: No cape found
[ 5.214747] bone_capemgr bone_capemgr: slot #2: No cape found
[ 5.274747] bone_capemgr bone_capemgr: slot #3: No cape found
[ 5.280591] bone_capemgr bone_capemgr: initialized OK.
[ 5.285974] cpu cpu0: of_pm_voltdm_notifier_register: Failed to get cpu0 reg7
[ 5.294718] cpu cpu0: cpu0 clock notifier not ready, retry
[ 5.300617] omap_rtc 44e3e000.rtc: setting system clock to 2000-01-01 00:00:)
[ 5.309339] of_cfs_init
[ 5.311902] of_cfs_init: OK
[ 5.317294] device-tree: Duplicate name in testcase-data, renamed to "duplic"
[ 5.328434] ### dt-test ### start of unittest - you will see error messages
[ 5.336158] /testcase-data/phandle-tests/consumer-a: could not get #phandle-1
[ 5.348169] /testcase-data/phandle-tests/consumer-a: could not get #phandle-1
[ 5.360147] /testcase-data/phandle-tests/consumer-a: could not find phandle
[ 5.367146] /testcase-data/phandle-tests/consumer-a: could not find phandle
[ 5.374137] /testcase-data/phandle-tests/consumer-a: arguments longer than py
[ 5.381834] /testcase-data/phandle-tests/consumer-a: arguments longer than py
[ 5.389822] ### dt-test ### FAIL of_unittest_changeset_helper():575 '/testcad
and then after a long wait :
[ 147.624751] random: nonblocking pool is initialized
and even later :
[ 240.684743] INFO: task swapper:1 blocked for more than 120 seconds.
[ 240.691039] Not tainted 4.4.0-4-ARCH #1
[ 240.695424] "echo 0 > /proc/sys/kernel/hung_task_timeout_secs" disables this.
[ 240.703287] swapper D c090722c 0 1 0 0x00000000
[ 240.709732] [<c090722c>] (__schedule) from [<c09075a8>] (schedule+0x50/0xa8)
[ 240.716831] [<c09075a8>] (schedule) from [<c09077e4>] (schedule_preempt_disa)
[ 240.725235] [<c09077e4>] (schedule_preempt_disabled) from [<c0908bc4>] (__mu)
[ 240.734771] [<c0908bc4>] (__mutex_lock_slowpath) from [<c0908c80>] (mutex_lo)
[ 240.742990] [<c0908c80>] (mutex_lock) from [<c0781498>] (of_changeset_revert)
[ 240.751057] [<c0781498>] (of_changeset_revert) from [<c0d66ff0>] (of_unittes)
[ 240.759550] [<c0d66ff0>] (of_unittest) from [<c0009674>] (do_one_initcall+0x)
[ 240.767434] [<c0009674>] (do_one_initcall) from [<c0d16f24>] (kernel_init_fr)
[ 240.776185] [<c0d16f24>] (kernel_init_freeable) from [<c090642c>] (kernel_in)
[ 240.784406] [<c090642c>] (kernel_init) from [<c0010738>] (ret_from_fork+0x14)

Edited :
NORMAL boot looks like this :
[ 5.345721] of_cfs_init
[ 5.348271] of_cfs_init: OK
[ 5.353624] device-tree: Duplicate name in testcase-data, renamed to "duplicate-name#1"
[ 5.364639] ### dt-test ### start of unittest - you will see error messages
[ 5.372377] /testcase-data/phandle-tests/consumer-a: could not get #phandle-cells-missing for /testcase-data/phandle-tests/provider1
[ 5.384389] /testcase-data/phandle-tests/consumer-a: could not get #phandle-cells-missing for /testcase-data/phandle-tests/provider1
[ 5.396367] /testcase-data/phandle-tests/consumer-a: could not find phandle
[ 5.403357] /testcase-data/phandle-tests/consumer-a: could not find phandle
[ 5.410357] /testcase-data/phandle-tests/consumer-a: arguments longer than property
[ 5.418055] /testcase-data/phandle-tests/consumer-a: arguments longer than property
[ 5.426038] ### dt-test ### FAIL of_unittest_changeset_helper():579 '/testcase-data/changeset/n2/n21' not added
[ 5.437190] irq: no irq domain found for /testcase-data/interrupts/intc0 !
[ 5.453185] overlay_is_topmost: #5 clashes #6 @/testcase-data/overlay-node/test-bus/test-unittest8
[ 5.462270] overlay_removal_is_ok: overlay #5 is not topmost
[ 5.467964] of_overlay_destroy: removal check failed for overlay #5
[ 5.478978] find_target_node_direct: target "/ocp/l4_wkup@44c00000/prcm@200000/clocks/l3_gclk" not under target_root "/testcase-data/overlay-node/test-bus/test-unittest19"
[ 5.494417] __of_overlay_create: of_build_overlay_info() failed for tree@/testcase-data/overlay19
[ 5.505320] i2c i2c-3: Added multiplexed i2c bus 4
[ 5.511885] i2c i2c-3: Added multiplexed i2c bus 5
[ 5.520828] ### dt-test ### end of unittest - 159 passed, 1 failed
[ 5.532040] EXT4-fs (mmcblk1p1): couldn't mount as ext3 due to feature incompatibilities
[ 5.541005] EXT4-fs (mmcblk1p1): couldn't mount as ext2 due to feature incompatibilities
[ 5.560488] EXT4-fs (mmcblk1p1): mounted filesystem with ordered data mode. Opts: (null)
[ 5.568757] VFS: Mounted root (ext4 filesystem) on device 179:9.
[ 5.575488] devtmpfs: mounted
[ 5.579105] Freeing unused kernel memory: 616K (c0d16000 - c0db0000)
[ 5.816123] ip_tables: (C) 2000-2006 Netfilter Core Team
[ 5.830847] random: systemd urandom read with 23 bits of entropy available
[ 5.858460] systemd[1]: systemd 228 running in system mode. (+PAM -AUDIT -SELINUX -IMA -APPARMOR +SMACK -SYSVINIT +UTMP +LIBCRYPTSETUP +GCRYPT +GNUTLS +ACL +XZ +LZ4 +SECCOMP +BLKID +ELFUTILS +KMOD +IDN)
[ 5.877292] systemd[1]: Detected architecture arm.

Welcome to Arch Linux ARM!

[WarheadsSE]

viewtopic.php?f=48&t=9451&p=49264&hilit=beaglebone+mmc+sysctl#p49264

[kleykenb]

Solution confirmed :
$this->bbcode_second_pass_code('', 'echo "vm.min_free_kbytes=16384" >>/etc/sysctl.d/10-vm.conf')

edit: code tags added

[WarheadsSE]

Please use code tags.