Bricked Turris Omnia: After Turris OS 5.0 -> sysupgrade OpenWRT 19.07.2

Hello,

I tried to sysupgrade to OpenWRT 19.07.2 from SSH in Turris OS 5.0. After that, the Omnia doesn’t function properly.

Using medkit file and USB, I’ve tried to revive the Omnia through console serial connection, but I reach this error:

ERROR: Did not find a cmdline Flattened Device Tree
Could not find a valid device tree

Is anyone familiar with this error? I’ve found it in another post, but it was un-resolved.

Thanks.

Bit of forum search might reveal the solution.


Never mind that TOS5.0 is currently based on OpenWrt 19.07.2 and thus there would be no benefit with that upgrade approach.

As far as I know OpenWrt does not fiddle with the u-boot (boot loader) image that ships on the device (/dev/mtd0) from the manufacturer but it does change the boot (env) variables as per OpenWrt specifications [1] and which are different from TOS.

You would have to decide whether to run OpenWrt or TOS and install accordingly but trying to switch between the two on same partition does not work so well.

Alternatively it should be feasible to install TOS on one partition and OpenWrt on another one and switch between the two (dual boot) from ssh. But that is a more complex topic and already discussed elsewhere in the forum.


[1] https://github.com/openwrt/openwrt/pull/2693/commits/bd8b290f4a61f08a9f50a80abae6c8c6070745fb

I’ve gotten as far as resetting uBoot, but when I do that I’m eventually prompted with a message related to bad zImage magic.

Unfortunately I haven’t found instructions on how to use the various uBoot commands. For example, I’m not sure how to manipulate a partition on the device from uBoot. I have found other topics in the forum covering similar issues, but I’ve yet to find a solution with enough detail with respect to uBoot commands that I’m able to follow.

Also, I expect I’ll need to transfer files to the device from a tftp server running on my machine, but as of right now the device doesnt seem to be finding my machine when I run the dhcp command from uBoot. It appears to connect to then I see roughly 14 BOOTP broadcast messages before it times out.

Any additional help on this topic is appreciated. Thanks.

u-boot commands
?       - alias for 'help'
base    - print or set address offset
bdinfo  - print Board Info structure
boot    - boot default, i.e., run 'bootcmd'
bootd   - boot default, i.e., run 'bootcmd'
bootm   - boot application image from memory
bootp   - boot image via network using BOOTP/TFTP protocol
bootz   - boot Linux zImage image from memory
btrload - load binary file from a btr filesystem
btrls   - list files in a directory (default /)
cmp     - memory compare
coninfo - print console devices and information
cp      - memory copy
crc32   - checksum calculation
dcache  - enable or disable data cache
dhcp    - boot image via network using DHCP/TFTP protocol
dm      - Driver model low level access
echo    - echo args to console
editenv - edit environment variable
env     - environment handling commands
exit    - exit script
ext2load- load binary file from a Ext2 filesystem
ext2ls  - list files in a directory (default /)
ext4load- load binary file from a Ext4 filesystem
ext4ls  - list files in a directory (default /)
ext4size- determine a file's size
false   - do nothing, unsuccessfully
fatinfo - print information about filesystem
fatload - load binary file from a dos filesystem
fatls   - list files in a directory (default /)
fatsize - determine a file's size
fdt     - flattened device tree utility commands
fstype  - Look up a filesystem type
go      - start application at address 'addr'
help    - print command description/usage
i2c     - I2C sub-system
icache  - enable or disable instruction cache
iminfo  - print header information for application image
imxtract- extract a part of a multi-image
itest   - return true/false on integer compare
load    - load binary file from a filesystem
loadb   - load binary file over serial line (kermit mode)
loads   - load S-Record file over serial line
loadx   - load binary file over serial line (xmodem mode)
loady   - load binary file over serial line (ymodem mode)
loop    - infinite loop on address range
ls      - list files in a directory (default /)
md      - memory display
mdio    - MDIO utility commands
mii     - MII utility commands
mm      - memory modify (auto-incrementing address)
mmc     - MMC sub system
mmcinfo - display MMC info
mw      - memory write (fill)
nfs     - boot image via network using NFS protocol
nm      - memory modify (constant address)
pci     - list and access PCI Configuration Space
ping    - send ICMP ECHO_REQUEST to network host
printenv- print environment variables
reset   - Perform RESET of the CPU
run     - run commands in an environment variable
save    - save file to a filesystem
saveenv - save environment variables to persistent storage
scsi    - SCSI sub-system
scsiboot- boot from SCSI device
setenv  - set environment variables
setexpr - set environment variable as the result of eval expression
sf      - SPI flash sub-system
showvar - print local hushshell variables
size    - determine a file's size
sleep   - delay execution for some time
source  - run script from memory
sspi    - SPI utility command
test    - minimal test like /bin/sh
tftpboot- boot image via network using TFTP protocol
tftpput - TFTP put command, for uploading files to a server
time    - run commands and summarize execution time
true    - do nothing, successfully
usb     - USB sub-system
usbboot - boot from USB device
version - print monitor, compiler and linker version

Which is typical for an OpenWrt installation but not TOS. If you wan to stay with OpenWrt they got plenty of documentation on the subject and also their own forum.


If you want to stick with TOS try the 4-LED reset with a medkit.

Even with the uBoot commands from the help menu, I haven’t been able to figure out how to change a partition.

I’ve used a TFTP server in the past to load OpenWRT files on another device in the past. I haven’t figured out how to make it work with the Omnia yet.

I’ve tried using the Medkit reset method for both TOS medkit files and the OpenWRT medkit file. In any case, this is my uBOOT output:

U-Boot SPL 2015.10-rc2 (Aug 18 2016 - 20:43:35)
High speed PHY - Version: 2.0
SERDES0 card detect: PEX

Initialize Turris board topology
Detected Device ID 6820
board SerDes lanes topology details:
 | Lane #  | Speed |  Type       |
 --------------------------------
 |   0    |  5   |  PCIe0       |
 |   1    |  5   |  USB3 HOST0  |
 |   2    |  5   |  PCIe1       |
 |   3    |  5   |  USB3 HOST1  |
 |   4    |  5   |  PCIe2       |
 |   5    |  0   |  SGMII2      |
 --------------------------------
:** Link is Gen1, check the EP capability
PCIe, Idx 0: remains Gen1
:** Link is Gen1, check the EP capability
PCIe, Idx 1: remains Gen1
PCIe, Idx 2: detected no link
High speed PHY - Ended Successfully
DDR3 Training Sequence - Ver TIP-1.29.0
Memory config in EEPROM: 0x02
DDR3 Training Sequence - Switching XBAR Window to FastPath Window
DDR3 Training Sequence - Ended Successfully


U-Boot 2015.10-rc2 (Aug 18 2016 - 20:43:35 +0200), Build: jenkins-omnia-master-23

SoC:   MV88F6820-A0
       Watchdog enabled
I2C:   ready
SPI:   ready
DRAM:  2 GiB (ECC not enabled)
Enabling Armada 385 watchdog.
Disabling MCU startup watchdog.
Regdomain set to **
MMC:   mv_sdh: 0
SF: Detected S25FL164K with page size 256 Bytes, erase size 64 KiB, total 8 MiB
PCI:
  00:01.0     - 168c:003c - Network controller
PCI:
  01:00.0     - 11ab:6820 - Memory controller
  01:01.0     - 168c:002e - Network controller
Model: Marvell Armada 385 GP
Board: Turris Omnia SN: 0000000C00009E06
Regdomain set to **
SCSI:  MVEBU SATA INIT
SATA link 0 timeout.
SATA link 1 timeout.
AHCI 0001.0000 32 slots 2 ports 6 Gbps 0x3 impl SATA mode
flags: 64bit ncq led only pmp fbss pio slum part sxs
Net:   neta2
Hit any key to stop autoboot:  0
Setting bus to 1
BOOT RESCUE
SF: Detected S25FL164K with page size 256 Bytes, erase size 64 KiB, total 8 MiB
device 0 offset 0x100000, size 0x700000
SF: 7340032 bytes @ 0x100000 Read: OK
Kernel image @ 0x1000000 [ 0x000000 - 0x689b30 ]

Starting kernel ...

[    0.000000] Booting Linux on physical CPU 0x0
[    0.000000] Linux version 4.4.13-369554f06f5670aea91212be2c6d6e58-7 (beast@slave01) (gcc version 4.8.3 (OpenWrt/Linaro GCC 4.8-2014.04 r49274) ) #4 SMP Thu Aug 18 20:46:34 CEST 2016
[    0.000000] CPU: ARMv7 Processor [414fc091] revision 1 (ARMv7), cr=10c5387d
[    0.000000] CPU: PIPT / VIPT nonaliasing data cache, VIPT aliasing instruction cache
[    0.000000] Machine model: Turris Omnia
[    0.000000] Memory policy: Data cache writealloc
[    0.000000] PERCPU: Embedded 11 pages/cpu @eefcb000 s13952 r8192 d22912 u45056
[    0.000000] Built 1 zonelists in Zone order, mobility grouping on.  Total pages: 522752
[    0.000000] Kernel command line: earlyprintk console=ttyS0,115200 rootfstype=btrfs rootdelay=2 root=b301 rootflags=subvol=@,commit=5 rw omniarescue=3
[    0.000000] PID hash table entries: 4096 (order: 2, 16384 bytes)
[    0.000000] Dentry cache hash table entries: 131072 (order: 7, 524288 bytes)
[    0.000000] Inode-cache hash table entries: 65536 (order: 6, 262144 bytes)
[    0.000000] Memory: 2069096K/2097152K available (4730K kernel code, 144K rwdata, 676K rodata, 4912K init, 182K bss, 28056K reserved, 0K cma-reserved, 1310720K highmem)
[    0.000000] Virtual kernel memory layout:
[    0.000000]     vector  : 0xffff0000 - 0xffff1000   (   4 kB)
[    0.000000]     fixmap  : 0xffc00000 - 0xfff00000   (3072 kB)
[    0.000000]     vmalloc : 0xf0800000 - 0xff800000   ( 240 MB)
[    0.000000]     lowmem  : 0xc0000000 - 0xf0000000   ( 768 MB)
[    0.000000]     pkmap   : 0xbfe00000 - 0xc0000000   (   2 MB)
[    0.000000]     modules : 0xbf000000 - 0xbfe00000   (  14 MB)
[    0.000000]       .text : 0xc0008000 - 0xc054fe6c   (5408 kB)
[    0.000000]       .init : 0xc0550000 - 0xc0a1c000   (4912 kB)
[    0.000000]       .data : 0xc0a1c000 - 0xc0a40274   ( 145 kB)
[    0.000000]        .bss : 0xc0a40274 - 0xc0a6dc38   ( 183 kB)
[    0.000000] Hierarchical RCU implementation.
[    0.000000]  RCU restricting CPUs from NR_CPUS=4 to nr_cpu_ids=2.
[    0.000000] RCU: Adjusting geometry for rcu_fanout_leaf=16, nr_cpu_ids=2
[    0.000000] NR_IRQS:16 nr_irqs:16 16
[    0.000000] mvebu_mbus: [Firmware Warn]: deprecated mbus-mvebu Device Tree, suspend/resume will not work
[    0.000000] L2C-310 enabling early BRESP for Cortex-A9
[    0.000000] L2C-310 full line of zeros enabled for Cortex-A9
[    0.000000] L2C-310 D prefetch enabled, offset 1 lines
[    0.000000] L2C-310 dynamic clock gating enabled, standby mode enabled
[    0.000000] L2C-310 Coherent cache controller enabled, 16 ways, 1024 kB
[    0.000000] L2C-310 Coherent: CACHE_ID 0x410054c9, AUX_CTRL 0x56070001
[    0.000000] Switching to timer-based delay loop, resolution 40ns
[    0.000003] sched_clock: 32 bits at 25MHz, resolution 40ns, wraps every 85899345900ns
[    0.000009] clocksource: armada_370_xp_clocksource: mask: 0xffffffff max_cycles: 0xffffffff, max_idle_ns: 76450417870 ns
[    0.000150] Calibrating delay loop (skipped), value calculated using timer frequency.. 50.00 BogoMIPS (lpj=250000)
[    0.000157] pid_max: default: 32768 minimum: 301
[    0.000205] Mount-cache hash table entries: 2048 (order: 1, 8192 bytes)
[    0.000210] Mountpoint-cache hash table entries: 2048 (order: 1, 8192 bytes)
[    0.000425] CPU: Testing write buffer coherency: ok
[    0.000532] CPU0: thread -1, cpu 0, socket 0, mpidr 80000000
[    0.000545] Setting up static identity map for 0x8280 - 0x82d8
[    0.000623] mvebu-soc-id: MVEBU SoC ID=0x6820, Rev=0x4
[    0.000703] mvebu-pmsu: Initializing Power Management Service Unit
[    0.001130] Booting CPU 1
[    0.001306] CPU1: thread -1, cpu 1, socket 0, mpidr 80000001
[    0.001336] Brought up 2 CPUs
[    0.001342] SMP: Total of 2 processors activated (100.00 BogoMIPS).
[    0.001345] CPU: All CPU(s) started in SVC mode.
[    0.003029] VFP support v0.3: implementor 41 architecture 3 part 30 variant 9 rev 4
[    0.003085] clocksource: jiffies: mask: 0xffffffff max_cycles: 0xffffffff, max_idle_ns: 19112604462750000 ns
[    0.003102] xor: measuring software checksum speed
[    0.099895]    arm4regs  :  2768.800 MB/sec
[    0.199897]    8regs     :  1859.200 MB/sec
[    0.299896]    32regs    :  1664.000 MB/sec
[    0.299899] xor: using function: arm4regs (2768.800 MB/sec)
[    0.299905] pinctrl core: initialized pinctrl subsystem
[    0.300235] NET: Registered protocol family 16
[    0.300735] DMA: preallocated 256 KiB pool for atomic coherent allocations
[    0.329919] cpuidle: using governor ladder
[    0.332545] mvebu-pmsu: CPU hotplug support is currently broken on Armada 38x: disabling
[    0.332553] mvebu-pmsu: CPU idle is currently broken on Armada 38x: disabling
[    0.530181] raid6: int32x1  gen()   155 MB/s
[    0.700036] raid6: int32x1  xor()   202 MB/s
[    0.869919] raid6: int32x2  gen()   255 MB/s
[    1.039919] raid6: int32x2  xor()   229 MB/s
[    1.209973] raid6: int32x4  gen()   284 MB/s
[    1.379984] raid6: int32x4  xor()   190 MB/s
[    1.549934] raid6: int32x8  gen()   371 MB/s
[    1.719947] raid6: int32x8  xor()   214 MB/s
[    1.719950] raid6: using algorithm int32x8 gen() 371 MB/s
[    1.719953] raid6: .... xor() 214 MB/s, rmw enabled
[    1.719956] raid6: using intx1 recovery algorithm
[    1.720547] clocksource: Switched to clocksource armada_370_xp_clocksource
[    1.720905] NET: Registered protocol family 2
[    1.721143] TCP established hash table entries: 8192 (order: 3, 32768 bytes)
[    1.721181] TCP bind hash table entries: 8192 (order: 4, 65536 bytes)
[    1.721242] TCP: Hash tables configured (established 8192 bind 8192)
[    1.721277] UDP hash table entries: 512 (order: 2, 16384 bytes)
[    1.721300] UDP-Lite hash table entries: 512 (order: 2, 16384 bytes)
[    1.721404] NET: Registered protocol family 1
[    2.856967] futex hash table entries: 512 (order: 3, 32768 bytes)
[    2.857297] squashfs: version 4.0 (2009/01/31) Phillip Lougher
[    2.857303] jffs2: version 2.2 (NAND) (SUMMARY) (LZMA) (RTIME) (CMODE_PRIORITY) (c) 2001-2006 Red Hat, Inc.
[    2.857631] bounce: pool size: 64 pages
[    2.857663] Block layer SCSI generic (bsg) driver version 0.4 loaded (major 252)
[    2.857669] io scheduler noop registered
[    2.857672] io scheduler deadline registered (default)
[    2.858046] armada-38x-pinctrl f1018000.pinctrl: registered pinctrl driver
[    2.858371] irq: Cannot allocate irq_descs @ IRQ48, assuming pre-allocated
[    2.858520] irq: Cannot allocate irq_descs @ IRQ80, assuming pre-allocated
[    2.858848] mvebu-pcie soc:pcie-controller: PCI host bridge to bus 0000:00
[    2.858857] pci_bus 0000:00: root bus resource [io  0x1000-0xfffff]
[    2.858862] pci_bus 0000:00: root bus resource [mem 0xe0000000-0xe7ffffff]
[    2.858867] pci_bus 0000:00: root bus resource [bus 00-ff]
[    2.859161] PCI: bus0: Fast back to back transfers disabled
[    2.859167] pci 0000:00:01.0: bridge configuration invalid ([bus 00-00]), reconfiguring
[    2.859175] pci 0000:00:02.0: bridge configuration invalid ([bus 00-00]), reconfiguring
[    2.859180] pci 0000:00:03.0: bridge configuration invalid ([bus 00-00]), reconfiguring
[    2.859436] PCI: bus1: Fast back to back transfers disabled
[    2.859704] PCI: bus2: Fast back to back transfers disabled
[    2.859761] PCI: bus3: Fast back to back transfers enabled
[    2.859822] pci 0000:00:01.0: BAR 8: assigned [mem 0xe0000000-0xe02fffff]
[    2.859829] pci 0000:00:02.0: BAR 8: assigned [mem 0xe0300000-0xe03fffff]
[    2.859836] pci 0000:01:00.0: BAR 0: assigned [mem 0xe0000000-0xe01fffff 64bit]
[    2.859848] pci 0000:01:00.0: BAR 6: assigned [mem 0xe0200000-0xe020ffff pref]
[    2.859853] pci 0000:00:01.0: PCI bridge to [bus 01]
[    2.859859] pci 0000:00:01.0:   bridge window [mem 0xe0000000-0xe02fffff]
[    2.859867] pci 0000:02:00.0: BAR 0: assigned [mem 0xe0300000-0xe030ffff 64bit]
[    2.859877] pci 0000:00:02.0: PCI bridge to [bus 02]
[    2.859882] pci 0000:00:02.0:   bridge window [mem 0xe0300000-0xe03fffff]
[    2.859888] pci 0000:00:03.0: PCI bridge to [bus 03]
[    2.859995] mv_xor f1060800.xor: Marvell shared XOR driver
[    2.900853] mv_xor f1060800.xor: Marvell XOR (Descriptor Mode): ( xor cpy intr )
[    2.900949] mv_xor f1060900.xor: Marvell shared XOR driver
[    2.940821] mv_xor f1060900.xor: Marvell XOR (Descriptor Mode): ( xor cpy intr )
[    2.940958] Serial: 8250/16550 driver, 2 ports, IRQ sharing disabled
[    2.941259] console [ttyS0] disabled
[    2.961326] f1012000.serial: ttyS0 at MMIO 0xf1012000 (irq = 22, base_baud = 15625000) is a 16550A
[    3.716226] console [ttyS0] enabled
[    3.739938] f1012100.serial: ttyS1 at MMIO 0xf1012100 (irq = 23, base_baud = 15625000) is a 16550A
[    3.749648] m25p80 spi0.0: s25fl164k (8192 Kbytes)
[    3.756013] 2 ofpart partitions found on MTD device spi0.0
[    3.761523] Creating 2 MTD partitions on "spi0.0":
[    3.766326] 0x000000000000-0x000000100000 : "U-Boot"
[    3.771659] 0x000000100000-0x000000800000 : "Rescue system"
[    3.777919] libphy: Fixed MDIO Bus: probed
[    3.782251] libphy: orion_mdio_bus: probed
[    3.788395] mvneta f1030000.ethernet eth0: Using hardware mac address d8:58:d7:00:a3:65
[    3.797184] mvneta f1034000.ethernet eth1: Using hardware mac address d8:58:d7:00:a3:66
[    3.806005] mvneta f1070000.ethernet eth2: Using hardware mac address d8:58:d7:00:a3:67
[    3.814252] armada38x-rtc f10a3800.rtc: rtc core: registered f10a3800.rtc as rtc0
[    4.330655] i2c /dev entries driver
[    4.334896] at24 1-0054: 8192 byte 24c64 EEPROM, writable, 1 bytes/write
[    4.341669] i2c i2c-0: Added multiplexed i2c bus 1
[    4.346540] i2c i2c-0: Added multiplexed i2c bus 2
[    4.351418] i2c i2c-0: Added multiplexed i2c bus 3
[    4.356282] i2c i2c-0: Added multiplexed i2c bus 4
[    4.361154] i2c i2c-0: Added multiplexed i2c bus 5
[    4.366013] i2c i2c-0: Added multiplexed i2c bus 6
[    4.370882] i2c i2c-0: Added multiplexed i2c bus 7
[    4.375776] i2c i2c-0: Added multiplexed i2c bus 8
[    4.380586] pca954x 0-0070: registered 8 multiplexed busses for I2C mux pca9547
[    4.388049] sdhci: Secure Digital Host Controller Interface driver
[    4.394249] sdhci: Copyright(c) Pierre Ossman
[    4.398761] sdhci-pxav3 f10d8000.sdhci: No vmmc regulator found
[    4.404705] sdhci-pxav3 f10d8000.sdhci: No vqmmc regulator found
[    4.450544] mmc0: SDHCI controller on f10d8000.sdhci [f10d8000.sdhci] using ADMA
[    4.457983] sdhci-pltfm: SDHCI platform and OF driver helper
[    4.472928] NET: Registered protocol family 10
[    4.477856] NET: Registered protocol family 17
[    4.482333] bridge: automatic filtering via arp/ip/ip6tables has been deprecated. Update your scripts to load br_netfilter if you need this.
[    4.493720] mmc0: MAN_BKOPS_EN bit is not set
[    4.495091] mmc0: new high speed MMC card at address 0001
[    4.495320] mmcblk0: mmc0:0001 008G30 7.28 GiB
[    4.495396] mmcblk0boot0: mmc0:0001 008G30 partition 1 4.00 MiB
[    4.500595] mmcblk0boot1: mmc0:0001 008G30 partition 2 4.00 MiB
[    4.500665] mmcblk0rpmb: mmc0:0001 008G30 partition 3 4.00 MiB
[    4.501777]  mmcblk0: p1 p2
[    4.529788] 8021q: 802.1Q VLAN Support v1.8
[    4.534034] Registering SWP/SWPB emulation handler
[    4.539403] Btrfs loaded
[    4.542563] mvsw61xx 10.mvsw61xx: Found MV88E6176 at f1072004.mdio-mi:10
[    4.549282] mvsw61xx 10.mvsw61xx: Using indirect addressing
[    4.595865] armada38x-rtc f10a3800.rtc: setting system clock to 2038-02-12 08:38:28 UTC (2149576708)
[    4.607741] Freeing unused kernel memory: 4912K (c0550000 - c0a1c000)
modprobe grace
modprobe libata
[    4.682161] SCSI subsystem initialized
modprobe async_raid6_rec[    4.694419] async_tx: api initialized (async)
ov
modprobe nls_base
modprobe sha256_generic
modprobe mac802[    4.704577] Loading modules backported from Linux version master-2015-12-03-0-g1677f62
11
[    4.712679] Backport generated by backports.git backports-20151120-0-g906a6b3
[    4.732332] cfg80211: World regulatory domain updated:
[    4.737490] cfg80211:  DFS Master region: unset
[    4.741884] cfg80211:   (start_freq - end_freq @ bandwidth), (max_antenna_gain, max_eirp), (dfs_cac_time)
[    4.751716] cfg80211:   (2402000 KHz - 2472000 KHz @ 40000 KHz), (N/A, 2000 mBm), (N/A)
[    4.759741] cfg80211:   (2457000 KHz - 2482000 KHz @ 20000 KHz, 92000 KHz AUTO), (N/A, 2000 mBm), (N/A)
[    4.769171] cfg80211:   (2474000 KHz - 2494000 KHz @ 20000 KHz), (N/A, 2000 mBm), (N/A)
[    4.777203] cfg80211:   (5170000 KHz - 5250000 KHz @ 80000 KHz, 160000 KHz AUTO), (N/A, 2000 mBm), (N/A)
[    4.786727] cfg80211:   (5250000 KHz - 5330000 KHz @ 80000 KHz, 160000 KHz AUTO), (N/A, 2000 mBm), (0 s)
[    4.796242] cfg80211:   (5490000 KHz - 5730000 KHz @ 160000 KHz), (N/A, 2000 mBm), (0 s)
[    4.804359] cfg80211:   (5735000 KHz - 5835000 KHz @ 80000 KHz), (N/A, 2000 mBm), (N/A)
[    4.812389] cfg80211:   (57240000 KHz - 63720000 KHz @ 2160000 KHz), (N/A, 0 mBm), (N/A)
modprobe fuse
[    4.824823] fuse init (API version 7.23)
modprobe dm-region-hash
[    4.834138] device-mapper: ioctl: 4.34.0-ioctl (2015-10-28) initialised: dm-devel@redhat.com
modprobe xfs
[    4.910341] SGI XFS with security attributes, no debug enabled
modprobe orion_wdt
[    4.918632] orion_wdt: Initial timeout 171 sec
modprobe md4
modprobe mvsdio
modprobe cifs
modprobe cryptodev
[    4.943741] cryptodev: driver 1.8 loaded.
modprobe async_xor
modprobe ahci_mvebu
[    4.953312] ahci-mvebu f10a8000.sata: AHCI 0001.0000 32 slots 2 ports 6 Gbps 0x3 impl platform mode
[    4.962412] ahci-mvebu f10a8000.sata: flags: 64bit ncq sntf led only pmp fbs pio slum part sxs
[    4.971893] scsi host0: ahci-mvebu
[    4.975457] scsi host1: ahci-mvebu
[    4.978958] ata1: SATA max UDMA/133 mmio [mem 0xf10a8000-0xf10a9fff] port 0x100 irq 44
[    4.986915] ata2: SATA max UDMA/133 mmio [mem 0xf10a8000-0xf10a9fff] port 0x180 irq 44
[    5.340541] ata2: SATA link down (SStatus 0 SControl 300)
[    5.345967] ata1: SATA link down (SStatus 0 SControl 300)
modprobe marvell-cesa
[    5.354730] marvell-cesa f1090000.crypto: CESA device successfully registered
modprobe libcrc32c
modprobe fat
modprobe dm-crypt
modprobe algif_hash
[    5.370827] NET: Registered protocol family 38
modprobe sunrpc
[    5.387641] RPC: Registered named UNIX socket transport module.
[    5.393608] RPC: Registered udp transport module.
[    5.398321] RPC: Registered tcp transport module.
[    5.403047] RPC: Registered tcp NFSv4.1 backchannel transport module.
modprobe nfs
modprobe af_alg
modprobe algif_skcipher
modprobe dm-mod
modprobe nls_utf8
modprobe vfat
modprobe nfsv3
modprobe raid1
[    5.437047] md: raid1 personality registered for level 1
modprobe sd_mod
modprobe loop
[    5.449630] loop: module loaded
modprobe ahci_platform
modprobe libahci_platform
modprobe md5
modprobe multipath
[    5.460756] md: multipath personality registered for level -4
modprobe usb-storage
[    5.476304] usbcore: registered new interface driver usbfs
[    5.481854] usbcore: registered new interface driver hub
[    5.487219] usbcore: registered new device driver usb
[    5.493511] usbcore: registered new interface driver usb-storage
modprobe nls_cp437
modprobe des_generic
modprobe lockd
modprobe usb-common
modprobe hwmon
modprobe seqiv
modprobe async_pq
modprobe armada_thermal
modprobe dm-mirror
modprobe ehci-orion
[    5.531298] ehci_hcd: USB 2.0 'Enhanced' Host Controller (EHCI) Driver
[    5.538038] ehci-orion: EHCI orion driver
[    5.542202] orion-ehci f1058000.usb: EHCI Host Controller
[    5.547624] orion-ehci f1058000.usb: new USB bus registered, assigned bus number 1
[    5.555295] orion-ehci f1058000.usb: irq 39, io mem 0xf1058000
[    5.580554] orion-ehci f1058000.usb: USB 2.0 started, EHCI 1.00
[    5.586751] hub 1-0:1.0: USB hub found
[    5.590523] hub 1-0:1.0: 1 port detected
modprobe gf128mul
modprobe cbc
modprobe cfg80211
modprobe thermal_sys
modprobe xhci-pci
modprobe async_memcpy
modprobe hmac
modprobe authenc
modprobe md-mod
modprobe sha512_generic
modprobe dm-log
modprobe xts
modprobe ehci-hcd
modprobe usbcore
modprobe aead
modprobe crypto_null
modprobe ath
modprobe linear
[    5.630756] md: linear personality registered for level -1
modprobe raid10
[    5.639037] md: raid10 personality registered for level 10
modprobe libahci
modprobe raid0
[    5.648448] md: raid0 personality registered for level 0
modprobe compat
modprobe xhci-hcd
modprobe xhci-plat-hcd
[    5.659283] xhci-hcd f10f0000.usb3: xHCI Host Controller
[    5.664792] xhci-hcd f10f0000.usb3: new USB bus registered, assigned bus number 2
[    5.672407] xhci-hcd f10f0000.usb3: hcc params 0x0a000990 hci version 0x100 quirks 0x00010010
[    5.680988] xhci-hcd f10f0000.usb3: irq 46, io mem 0xf10f0000
[    5.687018] hub 2-0:1.0: USB hub found
[    5.690836] hub 2-0:1.0: 1 port detected
[    5.694874] xhci-hcd f10f0000.usb3: xHCI Host Controller
[    5.700202] xhci-hcd f10f0000.usb3: new USB bus registered, assigned bus number 3
[    5.707777] usb usb3: We don't know the algorithms for LPM for this host, disabling LPM.
[    5.716128] hub 3-0:1.0: USB hub found
[    5.719898] hub 3-0:1.0: 1 port detected
[    5.724009] xhci-hcd f10f8000.usb3: xHCI Host Controller
[    5.729341] xhci-hcd f10f8000.usb3: new USB bus registered, assigned bus number 4
[    5.736957] xhci-hcd f10f8000.usb3: hcc params 0x0a000990 hci version 0x100 quirks 0x00010010
[    5.745536] xhci-hcd f10f8000.usb3: irq 47, io mem 0xf10f8000
[    5.751546] hub 4-0:1.0: USB hub found
[    5.755319] hub 4-0:1.0: 1 port detected
[    5.759344] xhci-hcd f10f8000.usb3: xHCI Host Controller
[    5.764693] xhci-hcd f10f8000.usb3: new USB bus registered, assigned bus number 5
[    5.772247] usb usb5: We don't know the algorithms for LPM for this host, disabling LPM.
[    5.780592] hub 5-0:1.0: USB hub found
[    5.784362] hub 5-0:1.0: 1 port detected
modprobe ehci-platform
[    5.790727] ehci-platform: EHCI generic platform driver
modprobe exportfs
modprobe async_tx
modprobe block2mtd
modprobe ecb
modprobe exfat
[    5.807489] exFAT: Version 1.2.9
modprobe raid456
[    5.816651] md: raid6 personality registered for level 6
[    5.822031] md: raid5 personality registered for level 5
[    5.827354] md: raid4 personality registered for level 4
modprobe scsi_mod
MODE=3
Mode: Reflash...
[    6.070554] usb 4-1: new high-speed USB device number 2 using xhci-hcd
[    6.077130] xhci-hcd f10f8000.usb3: ERROR: unexpected setup context command completion code 0x11.
[    6.086045] usb 4-1: hub failed to enable device, error -22
[    6.470559] usb 5-1: new SuperSpeed USB device number 2 using xhci-hcd
[    6.491937] usb-storage 5-1:1.0: USB Mass Storage device detected
[    6.498146] scsi host2: usb-storage 5-1:1.0
[    7.501102] scsi 2:0:0:0: Direct-Access     Kingston DataTraveler 3.0 PMAP PQ: 0 ANSI: 6
[    7.509656] sd 2:0:0:0: [sda] 121208832 512-byte logical blocks: (62.1 GB/57.8 GiB)
[    7.517591] sd 2:0:0:0: [sda] Write Protect is off
[    7.522657] sd 2:0:0:0: [sda] Write cache: disabled, read cache: enabled, doesn't support DPO or FUA
[    7.628939]  sda:
[    7.631925] sd 2:0:0:0: [sda] Attached SCSI removable disk
No medkit image found. Exit to shell.
Doing sysrq rebo[   16.141510] sysrq: SysRq : ot as busybox onChanging Loglevel
e doesn't work
[   16.147278] sysrq: Loglevel set to 0
[   16.152320] sysrq: SysRq : Resetting

U-Boot SPL 2015.10-rc2 (Aug 18 2016 - 20:43:35)
High speed PHY - Version: 2.0
SERDES0 card detect: PEX

Initialize Turris board topology
Detected Device ID 6820
board SerDes lanes topology details:
 | Lane #  | Speed |  Type       |
 --------------------------------
 |   0    |  5   |  PCIe0       |
 |   1    |  5   |  USB3 HOST0  |
 |   2    |  5   |  PCIe1       |
 |   3    |  5   |  USB3 HOST1  |
 |   4    |  5   |  PCIe2       |
 |   5    |  0   |  SGMII2      |
 --------------------------------
:** Link is Gen1, check the EP capability
PCIe, Idx 0: remains Gen1
:** Link is Gen1, check the EP capability
PCIe, Idx 1: remains Gen1
PCIe, Idx 2: detected no link
High speed PHY - Ended Successfully
DDR3 Training Sequence - Ver TIP-1.29.0
Memory config in EEPROM: 0x02
DDR3 Training Sequence - Switching XBAR Window to FastPath Window
DDR3 Training Sequence - Ended Successfully


U-Boot 2015.10-rc2 (Aug 18 2016 - 20:43:35 +0200), Build: jenkins-omnia-master-23

SoC:   MV88F6820-A0
       Watchdog enabled
I2C:   ready
SPI:   ready
DRAM:  2 GiB (ECC not enabled)
Enabling Armada 385 watchdog.
Disabling MCU startup watchdog.
Regdomain set to **
MMC:   mv_sdh: 0
SF: Detected S25FL164K with page size 256 Bytes, erase size 64 KiB, total 8 MiB
PCI:
  00:01.0     - 168c:003c - Network controller
PCI:
  01:00.0     - 11ab:6820 - Memory controller
  01:01.0     - 168c:002e - Network controller
Model: Marvell Armada 385 GP
Board: Turris Omnia SN: 0000000C00009E06
Regdomain set to **
SCSI:  MVEBU SATA INIT
SATA link 0 timeout.
SATA link 1 timeout.
AHCI 0001.0000 32 slots 2 ports 6 Gbps 0x3 impl SATA mode
flags: 64bit ncq led only pmp fbss pio slum part sxs
Net:   neta2
Hit any key to stop autoboot:  0
Setting bus to 1
BOOT eMMC FS
btrfs probe failed
** Unrecognized filesystem type **
btrfs probe failed
** Unrecognized filesystem type **
Kernel image @ 0x1000000 [ 0x000000 - 0x689b30 ]
ERROR: Did not find a cmdline Flattened Device Tree
Could not find a valid device tree

Make sure that the USB drive is correctly formatted and actually contains the medkit image

Thanks for the support. It was the USB… with a new USB, and after cleaning it using Windows diskpart tool, then reformatting using Linux Disks, it was recognized by the Omnia.