Can't stat /proc/sys/vm & K Panic when Flashing eMMC while Running with a Kernel built from Source

Jeff Andich

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Feb 13, 2018, 6:17:32 PM2/13/18

to BeagleBoard

Hi,

I burned a uSD card with bbx15-debian-8.10-console-armhf-2018-01-01-1gb.img.xz which I got from elinux.org. The kernel which comes with that image is 4.4.91-ti-r141. But I have been building kernel version 4.4.110-ti-r142 from source following the instructions on eewiki.net for the BB-X15, and copying the kernel image, dtbs, and modules to that same uSD card which still has the stock kernel on it. Both kernel's appear to run just fine from uSD card when uname-r is changed in uEnv.txt.

But when I run try to run the eMMC flasher script with the 4.4.110 (built from source) kernel running instead of the "stock kernel" running the flasher script dies when /proc/sys/vm/min_free_kbytes isn't there and then you see a kernel panic (please see console dump below). However, when I switch the running kernel back to the stock kernel, 4.4.91-ti-r141 which came with that image, the eMMC flasher script again works. I've tried running both, /opt/scripts/tools/eMMC/init-eMMC-flasher-v3-no-eeprom.sh and init-eMMC-flasher-v3-x15_b1.sh, both with the same result (I think).

I'm wondering what other crucial step needs to be followed which I missed... I didn't touch the filesystem which was already part of the 2018-01-01 console BB-X15 image on that uSD card, but when I run "mount" on both kernels, I get differences (see below).

Please take a look at what I've posted below and give me some clues as to where to look or what to read up on next..

Thanks!!

*When the kernel built from source (4.4.110) is running from uSD card, and I'm logged in as debian (or have typed sudo su from debian), I'm able to run /sbin/sysctl -n vm.min_free_kbytes both as "debian" and su. So proc appears to be present on the 4.4.110 kernel running from uSD card once logged in:

*When running both kernels from the uSD card, I ran "zcat /proc/config.gz" and the configurations were "pretty similar." (see diff below):

< # Linux/arm 4.4.91 Kernel Configuration

---

> # Linux/arm 4.4.110 Kernel Configuration

1208a1209

> # CONFIG_NET_DSA is not set

2809,2810c2810,2811

< CONFIG_SERIAL_8250_NR_UARTS=6

< CONFIG_SERIAL_8250_RUNTIME_UARTS=6

---

> CONFIG_SERIAL_8250_NR_UARTS=9

> CONFIG_SERIAL_8250_RUNTIME_UARTS=9

*One thing that's different is the outputs of the "mount" command run on the two kernels:

> /dev/mmcblk0p1 on / type ext4 (rw,relatime,errors=remount-ro,data=ordered)

> devtmpfs on /dev type devtmpfs (rw,relatime,size=824360k,nr_inodes=97302,mode=755)

3,6d4

< udev on /dev type devtmpfs (rw,relatime,size=10240k,nr_inodes=96053,mode=755)

< devpts on /dev/pts type devpts (rw,nosuid,noexec,relatime,gid=5,mode=620,ptmxmode=000)

< tmpfs on /run type tmpfs (rw,nosuid,relatime,size=372500k,mode=755)

< /dev/mmcblk0p1 on / type ext4 (rw,relatime,errors=remount-ro,data=ordered)

8a7,8

> devpts on /dev/pts type devpts (rw,nosuid,noexec,relatime,gid=5,mode=620,ptmxmode=000)

> tmpfs on /run type tmpfs (rw,nosuid,nodev,mode=755)

13,17d12

< cgroup on /sys/fs/cgroup/freezer type cgroup (rw,nosuid,nodev,noexec,relatime,freezer)

< cgroup on /sys/fs/cgroup/blkio type cgroup (rw,nosuid,nodev,noexec,relatime,blkio)

< cgroup on /sys/fs/cgroup/perf_event type cgroup (rw,nosuid,nodev,noexec,relatime,perf_event)

< cgroup on /sys/fs/cgroup/devices type cgroup (rw,nosuid,nodev,noexec,relatime,devices)

< cgroup on /sys/fs/cgroup/cpu,cpuacct type cgroup (rw,nosuid,nodev,noexec,relatime,cpu,cpuacct)

19c14,15

< cgroup on /sys/fs/cgroup/cpuset type cgroup (rw,nosuid,nodev,noexec,relatime,cpuset)

---

> cgroup on /sys/fs/cgroup/cpu,cpuacct type cgroup (rw,nosuid,nodev,noexec,relatime,cpu,cpuacct)

> cgroup on /sys/fs/cgroup/perf_event type cgroup (rw,nosuid,nodev,noexec,relatime,perf_event)

21c17,20

< systemd-1 on /proc/sys/fs/binfmt_misc type autofs (rw,relatime,fd=22,pgrp=1,timeout=0,minproto=5,maxproto=5,direct)

---

> cgroup on /sys/fs/cgroup/cpuset type cgroup (rw,nosuid,nodev,noexec,relatime,cpuset)

> cgroup on /sys/fs/cgroup/freezer type cgroup (rw,nosuid,nodev,noexec,relatime,freezer)

> cgroup on /sys/fs/cgroup/devices type cgroup (rw,nosuid,nodev,noexec,relatime,devices)

> cgroup on /sys/fs/cgroup/blkio type cgroup (rw,nosuid,nodev,noexec,relatime,blkio)

24c23

< configfs on /sys/kernel/config type configfs (rw,relatime)

---

> systemd-1 on /proc/sys/fs/binfmt_misc type autofs (rw,relatime,fd=33,pgrp=1,timeout=0,minproto=5,maxproto=5,direct)

26c25,26

< tmpfs on /run/user/1000 type tmpfs (rw,nosuid,nodev,relatime,size=186252k,mode=700,uid=1000,gid=1000)

---

> configfs on /sys/kernel/config type configfs (rw,relatime)

> tmpfs on /run/user/1000 type tmpfs (rw,nosuid,nodev,relatime,size=186248k,mode=700,uid=1000,gid=1000)

**** Console dump when attempting to flash the eMMC using kernel 4.4.110-ti-r142 compiled from source *****

================================================================================

Starting eMMC Flasher from microSD media

Version: [1.20171220: btrfs...]

================================================================================

Prepare environment for flashing

Starting at Mon Jan 1 00:28:24 UTC 2001

----------------------------------------

==> Giving system time to stablize...

5 4 3 2 1

==> Preparing /tmp

==> Preparing sysctl

sysctl: cannot stat /proc/sys/vm/min_free_kbytes: No such file or directory

Traceback (last called is first):

prepare_environment() in /opt/scripts/tools/eMMC/functions.sh:148

main() in /opt/scripts/tools/eMMC/init-eMMC-flasher-v3-x15_b1.sh:43

The command value_min_free_kbytes=$(sysctl -n vm.min_free_kbytes) exited with exit code 255.

================================================================================

Tearing Down script environment

==> Unmounting /tmp

Usage:

blockdev -V

blockdev --report [devices]

blockdev [-v|-q] commands devices

Available commands:

--getsz get size in 512-byte sectors

--setro set read-only

--setrw set read-write

--getro get read-only

--getdiscardzeroes get discard zeroes support status

--getss get logical block (sector) size

--getpbsz get physical block (sector) size

--getiomin get minimum I/O size

--getioopt get optimal I/O size

--getalignoff get alignment offset in bytes

--getmaxsect get max sectors per request

--getbsz get blocksize

--setbsz <bytes> set blocksize on file descriptor opening the block device

--getsize get 32-bit sector count (deprecated, use --getsz)

--getsize64 get size in bytes

--setra <sectors> set readahead

--getra get readahead

--setfra <sectors> set filesystem readahead

--getfra get filesystem readahead

--flushbufs flush buffers

--rereadpt reread partition table

!==> We don't know how to reset the leds as we are not a BBB compatible device

[ 9.441093] Kernel panic - not syncing: Attempted to kill init! exitcode=0x00000100

[ 9.441093]

[ 9.450268] CPU: 1 PID: 1 Comm: init-eMMC-flash Not tainted 4.4.110-ti-r142 #10

[ 9.457603] Hardware name: Generic DRA74X (Flattened Device Tree)

[ 9.463733] [<c001be78>] (unwind_backtrace) from [<c0015a90>] (show_stack+0x20/0x24)

[ 9.471510] [<c0015a90>] (show_stack) from [<c05c58e0>] (dump_stack+0x8c/0xa0)

[ 9.478765] [<c05c58e0>] (dump_stack) from [<c0162170>] (panic+0x100/0x288)

[ 9.485758] [<c0162170>] (panic) from [<c0048774>] (complete_and_exit+0x0/0x2c)

[ 9.493097] [<c0048774>] (complete_and_exit) from [<c0048810>] (do_group_exit+0x50/0xe0)

[ 9.501221] [<c0048810>] (do_group_exit) from [<c00488c0>] (__wake_up_parent+0x0/0x30)

[ 9.509171] [<c00488c0>] (__wake_up_parent) from [<c0010e20>] (ret_fast_syscall+0x0/0x50)

[ 9.517381] CPU0: stopping

[ 9.520099] CPU: 0 PID: 0 Comm: swapper/0 Not tainted 4.4.110-ti-r142 #10

[ 9.526910] Hardware name: Generic DRA74X (Flattened Device Tree)

[ 9.533032] [<c001be78>] (unwind_backtrace) from [<c0015a90>] (show_stack+0x20/0x24)

[ 9.540808] [<c0015a90>] (show_stack) from [<c05c58e0>] (dump_stack+0x8c/0xa0)

[ 9.548060] [<c05c58e0>] (dump_stack) from [<c001952c>] (handle_IPI+0x2ac/0x2cc)

[ 9.555486] [<c001952c>] (handle_IPI) from [<c00095f4>] (gic_handle_irq+0x98/0x9c)

[ 9.563090] [<c00095f4>] (gic_handle_irq) from [<c0ab2814>] (__irq_svc+0x54/0x70)

[ 9.570598] Exception stack(0xc1013ef8 to 0xc1013f40)

[ 9.575665] 3ee0: 00000001 00000000

[ 9.583875] 3f00: fe600000 00000000 c1012000 c1015b44 00000000 c10ea5a8 c0aba57c c0d4cb38

[ 9.592083] 3f20: 00000000 c1013f54 c1013f34 c1013f48 c0033280 c00119c0 600f0013 ffffffff

[ 9.600296] [<c0ab2814>] (__irq_svc) from [<c00119c0>] (arch_cpu_idle+0x30/0x4c)

[ 9.607724] [<c00119c0>] (arch_cpu_idle) from [<c008e0f8>] (default_idle_call+0x30/0x3c)

[ 9.615847] [<c008e0f8>] (default_idle_call) from [<c008e460>] (cpu_startup_entry+0x300/0)

[ 9.624493] [<c008e460>] (cpu_startup_entry) from [<c0aacc94>] (rest_init+0x88/0x8c)

[ 9.632271] [<c0aacc94>] (rest_init) from [<c0f54df4>] (start_kernel+0x434/0x454)

[ 9.639787] ---[ end Kernel panic - not syncing: Attempted to kill init! exitcode=0x000000

[ 9.639787]

Robert Nelson

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Feb 13, 2018, 6:25:57 PM2/13/18

to Beagle Board

Weird, for now just nuke that sysctr setting, it's not mandatory, it fixed some randomness on the bones, which have a quarter the memory of the x15..

Regards,

--
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Jeff Andich

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Feb 14, 2018, 3:21:08 PM2/14/18

to BeagleBoard

Nuking sysctl -n vm.min_free_kbytes in functions.sh::prepare_environment() gets rid of that problem, but script chokes on the next step, determining root drive, apparently due to issues with presence of proc at this point..

# echo_broadcast "==> Preparing sysctl"

# value_min_free_kbytes=$(sysctl -n vm.min_free_kbytes)

# echo_broadcast "==> sysctl: vm.min_free_kbytes=[${value_min_free_kbytes}]"

# echo_broadcast "==> sysctl: setting: [sysctl -w vm.min_free_kbytes=16384]"

# sysctl -w vm.min_free_kbytes=16384

# generate_line 40

One interesting thing... Regarding the flasher script/process, it ALMOST looks like something is tied to the original uname-r associated with the stock image on 2018-01-01..

I tried a brief (horrible hack) experiment where I renamed the stock kernel, from: 4.4.91-ti-r141 to: 4.4.91-ti-r141-stock.

I renamed the vmlinuz image to vmlinuz-4.4.91-ti-r141-stock, the modules directory to 4.4.91-ti-r141-stock, and the dtbs direcfory to uname-r-stock and then set uname-r in uEnv.txt to uname-r-stock and ran the flasher.

I saw the same flasher problem (cannot stat /proc/sys/vm) with the renamed uname-r as with the 4.4.110-ti-r142 image

================================================================================

Prepare environment for flashing

Starting at Mon Jan 1 00:00:01 UTC 2001

----------------------------------------

==> Giving system time to stablize...

5 4 3 2 1

==> Preparing /tmp

==> Preparing sysctl

sysctl: cannot stat /proc/sys/vm/min_free_kbytes: No such file or directory

Traceback (last called is first):

prepare_environment() in /opt/scripts/tools/eMMC/functions.sh:150

main() in /opt/scripts/tools/eMMC/init-eMMC-flasher-v3-no-eeprom.sh:41

The command value_min_free_kbytes=$(sysctl -n vm.min_free_kbytes) exited with exit code 255.

================================================================================

Tearing Down script environment

==> Unmounting /tmp

I then did something even potentially worse and renamed the 4.4.110-ti-r142 kernel to 4.4.91-ti-r141 (consistent with the original image name) and ran the flasher image got a bunch of errors, but it looks like the flash programming process got a lot further along (see below).

Next, I will try to re-build the 4.4.91-ti-r141 kernel with the same .config as on the 2018-01-01 image, copy that to the uSD card with uname-r = 4.4.91-ti-r141, and re-run the flasher.

In the meantime, is there a logical explanation for what I just saw?? Either that the flasher script or the presence of /proc somehow depends on the original uname-r? Recall that if I copy a kernel with a different uname-r to uSD card and change uname-r in uEnv.txt that the system boots with that kernel (from uSD card)..

Thanks!

Jeff

================================================================================

Starting eMMC Flasher from microSD media

Version: [1.20171220: btrfs...]

================================================================================

Prepare environment for flashing

Starting at Mon Jan 1 00:00:58 UTC 2001

----------------------------------------

==> Giving system time to stablize...

5 4 3 2 1

==> Preparing /tmp

==> Preparing sysctl

==> sysctl: vm.min_free_kbytes=[2479]

==> sysctl: setting: [sysctl -w vm.min_free_kbytes=16384]

vm.min_free_kbytes = 16384

----------------------------------------

==> Determining root drive

==> console=ttyO2,115200n8 root=/dev/mmcblk0p1 ro rootfstype=ext4 rootwait init=/opth

----------------------------------------

==> root_drive=[/dev/mmcblk0p1]

====> Root drive identified at [/dev/mmcblk0p1]

==> Boot Drive [/dev/mmcblk0p1]

==> Figuring out Source and Destination devices

====> Source identified: [/dev/mmcblk0]

====> Destination identified: [/dev/mmcblk1]

==> Figuring out machine

====> Machine is TI_AM572x_EVM_Rev_A3

====> Machine is compatible with BeagleBone Black

================================================================================

5 4 3 2 1

================================================================================

Checking running system

==> Copying: [/dev/mmcblk0] -> [/dev/mmcblk1]

==> lsblk:

----------------------------------------

NAME MAJ:MIN RM SIZE RO TYPE MOUNTPOINT

mmcblk1boot0 179:16 0 4M 1 disk

mmcblk1boot1 179:24 0 4M 1 disk

mmcblk0 179:0 0 29G 0 disk

`-mmcblk0p1 179:1 0 846M 0 part /

mmcblk1 179:8 0 3.6G 0 disk

`-mmcblk1p1 179:9 0 3.6G 0 part

----------------------------------------

==> df -h | grep rootfs:

----------------------------------------

modprobe: ERROR: ../libkmod/libkmod.c:557 kmod_search_moddep() could not open moddep'

==> Giving you time to check...

10 9 8 7 6 5 4 3 2 1

================================================================================

Preparing drives

----------------------------------------

==> Erasing: /dev/mmcblk1

----------------------------------------

108+0 records in

108+0 records out

113246208 bytes (113 MB) copied, 8.97986 s, 12.6 MB/s

----------------------------------------

108+0 records in

108+0 records out

113246208 bytes (113 MB) copied, 1.71958 s, 65.9 MB/s

----------------------------------------

==> Erasing: /dev/mmcblk1 complete

----------------------------------------

==> Loading /boot/SOC.sh

************************************************************

#!/bin/sh

format=1.0

board=beagle_x15

bootloader_location=dd_spl_uboot_boot

bootrom_gpt=

dd_spl_uboot_count=2

dd_spl_uboot_seek=1

dd_spl_uboot_conf=notrunc

dd_spl_uboot_bs=128k

dd_spl_uboot_backup=/opt/backup/uboot/MLO

dd_uboot_count=4

dd_uboot_seek=1

dd_uboot_conf=notrunc

dd_uboot_bs=384k

dd_uboot_backup=/opt/backup/uboot/u-boot.img

boot_fstype=ext4

conf_boot_startmb=4

conf_boot_endmb=

sfdisk_fstype=L

boot_label=BOOT

rootfs_label=rootfs

#Kernel

dtb=

serial_tty=ttyO2

usbnet_mem=

************************************************************

==> Loaded

----------------------------------------

================================================================================

Writing bootloader to [/dev/mmcblk1]

----------------------------------------

==> Figuring out options for SPL U-Boot copy ...

===> Will use : count=2 seek=1 conv=notrunc bs=128k

==> Figuring out options for U-Boot copy ...

===> Will use : count=4 seek=1 conv=notrunc bs=384k

==> Copying SPL U-Boot with dd if=/opt/backup/uboot/MLO of=/dev/mmcblk1 count=2 seekk

------------------------------------------------------------

0+1 records in

0+1 records out

122070 bytes (122 kB) copied, 0.0182185 s, 6.7 MB/s

------------------------------------------------------------

==> Copying U-Boot with dd if=/opt/backup/uboot/u-boot.img of=/dev/mmcblk1 count=4 sk

------------------------------------------------------------

2+1 records in

2+1 records out

1042348 bytes (1.0 MB) copied, 0.150472 s, 6.9 MB/s

------------------------------------------------------------

Writing bootloader completed

================================================================================

Partitionning /dev/mmcblk1

----------------------------------------

==> sfdisk parameters:

sfdisk: [sfdisk from util-linux 2.25.2]

sfdisk: [sfdisk --force --Linux --in-order --unit M /dev/mmcblk1]

sfdisk: [4,,L,*]

==> Partitionning

------------------------------------------------------------

[ 43.171121] mmcblk1: p1

sfdisk: Checking that no-one is using this disk right now ...

sfdisk: OK

Disk /dev/mmcblk1: 116736 cylinders, 4 heads, 16 sectors/track

sfdisk: /dev/mmcblk1: unrecognized partition table type

Old situation:

sfdisk: No partitions found

New situation:

Units: 1MiB = 1024*1024 bytes, blocks of 1024 bytes, counting from 0

Device Boot Start End MiB #blocks Id System

/dev/mmcblk1p1 * 4 3647 3644 3731456 83 Linux

/dev/mmcblk1p2 0 - 0 0 0 Empty

/dev/mmcblk1p3 0 - 0 0 0 Empty

/dev/mmcblk1p4 0 - 0 0 0 Empty

Successfully wrote the new partition table

Re-reading the partition table ...

sfdisk: 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).)

------------------------------------------------------------

==> Partitionning Completed

==> Generated Partitions:

------------------------------------------------------------

Disk /dev/mmcblk1: 116736 cylinders, 4 heads, 16 sectors/track

Units: cylinders of 32768 bytes, blocks of 1024 bytes, counting from 0

Device Boot Start End #cyls #blocks Id System

/dev/mmcblk1p1 * 128 116735 116608 3731456 83 Linux

/dev/mmcblk1p2 0 - 0 0 0 Empty

/dev/mmcblk1p3 0 - 0 0 0 Empty

/dev/mmcblk1p4 0 - 0 0 0 Empty

------------------------------------------------------------

================================================================================

Preparing future rootfs to receive files

----------------------------------------

==> Formatting rootfs with mkfs.ext4 -O ^metadata_csum,^64bit /dev/mmcblk1p1 -L roos

--------------------------------------------------------------------------------

mke2fs 1.43 (17-May-2016)

Discarding device blocks: done

Creating filesystem with 932864 4k blocks and 233392 inodes

Filesystem UUID: f1ba24df-0109-4b9b-8598-eb34ae259aca

Superblock backups stored on blocks:

32768, 98304, 163840, 229376, 294912, 819200, 884736

Allocating group tables: done

Writing inode tables: done

Creating journal (16384 blocks): done

Writing superblocks and filesystem accounting information: done

--------------------------------------------------------------------------------

==> Formatting rootfs: /dev/mmcblk1p1 complete

==> Creating temporary rootfs directory (/tmp/rootfs)

==> Mounting /dev/mmcblk1p1 to /tmp/rootfs

[ 53.866332] EXT4-fs (mmcblk1p1): mounted filesystem with ordered data mode. Opts:)

================================================================================

Copying: Current rootfs to /dev/mmcblk1p1

----------------------------------------

==> rsync: / -> /tmp/rootfs

----------------------------------------

[ 54.047765] random: nonblocking pool is initialized

----------------------------------------

==> Copying: Kernel modules

===> Creating directory for modules

===> rsync: /lib/modules/4.4.110-ti-r142/ -> /tmp/rootfs/lib/modules/4.4.110-ti-r142/

----------------------------------------

rsync: change_dir "/lib/modules/4.4.110-ti-r142" failed: No such file or directory ()

rsync error: some files/attrs were not transferred (see previous errors) (code 23) a]

writing to [/dev/mmcblk1] failed...

----------------------------------------

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Robert Nelson

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Feb 14, 2018, 3:31:34 PM2/14/18

to Beagle Board

On Wed, Feb 14, 2018 at 2:21 PM, Jeff Andich <jeff....@gmail.com> wrote:
> Nuking sysctl -n vm.min_free_kbytes in functions.sh::prepare_environment()
> gets rid of that problem, but script chokes on the next step, determining
> root drive, apparently due to issues with presence of proc at this point..
>
> # echo_broadcast "==> Preparing sysctl"
> # value_min_free_kbytes=$(sysctl -n vm.min_free_kbytes)
> # echo_broadcast "==> sysctl:
> vm.min_free_kbytes=[${value_min_free_kbytes}]"
> # echo_broadcast "==> sysctl: setting: [sysctl -w
> vm.min_free_kbytes=16384]"
> # sysctl -w vm.min_free_kbytes=16384
> # generate_line 40

This now checks for:

/proc/sys/vm/min_free_kbytes

https://github.com/RobertCNelson/boot-scripts/commit/89f2e9309c2322c15e2bb6b55afd214313d94842#diff-c483633eab46489e55e2e391823018ad

>
> ================================================================================
> Checking running system
> ==> Copying: [/dev/mmcblk0] -> [/dev/mmcblk1]
> ==> lsblk:
> ----------------------------------------
> NAME MAJ:MIN RM SIZE RO TYPE MOUNTPOINT
> mmcblk1boot0 179:16 0 4M 1 disk
> mmcblk1boot1 179:24 0 4M 1 disk
> mmcblk0 179:0 0 29G 0 disk
> `-mmcblk0p1 179:1 0 846M 0 part /
> mmcblk1 179:8 0 3.6G 0 disk
> `-mmcblk1p1 179:9 0 3.6G 0 part
> ----------------------------------------
> ==> df -h | grep rootfs:
> ----------------------------------------
> modprobe: ERROR: ../libkmod/libkmod.c:557 kmod_search_moddep() could not
> open moddep'
> ==> Giving you time to check...

Humm..

Maybe you need to boot once..

Run:

sudo depmod -a

might as well run, this too...

sudo update-initramfs -ck `uname -r`

or

sudo update-initramfs -uk `uname -r`

then, shutdown and try to flash it..

Regards,

--
Robert Nelson
https://rcn-ee.com/

Jeff Andich

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Feb 14, 2018, 4:49:22 PM2/14/18

to BeagleBoard

Thanks Robert!

Eureka it works!

so long as you keep, initrd.img-4.4.110-ti-r142 in /boot it's happy..

Regards,

Jeff

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