Problem of migrating from kernel overlays to uboot overlay

[BrentCC]

Hi,
I have packet sniffing device that consists of BBG and a cape(sniffer)
The device was running with an old image from 2017, and I updated it to the latest image.
However after the update, I couldn't initialize BBG any more. After some debugging, the issue is related to the overlays.
The device was configured with kernel overlays with bone cape manager and slots, but these are removed from the latest kernel.

I tried several methods to re-configure it.
i) Disable the uboot overlay and stick to the old solution.
As instructed in here, I put #enable_uboot_overlays=1 in the boot up file. However, it is automatically written into the file when BBG boots up

debug: [enable_uboot_overlays=] ...
loading /boot/dtbs/4.19.94-ti-r42/am335x-bonegreen-overlay-ni2c2.dtb ...
54543 bytes read in 72 ms (739.3 KiB/s)
uboot_overlays: add [enable_uboot_overlays=1] to /boot/uEnv.txt to enable...

ii) Override U-Boot external capes
As instructed here, I put overrode the uboot overlay with my customized ones.(using dtc to compile dts into dtbo)

uboot_overlay_addr0=/lib/firmware/am335x-bonegreen-overlay-ni2c2.dtbo
uboot_overlay_addr1=/lib/firmware/BB-GIRTC-00A0.dtbo
uboot_overlay_addr2=/lib/firmware/BBHDME8DMAPALL-00A0.dtbo
uboot_overlay_addr3=/lib/firmware/BBHDME8GPIOPALL-00A0.dtbo
uboot_overlay_addr4=/lib/firmware/lastditch-00A0.dtbo
uboot_overlay_addr5=/lib/firmware/RECLAIMI2C2-00A0.dtbo

Afterwards, I couldn't boot up BBG because, I have this error:

libfdt fdt_check_header(): FDT_ERR_BADMAGIC
failed on fdt_overlay_apply(): FDT_ERR_BADMAGIC
base fdt does did not have a /__symbols__ node
make sure you've compiled with -@

I googled this error, and I found someone had encountered similar issue as well.
I tried to follow the suggestion to make my dtbo file, but nothing need to be done. Do you know why it's not working in my case?

debian@beaglebone:~/bb.org-overlays$ make /home/debian/dtree/src/am335x-bonegreen-overlay-ni2c2.dtbo
make: Nothing to be done for '/home/debian/dtree/src/am335x-bonegreen-overlay-ni2c2.dtbo'.

Therefore, the issue still remains. Could you give me some hints about migrating from kernel overlays to uboot overlays?
(By the way, the old DT files also contain slots)

Image: bone-eMMC-flasher-debian-10.3-iot-armhf-2020-04-06-4gb.img
Hardware: SeeedStudio BeagleBone Green
Capes: Customized cape(packet sniffer)

sudo /opt/scripts/tools/version.sh
git:/opt/scripts/:[e4e4854ef8ff9ada5c85553376043ee7679167ca]
eeprom:[A335BNLTBBG1BBG217083985]
model:[TI_AM335x_BeagleBone_Green]
dogtag:[BeagleBoard.org Debian Buster IoT Image 2020-04-06]
bootloader:[eMMC-(default)]:[/dev/mmcblk1]:[U-Boot SPL 2019.04-00002-gc9b3922522                                                                                                              (Aug 24 2020 - 16:42:18 -0500)]:[location: dd MBR]
bootloader:[eMMC-(default)]:[/dev/mmcblk1]:[U-Boot 2019.04-00002-gc9b3922522]:[l                                                                                                             ocation: dd MBR]
UBOOT: Booted Device-Tree:[am335x-boneblack-uboot-univ.dts]
UBOOT: Loaded Overlay:[AM335X-PRU-RPROC-4-19-TI-00A0]
UBOOT: Loaded Overlay:[BB-ADC-00A0]
UBOOT: Loaded Overlay:[BB-BONE-eMMC1-01-00A0]
UBOOT: Loaded Overlay:[M-BB-BBG-00A0]
kernel:[4.19.94-ti-r59]
nodejs:[v10.15.2]
/boot/uEnv.txt Settings:
uboot_overlay_options:[enable_uboot_overlays=1]
uboot_overlay_options:[uboot_overlay_pru=/lib/firmware/AM335X-PRU-RPROC-4-19-TI-                                                                                                             00A0.dtbo]
uboot_overlay_options:[enable_uboot_cape_universal=1]
pkg check: to individually upgrade run: [sudo apt install --only-upgrade <pkg>]
pkg:[bb-cape-overlays]:[4.14.20201221.0-0~buster+20201221]
pkg:[bb-customizations]:[1.20200306.0-0rcnee0~buster+20200306]
pkg:[bb-usb-gadgets]:[1.20200322.0-0rcnee0~buster+20200322]
pkg:[bb-wl18xx-firmware]:[1.20200322.0-0rcnee0~buster+20200322]
pkg:[kmod]:[26-1]
pkg:[librobotcontrol]:[1.0.4-git20190227.1-0rcnee0~buster+20190327]
pkg:[firmware-ti-connectivity]:[20190717-2rcnee1~buster+20200305]
groups:[debian : debian adm kmem dialout cdrom floppy audio dip video plugdev us                                                                                                             ers systemd-journal bluetooth netdev i2c gpio pwm eqep remoteproc admin spi iio                                                                                                              docker tisdk weston-launch xenomai cloud9ide]
cmdline:[console=ttyO0,115200n8 bone_capemgr.uboot_capemgr_enabled=1 root=/dev/m                                                                                                             mcblk1p1 ro rootfstype=ext4 rootwait coherent_pool=1M net.ifnames=0 lpj=1990656                                                                                                              rng_core.default_quality=100 quiet]
dmesg | grep remote
[   44.087108] remoteproc remoteproc0: wkup_m3 is available
[   44.186052] remoteproc remoteproc0: powering up wkup_m3
[   44.186080] remoteproc remoteproc0: Booting fw image am335x-pm-firmware.elf,                                                                                                              size 217168
[   44.186332] remoteproc remoteproc0: remote processor wkup_m3 is now up
[   45.821693] remoteproc remoteproc1: 4a334000.pru is available
[   45.829753] remoteproc remoteproc2: 4a338000.pru is available
dmesg | grep pru
[   45.821693] remoteproc remoteproc1: 4a334000.pru is available
[   45.821861] pru-rproc 4a334000.pru: PRU rproc node pru@4a334000 probed succes                                                                                                             sfully
[   45.829753] remoteproc remoteproc2: 4a338000.pru is available
[   45.829932] pru-rproc 4a338000.pru: PRU rproc node pru@4a338000 probed succes                                                                                                             sfully
dmesg | grep pinctrl-single
[    0.987636] pinctrl-single 44e10800.pinmux: 142 pins, size 568
dmesg | grep gpio-of-helper
[    1.001404] gpio-of-helper ocp:cape-universal: ready
lsusb
Bus 001 Device 001: ID 1d6b:0002 Linux Foundation 2.0 root hub
END

Thank you so much in advance!

[RobertCNelson]

@BrentCC

However, it is automatically written into the file when BBG boots up

No, that statement is incorrect.. U-Boot just "reports" it is disabled and recommends for you to enable it..

In your /boot/uEnv.txt just make sure you have these set..

dtb=<your custom kernel>.dtb
#enable_uboot_overlays=1

and it'll boot the same way as before u-boot overlays...

failed on fdt_overlay_apply(): FDT_ERR_BADMAGIC
base fdt does did not have a /__symbols__ node
make sure you've compiled with -@

Yeah, your going to have to post the problem overlay, i can't help you with just that information..

Regards,

[BrentCC]

@RobertCNelson

However, it is automatically written into the file when BBG boots up

No, that statement is incorrect.. U-Boot just "reports" it is disabled and recommends for you to enable it..

In your /boot/uEnv.txt just make sure you have these set..

dtb=<your custom kernel>.dtb
#enable_uboot_overlays=1

Is it possible to put multiple customized customize there? I have six DT.

/lib/firmware/am335x-bonegreen-overlay-ni2c2.dtbo
/lib/firmware/BB-GIRTC-00A0.dtbo
/lib/firmware/BBHDME8DMAPALL-00A0.dtbo
/lib/firmware/BBHDME8GPIOPALL-00A0.dtbo
/lib/firmware/lastditch-00A0.dtbo
/lib/firmware/RECLAIMI2C2-00A0.dtbo

Thanks!

[RobertCNelson]

@BrentCC no... that's not how it works.

For u-boot overlays we start with a base ".dtb" this usually comes from the kernel tree.

For the beaglebone black this would be:

am335x-boneblack.dtb

Then for u-boot overlays you list the "overlays" you'd like to apply on top of those..

Which would be found under /lib/firmware/

and set via:

uboot_overlay_addrX=/lib/firmware/my-overlay.dtbo

Pre u-boot overlays, you'd just boot:

am335x-boneblack.dtb

Then in your case, you'd load these via 'slots'..

/lib/firmware/am335x-bonegreen-overlay-ni2c2.dtbo
/lib/firmware/BB-GIRTC-00A0.dtbo
/lib/firmware/BBHDME8DMAPALL-00A0.dtbo
/lib/firmware/BBHDME8GPIOPALL-00A0.dtbo
/lib/firmware/lastditch-00A0.dtbo
/lib/firmware/RECLAIMI2C2-00A0.dtbo

With u-boot overlays, the "load by slot" is done by u-boot instead of by the kernel..

Regards,

[RobertCNelson]

Here's another example to explain it: (with just 2 of your random overlays..)

U-Boot overlay's:

U-Boot Load: am335x-boneblack.dtb
U-Boot apply: BB-GIRTC-00A0.dtbo
U-Boot apply: RECLAIMI2C2-00A0.dtbo
Boot into Linux..

Linux Overlay:

U-Boot Load: am335x-boneblack.dtb
Boot into Linux..
Linux load: BB-GIRTC-00A0.dtbo
Linux load: RECLAIMI2C2-00A0.dtbo

See, we just "moved" where the device overlay load happens.. and best of all, since we do it u-boot, you don't have a random kernel "runtime" issues..

Regards,

[BrentCC]

Hi Robert

Thanks for the reply! It looks clearer to me.

am335x-boneblack.dtb

Where can I find the path of this file? so I can modify it.
In my case it is am335x-boneblack-uboot-univ.dts

debian@beaglebone:/opt/scripts/tools$ sudo ./version.sh | grep UBOOT
UBOOT: Booted Device-Tree:[am335x-boneblack-uboot-univ.dts]
UBOOT: Loaded Overlay:[AM335X-PRU-RPROC-4-19-TI-00A0]
UBOOT: Loaded Overlay:[BB-ADC-00A0]
UBOOT: Loaded Overlay:[BB-BONE-eMMC1-01-00A0]
UBOOT: Loaded Overlay:[M-BB-BBG-00A0]

I have a another question about correctly using bb.org-overlays to make the dtbo file.
Should I just download the repo and make with the exisiting dtbo file?

Thanks again!

[RobertCNelson]

@BrentCC the repo with the 4.19.94-ti device tree's can be found here:

https://github.com/beagleboard/BeagleBoard-DeviceTrees

just use the Makefile to build and install your *.dtb

Regards,

[BrentCC]

@RobertCNelson
I modified my /boot/uEnv.txt as below by disabling uboot

uname_r=4.19.94-ti-r59
#uuid=
dtb=/boot/dtbs/4.19.94-ti-r59/am335x-bonegreen-overlay-ni2c2.dtb
#enable_uboot_overlays=1
uboot_overlay_addr0=/lib/firmware/BB-GIRTC-00A0.dtbo
uboot_overlay_addr1=/lib/firmware/BBHDME8DMAPALL-00A0.dtbo
uboot_overlay_addr2=/lib/firmware/BBHDME8GPIOPALL-00A0.dtbo
uboot_overlay_addr3=/lib/firmware/lastditch-00A0.dtbo
uboot_overlay_addr4=/lib/firmware/RECLAIMI2C2-00A0.dtbo
uboot_overlay_pru=/lib/firmware/AM335X-PRU-RPROC-4-19-TI-00A0.dtbo
#enable_uboot_cape_universal=1
cmdline=coherent_pool=1M net.ifnames=0 lpj=1990656 rng_core.default_quality=100 quiet

However, I couldn't boot up afterwards. The boot up log is attached below.
boot up without uboot.txt

[RobertCNelson]

@BrentCC

dtb=/boot/dtbs/4.19.94-ti-r59/am335x-bonegreen-overlay-ni2c2.dtb

I have no idea what that would do.. you already have "uname_r=4.19.94-ti-r59" defined, so it'll auto pre-pend the path: "/boot/dtbs/4.19.94-ti-r59/"...

So just use:

dtb=am335x-bonegreen-overlay-ni2c2.dtb

Second:

#enable_uboot_overlays=1

Disables all uboot_overlays_addr*=

So if you want to use: uboot_overlays_addr*=

enable_uboot_overlays=1

Edit (looked at log)

debug: [enable_uboot_overlays=] ...
loading /boot//boot/dtbs/4.19.94-ti-r59/am335x-bonegreen-overlay-ni2c2.dtb ...
uboot_overlays: add [enable_uboot_overlays=1] to /boot/uEnv.txt to enable...

Yeap, it "gave" up finding your "am335x-bonegreen-overlay-ni2c2.dtb"... Hence the double "/boot/boot"..

Just use:

dtb=am335x-bonegreen-overlay-ni2c2.dtb

Regards,

[BrentCC]

Hi @RobertCNelson
Maybe I misunderstood what you said before.
This time I tried below settings, without overriding uboot overlays.

uname_r=4.19.94-ti-r42
#uuid=
dtb=am335x-bonegreen-overlay-ni2c2.dtb
#enable_uboot_overlays=1

But I run into another error that stops me from booting.

Gave up waiting for root file system device.  Common problems:
 - Boot args (cat /proc/cmdline)
   - Check rootdelay= (did the system wait long enough?)
 - Missing modules (cat /proc/modules; ls /dev)
ALERT!  /dev/mmcblk1p1 does not exist.  Dropping to a shell!
(initramfs)

disable_uboot.txt

Next step, I will try

enable_uboot_overlays=1

And add uboot_overlay_addrX

[RobertCNelson]

@BrentCC do you have both microSD/eMMC defined in your custom am335x-bonegreen-overlay-ni2c2.dtb ?

Waiting for /dev/mmcblk1p1 usually means it's waiting for eMMC.

Since i don't have access to your your am335x-bonegreen-overlay-ni2c2.dtb, you'll need to look at it to see if you have the eMMC enabled...

Regards,

[BrentCC]

Hi, @RobertCNelson

@BrentCC do you have both microSD/eMMC defined in your custom am335x-bonegreen-overlay-ni2c2.dtb ?

Waiting for /dev/mmcblk1p1 usually means it's waiting for eMMC.

Since i don't have access to your your am335x-bonegreen-overlay-ni2c2.dtb, you'll need to look at it to see if you have the eMMC enabled...

No, I only have eMMC to boot up. I flashed the image into eMMC through SDcard. I followed the guide here. BBG works perfectly before I used the custom kernel. I upload am335x-bonegreen-overlay-ni2c2.dts here.

In addition, I also tried to enable uboot overlays as below.

uname_r=4.19.94-ti-r42
dtb=am335x-bonegreen-overlay-ni2c2.dtb
enable_uboot_overlays=1
uboot_overlay_addr0=/lib/firmware/BB-GIRTC-00A0.dtbo
uboot_overlay_addr1=/lib/firmware/BBHDME8DMAPALL-00A0.dtbo
uboot_overlay_addr2=/lib/firmware/BBHDME8GPIOPALL-00A0.dtbo
uboot_overlay_addr3=/lib/firmware/lastditch-00A0.dtbo
uboot_overlay_addr4=/lib/firmware/RECLAIMI2C2-00A0.dtbo

However, maybe there is a conflict in i/o definition....

U-Boot SPL 2019.04-00002-g07d5700e21 (Mar 06 2020 - 11:24:55 -0600)
Trying to boot from MMC2
Loading Environment from EXT4... Card did not respond to voltage select!


U-Boot 2019.04-00002-g07d5700e21 (Mar 06 2020 - 11:24:55 -0600), Build: jenkins-github_Bootloader-Builder-137

CPU  : AM335X-GP rev 2.1
I2C:   ready
DRAM:  512 MiB
No match for driver 'omap_hsmmc'
No match for driver 'omap_hsmmc'
Some drivers were not found
Reset Source: Global external warm reset has occurred.
Reset Source: Global warm SW reset has occurred.
Reset Source: Power-on reset has occurred.
RTC 32KCLK Source: External.
MMC:   OMAP SD/MMC: 0, OMAP SD/MMC: 1
Loading Environment from EXT4... Card did not respond to voltage select!
Board: BeagleBone Black
<ethaddr> not set. Validating first E-fuse MAC
BeagleBone Black:
Model: SeeedStudio BeagleBone Green:
BeagleBone: cape eeprom: i2c_probe: 0x54:
BeagleBone: cape eeprom: i2c_probe: 0x55:
BeagleBone: cape eeprom: i2c_probe: 0x56:
BeagleBone: cape eeprom: i2c_probe: 0x57:
Net:   eth0: MII MODE
cpsw, usb_ether
Press SPACE to abort autoboot in 0 seconds
board_name=[BBG1] ...
Card did not respond to voltage select!
Card did not respond to voltage select!
Card did not respond to voltage select!
gpio: pin 56 (gpio 56) value is 0
gpio: pin 55 (gpio 55) value is 0
gpio: pin 54 (gpio 54) value is 0
gpio: pin 53 (gpio 53) value is 1
Card did not respond to voltage select!
Card did not respond to voltage select!
switch to partitions #0, OK
mmc1(part 0) is current device
Scanning mmc 1:1...
gpio: pin 56 (gpio 56) value is 0
gpio: pin 55 (gpio 55) value is 0
gpio: pin 54 (gpio 54) value is 0
gpio: pin 53 (gpio 53) value is 1
switch to partitions #0, OK
mmc1(part 0) is current device
gpio: pin 54 (gpio 54) value is 1
Checking for: /uEnv.txt ...
Checking for: /boot.scr ...
Checking for: /boot/boot.scr ...
Checking for: /boot/uEnv.txt ...
gpio: pin 55 (gpio 55) value is 1
2081 bytes read in 13 ms (156.3 KiB/s)
Loaded environment from /boot/uEnv.txt
debug: [dtb=am335x-bonegreen-overlay-ni2c2.dtb] ...
Using: dtb=am335x-bonegreen-overlay-ni2c2.dtb ...
Checking if uname_r is set in /boot/uEnv.txt...
gpio: pin 56 (gpio 56) value is 1
Running uname_boot ...
loading /boot/vmlinuz-4.19.94-ti-r42 ...
10095592 bytes read in 652 ms (14.8 MiB/s)
debug: [enable_uboot_overlays=1] ...
debug: [enable_uboot_cape_universal=] ...
debug: [uboot_base_dtb_univ=am335x-boneblack-uboot.dtb] ...
uboot_overlays: [uboot_base_dtb=am335x-boneblack-uboot.dtb] ...
uboot_overlays: Switching too: dtb=am335x-boneblack-uboot.dtb ...
loading /boot/dtbs/4.19.94-ti-r42/am335x-boneblack-uboot.dtb ...
57419 bytes read in 35 ms (1.6 MiB/s)
uboot_overlays: [fdt_buffer=0x60000] ...
uboot_overlays: loading /lib/firmware/M-BB-BBG-00A0.dtbo ...
423 bytes read in 197 ms (2 KiB/s)
uboot_overlays: loading /lib/firmware/BB-ADC-00A0.dtbo ...
867 bytes read in 334 ms (2 KiB/s)
uboot_overlays: loading /lib/firmware/BB-GIRTC-00A0.dtbo ...
1119 bytes read in 284 ms (2.9 KiB/s)
uboot_overlays: loading /lib/firmware/BBHDME8DMAPALL-00A0.dtbo ...
5008 bytes read in 368 ms (12.7 KiB/s)
uboot_overlays: loading /lib/firmware/BBHDME8GPIOPALL-00A0.dtbo ...
5281 bytes read in 119 ms (43 KiB/s)
uboot_overlays: loading /lib/firmware/lastditch-00A0.dtbo ...
842 bytes read in 287 ms (2 KiB/s)
uboot_overlays: loading /lib/firmware/RECLAIMI2C2-00A0.dtbo ...
350 bytes read in 119 ms (2 KiB/s)
uboot_overlays: loading /lib/firmware/BB-BONE-eMMC1-01-00A0.dtbo ...
1584 bytes read in 304 ms (4.9 KiB/s)
uboot_overlays: loading /lib/firmware/AM335X-PRU-RPROC-4-19-TI-00A0.dtbo ...
3801 bytes read in 237 ms (15.6 KiB/s)
uboot_overlays: add [enable_uboot_cape_universal=1] to /boot/uEnv.txt to enable...
loading /boot/initrd.img-4.19.94-ti-r42 ...
6589689 bytes read in 429 ms (14.6 MiB/s)
debug: [console=ttyO0,115200n8 bone_capemgr.uboot_capemgr_enabled=1 root=/dev/mmcblk1p1 ro rootfstype=ext4 rootwait coherent_pool=1M net.ifnames=0 lpj=1990656 rng_core.default_quality=100 quiet] ...
debug: [bootz 0x82000000 0x88080000:648cf9 88000000] ...
## Flattened Device Tree blob at 88000000
   Booting using the fdt blob at 0x88000000
   Loading Ramdisk to 8f9b7000, end 8ffffcf9 ... OK
   Loading Device Tree to 8f944000, end 8f9b6fff ... OK

Starting kernel ...

[    0.000850] timer_probe: no matching timers found
[    0.118310] l4_wkup_cm:clk:0010:0: failed to disable
[    0.903073] pinctrl-single 44e10800.pinmux: pin PIN95 already requested by ocp:valversled_helper; cannot claim for ocp:P9_19_pinmux
[    0.915123] pinctrl-single 44e10800.pinmux: pin-95 (ocp:P9_19_pinmux) status -22
[    0.922647] pinctrl-single 44e10800.pinmux: could not request pin 95 (PIN95) from group pinmux_P9_19_default_pin  on device pinctrl-single
[    0.935224] bone-pinmux-helper ocp:P9_19_pinmux: Error applying setting, reverse things back
[    0.944316] pinctrl-single 44e10800.pinmux: pin PIN94 already requested by ocp:valversled_helper; cannot claim for ocp:P9_20_pinmux
[    0.956329] pinctrl-single 44e10800.pinmux: pin-94 (ocp:P9_20_pinmux) status -22
[    0.963860] pinctrl-single 44e10800.pinmux: could not request pin 94 (PIN94) from group pinmux_P9_20_default_pin  on device pinctrl-single
[    0.976432] bone-pinmux-helper ocp:P9_20_pinmux: Error applying setting, reverse things back
[    1.188501] omap_voltage_late_init: Voltage driver support not added
[    4.941876] cc2520 spi2.7: fifo gpio is not valid
[    4.948071] cc2520 spi2.6: fifo gpio is not valid
[    4.953169] pinctrl-single 44e10800.pinmux: pin PIN51 already requested by i2c@0; cannot claim for spi2.5
[    4.962826] pinctrl-single 44e10800.pinmux: pin-51 (spi2.5) status -22
[    4.969414] pinctrl-single 44e10800.pinmux: could not request pin 51 (PIN51) from group pinmux_bb_cc_6_pins  on device pinctrl-single
[    4.981491] cc2520 spi2.5: Error applying setting, reverse things back
[    4.988254] cc2520 spi2.4: fifo gpio is not valid
[    4.993163] pinctrl-single 44e10800.pinmux: pin PIN5 already requested by 481d8000.mmc; cannot claim for spi2.3
[    5.003331] pinctrl-single 44e10800.pinmux: pin-5 (spi2.3) status -22
[    5.009830] pinctrl-single 44e10800.pinmux: could not request pin 5 (PIN5) from group pinmux_bb_cc_4_pins  on device pinctrl-single
[    5.021750] cc2520 spi2.3: Error applying setting, reverse things back
[    5.028541] cc2520 spi2.2: fifo gpio is not valid
[    5.033493] cc2520 spi2.1: fifo gpio is not valid
[    5.038361] pinctrl-single 44e10800.pinmux: pin PIN7 already requested by 481d8000.mmc; cannot claim for spi2.0
[    5.048534] pinctrl-single 44e10800.pinmux: pin-7 (spi2.0) status -22
[    5.055036] pinctrl-single 44e10800.pinmux: could not request pin 7 (PIN7) from group pinmux_bb_cc_1_pins  on device pinctrl-single
[    5.067026] cc2520 spi2.0: Error applying setting, reverse things back

[RobertCNelson]

No, I only have eMMC to boot up. I flashed the image into eMMC through SDcard. I followed the guide here. BBG works perfectly before I used the custom kernel. I upload am335x-bonegreen-overlay-ni2c2.dts here.

If we look at that file:

        mmc@48060000 {
            status = "okay";
        };
        mmc@481d8000 {
            status = "disabled";
        };
        mmc@47810000 {
            status = "disabled";
        };

Only microSD is enabled, thus your eMMC is disabled.. you need to pass root=/dev/mmcblk0p1

What was your old kernel?

[ 0.903073] pinctrl-single 44e10800.pinmux: pin PIN95 already requested by ocp:valversled_helper; cannot claim for ocp:P9_19_pinmux
[ 0.915123] pinctrl-single 44e10800.pinmux: pin-95 (ocp:P9_19_pinmux) status -22
[ 0.922647] pinctrl-single 44e10800.pinmux: could not request pin 95 (PIN95) from group pinmux_P9_19_default_pin on device pinctrl-single
[ 0.935224] bone-pinmux-helper ocp:P9_19_pinmux: Error applying setting, reverse things back
[ 0.944316] pinctrl-single 44e10800.pinmux: pin PIN94 already requested by ocp:valversled_helper; cannot claim for ocp:P9_20_pinmux
[ 0.956329] pinctrl-single 44e10800.pinmux: pin-94 (ocp:P9_20_pinmux) status -22
[ 0.963860] pinctrl-single 44e10800.pinmux: could not request pin 94 (PIN94) from group pinmux_P9_20_default_pin on device pinctrl-single
[ 0.976432] bone-pinmux-helper ocp:P9_20_pinmux: Error applying setting, reverse things back

You need to disable pin's your overlay uses..

That's this section:

https://github.com/beagleboard/bb.org-overlays/blob/master/src/arm/BB-SPIDEV0-00A0.dts#L49-L60

Regards,

[RobertCNelson]

PS, this is a bug:

debug: [dtb=am335x-bonegreen-overlay-ni2c2.dtb] ...
Using: dtb=am335x-bonegreen-overlay-ni2c2.dtb ...
Checking if uname_r is set in /boot/uEnv.txt...
gpio: pin 56 (gpio 56) value is 1
Running uname_boot ...
loading /boot/vmlinuz-4.19.94-ti-r42 ...
10095592 bytes read in 652 ms (14.8 MiB/s)
debug: [enable_uboot_overlays=1] ...
debug: [enable_uboot_cape_universal=] ...
debug: [uboot_base_dtb_univ=am335x-boneblack-uboot.dtb] ...
uboot_overlays: [uboot_base_dtb=am335x-boneblack-uboot.dtb] ...
uboot_overlays: Switching too: dtb=am335x-boneblack-uboot.dtb ...
loading /boot/dtbs/4.19.94-ti-r42/am335x-boneblack-uboot.dtb ...

I'll work on that it, it should not have swapped over...