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This is the same board as in AM335x board starts kernel from SD card but uses distro from eMMC. That problem has been fixed by setting vmmc-supply to vmmcsd_fixed.
But there is another problem with SD card when booting from the internal eMMC, I copied the relevant lines from dmesg output:
[ 1.066114] omap_hsmmc 48060000.mmc: Got CD GPIO
[ 1.101295] omap_hsmmc 48060000.mmc: no support for card's volts
[ 1.101313] mmc0: error -22 whilst initialising SD card
And there is no /dev/mmc0blk device when the system boots.
How can I fix the error?