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So I installed Raspbian Stretch Lite on a USB Flash key and can successfully boot from it. Now I wanted to attach and auto mount another USB HDD Seagate of 1TB to it. Manually I can mount this 1TB disk and it works okay. But when I reboot the Pi it does not boot. There appears nothing when it tries to reboot - just a blank screen.

I thought I may be making some mistake with fstab entry so I removed the added entry. Plug the HDD but it still goes to blank screen when rebooting.

HDD is connected to powered hub with 2.5A supply. Do I need to make some special changes if I want to attach another USB HDD when it is already booted off a USB flash key? Thank you!

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This seems to be a known problem. The Raspberry Pi does not have a boot order with its USB ports. It scans all ports and what bootable device it find first it will use. It seems the HDD is ready before the flash drive and the RasPi tries to boot from it.

Here I have found a user who seems to have a solution for your problem. He stated that the RasPi only looks for bootable devices and he was able to make his drives not bootable. Look at USB port boot order?.

Update
Finally here is the solution posted by @Naheed Ashraf in a comment:

I finally managed to get it working. I did two things differently. One, I formated my SD Card in a Windows machine as FAT32 instead of formatting FAT32 in a Linux machine. Second thing done was to download the bootcode.bin from [link]github.com/raspberrypi/firmware/raw/master/boot/bootcode.bin instead of copying it from USB flash key. I am too thankful to do one thing at a time to find the previous issue root cause :).

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  • I found that in my RPi 3b+, (in which there's four ports) I can plug in my external SSD on the bottom-right one and keep a usb wireless keyboard/mouse dongle plugged in on the bottom-left, and it boots correctly (from the SSD). In many different arrangements, it refused to boot with the dongle plugged in. – user96931 May 3 '19 at 18:19
  • Thank you @Ingo for the link to the user post and sharing some thoughts. There is nothing on the 2nd hard drive - it is formatted so I guess there is nothing on the HDD that indicates that it is for boot purposes so ideally Pi should skip if this is detected first. And I don't have SD card inserted as well. Anyway - thank you for your feedback. I might change the port as other user suggested here if that helps :( – Naheed Ashraf May 3 '19 at 22:25
  • Sorry - I guess I missed the point with my earlier post. I think the workaround is to have only Bootcode.bin on the SD Card. So I format a SD Card as FAT32 and just put this file on it. Then I keep the Bootcode.bin on my USB flash key or I need to delete that? Thank you. – Naheed Ashraf May 3 '19 at 23:40
  • @NaheedAshraf The RasPi will always use the bootcode.bin on the SD Card so it shouldn't matter if there is another bootcode.bin anywhere. If you have found a solution it would be nice if you make an answer to share it with the community. – Ingo May 4 '19 at 7:31
  • I did put the bootcode.ini on the sd card but it did not boot the Pi so I gave it up for now :( and now fully booting from sd card instead. I will give it another shot some other day perhaps. – Naheed Ashraf May 4 '19 at 14:17

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