[solutions]post OSX upgrade breaks GRUB, wipes bios_grub partition?

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ManTaRa
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[solutions]post OSX upgrade breaks GRUB, wipes bios_grub partition?

Post by ManTaRa »

readers:

I have a multi-system HD running in a '12 MacPro . . . two partitions for various flavors OSX, and LM 18 running at the tail end. I recently upgraded the second OSX partition to 10.12 and of course after that GRUB was broken and the LM/"windows" disk no longer showed up when booting with the option key. I did not have to use rEFInd to get the system to recognize and boot LM previously.

I have been through this before, but mostly in PPC computers where Yaboot is the linux bootloader, so GRUB seems a little different. I've read through a number of fixit posts, as well as running, "boot-repair," SG2, both of them said "successful" but, problem of not booting remains--and fiddled with Rescatux a bit today--but a couple problems remain.

I've needed to set up a separate "bios_grub" partition in the original LM install, that seems to help get GRUB installed, but, after upgrading the OSX side it seems in GParted to have wiped the data from that partition, and I can't get GParted to show an option of formatting it as "bios_grub" or anything relating to that . . . only the "ext4" or "fat32" and a few other options show up. I'm trying to avoid a re-install, since every few months OSX comes up with a security update, which will again wipe this data, so I'd like to "figure it out" if possible . . . how to get "bios_grub" flag back on that partition (10 MB).

And, from what I found on GRUB, the file to edit is /etc/default/grub . . . which I was hoping would show the root partition (which is now /dev/sda7) and/or the "boot" partition, which I believe should be the "bios_grub" partition??? but, is now "unallocated" and doesn't have an sda number; all the file shows is:

Code: Select all

  GNU nano 2.5.3           File: /etc/default/grub                              

# If you change this file, run 'update-grub' afterwards to update
# /boot/grub/grub.cfg.
# For full documentation of the options in this file, see:
#   info -f grub -n 'Simple configuration'

GRUB_DEFAULT=0
#GRUB_HIDDEN_TIMEOUT=0
GRUB_HIDDEN_TIMEOUT_QUIET=true
GRUB_TIMEOUT=10
GRUB_DISTRIBUTOR=`lsb_release -i -s 2> /dev/null || echo Debian`
GRUB_CMDLINE_LINUX_DEFAULT="quiet splash"
GRUB_CMDLINE_LINUX=""

# Uncomment to enable BadRAM filtering, modify to suit your needs
# This works with Linux (no patch required) and with any kernel that obtains
# the memory map information from GRUB (GNU Mach, kernel of FreeBSD ...)
#GRUB_BADRAM="0x01234567,0xfefefefe,0x89abcdef,0xefefefef"

# Uncomment to disable graphical terminal (grub-pc only)
                               [ Read 34 lines ]

Appreciate any thoughts on this,

MTR
Last edited by ManTaRa on Wed Nov 02, 2016 1:44 pm, edited 1 time in total.
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austin.texas
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Re: post OSX upgrade breaks GRUB, wipes bios_grub partition?

Post by austin.texas »

Is your OSX installed in UEFI mode or non-UEFI (Legacy)?
Please post the result of

Code: Select all

sudo parted --list
Mint 18.2 Cinnamon, Quad core AMD A8-3870 with Radeon HD Graphics 6550D, 8GB DDR3, Ralink RT2561/RT61 802.11g PCI
Linux Linx 2018
ManTaRa
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Re: post OSX upgrade breaks GRUB, wipes bios_grub partition?

Post by ManTaRa »

austin.texas wrote:Is your OSX installed in UEFI mode or non-UEFI (Legacy)?
Please post the result of

Code: Select all

sudo parted --list
@a.t:

Appreciate the reply, pretty sure OSX is installed in UEFI these days . . . here's the output to the suggested command; perhaps the "error" shows the "unallocated" 10 MB partition which is not showing up in this data?

Code: Select all

$ sudo parted --list
[sudo] password for ManTaRa: 
Model: ATA WDC WD10EZEX-00B (scsi)
Disk /dev/sda: 1000GB
Sector size (logical/physical): 512B/4096B
Partition Table: gpt
Disk Flags: 

Number  Start   End     Size    File system     Name                  Flags
 1      20.5kB  210MB   210MB   fat32           EFI System Partition  boot, esp
 2      210MB   226GB   226GB   hfs+            Untitled 1
 3      226GB   226GB   650MB   hfs+            Recovery HD
 4      226GB   478GB   251GB   hfs+            MacintoDos
 5      478GB   478GB   650MB   hfs+
 6      478GB   898GB   419GB   hfs+            MacintoTres
 7      898GB   947GB   49.3GB  ext4
 8      947GB   996GB   49.3GB  ext4
 9      996GB   1000GB  3999MB  linux-swap(v1)


Warning: Unable to open /dev/sr0 read-write (Read-only file system).  /dev/sr0
has been opened read-only.
Error: Can't have a partition outside the disk!
Ignore/Cancel?
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Re: post OSX upgrade breaks GRUB, wipes bios_grub partition?

Post by austin.texas »

You do have OSX installed it UEFI mode, which means that you need to install Mint in UEFI mode.
The "bios_grub" partition is only for non-UEFI installations, so you can forget about that.

These guides will give you the basics of installing in UEFI mode, for dual-booting. The error you mentioned comes from parted trying to read the CD/DVD drive, so that is not important.
Mint 18.2 Cinnamon, Quad core AMD A8-3870 with Radeon HD Graphics 6550D, 8GB DDR3, Ralink RT2561/RT61 802.11g PCI
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ManTaRa
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Re: post OSX upgrade breaks GRUB, wipes bios_grub partition?

Post by ManTaRa »

austin.texas wrote:You do have OSX installed it UEFI mode, which means that you need to install Mint in UEFI mode.
The "bios_grub" partition is only for non-UEFI installations, so you can forget about that.

These guides will give you the basics of installing in UEFI mode, for dual-booting. The error you mentioned comes from parted trying to read the CD/DVD drive, so that is not important.
@a.t:

Appreciate the links . . . I'll try to read through them. As far as the "bios_grub" partition goes, on two intel Macs I have LM installed on, if I don't do the "bios_grub" flag the install says "successful" but, the system doesn't boot. Previously I used rEFInd on the other unit, but for this computer using the "bios_grub" flag was what "worked" . . . . Also noticed that the OSX 10.12 install seems to have wiped the "name" of the first partition, also an older OSX partition . . . so OSX doesn't even play well with . . . other versions of itself . . . .

MTR
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Re: post OSX upgrade breaks GRUB, wipes bios_grub partition?

Post by prestonR »

Instructions of how to install on MBP by the chief-developer of Mint. Worked for my MBP.
https://community.linuxmint.com/tutorial/view/1643
Note that in my case I have to boot from USB and pick 'efi-boot' option from the apple boot screen; booting from DVD will boot in compatibility mode.
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Re: post OSX upgrade breaks GRUB, wipes bios_grub partition?

Post by ManTaRa »

prestonR wrote:Instructions of how to install on MBP by the chief-developer of Mint. Worked for my MBP.
https://community.linuxmint.com/tutorial/view/1643
Note that in my case I have to boot from USB and pick 'efi-boot' option from the apple boot screen; booting from DVD will boot in compatibility mode.
@prestonR:

Thanks for that link, I had seen it and generally used it for this MP install . . . I'm not sure if I did the "efibootmanager" . . . part of it, or if I did was there some error?

@a.t: I note in a quick read of Rod Smith's link that he says "OSX EFI is a different animal than other EFI's" . . . and therein is the "rub" . . . this is "dual-boot" with OSX . . . not windows.

@et al:

Anyway, one response I have is that I am looking to "repair" GRUB or repair the function where the "windows/linux" disk will again show up with the option key on restart, as it was before. I can boot LM 18 using the SuperGrub2 disk . . . and I can run updates . . . and I ran "recovery" from a Live DVD, but none of them seem to have fixed Grub . . . . Lost track of what all I've done to try to fix it; but, sure, I know I can nuke n pave for a fresh install, but if and when there is another OSX upgrade, again GRUB will be "unblessed"???

I compared the GRUB file I posted here with a copy of it from July, and those files look the same . . . so question is what other file or item needs to be adjusted to revive the boot capacity??? Of course I'll read on . . . .
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Re: post OSX upgrade breaks GRUB, wipes bios_grub partition?

Post by prestonR »

ManTaRa wrote:I'm not sure if I did the "efibootmanager" . . . part of it, or if I did was there some error?
That sounds like the error you get if your install was non-efi by picking the '"windows/linux" disk' option at the apple boot screen and you try to run 'efibootmanager'. Boot a liveUSB via the 'usb-efi' option and install in efi mode and you won't get the error. Now use efibootmanager to change the boot order.
this is "dual-boot" with OSX . . . not windows
So are the instructions in the link. :D
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Re: post OSX upgrade breaks GRUB, wipes bios_grub partition?

Post by ManTaRa »

prestonR wrote:
ManTaRa wrote:I'm not sure if I did the "efibootmanager" . . . part of it, or if I did was there some error?
That sounds like the error you get if your install was non-efi by picking the '"windows/linux" disk' option at the apple boot screen and you try to run 'efibootmanager'. Boot a liveUSB via the 'usb-efi' option and install in efi mode and you won't get the error. Now use efibootmanager to change the boot order.
this is "dual-boot" with OSX . . . not windows
So are the instructions in the link. :D
OK, thanks for the reply . . . this is still looking at fresh install as the solution, which it might be . . . original install was via Live DVD, possibly of 17.3 . . . no options for "efi" or non-efi were selected at the time . . . . But, as far as using efibootmanager to change the boot order, I spend more time in OSX, so I didn't mess with selecting LM as the first up in the boot order . . . .

Let's say I try this method, if I can find the choice in the Live DVD . . . and do a fresh install, would doing it this way then be "bullet-proof" against an OSX upgrade or security update? Or, back to fresh install each time?? I'm trying to figure out how to avoid the fresh install as the "solution" . . . if that is possible, etc???

MTR
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Re: post OSX upgrade breaks GRUB, wipes bios_grub partition?

Post by prestonR »

ManTaRa wrote:original install was via Live DVD, possibly of 17.3 . . . no options for "efi" or non-efi were selected at the time . . .
Yes, you did select an option: By booting 'windows/linux DVD' you selected non-efi compatibility mode.

To get the 'usb-efi' option:
- boot your Mint with SGD or boot the liveDVD
- use USB ImageWriter to write your Mint iso to an USB drive
- power down
- remove DVD
- boot with the MintUSB drive plugged in and hold 'options'
- the grey Apple boot menu should now show an 'usb-efi' option
- boot and install
- you now have installed Mint in 'efi' mode

If a major OSX update buggers this up re-install grub (now this will be done in efi mode) and do that efibootmanager fix.
Last edited by prestonR on Sat Oct 29, 2016 5:16 am, edited 1 time in total.
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Re: post OSX upgrade breaks GRUB, wipes bios_grub partition?

Post by ManTaRa »

prestonR wrote:
ManTaRa wrote:original install was via Live DVD, possibly of 17.3 . . . no options for "efi" or non-efi were selected at the time . . .
Yes, you did select an option: By booting 'windows/linux DVD' you selected non-efi compatibility mode.

If a major OSX buggers this up re-install grub (now this will be done in efi mode) and do that efibootmanager fix.
@Preston:

Thanks for the further thoughts . . . but, when I did my install I didn't use the option key and select "windows/linux DVD" . . . I booted the DVD with the "c" key . . . boots the DVD up similar I believe to booting via USB??? Or, no, any DVD iso is going to select "non-efi" compatibility mode; which also might explain why the "bios_grub" partition seemed to be "needed"???

Anyway, things will go into slo-mo on this one as I'm fresh out of unoccupied usb flash drives . . . I'll post back once I've tried the install via EFI/usb mode . . . .

MTR

[edit: I see that I can boot "efi" using the live DVD + option key . . . so things may speed up a tad bit . . . just need the approx 40+ mins to run the install and download stuff via 2 MB DSL line . . . . So we're back to "cooking with gas" on this one; I'm booted in "EFI" as we speak/type.]
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Re: post OSX upgrade breaks GRUB, wipes bios_grub partition?

Post by prestonR »

any DVD iso is going to select "non-efi" compatibility mode; which also might explain why the "bios_grub" partition seemed to be "needed"???
That is the case with my 2009 MBP but of course this may be different with other MBP. Still, to boot 'efi' the option chosen at the grey apple boot screen has to say something with 'efi', eg 'efi-usb'. Great, now we're moving.
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Re: post OSX upgrade breaks GRUB, wipes bios_grub partition?

Post by ManTaRa »

@et al:

Got the base install back in again . . . this time there were two (2) DVD "EFI boot" images to choose from in the grey "option" bootloader list of disks, along with the DVD "windows" choice . . .so I picked the "first" one. The install itself seemed to go pretty quick . . . the updates/upgrades seemed to take quite awhile to finish, with seemingly more yet to come.

The install has set itself as the "default" boot OS, I'd prefer my older OSX 10.9 system to be the default, so that might mean finding or installing the "efibootmanager" and/or fiddling with the boot order there??? as per the Clem tutorial for the MBPro? Or, likely with the next Security Update that might be excised?? question is whether or not after any upgrade of OSX would the LM system still show up as an "option" key listing . . . or again, busted flat in Baton Rouge??? Back to "Go, do not collect yr LM system . . ."????

Thanks though, it's always good times in linux-land . . . . I'll fiddle around with it a tad more before marking the thread as "solved."

MTR
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Re: post OSX upgrade breaks GRUB, wipes bios_grub partition?

Post by prestonR »

The install has set itself as the "default" boot OS, I'd prefer my older OSX 10.9 system to be the default, so that might mean finding or installing the "efibootmanager" and/or fiddling with the boot order there??? as per the Clem tutorial for the MBPro?
Yes.

The full instructions are only linked in Clem's post. To set this up so that OSX has the number one spot check the complete tutorial half-way down the page here: http://www.everydaylinuxuser.com/2014/0 ... e-osx.html

Can a major OSX upgrade do damage? Well, can't say for sure but the reason it got busted was that Legacy Mint can't join OSX on the efi boot but has to set-up it's own system. An OSX upgrade might damage this system but it won't damage the efi partition or OSX will fail to boot.

Even if Mint would disappear from the efi options, re-install grub, then fix the boot again.

Good luck.
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Re: post OSX upgrade breaks GRUB, wipes bios_grub partition?

Post by ManTaRa »

prestonR wrote:
The install has set itself as the "default" boot OS, I'd prefer my older OSX 10.9 system to be the default, so that might mean finding or installing the "efibootmanager" and/or fiddling with the boot order there??? as per the Clem tutorial for the MBPro?
Yes.
The full instructions are only linked in Clem's post. To set this up so that OSX has the number one spot check the complete tutorial half-way down the page here: http://www.everydaylinuxuser.com/2014/0 ... e-osx.html

Even if Mint would disappear from the efi options, re-install grub, then fix the boot again.
@PrestonR:

Thanks for that link, looks fairly similar to the Clem tutorial . . . appreciate the help on this one or more; it has been a problem for awhile, as I also have an 09 MBPro which is likely installed in "compatibility" . . . however I think when I first started messing with LM there was no "EFI boot" option, and rEFIt or rEFInd were the only options for installing to intel Macs at the time??? Somehow I missed the memo on the change . . . so, now I got it. Thnx. I might have to change my MBPro install to an "EFI-boot" install . . . if I get a spare moment . . . .

MTR
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Re: post OSX upgrade breaks GRUB, wipes bios_grub partition?

Post by fabien85 »

ManTaRa wrote:@et al:
question is whether or not after any upgrade of OSX would the LM system still show up as an "option" key listing . . . or again, busted flat in Baton Rouge??? Back to "Go, do not collect yr LM system . . ."????
If OSX makes its bootloader the default again, you can roll this back using instructions from this page :
http://www.rodsbooks.com/refind/bootcoup.html#bless
just adapt to your grub case instead of refind.
(i.e. grubx64.efi should be on the ESP, so after mounting it issue

Code: Select all

sudo bless --mount /Volumes/ESP --setBoot --file /Volumes/ESP/efi/ubuntu/grubx64.efi --shortform
)

By the way, everything would be simpler with refind, because you can install or reinstall it (or just rebless it) from either linux or OSX. Perso, I have had LM upgrades including switching release (16->17, and all the way to 17.3), OSX upgrades including firmware update and switching from 10.6 to 10.11, and I never had refind fall. Only troubles were with grub (updates, or when moving /home to a separate partition), that I am keeping as a side bootloader just in case.

To switch a legacy/BIOS install to an EFI install is possible but awkward. If you dual boot OSX and a legacy OS, you normally have an hybrid MBR, you can check this using gdisk : "sudo gdisk -l /dev/sda" (when issued from linux, from OSX use "sudo gdisk -l /dev/disk0") should give something like

Code: Select all

GPT fdisk (gdisk) version 0.7.2

Partition table scan:
  MBR: hybrid
  BSD: not present
  APM: not present
  GPT: present

Found valid GPT with hybrid MBR; using GPT.
You have to first install and register an EFI bootloader (again, refind is the simplest because you can install it from OSX, while if you boot linux in legacy mode I dont think it will let you install grub-efi, and most probably will not register it in the boot order). Then you have to recreate the protective MBR to destroy the legacy mode bootloader, this can also be done with gdisk ('n' option in the expert menu that you get with 'x').
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Re: post OSX upgrade breaks GRUB, wipes bios_grub partition?

Post by ManTaRa »

fabien85 wrote:
ManTaRa wrote:@et al:
question is whether or not after any upgrade of OSX would the LM system still show up as an "option" key listing . . . or again, busted flat in Baton Rouge??? Back to "Go, do not collect yr LM system . . ."????
If OSX makes its bootloader the default again, you can roll this back using instructions from this page :
http://www.rodsbooks.com/refind/bootcoup.html#bless
just adapt to your grub case instead of refind.
(i.e. grubx64.efi should be on the ESP, so after mounting it issue

Code: Select all

sudo bless --mount /Volumes/ESP --setBoot --file /Volumes/ESP/efi/ubuntu/grubx64.efi --shortform
)

By the way, everything would be simpler with refind, because you can install or reinstall it (or just rebless it) from either linux or OSX. Perso, I have had LM upgrades including switching release (16->17, and all the way to 17.3), OSX upgrades including firmware update and switching from 10.6 to 10.11, and I never had refind fall. Only troubles were with grub (updates, or when moving /home to a separate partition), that I am keeping as a side bootloader just in case.

.
@fabien85:

Thanks for the further details; since I went for the fresh EFI boot this time, we'll see how it goes on an upgrade . . . . But, as far as "rEFInd not falling" goes, on my MBPro I've had rEFIt & then rEFInd and with an OSX upgrade rEFInd would have to be "blessed" to get it to work again . . . but seemingly if I remember, GRUB would still work. At that time rEFInd was very easy to install in OSX, now apparently with 10.11 and up it requires more effort than the old, "drag the .sh file in the terminal to install" . . . very easy then. Now 10.11 has "SIP" (which I disabled) and some further complications to the process . . . and up until recently there were no apparent problems with having the dual+ boot system boot between OSX & LM with the option OSX bootloader. On my 09 MBPro it seemed like LM wouldn't boot w/o adding my "bios_grub" partition && rEFInd . . . which just means another layer to go through on the boot process.

Anyway, thanks for the additional info and links; I'll have some time in the near future to fine tune the LM boot situation . . . and hopefully it would be more easily repaired . . . either via "recovery" or "boot-repair" or "rescutux" or . . . via your suggested "blessings" . . . .

MTR
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Re: post OSX upgrade breaks GRUB, wipes bios_grub partition?

Post by prestonR »

To switch a legacy/BIOS install to an EFI install is possible
ManTaRa has already reinstalled in efi-mode and it seems to work.
as far as "rEFInd not falling" goes
It failed on me with an OSX update, bringing OSX down and making the legacy installed Mint and WinXP unbootable. Until then it had worked great.

Apple wanted 20 bucks to upgrade so I wiped OSX and re-installed Mint in efi. Grub and efibootmnger do the job of sorting boot; OSX and refind aren't really needed anymore (mind that a firmware upgrade of a component, should that become necessary, may require at least an install disk).

No issues so far ... knock, knock, knock...
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Re: post OSX upgrade breaks GRUB, wipes bios_grub partition?

Post by ManTaRa »

Code: Select all

sudo efibootmgr
BootCurrent: 0000
BootOrder: 0000,0080
Boot0000* ubuntu
Boot0080* Mac OS X
Boot0081* Mac OS X
BootFFFF* 
For technical reasons which are outside the scope of this tutorial, Linux Mint 17 uses the name "ubuntu" as its EFI identifier. So you can see your two operating system in efibootmgr's output:
Mint ("ubuntu") is at address "Boot0000"
Mac OS is at address "Boot0080"
Now, check the "BootOrder". It defines what to boot and in which order. Its value is at "0080", so it's basically booting Mac OS.
Let's change it with the following command, to make it boot Mint first (which is at "Boot0000", or "0") and then Mac OS (which is at "Boot0080" or "80"):

sudo efibootmgr -o 0,80

Run efibootmgr without arguments to check things up. The boot order should now indicate that it will run Mint first, and if that ever came to fail.. it would then run Mac OS. In other words our MacBook now boots into Grub. From there we can select Mint or press Escape and type "exit" to boot into Mac (we'll fix the Mac grub entries to make it exit without having to type anything later on in this tutorial).
So let's reboot now, and we should boot straight into Mint's Grub menu.
@readers
So it seems like efibootmgr was already installed, because I ran the command and got the shown results; so with a "hand's off" reboot we go to the grub menu and then into LM . . . but, technically since I'm on a Mac I'm thinking that I prefer to have OSX set to be the "default" or first up system?

My question now is on the "sudo efibootmgr -o 0,80" line . . . in which the "-o" is something like a short cut for "open"?? So if I was to change that line I would be using "sudo efibootmgr -o 80,0"??? Or, if I wanted to be fancy I could use "sudo efibootmgr -o 80,81,0" ???? And then it would search the available OSX items and then go to LM??

I'll have to see how well LM now runs on this computer, it certainly is "zippier" in some sense, but there have been functionality issues with "suspend" seeming to keep the computer warmer than OSX "sleep" . . . I'm thinking that in the next few years I'll be changing over to largely using LM as the first up system . . . but likely on a PC . . . . So far in the past OSX has kept the computers running cooler than LM has . . . so now we're again in "testing" . . . obviously I could always change the boot order to whatever is best choice at the time . . . and/or OSX update may do it as well, etc--my question is on how to write the command, and then whether you could have three selections there or just the two?

Thanks again,

MTR
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Re: post OSX upgrade breaks GRUB, wipes bios_grub partition?

Post by prestonR »

Code: Select all

sudo efibootmgr -o 80,0
That makes sense

Code: Select all

sudo efibootmgr -o 80,81,0
That will try to order what isn't there... How to use efibootmgr: https://www.linuxbabe.com/command-line/ ... r-examples
but there have been functionality issues
What kernel are you on? Try at least the latest of the series. Had similar hitches within the lower version numbers but in general, and this is purely my personal experience and may not be so for you, the later the kernel the better it runs. Currently I'm on 4.4.0-45, haven't noticed any regressions yet. Whatever new kernel you try, never de-install the 'old' one quickly, problems may take long to notice, having at least one fall-back is wise.
Last edited by prestonR on Tue Nov 01, 2016 4:00 pm, edited 1 time in total.
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