[Bio-linux-devel] 16.04.1 Upgrade Follies

[Tony Travis]

On 02/11/16 14:19, mckennep at mskcc.org wrote:
> Hi,
> 
> I made a stupid mistake and tried to upgrade to Ubuntu 16.04.1 on a
> Bio-Linux 8 installation.

Hi, Peter.

You didn't make a stupid mistake trying the upgrade!

I've got Bio-Linux 8 running under Ubuntu 16.04 LTS on my laptop. A few
things are terminally broken (e.g. Galaxy in particular). I've
work-arounds for some packages, but more work needs to be done before I
make a Bio-Linux 9 release based on Ubuntu 16.04.

> Now, after starting grub, I get a black screen with the following
> (xxx = large number):
> 
> lvmetad is not active yet, using direct activation during sysinit 
> /dev/mapper/biolinux--vg-root: recovering journal 
> /dev/mapper/biolinux--vg-root: clean, xxxxxxx/xxxxxxxx files,
> xxxxxx/xxxxxxx blocks
> 
> I searched and found this:
> 
> http://askubuntu.com/questions/769863/lvmetad-is-not-active-yet-using-direct-activation-during-sysinit/783977#783977
>
>  ...but those suggestions didn't work for me.  Adding 'nomodeset'
> after 'quiet splash' in the startup commands gives me the same black
> screen with the 'lvmetad' error message, but now I also get the
> Biolinux8 green startup dots cycling on the screen forever.
> 
> I looked up what lvmetad is, but I don't really understand what it
> does. Any ideas?

The BIG mistake you made was using LVM :-(

If you want to run Bio-Linux on a server, use "md" RAID instead of LVM.
You don't need LVM on a laptop or desktop anyway, but you should use
"md" RAID on a workstation if it has several disks.

What you need to do is fix your broken LVM from the command-line!

HTH,

  Tony.

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