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dracut-initqueue timeout and root LV missing, some LV's missing in rescue mode

Yesterday I had a machine that stopped booting after an update. What I didn't know was that during issues with yum update the LVM package was removed and after that the initramfs's (all of them) where regenerated. Which resulted in a machine that wasn't able to boot anymore.

The errors (list of search words, not actual since no log exists):

dracut-initqueue timeout
root does not exist
Starting dracut emergency shell
Entering emergency mode
dracut-initqueue[259]: Warning: dracut-initqueue timeout
dracut-initqueue[279] Warning: Could not boot
dracut-initqueue[279] Warning; /dev/mapper/rhel_...-root does not exit
in rescue mode
job timeout
Timed out waiting for dev-mapper-VG\LV.device
unable to mount logic volumes
vgchange missing
lvchange missing

This is how I solved it:

I started a live CD, configured the network and chrooted into the machine and ran (check kernel version and actual initramfs file):

lsinitrd -m –k /boot/initramfs-3.10.0-693.11.1.el7.x86_64.img | grep lvm (returned nothing)
yum install lvm2
dracut -f /boot/initramfs-3.10.0-693.11.1.el7.x86_64.img 3.10.0-693.11.1.el7.x86_64

Since this isn't standard behavior, you should check all services and make sure that your packages are consistent.

yum check all

Shrink a disk

This was tested on RHEL7 but should work on any recent Linux.

In case you have a too large disk or you want to roll back an expansion because for instance the need of extra disk space isn't relevant anymore, you can follow this guide.

! Always make sure you have a backup, these are dangerous commands to run that can lead to data corruption

There are a lot of tricks you can do but these ones are tested. Shifting around with new disks to swap should be the safest way but Red Hat's implementation of Grub and initramfs has some drawbacks which during my tests lead to an unbootable machine. This article describes how I did a move (over network if you like) in a Debian-based set up.

First things first, resize the actual file system(s). If you can't unmount the partition, start from a rescue disk (gparted-live for instance) to do this part and return to the installed system afterwards. Take a margin of 10% to make sure we don't have any conversion issues resulting in dataloss (repeat this for all partitions)

If you are on xfs or another filesystem that doesn't allow shrinking you can use fstransform (actually you can always use this). fstransform is in the EPEL directory but you can just download the RPM and install it with yum install too.

If you want to keep xfs

fstransform /dev/[volumegroup]/[logicalvolume] --new-size=[size] xfs

If you rather would have ext4

fstransform /dev/[volumegroup]/[logicalvolume] --new-size=[size] ext4

for ext4

e2fsck -f /dev/[volumegroup]/[logicalvolume]
resize2fs -p /dev/[volumegroup]/[logicalvolume] [size]
 
example:
resize2fs -p /dev/mapper/vg_system_lv_tmp 900M

Next we are going to reduce the LVM volume (if you can't manage the downtime, this part you can do with a mounted FS) (repeat this for all partitions)

lvreduce -L [newlvsize] /dev/[volumegroup]/[logicalvolume]
 
example:
lvreduce -L 900M /dev/mapper/vg_system_lv_tmp

Next if you want to drop a disk, now is the moment to clean it out. (if your LVM is on one disk, you can skip this part)

pvmove /dev/[the disk you want to remove]
vgreduce [volumegroup] /dev/[the disk you want to remove]
pvremove /dev/[the disk you want to remove]

Now you can drop/reuse this disk.

To shrink the LVM part on a disk with partition table you should first check the used and total extensions and ask LVM to move all extensions to the front of the LVM partition

vgdisplay
pvmove --alloc anywhere /dev/[partition]:[alloc PE + 1]-[total PE - 1]

Now check if all used extends are on the front of the disk and the only free portion is on the end. If not repeat the previous pvmove command until you get the desired result.

pvs -v --segments

This is how it should look

undefined

And now you can resize the volume group to match the wanted disk size

pvresize --setphysicalvolumesize [size] /dev/[lvm partition]
 
example:
pvresize --setphysicalvolumesize 38G /dev/sda2

Next you can resize the partition table to become small enough to fit the end size of your disk and next you can resize the virtual disk. Check the extends of an other virtual machine with the wanted disk size if you want to push it to the limit, otherwise keep a margin. I used 40G as an example.

fdisk /dev/sda
*d* -> select partition 2 if that is the LVM one
*n* -> create a new primary partition 2 with the default suggested start sector but for the end sector select 83886079 (for a 40G total disk with 500M boot partition)
*:wq* to save

Now resize the VM disk to the same size (40G in this example). Next you can use lvextend and resize2fs to fill up the margin again to get the desired result.

Since it seems impossible to shrink a disk in hyper-v (Gen 1). I added a 40G disk, started the live cd again and did:

dd if=/dev/sda of=/dev/sdb

Next I just removed the first disk (if you want to be safe, press remove but select "no" when hyper-v asks if you want to remove the disk from the host too) and made the new disk the primary disk and marked it "contains the operating system for the virtual machine" and it booted fine.

pvresize /dev/[lvm partition]
lvresize -L [oldlvsize] /dev/[volumegroup]/[logicalvolume]
resize2fs /dev/[volumegroup]/[logicalvolume]

And finally delete the old disk from the host if you kept it. For this go to the host running the VM, go into the directory you find when you open the disk settings of the VM and just delete the old disk with shift+delete.

MDADM and a single LVM to boot from (on a Debian based system)

Yesterday I moved a customer's server to new disks. To get some extra features like snapshotting I opted to convert the current static disk layout to LVM on top of MDADM. As a bonus I did the entire sync online to a new disk connected to my laptop which acted as a degraded mirror.

Yes I know GPT is the way to go but I started this move at 7 PM to minimise business impact and since the new disks are still only 500G I went for MBR which was already in place. For GPT "RAID" check this answer

This tutorial can also be used to move a non-RAID server to a RAID setup or to move a server to a new machine that will have MDADM RAID.

First create the partition table

parted /dev/sdz 
mklabel msdos
mkpart primary ext2 0% 100%
set 1 lvm on
quit

Create the MDADM mirror and LVM group + partitions (I will only use 2 in this tutorial but you can use this as a guide to get a better solution for a professional environment)

mdadm --create --verbose /dev/md0 --level=mirror --raid-devices=2 /dev/sdz1 missing
pvcreate /dev/md0
vgcreate lvm /dev/md0
lvcreate -L 500M lvm -n boot
lvcreate -L 20G lvm -n root
mkfs.ext4 /dev/mapper/lvm-boot
mkfs.ext4 /dev/mapper/lvm-root

 Next mount the new partitions and start cloning the old system

mount /dev/mapper/lvm-root /mnt
mkdir /mnt/boot
mount /dev/mapper/lvm-boot /mnt/boot
rsync -aAXv --exclude={"/dev/*","/proc/*","/sys/*","/tmp/*","/run/*","/mnt/*","/media/*","/lost+found"} user@src /mnt/
*here you should stop all services on the src and rerun the rsync command for a final sync*

Next we will set up the bootloader and adapt the system files

for i in /dev /dev/pts /proc /sys /run; do sudo mount -B $i /mnt$i; done
sudo cp /etc/resolv.conf /mnt/etc/resolv.conf
sudo chroot /mnt
blkid
*get the ID's for the LVM paritions*
vi /etc/fstab
*replace the ID's of the old /, /boot, ...*
apt-get install lvm2 mdadm
mdadm --examine --scan >> /etc/mdadm.conf
*delete the previous lines starting with ARRAY, if any*
vi /etc/mdadm/mdadm.conf
*now update initramfs to make sure it contains MDADM and LVM2 support and install grub to the new disk*
update-initramfs -k all -u -v
grub-install /dev/sdz

At this point you should be able to shut down the src server and boot from the new disk after replacement (or if you use this to move a server by starting the dst server). If you are able to boot succesfully and have the second disk already in place we are now going to "restore" the mirror.

*copy the MBR*
dd if=/dev/sdz of=/dev/sdy bs=512 count=1
partprobe /dev/sdy
*add the disk to the MDADM RAID to start rebuilding*
mdadm --manage /dev/md0 --add /dev/sdy1
*check if the rebuild is started*
cat /proc/mdstat
*just to make sure reinstall grub on boot disks, choose both /dev/sdz en /dev/sdy*
dpkg-reconfigure grub-pc

Another reboot after the rebuild is finished can be good to verify everything.

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