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booting nixos from lvm on top of mdadm using gpt

28 Apr 2012

#what is this?

i recently upgraded my hetzner root server and therefore had a system with 2x3tb disks. as fdisk can’t be used to partition disks > 2tb i had to use gpt instead which was quite tricky until it was working. so here is my installation guide. parts of it applies also to other distributions.

this guide uses concepts from the hetzner wiki OpenBSD installation guide [1].

note:

disk layout

update: 26.5.2012: updated the image according to the swap comment from nbp. swap should not be in the lvm as it might degrade the performance.

the installation

first remove old partitions/mdadm setups

uninstall:

lvremove /dev/myvolgrp/home
lvremove /dev/myvolgrp/system
lvremove /dev/myvolgrp/swap
vgremove myvolgrp
pvremote /dev/md0
mdadm --stop /dev/md0
# to remove the md0 permanently
mdadm --zero-superblock /dev/sda1
mdadm --zero-superblock /dev/sdb1

creating the partitions

update 26.5.2012: also add the swap partition here (not done below!).

parted /dev/sda
mklabel gpt
mkpart non-fs 0 2
mkpart primary 2 3001G
p
Number Start End Size File system Name Flags
1 17.4kB 2000kB 1983kB non-fs
2 2097kB 3001GB 3001GB primary
     
set 1 bios_grub on
p
Number Start End Size File system Name Flags
1 17.4kB 2000kB 1983kB non-fs bios_grub
2 2097kB 3001GB 3001GB primary

creating the new mdadm softraid device

mdadm --create /dev/md0 --level=1 --raid-devices=2 /dev/sda2 /dev/sdb2
mdadm: Note: this array has metadata at the start and
may not be suitable as a boot device. If you plan to
store '/boot' on this device please ensure that
your boot-loader understands md/v1.x metadata, or use
--metadata=0.90
Continue creating array? y
mdadm: Defaulting to version 1.2 metadata
mdadm: array /dev/md0 started.

LVM+filesystems

pvcreate /dev/md0
Physical volume "/dev/md0" successfully created

vgcreate myVolGrp /dev/md0
Volume group "myVolGrp" successfully created

lvcreate -n system -L50G myVolGrp
lvcreate -n swap -L8G myVolGrp

mkfs.ext4 -O dir_index -j -L system /dev/myVolGrp/system
mkswap -L swap /dev/myVolGrp/swap

note: the disk layout diagram mentiones a tmp partition which** happended to be added later ;-)**

using a virtual machine + vnc to boot the iso image

preparing the host system:

iptables -t nat -A POSTROUTING -o eth0 -j MASQUERADE
echo 1 > /proc/sys/net/ipv4/ip_forward

on the hostsystem

#download latest console only 64bit nixos installer
nixos-minimal-0.1pre33860-33874-x86_64-linux.iso

make sure /dev/myVolGrp/system and /dev/myVolGrp/swap are not in use:

apt-get install sudo
qemu-system-x86_64 -enable-kvm -m 1024 -hda /dev/md0 -net nic -net tap -cdrom nixos-minimal-0.1pre33860-33874-x86_64-linux.iso -boot d -vnc localhost:0

note: in contrast to original article [1] i use ‘-enable-kvm’ which speeds things up!

from your homecomputer

execute this two commands (in two different shells):

ssh -L 5900:localhost:5900 root@176.9.99.117
vncviewer localhost

inside the qemu/kvm system via vncviewer

how we have to prepare install the system on the devices we had preparted in the steps before:

inside do:
login as root
mount -L system /mnt

cd /mnt
nixos-option --install
vi /etc/nixos/configuration.nix

stop dhcpcd
ip a add 172.2.0.2/16 dev eth0
ip r add via 172.2.0.1
echo "nameserver 8.8.8.8" > /etc/resolv.conf
# use ping www.google.de to verfy that the routing is working

# example url, configuration.nix is appended to this article
curl http://lastlog.de/configuration.nix
mv configuration.nix /mnt/etc/nixos/configuration.nix
# now the installation, make sure you read the nixos installation guide as well, but in short:
nixos-install
# only the grub2 installation should have failed (as there is no /dev/sda1 in the virtual machine!)
#finally we halt the system
halt

im hostsystem we need to install grub2:

apt-get install grub2
grub-install --no-floppy --root-directory=/mnt --recheck /dev/sda
Installation finished. No error reported.

grub-install --no-floppy --root-directory=/mnt --recheck /dev/sdb
Installation finished. No error reported.

# now we add a ssh key so we can login into this system later on
cd /mnt
mkdir root
cd root
mkdir .ssh
chown 0700 .ssh/
cd .ssh
echo "ssh-rsa AAAAB3Nz.....aU79sGVhyOPRz joachim@ebooK" > authorized_keys

from your homecomputer login into the installed system (reboot the host) and then issue this command:

ssh root@176.9.99.117 -i ~/.ssh/myprivatekey

after the first login, nixos-rebuild switch might fail with this error message:

nixos-rebuild switch --fast
building the system configuration...
updating GRUB 2 menu...
installing the GRUB bootloader on /dev/sda...
/nix/store/iaypdz5mm1qk8izs9412cb28v9vwwcn4-grub-1.99/sbin/grub-probe: error: no such disk.
Auto-detection of a filesystem of /dev/mapper/myVolGrp-system failed.
Try with --recheck.
If the problem persists please report this together with the output of 
"/nix/store/iaypdz5mm1qk8izs9412cb28v9vwwcn4-grub-1.99/sbin/grub-probe --device-map="/boot/grub/device.map" 
--target=fs -v /boot/grub" to
grub-probe --device-map="/boot/grub/device.map" --target=fs -v /boot/grub
grub-probe: info: Cannot stat `/dev/disk/by-id/scsi-35000c5003f556643', skipping.
grub-probe: info: Cannot stat `/dev/disk/by-id/scsi-35000c5003f5363a6', skipping.
grub-probe: info: changing current directory to /dev.
grub-probe: info: changing current directory to pts.
grub-probe: info: changing current directory to shm.
grub-probe: info: changing current directory to myVolGrp.
grub-probe: info: changing current directory to md.
grub-probe: info: changing current directory to disk.
grub-probe: info: changing current directory to by-label.
grub-probe: info: changing current directory to by-uuid.
grub-probe: info: changing current directory to by-partlabel.
grub-probe: info: changing current directory to by-partuuid.
grub-probe: info: changing current directory to by-path.
grub-probe: info: changing current directory to by-id.
grub-probe: info: changing current directory to snd.
grub-probe: info: changing current directory to mapper.
grub-probe: info: opening myVolGrp-system.
grub-probe: error: no such disk.

so what is inside this device.map anyway?

cd /boot/grub
cat device.map
(hd0) /dev/disk/by-id/scsi-35000c5003f556643
(hd1) /dev/disk/by-id/scsi-35000c5003f5363a6

Jordan_U#grub@irc.freenode.net recommended to remove the device.map. that made it work:

rm /boot/grub/device.map

rescue system state by going to the previous version

in theory you should be able to use vkvm from hetzner, which does basically what i am doing here, but it didn’t work for me since non of my browsers worked with the java plugin and i had problems with the vncviewer on port 47774.

boot the hetzner 64 bit linux rescue system which contains qemu+kvm:

apt-get install sudo
qemu-system-x86_64 -enable-kvm -m 1024 -hda /dev/md0 -cdrom nixos-minimal-0.1pre33860-33874-x86_64-linux.iso -boot d -vnc localhost:0

ssh -L 5900:localhost:5900 root@176.9.99.117
vncviewer localhost

now inside the vncviewer

mount /dev/myVolGrp/system /mnt
cd /mnt
for a in dev proc sys; do mount --bind /$a /mnt/$a; done;
chroot . /bin/sh

now inside that new shell, type:

ls -l /nix/var/nix/profiles/system-*
lrwxrwxrwx 1 root root 76 Jul  3 23:31 /nix/var/nix/profiles/system-67-link -> /nix/store/d146zhm0mzdbb8v41yr782v96zncqhxa-nixos-0.2pre4832_edab9e4-e533af9
lrwxrwxrwx 1 root root 76 Jul  7 22:45 /nix/var/nix/profiles/system-68-link -> /nix/store/d0l5zg81x6yc3mxbrd3zxv3m4xhwabs7-nixos-0.2pre4832_edab9e4-9e98650

since we want to go to the previous boot entry, we type:

/nix/var/nix/profiles/system-67-link/bin/switch-to-configuration boot

since we are done here, type:

exit      # this will exit from the chroot into the rescue system
cd / 
umount /mnt
reboot

summary

took quite some time to figure all this out so i guess someone else might have interested in this guide as well. i also tried to install, using EFI, but soon discovered that this might be a very complicated road to go and therefore skipped that. it is cool to see that there is a very helpful community surrounding key projects required to get this installation done. i would have had to spend much more time if i wouldn’t have had someone to ask from time to time.

configuration.nix


# Edit this configuration file which defines what would be installed on the
# system. To Help while choosing option value, you can watch at the manual
# page of configuration.nix or at the last chapter of the manual available
# on the virtual console 8 (Alt+F8).

{config, pkgs, ...}:

{
require = [
# Include the configuration for part of your system which have been
# detected automatically.
./hardware-configuration.nix
];

boot.initrd.kernelModules = [
# Specify all kernel modules that are necessary for mounting the root
# file system.
#
# "ext4" "ata_piix"
"af_packet" "snd_pcm_oss" "snd_mixer_oss" "rtc_cmos" "rtc_core" "rtc_lib" "snd_hda_codec_via" "i915" 
"joydev" "drm_kms_helper" "snd_hda_intel" "rng_core" "drm" "snd_hda_codec" "thermal" "i2c_algo_bit" 
"button" "snd_hwdep" "intel_agp" "psmouse" "i2c_i801" "evdev" "snd_pcm" "video" "agpgart" "pcspkr" 
"serio_raw" "iTCO_wdt" "i2c_core" "snd_timer" "output" "e1000e" "snd" "soundcore" "snd_page_alloc" 
"sg" "loop" "ipv6" "kvm" "freq_table" "processor" "thermal_sys" "hwmon" "ext4" "mbcache" "jbd2" 
"crc16" "raid456" "async_pq" "async_xor" "xor" "async_memcpy" "async_raid6_recov" "raid6_pq" 
"async_tx" "md_mod" "sd_mod" "crc_t10dif" "sata_sil" "ata_piix" "dm_mod" "usb_storage" 
"usb_libusual" "usbhid" "hid" "ohci1394" "ieee1394" "ahci" "libata" "scsi_mod" "ehci_hcd" 
"uhci_hcd" "usbcore" "nls_base" "scsi_wait_scan" "unix"
];

boot.loader.grub = {
# Use grub 2 as boot loader.
enable = true;
version = 2;

# Define on which hard drive you want to install Grub.
devices = [ "/dev/sda" "/dev/sdb" ];
};
boot.extraKernelParams = [ "vga=normal" "nomodeset" ];

networking = {
hostName = "nix9000"; # Define your hostname.
# wireless.enable = true; # Enables Wireless.
};

# Add file system entries for each partition that you want to see mounted
# at boot time. You can add filesystems which are not mounted at boot by
# adding the noauto option.
fileSystems = [
# Mount the root file system
#
{ mountPoint = "/";
#device = "/dev/sda2";
label = "system";
}
#{ mountPoint = "/boot";
# label = "boot";
#}

# Copy & Paste & Uncomment & Modify to add any other file system.
#
# { mountPoint = "/data"; # where you want to mount the device
# device = "/dev/sdb"; # the device or the label of the device
# # label = "data";
# fsType = "ext3"; # the type of the partition.
# options = "data=journal";
# }
];

swapDevices = [
# List swap partitions that are mounted at boot time.
#
{ label = "swap"; }
];

# Select internationalisation properties.
# i18n = {
# consoleFont = "lat9w-16";
# consoleKeyMap = "us";
# defaultLocale = "en_US.UTF-8";
# };

# List services that you want to enable:

# Add an OpenSSH daemon.
services.openssh.enable = true;

# Add CUPS to print documents.
# services.printing.enable = true;

# Add XServer (default if you have used a graphical iso)
# services.xserver = {
# enable = true;
# layout = "us";
# xkbOptions = "eurosign:e";
# };

environment.systemPackages = with pkgs; [
zsh wget wgetpaste vimprobable2
];

# Add the NixOS Manual on virtual console 8
#services.nixosManual.showManual = true;
}