Replacing VDEV in a ZFS Pool

Several months ago I had an old 3TB hard drive (HDD) crashed on me. Luckily it was a hard drive that is primarily used for backup purposes, so the data lost can quickly be duplicated from source by performing another backup. Since it was not critical that I replace the damaged drive immediately, it was kind of left to fester until today.

Recently I acquired four additional WD Red 6TB HDD, and I wanted to install these new drives into my NAS chassis. Since I am opening the chassis, I will irradicate the damaged drive, and also take this opportunity to swap some old drives out of the ZFS pool that I created earlier and add these new drives into the pool.

I first use the following command to add two additional mirror vdev’s each composed of the two new WD Red drives.

sudo zpool add vault mirror {id_of_drive_1} {id_of_drive_2}

The drive id’s is located in the following path: /dev/disk/by-id and is typically prefixed with ata or wwn.

This created two vdev’s into the pool, and I can remove an existing vdev. Doing so will automatically start redistributing the data on the removing vdev to the other vdev’s in the pool. All of this is performed while the pool is still online and running to service the NAS. To remove the old vdev, I execute the following command:

sudo zpool remove vault {vdev_name}

In my case, the old vdev’s name is mirror-5.

Once the remove command is given, the copying of data from the old vdev to the other vdev’s begins. You can check the status with:

sudo zpool status -v vault

The above will show the copying status and the approximate time it will take to complete the job.

Once the removal is completed, the old HDD of mirror-5 is still labeled for ZFS use. I had to use the labelclear command to clean the drive so that I could repurpose the drives for backup duty. Below is an example of the command.

sudo zpool labelclear sdb1

The resulting pool now looks like this:

sudo zpool list -v vault

(Output truncated)
                                                                                                                     NAME                                                    SIZE  ALLOC   FREE
vault                                                  52.7T  38.5T  14.3T
  mirror-0                                             9.09T  9.00T  92.4G
    ata-ST10000VN0008-2JJ101_ZHZ1KMA0-part1                -      -      -
    ata-WDC_WD101EFAX-68LDBN0_VCG6VRWN-part1               -      -      -
  mirror-1                                             7.27T  7.19T  73.7G
    wwn-0x5000c500b41844d9-part1                           -      -      -
    ata-ST8000VN0022-2EL112_ZA1E8S0V-part1                 -      -      -
  mirror-2                                             9.09T  9.00T  93.1G
    wwn-0x5000c500c3d33191-part1                           -      -      -
    ata-ST10000VN0004-1ZD101_ZA2964KD-part1                -      -      -
  mirror-3                                             10.9T  10.8T   112G
    wwn-0x5000c500dc587450-part1                           -      -      -
    wwn-0x5000c500dcc525ab-part1                           -      -      -
  mirror-4                                             5.45T  1.74T  3.72T
    wwn-0x50014ee2b9f82b35-part1                           -      -      -
    wwn-0x50014ee2b96dac7c-part1                           -      -      -
  indirect-5                                               -      -      -
  mirror-6                                             5.45T   372G  5.09T
    wwn-0x50014ee265d315cd-part1                           -      -      -
    wwn-0x50014ee2bb37517e-part1                           -      -      -
  mirror-7                                             5.45T   373G  5.09T
    wwn-0x50014ee265d315b1-part1                           -      -      -
    wwn-0x50014ee2bb2898c2-part1                           -      -      -
cache                                                      -      -      -
  nvme-Samsung_SSD_970_EVO_Plus_500GB_S4P2NF0M419555D   466G   462G  4.05G

The above indirect-5 can be safely ignored. It is just a reference to the old mirror-5.

This time we replaced the entire vdev, another technique is to replace the actual drives within the vdev. To do this, we will have to use the zpool replace command. We may also have to perform a zpool offline first before the replace command. This can be successively done on all the old drives in the mirror with newer drives with larger capacities to increase an existing vdev’s size.

Found Two HBA Cards for My NAS

About three weeks ago, I was casually browsing eBay and found this little gem, a Host Bus Adapter that can do PCIe 2.0 x8 (~4 to 8GB/s). This is way better than the one that I purchased earlier (GLOTRENDS SA3116J PCIe SATA Adapter Card) which can operate on a single lane of PCIe 3.0 yielding only 1GB/s. I could not pass it up at a price of only $ 40 CAD, so I purchased two of these to replace the old adapter card I had.

LSI 6Gbps SAS HBA 9200-8i IT Mode ZFS FreeNAS unRAID + 2*SFF-8087 SATA

This new card LSI 6Gbps SAS HBA 9200-8i only supports 8 SATA ports per card, so I had to get two of them to support all of the hard drives that I have. These SAS HBA cards must have the IT (initiator target) mode firmware because the default firmware (IR mode) supports a version of hardware RAID, which I did not want. With the IT mode, the hard drives will be logically separated on the card and only share the physical bandwidth of the PCIe bus. This is a must for ZFS.

With these new cards, my write throughput to my NAS hard drives now averages around 500MB/s. Previously, I was only getting about half of this.

I wish I would have found these sooner. Now I have two spare PCIe SATA expansion cards, one supporting 8 ports, and the other supporting 16 ports. I will place them on another server. Perhaps in a future Proxmox cluster project.

LVM to ZFS Migration

In a previous post, I described the hardware changes that I made to facilitate additional drive slots on my NAS Media Server.

We now need to migrate from an LVM system consisting of 40TB of redundant mirrored storage using mdadm to a ZFS system consisting of a single pool and a dataset. Below is a diagram depicting the logical layout of the old and the intended new system.

40TB of Redundant Storage
40TB of Redundant Storage
Logical Volume (LV)
Logical Volume (LV)
EXT 4 File System for Media Storage
EXT 4 File System for Media Storage
Old Storage System
Old Storage System
50TB of Redundant Storage
50TB of Redundant Storage
ZFS Dataset
ZFS Dataset
New Storage System
New Storage System
LV Group of 4 Physical Volumes (PV)
LV Group of 4 Physical Volumes (PV)
PV
PV
10TB
mdadm mirror
10TB…
PV
PV
8TB
mdadm mirror
8TB…
PV
PV
10TB
mdadm mirror
10TB…
PV
PV
12TB
mdadm mirror
12TB…
ZFS Pool
ZFS Pool
12TB
Mirror VDEV
12TB…
10TB
Mirror VDEV
10TB…
8TB
Mirror VDEV
8TB…
10TB
Mirror VDEV
10TB…
6TB
Mirror VDEV
6TB…
4TB
Mirror VDEV
4TB…
512GB
L2ARC Cache
512GB…

Before the migration, we must backup all the data from the LVM system. I cobbled together a collection of old hard drives and then proceeded to create another LVM volume as the temporary storage of the content. This temporary volume will not have any redundancy capability, so if any one of the old hard drives fails, then out goes all the content. The original LVM system is mounted on /mnt/airvideo and the temporary LVM volume is mounted on /mnt/av2.

I used the command below to proceed with the backup.

sudo rsync --delete -aAXv /mnt/airvideo /mnt/av2 > ~/nohup.avs.rsync.out 2>&1 &

I can then monitor the progress of the backup with:

tail -f ~/nohup.avs.rsync.out

The backup took a little more than 7 days to copy around 32 TB of data from our NAS server. During this entire process, all of the NAS services continued to run, so that downtime was almost non-existent.

Once the backup is completed, I wanted to move all the services to the backup before I started to dismantle the old LVM volume. The following steps were done:

  • Stop all services on other machines that were using the NAS;
  • Stop all services on the NAS that were using the /mnt/airvideo LVM volume;
    • sudo systemctl stop apache2 smbd nmbd plexmediaserver
  • Unmount the /mnt/airvideo volume, and create a soft-link of the same name to the backup volume at /mnt/av2;
    • sudo umount /mnt/airvideo
    • sudo ln -s /mnt/av2 /mnt/airvideo
  • Restart all services on the NAS and the other machines;
    • sudo systemctl start apache2 smbd nmbd plexmediaserver
  • Once again, the downtime here was minimal;
  • Remove or comment out the entry in the /etc/fstab file that automatically mounts the old LVM volume on boot. This is no longer necessary because ZFS is remounted by default;

Now that the services are all up and running, we can then start destroying the old LVM volume (airvideovg2/airvideo) and volume group (airvideovg2). We can obtain a list of all the physical volumes that make up the volume group.

sudo pvdisplay -C --separator ' | ' -o pv_name,vg_name

  PV | VG
  /dev/md1 | airvideovg2
  /dev/md2 | airvideovg2
  /dev/md3 | airvideovg2
  /dev/md4 | airvideovg2
  /dev/nvme0n1p1 | airvideovg2

The /dev/mdX devices are the mdadm mirror devices, each consisting of a pair of hard drives.

sudo lvremove airvideovg2/airvideo
Do you really want to remove and DISCARD active logical volume airvideovg2/airvideo? [y/n]: y
  Flushing 0 blocks for cache airvideovg2/airvideo.
Do you really want to remove and DISCARD logical volume airvideovg2/lv_cache_cpool? [y/n]: y
  Logical volume "lv_cache_cpool" successfully removed
  Logical volume "airvideo" successfully removed

sudo vgremove airvideovg2
  Volume group "airvideovg2" successfully removed

At this point, both the logical volume and the volume group are removed. We say a little prayer to ensure nothing happens with our temporary volume (/mnt/av2), that is currently in operation.

We now have to disassociate the mdadm devices from LVM.

sudo pvremove /dev/md1
Labels on physical volume "/dev/md1" successfully wiped.
sudo pvremove /dev/md2
Labels on physical volume "/dev/md2" successfully wiped.
sudo pvremove /dev/md3
Labels on physical volume "/dev/md3" successfully wiped.
sudo pvremove /dev/md4
Labels on physical volume "/dev/md4" successfully wiped.
sudo pvremove /dev/nvme0n1p1
Labels on physical volume "/dev/nvme0n1p1" successfully wiped.

You can find the physical hard drives associated with each mdadm device using the following:

sudo mdadm --detail /dev/md1
#or
sudo cat /proc/mdstat

We then have to stop all the mdadm devices and zero their superblock so that we can reuse the hard drives to set up our ZFS pool.

sudo mdadm --stop /dev/md1
mdadm: stopped /dev/md1
sudo mdadm --stop /dev/md2
mdadm: stopped /dev/md2
sudo mdadm --stop /dev/md3
mdadm: stopped /dev/md3
sudo mdadm --stop /dev/md4
mdadm: stopped /dev/md4

# Normally you also need to do a --remove after the --stop,
# but it looks like the 6.5 kernel did the remove automatically.
#
# For all partitions used in the md device

for i in sdb1 sdc1 sdp1 sda1 sdo1 sdd1 sdg1 sdn1
do
	sudo mdadm --zero-superblock /dev/${i}
done

Now with all of the old hard drives freed up, we can repurpose them to create our ZFS pool. Instead of using the /dev/sdX reference of the physical device, it is recommended to use /dev/disk/by-id with the manufacturer’s model and serial number so that the ZFS pool can be moved to another machine in the future. We also used the -f switch to let ZFS know that it is okay to erase the existing content on those devices. The command to create the pool we named vault is this:

zpool create -f vault mirror /dev/disk/by-id/ata-ST10000VN0008-2JJ101_ZHZ1KMA0-part1 /dev/disk/by-id/ata-WDC_WD101EFAX-68LDBN0_VCG6VRWN-part1 mirror /dev/disk/by-id/ata-ST8000VN0022-2EL112_ZA1E8GW4-part1 /dev/disk/by-id/ata-ST8000VN0022-2EL112_ZA1E8S0V-part1 mirror /dev/disk/by-id/ata-ST10000VN0004-1ZD101_ZA2C69FN-part1 /dev/disk/by-id/ata-ST10000VN0004-1ZD101_ZA2964KD-part1 mirror /dev/disk/by-id/ata-ST12000VN0008-2YS101_ZRT008SC-part1 /dev/disk/by-id/ata-ST12000VN0008-2YS101_ZV701XQV-part1

# The above created the pool with the old drives from the old LVM volume group
# We then added 4 more drives, 2 x 6TB, and 2 x 4TB drives to the pool

# Adding another 6TB mirror:

sudo zpool add -f vault mirror /dev/disk/by-id/ata-WDC_WD60EFRX-68L0BN1_WD-WX31D87HDU09-part1 /dev/disk/by-id/ata-WDC_WD60EZRZ-00GZ5B1_WD-WX11D374490J-part1

# Adding another 4TB mirror:

sudo zpool add -f vault mirror /dev/disk/by-id/ata-ST4000DM004-2CV104_ZFN0GTAK-part1 /dev/disk/by-id/ata-WDC_WD40EZRX-00SPEB0_WD-WCC4E0354579-part1

We also want to add the old NVMe as ZFS L2ARC cache.

ls -lh /dev/disk/by-id/nvme-Samsung_SSD_970_EVO_Plus_500GB_S4P2NF0M419555D

lrwxrwxrwx 1 root root 13 Mar  2 16:02 /dev/disk/by-id/nvme-Samsung_SSD_970_EVO_Plus_500GB_S4P2NF0M419555D -> ../../nvme0n1

sudo zpool add vault cache /dev/disk/by-id/nvme-Samsung_SSD_970_EVO_Plus_500GB_S4P2NF0M419555D 

We can see the pool using this command:

sudo zpool list -v vault

NAME                                                    SIZE  ALLOC   FREE  CKPOINT  EXPANDSZ   FRAG    CAP  DEDUP    HEALTH  ALTROOT
vault                                                  45.4T  31.0T  14.4T        -         -     0%    68%  1.00x    ONLINE  -
  mirror-0                                             9.09T  8.05T  1.04T        -         -     0%  88.5%      -    ONLINE
    ata-ST10000VN0008-2JJ101_ZHZ1KMA0-part1                -      -      -        -         -      -      -      -    ONLINE
    ata-WDC_WD101EFAX-68LDBN0_VCG6VRWN-part1               -      -      -        -         -      -      -      -    ONLINE
  mirror-1                                             7.27T  6.49T   796G        -         -     0%  89.3%      -    ONLINE
    ata-ST8000VN0022-2EL112_ZA1E8GW4-part1                 -      -      -        -         -      -      -      -    ONLINE
    ata-ST8000VN0022-2EL112_ZA1E8S0V-part1                 -      -      -        -         -      -      -      -    ONLINE
  mirror-2                                             9.09T  7.54T  1.55T        -         -     0%  82.9%      -    ONLINE
    ata-ST10000VN0004-1ZD101_ZA2C69FN-part1                -      -      -        -         -      -      -      -    ONLINE
    ata-ST10000VN0004-1ZD101_ZA2964KD-part1                -      -      -        -         -      -      -      -    ONLINE
  mirror-3                                             10.9T  8.91T  2.00T        -         -     0%  81.7%      -    ONLINE
    ata-ST12000VN0008-2YS101_ZRT008SC-part1                -      -      -        -         -      -      -      -    ONLINE
    ata-ST12000VN0008-2YS101_ZV701XQV-part1                -      -      -        -         -      -      -      -    ONLINE
  mirror-4                                             5.45T  23.5G  5.43T        -         -     0%  0.42%      -    ONLINE
    ata-WDC_WD60EFRX-68L0BN1_WD-WX31D87HDU09-part1         -      -      -        -         -      -      -      -    ONLINE
    ata-WDC_WD60EZRZ-00GZ5B1_WD-WX11D374490J-part1         -      -      -        -         -      -      -      -    ONLINE
  mirror-5                                             3.62T  17.2G  3.61T        -         -     0%  0.46%      -    ONLINE
    ata-ST4000DM004-2CV104_ZFN0GTAK-part1                  -      -      -        -         -      -      -      -    ONLINE
    ata-WDC_WD40EZRX-00SPEB0_WD-WCC4E0354579-part1         -      -      -        -         -      -      -      -    ONLINE
cache                                                      -      -      -        -         -      -      -      -  -
  nvme-Samsung_SSD_970_EVO_Plus_500GB_S4P2NF0M419555D   466G  3.58G   462G        -         -     0%  0.76%      -    ONLINE

Once the pool is created, we wanted to set some pool properties so that in the future when we replace these drives with bigger drives, the pool will automatically expand.

zpool set autoexpand=on vault

With the pool created, we can then create our dataset or filesystem and its associated mount point. We also want to ensure that the filesystem also supports posixacl.

zfs create vault/airvideo
zfs set mountpoint=/mnt/av vault/airvideo
zfs set acltype=posixacl vault
zfs set acltype=posixacl vault/airvideo

We mount the new ZFS filesystem on /mnt/av because the /mnt/airvideo is soft-linked to the temporary /mnt/av2 volume that is still in operation. We first have to re-copy all our content from the temporary volume to the new ZFS filesystem.

sudo rsync --delete -aAXv /mnt/av2/ /mnt/av > ~/nohup.avs.rsync.out 2>&1 &

This took around 4 days to complete. We can all breathe easy again because all the data now have redundancy again! We can now bring the new ZFS filesystem live.

sudo systemctl stop apache2.service smbd nmbd plexmediaserver.service
sudo rm /mnt/airvideo
sudo zfs set mountpoint=/mnt/airvideo vault/airvideo
sudo systemctl start apache2.service smbd nmbd plexmediaserver.service

zfs list

NAME             USED  AVAIL     REFER  MOUNTPOINT
vault           31.0T  14.2T       96K  /vault
vault/airvideo  31.0T  14.2T     31.0T  /mnt/airvideo

The above did not take long and the migration is completed!

df -h /mnt/airvideo

Filesystem      Size  Used Avail Use% Mounted on
vault/airvideo   46T   32T   15T  69% /mnt/airvideo

Getting the capacity of our new ZFS filesystem shows that we now have 46TB to work with! This should last for at least a couple of years I hope.

I also did a quick reboot of the system to ensure it can come back up with the ZFS filesystem in tack and without issues. It has now been running for 2 days. I have not collected any performance statistics, but the services all feel faster.

Media Server Storage Hardware Reconfiguration

Our media server has reached 89% utilization and needs storage expansion. The storage makeup on the server uses Logical Volume Manager (LVM) and software RAID called mdadm. I can expand the storage by swapping out the hard drives with the least capacity with new hard drives with a larger capacity like I have previously done.

I thought I try something different this time around. I would like to switch from LVM to ZFS, an LVM alternative that is very popular with modern mass storage systems, especially with TrueNAS.

All filled with 8 drives

Before I can attempt the conversion, I will first need to backup all of the content from the media server. The second issue is that I needed more physical expansion space on the server to house more hard drives. The existing housings are all filled except for a single slot, which is going to be insufficient.

A related issue is that I no longer have any free SATA slots available for the new hard drives, so I purchased GLOTRENDS SA3116J PCIe SATA Adapter Card with 16 SATA Ports. Once this is installed, I have more than enough SATA ports for additional storage.

PCIe SATA Card Installed

One downside of the SATA card is that it is limited to PCIe 3.0 x1 speed. This means data transfer is limited to a theoretical maximum of 1GB/s. Given that the physical hard drives top out at 200MB/s, I don’t think we need to be too concerned about this bottleneck. We will see in terms of practical usage in the future.

I am so lucky to have extra SATA power cables and extension cables laying around and my 850W existing power supply has ample power for the additional hard drives.

How do we store the additional hard drives with a full cabinet? I went to Amazon again and purchased a hard drive cage, Jaquiain 3.5 Inch HDD Hard Drive Cage 8X3.5 Inch HDD Cage. I did not have to buy any new hard drives yet, because I had plenty of old hard drives laying around. After I put together the cage with 8 really old and used hard drives, it looks something like this:

With this new additional storage, I am now able to backup the media content from my media server. However, before I do that there is one last thing that I need to do, and that is to experiment with an optimal ZFS pool configuration that will work with my content and usage. I will perform this experimentation with the additional storage before reconfiguring the old storage with ZFS. Please stay tuned for my findings.

After booting the system with 16 hard drives, I measured the power usage and it was hovering around 180W. This is not too bad, less than 2 traditional incandescent light bulbs.


Addendum:

During my setup, I had to spend hours deciphering an issue. My system did not recognize my old hard drives. After many trials, I finally narrowed down that the GLOTRENDS card is not compatible with an old 2TB Western Digital Enterprise Drive. This is the first time that I came across SATA incompatibilities.

There is another possibility that these drives were damaged by the usage of an incorrect modular power cable. I found that these drives also do not work with my USB3.0 HDD external dock as well. This gives additional credence that the physical drive has been damaged.

The troubled drive with the SATA card

All my other drives worked fine with the card.

Another discovery is that not all modular power cables will work with my ASUS ROG STRIX 850W power supply. Initially, I thought I would use an 8-pin PCIe to 6-pin adapter along with a 6-pin to SATA power cable designed for Corsair power supplies.

PCIe Power Adapter from Amazon
OwlTree PCI-e 6 Pin Male to 4 SATA 1 to 4 SATA Female Power Supply Splitter Supply Cable for Corsair Modular RM650X RM750X RM850X RM1000X

Using the above cables will cause the power supply not to start. I had to hunt for the original cables that came with the STRIX power supply.

Learned a lot from rejigging this media server. My reward is to see my server boot up with 16 hard drives and 2 NVMe SSD drives recognized. I have never built a system with so many drives and storage before.

EXT4-fs Errors on NVME SSD

In my previous post, I replaced my NVME boot disk on our media server thinking that the disk was defective because the file system (EXT4-fs) was reporting numerous htree_dirblock_to_tree:1080 errors.

The errors continue to persist with the new disk, so I can eliminate the possibility of hardware as the cause of the issue.

I noticed that the htree_dirblock_to_tree:1080 errors were caused by the tar command and the time in which these errors occur coincided when the media server is being backed up. Apparently, the backup process is causing these errors with the tar command.

This backup process has remained unchanged for quite some time and has worked really well for us. I guess for some reason there is a bug in the kernel or in the tar command that is not quite compatible with NVME devices.

I had to resort to finding an alternative backup methodology. I ended up using the rsync method instead.

sudo rsync --delete \
  --exclude 'dev' \
  --exclude 'proc' \
  --exclude 'sys' \
  --exclude 'tmp' \
  --exclude 'run' \
  --exclude 'mnt' \
  --exclude 'media' \
  --exclude 'cdrom' \
  --exclude 'lost+found' \
  --exclude 'home/kang/log' \
  -aAXv / /mnt/backup

It looks like this method is faster and can perform incremental backup. However, instead of backing up to an archive file, which I later need to extract and prepare during the restoration process, I have to back it up to a dedicated backup device. Since the old NVME disk is perfectly fine, I reused it as my backup device. I have partitioned this backup device in the same layout as the current boot disk.

Device          Start        End    Sectors   Size Type
/dev/sdi1        2048    2203647    2201600     1G Microsoft basic data
/dev/sdi2     2203648 1921875967 1919672320 915.4G Linux filesystem
/dev/sdi3  1921875968 1953523711   31647744  15.1G Linux swap

The only exception is that the first partition is not marked as boot and esp, so during the restoration process I will have to mark that partition accordingly with the parted command by using the following commands:

set 1 boot on
set 1 esp on

The idea is that at 3am every night/morning, I will backup the root filesystem to the second partition of the backup drive. If anything happens with the current boot disk, the backup drive can act as an immediately available replacement, after a grub-install preparation as mentioned in the previous article.

Let us see how this new backup process works and hopefully, we can bid a final farewell to the htree_dirblock_to_tree:1080 errors!

Update: 2023-12-22

It looks like even with the rsync command, the htree_dirblock_to_tree:1080 errors still came back during the backup process. I decided to upgrade the kernel from vmlinuz-5.15.0-91-generic to vmlinuz-6.2.0-39-generic. Last night (2023-12-23 early morning) was the first backup after the kernel upgrade, and no errors were recorded. I hope this behavior persists and it is not a one-off.

Replacing NVME Boot Disk

A few months ago, the boot disk of our media server begin to incur some errors, such as the ones below:

Dec 17 03:01:35 avs kernel: [32515.068669] EXT4-fs error (device nvme1n1p2): htree_dirblock_to_tree:1080: inode #10354778: comm tar: Directory block failed checksum
Dec 17 03:02:35 avs kernel: [32575.183005] EXT4-fs error (device nvme1n1p2): htree_dirblock_to_tree:1080: inode #13500463: comm tar: Directory block failed checksum
Dec 17 03:02:35 avs kernel: [32575.183438] EXT4-fs error (device nvme1n1p2): htree_dirblock_to_tree:1080: inode #13500427: comm tar: Directory block failed checksum

The boot disk is a NVME device and I thought it may be due to over heating, so I purchased a heat sink and installed it. Unfortunately the errors persisted after the heat sink.

I decided to replace the boot disk with the exact same model which was the Samsung 980Pro 1TB. This should have been a pretty easy maintenance task. We clone the drive, and swap in the new drive. However, Murphy is sure to strike!

My usual goto cloning utility is Clonezilla, unfortunately this utility did not like cloning NVME drives. The utility resulted in a kernel panic after trying multiple versions. I am not sure what is the problem here. It could be Clonezilla or the USB 3.0 NVME enclosure that I was using for the new disk.

I resigned to using the dd command:

dd if=/dev/source of=/dev/target status=progress

Unfortunately this would have taken way too long something like 20+ hours, so I gave up with this approach.

I decided to do a good old restore of the nightly backup. I started by cloning the partition table:

sfdisk -d /dev/olddisk | sfdisk /dev/newdisk

I then proceeded with the restore of the nightly backup. Murphy strikes twice! The nightly backup was corrupted! I guess it is not surprising when the root directory’s integrity is in question. The whole reason why we are doing this exercise.

Without the nightly backup, I had to resort to a live backup. I booted system again, and performed:

sudo su -
mount /dev/new_disk_root_partition /mnt/newboot
cd /
tar -cvpf - --exclude=/tmp --exclude=/home/kang/log --exclude=/span --exclude="/var/lib/plexmediaserver/Library/Application Support/Plex Media Server/Cache" --one-file-system / | tar xvpzf - -C /mnt/newboot --numeric-owner

The above took about an hour. I then copy the /span directory manually, because this directory tends to change while the server is up and running.

With all the contents copied, I forgot how to install grub and had to re-teach myself again. I had to use a live copy Ubuntu USB and use that to boot up the machine, and then mount both the root and efi partitions respectively.

nvme1n1                              259:0    0 931.5G  0 disk
├─nvme1n1p1                          259:1    0     1G  0 part  /boot/efi
├─nvme1n1p2                          259:2    0 915.4G  0 part  /
└─nvme1n1p3                          259:3    0  15.1G  0 part  [SWAP]

And install GRUB.

sudo su -
mkdir /efi
mount /dev/nvme1n1p1 /efi
mount /dev/nvme1n1p2 /mnt
grub-install --efi-directory /efi --root-directory /mnt

I also have fix the /etc/fstab to ensure the root partition and /boot/efi partition are properly referenced by their corresponding, correct UUID. The blkid command came in handy to find the UUID. For the swap partition, I had to use the mkswap command before I get the UUID.

After I rebooted, I reinstalled GRUB one more time with the following as super user:

grub-install /dev/nvme1n1

I also updated the initramfs using:

update-initramfs -c -k all

For something that should have taken less than an hour, it took the majority of the day. The server is now running with the new NVME replacement disk. Hopefully this resolves the file system corruptions. We have to wait and see!

Update: The Day After

The same errors occurred again! I noticed that these corruptions occur when we do a system backup. How ironic! I later confirmed that performing the tar command on the root directory during the backup process can cause such an error. I now have to see why this is. I will disable the system backup for the next few days to see if the errors come back or not.

Managing Audio Books with Plex

Library Setup

I have a membership with Audible and I sometimes also get other audio book sources. Recently I experimented with combining all of my audio books into a centralized place. Since I already have a Plex server running, I thought it would be a good place to do this.

I did a little research and came across a couple of very helpful articles:

  • A Reddit article;
  • and some really detail information on GitHub;

The main points are:

  • I have a single folder to store all of my audio books. Inside the folder, each audio book is stored as an “m4b” file.
  • Ensure that audio books have a poster image and that its artist and album_artist tags are set to the author. Where appropriate, the audio book should also contain chapter metadata.
  • Download and install the Audnexus agent;
  • Create a music library on Plex by adding the audio book folder, and set the agent to Audnexus
Note the Agent setting
  • Ensure that the advanced option of “Store track progress” is checked.
Ensure that Store Track Progress is checked!

Each book in the library will be represented as an album, and the author will be mapped to album artist. Once the library is created, you can download and play the audio books from the desktop using the Plex app. However, the more common use case is to listen to the audio books while on the go.

Using Prologue to Play Audio Books

We first have to download the Prologue App. I did not get any of the In-App premium functionality, and just stayed with the free version.

Point the app to my Plex server’s URL, and all the audio books from the library should now be accessible and playable on the iPhone or iPad with chapter, bookmark, and last-left-position support.

This is a really neat solution, and I am impressed how Plex and Prologue together formed a dynamic duo in this manner.

Media Server Upgrade 2022 (Part 2)

Part 1

In the first part of this post, I talked about making sure all the new hardware that I recently purchased works. Yesterday, upgrading from Ubuntu 20.04 LTS to 22.04 LTS was super simple. Unfortunately, that was the end of the easy part.

I thought I could just image by old boot drive and make a carbon copy of it on my new boot drive. My old boot drive is a simple SATA 512GB SSD, and my new boot drive is an NVMe M.2 1TB SSD plugged directly to the motherboard. The copying was pretty simple, but because the drives differ in size, I had to relayout the partition table with the new drive once the copy is completed. I did this with the parted command.

Unfortunately the new boot drive did not want to boot. At this point I had to do some research. The most helpful articles were:

Both of the above articles were an excellent refresher on how GRUB works. I have used GRUB since the beginning, but one gets super rusty when these types of tasks are only performed once every three or six years!

Instead of detailing what went wrong, I will just explain what I should have done. This way if I need it again in the future, it is here for my reference.

Step 1: Perform a backup of the old boot drive from a Live USB in shell mode. This is done on my server on a nightly basis. This method is clearly described on the Ubuntu Community Help Wiki.

Following this method I will end up with a compressed tar archive for my entire root directory, skipping some runtime and other unwanted directories.

Step 2: After installing a fresh install of the new Ubuntu LTS Server operating system on the new server and boot drive, I proceeded to backup the new boot with the same technique used in Step 1. I stored the backup of the new install on another external SSD drive that I have lying around. Also it is important that new boot drive partition layout of the new install contains a swap partition.

Step 3: I then restore the most recent backup (done in Step 1) of the old boot drive to the new boot drive. I then replaced the /boot/grub directory with the new contents from the new install which was backed up in Step 2. The new GRUB is already installed when we performed a brand new installation on the drive. We just want to make sure the boot partition matches the /boot/grub contents.

Step 4: We also need to fix up the /etc/fstab file because it contains references to drive devices from the old hardware. Paid special attention the main data partition and the swap partition. It should look something like this:

# /etc/fstab: static file system information.
#
# Use 'blkid' to print the universally unique identifier for a
# device; this may be used with UUID= as a more robust way to name devices
# that works even if disks are added and removed. See fstab(5).
#
# <file system> <mount point>   <type>  <options>       <dump>  <pass>
# / was on /dev/nvme1n1p2 during curtin installation
UUID=fc939be4-5292-4252-8120-7ef59b177e5b / ext4 defaults 0 1

# /boot/efi was on /dev/nvme0n1p1 during curtin installation
UUID=5187-A8C6 /boot/efi vfat defaults 0 1

# Swap partition
UUID=512d611e-6944-4a57-9748-ea68e9ec3fad	none	swap	sw	0	0

# /dev/mapper/airvideovg2-airvideo /mnt/airvideo ext4 rw,noatime 0 0
UUID=9e78425c-c1f3-4285-9fa1-96cac9114c55 /mnt/airvideo ext4 rw,noatime 0 0

Noticed that I also added the LVM logical volume for /mnt/airvideo, which is my RAID-1 array. The UUID can be obtained by the blkid command. Below is a sample output:

% blkid
/dev/sdf1: UUID="60024298-9915-3ad8-ae6c-ed7adc98ee62" UUID_SUB="fe08d23c-8e11-e02b-63f9-1bb806046db7" LABEL="avs:4" TYPE="linux_raid_member" PARTLABEL="primary" PARTUUID="552bdff7-182f-40f0-a378-844fdb549f07"
/dev/nvme0n1p1: UUID="r2rLMD-BEnc-wcza-yvro-chkB-1vB6-6Jtzgz" TYPE="LVM2_member" PARTLABEL="primary" PARTUUID="6c85af69-19a0-4720-9588-808bc0d818f7"
/dev/sdd1: UUID="34c6a19f-98ea-0188-bb3f-a5f5c3be238d" UUID_SUB="4174d106-cae4-d934-3ed4-5057531acb3c" LABEL="avs:3" TYPE="linux_raid_member" PARTLABEL="primary" PARTUUID="2fc4e9ad-be4b-48aa-8115-f32472e61005"
/dev/sdb1: UUID="ac438ac6-344a-656b-387f-017036b0fafa" UUID_SUB="0924dc67-cd3f-dec5-1814-ab46ebdf2fbe" LABEL="avs:1" TYPE="linux_raid_member" PARTUUID="29e7cfce-9e7b-4067-a0ca-453b39e0bd3d"
/dev/md4: UUID="gjbtdL-homY-wyRG-rUBw-lFgm-t0vZ-Gi8gSz" TYPE="LVM2_member"
/dev/md2: UUID="0Nky5e-52t6-b1uZ-GAIl-4Ior-XWTz-wFpHh1" TYPE="LVM2_member"
/dev/sdi1: UUID="5b483ac2-5b7f-4951-84b2-08adc602f705" BLOCK_SIZE="4096" TYPE="ext4" PARTLABEL="data" PARTUUID="e0515517-9fbb-4d8a-88ad-674622f20e00"
/dev/sdg1: UUID="3d1afb64-8785-74e6-f9be-b68600eebdd5" UUID_SUB="c146cd05-8ee8-5804-b921-6d87cdd4a092" LABEL="avs:2" TYPE="linux_raid_member" PARTLABEL="lvm" PARTUUID="2f25ec17-83c4-4c0b-8653-600283d58109"
/dev/sde1: UUID="34c6a19f-98ea-0188-bb3f-a5f5c3be238d" UUID_SUB="8aabfe5b-af16-6e07-17c2-3f3ceb1514e3" LABEL="avs:3" TYPE="linux_raid_member" PARTLABEL="primary" PARTUUID="2fc4e9ad-be4b-48aa-8115-f32472e61005"
/dev/sdc1: UUID="ac438ac6-344a-656b-387f-017036b0fafa" UUID_SUB="c188f680-01a8-d5b2-f8bc-9f1cc1fc3598" LABEL="avs:1" TYPE="linux_raid_member" PARTUUID="29e7cfce-9e7b-4067-a0ca-453b39e0bd3d"
/dev/nvme1n1p2: UUID="fc939be4-5292-4252-8120-7ef59b177e5b" BLOCK_SIZE="4096" TYPE="ext4" PARTUUID="912e805d-fe68-48f8-b845-9bba0e3e8c78"
/dev/nvme1n1p3: UUID="512d611e-6944-4a57-9748-ea68e9ec3fad" TYPE="swap" PARTLABEL="swap" PARTUUID="04ac46ff-74f3-499a-814d-32082f6596d2"
/dev/nvme1n1p1: UUID="5187-A8C6" BLOCK_SIZE="512" TYPE="vfat" PARTUUID="fe91a6b2-9cd3-46af-813a-b053a181af52"
/dev/sda1: UUID="3d1afb64-8785-74e6-f9be-b68600eebdd5" UUID_SUB="87fe80a1-4a79-67f3-273e-949e577dd5ee" LABEL="avs:2" TYPE="linux_raid_member" PARTUUID="c8dce45e-5134-4957-aee9-769fa9d11d1f"
/dev/md3: UUID="XEJI0m-PEmZ-VFiI-o4h0-bnQc-Y3Be-3QHB9n" TYPE="LVM2_member"
/dev/md1: UUID="usz0sA-yO01-tlPL-12j2-2C5r-Ukhc-9RLCaX" TYPE="LVM2_member"
/dev/mapper/airvideovg2-airvideo: UUID="9e78425c-c1f3-4285-9fa1-96cac9114c55" BLOCK_SIZE="4096" TYPE="ext4"
/dev/sdh1: UUID="60024298-9915-3ad8-ae6c-ed7adc98ee62" UUID_SUB="a1291844-6587-78b0-fcd1-65bc367068e5" LABEL="avs:4" TYPE="linux_raid_member" PARTLABEL="primary" PARTUUID="ed0274b9-21dc-49bf-bdda-566b2727ddc2"

Step 4B (Potentially): If the system boots in the “grub>” prompt, then we will have persuade grub to manually boot by providing the following at the prompt:

grub> set root=(hd9,gpt2)
grub> linux /boot/vmlinuz root=/dev/nvme1n1p2
grub> initrd /boot/initrd.img
grub> boot

To find the root value on the first line, you have use the ls command which is explained in this article. The root parameter on the linux line references the partition which the root directory is mounted. In my case, it was /dev/nvme1n1p2.

After I rebooted, I reinstalled GRUB with the following as super user:

grub-install /dev/nvme1n1

It may also be required to update our initramfs using:

update-initramfs -c -k all

Step 5: At this point the system should reboot and all of the old server’s content should now be on the old hardware. Unfortunately we will need to fix the network interface.

First obtain the MAC address of the network interface using:

% sudo lshw -C network | grep serial   
    serial: 04:42:1a:05:d3:c4

And then we will have to edit the /etc/netplan/00-installer-config.yaml file.

% cat /etc/netplan/00-installer-config.yaml 
# This is the network config written by 'subiquity'
network:
  ethernets:
    enp6s0:
      dhcp4: true
      match:
        macaddress: 04:42:1a:05:d3:c4
      set-name: enp6s0
  version: 2

Ensuring the MAC address matches from lshw and that the name is the same as the old system. The name in this example is enp6s0. We then need to execute the following commands to generate the interface.

netplan generate
netplan apply

We need to ensure the name matches because many services on the server have configurations that references the interface name, such as:

  • Configurations in /var/network/interfaces
  • Samba (SMB) (/etc/samba/smb.conf)
  • Pihole (/etc/pihole/setupVars.conf)
  • Homebridge (/var/lib/homebridge/config.json)

Step 6: Fix the router provisioning DHCP IP addresses so that the new server has the same fixed IP address as the old server. This is important because there may be firewall rules referencing this IP address directly. The hostname should have been automatically restored when we restored the partition in Step 3.

Step 7: Our final step is to test the various services and ensure they are working properly. These include:

  • Mail
  • Our web site lufamily.ca
  • Homebridge
  • Plex
  • Pihole (DNS server)
  • SMB (File sharing)

Finally the new system is completed!

New system all up and running!

Media Server Upgrade 2022

On May 15th, 2019 (more than three years ago), I performed a performance boost to my media server by upgrading its CPU, Motherboard, and Memory. You can read that experience in this post.

Today, I am going to be doing the same. It looks like we are on a cadence of every 3 years or so to do a spec bump. This time around we are also changing the same items, but will include the power supply as well in the swap. I also decided to swap the boot drive hardware from an old SSD drive to an NVME drive. All of this resulted in the following hardware acquisitions, all from Amazon, which I find them to have lower pricing (when factoring free shipping through Prime), than Newegg even during Black Friday and Cyber Monday offers.

  • AMD Ryzen 7 5700G 8-Core, 16-Thread Unlocked Desktop Processor with Radeon Graphics
  • ASUS TUF GAMING B550-PLUS AMD AM4 (3rd Gen Ryzen™)
  • G.SKILL Ripjaws V Series DDR4 3600MHz 32GB(16GBx2) Memory Kit
  • ASUS ROG Strix 850W Gold PSU
  • Samsung 980 PRO SSD 1TB – M.2 NVMe

The above totalled $1045.60 CAD.

The plan is to spend the time today to roughly test out all the new hardware.

Test Setup

I quickly did a skeleton setup to make sure Ubuntu 22.04.01 Server Edition works with all hardware involved, especially the networking.

Memory Test

Once I know Ubuntu server is working good, I am now testing the server’s new 32GB DDR4 memory. This is running as I write this post and will let it run overnight.

The plan for tomorrow is to upgrade the current media server from Ubuntu 20.04.5 LTS to Ubuntu 22.04.1 LTS. Once this is done, I can then backup everything, and move the new hardware into the old casing and hope everything works.

Part 2