ZFS on NVMe massive performance drop after update from Proxmox 6.2 to 6.3

E

efinley

Member
Jul 16, 2018
25
1
23
54
Hello Proxmox community,

TL;DR
Huge performance hit after upgrading to 6.3-3, probably having to do with IO delay.
Replication from system to system will stall completely for up to a minute at a time.

Screenshot 2021-04-22 135205.png

This graph shows the sharp rise in IO delay. The rise corresponds precisely with the update. The load on this server did not change.

Screenshot 2021-04-22 140800.png

before the update the IO delay was generally between 0 and 1%.

Code: 
root@dbgp-vsys01:~# zpool status
  pool: rpool
 state: ONLINE
  scan: scrub repaired 0B in 0 days 00:07:07 with 0 errors on Sun Apr 11 00:31:08 2021
config:

        NAME        STATE     READ WRITE CKSUM
        rpool       ONLINE       0     0     0
          mirror-0  ONLINE       0     0     0
            sda2    ONLINE       0     0     0
            sdb2    ONLINE       0     0     0

errors: No known data errors

  pool: tank
 state: ONLINE
  scan: resilvered 196G in 0 days 00:10:27 with 0 errors on Sat Apr 17 00:32:39 2021
config:

        NAME                                             STATE     READ WRITE CKSUM
        tank                                             ONLINE       0     0     0
          mirror-0                                       ONLINE       0     0     0
            nvme-INTEL_SSDPE2KX040T7_PHLF810502XJ4P0IGN  ONLINE       0     0     0
            nvme-INTEL_SSDPE2KX040T7_PHLF810502W44P0IGN  ONLINE       0     0     0
          mirror-1                                       ONLINE       0     0     0
            nvme-INTEL_SSDPE2KX040T7_PHLF810502XE4P0IGN  ONLINE       0     0     0
            nvme-INTEL_SSDPE2KX040T7_PHLF810502V64P0IGN  ONLINE       0     0     0
          mirror-2                                       ONLINE       0     0     0
            nvme-INTEL_SSDPE2KX040T7_PHLF813200244P0IGN  ONLINE       0     0     0
            nvme-INTEL_SSDPE2KX040T7_PHLF813200AY4P0IGN  ONLINE       0     0     0
          mirror-3                                       ONLINE       0     0     0
            nvme-INTEL_SSDPE2KX040T7_PHLF810502XN4P0IGN  ONLINE       0     0     0
            nvme-INTEL_SSDPE2KX040T7_PHLF810503114P0IGN  ONLINE       0     0     0
          mirror-4                                       ONLINE       0     0     0
            nvme-INTEL_SSDPE2KX040T7_PHLF810502VL4P0IGN  ONLINE       0     0     0
            nvme-INTEL_SSDPE2KX040T7_PHLF813102KU4P0IGN  ONLINE       0     0     0
          mirror-5                                       ONLINE       0     0     0
            nvme-INTEL_SSDPE2KX040T7_PHLF810502W94P0IGN  ONLINE       0     0     0
            nvme-INTEL_SSDPE2KX040T7_PHLF810503F84P0IGN  ONLINE       0     0     0
          mirror-6                                       ONLINE       0     0     0
            nvme-INTEL_SSDPE2KX040T7_PHLF8132002L4P0IGN  ONLINE       0     0     0
            nvme-INTEL_SSDPE2KX040T7_PHLF810502VD4P0IGN  ONLINE       0     0     0
          mirror-7                                       ONLINE       0     0     0
            nvme-INTEL_SSDPE2KX040T7_PHLF813102JC4P0IGN  ONLINE       0     0     0
            nvme-INTEL_SSDPE2KX040T7_PHLF8105047S4P0IGN  ONLINE       0     0     0
          mirror-8                                       ONLINE       0     0     0
            nvme-INTEL_SSDPE2KX040T7_PHLF810503F14P0IGN  ONLINE       0     0     0
            nvme-INTEL_SSDPE2KX040T7_PHLF810502V54P0IGN  ONLINE       0     0     0
          mirror-9                                       ONLINE       0     0     0
            nvme-INTEL_SSDPE2KX040T7_PHLF8105031A4P0IGN  ONLINE       0     0     0
            nvme-INTEL_SSDPE2KX040T7_PHLF810504W44P0IGN  ONLINE       0     0     0
          mirror-10                                      ONLINE       0     0     0
            nvme-INTEL_SSDPE2KX040T7_PHLF810503FC4P0IGN  ONLINE       0     0     0
            nvme-INTEL_SSDPE2KX040T7_PHLF727500J34P0IGN  ONLINE       0     0     0
        logs
          nvme-INTEL_SSDPE21K375GA_PHKE751000AW375AGN    ONLINE       0     0     0
          nvme-INTEL_SSDPE21K375GA_PHKE75100081375AGN    ONLINE       0     0     0

errors: No known data errors

Code: 
root@dbgp-vsys01:~# zfs list
NAME                          USED  AVAIL     REFER  MOUNTPOINT
rpool                        91.2G   124G      104K  /rpool
rpool/ROOT                   82.5G   124G       96K  /rpool/ROOT
rpool/ROOT/pve-1             82.5G   124G     82.5G  /
rpool/data                     96K   124G       96K  /rpool/data
rpool/swap                   8.50G   131G     1.24G  -
tank                         2.01T  36.6T      104K  /tank
tank/config                  14.0M  36.6T     7.34M  /tank/config
tank/data                    1.99T  36.6T      176K  /tank/data
tank/data/migrate              96K  36.6T       96K  /tank/data/migrate
tank/data/subvol-100-disk-1  1.32G  6.74G     1.26G  /tank/data/subvol-100-disk-1
tank/data/subvol-100-disk-2   515G  36.6T      461G  /tank/data/subvol-100-disk-2
tank/data/subvol-100-disk-3  5.24G  7.13G      894M  /tank/data/subvol-100-disk-3
tank/data/subvol-104-disk-1  28.9G  36.6T     22.3G  /tank/data/subvol-104-disk-1
tank/data/subvol-132-disk-0   930M  7.11G      914M  /tank/data/subvol-132-disk-0
tank/data/subvol-172-disk-0  35.3G  70.7G     29.3G  /tank/data/subvol-172-disk-0
tank/data/subvol-174-disk-0  53.9G  47.2G     52.8G  /tank/data/subvol-174-disk-0
tank/data/subvol-176-disk-0  8.10G  42.2G     7.78G  /tank/data/subvol-176-disk-0
tank/data/subvol-196-disk-0  1.66G  6.51G     1.49G  /tank/data/subvol-196-disk-0
tank/data/subvol-197-disk-0  2.18G  6.02G     1.98G  /tank/data/subvol-197-disk-0
tank/data/vm-105-disk-0      4.68G  36.6T     4.68G  -
tank/data/vm-107-disk-0      54.6G  36.6T     53.0G  -
tank/data/vm-113-disk-0      10.8G  36.6T     10.5G  -
tank/data/vm-118-disk-0      17.0G  36.6T     17.0G  -
tank/data/vm-127-disk-0      52.4G  36.6T     41.9G  -
tank/data/vm-136-disk-0      12.2G  36.6T     12.2G  -
tank/data/vm-139-disk-0      26.6G  36.6T     25.2G  -
tank/data/vm-146-disk-0      2.57G  36.6T     2.42G  -
tank/data/vm-150-disk-0      18.2G  36.6T     17.1G  -
tank/data/vm-150-disk-1      2.30G  36.6T     2.30G  -
tank/data/vm-159-disk-0      29.6G  36.6T     28.6G  -
tank/data/vm-164-disk-0      5.01G  36.6T     4.20G  -
tank/data/vm-168-disk-0      29.2G  36.6T     28.3G  -
tank/data/vm-169-disk-0      16.8G  36.6T     16.8G  -
tank/data/vm-170-disk-0      30.7G  36.6T     30.7G  -
tank/data/vm-171-disk-0      35.2G  36.6T     35.2G  -
tank/data/vm-175-disk-0      24.8G  36.6T     17.8G  -
tank/data/vm-181-disk-0      16.3G  36.6T     16.3G  -
tank/data/vm-215-disk-0      26.0G  36.6T     25.8G  -
tank/data/vm-215-disk-1      6.91M  36.6T     6.91M  -
tank/data/vm-230-disk-0      24.1G  36.6T     19.3G  -
tank/data/vm-280-disk-0       111G  36.6T     92.7G  -
tank/data/vm-280-disk-1       209G  36.6T      172G  -
tank/data/vm-282-disk-0       185G  36.6T      150G  -
tank/data/vm-714-disk-0      42.8G  36.6T     41.7G  -
tank/data/vm-715-disk-0      44.2G  36.6T     40.4G  -
tank/data/vm-715-disk-1      32.0G  36.6T     32.0G  -
tank/data/vm-905-disk-0       241G  36.6T      202G  -
tank/data/vm-905-disk-1      83.2G  36.6T     31.6G  -
tank/data/vm-999-disk-1        56K  36.6T       56K  -
tank/encrypted_data           192K  36.6T      192K  /tank/encrypted_data

Code: 
root@dbgp-vsys01:~# pveversion -v
proxmox-ve: 6.3-1 (running kernel: 5.4.78-2-pve)
pve-manager: 6.3-3 (running version: 6.3-3/eee5f901)
pve-kernel-5.4: 6.3-3
pve-kernel-helper: 6.3-3
pve-kernel-5.3: 6.1-6
pve-kernel-5.4.78-2-pve: 5.4.78-2
pve-kernel-5.4.34-1-pve: 5.4.34-2
pve-kernel-4.15: 5.4-8
pve-kernel-5.3.18-3-pve: 5.3.18-3
pve-kernel-5.3.13-3-pve: 5.3.13-3
pve-kernel-4.15.18-20-pve: 4.15.18-46
pve-kernel-4.15.17-1-pve: 4.15.17-9
ceph-fuse: 12.2.11+dfsg1-2.1+b1
corosync: 3.1.0-pve1
criu: 3.11-3
glusterfs-client: 5.5-3
ifupdown: residual config
ifupdown2: 3.0.0-1+pve3
ksm-control-daemon: 1.3-1
libjs-extjs: 6.0.1-10
libknet1: 1.20-pve1
libproxmox-acme-perl: 1.0.7
libproxmox-backup-qemu0: 1.0.2-1
libpve-access-control: 6.1-3
libpve-apiclient-perl: 3.1-3
libpve-common-perl: 6.3-5
libpve-guest-common-perl: 3.1-5
libpve-http-server-perl: 3.1-1
libpve-storage-perl: 6.3-6
libqb0: 1.0.5-1
libspice-server1: 0.14.2-4~pve6+1
lvm2: 2.03.02-pve4
lxc-pve: 4.0.6-2
lxcfs: 4.0.6-pve1
novnc-pve: 1.1.0-1
proxmox-backup-client: 1.0.8-1
proxmox-mini-journalreader: 1.1-1
proxmox-widget-toolkit: 2.4-5
pve-cluster: 6.2-1
pve-container: 3.3-3
pve-docs: 6.3-1
pve-edk2-firmware: 2.20200531-1
pve-firewall: 4.1-3
pve-firmware: 3.1-3
pve-ha-manager: 3.1-1
pve-i18n: 2.2-2
pve-qemu-kvm: 5.1.0-8
pve-xtermjs: 4.7.0-3
qemu-server: 6.3-5
smartmontools: 7.1-pve2
spiceterm: 3.1-1
vncterm: 1.6-2
zfsutils-linux: 0.8.5-pve1

Code: 
root@dbgp-vsys01:~# zpool iostat tank 2
              capacity     operations     bandwidth
pool        alloc   free   read  write   read  write
----------  -----  -----  -----  -----  -----  -----
tank        2.01T  37.9T     88  6.87K   944K  66.9M
tank        2.01T  37.9T      0  52.0K      0   473M
tank        2.01T  37.9T      0  2.82K  37.9K  42.1M
tank        2.01T  37.9T      0  12.4K  7.97K   108M
tank        2.01T  37.9T      0  15.3K      0   143M
tank        2.01T  37.9T      0  10.2K  7.97K  99.2M
tank        2.01T  37.9T      0  12.6K  7.97K   108M
tank        2.01T  37.9T      0  9.60K      0   107M
tank        2.01T  37.9T      0  11.7K  5.98K   111M
tank        2.01T  37.9T      2  43.2K  13.9K   379M
tank        2.01T  37.9T      0  6.58K  5.98K  73.5M
tank        2.01T  37.9T      2    822  14.0K  16.9M
tank        2.01T  37.9T      2  57.2K  13.9K   519M
tank        2.01T  37.9T      0  7.28K  5.98K  72.0M
tank        2.01T  37.9T      5   110K  45.8K   976M
tank        2.01T  37.9T      6  72.2K  33.9K   646M
tank        2.01T  37.9T      3  21.0K  17.9K   200M
tank        2.01T  37.9T      0  13.9K      0   124M
tank        2.01T  37.9T      0  9.24K      0  83.4M
tank        2.01T  37.9T      2  8.92K  12.0K  82.0M
tank        2.01T  37.9T      0  7.79K      0  74.2M
tank        2.01T  37.9T      1  6.53K  12.0K  67.2M
tank        2.01T  37.9T      0    389      0  7.71M
tank        2.01T  37.9T      0  14.0K      0   138M
tank        2.01T  37.9T      0  1.16K  3.98K  16.4M
tank        2.01T  37.9T      0  14.0K  5.98K   121M
tank        2.01T  37.9T      5  23.5K  21.9K   209M
tank        2.01T  37.9T      0  4.53K      0  36.0M
tank        2.01T  37.9T      0  2.55K  3.98K  24.9M
tank        2.01T  37.9T      1  2.20K  7.97K  36.6M
tank        2.01T  37.9T      2  3.42K  13.9K  35.0M
tank        2.01T  37.9T      0  7.16K      0  79.7M
tank        2.01T  37.9T      0      0  5.98K      0
tank        2.01T  37.9T      2      0  9.96K      0
tank        2.01T  37.9T      0  9.20K      0  94.5M
tank        2.01T  37.9T      0  35.0K      0   309M
tank        2.01T  37.9T      0  12.8K  1.99K   115M
tank        2.01T  37.9T      0  20.1K      0   182M

I have a duplicate/identical system that is sitting idle, so I can do whatever tests necessary to troubleshoot this.

Any help would be appreciated.

Thanks,
Elliot
 
There is no other performance hit known and you're still on zfs 0.8.5

If you are up to date you should have zfs 2.0.x, does "apt update" show missing/broken updates ?

Try to boot the last kernel to see if it is kernel related.


There was a resilver exactly when the problem started.

So it seems like you did some hardware maintenance as well.

What does "zpool history" show for the time span april 16, 17, 18.


I would check all disks smart values, looks like one or more drives are dead.

SSD's tend to slow down instead of throwing errors when they die.

In that case the io delay of course goes up since the mirror has to wait for the slowest drive.

nvme-INTEL_SSDPE2KX040T7_PHLF727500J34P0IGN does not fit the other batches, did it recently get replaced ?
 
Last edited:
H4R0 said:
There is no other performance hit known and you're still on zfs 0.8.5
Click to expand...

so https://forum.proxmox.com/threads/z...p-after-update-from-proxmox-6-2-to-6-3.81820/ doesn't count?

same before and after version and exactly the same problem.

H4R0 said:
Try to boot the last kernel to see if it is kernel related.
Click to expand...
I will try this, thanks.

H4R0 said:
There was a resilver exactly when the problem started.

So it seems like you did some hardware maintenance as well.

What does "zpool history" show for the time span april 16, 17, 18.
Click to expand...
Yes, it's unfortunate that I replaced a drive and upgraded at the same time, because now the new drive will be pointed at as the cause.

S.M.A.R.T. shows all drives at 1% wearout except the new drive is at 0%. All pass the S.M.A.R.T. test.

H4R0 said:
I would check all disks smart values, looks like one or more drives are dead.
Click to expand...
none are dead and in fact, all are healthy and at 1% wearout or less.

H4R0 said:
nvme-INTEL_SSDPE2KX040T7_PHLF727500J34P0IGN does not fit the other batches, did it recently get replaced ?
Click to expand...
yes, this is the drive that was resilvered. it is at 0% wearout.
 
The question about broken update is still unanswered, proxmox subscription as well as no-sub repo has ZFS 2.0.x, you are on 0.8.5

So what does "apt update" show. Never upgrade with "apt upgrade" use "apt full-upgrade" or the gui option.


First try the old kernel, if it doesn't solve the issue make sure all packages are up to date.


On the testing system try the 5.11 kernel and if that does not work downgrade the ZFS packages.

Hard to tell if it is ZFS or Kernel related.


If the issue still persists I would do some troubleshooting.

Temporarily remove the optane log drives from the pool to see if it makes a difference since your workload is mainly write based.

I had some bad results with slog in the past.


Run fio benchmarks and check bandwidth, iops, temps and load.
 
Just to conclude this thread:

TL;DR
proxmox 6.2-4 -> zfs 0.8.3 normal IO delay
proxmox 6.3-3 -> zfs 0.8.5 has problems causing excessive IO delay, huge performance penalty
proxmox 6.3-6 -> zfs 2.0.4 normal IO delay

I moved all VMs to the identically configured host and had the identical problem (6.3-3). I upgraded the problem host to 6.3-6 which includes an update to ZFS 2.04 and moved all the VMs back and the IO delay is back down where it belongs below 1%.
 
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