Problem: Disk read/write request responses are too high (read > 20 ms for 15m or write > 20 ms for 15m)

[Razva]

Hello,

Zabbix is reporting this very often:

Problem: sda: Disk read/write request responses are too high (read > 20 ms for 15m or write > 20 ms for 15m)
Severity: Warning
Opdata: 40.74 ms, 0.55 ms
Application: Disk sda
Trigger description: This trigger might indicate disk sda saturation.

I've watched the activity with iotop, here's 1 minute of recording exactly when Zabbix was reporting the issue: https://www.screencast.com/t/jVUq92jLP

Here's the drive information:

Unique ID: 3OOL.aBG3oNNOhmB
Parent ID: abAj.GPRb67Bwnc2
SysFS ID: /class/block/sda
SysFS BusID: 0:0:0:0
SysFS Device Link: /devices/pci0000:00/0000:00:17.0/ata1/host0/target0:0:0/0:0:0:0
Hardware Class: disk
Model: "ST16000NM001G-2K"
Device: "ST16000NM001G-2K"
Revision: "SN03"
Serial ID: "ZL2CSKWB"
Driver: "ahci", "sd"
Driver Modules: "ahci"
Device File: /dev/sda
Device Files: /dev/sda, /dev/disk/by-id/ata-ST16000NM001G-2KK103_ZL2CSKWB, /dev/disk/by-path/pci-0000:00:17.0-ata-1, /dev/disk/by-id/wwn-0x5000c500c883def2
Device Number: block 8:0-8:15
BIOS id: 0x83
Geometry (Logical): CHS 1945332/255/63
Size: 31251759104 sectors a 512 bytes
Capacity: 14902 GB (16000900661248 bytes)
Config Status: cfg=new, avail=yes, need=no, active=unknown
Attached to: #17 (SATA controller

Here's the SMART information: https://www.screencast.com/t/dodeCQZtfzX

=== START OF INFORMATION SECTION ===
Model Family:     Seagate Exos X16
Device Model:     ST16000NM001G-2KK103
Serial Number:    ZL2CSKWB
LU WWN Device Id: 5 000c50 0c883def2
Firmware Version: SN03
User Capacity:    16,000,900,661,248 bytes [16.0 TB]
Sector Sizes:     512 bytes logical, 4096 bytes physical
Rotation Rate:    7200 rpm
Form Factor:      3.5 inches
Device is:        In smartctl database [for details use: -P show]
ATA Version is:   ACS-4 (minor revision not indicated)
SATA Version is:  SATA 3.3, 6.0 Gb/s (current: 6.0 Gb/s)
Local Time is:    Thu Feb 24 14:31:59 2022 EET
SMART support is: Available - device has SMART capability.
SMART support is: Enabled

=== START OF READ SMART DATA SECTION ===
SMART overall-health self-assessment test result: PASSED

General SMART Values:
Offline data collection status:  (0x82) Offline data collection activity
                                        was completed without error.
                                        Auto Offline Data Collection: Enabled.
Self-test execution status:      (   0) The previous self-test routine completed
                                        without error or no self-test has ever
                                        been run.
Total time to complete Offline
data collection:                (  567) seconds.
Offline data collection
capabilities:                    (0x7b) SMART execute Offline immediate.
                                        Auto Offline data collection on/off support.
                                        Suspend Offline collection upon new
                                        command.
                                        Offline surface scan supported.
                                        Self-test supported.
                                        Conveyance Self-test supported.
                                        Selective Self-test supported.
SMART capabilities:            (0x0003) Saves SMART data before entering
                                        power-saving mode.
                                        Supports SMART auto save timer.
Error logging capability:        (0x01) Error logging supported.
                                        General Purpose Logging supported.
Short self-test routine
recommended polling time:        (   1) minutes.
Extended self-test routine
recommended polling time:        (1407) minutes.
Conveyance self-test routine
recommended polling time:        (   2) minutes.
SCT capabilities:              (0x70bd) SCT Status supported.
                                        SCT Error Recovery Control supported.
                                        SCT Feature Control supported.
                                        SCT Data Table supported.

SMART Attributes Data Structure revision number: 10
Vendor Specific SMART Attributes with Thresholds:
ID# ATTRIBUTE_NAME          FLAG     VALUE WORST THRESH TYPE      UPDATED  WHEN_FAILED RAW_VALUE
  1 Raw_Read_Error_Rate     0x000f   070   064   044    Pre-fail  Always       -       9092416
  3 Spin_Up_Time            0x0003   094   094   000    Pre-fail  Always       -       0
  4 Start_Stop_Count        0x0032   100   100   020    Old_age   Always       -       6
  5 Reallocated_Sector_Ct   0x0033   100   100   010    Pre-fail  Always       -       0
  7 Seek_Error_Rate         0x000f   086   060   045    Pre-fail  Always       -       359240283
  9 Power_On_Hours          0x0032   091   091   000    Old_age   Always       -       8092
 10 Spin_Retry_Count        0x0013   100   100   097    Pre-fail  Always       -       0
 12 Power_Cycle_Count       0x0032   100   100   020    Old_age   Always       -       6
 18 Head_Health             0x000b   100   100   050    Pre-fail  Always       -       0
187 Reported_Uncorrect      0x0032   100   100   000    Old_age   Always       -       0
188 Command_Timeout         0x0032   100   100   000    Old_age   Always       -       0
190 Airflow_Temperature_Cel 0x0022   060   049   040    Old_age   Always       -       40 (Min/Max 35/47)
192 Power-Off_Retract_Count 0x0032   100   100   000    Old_age   Always       -       2
193 Load_Cycle_Count        0x0032   100   100   000    Old_age   Always       -       363
194 Temperature_Celsius     0x0022   040   047   000    Old_age   Always       -       40 (0 22 0 0 0)
197 Current_Pending_Sector  0x0012   100   100   000    Old_age   Always       -       0
198 Offline_Uncorrectable   0x0010   100   100   000    Old_age   Offline      -       0
199 UDMA_CRC_Error_Count    0x003e   200   200   000    Old_age   Always       -       0
200 Pressure_Limit          0x0023   100   100   001    Pre-fail  Always       -       0
240 Head_Flying_Hours       0x0000   100   253   000    Old_age   Offline      -       8031h+40m+01.909s
241 Total_LBAs_Written      0x0000   100   253   000    Old_age   Offline      -       58614631828
242 Total_LBAs_Read         0x0000   100   253   000    Old_age   Offline      -       184612154736

SMART Error Log Version: 1
No Errors Logged

SMART Self-test log structure revision number 1
Num  Test_Description    Status                  Remaining  LifeTime(hours)  LBA_of_first_error
# 1  Short offline       Completed without error       00%         1         -
# 2  Short offline       Completed without error       00%         0         -

SMART Selective self-test log data structure revision number 1
 SPAN  MIN_LBA  MAX_LBA  CURRENT_TEST_STATUS
    1        0        0  Not_testing
    2        0        0  Not_testing
    3        0        0  Not_testing
    4        0        0  Not_testing
    5        0        0  Not_testing
Selective self-test flags (0x0):
  After scanning selected spans, do NOT read-scan remainder of disk.
If Selective self-test is pending on power-up, resume after 0 minute delay.

Is this normal? Should I just ignore the warning and/or set a higher threshold?

Thank you!

 

[sombra3405]

Greetings, I have the same problem, I have 6 10k rpm disks with raid 5, I also try to restore a virtual machine and it gives me the following error "echo 0 > /proc/sys/kernel/hung_task_timeout_secs" disables this message.
I've read about the 120 sec blocking message that it could be the kernel, but I don't know about the zabbix message about disk saturation

 

[itNGO]

PBS creates millions of files in small chunks to deduplicate and optimize space usage.
When you use rotating disks, they burn like hell to read this data.
So yes, this is expected. That is why recommendation is to use SSDs for PBS.
If you can not, at least use special device in a ZFS Pool or if using Raid-Controller with XFS or EXT4 at least add CacheCade-SSDs or similar.

It is more or less by design in PBS...

 

[molnart]

what is the best practice for syncing long-term backups to rotating disk? garbage collection on a z-raid pool via NFS takes 10+ hours and often fails. i could use an ssd as the primary backup target for the most recent copies, but still i need to sync them to a larger capacity storage and probably also run garbage collection from there...