freebsd-update from 13.1 to 13.2 very slow

D

David the Swarfer

Hi all
I run 3 FBSD servers and am busy upgrading from 13.1 to 13.2.
One of them ran fine in an unremarkable length of time.
the 2nd one is taking a very long time to process the
freebsd-update upgrade -r 13.2-RELEASE
command and is stuck at the code
Code: 
 # Sanity check entries with type 'f'
        if grep -E '^f' sanitycheck.tmp |
            grep -qvE "^f\|${M}\|${H}\|${P}*\$"; then
                fetch_metadata_bogus ""
                return 1
        fi
using 100% CPU for the grep commands.

sanitycheck.tmp is not insanly large, just 127591 lines so this should not be taking hours (about 2.5 so far).

Now, the CPU is not the fastest ever, being a
Intel(R) Core(TM)2 CPU 6300 @ 1.86GHz (1864.87-MHz K8-class CPU) with 8GB RAM
but prior to reinstalling this machine with 64bit FBSD 13 (from 32bit FBSD12 on UFS) on a ZFS root this kind of upgrade was much much quicker.

I cannot see any disk activity at all so I don't think it is a disk problem.

oh, it finished while I was typing this up, great, not stuck forever, just uncomfortably long.
any ideas?
maybe that grep command can be made more efficient?

thanks
 
oh hell, it asked if things seems reasonable, I answered yes, and now it appears to be running that command again!

Code: 
 `-- /bin/sh /usr/sbin/freebsd-update upgrade -r 13.2-RELEASE
5591  0  S+     0:00.08 | |             |-- gunzip -c
5592  0  R+     2:47.17 | |             `-- grep -qvE ^[a-z]+\\|[0-9a-z-]+\\|[-+./:=,%@_[~[:alnum:]]+\\|[fdL-]\\|

100% CPU, mem used about 355M, no swap used
 
David the Swarfer said:
I cannot see any disk activity at all so I don't think it is a disk problem.
Click to expand...
Could still be a disk issue or perhaps even a controller issue. Have you checked /var/log/messages? Specifically look for time-outs, those can happen if the disk itself is on its last legs. This would cause disk activity to grind to halt or cause some sever slowdowns with I/O to/from the disk. Also check the SMART data of the disk.
 
SirDice said:
Could still be a disk issue or perhaps even a controller issue. Have you checked /var/log/messages? Specifically look for time-outs, those can happen if the disk itself is on its last legs. This would cause disk activity to grind to halt or cause some sever slowdowns with I/O to/from the disk. Also check the SMART data of the disk.
Click to expand...

I dont see any disk related messages in the logs.
it has been running now since 3pm, now nearly 9pm.
Top shows

last pid: 12391; load averages: 1.07, 1.22, 1.22 up 0+05:26:50 20:47:20
44 processes: 2 running, 42 sleeping
CPU: 49.0% user, 0.0% nice, 3.9% system, 0.0% interrupt, 47.1% idle
Mem: 27M Active, 262M Inact, 843M Wired, 116M Buf, 6715M Free
ARC: 243M Total, 199M MFU, 34M MRU, 264K Anon, 1533K Header, 8693K Other
212M Compressed, 474M Uncompressed, 2.23:1 Ratio
Swap: 4096M Total, 4096M Free

PID USERNAME THR PRI NICE SIZE RES STATE C TIME WCPU COMMAND
12329 root 1 102 0 13M 2240K CPU1 1 0:53 98.40% sha256

and that ARC data does not look like a problem to me (but this is my first use of ZFS), mem not full, swap not thrashing, just really slow.
Other disks in this box are UFS and work just fine but the ZFS stuff does seem slow.
No, no UPS, it failed earlier this year and the univerity has seen fit to not replace it.

I doubt it will finish the update fetch before 11pm when the power is due off, at this rate it will never get upgraded since we have regular outages (google 'south afrcia loadshedding') and
stuff has to happen in the 6 to 8 hour 'on' windows.

smartctl -d atacam -a ada0
Code: 
smartctl 7.3 2022-02-28 r5338 [FreeBSD 13.1-RELEASE-p8 amd64] (local build)
Copyright (C) 2002-22, Bruce Allen, Christian Franke, www.smartmontools.org

=== START OF INFORMATION SECTION ===
Model Family:     Seagate IronWolf
Device Model:     ST2000VN004-2E4164
Serial Number:    Z5240R13
LU WWN Device Id: 5 000c50 0af9b26f6
Firmware Version: SC60
User Capacity:    2,000,398,934,016 bytes [2.00 TB]
Sector Sizes:     512 bytes logical, 4096 bytes physical
Rotation Rate:    5900 rpm
Form Factor:      3.5 inches
Device is:        In smartctl database 7.3/5319
ATA Version is:   ACS-2, ACS-3 T13/2161-D revision 3b
SATA Version is:  SATA 3.1, 6.0 Gb/s (current: 3.0 Gb/s)
Local Time is:    Fri Jul  7 20:58:38 2023 SAST
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:  (0x00) Offline data collection activity
                                        was never started.
                                        Auto Offline Data Collection: Disabled.
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:                (  107) seconds.
Offline data collection
capabilities:                    (0x73) SMART execute Offline immediate.
                                        Auto Offline data collection on/off support.
                                        Suspend Offline collection upon new
                                        command.
                                        No 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:        ( 255) minutes.
Conveyance self-test routine
recommended polling time:        (   2) minutes.
SCT capabilities:              (0x10bd) 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   115   099   006    Pre-fail  Always       -       100123960
  3 Spin_Up_Time            0x0003   096   095   000    Pre-fail  Always       -       0
  4 Start_Stop_Count        0x0032   100   100   020    Old_age   Always       -       312
  5 Reallocated_Sector_Ct   0x0033   100   100   010    Pre-fail  Always       -       0
  7 Seek_Error_Rate         0x000f   067   060   030    Pre-fail  Always       -       5806069
  9 Power_On_Hours          0x0032   097   097   000    Old_age   Always       -       2854
 10 Spin_Retry_Count        0x0013   100   100   097    Pre-fail  Always       -       0
 12 Power_Cycle_Count       0x0032   100   100   020    Old_age   Always       -       312
184 End-to-End_Error        0x0032   100   100   099    Old_age   Always       -       0
187 Reported_Uncorrect      0x0032   100   100   000    Old_age   Always       -       0
188 Command_Timeout         0x0032   100   100   000    Old_age   Always       -       0
189 High_Fly_Writes         0x003a   094   094   000    Old_age   Always       -       6
190 Airflow_Temperature_Cel 0x0022   073   066   045    Old_age   Always       -       27 (Min/Max 25/28)
191 G-Sense_Error_Rate      0x0032   100   100   000    Old_age   Always       -       0
192 Power-Off_Retract_Count 0x0032   100   100   000    Old_age   Always       -       67
193 Load_Cycle_Count        0x0032   100   100   000    Old_age   Always       -       312
194 Temperature_Celsius     0x0022   027   040   000    Old_age   Always       -       27 (0 13 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

SMART Error Log Version: 1
No Errors Logged

SMART Self-test log structure revision number 1
No self-tests have been logged.  [To run self-tests, use: smartctl -t]

you say a controller problem, yet this system ran UFS just fine with no such speed problem, why would ZFS slow it down this drastically?
 
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