ASRock BeeBox N3150 - FreeBSD

Hardware info on main page.

storage device

root@www# camcontrol devlist
<TOSHIBA THNSNJ128GMCU JUT10101>   at scbus1 target 0 lun 0 (ada0,pass0)

old storage device

root@www# camcontrol devlist
<INTEL SSDMCEAC120A3 LLGi>         at scbus1 target 0 lun 0 (ada0,pass0)

storage layout of ada0

root@www# gpart show -p ada0
=>       34  250069613    ada0  GPT  (119G)
         34       1024  ada0p1  freebsd-boot  (512K)
       1058  241172480  ada0p2  freebsd-ufs  (115G)
  241173538    8896109  ada0p3  freebsd-swap  (4.2G)

old storage layout of ada0

root@www# gpart show -p ada0
=>       34  234441581    ada0  GPT  (112G)
         34       1024  ada0p1  freebsd-boot  (512K)
       1058  226491392  ada0p2  freebsd-ufs  (108G)
  226492450    7949164  ada0p3  freebsd-swap  (3.8G)
  234441614          1          - free -  (512B)

Links

MediaWiki HTTPS, Running Mediawiki on FreeBSD, How To Secure Apache with Let's Encrypt on FreeBSD 12.0,

work log

2024-11-04: ada0p2 - panic and reboot. From /var/log/messages

Nov  4 09:50:15 www kernel: Fatal trap 12: page fault while in kernel mode
Nov  4 09:50:15 www kernel: cpuid = 3; apic id = 06
Nov  4 09:50:15 www kernel: fault virtual address       = 0x18
Nov  4 09:50:15 www kernel: fault code          = supervisor read data, page not present
Nov  4 09:50:15 www kernel: instruction pointer = 0x20:0xffffffff80cae35d
Nov  4 09:50:15 www kernel: stack pointer               = 0x28:0xfffffe00c5396710
Nov  4 09:50:15 www kernel: frame pointer               = 0x28:0xfffffe00c5396780
Nov  4 09:50:15 www kernel: code segment                = base 0x0, limit 0xfffff, type 0x1b
Nov  4 09:50:15 www kernel:                     = DPL 0, pres 1, long 1, def32 0, gran 1
Nov  4 09:50:15 www kernel: processor eflags    = interrupt enabled, resume, IOPL = 0
Nov  4 09:50:15 www kernel: current process             = 12 (irq118: re0)
Nov  4 09:50:15 www kernel: trap number         = 12
Nov  4 09:50:15 www kernel: panic: page fault
Nov  4 09:50:15 www kernel: cpuid = 3
Nov  4 09:50:15 www kernel: time = 1730710177
Nov  4 09:50:15 www kernel: KDB: stack backtrace:
Nov  4 09:50:15 www kernel: #0 0xffffffff80c694a5 at kdb_backtrace+0x65
Nov  4 09:50:15 www kernel: #1 0xffffffff80c1bb5f at vpanic+0x17f
Nov  4 09:50:15 www kernel: #2 0xffffffff80c1b9d3 at panic+0x43
Nov  4 09:50:15 www kernel: #3 0xffffffff810afdf5 at trap_fatal+0x385
Nov  4 09:50:15 www kernel: #4 0xffffffff810afe4f at trap_pfault+0x4f
Nov  4 09:50:15 www kernel: #5 0xffffffff81087578 at calltrap+0x8
Nov  4 09:50:15 www kernel: #6 0xffffffff80de0809 at tcp_output+0x1339
Nov  4 09:50:15 www kernel: #7 0xffffffff80dd7f2d at tcp_do_segment+0x2cfd
Nov  4 09:50:15 www kernel: #8 0xffffffff80dd44f1 at tcp_input_with_port+0xb61
Nov  4 09:50:15 www kernel: #9 0xffffffff80dd519b at tcp_input+0xb
Nov  4 09:50:15 www kernel: #10 0xffffffff80dc695f at ip_input+0x11f
Nov  4 09:50:15 www kernel: #11 0xffffffff80d530c9 at netisr_dispatch_src+0xb9
Nov  4 09:50:15 www kernel: #12 0xffffffff80d36ee8 at ether_demux+0x138
Nov  4 09:50:15 www kernel: #13 0xffffffff80d38275 at ether_nh_input+0x355
Nov  4 09:50:15 www kernel: #14 0xffffffff80d530c9 at netisr_dispatch_src+0xb9
Nov  4 09:50:15 www kernel: #15 0xffffffff80d37319 at ether_input+0x69
Nov  4 09:50:15 www kernel: #16 0xffffffff8092179d at re_rxeof+0x5cd
Nov  4 09:50:15 www kernel: #17 0xffffffff8091f003 at re_intr_msi+0xf3
Nov  4 09:50:15 www kernel: Uptime: 7d17h34m8s
Nov  4 09:50:15 www kernel: Dumping 1059 out of 16016 MB:..2%..11%..22%..31%..41%..52%..61%..71%..81%..91%
---<<BOOT>>---

2024-10-27: ada0p2 - backup - finish up by unmounting the backup disk

root@www# umount /zb

2024-10-27: ada0p2 - backup - do a mysql backup

$ mysqldump -u user -p wikidb --set-gtid-purged=OFF > wikidb_backup_20241027.sql
Enter password: 

check the file

$ ll -h
total 118184
drwxr-xr-x  2 tingo  tingo  -  512B Oct 27 17:08 ./
drwxr-xr-x  4 tingo  tingo  -  512B Oct 27 17:06 ../
-rw-r--r--  1 tingo  tingo  -  115M Oct 27 17:08 wikidb_backup_20241027.sql

(user is just an example user name)

2024-10-27: ada0p2 - backup - mount backup disk

root@www# mount /dev/da0p1 /zb

make a directory

root@www# cd /zb/ndwiki-backups/
root@www# mkdir 20241027
root@www# cd 20241027/

do the backup

root@www# dump -C16 -0aLf /zb/ndwiki-backups/20241027/ada0p2_dump.file /dev/ada0p2
  DUMP: Date of this level 0 dump: Sun Oct 27 16:42:13 2024
  DUMP: Date of last level 0 dump: the epoch
  DUMP: Dumping snapshot of /dev/ada0p2 (/) to /zb/ndwiki-backups/20241027/ada0p2_dump.file
  DUMP: mapping (Pass I) [regular files]
  DUMP: Cache 16 MB, blocksize = 65536
  DUMP: mapping (Pass II) [directories]
  DUMP: estimated 84421254 tape blocks.
  DUMP: dumping (Pass III) [directories]
  DUMP: dumping (Pass IV) [regular files]
  DUMP: 26.19% done, finished in 0:14 at Sun Oct 27 17:01:18 2024
  DUMP: 52.95% done, finished in 0:08 at Sun Oct 27 17:01:06 2024
  DUMP: 79.19% done, finished in 0:03 at Sun Oct 27 17:01:09 2024
  DUMP: DUMP: 84419322 tape blocks on 1 volume
  DUMP: finished in 1146 seconds, throughput 73664 KBytes/sec
  DUMP: Closing /zb/ndwiki-backups/20241027/ada0p2_dump.file
  DUMP: DUMP IS DONE

check the file

root@www# ll -h /zb/ndwiki-backups/20241027/
total 84440008
drwxr-xr-x  2 root   wheel   512B Oct 27 16:42 ./
drwxr-xr-x  5 tingo  wheel   512B Oct 27 16:37 ../
-rw-r--r--  1 root   wheel    81G Oct 27 17:01 ada0p2_dump.file

2024-08-06: ada0p2 - and again - panic and reboot

Aug  6 18:46:45 www kernel: Fatal trap 12: page fault while in kernel mode
Aug  6 18:46:45 www kernel: cpuid = 3; apic id = 06
Aug  6 18:46:45 www kernel: fault virtual address       = 0x18
Aug  6 18:46:45 www kernel: fault code          = supervisor read data, page not present
Aug  6 18:46:45 www kernel: instruction pointer = 0x20:0xffffffff80cae35d
Aug  6 18:46:45 www kernel: stack pointer               = 0x0:0xfffffe00c5392710
Aug  6 18:46:45 www kernel: frame pointer               = 0x0:0xfffffe00c5392780
Aug  6 18:46:45 www kernel: code segment                = base 0x0, limit 0xfffff, type 0x1b
Aug  6 18:46:45 www kernel:                     = DPL 0, pres 1, long 1, def32 0, gran 1
Aug  6 18:46:45 www kernel: processor eflags    = interrupt enabled, resume, IOPL = 0
Aug  6 18:46:45 www kernel: current process             = 12 (irq118: re0)
Aug  6 18:46:45 www kernel: trap number         = 12
Aug  6 18:46:45 www kernel: panic: page fault
Aug  6 18:46:45 www kernel: cpuid = 3
Aug  6 18:46:45 www kernel: time = 1722962768
Aug  6 18:46:45 www kernel: KDB: stack backtrace:
Aug  6 18:46:45 www kernel: #0 0xffffffff80c694a5 at kdb_backtrace+0x65
Aug  6 18:46:45 www kernel: #1 0xffffffff80c1bb5f at vpanic+0x17f
Aug  6 18:46:45 www kernel: #2 0xffffffff80c1b9d3 at panic+0x43
Aug  6 18:46:45 www kernel: #3 0xffffffff810afdf5 at trap_fatal+0x385
Aug  6 18:46:45 www kernel: #4 0xffffffff810afe4f at trap_pfault+0x4f
Aug  6 18:46:45 www kernel: #5 0xffffffff81087578 at calltrap+0x8
Aug  6 18:46:45 www kernel: #6 0xffffffff80de0809 at tcp_output+0x1339
Aug  6 18:46:45 www kernel: #7 0xffffffff80dd7dac at tcp_do_segment+0x2b7c
Aug  6 18:46:45 www kernel: #8 0xffffffff80dd44f1 at tcp_input_with_port+0xb61
Aug  6 18:46:45 www kernel: #9 0xffffffff80dd519b at tcp_input+0xb
Aug  6 18:46:45 www kernel: #10 0xffffffff80dc695f at ip_input+0x11f
Aug  6 18:46:45 www kernel: #11 0xffffffff80d530c9 at netisr_dispatch_src+0xb9
Aug  6 18:46:45 www kernel: #12 0xffffffff80d36ee8 at ether_demux+0x138
Aug  6 18:46:45 www kernel: #13 0xffffffff80d38275 at ether_nh_input+0x355
Aug  6 18:46:45 www kernel: #14 0xffffffff80d530c9 at netisr_dispatch_src+0xb9
Aug  6 18:46:45 www kernel: #15 0xffffffff80d37319 at ether_input+0x69
Aug  6 18:46:45 www kernel: #16 0xffffffff8092179d at re_rxeof+0x5cd
Aug  6 18:46:45 www kernel: #17 0xffffffff8091f003 at re_intr_msi+0xf3
Aug  6 18:46:45 www kernel: Uptime: 1d4h20m6s

2024-08-05: ada0p2 - another panic, another reboot

Aug  5 14:26:13 www kernel: Fatal trap 12: page fault while in kernel mode
Aug  5 14:26:13 www kernel: cpuid = 3; apic id = 06
Aug  5 14:26:13 www kernel: fault virtual address       = 0x18
Aug  5 14:26:13 www kernel: fault code          = supervisor read data, page not present
Aug  5 14:26:13 www kernel: instruction pointer = 0x20:0xffffffff80cae402
Aug  5 14:26:13 www kernel: stack pointer               = 0x0:0xfffffe00c5396710
Aug  5 14:26:13 www kernel: frame pointer               = 0x0:0xfffffe00c5396780
Aug  5 14:26:13 www kernel: code segment                = base 0x0, limit 0xfffff, type 0x1b
Aug  5 14:26:13 www kernel:                     = DPL 0, pres 1, long 1, def32 0, gran 1
Aug  5 14:26:13 www kernel: processor eflags    = interrupt enabled, resume, IOPL = 0
Aug  5 14:26:13 www kernel: current process             = 12 (irq118: re0)
Aug  5 14:26:13 www kernel: trap number         = 12
Aug  5 14:26:13 www kernel: panic: page fault
Aug  5 14:26:13 www kernel: cpuid = 3
Aug  5 14:26:13 www kernel: time = 1722860734
Aug  5 14:26:13 www kernel: KDB: stack backtrace:
Aug  5 14:26:13 www kernel: #0 0xffffffff80c694a5 at kdb_backtrace+0x65
Aug  5 14:26:13 www kernel: #1 0xffffffff80c1bb5f at vpanic+0x17f
Aug  5 14:26:13 www kernel: #2 0xffffffff80c1b9d3 at panic+0x43
Aug  5 14:26:13 www kernel: #3 0xffffffff810afdf5 at trap_fatal+0x385
Aug  5 14:26:13 www kernel: #4 0xffffffff810afe4f at trap_pfault+0x4f
Aug  5 14:26:13 www kernel: #5 0xffffffff81087578 at calltrap+0x8
Aug  5 14:26:13 www kernel: #6 0xffffffff80de0809 at tcp_output+0x1339
Aug  5 14:26:13 www kernel: #7 0xffffffff80dd7f2d at tcp_do_segment+0x2cfd
Aug  5 14:26:13 www kernel: #8 0xffffffff80dd44f1 at tcp_input_with_port+0xb61
Aug  5 14:26:13 www kernel: #9 0xffffffff80dd519b at tcp_input+0xb
Aug  5 14:26:13 www kernel: #10 0xffffffff80dc695f at ip_input+0x11f
Aug  5 14:26:13 www kernel: #11 0xffffffff80d530c9 at netisr_dispatch_src+0xb9
Aug  5 14:26:13 www kernel: #12 0xffffffff80d36ee8 at ether_demux+0x138
Aug  5 14:26:13 www kernel: #13 0xffffffff80d38275 at ether_nh_input+0x355
Aug  5 14:26:13 www kernel: #14 0xffffffff80d530c9 at netisr_dispatch_src+0xb9
Aug  5 14:26:13 www kernel: #15 0xffffffff80d37319 at ether_input+0x69
Aug  5 14:26:13 www kernel: #16 0xffffffff8092179d at re_rxeof+0x5cd
Aug  5 14:26:13 www kernel: #17 0xffffffff8091f003 at re_intr_msi+0xf3
Aug  5 14:26:13 www kernel: Uptime: 4d4h54m12s

2024-08-01: ada0p2 - the machine had a panic and rebooted

Aug  1 04:11:17 www kernel: Fatal trap 12: page fault while in kernel mode
Aug  1 04:11:17 www kernel: cpuid = 3; apic id = 06
Aug  1 04:11:17 www kernel: fault virtual address       = 0x18
Aug  1 04:11:17 www kernel: fault code          = supervisor read data, page not present
Aug  1 04:11:17 www kernel: instruction pointer = 0x20:0xffffffff80cae35d
Aug  1 04:11:17 www kernel: stack pointer               = 0x28:0xfffffe00c53be710
Aug  1 04:11:17 www kernel: frame pointer               = 0x28:0xfffffe00c53be780
Aug  1 04:11:17 www kernel: code segment                = base 0x0, limit 0xfffff, type 0x1b
Aug  1 04:11:17 www kernel:                     = DPL 0, pres 1, long 1, def32 0, gran 1
Aug  1 04:11:17 www kernel: processor eflags    = interrupt enabled, resume, IOPL = 0
Aug  1 04:11:17 www kernel: current process             = 12 (irq118: re0)
Aug  1 04:11:17 www kernel: trap number         = 12
Aug  1 04:11:17 www kernel: panic: page fault
Aug  1 04:11:17 www kernel: cpuid = 3
Aug  1 04:11:17 www kernel: time = 1722478237
Aug  1 04:11:17 www kernel: KDB: stack backtrace:
Aug  1 04:11:17 www kernel: #0 0xffffffff80c694a5 at kdb_backtrace+0x65
Aug  1 04:11:17 www kernel: #1 0xffffffff80c1bb5f at vpanic+0x17f
Aug  1 04:11:17 www kernel: #2 0xffffffff80c1b9d3 at panic+0x43
Aug  1 04:11:17 www kernel: #3 0xffffffff810afdf5 at trap_fatal+0x385
Aug  1 04:11:17 www kernel: #4 0xffffffff810afe4f at trap_pfault+0x4f
Aug  1 04:11:17 www kernel: #5 0xffffffff81087578 at calltrap+0x8
Aug  1 04:11:17 www kernel: #6 0xffffffff80de0809 at tcp_output+0x1339
Aug  1 04:11:17 www kernel: #7 0xffffffff80dd7dac at tcp_do_segment+0x2b7c
Aug  1 04:11:17 www kernel: #8 0xffffffff80dd44f1 at tcp_input_with_port+0xb61
Aug  1 04:11:17 www kernel: #9 0xffffffff80dd519b at tcp_input+0xb
Aug  1 04:11:17 www kernel: #10 0xffffffff80dc695f at ip_input+0x11f
Aug  1 04:11:17 www kernel: #11 0xffffffff80d530c9 at netisr_dispatch_src+0xb9
Aug  1 04:11:17 www kernel: #12 0xffffffff80d36ee8 at ether_demux+0x138
Aug  1 04:11:17 www kernel: #13 0xffffffff80d38275 at ether_nh_input+0x355
Aug  1 04:11:17 www kernel: #14 0xffffffff80d530c9 at netisr_dispatch_src+0xb9
Aug  1 04:11:17 www kernel: #15 0xffffffff80d37319 at ether_input+0x69
Aug  1 04:11:17 www kernel: #16 0xffffffff8092179d at re_rxeof+0x5cd
Aug  1 04:11:17 www kernel: #17 0xffffffff8091f003 at re_intr_msi+0xf3
Aug  1 04:11:17 www kernel: Uptime: 1d12h56m42s

and another one, just a few hours after

Aug  1 09:31:33 www kernel: Fatal trap 12: page fault while in kernel mode
Aug  1 09:31:33 www kernel: cpuid = 3; apic id = 06
Aug  1 09:31:33 www kernel: fault virtual address       = 0x18
Aug  1 09:31:33 www kernel: fault code          = supervisor read data, page not present
Aug  1 09:31:33 www kernel: instruction pointer = 0x20:0xffffffff80cae35d
Aug  1 09:31:33 www kernel: stack pointer               = 0x0:0xfffffe00c5396710
Aug  1 09:31:33 www kernel: frame pointer               = 0x0:0xfffffe00c5396780
Aug  1 09:31:33 www kernel: code segment                = base 0x0, limit 0xfffff, type 0x1b
Aug  1 09:31:33 www kernel:                     = DPL 0, pres 1, long 1, def32 0, gran 1
Aug  1 09:31:33 www kernel: processor eflags    = interrupt enabled, resume, IOPL = 0
Aug  1 09:31:33 www kernel: current process             = 12 (irq118: re0)
Aug  1 09:31:33 www kernel: trap number         = 12
Aug  1 09:31:33 www kernel: panic: page fault
Aug  1 09:31:33 www kernel: cpuid = 3
Aug  1 09:31:33 www kernel: time = 1722497457
Aug  1 09:31:33 www kernel: KDB: stack backtrace:
Aug  1 09:31:33 www kernel: #0 0xffffffff80c694a5 at kdb_backtrace+0x65
Aug  1 09:31:33 www kernel: #1 0xffffffff80c1bb5f at vpanic+0x17f
Aug  1 09:31:33 www kernel: #2 0xffffffff80c1b9d3 at panic+0x43
Aug  1 09:31:33 www kernel: #3 0xffffffff810afdf5 at trap_fatal+0x385
Aug  1 09:31:33 www kernel: #4 0xffffffff810afe4f at trap_pfault+0x4f
Aug  1 09:31:33 www kernel: #5 0xffffffff81087578 at calltrap+0x8
Aug  1 09:31:33 www kernel: #6 0xffffffff80de0809 at tcp_output+0x1339
Aug  1 09:31:33 www kernel: #7 0xffffffff80dd7f2d at tcp_do_segment+0x2cfd
Aug  1 09:31:33 www kernel: #8 0xffffffff80dd44f1 at tcp_input_with_port+0xb61
Aug  1 09:31:33 www kernel: #9 0xffffffff80dd519b at tcp_input+0xb
Aug  1 09:31:33 www kernel: #10 0xffffffff80dc695f at ip_input+0x11f
Aug  1 09:31:33 www kernel: #11 0xffffffff80d530c9 at netisr_dispatch_src+0xb9
Aug  1 09:31:33 www kernel: #12 0xffffffff80d36ee8 at ether_demux+0x138
Aug  1 09:31:33 www kernel: #13 0xffffffff80d38275 at ether_nh_input+0x355
Aug  1 09:31:33 www kernel: #14 0xffffffff80d530c9 at netisr_dispatch_src+0xb9
Aug  1 09:31:33 www kernel: #15 0xffffffff80d37319 at ether_input+0x69
Aug  1 09:31:33 www kernel: #16 0xffffffff8092179d at re_rxeof+0x5cd
Aug  1 09:31:33 www kernel: #17 0xffffffff8091f003 at re_intr_msi+0xf3
Aug  1 09:31:33 www kernel: Uptime: 5h19m52s

2024-07-30: ada0p2 - the machine had a panic and rebooted

Jul 30 15:14:07 www kernel: Fatal trap 12: page fault while in kernel mode
Jul 30 15:14:07 www kernel: cpuid = 3; apic id = 06
Jul 30 15:14:07 www kernel: fault virtual address       = 0x18
Jul 30 15:14:07 www kernel: fault code          = supervisor read data, page not present
Jul 30 15:14:07 www kernel: instruction pointer = 0x20:0xffffffff80cae402
Jul 30 15:14:07 www kernel: stack pointer               = 0x28:0xfffffe00c5396710
Jul 30 15:14:07 www kernel: frame pointer               = 0x28:0xfffffe00c5396780
Jul 30 15:14:07 www kernel: code segment                = base 0x0, limit 0xfffff, type 0x1b
Jul 30 15:14:07 www kernel:                     = DPL 0, pres 1, long 1, def32 0, gran 1
Jul 30 15:14:07 www kernel: processor eflags    = interrupt enabled, resume, IOPL = 0
Jul 30 15:14:07 www kernel: current process             = 12 (irq118: re0)
Jul 30 15:14:07 www kernel: trap number         = 12
Jul 30 15:14:07 www kernel: panic: page fault
Jul 30 15:14:07 www kernel: cpuid = 3
Jul 30 15:14:07 www kernel: time = 1722345209
Jul 30 15:14:07 www kernel: KDB: stack backtrace:
Jul 30 15:14:07 www kernel: #0 0xffffffff80c694a5 at kdb_backtrace+0x65
Jul 30 15:14:07 www kernel: #1 0xffffffff80c1bb5f at vpanic+0x17f
Jul 30 15:14:07 www kernel: #2 0xffffffff80c1b9d3 at panic+0x43
Jul 30 15:14:07 www kernel: #3 0xffffffff810afdf5 at trap_fatal+0x385
Jul 30 15:14:07 www kernel: #4 0xffffffff810afe4f at trap_pfault+0x4f
Jul 30 15:14:07 www kernel: #5 0xffffffff81087578 at calltrap+0x8
Jul 30 15:14:07 www kernel: #6 0xffffffff80de0809 at tcp_output+0x1339
Jul 30 15:14:07 www kernel: #7 0xffffffff80dd7f2d at tcp_do_segment+0x2cfd
Jul 30 15:14:07 www kernel: #8 0xffffffff80dd44f1 at tcp_input_with_port+0xb61
Jul 30 15:14:07 www kernel: #9 0xffffffff80dd519b at tcp_input+0xb
Jul 30 15:14:07 www kernel: #10 0xffffffff80dc695f at ip_input+0x11f
Jul 30 15:14:07 www kernel: #11 0xffffffff80d530c9 at netisr_dispatch_src+0xb9
Jul 30 15:14:07 www kernel: #12 0xffffffff80d36ee8 at ether_demux+0x138
Jul 30 15:14:07 www kernel: #13 0xffffffff80d38275 at ether_nh_input+0x355
Jul 30 15:14:07 www kernel: #14 0xffffffff80d530c9 at netisr_dispatch_src+0xb9
Jul 30 15:14:07 www kernel: #15 0xffffffff80d37319 at ether_input+0x69
Jul 30 15:14:07 www kernel: #16 0xffffffff8092179d at re_rxeof+0x5cd
Jul 30 15:14:07 www kernel: #17 0xffffffff8091f003 at re_intr_msi+0xf3
Jul 30 15:14:07 www kernel: Uptime: 33d12h15m57s

2024-06-27: ada0p2 - the machine had a panic. From /var/log/messages

Jun 27 02:57:43 www kernel: Fatal trap 12: page fault while in kernel mode
Jun 27 02:57:43 www kernel: cpuid = 3; apic id = 06
Jun 27 02:57:43 www kernel: fault virtual address       = 0x18
Jun 27 02:57:43 www kernel: fault code          = supervisor read data, page not present
Jun 27 02:57:43 www kernel: instruction pointer = 0x20:0xffffffff80cae35d
Jun 27 02:57:43 www kernel: stack pointer               = 0x28:0xfffffe00c5396710
Jun 27 02:57:43 www kernel: frame pointer               = 0x28:0xfffffe00c5396780
Jun 27 02:57:43 www kernel: code segment                = base 0x0, limit 0xfffff, type 0x1b
Jun 27 02:57:43 www kernel:                     = DPL 0, pres 1, long 1, def32 0, gran 1
Jun 27 02:57:43 www kernel: processor eflags    = interrupt enabled, resume, IOPL = 0
Jun 27 02:57:43 www kernel: current process             = 12 (irq118: re0)
Jun 27 02:57:43 www kernel: trap number         = 12
Jun 27 02:57:43 www kernel: panic: page fault
Jun 27 02:57:43 www kernel: cpuid = 3
Jun 27 02:57:43 www kernel: time = 1719449825
Jun 27 02:57:43 www kernel: KDB: stack backtrace:
Jun 27 02:57:43 www kernel: #0 0xffffffff80c694a5 at kdb_backtrace+0x65
Jun 27 02:57:43 www kernel: #1 0xffffffff80c1bb5f at vpanic+0x17f
Jun 27 02:57:43 www kernel: #2 0xffffffff80c1b9d3 at panic+0x43
Jun 27 02:57:43 www kernel: #3 0xffffffff810afdf5 at trap_fatal+0x385
Jun 27 02:57:43 www kernel: #4 0xffffffff810afe4f at trap_pfault+0x4f
Jun 27 02:57:43 www kernel: #5 0xffffffff81087578 at calltrap+0x8
Jun 27 02:57:43 www kernel: #6 0xffffffff80de0809 at tcp_output+0x1339
Jun 27 02:57:43 www kernel: #7 0xffffffff80dd7dac at tcp_do_segment+0x2b7c
Jun 27 02:57:43 www kernel: #8 0xffffffff80dd44f1 at tcp_input_with_port+0xb61
Jun 27 02:57:43 www kernel: #9 0xffffffff80dd519b at tcp_input+0xb
Jun 27 02:57:43 www kernel: #10 0xffffffff80dc695f at ip_input+0x11f
Jun 27 02:57:43 www kernel: #11 0xffffffff80d530c9 at netisr_dispatch_src+0xb9
Jun 27 02:57:43 www kernel: #12 0xffffffff80d36ee8 at ether_demux+0x138
Jun 27 02:57:43 www kernel: #13 0xffffffff80d38275 at ether_nh_input+0x355
Jun 27 02:57:43 www kernel: #14 0xffffffff80d530c9 at netisr_dispatch_src+0xb9
Jun 27 02:57:43 www kernel: #15 0xffffffff80d37319 at ether_input+0x69
Jun 27 02:57:43 www kernel: #16 0xffffffff8092179d at re_rxeof+0x5cd
Jun 27 02:57:43 www kernel: #17 0xffffffff8091f003 at re_intr_msi+0xf3
Jun 27 02:57:43 www kernel: Uptime: 50d6h43m39s
Jun 27 02:57:43 www kernel: Dumping 1007 out of 16016 MB:..2%..12%..21%..31%..42%..51%..61%..72%..81%..91%---<<BOOT>>---

and then it booted again.

2024-05-20: ada0p2 - mysql - mysqldump backups

$ mysqldump -u user -p wikidb --set-gtid-purged=OFF > wikidb_backup_202405202152.sql
Enter password: 
mysqldump: Error: 'Access denied; you need (at least one of) the PROCESS privilege(s) for this operation' when trying to dump tablespaces

let me try with '--no-tablespaces':

$ mysqldump -u user -p wikidb --set-gtid-purged=OFF --no-tablespaces > wikidb_backup_202405202159.sql
Enter password: 

yes, that works.

2024-05-20: ada0p2 - mysql - in the end, I just restored a "fresh" mysql directory, started the server, created wiki db user and added neccessary grants, created the database. Then I restored it from a backup created with

$ mysqldump -u user -p wikidb > wikidb_backup.sql
Enter password: 
Warning: A partial dump from a server that has GTIDs will by default include the GTIDs of all transactions, even those that changed suppressed parts of the database. If you don't want to restore
GTIDs, pass --set-gtid-purged=OFF. To make a complete dump, pass --all-databases --triggers --routines --events. 

(user is just an example username). In retrospect, I should have used mysqldump -u user -p wikidb --set-gtid-purged=OFF > wikidb_backup.sql so I didn't need to edit the backup sql file. Restored with

$ mysql -u user -p wikidb < wikidb_backup.sql
Enter password: 

2024-05-20: ada0p2 - mysql - try mysql_upgrade

root@www# mysql_upgrade -u root -p
Enter password: 
Checking if update is needed.
This installation of MySQL is already upgraded to 5.7.38, use --force if you still need to run mysql_upgrade

ok, try with --force

root@www# mysql_upgrade -u root -p --force
Enter password: 
Checking server version.
Running queries to upgrade MySQL server.
mysql_upgrade: [ERROR] 1146: Table 'mysql.plugin' doesn't exist
mysql_upgrade: [ERROR] 1812: Tablespace is missing for table `mysql`.`servers`.
mysql_upgrade: [ERROR] 1146: Table 'mysql.help_topic' doesn't exist
mysql_upgrade: [ERROR] 1146: Table 'mysql.help_category' doesn't exist
mysql_upgrade: [ERROR] 1146: Table 'mysql.help_relation' doesn't exist
mysql_upgrade: [ERROR] 1146: Table 'mysql.help_keyword' doesn't exist
mysql_upgrade: [ERROR] 1146: Table 'mysql.time_zone_name' doesn't exist
mysql_upgrade: [ERROR] 1146: Table 'mysql.time_zone' doesn't exist
mysql_upgrade: [ERROR] 1146: Table 'mysql.time_zone_transition' doesn't exist
mysql_upgrade: [ERROR] 1146: Table 'mysql.time_zone_transition_type' doesn't exist
mysql_upgrade: [ERROR] 1812: Tablespace is missing for table `mysql`.`innodb_table_stats`.
mysql_upgrade: [ERROR] 1243: Unknown prepared statement handler (stmt) given to EXECUTE
mysql_upgrade: [ERROR] 1243: Unknown prepared statement handler (stmt) given to DEALLOCATE PREPARE
mysql_upgrade: [ERROR] 1812: Tablespace is missing for table `mysql`.`innodb_index_stats`.
mysql_upgrade: [ERROR] 1243: Unknown prepared statement handler (stmt) given to EXECUTE
mysql_upgrade: [ERROR] 1243: Unknown prepared statement handler (stmt) given to DEALLOCATE PREPARE
mysql_upgrade: [ERROR] 1146: Table 'mysql.slave_relay_log_info' doesn't exist
mysql_upgrade: [ERROR] 1243: Unknown prepared statement handler (stmt) given to EXECUTE
mysql_upgrade: [ERROR] 1243: Unknown prepared statement handler (stmt) given to DEALLOCATE PREPARE
mysql_upgrade: [ERROR] 1146: Table 'mysql.slave_master_info' doesn't exist
mysql_upgrade: [ERROR] 1243: Unknown prepared statement handler (stmt) given to EXECUTE
mysql_upgrade: [ERROR] 1243: Unknown prepared statement handler (stmt) given to DEALLOCATE PREPARE
mysql_upgrade: [ERROR] 1146: Table 'mysql.slave_worker_info' doesn't exist
mysql_upgrade: [ERROR] 1243: Unknown prepared statement handler (stmt) given to EXECUTE
mysql_upgrade: [ERROR] 1243: Unknown prepared statement handler (stmt) given to DEALLOCATE PREPARE
mysql_upgrade: [ERROR] 1146: Table 'mysql.gtid_executed' doesn't exist
mysql_upgrade: [ERROR] 1243: Unknown prepared statement handler (stmt) given to EXECUTE
mysql_upgrade: [ERROR] 1243: Unknown prepared statement handler (stmt) given to DEALLOCATE PREPARE
mysql_upgrade: [ERROR] 1812: Tablespace is missing for table `mysql`.`server_cost`.
mysql_upgrade: [ERROR] 1812: Tablespace is missing for table `mysql`.`server_cost`.
mysql_upgrade: [ERROR] 1146: Table 'mysql.engine_cost' doesn't exist
mysql_upgrade: [ERROR] 1146: Table 'mysql.engine_cost' doesn't exist
mysql_upgrade: [ERROR] 1146: Table 'mysql.plugin' doesn't exist
mysql_upgrade: [ERROR] 1812: Tablespace is missing for table `mysql`.`servers`.
mysql_upgrade: [ERROR] 1146: Table 'mysql.slave_master_info' doesn't exist
mysql_upgrade: [ERROR] 1146: Table 'mysql.slave_master_info' doesn't exist
mysql_upgrade: [ERROR] 1146: Table 'mysql.slave_master_info' doesn't exist
mysql_upgrade: [ERROR] 1146: Table 'mysql.slave_worker_info' doesn't exist
mysql_upgrade: [ERROR] 1146: Table 'mysql.slave_relay_log_info' doesn't exist
mysql_upgrade: [ERROR] 1146: Table 'mysql.gtid_executed' doesn't exist
mysql_upgrade: [ERROR] 1146: Table 'mysql.slave_master_info' doesn't exist
mysql_upgrade: [ERROR] 1146: Table 'mysql.slave_relay_log_info' doesn't exist
mysql_upgrade: [ERROR] 1146: Table 'mysql.slave_worker_info' doesn't exist
mysql_upgrade: [ERROR] 1146: Table 'mysql.slave_master_info' doesn't exist
mysql_upgrade: [ERROR] 1146: Table 'mysql.slave_master_info' doesn't exist
mysql_upgrade: [ERROR] 1812: Tablespace is missing for table `mysql`.`innodb_table_stats`.
mysql_upgrade: [ERROR] 1812: Tablespace is missing for table `mysql`.`innodb_index_stats`.
mysql_upgrade: [ERROR] 1146: Table 'mysql.help_category' doesn't exist
mysql_upgrade: [ERROR] 1146: Table 'mysql.help_topic' doesn't exist
mysql_upgrade: [ERROR] 1146: Table 'mysql.help_topic' doesn't exist
mysql_upgrade: [ERROR] 1146: Table 'mysql.help_category' doesn't exist
mysql_upgrade: [ERROR] 1146: Table 'mysql.help_relation' doesn't exist
mysql_upgrade: [ERROR] 1146: Table 'mysql.help_keyword' doesn't exist
mysql_upgrade: [ERROR] 1146: Table 'mysql.plugin' doesn't exist
mysql_upgrade: [ERROR] 1812: Tablespace is missing for table `mysql`.`servers`.
mysql_upgrade: [ERROR] 1146: Table 'mysql.time_zone' doesn't exist
mysql_upgrade: [ERROR] 1146: Table 'mysql.time_zone_name' doesn't exist
mysql_upgrade: [ERROR] 1146: Table 'mysql.time_zone_transition' doesn't exist
mysql_upgrade: [ERROR] 1146: Table 'mysql.time_zone_transition_type' doesn't exist
mysql_upgrade: [ERROR] 1812: Tablespace is missing for table `mysql`.`servers`.
mysql_upgrade: [ERROR] 1812: Tablespace is missing for table `mysql`.`innodb_table_stats`.
mysql_upgrade: [ERROR] 1812: Tablespace is missing for table `mysql`.`innodb_index_stats`.
Checking system database.
mysql.columns_priv                                 OK
mysql.db                                           OK
mysql.engine_cost
Error    : Table 'mysql.engine_cost' doesn't exist
status   : Operation failed
mysql.event                                        OK
mysql.func                                         OK
mysql.general_log                                  OK
mysql.gtid_executed
Error    : Table 'mysql.gtid_executed' doesn't exist
status   : Operation failed
mysql.help_category
Error    : Table 'mysql.help_category' doesn't exist
status   : Operation failed
mysql.help_keyword
Error    : Table 'mysql.help_keyword' doesn't exist
status   : Operation failed
mysql.help_relation
Error    : Table 'mysql.help_relation' doesn't exist
status   : Operation failed
mysql.help_topic
Error    : Table 'mysql.help_topic' doesn't exist
status   : Operation failed
mysql.innodb_index_stats
Warning  : InnoDB: Tablespace is missing for table mysql/innodb_index_stats.
Error    : Tablespace is missing for table `mysql`.`innodb_index_stats`.
error    : Corrupt
mysql.innodb_table_stats
Warning  : InnoDB: Tablespace is missing for table mysql/innodb_table_stats.
Error    : Tablespace is missing for table `mysql`.`innodb_table_stats`.
error    : Corrupt
mysql.ndb_binlog_index                             OK
mysql.plugin
Error    : Table 'mysql.plugin' doesn't exist
status   : Operation failed
mysql.proc                                         OK
mysql.procs_priv                                   OK
mysql.proxies_priv                                 OK
mysql.server_cost
Warning  : InnoDB: Tablespace is missing for table mysql/server_cost.
Error    : Tablespace is missing for table `mysql`.`server_cost`.
error    : Corrupt
mysql.servers
Warning  : InnoDB: Tablespace is missing for table mysql/servers.
Error    : Tablespace is missing for table `mysql`.`servers`.
error    : Corrupt
mysql.slave_master_info
Error    : Table 'mysql.slave_master_info' doesn't exist
status   : Operation failed
mysql.slave_relay_log_info
Error    : Table 'mysql.slave_relay_log_info' doesn't exist
status   : Operation failed
mysql.slave_worker_info
Error    : Table 'mysql.slave_worker_info' doesn't exist
status   : Operation failed
mysql.slow_log                                     OK
mysql.tables_priv                                  OK
mysql.time_zone
Error    : Table 'mysql.time_zone' doesn't exist
status   : Operation failed
mysql.time_zone_leap_second                        OK
mysql.time_zone_name
Error    : Table 'mysql.time_zone_name' doesn't exist
status   : Operation failed
mysql.time_zone_transition
Error    : Table 'mysql.time_zone_transition' doesn't exist
status   : Operation failed
mysql.time_zone_transition_type
Error    : Table 'mysql.time_zone_transition_type' doesn't exist
status   : Operation failed
mysql.user                                         OK

Repairing tables
mysql.engine_cost
Error    : Table 'mysql.engine_cost' doesn't exist
status   : Operation failed
mysql.gtid_executed
Error    : Table 'mysql.gtid_executed' doesn't exist
status   : Operation failed
mysql.help_category
Error    : Table 'mysql.help_category' doesn't exist
status   : Operation failed
mysql.help_keyword
Error    : Table 'mysql.help_keyword' doesn't exist
status   : Operation failed
mysql.help_relation
Error    : Table 'mysql.help_relation' doesn't exist
status   : Operation failed
mysql.help_topic
Error    : Table 'mysql.help_topic' doesn't exist
status   : Operation failed
mysql.innodb_index_stats
Warning  : InnoDB: Tablespace is missing for table mysql/innodb_index_stats.
Error    : Tablespace is missing for table `mysql`.`innodb_index_stats`.
error    : Corrupt
mysql.innodb_table_stats
Warning  : InnoDB: Tablespace is missing for table mysql/innodb_table_stats.
Error    : Tablespace is missing for table `mysql`.`innodb_table_stats`.
error    : Corrupt
mysql.plugin
Error    : Table 'mysql.plugin' doesn't exist
status   : Operation failed
mysql.server_cost
Warning  : InnoDB: Tablespace is missing for table mysql/server_cost.
Error    : Tablespace is missing for table `mysql`.`server_cost`.
error    : Corrupt
mysql.servers
Warning  : InnoDB: Tablespace is missing for table mysql/servers.
Error    : Tablespace is missing for table `mysql`.`servers`.
error    : Corrupt
mysql.slave_master_info
Error    : Table 'mysql.slave_master_info' doesn't exist
status   : Operation failed
mysql.slave_relay_log_info
Error    : Table 'mysql.slave_relay_log_info' doesn't exist
status   : Operation failed
mysql.slave_worker_info
Error    : Table 'mysql.slave_worker_info' doesn't exist
status   : Operation failed
mysql.time_zone
Error    : Table 'mysql.time_zone' doesn't exist
status   : Operation failed
mysql.time_zone_name
Error    : Table 'mysql.time_zone_name' doesn't exist
status   : Operation failed
mysql.time_zone_transition
Error    : Table 'mysql.time_zone_transition' doesn't exist
status   : Operation failed
mysql.time_zone_transition_type
Error    : Table 'mysql.time_zone_transition_type' doesn't exist
status   : Operation failed
The sys schema is already up to date (version 1.5.2).
Checking databases.
sys.sys_config
Error    : Table 'sys.sys_config' doesn't exist
status   : Operation failed
wikidb.actor                                       OK
wikidb.archive                                     OK
wikidb.bot_passwords                               OK
wikidb.category                                    OK
wikidb.categorylinks                               OK
wikidb.change_tag                                  OK
wikidb.change_tag_def                              OK
wikidb.comment                                     OK
wikidb.content                                     OK
wikidb.content_models                              OK
wikidb.cu_changes                                  OK
wikidb.cu_log                                      OK
wikidb.dymnorm                                     OK
wikidb.dympage                                     OK
wikidb.external_user                               OK
wikidb.externallinks                               OK
wikidb.filearchive                                 OK
wikidb.image                                       OK
wikidb.imagelinks                                  OK
wikidb.interwiki                                   OK
wikidb.ip_changes                                  OK
wikidb.ipblocks                                    OK
wikidb.ipblocks_restrictions                       OK
wikidb.iwlinks                                     OK
wikidb.job                                         OK
wikidb.l10n_cache                                  OK
wikidb.langlinks                                   OK
wikidb.linktarget                                  OK
wikidb.log_search                                  OK
wikidb.logging                                     OK
wikidb.math                                        OK
wikidb.metric                                      OK
wikidb.module_deps                                 OK
wikidb.objectcache                                 OK
wikidb.oldimage                                    OK
wikidb.online                                      OK
wikidb.online_chat                                 OK
wikidb.online_config                               OK
wikidb.page                                        OK
wikidb.page_props                                  OK
wikidb.page_restrictions                           OK
wikidb.pagelinks                                   OK
wikidb.protected_titles                            OK
wikidb.querycache                                  OK
wikidb.querycache_info                             OK
wikidb.querycachetwo                               OK
wikidb.recentchanges                               OK
wikidb.redirect                                    OK
wikidb.revision                                    OK
wikidb.revision_actor_temp                         OK
wikidb.revision_comment_temp                       OK
wikidb.searchindex                                 OK
wikidb.site_identifiers                            OK
wikidb.site_stats                                  OK
wikidb.sites                                       OK
wikidb.slot_roles                                  OK
wikidb.slots                                       OK
wikidb.templatelinks                               OK
wikidb.text                                        OK
wikidb.trackbacks                                  OK
wikidb.updatelog                                   OK
wikidb.uploadstash                                 OK
wikidb.user                                        OK
wikidb.user_former_groups                          OK
wikidb.user_groups                                 OK
wikidb.user_newtalk                                OK
wikidb.user_properties                             OK
wikidb.watchlist                                   OK
wikidb.watchlist_expiry                            OK

Repairing tables
mysql.engine_cost
Error    : Table 'mysql.engine_cost' doesn't exist
status   : Operation failed
mysql.gtid_executed
Error    : Table 'mysql.gtid_executed' doesn't exist
status   : Operation failed
mysql.help_category
Error    : Table 'mysql.help_category' doesn't exist
status   : Operation failed
mysql.help_keyword
Error    : Table 'mysql.help_keyword' doesn't exist
status   : Operation failed
mysql.help_relation
Error    : Table 'mysql.help_relation' doesn't exist
status   : Operation failed
mysql.help_topic
Error    : Table 'mysql.help_topic' doesn't exist
status   : Operation failed
mysql.innodb_index_stats
Warning  : InnoDB: Tablespace is missing for table mysql/innodb_index_stats.
Error    : Tablespace is missing for table `mysql`.`innodb_index_stats`.
error    : Corrupt
mysql.innodb_table_stats
Warning  : InnoDB: Tablespace is missing for table mysql/innodb_table_stats.
Error    : Tablespace is missing for table `mysql`.`innodb_table_stats`.
error    : Corrupt
mysql.plugin
Error    : Table 'mysql.plugin' doesn't exist
status   : Operation failed
mysql.server_cost
Warning  : InnoDB: Tablespace is missing for table mysql/server_cost.
Error    : Tablespace is missing for table `mysql`.`server_cost`.
error    : Corrupt
mysql.servers
Warning  : InnoDB: Tablespace is missing for table mysql/servers.
Error    : Tablespace is missing for table `mysql`.`servers`.
error    : Corrupt
mysql.slave_master_info
Error    : Table 'mysql.slave_master_info' doesn't exist
status   : Operation failed
mysql.slave_relay_log_info
Error    : Table 'mysql.slave_relay_log_info' doesn't exist
status   : Operation failed
mysql.slave_worker_info
Error    : Table 'mysql.slave_worker_info' doesn't exist
status   : Operation failed
mysql.time_zone
Error    : Table 'mysql.time_zone' doesn't exist
status   : Operation failed
mysql.time_zone_name
Error    : Table 'mysql.time_zone_name' doesn't exist
status   : Operation failed
mysql.time_zone_transition
Error    : Table 'mysql.time_zone_transition' doesn't exist
status   : Operation failed
mysql.time_zone_transition_type
Error    : Table 'mysql.time_zone_transition_type' doesn't exist
status   : Operation failed
sys.sys_config
Error    : Table 'sys.sys_config' doesn't exist
status   : Operation failed
Upgrade process completed successfully.
Checking if update is needed.

2024-05-20: ada0p2 - mysql - check with mysqlcheck

root@www# mysqlcheck -u root -p --all-databases
Enter password: 
mysql.columns_priv                                 OK
mysql.db                                           OK
mysql.engine_cost
Error    : Table 'mysql.engine_cost' doesn't exist
status   : Operation failed
mysql.event                                        OK
mysql.func                                         OK
mysql.general_log                                  OK
mysql.gtid_executed
Error    : Table 'mysql.gtid_executed' doesn't exist
status   : Operation failed
mysql.help_category
Error    : Table 'mysql.help_category' doesn't exist
status   : Operation failed
mysql.help_keyword
Error    : Table 'mysql.help_keyword' doesn't exist
status   : Operation failed
mysql.help_relation
Error    : Table 'mysql.help_relation' doesn't exist
status   : Operation failed
mysql.help_topic
Error    : Table 'mysql.help_topic' doesn't exist
status   : Operation failed
mysql.innodb_index_stats
Warning  : InnoDB: Tablespace is missing for table mysql/innodb_index_stats.
Error    : Tablespace is missing for table `mysql`.`innodb_index_stats`.
error    : Corrupt
mysql.innodb_table_stats
Warning  : InnoDB: Tablespace is missing for table mysql/innodb_table_stats.
Error    : Tablespace is missing for table `mysql`.`innodb_table_stats`.
error    : Corrupt
mysql.ndb_binlog_index                             OK
mysql.plugin
Error    : Table 'mysql.plugin' doesn't exist
status   : Operation failed
mysql.proc                                         OK
mysql.procs_priv                                   OK
mysql.proxies_priv                                 OK
mysql.server_cost
Warning  : InnoDB: Tablespace is missing for table mysql/server_cost.
Error    : Tablespace is missing for table `mysql`.`server_cost`.
error    : Corrupt
mysql.servers
Warning  : InnoDB: Tablespace is missing for table mysql/servers.
Error    : Tablespace is missing for table `mysql`.`servers`.
error    : Corrupt
mysql.slave_master_info
Error    : Table 'mysql.slave_master_info' doesn't exist
status   : Operation failed
mysql.slave_relay_log_info
Error    : Table 'mysql.slave_relay_log_info' doesn't exist
status   : Operation failed
mysql.slave_worker_info
Error    : Table 'mysql.slave_worker_info' doesn't exist
status   : Operation failed
mysql.slow_log                                     OK
mysql.tables_priv                                  OK
mysql.time_zone
Error    : Table 'mysql.time_zone' doesn't exist
status   : Operation failed
mysql.time_zone_leap_second                        OK
mysql.time_zone_name
Error    : Table 'mysql.time_zone_name' doesn't exist
status   : Operation failed
mysql.time_zone_transition
Error    : Table 'mysql.time_zone_transition' doesn't exist
status   : Operation failed
mysql.time_zone_transition_type
Error    : Table 'mysql.time_zone_transition_type' doesn't exist
status   : Operation failed
mysql.user                                         OK
sys.sys_config
Error    : Table 'sys.sys_config' doesn't exist
status   : Operation failed
wikidb.actor                                       OK
wikidb.archive                                     OK
wikidb.bot_passwords                               OK
wikidb.category                                    OK
wikidb.categorylinks                               OK
wikidb.change_tag                                  OK
wikidb.change_tag_def                              OK
wikidb.comment                                     OK
wikidb.content                                     OK
wikidb.content_models                              OK
wikidb.cu_changes                                  OK
wikidb.cu_log                                      OK
wikidb.dymnorm                                     OK
wikidb.dympage                                     OK
wikidb.external_user                               OK
wikidb.externallinks                               OK
wikidb.filearchive                                 OK
wikidb.image                                       OK
wikidb.imagelinks                                  OK
wikidb.interwiki                                   OK
wikidb.ip_changes                                  OK
wikidb.ipblocks                                    OK
wikidb.ipblocks_restrictions                       OK
wikidb.iwlinks                                     OK
wikidb.job                                         OK
wikidb.l10n_cache                                  OK
wikidb.langlinks                                   OK
wikidb.linktarget                                  OK
wikidb.log_search                                  OK
wikidb.logging                                     OK
wikidb.math                                        OK
wikidb.metric                                      OK
wikidb.module_deps                                 OK
wikidb.objectcache                                 OK
wikidb.oldimage                                    OK
wikidb.online                                      OK
wikidb.online_chat                                 OK
wikidb.online_config                               OK
wikidb.page                                        OK
wikidb.page_props                                  OK
wikidb.page_restrictions                           OK
wikidb.pagelinks                                   OK
wikidb.protected_titles                            OK
wikidb.querycache                                  OK
wikidb.querycache_info                             OK
wikidb.querycachetwo                               OK
wikidb.recentchanges                               OK
wikidb.redirect                                    OK
wikidb.revision                                    OK
wikidb.revision_actor_temp                         OK
wikidb.revision_comment_temp                       OK
wikidb.searchindex                                 OK
wikidb.site_identifiers                            OK
wikidb.site_stats                                  OK
wikidb.sites                                       OK
wikidb.slot_roles                                  OK
wikidb.slots                                       OK
wikidb.templatelinks                               OK
wikidb.text                                        OK
wikidb.trackbacks                                  OK
wikidb.updatelog                                   OK
wikidb.uploadstash                                 OK
wikidb.user                                        OK
wikidb.user_former_groups                          OK
wikidb.user_groups                                 OK
wikidb.user_newtalk                                OK
wikidb.user_properties                             OK
wikidb.watchlist                                   OK
wikidb.watchlist_expiry                            OK

2024-05-20: ada0p2 - mysql - doing a manual backup

$ mysqldump -u wikidb_user -p wikidb > wikidb_backup.sql
Enter password: 
Warning: A partial dump from a server that has GTIDs will by default include the GTIDs of all transactions, even those that changed suppressed parts of the database. If you don't want to restore GTIDs, pass --set-gtid-purged=OFF. To make a complete dump, pass --all-databases --triggers --routines --events. 

2022-11-30: ada0p2 - restarted the machine after a power outage, mysql wouldn't start. The error message in /var/db/mysql/www.ndwiki.org.err was

2022-11-30T22:08:11.993103Z 0 [Note] InnoDB: Highest supported file format is Barracuda.
2022-11-30T22:08:12.003256Z 0 [ERROR] InnoDB: Ignoring the redo log due to missing MLOG_CHECKPOINT between the checkpoint 362685108184 and the end 362685107712.
2022-11-30T22:08:12.003340Z 0 [ERROR] InnoDB: Plugin initialization aborted with error Generic error
2022-11-30T22:08:12.322948Z 0 [ERROR] Plugin 'InnoDB' init function returned error.
2022-11-30T22:08:12.323013Z 0 [ERROR] Plugin 'InnoDB' registration as a STORAGE ENGINE failed.
2022-11-30T22:08:12.323043Z 0 [ERROR] Failed to initialize builtin plugins.
2022-11-30T22:08:12.323065Z 0 [ERROR] Aborting

2022-11-30T22:08:12.323092Z 0 [Note] Binlog end
2022-11-30T22:08:12.323228Z 0 [Note] Shutting down plugin 'CSV'
2022-11-30T22:08:12.327396Z 0 [Note] /usr/local/libexec/mysqld: Shutdown complete

I removed (ok, renamed) ib_logfile0 and ib_logfile1, then restarted mysql. It works, but shows many errors in the log file

2022-11-30T23:27:22.713338Z 731 [ERROR] InnoDB: Page [page id: space=242, page number=13] log sequence number 339849315309 is in the future! Current system log sequence number 338255494511.
2022-11-30T23:27:22.713464Z 731 [ERROR] InnoDB: Your database may be corrupt or you may have copied the InnoDB tablespace but not the InnoDB log files. Please refer to http://dev.mysql.com/doc/refman/5.7/en/forcing-innodb-recovery.html for information about forcing recovery.
2022-11-30T23:31:40.922890Z 739 [ERROR] InnoDB: Page [page id: space=236, page number=74] log sequence number 345179832483 is in the future! Current system log sequence number 338255548591.
2022-11-30T23:31:40.922963Z 739 [ERROR] InnoDB: Your database may be corrupt or you may have copied the InnoDB tablespace but not the InnoDB log files. Please refer to http://dev.mysql.com/doc/refman/5.7/en/forcing-innodb-recovery.html for information about forcing recovery.
2022-11-30T23:31:40.925794Z 739 [ERROR] InnoDB: Page [page id: space=196, page number=18] log sequence number 338316034383 is in the future! Current system log sequence number 338255548591.
2022-11-30T23:31:40.925869Z 739 [ERROR] InnoDB: Your database may be corrupt or you may have copied the InnoDB tablespace but not the InnoDB log files. Please refer to http://dev.mysql.com/doc/refman/5.7/en/forcing-innodb-recovery.html for information about forcing recovery.
2022-11-30T23:32:49.571143Z 747 [ERROR] InnoDB: Page [page id: space=240, page number=64] log sequence number 338323902006 is in the future! Current system log sequence number 338255610748.
2022-11-30T23:32:49.571204Z 747 [ERROR] InnoDB: Your database may be corrupt or you may have copied the InnoDB tablespace but not the InnoDB log files. Please refer to http://dev.mysql.com/doc/refman/5.7/en/forcing-innodb-recovery.html for information about forcing recovery.
2022-11-30T23:32:49.571984Z 747 [ERROR] InnoDB: Page [page id: space=240, page number=68] log sequence number 338323902024 is in the future! Current system log sequence number 338255610748.
2022-11-30T23:32:49.572087Z 747 [ERROR] InnoDB: Your database may be corrupt or you may have copied the InnoDB tablespace but not the InnoDB log files. Please refer to http://dev.mysql.com/doc/refman/5.7/en/forcing-innodb-recovery.html for information about forcing recovery.
2022-11-30T23:33:47.418607Z 757 [ERROR] InnoDB: Page [page id: space=236, page number=30] log sequence number 338317490121 is in the future! Current system log sequence number 338255652386.
2022-11-30T23:33:47.418674Z 757 [ERROR] InnoDB: Your database may be corrupt or you may have copied the InnoDB tablespace but not the InnoDB log files. Please refer to http://dev.mysql.com/doc/refman/5.7/en/forcing-innodb-recovery.html for information about forcing recovery.
2022-11-30T23:33:47.644614Z 757 [ERROR] InnoDB: Page [page id: space=280, page number=10] log sequence number 338335102364 is in the future! Current system log sequence number 338255666007.
2022-11-30T23:33:47.644674Z 757 [ERROR] InnoDB: Your database may be corrupt or you may have copied the InnoDB tablespace but not the InnoDB log files. Please refer to http://dev.mysql.com/doc/refman/5.7/en/forcing-innodb-recovery.html for information about forcing recovery.
2022-11-30T23:33:47.765197Z 757 [ERROR] InnoDB: Page [page id: space=189, page number=119] log sequence number 338351690518 is in the future! Current system log sequence number 338255666007.
2022-11-30T23:33:47.765260Z 757 [ERROR] InnoDB: Your database may be corrupt or you may have copied the InnoDB tablespace but not the InnoDB log files. Please refer to http://dev.mysql.com/doc/refman/5.7/en/forcing-innodb-recovery.html for information about forcing recovery.
2022-11-30T23:35:52.806089Z 763 [ERROR] InnoDB: Page [page id: space=240, page number=33] log sequence number 338323904391 is in the future! Current system log sequence number 338255707206.
2022-11-30T23:35:52.806150Z 763 [ERROR] InnoDB: Your database may be corrupt or you may have copied the InnoDB tablespace but not the InnoDB log files. Please refer to http://dev.mysql.com/doc/refman/5.7/en/forcing-innodb-recovery.html for information about forcing recovery.
2022-11-30T23:35:52.807256Z 763 [ERROR] InnoDB: Page [page id: space=240, page number=37] log sequence number 338323905954 is in the future! Current system log sequence number 338255707206.
2022-11-30T23:35:52.807300Z 763 [ERROR] InnoDB: Your database may be corrupt or you may have copied the InnoDB tablespace but not the InnoDB log files. Please refer to http://dev.mysql.com/doc/refman/5.7/en/forcing-innodb-recovery.html for information about forcing recovery.
2022-11-30T23:35:52.808669Z 763 [ERROR] InnoDB: Page [page id: space=240, page number=7] log sequence number 338322788212 is in the future! Current system log sequence number 338255707206.
2022-11-30T23:35:52.808723Z 763 [ERROR] InnoDB: Your database may be corrupt or you may have copied the InnoDB tablespace but not the InnoDB log files. Please refer to http://dev.mysql.com/doc/refman/5.7/en/forcing-innodb-recovery.html for information about forcing recovery.
2022-11-30T23:35:52.809371Z 763 [ERROR] InnoDB: Page [page id: space=240, page number=65] log sequence number 338323900428 is in the future! Current system log sequence number 338255707206.
2022-11-30T23:35:52.809403Z 763 [ERROR] InnoDB: Your database may be corrupt or you may have copied the InnoDB tablespace but not the InnoDB log files. Please refer to http://dev.mysql.com/doc/refman/5.7/en/forcing-innodb-recovery.html for information about forcing recovery.
2022-11-30T23:37:50.695408Z 767 [ERROR] InnoDB: Page [page id: space=179, page number=38] log sequence number 338297978288 is in the future! Current system log sequence number 338255724903.
2022-11-30T23:37:50.695474Z 767 [ERROR] InnoDB: Your database may be corrupt or you may have copied the InnoDB tablespace but not the InnoDB log files. Please refer to http://dev.mysql.com/doc/refman/5.7/en/forcing-innodb-recovery.html for information about forcing recovery.
2022-11-30T23:39:44.466529Z 769 [ERROR] InnoDB: Page [page id: space=236, page number=27] log sequence number 338317490031 is in the future! Current system log sequence number 338255753645.
2022-11-30T23:39:44.466601Z 769 [ERROR] InnoDB: Your database may be corrupt or you may have copied the InnoDB tablespace but not the InnoDB log files. Please refer to http://dev.mysql.com/doc/refman/5.7/en/forcing-innodb-recovery.html for information about forcing recovery.
2022-11-30T23:39:45.189494Z 0 [ERROR] InnoDB: Tablespace for table `mysql`.`innodb_table_stats` is missing.
2022-11-30T23:39:45.189578Z 0 [Warning] InnoDB: Recalculation of persistent statistics requested for table `wikidb`.`objectcache` but the required persistent statistics storage is not present or is corrupted. Using transient stats instead.
2022-11-30T23:39:56.722256Z 771 [ERROR] InnoDB: Page [page id: space=274, page number=20] log sequence number 338334466935 is in the future! Current system log sequence number 338255789206.
2022-11-30T23:39:56.722318Z 771 [ERROR] InnoDB: Your database may be corrupt or you may have copied the InnoDB tablespace but not the InnoDB log files. Please refer to http://dev.mysql.com/doc/refman/5.7/en/forcing-innodb-recovery.html for information about forcing recovery.
2022-11-30T23:39:57.267300Z 771 [ERROR] InnoDB: Page [page id: space=274, page number=54] log sequence number 344178102906 is in the future! Current system log sequence number 338255806015.
2022-11-30T23:39:57.267362Z 771 [ERROR] InnoDB: Your database may be corrupt or you may have copied the InnoDB tablespace but not the InnoDB log files. Please refer to http://dev.mysql.com/doc/refman/5.7/en/forcing-innodb-recovery.html for information about forcing recovery.
2022-11-30T23:41:56.230928Z 777 [ERROR] InnoDB: Page [page id: space=236, page number=15] log sequence number 345589768157 is in the future! Current system log sequence number 338255833340.
2022-11-30T23:41:56.231000Z 777 [ERROR] InnoDB: Your database may be corrupt or you may have copied the InnoDB tablespace but not the InnoDB log files. Please refer to http://dev.mysql.com/doc/refman/5.7/en/forcing-innodb-recovery.html for information about forcing recovery.
2022-11-30T23:43:29.899085Z 781 [ERROR] InnoDB: Page [page id: space=240, page number=57] log sequence number 338323785292 is in the future! Current system log sequence number 338255878256.
2022-11-30T23:43:29.899146Z 781 [ERROR] InnoDB: Your database may be corrupt or you may have copied the InnoDB tablespace but not the InnoDB log files. Please refer to http://dev.mysql.com/doc/refman/5.7/en/forcing-innodb-recovery.html for information about forcing recovery.
2022-11-30T23:43:29.899831Z 781 [ERROR] InnoDB: Page [page id: space=240, page number=61] log sequence number 338323842997 is in the future! Current system log sequence number 338255878256.
2022-11-30T23:43:29.899864Z 781 [ERROR] InnoDB: Your database may be corrupt or you may have copied the InnoDB tablespace but not the InnoDB log files. Please refer to http://dev.mysql.com/doc/refman/5.7/en/forcing-innodb-recovery.html for information about forcing recovery.

so I should probably do a proper recovery real soon now.

2022-10-22: ada0p2 - certbot renewal - from weekly run output mail

Renewing Let's Encrypt certificates:
Saving debug log to /var/log/letsencrypt/letsencrypt.log

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Processing /usr/local/etc/letsencrypt/renewal/www.ndwiki.org.conf
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Unable to read ssl_module file; not disabling session tickets.
Renewing an existing certificate for ndwiki.org and www.ndwiki.org
Reloading apache server after certificate renewal

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Congratulations, all renewals succeeded: 
  /usr/local/etc/letsencrypt/live/www.ndwiki.org/fullchain.pem (success)
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Hook 'post-hook' ran with output:
 Performing sanity check on apache24 configuration:
 Performing sanity check on apache24 configuration:
 Performing a graceful restart
Hook 'post-hook' ran with error output:
 Syntax OK
 Syntax OK

-- End of weekly output --

let me check with certbot - yes certbot certificates show that the certificates got updated. And the wiki works, so apache got restarted correctly. Good.

2022-08-19: ada0p2 - certbot - renewals. I tested with

root@www# certbot renew --dry-run
Saving debug log to /var/log/letsencrypt/letsencrypt.log

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Processing /usr/local/etc/letsencrypt/renewal/www.ndwiki.org.conf
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Unable to read ssl_module file; not disabling session tickets.
Account registered.
Simulating renewal of an existing certificate for ndwiki.org and www.ndwiki.org

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Congratulations, all simulated renewals succeeded: 
  /usr/local/etc/letsencrypt/live/www.ndwiki.org/fullchain.pem (success)
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

good. Then I configureed in /etc/periodic.conf

weekly_certbot_enable="YES"
weekly_certbot_post_hook="service apache24 onereload"

Must be checked after a week to verify that it actually works.

2022-08-19: ada0p2 - certbot - I messed with it for a bit, then found an article that helped, reconfigured apache, and ran

root@www# certbot --apache -d ndwiki.org -d www.ndwiki.org
Saving debug log to /var/log/letsencrypt/letsencrypt.log
[..]
Successfully deployed certificate for ndwiki.org to /usr/local/etc/apache24/extra/httpd-vhosts-le-ssl.conf
Successfully deployed certificate for www.ndwiki.org to /usr/local/etc/apache24/extra/httpd-vhosts-le-ssl.conf
Added an HTTP->HTTPS rewrite in addition to other RewriteRules; you may wish to check for overall consistency.
[..]
NEXT STEPS:
- The certificate will need to be renewed before it expires. Certbot can automatically renew the certificate in the background, 

then I fixed up the apache configuration, and changed $wgServer in LocalSettings.php from 'http://' to 'https://'. 2022-08-19: ada0p2 - pkg - install certbot-apache, messages

Message from py39-certbot-1.27.0,1:

--
This port installs the "standalone" client only, which does not use and
is not the certbot-auto bootstrap/wrapper script.

The simplest form of usage to obtain certificates is:

 # sudo certbot certonly --standalone -d <domain>, [domain2, ... domainN]>

NOTE:

The client requires the ability to bind on TCP port 80 or 443 (depending
on the --preferred-challenges option used). If a server is running on that
port, it will need to be temporarily stopped so that the standalone server
can listen on that port to complete the challenge authentication process.

For more information on the 'standalone' mode, see:

  https://certbot.eff.org/docs/using.html#standalone

The certbot plugins to support apache and nginx certificate installation
will be made available in the following ports:

 * Apache plugin: security/py-certbot-apache
 * Nginx plugin: security/py-certbot-nginx

In order to automatically renew the certificates, add this line to
/etc/periodic.conf:

    weekly_certbot_enable="YES"

More config details in the certbot periodic script:

    /usr/local/etc/periodic/weekly/500.certbot-3.9

packages

Aug 19 15:45:39 www pkg[16619]: py39-setuptools-62.1.0_1 installed
Aug 19 15:45:39 www pkg[16619]: py39-pycparser-2.21 installed
Aug 19 15:45:39 www pkg[16619]: py39-cffi-1.15.0_1 installed
Aug 19 15:45:39 www pkg[16619]: py39-cryptography-3.4.8 installed
Aug 19 15:45:39 www pkg[16619]: py39-six-1.16.0 installed
Aug 19 15:45:39 www pkg[16619]: py39-openssl-20.0.1,1 installed
Aug 19 15:45:39 www pkg[16619]: py39-certifi-2022.5.18.1 installed
Aug 19 15:45:39 www pkg[16619]: py39-pysocks-1.7.1 installed
Aug 19 15:45:39 www pkg[16619]: py39-idna-3.3 installed
Aug 19 15:45:39 www pkg[16619]: py39-charset-normalizer-2.0.12 installed
Aug 19 15:45:40 www pkg[16619]: py39-urllib3-1.26.9,1 installed
Aug 19 15:45:40 www pkg[16619]: py39-requests-2.28.0 installed
Aug 19 15:45:40 www pkg[16619]: py39-pytz-2021.3,1 installed
Aug 19 15:45:40 www pkg[16619]: py39-requests-toolbelt-0.9.1_1 installed
Aug 19 15:45:40 www pkg[16619]: py39-zope.interface-5.3.0 installed
Aug 19 15:45:41 www pkg[16619]: py39-josepy-1.13.0 installed
Aug 19 15:45:41 www pkg[16619]: py39-pyrfc3339-1.1 installed
Aug 19 15:45:41 www pkg[16619]: py39-zope.event-4.1.0 installed
Aug 19 15:45:41 www pkg[16619]: py39-configobj-5.0.6_1 installed
Aug 19 15:45:41 www pkg[16619]: py39-zope.component-4.2.2 installed
Aug 19 15:45:41 www pkg[16619]: py39-parsedatetime-2.6 installed
Aug 19 15:45:41 www pkg[16619]: augeas-1.12.0_3 installed
Aug 19 15:45:41 www pkg[16619]: py39-configargparse-1.5.3 installed
Aug 19 15:45:41 www pkg[16619]: py39-distro-1.7.0 installed
Aug 19 15:45:41 www pkg[16619]: py39-acme-1.27.0,1 installed
Aug 19 15:45:42 www pkg[16619]: py39-certbot-1.27.0,1 installed
Aug 19 15:45:42 www pkg[16619]: py39-python-augeas-1.0.3 installed
Aug 19 15:45:42 www pkg[16619]: py39-certbot-apache-1.27.0 installed

2022-08-18: ada0p2 - mysql - the complete set of privileges needed for the wiki database user

grant select, update, insert, delete, usage on wikidb.* to '_user'@'localhost';
grant create, drop on wikidb.* to '_user'@'localhost';
grant alter on wikidb.* to '_user'@'localhost';
grant lock tables on wikidb.* to '_user'@'localhost';
grant index on wikidb.* to '_user'@'localhost';

(the name of the user here is just an example).

2022-08-18: ada0p2 - pkg - install mediawiki 1.38 again, and run the update script

root@www# php update.php
MediaWiki 1.38.2 Updater

Your composer.lock file is up to date with current dependencies!
Going to run database updates for wikidb
Depending on the size of your database this may take a while!
Abort with control-c in the next five seconds (skip this countdown with --quick) ...0
...collations up-to-date.
...have el_index_60 field in externallinks table.
...ug_user_group key doesn't exist.
...have ug_expiry field in user_groups table.
...img_media_type in table image already modified by patch patch-add-3d.sql.
...ip_changes table already exists.
...index PRIMARY already set on categorylinks table.
...index PRIMARY already set on templatelinks table.
...index PRIMARY already set on pagelinks table.
...index PRIMARY already set on text table.
...index PRIMARY already set on imagelinks table.
...index PRIMARY already set on iwlinks table.
...index PRIMARY already set on langlinks table.
...index PRIMARY already set on log_search table.
...index PRIMARY already set on module_deps table.
...index PRIMARY already set on objectcache table.
...index PRIMARY already set on querycache_info table.
...index PRIMARY already set on site_stats table.
...index PRIMARY already set on user_former_groups table.
...index PRIMARY already set on user_properties table.
...comment table already exists.
...revision_comment_temp table already exists.
...have ar_comment_id field in archive table.
...have fa_description_id field in filearchive table.
...img_description field does not exist in image table, skipping modify field patch.
...have ipb_reason_id field in ipblocks table.
...have log_comment_id field in logging table.
...have oi_description_id field in oldimage table.
...have pt_reason_id field in protected_titles table.
...have rc_comment_id field in recentchanges table.
...have img_description_id field in image table.
...index PRIMARY already set on l10n_cache table.
...bot_passwords.bp_user is already unsigned int.
...change_tag.ct_log_id is already unsigned int.
...change_tag.ct_rev_id is already unsigned int.
...user_newtalk.user_id is already unsigned int.
...user_properties.up_user is already unsigned int.
...change_tag.ct_rc_id is already unsigned int.
...slots table already exists.
...have slot_origin field in slots table.
...content table already exists.
...slot_roles table already exists.
...content_models table already exists.
...actor table already exists.
...revision_actor_temp table already exists.
...have ar_actor field in archive table.
...have ipb_by_actor field in ipblocks table.
...have img_actor field in image table.
...have oi_actor field in oldimage table.
...have fa_actor field in filearchive table.
...have rc_actor field in recentchanges table.
...have log_actor field in logging table.
...table site_stats already modified by patch patch-site_stats-modify.sql.
...index rc_namespace_title_timestamp already set on recentchanges table.
...change_tag_def table already exists.
Running maintenance/deduplicateArchiveRevId.php...
...Update 'DeduplicateArchiveRevId' already logged as completed. Use --force to run it again.
done.
...have ct_tag_id field in change_tag table.
...index ar_revid_uniq already set on archive table.
...index log_type_action already set on logging table.
...type_action key doesn't exist.
...index PRIMARY already set on interwiki table.
...index PRIMARY already set on page_props table.
...index PRIMARY already set on protected_titles table.
...index PRIMARY already set on site_identifiers table.
...index rc_this_oldid already set on recentchanges table.
...transcache doesn't exist.
Running maintenance/populateChangeTagDef.php...
...Update 'PopulateChangeTagDef' already logged as completed. Use --force to run it again.
done.
...change_tag_rc_tag key doesn't exist.
...have ipb_sitewide field in ipblocks table.
...ipblocks_restrictions table already exists.
...change_tag table does not contain ct_tag field.
...valid_tag doesn't exist.
...tag_summary doesn't exist.
...archive table does not contain ar_comment field.
...ipblocks table does not contain ipb_reason field.
...image table does not contain img_description field.
...oldimage table does not contain oi_description field.
...filearchive table does not contain fa_description field.
...recentchanges table does not contain rc_comment field.
...logging table does not contain log_comment field.
...protected_titles table does not contain pt_reason field.
...table job already modified by patch patch-job-params-mediumblob.sql.
...ar_usertext_timestamp key doesn't exist.
...usertext_timestamp key doesn't exist.
...archive table does not contain ar_user field.
...ipblocks table does not contain ip_by field.
...img_user_timestamp key doesn't exist.
...image table does not contain img_user field.
...oldimage table does not contain oi_user field.
...filearchive table does not contain fa_user field.
...recentchanges table does not contain rc_user field.
...logging table does not contain log_user field.
...index un_user_ip already set on user_newtalk table.
...watchlist_expiry table already exists.
...page_restrictions in table page already modified by patch patch-page_restrictions-null.sql.
...index ipb_address_unique already set on ipblocks table.
...have rev_actor field in revision table.
...archive table does not contain ar_text_id field.
...lc_lang is up-to-date.
...ll_lang is up-to-date.
...site_language is up-to-date.
...index ipb_address_unique on table ipblocks has no field ipb_anon_only; added.
...ipb_address_unique index up-to-date.
...actor_name in table actor already modified by patch patch-actor-actor_name-varbinary.sql.
...site_global_key in table sites already modified by patch patch-sites-site_global_key.sql.
...iwl_prefix in table iwlinks already modified by patch patch-extend-iwlinks-iwl_prefix.sql.
...rd_title in table redirect already modified by patch patch-redirect-rd_title-varbinary.sql.
...pl_title in table pagelinks already modified by patch patch-pagelinks-pl_title-varbinary.sql.
...tl_title in table templatelinks already modified by patch patch-templatelinks-tl_title-varbinary.sql.
...il_to in table imagelinks already modified by patch patch-imagelinks-il_to-varbinary.sql.
...ll_title in table langlinks already modified by patch patch-langlinks-ll_title-varbinary.sql.
...iwl_title in table iwlinks already modified by patch patch-iwlinks-iwl_title-varbinary.sql.
...cat_title in table category already modified by patch patch-category-cat_title-varbinary.sql.
...qc_title in table querycache already modified by patch patch-querycache-qc_title-varbinary.sql.
...qcc_title in table querycachetwo already modified by patch patch-querycachetwo-qcc_title-varbinary.sql.
...wl_title in table watchlist already modified by patch patch-watchlist-wl_title-varbinary.sql.
...user_last_timestamp in table user_newtalk already modified by patch patch-user_newtalk-user_last_timestamp-binary.sql.
...pt_title in table protected_titles already modified by patch patch-protected_titles-pt_title-varbinary.sql.
...ir_type in table ipblocks_restrictions already modified by patch patch-ipblocks_restrictions-ir_type.sql.
...index wl_namespace_title already set on watchlist table.
...job_title in table job already modified by patch patch-job-job_title-varbinary.sql.
...job_timestamp in table job already modified by patch patch-job_job_timestamp.sql.
...job_token_timestamp in table job already modified by patch patch-job_job_token_timestamp.sql.
...wl_notificationtimestamp in table watchlist already modified by patch patch-watchlist-wl_notificationtimestamp.sql.
...role_id in table slot_roles already modified by patch patch-slot_roles-role_id.sql.
...model_id in table content_models already modified by patch patch-content_models-model_id.sql.
...cl_to in table categorylinks already modified by patch patch-categorylinks-cl_to-varbinary.sql.
...log_title in table logging already modified by patch patch-logging-log_title-varbinary.sql.
...us_timestamp in table uploadstash already modified by patch patch-uploadstash-us_timestamp.sql.
...index up_property already set on user_properties table.
...index site_global_key already set on sites table.
...index log_type_time already set on logging table.
...fa_name in table filearchive already modified by patch patch-filearchive-fa_name.sql.
...oi_name in table oldimage already modified by patch patch-oldimage-oi_name-varbinary.sql.
...exptime in table objectcache already modified by patch patch-objectcache-exptime-notnull.sql.
...index ar_name_title_timestamp already set on archive table.
...img_name in table image already modified by patch patch-image-img_name-varbinary.sql.
...img_timestamp in table image already modified by patch patch-image-img_timestamp.sql.
...index si_key already set on site_identifiers table.
...rc_title in table recentchanges already modified by patch patch-recentchanges-rc_title-varbinary.sql.
...rc_timestamp in table recentchanges already modified by patch patch-recentchanges-rc_timestamp.sql.
...rc_id in table recentchanges already modified by patch patch-recentchanges-rc_id.sql.
...index rc_new_name_timestamp already set on recentchanges table.
...ar_title in table archive already modified by patch patch-archive-ar_title-varbinary.sql.
...page_title in table page already modified by patch patch-page-page_title-varbinary.sql.
...user_name in table user already modified by patch patch-user_table-updates.sql.
...index rev_page_timestamp already set on revision table.
...have modtoken field in objectcache table.
...index oi_timestamp already set on oldimage table.
...index page_name_title already set on page table.
...index ct_rc_tag_id already set on change_tag table.
...page_restrictions table does not contain pr_user field.
...fa_id in table filearchive already modified by patch patch-filearchive-fa_id.sql.
...img_major_mime in table image already modified by patch patch-image-img_major_mime-default.sql.
...linktarget table already exists.
...rev_page_id key doesn't exist.
...pr_page in table page_restrictions already modified by patch patch-page_restrictions-pr_page.sql.
...pp_page in table page_props already modified by patch patch-page_props-pp_page.sql.
...ir_value in table ipblocks_restrictions already modified by patch patch-ipblocks_restrictions-ir_value.sql.
...have tl_target_id field in templatelinks table.
...site_stats is populated...done.
...Update 'populate rev_len and ar_len' already logged as completed. Use --force to run it again.
...Update 'populate rev_sha1' already logged as completed. Use --force to run it again.
...img_sha1 column of image table already populated.
...protocol-relative URLs in externallinks table already fixed.
...fa_sha1 column of filearchive table already populated.
...*_from_namespace column of backlink tables already populated.
...Update 'FixDefaultJsonContentPages' already logged as completed. Use --force to run it again.
...Update 'cleanup empty categories' already logged as completed. Use --force to run it again.
...RFC and PMID already added to interwiki database table.
...Update 'populate pp_sortkey' already logged as completed. Use --force to run it again.
...Update 'populate ip_changes' already logged as completed. Use --force to run it again.
...externallinks table indexes up to date
Set the local repo temp zone container to be private.
Purging caches...done.

Done in 0.5 s.

(I got a ssh disconnect the first time, so I had to re-run it). Anyway, the wiki works now. some of the extensions needs to be updated. 2022-08-18: ada0p2 - mediawiki 1.35 update

root@www# php update.php
MediaWiki 1.35.7 Updater

Your composer.lock file is up to date with current dependencies!
Going to run database updates for wikidb
Depending on the size of your database this may take a while!
Abort with control-c in the next five seconds (skip this countdown with --quick) ... 0
...have ipb_id field in ipblocks table.
...have ipb_expiry field in ipblocks table.
...already have interwiki table
...indexes seem up to 20031107 standards.
...have rc_type field in recentchanges table.
...index new_name_timestamp already set on recentchanges table.
...have user_real_name field in user table.
...querycache table already exists.
...objectcache table already exists.
...categorylinks table already exists.
...have pagelinks; skipping old links table updates
...il_from OK
...have rc_ip field in recentchanges table.
...index PRIMARY already set on image table.
...have rc_id field in recentchanges table.
...have rc_patrolled field in recentchanges table.
...logging table already exists.
...have user_token field in user table.
...have wl_notificationtimestamp field in watchlist table.
...watchlist talk page rows already present.
...user table does not contain user_emailauthenticationtimestamp field.
...page table already exists.
...have log_params field in logging table.
...logging table has correct log_title encoding.
...have ar_rev_id field in archive table.
...have page_len field in page table.
...revision table does not contain inverse_timestamp field.
...have rev_text_id field in revision table.
...have rev_deleted field in revision table.
...have img_width field in image table.
...have img_metadata field in image table.
...have user_email_token field in user table.
...have ar_text_id field in archive table.
...page_namespace is already a full int (int(11)).
...ar_namespace is already a full int (int(11)).
...rc_namespace is already a full int (int(11)).
...wl_namespace is already a full int (int(11)).
...qc_namespace is already a full int (int(11)).
...log_namespace is already a full int (int(11)).
...have img_media_type field in image table.
...already have pagelinks table.
...image table does not contain img_type field.
...already have unique user_name index.
...user_groups table exists and is in current format.
...have ss_total_pages field in site_stats table.
...user_newtalk table already exists.
...have iw_trans field in interwiki table.
...wl_notificationtimestamp is already nullable.
...index times already set on logging table.
...have ipb_range_start field in ipblocks table.
...no page_random rows needed to be set
...have user_registration field in user table.
...templatelinks table already exists
...externallinks table already exists.
...job table already exists.
...have ss_images field in site_stats table.
...langlinks table already exists.
...querycache_info table already exists.
...filearchive table already exists.
...have ipb_anon_only field in ipblocks table.
...index rc_ns_usertext already set on recentchanges table.
...index rc_user_text already set on recentchanges table.
...have user_newpass_time field in user table.
...redirect table already exists.
...querycachetwo table already exists.
...have ipb_enable_autoblock field in ipblocks table.
...index pl_namespace on table pagelinks includes field pl_from.
...index tl_namespace on table templatelinks includes field tl_from.
...index il_to on table imagelinks includes field il_from.
...have rc_old_len field in recentchanges table.
...have user_editcount field in user table.
...page_restrictions table already exists.
...have log_id field in logging table.
...have rev_parent_id field in revision table.
...have pr_id field in page_restrictions table.
...have rev_len field in revision table.
...have rc_deleted field in recentchanges table.
...have log_deleted field in logging table.
...have ar_deleted field in archive table.
...have ipb_deleted field in ipblocks table.
...have fa_deleted field in filearchive table.
...have ar_len field in archive table.
...have ipb_block_email field in ipblocks table.
...index cl_sortkey on table categorylinks includes field cl_from.
...have oi_metadata field in oldimage table.
...index usertext_timestamp already set on archive table.
...index img_usertext_timestamp already set on image table.
...index oi_usertext_timestamp already set on oldimage table.
...have ar_page_id field in archive table.
...have img_sha1 field in image table.
...protected_titles table already exists.
...have ipb_by_text field in ipblocks table.
...page_props table already exists.
...updatelog table already exists.
...category table already exists.
...category table already populated.
...have ar_parent_id field in archive table.
...have user_last_timestamp field in user_newtalk table.
...protected_titles table has correct pt_title encoding.
...have ss_active_users field in site_stats table.
...ss_active_users user count set...
...have ipb_allow_usertalk field in ipblocks table.
...change_tag table already exists.
...user_properties table already exists.
...log_search table already exists.
...have log_user_text field in logging table.
...l10n_cache table already exists.
...ct_rc_id key doesn't exist.
...have rd_interwiki field in redirect table.
...*_mime_minor fields are already long enough.
...iwlinks table already exists.
...index iwl_prefix_title_from already set on iwlinks table.
...have ul_value field in updatelog table.
...have iw_api field in interwiki table.
...iwl_prefix key doesn't exist.
...have cl_collation field in categorylinks table.
...categorylinks up-to-date.
...module_deps table already exists.
...ar_page_revid key doesn't exist.
...skipping index ar_revid because index ar_revid already set on archive table.
...user_last_timestamp is already nullable.
...index user_email already set on user table.
...up_property in table user_properties already modified by patch patch-up_property.sql.
...uploadstash table already exists.
...user_former_groups table already exists.
...have rev_sha1 field in revision table.
...batch conversion of user_options: nothing to migrate. done.
...user table does not contain user_options field.
...have ar_sha1 field in archive table.
...index page_redirect_namespace_len already set on page table.
...have us_chunk_inx field in uploadstash table.
...have job_timestamp field in job table.
...index page_user_timestamp already set on revision table.
...have ipb_parent_block_id field in ipblocks table.
...index ipb_parent_block_id already set on ipblocks table.
...category table does not contain cat_hidden field.
...have rev_content_format field in revision table.
...have rev_content_model field in revision table.
...have ar_content_format field in archive table.
...have ar_content_model field in archive table.
...have page_content_model field in page table.
...site_stats table does not contain ss_admins field.
...recentchanges table does not contain rc_moved_to_title field.
...sites table already exists.
...have fa_sha1 field in filearchive table.
...have job_token field in job table.
...have job_attempts field in job table.
...have us_props field in uploadstash table.
...ug_group in table user_groups already modified by patch patch-ug_group-length-increase-255.sql.
...ufg_group in table user_former_groups already modified by patch patch-ufg_group-length-increase-255.sql.
...index pp_propname_page already set on page_props table.
...index img_media_mime already set on image table.
...iwl_prefix_title_from index is already non-UNIQUE.
...index iwl_prefix_from_title already set on iwlinks table.
...have ar_id field in archive table.
...have el_id field in externallinks table.
...have rc_source field in recentchanges table.
...index log_user_text_type_time already set on logging table.
...index log_user_text_time already set on logging table.
...have page_links_updated field in page table.
...have user_password_expires field in user table.
...have pp_sortkey field in page_props table.
...recentchanges table does not contain rc_cur_time field.
...index wl_user_notificationtimestamp already set on watchlist table.
...have page_lang field in page table.
...have pl_from_namespace field in pagelinks table.
...have tl_from_namespace field in templatelinks table.
...have il_from_namespace field in imagelinks table.
...img_major_mime in table image already modified by patch patch-img_major_mime-chemical.sql.
...oi_major_mime in table oldimage already modified by patch patch-oi_major_mime-chemical.sql.
...fa_major_mime in table filearchive already modified by patch patch-fa_major_mime-chemical.sql.
...comment fields are up to date.
...hitcounter doesn't exist.
...site_stats table does not contain ss_total_views field.
...page table does not contain page_counter field.
...msg_resource_links doesn't exist.
...msg_resource doesn't exist.
...bot_passwords table already exists.
...have wl_id field in watchlist table.
Dropping cl_collation index from table categorylinks ...done.
Adding index cl_collation_ext to table categorylinks ...done.
...collations up-to-date.
Adding index rc_name_type_patrolled_timestamp to table recentchanges ...done.
...rev_page_id index not found on revision.
Making pl_namespace, tl_namespace and il_to indices non-UNIQUE ...done.
Adding ct_id field to table change_tag ...done.
Modifying rc_ip field of table recentchanges ...done.
...index usertext_timestamp already set on archive table.
Adding el_index_60 field to table externallinks ...done.
...ug_user_group key doesn't exist.
Adding ug_expiry field to table user_groups ...done.
Adding index img_user_timestamp to table image ...done.
Modifying img_media_type field of table image ...done.
Creating ip_changes table ...done.
Renaming index cl_from into PRIMARY to table categorylinks ...done.
Renaming index tl_from into PRIMARY to table templatelinks ...done.
Renaming index pl_from into PRIMARY to table pagelinks ...done.
...index PRIMARY already set on text table.
Renaming index il_from into PRIMARY to table imagelinks ...done.
Renaming index iwl_from into PRIMARY to table iwlinks ...done.
Renaming index ll_from into PRIMARY to table langlinks ...done.
Renaming index ls_field_val into PRIMARY to table log_search ...done.
Renaming index md_module_skin into PRIMARY to table module_deps ...done.
Renaming index keyname into PRIMARY to table objectcache ...done.
Renaming index qci_type into PRIMARY to table querycache_info ...done.
Renaming index ss_row_id into PRIMARY to table site_stats ...done.
Renaming index ufg_user_group into PRIMARY to table user_former_groups ...done.
Renaming index user_properties_user_property into PRIMARY to table user_properties ...done.
Creating comment table ...done.
Creating revision_comment_temp table ...done.
Adding ar_comment_id field to table archive ...done.
Adding fa_description_id field to table filearchive ...done.
Modifying img_description field of table image ...done.
Adding ipb_reason_id field to table ipblocks ...done.
Adding log_comment_id field to table logging ...done.
Adding oi_description_id field to table oldimage ...done.
Adding pt_reason_id field to table protected_titles ...done.
Adding rc_comment_id field to table recentchanges ...done.
Modifying rev_comment field of table revision ...done.
Adding img_description_id field to table image ...done.
Migrating comments to the 'comments' table, printing progress markers. For large
databases, you may want to hit Ctrl-C and do this manually with
maintenance/migrateComments.php.
Beginning migration of revision.rev_comment to revision_comment_temp.revcomment_comment_id
... 112
... 216
... 322
... 424
... 524
... 625
... 726
... 828
... 931
... 1031
... 1131
... 1232
... 1332
... 1432
... 1534
... 1636
... 1738
... 1856
... 1956
... 2059
... 2159
... 2259
... 2359
... 2459
... 2559
... 2659
... 2759
... 2859
... 2959
... 3059
... 3159
... 3260
... 3360
... 3461
... 3562
... 3662
... 3762
... 3863
... 3964
... 4069
... 4175
... 4275
... 4375
... 4475
... 4575
... 4675
... 4775
... 4875
... 4975
... 5075
... 5175
... 5275
... 5375
... 5475
... 5575
... 5675
... 5775
... 5875
... 5975
... 6075
... 6175
... 6275
... 6375
... 6475
... 6575
... 6675
... 6723
Completed migration, updated 6648 row(s) with 5252 new comment(s)
Beginning migration of archive.ar_comment to archive.ar_comment_id
... 77
Completed migration, updated 75 row(s) with 42 new comment(s)
Beginning migration of ipblocks.ipb_reason to ipblocks.ipb_reason_id
... 19
Completed migration, updated 13 row(s) with 3 new comment(s)
Beginning migration of image.img_description to image.img_description_id
... 3009_nd100_local_io.jpg
... Disk_Media_Maint_1988-09-30.jpg
... ND-100.843-back_side.jpg
... ND110.zip
... NORD-1_card_135-s.jpg
... Nd246_keyboard_1_IMG_20210326_155446988.jpg
... TDV2200_9_inside_back_and_top_cover_off_IMG_20210315_193816713.jpg
... Tdv2200_9_s_EPROM_U63.jpg
... Yes_check.svg
Completed migration, updated 868 row(s) with 20 new comment(s)
Beginning migration of oldimage.oi_description to oldimage.oi_description_id
... Yes_check.svg 20081021222306
Completed migration, updated 37 row(s) with 4 new comment(s)
Beginning migration of filearchive.fa_deleted_reason to filearchive.fa_deleted_reason_id
... 13
Completed migration, updated 13 row(s) with 9 new comment(s)
Beginning migration of filearchive.fa_description to filearchive.fa_description_id
... 13
Completed migration, updated 13 row(s) with 0 new comment(s)
Beginning migration of recentchanges.rc_comment to recentchanges.rc_comment_id
... 6833
Completed migration, updated 13 row(s) with 0 new comment(s)
Beginning migration of logging.log_comment to logging.log_comment_id
... 100
... 200
... 300
... 400
... 500
... 600
... 700
... 800
... 900
... 1000
... 1100
... 1200
... 1300
... 1400
... 1500
... 1600
... 1700
... 1800
... 1900
... 2000
... 2100
... 2200
... 2300
... 2400
... 2500
... 2600
... 2700
... 2800
... 2900
... 3000
... 3100
... 3200
... 3300
... 3400
... 3500
... 3600
... 3700
... 3800
... 3900
... 4000
... 4100
... 4200
... 4300
... 4400
... 4500
... 4600
... 4615
Completed migration, updated 4615 row(s) with 65 new comment(s)
Beginning migration of protected_titles.pt_reason to protected_titles.pt_reason_id
Completed migration, updated 0 row(s) with 0 new comment(s)
done.
Renaming index lc_lang_key into PRIMARY to table l10n_cache ...done.
Making bot_passwords.bp_user into an unsigned int ...done.
Making change_tag.ct_log_id into an unsigned int ...done.
Making change_tag.ct_rev_id into an unsigned int ...done.
Making page_restrictions.pr_user into an unsigned int ...done.
...user_newtalk.user_id is already unsigned int.
Making user_properties.up_user into an unsigned int ...done.
Creating slots table ...done.
...have slot_origin field in slots table.
Creating content table ...done.
Creating slot_roles table ...done.
Creating content_models table ...done.
Migrating archive ar_text to modern storage.
Migrating ar_text to modern storage...
Completed ar_text migration, 0 rows updated, 0 missing data.
Dropping ar_text and ar_flags columns ...done.
Creating actor table ...done.
Creating revision_actor_temp table ...done.
Adding ar_actor field to table archive ...done.
Adding ipb_by_actor field to table ipblocks ...done.
Adding img_actor field to table image ...done.
Adding oi_actor field to table oldimage ...done.
Adding fa_actor field to table filearchive ...done.
Adding rc_actor field to table recentchanges ...done.
Adding log_actor field to table logging ...done.
Migrating actors to the 'actor' table, printing progress markers. For large
databases, you may want to hit Ctrl-C and do this manually with
maintenance/migrateActors.php.
Creating actor entries for all registered users
... 1 - 71
Completed actor creation, added 71 new actor(s)
Beginning migration of revision.rev_user and revision.rev_user_text to revision_actor_temp.revactor_actor
... rev_id=112
... rev_id=216
... rev_id=322
... rev_id=424
... rev_id=524
... rev_id=625
... rev_id=726
... rev_id=828
... rev_id=931
... rev_id=1031
... rev_id=1131
... rev_id=1232
... rev_id=1332
... rev_id=1432
... rev_id=1534
... rev_id=1636
... rev_id=1738
... rev_id=1856
... rev_id=1956
... rev_id=2059
... rev_id=2159
... rev_id=2259
... rev_id=2359
... rev_id=2459
... rev_id=2559
... rev_id=2659
... rev_id=2759
... rev_id=2859
... rev_id=2959
... rev_id=3059
... rev_id=3159
... rev_id=3260
... rev_id=3360
... rev_id=3461
... rev_id=3562
... rev_id=3662
... rev_id=3762
... rev_id=3863
... rev_id=3964
... rev_id=4069
... rev_id=4175
... rev_id=4275
... rev_id=4375
... rev_id=4475
... rev_id=4575
... rev_id=4675
... rev_id=4775
... rev_id=4875
... rev_id=4975
... rev_id=5075
... rev_id=5175
... rev_id=5275
... rev_id=5375
... rev_id=5475
... rev_id=5575
... rev_id=5675
... rev_id=5775
... rev_id=5875
... rev_id=5975
... rev_id=6075
... rev_id=6175
... rev_id=6275
... rev_id=6375
... rev_id=6475
... rev_id=6575
... rev_id=6675
... rev_id=6723
Completed migration, updated 6648 row(s) with 1 new actor(s), 0 error(s)
Beginning migration of archive.ar_user and archive.ar_user_text to archive.ar_actor
... ar_id=77
Completed migration, updated 75 row(s) with 0 new actor(s), 0 error(s)
Beginning migration of ipblocks.ipb_by and ipblocks.ipb_by_text to ipblocks.ipb_by_actor
... ipb_id=19
Completed migration, updated 13 row(s) with 0 new actor(s), 0 error(s)
Beginning migration of image.img_user and image.img_user_text to image.img_actor
... img_name=3009_nd100_local_io.jpg
... img_name=Disk_Media_Maint_1988-09-30.jpg
... img_name=ND-100.843-back_side.jpg
... img_name=ND110.zip
... img_name=NORD-1_card_135-s.jpg
... img_name=Nd246_keyboard_1_IMG_20210326_155446988.jpg
... img_name=TDV2200_9_inside_back_and_top_cover_off_IMG_20210315_193816713.jpg
... img_name=Tdv2200_9_s_EPROM_U63.jpg
... img_name=Yes_check.svg
Completed migration, updated 868 row(s) with 0 new actor(s), 0 error(s)
Beginning migration of oldimage.oi_user and oldimage.oi_user_text to oldimage.oi_actor
... oi_name=Yes_check.svg oi_timestamp=20081021222306
Completed migration, updated 37 row(s) with 0 new actor(s), 0 error(s)
Beginning migration of filearchive.fa_user and filearchive.fa_user_text to filearchive.fa_actor
... fa_id=13
Completed migration, updated 13 row(s) with 0 new actor(s), 0 error(s)
Beginning migration of recentchanges.rc_user and recentchanges.rc_user_text to recentchanges.rc_actor
... rc_id=6833
Completed migration, updated 13 row(s) with 0 new actor(s), 0 error(s)
Beginning migration of logging.log_user and logging.log_user_text to logging.log_actor
... log_id=100
... log_id=200
... log_id=300
... log_id=400
... log_id=500
... log_id=600
... log_id=700
... log_id=800
... log_id=900
... log_id=1000
... log_id=1100
... log_id=1200
... log_id=1300
... log_id=1400
... log_id=1500
... log_id=1600
... log_id=1700
... log_id=1800
... log_id=1900
... log_id=2000
... log_id=2100
... log_id=2200
... log_id=2300
... log_id=2400
... log_id=2500
... log_id=2600
... log_id=2700
... log_id=2800
... log_id=2900
... log_id=3000
... log_id=3100
... log_id=3200
... log_id=3300
... log_id=3400
... log_id=3500
... log_id=3600
... log_id=3700
... log_id=3800
... log_id=3900
... log_id=4000
... log_id=4100
... log_id=4200
... log_id=4300
... log_id=4400
... log_id=4500
... log_id=4600
... log_id=4615
Completed migration, updated 4615 row(s) with 0 new actor(s), 0 error(s)
Beginning migration of log_search
Completed migration, inserted 0 row(s) with 0 new actor(s), 0 error(s)
done.
Modifying rev_text_id field of table revision ...done.
Modifying table site_stats ...done.
Populating ar_rev_id.
Populating ar_rev_id...
Completed ar_rev_id population, 0 rows updated.
Making ar_rev_id not nullable ...done.
Adding index rc_namespace_title_timestamp to table recentchanges ...done.
Creating change_tag_def table ...done.
Populating el_index_60 field, printing progress markers. For large
databases, you may want to hit Ctrl-C and do this manually with
maintenance/populateExternallinksIndex60.php.
Populating externallinks.el_index_60...
el_id 0 - 200 of 2403
el_id 200 - 400 of 2403
el_id 400 - 600 of 2403
el_id 600 - 800 of 2403
el_id 800 - 1000 of 2403
el_id 1000 - 1200 of 2403
el_id 1200 - 1400 of 2403
el_id 1400 - 1600 of 2403
el_id 1600 - 1800 of 2403
el_id 1800 - 2000 of 2403
el_id 2000 - 2200 of 2403
el_id 2200 - 2400 of 2403
el_id 2400 - 2600 of 2403
Done, 2342 rows updated.
done.
Modifying el_index_60 field of table externallinks ...done.
Running maintenance/deduplicateArchiveRevId.php...
Deduplicating ar_rev_id...
Row 37 conflicts with revision row for rev_id 1673, reassigning
Row 38 conflicts with revision row for rev_id 1674, reassigning
... 9-4136
Finished deduplicating ar_rev_id. 0 rows deleted, 2 assigned new IDs.
done.
Adding ct_tag_id field to table change_tag ...done.
Adding index ar_revid_uniq to table archive ...done.
Migrating revision data to the MCR 'slot' and 'content' tables, printing progress markers.
For large databases, you may want to hit Ctrl-C and do this manually with
maintenance/populateContentTables.php.
Populating revision...
... revision processed up to revision id 500 of 6723 (476 rows in 1.05863904953 seconds)
... revision processed up to revision id 1000 of 6723 (969 rows in 2.2936339378357 seconds)
... revision processed up to revision id 1500 of 6723 (1468 rows in 3.5361518859863 seconds)
... revision processed up to revision id 2000 of 6723 (1944 rows in 4.6322391033173 seconds)
... revision processed up to revision id 2500 of 6723 (2441 rows in 5.4795908927917 seconds)
... revision processed up to revision id 3000 of 6723 (2941 rows in 5.6425759792328 seconds)
... revision processed up to revision id 3500 of 6723 (3438 rows in 5.8021569252014 seconds)
... revision processed up to revision id 4000 of 6723 (3936 rows in 5.9682450294495 seconds)
... revision processed up to revision id 4500 of 6723 (4425 rows in 6.1259860992432 seconds)
... revision processed up to revision id 5000 of 6723 (4925 rows in 6.2875409126282 seconds)
... revision processed up to revision id 5500 of 6723 (5425 rows in 6.4554059505463 seconds)
... revision processed up to revision id 6000 of 6723 (5925 rows in 6.6151750087738 seconds)
... revision processed up to revision id 6500 of 6723 (6425 rows in 6.7829020023346 seconds)
... revision processed up to revision id 6723 of 6723 (6648 rows in 6.8601369857788 seconds)
Done populating revision table. Processed 6648 rows in 6.8602089881897 seconds
Populating archive...
... archive processed up to revision id 508 of 6727 (22 rows in 0.05457615852356 seconds)
... archive processed up to revision id 1008 of 6727 (29 rows in 0.075898170471191 seconds)
... archive processed up to revision id 1508 of 6727 (32 rows in 0.091788053512573 seconds)
... archive processed up to revision id 2008 of 6727 (57 rows in 0.16466808319092 seconds)
... archive processed up to revision id 2508 of 6727 (57 rows in 0.16599822044373 seconds)
... archive processed up to revision id 3008 of 6727 (57 rows in 0.16702318191528 seconds)
... archive processed up to revision id 3508 of 6727 (60 rows in 0.1760241985321 seconds)
... archive processed up to revision id 4008 of 6727 (62 rows in 0.18403005599976 seconds)
... archive processed up to revision id 4508 of 6727 (73 rows in 0.19349002838135 seconds)
... archive processed up to revision id 5008 of 6727 (73 rows in 0.19481110572815 seconds)
... archive processed up to revision id 5508 of 6727 (73 rows in 0.19583702087402 seconds)
... archive processed up to revision id 6008 of 6727 (73 rows in 0.19691514968872 seconds)
... archive processed up to revision id 6508 of 6727 (73 rows in 0.19788217544556 seconds)
... archive processed up to revision id 6727 of 6727 (75 rows in 0.2083101272583 seconds)
Done populating archive table. Processed 75 rows in 0.20837020874023 seconds
Done. Processed 6723 rows in 7.0772159099579 seconds
done.
Adding index log_type_action to table logging ...done.
Dropping type_action index from table logging ...done.
Renaming index iw_prefix into PRIMARY to table interwiki ...done.
...index PRIMARY already set on page_props table.
...index PRIMARY already set on protected_titles table.
Renaming index site_ids_type into PRIMARY to table site_identifiers ...done.
Adding index rc_this_oldid to table recentchanges ...done.
Dropping table transcache ...done.
Running maintenance/populateChangeTagDef.php...
No user defined tags to set, moving on...
done.
Adding index change_tag_rc_tag_id to table change_tag ...done.
Adding ipb_sitewide field to table ipblocks ...done.
Creating ipblocks_restrictions table ...done.
Table change_tag contains ct_tag field. Dropping ...done.
Dropping table valid_tag ...done.
Dropping table tag_summary ...done.
Table archive contains ar_comment field. Dropping ...done.
Table ipblocks contains ipb_reason field. Dropping ...done.
Table image contains img_description field. Dropping ...done.
Table oldimage contains oi_description field. Dropping ...done.
Table filearchive contains fa_description field. Dropping ...done.
Table recentchanges contains rc_comment field. Dropping ...done.
Table logging contains log_comment field. Dropping ...done.
Table protected_titles contains pt_reason field. Dropping ...done.
Modifying table job ...done.
...ar_usertext_timestamp key doesn't exist.
Dropping usertext_timestamp index from table archive ...done.
Table archive contains ar_user field. Dropping ...done.
...ipblocks table does not contain ip_by field.
Dropping img_user_timestamp index from table image ...done.
Table image contains img_user field. Dropping ...done.
Table oldimage contains oi_user field. Dropping ...done.
Table filearchive contains fa_user field. Dropping ...done.
Table recentchanges contains rc_user field. Dropping ...done.
Table logging contains log_user field. Dropping ...done.
Adding index un_user_ip to table user_newtalk ...done.
Creating watchlist_expiry table ...done.
Modifying page_restrictions field of table page ...done.
Renaming index ipb_address into ipb_address_unique to table ipblocks ...done.
Adding rev_actor field to table revision ...done.
Table archive contains ar_text_id field. Dropping ...done.
Updating length of lc_lang in `l10n_cache` ...done.
Updating length of ll_lang in `langlinks` ...done.
Updating length of site_language in `sites` ...done.
...index ipb_address_unique on table ipblocks has no field ipb_anon_only; added.
...ipb_address_unique index up-to-date.
Modifying actor_name field of table actor ...done.
Modifying site_global_key field of table sites ...done.
Modifying iwl_prefix field of table iwlinks ...done.
...site_stats is populated...done.
Populating rev_len column
...doing rev_id from 1 to 200
...doing rev_id from 201 to 400
...doing rev_id from 401 to 600
...doing rev_id from 601 to 800
...doing rev_id from 801 to 1000
...doing rev_id from 1001 to 1200
...doing rev_id from 1201 to 1400
...doing rev_id from 1401 to 1600
...doing rev_id from 1601 to 1800
...doing rev_id from 1801 to 2000
...doing rev_id from 2001 to 2200
...doing rev_id from 2201 to 2400
...doing rev_id from 2401 to 2600
...doing rev_id from 2601 to 2800
...doing rev_id from 2801 to 3000
...doing rev_id from 3001 to 3200
...doing rev_id from 3201 to 3400
...doing rev_id from 3401 to 3600
...doing rev_id from 3601 to 3800
...doing rev_id from 3801 to 4000
...doing rev_id from 4001 to 4200
...doing rev_id from 4201 to 4400
...doing rev_id from 4401 to 4600
...doing rev_id from 4601 to 4800
...doing rev_id from 4801 to 5000
...doing rev_id from 5001 to 5200
...doing rev_id from 5201 to 5400
...doing rev_id from 5401 to 5600
...doing rev_id from 5601 to 5800
...doing rev_id from 5801 to 6000
...doing rev_id from 6001 to 6200
...doing rev_id from 6201 to 6400
...doing rev_id from 6401 to 6600
...doing rev_id from 6601 to 6800
Populating ar_len column
...doing ar_id from 1 to 200
rev_len and ar_len population complete [3 revision rows, 8 archive rows].
...Update 'populate rev_sha1' already logged as completed. Use --force to run it again.
...img_sha1 column of image table already populated.
...protocol-relative URLs in externallinks table already fixed.
...fa_sha1 column of filearchive table already populated.
Updating *_from_namespace fields in links tables.
...doing page_id from 1 to 200
...doing page_id from 200 to 399
...doing page_id from 399 to 598
...doing page_id from 598 to 797
...doing page_id from 797 to 996
...doing page_id from 996 to 1195
...doing page_id from 1195 to 1394
...doing page_id from 1394 to 1593
...doing page_id from 1593 to 1792
...doing page_id from 1792 to 1991
...doing page_id from 1991 to 2190
...doing page_id from 2190 to 2389
Adding empty categories with description pages...
--mode=both --begin=ND-10408
Removing empty categories without description pages...
--mode=remove --begin=Spammer
Category cleanup complete.
Populating page_props.pp_sortkey...
Populating page_props.pp_sortkey complete.
Updated a total of 0 rows
Copying IP revisions to ip_changes, from rev_id 0 to rev_id 6723
...checking 1 revisions for IP edits that need copying, between rev_ids 0 and 200
Attempted to insert 0 IP revisions, 0 actually done.
Updating externallinks table index fields
el_id 0 - 2403 of 2403
Done, 2 rows updated, 0 deleted.
Set the local repo temp zone container to be private.
Purging caches...done.

Done in 55 s.

nice.

2022-08-18: ada0p2 - mysql, at first the mediawiki update script complained again, I needed to give the wiki databse user the index privilege on the databse via a 'grant index on wikidb.* to 'user'@'localhost;' statement.

2022-08-18: ada0p2 - mediawiki

root@www# pwd
/usr/local/www/mediawiki/maintenance
root@www# php update.php
MediaWiki 1.38.2 Updater

Your composer.lock file is up to date with current dependencies!
Going to run database updates for wikidb
Depending on the size of your database this may take a while!
Abort with control-c in the next five seconds (skip this countdown with --quick) ...0
Can not upgrade from versions older than 1.29, please upgrade to that version or later first.

ok, so (temporarily) install mediawiki 1.35, and see if that will upgrade it.

2022-08-18: ada0p2 - apache - at first it didn't start

root@www# service apache24 start
Performing sanity check on apache24 configuration:
httpd: Syntax error on line 177 of /usr/local/etc/apache24/httpd.conf: Cannot load libexec/apache24/libphp5.so into server: Cannot open "/usr/local/libexec/apache24/libphp5.so"
Starting apache24.
httpd: Syntax error on line 177 of /usr/local/etc/apache24/httpd.conf: Cannot load libexec/apache24/libphp5.so into server: Cannot open "/usr/local/libexec/apache24/libphp5.so"
/usr/local/etc/rc.d/apache24: WARNING: failed to start apache24

so I fixed the config in /usr/local/etc/apache24/httpd.conf, changing php5 to php7, and now

root@www# service apache24 start
Performing sanity check on apache24 configuration:
Syntax OK
Starting apache24.
root@www# service apache24 status
apache24 is running as pid 12943.

2022-08-18: ada0p2 - mysql - I stopped the mysql server, copied in the old ib* files, and changed

innodb_data_file_path           = ibdata1:128M:autoextend

to

innodb_data_file_path           = ibdata1:76M:autoextend

in /usr/local/etc/mysql/my.cnf, and now the mysql server starts up aagain. Let me check it

root@www# mysqlcheck -u root -p wikidb
Enter password: 
wikidb.archive                                     OK
wikidb.category                                    OK
wikidb.categorylinks                               OK
wikidb.change_tag                                  OK
wikidb.cu_changes                                  OK
wikidb.cu_log                                      OK
wikidb.dymnorm                                     OK
wikidb.dympage                                     OK
wikidb.external_user                               OK
wikidb.externallinks                               OK
wikidb.filearchive                                 OK
wikidb.image                                       OK
wikidb.imagelinks                                  OK
wikidb.interwiki                                   OK
wikidb.ipblocks                                    OK
wikidb.iwlinks                                     OK
wikidb.job                                         OK
wikidb.l10n_cache                                  OK
wikidb.langlinks                                   OK
wikidb.log_search                                  OK
wikidb.logging                                     OK
wikidb.math                                        OK
wikidb.metric                                      OK
wikidb.module_deps                                 OK
wikidb.msg_resource                                OK
wikidb.msg_resource_links                          OK
wikidb.objectcache                                 OK
wikidb.oldimage                                    OK
wikidb.online                                      OK
wikidb.online_chat                                 OK
wikidb.online_config                               OK
wikidb.page                                        OK
wikidb.page_props                                  OK
wikidb.page_restrictions                           OK
wikidb.pagelinks                                   OK
wikidb.protected_titles                            OK
wikidb.querycache                                  OK
wikidb.querycache_info                             OK
wikidb.querycachetwo                               OK
wikidb.recentchanges                               OK
wikidb.redirect                                    OK
wikidb.revision                                    OK
wikidb.searchindex                                 OK
wikidb.site_identifiers                            OK
wikidb.site_stats                                  OK
wikidb.sites                                       OK
wikidb.tag_summary                                 OK
wikidb.templatelinks                               OK
wikidb.text                                        OK
wikidb.trackbacks                                  OK
wikidb.transcache                                  OK
wikidb.updatelog                                   OK
wikidb.uploadstash                                 OK
wikidb.user                                        OK
wikidb.user_former_groups                          OK
wikidb.user_groups                                 OK
wikidb.user_newtalk                                OK
wikidb.user_properties                             OK
wikidb.valid_tag                                   OK
wikidb.watchlist                                   OK

2022-08-18: ada0p2 - mysql - run mysql_upgrade

root@www# mysql_upgrade -u root -p
Enter password: 
Checking if update is needed.
Checking server version.
Running queries to upgrade MySQL server.
Checking system database.
mysql.columns_priv                                 OK
mysql.db                                           OK
mysql.engine_cost                                  OK
mysql.event                                        OK
mysql.func                                         OK
mysql.general_log                                  OK
mysql.gtid_executed                                OK
mysql.help_category                                OK
mysql.help_keyword                                 OK
mysql.help_relation                                OK
mysql.help_topic                                   OK
mysql.innodb_index_stats                           OK
mysql.innodb_table_stats                           OK
mysql.ndb_binlog_index                             OK
mysql.plugin                                       OK
mysql.proc                                         OK
mysql.procs_priv                                   OK
mysql.proxies_priv                                 OK
mysql.server_cost                                  OK
mysql.servers                                      OK
mysql.slave_master_info                            OK
mysql.slave_relay_log_info                         OK
mysql.slave_worker_info                            OK
mysql.slow_log                                     OK
mysql.tables_priv                                  OK
mysql.time_zone                                    OK
mysql.time_zone_leap_second                        OK
mysql.time_zone_name                               OK
mysql.time_zone_transition                         OK
mysql.time_zone_transition_type                    OK
mysql.user                                         OK
The sys schema is already up to date (version 1.5.2).
Checking databases.
sys.sys_config                                     OK
wikidb.archive
Error    : Table 'wikidb.archive' doesn't exist
status   : Operation failed
wikidb.category
Error    : Table 'wikidb.category' doesn't exist
status   : Operation failed
wikidb.categorylinks
Error    : Table 'wikidb.categorylinks' doesn't exist
status   : Operation failed
wikidb.change_tag
Error    : Table 'wikidb.change_tag' doesn't exist
status   : Operation failed
wikidb.cu_changes
Error    : Table 'wikidb.cu_changes' doesn't exist
status   : Operation failed
wikidb.cu_log
Error    : Table 'wikidb.cu_log' doesn't exist
status   : Operation failed
wikidb.dymnorm                                     OK
wikidb.dympage                                     OK
wikidb.external_user
Error    : Table 'wikidb.external_user' doesn't exist
status   : Operation failed
wikidb.externallinks
Error    : Table 'wikidb.externallinks' doesn't exist
status   : Operation failed
wikidb.filearchive
Error    : Table 'wikidb.filearchive' doesn't exist
status   : Operation failed
wikidb.image
Error    : Table 'wikidb.image' doesn't exist
status   : Operation failed
wikidb.imagelinks
Error    : Table 'wikidb.imagelinks' doesn't exist
status   : Operation failed
wikidb.interwiki
Error    : Table 'wikidb.interwiki' doesn't exist
status   : Operation failed
wikidb.ipblocks
Error    : Table 'wikidb.ipblocks' doesn't exist
status   : Operation failed
wikidb.iwlinks
Error    : Table 'wikidb.iwlinks' doesn't exist
status   : Operation failed
wikidb.job
Error    : Table 'wikidb.job' doesn't exist
status   : Operation failed
wikidb.l10n_cache
Error    : Table 'wikidb.l10n_cache' doesn't exist
status   : Operation failed
wikidb.langlinks
Error    : Table 'wikidb.langlinks' doesn't exist
status   : Operation failed
wikidb.log_search
Error    : Table 'wikidb.log_search' doesn't exist
status   : Operation failed
wikidb.logging
Error    : Table 'wikidb.logging' doesn't exist
status   : Operation failed
wikidb.math
Error    : Table 'wikidb.math' doesn't exist
status   : Operation failed
wikidb.metric                                      OK
wikidb.module_deps
Error    : Table 'wikidb.module_deps' doesn't exist
status   : Operation failed
wikidb.msg_resource
Error    : Table 'wikidb.msg_resource' doesn't exist
status   : Operation failed
wikidb.msg_resource_links
Error    : Table 'wikidb.msg_resource_links' doesn't exist
status   : Operation failed
wikidb.objectcache
Error    : Table 'wikidb.objectcache' doesn't exist
status   : Operation failed
wikidb.oldimage
Error    : Table 'wikidb.oldimage' doesn't exist
status   : Operation failed
wikidb.online                                      OK
wikidb.online_chat                                 OK
wikidb.online_config                               OK
wikidb.page
Error    : Table 'wikidb.page' doesn't exist
status   : Operation failed
wikidb.page_props
Error    : Table 'wikidb.page_props' doesn't exist
status   : Operation failed
wikidb.page_restrictions
Error    : Table 'wikidb.page_restrictions' doesn't exist
status   : Operation failed
wikidb.pagelinks
Error    : Table 'wikidb.pagelinks' doesn't exist
status   : Operation failed
wikidb.protected_titles
Error    : Table 'wikidb.protected_titles' doesn't exist
status   : Operation failed
wikidb.querycache
Error    : Table 'wikidb.querycache' doesn't exist
status   : Operation failed
wikidb.querycache_info
Error    : Table 'wikidb.querycache_info' doesn't exist
status   : Operation failed
wikidb.querycachetwo
Error    : Table 'wikidb.querycachetwo' doesn't exist
status   : Operation failed
wikidb.recentchanges
Error    : Table 'wikidb.recentchanges' doesn't exist
status   : Operation failed
wikidb.redirect
Error    : Table 'wikidb.redirect' doesn't exist
status   : Operation failed
wikidb.revision
Error    : Table 'wikidb.revision' doesn't exist
status   : Operation failed
wikidb.searchindex                                 OK
wikidb.site_identifiers
Error    : Table 'wikidb.site_identifiers' doesn't exist
status   : Operation failed
wikidb.site_stats
Error    : Table 'wikidb.site_stats' doesn't exist
status   : Operation failed
wikidb.sites
Error    : Table 'wikidb.sites' doesn't exist
status   : Operation failed
wikidb.tag_summary
Error    : Table 'wikidb.tag_summary' doesn't exist
status   : Operation failed
wikidb.templatelinks
Error    : Table 'wikidb.templatelinks' doesn't exist
status   : Operation failed
wikidb.text
Error    : Table 'wikidb.text' doesn't exist
status   : Operation failed
wikidb.trackbacks
Error    : Table 'wikidb.trackbacks' doesn't exist
status   : Operation failed
wikidb.transcache
Error    : Table 'wikidb.transcache' doesn't exist
status   : Operation failed
wikidb.updatelog
Error    : Table 'wikidb.updatelog' doesn't exist
status   : Operation failed
wikidb.uploadstash
Error    : Table 'wikidb.uploadstash' doesn't exist
status   : Operation failed
wikidb.user
Error    : Table 'wikidb.user' doesn't exist
status   : Operation failed
wikidb.user_former_groups
Error    : Table 'wikidb.user_former_groups' doesn't exist
status   : Operation failed
wikidb.user_groups
Error    : Table 'wikidb.user_groups' doesn't exist
status   : Operation failed
wikidb.user_newtalk
Error    : Table 'wikidb.user_newtalk' doesn't exist
status   : Operation failed
wikidb.user_properties
Error    : Table 'wikidb.user_properties' doesn't exist
status   : Operation failed
wikidb.valid_tag
Error    : Table 'wikidb.valid_tag' doesn't exist
status   : Operation failed
wikidb.watchlist
Error    : Table 'wikidb.watchlist' doesn't exist
status   : Operation failed

Repairing tables
wikidb.archive
Error    : Table 'wikidb.archive' doesn't exist
status   : Operation failed
wikidb.category
Error    : Table 'wikidb.category' doesn't exist
status   : Operation failed
wikidb.categorylinks
Error    : Table 'wikidb.categorylinks' doesn't exist
status   : Operation failed
wikidb.change_tag
Error    : Table 'wikidb.change_tag' doesn't exist
status   : Operation failed
wikidb.cu_changes
Error    : Table 'wikidb.cu_changes' doesn't exist
status   : Operation failed
wikidb.cu_log
Error    : Table 'wikidb.cu_log' doesn't exist
status   : Operation failed
wikidb.external_user
Error    : Table 'wikidb.external_user' doesn't exist
status   : Operation failed
wikidb.externallinks
Error    : Table 'wikidb.externallinks' doesn't exist
status   : Operation failed
wikidb.filearchive
Error    : Table 'wikidb.filearchive' doesn't exist
status   : Operation failed
wikidb.image
Error    : Table 'wikidb.image' doesn't exist
status   : Operation failed
wikidb.imagelinks
Error    : Table 'wikidb.imagelinks' doesn't exist
status   : Operation failed
wikidb.interwiki
Error    : Table 'wikidb.interwiki' doesn't exist
status   : Operation failed
wikidb.ipblocks
Error    : Table 'wikidb.ipblocks' doesn't exist
status   : Operation failed
wikidb.iwlinks
Error    : Table 'wikidb.iwlinks' doesn't exist
status   : Operation failed
wikidb.job
Error    : Table 'wikidb.job' doesn't exist
status   : Operation failed
wikidb.l10n_cache
Error    : Table 'wikidb.l10n_cache' doesn't exist
status   : Operation failed
wikidb.langlinks
Error    : Table 'wikidb.langlinks' doesn't exist
status   : Operation failed
wikidb.log_search
Error    : Table 'wikidb.log_search' doesn't exist
status   : Operation failed
wikidb.logging
Error    : Table 'wikidb.logging' doesn't exist
status   : Operation failed
wikidb.math
Error    : Table 'wikidb.math' doesn't exist
status   : Operation failed
wikidb.module_deps
Error    : Table 'wikidb.module_deps' doesn't exist
status   : Operation failed
wikidb.msg_resource
Error    : Table 'wikidb.msg_resource' doesn't exist
status   : Operation failed
wikidb.msg_resource_links
Error    : Table 'wikidb.msg_resource_links' doesn't exist
status   : Operation failed
wikidb.objectcache
Error    : Table 'wikidb.objectcache' doesn't exist
status   : Operation failed
wikidb.oldimage
Error    : Table 'wikidb.oldimage' doesn't exist
status   : Operation failed
wikidb.page
Error    : Table 'wikidb.page' doesn't exist
status   : Operation failed
wikidb.page_props
Error    : Table 'wikidb.page_props' doesn't exist
status   : Operation failed
wikidb.page_restrictions
Error    : Table 'wikidb.page_restrictions' doesn't exist
status   : Operation failed
wikidb.pagelinks
Error    : Table 'wikidb.pagelinks' doesn't exist
status   : Operation failed
wikidb.protected_titles
Error    : Table 'wikidb.protected_titles' doesn't exist
status   : Operation failed
wikidb.querycache
Error    : Table 'wikidb.querycache' doesn't exist
status   : Operation failed
wikidb.querycache_info
Error    : Table 'wikidb.querycache_info' doesn't exist
status   : Operation failed
wikidb.querycachetwo
Error    : Table 'wikidb.querycachetwo' doesn't exist
status   : Operation failed
wikidb.recentchanges
Error    : Table 'wikidb.recentchanges' doesn't exist
status   : Operation failed
wikidb.redirect
Error    : Table 'wikidb.redirect' doesn't exist
status   : Operation failed
wikidb.revision
Error    : Table 'wikidb.revision' doesn't exist
status   : Operation failed
wikidb.site_identifiers
Error    : Table 'wikidb.site_identifiers' doesn't exist
status   : Operation failed
wikidb.site_stats
Error    : Table 'wikidb.site_stats' doesn't exist
status   : Operation failed
wikidb.sites
Error    : Table 'wikidb.sites' doesn't exist
status   : Operation failed
wikidb.tag_summary
Error    : Table 'wikidb.tag_summary' doesn't exist
status   : Operation failed
wikidb.templatelinks
Error    : Table 'wikidb.templatelinks' doesn't exist
status   : Operation failed
wikidb.text
Error    : Table 'wikidb.text' doesn't exist
status   : Operation failed
wikidb.trackbacks
Error    : Table 'wikidb.trackbacks' doesn't exist
status   : Operation failed
wikidb.transcache
Error    : Table 'wikidb.transcache' doesn't exist
status   : Operation failed
wikidb.updatelog
Error    : Table 'wikidb.updatelog' doesn't exist
status   : Operation failed
wikidb.uploadstash
Error    : Table 'wikidb.uploadstash' doesn't exist
status   : Operation failed
wikidb.user
Error    : Table 'wikidb.user' doesn't exist
status   : Operation failed
wikidb.user_former_groups
Error    : Table 'wikidb.user_former_groups' doesn't exist
status   : Operation failed
wikidb.user_groups
Error    : Table 'wikidb.user_groups' doesn't exist
status   : Operation failed
wikidb.user_newtalk
Error    : Table 'wikidb.user_newtalk' doesn't exist
status   : Operation failed
wikidb.user_properties
Error    : Table 'wikidb.user_properties' doesn't exist
status   : Operation failed
wikidb.valid_tag
Error    : Table 'wikidb.valid_tag' doesn't exist
status   : Operation failed
wikidb.watchlist
Error    : Table 'wikidb.watchlist' doesn't exist
status   : Operation failed
Upgrade process completed successfully.
Checking if update is needed.

of course mysqlcheck is the same

root@www# mysqlcheck -u root -p wikidb
Enter password: 
wikidb.archive
Error    : Table 'wikidb.archive' doesn't exist
status   : Operation failed
wikidb.category
Error    : Table 'wikidb.category' doesn't exist
status   : Operation failed
wikidb.categorylinks
Error    : Table 'wikidb.categorylinks' doesn't exist
status   : Operation failed
wikidb.change_tag
Error    : Table 'wikidb.change_tag' doesn't exist
status   : Operation failed
wikidb.cu_changes
Error    : Table 'wikidb.cu_changes' doesn't exist
status   : Operation failed
wikidb.cu_log
Error    : Table 'wikidb.cu_log' doesn't exist
status   : Operation failed
wikidb.dymnorm                                     OK
wikidb.dympage                                     OK
wikidb.external_user
Error    : Table 'wikidb.external_user' doesn't exist
status   : Operation failed
wikidb.externallinks
Error    : Table 'wikidb.externallinks' doesn't exist
status   : Operation failed
wikidb.filearchive
Error    : Table 'wikidb.filearchive' doesn't exist
status   : Operation failed
wikidb.image
Error    : Table 'wikidb.image' doesn't exist
status   : Operation failed
wikidb.imagelinks
Error    : Table 'wikidb.imagelinks' doesn't exist
status   : Operation failed
wikidb.interwiki
Error    : Table 'wikidb.interwiki' doesn't exist
status   : Operation failed
wikidb.ipblocks
Error    : Table 'wikidb.ipblocks' doesn't exist
status   : Operation failed
wikidb.iwlinks
Error    : Table 'wikidb.iwlinks' doesn't exist
status   : Operation failed
wikidb.job
Error    : Table 'wikidb.job' doesn't exist
status   : Operation failed
wikidb.l10n_cache
Error    : Table 'wikidb.l10n_cache' doesn't exist
status   : Operation failed
wikidb.langlinks
Error    : Table 'wikidb.langlinks' doesn't exist
status   : Operation failed
wikidb.log_search
Error    : Table 'wikidb.log_search' doesn't exist
status   : Operation failed
wikidb.logging
Error    : Table 'wikidb.logging' doesn't exist
status   : Operation failed
wikidb.math
Error    : Table 'wikidb.math' doesn't exist
status   : Operation failed
wikidb.metric                                      OK
wikidb.module_deps
Error    : Table 'wikidb.module_deps' doesn't exist
status   : Operation failed
wikidb.msg_resource
Error    : Table 'wikidb.msg_resource' doesn't exist
status   : Operation failed
wikidb.msg_resource_links
Error    : Table 'wikidb.msg_resource_links' doesn't exist
status   : Operation failed
wikidb.objectcache
Error    : Table 'wikidb.objectcache' doesn't exist
status   : Operation failed
wikidb.oldimage
Error    : Table 'wikidb.oldimage' doesn't exist
status   : Operation failed
wikidb.online                                      OK
wikidb.online_chat                                 OK
wikidb.online_config                               OK
wikidb.page
Error    : Table 'wikidb.page' doesn't exist
status   : Operation failed
wikidb.page_props
Error    : Table 'wikidb.page_props' doesn't exist
status   : Operation failed
wikidb.page_restrictions
Error    : Table 'wikidb.page_restrictions' doesn't exist
status   : Operation failed
wikidb.pagelinks
Error    : Table 'wikidb.pagelinks' doesn't exist
status   : Operation failed
wikidb.protected_titles
Error    : Table 'wikidb.protected_titles' doesn't exist
status   : Operation failed
wikidb.querycache
Error    : Table 'wikidb.querycache' doesn't exist
status   : Operation failed
wikidb.querycache_info
Error    : Table 'wikidb.querycache_info' doesn't exist
status   : Operation failed
wikidb.querycachetwo
Error    : Table 'wikidb.querycachetwo' doesn't exist
status   : Operation failed
wikidb.recentchanges
Error    : Table 'wikidb.recentchanges' doesn't exist
status   : Operation failed
wikidb.redirect
Error    : Table 'wikidb.redirect' doesn't exist
status   : Operation failed
wikidb.revision
Error    : Table 'wikidb.revision' doesn't exist
status   : Operation failed
wikidb.searchindex
warning  : 12 clients are using or haven't closed the table properly
status   : OK
wikidb.site_identifiers
Error    : Table 'wikidb.site_identifiers' doesn't exist
status   : Operation failed
wikidb.site_stats
Error    : Table 'wikidb.site_stats' doesn't exist
status   : Operation failed
wikidb.sites
Error    : Table 'wikidb.sites' doesn't exist
status   : Operation failed
wikidb.tag_summary
Error    : Table 'wikidb.tag_summary' doesn't exist
status   : Operation failed
wikidb.templatelinks
Error    : Table 'wikidb.templatelinks' doesn't exist
status   : Operation failed
wikidb.text
Error    : Table 'wikidb.text' doesn't exist
status   : Operation failed
wikidb.trackbacks
Error    : Table 'wikidb.trackbacks' doesn't exist
status   : Operation failed
wikidb.transcache
Error    : Table 'wikidb.transcache' doesn't exist
status   : Operation failed
wikidb.updatelog
Error    : Table 'wikidb.updatelog' doesn't exist
status   : Operation failed
wikidb.uploadstash
Error    : Table 'wikidb.uploadstash' doesn't exist
status   : Operation failed
wikidb.user
Error    : Table 'wikidb.user' doesn't exist
status   : Operation failed
wikidb.user_former_groups
Error    : Table 'wikidb.user_former_groups' doesn't exist
status   : Operation failed
wikidb.user_groups
Error    : Table 'wikidb.user_groups' doesn't exist
status   : Operation failed
wikidb.user_newtalk
Error    : Table 'wikidb.user_newtalk' doesn't exist
status   : Operation failed
wikidb.user_properties
Error    : Table 'wikidb.user_properties' doesn't exist
status   : Operation failed
wikidb.valid_tag
Error    : Table 'wikidb.valid_tag' doesn't exist
status   : Operation failed
wikidb.watchlist
Error    : Table 'wikidb.watchlist' doesn't exist
status   : Operation failed

2022-08-18: ada0p2 - mysql server - mv the old /var/db/mysql directory out of the way, then start with an empty one. Stop the mysql server and copy in the wikidb database. Then re-create the wikidb user, and give it all privileges it needs on wikidb. Test with mysql that you can connect to the databse and show all tables. It works.

2022-08-18: ada0p2 - pkg - install everything we need again (plus some nice to have things)

Aug 18 16:43:55 www pkg[1391]: indexinfo-0.3.1 installed
Aug 18 16:43:55 www pkg[1391]: libunistring-1.0 installed
Aug 18 16:43:56 www pkg[1391]: readline-8.1.2 installed
Aug 18 16:43:56 www pkg[1391]: libxml2-2.9.13_2 installed
Aug 18 16:43:56 www pkg[1391]: libidn2-2.3.2 installed
Aug 18 16:43:56 www pkg[1391]: libpaper-1.1.28 installed
Aug 18 16:43:57 www pkg[1391]: libargon2-20190702 installed
Aug 18 16:43:57 www pkg[1391]: pcre2-10.40 installed
Aug 18 16:43:57 www pkg[1391]: gettext-runtime-0.21 installed
Aug 18 16:43:58 www pkg[1391]: cyrus-sasl-2.1.28 installed
Aug 18 16:43:58 www pkg[1391]: libnghttp2-1.48.0 installed
Aug 18 16:43:58 www pkg[1391]: psutils-1.17_5 installed
Aug 18 16:44:11 www pkg[1391]: perl5-5.32.1_1 installed
Aug 18 16:44:12 www pkg[1391]: php74-7.4.30 installed
Aug 18 16:44:12 www pkg[1391]: libssh2-1.10.0,3 installed
Aug 18 16:44:12 www pkg[1391]: libpsl-0.21.1_4 installed
Aug 18 16:44:13 www pkg[1391]: libiconv-1.16 installed
Aug 18 16:44:13 www pkg[1391]: ca_root_nss-3.78 installed
Aug 18 16:44:13 www pkg[1391]: uchardet-0.0.7 installed
Aug 18 16:44:13 www pkg[1391]: libedit-3.1.20210910,1 installed
Aug 18 16:44:15 www pkg[1391]: icu-71.1,1 installed
Aug 18 16:44:16 www pkg[1391]: openldap24-client-2.4.59_4 installed
Aug 18 16:44:17 www pkg[1391]: groff-1.22.4_4 installed
Aug 18 16:44:17 www pkg[1391]: liblz4-1.9.3,1 installed
Aug 18 16:44:18 www pkg[1391]: protobuf-3.20.1,1 installed
Aug 18 16:44:18 www pkg[1391]: oniguruma-6.9.8_1 installed
Aug 18 16:44:19 www pkg[1391]: curl-7.84.0 installed
Aug 18 16:44:19 www pkg[1391]: libevent-2.1.12 installed
Aug 18 16:44:19 www pkg[1391]: php74-dom-7.4.30 installed
Aug 18 16:44:19 www pkg[1391]: php74-json-7.4.30 installed
Aug 18 16:44:19 www pkg[1391]: php74-ctype-7.4.30 installed
Aug 18 16:44:19 www pkg[1391]: php74-iconv-7.4.30 installed
Aug 18 16:44:19 www pkg[1391]: php74-filter-7.4.30 installed
Aug 18 16:44:20 www pkg[1391]: mysql57-client-5.7.38 installed
Aug 18 16:44:20 www pkg[1391]: php74-fileinfo-7.4.30 installed
Aug 18 16:44:20 www pkg[1391]: php74-zlib-7.4.30 installed
Aug 18 16:44:20 www pkg[1391]: php74-session-7.4.30 installed
Aug 18 16:44:20 www pkg[1391]: php74-xml-7.4.30 installed
Aug 18 16:44:21 www pkg[1391]: php74-mbstring-7.4.30 installed
Aug 18 16:44:21 www pkg[1391]: php74-mysqli-7.4.30 installed
Aug 18 16:44:21 www pkg[1391]: php74-xmlreader-7.4.30 installed
Aug 18 16:44:21 www pkg[1391]: php74-sockets-7.4.30 installed
Aug 18 16:44:21 www pkg[1391]: php74-readline-7.4.30 installed
Aug 18 16:44:21 www pkg[1391]: php74-openssl-7.4.30 installed
Aug 18 16:44:21 www pkg[1391]: php74-intl-7.4.30 installed
Aug 18 16:44:49 www pkg[1391]: mediawiki138-php74-1.38.2 installed
Aug 18 16:44:49 www pkg[1391]: mediawiki138-php74-1.38.2 installed
Aug 18 16:47:02 www pkg[1775]: db5-5.3.28_8 installed
Aug 18 16:47:02 www pkg[1775]: expat-2.4.8 installed
Aug 18 16:47:03 www pkg[1775]: gdbm-1.23 installed
Aug 18 16:47:03 www pkg[1775]: apr-1.7.0.1.6.1_2 installed
Aug 18 16:47:03 www pkg[1775]: jansson-2.14 installed
Aug 18 16:47:05 www pkg[1775]: apache24-2.4.54 installed
Aug 18 16:49:08 www pkg[1871]: xorgproto-2022.1 installed
Aug 18 16:49:08 www pkg[1871]: libXau-1.0.9 installed
Aug 18 16:49:08 www pkg[1871]: mpdecimal-2.5.1 installed
Aug 18 16:49:08 www pkg[1871]: libpthread-stubs-0.4 installed
Aug 18 16:49:08 www pkg[1871]: libffi-3.4.2 installed
Aug 18 16:49:08 www pkg[1871]: libXdmcp-1.1.3 installed
Aug 18 16:49:10 www pkg[1871]: libxcb-1.15 installed
Aug 18 16:49:10 www pkg[1871]: libICE-1.0.10,1 installed
Aug 18 16:49:20 www pkg[1871]: python39-3.9.13 installed
Aug 18 16:49:20 www pkg[1871]: pcre-8.45_1 installed
Aug 18 16:49:21 www pkg[1871]: jpeg-turbo-2.1.3 installed
Aug 18 16:49:21 www pkg[1871]: libSM-1.2.3,1 installed
Aug 18 16:49:23 www pkg[1871]: libX11-1.7.2,1 installed
Aug 18 16:49:25 www pkg[1871]: glib-2.72.2,2 installed
Aug 18 16:49:25 www pkg[1871]: jbigkit-2.1_1 installed
Aug 18 16:49:26 www pkg[1871]: png-1.6.37_1 installed
Aug 18 16:49:26 www pkg[1871]: dbus-1.14.0,1 installed
Aug 18 16:49:26 www pkg[1871]: gmp-6.2.1 installed
Aug 18 16:49:26 www pkg[1871]: Imath-3.1.5_1 installed
Aug 18 16:49:27 www pkg[1871]: tiff-4.3.0 installed
Aug 18 16:49:27 www pkg[1871]: shared-mime-info-2.2_1 installed
Aug 18 16:49:27 www pkg[1871]: libtasn1-4.18.0 installed
Aug 18 16:49:27 www pkg[1871]: p11-kit-0.24.1_1 installed
Aug 18 16:49:28 www pkg[1871]: dbus-glib-0.112 installed
Aug 18 16:49:28 www pkg[1871]: gnome_subr-1.0 installed
Aug 18 16:49:28 www pkg[1871]: freetype2-2.12.1 installed
Aug 18 16:49:28 www pkg[1871]: gdk-pixbuf2-2.40.0_4 installed
Aug 18 16:49:29 www pkg[1871]: highway-0.17.0 installed
Aug 18 16:49:29 www pkg[1871]: nettle-3.8 installed
Aug 18 16:49:29 www pkg[1871]: giflib-5.2.1 installed
Aug 18 16:49:30 www pkg[1871]: openexr-3.1.5 installed
Aug 18 16:49:30 www pkg[1871]: libdaemon-0.14_1 installed
Aug 18 16:49:30 www pkg[1871]: brotli-1.0.9,1 installed
Aug 18 16:49:30 www pkg[1871]: avahi-app-0.8 installed
Aug 18 16:49:31 www pkg[1871]: fontconfig-2.13.94_2,1 installed
Aug 18 16:49:33 www pkg[1871]: gnutls-3.7.7 installed
Aug 18 16:49:33 www pkg[1871]: libimagequant-2.17.0 installed
Aug 18 16:49:35 www pkg[1871]: libjxl-0.6.1_5 installed
Aug 18 16:49:35 www pkg[1871]: lcms2-2.13.1 installed
Aug 18 16:49:35 www pkg[1871]: webp-1.2.2 installed
Aug 18 16:49:36 www pkg[1871]: vmaf-2.3.1 installed
Aug 18 16:49:36 www pkg[1871]: jbig2dec-0.19 installed
Aug 18 16:49:37 www pkg[1871]: aom-3.4.0 installed
Aug 18 16:49:37 www pkg[1871]: libgd-2.3.3_1,1 installed
Aug 18 16:49:38 www pkg[1871]: cups-2.4.2 installed
Aug 18 16:49:39 www pkg[1871]: x265-3.4_2 installed
Aug 18 16:49:39 www pkg[1871]: libde265-1.0.8 installed
Aug 18 16:49:39 www pkg[1871]: dav1d-1.0.0_1 installed
Aug 18 16:49:39 www pkg[1871]: openjpeg-2.5.0 installed
Aug 18 16:49:39 www pkg[1871]: libidn-1.38 installed
Aug 18 16:49:40 www pkg[1871]: poppler-data-0.4.11 installed
Aug 18 16:49:40 www pkg[1871]: liblqr-1-0.4.2 installed
Aug 18 16:49:41 www pkg[1871]: libwmf-nox11-0.2.12 installed
Aug 18 16:49:41 www pkg[1871]: fftw3-3.3.10_2 installed
Aug 18 16:49:44 www pkg[1871]: ghostscript9-agpl-base-9.56.1_1 installed
Aug 18 16:49:44 www pkg[1871]: libheif-1.12.0.62_1 installed
Aug 18 16:49:44 www pkg[1871]: libraw-0.20.2_3 installed
Aug 18 16:49:44 www pkg[1871]: libltdl-2.4.7 installed
Aug 18 16:49:44 www pkg[1871]: libzip-1.7.3 installed
Aug 18 16:49:45 www pkg[1871]: pkgconf-1.8.0,1 installed
Aug 18 16:49:45 www pkg[1871]: gsfonts-8.11_8 installed
Aug 18 16:49:48 www pkg[1871]: ImageMagick7-nox11-7.1.0.34_1 installed
Aug 18 16:50:11 www pkg[2634]: p5-TimeDate-2.33,1 installed
Aug 18 16:50:11 www pkg[2634]: p5-URI-5.10 installed
Aug 18 16:50:11 www pkg[2634]: p5-Clone-0.45 installed
Aug 18 16:50:11 www pkg[2634]: p5-HTTP-Date-6.05 installed
Aug 18 16:50:11 www pkg[2634]: p5-Encode-Locale-1.05 installed
Aug 18 16:50:11 www pkg[2634]: p5-LWP-MediaTypes-6.04 installed
Aug 18 16:50:11 www pkg[2634]: p5-IO-HTML-1.004 installed
Aug 18 16:50:11 www pkg[2634]: p5-HTML-Tagset-3.20_1 installed
Aug 18 16:50:11 www pkg[2634]: p5-Socket6-0.29 installed
Aug 18 16:50:12 www pkg[2634]: p5-HTTP-Message-6.37 installed
Aug 18 16:50:12 www pkg[2634]: p5-Net-SSLeay-1.92 installed
Aug 18 16:50:12 www pkg[2634]: p5-GSSAPI-0.28_2 installed
Aug 18 16:50:12 www pkg[2634]: p5-IO-Socket-INET6-2.72_1 installed
Aug 18 16:50:12 www pkg[2634]: p5-HTML-Parser-3.78 installed
Aug 18 16:50:12 www pkg[2634]: p5-Mozilla-CA-20211001 installed
Aug 18 16:50:12 www pkg[2634]: p5-Digest-HMAC-1.04 installed
Aug 18 16:50:12 www pkg[2634]: p5-IO-Socket-SSL-2.074 installed
Aug 18 16:50:12 www pkg[2634]: p5-CGI-4.54 installed
Aug 18 16:50:12 www pkg[2634]: p5-Error-0.17029 installed
Aug 18 16:50:12 www pkg[2634]: p5-Authen-SASL-2.16_1 installed
Aug 18 16:50:14 www pkg[2634]: git-2.37.1 installed
Aug 18 16:51:53 www pkg[2649]: lua54-5.4.2 installed
Aug 18 16:52:40 www pkg[2670]: mod_php74-7.4.30 installed
Aug 18 16:54:03 www pkg[2687]: mysql57-server-5.7.38 installed
Aug 18 16:55:40 www pkg[2725]: php74-pecl-imagick-im7-3.5.1_1 installed
Aug 18 16:58:51 www pkg[2746]: php74-pcntl-7.4.30 installed
Aug 18 17:00:20 www pkg[2770]: smartmontools-7.3 installed

2022-08-18: ada0p2 - pkg - delete all packages

root@www# pkg delete -a
[..]
Number of packages to be removed: 108

The operation will free 747 MiB.

Proceed with deinstalling packages? [y/N]: y
[..]
[107/108] Deleting files for libevent-2.1.8: 100%

2022-08-18: ada0p2 - pkg - try to fix pkg

root@www# pkg-static install -f pkg
pkg-static: Warning: Major OS version upgrade detected.  Running "pkg-static install -f pkg" recommended
Updating FreeBSD repository catalogue...
pkg-static: repository meta /var/db/pkg/FreeBSD.meta has wrong version 2
pkg-static: Repository FreeBSD load error: meta cannot be loaded No error: 0
Fetching meta.txz: 100%    916 B   0.9kB/s    00:01    
pkg-static: repository meta /var/db/pkg/FreeBSD.meta has wrong version 2
repository FreeBSD has no meta file, using default settings
Fetching packagesite.txz: 100%    6 MiB   6.6MB/s    00:01    
pkg-static: repository meta /var/db/pkg/FreeBSD.meta has wrong version 2
pkg-static: Repository FreeBSD load error: meta cannot be loaded No error: 0
Unable to open created repository FreeBSD
Unable to update repository FreeBSD
Error updating repositories!

ok, try this one instead

root@www# pkg bootstrap -f
The package management tool is not yet installed on your system.
Do you want to fetch and install it now? [y/N]: y
Bootstrapping pkg from pkg+http://pkg.FreeBSD.org/FreeBSD:13:amd64/quarterly, please wait...
Verifying signature with trusted certificate pkg.freebsd.org.2013102301... done
Installing pkg-1.18.3...
package pkg is already installed, forced install
Extracting pkg-1.18.3: 100%
root@www# pkg update -f
Updating FreeBSD repository catalogue...
pkg: Repository FreeBSD has a wrong packagesite, need to re-create database
Fetching meta.conf: 100%    163 B   0.2kB/s    00:01    
Fetching packagesite.pkg: 100%    6 MiB   6.6MB/s    00:01    
Processing entries: 100%
FreeBSD repository update completed. 31603 packages processed.
All repositories are up to date.

Yes, that worked better.

2022-08-18: ada0p2 - reboot, FreeBSD 13.1-release-p1 is in

root@www# freebsd-version -ku
13.1-RELEASE-p1
13.1-RELEASE-p1

kernel

root@www# uname -a
FreeBSD www.ndwiki.org 13.1-RELEASE-p1 FreeBSD 13.1-RELEASE-p1 GENERIC amd64

2022-08-18: ada0p2 - freebsd-update - upgrade to 13.1-release

root@www# freebsd-update -r 13.1-RELEASE upgrade
src component not installed, skipped
Looking up update.FreeBSD.org mirrors... 2 mirrors found.
Fetching metadata signature for 11.4-RELEASE from update2.freebsd.org... done.
Fetching metadata index... done.
Fetching 1 metadata patches. done.
Applying metadata patches... done.
Fetching 1 metadata files... done.
Inspecting system... done.

The following components of FreeBSD seem to be installed:
kernel/generic world/base world/lib32

The following components of FreeBSD do not seem to be installed:
kernel/generic-dbg world/base-dbg world/doc world/lib32-dbg

Does this look reasonable (y/n)? y
[..]
The following changes, which occurred between FreeBSD 11.4-RELEASE and
FreeBSD 13.1-RELEASE have been merged into /etc/group:
[..]
The following files are affected by updates. No changes have
been downloaded, however, because the files have been modified
locally:
/.profile
/root/.profile
/root/.shrc
/var/log/sendmail.st
[..]
The following files will be removed as part of updating to
13.1-RELEASE-p1:
The following files will be added as part of updating to
13.1-RELEASE-p1:
The following files will be updated as part of updating to
13.1-RELEASE-p1:
[..]
/var/db/services.db
/var/yp/Makefile.dist
To install the downloaded upgrades, run "/usr/sbin/freebsd-update install".

install

root@www# freebsd-update install
src component not installed, skipped
Installing updates...
Kernel updates have been installed.  Please reboot and run
"/usr/sbin/freebsd-update install" again to finish installing updates.

reboot, install

root@www# freebsd-update install
src component not installed, skipped
Installing updates...Scanning //usr/share/certs/blacklisted for certificates...
Scanning //usr/share/certs/trusted for certificates...
Scanning //usr/local/share/certs for certificates...
find: ///usr/share/man/mandoc.db: No such file or directory
find: ///usr/share/openssl/man/mandoc.db: No such file or directory

Completing this upgrade requires removing old shared object files.
Please rebuild all installed 3rd party software (e.g., programs
installed from the ports tree) and then run "/usr/sbin/freebsd-update install"
again to finish installing updates.

just install again (I'm going to reinstall all packages anyway)

root@www# freebsd-update install
src component not installed, skipped
Installing updates...rmdir: ///var/db/etcupdate/current/usr/share/openssl/man/en.ISO8859-1: Directory not empty
rmdir: ///var/db/etcupdate/current/usr/share/openssl/man: Directory not empty
rmdir: ///var/db/etcupdate/current/usr/share/openssl: Directory not empty
rmdir: ///var/db/etcupdate/current/usr/share/man/en.UTF-8: Directory not empty
rmdir: ///var/db/etcupdate/current/usr/share/man/en.ISO8859-1: Directory not empty
rmdir: ///var/db/etcupdate/current/usr/share/man: Directory not empty
rmdir: ///usr/share/openssl/man/en.ISO8859-1: Directory not empty
rmdir: ///usr/share/man/en.UTF-8: Directory not empty
rmdir: ///usr/share/man/en.ISO8859-1: Directory not empty
 done.

2022-08-18: ada0p2 - freebsd-update - upgrade, first to 11.4

root@www# freebsd-update -r 11.4-RELEASE upgrade
src component not installed, skipped
Looking up update.FreeBSD.org mirrors... 2 mirrors found.
Fetching metadata signature for 10.4-RELEASE from update2.freebsd.org... done.
Fetching metadata index... done.
Inspecting system... done.

The following components of FreeBSD seem to be installed:
kernel/generic world/base world/lib32

The following components of FreeBSD do not seem to be installed:
world/doc world/games

Does this look reasonable (y/n)? y
[..]
Attempting to automatically merge changes in files... done.

The following changes, which occurred between FreeBSD 10.4-RELEASE and
FreeBSD 11.4-RELEASE have been merged into /etc/group:
[..]
The following files are affected by updates, but no changes have
been downloaded because the files have been modified locally:
/.profile
/root/.profile
[..]
The following files will be removed as part of updating to 11.4-RELEASE-p13:
The following files will be added as part of updating to 11.4-RELEASE-p13:
The following files will be updated as part of updating to 11.4-RELEASE-p13:
[..]
/var/yp/Makefile.dist
To install the downloaded upgrades, run "/usr/sbin/freebsd-update install".

install

root@www# freebsd-update install
src component not installed, skipped
Installing updates...
Kernel updates have been installed.  Please reboot and run
"/usr/sbin/freebsd-update install" again to finish installing updates.

reboot, install

root@www# freebsd-update install
src component not installed, skipped
Installing updates...
Completing this upgrade requires removing old shared object files.
Please rebuild all installed 3rd party software (e.g., programs
installed from the ports tree) and then run "/usr/sbin/freebsd-update install"
again to finish installing updates.

just install again, I'm going to reinstall all packages anyway

root@www# freebsd-update install
src component not installed, skipped
Installing updates... done.

FreeBSD 11.4-release-p13 is in

root@www# freebsd-version -ku
11.4-RELEASE-p9
11.4-RELEASE-p13

2022-08-18: ada0p2 - I also made a databasebackup (using mysqldump), and copies of various files. A list of installed packages as well. Check various settings

root@www# pkg -vv | grep url
    url             : "pkg+http://pkg.FreeBSD.org/FreeBSD:10:amd64/quarterly",

and

root@www# cat /boot/loader.conf
coretemp_load="YES"

2022-08-18: ada0p2 - do a backup

root@www# dump -C16 -0aLf /zb/ndwiki-backups/20220817/ada0p2_dump.file /dev/ada0p2
  DUMP: Date of this level 0 dump: Thu Aug 18 11:28:05 2022
  DUMP: Date of last level 0 dump: the epoch
  DUMP: Dumping snapshot of /dev/ada0p2 (/) to /zb/ndwiki-backups/20220817/ada0p2_dump.file
  DUMP: mapping (Pass I) [regular files]
  DUMP: Cache 16 MB, blocksize = 65536
  DUMP: mapping (Pass II) [directories]
  DUMP: estimated 13325280 tape blocks.
  DUMP: dumping (Pass III) [directories]
  DUMP: dumping (Pass IV) [regular files]
  DUMP: DUMP: 13324160 tape blocks on 1 volume
  DUMP: finished in 189 seconds, throughput 70498 KBytes/sec
  DUMP: Closing /zb/ndwiki-backups/20220817/ada0p2_dump.file
  DUMP: DUMP IS DONE

check backup file

root@www# ll -h /zb/ndwiki-backups/20220818/
total 13327464
drwxr-xr-x  2 root   wheel   512B Aug 18 11:28 ./
drwxr-xr-x  3 tingo  wheel   512B Aug 18 11:34 ../
-rw-r--r--  1 root   wheel    13G Aug 18 11:31 ada0p2_dump.file

(I realized the mistake, and renamed the backup directory)

2022-08-18: ada0p2 - connecting a (usb) hard drive (for backups) to the machine. From /var/log/messages

Aug 18 10:57:54 www kernel: ugen0.2: <Western Digital My Passport 2626> at usbus0
Aug 18 10:57:54 www kernel: umass0: <Western Digital My Passport 2626, class 0/0, rev 3.20/10.34, addr 3> on usbus0
Aug 18 10:57:54 www kernel: umass0:  SCSI over Bulk-Only; quirks = 0xc001
Aug 18 10:57:54 www kernel: umass0:2:0:-1: Attached to scbus2
Aug 18 10:57:54 www kernel: da0 at umass-sim0 bus 0 scbus2 target 0 lun 0
Aug 18 10:57:54 www kernel: da0: <WD My Passport 2626 1034> Fixed Direct Access SPC-4 SCSI device
Aug 18 10:57:54 www kernel: da0: Serial Number 57583832413731304E394E37
Aug 18 10:57:54 www kernel: da0: 400.000MB/s transfers
Aug 18 10:57:54 www kernel: da0: 1907697MB (3906963456 512 byte sectors)
Aug 18 10:57:54 www kernel: da0: quirks=0x2<NO_6_BYTE>
Aug 18 10:57:54 www kernel: ses0 at umass-sim0 bus 0 scbus2 target 0 lun 1
Aug 18 10:57:54 www kernel: ses0: <WD SES Device 1034> Fixed Enclosure Services SPC-4 SCSI device
Aug 18 10:57:54 www kernel: ses0: Serial Number 57583832413731304E394E37
Aug 18 10:57:54 www kernel: ses0: 400.000MB/s transfers
Aug 18 10:57:54 www kernel: 
Aug 18 10:57:54 www kernel: ses0: SCSI-3 ENC Device

usbconfig shows

root@www# usbconfig -d ugen0.2
ugen0.2: <Western Digital My Passport 2626> at usbus0, cfg=0 md=HOST spd=SUPER (5.0Gbps) pwr=ON (224mA)

mount the drive

root@www# mount /dev/da0p1 /zb

check it

root@www# ll /zb
total 20
drwxrwxr-x   5 root   wheel     512 Aug 17 21:23 ./
drwxr-xr-x  19 root   wheel     512 Aug 16 10:39 ../
drwxrwxr-x   2 root   operator  512 Aug 17 17:24 .snap/
drwxr-xr-x   2 tingo  wheel     512 Aug 17 19:14 fio_test/
drwxr-xr-x   2 tingo  wheel     512 Aug 17 21:23 ndwiki-backups/

we're ready.

2020-09-30: ada0p2 - freebsd-update fetch

root@www# freebsd-update fetch
[..]
No updates needed to update system to 10.4-RELEASE-p13.

WARNING: FreeBSD 10.4-RELEASE-p13 HAS PASSED ITS END-OF-LIFE DATE.
Any security issues discovered after Thu Nov  1 01:00:00 CET 2018
will not have been corrected.

ok, at least I know.

2020-09-30: ada0p2 - after power on (due to power outage) fsck revealed that ada0p2 (root fs) wasn't completely clean, so I rebooted the machine into single-user and ran fsck manually.

2019-03-08: ada0p2 - I can't find any reason in /var/log/messages or dmesg for yesterday's problem.

2019-03-08: ada0p2 - rebooted the server.

2019-03-07: web server not responding, server responds to ping, can ssh to it, but don't get a shell.

2019-01-20: ada0p2 - after a reboot, the machine now runs FreeBSD 10.4-release-p13:

$ freebsd-version -ku
10.4-RELEASE-p13
10.4-RELEASE-p13

kernel

$ uname -a
FreeBSD www.ndwiki.org 10.4-RELEASE-p13 FreeBSD 10.4-RELEASE-p13 #0: Thu Sep 27 10:09:35 UTC 2018     root@amd64-builder.daemonology.net:/usr/obj/usr/src/sys/GENERIC  amd64

ok

2019-01-20: ada0p2 - freebsd-update - upgrade to FreeBSD 10.4-release

root@www# freebsd-update upgrade -r 10.4-RELEASE
[..]
The following components of FreeBSD seem to be installed:
kernel/generic world/base world/lib32

The following components of FreeBSD do not seem to be installed:
world/doc world/games
[..]
Fetching metadata signature for 10.4-RELEASE from update1.freebsd.org... done.
[..]
Applying patches... done.
Fetching 145 files... done.
Attempting to automatically merge changes in files... done.

The following files are affected by updates, but no changes have
been downloaded because the files have been modified locally:
/.profile
/root/.profile
The following files will be removed as part of updating to 10.4-RELEASE-p13:
/boot/kernel/hv_ata_pci_disengage.ko
/boot/kernel/hv_ata_pci_disengage.ko.symbols
/usr/share/man/man2/cap_rights_get.2.gz
/usr/share/man/man4/hv_ata_pci_disengage.4.gz
/usr/share/man/man9/rman_await_resource.9.gz
The following files will be added as part of updating to 10.4-RELEASE-p13:
/boot/kernel/geom_flashmap.ko
/boot/kernel/geom_flashmap.ko.symbols
[..]
The following files will be updated as part of updating to 10.4-RELEASE-p13:
/.cshrc
[..]
/var/db/etcupdate/log
/var/db/mergemaster.mtree
/var/yp/Makefile.dist
To install the downloaded upgrades, run "/usr/sbin/freebsd-update install".

install

root@www# freebsd-update install
src component not installed, skipped
Installing updates...
Kernel updates have been installed.  Please reboot and run
"/usr/sbin/freebsd-update install" again to finish installing updates.
reboot, then freebsd-update install again
root@www# freebsd-update install
src component not installed, skipped
Installing updates... done.

ok

2019-01-20: ada0p2 - after a reboot, FreeBSD 10.3-release-p29 is in

$ freebsd-version -ku
10.3-RELEASE-p29
10.3-RELEASE-p29

kernel

$ uname -a
FreeBSD www.ndwiki.org 10.3-RELEASE-p29 FreeBSD 10.3-RELEASE-p29 #0: Tue Apr  3 19:55:05 UTC 2018     root@amd64-builder.daemonology.net:/usr/obj/usr/src/sys/GENERIC  amd64

and

2019-01-20: ada0p2 - the machine has been up 242 days

root@www# date;uptime
Sun Jan 20 18:10:23 CET 2019
 6:10PM  up 242 days,  6:17, 1 user, load averages: 1.32, 1.32, 1.22

ok.

2019-01-20: ada0p2 - freebsd-update fetch

root@www# freebsd-update fetch
[..]
The following files will be removed as part of updating to 10.3-RELEASE-p29:
/usr/share/zoneinfo/Pacific/Johnston
The following files will be added as part of updating to 10.3-RELEASE-p29:
/usr/share/zoneinfo/America/Punta_Arenas
/usr/share/zoneinfo/Asia/Atyrau
/usr/share/zoneinfo/Europe/Saratov
The following files will be updated as part of updating to 10.3-RELEASE-p29:
/bin/freebsd-version
/boot/boot1.efi
/boot/boot1.efifat
/boot/kernel/cam.ko
/boot/kernel/cam.ko.symbols
[..]
/var/db/mergemaster.mtree

WARNING: FreeBSD 10.3-RELEASE-p18 HAS PASSED ITS END-OF-LIFE DATE.
Any security issues discovered after Tue May  1 02:00:00 CEST 2018
will not have been corrected.

install

root@www# freebsd-update install
src component not installed, skipped
Installing updates... done.

now only reboot remains.

2017-09-13: ada0p2 - bluetooth is enabled:

root@www# hccontrol -n ubt0hci read_local_name
Local name: www.ndwiki.org (ubt0)
root@www# hccontrol -n ubt0hci read_local_version_information
HCI version: ? [0x6]
HCI revision: 0x0a
LMP version: ? [0x6]
LMP sub-version: 0x8821
Manufacturer: ? [0x5d]
root@www# hccontrol -n ubt0hci read_local_supported_features
Features: 0xff 0xff 0xff 0xfe 0xdb 0xff 0x7b 0x87
<3-Slot> <5-Slot> <Encryption> <Slot offset>
<Timing accuracy> <Switch> <Hold mode> <Sniff mode>
<Park mode> <RSSI> <Channel quality> <SCO link>
<HV2 packets> <HV3 packets> <u-law log> <A-law log> <CVSD>
<Paging scheme> <Power control> <Transparent SCO data>
<Flow control lag (bit0)> <Flow control lag (bit1)>
<Flow control lag (bit2)> <Unknown2.7>

I can even do an inquiry

root@www# hccontrol -n ubt0hci inquiry
Inquiry complete. Status: No error [00]

even if it doesn't return results, I don't want that.

root@www# service bluetooth status
/etc/rc.d/bluetooth: unknown directive 'status'.
Usage: /etc/rc.d/bluetooth [fast|force|one|quiet](start|stop|restart|rcvar|enabled)
root@www# service bluetooth rcvar
# bluetooth
#

ok, no status, and no enable variable.

root@www# service bluetooth stop
/etc/rc.d/bluetooth: ERROR: Unsupported device:

that's funny. Ok, the name is needed:

root@www# service bluetooth stop ubt0

test

root@www# hccontrol -n ubt0hci read_local_name
hccontrol: Could not find HCI nodes

looks better.

2017-08-22: ada0p2 - mediawiki - today I uploaded a large picture and got an error message "Error creating thumbnail: File with dimensions greater than 12.5 MP". Turns out I have to set

# 2017-08-22: $wgMaxImageArea defaults to 1.25e7 (12.5 MP, or 3500 x 3500) which is too little
#             increase to 7.2e7 (72 MP, 9000 x 9000)
$wgMaxImageArea = 7.2e7;

in LocalSettings.php. Works now.

2017-07-30: ada0p2 - pkg - check all packages

root@www# pkg check -sa
Checking all packages: 100%

ok.

2017-07-30: ada0p2 - pkg - reinstall mediawiki package

root@www# pkg install --no-repo-update --force mediawiki126-1.26.4
The following 1 package(s) will be affected (of 0 checked):

Installed packages to be REINSTALLED:
 mediawiki126-1.26.4

Number of packages to be reinstalled: 1

17 MiB to be downloaded.

Proceed with this action? [y/N]: y
[1/1] Fetching mediawiki126-1.26.4.txz: 100%   17 MiB   3.6MB/s    00:05    
Checking integrity... done (0 conflicting)
[1/1] Reinstalling mediawiki126-1.26.4...
Extracting mediawiki126-1.26.4: 100%
Message from mediawiki126-1.26.4:
**** NOTE ****
Remember to check

/usr/local/www/mediawiki/INSTALL

and

/usr/local/www/mediawiki/UPGRADE

for details

===>   NOTICE:

This port is deprecated; you may wish to reconsider installing it:

Upstream support EoL.

It is scheduled to be removed on or after 2017-07-08.

worked nicely. And now the wiki works again.

2017-07-30: ada0p2 - after replacing he SSD and rebooting:

root@www# smartctl -i /dev/ada0
smartctl 6.5 2016-05-07 r4318 [FreeBSD 10.3-RELEASE-p18 amd64] (local build)
Copyright (C) 2002-16, Bruce Allen, Christian Franke, www.smartmontools.org

=== START OF INFORMATION SECTION ===
Device Model:     TOSHIBA THNSNJ128GMCU
Serial Number:    45UB31AQK8XX
LU WWN Device Id: 5 00080d c0022a914
Firmware Version: JUT10101
User Capacity:    128,035,676,160 bytes [128 GB]
Sector Size:      512 bytes logical/physical
Rotation Rate:    Solid State Device
Form Factor:      < 1.8 inches
Device is:        Not in smartctl database [for details use: -P showall]
ATA Version is:   ACS-2 (minor revision not indicated)
SATA Version is:  SATA 3.1, 6.0 Gb/s (current: 6.0 Gb/s)
Local Time is:    Sun Jul 30 00:07:38 2017 CEST
SMART support is: Available - device has SMART capability.
SMART support is: Enabled

ok.

2017-07-29: ada0p2 - do a backup to da0p2:

root@www# mount /dev/da0p2 /zb
root@www# cd /zb

do dump and restore

root@www# dump -C16 -0af - /dev/ada0p2 | restore -r -f -
  DUMP: WARNING: should use -L when dumping live read-write filesystems!
  DUMP: Date of this level 0 dump: Sat Jul 29 23:40:14 2017
  DUMP: Date of last level 0 dump: the epoch
  DUMP: Dumping /dev/ada0p2 (/) to standard output
  DUMP: mapping (Pass I) [regular files]
  DUMP: Cache 16 MB, blocksize = 65536
  DUMP: mapping (Pass II) [directories]
  DUMP: estimated 7780055 tape blocks.
  DUMP: dumping (Pass III) [directories]
  DUMP: dumping (Pass IV) [regular files]
warning: ./.snap: File exists
Warning: `.' missing from directory ./usr/local/www/mediawiki/resources/src/mediawiki.skinning/images
Warning: `..' missing from directory ./usr/local/www/mediawiki/resources/src/mediawiki.skinning/images
expected next file 963227, got 963223
expected next file 963227, got 963224
expected next file 963227, got 963225
expected next file 963227, got 963226
expected next file 963231, got 963228
expected next file 963231, got 963229
expected next file 963231, got 963230
expected next file 10677646, got 10677636
expected next file 10677646, got 10677637
expected next file 10677646, got 10677638
expected next file 10677646, got 10677639
expected next file 10677646, got 10677640
expected next file 10677646, got 10677641
expected next file 10677646, got 10677642
expected next file 10677646, got 10677643
expected next file 10677646, got 10677644
expected next file 10677646, got 10677645
expected next file 10684844, got 10684815
expected next file 10684844, got 10684822
expected next file 10684844, got 10684823
expected next file 10684844, got 10684824
expected next file 10684844, got 10684825
expected next file 10684844, got 10684826
expected next file 10684844, got 10684827
expected next file 10684844, got 10684828
expected next file 10684844, got 10684829
expected next file 10684844, got 10684830
expected next file 10684844, got 10684831
expected next file 10684844, got 10684832
expected next file 10684844, got 10684833
expected next file 10684844, got 10684834
expected next file 10684844, got 10684835
expected next file 10684844, got 10684836
expected next file 10684844, got 10684837
expected next file 10684844, got 10684838
expected next file 10684844, got 10684839
expected next file 10684844, got 10684840
expected next file 10684844, got 10684841
expected next file 10684844, got 10684842
expected next file 10684844, got 10684843
  DUMP: DUMP: 7779018 tape blocks
  DUMP: finished in 243 seconds, throughput 32012 KBytes/sec
  DUMP: DUMP IS DONE

ok.

2017-07-29: ada0p2 - create a filesystem on da0p2

root@www# newfs -U /dev/da0p2
/dev/da0p2: 117760.0MB (241172480 sectors) block size 32768, fragment size 4096
 using 189 cylinder groups of 626.09MB, 20035 blks, 80256 inodes.
 with soft updates
super-block backups (for fsck_ffs -b #) at:
 192, 1282432, 2564672, 3846912, 5129152, 6411392, 7693632, 8975872, 10258112, 11540352, 12822592, 14104832, 15387072,
 16669312, 17951552, 19233792, 20516032, 21798272, 23080512, 24362752, 25644992, 26927232, 28209472, 29491712, 30773952,
 32056192, 33338432, 34620672, 35902912, 37185152, 38467392, 39749632, 41031872, 42314112, 43596352, 44878592, 46160832,
 47443072, 48725312, 50007552, 51289792, 52572032, 53854272, 55136512, 56418752, 57700992, 58983232, 60265472, 61547712,
 62829952, 64112192, 65394432, 66676672, 67958912, 69241152, 70523392, 71805632, 73087872, 74370112, 75652352, 76934592,
 78216832, 79499072, 80781312, 82063552, 83345792, 84628032, 85910272, 87192512, 88474752, 89756992, 91039232, 92321472,
 93603712, 94885952, 96168192, 97450432, 98732672, 100014912, 101297152, 102579392, 103861632, 105143872, 106426112, 107708352,
 108990592, 110272832, 111555072, 112837312, 114119552, 115401792, 116684032, 117966272, 119248512, 120530752, 121812992,
 123095232, 124377472, 125659712, 126941952, 128224192, 129506432, 130788672, 132070912, 133353152, 134635392, 135917632,
 137199872, 138482112, 139764352, 141046592, 142328832, 143611072, 144893312, 146175552, 147457792, 148740032, 150022272,
 151304512, 152586752, 153868992, 155151232, 156433472, 157715712, 158997952, 160280192, 161562432, 162844672, 164126912,
 165409152, 166691392, 167973632, 169255872, 170538112, 171820352, 173102592, 174384832, 175667072, 176949312, 178231552,
 179513792, 180796032, 182078272, 183360512, 184642752, 185924992, 187207232, 188489472, 189771712, 191053952, 192336192,
 193618432, 194900672, 196182912, 197465152, 198747392, 200029632, 201311872, 202594112, 203876352, 205158592, 206440832,
 207723072, 209005312, 210287552, 211569792, 212852032, 214134272, 215416512, 216698752, 217980992, 219263232, 220545472,
 221827712, 223109952, 224392192, 225674432, 226956672, 228238912, 229521152, 230803392, 232085632, 233367872, 234650112,
 235932352, 237214592, 238496832, 239779072, 241061312

ok.

2017-07-29: ada0p2 - add bootcode to da0p1

root@www# gpart bootcode -b /boot/pmbr -p /boot/gptboot -i1 da0
bootcode written to da0

ok.

2017-07-29: ada0p2 - add partitions on da0 (mimic ada0)

root@www# gpart add -t freebsd-boot -s 512k da0
da0p1 added
root@www# gpart add -t freebsd-ufs -s 115G da0
da0p2 added
root@www# gpart add -t freebsd-swap da0
da0p3 added

show

root@www# gpart show -p /dev/da0
=>       34  250069613    da0  GPT  (119G)
         34       1024  da0p1  freebsd-boot  (512K)
       1058  241172480  da0p2  freebsd-ufs  (115G)
  241173538    8896109  da0p3  freebsd-swap  (4.2G)

ok.

2017-07-29: ada0p2 - delete all partitions on da0, and create a new one.

root@www# gpart delete -i 5 da0
da0p5 deleted
root@www# gpart delete -i 4 da0
da0p4 deleted
root@www# gpart delete -i 3 da0
da0p3 deleted
root@www# gpart delete -i 2 da0
da0p2 deleted
root@www# gpart delete -i 1 da0
da0p1 deleted

delete the GPT partition too

root@www# gpart destroy /dev/da0
da0 destroyed

create a new GPT

root@www# gpart create -s GPT da0
da0 created
root@www# gpart show -p /dev/da0
=>       34  250069613  da0  GPT  (119G)
         34  250069613       - free -  (119G)

ok.

2017-07-29: ada0p2 - partition layout of new SSD:

root@www# gpart show -p /dev/da0
=>       34  250069613    da0  GPT  (119G)
         34       2014         - free -  (1.0M)
       2048    2097152  da0p1  !de94bba4-06d1-4d40-a16a-bfd50179d6ac  (1.0G)
    2099200     204800  da0p2  efi  (100M)
    2304000     262144  da0p3  ms-reserved  (128M)
    2566144  223301632  da0p4  ms-basic-data  (106G)
  225867776   24200290  da0p5  !de94bba4-06d1-4d40-a16a-bfd50179d6ac  (12G)
  250068066       1581         - free -  (791K)

ok. The internal SSD looks like this:

root@www# gpart show -p ada0
=>       34  234441581    ada0  GPT  (112G)
         34       1024  ada0p1  freebsd-boot  (512K)
       1058  226491392  ada0p2  freebsd-ufs  (108G)
  226492450    7949164  ada0p3  freebsd-swap  (3.8G)
  234441614          1          - free -  (512B)

ok.

2017-07-29: ada0p2 - pkg - reinstall mediawiki

root@www# pkg install --no-repo-update mediawiki126-1.26.4
Checking integrity... done (0 conflicting)
The most recent version of packages are already installed
root@www# pkg install --no-repo-update --force mediawiki126-1.26.4
Checking integrity... done (0 conflicting)
The following 1 package(s) will be affected (of 0 checked):

Installed packages to be REINSTALLED:
    mediawiki126-1.26.4

Number of packages to be reinstalled: 1

Proceed with this action? [y/N]: y
[1/1] Reinstalling mediawiki126-1.26.4...
[1/1] Extracting mediawiki126-1.26.4: 100%
pkg: Fail to rename /usr/local/www/mediawiki/resources/src/mediawiki.skinning/images/.document-rtl.svg.CPDVDdmzwDCE -> /usr/local/www/mediawiki/resources/src/mediawiki.skinning/images/document-rtl.svg:Input/output error

Hmmm, I got this in /var/log/messages:

Jul 29 15:03:40 www kernel: g_vfs_done():ada0p2[READ(offset=4478702714880, length=32768)]error = 5
Jul 29 15:03:40 www kernel: g_vfs_done():ada0p2[READ(offset=4478702714880, length=32768)]error = 5

not good. Tried once more and got a kernel crash

Jul 29 15:11:29 www kernel: panic: ufsdirhash_findfree: free mismatch
Jul 29 15:11:29 www kernel: cpuid = 1
Jul 29 15:11:29 www kernel: KDB: stack backtrace:
Jul 29 15:11:29 www kernel: #0 0xffffffff8098e7e0 at kdb_backtrace+0x60
Jul 29 15:11:29 www kernel: #1 0xffffffff809514b6 at vpanic+0x126
Jul 29 15:11:29 www kernel: #2 0xffffffff80951383 at panic+0x43
Jul 29 15:11:29 www kernel: #3 0xffffffff80bb5641 at ufsdirhash_findfree+0x181
Jul 29 15:11:29 www kernel: #4 0xffffffff80bb72e0 at ufs_lookup_ino+0x2c0
Jul 29 15:11:29 www kernel: #5 0xffffffff80e80bc1 at VOP_CACHEDLOOKUP_APV+0xa1
Jul 29 15:11:29 www kernel: #6 0xffffffff809e48d6 at vfs_cache_lookup+0xd6
Jul 29 15:11:29 www kernel: #7 0xffffffff80e80ab1 at VOP_LOOKUP_APV+0xa1
Jul 29 15:11:29 www kernel: #8 0xffffffff809ecff1 at lookup+0x5a1
Jul 29 15:11:29 www kernel: #9 0xffffffff809ec754 at namei+0x4d4
Jul 29 15:11:29 www kernel: #10 0xffffffff80a05d17 at vn_open_cred+0xf7
Jul 29 15:11:29 www kernel: #11 0xffffffff809ff14f at kern_openat+0x26f
Jul 29 15:11:29 www kernel: #12 0xffffffff80d56e3f at amd64_syscall+0x40f
Jul 29 15:11:29 www kernel: #13 0xffffffff80d3c09b at Xfast_syscall+0xfb
Jul 29 15:11:29 www kernel: Uptime: 31d2h21m15s
Jul 29 15:11:29 www kernel: Dumping 1049 out of 16025 MB:..2%..11%..22%..31%..42%..51%..62%..71%..81%..92%Copyright

really not good.

2017-07-29: ada0p2 - ndwiki - I got an error message instead of the wiki page today:

Warning: Unexpected character in input: '.' (ASCII=4) state=0 in /usr/local/www/mediawiki/includes/Html.php on line 779

Parse error: syntax error, unexpected 'area' (T_STRING), expecting '(' in /usr/local/www/mediawiki/includes/Html.php on line 779

So I inspected the file:

root@www# file includes/Html.php
includes/Html.php: data

the other files look ok:

root@www# file includes/H*
includes/HistoryBlob.php:   PHP script, ASCII text
includes/Hooks.php:         PHP script, ASCII text
includes/Html.php:          data
includes/HtmlFormatter.php: PHP script, ASCII text
includes/HttpFunctions.php: PHP script, ASCII text
root@www# ll includes/H*
-rw-r--r--  1 root  wheel  16639 Aug 23  2016 includes/HistoryBlob.php
-rw-r--r--  1 root  wheel   6690 Aug 23  2016 includes/Hooks.php
-rw-r--r--  1 root  wheel  32871 Aug 23  2016 includes/Html.php
-rw-r--r--  1 root  wheel  11586 Aug 23  2016 includes/HtmlFormatter.php
-rw-r--r--  1 root  wheel  31482 Aug 23  2016 includes/HttpFunctions.php

looking closer at the file, it is mostly correct, with some corrupted characters. Strange. I fixed that file, but there are other corrupted files in includes. Perhaps I should reinstall mediawiki?

2017-06-30: ada0p2 - backup - borgbackup (archivers/py-borgbackup) is a nice tool, but it looks like the package is missing.

2017-06-30: ada0p2 - pkg - this machine uses the quarterly repository.

root@www# pkg -vv | grep url
    url             : "pkg+http://pkg.FreeBSD.org/FreeBSD:10:amd64/quarterly",

ok.

2017-06-28: ada0p2 - backup - try to do a backup

root@www# dump -C16 -0aLf /zb/ndwiki-backups/20170628/ada0p2_dump.file /dev/ada0p2
mksnap_ffs: Cannot create snapshot //.snap/dump_snapshot: /: Snapshots are not yet supported when running with journaled soft updates: Operation not supported
dump: Cannot create //.snap/dump_snapshot: No such file or directory

oh, that's not good.

root@www# mount
/dev/ada0p2 on / (ufs, local, journaled soft-updates)
devfs on /dev (devfs, local, multilabel)
/dev/da0p1 on /zb (ufs, local, soft-updates)

hmm, what do we do now? Try without '-L'?

root@www# dump -C16 -0af /zb/ndwiki-backups/20170628/ada0p2_dump.file /dev/ada0p2
  DUMP: WARNING: should use -L when dumping live read-write filesystems!
  DUMP: Date of this level 0 dump: Wed Jun 28 14:37:39 2017
  DUMP: Date of last level 0 dump: the epoch
  DUMP: Dumping /dev/ada0p2 (/) to /zb/ndwiki-backups/20170628/ada0p2_dump.file
  DUMP: mapping (Pass I) [regular files]
  DUMP: Cache 16 MB, blocksize = 65536
  DUMP: mapping (Pass II) [directories]
  DUMP: estimated 5344566 tape blocks.
  DUMP: dumping (Pass III) [directories]
  DUMP: dumping (Pass IV) [regular files]
  DUMP: DUMP: 5344332 tape blocks on 1 volume
  DUMP: finished in 88 seconds, throughput 60731 KBytes/sec
  DUMP: Closing /zb/ndwiki-backups/20170628/ada0p2_dump.file
  DUMP: DUMP IS DONE

and the files is

root@www# ls -lh /zb/ndwiki-backups/20170628/ada0p2_dump.file
-rw-r--r--  1 root  wheel   5.1G Jun 28 14:39 /zb/ndwiki-backups/20170628/ada0p2_dump.file

finally unmount the usb drive

root@www# umount /zb

ok.

2017-06-28: ada0p2 - backup - I'll do a manual backup on an external drive, just to be on the safe side. the drive is a 2 TB Seagate, USB 3.0.

root@www# usbconfig -d ugen0.2
ugen0.2: <BUP Slim BK Seagate> at usbus0, cfg=0 md=HOST spd=SUPER (5.0Gbps) pwr=ON (36mA)

from /var/log/messages

Jun 28 13:25:10 www kernel: ugen0.2: <Seagate> at usbus0
Jun 28 13:25:10 www kernel: umass0: <Seagate BUP Slim BK, class 0/0, rev 3.00/1.00, addr 3> on usbus0
Jun 28 13:25:10 www kernel: umass0:  SCSI over Bulk-Only; quirks = 0xc101
Jun 28 13:25:10 www kernel: umass0:2:0:-1: Attached to scbus2
Jun 28 13:25:10 www kernel: da0 at umass-sim0 bus 0 scbus2 target 0 lun 0
Jun 28 13:25:10 www kernel: da0: <Seagate BUP Slim BK 0304> Fixed Direct Access SPC-4 SCSI device
Jun 28 13:25:10 www kernel: da0: Serial Number NA7WAYTC
Jun 28 13:25:10 www kernel: da0: 400.000MB/s transfers
Jun 28 13:25:10 www kernel: da0: 1907729MB (3907029167 512 byte sectors)
Jun 28 13:25:10 www kernel: da0: quirks=0x2<NO_6_BYTE>

gpart says

root@www# gpart show -p da0
=>        63  3907029104    da0  MBR  (1.8T)
          63        1985         - free -  (993K)
        2048  3907027119  da0s1  ntfs  [active]  (1.8T)

that won't do.

root@www# gpart destroy -F da0
da0 destroyed

and create gpt partitioning

root@www# gpart create -s GPT da0
da0 created

add a freebsd-ufs partition

root@www# gpart add -t freebsd-ufs da0
da0p1 added

how does it look?

root@www# gpart show -p da0
=>        34  3907029100    da0  GPT  (1.8T)
          34           6         - free -  (3.0K)
          40  3907029088  da0p1  freebsd-ufs  (1.8T)
  3907029128           6         - free -  (3.0K)

ok, add filesystem

root@www# newfs -U /dev/da0p1
/dev/da0p1: 1907729.0MB (3907029088 sectors) block size 32768, fragment size 4096
    using 3048 cylinder groups of 626.09MB, 20035 blks, 80256 inodes.
    with soft updates
super-block backups (for fsck_ffs -b #) at:
 192, 1282432, 2564672, 3846912, 5129152, 6411392, 7693632, 8975872, 10258112, 11540352, 12822592, 14104832, 15387072,
[...]
 3885187392, 3886469632, 3887751872, 3889034112, 3890316352, 3891598592, 3892880832, 3894163072, 3895445312,
 3896727552, 3898009792, 3899292032, 3900574272, 3901856512, 3903138752, 3904420992, 3905703232, 3906985472

ok.

make a backup mount point

root@www# mkdir /zb

mount it

root@www# mount /dev/da0p1 /zb

create directories

root@www# mkdir -p /zb/ndwiki-backups/20170628

ok

2016-06-28: ada0p2 - after upgrading all packages, I rebooted the server - the wiki still works. I ran mysqlcheck -p --all-databases and it was ok.

2016-06-28: ada0p2 - pkg - run 'pkg upgrade' (I first ran 'pkg upgrade -n' to look at the list of upgrades)

root@www# pkg upgrade
Updating FreeBSD repository catalogue...
FreeBSD repository is up to date.
All repositories are up to date.
Checking for upgrades (78 candidates): 100%
Processing candidates (78 candidates): 100%
The following 84 package(s) will be affected (of 0 checked):

New packages to be INSTALLED:
    trousers: 0.3.14_1
    tpm-emulator: 0.7.4_1
    libunistring: 0.9.7
    libevent: 2.1.8
    liblz4: 1.7.5,1
    libnghttp2: 1.21.0

Installed packages to be UPGRADED:
    xproto: 7.0.28 -> 7.0.31
    webp: 0.5.0 -> 0.5.2_1
    tiff: 4.0.6_1 -> 4.0.8
    smartmontools: 6.4_2 -> 6.5_2
    python27: 2.7.11_2 -> 2.7.13_3
    png: 1.6.21 -> 1.6.29
    pkgconf: 0.9.12_1 -> 1.3.0,1
    php56-zlib: 5.6.21 -> 5.6.30
    php56-xmlreader: 5.6.21 -> 5.6.30
    php56-xml: 5.6.21 -> 5.6.30
    php56-sockets: 5.6.21 -> 5.6.30
    php56-session: 5.6.21 -> 5.6.30
    php56-readline: 5.6.21 -> 5.6.30
    php56-pcntl: 5.6.21 -> 5.6.30
    php56-mysql: 5.6.21 -> 5.6.30
    php56-mbstring: 5.6.21 -> 5.6.30
    php56-json: 5.6.21 -> 5.6.30
    php56-iconv: 5.6.21 -> 5.6.30
    php56-hash: 5.6.21 -> 5.6.30
    php56-dom: 5.6.21 -> 5.6.30
    php56-ctype: 5.6.21 -> 5.6.30
    php56: 5.6.21 -> 5.6.30
    perl5: 5.20.3_12 -> 5.24.1
    pecl-intl: 3.0.0_2 -> 3.0.0_7
    pecl-imagick: 3.4.1 -> 3.4.3
    pcre: 8.38_1 -> 8.40
    p5-Socket: 2.021 -> 2.024
    p5-Net-SSLeay: 1.72 -> 1.81
    p5-Net-SMTP-SSL: 1.03 -> 1.04
    p5-IO-Socket-SSL: 2.024 -> 2.044
    p5-IO-Socket-IP: 0.37 -> 0.39
    p11-kit: 0.23.2 -> 0.23.5
    openjpeg: 2.1.1 -> 2.1.2_1
    nettle: 3.2 -> 3.3
    mysql56-server: 5.6.30 -> 5.6.36
    mysql56-client: 5.6.30 -> 5.6.36
    mod_php56: 5.6.21 -> 5.6.30
    mediawiki126: 1.26.2 -> 1.26.4
    libxml2: 2.9.3 -> 2.9.4
    libxcb: 1.11.1 -> 1.12_2
    libtasn1: 4.8 -> 4.10
    libpthread-stubs: 0.3_6 -> 0.4
    liblqr-1: 0.4.1_8 -> 0.4.2
    libidn: 1.31 -> 1.33_1
    libiconv: 1.14_9 -> 1.14_10
    libedit: 3.1.20150325_2 -> 3.1.20150325_2,1
    libX11: 1.6.3,1 -> 1.6.5,1
    lcms2: 2.7_2 -> 2.8
    jpeg-turbo: 1.4.2 -> 1.5.1
    jbig2dec: 0.12 -> 0.13
    indexinfo: 0.2.4 -> 0.2.6
    icu: 55.1 -> 58.2_2,1
    gsfonts: 8.11_6 -> 8.11_8
    gnutls: 3.4.10 -> 3.5.13
    gmp: 5.1.3_3 -> 6.1.2
    glib: 2.46.2 -> 2.46.2_5
    git: 2.7.4_1 -> 2.13.0_1
    giflib: 5.1.3 -> 5.1.4
    gettext-runtime: 0.19.7 -> 0.19.8.1_1
    gdbm: 1.11_2 -> 1.12
    freetype2: 2.6.3 -> 2.8
    fontconfig: 2.11.1_1,1 -> 2.12.1,1
    fftw3: 3.3.3_2 -> 3.3.6.p1_1
    expat: 2.1.0_3 -> 2.2.0_1
    dbus: 1.8.20 -> 1.10.14_2
    db5: 5.3.28_3 -> 5.3.28_6
    cvsps: 2.1_1 -> 2.1_2
    curl: 7.48.0_1 -> 7.54.1
    cups: 2.1.3_2 -> 2.2.2_1
    ca_root_nss: 3.22.2 -> 3.31
    apr: 1.5.2.1.5.4 -> 1.5.2.1.5.4_2
    apache24: 2.4.20_1 -> 2.4.26
    ImageMagick-nox11: 6.9.4.1,1 -> 6.9.6.4_2,1

Installed packages to be REINSTALLED:
    p5-Mozilla-CA-20160104 (direct dependency changed: perl5)
    p5-GSSAPI-0.28_1 (direct dependency changed: perl5)
    p5-Error-0.17024 (direct dependency changed: perl5)
    p5-Digest-HMAC-1.03_1 (direct dependency changed: perl5)
    p5-Authen-SASL-2.16_1 (direct dependency changed: perl5)

Number of packages to be installed: 6
Number of packages to be upgraded: 73
Number of packages to be reinstalled: 5

The operation will free 12 MiB.
120 MiB to be downloaded.

Proceed with this action? [y/N]: y
[...]
Checking integrity... done (1 conflicting)
  - trousers-0.3.14_1 conflicts with trousers-tddl-0.3.10_7 on /usr/local/include/trousers/trousers.h
Checking integrity... done (0 conflicting)
Conflicts with the existing packages have been found.
One more solver iteration is needed to resolve them.
The following 85 package(s) will be affected (of 0 checked):
[...]

ok. From /var/log/messages

Jun 28 12:35:01 www pkg: pkg upgraded: 1.7.2 -> 1.10.1
Jun 28 12:42:39 www pkg: indexinfo upgraded: 0.2.4 -> 0.2.6
Jun 28 12:42:39 www pkg: gettext-runtime upgraded: 0.19.7 -> 0.19.8.1_1
Jun 28 12:42:39 www pkg: jpeg-turbo upgraded: 1.4.2 -> 1.5.1
Jun 28 12:42:39 www pkg: xproto upgraded: 7.0.28 -> 7.0.31
Jun 28 12:42:39 www pkg: libxml2 upgraded: 2.9.3 -> 2.9.4
Jun 28 12:42:48 www pkg: python27 upgraded: 2.7.11_2 -> 2.7.13_3
Jun 28 12:42:55 www pkg: perl5 upgraded: 5.20.3_12 -> 5.24.1
Jun 28 12:42:56 www pkg: pcre upgraded: 8.38_1 -> 8.40
Jun 28 12:42:56 www pkg: libiconv upgraded: 1.14_9 -> 1.14_10
Jun 28 12:42:56 www pkg: tiff upgraded: 4.0.6_1 -> 4.0.8
Jun 28 12:42:56 www pkg: libpthread-stubs upgraded: 0.3_6 -> 0.4
Jun 28 12:42:56 www pkg: expat upgraded: 2.1.0_3 -> 2.2.0_1
Jun 28 12:42:58 www pkg: glib upgraded: 2.46.2 -> 2.46.2_5
Jun 28 12:42:58 www pkg: png upgraded: 1.6.21 -> 1.6.29
Jun 28 12:42:58 www pkg: freetype2 upgraded: 2.6.3 -> 2.8
Jun 28 12:42:59 www pkg: php56 upgraded: 5.6.21 -> 5.6.30
Jun 28 12:43:00 www pkg: lcms2 upgraded: 2.7_2 -> 2.8
Jun 28 12:43:00 www pkg: giflib upgraded: 5.1.3 -> 5.1.4
Jun 28 12:43:03 www pkg: libxcb upgraded: 1.11.1 -> 1.12_2
Jun 28 12:43:03 www pkg: fontconfig upgraded: 2.11.1_1,1 -> 2.12.1,1
Jun 28 12:43:03 www pkg: webp upgraded: 0.5.0 -> 0.5.2_1
Jun 28 12:43:03 www pkg: pkgconf upgraded: 0.9.12_1 -> 1.3.0,1
Jun 28 12:43:03 www pkg: openjpeg upgraded: 2.1.1 -> 2.1.2_1
Jun 28 12:43:03 www pkg: liblqr-1 upgraded: 0.4.1_8 -> 0.4.2
Jun 28 12:43:04 www pkg: fftw3 upgraded: 3.3.3_2 -> 3.3.6.p1_1
Jun 28 12:43:05 www pkg: libX11 upgraded: 1.6.3,1 -> 1.6.5,1
Jun 28 12:43:05 www pkg: libidn upgraded: 1.31 -> 1.33_1
Jun 28 12:43:06 www pkg: gmp upgraded: 5.1.3_3 -> 6.1.2
Jun 28 12:43:06 www pkg: libtasn1 upgraded: 4.8 -> 4.10
Jun 28 12:43:06 www pkg: dbus upgraded: 1.8.20 -> 1.10.14_2
Jun 28 12:43:06 www pkg: ca_root_nss upgraded: 3.22.2 -> 3.31
Jun 28 12:43:06 www pkg: trousers-tddl-0.3.10_7 deinstalled
Jun 28 12:43:07 www pkg: p11-kit upgraded: 0.23.2 -> 0.23.5
Jun 28 12:43:07 www pkg: nettle upgraded: 3.2 -> 3.3
Jun 28 12:43:07 www pkg: gdbm upgraded: 1.11_2 -> 1.12
Jun 28 12:43:07 www pkg: tpm-emulator-0.7.4_1 installed
Jun 28 12:43:07 www pkg: p5-Socket upgraded: 2.021 -> 2.024
Jun 28 12:43:13 www pkg: db5 upgraded: 5.3.28_3 -> 5.3.28_6
Jun 28 12:43:13 www pkg: trousers-0.3.14_1 installed
Jun 28 12:43:13 www pkg: libunistring-0.9.7 installed
Jun 28 12:43:13 www pkg: php56-dom upgraded: 5.6.21 -> 5.6.30
Jun 28 12:43:14 www pkg: p5-Net-SSLeay upgraded: 1.72 -> 1.81
Jun 28 12:43:14 www pkg: p5-Mozilla-CA reinstalled: 20160104 -> 20160104
Jun 28 12:43:14 www pkg: p5-IO-Socket-IP upgraded: 0.37 -> 0.39
Jun 28 12:43:14 www pkg: p5-GSSAPI reinstalled: 0.28_1 -> 0.28_1
Jun 28 12:43:14 www pkg: p5-Digest-HMAC reinstalled: 1.03_1 -> 1.03_1
Jun 28 12:43:14 www pkg: libedit upgraded: 3.1.20150325_2 -> 3.1.20150325_2,1
Jun 28 12:43:14 www pkg: apr upgraded: 1.5.2.1.5.4 -> 1.5.2.1.5.4_2
Jun 28 12:43:14 www pkg: libevent-2.1.8 installed
Jun 28 12:43:14 www pkg: liblz4-1.7.5,1 installed
Jun 28 12:43:14 www pkg: libnghttp2-1.21.0 installed
Jun 28 12:43:16 www pkg: gnutls upgraded: 3.4.10 -> 3.5.13
Jun 28 12:43:17 www pkg: php56-zlib upgraded: 5.6.21 -> 5.6.30
Jun 28 12:43:17 www pkg: php56-xmlreader upgraded: 5.6.21 -> 5.6.30
Jun 28 12:43:17 www pkg: php56-xml upgraded: 5.6.21 -> 5.6.30
Jun 28 12:43:17 www pkg: php56-sockets upgraded: 5.6.21 -> 5.6.30
Jun 28 12:43:17 www pkg: php56-session upgraded: 5.6.21 -> 5.6.30
Jun 28 12:43:17 www pkg: php56-readline upgraded: 5.6.21 -> 5.6.30
Jun 28 12:43:17 www pkg: php56-mysql upgraded: 5.6.21 -> 5.6.30
Jun 28 12:43:17 www pkg: php56-mbstring upgraded: 5.6.21 -> 5.6.30
Jun 28 12:43:17 www pkg: php56-json upgraded: 5.6.21 -> 5.6.30
Jun 28 12:43:17 www pkg: php56-iconv upgraded: 5.6.21 -> 5.6.30
Jun 28 12:43:17 www pkg: php56-hash upgraded: 5.6.21 -> 5.6.30
Jun 28 12:43:18 www pkg: php56-ctype upgraded: 5.6.21 -> 5.6.30
Jun 28 12:43:18 www pkg: p5-IO-Socket-SSL upgraded: 2.024 -> 2.044
Jun 28 12:43:18 www pkg: p5-Error reinstalled: 0.17024 -> 0.17024
Jun 28 12:43:18 www pkg: p5-Authen-SASL reinstalled: 2.16_1 -> 2.16_1
Jun 28 12:43:18 www pkg: mysql56-client upgraded: 5.6.30 -> 5.6.36
Jun 28 12:43:21 www pkg: icu upgraded: 55.1 -> 58.2_2,1
Jun 28 12:43:21 www pkg: cvsps upgraded: 2.1_1 -> 2.1_2
Jun 28 12:43:22 www pkg: curl upgraded: 7.48.0_1 -> 7.54.1
Jun 28 12:43:26 www pkg: apache24 upgraded: 2.4.20_1 -> 2.4.26
Jun 28 12:43:29 www pkg: ImageMagick-nox11 upgraded: 6.9.4.1,1 -> 6.9.6.4_2,1
Jun 28 12:43:29 www pkg: jbig2dec upgraded: 0.12 -> 0.13
Jun 28 12:43:30 www pkg: gsfonts upgraded: 8.11_6 -> 8.11_8
Jun 28 12:43:31 www pkg: cups upgraded: 2.1.3_2 -> 2.2.2_1
Jun 28 12:43:31 www pkg: smartmontools upgraded: 6.4_2 -> 6.5_2
Jun 28 12:43:32 www pkg: php56-pcntl upgraded: 5.6.21 -> 5.6.30
Jun 28 12:43:32 www pkg: pecl-intl upgraded: 3.0.0_2 -> 3.0.0_7
Jun 28 12:43:32 www pkg: pecl-imagick upgraded: 3.4.1 -> 3.4.3
Jun 28 12:43:32 www pkg: p5-Net-SMTP-SSL upgraded: 1.03 -> 1.04
Jun 28 12:43:34 www pkg: mysql56-server upgraded: 5.6.30 -> 5.6.36
Jun 28 12:43:35 www pkg: mod_php56 upgraded: 5.6.21 -> 5.6.30
Jun 28 12:43:53 www pkg: mediawiki126 upgraded: 1.26.2 -> 1.26.4
Jun 28 12:43:55 www pkg: git upgraded: 2.7.4_1 -> 2.13.0_1

ok.

2016-06-28: ada0p2 - pkg - upgrade pkg

root@www# pkg upgrade pkg
Updating FreeBSD repository catalogue...
FreeBSD repository is up-to-date.
All repositories are up-to-date.
New version of pkg detected; it needs to be installed first.
The following 1 package(s) will be affected (of 0 checked):

Installed packages to be UPGRADED:
    pkg: 1.7.2 -> 1.10.1

3 MiB to be downloaded.

Proceed with this action? [y/N]: y
Fetching pkg-1.10.1.txz: 100%    3 MiB   2.6MB/s    00:01   
Checking integrity... done (0 conflicting)
[1/1] Upgrading pkg from 1.7.2 to 1.10.1...
[1/1] Extracting pkg-1.10.1: 100%
Updating FreeBSD repository catalogue...
Repo "FreeBSD" upgrade schema 2013 to 2014: DROP TABLE pkg_search;
FreeBSD repository is up to date.
All repositories are up to date.
Checking integrity... done (0 conflicting)
Your packages are up to date.

ok.

2016-06-28: ada0p2 - after a reboot, the server now runs FreeBSD 10.3-release-p19

root@www# freebsd-version -ku
10.3-RELEASE-p18
10.3-RELEASE-p19
root@www# uname -a
FreeBSD www.ndwiki.org 10.3-RELEASE-p18 FreeBSD 10.3-RELEASE-p18 #0: Tue Apr 11 10:31:00 UTC 2017     root@amd64-builder.daemonology.net:/usr/obj/usr/src/sys/GENERIC  amd64

ok.

2016-06-28: ada0p2 - run freebsd-update fetch

root@www# freebsd-update fetch
src component not installed, skipped
Looking up update.FreeBSD.org mirrors... 4 mirrors found.
Fetching metadata signature for 10.3-RELEASE from update4.freebsd.org... done.
Fetching metadata index... done.
Fetching 2 metadata files... done.
Inspecting system... done.
Preparing to download files... done.
Fetching 213 patches.....10....20....30....40....50....60....70....80....90....100....110....120....130....140....150....160....170....180....190....200....210. done.
Applying patches... done.
Fetching 6 files... done.
[...]
The following files will be removed as part of updating to 10.3-RELEASE-p19:
/usr/share/zoneinfo/America/Santa_Isabel
/usr/share/zoneinfo/Asia/Rangoon
The following files will be added as part of updating to 10.3-RELEASE-p19:
/usr/share/zoneinfo/Asia/Barnaul
/usr/share/zoneinfo/Asia/Famagusta
/usr/share/zoneinfo/Asia/Tomsk
/usr/share/zoneinfo/Asia/Yangon
/usr/share/zoneinfo/Europe/Astrakhan
/usr/share/zoneinfo/Europe/Kirov
/usr/share/zoneinfo/Europe/Ulyanovsk
The following files will be updated as part of updating to 10.3-RELEASE-p19:
/bin/freebsd-version
/boot/boot1.efi
/boot/boot1.efifat
/boot/kernel/hv_storvsc.ko
/boot/kernel/hv_storvsc.ko.symbols
/boot/kernel/hv_vmbus.ko
/boot/kernel/hv_vmbus.ko.symbols
/boot/kernel/ipl.ko
/boot/kernel/ipl.ko.symbols
/boot/kernel/kernel
/boot/kernel/kernel.symbols
/boot/kernel/linux.ko
/boot/kernel/linux.ko.symbols
/boot/kernel/linux64.ko
/boot/kernel/linux64.ko.symbols
/boot/kernel/sysvshm.ko
/boot/kernel/sysvshm.ko.symbols
/boot/kernel/tmpfs.ko
/boot/kernel/tmpfs.ko.symbols
/boot/kernel/zfs.ko
/boot/kernel/zfs.ko.symbols
/boot/loader.efi
/lib/libc.so.7
/lib/libcrypto.so.7
/rescue/[
/rescue/atmconfig
/rescue/badsect
/rescue/bsdlabel
/rescue/bunzip2
/rescue/bzcat
/rescue/bzip2
/rescue/camcontrol
/rescue/cat
/rescue/ccdconfig
/rescue/chflags
/rescue/chgrp
/rescue/chio
/rescue/chmod
/rescue/chown
/rescue/chroot
/rescue/clri
/rescue/cp
/rescue/csh
/rescue/date
/rescue/dd
/rescue/devfs
/rescue/df
/rescue/dhclient
/rescue/disklabel
/rescue/dmesg
/rescue/dump
/rescue/dumpfs
/rescue/dumpon
/rescue/echo
/rescue/ed
/rescue/ex
/rescue/expr
/rescue/fastboot
/rescue/fasthalt
/rescue/fdisk
/rescue/fsck
/rescue/fsck_4.2bsd
/rescue/fsck_ffs
/rescue/fsck_msdosfs
/rescue/fsck_ufs
/rescue/fsdb
/rescue/fsirand
/rescue/gbde
/rescue/geom
/rescue/getfacl
/rescue/glabel
/rescue/gpart
/rescue/groups
/rescue/gunzip
/rescue/gzcat
/rescue/gzip
/rescue/halt
/rescue/head
/rescue/hostname
/rescue/id
/rescue/ifconfig
/rescue/init
/rescue/ipf
/rescue/iscsictl
/rescue/iscsid
/rescue/kenv
/rescue/kill
/rescue/kldconfig
/rescue/kldload
/rescue/kldstat
/rescue/kldunload
/rescue/ldconfig
/rescue/less
/rescue/link
/rescue/ln
/rescue/ls
/rescue/lzcat
/rescue/lzma
/rescue/md5
/rescue/mdconfig
/rescue/mdmfs
/rescue/mkdir
/rescue/mknod
/rescue/more
/rescue/mount
/rescue/mount_cd9660
/rescue/mount_msdosfs
/rescue/mount_nfs
/rescue/mount_nullfs
/rescue/mount_udf
/rescue/mount_unionfs
/rescue/mt
/rescue/mv
/rescue/nc
/rescue/newfs
/rescue/newfs_msdos
/rescue/nos-tun
/rescue/pgrep
/rescue/ping
/rescue/ping6
/rescue/pkill
/rescue/ps
/rescue/pwd
/rescue/rcorder
/rescue/rcp
/rescue/rdump
/rescue/realpath
/rescue/reboot
/rescue/red
/rescue/rescue
/rescue/restore
/rescue/rm
/rescue/rmdir
/rescue/route
/rescue/routed
/rescue/rrestore
/rescue/rtquery
/rescue/rtsol
/rescue/savecore
/rescue/sed
/rescue/setfacl
/rescue/sh
/rescue/sleep
/rescue/spppcontrol
/rescue/stty
/rescue/swapon
/rescue/sync
/rescue/sysctl
/rescue/tail
/rescue/tar
/rescue/tcsh
/rescue/tee
/rescue/test
/rescue/tunefs
/rescue/umount
/rescue/unlink
/rescue/unlzma
/rescue/unxz
/rescue/vi
/rescue/whoami
/rescue/xz
/rescue/xzcat
/rescue/zcat
/rescue/zdb
/rescue/zfs
/rescue/zpool
/sbin/dhclient
/sbin/ifconfig
/sbin/ipftest
/sbin/route
/usr/bin/ar
/usr/bin/bsdcpio
/usr/bin/bspatch
/usr/bin/netstat
/usr/bin/ntpq
/usr/bin/openssl
/usr/bin/ranlib
/usr/bin/slogin
/usr/bin/ssh
/usr/bin/ssh-agent
/usr/include/archive.h
/usr/include/openssl/ssl.h
/usr/include/openssl/ssl3.h
/usr/include/vm/vm_object.h
/usr/lib/libarchive.a
/usr/lib/libarchive.so.6
/usr/lib/libarchive_p.a
/usr/lib/libc.a
/usr/lib/libc_p.a
/usr/lib/libc_pic.a
/usr/lib/libcrypto.a
/usr/lib/libcrypto_p.a
/usr/lib/libmp.so.7
/usr/lib/libssl.a
/usr/lib/libssl.so.7
/usr/lib/libssl_p.a
/usr/lib/libvmmapi.a
/usr/lib/libvmmapi.so.5
/usr/lib/libvmmapi_p.a
/usr/lib/private/libssh.a
/usr/lib/private/libssh.so.5
/usr/lib/private/libssh_p.a
/usr/lib32/libarchive.a
/usr/lib32/libarchive.so.6
/usr/lib32/libarchive_p.a
/usr/lib32/libc.a
/usr/lib32/libc.so.7
/usr/lib32/libc_p.a
/usr/lib32/libc_pic.a
/usr/lib32/libcrypto.a
/usr/lib32/libcrypto.so.7
/usr/lib32/libcrypto_p.a
/usr/lib32/libmp.so.7
/usr/lib32/libssl.a
/usr/lib32/libssl.so.7
/usr/lib32/libssl_p.a
/usr/lib32/private/libssh.a
/usr/lib32/private/libssh.so.5
/usr/lib32/private/libssh_p.a
/usr/libexec/sendmail/sendmail
/usr/libexec/telnetd
/usr/sbin/arp
/usr/sbin/bhyve
/usr/sbin/bhyveload
/usr/sbin/freebsd-update
/usr/sbin/ifmcstat
/usr/sbin/ndp
/usr/sbin/ntp-keygen
/usr/sbin/ntpd
/usr/sbin/ntpdate
/usr/sbin/ntpdc
/usr/sbin/ntptime
/usr/sbin/portsnap
/usr/sbin/sntp
/usr/sbin/sshd
/usr/sbin/zdump
/usr/sbin/zic
/usr/share/doc/ntp/copyright.html
[...]
/usr/share/zoneinfo/zone.tab
/var/db/mergemaster.mtree

install

root@www# freebsd-update install
src component not installed, skipped
Installing updates... done.

and do a reboot.

2016-06-28: ada0p2 - pkg update repository

root@www# pkg update
Updating FreeBSD repository catalogue...
Fetching meta.txz: 100%    944 B   0.9kB/s    00:01   
Fetching packagesite.txz: 100%    6 MiB   6.0MB/s    00:01   
Processing entries: 100%
FreeBSD repository update completed. 26282 packages processed.

ok.

2016-06-28: ada0p2 - run the fetch job for a new leapseconds file

root@www# service ntpd onefetch
root@www# ll /var/run/ntpd.leap-seconds.list
-rw-r--r--  1 root  wheel  10408 Mar 20 19:53 /var/run/ntpd.leap-seconds.list

I forgot to check it before running the command. Oh well.

2016-06-28: ada0p2 - I connected a monitor (HDMI to DVI cable works) and a usb keyboard. The machine had panicked, and needed a manual fsck. So I ran fsck two or three times, and the machine booted up.

root@www# cat /var/crash/info.0
Dump header from device /dev/ada0p3
  Architecture: amd64
  Architecture Version: 2
  Dump Length: 891301888B (850 MB)
  Blocksize: 512
  Dumptime: Wed Jun 28 00:38:50 2017
  Hostname: www.ndwiki.org
  Magic: FreeBSD Kernel Dump
  Version String: FreeBSD 10.3-RELEASE-p2 #0: Wed May  4 06:03:51 UTC 2016
    root@amd64-builder.daemonology.net:/usr/obj/usr/src/sys/GENERIC
  Panic String: page fault
  Dump Parity: 2107600417
  Bounds: 0
  Dump Status: good

from /var/log/messages

Jun 28 10:35:29 www syslogd: kernel boot file is /boot/kernel/kernel
Jun 28 10:35:29 www kernel: panic: page fault
Jun 28 10:35:29 www kernel: cpuid = 2
Jun 28 10:35:29 www kernel: KDB: stack backtrace:
Jun 28 10:35:29 www kernel: #0 0xffffffff8098e390 at kdb_backtrace+0x60
Jun 28 10:35:29 www kernel: #1 0xffffffff80951066 at vpanic+0x126
Jun 28 10:35:29 www kernel: #2 0xffffffff80950f33 at panic+0x43
Jun 28 10:35:29 www kernel: #3 0xffffffff80d55f7b at trap_fatal+0x36b
Jun 28 10:35:29 www kernel: #4 0xffffffff80d5627d at trap_pfault+0x2ed
Jun 28 10:35:29 www kernel: #5 0xffffffff80d558fa at trap+0x47a
Jun 28 10:35:29 www kernel: #6 0xffffffff80d3b8d2 at calltrap+0x8
Jun 28 10:35:29 www kernel: #7 0xffffffff80b7cd21 at ffs_alloc+0x1e1
Jun 28 10:35:29 www kernel: #8 0xffffffff80b85664 at ffs_balloc_ufs2+0x12d4
Jun 28 10:35:29 www kernel: #9 0xffffffff80bafe88 at ffs_write+0x288
Jun 28 10:35:29 www kernel: #10 0xffffffff80e81549 at VOP_WRITE_APV+0x149
Jun 28 10:35:29 www kernel: #11 0xffffffff80a08f50 at vn_io_fault_doio+0x60
Jun 28 10:35:29 www kernel: #12 0xffffffff80a06bd9 at vn_io_fault1+0x349
Jun 28 10:35:29 www kernel: #13 0xffffffff80a06789 at vn_rdwr+0x289
Jun 28 10:35:29 www kernel: #14 0xffffffff80a06d47 at vn_rdwr_inchunks+0xa7
Jun 28 10:35:29 www kernel: #15 0xffffffff808f0e63 at elf64_coredump+0xa13
Jun 28 10:35:29 www kernel: #16 0xffffffff8095481c at sigexit+0xb6c
Jun 28 10:35:29 www kernel: #17 0xffffffff80954e76 at postsig+0x286
Jun 28 10:35:29 www kernel: Uptime: 60d22h58m7s
Jun 28 10:35:29 www kernel: Dumping 850 out of 16025 MB:..2%..12%..21%..31%..42%..51%..61%..72%..81%..91%

and smartctl info

root@www# smartctl -i /dev/ada0
smartctl 6.4 2015-06-04 r4109 [FreeBSD 10.3-RELEASE-p2 amd64] (local build)
Copyright (C) 2002-15, Bruce Allen, Christian Franke, www.smartmontools.org

=== START OF INFORMATION SECTION ===
Device Model:     INTEL SSDMCEAC120A3
Serial Number:    CVLI31710006120B
LU WWN Device Id: 5 5cd2e4 0000e1878
Firmware Version: LLGi
User Capacity:    120,034,123,776 bytes [120 GB]
Sector Size:      512 bytes logical/physical
Rotation Rate:    Solid State Device
Device is:        Not in smartctl database [for details use: -P showall]
ATA Version is:   ACS-2 (minor revision not indicated)
SATA Version is:  SATA 3.0, 6.0 Gb/s (current: 6.0 Gb/s)
Local Time is:    Wed Jun 28 10:45:10 2017 CEST
SMART support is: Available - device has SMART capability.
SMART support is: Enabled

root@www# smartctl -H /dev/ada0
smartctl 6.4 2015-06-04 r4109 [FreeBSD 10.3-RELEASE-p2 amd64] (local build)
Copyright (C) 2002-15, Bruce Allen, Christian Franke, www.smartmontools.org

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

hmm, doesn't look wrong. run 'smartctl -a'

root@www# smartctl -a /dev/ada0
smartctl 6.4 2015-06-04 r4109 [FreeBSD 10.3-RELEASE-p2 amd64] (local build)
Copyright (C) 2002-15, Bruce Allen, Christian Franke, www.smartmontools.org

=== START OF INFORMATION SECTION ===
Device Model:     INTEL SSDMCEAC120A3
Serial Number:    CVLI31710006120B
LU WWN Device Id: 5 5cd2e4 0000e1878
Firmware Version: LLGi
User Capacity:    120,034,123,776 bytes [120 GB]
Sector Size:      512 bytes logical/physical
Rotation Rate:    Solid State Device
Device is:        Not in smartctl database [for details use: -P showall]
ATA Version is:   ACS-2 (minor revision not indicated)
SATA Version is:  SATA 3.0, 6.0 Gb/s (current: 6.0 Gb/s)
Local Time is:    Wed Jun 28 10:48:35 2017 CEST
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:         ( 2930) seconds.
Offline data collection
capabilities:              (0x7f) SMART execute Offline immediate.
                    Auto Offline data collection on/off support.
                    Abort 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:      (  48) minutes.
Conveyance self-test routine
recommended polling time:      (   2) minutes.
SCT capabilities:            (0x0021)    SCT Status 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
  5 Reallocated_Sector_Ct   0x0032   100   100   000    Old_age   Always       -       0
  9 Power_On_Hours          0x0032   100   100   000    Old_age   Always       -       9769 (17 232 0)
 12 Power_Cycle_Count       0x0032   100   100   000    Old_age   Always       -       13
170 Unknown_Attribute       0x0033   100   100   010    Pre-fail  Always       -       0
171 Unknown_Attribute       0x0032   100   100   000    Old_age   Always       -       0
172 Unknown_Attribute       0x0032   100   100   000    Old_age   Always       -       0
174 Unknown_Attribute       0x0032   100   100   000    Old_age   Always       -       5
183 Runtime_Bad_Block       0x0032   100   100   000    Old_age   Always       -       0
184 End-to-End_Error        0x0033   100   100   090    Pre-fail  Always       -       0
187 Reported_Uncorrect      0x0032   100   100   050    Old_age   Always       -       0
192 Power-Off_Retract_Count 0x0032   100   100   000    Old_age   Always       -       5
199 UDMA_CRC_Error_Count    0x0032   100   100   000    Old_age   Always       -       0
225 Unknown_SSD_Attribute   0x0032   100   100   000    Old_age   Always       -       59008
226 Unknown_SSD_Attribute   0x0032   100   100   000    Old_age   Always       -       65535
227 Unknown_SSD_Attribute   0x0032   100   100   000    Old_age   Always       -       0
228 Power-off_Retract_Count 0x0032   100   100   000    Old_age   Always       -       65535
232 Available_Reservd_Space 0x0033   100   100   010    Pre-fail  Always       -       0
233 Media_Wearout_Indicator 0x0032   100   100   000    Old_age   Always       -       0
241 Total_LBAs_Written      0x0032   100   100   000    Old_age   Always       -       59008
242 Total_LBAs_Read         0x0032   100   100   000    Old_age   Always       -       120
249 Unknown_Attribute       0x0013   100   100   000    Pre-fail  Always       -       1481

SMART Error Log not supported

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

SMART Selective self-test log data structure revision number 0
Note: revision number not 1 implies that no selective self-test has ever been run
 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.

doesn't look wrong either.

2017-06-27: ada0p2 -from /var/log/messages:

Jun 27 22:12:45 www kernel: pid 70925 (httpd), uid 80: exited on signal 10
Jun 27 22:15:22 www kernel: pid 80525 (httpd), uid 80: exited on signal 10

Jun 27 22:19:49 www kernel: pid 80656 (httpd), uid 80: exited on signal 10
Jun 27 22:20:04 www kernel: pid 80526 (httpd), uid 80: exited on signal 10

(heaps of those)

Jun 27 23:47:06 www kernel: pid 81201 (sshd), uid 0: exited on signal 11
Jun 27 23:47:06 www kernel: pid 81166 (httpd), uid 80: exited on signal 10
Jun 27 23:47:19 www kernel: pid 81232 (sshd), uid 0: exited on signal 11
Jun 27 23:47:30 www sshd[81259]: error: rexec: line 8: Bad configuration option: \b
Jun 27 23:47:30 www sshd[81259]: error: rexec: line 39: Bad configuration option: \216
Jun 27 23:47:30 www sshd[81259]: error: rexec: line 46: Bad configuration option: \b
Jun 27 23:47:30 www sshd[81259]: fatal: rexec: terminating, 3 bad configuration options
Jun 27 23:49:50 www sshd[81260]: error: rexec: line 8: Bad configuration option: \b
Jun 27 23:49:50 www sshd[81260]: error: rexec: line 39: Bad configuration option: \216

(and more)

Jun 28 00:10:59 www kernel: g_vfs_done():ada0p2[READ(offset=459226424037179392, length=32768)]error = 5
Jun 28 00:10:59 www kernel: g_vfs_done():ada0p2[READ(offset=983614305834237952, length=32768)]error = 5
Jun 28 00:10:59 www kernel: g_vfs_done():ada0p2[READ(offset=1967228611668344832, length=32768)]error = 5
Jun 28 00:10:59 www kernel: g_vfs_done():ada0p2[READ(offset=1639451001289900032, length=32768)]error = 5
Jun 28 00:10:59 www kernel: g_vfs_done():ada0p2[READ(offset=983614305834237952, length=32768)]error = 5
Jun 28 00:10:59 www kernel: g_vfs_done():ada0p2[READ(offset=1901222730468524032, length=32768)]error = 5
Jun 28 00:10:59 www kernel: g_vfs_done():ada0p2[READ(offset=983614305834237952, length=32768)]error = 5
Jun 28 00:10:59 www last message repeated 2 times
Jun 28 00:10:59 www kernel: g_vfs_done():ada0p2[READ(offset=1639451001289900032, length=32768)]error = 5
Jun 28 00:10:59 www kernel: g_vfs_done():ada0p2[READ(offset=983614305834237952, length=32768)]error = 5
Jun 28 00:10:59 www kernel: g_vfs_done():ada0p2[READ(offset=1639451001289900032, length=32768)]error = 5
Jun 28 00:10:59 www kernel: g_vfs_done():ada0p2[READ(offset=1639451001289900032, length=32768)]error = 5

Jun 28 00:27:07 www kernel: g_vfs_done():ada0p2[READ(offset=1574008069487624192, length=32768)]error = 5
Jun 28 00:27:07 www kernel: g_vfs_done():ada0p2[READ(offset=1508002188287803392, length=32768)]error = 5
Jun 28 00:27:07 www kernel: g_vfs_done():ada0p2[READ(offset=1442840730527793152, length=32768)]error = 5
Jun 28 00:27:07 www kernel: g_vfs_done():ada0p2[READ(offset=1311110442170417152, length=32768)]error = 5
Jun 28 00:27:07 www kernel: g_vfs_done():ada0p2[READ(offset=983614305834237952, length=32768)]error = 5
Jun 28 00:27:07 www kernel: g_vfs_done():ada0p2[READ(offset=1967228611668344832, length=32768)]error = 5
Jun 28 00:27:07 www kernel: g_vfs_done():ada0p2[READ(offset=2229563290244513792, length=32768)]error = 5
Jun 28 00:27:07 www kernel: pid 81816 (smartctl), uid 0: exited on signal 11 (core dumped)
Jun 28 00:27:11 www kernel: pid 81833 (env), uid 0: exited on signal 10 (core dumped)

Jun 28 00:29:05 www sshd[81850]: error: rexec: line 8: Bad configuration option: \b
Jun 28 00:29:05 www sshd[81850]: error: rexec: line 39: Bad configuration option: \216
Jun 28 00:29:05 www sshd[81850]: error: rexec: line 46: Bad configuration option: \b
Jun 28 00:29:05 www sshd[81850]: fatal: rexec: terminating, 3 bad configuration options
Jun 28 00:29:14 www sshd[81851]: error: rexec: line 8: Bad configuration option: \b
Jun 28 00:29:14 www sshd[81851]: error: rexec: line 39: Bad configuration option: \216
Jun 28 00:29:14 www sshd[81851]: error: rexec: line 46: Bad configuration option: \b
Jun 28 00:29:14 www sshd[81851]: fatal: rexec: terminating, 3 bad configuration options
Jun 28 00:30:28 www kernel: pid 81854 (less), uid 0: exited on signal 10 (core dumped)
Jun 28 00:30:30 www kernel: pid 81855 (less), uid 0: exited on signal 10 (core dumped)
Jun 28 00:31:32 www kernel: pid 81737 (httpd), uid 80: exited on signal 10
Jun 28 00:32:52 www kernel: pid 81738 (httpd), uid 80: exited on signal 10

perhaps the SSD is going bad. I'll need to check tomorrow.

2016-06-01: ada0p2 - ntp - these annoying messages show up in /var/log/messages:

May 31 16:41:28 www ntpd[570]: leapsecond file ('/var/db/ntpd.leap-seconds.list'): will expire in less than one day
May 31 17:41:28 www ntpd[570]: leapsecond file ('/var/db/ntpd.leap-seconds.list'): will expire in less than one day
May 31 18:41:28 www ntpd[570]: leapsecond file ('/var/db/ntpd.leap-seconds.list'): will expire in less than one day
May 31 19:41:28 www ntpd[570]: leapsecond file ('/var/db/ntpd.leap-seconds.list'): will expire in less than one day
May 31 20:41:28 www ntpd[570]: leapsecond file ('/var/db/ntpd.leap-seconds.list'): will expire in less than one day
May 31 21:41:28 www ntpd[570]: leapsecond file ('/var/db/ntpd.leap-seconds.list'): will expire in less than one day
May 31 22:41:29 www ntpd[570]: leapsecond file ('/var/db/ntpd.leap-seconds.list'): will expire in less than one day
May 31 23:41:28 www ntpd[570]: leapsecond file ('/var/db/ntpd.leap-seconds.list'): will expire in less than one day
Jun  1 00:41:29 www ntpd[570]: leapsecond file ('/var/db/ntpd.leap-seconds.list'): will expire in less than one day
Jun  1 01:41:28 www ntpd[570]: leapsecond file ('/var/db/ntpd.leap-seconds.list'): will expire in less than one day

To shut it up, I add to /etc/periodic.conf:

root@www# more /etc/periodic.conf
daily_ntpd_leapfile_enable="YES"

tomorrow we will see.

2016-05-20: ada0p2 - pkg - installed more packages:

May 20 11:25:56 www pkg: pecl-APCu-4.0.10 installed
May 20 11:28:38 www pkg: p5-Socket-2.021 installed
May 20 11:28:38 www pkg: p5-Net-SSLeay-1.72 installed
May 20 11:28:38 www pkg: p5-IO-Socket-IP-0.37 installed
May 20 11:28:38 www pkg: p5-Mozilla-CA-20160104 installed
May 20 11:28:38 www pkg: p5-Digest-HMAC-1.03_1 installed
May 20 11:28:38 www pkg: p5-GSSAPI-0.28_1 installed
May 20 11:28:38 www pkg: p5-IO-Socket-SSL-2.024 installed
May 20 11:28:38 www pkg: p5-Error-0.17024 installed
May 20 11:28:38 www pkg: cvsps-2.1_1 installed
May 20 11:28:38 www pkg: p5-Authen-SASL-2.16_1 installed
May 20 11:28:39 www pkg: curl-7.48.0_1 installed
May 20 11:28:39 www pkg: p5-Net-SMTP-SSL-1.03 installed
May 20 11:28:40 www pkg: git-2.7.4_1 installed

Mediawiki wants pecl-APC not pecl-APCu, but pecl-APC doesn't exist as a package. Also installed php56-pcntl and lua 5.1, it is required for Scribunto extension:

May 20 15:40:44 www pkg: php56-pcntl-5.6.21 installed
May 20 15:48:42 www pkg: lua51-5.1.5_9 installed

ok

2016-05-19: ada0p2 - mediawiki - upgrade script ran with success. Unfortunately, afterwards, the main wiki page doesn't show up. Not sure if this is caused by lacking name resolution, or a misconfiguration on my part.

2016-05-19: ada0p2 - mysql - the wikidb_user needs a grant for INDEX on wikidb.

2016-05-19: ada0p2 - pkg - installed a few more packages:

May 19 23:18:41 ndwiki pkg: icu-55.1 installed
May 19 23:18:41 ndwiki pkg: pecl-intl-3.0.0_2 installed
May 19 23:26:07 ndwiki pkg: xproto-7.0.28 installed
May 19 23:26:07 ndwiki pkg: libXdmcp-1.1.2 installed
May 19 23:26:07 ndwiki pkg: libpthread-stubs-0.3_6 installed
May 19 23:26:07 ndwiki pkg: libXau-1.0.8_3 installed
May 19 23:26:07 ndwiki pkg: libffi-3.2.1 installed
May 19 23:26:08 ndwiki pkg: libxcb-1.11.1 installed
May 19 23:26:08 ndwiki pkg: kbproto-1.0.7 installed
May 19 23:26:08 ndwiki pkg: libICE-1.0.9_1,1 installed
May 19 23:26:13 ndwiki pkg: python27-2.7.11_2 installed
May 19 23:26:13 ndwiki pkg: gnome_subr-1.0 installed
May 19 23:26:14 ndwiki pkg: libX11-1.6.3,1 installed
May 19 23:26:14 ndwiki pkg: libSM-1.2.2_3,1 installed
May 19 23:26:15 ndwiki pkg: glib-2.46.2 installed
May 19 23:26:15 ndwiki pkg: dbus-1.8.20 installed
May 19 23:26:15 ndwiki pkg: python2-2_3 installed
May 19 23:26:15 ndwiki pkg: gmp-5.1.3_3 installed
May 19 23:26:15 ndwiki pkg: ca_root_nss-3.22.2 installed
May 19 23:26:15 ndwiki pkg: libtasn1-4.8 installed
May 19 23:26:15 ndwiki pkg: jbigkit-2.1_1 installed
May 19 23:26:15 ndwiki pkg: libidn-1.31 installed
May 19 23:26:16 ndwiki pkg: jpeg-turbo-1.4.2 installed
May 19 23:26:16 ndwiki pkg: dbus-glib-0.104 installed
May 19 23:26:16 ndwiki pkg: gobject-introspection-1.46.0 installed
May 19 23:26:16 ndwiki pkg: libdaemon-0.14_1 installed
May 19 23:26:16 ndwiki pkg: nettle-3.2 installed
May 19 23:26:17 ndwiki pkg: p11-kit-0.23.2 installed
May 19 23:26:17 ndwiki pkg: trousers-tddl-0.3.10_7 installed
May 19 23:26:17 ndwiki pkg: png-1.6.21 installed
May 19 23:26:17 ndwiki pkg: freetype2-2.6.3 installed
May 19 23:26:17 ndwiki pkg: libpaper-1.1.24.4 installed
May 19 23:26:17 ndwiki pkg: tiff-4.0.6_1 installed
May 19 23:26:18 ndwiki pkg: avahi-app-0.6.31_5 installed
May 19 23:26:19 ndwiki pkg: gnutls-3.4.10 installed
May 19 23:26:19 ndwiki pkg: jbig2dec-0.12 installed
May 19 23:26:19 ndwiki pkg: svgalib-1.4.3_7 installed
May 19 23:26:19 ndwiki pkg: fontconfig-2.11.1_1,1 installed
May 19 23:26:20 ndwiki pkg: cups-2.1.3_2 installed
May 19 23:26:21 ndwiki pkg: gsfonts-8.11_6 installed
May 19 23:26:21 ndwiki pkg: lcms2-2.7_2 installed
May 19 23:26:21 ndwiki pkg: giflib-5.1.3 installed
May 19 23:26:21 ndwiki pkg: libfpx-1.3.1.4_1 installed
May 19 23:26:21 ndwiki pkg: liblqr-1-0.4.1_8 installed
May 19 23:26:24 ndwiki pkg: ghostscript9-agpl-base-9.16_5 installed
May 19 23:26:24 ndwiki pkg: fftw3-3.3.3_2 installed
May 19 23:26:25 ndwiki pkg: openjpeg-2.1.1 installed
May 19 23:26:25 ndwiki pkg: pkgconf-0.9.12_1 installed
May 19 23:26:25 ndwiki pkg: libwmf-nox11-0.2.8.4_15 installed
May 19 23:26:25 ndwiki pkg: libltdl-2.4.6 installed
May 19 23:26:25 ndwiki pkg: webp-0.5.0 installed
May 19 23:26:27 ndwiki pkg: ImageMagick-nox11-6.9.4.1,1 installed
May 19 23:26:27 ndwiki pkg: pecl-imagick-3.4.1 installed

ok.

2016-05-19: ada0p2 - mediawiki copied old files, configured apache.

2016-05-18: ada0p2 - database - to be safe, run mysql_upgrade too:

root@ndweb# mysql_upgrade -u root -p
Enter password:
Looking for 'mysql' as: mysql
Looking for 'mysqlcheck' as: mysqlcheck
Running 'mysqlcheck with default connection arguments
Warning: Using a password on the command line interface can be insecure.
Running 'mysqlcheck with default connection arguments
Warning: Using a password on the command line interface can be insecure.
mysql.columns_priv                                 OK
mysql.db                                           OK
mysql.event                                        OK
mysql.func                                         OK
mysql.general_log                                  OK
mysql.help_category                                OK
mysql.help_keyword                                 OK
mysql.help_relation                                OK
mysql.help_topic                                   OK
mysql.innodb_index_stats                           OK
mysql.innodb_table_stats                           OK
mysql.ndb_binlog_index                             OK
mysql.plugin                                       OK
mysql.proc                                         OK
mysql.procs_priv                                   OK
mysql.proxies_priv                                 OK
mysql.servers                                      OK
mysql.slave_master_info                            OK
mysql.slave_relay_log_info                         OK
mysql.slave_worker_info                            OK
mysql.slow_log                                     OK
mysql.tables_priv                                  OK
mysql.time_zone                                    OK
mysql.time_zone_leap_second                        OK
mysql.time_zone_name                               OK
mysql.time_zone_transition                         OK
mysql.time_zone_transition_type                    OK
mysql.user                                         OK
Running 'mysql_fix_privilege_tables'...
Warning: Using a password on the command line interface can be insecure.
Running 'mysqlcheck with default connection arguments
Warning: Using a password on the command line interface can be insecure.
Running 'mysqlcheck with default connection arguments
Warning: Using a password on the command line interface can be insecure.
wikidb.archive                                     OK
wikidb.category                                    OK
wikidb.categorylinks                               OK
wikidb.change_tag                                  OK
wikidb.cu_changes                                  OK
wikidb.cu_log                                      OK
wikidb.dymnorm                                     OK
wikidb.dympage                                     OK
wikidb.external_user                               OK
wikidb.externallinks                               OK
wikidb.filearchive                                 OK
wikidb.hitcounter                                  OK
wikidb.image                                       OK
wikidb.imagelinks                                  OK
wikidb.interwiki                                   OK
wikidb.ipblocks                                    OK
wikidb.iwlinks                                     OK
wikidb.job                                         OK
wikidb.l10n_cache                                  OK
wikidb.langlinks                                   OK
wikidb.log_search                                  OK
wikidb.logging                                     OK
wikidb.math                                        OK
wikidb.metric                                      OK
wikidb.module_deps                                 OK
wikidb.msg_resource                                OK
wikidb.msg_resource_links                          OK
wikidb.objectcache                                 OK
wikidb.oldimage                                    OK
wikidb.online                                      OK
wikidb.online_chat                                 OK
wikidb.online_config                               OK
wikidb.page                                        OK
wikidb.page_props                                  OK
wikidb.page_restrictions                           OK
wikidb.pagelinks                                   OK
wikidb.protected_titles                            OK
wikidb.querycache                                  OK
wikidb.querycache_info                             OK
wikidb.querycachetwo                               OK
wikidb.recentchanges                               OK
wikidb.redirect                                    OK
wikidb.revision                                    OK
wikidb.searchindex                                 OK
wikidb.site_identifiers                            OK
wikidb.site_stats                                  OK
wikidb.sites                                       OK
wikidb.tag_summary                                 OK
wikidb.templatelinks                               OK
wikidb.text                                        OK
wikidb.trackbacks                                  OK
wikidb.transcache                                  OK
wikidb.updatelog                                   OK
wikidb.uploadstash                                 OK
wikidb.user                                        OK
wikidb.user_former_groups                          OK
wikidb.user_groups                                 OK
wikidb.user_newtalk                                OK
wikidb.user_properties                             OK
wikidb.valid_tag                                   OK
wikidb.watchlist                                   OK
OK

nothing more.

2016-05-18: ada0p2 - database - check databases. system:

root@ndweb# mysqlcheck -u root -p mysql
Enter password:
mysql.columns_priv                                 OK
mysql.db                                           OK
mysql.event                                        OK
mysql.func                                         OK
mysql.general_log                                  OK
mysql.help_category                                OK
mysql.help_keyword                                 OK
mysql.help_relation                                OK
mysql.help_topic                                   OK
mysql.innodb_index_stats                           OK
mysql.innodb_table_stats                           OK
mysql.ndb_binlog_index                             OK
mysql.plugin                                       OK
mysql.proc                                         OK
mysql.procs_priv                                   OK
mysql.proxies_priv                                 OK
mysql.servers                                      OK
mysql.slave_master_info                            OK
mysql.slave_relay_log_info                         OK
mysql.slave_worker_info                            OK
mysql.slow_log                                     OK
mysql.tables_priv                                  OK
mysql.time_zone                                    OK
mysql.time_zone_leap_second                        OK
mysql.time_zone_name                               OK
mysql.time_zone_transition                         OK
mysql.time_zone_transition_type                    OK
mysql.user                                         OK

wikidb:

root@ndweb# mysqlcheck -u root -p wikidb
Enter password:
wikidb.archive                                     OK
wikidb.category                                    OK
wikidb.categorylinks                               OK
wikidb.change_tag                                  OK
wikidb.cu_changes                                  OK
wikidb.cu_log                                      OK
wikidb.dymnorm                                     OK
wikidb.dympage                                     OK
wikidb.external_user                               OK
wikidb.externallinks                               OK
wikidb.filearchive                                 OK
wikidb.hitcounter
note     : The storage engine for the table doesn't support check
wikidb.image                                       OK
wikidb.imagelinks                                  OK
wikidb.interwiki                                   OK
wikidb.ipblocks                                    OK
wikidb.iwlinks                                     OK
wikidb.job                                         OK
wikidb.l10n_cache                                  OK
wikidb.langlinks                                   OK
wikidb.log_search                                  OK
wikidb.logging                                     OK
wikidb.math                                        OK
wikidb.metric                                      OK
wikidb.module_deps                                 OK
wikidb.msg_resource                                OK
wikidb.msg_resource_links                          OK
wikidb.objectcache                                 OK
wikidb.oldimage                                    OK
wikidb.online                                      OK
wikidb.online_chat                                 OK
wikidb.online_config                               OK
wikidb.page                                        OK
wikidb.page_props                                  OK
wikidb.page_restrictions                           OK
wikidb.pagelinks                                   OK
wikidb.protected_titles                            OK
wikidb.querycache                                  OK
wikidb.querycache_info                             OK
wikidb.querycachetwo                               OK
wikidb.recentchanges                               OK
wikidb.redirect                                    OK
wikidb.revision                                    OK
wikidb.searchindex                                 OK
wikidb.site_identifiers                            OK
wikidb.site_stats                                  OK
wikidb.sites                                       OK
wikidb.tag_summary                                 OK
wikidb.templatelinks                               OK
wikidb.text                                        OK
wikidb.trackbacks                                  OK
wikidb.transcache                                  OK
wikidb.updatelog                                   OK
wikidb.uploadstash                                 OK
wikidb.user                                        OK
wikidb.user_former_groups                          OK
wikidb.user_groups                                 OK
wikidb.user_newtalk                                OK
wikidb.user_properties                             OK
wikidb.valid_tag                                   OK
wikidb.watchlist                                   OK

seems ok.

2016-05-18: ada0p2 - database - next hurdle, now I get this:

root@ndweb# mysql -u wikidb_user -p wikidb < /home/tingo/dl/ndwiki/wikidb_db_dump-2015-04-01.sql
Enter password:
ERROR 1406 (22001) at line 711: Data too long for column 'log_comment' at row 36

oh, crap. Ok, this article seems to indicate that this is a new feature of MySQL 5.6. I'll add

SET SESSION sql_mode='';

at the top of the import file and try again. Again:

root@ndweb# mysql -u wikidb_user -p wikidb < /home/tingo/dl/ndwiki/wikidb_db_dump-2015-04-01.sql
Enter password:
ERROR 1231 (42000) at line 1860: Variable 'time_zone' can't be set to the value of 'NULL'

Oh, another problem. I added these lines to the top of the import file:

/*!40101 SET @OLD_CHARACTER_SET_CLIENT=@@CHARACTER_SET_CLIENT */;
/*!40101 SET @OLD_CHARACTER_SET_RESULTS=@@CHARACTER_SET_RESULTS */;
/*!40101 SET @OLD_COLLATION_CONNECTION=@@COLLATION_CONNECTION */;
/*!40101 SET NAMES utf8 */;
/*!40103 SET @OLD_TIME_ZONE=@@TIME_ZONE */;
/*!40103 SET TIME_ZONE='+00:00' */;
/*!40014 SET @OLD_UNIQUE_CHECKS=@@UNIQUE_CHECKS, UNIQUE_CHECKS=0 */;
/*!40014 SET @OLD_FOREIGN_KEY_CHECKS=@@FOREIGN_KEY_CHECKS, FOREIGN_KEY_CHECKS=0 */;
/*!40101 SET @OLD_SQL_MODE=@@SQL_MODE, SQL_MODE='NO_AUTO_VALUE_ON_ZERO' */;
/*!40111 SET @OLD_SQL_NOTES=@@SQL_NOTES, SQL_NOTES=0 */;

and finally:

root@ndweb# mysql -u wikidb_user -p wikidb < /home/tingo/dl/ndwiki/wikidb_db_dump-2015-04-01.sql
Enter password:
root@ndweb#

nice.

2016-05-18: ada0p2 - database - in the end, I split the import file so that just the wikidb database was left. Still get this:

root@ndweb# mysql -u wikidb_user -p wikidb < /home/tingo/dl/ndwiki/wikidb_db_dump-2015-04-01.sql
Enter password:
ERROR 1044 (42000) at line 5: Access denied for user 'wikidb_user'@'localhost' to database 'wikidb'

Hmm... aha! The user lacks CREATE and DROP privileges on that database. And ALTER and LOCK TABLES too.

2016-05-18: ada0p2 - database - import from the backup:

root@ndweb# mysql -u wikidb_user -p wikidb < /home/tingo/dl/ndwiki/full_db_dump-2015-04-01.sql
Enter password:
ERROR 1044 (42000) at line 22: Access denied for user 'wikiuser'@'localhost' to database 'dbmail'

ok, a bit of trouble there. Not sure why the dbmail is in the backup. Create it, grant access, and retry. On second thought, check the dump file - yep, it contains all databases.

2016-05-18: ada0p2 - create a database for the wiki:

root@ndweb# mysql -u root -p
Enter password:
Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 8
Server version: 5.6.30 Source distribution

Copyright (c) 2000, 2016, Oracle and/or its affiliates. All rights reserved.

Oracle is a registered trademark of Oracle Corporation and/or its
affiliates. Other names may be trademarks of their respective
owners.

Type 'help;' or '\h' for help. Type '\c' to clear the current input statement.
mysql> create database wikidb;
Query OK, 1 row affected (0.00 sec)

mysql> create user wikidb_user identified by 'wikidb_user_password';
Query OK, 0 rows affected (0.00 sec)

(no, that is not the real username or password)

mysql> use wikidb;
Database changed

mysql> grant select, update, insert, delete, usage on wikidb.* to wikidb_user;
Query OK, 0 rows affected (0.00 sec)

mysql> quit;
Bye

ok. Actually, that didn't work, I got this:

root@ndweb# mysql -u wikidb_user -p wikidb
Enter password:
ERROR 1045 (28000): Access denied for user 'wikidb_user'@'localhost' (using password: YES)

Looking at the user table in mysql, it is clear that "wikidb_user" and "wikidb_user@'localhost'" are different users. Easily fixed.

2016-05-18: ada0p2 - pkg - install mediawiki (I'm following the guide in the link above) and other bits: database server:

root@ndweb# pkg install mysql56-server
Updating FreeBSD repository catalogue...
FreeBSD repository is up-to-date.
All repositories are up-to-date.
The following 4 package(s) will be affected (of 0 checked):

New packages to be INSTALLED:
    mysql56-server: 5.6.30
    mysql56-client: 5.6.30
    libedit: 3.1.20150325_2
    perl5: 5.20.3_12

The process will require 179 MiB more space.
23 MiB to be downloaded.

Proceed with this action? [y/N]: y
[...]
Checking integrity... done (0 conflicting)
[1/4] Installing libedit-3.1.20150325_2...
[1/4] Extracting libedit-3.1.20150325_2: 100%
[2/4] Installing mysql56-client-5.6.30...
[2/4] Extracting mysql56-client-5.6.30: 100%
[3/4] Installing perl5-5.20.3_12...
[3/4] Extracting perl5-5.20.3_12: 100%
[4/4] Installing mysql56-server-5.6.30...
===> Creating users and/or groups.
Creating group 'mysql' with gid '88'.
Creating user 'mysql' with uid '88'.
[4/4] Extracting mysql56-server-5.6.30: 100%
Message from mysql56-client-5.6.30:
* * * * * * * * * * * * * * * * * * * * * * * *

Please be aware the database client is vulnerable
to CVE-2015-3152 - SSL Downgrade aka "BACKRONYM".
You may find more information at the following URL:

http://www.vuxml.org/freebsd/36bd352d-299b-11e5-86ff-14dae9d210b8.html

Although this database client is not listed as
"affected", it is vulnerable and will not be
receiving a patch. Please take note of this when
deploying this software.

* * * * * * * * * * * * * * * * * * * * * * * *
Message from perl5-5.20.3_12:
The /usr/bin/perl symlink has been removed starting with Perl 5.20.
For shebangs, you should either use:

#!/usr/local/bin/perl

or

#!/usr/bin/env perl

The first one will only work if you have a /usr/local/bin/perl,
the second will work as long as perl is in PATH.
Message from mysql56-server-5.6.30:
************************************************************************

Remember to run mysql_upgrade the first time you start the MySQL server
after an upgrade from an earlier version.

************************************************************************

web server

root@ndweb# pkg install apache24
Updating FreeBSD repository catalogue...
FreeBSD repository is up-to-date.
All repositories are up-to-date.
The following 9 package(s) will be affected (of 0 checked):

New packages to be INSTALLED:
    apache24: 2.4.20_1
    libxml2: 2.9.3
    expat: 2.1.0_3
    apr: 1.5.2.1.5.4
    gdbm: 1.11_2
    indexinfo: 0.2.4
    gettext-runtime: 0.19.7
    db5: 5.3.28_3
    pcre: 8.38_1

The process will require 87 MiB more space.
19 MiB to be downloaded.

Proceed with this action? [y/N]: y
[...]   
Checking integrity... done (0 conflicting)
[1/9] Installing indexinfo-0.2.4...
[1/9] Extracting indexinfo-0.2.4: 100%
[2/9] Installing gettext-runtime-0.19.7...
[2/9] Extracting gettext-runtime-0.19.7: 100%
[3/9] Installing expat-2.1.0_3...
[3/9] Extracting expat-2.1.0_3: 100%
[4/9] Installing gdbm-1.11_2...
[4/9] Extracting gdbm-1.11_2: 100%
[5/9] Installing db5-5.3.28_3...
[5/9] Extracting db5-5.3.28_3: 100%
[6/9] Installing libxml2-2.9.3...
[6/9] Extracting libxml2-2.9.3: 100%
[7/9] Installing apr-1.5.2.1.5.4...
[7/9] Extracting apr-1.5.2.1.5.4: 100%
[8/9] Installing pcre-8.38_1...
[8/9] Extracting pcre-8.38_1: 100%
[9/9] Installing apache24-2.4.20_1...
===> Creating users and/or groups.
Using existing group 'www'.
Using existing user 'www'.
[9/9] Extracting apache24-2.4.20_1: 100%
Message from apache24-2.4.20_1:
To run apache www server from startup, add apache24_enable="yes"
in your /etc/rc.conf. Extra options can be found in startup script.

Your hostname must be resolvable using at least 1 mechanism in
/etc/nsswitch.conf typically DNS or /etc/hosts or apache might
have issues starting depending on the modules you are using.

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

- apache24 default build changed from static MPM to modular MPM
- more modules are now enabled per default in the port
- icons and error pages moved from WWWDIR to DATADIR

   If build with modular MPM and no MPM is activated in
   httpd.conf, then mpm_prefork will be activated as default
   MPM in etc/apache24/modules.d to keep compatibility with
   existing php/perl/python modules!

Please compare the existing httpd.conf with httpd.conf.sample
and merge missing modules/instructions into httpd.conf!

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

php module for web server

root@ndweb# pkg install mod_php56
Updating FreeBSD repository catalogue...
FreeBSD repository is up-to-date.
All repositories are up-to-date.
The following 2 package(s) will be affected (of 0 checked):

New packages to be INSTALLED:
    mod_php56: 5.6.21
    php56: 5.6.21

The process will require 21 MiB more space.
3 MiB to be downloaded.

Proceed with this action? [y/N]: y
[...]
Checking integrity... done (0 conflicting)
[1/2] Installing php56-5.6.21...
[1/2] Extracting php56-5.6.21: 100%
[2/2] Installing mod_php56-5.6.21...
[2/2] Extracting mod_php56-5.6.21: 100%
[activating module 'php5' in /usr/local/etc/apache24/httpd.conf]
Message from mod_php56-5.6.21:
***************************************************************

Make sure index.php is part of your DirectoryIndex.

You should add the following to your Apache configuration file:

<FilesMatch "\.php$">
    SetHandler application/x-httpd-php
</FilesMatch>
<FilesMatch "\.phps$">
    SetHandler application/x-httpd-php-source
</FilesMatch>

***************************************************************

install mediawiki126:

root@ndweb# pkg install mediawiki126
Updating FreeBSD repository catalogue...
FreeBSD repository is up-to-date.
All repositories are up-to-date.
The following 16 package(s) will be affected (of 0 checked):

New packages to be INSTALLED:
    mediawiki126: 1.26.2
    php56-session: 5.6.21
    php56-xml: 5.6.21
    php56-hash: 5.6.21
    php56-xmlreader: 5.6.21
    php56-dom: 5.6.21
    php56-ctype: 5.6.21
    php56-iconv: 5.6.21
    libiconv: 1.14_9
    php56-sockets: 5.6.21
    php56-mysql: 5.6.21
    php56-mbstring: 5.6.21
    oniguruma5: 5.9.6_1
    php56-json: 5.6.21
    php56-readline: 5.6.21
    php56-zlib: 5.6.21

The process will require 100 MiB more space.
19 MiB to be downloaded.

Proceed with this action? [y/N]: y
[...]
Checking integrity... done (0 conflicting)
[...]
Message from mediawiki126-1.26.2:
**** NOTE ****
Remember to check

/usr/local/www/mediawiki/INSTALL

and

/usr/local/www/mediawiki/UPGRADE

for details

ok.

2016-05-17: ada0p2 - pkg - install smartmontools:

root@ndweb# pkg install smartmontools
Updating FreeBSD repository catalogue...
FreeBSD repository is up-to-date.
All repositories are up-to-date.
Updating database digests format: 100%
The following 1 package(s) will be affected (of 0 checked):

New packages to be INSTALLED:
    smartmontools: 6.4_2

The process will require 1 MiB more space.
377 KiB to be downloaded.

Proceed with this action? [y/N]: y
Fetching smartmontools-6.4_2.txz: 100%  377 KiB 386.3kB/s    00:01   
Checking integrity... done (0 conflicting)
[1/1] Installing smartmontools-6.4_2...
[1/1] Extracting smartmontools-6.4_2: 100%
Message from smartmontools-6.4_2:
smartmontools has been installed

To check the status of drives, use the following:

    /usr/local/sbin/smartctl -a /dev/ad0    for first ATA/SATA drive
    /usr/local/sbin/smartctl -a /dev/da0    for first SCSI drive
    /usr/local/sbin/smartctl -a /dev/ada0    for first SATA drive

To include drive health information in your daily status reports,
add a line like the following to /etc/periodic.conf:
    daily_status_smart_devices="/dev/ad0 /dev/da0"
substituting the appropriate device names for your SMART-capable disks.

To enable drive monitoring, you can use /usr/local/sbin/smartd.
A sample configuration file has been installed as
/usr/local/etc/smartd.conf.sample
Copy this file to /usr/local/etc/smartd.conf and edit appropriately

To have smartd start at boot
    echo 'smartd_enable="YES"' >> /etc/rc.conf

ok.

2016-05-17: ada0p2 - install pkg:

root@ndweb# pkg
The package management tool is not yet installed on your system.
Do you want to fetch and install it now? [y/N]: y
Bootstrapping pkg from pkg+http://pkg.FreeBSD.org/FreeBSD:10:amd64/quarterly, please wait...
Verifying signature with trusted certificate pkg.freebsd.org.2013102301... done
Installing pkg-1.7.2...
Extracting pkg-1.7.2: 100%
pkg: not enough arguments
Usage: pkg [-v] [-d] [-l] [-N] [-j <jail name or id>|-c <chroot path>|-r <rootdir>] [-C <configuration file>] [-R <repo config dir>] [-o var=value] [-4|-6] <command> [<args>]

For more information on available commands and options see 'pkg help'.

test it

root@ndweb# pkg -v
1.7.2
root@ndweb# pkg version
Updating FreeBSD repository catalogue...
Fetching meta.txz: 100%    944 B   0.9kB/s    00:01   
Fetching packagesite.txz: 100%    5 MiB   1.9MB/s    00:03   
Processing entries: 100%
FreeBSD repository update completed. 25088 packages processed.
pkg-1.7.2                          =

ok.

2016-05-17: ada0p2 - the machine now runs FreeBSD 10.3-release-p2:

root@ndweb# uname -a
FreeBSD ndweb 10.3-RELEASE-p2 FreeBSD 10.3-RELEASE-p2 #0: Wed May  4 06:03:51 UTC 2016     root@amd64-builder.daemonology.net:/usr/obj/usr/src/sys/GENERIC  amd64

freebsd-version

root@ndweb# freebsd-version -ku
10.3-RELEASE-p2
10.3-RELEASE-p2

ok.

2016-05-17: ada0p2 - run freebsd-update: fetch

root@ndweb# freebsd-update fetch
src component not installed, skipped
Looking up update.FreeBSD.org mirrors... none found.
Fetching public key from update.FreeBSD.org... done.
Fetching metadata signature for 10.3-RELEASE from update.FreeBSD.org... done.
Fetching metadata index... done.
Fetching 2 metadata files... done.
Inspecting system... done.
Preparing to download files... done.
Fetching 61 patches.....10....20....30....40....50....60 done.
Applying patches... done.

The following files will be updated as part of updating to 10.3-RELEASE-p2:
/bin/freebsd-version
/boot/kernel/kernel
/boot/kernel/kernel.symbols
/boot/kernel/zfs.ko
/boot/kernel/zfs.ko.symbols
/etc/mail/freebsd.cf
/etc/mail/freebsd.submit.cf
/etc/mail/sendmail.cf
/etc/mail/submit.cf
/lib/libc.so.7
/lib/libcrypto.so.7
/rescue/[
/rescue/atmconfig
/rescue/badsect
/rescue/bsdlabel
/rescue/bunzip2
/rescue/bzcat
/rescue/bzip2
/rescue/camcontrol
/rescue/cat
/rescue/ccdconfig
/rescue/chflags
/rescue/chgrp
/rescue/chio
/rescue/chmod
/rescue/chown
/rescue/chroot
/rescue/clri
/rescue/cp
/rescue/csh
/rescue/date
/rescue/dd
/rescue/devfs
/rescue/df
/rescue/dhclient
/rescue/disklabel
/rescue/dmesg
/rescue/dump
/rescue/dumpfs
/rescue/dumpon
/rescue/echo
/rescue/ed
/rescue/ex
/rescue/expr
/rescue/fastboot
/rescue/fasthalt
/rescue/fdisk
/rescue/fsck
/rescue/fsck_4.2bsd
/rescue/fsck_ffs
/rescue/fsck_msdosfs
/rescue/fsck_ufs
/rescue/fsdb
/rescue/fsirand
/rescue/gbde
/rescue/geom
/rescue/getfacl
/rescue/glabel
/rescue/gpart
/rescue/groups
/rescue/gunzip
/rescue/gzcat
/rescue/gzip
/rescue/halt
/rescue/head
/rescue/hostname
/rescue/id
/rescue/ifconfig
/rescue/init
/rescue/ipf
/rescue/iscsictl
/rescue/iscsid
/rescue/kenv
/rescue/kill
/rescue/kldconfig
/rescue/kldload
/rescue/kldstat
/rescue/kldunload
/rescue/ldconfig
/rescue/less
/rescue/link
/rescue/ln
/rescue/ls
/rescue/lzcat
/rescue/lzma
/rescue/md5
/rescue/mdconfig
/rescue/mdmfs
/rescue/mkdir
/rescue/mknod
/rescue/more
/rescue/mount
/rescue/mount_cd9660
/rescue/mount_msdosfs
/rescue/mount_nfs
/rescue/mount_nullfs
/rescue/mount_udf
/rescue/mount_unionfs
/rescue/mt
/rescue/mv
/rescue/nc
/rescue/newfs
/rescue/newfs_msdos
/rescue/nos-tun
/rescue/pgrep
/rescue/ping
/rescue/ping6
/rescue/pkill
/rescue/ps
/rescue/pwd
/rescue/rcorder
/rescue/rcp
/rescue/rdump
/rescue/realpath
/rescue/reboot
/rescue/red
/rescue/rescue
/rescue/restore
/rescue/rm
/rescue/rmdir
/rescue/route
/rescue/routed
/rescue/rrestore
/rescue/rtquery
/rescue/rtsol
/rescue/savecore
/rescue/sed
/rescue/setfacl
/rescue/sh
/rescue/sleep
/rescue/spppcontrol
/rescue/stty
/rescue/swapon
/rescue/sync
/rescue/sysctl
/rescue/tail
/rescue/tar
/rescue/tcsh
/rescue/tee
/rescue/test
/rescue/tunefs
/rescue/umount
/rescue/unlink
/rescue/unlzma
/rescue/unxz
/rescue/vi
/rescue/whoami
/rescue/xz
/rescue/xzcat
/rescue/zcat
/rescue/zdb
/rescue/zfs
/rescue/zpool
/sbin/init
/usr/bin/ar
/usr/bin/c++
/usr/bin/cc
/usr/bin/clang
/usr/bin/clang++
/usr/bin/clang-cpp
/usr/bin/cpp
/usr/bin/ntpq
/usr/bin/openssl
/usr/bin/ranlib
/usr/lib/libbsnmp.so.6
/usr/lib/libc.a
/usr/lib/libc_p.a
/usr/lib/libc_pic.a
/usr/lib/libcrypto.a
/usr/lib/libcrypto_p.a
/usr/lib/libssl.so.7
/usr/lib32/libbsnmp.so.6
/usr/lib32/libc.a
/usr/lib32/libc.so.7
/usr/lib32/libc_p.a
/usr/lib32/libc_pic.a
/usr/lib32/libcrypto.a
/usr/lib32/libcrypto.so.7
/usr/lib32/libcrypto_p.a
/usr/lib32/libssl.so.7
/usr/sbin/amd
/usr/sbin/hostapd
/usr/sbin/ntp-keygen
/usr/sbin/ntpd
/usr/sbin/ntpdate
/usr/sbin/ntpdc
/usr/sbin/ntptime
/usr/sbin/sntp
/usr/sbin/wpa_supplicant
/usr/share/doc/ntp/authentic.html
/usr/share/doc/ntp/monopt.html
/usr/share/doc/ntp/ntp-keygen.html
/usr/share/doc/ntp/ntp.conf.html
/usr/share/doc/ntp/ntp.keys.html
/usr/share/doc/ntp/ntpsnmpd.html
/usr/share/doc/ntp/xleave.html
/usr/share/man/man5/ntp.conf.5.gz
/usr/share/man/man5/ntp.keys.5.gz
/usr/share/man/man8/ntp-keygen.8.gz
/usr/share/man/man8/ntpd.8.gz
/usr/share/man/man8/ntpdc.8.gz
/usr/share/man/man8/ntpq.8.gz
/usr/share/man/man8/sntp.8.gz
/var/db/etcupdate/current/etc/mail/freebsd.cf
/var/db/etcupdate/current/etc/mail/freebsd.submit.cf
/var/db/etcupdate/current/etc/mail/sendmail.cf
/var/db/etcupdate/current/etc/mail/submit.cf

install

root@ndweb# freebsd-update install
src component not installed, skipped
Installing updates... done.

ok.

2016-05-17: ada0p2 - FreeBSD 10.3-release installed. dmesg output: normal, verbose.

root@ndweb:~ # uname -a
FreeBSD ndweb 10.3-RELEASE FreeBSD 10.3-RELEASE #0 r297264: Fri Mar 25 02:10:02 UTC 2016     root@releng1.nyi.freebsd.org:/usr/obj/usr/src/sys/GENERIC  amd64

disk layout

root@ndweb:~ # swapinfo -h;df -h
Device          1K-blocks     Used    Avail Capacity
/dev/ada0p3       3974580       0B     3.8G     0%
Filesystem     Size    Used   Avail Capacity  Mounted on
/dev/ada0p2    105G    926M     95G     1%    /
devfs          1.0K    1.0K      0B   100%    /dev

partition info

root@ndweb:~ # gpart show -p ada0
=>       34  234441581    ada0  GPT  (112G)
         34       1024  ada0p1  freebsd-boot  (512K)
       1058  226491392  ada0p2  freebsd-ufs  (108G)
  226492450    7949164  ada0p3  freebsd-swap  (3.8G)
  234441614          1          - free -  (512B)

PCI info

root@ndweb:~ # pciconf -lv
hostb0@pci0:0:0:0:    class=0x060000 card=0x22b11849 chip=0x22808086 rev=0x21 hdr=0x00
    vendor     = 'Intel Corporation'
    class      = bridge
    subclass   = HOST-PCI
vgapci0@pci0:0:2:0:    class=0x030000 card=0x22b11849 chip=0x22b18086 rev=0x21 hdr=0x00
    vendor     = 'Intel Corporation'
    class      = display
    subclass   = VGA
ahci0@pci0:0:19:0:    class=0x010601 card=0x22a31849 chip=0x22a38086 rev=0x21 hdr=0x00
    vendor     = 'Intel Corporation'
    class      = mass storage
    subclass   = SATA
xhci0@pci0:0:20:0:    class=0x0c0330 card=0x22b51849 chip=0x22b58086 rev=0x21 hdr=0x00
    vendor     = 'Intel Corporation'
    class      = serial bus
    subclass   = USB
none0@pci0:0:26:0:    class=0x108000 card=0x22981849 chip=0x22988086 rev=0x21 hdr=0x00
    vendor     = 'Intel Corporation'
    class      = encrypt/decrypt
hdac0@pci0:0:27:0:    class=0x040300 card=0x02831849 chip=0x22848086 rev=0x21 hdr=0x00
    vendor     = 'Intel Corporation'
    class      = multimedia
    subclass   = HDA
pcib1@pci0:0:28:0:    class=0x060400 card=0x22c81849 chip=0x22c88086 rev=0x21 hdr=0x01
    vendor     = 'Intel Corporation'
    class      = bridge
    subclass   = PCI-PCI
pcib2@pci0:0:28:1:    class=0x060400 card=0x22ca1849 chip=0x22ca8086 rev=0x21 hdr=0x01
    vendor     = 'Intel Corporation'
    class      = bridge
    subclass   = PCI-PCI
isab0@pci0:0:31:0:    class=0x060100 card=0x229c1849 chip=0x229c8086 rev=0x21 hdr=0x00
    vendor     = 'Intel Corporation'
    class      = bridge
    subclass   = PCI-ISA
none1@pci0:0:31:3:    class=0x0c0500 card=0x22921849 chip=0x22928086 rev=0x21 hdr=0x00
    vendor     = 'Intel Corporation'
    class      = serial bus
    subclass   = SMBus
none2@pci0:1:0:0:    class=0x028000 card=0x882110ec chip=0x882110ec rev=0x00 hdr=0x00
    vendor     = 'Realtek Semiconductor Co., Ltd.'
    device     = 'RTL8821AE 802.11ac PCIe Wireless Network Adapter'
    class      = network
re0@pci0:2:0:0:    class=0x020000 card=0x81681849 chip=0x816810ec rev=0x11 hdr=0x00
    vendor     = 'Realtek Semiconductor Co., Ltd.'
    device     = 'RTL8111/8168/8411 PCI Express Gigabit Ethernet Controller'
    class      = network
    subclass   = ethernet

The wireless interface is not supported (none2), but I am not using it, so it doesn't matter.

2016-05-17: I installed FreeBSD 10.3-release on the ssd (ada0). Norwegian keymap, named the machine ndweb, I removed games and ports from additional components, I used Guided disk setup, selected ada0, Partition, GPT, which gave me a 512kB freebsd-boot, 108 GB freebsd-ufs and 3.8 GB freebsd-swap. After writing partitions, the install started. After everything was extracted, a root password was set, select network interface (re0), IPv4, DHCP, I said no to IPv6 (I can always change it later. Resolver is set to 10.1.10.1 - this will need to change! For services, I slected sshd, ntpd and dumpdev.

2016-05-17: I booted of a FreeBSD 10.3-release install usb stick.