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Subject[BUG] Slow SATA disk - waiting in balance_dirty_pages() on i686-pae.html
Date
Hello,

;TL,DR: apt-get is blocked by balance_dirty_pages() with linux-{3,16
4.2, 4.9}, but fast after reboot.


We still have several systems running 4.9.0-ucs104-686-pae. They have 16
GiB RAM and two disk:
> # lsblk -S
> NAME HCTL TYPE VENDOR MODEL REV TRAN
> sdb 5:0:0:0 disk ATA ST32000644NS SN12 sata
> sr0 6:0:0:0 rom Optiarc DVD RW AD-7260S 1.03 sata
> sda 4:0:0:0 disk ATA ST32000644NS SN12 sata

After some time they get really slow, for example when running "apt-get
update" to update the list of available Debian packages. "vmstat" shows
a very hight "wait time":
> # vmstat 1
> procs -----------memory---------- ---swap-- -----io---- -system-- ------cpu-----
> r b swpd free buff cache si so bi bo in cs us sy id wa st
> 0 1 0 13545436 361480 1786148 0 0 2 21 25 35 2 1 95 2 0
> 0 2 0 13545312 361484 1786144 0 0 0 636 596 939 0 0 83 17 0
> 1 1 0 13543700 361488 1786148 0 0 4 464 3472 872 3 4 79 14 0
> 0 1 0 13545072 361488 1786148 0 0 0 2176 2504 905 3 4 79 13 0
> 0 1 0 13545188 361488 1786276 0 0 0 1832 1173 969 0 0 87 13 0
> 0 1 0 13545088 361488 1786276 0 0 0 1360 862 1036 0 0 87 12 0
> 0 2 0 13544560 361492 1786276 0 0 0 2276 1739 921 0 0 87 13 0
> 0 1 0 13545304 361500 1786276 0 0 0 468 581 1030 0 0 81 19 0
> 1 1 0 13543228 361500 1786284 0 0 0 520 1219 1078 2 3 82 13 0
> 0 2 0 13545228 361500 1786284 0 0 0 608 673 1054 3 5 75 17 0
> 0 1 0 13545436 361500 1786280 0 0 0 900 1343 1126 0 0 82 17 0
> 4 4 0 13526320 359140 1786280 0 0 0 440 2126 5782 30 6 50 14 0
> 0 2 0 13529640 359144 1786280 0 0 0 1480 2764 6362 2 3 65 30 0
> 0 2 0 13529744 359144 1786280 0 0 0 968 769 1737 0 0 74 25 0
> 0 2 0 13529884 359152 1786276 0 0 0 1036 688 1516 0 0 74 26 0
> 1 2 0 13530000 359152 1786408 0 0 0 1200 884 1402 1 1 75 23 0
> 1 2 0 13528500 359152 1786408 0 0 0 1492 1027 1340 3 4 70 23 0
> 0 3 0 13539544 359160 1786408 0 0 4 1892 1105 1204 1 1 70 28 0
> 0 2 0 13522632 359160 1786408 0 0 0 1056 3320 1838 6 4 64 26 0
> 0 1 0 13543488 359160 1786408 0 0 0 2604 1499 1200 1 0 82 17 0
> 0 1 0 13543728 359168 1786412 0 0 0 2508 1229 693 0 0 81 19 0

Loocking as 'wchan' I see it stuck in
> # ps -eo pid,tid,class,rtprio,ni,pri,psr,pcpu,stat,wchan:32,cgroup:48,comm | grep apt
> 21403 21403 TS - 0 19 5 0.2 D+ balance_dirty_pages.isra.24 1:name=systemd:/system.slice/ssh.service apt-get

"iostat" tell me that the system is constantly writing:
> avg-cpu: %user %nice %system %iowait %steal %idle
> 1,97 0,00 2,43 15,68 0,00 79,92
>
> Device: rrqm/s wrqm/s r/s w/s rMB/s wMB/s avgrq-sz avgqu-sz await r_await w_await svctm %util
> sdb 0,00 6,33 0,00 220,67 0,00 1,03 9,55 3,18 14,40 0,00 14,40 0,83 18,27
> sda 0,00 6,00 0,33 221,00 0,00 1,03 9,53 3,15 14,25 60,00 14,18 0,73 16,27
> md0 0,00 0,00 0,00 0,00 0,00 0,00 0,00 0,00 0,00 0,00 0,00 0,00 0,00
> md1 0,00 0,00 0,33 227,00 0,00 1,03 9,28 0,00 0,00 0,00 0,00 0,00 0,00
> dm-0 0,00 0,00 0,33 224,33 0,00 1,02 9,33 3,50 15,58 60,00 15,51 0,81 18,27
> dm-1 0,00 0,00 0,00 0,00 0,00 0,00 0,00 0,00 0,00 0,00 0,00 0,00 0,00
> dm-2 0,00 0,00 0,00 1,67 0,00 0,01 8,00 0,03 18,40 0,00 18,40 18,40 3,07
> dm-3 0,00 0,00 0,00 0,00 0,00 0,00 0,00 0,00 0,00 0,00 0,00 0,00 0,00
> dm-4 0,00 0,00 0,00 0,00 0,00 0,00 0,00 0,00 0,00 0,00 0,00 0,00 0,00
> dm-5 0,00 0,00 0,00 0,00 0,00 0,00 0,00 0,00 0,00 0,00 0,00 0,00 0,00

"echo 1 >/proc/sys/vm/block_dump" did now show any useful (to my
untrained eye):
> [142980.159166] apt-get(1010): dirtied inode 786560 (pkgcache.bin.Vv0g4q) on dm-0
> [142980.159183] apt-get(1010): dirtied inode 786560 (pkgcache.bin.Vv0g4q) on dm-0
> [142980.159438] kworker/u16:1(5188): WRITE block 49666728 on dm-0 (8 sectors)
> [142980.159450] kworker/u16:1(5188): WRITE block 49666968 on dm-0 (8 sectors)
> [142980.159455] kworker/u16:1(5188): WRITE block 49667384 on dm-0 (8 sectors)
> [142980.159460] kworker/u16:1(5188): WRITE block 49667568 on dm-0 (8 sectors)
> [142980.159465] kworker/u16:1(5188): WRITE block 49667584 on dm-0 (8 sectors)
> [142980.159470] kworker/u16:1(5188): WRITE block 49667616 on dm-0 (8 sectors)
> [142980.159474] kworker/u16:1(5188): WRITE block 49667664 on dm-0 (8 sectors)
> [142980.159479] kworker/u16:1(5188): WRITE block 49667704 on dm-0 (8 sectors)
> [142980.159489] kworker/u16:1(5188): WRITE block 49643520 on dm-0 (8 sectors)
> [142980.159494] kworker/u16:1(5188): WRITE block 49643680 on dm-0 (8 sectors)
> [142980.159499] kworker/u16:1(5188): WRITE block 49643920 on dm-0 (8 sectors)
> [142980.159503] kworker/u16:1(5188): WRITE block 49644240 on dm-0 (8 sectors)
> [142980.159508] kworker/u16:1(5188): WRITE block 49644408 on dm-0 (8 sectors)
> [142980.159513] kworker/u16:1(5188): WRITE block 49644872 on dm-0 (8 sectors)
> [142980.159517] kworker/u16:1(5188): WRITE block 49644888 on dm-0 (8 sectors)
> [142980.159522] kworker/u16:1(5188): WRITE block 49645048 on dm-0 (8 sectors)
> [142980.159527] kworker/u16:1(5188): WRITE block 49645072 on dm-0 (8 sectors)
> [142980.159531] kworker/u16:1(5188): WRITE block 49646088 on dm-0 (8 sectors)
> [142980.159536] kworker/u16:1(5188): WRITE block 49922424 on dm-0 (8 sectors)
> [142980.159541] kworker/u16:1(5188): WRITE block 49929072 on dm-0 (8 sectors)
> [142980.159545] kworker/u16:1(5188): WRITE block 49929296 on dm-0 (8 sectors)
> [142980.159551] kworker/u16:1(5188): WRITE block 49665288 on dm-0 (8 sectors)
> [142980.159555] kworker/u16:1(5188): WRITE block 49666272 on dm-0 (8 sectors)
> [142980.163173] rs:main Q:Reg(1284): dirtied inode 266 (debug) on dm-2
> [142980.163185] rs:main Q:Reg(1284): dirtied inode 266 (debug) on dm-2
> [142980.163251] kworker/u16:1(5188): WRITE block 14423192 on dm-2 (8 sectors)
> [142980.175161] rs:main Q:Reg(1284): dirtied inode 266 (debug) on dm-2
> [142980.175164] apt-get(1010): dirtied inode 786560 (pkgcache.bin.Vv0g4q) on dm-0
> [142980.175172] apt-get(1010): dirtied inode 786560 (pkgcache.bin.Vv0g4q) on dm-0
...
(I forgot to filter out those messages from syslog, so rsyslog is
constantly dirtying the log files with those messages)

On the other hand there doesn't seem to be much dirty data:
> # cat /proc/meminfo
> MemTotal: 16519788 kB
> MemFree: 13524100 kB
> MemAvailable: 14599184 kB
> Buffers: 361420 kB
> Cached: 1808348 kB
> SwapCached: 0 kB
> Active: 1660840 kB
> Inactive: 973144 kB
> Active(anon): 467196 kB
> Inactive(anon): 40420 kB
> Active(file): 1193644 kB
> Inactive(file): 932724 kB
> Unevictable: 0 kB
> Mlocked: 0 kB
> HighTotal: 15778484 kB
> HighFree: 13476176 kB
> LowTotal: 741304 kB
> LowFree: 47924 kB
> SwapTotal: 25165820 kB
> SwapFree: 25165820 kB
> Dirty: 4 kB
> Writeback: 268 kB
> AnonPages: 464272 kB
> Mapped: 514240 kB
> Shmem: 43344 kB
> Slab: 306304 kB
> SReclaimable: 282876 kB
> SUnreclaim: 23428 kB
> KernelStack: 3152 kB
> PageTables: 9620 kB
> NFS_Unstable: 0 kB
> Bounce: 536 kB
> WritebackTmp: 0 kB
> CommitLimit: 33425712 kB
> Committed_AS: 1957408 kB
> VmallocTotal: 122880 kB
> VmallocUsed: 0 kB
> VmallocChunk: 0 kB
> HardwareCorrupted: 0 kB
> AnonHugePages: 0 kB
> ShmemHugePages: 0 kB
> ShmemPmdMapped: 0 kB
> HugePages_Total: 0
> HugePages_Free: 0
> HugePages_Rsvd: 0
> HugePages_Surp: 0
> Hugepagesize: 2048 kB
> DirectMap4k: 10232 kB
> DirectMap2M: 899072 kB

Running "blktrace -d /dev/sda -d /dev/sdb -w 60" shows the disk to have
a very low write performance:
> Total (sda):
> Reads Queued: 6, 24KiB Writes Queued: 1091, 4076KiB
> Read Dispatches: 6, 24KiB Write Dispatches: 730, 4076KiB
> Reads Requeued: 0 Writes Requeued: 6
> Reads Completed: 6, 24KiB Writes Completed: 992, 4076KiB
> Read Merges: 0, 0KiB Write Merges: 267, 1068KiB
> PC Reads Queued: 0, 0KiB PC Writes Queued: 0, 0KiB
> PC Read Disp.: 20, 4KiB PC Write Disp.: 0, 0KiB
> PC Reads Req.: 7 PC Writes Req.: 0
> PC Reads Compl.: 13 PC Writes Compl.: 0
> IO unplugs: 508 Timer unplugs: 0
>
> Throughput (R/W): 0KiB/s / 68KiB/s
> Events (sda): 12188 entries
> Skips: 0 forward (0 - 0.0%)
...
> Total (sdb):
> Reads Queued: 2, 8KiB Writes Queued: 1091, 4076KiB
> Read Dispatches: 2, 8KiB Write Dispatches: 727, 4076KiB
> Reads Requeued: 0 Writes Requeued: 4
> Reads Completed: 2, 8KiB Writes Completed: 991, 4076KiB
> Read Merges: 0, 0KiB Write Merges: 268, 1072KiB
> PC Reads Queued: 0, 0KiB PC Writes Queued: 0, 0KiB
> PC Read Disp.: 18, 4KiB PC Write Disp.: 0, 0KiB
> PC Reads Req.: 5 PC Writes Req.: 0
> PC Reads Compl.: 13 PC Writes Compl.: 0
> IO unplugs: 507 Timer unplugs: 0
>
> Throughput (R/W): 0KiB/s / 68KiB/s
> Events (sdb): 12011 entries
> Skips: 0 forward (0 - 0.0%)
"sysctl" was not changes (to my knowledge):
> # sysctl -a | grep ^vm
> vm.admin_reserve_kbytes = 8192
> vm.block_dump = 0
> vm.compact_unevictable_allowed = 1
> vm.dirty_background_bytes = 0
> vm.dirty_background_ratio = 10
> vm.dirty_bytes = 0
> vm.dirty_expire_centisecs = 3000
> vm.dirty_ratio = 20
> vm.dirty_writeback_centisecs = 500
> vm.dirtytime_expire_seconds = 43200
> vm.drop_caches = 0
> vm.extfrag_threshold = 500
> vm.highmem_is_dirtyable = 0
> vm.hugepages_treat_as_movable = 0
> vm.hugetlb_shm_group = 0
> vm.laptop_mode = 0
> vm.legacy_va_layout = 0
> vm.lowmem_reserve_ratio = 256 32 32
> vm.max_map_count = 65530
> vm.memory_failure_early_kill = 0
> vm.memory_failure_recovery = 1
> vm.min_free_kbytes = 35204
> vm.mmap_min_addr = 65536
> vm.mmap_rnd_bits = 8
> vm.nr_hugepages = 0
> vm.nr_overcommit_hugepages = 0
> vm.nr_pdflush_threads = 0
> vm.oom_dump_tasks = 1
> vm.oom_kill_allocating_task = 0
> vm.overcommit_kbytes = 0
> vm.overcommit_memory = 0
> vm.overcommit_ratio = 50
> vm.page-cluster = 3
> vm.panic_on_oom = 0
> vm.percpu_pagelist_fraction = 0
> vm.stat_interval = 1
> vm.swappiness = 60
> vm.user_reserve_kbytes = 131072
> vm.vdso_enabled = 1
> vm.vfs_cache_pressure = 100
> vm.watermark_scale_factor = 10

Here's the 'SysRq-t' output (for that process):
> [148498.778772] apt-get D 0 21403 10119 0x00000000
> [148498.778773] 00000000 e99c9480 c17756c0 e7243d0c c15afda5 f6a5f968 e7243d84 f5f07c00
> [148498.778776] f5d90c00 10ea48c6 0000870f 10ea0f6b 0000870f e7c35e00 0000870f f7965e80
> [148498.778778] e7243d18 e99c9480 f795fa40 f795fa40 e7243d18 c15b022e e7243d38 e7243d60
> [148498.778780] Call Trace:
> [148498.778782] [<c15afda5>] ? __schedule+0x2b5/0x710
> [148498.778783] [<c15b022e>] ? schedule+0x2e/0x80
> [148498.778784] [<c15b2ff1>] ? schedule_timeout+0x131/0x2a0
> [148498.778786] [<f85221a4>] ? jbd2_journal_stop+0xc4/0x3e0 [jbd2]
> [148498.778788] [<c12f6457>] ? fprop_fraction_percpu+0x27/0xb0
> [148498.778790] [<c10d5240>] ? lock_timer_base+0x80/0x80
> [148498.778791] [<c15afa7b>] ? io_schedule_timeout+0x9b/0x110
> [148498.778793] [<c11721d6>] ? balance_dirty_pages.isra.24+0x316/0xec0
> [148498.778794] [<c12fa594>] ? radix_tree_tag_set+0x84/0xf0
> [148498.778796] [<c11717d9>] ? set_page_dirty+0x49/0xb0
> [148498.778798] [<c120e095>] ? block_page_mkwrite+0xe5/0x120
> [148498.778801] [<c1173003>] ? balance_dirty_pages_ratelimited+0x283/0x3c0
> [148498.778804] [<c119645c>] ? do_wp_page+0x6ac/0x7c0
> [148498.778807] [<c105f92b>] ? kmap_atomic_prot+0xdb/0x100
> [148498.778810] [<c1199a56>] ? handle_mm_fault+0x7e6/0x10d0
> [148498.778812] [<c11d6f6f>] ? vfs_read+0x10f/0x140
> [148498.778815] [<c10562f0>] ? __do_page_fault+0x1d0/0x510
> [148498.778818] [<c1056630>] ? __do_page_fault+0x510/0x510
> [148498.778820] [<c15b5643>] ? error_code+0x67/0x6c

There is a similar reports at
<https://askubuntu.com/questions/251781/reading-package-list-takes-forever/327444>
and we're seeing it at a regular interval.
Rebooting system fixes it (apt-get is fast again), but re-occurs after
some time.

We have used several different Linux kernel versions by now (3.16, 4.2,
4.9), but all show the same bug.
It is not limited to 'apt', we have seen it with 'slapadd' as well.
We only observed this on 686-pae, never on amd64 - may be an 32 bit
overflow bug?

Any other idea?

What other data should I collect to help diagnose this?

Philipp
--
Philipp Hahn
Open Source Software Engineer

Univention GmbH
be open.
Mary-Somerville-Str. 1
D-28359 Bremen
Tel.: +49 421 22232-0
Fax : +49 421 22232-99
hahn@univention.de

http://www.univention.de/
Geschäftsführer: Peter H. Ganten
HRB 20755 Amtsgericht Bremen
Steuer-Nr.: 71-597-02876

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