I'm trying to diagnose a slow filesystem issue on a server I look after. It's been ongoing for quite some time, and I've run out of ideas as to what I can try. Here's the thick of it.
The server itself is a Dell Poweredge T310. It has 4 SAS hard drives in it, configured at RAID5, and is running Citrix XenServer 5.6. The VM is a (relatively) old Debian 5.0.6 installation. It's given 4 cores, and 4Gb's of RAM. It has 3 volumes. A 10Gb volume (ext3) for the system, 980Gb volume (xfs) for data (~94% full), and another 200Gb volume (xfs) for data (~13% full).
Now here's the weird thing. Read/write access to the 980Gb volume is really slow. I might get 5Mb/s out of it if I'm lucky. At first I figured it was actually disk access in the system, or at a hypervisor level, but ruled that out entirely as other VMs on the same host are running perfectly fine (a good couple hundred Mb/s disk r/w access). So then I started to target this particular VM. I started thinking it was XFS, but to prove it I wasn't going to attempt to change the filesystem on the 980Gb drive, with years and years of billions of files on there. So I provisioned the 200Gb drive, and did the same read/write test (basically dd), and got a good couple hundred Mb/s r/w access to it. So that ruled out the VM, the hardware, and the filesystem type.
There's also a lot of these in /var/log/kern.log; (sorry, this is quite long)
Sep 4 10:16:59 uriel kernel: [32571790.564689] httpd: page allocation failure. order:5, mode:0x4020
Sep 4 10:16:59 uriel kernel: [32571790.564693] Pid: 7318, comm: httpd Not tainted 2.6.32-4-686-bigmem #1
Sep 4 10:16:59 uriel kernel: [32571790.564696] Call Trace:
Sep 4 10:16:59 uriel kernel: [32571790.564705] [<c1092a4d>] ? __alloc_pages_nodemask+0x476/0x4e0
Sep 4 10:16:59 uriel kernel: [32571790.564711] [<c1092ac3>] ? __get_free_pages+0xc/0x17
Sep 4 10:16:59 uriel kernel: [32571790.564716] [<c10b632e>] ? __kmalloc+0x30/0x128
Sep 4 10:16:59 uriel kernel: [32571790.564722] [<c11dd774>] ? pskb_expand_head+0x4f/0x157
Sep 4 10:16:59 uriel kernel: [32571790.564727] [<c11ddbbf>] ? __pskb_pull_tail+0x41/0x1fb
Sep 4 10:16:59 uriel kernel: [32571790.564732] [<c11e4882>] ? dev_queue_xmit+0xe4/0x38e
Sep 4 10:16:59 uriel kernel: [32571790.564738] [<c1205902>] ? ip_finish_output+0x0/0x5c
Sep 4 10:16:59 uriel kernel: [32571790.564742] [<c12058c7>] ? ip_finish_output2+0x187/0x1c2
Sep 4 10:16:59 uriel kernel: [32571790.564747] [<c1204dc8>] ? ip_local_out+0x15/0x17
Sep 4 10:16:59 uriel kernel: [32571790.564751] [<c12055a9>] ? ip_queue_xmit+0x31e/0x379
Sep 4 10:16:59 uriel kernel: [32571790.564758] [<c1279a90>] ? _spin_lock_bh+0x8/0x1e
Sep 4 10:16:59 uriel kernel: [32571790.564767] [<eda15a8d>] ? __nf_ct_refresh_acct+0x66/0xa4 [nf_conntrack]
Sep 4 10:16:59 uriel kernel: [32571790.564773] [<c103bf42>] ? _local_bh_enable_ip+0x16/0x6e
Sep 4 10:16:59 uriel kernel: [32571790.564779] [<c1214593>] ? tcp_transmit_skb+0x595/0x5cc
Sep 4 10:16:59 uriel kernel: [32571790.564785] [<c1005c4f>] ? xen_restore_fl_direct_end+0x0/0x1
Sep 4 10:16:59 uriel kernel: [32571790.564791] [<c12165ea>] ? tcp_write_xmit+0x7a3/0x874
Sep 4 10:16:59 uriel kernel: [32571790.564796] [<c121203a>] ? tcp_ack+0x1611/0x1802
Sep 4 10:16:59 uriel kernel: [32571790.564801] [<c10055ec>] ? xen_force_evtchn_callback+0xc/0x10
Sep 4 10:16:59 uriel kernel: [32571790.564806] [<c121392f>] ? tcp_established_options+0x1d/0x8b
Sep 4 10:16:59 uriel kernel: [32571790.564811] [<c1213be4>] ? tcp_current_mss+0x38/0x53
Sep 4 10:16:59 uriel kernel: [32571790.564816] [<c1216701>] ? __tcp_push_pending_frames+0x1e/0x50
Sep 4 10:16:59 uriel kernel: [32571790.564821] [<c1212246>] ? tcp_data_snd_check+0x1b/0xd2
Sep 4 10:16:59 uriel kernel: [32571790.564825] [<c1212de3>] ? tcp_rcv_established+0x5d0/0x626
Sep 4 10:16:59 uriel kernel: [32571790.564831] [<c121902c>] ? tcp_v4_do_rcv+0x15f/0x2cf
Sep 4 10:16:59 uriel kernel: [32571790.564835] [<c1219561>] ? tcp_v4_rcv+0x3c5/0x5c0
Sep 4 10:16:59 uriel kernel: [32571790.564841] [<c120197e>] ? ip_local_deliver_finish+0x10c/0x18c
Sep 4 10:16:59 uriel kernel: [32571790.564846] [<c12015a4>] ? ip_rcv_finish+0x2c4/0x2d8
Sep 4 10:16:59 uriel kernel: [32571790.564852] [<c11e3b71>] ? netif_receive_skb+0x3bb/0x3d6
Sep 4 10:16:59 uriel kernel: [32571790.564864] [<ed823efc>] ? xennet_poll+0x9b8/0xafc [xen_netfront]
Sep 4 10:16:59 uriel kernel: [32571790.564869] [<c11e40ee>] ? net_rx_action+0x96/0x194
Sep 4 10:16:59 uriel kernel: [32571790.564874] [<c103bd4c>] ? __do_softirq+0xaa/0x151
Sep 4 10:16:59 uriel kernel: [32571790.564878] [<c103be24>] ? do_softirq+0x31/0x3c
Sep 4 10:16:59 uriel kernel: [32571790.564883] [<c103befa>] ? irq_exit+0x26/0x58
Sep 4 10:16:59 uriel kernel: [32571790.564890] [<c118ff9f>] ? xen_evtchn_do_upcall+0x12c/0x13e
Sep 4 10:16:59 uriel kernel: [32571790.564896] [<c1008c3f>] ? xen_do_upcall+0x7/0xc
Sep 4 10:16:59 uriel kernel: [32571790.564899] Mem-Info:
Sep 4 10:16:59 uriel kernel: [32571790.564902] DMA per-cpu:
Sep 4 10:16:59 uriel kernel: [32571790.564905] CPU 0: hi: 0, btch: 1 usd: 0
Sep 4 10:16:59 uriel kernel: [32571790.564908] CPU 1: hi: 0, btch: 1 usd: 0
Sep 4 10:16:59 uriel kernel: [32571790.564911] CPU 2: hi: 0, btch: 1 usd: 0
Sep 4 10:16:59 uriel kernel: [32571790.564914] CPU 3: hi: 0, btch: 1 usd: 0
Sep 4 10:16:59 uriel kernel: [32571790.564916] Normal per-cpu:
Sep 4 10:16:59 uriel kernel: [32571790.564919] CPU 0: hi: 186, btch: 31 usd: 175
Sep 4 10:16:59 uriel kernel: [32571790.564922] CPU 1: hi: 186, btch: 31 usd: 165
Sep 4 10:16:59 uriel kernel: [32571790.564925] CPU 2: hi: 186, btch: 31 usd: 30
Sep 4 10:16:59 uriel kernel: [32571790.564928] CPU 3: hi: 186, btch: 31 usd: 140
Sep 4 10:16:59 uriel kernel: [32571790.564931] HighMem per-cpu:
Sep 4 10:16:59 uriel kernel: [32571790.564933] CPU 0: hi: 186, btch: 31 usd: 159
Sep 4 10:16:59 uriel kernel: [32571790.564936] CPU 1: hi: 186, btch: 31 usd: 22
Sep 4 10:16:59 uriel kernel: [32571790.564939] CPU 2: hi: 186, btch: 31 usd: 24
Sep 4 10:16:59 uriel kernel: [32571790.564942] CPU 3: hi: 186, btch: 31 usd: 13
Sep 4 10:16:59 uriel kernel: [32571790.564947] active_anon:485974 inactive_anon:121138 isolated_anon:0
Sep 4 10:16:59 uriel kernel: [32571790.564948] active_file:75215 inactive_file:79510 isolated_file:0
Sep 4 10:16:59 uriel kernel: [32571790.564949] unevictable:0 dirty:516 writeback:15 unstable:0
Sep 4 10:16:59 uriel kernel: [32571790.564950] free:230770 slab_reclaimable:36661 slab_unreclaimable:21249
Sep 4 10:16:59 uriel kernel: [32571790.564952] mapped:20016 shmem:29450 pagetables:5600 bounce:0
Sep 4 10:16:59 uriel kernel: [32571790.564958] DMA free:2884kB min:72kB low:88kB high:108kB active_anon:0kB inactive_anon:0kB active_file:5692kB inactive_file:724kB unevictable:0kB isolated(anon):0kB isolated(file):0kB present:15872kB mlocked:0kB dirty:8kB writeback:0kB mapped:0kB shmem:0kB slab_reclaimable:5112kB slab_unreclaimable:156kB kernel_stack:56kB pagetables:0kB unstable:0kB bounce:0kB writeback_tmp:0kB pages_scanned:0 all_unreclaimable? no
Sep 4 10:16:59 uriel kernel: [32571790.564964] lowmem_reserve[]: 0 698 4143 4143
Sep 4 10:16:59 uriel kernel: [32571790.564977] Normal free:143468kB min:3344kB low:4180kB high:5016kB active_anon:56kB inactive_anon:2068kB active_file:131812kB inactive_file:131728kB unevictable:0kB isolated(anon):0kB isolated(file):0kB present:715256kB mlocked:0kB dirty:156kB writeback:0kB mapped:308kB shmem:4kB slab_reclaimable:141532kB slab_unreclaimable:84840kB kernel_stack:1928kB pagetables:22400kB unstable:0kB bounce:0kB writeback_tmp:0kB pages_scanned:0 all_unreclaimable? no
Sep 4 10:16:59 uriel kernel: [32571790.564983] lowmem_reserve[]: 0 0 27559 27559
Sep 4 10:16:59 uriel kernel: [32571790.564995] HighMem free:776728kB min:512kB low:4636kB high:8760kB active_anon:1943840kB inactive_anon:482484kB active_file:163356kB inactive_file:185588kB unevictable:0kB isolated(anon):0kB isolated(file):0kB present:3527556kB mlocked:0kB dirty:1900kB writeback:60kB mapped:79756kB shmem:117796kB slab_reclaimable:0kB slab_unreclaimable:0kB kernel_stack:0kB pagetables:0kB unstable:0kB bounce:0kB writeback_tmp:0kB pages_scanned:0 all_unreclaimable? no
Sep 4 10:16:59 uriel kernel: [32571790.565001] lowmem_reserve[]: 0 0 0 0
Sep 4 10:16:59 uriel kernel: [32571790.565011] DMA: 385*4kB 16*8kB 3*16kB 9*32kB 6*64kB 2*128kB 1*256kB 0*512kB 0*1024kB 0*2048kB 0*4096kB = 2900kB
Sep 4 10:16:59 uriel kernel: [32571790.565032] Normal: 21505*4kB 6508*8kB 273*16kB 24*32kB 3*64kB 0*128kB 0*256kB 0*512kB 0*1024kB 0*2048kB 0*4096kB = 143412kB
Sep 4 10:16:59 uriel kernel: [32571790.565054] HighMem: 949*4kB 8859*8kB 7063*16kB 6186*32kB 4631*64kB 727*128kB 6*256kB 0*512kB 0*1024kB 0*2048kB 0*4096kB = 776604kB
Sep 4 10:16:59 uriel kernel: [32571790.565076] 198980 total pagecache pages
Sep 4 10:16:59 uriel kernel: [32571790.565079] 14850 pages in swap cache
Sep 4 10:16:59 uriel kernel: [32571790.565082] Swap cache stats: add 2556273, delete 2541423, find 82961339/83153719
Sep 4 10:16:59 uriel kernel: [32571790.565085] Free swap = 250592kB
Sep 4 10:16:59 uriel kernel: [32571790.565087] Total swap = 385520kB
Sep 4 10:16:59 uriel kernel: [32571790.575454] 1073152 pages RAM
Sep 4 10:16:59 uriel kernel: [32571790.575458] 888834 pages HighMem
Sep 4 10:16:59 uriel kernel: [32571790.575461] 11344 pages reserved
Sep 4 10:16:59 uriel kernel: [32571790.575463] 1090481 pages shared
Sep 4 10:16:59 uriel kernel: [32571790.575465] 737188 pages non-shared
Now, I've no idea what this means. There's plenty of free memory;
total used free shared buffers cached
Mem: 4247232 3455904 791328 0 5348 736412
-/+ buffers/cache: 2714144 1533088
Swap: 385520 131004 254516
Though now I see the swap is relatively low in size, but would that matter?
I've been starting to think about fragmentation, or inode usage on that large partition, but a recent fsck on it showed is as only like 0.5% fragmented. Which leaves me with inode usage, but how much of an effect really would a large inode table or filesystem TOC have?
I've love to hear people's opinions on this. It's driving me potty!
df -h output;
Filesystem Size Used Avail Use% Mounted on
/dev/xvda1 9.5G 6.6G 2.4G 74% /
tmpfs 2.1G 0 2.1G 0% /lib/init/rw
udev 10M 520K 9.5M 6% /dev
tmpfs 2.1G 0 2.1G 0% /dev/shm
/dev/xvdb 980G 921G 59G 94% /data
xfs_db output;
# xfs_db -r -c frag /dev/xvdb
actual 15687263, ideal 15385050, fragmentation factor 1.93%
Best Answer
It could still be the XFS filesystem in this case. You may have heavy fragmentation issues as well as the slowdown that comes with a nearly-full filesystem. You could benefit from more space in either case.
Please check the XFS filesystem's fragmentation. You can do this with the
xfs_dbcommand. If the filesystem is/dev/sdb1, for example, then you command would look like:That will output a fragmentation factor:
You can run the online defragmentation utility,
xfs_fsr -v, in ascreensession to try to rectify this. By default, the command runs for 2 hours or TEN passes on the filesystem. You may have to run it multiple times. Check the fragmentation factor between runs.