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SubjectRe: iotop: khugepaged at 99.99% (2.6.38.3)
Date
I didn't have to wait until tomorrow, the problem just occurred again. I was
using Gnome Shell with three instances of R in separate EMACS sessions, Java
(JabRef), Evolution and Totem playing a video file. Shortly after starting the
video, Gnome Shell froze. I could switch to a tty and iotop showed totem,
gnome-shell and khugepaged at 99% IO. I managed to kill Totem and then Gnome
Shell, which respawned and let me save my work before rebooting.

I did a "cat /proc/zoneinfo" four times, the last time is after killing and
restartong Gnome Shell. I forgot to do SYSRQ+T, sorry. I'll remember it the next
time, shouldn't be long...

1st /proc/zoneinfo:

Node 0, zone DMA
pages free 3270
min 196
low 245
high 294
scanned 0
spanned 4080
present 3951
nr_free_pages 3270
nr_inactive_anon 0
nr_active_anon 0
nr_inactive_file 594
nr_active_file 0
nr_unevictable 0
nr_mlock 0
nr_anon_pages 0
nr_mapped 0
nr_file_pages 706
nr_dirty 0
nr_writeback 0
nr_slab_reclaimable 0
nr_slab_unreclaimable 2
nr_page_table_pages 0
nr_kernel_stack 0
nr_unstable 0
nr_bounce 0
nr_vmscan_write 0
nr_writeback_temp 0
nr_isolated_anon 0
nr_isolated_file 298
nr_shmem 0
nr_dirtied 1414
nr_written 1414
nr_anon_transparent_hugepages 0
protection: (0, 865, 3023, 3023)
pagesets
cpu: 0
count: 0
high: 0
batch: 1
vm stats threshold: 4
cpu: 1
count: 0
high: 0
batch: 1
vm stats threshold: 4
all_unreclaimable: 0
start_pfn: 16
inactive_ratio: 1
Node 0, zone Normal
pages free 18200
min 11003
low 13753
high 16504
scanned 0
spanned 223230
present 221486
nr_free_pages 18200
nr_inactive_anon 69521
nr_active_anon 48778
nr_inactive_file 37202
nr_active_file 16530
nr_unevictable 0
nr_mlock 0
nr_anon_pages 14029
nr_mapped 175
nr_file_pages 55304
nr_dirty 91
nr_writeback 0
nr_slab_reclaimable 15225
nr_slab_unreclaimable 2797
nr_page_table_pages 1134
nr_kernel_stack 319
nr_unstable 0
nr_bounce 0
nr_vmscan_write 1023
nr_writeback_temp 0
nr_isolated_anon 0
nr_isolated_file 0
nr_shmem 1750
nr_dirtied 1215288
nr_written 958209
nr_anon_transparent_hugepages 100
protection: (0, 0, 17262, 17262)
pagesets
cpu: 0
count: 174
high: 186
batch: 31
vm stats threshold: 16
cpu: 1
count: 144
high: 186
batch: 31
vm stats threshold: 16
all_unreclaimable: 0
start_pfn: 4096
inactive_ratio: 1
Node 0, zone HighMem
pages free 150806
min 128
low 6989
high 13850
scanned 0
spanned 556754
present 552404
nr_free_pages 150806
nr_inactive_anon 54225
nr_active_anon 143153
nr_inactive_file 142731
nr_active_file 63382
nr_unevictable 12
nr_mlock 12
nr_anon_pages 134200
nr_mapped 15674
nr_file_pages 245898
nr_dirty 862
nr_writeback 0
nr_slab_reclaimable 0
nr_slab_unreclaimable 0
nr_page_table_pages 0
nr_kernel_stack 0
nr_unstable 0
nr_bounce 0
nr_vmscan_write 4921
nr_writeback_temp 0
nr_isolated_anon 0
nr_isolated_file 0
nr_shmem 39003
nr_dirtied 4316856
nr_written 3258730
nr_anon_transparent_hugepages 23
protection: (0, 0, 0, 0)
pagesets
cpu: 0
count: 181
high: 186
batch: 31
vm stats threshold: 24
cpu: 1
count: 148
high: 186
batch: 31
vm stats threshold: 24
all_unreclaimable: 0
start_pfn: 227326
inactive_ratio: 4


2nd /proc/zoneinfo:

Node 0, zone DMA
pages free 3270
min 196
low 245
high 294
scanned 0
spanned 4080
present 3951
nr_free_pages 3270
nr_inactive_anon 0
nr_active_anon 0
nr_inactive_file 594
nr_active_file 0
nr_unevictable 0
nr_mlock 0
nr_anon_pages 0
nr_mapped 0
nr_file_pages 706
nr_dirty 0
nr_writeback 0
nr_slab_reclaimable 0
nr_slab_unreclaimable 2
nr_page_table_pages 0
nr_kernel_stack 0
nr_unstable 0
nr_bounce 0
nr_vmscan_write 0
nr_writeback_temp 0
nr_isolated_anon 0
nr_isolated_file 298
nr_shmem 0
nr_dirtied 1414
nr_written 1414
nr_anon_transparent_hugepages 0
protection: (0, 865, 3023, 3023)
pagesets
cpu: 0
count: 0
high: 0
batch: 1
vm stats threshold: 4
cpu: 1
count: 0
high: 0
batch: 1
vm stats threshold: 4
all_unreclaimable: 0
start_pfn: 16
inactive_ratio: 1
Node 0, zone Normal
pages free 18165
min 11003
low 13753
high 16504
scanned 0
spanned 223230
present 221486
nr_free_pages 18165
nr_inactive_anon 69521
nr_active_anon 48778
nr_inactive_file 37220
nr_active_file 16531
nr_unevictable 0
nr_mlock 0
nr_anon_pages 14029
nr_mapped 175
nr_file_pages 55324
nr_dirty 16
nr_writeback 0
nr_slab_reclaimable 15224
nr_slab_unreclaimable 2805
nr_page_table_pages 1134
nr_kernel_stack 319
nr_unstable 0
nr_bounce 0
nr_vmscan_write 1023
nr_writeback_temp 0
nr_isolated_anon 0
nr_isolated_file 0
nr_shmem 1750
nr_dirtied 1215307
nr_written 958303
nr_anon_transparent_hugepages 100
protection: (0, 0, 17262, 17262)
pagesets
cpu: 0
count: 156
high: 186
batch: 31
vm stats threshold: 16
cpu: 1
count: 168
high: 186
batch: 31
vm stats threshold: 16
all_unreclaimable: 0
start_pfn: 4096
inactive_ratio: 1
Node 0, zone HighMem
pages free 146280
min 128
low 6989
high 13850
scanned 0
spanned 556754
present 552404
nr_free_pages 146280
nr_inactive_anon 54225
nr_active_anon 143128
nr_inactive_file 146871
nr_active_file 63760
nr_unevictable 12
nr_mlock 12
nr_anon_pages 134163
nr_mapped 15674
nr_file_pages 250402
nr_dirty 1820
nr_writeback 0
nr_slab_reclaimable 0
nr_slab_unreclaimable 0
nr_page_table_pages 0
nr_kernel_stack 0
nr_unstable 0
nr_bounce 0
nr_vmscan_write 4921
nr_writeback_temp 0
nr_isolated_anon 0
nr_isolated_file 0
nr_shmem 39003
nr_dirtied 4323393
nr_written 3262270
nr_anon_transparent_hugepages 23
protection: (0, 0, 0, 0)
pagesets
cpu: 0
count: 184
high: 186
batch: 31
vm stats threshold: 24
cpu: 1
count: 164
high: 186
batch: 31
vm stats threshold: 24
all_unreclaimable: 0
start_pfn: 227326
inactive_ratio: 4


3rd /proc/zoneinfo:

Node 0, zone DMA
pages free 3270
min 196
low 245
high 294
scanned 0
spanned 4080
present 3951
nr_free_pages 3270
nr_inactive_anon 0
nr_active_anon 0
nr_inactive_file 594
nr_active_file 0
nr_unevictable 0
nr_mlock 0
nr_anon_pages 0
nr_mapped 0
nr_file_pages 706
nr_dirty 0
nr_writeback 0
nr_slab_reclaimable 0
nr_slab_unreclaimable 2
nr_page_table_pages 0
nr_kernel_stack 0
nr_unstable 0
nr_bounce 0
nr_vmscan_write 0
nr_writeback_temp 0
nr_isolated_anon 0
nr_isolated_file 298
nr_shmem 0
nr_dirtied 1414
nr_written 1414
nr_anon_transparent_hugepages 0
protection: (0, 865, 3023, 3023)
pagesets
cpu: 0
count: 0
high: 0
batch: 1
vm stats threshold: 4
cpu: 1
count: 0
high: 0
batch: 1
vm stats threshold: 4
all_unreclaimable: 0
start_pfn: 16
inactive_ratio: 1
Node 0, zone Normal
pages free 18200
min 11003
low 13753
high 16504
scanned 0
spanned 223230
present 221486
nr_free_pages 18200
nr_inactive_anon 69521
nr_active_anon 48778
nr_inactive_file 37228
nr_active_file 16534
nr_unevictable 0
nr_mlock 0
nr_anon_pages 14029
nr_mapped 175
nr_file_pages 55334
nr_dirty 5
nr_writeback 0
nr_slab_reclaimable 15224
nr_slab_unreclaimable 2801
nr_page_table_pages 1134
nr_kernel_stack 319
nr_unstable 0
nr_bounce 0
nr_vmscan_write 1023
nr_writeback_temp 0
nr_isolated_anon 0
nr_isolated_file 0
nr_shmem 1750
nr_dirtied 1215316
nr_written 958323
nr_anon_transparent_hugepages 100
protection: (0, 0, 17262, 17262)
pagesets
cpu: 0
count: 127
high: 186
batch: 31
vm stats threshold: 16
cpu: 1
count: 132
high: 186
batch: 31
vm stats threshold: 16
all_unreclaimable: 0
start_pfn: 4096
inactive_ratio: 1
Node 0, zone HighMem
pages free 143087
min 128
low 6989
high 13850
scanned 0
spanned 556754
present 552404
nr_free_pages 143087
nr_inactive_anon 54225
nr_active_anon 143127
nr_inactive_file 150208
nr_active_file 63776
nr_unevictable 12
nr_mlock 12
nr_anon_pages 134163
nr_mapped 15674
nr_file_pages 253755
nr_dirty 740
nr_writeback 0
nr_slab_reclaimable 0
nr_slab_unreclaimable 0
nr_page_table_pages 0
nr_kernel_stack 0
nr_unstable 0
nr_bounce 0
nr_vmscan_write 4921
nr_writeback_temp 0
nr_isolated_anon 0
nr_isolated_file 0
nr_shmem 39003
nr_dirtied 4329000
nr_written 3266708
nr_anon_transparent_hugepages 23
protection: (0, 0, 0, 0)
pagesets
cpu: 0
count: 166
high: 186
batch: 31
vm stats threshold: 24
cpu: 1
count: 22
high: 186
batch: 31
vm stats threshold: 24
all_unreclaimable: 0
start_pfn: 227326
inactive_ratio: 4


4th /proc/zoneinfo:

Node 0, zone DMA
pages free 3270
min 196
low 245
high 294
scanned 0
spanned 4080
present 3951
nr_free_pages 3270
nr_inactive_anon 0
nr_active_anon 0
nr_inactive_file 594
nr_active_file 0
nr_unevictable 0
nr_mlock 0
nr_anon_pages 0
nr_mapped 0
nr_file_pages 706
nr_dirty 0
nr_writeback 0
nr_slab_reclaimable 0
nr_slab_unreclaimable 2
nr_page_table_pages 0
nr_kernel_stack 0
nr_unstable 0
nr_bounce 0
nr_vmscan_write 0
nr_writeback_temp 0
nr_isolated_anon 0
nr_isolated_file 298
nr_shmem 0
nr_dirtied 1414
nr_written 1414
nr_anon_transparent_hugepages 0
protection: (0, 865, 3023, 3023)
pagesets
cpu: 0
count: 0
high: 0
batch: 1
vm stats threshold: 4
cpu: 1
count: 0
high: 0
batch: 1
vm stats threshold: 4
all_unreclaimable: 0
start_pfn: 16
inactive_ratio: 1
Node 0, zone Normal
pages free 128730
min 11003
low 13753
high 16504
scanned 0
spanned 223230
present 221486
nr_free_pages 128730
nr_inactive_anon 8337
nr_active_anon 3
nr_inactive_file 37354
nr_active_file 16679
nr_unevictable 0
nr_mlock 0
nr_anon_pages 140
nr_mapped 7
nr_file_pages 53743
nr_dirty 55
nr_writeback 0
nr_slab_reclaimable 15233
nr_slab_unreclaimable 2654
nr_page_table_pages 622
nr_kernel_stack 251
nr_unstable 0
nr_bounce 0
nr_vmscan_write 1023
nr_writeback_temp 0
nr_isolated_anon 0
nr_isolated_file 0
nr_shmem 3
nr_dirtied 1215764
nr_written 958721
nr_anon_transparent_hugepages 8
protection: (0, 0, 17262, 17262)
pagesets
cpu: 0
count: 163
high: 186
batch: 31
vm stats threshold: 16
cpu: 1
count: 133
high: 186
batch: 31
vm stats threshold: 16
all_unreclaimable: 0
start_pfn: 4096
inactive_ratio: 1
Node 0, zone HighMem
pages free 263502
min 128
low 6989
high 13850
scanned 0
spanned 556754
present 552404
nr_free_pages 263502
nr_inactive_anon 24892
nr_active_anon 26289
nr_inactive_file 174037
nr_active_file 65827
nr_unevictable 12
nr_mlock 12
nr_anon_pages 29472
nr_mapped 11150
nr_file_pages 259669
nr_dirty 9
nr_writeback 0
nr_slab_reclaimable 0
nr_slab_unreclaimable 0
nr_page_table_pages 0
nr_kernel_stack 0
nr_unstable 0
nr_bounce 0
nr_vmscan_write 4921
nr_writeback_temp 0
nr_isolated_anon 0
nr_isolated_file 0
nr_shmem 18959
nr_dirtied 4364710
nr_written 3290304
nr_anon_transparent_hugepages 2
protection: (0, 0, 0, 0)
pagesets
cpu: 0
count: 149
high: 186
batch: 31
vm stats threshold: 24
cpu: 1
count: 74
high: 186
batch: 31
vm stats threshold: 24
all_unreclaimable: 0
start_pfn: 227326
inactive_ratio: 4



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