A misconfigured logrotate produced a lot of files in a directory on my server. ls | wc -l showed 5,387,172 files and according to du -sh this summed up to about 8 GB. dmesg showed many errors like this:
[16718682.749947] EXT4-fs warning (device dm-5): ext4_dx_add_entry:2209: Directory (ino: 4194315) index full, reach max htree level :2
[16718682.750028] EXT4-fs warning (device dm-5): ext4_dx_add_entry:2213: Large directory feature is not enabled on this filesystem
The configuration is fixed now and I deleted all the files that were not supposed to be there. After cleaning up, I got this:
# ls -l roundcube/logs/
total 20
-rw-r--r-- 1 www-data www-data 0 Mär 21 06:25 errors.log
-rw-r--r-- 1 www-data www-data 315 Mär 21 06:25 errors.log.1
-rw-r--r-- 1 www-data www-data 0 Jan 7 06:36 errors.log.10.gz
-rw-r--r-- 1 www-data www-data 0 Dez 18 06:26 errors.log.11.gz
-rw-r--r-- 1 www-data www-data 0 Dez 10 06:25 errors.log.12.gz
-rw-r--r-- 1 www-data www-data 321 Mär 14 06:25 errors.log.2.gz
-rw-r--r-- 1 www-data www-data 272 Mär 7 06:25 errors.log.3.gz
-rw-r--r-- 1 www-data www-data 354 Feb 28 06:25 errors.log.4.gz
-rw-r--r-- 1 www-data www-data 20 Feb 18 16:07 errors.log.5.gz
-rw-r--r-- 1 www-data www-data 0 Feb 18 18:14 errors.log.6.gz
-rw-r--r-- 1 www-data www-data 0 Feb 5 13:36 errors.log.7.gz
-rw-r--r-- 1 www-data www-data 0 Jan 29 09:17 errors.log.8.gz
-rw-r--r-- 1 www-data www-data 0 Jan 14 06:49 errors.log.9.gz
# du -sh roundcube/logs/
632M roundcube/logs/
However the ls call still took a long time (I did not look at the clock but I think it was >10 minutes). Might also be >60 minutes. And also it is strange, that du still reports 632MB.
I started a rescue system and ran fsck:
root@rescue /dev/mapper # fsck.ext4 vg0-mail
e2fsck 1.44.5 (15-Dec-2018)
vg0-mail: clean, 300078/13107200 files, 13579986/52428800 blocks
root@rescue /dev/mapper # fsck.ext4 -f vg0-mail
e2fsck 1.44.5 (15-Dec-2018)
Pass 1: Checking inodes, blocks, and sizes
Pass 2: Checking directory structure
Pass 3: Checking directory connectivity
Pass 4: Checking reference counts
Pass 5: Checking group summary information
vg0-mail: 300078/13107200 files (0.5% non-contiguous), 13579986/52428800 blocks
So it does seem like everything is alright. I rebooted back into the normal system, but ls is still slow.
Just to make sure that there are no processes interfering, I rebooted back into the rescue system, mounted the volume there and tried to list directory contents. It also hangs.
strace ls shows many lines. The last couple of lines are:
fstat(3, {st_mode=S_IFREG|0444, st_size=0, ...}) = 0
read(3, "nodev\tsysfs\nnodev\ttmpfs\nnodev\tbd"..., 1024) = 309
read(3, "", 1024) = 0
close(3) = 0
access("/etc/selinux/config", F_OK) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/usr/lib/locale/locale-archive", O_RDONLY|O_CLOEXEC) = 3
fstat(3, {st_mode=S_IFREG|0644, st_size=5547600, ...}) = 0
mmap(NULL, 5547600, PROT_READ, MAP_PRIVATE, 3, 0) = 0x7f0bd79c6000
close(3) = 0
ioctl(1, TCGETS, {B38400 opost isig icanon echo ...}) = 0
ioctl(1, TIOCGWINSZ, {ws_row=66, ws_col=271, ws_xpixel=0, ws_ypixel=0}) = 0
stat("roundcube/logs/", {st_mode=S_IFDIR|0755, st_size=662331392, ...}) = 0
openat(AT_FDCWD, "roundcube/logs/", O_RDONLY|O_NONBLOCK|O_CLOEXEC|O_DIRECTORY) = 3
fstat(3, {st_mode=S_IFDIR|0755, st_size=662331392, ...}) = 0
getdents64(3
So it seems to hang on getdents64? I am somewhat confused that it ends with seemingly an incomplete line.
I read that this might be caused by a hardware defect, so I tried to run an smartctl -t long analysis on both disks (raid 1). Here are the results:
/dev/sda
smartctl 6.6 2017-11-05 r4594 [x86_64-linux-4.19.0-14-amd64] (local build)
Copyright (C) 2002-17, Bruce Allen, Christian Franke, www.smartmontools.org
=== START OF INFORMATION SECTION ===
Model Family: Seagate Constellation ES.3
Device Model: ST2000NM0033-9ZM175
Serial Number: Z1X0QWWG
LU WWN Device Id: 5 000c50 064a202c3
Firmware Version: SN07
User Capacity: 2.000.398.934.016 bytes [2,00 TB]
Sector Size: 512 bytes logical/physical
Rotation Rate: 7200 rpm
Form Factor: 3.5 inches
Device is: In smartctl database [for details use: -P show]
ATA Version is: ACS-2 (minor revision not indicated)
SATA Version is: SATA 3.0, 6.0 Gb/s (current: 3.0 Gb/s)
Local Time is: Tue Mar 23 21:24:30 2021 CET
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: (0x82) Offline data collection activity
was completed without error.
Auto Offline Data Collection: Enabled.
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: ( 592) seconds.
Offline data collection
capabilities: (0x7b) SMART execute Offline immediate.
Auto Offline data collection on/off support.
Suspend 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: ( 245) minutes.
Conveyance self-test routine
recommended polling time: ( 2) minutes.
SCT capabilities: (0x50bd) SCT Status supported.
SCT Error Recovery Control supported.
SCT Feature Control supported.
SCT Data Table supported.
SMART Attributes Data Structure revision number: 10
Vendor Specific SMART Attributes with Thresholds:
ID# ATTRIBUTE_NAME FLAG VALUE WORST THRESH TYPE UPDATED WHEN_FAILED RAW_VALUE
1 Raw_Read_Error_Rate 0x000f 070 063 044 Pre-fail Always - 11974882
3 Spin_Up_Time 0x0003 096 096 000 Pre-fail Always - 0
4 Start_Stop_Count 0x0032 100 100 020 Old_age Always - 25
5 Reallocated_Sector_Ct 0x0033 100 100 010 Pre-fail Always - 0
7 Seek_Error_Rate 0x000f 088 060 030 Pre-fail Always - 706711710
9 Power_On_Hours 0x0032 033 033 000 Old_age Always - 59193
10 Spin_Retry_Count 0x0013 100 100 097 Pre-fail Always - 0
12 Power_Cycle_Count 0x0032 100 100 020 Old_age Always - 24
184 End-to-End_Error 0x0032 100 100 099 Old_age Always - 0
187 Reported_Uncorrect 0x0032 100 100 000 Old_age Always - 0
188 Command_Timeout 0x0032 100 100 000 Old_age Always - 0
189 High_Fly_Writes 0x003a 059 059 000 Old_age Always - 41
190 Airflow_Temperature_Cel 0x0022 060 050 045 Old_age Always - 40 (Min/Max 36/44)
191 G-Sense_Error_Rate 0x0032 100 100 000 Old_age Always - 0
192 Power-Off_Retract_Count 0x0032 100 100 000 Old_age Always - 18
193 Load_Cycle_Count 0x0032 099 099 000 Old_age Always - 2459
194 Temperature_Celsius 0x0022 040 050 000 Old_age Always - 40 (0 21 0 0 0)
195 Hardware_ECC_Recovered 0x001a 042 015 000 Old_age Always - 11974882
197 Current_Pending_Sector 0x0012 100 100 000 Old_age Always - 0
198 Offline_Uncorrectable 0x0010 100 100 000 Old_age Offline - 0
199 UDMA_CRC_Error_Count 0x003e 200 200 000 Old_age Always - 0
SMART Error Log Version: 1
No Errors Logged
SMART Self-test log structure revision number 1
Num Test_Description Status Remaining LifeTime(hours) LBA_of_first_error
# 1 Extended offline Completed without error 00% 59192 -
# 2 Short offline Interrupted (host reset) 10% 59185 -
# 3 Extended offline Completed without error 00% 53208 -
# 4 Extended offline Completed without error 00% 53191 -
# 5 Extended offline Completed without error 00% 53178 -
# 6 Short offline Completed without error 00% 53170 -
# 7 Extended offline Completed without error 00% 53056 -
# 8 Extended offline Completed without error 00% 53040 -
# 9 Extended offline Completed without error 00% 53025 -
#10 Short offline Completed without error 00% 53017 -
#11 Extended offline Completed without error 00% 51660 -
#12 Extended offline Completed without error 00% 51643 -
#13 Extended offline Completed without error 00% 2411 -
#14 Extended offline Completed without error 00% 2383 -
SMART Selective self-test log data structure revision number 1
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.
/dev/sdb
smartctl 6.6 2017-11-05 r4594 [x86_64-linux-4.19.0-14-amd64] (local build)
Copyright (C) 2002-17, Bruce Allen, Christian Franke, www.smartmontools.org
=== START OF INFORMATION SECTION ===
Model Family: Hitachi/HGST Ultrastar 7K4000
Device Model: HGST HUS724020ALA640
Serial Number: PN2138P2GNK30J
LU WWN Device Id: 5 000cca 24bc9579a
Firmware Version: MF6OAA70
User Capacity: 2.000.398.934.016 bytes [2,00 TB]
Sector Size: 512 bytes logical/physical
Rotation Rate: 7200 rpm
Form Factor: 3.5 inches
Device is: In smartctl database [for details use: -P show]
ATA Version is: ATA8-ACS T13/1699-D revision 4
SATA Version is: SATA 3.0, 6.0 Gb/s (current: 3.0 Gb/s)
Local Time is: Tue Mar 23 22:38:27 2021 CET
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: (0x84) Offline data collection activity
was suspended by an interrupting command from host.
Auto Offline Data Collection: Enabled.
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: ( 24) seconds.
Offline data collection
capabilities: (0x5b) SMART execute Offline immediate.
Auto Offline data collection on/off support.
Suspend Offline collection upon new
command.
Offline surface scan supported.
Self-test supported.
No 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: ( 314) minutes.
SCT capabilities: (0x003d) SCT Status supported.
SCT Error Recovery Control supported.
SCT Feature Control supported.
SCT Data Table supported.
SMART Attributes Data Structure revision number: 16
Vendor Specific SMART Attributes with Thresholds:
ID# ATTRIBUTE_NAME FLAG VALUE WORST THRESH TYPE UPDATED WHEN_FAILED RAW_VALUE
1 Raw_Read_Error_Rate 0x000b 100 100 016 Pre-fail Always - 0
2 Throughput_Performance 0x0005 136 136 054 Pre-fail Offline - 80
3 Spin_Up_Time 0x0007 163 163 024 Pre-fail Always - 367 (Average 396)
4 Start_Stop_Count 0x0012 100 100 000 Old_age Always - 28
5 Reallocated_Sector_Ct 0x0033 100 100 005 Pre-fail Always - 0
7 Seek_Error_Rate 0x000b 100 100 067 Pre-fail Always - 0
8 Seek_Time_Performance 0x0005 145 145 020 Pre-fail Offline - 24
9 Power_On_Hours 0x0012 095 095 000 Old_age Always - 37639
10 Spin_Retry_Count 0x0013 100 100 060 Pre-fail Always - 0
12 Power_Cycle_Count 0x0032 100 100 000 Old_age Always - 27
192 Power-Off_Retract_Count 0x0032 099 099 000 Old_age Always - 1311
193 Load_Cycle_Count 0x0012 099 099 000 Old_age Always - 1311
194 Temperature_Celsius 0x0002 150 150 000 Old_age Always - 40 (Min/Max 22/60)
196 Reallocated_Event_Count 0x0032 100 100 000 Old_age Always - 0
197 Current_Pending_Sector 0x0022 100 100 000 Old_age Always - 0
198 Offline_Uncorrectable 0x0008 100 100 000 Old_age Offline - 0
199 UDMA_CRC_Error_Count 0x000a 200 200 000 Old_age Always - 0
SMART Error Log Version: 1
No Errors Logged
SMART Self-test log structure revision number 1
Num Test_Description Status Remaining LifeTime(hours) LBA_of_first_error
# 1 Extended offline Completed without error 00% 37638 -
# 2 Short offline Interrupted (host reset) 90% 37630 -
# 3 Extended offline Completed without error 00% 31654 -
# 4 Extended offline Completed without error 00% 31637 -
# 5 Extended offline Completed without error 00% 30951 -
# 6 Extended offline Completed without error 00% 30932 -
# 7 Extended offline Completed without error 00% 30927 -
# 8 Short offline Completed without error 00% 30919 -
# 9 Extended offline Completed without error 00% 30882 -
#10 Extended offline Completed without error 00% 30866 -
#11 Extended offline Completed without error 00% 19849 -
#12 Extended offline Completed without error 00% 19832 -
SMART Selective self-test log data structure revision number 1
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.
I don't understand most of it, but it does not look "bad" to me?!
Eventually I just executed mv logs logs-old; mv logs-old/* logs; rm -r logs-old And this does seem to "solve" my problem for now. But I wonder if this could really be it or whether there might be more to it.
What could have happened here to cause this behaviour of extremely slow directory listing? Could the problem be gone now? Could there be some damage that I should find?
