Experiencing Freezes on Fedora 32, possibly related to mdraid

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1

I’m experincing system freezes on Fedora 32. After the following hard reset and reboot, one of my hdd drives (/dev/sdh) keeps getting kicked out of my RAID6 (/dev/md1) and mdadm --examine cannot even find a superblock on it anymore:
# mdadm --detail /dev/md1
/dev/md1:
Version : 1.2
Creation Time : Sat Mar 8 20:10:04 2014
Raid Level : raid6
Array Size : 11721060352 (11178.07 GiB 12002.37 GB)
Used Dev Size : 2930265088 (2794.52 GiB 3000.59 GB)
Raid Devices : 6
Total Devices : 5
Persistence : Superblock is persistent

       Update Time : Tue Aug 11 15:55:38 2020
             State : clean, degraded
    Active Devices : 5
   Working Devices : 5
    Failed Devices : 0
     Spare Devices : 0

            Layout : left-symmetric
        Chunk Size : 512K

Consistency Policy : resync

              Name : hal01:md1
              UUID : 8252380b:1c2d391a:1b8454fc:f1054b90
            Events : 617244

    Number   Major   Minor   RaidDevice State
       0       8       16        0      active sync   /dev/sdb
       6       8       96        1      active sync   /dev/sdg
       7       8       48        2      active sync   /dev/sdd
       5       8       32        3      active sync   /dev/sdc
       -       0        0        4      removed
       8       8        0        5      active sync   /dev/sda
# mdadm --examine /dev/sdh
/dev/sdh:
   MBR Magic : aa55
Partition[0] :   4294967295 sectors at            1 (type ee)

Related logs are at https://pastebin.com/WdTfUsXx

About my system:

uname -a

Linux PC-192-168-137-3.fritz.box 5.7.11-200.fc32.x86_64 #1 SMP Wed Jul 29 17:15:52 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux

cat /proc/cpuinfo

processor : 0
vendor_id : AuthenticAMD
cpu family : 23
model : 24
model name : AMD Ryzen 3 3200G with Radeon Vega Graphics
stepping : 1
microcode : 0x8108109
cpu MHz : 1256.452
cache size : 512 KB
physical id : 0
siblings : 4
core id : 0
cpu cores : 4
apicid : 0
initial apicid : 0
fpu : yes
fpu_exception : yes
cpuid level : 13
wp : yes
flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx mmxext fxsr_opt pdpe1gb rdtscp lm constant_tsc rep_good nopl nonstop_tsc cpuid extd_apicid aperfmperf pni pclmulqdq monitor ssse3 fma cx16 sse4_1 sse4_2 movbe popcnt aes xsave avx f16c rdrand lahf_lm cmp_legacy svm extapic cr8_legacy abm sse4a misalignsse 3dnowprefetch osvw skinit wdt tce topoext perfctr_core perfctr_nb bpext perfctr_llc mwaitx cpb hw_pstate sme ssbd sev ibpb vmmcall fsgsbase bmi1 avx2 smep bmi2 rdseed adx smap clflushopt sha_ni xsaveopt xsavec xgetbv1 xsaves clzero irperf xsaveerptr arat npt lbrv svm_lock nrip_save tsc_scale vmcb_clean flushbyasid decodeassists pausefilter pfthreshold avic v_vmsave_vmload vgif overflow_recov succor smca
bugs : sysret_ss_attrs null_seg spectre_v1 spectre_v2 spec_store_bypass
bogomips : 7187.29
TLB size : 2560 4K pages
clflush size : 64
cache_alignment : 64
address sizes : 43 bits physical, 48 bits virtual
power management: ts ttp tm hwpstate eff_freq_ro [13] [14]

processor : 1
vendor_id : AuthenticAMD
cpu family : 23
model : 24
model name : AMD Ryzen 3 3200G with Radeon Vega Graphics
stepping : 1
microcode : 0x8108109
cpu MHz : 1257.062
cache size : 512 KB
physical id : 0
siblings : 4
core id : 1
cpu cores : 4
apicid : 1
initial apicid : 1
fpu : yes
fpu_exception : yes
cpuid level : 13
wp : yes
flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx mmxext fxsr_opt pdpe1gb rdtscp lm constant_tsc rep_good nopl nonstop_tsc cpuid extd_apicid aperfmperf pni pclmulqdq monitor ssse3 fma cx16 sse4_1 sse4_2 movbe popcnt aes xsave avx f16c rdrand lahf_lm cmp_legacy svm extapic cr8_legacy abm sse4a misalignsse 3dnowprefetch osvw skinit wdt tce topoext perfctr_core perfctr_nb bpext perfctr_llc mwaitx cpb hw_pstate sme ssbd sev ibpb vmmcall fsgsbase bmi1 avx2 smep bmi2 rdseed adx smap clflushopt sha_ni xsaveopt xsavec xgetbv1 xsaves clzero irperf xsaveerptr arat npt lbrv svm_lock nrip_save tsc_scale vmcb_clean flushbyasid decodeassists pausefilter pfthreshold avic v_vmsave_vmload vgif overflow_recov succor smca
bugs : sysret_ss_attrs null_seg spectre_v1 spectre_v2 spec_store_bypass
bogomips : 7187.29
TLB size : 2560 4K pages
clflush size : 64
cache_alignment : 64
address sizes : 43 bits physical, 48 bits virtual
power management: ts ttp tm hwpstate eff_freq_ro [13] [14]

processor : 2
vendor_id : AuthenticAMD
cpu family : 23
model : 24
model name : AMD Ryzen 3 3200G with Radeon Vega Graphics
stepping : 1
microcode : 0x8108109
cpu MHz : 1266.412
cache size : 512 KB
physical id : 0
siblings : 4
core id : 2
cpu cores : 4
apicid : 2
initial apicid : 2
fpu : yes
fpu_exception : yes
cpuid level : 13
wp : yes
flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx mmxext fxsr_opt pdpe1gb rdtscp lm constant_tsc rep_good nopl nonstop_tsc cpuid extd_apicid aperfmperf pni pclmulqdq monitor ssse3 fma cx16 sse4_1 sse4_2 movbe popcnt aes xsave avx f16c rdrand lahf_lm cmp_legacy svm extapic cr8_legacy abm sse4a misalignsse 3dnowprefetch osvw skinit wdt tce topoext perfctr_core perfctr_nb bpext perfctr_llc mwaitx cpb hw_pstate sme ssbd sev ibpb vmmcall fsgsbase bmi1 avx2 smep bmi2 rdseed adx smap clflushopt sha_ni xsaveopt xsavec xgetbv1 xsaves clzero irperf xsaveerptr arat npt lbrv svm_lock nrip_save tsc_scale vmcb_clean flushbyasid decodeassists pausefilter pfthreshold avic v_vmsave_vmload vgif overflow_recov succor smca
bugs : sysret_ss_attrs null_seg spectre_v1 spectre_v2 spec_store_bypass
bogomips : 7187.29
TLB size : 2560 4K pages
clflush size : 64
cache_alignment : 64
address sizes : 43 bits physical, 48 bits virtual
power management: ts ttp tm hwpstate eff_freq_ro [13] [14]

processor : 3
vendor_id : AuthenticAMD
cpu family : 23
model : 24
model name : AMD Ryzen 3 3200G with Radeon Vega Graphics
stepping : 1
microcode : 0x8108109
cpu MHz : 1257.557
cache size : 512 KB
physical id : 0
siblings : 4
core id : 3
cpu cores : 4
apicid : 3
initial apicid : 3
fpu : yes
fpu_exception : yes
cpuid level : 13
wp : yes
flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx mmxext fxsr_opt pdpe1gb rdtscp lm constant_tsc rep_good nopl nonstop_tsc cpuid extd_apicid aperfmperf pni pclmulqdq monitor ssse3 fma cx16 sse4_1 sse4_2 movbe popcnt aes xsave avx f16c rdrand lahf_lm cmp_legacy svm extapic cr8_legacy abm sse4a misalignsse 3dnowprefetch osvw skinit wdt tce topoext perfctr_core perfctr_nb bpext perfctr_llc mwaitx cpb hw_pstate sme ssbd sev ibpb vmmcall fsgsbase bmi1 avx2 smep bmi2 rdseed adx smap clflushopt sha_ni xsaveopt xsavec xgetbv1 xsaves clzero irperf xsaveerptr arat npt lbrv svm_lock nrip_save tsc_scale vmcb_clean flushbyasid decodeassists pausefilter pfthreshold avic v_vmsave_vmload vgif overflow_recov succor smca
bugs : sysret_ss_attrs null_seg spectre_v1 spectre_v2 spec_store_bypass
bogomips : 7187.29
TLB size : 2560 4K pages
clflush size : 64
cache_alignment : 64
address sizes : 43 bits physical, 48 bits virtual
power management: ts ttp tm hwpstate eff_freq_ro [13] [14]

cat /proc/mdstat

Personalities : [raid1] [raid6] [raid5] [raid4]
md1 : active raid6 sdc[5] sdb[0] sdg[6] sdd[7] sda[8]
11721060352 blocks super 1.2 level 6, 512k chunk, algorithm 2 [6/5] [UUUU_U]

md125 : active raid1 sdf1[1] sde1[0]
1046528 blocks super 1.2 [2/2] [UU]
bitmap: 0/1 pages [0KB], 65536KB chunk

md126 : active raid1 sde3[0] sdf3[1]
450891776 blocks super 1.2 [2/2] [UU]
bitmap: 0/4 pages [0KB], 65536KB chunk

md127 : active raid1 sde2[0] sdf2[1]
16759808 blocks super 1.2 [2/2] [UU]

unused devices:

2

That looks like the drive failed and will need to be replaced.

3

Sure? smartctl -t long does not report any errors. And a failed drive should not cause the whole system to freeze.

4

Well, it obviously is not seen as a active raid device in your original post.
In the output of /proc/mdstat it shows as missing

and in

it is listed as “removed”

Apparently it has either been manually removed physically, configuration wise using mdadm, or has failed. Your system shows there should be 6 devices in the raid but only sees 5. If the drive is functional you likely can add it back to the array.

Wikipedia may explain the freezes under the performance part in that raid 6 is trying to write the extra parity but cannot.

5

The drive is available in the system as /dev/sdh and according to smartctl everything is fine. However, mdadm --examine doesn’t even find a superblock on it. I can add the drive back to the array and it syncs without any issues … until the next time the system freezes. I still feel there is more going on here than just a failed drive. The whole reason for a RAID array is to keep the system running in case of a failed drive. A drive failure should not cause a system freeze that can only be recovered by a cold boot.

Did you take a look at the logs at https://pastebin.com/WdTfUsXx ? I don’t understand the half of it, but even the very first line “kernel: general protection fault, probably for non-canonical address 0xdbe0234e968c12d5: 0000 [#1] SMP NOPTI” sounds like something that shouldn’t happen.

And going from there: If you google “general protection fault SMP NOPTI” you will find quite a few bug reports related to amdgpu kernel module running on AMD Vega graphics. And my system is a Ryzen 3200G with Radeon Vega 8 graphics… That wouldn’t explain why the drive gets kicked from the raid or why the md superblock is missing from the drive, but then maybe I’m seeing two completely unrelated issues.

# mdadm --examine /dev/sdh
/dev/sdh:
   MBR Magic : aa55
Partition[0] :   4294967295 sectors at            1 (type ee)


# smartctl -a /dev/sdh
smartctl 7.1 2019-12-30 r5022 [x86_64-linux-5.7.11-200.fc32.x86_64] (local build                                                                                                                                                             )
Copyright (C) 2002-19, Bruce Allen, Christian Franke, www.smartmontools.org

=== START OF INFORMATION SECTION ===
Model Family:     Seagate Surveillance
Device Model:     ST3000VX000-1CU166
Serial Number:    W1F4B3GL
LU WWN Device Id: 5 000c50 03d26d7b3
Firmware Version: CV23
User Capacity:    3.000.592.982.016 bytes [3,00 TB]
Sector Sizes:     512 bytes logical, 4096 bytes 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: 6.0 Gb/s)
Local Time is:    Fri Aug 14 22:25:15 2020 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:  (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:                (   97) seconds.
Offline data collection
capabilities:                    (0x7b) SMART execute Offline immediate.
                                        Auto Offline data collection on/off supp                                                                                                                                                             ort.
                                        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:        ( 329) minutes.
Conveyance self-test routine
recommended polling time:        (   2) minutes.
SCT capabilities:              (0x10b9) 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   114   099   006    Pre-fail  Always       -                                                                                                                                                                    74138232
  3 Spin_Up_Time            0x0003   094   094   000    Pre-fail  Always       -                                                                                                                                                                    0
  4 Start_Stop_Count        0x0032   100   100   020    Old_age   Always       -                                                                                                                                                                    87
  5 Reallocated_Sector_Ct   0x0033   100   100   010    Pre-fail  Always       -                                                                                                                                                                    0
  7 Seek_Error_Rate         0x000f   076   060   030    Pre-fail  Always       -                                                                                                                                                                    43832099
  9 Power_On_Hours          0x0032   036   036   000    Old_age   Always       -                                                                                                                                                                    56213
 10 Spin_Retry_Count        0x0013   100   100   097    Pre-fail  Always       -                                                                                                                                                                    0
 12 Power_Cycle_Count       0x0032   100   100   020    Old_age   Always       -                                                                                                                                                                    79
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       -                                                                                                                                                                    4295032833
189 High_Fly_Writes         0x003a   001   001   000    Old_age   Always       -                                                                                                                                                                    859
190 Airflow_Temperature_Cel 0x0022   069   054   045    Old_age   Always       -                                                                                                                                                                    31 (Min/Max 27/32)
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       -                                                                                                                                                                    54
193 Load_Cycle_Count        0x0032   100   100   000    Old_age   Always       -                                                                                                                                                                    89
194 Temperature_Celsius     0x0022   031   046   000    Old_age   Always       -                                                                                                                                                                    31 (0 17 0 0 0)
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%     55298         -
# 2  Short offline       Completed without error       00%     55292         -

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.

# mdadm /dev/md1 --add /dev/sdh
mdadm: added /dev/sdh

# mdadm --detail /dev/md1
/dev/md1:
           Version : 1.2
     Creation Time : Sat Mar  8 20:10:04 2014
        Raid Level : raid6
        Array Size : 11721060352 (11178.07 GiB 12002.37 GB)
     Used Dev Size : 2930265088 (2794.52 GiB 3000.59 GB)
      Raid Devices : 6
     Total Devices : 6
       Persistence : Superblock is persistent

       Update Time : Fri Aug 14 23:02:02 2020
             State : clean, degraded, recovering
    Active Devices : 5
   Working Devices : 6
    Failed Devices : 0
     Spare Devices : 1

            Layout : left-symmetric
        Chunk Size : 512K

Consistency Policy : resync

    Rebuild Status : 0% complete

              Name : hal01:md1
              UUID : 8252380b:1c2d391a:1b8454fc:f1054b90
            Events : 619212

    Number   Major   Minor   RaidDevice State
       0       8       16        0      active sync   /dev/sdb
       6       8       96        1      active sync   /dev/sdg
       7       8       48        2      active sync   /dev/sdd
       5       8       32        3      active sync   /dev/sdc
       9       8      112        4      spare rebuilding   /dev/sdh
       8       8        0        5      active sync   /dev/sda
6

I have no explanation for why your drive dropped out, but from your latest post it shows as rebuilding so hopefully that fixes that for you. You will have to see if the freeze situation is fixed after the array is rebuilt.