Removing E (DiskError) flag on system drive of a Synology NAS
Recently, I came across the following problem: A user of a Synology DiskStation wanted upgrade the disk drives to bigger ones. So he tried to do everything correctly:
First, he identified the list of possible disk drives officially supported for his Disk Station and bought the appropriate hard disk.
Then removed one disk drive (drive 2) in the bay and exchanged it with one of the newly bought disks and tols the NAS to repair the volume in order to sync system and data to the new drive.
And here is, where the problems started: The data RAID fortunately synced fine to the second drive, but the System RAID did not sync and left him with a faulty system volume.
This is where I came into play. A quick check via commandline revealed the following status:
sh-4.3# cat /proc/mdstat Personalities : [linear] [raid0] [raid1] [raid10] [raid6] [raid5] [raid4] md2 : active raid1 sda5[2] sdb5[1] 1948779648 blocks super 1.2 [2/2] [UU] md1 : active raid1 sda2[0] sdb2[1] 2097088 blocks [2/2] [UU] md0 : active raid1 sdb1[1](E) 2490176 blocks [2/1] [_E]
Now my first thought was: Status E? I’m used to Linux Software RAID, but I never saw such a RAID status code. Checked documentation, no mention if it either. It’s not “F” for faulty, it’s “E”.
After digging around in Google I finally figured out that this is a proprietary status code from Synology RAIDs not implemented in official Linux kernel.
Now how to find out more about it? I found an article on how to reset the “Faulty” flag on an existing array disk, but it didn’t sound very safe given the fact that I didn’t know the original RAID parameters of the RAID.
Now the first thing to do when working with such volumes obviously is to make a copy and work only with the copied drive to have the original drive secured in case something goes wrong. So I dug out another good spare drive of the same size from my collection and copied the existing drive to it sector per sector with dd.
During copying, it turned out there was a bad block (fortunately only one!) on the original drive within the system partition, so that was the reason why the drive’s state went to “E”, which seems to indicate “Disk error”. ddrescue to the rescue! It skipped the bad sector and I had a working copy of the drive to mess around with. I later checked the location of the bad sector and there were sectors with 00s around it, so I guess that there was nothing important on that bad sector anyway.
Now how to reset this damn E flag? First, I needed to identify the Superblock of the RAID volume that went bed. So obviously, just examine it with
mdadm --examine /dev/sdb1
right? BOOM:
mdadm: No md superblock detected on /dev/sdb1.
Where the heck is it? After much googling around, I found a hint, that the Superblock has swapped endianness and was in fact version 0.9 as opposed to the data partition which has a version 1.2 superblock:
# mdadm --examine /dev/sdb1 -e 0 mdadm: No super block found on /dev/sdb1 (Expected magic a92b4efc, got fc4e2ba9)
Now the author of the article changed byte endianness to use the RAID on a PC, but my intention was to just remove the E flag and not mess around with the partition style. By looking at the mdadm source code, I found out that there already was a parameter to obey the different endianness of the superblock, the parameter to be specified is: “-e 0.9”
So I finally was able to dump the superblock of the disk with:
# ./mdadm.synology --examine /dev/sdb1 -e 0.9 /dev/sdb1: Magic : a92b4efc Version : 0.90.00 UUID : 5b116fc2:267b242b:3017a5a8:c86610be Creation Time : Sat Jan 1 00:00:02 2000 Raid Level : raid1 Used Dev Size : 2490176 (2.37 GiB 2.55 GB) Array Size : 2490176 (2.37 GiB 2.55 GB) Raid Devices : 2 Total Devices : 1 Preferred Minor : 0 Update Time : Wed Mar 8 16:25:39 2023 State : clean Active Devices : 1 Working Devices : 1 Failed Devices : 0 Spare Devices : 0 Checksum : c15399ef - correct Events : 12649239 Number Major Minor RaidDevice State this 1 8 17 1 active sync /dev/sdb1 0 0 0 0 0 removed 1 1 8 17 1 active sync /dev/sdb1
When looking at the output, the array component seemed to be in a perfectly fine condition, no sign of the failure indication from Synology. So I checked the available open source of the Synology Linux kernel for this disk error flag. Turns out that it can be found in md_p.h header file:
#ifdef MY_ABC_HERE #define MD_DISK_ERROR 6 #endif
Fortunately, Synology marked all their changes to the Stock Linux kernel with the #define MY_ABC_HERE, so specific code paths are easy to spot in the source.
Next, I had to identify the location of the flag in the superblock to confirm my findings. I hexdumped the superblock of the affected device. The 0.90 superblock is of struct mdp_superblock_s, which -according to md_p.h has the following structure:
typedef struct mdp_superblock_s {
/*
* Constant generic information
*/
__u32 md_magic; /* 0 MD identifier */
__u32 major_version; /* 1 major version to which the set conforms */
__u32 minor_version; /* 2 minor version ... */
__u32 patch_version; /* 3 patchlevel version ... */
...
/*
* Disks information
*/
mdp_disk_t disks[MD_SB_DISKS];
/*
* Reserved
*/
__u32 reserved[MD_SB_RESERVED_WORDS];
/*
* Active descriptor
*/
mdp_disk_t this_disk;
} mdp_super_t;
typedef struct mdp_device_descriptor_s {
__u32 number; /* 0 Device number in the entire set */
__u32 major; /* 1 Device major number */
__u32 minor; /* 2 Device minor number */
__u32 raid_disk; /* 3 The role of the device in the raid set */
__u32 state; /* 4 Operational state */
__u32 reserved[MD_SB_DESCRIPTOR_WORDS - 5];
} mdp_disk_t;
So the state of the individual disks is in the state field of the mdp_disk_t structure. Let’s check the dump and interpret it:
mdp_super_t: ------------ 0000 A9 2B 4E FC 00 00 00 00 00 00 00 5A 00 00 00 00 0010 00 00 00 00 5B 11 6F C2 38 6D 43 82 00 00 00 01 0020 00 25 FF 40 00 00 00 01 00 00 00 02 00 00 00 00 0030 00 00 00 00 26 7B 24 2B 30 17 A5 A8 C8 66 10 BE 0040 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0050 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0060 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0070 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0080 64 08 B7 03 00 00 00 01 00 00 00 01 00 00 00 01 0090 00 00 00 00 00 00 00 00 C1 53 9A 6F 00 00 00 00 00A0 00 C1 03 17 00 00 00 00 00 C1 03 17 FF FF FF FF 00B0 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00C0 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00D0 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00E0 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00F0 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0100 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0110 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0120 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0130 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0140 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0150 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0160 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0170 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0180 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0190 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 01A0 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 01B0 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 01C0 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 01D0 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 01E0 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 01F0 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0200 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0210 00 00 00 08 00 00 00 00 00 00 00 00 00 00 00 00 0220 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0230 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0240 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0250 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0260 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0270 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 mdp_disk_t disks[MD_SB_DISKS]; 0280 00 00 00 01 00 00 00 08 00 00 00 11 00 00 00 01 0290 00 00 00 46 00 00 00 00 00 00 00 00 00 00 00 00 02A0 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 02B0 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 02C0 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 02D0 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 02E0 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 02F0 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0300 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0310 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0320 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0330 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0340 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0350 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0360 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0370 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0380 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0390 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 03A0 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 03B0 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 03C0 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 03D0 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 03E0 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 03F0 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0400 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0410 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0420 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0430 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0440 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0450 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0460 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0470 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0480 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0490 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 04A0 00 00 00 00 00 00 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00 00 00 00 00 00 00 00 00 0E20 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0E30 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0E40 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0E50 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0E60 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0E70 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0E80 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0E90 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0EA0 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0EB0 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0EC0 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0ED0 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0EE0 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0EF0 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0F00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0F10 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0F20 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0F30 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0F40 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0F50 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0F60 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0F70 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 mdp_disk_t this_disk; 0F80 00 00 00 01 00 00 00 08 00 00 00 11 00 00 00 01 0F90 00 00 00 46 00 00 00 00 00 00 00 00 00 00 00 00 0FA0 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0FB0 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0FC0 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0FD0 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0FE0 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0FF0 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00
I marked the significant fields in the dump. It can be seen that the state flag is 0x46 (that is 1000110b) which indicates:
#define MD_DISK_FAULTY 0 #define MD_DISK_ACTIVE 1 #define MD_DISK_SYNC 2 #define MD_DISK_REMOVED 3 #define MD_DISK_CLUSTER_ADD 4 #define MD_DISK_CANDIDATE 5 #define MD_DISK_ERROR 6 #define MD_DISK_WRITEMOSTLY 9 #define MD_DISK_JOURNAL 18
Bingo, there it is, MD_DISK_ERROR! So I was temtped to just remove the flag with a Hex editor, but beware: There is a checksum for the superblock header! So what’s the easiest thing to do?
First, check if Synology’s mdadm fork contained functions to maybe already clear the error flag. There must be a custom implementation, because it is able to display the E flag.
Turns out, there is no such function, so I had to extend the mdadm source code to introduce such a feature.
So, in short, I forked mdadm and implemented it, it can be downlaoded here together with a description on how to use it, so read the README there for a continuation of this story.
In short, I cleared the errorflag of the partition with my patched mdadm:
./mdadm.synology --misc --no-diskerr /dev/sdb1 -e 0.9
and put the disk back in the Synology, booted up, repaired system partition and got back a running system without having to reinstall the Synology DSM Software and its settings.
System programmer