Diagnosing unwriteable HDD

Question

I am currently dealing with an HDD, which I cannot write to, but I do not understand the reason for it. Here is what I have observed about the problem:

1. Running a read-only benchmark works fine; read speed and access time seem fine

2. Running a write benchmark does not produce results and seems to "hang"

3. Any application or process that attempts to write to the disk hangs until terminated, including gparted when attempting to format the disk. At some point during the formatting attempt, "Input/Output Error during write on /dev/sda" was raised. The only other discernible error message I have seen is something along the lines of Buffer I/O logical block <some_number> lost during async write which is sometimes showing during shutdown.

4. Smartctl output of self test seems fine, leading me to believe that it might not be a physical problem

5. The command fdisk -l returns the following output for the affected disk:

Device         Start        End    Sectors   Size Type
/dev/sda1         63     532542     532480   260M EFI System
/dev/sda2     532543  498340557  497808015 237,4G Microsoft basic data
/dev/sda5  498341888 1953519615 1455177728 693,9G Linux filesystem

Partition 1 does not start on physical sector boundary.
Partition 2 does not start on physical sector boundary.


GPT PMBR size mismatch (4100491 != 15701758) will be corrected by write.
The backup GPT table is not on the end of the device. This problem will be corrected by write.

6. I did hear some scratch-like sounds coming from the disk a while ago.

So especially due to point 6, I am assuming that there is something physically broken in the HDD, but then again, I would expect smartctl to indicate that. I am unfortunately not very experienced with these kinds of issues, so if someone has an idea about any additional diagnostic steps I could take to confirm, that the disk is indeed broken, I would appreciate that.

Edit: As requested, I am adding here the output from \dmesg when running a write benchmark. The benchmark itself is stuck at the first sample, as you can see below.

[ 1090.321553] ata5.00: exception Emask 0x0 SAct 0x9801ffff SErr 0x50000 action 0x6 frozen
[ 1090.321562] ata5: SError: { PHYRdyChg CommWake }
[ 1090.321569] ata5.00: failed command: WRITE FPDMA QUEUED
[ 1090.321580] ata5.00: cmd 61/d0:00:40:0d:00/02:00:00:00:00/40 tag 0 ncq dma 368640 out
                        res 40/00:ff:ff:00:00/00:00:00:00:00/00 Emask 0x4 (timeout)
[ 1090.321584] ata5.00: status: { DRDY }
[ 1090.321588] ata5.00: failed command: WRITE FPDMA QUEUED
[ 1090.321598] ata5.00: cmd 61/40:08:10:10:00/05:00:00:00:00/40 tag 1 ncq dma 688128 out
                        res 40/00:ff:ff:00:00/00:00:00:00:00/00 Emask 0x4 (timeout)
[ 1090.321602] ata5.00: status: { DRDY }
[ 1090.321605] ata5.00: failed command: WRITE FPDMA QUEUED
[ 1090.321614] ata5.00: cmd 61/c8:10:50:15:00/02:00:00:00:00/40 tag 2 ncq dma 364544 out
                        res 40/00:ff:ff:00:00/00:00:00:00:00/00 Emask 0x4 (timeout)
[ 1090.321618] ata5.00: status: { DRDY }
[ 1090.321622] ata5.00: failed command: WRITE FPDMA QUEUED
[ 1090.321630] ata5.00: cmd 61/48:18:18:18:00/05:00:00:00:00/40 tag 3 ncq dma 692224 out
                        res 40/00:ff:ff:00:00/00:00:00:00:00/00 Emask 0x4 (timeout)
[ 1090.321634] ata5.00: status: { DRDY }
[ 1090.321638] ata5.00: failed command: WRITE FPDMA QUEUED
[ 1090.321646] ata5.00: cmd 61/c0:20:60:1d:00/02:00:00:00:00/40 tag 4 ncq dma 360448 out
                        res 40/00:ff:ff:00:00/00:00:00:00:00/00 Emask 0x4 (timeout)
[ 1090.321650] ata5.00: status: { DRDY }
[ 1090.321654] ata5.00: failed command: WRITE FPDMA QUEUED
[ 1090.321662] ata5.00: cmd 61/48:28:20:20:00/05:00:00:00:00/40 tag 5 ncq dma 692224 out
                        res 40/00:ff:ff:00:00/00:00:00:00:00/00 Emask 0x4 (timeout)
[ 1090.321666] ata5.00: status: { DRDY }
[ 1090.321670] ata5.00: failed command: WRITE FPDMA QUEUED
[ 1090.321678] ata5.00: cmd 61/c0:30:68:25:00/02:00:00:00:00/40 tag 6 ncq dma 360448 out
                        res 40/00:ff:ff:00:00/00:00:00:00:00/00 Emask 0x4 (timeout)
[ 1090.321682] ata5.00: status: { DRDY }
[ 1090.321686] ata5.00: failed command: WRITE FPDMA QUEUED
[ 1090.321694] ata5.00: cmd 61/40:38:28:28:00/05:00:00:00:00/40 tag 7 ncq dma 688128 out
                        res 40/00:ff:ff:00:00/00:00:00:00:00/00 Emask 0x4 (timeout)
[ 1090.321698] ata5.00: status: { DRDY }
[ 1090.321701] ata5.00: failed command: WRITE FPDMA QUEUED
[ 1090.321710] ata5.00: cmd 61/c0:40:68:2d:00/02:00:00:00:00/40 tag 8 ncq dma 360448 out
                        res 40/00:ff:ff:00:00/00:00:00:00:00/00 Emask 0x4 (timeout)
[ 1090.321714] ata5.00: status: { DRDY }
[ 1090.321717] ata5.00: failed command: WRITE FPDMA QUEUED
[ 1090.321726] ata5.00: cmd 61/40:48:28:30:00/05:00:00:00:00/40 tag 9 ncq dma 688128 out
                        res 40/00:ff:ff:00:00/00:00:00:00:00/00 Emask 0x4 (timeout)
[ 1090.321730] ata5.00: status: { DRDY }
[ 1090.321733] ata5.00: failed command: WRITE FPDMA QUEUED
[ 1090.321742] ata5.00: cmd 61/c8:50:68:35:00/02:00:00:00:00/40 tag 10 ncq dma 364544 out
                        res 40/00:ff:ff:00:00/00:00:00:00:00/00 Emask 0x4 (timeout)
[ 1090.321746] ata5.00: status: { DRDY }
[ 1090.321749] ata5.00: failed command: WRITE FPDMA QUEUED
[ 1090.321758] ata5.00: cmd 61/40:58:30:38:00/05:00:00:00:00/40 tag 11 ncq dma 688128 out
                        res 40/00:ff:ff:00:00/00:00:00:00:00/00 Emask 0x4 (timeout)
[ 1090.321762] ata5.00: status: { DRDY }
[ 1090.321765] ata5.00: failed command: WRITE FPDMA QUEUED
[ 1090.321774] ata5.00: cmd 61/c0:60:70:3d:00/02:00:00:00:00/40 tag 12 ncq dma 360448 out
                        res 40/00:ff:ff:00:00/00:00:00:00:00/00 Emask 0x4 (timeout)
[ 1090.321778] ata5.00: status: { DRDY }
[ 1090.321781] ata5.00: failed command: WRITE FPDMA QUEUED
[ 1090.321790] ata5.00: cmd 61/40:68:30:40:00/05:00:00:00:00/40 tag 13 ncq dma 688128 out
                        res 40/00:ff:ff:00:00/00:00:00:00:00/00 Emask 0x4 (timeout)
[ 1090.321794] ata5.00: status: { DRDY }
[ 1090.321797] ata5.00: failed command: WRITE FPDMA QUEUED
[ 1090.321806] ata5.00: cmd 61/c8:70:70:45:00/02:00:00:00:00/40 tag 14 ncq dma 364544 out
                        res 40/00:ff:ff:00:00/00:00:00:00:00/00 Emask 0x4 (timeout)
[ 1090.321810] ata5.00: status: { DRDY }
[ 1090.321813] ata5.00: failed command: WRITE FPDMA QUEUED
[ 1090.321822] ata5.00: cmd 61/48:78:38:48:00/05:00:00:00:00/40 tag 15 ncq dma 692224 out
                        res 40/00:01:00:00:00/00:00:00:00:00/00 Emask 0x4 (timeout)
[ 1090.321826] ata5.00: status: { DRDY }
[ 1090.321829] ata5.00: failed command: WRITE FPDMA QUEUED
[ 1090.321838] ata5.00: cmd 61/80:80:80:4d:00/02:00:00:00:00/40 tag 16 ncq dma 327680 out
                        res 40/00:ff:ff:00:00/00:00:00:00:00/00 Emask 0x4 (timeout)
[ 1090.321841] ata5.00: status: { DRDY }
[ 1090.321845] ata5.00: failed command: WRITE FPDMA QUEUED
[ 1090.321854] ata5.00: cmd 61/40:d8:00:00:00/05:00:00:00:00/40 tag 27 ncq dma 688128 out
                        res 40/00:01:00:4f:c2/00:00:00:00:00/00 Emask 0x4 (timeout)
[ 1090.321858] ata5.00: status: { DRDY }
[ 1090.321861] ata5.00: failed command: WRITE FPDMA QUEUED
[ 1090.321870] ata5.00: cmd 61/c0:e0:40:05:00/02:00:00:00:00/40 tag 28 ncq dma 360448 out
                        res 40/00:00:00:4f:c2/00:00:00:00:00/00 Emask 0x4 (timeout)
[ 1090.321874] ata5.00: status: { DRDY }
[ 1090.321877] ata5.00: failed command: WRITE FPDMA QUEUED
[ 1090.321886] ata5.00: cmd 61/40:f8:00:08:00/05:00:00:00:00/40 tag 31 ncq dma 688128 out
                        res 40/00:ff:ff:00:00/00:00:00:00:00/00 Emask 0x4 (timeout)
[ 1090.321890] ata5.00: status: { DRDY }
[ 1090.321896] ata5: hard resetting link
[ 1090.636674] ata5: SATA link up 6.0 Gbps (SStatus 133 SControl 300)
[ 1090.646800] ata5.00: ACPI cmd ef/10:06:00:00:00:00 (SET FEATURES) succeeded
[ 1090.646806] ata5.00: ACPI cmd f5/00:00:00:00:00:00 (SECURITY FREEZE LOCK) filtered out
[ 1090.646811] ata5.00: ACPI cmd b1/c1:00:00:00:00:00 (DEVICE CONFIGURATION OVERLAY) filtered out
[ 1090.651025] ata5.00: ACPI cmd ef/10:06:00:00:00:00 (SET FEATURES) succeeded
[ 1090.651032] ata5.00: ACPI cmd f5/00:00:00:00:00:00 (SECURITY FREEZE LOCK) filtered out
[ 1090.651036] ata5.00: ACPI cmd b1/c1:00:00:00:00:00 (DEVICE CONFIGURATION OVERLAY) filtered out
[ 1090.652207] ata5.00: configured for UDMA/100
[ 1090.652755] ata5: EH complete
[ 1121.030386] ata5.00: exception Emask 0x0 SAct 0xfcfffc SErr 0x40000 action 0x6 frozen
[ 1121.030399] ata5: SError: { CommWake }
[ 1121.030408] ata5.00: failed command: WRITE FPDMA QUEUED
[ 1121.030425] ata5.00: cmd 61/40:10:00:08:00/05:00:00:00:00/40 tag 2 ncq dma 688128 out
                        res 40/00:ff:ff:00:00/00:00:00:00:00/00 Emask 0x4 (timeout)
[ 1121.030430] ata5.00: status: { DRDY }
[ 1121.030436] ata5.00: failed command: WRITE FPDMA QUEUED
[ 1121.030451] ata5.00: cmd 61/c0:18:40:05:00/02:00:00:00:00/40 tag 3 ncq dma 360448 out
                        res 40/00:ff:ff:00:00/00:00:00:00:00/00 Emask 0x4 (timeout)
[ 1121.030457] ata5.00: status: { DRDY }
[ 1121.030462] ata5.00: failed command: WRITE FPDMA QUEUED
[ 1121.030471] ata5.00: cmd 61/40:20:00:00:00/05:00:00:00:00/40 tag 4 ncq dma 688128 out
                        res 40/00:ff:ff:00:00/00:00:00:00:00/00 Emask 0x4 (timeout)
[ 1121.030475] ata5.00: status: { DRDY }
[ 1121.030479] ata5.00: failed command: WRITE FPDMA QUEUED
[ 1121.030488] ata5.00: cmd 61/80:28:80:4d:00/02:00:00:00:00/40 tag 5 ncq dma 327680 out
                        res 40/00:ff:ff:00:00/00:00:00:00:00/00 Emask 0x4 (timeout)
[ 1121.030491] ata5.00: status: { DRDY }
[ 1121.030495] ata5.00: failed command: WRITE FPDMA QUEUED
[ 1121.030504] ata5.00: cmd 61/48:30:38:48:00/05:00:00:00:00/40 tag 6 ncq dma 692224 out
                        res 40/00:ff:ff:00:00/00:00:00:00:00/00 Emask 0x4 (timeout)
[ 1121.030507] ata5.00: status: { DRDY }
[ 1121.030511] ata5.00: failed command: WRITE FPDMA QUEUED
[ 1121.030520] ata5.00: cmd 61/c8:38:70:45:00/02:00:00:00:00/40 tag 7 ncq dma 364544 out
                        res 40/00:ff:ff:00:00/00:00:00:00:00/00 Emask 0x4 (timeout)
[ 1121.030523] ata5.00: status: { DRDY }
[ 1121.030527] ata5.00: failed command: WRITE FPDMA QUEUED
[ 1121.030535] ata5.00: cmd 61/40:40:30:40:00/05:00:00:00:00/40 tag 8 ncq dma 688128 out
                        res 40/00:ff:ff:00:00/00:00:00:00:00/00 Emask 0x4 (timeout)
[ 1121.030539] ata5.00: status: { DRDY }
[ 1121.030543] ata5.00: failed command: WRITE FPDMA QUEUED
[ 1121.030551] ata5.00: cmd 61/c0:48:70:3d:00/02:00:00:00:00/40 tag 9 ncq dma 360448 out
                        res 40/00:ff:ff:00:00/00:00:00:00:00/00 Emask 0x4 (timeout)
[ 1121.030555] ata5.00: status: { DRDY }
[ 1121.030558] ata5.00: failed command: WRITE FPDMA QUEUED
[ 1121.030568] ata5.00: cmd 61/40:50:30:38:00/05:00:00:00:00/40 tag 10 ncq dma 688128 out
                        res 40/00:ff:ff:00:00/00:00:00:00:00/00 Emask 0x4 (timeout)
[ 1121.030571] ata5.00: status: { DRDY }
[ 1121.030575] ata5.00: failed command: WRITE FPDMA QUEUED
[ 1121.030584] ata5.00: cmd 61/c8:58:68:35:00/02:00:00:00:00/40 tag 11 ncq dma 364544 out
                        res 40/00:ff:ff:00:00/00:00:00:00:00/00 Emask 0x4 (timeout)
[ 1121.030587] ata5.00: status: { DRDY }
[ 1121.030591] ata5.00: failed command: WRITE FPDMA QUEUED
[ 1121.030600] ata5.00: cmd 61/40:60:28:30:00/05:00:00:00:00/40 tag 12 ncq dma 688128 out
                        res 40/00:ff:ff:00:00/00:00:00:00:00/00 Emask 0x4 (timeout)
[ 1121.030603] ata5.00: status: { DRDY }
[ 1121.030607] ata5.00: failed command: WRITE FPDMA QUEUED
[ 1121.030616] ata5.00: cmd 61/c0:68:68:2d:00/02:00:00:00:00/40 tag 13 ncq dma 360448 out
                        res 40/00:ff:ff:00:00/00:00:00:00:00/00 Emask 0x4 (timeout)
[ 1121.030619] ata5.00: status: { DRDY }
[ 1121.030623] ata5.00: failed command: WRITE FPDMA QUEUED
[ 1121.030632] ata5.00: cmd 61/40:70:28:28:00/05:00:00:00:00/40 tag 14 ncq dma 688128 out
                        res 40/00:ff:ff:00:00/00:00:00:00:00/00 Emask 0x4 (timeout)
[ 1121.030635] ata5.00: status: { DRDY }
[ 1121.030639] ata5.00: failed command: WRITE FPDMA QUEUED
[ 1121.030648] ata5.00: cmd 61/c0:78:68:25:00/02:00:00:00:00/40 tag 15 ncq dma 360448 out
                        res 40/00:01:00:00:00/00:00:00:00:00/00 Emask 0x4 (timeout)
[ 1121.030651] ata5.00: status: { DRDY }
[ 1121.030655] ata5.00: failed command: WRITE FPDMA QUEUED
[ 1121.030664] ata5.00: cmd 61/48:90:20:20:00/05:00:00:00:00/40 tag 18 ncq dma 692224 out
                        res 40/00:ff:ff:00:00/00:00:00:00:00/00 Emask 0x4 (timeout)
[ 1121.030667] ata5.00: status: { DRDY }
[ 1121.030671] ata5.00: failed command: WRITE FPDMA QUEUED
[ 1121.030680] ata5.00: cmd 61/c0:98:60:1d:00/02:00:00:00:00/40 tag 19 ncq dma 360448 out
                        res 40/00:ff:ff:00:00/00:00:00:00:00/00 Emask 0x4 (timeout)
[ 1121.030683] ata5.00: status: { DRDY }
[ 1121.030687] ata5.00: failed command: WRITE FPDMA QUEUED
[ 1121.030696] ata5.00: cmd 61/48:a0:18:18:00/05:00:00:00:00/40 tag 20 ncq dma 692224 out
                        res 40/00:01:00:4f:c2/00:00:00:00:00/00 Emask 0x4 (timeout)
[ 1121.030699] ata5.00: status: { DRDY }
[ 1121.030703] ata5.00: failed command: WRITE FPDMA QUEUED
[ 1121.030712] ata5.00: cmd 61/c8:a8:50:15:00/02:00:00:00:00/40 tag 21 ncq dma 364544 out
                        res 40/00:ff:ff:00:00/00:00:00:00:00/00 Emask 0x4 (timeout)
[ 1121.030715] ata5.00: status: { DRDY }
[ 1121.030719] ata5.00: failed command: WRITE FPDMA QUEUED
[ 1121.030728] ata5.00: cmd 61/40:b0:10:10:00/05:00:00:00:00/40 tag 22 ncq dma 688128 out
                        res 40/00:00:00:4f:c2/00:00:00:00:00/00 Emask 0x4 (timeout)
[ 1121.030731] ata5.00: status: { DRDY }
[ 1121.030735] ata5.00: failed command: WRITE FPDMA QUEUED
[ 1121.030743] ata5.00: cmd 61/d0:b8:40:0d:00/02:00:00:00:00/40 tag 23 ncq dma 368640 out
                        res 40/00:00:00:4f:c2/00:00:00:00:00/00 Emask 0x4 (timeout)
[ 1121.030747] ata5.00: status: { DRDY }
[ 1121.030753] ata5: hard resetting link
[ 1121.345937] ata5: SATA link up 6.0 Gbps (SStatus 133 SControl 300)
[ 1121.358873] ata5.00: ACPI cmd ef/10:06:00:00:00:00 (SET FEATURES) succeeded
[ 1121.358880] ata5.00: ACPI cmd f5/00:00:00:00:00:00 (SECURITY FREEZE LOCK) filtered out
[ 1121.358884] ata5.00: ACPI cmd b1/c1:00:00:00:00:00 (DEVICE CONFIGURATION OVERLAY) filtered out
[ 1121.363203] ata5.00: ACPI cmd ef/10:06:00:00:00:00 (SET FEATURES) succeeded
[ 1121.363209] ata5.00: ACPI cmd f5/00:00:00:00:00:00 (SECURITY FREEZE LOCK) filtered out
[ 1121.363214] ata5.00: ACPI cmd b1/c1:00:00:00:00:00 (DEVICE CONFIGURATION OVERLAY) filtered out
[ 1121.364412] ata5.00: configured for UDMA/100
[ 1121.364968] ata5: EH complete
[ 1209.075840] INFO: task gnome-disks:8463 blocked for more than 120 seconds.
[ 1209.075852]       Tainted: P           OE     5.4.0-153-generic #170-Ubuntu
[ 1209.075854] "echo 0 > /proc/sys/kernel/hung_task_timeout_secs" disables this message.
[ 1209.075858] gnome-disks     D    0  8463   2344 0x00004000
[ 1209.075863] Call Trace:
[ 1209.075878]  __schedule+0x2e3/0x740
[ 1209.075885]  schedule+0x42/0xb0
[ 1209.075891]  io_schedule+0x16/0x40
[ 1209.075899]  __blkdev_direct_IO+0x353/0x450
[ 1209.075906]  ? check_preempt_curr+0x4e/0x90
[ 1209.075911]  blkdev_direct_IO+0x4d/0x70
[ 1209.075919]  generic_file_direct_write+0x9c/0x170
[ 1209.075926]  __generic_file_write_iter+0xbc/0x1d0
[ 1209.075931]  blkdev_write_iter+0xb8/0x160
[ 1209.075940]  new_sync_write+0x125/0x1c0
[ 1209.075949]  __vfs_write+0x29/0x40
[ 1209.075952]  vfs_write+0xb9/0x1a0
[ 1209.075957]  ksys_write+0x67/0xe0
[ 1209.075962]  __x64_sys_write+0x1a/0x20
[ 1209.075975]  do_syscall_64+0x57/0x190
[ 1209.075980]  entry_SYSCALL_64_after_hwframe+0x5c/0xc1
[ 1209.075984] RIP: 0033:0x7efc3d2f132f
[ 1209.075992] Code: Bad RIP value.
[ 1209.075995] RSP: 002b:00007efc32dc59a0 EFLAGS: 00000293 ORIG_RAX: 0000000000000001
[ 1209.075999] RAX: ffffffffffffffda RBX: 0000000000000000 RCX: 00007efc3d2f132f
[ 1209.076002] RDX: 0000000000a00000 RSI: 00007efc313c4000 RDI: 000000000000000b
[ 1209.076004] RBP: 000055a1a5d5d010 R08: 0000000000000000 R09: 0000000000000423
[ 1209.076005] R10: 00007ffdf2cc2090 R11: 0000000000000293 R12: 000000000000000b
[ 1209.076007] R13: 00007efc313c4000 R14: 0000000000001000 R15: 00007efc32dc5a50
[ 1213.183836] ata5.00: exception Emask 0x0 SAct 0x0 SErr 0x40000 action 0x6 frozen
[ 1213.183845] ata5: SError: { CommWake }
[ 1213.183852] ata5.00: failed command: WRITE DMA EXT
[ 1213.183865] ata5.00: cmd 35/00:c8:68:35:00/00:02:00:00:00/e0 tag 17 dma 364544 out
                        res 40/00:ff:ff:00:00/00:00:00:00:00/00 Emask 0x4 (timeout)
[ 1213.183869] ata5.00: status: { DRDY }
[ 1213.183876] ata5: hard resetting link
[ 1213.498788] ata5: SATA link up 6.0 Gbps (SStatus 133 SControl 300)
[ 1213.501523] ata5.00: ACPI cmd ef/10:06:00:00:00:00 (SET FEATURES) succeeded
[ 1213.501530] ata5.00: ACPI cmd f5/00:00:00:00:00:00 (SECURITY FREEZE LOCK) filtered out
[ 1213.501534] ata5.00: ACPI cmd b1/c1:00:00:00:00:00 (DEVICE CONFIGURATION OVERLAY) filtered out
[ 1213.505634] ata5.00: ACPI cmd ef/10:06:00:00:00:00 (SET FEATURES) succeeded
[ 1213.505640] ata5.00: ACPI cmd f5/00:00:00:00:00:00 (SECURITY FREEZE LOCK) filtered out
[ 1213.505645] ata5.00: ACPI cmd b1/c1:00:00:00:00:00 (DEVICE CONFIGURATION OVERLAY) filtered out
[ 1213.506879] ata5.00: configured for UDMA/100
[ 1213.507257] ata5: EH complete

Benchmark stuck at first sample:

Answer 1

• From the above dmesg output it becomes clear, that this HDD is broken beyond repair (software-wise).

• I recommend to stop fiddling with it right now assuming you need the data from it.

• In case you DO need the data from it, please contact some reputable recovery company, and be prepared it could cost a small fortune.

• In case you DON'T need the data from it, throw it to the junk yard.

I hope I did make things clearer a bit for your decision.