Mounted fsck for home directory

dmesg.md

Kernel: Linux thinkpad 6.14.5 #1-NixOS SMP PREEMPT_DYNAMIC Fri May 2 06:02:16 UTC 2025 x86_64 GNU/Linux bcachefs version v1.25.2 (but when it runs, it finds extents with 1.20, even though I formatted with 1.25.2 tool chain)

Got asked multiple times for (y,n, or Y,N for all errors of this type) Y => captial Y didn't seem to be working? I got asked for each occurance after. I have two volumes, a home directory and an extra data volume. Both use snapshots. dm-3 is home directory and dm-4 is the extra volume.

When booting (boot failed even with "fsck" as a mount option)

[May14 09:04] bcachefs (dm-3): journal read done, replaying entries 595600-595600
[  +0.026529] bcachefs (dm-3): accounting_read... done
[  +0.019089] bcachefs (dm-3): alloc_read... done
[  +0.003614] bcachefs (dm-3): stripes_read... done
[  +0.000003] bcachefs (dm-3): snapshots_read... done
[  +0.000027] bcachefs (dm-3): check_allocations... done
[  +9.705253] bcachefs (dm-3): going read-write
[  +0.000961] bcachefs (dm-3): journal_replay... done
[  +0.000007] bcachefs (dm-3): check_alloc_info... done
[  +0.868895] bcachefs (dm-3): check_lrus... done
[  +0.004277] bcachefs (dm-3): check_btree_backpointers... done
[  +3.788493] bcachefs (dm-3): check_extents_to_backpointers... done
[  +1.046408] bcachefs (dm-3): check_alloc_to_lru_refs... done
[  +0.101477] bcachefs (dm-3): check_snapshot_trees... done
[  +0.000015] bcachefs (dm-3): check_snapshots... done
[  +0.000069] bcachefs (dm-3): check_subvols...
[  +0.000023] subvol root 4096:4294967133 has wrong bi_subvol field: got 0, should be 1, exiting
[  +0.000003] bcachefs (dm-3): Unable to continue, halting
[  +0.000001] bcachefs (dm-3): bch2_check_subvols(): error fsck_errors_not_fixed
[  +0.001323] bcachefs (dm-3): bch2_fs_recovery(): error fsck_errors_not_fixed
[  +0.000002] bcachefs (dm-3): bch2_fs_start(): error starting filesystem fsck_errors_not_fixed
[  +0.001537] bcachefs (dm-3): unclean shutdown complete, journal seq 595608
[  +0.155283] bcachefs: bch2_fs_get_tree() error: fsck_errors_not_fixed
[  +0.049731] bcachefs (dm-4): starting version 1.20: directory_size opts=background_compression=zstd:15,fsck
[  +0.000005] bcachefs (dm-4): recovering from unclean shutdown
[ +14.355908] bcachefs (dm-4): journal read done, replaying entries 64678-64678
[  +0.013666] bcachefs (dm-4): accounting_read... done
[  +0.014887] bcachefs (dm-4): alloc_read... done
[  +0.001530] bcachefs (dm-4): stripes_read... done
[  +0.000002] bcachefs (dm-4): snapshots_read... done
[  +0.000013] bcachefs (dm-4): check_allocations... done
[ +12.512120] bcachefs (dm-4): going read-write
[  +0.010250] bcachefs (dm-4): journal_replay... done
[  +0.000008] bcachefs (dm-4): check_alloc_info... done
[  +0.395574] bcachefs (dm-4): check_lrus... done
[  +0.003239] bcachefs (dm-4): check_btree_backpointers... done
[  +6.616244] bcachefs (dm-4): check_extents_to_backpointers... done
[  +1.668524] bcachefs (dm-4): check_alloc_to_lru_refs... done
[  +0.162440] bcachefs (dm-4): check_snapshot_trees... done
[  +0.000028] bcachefs (dm-4): check_snapshots... done
[  +0.000045] bcachefs (dm-4): check_subvols...
[  +0.000018] subvol root 4096:4294967254 has wrong bi_subvol field: got 0, should be 1, exiting
[  +0.000003] bcachefs (dm-4): Unable to continue, halting
[  +0.000001] bcachefs (dm-4): bch2_check_subvols(): error fsck_errors_not_fixed
[  +0.000128] bcachefs (dm-4): bch2_fs_recovery(): error fsck_errors_not_fixed
[  +0.000001] bcachefs (dm-4): bch2_fs_start(): error starting filesystem fsck_errors_not_fixed
[  +0.001288] bcachefs (dm-4): unclean shutdown complete, journal seq 64686
[  +0.111479] bcachefs: bch2_fs_get_tree() error: fsck_errors_not_fixed
[May14 09:05] bcachefs (dm-4): starting version 1.20: directory_size opts=background_compression=zstd:15
[  +0.000005] bcachefs (dm-4): recovering from unclean shutdown
[ +14.249633] bcachefs (dm-4): journal read done, replaying entries 64678-64678
[  +0.015013] bcachefs (dm-4): accounting_read... done
[  +0.014769] bcachefs (dm-4): alloc_read... done
[  +0.001717] bcachefs (dm-4): stripes_read... done
[  +0.000003] bcachefs (dm-4): snapshots_read... done
[  +0.014470] bcachefs (dm-4): going read-write
[  +0.002666] bcachefs (dm-4): journal_replay... done
[  +0.000008] bcachefs (dm-4): resume_logged_ops... done
[  +0.000002] bcachefs (dm-4): delete_dead_inodes... done
[May14 09:10] bcachefs (dm-3): starting version 1.20: directory_size opts=background_compression=lz4
[  +0.000004] bcachefs (dm-3): recovering from unclean shutdown
[ +11.879696] bcachefs (dm-3): journal read done, replaying entries 595600-595600
[  +0.027066] bcachefs (dm-3): accounting_read... done
[  +0.011949] bcachefs (dm-3): alloc_read... done
[  +0.005158] bcachefs (dm-3): stripes_read... done
[  +0.000003] bcachefs (dm-3): snapshots_read... done
[  +0.012504] bcachefs (dm-3): going read-write
[  +0.001536] bcachefs (dm-3): journal_replay... done
[  +0.000014] bcachefs (dm-3): resume_logged_ops... done
[  +0.001085] bcachefs (dm-3): delete_dead_inodes... done
[May14 09:16] bcachefs (dm-4): clean shutdown complete, journal seq 65358
[  +2.680376] bcachefs (dm-4): starting version 1.20: directory_size opts=background_compression=zstd:15,fsck
[  +0.000008] bcachefs (dm-4): recovering from clean shutdown, journal seq 65358
[  +0.013469] bcachefs (dm-4): accounting_read... done
[  +0.004957] bcachefs (dm-4): alloc_read... done
[  +0.001588] bcachefs (dm-4): stripes_read... done
[  +0.000002] bcachefs (dm-4): snapshots_read... done
[  +0.000012] bcachefs (dm-4): check_allocations... done
[ +12.952239] bcachefs (dm-4): going read-write
[  +0.009793] bcachefs (dm-4): journal_replay... done
[  +0.000004] bcachefs (dm-4): check_alloc_info... done
[  +0.453924] bcachefs (dm-4): check_lrus... done
[  +0.003126] bcachefs (dm-4): check_btree_backpointers... done
[  +6.827293] bcachefs (dm-4): check_extents_to_backpointers... done
[  +1.803105] bcachefs (dm-4): check_alloc_to_lru_refs... done
[  +0.166978] bcachefs (dm-4): check_snapshot_trees... done
[  +0.000032] bcachefs (dm-4): check_snapshots... done
[  +0.000050] bcachefs (dm-4): check_subvols...
[  +0.000022] subvol root 4096:4294967254 has wrong bi_subvol field: got 0, should be 1, exiting
[  +0.000004] bcachefs (dm-4): Unable to continue, halting
[  +0.000001] bcachefs (dm-4): bch2_check_subvols(): error fsck_errors_not_fixed
[  +0.000010] bcachefs (dm-4): bch2_fs_recovery(): error fsck_errors_not_fixed
[  +0.000001] bcachefs (dm-4): bch2_fs_start(): error starting filesystem fsck_errors_not_fixed
[  +0.001245] bcachefs (dm-4): unclean shutdown complete, journal seq 65360
[  +0.021292] bcachefs: bch2_fs_get_tree() error: fsck_errors_not_fixed
[ +22.842419] bcachefs (dm-4): starting version 1.20: directory_size opts=background_compression=zstd:15
[  +0.000004] bcachefs (dm-4): recovering from unclean shutdown
[May14 09:17] bcachefs (dm-4): journal read done, replaying entries 65360-65360
[  +0.013048] bcachefs (dm-4): accounting_read... done
[  +0.014550] bcachefs (dm-4): alloc_read... done
[  +0.001495] bcachefs (dm-4): stripes_read... done
[  +0.000002] bcachefs (dm-4): snapshots_read... done
[  +0.013094] bcachefs (dm-4): going read-write
[  +0.002274] bcachefs (dm-4): journal_replay... done
[  +0.000867] bcachefs (dm-4): resume_logged_ops... done
[  +0.000009] bcachefs (dm-4): delete_dead_inodes... done
[ +15.652734] bcachefs (dm-4): clean shutdown complete, journal seq 65389
[  +1.558912] bcachefs (dm-4): starting version 1.20: directory_size opts=background_compression=zstd:15,fsck
[  +0.000008] bcachefs (dm-4): recovering from clean shutdown, journal seq 65389
[  +0.011783] bcachefs (dm-4): accounting_read... done
[  +0.004574] bcachefs (dm-4): alloc_read... done
[  +0.001435] bcachefs (dm-4): stripes_read... done
[  +0.000002] bcachefs (dm-4): snapshots_read... done
[  +0.000011] bcachefs (dm-4): check_allocations... done
[ +12.578447] bcachefs (dm-4): going read-write
[  +0.010152] bcachefs (dm-4): journal_replay... done
[  +0.000867] bcachefs (dm-4): check_alloc_info... done
[  +0.413167] bcachefs (dm-4): check_lrus... done
[  +0.002890] bcachefs (dm-4): check_btree_backpointers... done
[  +6.755346] bcachefs (dm-4): check_extents_to_backpointers... done
[  +1.767021] bcachefs (dm-4): check_alloc_to_lru_refs... done
[  +0.169542] bcachefs (dm-4): check_snapshot_trees... done
[  +0.000014] bcachefs (dm-4): check_snapshots... done
[  +0.000045] bcachefs (dm-4): check_subvols...
[  +0.000016] subvol root 4096:4294967254 has wrong bi_subvol field: got 0, should be 1, exiting
[  +0.000003] bcachefs (dm-4): Unable to continue, halting
[  +0.000001] bcachefs (dm-4): bch2_check_subvols(): error fsck_errors_not_fixed
[  +0.000012] bcachefs (dm-4): bch2_fs_recovery(): error fsck_errors_not_fixed
[  +0.000002] bcachefs (dm-4): bch2_fs_start(): error starting filesystem fsck_errors_not_fixed
[  +0.001106] bcachefs (dm-4): unclean shutdown complete, journal seq 65392
[  +0.034750] bcachefs: bch2_fs_get_tree() error: fsck_errors_not_fixed

Mounting home manually once recovered boot

Running fsck online
bcachefs (dm-3): check_alloc_info... done
bcachefs (dm-3): check_lrus... done
bcachefs (dm-3): check_btree_backpointers... done
bcachefs (dm-3): check_backpointers_to_extents...bcachefs (dm-3): backpointers_to_extents: 45%, done 1391/3057 nodes, at backpointers:0:297554411520:0
 done
bcachefs (dm-3): check_extents_to_backpointers... done
bcachefs (dm-3): check_alloc_to_lru_refs... done
bcachefs (dm-3): check_snapshot_trees... done
bcachefs (dm-3): check_snapshots... done
bcachefs (dm-3): check_subvols...subvol root 4096:4294967133 has wrong bi_subvol field: got 0, should be 1, fix? (y,n, or Y,N for all errors of this type) Y
 done
bcachefs (dm-3): check_subvol_children... done
bcachefs (dm-3): delete_dead_snapshots... done
bcachefs (dm-3): check_indirect_extents... done
bcachefs (dm-3): check_root... done
bcachefs (dm-3): check_subvolume_structure...subvolume loop, fix? (y,n, or Y,N for all errors of this type) Y
bcachefs (dm-3): bch2_check_subvolume_structure(): error ENOENT_bkey_type_mismatch
bcachefs (dm-3): bch2_fsck_online_thread_fn(): error ENOENT_bkey_type_mismatch
error closing fd: Unknown error 2151 at c_src/cmd_fsck.c:89

Mounting volume manually

[  +1.333192] bcachefs (dm-3): dirent points to inode that does not point back:
                u64s 8 type dirent 1185863:7978347666253517277:4294967257 len 0 ver 0: wireplumber -> 1539556 type dir
                inum: 1539556:4294967135 
                mode=40700
                flags=(19300000)
                journal_seq=595070
                hash_seed=40453bf795df7029
                hash_type=siphash
                bi_size=0
                bi_sectors=0
                bi_version=0
                bi_atime=44188747530185
                bi_ctime=561230813172379
                bi_mtime=561230813172379
                bi_otime=3270941005684
                bi_uid=1000
                bi_gid=1000
                bi_nlink=0
                bi_generation=0
                bi_dev=0
                bi_data_checksum=0
                bi_compression=0
                bi_project=0
                bi_background_compression=0
                bi_data_replicas=0
                bi_promote_target=0
                bi_foreground_target=0
                bi_background_target=0
                bi_erasure_code=0
                bi_fields_set=0
                bi_dir=0
                bi_dir_offset=0
                bi_subvol=0
                bi_parent_subvol=0
                bi_nocow=0
                bi_depth=2
                bi_inodes_32bit=0
[  +0.000014] bcachefs (dm-3): inconsistency detected - emergency read only at journal seq 595673
[  +0.023768] bcachefs (dm-3): unclean shutdown complete, journal seq 595673
[  +0.136384] Initializing XFRM netlink socket
[  +0.097383] rfkill: input handler enabled
[  +0.988851] bcachefs (dm-3): dirent points to inode that does not point back:
                u64s 8 type dirent 4115:4788777817878249414:4294967257 len 0 ver 0: gstreamer-1.0 -> 10241 type dir
                inum: 10241:4294967135 
                mode=40775
                flags=(19300000)
                journal_seq=595063
                hash_seed=fd5f451d87ca12
                hash_type=siphash
                bi_size=0
                bi_sectors=0
                bi_version=0
                bi_atime=44178662298638
                bi_ctime=561233699238565
                bi_mtime=561233699238565
                bi_otime=1512841998542
                bi_uid=1000
                bi_gid=1000
                bi_nlink=0
                bi_generation=0
                bi_dev=0
                bi_data_checksum=0
                bi_compression=0
                bi_project=0
                bi_background_compression=0
                bi_data_replicas=0
                bi_promote_target=0
                bi_foreground_target=0
                bi_background_target=0
                bi_erasure_code=0
                bi_fields_set=0
                bi_dir=0
                bi_dir_offset=0
                bi_subvol=0
                bi_parent_subvol=0
                bi_nocow=0
                bi_depth=1
                bi_inodes_32bit=0
[  +0.107900] rfkill: input handler disabled
[  +0.070952] nvme nvme0: using unchecked data buffer
[  +0.474851] bcachefs (dm-3): dirent points to inode that does not point back:
                u64s 7 type dirent 1247259:1334536482454387248:4294967257 len 0 ver 0: tags -> 1490909 type dir
                inum: 1490909:4294967135 
                mode=40755
                flags=(19300000)
                journal_seq=595069
                hash_seed=6f64e5f375e3a899
                hash_type=siphash
                bi_size=0
                bi_sectors=0
                bi_version=0
                bi_atime=44188644527820
                bi_ctime=561243516435990
                bi_mtime=561243516435990
                bi_otime=3102359751064
                bi_uid=1000
                bi_gid=1000
                bi_nlink=0
                bi_generation=0
                bi_dev=0
                bi_data_checksum=0
                bi_compression=0
                bi_project=0
                bi_background_compression=0
                bi_data_replicas=0
                bi_promote_target=0
                bi_foreground_target=0
                bi_background_target=0
                bi_erasure_code=0
                bi_fields_set=0
                bi_dir=0
                bi_dir_offset=0
                bi_subvol=0
                bi_parent_subvol=0
                bi_nocow=0
                bi_depth=2
                bi_inodes_32bit=0

Some additional errors I have seen but weren't able to capture in the recovery console:

EEXIST_str_hash_set, exit code -1. I deleted all snapshots and this error went away, but the ones above persist.

Mounting the Extra volume manually succeeds, but is unusable:

ls -al tmpfs
ls: cannot access 'tmpfs/.Trash-1000': No such file or directory
ls: cannot access 'tmpfs/Games': No such file or directory
ls: cannot access 'tmpfs/rpi-backups': No such file or directory
ls: cannot access 'tmpfs/ISOs': No such file or directory
ls: cannot access 'tmpfs/gdrive-backup': No such file or directory
ls: cannot access 'tmpfs/accident-09152022': No such file or directory
ls: cannot access 'tmpfs/pve-backup': No such file or directory
ls: cannot access 'tmpfs/lost+found': No such file or directory
ls: cannot access 'tmpfs/photos': No such file or directory
ls: cannot access 'tmpfs/quickemu': No such file or directory
ls: cannot access 'tmpfs/USB-Backup': No such file or directory
ls: cannot access 'tmpfs/lepotato.img': No such file or directory
ls: cannot access 'tmpfs/linux-vol': No such file or directory
ls: cannot access 'tmpfs/VMs': No such file or directory
ls: cannot access 'tmpfs/ventoy-backup': No such file or directory
total 4
drwxr-xr-x 2 root root    0 May 14 09:17 .
drwxr-xr-x 5 root root 4096 May  7 20:05 ..
d????????? ? ?    ?       ?            ? accident-09152022
d????????? ? ?    ?       ?            ? Games
d????????? ? ?    ?       ?            ? gdrive-backup
d????????? ? ?    ?       ?            ? ISOs
-????????? ? ?    ?       ?            ? lepotato.img
d????????? ? ?    ?       ?            ? linux-vol
d????????? ? ?    ?       ?            ? lost+found
d????????? ? ?    ?       ?            ? photos
d????????? ? ?    ?       ?            ? pve-backup
d????????? ? ?    ?       ?            ? quickemu
d????????? ? ?    ?       ?            ? rpi-backups
d????????? ? ?    ?       ?            ? .Trash-1000
d????????? ? ?    ?       ?            ? USB-Backup
d????????? ? ?    ?       ?            ? ventoy-backup
d????????? ? ?    ?       ?            ? VMs

Note: I added the fsck mount option because if there was an unclean shutdown, the system failed to boot due to some cleanup needing to be done.