Ubuntu: fsck shows ext4 file system errors, but only when booting from system partition



Question:

I'm having a problem with my ext4 system partition. I'm running 17.04 (upgraded from 16.10), but the problem was already present in 16.10.

Occasionally (most commonly after waking the system from suspend) the system crashes with a bunch of ext4 filesystem errors.

Now when checking the filesystem with

sudo fsck -n /dev/nvme0n1p2  

fsck claims that the filesystem is clean

fsck from util-linux 2.29  e2fsck 1.43.4 (31-Jan-2017)  Warning!  /dev/nvme0n1p2 is mounted.  Warning: skipping journal recovery because doing a read-only filesystem check.  /dev/nvme0n1p2: clean, 434755/15089664 files, 46490132/60347136 blocks  

However if I force a check, I get a whole bunch of errors:

sudo fsck -nf /dev/nvme0n1p2  fsck from util-linux 2.29  e2fsck 1.43.4 (31-Jan-2017)  Warning!  /dev/nvme0n1p2 is mounted.  Warning: skipping journal recovery because doing a read-only filesystem check.  Pass 1: Checking inodes, blocks, and sizes  Inodes that were part of a corrupted orphan linked list found.  Fix? no    Inode 131275 was part of the orphaned inode list.  IGNORED.  Inode 135221 was part of the orphaned inode list.  IGNORED.  Inode 135244 was part of the orphaned inode list.  IGNORED.  Inode 135260 was part of the orphaned inode list.  IGNORED.  Inode 135263 was part of the orphaned inode list.  IGNORED.  Inode 135268 was part of the orphaned inode list.  IGNORED.  Deleted inode 135272 has zero dtime.  Fix? no    Inode 135274 was part of the orphaned inode list.  IGNORED.  Inode 135384 was part of the orphaned inode list.  IGNORED.  Inode 135396 was part of the orphaned inode list.  IGNORED.  Inode 135697 was part of the orphaned inode list.  IGNORED.  Inode 135711 was part of the orphaned inode list.  IGNORED.  Inode 135713 was part of the orphaned inode list.  IGNORED.  Inode 12059086 was part of the orphaned inode list.  IGNORED.  Inode 12061077 was part of the orphaned inode list.  IGNORED.  Inode 12062594 was part of the orphaned inode list.  IGNORED.  Pass 2: Checking directory structure  Pass 3: Checking directory connectivity  Pass 4: Checking reference counts  Pass 5: Checking group summary information  Block bitmap differences:  -(40927357--40927367) -(40927563--40927569) -(40940652--40940653) -(40940676--40940681) -(48296964--48296970) -(48296978--48296984) -(48304145--48304165) -(48304315--48304321) -(48326677--48326690) -(48326733--48326739) -(48326775--48326781)  Fix? no    Free blocks count wrong (13857004, counted=13856542).  Fix? no    Inode bitmap differences:  -131275 -135221 -135244 -135260 -135263 -135268 -135272 -135274 -135384 -135396 -135697 -135711 -135713 -12059086 -12061077 -12062594  Fix? no    Free inodes count wrong (14654909, counted=14654758).  Fix? no      /dev/nvme0n1p2: ********** WARNING: Filesystem still has errors **********    /dev/nvme0n1p2: 434755/15089664 files (0.3% non-contiguous), 46490132/60347136 blocks  

Now my problem is that I cannot fix those errors, since it is my system partition, which I cannot unmount. But when I boot from an external drive or in recovery mode, fsck does not report any errors, even with -f. After rebooting my system, however, the errors persist. I'm currently at a loss how I might be able to fix the filesystem. Any help would be greatly appreciated.


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