[RHEL5.6] e2fsck hangs in "Pass 2: Checking directory structure" on 400GB volume containing many hard links

Issue

• fsck hangs on 400 GB volume used for rsync backups and containing lots of hard links

• Disk checks hanging. We have multi TB disks that are marked as clean with errors.
  When I run e2fsck -fptt it hangs on pass two.

• strace of fsck shows hung in "Pass 2: Checking directory structure", after a 4k read:

  1963  20:50:27 write(1, "                                "..., 80) = 80
  1963  20:50:27 write(1, "Pass 2: Checking ", 17) = 17
  1963  20:50:27 write(1, "directory", 9) = 9
  1963  20:50:27 write(1, " structure\n", 11) = 11
  1963  20:50:27 brk(0x4a2b000)           = 0x4a2b000
  1963  20:50:27 brk(0x56ab000)           = 0x56ab000
  1963  20:50:27 mmap(NULL, 154857472, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS, -1, 0) = 0x2ab37bef3000
  1963  20:50:27 mmap(NULL, 200712192, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS, -1, 0) = 0x2ab3852a2000
  1963  20:50:33 munmap(0x2ab3852a2000, 200712192) = 0
  1963  20:50:33 lseek(3, 6303744, SEEK_SET) = 6303744
  1963  20:50:33 read(3, "\2\0\0\0\f\0\1\2.\0\0\0\2\0\0\0\f\0\2\2..\0\0\v\0\0\0\24\0\n\2"..., 4096) = 4096
  ...
  1963  20:50:33 lseek(3, 147316736, SEEK_SET) = 147316736
  1963  20:50:33 read(3, "\347G\0\0\f\0\1\2.\0\0\0\231\307?\6\364\17\2\2..\0\0\0\0\0\0\0\0\0\0"..., 4096) = 4096
  1963  21:09:07 --- SIGINT (Interrupt) @ 0 (0) ---
  1963  21:09:07 rt_sigreturn(0x2)        = 104843161
  

• A backtrace of fsck during execution shows the following:

  (gdb) bt
  0  get_icount_el (icount=0x19948d40, ino=104843161, create=1) at icount.c:257
  1  0x000000000041cd0b in ext2fs_icount_increment (icount=0x19948d40, ino=104843161, ret=0x7fff4e11e74e) at icount.c:340
  2  0x000000000040ada4 in check_dir_block (fs=0x1990ce20, db=0x2adcd60a13e8, priv_data=0x7fff4e11e7d0) at pass2.c:1014
  3  0x000000000041a673 in ext2fs_dblist_iterate (dblist=0x199349c0, func=0x40a720 , priv_data=0x7fff4e11e7d0) at dblist.c:235
  4  0x000000000040a2d7 in e2fsck_pass2 (ctx=0x1990cad0) at pass2.c:149
  5  0x00000000004030a6 in e2fsck_run (ctx=0x1990cad0) at e2fsck.c:203
  6  0x00000000004023af in main (argc=, argv=) at unix.c:1148