[Bug 1716653] [NEW] update-apt-xapian-index burning 100% CPU for two weeks

Tue Sep 12 10:43:36 UTC 2017

Public bug reported:

I accidentally noticed that one of my Ubuntu 14.04 LTS servers hasn't
been applying unattended updates for a while.  Some digging shows that
this is because update-apt-xapian-index started on August 27 is still
running (and eating 100% CPU, for over two weeks)!, which blocks all
other /etc/cron.daily/ scripts from running.  Every night cron starts a
new run, which gets blocked by a new instance of update-apt-xapian-
index:

     $ pstree
     ...
     |-cron-+-16*[cron---sh---run-parts---apt---update-apt-xapi]
     |      |-2*[cron---sh---run-parts---apt-xapian-inde---update-apt-xapi]
     |      |-cron---sh---run-parts---apt-xapian-inde---update-apt-xapi---cat
     |      `-cron---sh---python

strace shows that it's repeatedly reading and writing the same locations
in /var/cache/apt-xapian-index/index.2/postlist.DB:

pread64(83, "\0\0\0\3\0\rH\rH\0=\30\25\r\205\30\1\27\345\27\321\27\270\27\205\27o\27Z\27\21\26"..., 8192, 8880128) = 8192
pwrite64(83, "\0\0\0\3\0\rH\rH\0=\30\25\r\205\30\1\27\345\27\321\27\270\27\205\27o\27Z\27\21\26"..., 8192, 8880128) = 8192
pread64(83, "\0\0\0\3\0\10F\10F\0\21\30\34\10W\0209\20%\20\t\17\365\17\334\17\251\17\223\17~\17"..., 8192, 8871936) = 8192
pwrite64(83, "\0\0\0\3\0\10F\10F\0\21\30\34\10W\0209\20%\20\t\17\365\17\334\17\251\17\223\17~\17"..., 8192, 8871936) = 8192
pread64(83, "\0\0\0\3\0\rH\rH\0=\30\25\r\205\30\1\27\345\27\321\27\270\27\205\27o\27Z\27\21\26"..., 8192, 8880128) = 8192
pwrite64(83, "\0\0\0\3\0\rH\rH\0=\30\25\r\205\30\1\27\345\27\321\27\270\27\205\27o\27Z\27\21\26"..., 8192, 8880128) = 8192
pread64(83, "\0\0\0\3\0\10F\10F\0\21\30\34\10W\0209\20%\20\t\17\365\17\334\17\251\17\223\17~\17"..., 8192, 8871936) = 8192
pwrite64(83, "\0\0\0\3\0\10F\10F\0\21\30\34\10W\0209\20%\20\t\17\365\17\334\17\251\17\223\17~\17"..., 8192, 8871936) = 8192
pread64(83, "\0\0\0\3\0\rH\rH\0=\30\25\r\205\30\1\27\345\27\321\27\270\27\205\27o\27Z\27\21\26"..., 8192, 8880128) = 8192
pwrite64(83, "\0\0\0\3\0\rH\rH\0=\30\25\r\205\30\1\27\345\27\321\27\270\27\205\27o\27Z\27\21\26"..., 8192, 8880128) = 8192
pread64(83, "\0\0\0\3\0\10F\10F\0\21\30\34\10W\0209\20%\20\t\17\365\17\334\17\251\17\223\17~\17"..., 8192, 8871936) = 8192
pwrite64(83, "\0\0\0\3\0\10F\10F\0\21\30\34\10W\0209\20%\20\t\17\365\17\334\17\251\17\223\17~\17"..., 8192, 8871936) = 8192
pread64(83, "\0\0\0\3\0\rH\rH\0=\30\25\r\205\30\1\27\345\27\321\27\270\27\205\27o\27Z\27\21\26"..., 8192, 8880128) = 8192
pwrite64(83, "\0\0\0\3\0\rH\rH\0=\30\25\r\205\30\1\27\345\27\321\27\270\27\205\27o\27Z\27\21\26"..., 8192, 8880128) = 8192
pread64(83, "\0\0\0\3\0\10F\10F\0\21\30\34\10W\0209\20%\20\t\17\365\17\334\17\251\17\223\17~\17"..., 8192, 8871936) = 8192
pwrite64(83, "\0\0\0\3\0\10F\10F\0\21\30\34\10W\0209\20%\20\t\17\365\17\334\17\251\17\223\17~\17"..., 8192, 8871936) = 8192
pread64(83, "\0\0\0\3\0\rH\rH\0=\30\25\r\205\30\1\27\345\27\321\27\270\27\205\27o\27Z\27\21\26"..., 8192, 8880128) = 8192
pwrite64(83, "\0\0\0\3\0\rH\rH\0=\30\25\r\205\30\1\27\345\27\321\27\270\27\205\27o\27Z\27\21\26"..., 8192, 8880128) = 8192

I poked around a bit with gdb and dumped the C and Python stack frames,
but I'm not sure what to look for.

ProblemType: Bug
DistroRelease: Ubuntu 14.04
Package: apt-xapian-index 0.45ubuntu4
ProcVersionSignature: Ubuntu 3.13.0-128.177-generic 3.13.11-ckt39
Uname: Linux 3.13.0-128-generic i686
ApportVersion: 2.14.1-0ubuntu3.25
Architecture: i386
Date: Tue Sep 12 13:21:42 2017
PackageArchitecture: all
SourcePackage: apt-xapian-index
UpgradeStatus: Upgraded to trusty on 2016-03-31 (530 days ago)

** Affects: apt-xapian-index (Ubuntu)
     Importance: Undecided
         Status: New

** Tags: apport-bug i386 trusty

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https://bugs.launchpad.net/bugs/1716653

Title:
  update-apt-xapian-index burning 100% CPU for two weeks

Status in apt-xapian-index package in Ubuntu:
  New

Bug description:
  I accidentally noticed that one of my Ubuntu 14.04 LTS servers hasn't
  been applying unattended updates for a while.  Some digging shows that
  this is because update-apt-xapian-index started on August 27 is still
  running (and eating 100% CPU, for over two weeks)!, which blocks all
  other /etc/cron.daily/ scripts from running.  Every night cron starts
  a new run, which gets blocked by a new instance of update-apt-xapian-
  index:

       $ pstree
       ...
       |-cron-+-16*[cron---sh---run-parts---apt---update-apt-xapi]
       |      |-2*[cron---sh---run-parts---apt-xapian-inde---update-apt-xapi]
       |      |-cron---sh---run-parts---apt-xapian-inde---update-apt-xapi---cat
       |      `-cron---sh---python

  strace shows that it's repeatedly reading and writing the same
  locations in /var/cache/apt-xapian-index/index.2/postlist.DB:

  pread64(83, "\0\0\0\3\0\rH\rH\0=\30\25\r\205\30\1\27\345\27\321\27\270\27\205\27o\27Z\27\21\26"..., 8192, 8880128) = 8192
  pwrite64(83, "\0\0\0\3\0\rH\rH\0=\30\25\r\205\30\1\27\345\27\321\27\270\27\205\27o\27Z\27\21\26"..., 8192, 8880128) = 8192
  pread64(83, "\0\0\0\3\0\10F\10F\0\21\30\34\10W\0209\20%\20\t\17\365\17\334\17\251\17\223\17~\17"..., 8192, 8871936) = 8192
  pwrite64(83, "\0\0\0\3\0\10F\10F\0\21\30\34\10W\0209\20%\20\t\17\365\17\334\17\251\17\223\17~\17"..., 8192, 8871936) = 8192
  pread64(83, "\0\0\0\3\0\rH\rH\0=\30\25\r\205\30\1\27\345\27\321\27\270\27\205\27o\27Z\27\21\26"..., 8192, 8880128) = 8192
  pwrite64(83, "\0\0\0\3\0\rH\rH\0=\30\25\r\205\30\1\27\345\27\321\27\270\27\205\27o\27Z\27\21\26"..., 8192, 8880128) = 8192
  pread64(83, "\0\0\0\3\0\10F\10F\0\21\30\34\10W\0209\20%\20\t\17\365\17\334\17\251\17\223\17~\17"..., 8192, 8871936) = 8192
  pwrite64(83, "\0\0\0\3\0\10F\10F\0\21\30\34\10W\0209\20%\20\t\17\365\17\334\17\251\17\223\17~\17"..., 8192, 8871936) = 8192
  pread64(83, "\0\0\0\3\0\rH\rH\0=\30\25\r\205\30\1\27\345\27\321\27\270\27\205\27o\27Z\27\21\26"..., 8192, 8880128) = 8192
  pwrite64(83, "\0\0\0\3\0\rH\rH\0=\30\25\r\205\30\1\27\345\27\321\27\270\27\205\27o\27Z\27\21\26"..., 8192, 8880128) = 8192
  pread64(83, "\0\0\0\3\0\10F\10F\0\21\30\34\10W\0209\20%\20\t\17\365\17\334\17\251\17\223\17~\17"..., 8192, 8871936) = 8192
  pwrite64(83, "\0\0\0\3\0\10F\10F\0\21\30\34\10W\0209\20%\20\t\17\365\17\334\17\251\17\223\17~\17"..., 8192, 8871936) = 8192
  pread64(83, "\0\0\0\3\0\rH\rH\0=\30\25\r\205\30\1\27\345\27\321\27\270\27\205\27o\27Z\27\21\26"..., 8192, 8880128) = 8192
  pwrite64(83, "\0\0\0\3\0\rH\rH\0=\30\25\r\205\30\1\27\345\27\321\27\270\27\205\27o\27Z\27\21\26"..., 8192, 8880128) = 8192
  pread64(83, "\0\0\0\3\0\10F\10F\0\21\30\34\10W\0209\20%\20\t\17\365\17\334\17\251\17\223\17~\17"..., 8192, 8871936) = 8192
  pwrite64(83, "\0\0\0\3\0\10F\10F\0\21\30\34\10W\0209\20%\20\t\17\365\17\334\17\251\17\223\17~\17"..., 8192, 8871936) = 8192
  pread64(83, "\0\0\0\3\0\rH\rH\0=\30\25\r\205\30\1\27\345\27\321\27\270\27\205\27o\27Z\27\21\26"..., 8192, 8880128) = 8192
  pwrite64(83, "\0\0\0\3\0\rH\rH\0=\30\25\r\205\30\1\27\345\27\321\27\270\27\205\27o\27Z\27\21\26"..., 8192, 8880128) = 8192

  I poked around a bit with gdb and dumped the C and Python stack
  frames, but I'm not sure what to look for.

  ProblemType: Bug
  DistroRelease: Ubuntu 14.04
  Package: apt-xapian-index 0.45ubuntu4
  ProcVersionSignature: Ubuntu 3.13.0-128.177-generic 3.13.11-ckt39
  Uname: Linux 3.13.0-128-generic i686
  ApportVersion: 2.14.1-0ubuntu3.25
  Architecture: i386
  Date: Tue Sep 12 13:21:42 2017
  PackageArchitecture: all
  SourcePackage: apt-xapian-index
  UpgradeStatus: Upgraded to trusty on 2016-03-31 (530 days ago)

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