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I am trying to do yum update and getting "MemoryError". The server (OpenVZ box) has 2G RAM and Percona MySQL server running with 1G InnoDB buffer configured. The OS is CentOS 6.5, kernel 2.6.32-openvz-042stab088.4-amd64.

free -m output:

             total       used       free     shared    buffers     cached
Mem:          2048        728       1319          0          0         21
-/+ buffers/cache:        706       1341
Swap:         2048          0       2048

On the host machine, the box memory configuration is:

vzctl set 101 --physpages 0:2G --swappages 0:2G --kmemsize unlimited --privvmpages 2000M:2G --vmguarpages 2000M:2G --oomguarpages 2G --save

When I stop MySQL, yum update works fine. Why would MySQL make yum update fail if there is still more than 1G RAM free?

The full error output is:

yum update
Loaded plugins: fastestmirror, priorities
Loading mirror speeds from cached hostfile
 * base: mirror.mel.bkb.net.au
 * contrib: mirror.mel.bkb.net.au
 * epel: mirror.overthewire.com.au
 * extras: mirror.mel.bkb.net.au
 * updates: mirror.optus.net
Traceback (most recent call last):
  File "/usr/bin/yum", line 29, in <module>
    yummain.user_main(sys.argv[1:], exit_code=True)
  File "/usr/share/yum-cli/yummain.py", line 285, in user_main
    errcode = main(args)
  File "/usr/share/yum-cli/yummain.py", line 136, in main
    result, resultmsgs = base.doCommands()
  File "/usr/share/yum-cli/cli.py", line 434, in doCommands
    self._getTs(needTsRemove)
  File "/usr/lib/python2.6/site-packages/yum/depsolve.py", line 99, in _getTs
    self._getTsInfo(remove_only)
  File "/usr/lib/python2.6/site-packages/yum/depsolve.py", line 110, in _getTsInfo
    pkgSack = self.pkgSack
  File "/usr/lib/python2.6/site-packages/yum/__init__.py", line 887, in <lambda>
    pkgSack = property(fget=lambda self: self._getSacks(),
  File "/usr/lib/python2.6/site-packages/yum/__init__.py", line 683, in _getSacks
    self.plugins.run('exclude')
  File "/usr/lib/python2.6/site-packages/yum/plugins.py", line 184, in run
    func(conduitcls(self, self.base, conf, **kwargs))
  File "/usr/lib/yum-plugins/priorities.py", line 129, in exclude_hook
    repopkgs_archless = _pkglist_to_dict(conduit.getPackages(repo), repo.priority)
  File "/usr/lib/python2.6/site-packages/yum/plugins.py", line 592, in getPackages
    return self._base.pkgSack.returnPackages(arg)
  File "/usr/lib/python2.6/site-packages/yum/packageSack.py", line 499, in returnPackages
    ignore_case=ignore_case)
  File "/usr/lib/python2.6/site-packages/yum/sqlitesack.py", line 1646, in returnPackages
    pkgobjlist = self._buildPkgObjList(repoid, patterns, ignore_case)
  File "/usr/lib/python2.6/site-packages/yum/sqlitesack.py", line 1610, in _buildPkgObjList
    po = self._packageByKeyData(repo, x['pkgKey'], x)
  File "/usr/lib/python2.6/site-packages/yum/sqlitesack.py", line 754, in _packageByKeyData
    po = self.pc(repo, data)
  File "/usr/lib/python2.6/site-packages/yum/sqlitesack.py", line 187, in __init__
    self._loadedfiles = False
MemoryError

Similar question here but not helpful as I have way more RAM.

1

At first I recommends you to enable vSwap memory model because it's simpler and more reliable than old UBC styled system. With it you can replace this vzctl set 101 --physpages 0:2G --swappages 0:2G --kmemsize unlimited --privvmpages 2000M:2G --vmguarpages 2000M:2G --oomguarpages 2G --save by vzctl set 101 --physpages 2G --swappages 2G --save

After this please show me this command result: cat /proc/user_beancounters

This problems looks like memory problem but it related with secondary memory limits which can't show by free or top (only with cat /proc/user_beancounters).

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