Thank you, Rayson. I will watch out if the error happens again and run the
command that you suggested.
On the other hand, I encountered another odd behavior of loadbalance. It
seems that when loadbalance attempts to remove nodes, there is a timing gap
between the node is marked to be removed and it's actually being
inaccessible to job submission. In most cases it worked fine, but today a
job was submitted to the node *after* it's marked for removal by the
loadbalance. So the node was terminated by loadbalance, but the job was
submitted to this node before it's killed and that job shows up on that
node in qstat with "auo" states. When I tried to remove that node again by
explicitly use the removenode command, it failed because the node is no
longer there. I understand that loadbalance is still experimental. But it
seems a good idea to tighten the timing of events so that a node is off
limits to further job submission at the exact moment it is marked to be
removed by loadbalance. Any gap may have unintended side effects.
Thanks!
-Wei
On Wed, Jan 11, 2012 at 1:39 PM, Rayson Ho <raysonlogin_at_yahoo.com> wrote:
> The XML parser does not like the output of "qhost -xml". (We changed some
> minor XML output code in Grid Scheduler recently,
> but as you have encountered this before in earlier versions, looks like
> our changes are not the cause of this issue.)
>
>
> I just started a 1 node cluster and let the loadbalancer add another node,
> and it all seemed to work fine...from the error message
> in your email, qhost exited with 1, and a number of things can cause qhost
> to exit with code 1.
>
>
> Can you run from the interactive shell the following command on one of the
> nodes on EC2 when you encounter this problem
> again??
>
> % qhost -xml
>
> And then send us the output. It can be an issue related to how the XML is
> generated in Grid Engine/Grid Scheduler, or it can be
> something else in the XML parser.
>
> Rayson
>
> =================================
> Open Grid Scheduler / Grid Engine
> http://gridscheduler.sourceforge.net/
>
> Scalable Grid Engine Support Program
> http://www.scalablelogic.com/
>
>
>
> ________________________________
> From: Wei Tao <wei.tao_at_tsibiocomputing.com>
> To: starcluster_at_mit.edu
> Sent: Wednesday, January 11, 2012 10:01 AM
> Subject: [StarCluster] loadbalance error
>
>
> Hi all,
>
> I was running loadbalance. After a while, I got the following error. Can
> someone shed some light on this? This happened before with earlier versions
> of Starcluster as well.
>
> >>> Loading full job history
> !!! ERROR - command 'source /etc/profile && qhost -xml' failed with status
> 1
> Traceback (most recent call last):
> File
> "/usr/local/lib/python2.6/dist-packages/StarCluster-0.93-py2.6.egg/starcluster/cli.py",
> line 251, in main
> sc.execute(args)
> File
> "/usr/local/lib/python2.6/dist-packages/StarCluster-0.93-py2.6.egg/starcluster/commands/loadbalance.py",
> line 89, in execute
> lb.run(cluster)
> File
> "/usr/local/lib/python2.6/dist-packages/StarCluster-0.93-py2.6.egg/starcluster/balancers/sge/__init__.py",
> line 583, in run
> if self.get_stats() == -1:
> File
> "/usr/local/lib/python2.6/dist-packages/StarCluster-0.93-py2.6.egg/starcluster/balancers/sge/__init__.py",
> line 529, in get_stats
> self.stat.parse_qhost(qhostxml)
> File
> "/usr/local/lib/python2.6/dist-packages/StarCluster-0.93-py2.6.egg/starcluster/balancers/sge/__init__.py",
> line 49, in parse_qhost
> doc = xml.dom.minidom.parseString(string)
> File "/usr/lib/python2.6/xml/dom/minidom.py", line 1928, in parseString
> return expatbuilder.parseString(string)
> File "/usr/lib/python2.6/xml/dom/expatbuilder.py", line 940, in
> parseString
> return builder.parseString(string)
> File "/usr/lib/python2.6/xml/dom/expatbuilder.py", line 223, in
> parseString
> parser.Parse(string, True)
> ExpatError: syntax error: line 1, column 0
>
> ---------------------------------------------------------------------------
> MemoryError Traceback (most recent call last)
>
> /usr/local/bin/starcluster in <module>()
> 7 if __name__ == '__main__':
> 8 sys.exit(
> ----> 9 load_entry_point('StarCluster==0.93', 'console_scripts',
> 'starcluster')()
> 10 )
> 11
>
> /usr/local/lib/python2.6/dist-packages/StarCluster-0.93-py2.6.egg/starcluster/cli.pyc
> in main()
> 306 logger.configure_sc_logging()
> 307 warn_debug_file_moved()
> --> 308 StarClusterCLI().main()
> 309
> 310 if __name__ == '__main__':
>
> /usr/local/lib/python2.6/dist-packages/StarCluster-0.93-py2.6.egg/starcluster/cli.pyc
> in main(self)
> 283 log.debug(traceback.format_exc())
> 284 print
> --> 285 self.bug_found()
> 286
> 287
>
> /usr/local/lib/python2.6/dist-packages/StarCluster-0.93-py2.6.egg/starcluster/cli.pyc
> in bug_found(self)
> 150 crashfile = open(static.CRASH_FILE, 'w')
> 151 crashfile.write(header % "CRASH DETAILS")
> --> 152 crashfile.write(session.stream.getvalue())
> 153 crashfile.write(header % "SYSTEM INFO")
> 154 crashfile.write("StarCluster: %s\n" % __version__)
>
> /usr/lib/python2.6/StringIO.pyc in getvalue(self)
> 268 """
> 269 if self.buflist:
> --> 270 self.buf += ''.join(self.buflist)
> 271 self.buflist = []
> 272 return self.buf
>
> MemoryError:
>
> Thanks!
>
> -Wei
> _______________________________________________
> StarCluster mailing list
> StarCluster_at_mit.edu
> http://mailman.mit.edu/mailman/listinfo/starcluster
>
--
Wei Tao, Ph.D.
TSI Biocomputing LLC
617-564-0934
Received on Wed Jan 11 2012 - 15:54:52 EST