[CIG-SHORT] Updated PyLith/Python - Error
Matthew Knepley
knepley at mcs.anl.gov
Thu Oct 29 18:34:28 PDT 2015
On Thu, Oct 29, 2015 at 8:44 PM, bok10 <bok10 at pitt.edu> wrote:
> Yes, sorry for that confusion.
>
> I ran things on a Linux machine just now and got the same errors. Would
> this suggest anything more specific that may need adressed?
>
Please check again. This error is not possible on Linux:
OSError: [Errno 11] Resource temporarily unavailable
> /usr/bin/pylith: /usr/bin/nemesis: exit 1
Thanks,
Matt
> Bobby
>
>
> -------- Original message --------
> From: Brad Aagaard <baagaard at usgs.gov>
> Date: 10/29/2015 8:04 PM (GMT-05:00)
> To: cig-short at geodynamics.org
> Subject: Re: [CIG-SHORT] Updated PyLith/Python - Error
>
> Bobak,
>
> I think you must mean the v2.1.0 binary (we don't have a PyLith version
> 2.7.1).
>
> Cygwin/Windows is very opaque about loading libraries and remapping
> memory. Based on other people reporting this type of error on various
> cygwin related email lists, this appears to be related to those issues.
> Memory remapping generally requires running a cygwin rebase utility. Due
> to changes in the CIG Windows buildbot it might take us a while to
> recreate a Windows binary in hopes that might fix the problem. The
> problem can also be related to the number of processes running, which is
> why rebooting sometimes helps. It seems sort of hit or miss on whether
> this error occurs, so it is very difficult to debug or find a good
> workaround.
>
> We develop Pylith on Unix-like machines (Linux and OS X) and the PyLith
> binary and builds are much more robust on those operating systems. You
> might want to consider using a Linux virtual machine or making your
> machine dual boot (Windows + Linux) so that you can use the Linux binary.
>
> Regards,
> Brad
>
>
> On 10/29/2015 04:47 PM, Karimi, Bobak wrote:
> > Sorry, Brad. To answer your questions: I'm using the binary, V 2.7.1,
> and when I run the examples, I get the same error as I just sent (2nd
> email).
> >
> > Bobby
> >
> >
> > ________________________________________
> > From: Karimi, Bobak
> > Sent: Thursday, October 29, 2015 7:33 PM
> > To: cig-short at geodynamics.org
> > Subject: Re: [CIG-SHORT] Updated PyLith/Python - Error
> >
> > So, I just happened to find one line of reference text that I forgot to
> turn off, and that seemed to change my error to what is below. I tried
> rebooting (I read on a previous thread that suggestion was made for windows
> users).
> >
> > $ pylith WNAF.cfg
> > 0 [main] nemesis 656 child_info_fork::abort: unable to remap
> _collections.
> > dll to same address as parent (00360000) - try running rebaseall
> > Traceback (most recent call last):
> > File "<string>", line 1, in <module>
> > File
> "/usr/lib/python2.7/site-packages/pythia-0.8.1.15-py2.7.egg/pyre/schedule
> > rs/__init__.py", line 53, in jobstart
> > kwds = kwds)
> > File
> "/usr/lib/python2.7/site-packages/pythia-0.8.1.15-py2.7.egg/pyre/applicat
> > ions/__init__.py", line 41, in start
> > shell.run(**kwds)
> > File
> "/usr/lib/python2.7/site-packages/pythia-0.8.1.15-py2.7.egg/pyre/applicat
> > ions/Shell.py", line 143, in run
> > method(*args, **kwds)
> > File
> "/usr/lib/python2.7/site-packages/pythia-0.8.1.15-py2.7.egg/pyre/applicat
> > ions/SuperScript.py", line 49, in execute
> > self.main(*args, **kwds)
> > File
> "/usr/lib/python2.7/site-packages/pythia-0.8.1.15-py2.7.egg/pyre/applicat
> > ions/SuperScript.py", line 58, in main
> > self.runSubscript(*args, **kwds)
> > File
> "/usr/lib/python2.7/site-packages/pythia-0.8.1.15-py2.7.egg/pyre/schedule
> > rs/BatchScript.py", line 39, in runSubscript
> > super(BatchScript, self).runSubscript(*args, **kwds)
> > File
> "/usr/lib/python2.7/site-packages/pythia-0.8.1.15-py2.7.egg/pyre/applicat
> > ions/SuperScript.py", line 62, in runSubscript
> > self.subscript.run(*args, **kwds)
> > File
> "/usr/lib/python2.7/site-packages/pythia-0.8.1.15-py2.7.egg/pyre/applicat
> > ions/Application.py", line 42, in run
> > shell.run(*args, **kwds)
> > File
> "/usr/lib/python2.7/site-packages/pythia-0.8.1.15-py2.7.egg/pyre/applicat
> > ions/Shell.py", line 143, in run
> > method(*args, **kwds)
> > File
> "/usr/lib/python2.7/site-packages/pythia-0.8.1.15-py2.7.egg/mpi/Applicati
> > on.py", line 90, in _onLauncherNode
> > self.onLauncherNode(*args, **kwds)
> > File
> "/usr/lib/python2.7/site-packages/pythia-0.8.1.15-py2.7.egg/mpi/Applicati
> > on.py", line 94, in onLauncherNode
> > self.launchParallelRun(*args, **kwds)
> > File
> "/usr/lib/python2.7/site-packages/pythia-0.8.1.15-py2.7.egg/mpi/Applicati
> > on.py", line 103, in launchParallelRun
> > launcher.launch()
> > File
> "/usr/lib/python2.7/site-packages/pythia-0.8.1.15-py2.7.egg/mpi/Launcher.
> > py", line 45, in launch
> > pid = os.fork()
> > OSError: [Errno 11] Resource temporarily unavailable
> > /usr/bin/pylith: /usr/bin/nemesis: exit 1
> >
> >
> > ________________________________________
> > From: CIG-SHORT <cig-short-bounces at geodynamics.org> on behalf of Brad
> Aagaard <baagaard at usgs.gov>
> > Sent: Thursday, October 29, 2015 7:21 PM
> > To: cig-short at geodynamics.org
> > Subject: Re: [CIG-SHORT] Updated PyLith/Python - Error
> >
> > Bobak,
> >
> > Are you using the binary or building from source? Are you using v2.1.0?
> > Can you run the examples? If you built from source, did you run the test
> > suite via "make check"?
> >
> > Thanks,
> > Brad
> >
> >
> > On 10/29/2015 03:38 PM, Karimi, Bobak wrote:
> >> Hello all,
> >>
> >>
> >> I recently updated PyLith to the most recent version, and python to
> 2.7.1, and am getting the error:
> >>
> >>
> >> $ pylith WNAF.cfg
> >> Traceback (most recent call last):
> >> File "/usr/bin/pylith", line 27, in <module>
> >> start(applicationClass=PyLithApp)
> >> File
> "/usr/lib/python2.7/site-packages/pythia-0.8.1.15-py2.7.egg/pyre/applicat
> >> ions/__init__.py", line 41, in start
> >> shell.run(**kwds)
> >> File
> "/usr/lib/python2.7/site-packages/pythia-0.8.1.15-py2.7.egg/pyre/applicat
> >> ions/Shell.py", line 73, in run
> >> self.initializeConfiguration(context)
> >> File
> "/usr/lib/python2.7/site-packages/pythia-0.8.1.15-py2.7.egg/pyre/inventor
> >> y/Configurable.py", line 55, in initializeConfiguration
> >> return self.inventory.initializeConfiguration(context)
> >> File
> "/usr/lib/python2.7/site-packages/pythia-0.8.1.15-py2.7.egg/pyre/inventor
> >> y/Inventory.py", line 26, in initializeConfiguration
> >> extraDepositories=self._priv_depositories)
> >> File
> "/usr/lib/python2.7/site-packages/pythia-0.8.1.15-py2.7.egg/pyre/inventor
> >> y/odb/Curator.py", line 37, in getTraits
> >> errorHandler=self._recordTraitLookup):
> >> File
> "/usr/lib/python2.7/site-packages/pythia-0.8.1.15-py2.7.egg/pyre/odb/fs/C
> >> urator.py", line 70, in loadSymbol
> >> shelf = codec.open(spec, 'r')
> >> File
> "/usr/lib/python2.7/site-packages/pythia-0.8.1.15-py2.7.egg/pyre/odb/fs/C
> >> odecODB.py", line 33, in open
> >> self._decode(shelf)
> >> File
> "/usr/lib/python2.7/site-packages/pythia-0.8.1.15-py2.7.egg/pyre/inventor
> >> y/cfg/CodecConfig.py", line 37, in _decode
> >> parser.read(shelf.name)
> >> File "/usr/lib/python2.7/ConfigParser.py", line 305, in read
> >> self._read(fp, filename)
> >> File
> "/usr/lib/python2.7/site-packages/pythia-0.8.1.15-py2.7.egg/pyre/inventor
> >> y/cfg/Parser.py", line 98, in _read
> >> SafeConfigParser._read(self, self._sections.fp, fpname)
> >> File "/usr/lib/python2.7/ConfigParser.py", line 493, in _read
> >> cursect[optname].append(value)
> >> AttributeError: 'str' object has no attribute 'append'
> >>
> >>
> >>
> >> I think, If I'm understanding right, that the error has something to do
> with PyLith reaching out to the Python libraries, but I'm unsure of how to
> fix this (if that is the source of the problem).
> >>
> >>
> >> Any help would be much appreciated!
> >>
> >>
> >> Thanks,
> >> Bobby
> >>
> >>
> >>
> >>
> >>
> >> _______________________________________________
> >> CIG-SHORT mailing list
> >> CIG-SHORT at geodynamics.org
> >> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
> >>
> >
> > _______________________________________________
> > CIG-SHORT mailing list
> > CIG-SHORT at geodynamics.org
> > http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
> > _______________________________________________
> > CIG-SHORT mailing list
> > CIG-SHORT at geodynamics.org
> > http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
> >
>
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--
What most experimenters take for granted before they begin their
experiments is infinitely more interesting than any results to which their
experiments lead.
-- Norbert Wiener
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