[CIG-SHORT] Updated PyLith/Python - Error
Karimi, Bobak
bok10 at pitt.edu
Thu Oct 29 18:41:21 PDT 2015
Matt, thank you for that suggestion! I was remotely accessing my computers, and I most definitely did not send to the right machine the first time. It looks like it is functioning now. Thank you!
Is there a reason why CellFilterAverageMesh is now just CellFilterAverage? The examples provided with PyLith (at least the ones I ran) use CellFilterAverageMesh, but I get an error unless I removed the "Mesh" part. Just curious on that one, really.
Again, thank you again!
Bobby
________________________________
From: CIG-SHORT <cig-short-bounces at geodynamics.org> on behalf of Matthew Knepley <knepley at mcs.anl.gov>
Sent: Thursday, October 29, 2015 9:34 PM
To: cig-short at geodynamics.org
Subject: Re: [CIG-SHORT] Updated PyLith/Python - Error
On Thu, Oct 29, 2015 at 8:44 PM, bok10 <bok10 at pitt.edu<mailto: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<mailto:baagaard at usgs.gov>>
Date: 10/29/2015 8:04 PM (GMT-05:00)
To: cig-short at geodynamics.org<mailto: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<mailto: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<mailto:cig-short-bounces at geodynamics.org>> on behalf of Brad Aagaard <baagaard at usgs.gov<mailto:baagaard at usgs.gov>>
> Sent: Thursday, October 29, 2015 7:21 PM
> To: cig-short at geodynamics.org<mailto: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<http://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<mailto:CIG-SHORT at geodynamics.org>
>> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>>
>
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