[CIG-SHORT] Updated PyLith/Python - Error

Thu Oct 29 17:04:18 PDT 2015

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
>>
>
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