[CIG-SHORT] Pylithapp error
Rishabh Dutta
rishabh.dutta at kaust.edu.sa
Thu Nov 27 07:17:01 PST 2014
Hi,
I have been trying to run the same problem in 3d and am looking for the
displacement on the surface. I mentioned a nodeset of the surface where I
intend to find the displacement values. I have attached the .cfg file which
I am running. And it's not giving me the output for the surface nodeset. It
gives me the output for the whole domain though.
Thanks in advance,
Rishabh
On Tue, Nov 11, 2014 at 12:01 AM, Brad Aagaard <baagaard at usgs.gov> wrote:
> Rishabh,
>
> The error message provides a lot of important information you need to fix
> the error.
>
> Notice the backtrace:
>
> >> Backtrace - Component simpleioascii, iohandler
> >> Backtrace - Component simpledb, slip
> >> Backtrace - Component stepslipfn, slip_function
> >> Backtrace - Component eqkinsrc, rupture
> >> Backtrace - Component singlerupture, eq_srcs
> >> Backtrace - Component faultcohesivekin, compliant_fault
> >> Backtrace - Component interfaces
> >> Backtrace - Component timedependent, problem
> >> Backtrace - Component pylithapp
>
> This means that if you look in your .cfg file(s), you should look in the
> section
>
> pylithapp.problem.interfaces.compliant_fault
>
> If you don't have such a section "compliant_fault", because you used
> "compliant_zone", then you have identified the error. It is really that
> simple!
>
> Regards,
> Brad
>
>
>
> On 11/10/2014 12:40 PM, Charles Williams wrote:
>
>> Dear Rishabh,
>>
>> I notice that in your CFZ.cfg you have:
>>
>> [pylithapp.timedependent.interfaces.compliant_zone.eq_
>> srcs.rupture.slip_function]
>>
>> Elsewhere you refer to it as compliant_fault rather than compliant_zone.
>> Try fixing that.
>>
>> Cheers,
>> Charles
>>
>>
>> On 11/11/2014, at 1:06 am, Rishabh Dutta <rishabh.dutta at kaust.edu.sa>
>>> wrote:
>>>
>>> Dear Charles,
>>>
>>> Thanks for the quick reply.
>>>
>>> I have decided on taking one step at a time and running the problem
>>> without the fault friction. So, now I give the fault a zero slip.
>>> When I run: $ pylith pylithapp.cfg , it runs all fine. But I have the
>>> following error when I run: $ pylith CFZ.cfg
>>> Seems I have some error in the spatial database files.
>>>
>>> -------------------
>>> Traceback (most recent call last):
>>> File "/home/duttar/Desktop/softwares/pylith-2.0.3-linux-x86_64/bin/pylith",
>>> line 27, in <module>
>>> start(applicationClass=PyLithApp)
>>> File "/home/duttar/Desktop/softwares/pylith-2.0.3-linux-
>>> x86_64/lib/python2.7/site-packages/pythia-0.8.1.16-py2.
>>> 7.egg/pyre/applications/__init__.py", line 41, in start
>>> shell.run(**kwds)
>>> File "/home/duttar/Desktop/softwares/pylith-2.0.3-linux-
>>> x86_64/lib/python2.7/site-packages/pythia-0.8.1.16-py2.
>>> 7.egg/pyre/applications/Shell.py", line 125, in run
>>> app.applyConfiguration(context)
>>> File "/home/duttar/Desktop/softwares/pylith-2.0.3-linux-
>>> x86_64/lib/python2.7/site-packages/pythia-0.8.1.16-py2.
>>> 7.egg/pyre/inventory/Configurable.py", line 84, in applyConfiguration
>>> raise ValueError("%s\nBacktrace - Component %s" % (err.message,
>>> aliases))
>>> ValueError: Error while configuring spatial database reader
>>> (simpleioascii, iohandler):
>>> Filename for spatial database not specified.
>>> Backtrace - Component simpleioascii, iohandler
>>> Backtrace - Component simpledb, slip
>>> Backtrace - Component stepslipfn, slip_function
>>> Backtrace - Component eqkinsrc, rupture
>>> Backtrace - Component singlerupture, eq_srcs
>>> Backtrace - Component faultcohesivekin, compliant_fault
>>> Backtrace - Component interfaces
>>> Backtrace - Component timedependent, problem
>>> Backtrace - Component pylithapp
>>> --------------------
>>>
>>> Could this error be due to the end-points which are shared by the arrays
>>> for which I specify the boundary conditions?
>>> I am attaching all the config files and spatial database files that I
>>> use. Also, attached is a figure which shows the boundary condition that I
>>> intend to put.
>>>
>>> Thanks,
>>> Rishabh
>>>
>>> On Mon, Nov 10, 2014 at 1:40 AM, Charles Williams <willic3 at gmail.com
>>> <mailto:willic3 at gmail.com>> wrote:
>>> Dear Rishabh,
>>>
>>> This looks like a configuration problem. You must have one or more
>>> additional .cfg files, correct? It would be helpful to see those as well,
>>> and the command you are using to run PyLith.
>>>
>>> Cheers,
>>> Charles
>>>
>>>
>>> On 10/11/2014, at 5:26 am, Rishabh Dutta <rishabh.dutta at kaust.edu.sa
>>>> <mailto:rishabh.dutta at kaust.edu.sa>> wrote:
>>>>
>>>> Dear Brad et. al.,
>>>>
>>>> I am trying to run a 2D toy problem where a give a displacement field
>>>> on the boundary of the domain and try to estimate the response of a fault
>>>> with static friction. It is a compliant fault zone problem. I am using
>>>> pylith2.0.3.
>>>>
>>>> I am getting an error with the mesh reader I guess. The error comes
>>>> before the mesh is read:
>>>>
>>>> ---------------------
>>>> Traceback (most recent call last):
>>>> File "/home/duttar/Desktop/softwares/pylith-2.0.3-linux-x86_64/bin/pylith",
>>>> line 27, in <module>
>>>> start(applicationClass=PyLithApp)
>>>> File "/home/duttar/Desktop/softwares/pylith-2.0.3-linux-
>>>> x86_64/lib/python2.7/site-packages/pythia-0.8.1.16-py2.
>>>> 7.egg/pyre/applications/__init__.py", line 41, in start
>>>> shell.run(**kwds)
>>>> File "/home/duttar/Desktop/softwares/pylith-2.0.3-linux-
>>>> x86_64/lib/python2.7/site-packages/pythia-0.8.1.16-py2.
>>>> 7.egg/pyre/applications/Shell.py", line 73, in run
>>>> self.initializeConfiguration(context)
>>>> File "/home/duttar/Desktop/softwares/pylith-2.0.3-linux-
>>>> x86_64/lib/python2.7/site-packages/pythia-0.8.1.16-py2.
>>>> 7.egg/pyre/inventory/Configurable.py", line 55, in
>>>> initializeConfiguration
>>>> return self.inventory.initializeConfiguration(context)
>>>> File "/home/duttar/Desktop/softwares/pylith-2.0.3-linux-
>>>> x86_64/lib/python2.7/site-packages/pythia-0.8.1.16-py2.
>>>> 7.egg/pyre/inventory/Inventory.py", line 26, in initializeConfiguration
>>>> extraDepositories=self._priv_depositories)
>>>> File "/home/duttar/Desktop/softwares/pylith-2.0.3-linux-
>>>> x86_64/lib/python2.7/site-packages/pythia-0.8.1.16-py2.
>>>> 7.egg/pyre/inventory/odb/Curator.py", line 37, in getTraits
>>>> errorHandler=self._recordTraitLookup):
>>>> File "/home/duttar/Desktop/softwares/pylith-2.0.3-linux-
>>>> x86_64/lib/python2.7/site-packages/pythia-0.8.1.16-py2.7.egg/pyre/odb/fs/Curator.py",
>>>> line 70, in loadSymbol
>>>> shelf = codec.open(spec, 'r')
>>>> File "/home/duttar/Desktop/softwares/pylith-2.0.3-linux-
>>>> x86_64/lib/python2.7/site-packages/pythia-0.8.1.16-py2.
>>>> 7.egg/pyre/odb/fs/CodecODB.py", line 33, in open
>>>> self._decode(shelf)
>>>> File "/home/duttar/Desktop/softwares/pylith-2.0.3-linux-
>>>> x86_64/lib/python2.7/site-packages/pythia-0.8.1.16-py2.
>>>> 7.egg/pyre/inventory/cfg/CodecConfig.py", line 37, in _decode
>>>> parser.read(shelf.name <http://shelf.name/>)
>>>> File "/home/duttar/Desktop/softwares/pylith-2.0.3-linux-
>>>> x86_64/lib/python2.7/ConfigParser.py", line 305, in read
>>>> self._read(fp, filename)
>>>> File "/home/duttar/Desktop/softwares/pylith-2.0.3-linux-
>>>> x86_64/lib/python2.7/site-packages/pythia-0.8.1.16-py2.
>>>> 7.egg/pyre/inventory/cfg/Parser.py", line 98, in _read
>>>> SafeConfigParser._read(self, self._sections.fp, fpname)
>>>> File "/home/duttar/Desktop/softwares/pylith-2.0.3-linux-
>>>> x86_64/lib/python2.7/ConfigParser.py", line 493, in _read
>>>> cursect[optname].append(value)
>>>> AttributeError: 'str' object has no attribute 'append'
>>>> ----------------------------------------------------------
>>>>
>>>> I am attaching the .exo file (created in Trelis 15) and the
>>>> pylithapp.cfg file.
>>>>
>>>> Thanks,
>>>> Rishabh Dutta
>>>>
>>>> --
>>>> Rishabh Dutta,
>>>>
>>>> Ph. D. Student, Department of Earth Sciences
>>>> King Abdullah University of Science and Technology (KAUST)
>>>> Al-Khawarizmi Applied Mathematics Building (Bldg. #1) | Office Cubicle
>>>> # 3139-WS55
>>>> Mail Box 1720 | Thuwal 23955-6900 | Makkah Province | Kingdom of Saudi
>>>> Arabia
>>>>
>>>> Office Phone: +966 2 808-0351 <>
>>>> Personal Mobile No, : +966 544 700 852 <>
>>>> Email: rishabh.dutta at kaust.edu.sa <mailto:rishabh.dutta at kaust.edu.sa>
>>>> Website: http://cdi.kaust.edu.sa/Pages/Dutta.aspx <
>>>> http://cdi.kaust.edu.sa/Pages/Dutta.aspx>
>>>> This message and its contents, including attachments are intended
>>>> solely for the original recipient. If you are not the intended recipient or
>>>> have received this message in error, please notify me immediately and
>>>> delete this message from your computer system. Any unauthorized use or
>>>> distribution is prohibited. Please consider the environment before printing
>>>> this email.<pylithapp.cfg><CFZ.exo>______________________________
>>>> _________________
>>>> 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 <
>>>> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short>
>>>>
>>> Charles A. Williams
>>> Scientist
>>> GNS Science
>>> 1 Fairway Drive, Avalon
>>> PO Box 30368
>>> Lower Hutt 5040
>>> New Zealand
>>> ph (office): 0064-4570-4566
>>> fax (office): 0064-4570-4600
>>> C.Williams at gns.cri.nz <mailto:C.Williams at gns.cri.nz>
>>>
>>> _______________________________________________
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>>> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short <
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>>>
>>>
>>>
>>> --
>>> Rishabh Dutta,
>>>
>>> Ph. D. Student, Department of Earth Sciences
>>> King Abdullah University of Science and Technology (KAUST)
>>> Al-Khawarizmi Applied Mathematics Building (Bldg. #1) | Office Cubicle #
>>> 3139-WS55
>>> Mail Box 1720 | Thuwal 23955-6900 | Makkah Province | Kingdom of Saudi
>>> Arabia
>>>
>>> Office Phone: +966 2 808-0351 <>
>>> Personal Mobile No, : +966 544 700 852 <>
>>> Email: rishabh.dutta at kaust.edu.sa <mailto:rishabh.dutta at kaust.edu.sa>
>>> Website: http://cdi.kaust.edu.sa/Pages/Dutta.aspx <
>>> http://cdi.kaust.edu.sa/Pages/Dutta.aspx>
>>> This message and its contents, including attachments are intended solely
>>> for the original recipient. If you are not the intended recipient or have
>>> received this message in error, please notify me immediately and delete
>>> this message from your computer system. Any unauthorized use or
>>> distribution is prohibited. Please consider the environment before printing
>>> this email.<compliant_zone_const_elastic.spatialdb><faultslip.
>>> spatialdb><outer_const_elastic.spatialdb><sliptime.
>>> spatialdb><xneg.spatialdb><xpos.spatialdb><yneg.
>>> spatialdb><ypos.spatialdb><CFZ.cfg><pylithapp.cfg><CFZ.
>>> exo><CFZ.jou><bndycond.png>_________________________________
>>> ______________
>>> CIG-SHORT mailing list
>>> CIG-SHORT at geodynamics.org
>>> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>>>
>>
>> Charles A. Williams
>> Scientist
>> GNS Science
>> 1 Fairway Drive, Avalon
>> PO Box 30368
>> Lower Hutt 5040
>> New Zealand
>> ph (office): 0064-4570-4566
>> fax (office): 0064-4570-4600
>> C.Williams at gns.cri.nz <mailto:C.Williams at gns.cri.nz>
>>
>>
>>
>> _______________________________________________
>> 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
>
--
Rishabh Dutta,
Ph. D. Student, Department of Earth Sciences
King Abdullah University of Science and Technology (KAUST)
Al-Khawarizmi Applied Mathematics Building (Bldg. #1) | Office Cubicle #
3139-WS55
Mail Box 1720 | Thuwal 23955-6900 | Makkah Province | Kingdom of Saudi
Arabia
Office Phone: +966 2 808-0351
Personal Mobile No, : +966 544 700 852
Email: rishabh.dutta at kaust.edu.sa
Website: http://cdi.kaust.edu.sa/Pages/Dutta.aspx
--
------------------------------
This message and its contents, including attachments are intended solely
for the original recipient. If you are not the intended recipient or have
received this message in error, please notify me immediately and delete
this message from your computer system. Any unauthorized use or
distribution is prohibited. Please consider the environment before printing
this email.
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