[aspect-devel] Error on a depth dependent material model
Eleonora Ficini
eleonora.ficini at uniroma1.it
Thu May 10 22:28:29 PDT 2018
Dear all,
sorry Wolfgang, you are right! I didn't copy/paste the backtrace because it
was similar to what I got from running gdb and I didn't what to repeat
useless messages in the mailing list :) However, the bt I got was very
different from what John (by the way, thank you for the work you've done!) got.
Below you can find my bt copy/pasted. However I am sure this is related to
the fact that it is my first time with gdb and I am not really familiar
with it! Sorry :(
Thank you all for your support!
All the best,
Eleonora
(gdb) exec-file aspect
(gdb) run depth-dependent_test.prm
Starting program: /home/aspect/aspect/aspect depth-dependent_test.prm
[Thread debugging using libthread_db enabled]
Using host libthread_db library "/lib/x86_64-linux-gnu/libthread_db.so.1".
[New Thread 0x7fffcde85700 (LWP 31486)]
------------------------------------------------------------
-----------------
-- This is ASPECT, the Advanced Solver for Problems in Earth's ConvecTion.
-- . version 2.0.0-pre (master, 38f3849)
-- . using deal.II 8.5.1
-- . using Trilinos 12.10.1
-- . using p4est 2.0.0
-- . running in DEBUG mode
-- . running with 1 MPI process
------------------------------------------------------------
-----------------
Setting up GPlates boundary velocity plugin.
Input point 1 spherical coordinates: 1.571 4.870
Input point 1 normalized cartesian coordinates: 0.157 -0.988 -0.000
Input point 1 rotated model coordinates: 0.157 -0.988 -0.000
Input point 2 spherical coordinates: 1.571 5.240
Input point 2 normalized cartesian coordinates: 0.503 -0.864 -0.000
Input point 2 rotated model coordinates: 0.503 -0.864 -0.000
Model will be rotated by -0.00 degrees around axis 0.00 0.00 1.00
The ParaView rotation angles are: 0.00 -0.00 0.00
The inverse ParaView rotation angles are: 0.00 -0.00 0.00
Loading GPlates data boundary file /home/aspect/aspect/data/bound
ary-velocity/gplates/current_day.gpml.
Loading new velocity file did not succeed.
Assuming constant boundary conditions for rest of model run.
Number of active cells: 12,288 (on 6 levels)
Number of degrees of freedom: 162,432 (99,840+12,672+49,920)
Thread 1 "aspect" received signal SIGSEGV, Segmentation fault.
0x0000000000be5756 in ?? ()
(gdb) bt
#0 0x0000000000be5756 in ?? ()
#1 0x0000000001cddee0 in ?? ()
#2 0x0000000000be6a37 in ?? ()
#3 0x00000000000003dc in ?? ()
#4 0x0000000000d1cad1 in ?? ()
#5 0x0000000000000018 in ?? ()
#6 0x0000000001cddf60 in ?? ()
#7 0x00007fffffff9010 in ?? ()
#8 0x0000000000000000 in ?? ()
2018-05-10 22:29 GMT+02:00 <aspect-devel-request at geodynamics.org>:
> Send Aspect-devel mailing list submissions to
> aspect-devel at geodynamics.org
>
> To subscribe or unsubscribe via the World Wide Web, visit
> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel
> or, via email, send a message with subject or body 'help' to
> aspect-devel-request at geodynamics.org
>
> You can reach the person managing the list at
> aspect-devel-owner at geodynamics.org
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Aspect-devel digest..."
>
>
> Today's Topics:
>
> 1. Re: Error on a depth dependent material model (John Naliboff)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 10 May 2018 13:28:03 -0700
> From: John Naliboff <jbnaliboff at ucdavis.edu>
> To: aspect-devel at geodynamics.org
> Subject: Re: [aspect-devel] Error on a depth dependent material model
> Message-ID: <7e31ed96-8567-b4b6-bd8a-8ea092218742 at ucdavis.edu>
> Content-Type: text/plain; charset="utf-8"; Format="flowed"
>
> Hi all,
>
> I modified one of the burman tests (burnman_test.prm, uses Ascii
> reference profile material model) to use the depth dependent material
> model functionality (see attached). Even without depth-dependence
> enabled, this results in a segmentation fault. Eleonora - I ran your
> files and got the same error.
>
> The stack trace from gdb is at the base of the email. I need to get
> setup for the webinar, so without going into too much detail it looks
> there is an issue reading in data values from an ascii file when the
> depth_dependent functionality is enabled (see strack frames 1-3). I'll
> have a chance to look at this in more detail later in the afternoon.
>
> Eleonora - good find, this appears to be a bug. However, I'm still not
> sure why your output did not show a stacktrace either in gdb or running
> through a terminal in debug mode.
>
> Cheers,
> John
>
> *-----------------------------------------------------------
> ------------------**
> **-- This is ASPECT, the Advanced Solver for Problems in Earth's
> ConvecTion.**
> **-- . version 2.0.0-pre (master, b720dae)**
> **-- . using deal.II 8.5.1 (v8.5.1, 0e5d7e8)**
> **-- . using Trilinos 12.10.1**
> **-- . using p4est 1.1.0**
> **-- . running in DEBUG mode**
> **-- . running with 1 MPI process**
> **----------------------------------------------------------
> -------------------**
> **
> **
> ** Setting up GPlates boundary velocity plugin.**
> **
> ** Input point 1 spherical coordinates: 1.571 4.870**
> ** Input point 1 normalized cartesian coordinates: 0.157 -0.988 -0.000**
> ** Input point 1 rotated model coordinates: 0.157 -0.988 -0.000**
> ** Input point 2 spherical coordinates: 1.571 5.240**
> ** Input point 2 normalized cartesian coordinates: 0.503 -0.864 -0.000**
> ** Input point 2 rotated model coordinates: 0.503 -0.864 -0.000**
> **
> ** Model will be rotated by -0.00 degrees around axis 0.00 0.00 1.00**
> ** The ParaView rotation angles are: 0.00 -0.00 0.00**
> ** The inverse ParaView rotation angles are: 0.00 -0.00 0.00**
> **
> ** Loading GPlates data boundary file
> /data1/Software/aspect/master/aspect/data/boundary-velocity/
> gplates/current_day.gpml.**
> **
> **
> ** Loading new velocity file did not succeed.**
> ** Assuming constant boundary conditions for rest of model run.**
> **
> **Number of active cells: 192 (on 3 levels)**
> **Number of degrees of freedom: 2,832 (1,728+240+864)**
> **
> **
> **Thread 1 "aspect" received signal SIGSEGV, Segmentation fault.**
> **0x0000000000861062 in std::vector<dealii::Function<1, double>*,
> std::allocator<dealii::Function<1, double>*> >::operator[]
> (__n=<optimized out>, this=0x20) at
> /usr/include/c++/5/bits/stl_vector.h:795**
> **795 { return *(this->_M_impl._M_start + __n); }**
> **(gdb) bt**
> **#0 0x0000000000861062 in std::vector<dealii::Function<1, double>*,
> std::allocator<dealii::Function<1, double>*> >::operator[]
> (__n=<optimized out>, this=0x20) at
> /usr/include/c++/5/bits/stl_vector.h:795**
> **#1 aspect::Utilities::AsciiDataLookup<1>::get_data (this=0x0,
> position=..., component=<optimized out>)**
> ** at /data1/Software/aspect/master/aspect/source/utilities.cc:1459**
> **#2 0x000000000086233d in
> aspect::Utilities::AsciiDataProfile<2>::get_data_component (**
> ** this=this at entry=0x1c154b0, position=..., component=<optimized
> out>)**
> ** at /data1/Software/aspect/master/aspect/source/utilities.cc:2110**
> **#3 0x0000000000ab27e1 in
> aspect::MaterialModel::AsciiReferenceProfile<2>::evaluate
> (this=0x1c15430, in=..., **
> ** out=...) at
> /data1/Software/aspect/master/aspect/source/material_model/a
> scii_reference_profile.cc:93**
> **#4 0x0000000000a8b5fa in
> aspect::MaterialModel::DepthDependent<2>::evaluate (this=0x1c0a9d0,
> in=..., out=...)**
> ** at
> /data1/Software/aspect/master/aspect/source/material_model/d
> epth_dependent.cc:134**
> **#5 0x00000000009b44f6 in
> aspect::InitialTemperature::Adiabatic<2>::initial_temperature
> (this=0x1c17d70, **
> ** position=...) at
> /data1/Software/aspect/master/aspect/source/initial_temperat
> ure/adiabatic.cc:90**
> **#6 0x00000000009a76e8 in
> aspect::InitialTemperature::Manager<2>::initial_temperature
> (this=0x7fffffffbcb0, **
> ** position=...) at
> /data1/Software/aspect/master/aspect/source/initial_temperat
> ure/interface.cc:160**
> **#7 0x0000000000aec0c2 in std::_Mem_fn_base<double
> (aspect::InitialTemperature::Manager<2>::*)(dealii::Point<2, double>
> const&) const, true>::operator()<dealii::Point<2, double> const&, void>
> (__object=..., **
> ** this=0x1c72410) at /usr/include/c++/5/functional:583**
> **#8 std::_Bind<std::_Mem_fn<double
> (aspect::InitialTemperature::Manager<2>::*)(dealii::Point<2, double>
> const&) const>
> (std::reference_wrapper<aspect::InitialTemperature::Manager<2> >,
> std::_Placeholder<1>)>::__call<double, dealii::Point<2, double> const&,
> 0ul, 1ul>(std::tuple<dealii::Point<2, double> const&>&&,
> std::_Index_tuple<0ul, 1ul>) (__args=<unknown type in
> /data1/Software/aspect/master/aspect/aspect, CU 0x2e433f5, DIE
> 0x2f641dc>, **
> ** this=0x1c72410) at /usr/include/c++/5/functional:1074**
> **#9 std::_Bind<std::_Mem_fn<double
> (aspect::InitialTemperature::Manager<2>::*)(dealii::Point<2, double>
> const&) const>
> (std::reference_wrapper<aspect::InitialTemperature::Manager<2> >,
> std::_Placeholder<1>)>::operator()<dealii::Point<2, double> const&,
> double>(dealii::Point<2, double> const&) (this=0x1c72410)**
> ** at /usr/include/c++/5/functional:1133**
> **#10 std::_Function_handler<double (dealii::Point<2, double> const&),
> std::_Bind<std::_Mem_fn<double
> (aspect::InitialTemperature::Manager<2>::*)(dealii::Point<2, double>
> const&) const>
> (std::reference_wrapper<aspect::InitialTemperature::Manager<2> >,
> std::_Placeholder<1>)> >::_M_invoke(std::_Any_data const&,
> dealii::Point<2, double> const&) (__functor=..., __args#0=...) at
> /usr/include/c++/5/functional:1857**
> **#11 0x00007ffff4e35609 in std::function<double (dealii::Point<2,
> double> const&)>::operator()(dealii::Point<2, double> const&) const
> (this=this at entry=0x7fffffff9dc0, __args#0=...) at
> /usr/include/c++/5/functional:2267**
> **#12 0x00007ffff4e3589d in
> dealii::VectorFunctionFromScalarFunctionObject<2, double>::vector_value
> (**
> ** this=<optimized out>, p=..., values=...)**
> ** at
> /data1/Software/dealii/v8.5.1/dealii/include/deal.II/base/fu
> nction.templates.h:708**
> **#13 0x00007ffff4e13c49 in dealii::Function<2,
> double>::vector_value_list (this=0x7fffffff9d60, **
> ** points=std::vector of length 9, capacity 9 = {...},
> values=std::vector of length 9, capacity 9 = {...})**
> ** at
> /data1/Software/dealii/v8.5.1/dealii/include/deal.II/base/fu
> nction.templates.h:107**
> **#14 0x00007ffff1fdc570 in dealii::VectorTools::interpolate<2, 2,
> dealii::TrilinosWrappers::MPI::BlockVector, dealii::DoFHandler>
> (mapping=..., dof=..., function=..., vec=..., component_mask=...)**
> ** at
> /data1/Software/dealii/v8.5.1/dealii/include/deal.II/numeric
> s/vector_tools.templates.h:255**
> **#15 0x0000000000aec6dd in
> aspect::Simulator<2>::set_initial_temperature_and_compositional_fields (**
> ** this=this at entry=0x7fffffffad80)**
> ** at
> /data1/Software/aspect/master/aspect/source/simulator/initia
> l_conditions.cc:117**
> **#16 0x0000000000bae2d2 in aspect::Simulator<2>::run
> (this=this at entry=0x7fffffffad80)**
> ** at
> /data1/Software/aspect/master/aspect/source/simulator/core.cc:1601**
> **#17 0x00000000009c9d74 in run_simulator<2> (**
> ** input_as_string="# A test using adiabatic conditions and a gravity
> \n# profile generated by a mineral physics toolkit and read in\n#
> through an ascii data file. In this example, material properties\n# are
> based on a Birc"..., output_xml=output_xml at entry=false,
> output_plugin_graph=output_plugin_graph at entry=false)**
> ** at /data1/Software/aspect/master/aspect/source/main.cc:519**
> **#18 0x00000000009c9554 in main (argc=2, argv=0x7fffffffd778)**
> **---Type <return> to continue, or q <return> to quit---**
> ** at /data1/Software/aspect/master/aspect/source/main.cc:666**
> **(gdb) *
>
> On 05/10/2018 02:28 AM, Wolfgang Bangerth wrote:
> > On 05/10/2018 04:09 PM, Eleonora Ficini wrote:
> >> I did a backtrace but I didn't get any further info about where the
> >> error could be.
> >> I also tried to run the code with 1 process but nothing new happened.
> >
> > Eleonore -- I'm sure we all would love to help you more, but you're
> > not making it easy for us :-)
> >
> > When you say "didn't get any further info", what exactly did you get?
> > What did the backtrace show?
> >
> > Other than that, we can really only speculate. Without a backtrace, or
> > alternatively a way for us to reproduce the error, there is really not
> > very much any of us can help :-(
> >
> > Best
> > Wolfgang
> >
>
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: <http://lists.geodynamics.org/pipermail/aspect-devel/attachm
> ents/20180510/09307b04/attachment.html>
> -------------- next part --------------
> # A test using adiabatic conditions and a gravity
> # profile generated by a mineral physics toolkit and read in
> # through an ascii data file. In this example, material properties
> # are based on a Birch-Murnaghan equation of state.
>
> set Dimension = 2
> set Use years in output instead of seconds = true
> set End time = 1e6
>
>
> subsection Material model
> set Model name = depth dependent
>
> subsection Depth dependent model
> set Base model = ascii reference profile
> set Depth dependence method = None
> end
>
> subsection Ascii reference profile
> set Thermal viscosity exponent = 0
> set Viscosity prefactors = 1.0, 1.0, 1.0, 1.0
> subsection Ascii data model
> set Data file name = example_isentrope.txt
> set Data directory = $ASPECT_SOURCE_DIR/data/adiaba
> tic-conditions/ascii-data/
> end
> end
>
> set Material averaging = harmonic average
> end
>
> # The geometry is a spherical shell with the inner and
> # outer radius of the Earth's mantle.
> subsection Geometry model
> set Model name = spherical shell
>
> subsection Spherical shell
> set Inner radius = 3481000
> set Outer radius = 6336000
> end
> end
>
> subsection Adiabatic conditions model
> set Model name = ascii data
>
> subsection Ascii data model
> set Data directory = $ASPECT_SOURCE_DIR/data/adiaba
> tic-conditions/ascii-data/
> set Data file name = example_isentrope.txt
> end
> end
>
>
> # The gravity model reads an ascii data file that contains a gravity
> # profile consistent with the material properties computed using the
> # Birch-Murnaghan equation of state. It automatically uses the same file
> # specified in the adiabatic conditions model.
> subsection Gravity model
> set Model name = ascii data
> subsection Ascii data model
> set Data directory = $ASPECT_SOURCE_DIR/data/adiaba
> tic-conditions/ascii-data/
> set Data file name = example_isentrope.txt
> end
> end
>
> # The model uses the anelastic liquid approximation.
> subsection Formulation
> set Formulation = anelastic liquid approximation
> end
>
> # The present-day plate velocities are imposed on the upper model
> # boundary.
> # The parameters below this comment were created by the update script
> # as replacement for the old 'Model settings' subsection. They can be
> # safely merged with any existing subsections with the same name.
>
> subsection Boundary velocity model
> set Prescribed velocity boundary indicators = outer:gplates
> end
>
> subsection Boundary velocity model
> set Tangential velocity boundary indicators = inner
> end
>
> subsection Boundary temperature model
> set Fixed temperature boundary indicators = inner, outer
> end
>
>
> subsection Boundary velocity model
> subsection GPlates model
> set Data directory = $ASPECT_SOURCE_DIR/data/bounda
> ry-velocity/gplates/
> set Velocity file name = current_day.gpml
> set Data file time step = 1e6
> set Point one = 1.5708,4.87
> set Point two = 1.5708,5.24
> end
> end
>
>
> subsection Boundary temperature model
> set List of model names = spherical constant
> subsection Spherical constant
> set Inner temperature = 3500
> set Outer temperature = 273
> end
> end
>
> # The initial temperature is an adiabatic profile, which is
> # taken from the adabatic conditions model. In this case, this is
> # is the ascii data model that loads a file containing profiles
> # corresponding to the Birch-Murnaghan equation of state.
> # In addition to the adiabatic profile, there are thermal boundary
> # layers at the sirface and the core-mantle boundary.
> subsection Initial temperature model
> set Model name = adiabatic
>
> subsection Adiabatic
> set Age top boundary layer = 5e7
> end
> end
>
>
> subsection Mesh refinement
> set Refinement fraction = 0.4
> set Coarsening fraction = 0.05
> set Initial adaptive refinement = 1
> set Initial global refinement = 2
> set Strategy = temperature
> set Time steps between mesh refinement = 5
> end
>
>
> subsection Heating model
> set List of model names = adiabatic heating, shear heating
>
> subsection Adiabatic heating
> set Use simplified adiabatic heating = true
> end
> end
>
> subsection Postprocess
> set List of postprocessors = velocity statistics, temperature
> statistics, heat flux statistics, depth average
>
> subsection Depth average
> set Time between graphical output = 1e6
> end
> end
>
> ------------------------------
>
> Subject: Digest Footer
>
> _______________________________________________
> Aspect-devel mailing list
> Aspect-devel at geodynamics.org
> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel
>
> ------------------------------
>
> End of Aspect-devel Digest, Vol 78, Issue 24
> ********************************************
>
--
Eleonora Ficini, PhD student
Department of Earth Sciences
Sapienza University of Rome
P.le A. Moro, 5 - 00185, Rome, Italy
--
___________________________________________
*Il tuo 5 diventa 1000*
Fai
crescere la tua università
Dona il 5 per mille alla Sapienza
Codice
fiscale: *80209930587*
https://www.uniroma1.it/it/pagina/fai-crescere-la-tua-universita-con-il-cinque-mille
<https://www.uniroma1.it/it/pagina/fai-crescere-la-tua-universita-con-il-cinque-mille>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.geodynamics.org/pipermail/aspect-devel/attachments/20180511/b57dc378/attachment-0001.html>
More information about the Aspect-devel
mailing list