From c.thieulot at uu.nl  Wed Nov  2 05:25:50 2016
From: c.thieulot at uu.nl (Thieulot, C.A.P. (Cedric))
Date: Wed, 2 Nov 2016 12:25:50 +0000
Subject: [aspect-devel] Q2P-1 question
Message-ID: <6DCDF056-77D8-4A7F-949F-DE4033EC20C9@uu.nl>

Hi all,

I was reading on the Q2P-1 element recently when I came across the literature about the mapping of the pressure (e.g. Finite element approximation on quadrilateral meshes,
Arnold et al, Commun. Numer. Meth. Engng 2001; 17:805–812 (DOI: 10.1002/cnm.450) ). To summarize it I rereby attach a slide from a presentation of Arnold.
I was then wondering which option is implemented in ASPECT ?

Cedric.





[cid:EDFD84B3-8088-4F01-AED2-814331D4F09D at geo.uu.nl]
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From lev.karatun at gmail.com  Wed Nov  2 06:45:24 2016
From: lev.karatun at gmail.com (Lev Karatun)
Date: Wed, 2 Nov 2016 09:45:24 -0400
Subject: [aspect-devel] compilation error
Message-ID: <CAPGyz26PLEocxz9UVakPWYQOej=9YAe=ZaUyzmMY-bJtWd35gA@mail.gmail.com>

Hi,

I was trying to update Aspect to the latest version and got the following
error:

[  0%] Building CXX object CMakeFiles/aspect.dir/source/simulator/core.cc.o
In file included from
/home/lev/aspect/aspect_debug/include/aspect/simulator.h:30,
                 from
/home/lev/aspect/aspect_debug/source/simulator/core.cc:22:
/home/lev/aspect/dealii_debug/include/deal.II/lac/trilinos_block_vector.h:
In member function ‘void std::vector<_Tp, _Alloc>::resize(size_t, _Tp)
[with _Tp = dealii::TrilinosWrappers::Vector, _Alloc =
std::allocator<dealii::TrilinosWrappers::Vector>]’:
/home/lev/aspect/dealii_debug/include/deal.II/lac/trilinos_block_vector.h:399:
warning: ‘dealii::TrilinosWrappers::Vector::Vector()’ is deprecated
(declared at
/home/lev/aspect/dealii_debug/include/deal.II/lac/trilinos_vector.h:770)
In file included from /home/lev/aspect/trilinos/include/Amesos.h:34,
                 from
/home/lev/aspect/dealii_debug/include/deal.II/lac/trilinos_solver.h:34,
                 from
/home/lev/aspect/dealii_debug/include/deal.II/lac/generic_linear_algebra.h:143,
                 from
/home/lev/aspect/aspect_debug/include/aspect/global.h:35,
                 from
/home/lev/aspect/aspect_debug/include/aspect/simulator.h:42,
                 from
/home/lev/aspect/aspect_debug/source/simulator/core.cc:22:
/home/lev/aspect/trilinos/include/Amesos_BaseSolver.h: At global scope:
/home/lev/aspect/trilinos/include/Amesos_BaseSolver.h:410: warning: unused
parameter ‘paramList’
/home/lev/aspect/trilinos/include/Amesos_BaseSolver.h:432: warning: unused
parameter ‘TimingParameterList’
In file included from
/home/lev/aspect/dealii_debug/include/deal.II/base/parameter_handler.h:24,
                 from
/home/lev/aspect/aspect_debug/include/aspect/simulator.h:26,
                 from
/home/lev/aspect/aspect_debug/source/simulator/core.cc:22:
/home/lev/aspect/dealii_debug/include/deal.II/bundled/boost/smart_ptr/scoped_ptr.hpp:
In copy constructor ‘dealii::std_cxx11::unique_ptr<dealii::Mapping<2, 2>
>::unique_ptr(const dealii::std_cxx11::unique_ptr<dealii::Mapping<2, 2>
>&)’:
/home/lev/aspect/dealii_debug/include/deal.II/base/std_cxx11/unique_ptr.h:60:
  instantiated from
‘aspect::Simulator<dim>::Simulator(ompi_communicator_t*,
dealii::ParameterHandler&) [with int dim = 2]’
/home/lev/aspect/aspect_debug/source/simulator/core.cc:2471:   instantiated
from here
/home/lev/aspect/dealii_debug/include/deal.II/bundled/boost/smart_ptr/scoped_ptr.hpp:47:
error: ‘boost::scoped_ptr<T>::scoped_ptr(const boost::scoped_ptr<T>&) [with
T = dealii::Mapping<2, 2>]’ is private
/home/lev/aspect/dealii_debug/include/deal.II/base/std_cxx11/unique_ptr.h:60:
error: within this context
/home/lev/aspect/aspect_debug/source/simulator/core.cc: In constructor
‘aspect::Simulator<dim>::Simulator(ompi_communicator_t*,
dealii::ParameterHandler&) [with int dim = 2]’:
/home/lev/aspect/aspect_debug/source/simulator/core.cc:2471:   instantiated
from here
/home/lev/aspect/aspect_debug/source/simulator/core.cc:218: note:
synthesized method ‘dealii::std_cxx11::unique_ptr<dealii::Mapping<2, 2>
>::unique_ptr(const dealii::std_cxx11::unique_ptr<dealii::Mapping<2, 2>
>&)’ first required here
In file included from
/home/lev/aspect/dealii_debug/include/deal.II/base/parameter_handler.h:24,
                 from
/home/lev/aspect/aspect_debug/include/aspect/simulator.h:26,
                 from
/home/lev/aspect/aspect_debug/source/simulator/core.cc:22:
/home/lev/aspect/dealii_debug/include/deal.II/bundled/boost/smart_ptr/scoped_ptr.hpp:
In copy constructor ‘dealii::std_cxx11::unique_ptr<dealii::Mapping<3, 3>
>::unique_ptr(const dealii::std_cxx11::unique_ptr<dealii::Mapping<3, 3>
>&)’:
/home/lev/aspect/dealii_debug/include/deal.II/base/std_cxx11/unique_ptr.h:60:
  instantiated from
‘aspect::Simulator<dim>::Simulator(ompi_communicator_t*,
dealii::ParameterHandler&) [with int dim = 3]’
/home/lev/aspect/aspect_debug/source/simulator/core.cc:2471:   instantiated
from here
/home/lev/aspect/dealii_debug/include/deal.II/bundled/boost/smart_ptr/scoped_ptr.hpp:47:
error: ‘boost::scoped_ptr<T>::scoped_ptr(const boost::scoped_ptr<T>&) [with
T = dealii::Mapping<3, 3>]’ is private
/home/lev/aspect/dealii_debug/include/deal.II/base/std_cxx11/unique_ptr.h:60:
error: within this context
/home/lev/aspect/aspect_debug/source/simulator/core.cc: In constructor
‘aspect::Simulator<dim>::Simulator(ompi_communicator_t*,
dealii::ParameterHandler&) [with int dim = 3]’:
/home/lev/aspect/aspect_debug/source/simulator/core.cc:2471:   instantiated
from here
/home/lev/aspect/aspect_debug/source/simulator/core.cc:218: note:
synthesized method ‘dealii::std_cxx11::unique_ptr<dealii::Mapping<3, 3>
>::unique_ptr(const dealii::std_cxx11::unique_ptr<dealii::Mapping<3, 3>
>&)’ first required here
/home/lev/aspect/dealii_debug/include/deal.II/bundled/boost/system/error_code.hpp:
At global scope:
/home/lev/aspect/dealii_debug/include/deal.II/bundled/boost/system/error_code.hpp:221:
warning: ‘boost::system::posix_category’ defined but not used
/home/lev/aspect/dealii_debug/include/deal.II/bundled/boost/system/error_code.hpp:222:
warning: ‘boost::system::errno_ecat’ defined but not used
/home/lev/aspect/dealii_debug/include/deal.II/bundled/boost/system/error_code.hpp:223:
warning: ‘boost::system::native_ecat’ defined but not used
make[2]: *** [CMakeFiles/aspect.dir/source/simulator/core.cc.o] Error 1
make[1]: *** [CMakeFiles/aspect.dir/all] Error 2
make: *** [all] Error 2

Tips on how to solve it would be appreciated.

Best regards,
Lev Karatun.
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From jbnaliboff at ucdavis.edu  Wed Nov  2 09:00:03 2016
From: jbnaliboff at ucdavis.edu (John Naliboff)
Date: Wed, 2 Nov 2016 09:00:03 -0700
Subject: [aspect-devel] compilation error
In-Reply-To: <CAPGyz26PLEocxz9UVakPWYQOej=9YAe=ZaUyzmMY-bJtWd35gA@mail.gmail.com>
References: <CAPGyz26PLEocxz9UVakPWYQOej=9YAe=ZaUyzmMY-bJtWd35gA@mail.gmail.com>
Message-ID: <5a8fdc94-a0e6-b869-7f6c-c7ae88654b4c@ucdavis.edu>

Hi Lev,

What Trilinos and dealii version are you using?  If you are using the 
development version of dealii, when was the last update? Also, did you 
do 'make distclean' before reconfiguring and compiling ASPECT?  I'm not 
sure what the error below is related to, but the aforementioned 
information is always helpful when debugging an installation issue.

Cheers,
John

*************************************************
John Naliboff
Assistant Project Scientist, CIG
Earth & Planetary Sciences Dept., UC Davis

On 11/02/2016 06:45 AM, Lev Karatun wrote:
> Hi,
>
> I was trying to update Aspect to the latest version and got the 
> following error:
>
> [  0%] Building CXX object 
> CMakeFiles/aspect.dir/source/simulator/core.cc.o
> In file included from 
> /home/lev/aspect/aspect_debug/include/aspect/simulator.h:30,
>                  from 
> /home/lev/aspect/aspect_debug/source/simulator/core.cc:22:
> /home/lev/aspect/dealii_debug/include/deal.II/lac/trilinos_block_vector.h: 
> In member function ‘void std::vector<_Tp, _Alloc>::resize(size_t, _Tp) 
> [with _Tp = dealii::TrilinosWrappers::Vector, _Alloc = 
> std::allocator<dealii::TrilinosWrappers::Vector>]’:
> /home/lev/aspect/dealii_debug/include/deal.II/lac/trilinos_block_vector.h:399: 
> warning: ‘dealii::TrilinosWrappers::Vector::Vector()’ is deprecated 
> (declared at 
> /home/lev/aspect/dealii_debug/include/deal.II/lac/trilinos_vector.h:770)
> In file included from /home/lev/aspect/trilinos/include/Amesos.h:34,
>                  from 
> /home/lev/aspect/dealii_debug/include/deal.II/lac/trilinos_solver.h:34,
>                  from 
> /home/lev/aspect/dealii_debug/include/deal.II/lac/generic_linear_algebra.h:143,
>                  from 
> /home/lev/aspect/aspect_debug/include/aspect/global.h:35,
>                  from 
> /home/lev/aspect/aspect_debug/include/aspect/simulator.h:42,
>                  from 
> /home/lev/aspect/aspect_debug/source/simulator/core.cc:22:
> /home/lev/aspect/trilinos/include/Amesos_BaseSolver.h: At global scope:
> /home/lev/aspect/trilinos/include/Amesos_BaseSolver.h:410: warning: 
> unused parameter ‘paramList’
> /home/lev/aspect/trilinos/include/Amesos_BaseSolver.h:432: warning: 
> unused parameter ‘TimingParameterList’
> In file included from 
> /home/lev/aspect/dealii_debug/include/deal.II/base/parameter_handler.h:24,
>                  from 
> /home/lev/aspect/aspect_debug/include/aspect/simulator.h:26,
>                  from 
> /home/lev/aspect/aspect_debug/source/simulator/core.cc:22:
> /home/lev/aspect/dealii_debug/include/deal.II/bundled/boost/smart_ptr/scoped_ptr.hpp: 
> In copy constructor ‘dealii::std_cxx11::unique_ptr<dealii::Mapping<2, 
> 2> >::unique_ptr(const 
> dealii::std_cxx11::unique_ptr<dealii::Mapping<2, 2> >&)’:
> /home/lev/aspect/dealii_debug/include/deal.II/base/std_cxx11/unique_ptr.h:60: 
>   instantiated from 
> ‘aspect::Simulator<dim>::Simulator(ompi_communicator_t*, 
> dealii::ParameterHandler&) [with int dim = 2]’
> /home/lev/aspect/aspect_debug/source/simulator/core.cc:2471:   
> instantiated from here
> /home/lev/aspect/dealii_debug/include/deal.II/bundled/boost/smart_ptr/scoped_ptr.hpp:47: 
> error: ‘boost::scoped_ptr<T>::scoped_ptr(const boost::scoped_ptr<T>&) 
> [with T = dealii::Mapping<2, 2>]’ is private
> /home/lev/aspect/dealii_debug/include/deal.II/base/std_cxx11/unique_ptr.h:60: 
> error: within this context
> /home/lev/aspect/aspect_debug/source/simulator/core.cc: In constructor 
> ‘aspect::Simulator<dim>::Simulator(ompi_communicator_t*, 
> dealii::ParameterHandler&) [with int dim = 2]’:
> /home/lev/aspect/aspect_debug/source/simulator/core.cc:2471:   
> instantiated from here
> /home/lev/aspect/aspect_debug/source/simulator/core.cc:218: note: 
> synthesized method ‘dealii::std_cxx11::unique_ptr<dealii::Mapping<2, 
> 2> >::unique_ptr(const 
> dealii::std_cxx11::unique_ptr<dealii::Mapping<2, 2> >&)’ first 
> required here
> In file included from 
> /home/lev/aspect/dealii_debug/include/deal.II/base/parameter_handler.h:24,
>                  from 
> /home/lev/aspect/aspect_debug/include/aspect/simulator.h:26,
>                  from 
> /home/lev/aspect/aspect_debug/source/simulator/core.cc:22:
> /home/lev/aspect/dealii_debug/include/deal.II/bundled/boost/smart_ptr/scoped_ptr.hpp: 
> In copy constructor ‘dealii::std_cxx11::unique_ptr<dealii::Mapping<3, 
> 3> >::unique_ptr(const 
> dealii::std_cxx11::unique_ptr<dealii::Mapping<3, 3> >&)’:
> /home/lev/aspect/dealii_debug/include/deal.II/base/std_cxx11/unique_ptr.h:60: 
>   instantiated from 
> ‘aspect::Simulator<dim>::Simulator(ompi_communicator_t*, 
> dealii::ParameterHandler&) [with int dim = 3]’
> /home/lev/aspect/aspect_debug/source/simulator/core.cc:2471:   
> instantiated from here
> /home/lev/aspect/dealii_debug/include/deal.II/bundled/boost/smart_ptr/scoped_ptr.hpp:47: 
> error: ‘boost::scoped_ptr<T>::scoped_ptr(const boost::scoped_ptr<T>&) 
> [with T = dealii::Mapping<3, 3>]’ is private
> /home/lev/aspect/dealii_debug/include/deal.II/base/std_cxx11/unique_ptr.h:60: 
> error: within this context
> /home/lev/aspect/aspect_debug/source/simulator/core.cc: In constructor 
> ‘aspect::Simulator<dim>::Simulator(ompi_communicator_t*, 
> dealii::ParameterHandler&) [with int dim = 3]’:
> /home/lev/aspect/aspect_debug/source/simulator/core.cc:2471:   
> instantiated from here
> /home/lev/aspect/aspect_debug/source/simulator/core.cc:218: note: 
> synthesized method ‘dealii::std_cxx11::unique_ptr<dealii::Mapping<3, 
> 3> >::unique_ptr(const 
> dealii::std_cxx11::unique_ptr<dealii::Mapping<3, 3> >&)’ first 
> required here
> /home/lev/aspect/dealii_debug/include/deal.II/bundled/boost/system/error_code.hpp: 
> At global scope:
> /home/lev/aspect/dealii_debug/include/deal.II/bundled/boost/system/error_code.hpp:221: 
> warning: ‘boost::system::posix_category’ defined but not used
> /home/lev/aspect/dealii_debug/include/deal.II/bundled/boost/system/error_code.hpp:222: 
> warning: ‘boost::system::errno_ecat’ defined but not used
> /home/lev/aspect/dealii_debug/include/deal.II/bundled/boost/system/error_code.hpp:223: 
> warning: ‘boost::system::native_ecat’ defined but not used
> make[2]: *** [CMakeFiles/aspect.dir/source/simulator/core.cc.o] Error 1
> make[1]: *** [CMakeFiles/aspect.dir/all] Error 2
> make: *** [all] Error 2
>
> Tips on how to solve it would be appreciated.
>
> Best regards,
> Lev Karatun.
>
>
> _______________________________________________
> Aspect-devel mailing list
> Aspect-devel at geodynamics.org
> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel

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From heister at clemson.edu  Wed Nov  2 09:34:19 2016
From: heister at clemson.edu (Timo Heister)
Date: Wed, 2 Nov 2016 12:34:19 -0400
Subject: [aspect-devel] compilation error
In-Reply-To: <5a8fdc94-a0e6-b869-7f6c-c7ae88654b4c@ucdavis.edu>
References: <CAPGyz26PLEocxz9UVakPWYQOej=9YAe=ZaUyzmMY-bJtWd35gA@mail.gmail.com>
 <5a8fdc94-a0e6-b869-7f6c-c7ae88654b4c@ucdavis.edu>
Message-ID: <CAMRj59H-Awq9XF0wYct=iaKEYaRHH2+d3F+sRkaFAVCAjiUkRA@mail.gmail.com>

Can you please post your detailed.log from your deal.II build
directory? That will show us what compiler/settings you are using.

On Wed, Nov 2, 2016 at 12:00 PM, John Naliboff <jbnaliboff at ucdavis.edu> wrote:
> Hi Lev,
>
> What Trilinos and dealii version are you using?  If you are using the
> development version of dealii, when was the last update?  Also, did you do
> 'make distclean' before reconfiguring and compiling ASPECT?  I'm not sure
> what the error below is related to, but the aforementioned information is
> always helpful when debugging an installation issue.
>
> Cheers,
> John
>
>
> *************************************************
> John Naliboff
> Assistant Project Scientist, CIG
> Earth & Planetary Sciences Dept., UC Davis
>
> On 11/02/2016 06:45 AM, Lev Karatun wrote:
>
> Hi,
>
> I was trying to update Aspect to the latest version and got the following
> error:
>
> [  0%] Building CXX object CMakeFiles/aspect.dir/source/simulator/core.cc.o
> In file included from
> /home/lev/aspect/aspect_debug/include/aspect/simulator.h:30,
>                  from
> /home/lev/aspect/aspect_debug/source/simulator/core.cc:22:
> /home/lev/aspect/dealii_debug/include/deal.II/lac/trilinos_block_vector.h:
> In member function ‘void std::vector<_Tp, _Alloc>::resize(size_t, _Tp) [with
> _Tp = dealii::TrilinosWrappers::Vector, _Alloc =
> std::allocator<dealii::TrilinosWrappers::Vector>]’:
> /home/lev/aspect/dealii_debug/include/deal.II/lac/trilinos_block_vector.h:399:
> warning: ‘dealii::TrilinosWrappers::Vector::Vector()’ is deprecated
> (declared at
> /home/lev/aspect/dealii_debug/include/deal.II/lac/trilinos_vector.h:770)
> In file included from /home/lev/aspect/trilinos/include/Amesos.h:34,
>                  from
> /home/lev/aspect/dealii_debug/include/deal.II/lac/trilinos_solver.h:34,
>                  from
> /home/lev/aspect/dealii_debug/include/deal.II/lac/generic_linear_algebra.h:143,
>                  from
> /home/lev/aspect/aspect_debug/include/aspect/global.h:35,
>                  from
> /home/lev/aspect/aspect_debug/include/aspect/simulator.h:42,
>                  from
> /home/lev/aspect/aspect_debug/source/simulator/core.cc:22:
> /home/lev/aspect/trilinos/include/Amesos_BaseSolver.h: At global scope:
> /home/lev/aspect/trilinos/include/Amesos_BaseSolver.h:410: warning: unused
> parameter ‘paramList’
> /home/lev/aspect/trilinos/include/Amesos_BaseSolver.h:432: warning: unused
> parameter ‘TimingParameterList’
> In file included from
> /home/lev/aspect/dealii_debug/include/deal.II/base/parameter_handler.h:24,
>                  from
> /home/lev/aspect/aspect_debug/include/aspect/simulator.h:26,
>                  from
> /home/lev/aspect/aspect_debug/source/simulator/core.cc:22:
> /home/lev/aspect/dealii_debug/include/deal.II/bundled/boost/smart_ptr/scoped_ptr.hpp:
> In copy constructor ‘dealii::std_cxx11::unique_ptr<dealii::Mapping<2, 2>
>>::unique_ptr(const dealii::std_cxx11::unique_ptr<dealii::Mapping<2, 2>
>>&)’:
> /home/lev/aspect/dealii_debug/include/deal.II/base/std_cxx11/unique_ptr.h:60:
> instantiated from ‘aspect::Simulator<dim>::Simulator(ompi_communicator_t*,
> dealii::ParameterHandler&) [with int dim = 2]’
> /home/lev/aspect/aspect_debug/source/simulator/core.cc:2471:   instantiated
> from here
> /home/lev/aspect/dealii_debug/include/deal.II/bundled/boost/smart_ptr/scoped_ptr.hpp:47:
> error: ‘boost::scoped_ptr<T>::scoped_ptr(const boost::scoped_ptr<T>&) [with
> T = dealii::Mapping<2, 2>]’ is private
> /home/lev/aspect/dealii_debug/include/deal.II/base/std_cxx11/unique_ptr.h:60:
> error: within this context
> /home/lev/aspect/aspect_debug/source/simulator/core.cc: In constructor
> ‘aspect::Simulator<dim>::Simulator(ompi_communicator_t*,
> dealii::ParameterHandler&) [with int dim = 2]’:
> /home/lev/aspect/aspect_debug/source/simulator/core.cc:2471:   instantiated
> from here
> /home/lev/aspect/aspect_debug/source/simulator/core.cc:218: note:
> synthesized method ‘dealii::std_cxx11::unique_ptr<dealii::Mapping<2, 2>
>>::unique_ptr(const dealii::std_cxx11::unique_ptr<dealii::Mapping<2, 2> >&)’
> first required here
> In file included from
> /home/lev/aspect/dealii_debug/include/deal.II/base/parameter_handler.h:24,
>                  from
> /home/lev/aspect/aspect_debug/include/aspect/simulator.h:26,
>                  from
> /home/lev/aspect/aspect_debug/source/simulator/core.cc:22:
> /home/lev/aspect/dealii_debug/include/deal.II/bundled/boost/smart_ptr/scoped_ptr.hpp:
> In copy constructor ‘dealii::std_cxx11::unique_ptr<dealii::Mapping<3, 3>
>>::unique_ptr(const dealii::std_cxx11::unique_ptr<dealii::Mapping<3, 3>
>>&)’:
> /home/lev/aspect/dealii_debug/include/deal.II/base/std_cxx11/unique_ptr.h:60:
> instantiated from ‘aspect::Simulator<dim>::Simulator(ompi_communicator_t*,
> dealii::ParameterHandler&) [with int dim = 3]’
> /home/lev/aspect/aspect_debug/source/simulator/core.cc:2471:   instantiated
> from here
> /home/lev/aspect/dealii_debug/include/deal.II/bundled/boost/smart_ptr/scoped_ptr.hpp:47:
> error: ‘boost::scoped_ptr<T>::scoped_ptr(const boost::scoped_ptr<T>&) [with
> T = dealii::Mapping<3, 3>]’ is private
> /home/lev/aspect/dealii_debug/include/deal.II/base/std_cxx11/unique_ptr.h:60:
> error: within this context
> /home/lev/aspect/aspect_debug/source/simulator/core.cc: In constructor
> ‘aspect::Simulator<dim>::Simulator(ompi_communicator_t*,
> dealii::ParameterHandler&) [with int dim = 3]’:
> /home/lev/aspect/aspect_debug/source/simulator/core.cc:2471:   instantiated
> from here
> /home/lev/aspect/aspect_debug/source/simulator/core.cc:218: note:
> synthesized method ‘dealii::std_cxx11::unique_ptr<dealii::Mapping<3, 3>
>>::unique_ptr(const dealii::std_cxx11::unique_ptr<dealii::Mapping<3, 3> >&)’
> first required here
> /home/lev/aspect/dealii_debug/include/deal.II/bundled/boost/system/error_code.hpp:
> At global scope:
> /home/lev/aspect/dealii_debug/include/deal.II/bundled/boost/system/error_code.hpp:221:
> warning: ‘boost::system::posix_category’ defined but not used
> /home/lev/aspect/dealii_debug/include/deal.II/bundled/boost/system/error_code.hpp:222:
> warning: ‘boost::system::errno_ecat’ defined but not used
> /home/lev/aspect/dealii_debug/include/deal.II/bundled/boost/system/error_code.hpp:223:
> warning: ‘boost::system::native_ecat’ defined but not used
> make[2]: *** [CMakeFiles/aspect.dir/source/simulator/core.cc.o] Error 1
> make[1]: *** [CMakeFiles/aspect.dir/all] Error 2
> make: *** [all] Error 2
>
> Tips on how to solve it would be appreciated.
>
> Best regards,
> Lev Karatun.
>
>
> _______________________________________________
> Aspect-devel mailing list
> Aspect-devel at geodynamics.org
> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.geodynamics.org_cgi-2Dbin_mailman_listinfo_aspect-2Ddevel&d=CwIFaQ&c=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4&r=c08Btfq4m9QEScXN3ZQwLZzzWQE7S8CYq1IYuzKV_Zk&m=sG5zs-MssNAki6AoJRSXnOd8lnZ2bTe7bzYIj6rACMg&s=lWFdAvA2UoEemNQpJUKtwxvxX8EQ0yAK-8FTD4Ql1Wk&e= 
>
>
>
> _______________________________________________
> Aspect-devel mailing list
> Aspect-devel at geodynamics.org
> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.geodynamics.org_cgi-2Dbin_mailman_listinfo_aspect-2Ddevel&d=CwIGaQ&c=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4&r=R5lvg9JC99XvuTgScgbY_QFS80R7PEA2q0EPwDy7VQw&m=OIIEI8hxr1JRrRi4Ei99VvnoHw-rMaGpCXN5gB4y0KY&s=deLeS1iORFsQapfDDlK1jY2ggkY2jGekbwNjNh4PxfA&e=



-- 
Timo Heister
http://www.math.clemson.edu/~heister/

From lev.karatun at gmail.com  Wed Nov  2 09:55:49 2016
From: lev.karatun at gmail.com (Lev Karatun)
Date: Wed, 2 Nov 2016 12:55:49 -0400
Subject: [aspect-devel] compilation error
In-Reply-To: <CAMRj59H-Awq9XF0wYct=iaKEYaRHH2+d3F+sRkaFAVCAjiUkRA@mail.gmail.com>
References: <CAPGyz26PLEocxz9UVakPWYQOej=9YAe=ZaUyzmMY-bJtWd35gA@mail.gmail.com>
 <5a8fdc94-a0e6-b869-7f6c-c7ae88654b4c@ucdavis.edu>
 <CAMRj59H-Awq9XF0wYct=iaKEYaRHH2+d3F+sRkaFAVCAjiUkRA@mail.gmail.com>
Message-ID: <CAPGyz26EhecZ3BM4iAshMq94EeAUJ2-hAzGc5DP+W04JTpiTqA@mail.gmail.com>

Hi Timo,

it's attached.

Best regards,
Lev Karatun.

2016-11-02 12:34 GMT-04:00 Timo Heister <heister at clemson.edu>:

> Can you please post your detailed.log from your deal.II build
> directory? That will show us what compiler/settings you are using.
>
> On Wed, Nov 2, 2016 at 12:00 PM, John Naliboff <jbnaliboff at ucdavis.edu>
> wrote:
> > Hi Lev,
> >
> > What Trilinos and dealii version are you using?  If you are using the
> > development version of dealii, when was the last update?  Also, did you
> do
> > 'make distclean' before reconfiguring and compiling ASPECT?  I'm not sure
> > what the error below is related to, but the aforementioned information is
> > always helpful when debugging an installation issue.
> >
> > Cheers,
> > John
> >
> >
> > *************************************************
> > John Naliboff
> > Assistant Project Scientist, CIG
> > Earth & Planetary Sciences Dept., UC Davis
> >
> > On 11/02/2016 06:45 AM, Lev Karatun wrote:
> >
> > Hi,
> >
> > I was trying to update Aspect to the latest version and got the following
> > error:
> >
> > [  0%] Building CXX object CMakeFiles/aspect.dir/source/
> simulator/core.cc.o
> > In file included from
> > /home/lev/aspect/aspect_debug/include/aspect/simulator.h:30,
> >                  from
> > /home/lev/aspect/aspect_debug/source/simulator/core.cc:22:
> > /home/lev/aspect/dealii_debug/include/deal.II/lac/trilinos_
> block_vector.h:
> > In member function ‘void std::vector<_Tp, _Alloc>::resize(size_t, _Tp)
> [with
> > _Tp = dealii::TrilinosWrappers::Vector, _Alloc =
> > std::allocator<dealii::TrilinosWrappers::Vector>]’:
> > /home/lev/aspect/dealii_debug/include/deal.II/lac/trilinos_
> block_vector.h:399:
> > warning: ‘dealii::TrilinosWrappers::Vector::Vector()’ is deprecated
> > (declared at
> > /home/lev/aspect/dealii_debug/include/deal.II/lac/trilinos_vector.h:770)
> > In file included from /home/lev/aspect/trilinos/include/Amesos.h:34,
> >                  from
> > /home/lev/aspect/dealii_debug/include/deal.II/lac/trilinos_solver.h:34,
> >                  from
> > /home/lev/aspect/dealii_debug/include/deal.II/lac/generic_
> linear_algebra.h:143,
> >                  from
> > /home/lev/aspect/aspect_debug/include/aspect/global.h:35,
> >                  from
> > /home/lev/aspect/aspect_debug/include/aspect/simulator.h:42,
> >                  from
> > /home/lev/aspect/aspect_debug/source/simulator/core.cc:22:
> > /home/lev/aspect/trilinos/include/Amesos_BaseSolver.h: At global scope:
> > /home/lev/aspect/trilinos/include/Amesos_BaseSolver.h:410: warning:
> unused
> > parameter ‘paramList’
> > /home/lev/aspect/trilinos/include/Amesos_BaseSolver.h:432: warning:
> unused
> > parameter ‘TimingParameterList’
> > In file included from
> > /home/lev/aspect/dealii_debug/include/deal.II/base/
> parameter_handler.h:24,
> >                  from
> > /home/lev/aspect/aspect_debug/include/aspect/simulator.h:26,
> >                  from
> > /home/lev/aspect/aspect_debug/source/simulator/core.cc:22:
> > /home/lev/aspect/dealii_debug/include/deal.II/bundled/boost/
> smart_ptr/scoped_ptr.hpp:
> > In copy constructor ‘dealii::std_cxx11::unique_ptr<dealii::Mapping<2, 2>
> >>::unique_ptr(const dealii::std_cxx11::unique_ptr<dealii::Mapping<2, 2>
> >>&)’:
> > /home/lev/aspect/dealii_debug/include/deal.II/base/std_
> cxx11/unique_ptr.h:60:
> > instantiated from ‘aspect::Simulator<dim>::
> Simulator(ompi_communicator_t*,
> > dealii::ParameterHandler&) [with int dim = 2]’
> > /home/lev/aspect/aspect_debug/source/simulator/core.cc:2471:
>  instantiated
> > from here
> > /home/lev/aspect/dealii_debug/include/deal.II/bundled/boost/
> smart_ptr/scoped_ptr.hpp:47:
> > error: ‘boost::scoped_ptr<T>::scoped_ptr(const boost::scoped_ptr<T>&)
> [with
> > T = dealii::Mapping<2, 2>]’ is private
> > /home/lev/aspect/dealii_debug/include/deal.II/base/std_
> cxx11/unique_ptr.h:60:
> > error: within this context
> > /home/lev/aspect/aspect_debug/source/simulator/core.cc: In constructor
> > ‘aspect::Simulator<dim>::Simulator(ompi_communicator_t*,
> > dealii::ParameterHandler&) [with int dim = 2]’:
> > /home/lev/aspect/aspect_debug/source/simulator/core.cc:2471:
>  instantiated
> > from here
> > /home/lev/aspect/aspect_debug/source/simulator/core.cc:218: note:
> > synthesized method ‘dealii::std_cxx11::unique_ptr<dealii::Mapping<2, 2>
> >>::unique_ptr(const dealii::std_cxx11::unique_ptr<dealii::Mapping<2, 2>
> >&)’
> > first required here
> > In file included from
> > /home/lev/aspect/dealii_debug/include/deal.II/base/
> parameter_handler.h:24,
> >                  from
> > /home/lev/aspect/aspect_debug/include/aspect/simulator.h:26,
> >                  from
> > /home/lev/aspect/aspect_debug/source/simulator/core.cc:22:
> > /home/lev/aspect/dealii_debug/include/deal.II/bundled/boost/
> smart_ptr/scoped_ptr.hpp:
> > In copy constructor ‘dealii::std_cxx11::unique_ptr<dealii::Mapping<3, 3>
> >>::unique_ptr(const dealii::std_cxx11::unique_ptr<dealii::Mapping<3, 3>
> >>&)’:
> > /home/lev/aspect/dealii_debug/include/deal.II/base/std_
> cxx11/unique_ptr.h:60:
> > instantiated from ‘aspect::Simulator<dim>::
> Simulator(ompi_communicator_t*,
> > dealii::ParameterHandler&) [with int dim = 3]’
> > /home/lev/aspect/aspect_debug/source/simulator/core.cc:2471:
>  instantiated
> > from here
> > /home/lev/aspect/dealii_debug/include/deal.II/bundled/boost/
> smart_ptr/scoped_ptr.hpp:47:
> > error: ‘boost::scoped_ptr<T>::scoped_ptr(const boost::scoped_ptr<T>&)
> [with
> > T = dealii::Mapping<3, 3>]’ is private
> > /home/lev/aspect/dealii_debug/include/deal.II/base/std_
> cxx11/unique_ptr.h:60:
> > error: within this context
> > /home/lev/aspect/aspect_debug/source/simulator/core.cc: In constructor
> > ‘aspect::Simulator<dim>::Simulator(ompi_communicator_t*,
> > dealii::ParameterHandler&) [with int dim = 3]’:
> > /home/lev/aspect/aspect_debug/source/simulator/core.cc:2471:
>  instantiated
> > from here
> > /home/lev/aspect/aspect_debug/source/simulator/core.cc:218: note:
> > synthesized method ‘dealii::std_cxx11::unique_ptr<dealii::Mapping<3, 3>
> >>::unique_ptr(const dealii::std_cxx11::unique_ptr<dealii::Mapping<3, 3>
> >&)’
> > first required here
> > /home/lev/aspect/dealii_debug/include/deal.II/bundled/boost/
> system/error_code.hpp:
> > At global scope:
> > /home/lev/aspect/dealii_debug/include/deal.II/bundled/boost/
> system/error_code.hpp:221:
> > warning: ‘boost::system::posix_category’ defined but not used
> > /home/lev/aspect/dealii_debug/include/deal.II/bundled/boost/
> system/error_code.hpp:222:
> > warning: ‘boost::system::errno_ecat’ defined but not used
> > /home/lev/aspect/dealii_debug/include/deal.II/bundled/boost/
> system/error_code.hpp:223:
> > warning: ‘boost::system::native_ecat’ defined but not used
> > make[2]: *** [CMakeFiles/aspect.dir/source/simulator/core.cc.o] Error 1
> > make[1]: *** [CMakeFiles/aspect.dir/all] Error 2
> > make: *** [all] Error 2
> >
> > Tips on how to solve it would be appreciated.
> >
> > Best regards,
> > Lev Karatun.
> >
> >
> > _______________________________________________
> > Aspect-devel mailing list
> > Aspect-devel at geodynamics.org
> > https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.
> geodynamics.org_cgi-2Dbin_mailman_listinfo_aspect-2Ddevel&d=CwIFaQ&c=Ngd-
> ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4&r=c08Btfq4m9QEScXN3ZQwLZzzWQE7S8
> CYq1IYuzKV_Zk&m=sG5zs-MssNAki6AoJRSXnOd8lnZ2bTe7bzYIj6rACMg&s=
> lWFdAvA2UoEemNQpJUKtwxvxX8EQ0yAK-8FTD4Ql1Wk&e=
> >
> >
> >
> > _______________________________________________
> > Aspect-devel mailing list
> > Aspect-devel at geodynamics.org
> > https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.
> geodynamics.org_cgi-2Dbin_mailman_listinfo_aspect-2Ddevel&d=CwIGaQ&c=Ngd-
> ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4&r=R5lvg9JC99XvuTgScgbY_
> QFS80R7PEA2q0EPwDy7VQw&m=OIIEI8hxr1JRrRi4Ei99VvnoHw-rMaGpCXN5gB4y0KY&s=
> deLeS1iORFsQapfDDlK1jY2ggkY2jGekbwNjNh4PxfA&e=
>
>
>
> --
> Timo Heister
> http://www.math.clemson.edu/~heister/
> _______________________________________________
> Aspect-devel mailing list
> Aspect-devel at geodynamics.org
> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel
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From bangerth at tamu.edu  Wed Nov  2 11:46:21 2016
From: bangerth at tamu.edu (Wolfgang Bangerth)
Date: Wed, 2 Nov 2016 12:46:21 -0600
Subject: [aspect-devel] Q2P-1 question
In-Reply-To: <6DCDF056-77D8-4A7F-949F-DE4033EC20C9@uu.nl>
References: <6DCDF056-77D8-4A7F-949F-DE4033EC20C9@uu.nl>
Message-ID: <65f4d67c-116f-5775-6a57-aa557bce6007@tamu.edu>

On 11/02/2016 06:25 AM, Thieulot, C.A.P. (Cedric) wrote:
>
> I was reading on the Q2P-1 element recently when I came across the
> literature about the mapping of the pressure (e.g. Finite element
> approximation on quadrilateral meshes,
> Arnold et al, Commun. Numer. Meth. Engng 2001; 17:805–812 (DOI:
> 10.1002/cnm.450) ). To summarize it I rereby attach a slide from a
> presentation of Arnold.
> I was then wondering which option is implemented in ASPECT ?
>

You mean whether we do or do not map the pressure from the reference 
cell to the real cell?

We use FE_DGP if we want to use a discontinuous pressure, which is 
mapped from the reference cell. Arnold's answer is not wrong, but it 
only matters if you have cells that deviate strongly from cubes because 
in that case the norm of the Jacobian of the mapping is large and the 
norm enters the approximation quality. For the cells we use, I would 
venture the guess that the norm is never much larger than 2 or 3 -- 
almost all of our cells are close to cubes. In that case, I doubt that 
it would make much of a difference.

But if you'd like to try, you can change the new_FE_Q_or_DGQ in 
source/simulator/introspection.cc from using FE_DGP to using 
FE_DGPNonparametric, and in that case we use a non-mapped element. It's 
a one-line change. You could try whether that makes any noticeable 
difference.

Best
  W.

-- 
------------------------------------------------------------------------
Wolfgang Bangerth          email:                 bangerth at colostate.edu
                            www: http://www.math.colostate.edu/~bangerth/

From f_orellana at berkeley.edu  Wed Nov  2 11:20:10 2016
From: f_orellana at berkeley.edu (FELIPE ORELLANA ROVIROSA)
Date: Wed, 2 Nov 2016 11:20:10 -0700
Subject: [aspect-devel] compilation error
In-Reply-To: <CAPGyz26PLEocxz9UVakPWYQOej=9YAe=ZaUyzmMY-bJtWd35gA@mail.gmail.com>
References: <CAPGyz26PLEocxz9UVakPWYQOej=9YAe=ZaUyzmMY-bJtWd35gA@mail.gmail.com>
Message-ID: <CANEUqvg74W-zrSG7TosfWb5Cvitq8Lkpn2jWaG38pwi_T==WfQ@mail.gmail.com>

 Hi Lev,

  When I installed Aspect 1.5 pre like 2 months ago I got a similar error.

  The problem was related to the path and access to Trilinos and Deal ii.
Try to check that paths are correct, in relation with the actual
directories, etc.

Felipe

On Wed, Nov 2, 2016 at 6:45 AM, Lev Karatun <lev.karatun at gmail.com> wrote:

> Hi,
>
> I was trying to update Aspect to the latest version and got the following
> error:
>
> [  0%] Building CXX object CMakeFiles/aspect.dir/source/
> simulator/core.cc.o
> In file included from /home/lev/aspect/aspect_debug/
> include/aspect/simulator.h:30,
>                  from /home/lev/aspect/aspect_debug/
> source/simulator/core.cc:22:
> /home/lev/aspect/dealii_debug/include/deal.II/lac/trilinos_block_vector.h:
> In member function ‘void std::vector<_Tp, _Alloc>::resize(size_t, _Tp)
> [with _Tp = dealii::TrilinosWrappers::Vector, _Alloc =
> std::allocator<dealii::TrilinosWrappers::Vector>]’:
> /home/lev/aspect/dealii_debug/include/deal.II/lac/trilinos_block_vector.h:399:
> warning: ‘dealii::TrilinosWrappers::Vector::Vector()’ is deprecated
> (declared at /home/lev/aspect/dealii_debug/include/deal.II/lac/trilinos_
> vector.h:770)
> In file included from /home/lev/aspect/trilinos/include/Amesos.h:34,
>                  from /home/lev/aspect/dealii_debug/
> include/deal.II/lac/trilinos_solver.h:34,
>                  from /home/lev/aspect/dealii_debug/
> include/deal.II/lac/generic_linear_algebra.h:143,
>                  from /home/lev/aspect/aspect_debug/
> include/aspect/global.h:35,
>                  from /home/lev/aspect/aspect_debug/
> include/aspect/simulator.h:42,
>                  from /home/lev/aspect/aspect_debug/
> source/simulator/core.cc:22:
> /home/lev/aspect/trilinos/include/Amesos_BaseSolver.h: At global scope:
> /home/lev/aspect/trilinos/include/Amesos_BaseSolver.h:410: warning:
> unused parameter ‘paramList’
> /home/lev/aspect/trilinos/include/Amesos_BaseSolver.h:432: warning:
> unused parameter ‘TimingParameterList’
> In file included from /home/lev/aspect/dealii_debug/include/deal.II/base/
> parameter_handler.h:24,
>                  from /home/lev/aspect/aspect_debug/
> include/aspect/simulator.h:26,
>                  from /home/lev/aspect/aspect_debug/
> source/simulator/core.cc:22:
> /home/lev/aspect/dealii_debug/include/deal.II/bundled/boost/smart_ptr/scoped_ptr.hpp:
> In copy constructor ‘dealii::std_cxx11::unique_ptr<dealii::Mapping<2, 2>
> >::unique_ptr(const dealii::std_cxx11::unique_ptr<dealii::Mapping<2, 2>
> >&)’:
> /home/lev/aspect/dealii_debug/include/deal.II/base/std_cxx11/unique_ptr.h:60:
>   instantiated from ‘aspect::Simulator<dim>::
> Simulator(ompi_communicator_t*, dealii::ParameterHandler&) [with int dim
> = 2]’
> /home/lev/aspect/aspect_debug/source/simulator/core.cc:2471:
> instantiated from here
> /home/lev/aspect/dealii_debug/include/deal.II/bundled/boost/smart_ptr/scoped_ptr.hpp:47:
> error: ‘boost::scoped_ptr<T>::scoped_ptr(const boost::scoped_ptr<T>&)
> [with T = dealii::Mapping<2, 2>]’ is private
> /home/lev/aspect/dealii_debug/include/deal.II/base/std_cxx11/unique_ptr.h:60:
> error: within this context
> /home/lev/aspect/aspect_debug/source/simulator/core.cc: In constructor
> ‘aspect::Simulator<dim>::Simulator(ompi_communicator_t*,
> dealii::ParameterHandler&) [with int dim = 2]’:
> /home/lev/aspect/aspect_debug/source/simulator/core.cc:2471:
> instantiated from here
> /home/lev/aspect/aspect_debug/source/simulator/core.cc:218: note:
> synthesized method ‘dealii::std_cxx11::unique_ptr<dealii::Mapping<2, 2>
> >::unique_ptr(const dealii::std_cxx11::unique_ptr<dealii::Mapping<2, 2>
> >&)’ first required here
> In file included from /home/lev/aspect/dealii_debug/include/deal.II/base/
> parameter_handler.h:24,
>                  from /home/lev/aspect/aspect_debug/
> include/aspect/simulator.h:26,
>                  from /home/lev/aspect/aspect_debug/
> source/simulator/core.cc:22:
> /home/lev/aspect/dealii_debug/include/deal.II/bundled/boost/smart_ptr/scoped_ptr.hpp:
> In copy constructor ‘dealii::std_cxx11::unique_ptr<dealii::Mapping<3, 3>
> >::unique_ptr(const dealii::std_cxx11::unique_ptr<dealii::Mapping<3, 3>
> >&)’:
> /home/lev/aspect/dealii_debug/include/deal.II/base/std_cxx11/unique_ptr.h:60:
>   instantiated from ‘aspect::Simulator<dim>::
> Simulator(ompi_communicator_t*, dealii::ParameterHandler&) [with int dim
> = 3]’
> /home/lev/aspect/aspect_debug/source/simulator/core.cc:2471:
> instantiated from here
> /home/lev/aspect/dealii_debug/include/deal.II/bundled/boost/smart_ptr/scoped_ptr.hpp:47:
> error: ‘boost::scoped_ptr<T>::scoped_ptr(const boost::scoped_ptr<T>&)
> [with T = dealii::Mapping<3, 3>]’ is private
> /home/lev/aspect/dealii_debug/include/deal.II/base/std_cxx11/unique_ptr.h:60:
> error: within this context
> /home/lev/aspect/aspect_debug/source/simulator/core.cc: In constructor
> ‘aspect::Simulator<dim>::Simulator(ompi_communicator_t*,
> dealii::ParameterHandler&) [with int dim = 3]’:
> /home/lev/aspect/aspect_debug/source/simulator/core.cc:2471:
> instantiated from here
> /home/lev/aspect/aspect_debug/source/simulator/core.cc:218: note:
> synthesized method ‘dealii::std_cxx11::unique_ptr<dealii::Mapping<3, 3>
> >::unique_ptr(const dealii::std_cxx11::unique_ptr<dealii::Mapping<3, 3>
> >&)’ first required here
> /home/lev/aspect/dealii_debug/include/deal.II/bundled/boost/system/error_code.hpp:
> At global scope:
> /home/lev/aspect/dealii_debug/include/deal.II/bundled/boost/system/error_code.hpp:221:
> warning: ‘boost::system::posix_category’ defined but not used
> /home/lev/aspect/dealii_debug/include/deal.II/bundled/boost/system/error_code.hpp:222:
> warning: ‘boost::system::errno_ecat’ defined but not used
> /home/lev/aspect/dealii_debug/include/deal.II/bundled/boost/system/error_code.hpp:223:
> warning: ‘boost::system::native_ecat’ defined but not used
> make[2]: *** [CMakeFiles/aspect.dir/source/simulator/core.cc.o] Error 1
> make[1]: *** [CMakeFiles/aspect.dir/all] Error 2
> make: *** [all] Error 2
>
> Tips on how to solve it would be appreciated.
>
> Best regards,
> Lev Karatun.
>
> _______________________________________________
> Aspect-devel mailing list
> Aspect-devel at geodynamics.org
> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel
>
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From lev.karatun at gmail.com  Wed Nov  2 09:36:53 2016
From: lev.karatun at gmail.com (Lev Karatun)
Date: Wed, 2 Nov 2016 12:36:53 -0400
Subject: [aspect-devel] compilation error
In-Reply-To: <5a8fdc94-a0e6-b869-7f6c-c7ae88654b4c@ucdavis.edu>
References: <CAPGyz26PLEocxz9UVakPWYQOej=9YAe=ZaUyzmMY-bJtWd35gA@mail.gmail.com>
 <5a8fdc94-a0e6-b869-7f6c-c7ae88654b4c@ucdavis.edu>
Message-ID: <CAPGyz26eGg7VXswcD=EiEt3ZhTuuubNz_+7J2msJka3BFTpG9A@mail.gmail.com>

Hi John,

I'm using the latest version of dealII (commit 0e395a1 - 16 hours ago),
updated it just before updating aspect. Trilinos version is 11.12.1. I
donwnloaded aspect into a separate empty directory, it doesn't compile from
there.

Best regards,
Lev Karatun.

2016-11-02 12:00 GMT-04:00 John Naliboff <jbnaliboff at ucdavis.edu>:

> Hi Lev,
>
> What Trilinos and dealii version are you using?  If you are using the
> development version of dealii, when was the last update?  Also, did you do
> 'make distclean' before reconfiguring and compiling ASPECT?  I'm not sure
> what the error below is related to, but the aforementioned information is
> always helpful when debugging an installation issue.
>
> Cheers,
> John
>
>
> *************************************************
> John Naliboff
> Assistant Project Scientist, CIG
> Earth & Planetary Sciences Dept., UC Davis
>
> On 11/02/2016 06:45 AM, Lev Karatun wrote:
>
> Hi,
>
> I was trying to update Aspect to the latest version and got the following
> error:
>
> [  0%] Building CXX object CMakeFiles/aspect.dir/source/
> simulator/core.cc.o
> In file included from /home/lev/aspect/aspect_debug/
> include/aspect/simulator.h:30,
>                  from /home/lev/aspect/aspect_debug/
> source/simulator/core.cc:22:
> /home/lev/aspect/dealii_debug/include/deal.II/lac/trilinos_block_vector.h:
> In member function ‘void std::vector<_Tp, _Alloc>::resize(size_t, _Tp)
> [with _Tp = dealii::TrilinosWrappers::Vector, _Alloc =
> std::allocator<dealii::TrilinosWrappers::Vector>]’:
> /home/lev/aspect/dealii_debug/include/deal.II/lac/trilinos_block_vector.h:399:
> warning: ‘dealii::TrilinosWrappers::Vector::Vector()’ is deprecated
> (declared at /home/lev/aspect/dealii_debug/include/deal.II/lac/trilinos_
> vector.h:770)
> In file included from /home/lev/aspect/trilinos/include/Amesos.h:34,
>                  from /home/lev/aspect/dealii_debug/
> include/deal.II/lac/trilinos_solver.h:34,
>                  from /home/lev/aspect/dealii_debug/
> include/deal.II/lac/generic_linear_algebra.h:143,
>                  from /home/lev/aspect/aspect_debug/
> include/aspect/global.h:35,
>                  from /home/lev/aspect/aspect_debug/
> include/aspect/simulator.h:42,
>                  from /home/lev/aspect/aspect_debug/
> source/simulator/core.cc:22:
> /home/lev/aspect/trilinos/include/Amesos_BaseSolver.h: At global scope:
> /home/lev/aspect/trilinos/include/Amesos_BaseSolver.h:410: warning:
> unused parameter ‘paramList’
> /home/lev/aspect/trilinos/include/Amesos_BaseSolver.h:432: warning:
> unused parameter ‘TimingParameterList’
> In file included from /home/lev/aspect/dealii_debug/include/deal.II/base/
> parameter_handler.h:24,
>                  from /home/lev/aspect/aspect_debug/
> include/aspect/simulator.h:26,
>                  from /home/lev/aspect/aspect_debug/
> source/simulator/core.cc:22:
> /home/lev/aspect/dealii_debug/include/deal.II/bundled/boost/smart_ptr/scoped_ptr.hpp:
> In copy constructor ‘dealii::std_cxx11::unique_ptr<dealii::Mapping<2, 2>
> >::unique_ptr(const dealii::std_cxx11::unique_ptr<dealii::Mapping<2, 2>
> >&)’:
> /home/lev/aspect/dealii_debug/include/deal.II/base/std_cxx11/unique_ptr.h:60:
>   instantiated from ‘aspect::Simulator<dim>::
> Simulator(ompi_communicator_t*, dealii::ParameterHandler&) [with int dim
> = 2]’
> /home/lev/aspect/aspect_debug/source/simulator/core.cc:2471:
> instantiated from here
> /home/lev/aspect/dealii_debug/include/deal.II/bundled/boost/smart_ptr/scoped_ptr.hpp:47:
> error: ‘boost::scoped_ptr<T>::scoped_ptr(const boost::scoped_ptr<T>&)
> [with T = dealii::Mapping<2, 2>]’ is private
> /home/lev/aspect/dealii_debug/include/deal.II/base/std_cxx11/unique_ptr.h:60:
> error: within this context
> /home/lev/aspect/aspect_debug/source/simulator/core.cc: In constructor
> ‘aspect::Simulator<dim>::Simulator(ompi_communicator_t*,
> dealii::ParameterHandler&) [with int dim = 2]’:
> /home/lev/aspect/aspect_debug/source/simulator/core.cc:2471:
> instantiated from here
> /home/lev/aspect/aspect_debug/source/simulator/core.cc:218: note:
> synthesized method ‘dealii::std_cxx11::unique_ptr<dealii::Mapping<2, 2>
> >::unique_ptr(const dealii::std_cxx11::unique_ptr<dealii::Mapping<2, 2>
> >&)’ first required here
> In file included from /home/lev/aspect/dealii_debug/include/deal.II/base/
> parameter_handler.h:24,
>                  from /home/lev/aspect/aspect_debug/
> include/aspect/simulator.h:26,
>                  from /home/lev/aspect/aspect_debug/
> source/simulator/core.cc:22:
> /home/lev/aspect/dealii_debug/include/deal.II/bundled/boost/smart_ptr/scoped_ptr.hpp:
> In copy constructor ‘dealii::std_cxx11::unique_ptr<dealii::Mapping<3, 3>
> >::unique_ptr(const dealii::std_cxx11::unique_ptr<dealii::Mapping<3, 3>
> >&)’:
> /home/lev/aspect/dealii_debug/include/deal.II/base/std_cxx11/unique_ptr.h:60:
>   instantiated from ‘aspect::Simulator<dim>::
> Simulator(ompi_communicator_t*, dealii::ParameterHandler&) [with int dim
> = 3]’
> /home/lev/aspect/aspect_debug/source/simulator/core.cc:2471:
> instantiated from here
> /home/lev/aspect/dealii_debug/include/deal.II/bundled/boost/smart_ptr/scoped_ptr.hpp:47:
> error: ‘boost::scoped_ptr<T>::scoped_ptr(const boost::scoped_ptr<T>&)
> [with T = dealii::Mapping<3, 3>]’ is private
> /home/lev/aspect/dealii_debug/include/deal.II/base/std_cxx11/unique_ptr.h:60:
> error: within this context
> /home/lev/aspect/aspect_debug/source/simulator/core.cc: In constructor
> ‘aspect::Simulator<dim>::Simulator(ompi_communicator_t*,
> dealii::ParameterHandler&) [with int dim = 3]’:
> /home/lev/aspect/aspect_debug/source/simulator/core.cc:2471:
> instantiated from here
> /home/lev/aspect/aspect_debug/source/simulator/core.cc:218: note:
> synthesized method ‘dealii::std_cxx11::unique_ptr<dealii::Mapping<3, 3>
> >::unique_ptr(const dealii::std_cxx11::unique_ptr<dealii::Mapping<3, 3>
> >&)’ first required here
> /home/lev/aspect/dealii_debug/include/deal.II/bundled/boost/system/error_code.hpp:
> At global scope:
> /home/lev/aspect/dealii_debug/include/deal.II/bundled/boost/system/error_code.hpp:221:
> warning: ‘boost::system::posix_category’ defined but not used
> /home/lev/aspect/dealii_debug/include/deal.II/bundled/boost/system/error_code.hpp:222:
> warning: ‘boost::system::errno_ecat’ defined but not used
> /home/lev/aspect/dealii_debug/include/deal.II/bundled/boost/system/error_code.hpp:223:
> warning: ‘boost::system::native_ecat’ defined but not used
> make[2]: *** [CMakeFiles/aspect.dir/source/simulator/core.cc.o] Error 1
> make[1]: *** [CMakeFiles/aspect.dir/all] Error 2
> make: *** [all] Error 2
>
> Tips on how to solve it would be appreciated.
>
> Best regards,
> Lev Karatun.
>
>
> _______________________________________________
> Aspect-devel mailing listAspect-devel at geodynamics.orghttp://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel
>
>
>
> _______________________________________________
> Aspect-devel mailing list
> Aspect-devel at geodynamics.org
> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel
>
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From lokavarapuh at gmail.com  Wed Nov  2 17:11:57 2016
From: lokavarapuh at gmail.com (Harsha Lokavarapu)
Date: Wed, 2 Nov 2016 17:11:57 -0700
Subject: [aspect-devel] compilation error (Harsha Lv)
In-Reply-To: <mailman.6.1478109588.22305.aspect-devel@geodynamics.org>
References: <mailman.6.1478109588.22305.aspect-devel@geodynamics.org>
Message-ID: <67578bf6-c0bd-da07-79f0-6f7bf9484811@gmail.com>

This may not help but as a last attempt, try building with CXX11 support.
The cmake flag is:

    -DDEAL_II_WITH_CXX11=ON

Note that this will require building Trilinos with c++11 support as well.

On Wednesday 02 November 2016 10:59 AM, 
aspect-devel-request at geodynamics.org wrote:
> 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
>
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> 	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: compilation error (Timo Heister)
>     2. Re: compilation error (Lev Karatun)
>
>
> _______________________________________________
> Aspect-devel mailing list
> Aspect-devel at geodynamics.org
> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel

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From jbnaliboff at ucdavis.edu  Wed Nov  2 23:35:06 2016
From: jbnaliboff at ucdavis.edu (John Naliboff)
Date: Wed, 2 Nov 2016 23:35:06 -0700
Subject: [aspect-devel] compilation error
In-Reply-To: <CAPGyz26eGg7VXswcD=EiEt3ZhTuuubNz_+7J2msJka3BFTpG9A@mail.gmail.com>
References: <CAPGyz26PLEocxz9UVakPWYQOej=9YAe=ZaUyzmMY-bJtWd35gA@mail.gmail.com>
 <5a8fdc94-a0e6-b869-7f6c-c7ae88654b4c@ucdavis.edu>
 <CAPGyz26eGg7VXswcD=EiEt3ZhTuuubNz_+7J2msJka3BFTpG9A@mail.gmail.com>
Message-ID: <CB2D02C4-4B5A-4B59-B2F4-C9099953447A@ucdavis.edu>

Hi Lev,

Does dealii example-32 compile with your latest dealii update?  That is a good indicator to see if the problem lies directly with the dealii installation, independent of ASPECT.

Cheers,
John

*************************************************
John Naliboff
Assistant Project Scientist, CIG
Earth & Planetary Sciences Dept., UC Davis



> On Nov 2, 2016, at 9:36 AM, Lev Karatun <lev.karatun at gmail.com> wrote:
> 
> Hi John,
> 
> I'm using the latest version of dealII (commit 0e395a1 - 16 hours ago), updated it just before updating aspect. Trilinos version is 11.12.1. I donwnloaded aspect into a separate empty directory, it doesn't compile from there.
> 
> Best regards,
> Lev Karatun.
> 
> 2016-11-02 12:00 GMT-04:00 John Naliboff <jbnaliboff at ucdavis.edu <mailto:jbnaliboff at ucdavis.edu>>:
> Hi Lev,
> 
> What Trilinos and dealii version are you using?  If you are using the development version of dealii, when was the last update?  Also, did you do 'make distclean' before reconfiguring and compiling ASPECT?  I'm not sure what the error below is related to, but the aforementioned information is always helpful when debugging an installation issue.
> 
> Cheers,
> John
>  
>  *************************************************
> John Naliboff
> Assistant Project Scientist, CIG
> Earth & Planetary Sciences Dept., UC Davis
> On 11/02/2016 06:45 AM, Lev Karatun wrote:
>> Hi,
>> 
>> I was trying to update Aspect to the latest version and got the following error:
>> 
>> [  0%] Building CXX object CMakeFiles/aspect.dir/source/simulator/core.cc.o
>> In file included from /home/lev/aspect/aspect_debug/include/aspect/simulator.h:30,
>>                  from /home/lev/aspect/aspect_debug/source/simulator/core.cc:22:
>> /home/lev/aspect/dealii_debug/include/deal.II/lac/trilinos_block_vector.h: In member function ‘void std::vector<_Tp, _Alloc>::resize(size_t, _Tp) [with _Tp = dealii::TrilinosWrappers::Vector, _Alloc = std::allocator<dealii::TrilinosWrappers::Vector>]’:
>> /home/lev/aspect/dealii_debug/include/deal.II/lac/trilinos_block_vector.h:399: warning: ‘dealii::TrilinosWrappers::Vector::Vector()’ is deprecated (declared at /home/lev/aspect/dealii_debug/include/deal.II/lac/trilinos_vector.h:770)
>> In file included from /home/lev/aspect/trilinos/include/Amesos.h:34,
>>                  from /home/lev/aspect/dealii_debug/include/deal.II/lac/trilinos_solver.h:34,
>>                  from /home/lev/aspect/dealii_debug/include/deal.II/lac/generic_linear_algebra.h:143,
>>                  from /home/lev/aspect/aspect_debug/include/aspect/global.h:35,
>>                  from /home/lev/aspect/aspect_debug/include/aspect/simulator.h:42,
>>                  from /home/lev/aspect/aspect_debug/source/simulator/core.cc:22:
>> /home/lev/aspect/trilinos/include/Amesos_BaseSolver.h: At global scope:
>> /home/lev/aspect/trilinos/include/Amesos_BaseSolver.h:410: warning: unused parameter ‘paramList’
>> /home/lev/aspect/trilinos/include/Amesos_BaseSolver.h:432: warning: unused parameter ‘TimingParameterList’
>> In file included from /home/lev/aspect/dealii_debug/include/deal.II/base/parameter_handler.h:24,
>>                  from /home/lev/aspect/aspect_debug/include/aspect/simulator.h:26,
>>                  from /home/lev/aspect/aspect_debug/source/simulator/core.cc:22:
>> /home/lev/aspect/dealii_debug/include/deal.II/bundled/boost/smart_ptr/scoped_ptr.hpp: In copy constructor ‘dealii::std_cxx11::unique_ptr<dealii::Mapping<2, 2> >::unique_ptr(const dealii::std_cxx11::unique_ptr<dealii::Mapping<2, 2> >&)’:
>> /home/lev/aspect/dealii_debug/include/deal.II/base/std_cxx11/unique_ptr.h:60:   instantiated from ‘aspect::Simulator<dim>::Simulator(ompi_communicator_t*, dealii::ParameterHandler&) [with int dim = 2]’
>> /home/lev/aspect/aspect_debug/source/simulator/core.cc:2471:   instantiated from here
>> /home/lev/aspect/dealii_debug/include/deal.II/bundled/boost/smart_ptr/scoped_ptr.hpp:47: error: ‘boost::scoped_ptr<T>::scoped_ptr(const boost::scoped_ptr<T>&) [with T = dealii::Mapping<2, 2>]’ is private
>> /home/lev/aspect/dealii_debug/include/deal.II/base/std_cxx11/unique_ptr.h:60: error: within this context
>> /home/lev/aspect/aspect_debug/source/simulator/core.cc: In constructor ‘aspect::Simulator<dim>::Simulator(ompi_communicator_t*, dealii::ParameterHandler&) [with int dim = 2]’:
>> /home/lev/aspect/aspect_debug/source/simulator/core.cc:2471:   instantiated from here
>> /home/lev/aspect/aspect_debug/source/simulator/core.cc:218: note: synthesized method ‘dealii::std_cxx11::unique_ptr<dealii::Mapping<2, 2> >::unique_ptr(const dealii::std_cxx11::unique_ptr<dealii::Mapping<2, 2> >&)’ first required here
>> In file included from /home/lev/aspect/dealii_debug/include/deal.II/base/parameter_handler.h:24,
>>                  from /home/lev/aspect/aspect_debug/include/aspect/simulator.h:26,
>>                  from /home/lev/aspect/aspect_debug/source/simulator/core.cc:22:
>> /home/lev/aspect/dealii_debug/include/deal.II/bundled/boost/smart_ptr/scoped_ptr.hpp: In copy constructor ‘dealii::std_cxx11::unique_ptr<dealii::Mapping<3, 3> >::unique_ptr(const dealii::std_cxx11::unique_ptr<dealii::Mapping<3, 3> >&)’:
>> /home/lev/aspect/dealii_debug/include/deal.II/base/std_cxx11/unique_ptr.h:60:   instantiated from ‘aspect::Simulator<dim>::Simulator(ompi_communicator_t*, dealii::ParameterHandler&) [with int dim = 3]’
>> /home/lev/aspect/aspect_debug/source/simulator/core.cc:2471:   instantiated from here
>> /home/lev/aspect/dealii_debug/include/deal.II/bundled/boost/smart_ptr/scoped_ptr.hpp:47: error: ‘boost::scoped_ptr<T>::scoped_ptr(const boost::scoped_ptr<T>&) [with T = dealii::Mapping<3, 3>]’ is private
>> /home/lev/aspect/dealii_debug/include/deal.II/base/std_cxx11/unique_ptr.h:60: error: within this context
>> /home/lev/aspect/aspect_debug/source/simulator/core.cc: In constructor ‘aspect::Simulator<dim>::Simulator(ompi_communicator_t*, dealii::ParameterHandler&) [with int dim = 3]’:
>> /home/lev/aspect/aspect_debug/source/simulator/core.cc:2471:   instantiated from here
>> /home/lev/aspect/aspect_debug/source/simulator/core.cc:218: note: synthesized method ‘dealii::std_cxx11::unique_ptr<dealii::Mapping<3, 3> >::unique_ptr(const dealii::std_cxx11::unique_ptr<dealii::Mapping<3, 3> >&)’ first required here
>> /home/lev/aspect/dealii_debug/include/deal.II/bundled/boost/system/error_code.hpp: At global scope:
>> /home/lev/aspect/dealii_debug/include/deal.II/bundled/boost/system/error_code.hpp:221: warning: ‘boost::system::posix_category’ defined but not used
>> /home/lev/aspect/dealii_debug/include/deal.II/bundled/boost/system/error_code.hpp:222: warning: ‘boost::system::errno_ecat’ defined but not used
>> /home/lev/aspect/dealii_debug/include/deal.II/bundled/boost/system/error_code.hpp:223: warning: ‘boost::system::native_ecat’ defined but not used
>> make[2]: *** [CMakeFiles/aspect.dir/source/simulator/core.cc.o] Error 1
>> make[1]: *** [CMakeFiles/aspect.dir/all] Error 2
>> make: *** [all] Error 2
>> 
>> Tips on how to solve it would be appreciated.
>> 
>> Best regards,
>> Lev Karatun.
>> 
>> 
>> _______________________________________________
>> Aspect-devel mailing list
>> Aspect-devel at geodynamics.org <mailto:Aspect-devel at geodynamics.org>
>> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel <http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel>
> 
> _______________________________________________
> Aspect-devel mailing list
> Aspect-devel at geodynamics.org <mailto:Aspect-devel at geodynamics.org>
> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel <http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel>
> 
> _______________________________________________
> Aspect-devel mailing list
> Aspect-devel at geodynamics.org
> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel

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From heister at clemson.edu  Thu Nov  3 05:19:48 2016
From: heister at clemson.edu (Timo Heister)
Date: Thu, 3 Nov 2016 08:19:48 -0400
Subject: [aspect-devel] compilation error
In-Reply-To: <CB2D02C4-4B5A-4B59-B2F4-C9099953447A@ucdavis.edu>
References: <CAPGyz26PLEocxz9UVakPWYQOej=9YAe=ZaUyzmMY-bJtWd35gA@mail.gmail.com>
 <5a8fdc94-a0e6-b869-7f6c-c7ae88654b4c@ucdavis.edu>
 <CAPGyz26eGg7VXswcD=EiEt3ZhTuuubNz_+7J2msJka3BFTpG9A@mail.gmail.com>
 <CB2D02C4-4B5A-4B59-B2F4-C9099953447A@ucdavis.edu>
Message-ID: <CAMRj59HgpCwp91sLtWv6Y2mEf=qDMXOovM0V06A7TWNGLc8_pg@mail.gmail.com>

Lev, John,

this is a bug in ASPECT when compiling with an old compiler without
c++11 support. We will get this fixed as soon as possible.



On Thu, Nov 3, 2016 at 2:35 AM, John Naliboff <jbnaliboff at ucdavis.edu> wrote:
> Hi Lev,
>
> Does dealii example-32 compile with your latest dealii update?  That is a
> good indicator to see if the problem lies directly with the dealii
> installation, independent of ASPECT.
>
> Cheers,
> John
>
> *************************************************
> John Naliboff
> Assistant Project Scientist, CIG
> Earth & Planetary Sciences Dept., UC Davis
>
>
>
> On Nov 2, 2016, at 9:36 AM, Lev Karatun <lev.karatun at gmail.com> wrote:
>
> Hi John,
>
> I'm using the latest version of dealII (commit 0e395a1 - 16 hours ago),
> updated it just before updating aspect. Trilinos version is 11.12.1. I
> donwnloaded aspect into a separate empty directory, it doesn't compile from
> there.
>
> Best regards,
> Lev Karatun.
>
> 2016-11-02 12:00 GMT-04:00 John Naliboff <jbnaliboff at ucdavis.edu>:
>>
>> Hi Lev,
>>
>> What Trilinos and dealii version are you using?  If you are using the
>> development version of dealii, when was the last update?  Also, did you do
>> 'make distclean' before reconfiguring and compiling ASPECT?  I'm not sure
>> what the error below is related to, but the aforementioned information is
>> always helpful when debugging an installation issue.
>>
>> Cheers,
>> John
>>
>>
>> *************************************************
>> John Naliboff
>> Assistant Project Scientist, CIG
>> Earth & Planetary Sciences Dept., UC Davis
>>
>> On 11/02/2016 06:45 AM, Lev Karatun wrote:
>>
>> Hi,
>>
>> I was trying to update Aspect to the latest version and got the following
>> error:
>>
>> [  0%] Building CXX object
>> CMakeFiles/aspect.dir/source/simulator/core.cc.o
>> In file included from
>> /home/lev/aspect/aspect_debug/include/aspect/simulator.h:30,
>>                  from
>> /home/lev/aspect/aspect_debug/source/simulator/core.cc:22:
>> /home/lev/aspect/dealii_debug/include/deal.II/lac/trilinos_block_vector.h:
>> In member function ‘void std::vector<_Tp, _Alloc>::resize(size_t, _Tp) [with
>> _Tp = dealii::TrilinosWrappers::Vector, _Alloc =
>> std::allocator<dealii::TrilinosWrappers::Vector>]’:
>>
>> /home/lev/aspect/dealii_debug/include/deal.II/lac/trilinos_block_vector.h:399:
>> warning: ‘dealii::TrilinosWrappers::Vector::Vector()’ is deprecated
>> (declared at
>> /home/lev/aspect/dealii_debug/include/deal.II/lac/trilinos_vector.h:770)
>> In file included from /home/lev/aspect/trilinos/include/Amesos.h:34,
>>                  from
>> /home/lev/aspect/dealii_debug/include/deal.II/lac/trilinos_solver.h:34,
>>                  from
>> /home/lev/aspect/dealii_debug/include/deal.II/lac/generic_linear_algebra.h:143,
>>                  from
>> /home/lev/aspect/aspect_debug/include/aspect/global.h:35,
>>                  from
>> /home/lev/aspect/aspect_debug/include/aspect/simulator.h:42,
>>                  from
>> /home/lev/aspect/aspect_debug/source/simulator/core.cc:22:
>> /home/lev/aspect/trilinos/include/Amesos_BaseSolver.h: At global scope:
>> /home/lev/aspect/trilinos/include/Amesos_BaseSolver.h:410: warning: unused
>> parameter ‘paramList’
>> /home/lev/aspect/trilinos/include/Amesos_BaseSolver.h:432: warning: unused
>> parameter ‘TimingParameterList’
>> In file included from
>> /home/lev/aspect/dealii_debug/include/deal.II/base/parameter_handler.h:24,
>>                  from
>> /home/lev/aspect/aspect_debug/include/aspect/simulator.h:26,
>>                  from
>> /home/lev/aspect/aspect_debug/source/simulator/core.cc:22:
>>
>> /home/lev/aspect/dealii_debug/include/deal.II/bundled/boost/smart_ptr/scoped_ptr.hpp:
>> In copy constructor ‘dealii::std_cxx11::unique_ptr<dealii::Mapping<2, 2>
>> >::unique_ptr(const dealii::std_cxx11::unique_ptr<dealii::Mapping<2, 2>
>> >&)’:
>>
>> /home/lev/aspect/dealii_debug/include/deal.II/base/std_cxx11/unique_ptr.h:60:
>> instantiated from ‘aspect::Simulator<dim>::Simulator(ompi_communicator_t*,
>> dealii::ParameterHandler&) [with int dim = 2]’
>> /home/lev/aspect/aspect_debug/source/simulator/core.cc:2471:
>> instantiated from here
>>
>> /home/lev/aspect/dealii_debug/include/deal.II/bundled/boost/smart_ptr/scoped_ptr.hpp:47:
>> error: ‘boost::scoped_ptr<T>::scoped_ptr(const boost::scoped_ptr<T>&) [with
>> T = dealii::Mapping<2, 2>]’ is private
>>
>> /home/lev/aspect/dealii_debug/include/deal.II/base/std_cxx11/unique_ptr.h:60:
>> error: within this context
>> /home/lev/aspect/aspect_debug/source/simulator/core.cc: In constructor
>> ‘aspect::Simulator<dim>::Simulator(ompi_communicator_t*,
>> dealii::ParameterHandler&) [with int dim = 2]’:
>> /home/lev/aspect/aspect_debug/source/simulator/core.cc:2471:
>> instantiated from here
>> /home/lev/aspect/aspect_debug/source/simulator/core.cc:218: note:
>> synthesized method ‘dealii::std_cxx11::unique_ptr<dealii::Mapping<2, 2>
>> >::unique_ptr(const dealii::std_cxx11::unique_ptr<dealii::Mapping<2, 2> >&)’
>> first required here
>> In file included from
>> /home/lev/aspect/dealii_debug/include/deal.II/base/parameter_handler.h:24,
>>                  from
>> /home/lev/aspect/aspect_debug/include/aspect/simulator.h:26,
>>                  from
>> /home/lev/aspect/aspect_debug/source/simulator/core.cc:22:
>>
>> /home/lev/aspect/dealii_debug/include/deal.II/bundled/boost/smart_ptr/scoped_ptr.hpp:
>> In copy constructor ‘dealii::std_cxx11::unique_ptr<dealii::Mapping<3, 3>
>> >::unique_ptr(const dealii::std_cxx11::unique_ptr<dealii::Mapping<3, 3>
>> >&)’:
>>
>> /home/lev/aspect/dealii_debug/include/deal.II/base/std_cxx11/unique_ptr.h:60:
>> instantiated from ‘aspect::Simulator<dim>::Simulator(ompi_communicator_t*,
>> dealii::ParameterHandler&) [with int dim = 3]’
>> /home/lev/aspect/aspect_debug/source/simulator/core.cc:2471:
>> instantiated from here
>>
>> /home/lev/aspect/dealii_debug/include/deal.II/bundled/boost/smart_ptr/scoped_ptr.hpp:47:
>> error: ‘boost::scoped_ptr<T>::scoped_ptr(const boost::scoped_ptr<T>&) [with
>> T = dealii::Mapping<3, 3>]’ is private
>>
>> /home/lev/aspect/dealii_debug/include/deal.II/base/std_cxx11/unique_ptr.h:60:
>> error: within this context
>> /home/lev/aspect/aspect_debug/source/simulator/core.cc: In constructor
>> ‘aspect::Simulator<dim>::Simulator(ompi_communicator_t*,
>> dealii::ParameterHandler&) [with int dim = 3]’:
>> /home/lev/aspect/aspect_debug/source/simulator/core.cc:2471:
>> instantiated from here
>> /home/lev/aspect/aspect_debug/source/simulator/core.cc:218: note:
>> synthesized method ‘dealii::std_cxx11::unique_ptr<dealii::Mapping<3, 3>
>> >::unique_ptr(const dealii::std_cxx11::unique_ptr<dealii::Mapping<3, 3> >&)’
>> first required here
>>
>> /home/lev/aspect/dealii_debug/include/deal.II/bundled/boost/system/error_code.hpp:
>> At global scope:
>>
>> /home/lev/aspect/dealii_debug/include/deal.II/bundled/boost/system/error_code.hpp:221:
>> warning: ‘boost::system::posix_category’ defined but not used
>>
>> /home/lev/aspect/dealii_debug/include/deal.II/bundled/boost/system/error_code.hpp:222:
>> warning: ‘boost::system::errno_ecat’ defined but not used
>>
>> /home/lev/aspect/dealii_debug/include/deal.II/bundled/boost/system/error_code.hpp:223:
>> warning: ‘boost::system::native_ecat’ defined but not used
>> make[2]: *** [CMakeFiles/aspect.dir/source/simulator/core.cc.o] Error 1
>> make[1]: *** [CMakeFiles/aspect.dir/all] Error 2
>> make: *** [all] Error 2
>>
>> Tips on how to solve it would be appreciated.
>>
>> Best regards,
>> Lev Karatun.
>>
>>
>> _______________________________________________
>> Aspect-devel mailing list
>> Aspect-devel at geodynamics.org
>> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.geodynamics.org_cgi-2Dbin_mailman_listinfo_aspect-2Ddevel&d=CwIFaQ&c=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4&r=c08Btfq4m9QEScXN3ZQwLZzzWQE7S8CYq1IYuzKV_Zk&m=tJ1AVo2FsV-Q84Fz6OS2qIZMpTUeSn73iBh1vOoL-4I&s=S5AxEYm2M51bBBYwKjekwC4X0fPFVN41NEhcRyvw3Hg&e= 
>>
>>
>>
>> _______________________________________________
>> Aspect-devel mailing list
>> Aspect-devel at geodynamics.org
>> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.geodynamics.org_cgi-2Dbin_mailman_listinfo_aspect-2Ddevel&d=CwIFaQ&c=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4&r=c08Btfq4m9QEScXN3ZQwLZzzWQE7S8CYq1IYuzKV_Zk&m=tJ1AVo2FsV-Q84Fz6OS2qIZMpTUeSn73iBh1vOoL-4I&s=S5AxEYm2M51bBBYwKjekwC4X0fPFVN41NEhcRyvw3Hg&e= 
>
>
> _______________________________________________
> Aspect-devel mailing list
> Aspect-devel at geodynamics.org
> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.geodynamics.org_cgi-2Dbin_mailman_listinfo_aspect-2Ddevel&d=CwIFaQ&c=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4&r=c08Btfq4m9QEScXN3ZQwLZzzWQE7S8CYq1IYuzKV_Zk&m=tJ1AVo2FsV-Q84Fz6OS2qIZMpTUeSn73iBh1vOoL-4I&s=S5AxEYm2M51bBBYwKjekwC4X0fPFVN41NEhcRyvw3Hg&e= 
>
>
>
> _______________________________________________
> Aspect-devel mailing list
> Aspect-devel at geodynamics.org
> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.geodynamics.org_cgi-2Dbin_mailman_listinfo_aspect-2Ddevel&d=CwIGaQ&c=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4&r=R5lvg9JC99XvuTgScgbY_QFS80R7PEA2q0EPwDy7VQw&m=hQ2ClMQtaiXOLdBNbZSCUQKZqCsXZT517zxswRk1j-s&s=XRsatNYOGKjztBbXCCQNnZADxPi7Ehgp7vphUTYhDSc&e=


-- 
Timo Heister
http://www.math.clemson.edu/~heister/

From heister at clemson.edu  Thu Nov  3 05:21:33 2016
From: heister at clemson.edu (Timo Heister)
Date: Thu, 3 Nov 2016 08:21:33 -0400
Subject: [aspect-devel] compilation error
In-Reply-To: <CAMRj59HgpCwp91sLtWv6Y2mEf=qDMXOovM0V06A7TWNGLc8_pg@mail.gmail.com>
References: <CAPGyz26PLEocxz9UVakPWYQOej=9YAe=ZaUyzmMY-bJtWd35gA@mail.gmail.com>
 <5a8fdc94-a0e6-b869-7f6c-c7ae88654b4c@ucdavis.edu>
 <CAPGyz26eGg7VXswcD=EiEt3ZhTuuubNz_+7J2msJka3BFTpG9A@mail.gmail.com>
 <CB2D02C4-4B5A-4B59-B2F4-C9099953447A@ucdavis.edu>
 <CAMRj59HgpCwp91sLtWv6Y2mEf=qDMXOovM0V06A7TWNGLc8_pg@mail.gmail.com>
Message-ID: <CAMRj59HvxOQpRtqcfOckve3HeGsjUeTCYu4Hx+EMWimsTx2VMA@mail.gmail.com>

> This may not help but as a last attempt, try building with CXX11 support.
> The cmake flag is:
>
> -DDEAL_II_WITH_CXX11=ON

This is on by default so I assume it got disabled automatically
because his compiler is too old to support it.


On Thu, Nov 3, 2016 at 8:19 AM, Timo Heister <heister at clemson.edu> wrote:
> Lev, John,
>
> this is a bug in ASPECT when compiling with an old compiler without
> c++11 support. We will get this fixed as soon as possible.
>
>
>
> On Thu, Nov 3, 2016 at 2:35 AM, John Naliboff <jbnaliboff at ucdavis.edu> wrote:
>> Hi Lev,
>>
>> Does dealii example-32 compile with your latest dealii update?  That is a
>> good indicator to see if the problem lies directly with the dealii
>> installation, independent of ASPECT.
>>
>> Cheers,
>> John
>>
>> *************************************************
>> John Naliboff
>> Assistant Project Scientist, CIG
>> Earth & Planetary Sciences Dept., UC Davis
>>
>>
>>
>> On Nov 2, 2016, at 9:36 AM, Lev Karatun <lev.karatun at gmail.com> wrote:
>>
>> Hi John,
>>
>> I'm using the latest version of dealII (commit 0e395a1 - 16 hours ago),
>> updated it just before updating aspect. Trilinos version is 11.12.1. I
>> donwnloaded aspect into a separate empty directory, it doesn't compile from
>> there.
>>
>> Best regards,
>> Lev Karatun.
>>
>> 2016-11-02 12:00 GMT-04:00 John Naliboff <jbnaliboff at ucdavis.edu>:
>>>
>>> Hi Lev,
>>>
>>> What Trilinos and dealii version are you using?  If you are using the
>>> development version of dealii, when was the last update?  Also, did you do
>>> 'make distclean' before reconfiguring and compiling ASPECT?  I'm not sure
>>> what the error below is related to, but the aforementioned information is
>>> always helpful when debugging an installation issue.
>>>
>>> Cheers,
>>> John
>>>
>>>
>>> *************************************************
>>> John Naliboff
>>> Assistant Project Scientist, CIG
>>> Earth & Planetary Sciences Dept., UC Davis
>>>
>>> On 11/02/2016 06:45 AM, Lev Karatun wrote:
>>>
>>> Hi,
>>>
>>> I was trying to update Aspect to the latest version and got the following
>>> error:
>>>
>>> [  0%] Building CXX object
>>> CMakeFiles/aspect.dir/source/simulator/core.cc.o
>>> In file included from
>>> /home/lev/aspect/aspect_debug/include/aspect/simulator.h:30,
>>>                  from
>>> /home/lev/aspect/aspect_debug/source/simulator/core.cc:22:
>>> /home/lev/aspect/dealii_debug/include/deal.II/lac/trilinos_block_vector.h:
>>> In member function ‘void std::vector<_Tp, _Alloc>::resize(size_t, _Tp) [with
>>> _Tp = dealii::TrilinosWrappers::Vector, _Alloc =
>>> std::allocator<dealii::TrilinosWrappers::Vector>]’:
>>>
>>> /home/lev/aspect/dealii_debug/include/deal.II/lac/trilinos_block_vector.h:399:
>>> warning: ‘dealii::TrilinosWrappers::Vector::Vector()’ is deprecated
>>> (declared at
>>> /home/lev/aspect/dealii_debug/include/deal.II/lac/trilinos_vector.h:770)
>>> In file included from /home/lev/aspect/trilinos/include/Amesos.h:34,
>>>                  from
>>> /home/lev/aspect/dealii_debug/include/deal.II/lac/trilinos_solver.h:34,
>>>                  from
>>> /home/lev/aspect/dealii_debug/include/deal.II/lac/generic_linear_algebra.h:143,
>>>                  from
>>> /home/lev/aspect/aspect_debug/include/aspect/global.h:35,
>>>                  from
>>> /home/lev/aspect/aspect_debug/include/aspect/simulator.h:42,
>>>                  from
>>> /home/lev/aspect/aspect_debug/source/simulator/core.cc:22:
>>> /home/lev/aspect/trilinos/include/Amesos_BaseSolver.h: At global scope:
>>> /home/lev/aspect/trilinos/include/Amesos_BaseSolver.h:410: warning: unused
>>> parameter ‘paramList’
>>> /home/lev/aspect/trilinos/include/Amesos_BaseSolver.h:432: warning: unused
>>> parameter ‘TimingParameterList’
>>> In file included from
>>> /home/lev/aspect/dealii_debug/include/deal.II/base/parameter_handler.h:24,
>>>                  from
>>> /home/lev/aspect/aspect_debug/include/aspect/simulator.h:26,
>>>                  from
>>> /home/lev/aspect/aspect_debug/source/simulator/core.cc:22:
>>>
>>> /home/lev/aspect/dealii_debug/include/deal.II/bundled/boost/smart_ptr/scoped_ptr.hpp:
>>> In copy constructor ‘dealii::std_cxx11::unique_ptr<dealii::Mapping<2, 2>
>>> >::unique_ptr(const dealii::std_cxx11::unique_ptr<dealii::Mapping<2, 2>
>>> >&)’:
>>>
>>> /home/lev/aspect/dealii_debug/include/deal.II/base/std_cxx11/unique_ptr.h:60:
>>> instantiated from ‘aspect::Simulator<dim>::Simulator(ompi_communicator_t*,
>>> dealii::ParameterHandler&) [with int dim = 2]’
>>> /home/lev/aspect/aspect_debug/source/simulator/core.cc:2471:
>>> instantiated from here
>>>
>>> /home/lev/aspect/dealii_debug/include/deal.II/bundled/boost/smart_ptr/scoped_ptr.hpp:47:
>>> error: ‘boost::scoped_ptr<T>::scoped_ptr(const boost::scoped_ptr<T>&) [with
>>> T = dealii::Mapping<2, 2>]’ is private
>>>
>>> /home/lev/aspect/dealii_debug/include/deal.II/base/std_cxx11/unique_ptr.h:60:
>>> error: within this context
>>> /home/lev/aspect/aspect_debug/source/simulator/core.cc: In constructor
>>> ‘aspect::Simulator<dim>::Simulator(ompi_communicator_t*,
>>> dealii::ParameterHandler&) [with int dim = 2]’:
>>> /home/lev/aspect/aspect_debug/source/simulator/core.cc:2471:
>>> instantiated from here
>>> /home/lev/aspect/aspect_debug/source/simulator/core.cc:218: note:
>>> synthesized method ‘dealii::std_cxx11::unique_ptr<dealii::Mapping<2, 2>
>>> >::unique_ptr(const dealii::std_cxx11::unique_ptr<dealii::Mapping<2, 2> >&)’
>>> first required here
>>> In file included from
>>> /home/lev/aspect/dealii_debug/include/deal.II/base/parameter_handler.h:24,
>>>                  from
>>> /home/lev/aspect/aspect_debug/include/aspect/simulator.h:26,
>>>                  from
>>> /home/lev/aspect/aspect_debug/source/simulator/core.cc:22:
>>>
>>> /home/lev/aspect/dealii_debug/include/deal.II/bundled/boost/smart_ptr/scoped_ptr.hpp:
>>> In copy constructor ‘dealii::std_cxx11::unique_ptr<dealii::Mapping<3, 3>
>>> >::unique_ptr(const dealii::std_cxx11::unique_ptr<dealii::Mapping<3, 3>
>>> >&)’:
>>>
>>> /home/lev/aspect/dealii_debug/include/deal.II/base/std_cxx11/unique_ptr.h:60:
>>> instantiated from ‘aspect::Simulator<dim>::Simulator(ompi_communicator_t*,
>>> dealii::ParameterHandler&) [with int dim = 3]’
>>> /home/lev/aspect/aspect_debug/source/simulator/core.cc:2471:
>>> instantiated from here
>>>
>>> /home/lev/aspect/dealii_debug/include/deal.II/bundled/boost/smart_ptr/scoped_ptr.hpp:47:
>>> error: ‘boost::scoped_ptr<T>::scoped_ptr(const boost::scoped_ptr<T>&) [with
>>> T = dealii::Mapping<3, 3>]’ is private
>>>
>>> /home/lev/aspect/dealii_debug/include/deal.II/base/std_cxx11/unique_ptr.h:60:
>>> error: within this context
>>> /home/lev/aspect/aspect_debug/source/simulator/core.cc: In constructor
>>> ‘aspect::Simulator<dim>::Simulator(ompi_communicator_t*,
>>> dealii::ParameterHandler&) [with int dim = 3]’:
>>> /home/lev/aspect/aspect_debug/source/simulator/core.cc:2471:
>>> instantiated from here
>>> /home/lev/aspect/aspect_debug/source/simulator/core.cc:218: note:
>>> synthesized method ‘dealii::std_cxx11::unique_ptr<dealii::Mapping<3, 3>
>>> >::unique_ptr(const dealii::std_cxx11::unique_ptr<dealii::Mapping<3, 3> >&)’
>>> first required here
>>>
>>> /home/lev/aspect/dealii_debug/include/deal.II/bundled/boost/system/error_code.hpp:
>>> At global scope:
>>>
>>> /home/lev/aspect/dealii_debug/include/deal.II/bundled/boost/system/error_code.hpp:221:
>>> warning: ‘boost::system::posix_category’ defined but not used
>>>
>>> /home/lev/aspect/dealii_debug/include/deal.II/bundled/boost/system/error_code.hpp:222:
>>> warning: ‘boost::system::errno_ecat’ defined but not used
>>>
>>> /home/lev/aspect/dealii_debug/include/deal.II/bundled/boost/system/error_code.hpp:223:
>>> warning: ‘boost::system::native_ecat’ defined but not used
>>> make[2]: *** [CMakeFiles/aspect.dir/source/simulator/core.cc.o] Error 1
>>> make[1]: *** [CMakeFiles/aspect.dir/all] Error 2
>>> make: *** [all] Error 2
>>>
>>> Tips on how to solve it would be appreciated.
>>>
>>> Best regards,
>>> Lev Karatun.
>>>
>>>
>>> _______________________________________________
>>> Aspect-devel mailing list
>>> Aspect-devel at geodynamics.org
>>> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.geodynamics.org_cgi-2Dbin_mailman_listinfo_aspect-2Ddevel&d=CwIFaQ&c=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4&r=c08Btfq4m9QEScXN3ZQwLZzzWQE7S8CYq1IYuzKV_Zk&m=syxgWvWwIaL0Qr_hsPI90TnRuFsyMyEcb4OEIwaMybE&s=G5gPR8_CRWvpRyCcP0237nJcyqAG7xa2si02at4gU5o&e= 
>>>
>>>
>>>
>>> _______________________________________________
>>> Aspect-devel mailing list
>>> Aspect-devel at geodynamics.org
>>> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.geodynamics.org_cgi-2Dbin_mailman_listinfo_aspect-2Ddevel&d=CwIFaQ&c=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4&r=c08Btfq4m9QEScXN3ZQwLZzzWQE7S8CYq1IYuzKV_Zk&m=syxgWvWwIaL0Qr_hsPI90TnRuFsyMyEcb4OEIwaMybE&s=G5gPR8_CRWvpRyCcP0237nJcyqAG7xa2si02at4gU5o&e= 
>>
>>
>> _______________________________________________
>> Aspect-devel mailing list
>> Aspect-devel at geodynamics.org
>> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.geodynamics.org_cgi-2Dbin_mailman_listinfo_aspect-2Ddevel&d=CwIFaQ&c=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4&r=c08Btfq4m9QEScXN3ZQwLZzzWQE7S8CYq1IYuzKV_Zk&m=syxgWvWwIaL0Qr_hsPI90TnRuFsyMyEcb4OEIwaMybE&s=G5gPR8_CRWvpRyCcP0237nJcyqAG7xa2si02at4gU5o&e= 
>>
>>
>>
>> _______________________________________________
>> Aspect-devel mailing list
>> Aspect-devel at geodynamics.org
>> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.geodynamics.org_cgi-2Dbin_mailman_listinfo_aspect-2Ddevel&d=CwIGaQ&c=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4&r=R5lvg9JC99XvuTgScgbY_QFS80R7PEA2q0EPwDy7VQw&m=hQ2ClMQtaiXOLdBNbZSCUQKZqCsXZT517zxswRk1j-s&s=XRsatNYOGKjztBbXCCQNnZADxPi7Ehgp7vphUTYhDSc&e=
>
>
> --
> Timo Heister
> http://www.math.clemson.edu/~heister/



-- 
Timo Heister
http://www.math.clemson.edu/~heister/

From heister at clemson.edu  Thu Nov  3 05:57:08 2016
From: heister at clemson.edu (Timo Heister)
Date: Thu, 3 Nov 2016 08:57:08 -0400
Subject: [aspect-devel] compilation error
In-Reply-To: <CAMRj59HvxOQpRtqcfOckve3HeGsjUeTCYu4Hx+EMWimsTx2VMA@mail.gmail.com>
References: <CAPGyz26PLEocxz9UVakPWYQOej=9YAe=ZaUyzmMY-bJtWd35gA@mail.gmail.com>
 <5a8fdc94-a0e6-b869-7f6c-c7ae88654b4c@ucdavis.edu>
 <CAPGyz26eGg7VXswcD=EiEt3ZhTuuubNz_+7J2msJka3BFTpG9A@mail.gmail.com>
 <CB2D02C4-4B5A-4B59-B2F4-C9099953447A@ucdavis.edu>
 <CAMRj59HgpCwp91sLtWv6Y2mEf=qDMXOovM0V06A7TWNGLc8_pg@mail.gmail.com>
 <CAMRj59HvxOQpRtqcfOckve3HeGsjUeTCYu4Hx+EMWimsTx2VMA@mail.gmail.com>
Message-ID: <CAMRj59F6EBqx3zVXx4UzEgP1vny6EEHD3K=542md-6eDzgkOww@mail.gmail.com>

see https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_geodynamics_aspect_pull_1267&d=CwIFaQ&c=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4&r=c08Btfq4m9QEScXN3ZQwLZzzWQE7S8CYq1IYuzKV_Zk&m=5r5_DItWuONwoXvldIba3ADkcnN7FquA2JnGyXmTzmE&s=UhFn-WbTnWDY3DxqufF0zkfaJiOXBGD0q0C9F2WSpvU&e=  for a proposed fix.

On Thu, Nov 3, 2016 at 8:21 AM, Timo Heister <heister at clemson.edu> wrote:
>> This may not help but as a last attempt, try building with CXX11 support.
>> The cmake flag is:
>>
>> -DDEAL_II_WITH_CXX11=ON
>
> This is on by default so I assume it got disabled automatically
> because his compiler is too old to support it.
>
>
> On Thu, Nov 3, 2016 at 8:19 AM, Timo Heister <heister at clemson.edu> wrote:
>> Lev, John,
>>
>> this is a bug in ASPECT when compiling with an old compiler without
>> c++11 support. We will get this fixed as soon as possible.
>>
>>
>>
>> On Thu, Nov 3, 2016 at 2:35 AM, John Naliboff <jbnaliboff at ucdavis.edu> wrote:
>>> Hi Lev,
>>>
>>> Does dealii example-32 compile with your latest dealii update?  That is a
>>> good indicator to see if the problem lies directly with the dealii
>>> installation, independent of ASPECT.
>>>
>>> Cheers,
>>> John
>>>
>>> *************************************************
>>> John Naliboff
>>> Assistant Project Scientist, CIG
>>> Earth & Planetary Sciences Dept., UC Davis
>>>
>>>
>>>
>>> On Nov 2, 2016, at 9:36 AM, Lev Karatun <lev.karatun at gmail.com> wrote:
>>>
>>> Hi John,
>>>
>>> I'm using the latest version of dealII (commit 0e395a1 - 16 hours ago),
>>> updated it just before updating aspect. Trilinos version is 11.12.1. I
>>> donwnloaded aspect into a separate empty directory, it doesn't compile from
>>> there.
>>>
>>> Best regards,
>>> Lev Karatun.
>>>
>>> 2016-11-02 12:00 GMT-04:00 John Naliboff <jbnaliboff at ucdavis.edu>:
>>>>
>>>> Hi Lev,
>>>>
>>>> What Trilinos and dealii version are you using?  If you are using the
>>>> development version of dealii, when was the last update?  Also, did you do
>>>> 'make distclean' before reconfiguring and compiling ASPECT?  I'm not sure
>>>> what the error below is related to, but the aforementioned information is
>>>> always helpful when debugging an installation issue.
>>>>
>>>> Cheers,
>>>> John
>>>>
>>>>
>>>> *************************************************
>>>> John Naliboff
>>>> Assistant Project Scientist, CIG
>>>> Earth & Planetary Sciences Dept., UC Davis
>>>>
>>>> On 11/02/2016 06:45 AM, Lev Karatun wrote:
>>>>
>>>> Hi,
>>>>
>>>> I was trying to update Aspect to the latest version and got the following
>>>> error:
>>>>
>>>> [  0%] Building CXX object
>>>> CMakeFiles/aspect.dir/source/simulator/core.cc.o
>>>> In file included from
>>>> /home/lev/aspect/aspect_debug/include/aspect/simulator.h:30,
>>>>                  from
>>>> /home/lev/aspect/aspect_debug/source/simulator/core.cc:22:
>>>> /home/lev/aspect/dealii_debug/include/deal.II/lac/trilinos_block_vector.h:
>>>> In member function ‘void std::vector<_Tp, _Alloc>::resize(size_t, _Tp) [with
>>>> _Tp = dealii::TrilinosWrappers::Vector, _Alloc =
>>>> std::allocator<dealii::TrilinosWrappers::Vector>]’:
>>>>
>>>> /home/lev/aspect/dealii_debug/include/deal.II/lac/trilinos_block_vector.h:399:
>>>> warning: ‘dealii::TrilinosWrappers::Vector::Vector()’ is deprecated
>>>> (declared at
>>>> /home/lev/aspect/dealii_debug/include/deal.II/lac/trilinos_vector.h:770)
>>>> In file included from /home/lev/aspect/trilinos/include/Amesos.h:34,
>>>>                  from
>>>> /home/lev/aspect/dealii_debug/include/deal.II/lac/trilinos_solver.h:34,
>>>>                  from
>>>> /home/lev/aspect/dealii_debug/include/deal.II/lac/generic_linear_algebra.h:143,
>>>>                  from
>>>> /home/lev/aspect/aspect_debug/include/aspect/global.h:35,
>>>>                  from
>>>> /home/lev/aspect/aspect_debug/include/aspect/simulator.h:42,
>>>>                  from
>>>> /home/lev/aspect/aspect_debug/source/simulator/core.cc:22:
>>>> /home/lev/aspect/trilinos/include/Amesos_BaseSolver.h: At global scope:
>>>> /home/lev/aspect/trilinos/include/Amesos_BaseSolver.h:410: warning: unused
>>>> parameter ‘paramList’
>>>> /home/lev/aspect/trilinos/include/Amesos_BaseSolver.h:432: warning: unused
>>>> parameter ‘TimingParameterList’
>>>> In file included from
>>>> /home/lev/aspect/dealii_debug/include/deal.II/base/parameter_handler.h:24,
>>>>                  from
>>>> /home/lev/aspect/aspect_debug/include/aspect/simulator.h:26,
>>>>                  from
>>>> /home/lev/aspect/aspect_debug/source/simulator/core.cc:22:
>>>>
>>>> /home/lev/aspect/dealii_debug/include/deal.II/bundled/boost/smart_ptr/scoped_ptr.hpp:
>>>> In copy constructor ‘dealii::std_cxx11::unique_ptr<dealii::Mapping<2, 2>
>>>> >::unique_ptr(const dealii::std_cxx11::unique_ptr<dealii::Mapping<2, 2>
>>>> >&)’:
>>>>
>>>> /home/lev/aspect/dealii_debug/include/deal.II/base/std_cxx11/unique_ptr.h:60:
>>>> instantiated from ‘aspect::Simulator<dim>::Simulator(ompi_communicator_t*,
>>>> dealii::ParameterHandler&) [with int dim = 2]’
>>>> /home/lev/aspect/aspect_debug/source/simulator/core.cc:2471:
>>>> instantiated from here
>>>>
>>>> /home/lev/aspect/dealii_debug/include/deal.II/bundled/boost/smart_ptr/scoped_ptr.hpp:47:
>>>> error: ‘boost::scoped_ptr<T>::scoped_ptr(const boost::scoped_ptr<T>&) [with
>>>> T = dealii::Mapping<2, 2>]’ is private
>>>>
>>>> /home/lev/aspect/dealii_debug/include/deal.II/base/std_cxx11/unique_ptr.h:60:
>>>> error: within this context
>>>> /home/lev/aspect/aspect_debug/source/simulator/core.cc: In constructor
>>>> ‘aspect::Simulator<dim>::Simulator(ompi_communicator_t*,
>>>> dealii::ParameterHandler&) [with int dim = 2]’:
>>>> /home/lev/aspect/aspect_debug/source/simulator/core.cc:2471:
>>>> instantiated from here
>>>> /home/lev/aspect/aspect_debug/source/simulator/core.cc:218: note:
>>>> synthesized method ‘dealii::std_cxx11::unique_ptr<dealii::Mapping<2, 2>
>>>> >::unique_ptr(const dealii::std_cxx11::unique_ptr<dealii::Mapping<2, 2> >&)’
>>>> first required here
>>>> In file included from
>>>> /home/lev/aspect/dealii_debug/include/deal.II/base/parameter_handler.h:24,
>>>>                  from
>>>> /home/lev/aspect/aspect_debug/include/aspect/simulator.h:26,
>>>>                  from
>>>> /home/lev/aspect/aspect_debug/source/simulator/core.cc:22:
>>>>
>>>> /home/lev/aspect/dealii_debug/include/deal.II/bundled/boost/smart_ptr/scoped_ptr.hpp:
>>>> In copy constructor ‘dealii::std_cxx11::unique_ptr<dealii::Mapping<3, 3>
>>>> >::unique_ptr(const dealii::std_cxx11::unique_ptr<dealii::Mapping<3, 3>
>>>> >&)’:
>>>>
>>>> /home/lev/aspect/dealii_debug/include/deal.II/base/std_cxx11/unique_ptr.h:60:
>>>> instantiated from ‘aspect::Simulator<dim>::Simulator(ompi_communicator_t*,
>>>> dealii::ParameterHandler&) [with int dim = 3]’
>>>> /home/lev/aspect/aspect_debug/source/simulator/core.cc:2471:
>>>> instantiated from here
>>>>
>>>> /home/lev/aspect/dealii_debug/include/deal.II/bundled/boost/smart_ptr/scoped_ptr.hpp:47:
>>>> error: ‘boost::scoped_ptr<T>::scoped_ptr(const boost::scoped_ptr<T>&) [with
>>>> T = dealii::Mapping<3, 3>]’ is private
>>>>
>>>> /home/lev/aspect/dealii_debug/include/deal.II/base/std_cxx11/unique_ptr.h:60:
>>>> error: within this context
>>>> /home/lev/aspect/aspect_debug/source/simulator/core.cc: In constructor
>>>> ‘aspect::Simulator<dim>::Simulator(ompi_communicator_t*,
>>>> dealii::ParameterHandler&) [with int dim = 3]’:
>>>> /home/lev/aspect/aspect_debug/source/simulator/core.cc:2471:
>>>> instantiated from here
>>>> /home/lev/aspect/aspect_debug/source/simulator/core.cc:218: note:
>>>> synthesized method ‘dealii::std_cxx11::unique_ptr<dealii::Mapping<3, 3>
>>>> >::unique_ptr(const dealii::std_cxx11::unique_ptr<dealii::Mapping<3, 3> >&)’
>>>> first required here
>>>>
>>>> /home/lev/aspect/dealii_debug/include/deal.II/bundled/boost/system/error_code.hpp:
>>>> At global scope:
>>>>
>>>> /home/lev/aspect/dealii_debug/include/deal.II/bundled/boost/system/error_code.hpp:221:
>>>> warning: ‘boost::system::posix_category’ defined but not used
>>>>
>>>> /home/lev/aspect/dealii_debug/include/deal.II/bundled/boost/system/error_code.hpp:222:
>>>> warning: ‘boost::system::errno_ecat’ defined but not used
>>>>
>>>> /home/lev/aspect/dealii_debug/include/deal.II/bundled/boost/system/error_code.hpp:223:
>>>> warning: ‘boost::system::native_ecat’ defined but not used
>>>> make[2]: *** [CMakeFiles/aspect.dir/source/simulator/core.cc.o] Error 1
>>>> make[1]: *** [CMakeFiles/aspect.dir/all] Error 2
>>>> make: *** [all] Error 2
>>>>
>>>> Tips on how to solve it would be appreciated.
>>>>
>>>> Best regards,
>>>> Lev Karatun.
>>>>
>>>>
>>>> _______________________________________________
>>>> Aspect-devel mailing list
>>>> Aspect-devel at geodynamics.org
>>>> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.geodynamics.org_cgi-2Dbin_mailman_listinfo_aspect-2Ddevel&d=CwIFaQ&c=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4&r=c08Btfq4m9QEScXN3ZQwLZzzWQE7S8CYq1IYuzKV_Zk&m=5r5_DItWuONwoXvldIba3ADkcnN7FquA2JnGyXmTzmE&s=tHVqWLlk_265tEXD1zrOhkNBE6fpd4_xM7l5tib7E9U&e= 
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> Aspect-devel mailing list
>>>> Aspect-devel at geodynamics.org
>>>> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.geodynamics.org_cgi-2Dbin_mailman_listinfo_aspect-2Ddevel&d=CwIFaQ&c=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4&r=c08Btfq4m9QEScXN3ZQwLZzzWQE7S8CYq1IYuzKV_Zk&m=5r5_DItWuONwoXvldIba3ADkcnN7FquA2JnGyXmTzmE&s=tHVqWLlk_265tEXD1zrOhkNBE6fpd4_xM7l5tib7E9U&e= 
>>>
>>>
>>> _______________________________________________
>>> Aspect-devel mailing list
>>> Aspect-devel at geodynamics.org
>>> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.geodynamics.org_cgi-2Dbin_mailman_listinfo_aspect-2Ddevel&d=CwIFaQ&c=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4&r=c08Btfq4m9QEScXN3ZQwLZzzWQE7S8CYq1IYuzKV_Zk&m=5r5_DItWuONwoXvldIba3ADkcnN7FquA2JnGyXmTzmE&s=tHVqWLlk_265tEXD1zrOhkNBE6fpd4_xM7l5tib7E9U&e= 
>>>
>>>
>>>
>>> _______________________________________________
>>> Aspect-devel mailing list
>>> Aspect-devel at geodynamics.org
>>> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.geodynamics.org_cgi-2Dbin_mailman_listinfo_aspect-2Ddevel&d=CwIGaQ&c=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4&r=R5lvg9JC99XvuTgScgbY_QFS80R7PEA2q0EPwDy7VQw&m=hQ2ClMQtaiXOLdBNbZSCUQKZqCsXZT517zxswRk1j-s&s=XRsatNYOGKjztBbXCCQNnZADxPi7Ehgp7vphUTYhDSc&e=
>>
>>
>> --
>> Timo Heister
>> http://www.math.clemson.edu/~heister/
>
>
>
> --
> Timo Heister
> http://www.math.clemson.edu/~heister/



-- 
Timo Heister
http://www.math.clemson.edu/~heister/

From lev.karatun at gmail.com  Thu Nov  3 07:33:46 2016
From: lev.karatun at gmail.com (Lev Karatun)
Date: Thu, 3 Nov 2016 10:33:46 -0400
Subject: [aspect-devel] compilation error
In-Reply-To: <CAMRj59F6EBqx3zVXx4UzEgP1vny6EEHD3K=542md-6eDzgkOww@mail.gmail.com>
References: <CAPGyz26PLEocxz9UVakPWYQOej=9YAe=ZaUyzmMY-bJtWd35gA@mail.gmail.com>
 <5a8fdc94-a0e6-b869-7f6c-c7ae88654b4c@ucdavis.edu>
 <CAPGyz26eGg7VXswcD=EiEt3ZhTuuubNz_+7J2msJka3BFTpG9A@mail.gmail.com>
 <CB2D02C4-4B5A-4B59-B2F4-C9099953447A@ucdavis.edu>
 <CAMRj59HgpCwp91sLtWv6Y2mEf=qDMXOovM0V06A7TWNGLc8_pg@mail.gmail.com>
 <CAMRj59HvxOQpRtqcfOckve3HeGsjUeTCYu4Hx+EMWimsTx2VMA@mail.gmail.com>
 <CAMRj59F6EBqx3zVXx4UzEgP1vny6EEHD3K=542md-6eDzgkOww@mail.gmail.com>
Message-ID: <CAPGyz24H8WNVtUbCQuQ5emv-Q9j9oQTwS3uMbQdXb2Safq9Mug@mail.gmail.com>

Thank you Timo! That fixed it.

Best regards,
Lev Karatun.

2016-11-03 8:57 GMT-04:00 Timo Heister <heister at clemson.edu>:

> see https://urldefense.proofpoint.com/v2/url?u=https-3A__github.
> com_geodynamics_aspect_pull_1267&d=CwIFaQ&c=Ngd-
> ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4&r=c08Btfq4m9QEScXN3ZQwLZzzWQE7S8
> CYq1IYuzKV_Zk&m=5r5_DItWuONwoXvldIba3ADkcnN7FquA2JnGyXmTzmE&s=UhFn-
> WbTnWDY3DxqufF0zkfaJiOXBGD0q0C9F2WSpvU&e=  for a proposed fix.
>
> On Thu, Nov 3, 2016 at 8:21 AM, Timo Heister <heister at clemson.edu> wrote:
> >> This may not help but as a last attempt, try building with CXX11
> support.
> >> The cmake flag is:
> >>
> >> -DDEAL_II_WITH_CXX11=ON
> >
> > This is on by default so I assume it got disabled automatically
> > because his compiler is too old to support it.
> >
> >
> > On Thu, Nov 3, 2016 at 8:19 AM, Timo Heister <heister at clemson.edu>
> wrote:
> >> Lev, John,
> >>
> >> this is a bug in ASPECT when compiling with an old compiler without
> >> c++11 support. We will get this fixed as soon as possible.
> >>
> >>
> >>
> >> On Thu, Nov 3, 2016 at 2:35 AM, John Naliboff <jbnaliboff at ucdavis.edu>
> wrote:
> >>> Hi Lev,
> >>>
> >>> Does dealii example-32 compile with your latest dealii update?  That
> is a
> >>> good indicator to see if the problem lies directly with the dealii
> >>> installation, independent of ASPECT.
> >>>
> >>> Cheers,
> >>> John
> >>>
> >>> *************************************************
> >>> John Naliboff
> >>> Assistant Project Scientist, CIG
> >>> Earth & Planetary Sciences Dept., UC Davis
> >>>
> >>>
> >>>
> >>> On Nov 2, 2016, at 9:36 AM, Lev Karatun <lev.karatun at gmail.com> wrote:
> >>>
> >>> Hi John,
> >>>
> >>> I'm using the latest version of dealII (commit 0e395a1 - 16 hours ago),
> >>> updated it just before updating aspect. Trilinos version is 11.12.1. I
> >>> donwnloaded aspect into a separate empty directory, it doesn't compile
> from
> >>> there.
> >>>
> >>> Best regards,
> >>> Lev Karatun.
> >>>
> >>> 2016-11-02 12:00 GMT-04:00 John Naliboff <jbnaliboff at ucdavis.edu>:
> >>>>
> >>>> Hi Lev,
> >>>>
> >>>> What Trilinos and dealii version are you using?  If you are using the
> >>>> development version of dealii, when was the last update?  Also, did
> you do
> >>>> 'make distclean' before reconfiguring and compiling ASPECT?  I'm not
> sure
> >>>> what the error below is related to, but the aforementioned
> information is
> >>>> always helpful when debugging an installation issue.
> >>>>
> >>>> Cheers,
> >>>> John
> >>>>
> >>>>
> >>>> *************************************************
> >>>> John Naliboff
> >>>> Assistant Project Scientist, CIG
> >>>> Earth & Planetary Sciences Dept., UC Davis
> >>>>
> >>>> On 11/02/2016 06:45 AM, Lev Karatun wrote:
> >>>>
> >>>> Hi,
> >>>>
> >>>> I was trying to update Aspect to the latest version and got the
> following
> >>>> error:
> >>>>
> >>>> [  0%] Building CXX object
> >>>> CMakeFiles/aspect.dir/source/simulator/core.cc.o
> >>>> In file included from
> >>>> /home/lev/aspect/aspect_debug/include/aspect/simulator.h:30,
> >>>>                  from
> >>>> /home/lev/aspect/aspect_debug/source/simulator/core.cc:22:
> >>>> /home/lev/aspect/dealii_debug/include/deal.II/lac/trilinos_
> block_vector.h:
> >>>> In member function ‘void std::vector<_Tp, _Alloc>::resize(size_t,
> _Tp) [with
> >>>> _Tp = dealii::TrilinosWrappers::Vector, _Alloc =
> >>>> std::allocator<dealii::TrilinosWrappers::Vector>]’:
> >>>>
> >>>> /home/lev/aspect/dealii_debug/include/deal.II/lac/trilinos_
> block_vector.h:399:
> >>>> warning: ‘dealii::TrilinosWrappers::Vector::Vector()’ is deprecated
> >>>> (declared at
> >>>> /home/lev/aspect/dealii_debug/include/deal.II/lac/trilinos_
> vector.h:770)
> >>>> In file included from /home/lev/aspect/trilinos/include/Amesos.h:34,
> >>>>                  from
> >>>> /home/lev/aspect/dealii_debug/include/deal.II/lac/trilinos_
> solver.h:34,
> >>>>                  from
> >>>> /home/lev/aspect/dealii_debug/include/deal.II/lac/generic_
> linear_algebra.h:143,
> >>>>                  from
> >>>> /home/lev/aspect/aspect_debug/include/aspect/global.h:35,
> >>>>                  from
> >>>> /home/lev/aspect/aspect_debug/include/aspect/simulator.h:42,
> >>>>                  from
> >>>> /home/lev/aspect/aspect_debug/source/simulator/core.cc:22:
> >>>> /home/lev/aspect/trilinos/include/Amesos_BaseSolver.h: At global
> scope:
> >>>> /home/lev/aspect/trilinos/include/Amesos_BaseSolver.h:410: warning:
> unused
> >>>> parameter ‘paramList’
> >>>> /home/lev/aspect/trilinos/include/Amesos_BaseSolver.h:432: warning:
> unused
> >>>> parameter ‘TimingParameterList’
> >>>> In file included from
> >>>> /home/lev/aspect/dealii_debug/include/deal.II/base/
> parameter_handler.h:24,
> >>>>                  from
> >>>> /home/lev/aspect/aspect_debug/include/aspect/simulator.h:26,
> >>>>                  from
> >>>> /home/lev/aspect/aspect_debug/source/simulator/core.cc:22:
> >>>>
> >>>> /home/lev/aspect/dealii_debug/include/deal.II/bundled/boost/
> smart_ptr/scoped_ptr.hpp:
> >>>> In copy constructor ‘dealii::std_cxx11::unique_ptr<dealii::Mapping<2,
> 2>
> >>>> >::unique_ptr(const dealii::std_cxx11::unique_ptr<dealii::Mapping<2,
> 2>
> >>>> >&)’:
> >>>>
> >>>> /home/lev/aspect/dealii_debug/include/deal.II/base/std_
> cxx11/unique_ptr.h:60:
> >>>> instantiated from ‘aspect::Simulator<dim>::
> Simulator(ompi_communicator_t*,
> >>>> dealii::ParameterHandler&) [with int dim = 2]’
> >>>> /home/lev/aspect/aspect_debug/source/simulator/core.cc:2471:
> >>>> instantiated from here
> >>>>
> >>>> /home/lev/aspect/dealii_debug/include/deal.II/bundled/boost/
> smart_ptr/scoped_ptr.hpp:47:
> >>>> error: ‘boost::scoped_ptr<T>::scoped_ptr(const
> boost::scoped_ptr<T>&) [with
> >>>> T = dealii::Mapping<2, 2>]’ is private
> >>>>
> >>>> /home/lev/aspect/dealii_debug/include/deal.II/base/std_
> cxx11/unique_ptr.h:60:
> >>>> error: within this context
> >>>> /home/lev/aspect/aspect_debug/source/simulator/core.cc: In
> constructor
> >>>> ‘aspect::Simulator<dim>::Simulator(ompi_communicator_t*,
> >>>> dealii::ParameterHandler&) [with int dim = 2]’:
> >>>> /home/lev/aspect/aspect_debug/source/simulator/core.cc:2471:
> >>>> instantiated from here
> >>>> /home/lev/aspect/aspect_debug/source/simulator/core.cc:218: note:
> >>>> synthesized method ‘dealii::std_cxx11::unique_ptr<dealii::Mapping<2,
> 2>
> >>>> >::unique_ptr(const dealii::std_cxx11::unique_ptr<dealii::Mapping<2,
> 2> >&)’
> >>>> first required here
> >>>> In file included from
> >>>> /home/lev/aspect/dealii_debug/include/deal.II/base/
> parameter_handler.h:24,
> >>>>                  from
> >>>> /home/lev/aspect/aspect_debug/include/aspect/simulator.h:26,
> >>>>                  from
> >>>> /home/lev/aspect/aspect_debug/source/simulator/core.cc:22:
> >>>>
> >>>> /home/lev/aspect/dealii_debug/include/deal.II/bundled/boost/
> smart_ptr/scoped_ptr.hpp:
> >>>> In copy constructor ‘dealii::std_cxx11::unique_ptr<dealii::Mapping<3,
> 3>
> >>>> >::unique_ptr(const dealii::std_cxx11::unique_ptr<dealii::Mapping<3,
> 3>
> >>>> >&)’:
> >>>>
> >>>> /home/lev/aspect/dealii_debug/include/deal.II/base/std_
> cxx11/unique_ptr.h:60:
> >>>> instantiated from ‘aspect::Simulator<dim>::
> Simulator(ompi_communicator_t*,
> >>>> dealii::ParameterHandler&) [with int dim = 3]’
> >>>> /home/lev/aspect/aspect_debug/source/simulator/core.cc:2471:
> >>>> instantiated from here
> >>>>
> >>>> /home/lev/aspect/dealii_debug/include/deal.II/bundled/boost/
> smart_ptr/scoped_ptr.hpp:47:
> >>>> error: ‘boost::scoped_ptr<T>::scoped_ptr(const
> boost::scoped_ptr<T>&) [with
> >>>> T = dealii::Mapping<3, 3>]’ is private
> >>>>
> >>>> /home/lev/aspect/dealii_debug/include/deal.II/base/std_
> cxx11/unique_ptr.h:60:
> >>>> error: within this context
> >>>> /home/lev/aspect/aspect_debug/source/simulator/core.cc: In
> constructor
> >>>> ‘aspect::Simulator<dim>::Simulator(ompi_communicator_t*,
> >>>> dealii::ParameterHandler&) [with int dim = 3]’:
> >>>> /home/lev/aspect/aspect_debug/source/simulator/core.cc:2471:
> >>>> instantiated from here
> >>>> /home/lev/aspect/aspect_debug/source/simulator/core.cc:218: note:
> >>>> synthesized method ‘dealii::std_cxx11::unique_ptr<dealii::Mapping<3,
> 3>
> >>>> >::unique_ptr(const dealii::std_cxx11::unique_ptr<dealii::Mapping<3,
> 3> >&)’
> >>>> first required here
> >>>>
> >>>> /home/lev/aspect/dealii_debug/include/deal.II/bundled/boost/
> system/error_code.hpp:
> >>>> At global scope:
> >>>>
> >>>> /home/lev/aspect/dealii_debug/include/deal.II/bundled/boost/
> system/error_code.hpp:221:
> >>>> warning: ‘boost::system::posix_category’ defined but not used
> >>>>
> >>>> /home/lev/aspect/dealii_debug/include/deal.II/bundled/boost/
> system/error_code.hpp:222:
> >>>> warning: ‘boost::system::errno_ecat’ defined but not used
> >>>>
> >>>> /home/lev/aspect/dealii_debug/include/deal.II/bundled/boost/
> system/error_code.hpp:223:
> >>>> warning: ‘boost::system::native_ecat’ defined but not used
> >>>> make[2]: *** [CMakeFiles/aspect.dir/source/simulator/core.cc.o]
> Error 1
> >>>> make[1]: *** [CMakeFiles/aspect.dir/all] Error 2
> >>>> make: *** [all] Error 2
> >>>>
> >>>> Tips on how to solve it would be appreciated.
> >>>>
> >>>> Best regards,
> >>>> Lev Karatun.
> >>>>
> >>>>
> >>>> _______________________________________________
> >>>> Aspect-devel mailing list
> >>>> Aspect-devel at geodynamics.org
> >>>> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.
> geodynamics.org_cgi-2Dbin_mailman_listinfo_aspect-2Ddevel&d=CwIFaQ&c=Ngd-
> ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4&r=c08Btfq4m9QEScXN3ZQwLZzzWQE7S8
> CYq1IYuzKV_Zk&m=5r5_DItWuONwoXvldIba3ADkcnN7FquA2JnGyXmTzmE&s=tHVqWLlk_
> 265tEXD1zrOhkNBE6fpd4_xM7l5tib7E9U&e=
> >>>>
> >>>>
> >>>>
> >>>> _______________________________________________
> >>>> Aspect-devel mailing list
> >>>> Aspect-devel at geodynamics.org
> >>>> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.
> geodynamics.org_cgi-2Dbin_mailman_listinfo_aspect-2Ddevel&d=CwIFaQ&c=Ngd-
> ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4&r=c08Btfq4m9QEScXN3ZQwLZzzWQE7S8
> CYq1IYuzKV_Zk&m=5r5_DItWuONwoXvldIba3ADkcnN7FquA2JnGyXmTzmE&s=tHVqWLlk_
> 265tEXD1zrOhkNBE6fpd4_xM7l5tib7E9U&e=
> >>>
> >>>
> >>> _______________________________________________
> >>> Aspect-devel mailing list
> >>> Aspect-devel at geodynamics.org
> >>> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.
> geodynamics.org_cgi-2Dbin_mailman_listinfo_aspect-2Ddevel&d=CwIFaQ&c=Ngd-
> ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4&r=c08Btfq4m9QEScXN3ZQwLZzzWQE7S8
> CYq1IYuzKV_Zk&m=5r5_DItWuONwoXvldIba3ADkcnN7FquA2JnGyXmTzmE&s=tHVqWLlk_
> 265tEXD1zrOhkNBE6fpd4_xM7l5tib7E9U&e=
> >>>
> >>>
> >>>
> >>> _______________________________________________
> >>> Aspect-devel mailing list
> >>> Aspect-devel at geodynamics.org
> >>> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.
> geodynamics.org_cgi-2Dbin_mailman_listinfo_aspect-2Ddevel&d=CwIGaQ&c=Ngd-
> ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4&r=R5lvg9JC99XvuTgScgbY_
> QFS80R7PEA2q0EPwDy7VQw&m=hQ2ClMQtaiXOLdBNbZSCUQKZqCsXZT517zxswRk1j-s&s=
> XRsatNYOGKjztBbXCCQNnZADxPi7Ehgp7vphUTYhDSc&e=
> >>
> >>
> >> --
> >> Timo Heister
> >> http://www.math.clemson.edu/~heister/
> >
> >
> >
> > --
> > Timo Heister
> > http://www.math.clemson.edu/~heister/
>
>
>
> --
> Timo Heister
> http://www.math.clemson.edu/~heister/
> _______________________________________________
> Aspect-devel mailing list
> Aspect-devel at geodynamics.org
> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel
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From payman.janbakhsh at mail.utoronto.ca  Sun Nov  6 12:58:31 2016
From: payman.janbakhsh at mail.utoronto.ca (Payman Janbakhsh)
Date: Sun, 6 Nov 2016 20:58:31 +0000
Subject: [aspect-devel] Dynamic Topography vs Topography
Message-ID: <CY1PR03MB151850DB7C7A6869B0548BB3ADA40@CY1PR03MB1518.namprd03.prod.outlook.com>

Hi
When running a model, postprocessor outputs min and max topography at the end of each time step. In my case shows  values around + - 1.5m  (early steps).
Then when using dynamic topography postprocessor to plot dynamic topography vs X, with or without the option of Subtract mean of topography, my plot  shows values between -150m to 200m in some areas and zero(in the case of subtracted mean)  for the rest of the x dimension.
Why is there a discrepancy between Topography min/max  and dynamic topography at the same time step? Shouldn't the topography min/max reflect the min /max on my dynamic topography plot?

Thank you

Payman
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From rene.gassmoeller at mailbox.org  Mon Nov  7 11:58:03 2016
From: rene.gassmoeller at mailbox.org (Rene Gassmoeller)
Date: Mon, 7 Nov 2016 12:58:03 -0700
Subject: [aspect-devel] Dynamic Topography vs Topography
In-Reply-To: <CY1PR03MB151850DB7C7A6869B0548BB3ADA40@CY1PR03MB1518.namprd03.prod.outlook.com>
References: <CY1PR03MB151850DB7C7A6869B0548BB3ADA40@CY1PR03MB1518.namprd03.prod.outlook.com>
Message-ID: <e1ee9f21-63a0-b000-3d37-9b28feeba640@mailbox.org>

Hi Payman,

I guess the short answer is: They do different things. The topography
postprocessor measures the actual deformation of the mesh (i.e. you will
only see significant values, if you use a deforming mesh / free
surface). The dynamic topography however is calculated as: How much
topography would be here, if the pressure were to be balanced by
overlying topography (for a longer explanation including formulas take a
look at the postprocessor description in the manual or the source code).

So as long as you do not use a free surface, the values of the
'topography' postprocessor will be close to zero (there might be a tiny
value). And if you use a free surface the 'dynamic topography'
postprocessor will likely no longer calculate anything useful (because
the pressure is already compensated by building a topography).

Hope that helps,

Best,

Rene


On 11/06/2016 01:58 PM, Payman Janbakhsh wrote:
>
> Hi
>
> When running a model, postprocessor outputs min and max topography at
> the end of each time step. In my case shows  values around + - 1.5m
>  (early steps).
>
> Then when using dynamic topography postprocessor to plot dynamic
> topography vs X, with or without the option of Subtract mean of
> topography, my plot  shows values between -150m to 200m in some areas
> and zero(in the case of subtracted mean)  for the rest of the x
> dimension.
>
> Why is there a discrepancy between Topography min/max  and dynamic
> topography at the same time step? Shouldn’t the topography min/max
> reflect the min /max on my dynamic topography plot?
>
>  
>
> Thank you
>
>  
>
> Payman
>
>
>
> _______________________________________________
> Aspect-devel mailing list
> Aspect-devel at geodynamics.org
> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel

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From payman.janbakhsh at mail.utoronto.ca  Wed Nov  9 05:40:05 2016
From: payman.janbakhsh at mail.utoronto.ca (Payman Janbakhsh)
Date: Wed, 9 Nov 2016 13:40:05 +0000
Subject: [aspect-devel] Dynamic Topography vs Topography
In-Reply-To: <e1ee9f21-63a0-b000-3d37-9b28feeba640@mailbox.org>
References: <CY1PR03MB151850DB7C7A6869B0548BB3ADA40@CY1PR03MB1518.namprd03.prod.outlook.com>
 <e1ee9f21-63a0-b000-3d37-9b28feeba640@mailbox.org>
Message-ID: <CY1PR03MB15183F9604C68A2233770D0DADB90@CY1PR03MB1518.namprd03.prod.outlook.com>

Thanks Rene, sorry for late reply
It was my misunderstanding that for a free surface I can use the generated dynamic topography text files and see the surface evolution across my model domain at any given time step.
Is there an implemented option for it currently ?  (for a free surface).
Not the Topography postprocessor since it gives the max(min)  vs time(run time) ,
   Looking for a measure of surface mesh elevation(from its initial datum or a mean) vs X lateral dimension, at any given time step.
Thanks

payman
From: Aspect-devel [mailto:aspect-devel-bounces at geodynamics.org] On Behalf Of Rene Gassmoeller
Sent: November 7, 2016 2:58 PM
To: aspect-devel at geodynamics.org
Subject: Re: [aspect-devel] Dynamic Topography vs Topography


Hi Payman,

I guess the short answer is: They do different things. The topography postprocessor measures the actual deformation of the mesh (i.e. you will only see significant values, if you use a deforming mesh / free surface). The dynamic topography however is calculated as: How much topography would be here, if the pressure were to be balanced by overlying topography (for a longer explanation including formulas take a look at the postprocessor description in the manual or the source code).

So as long as you do not use a free surface, the values of the 'topography' postprocessor will be close to zero (there might be a tiny value). And if you use a free surface the 'dynamic topography' postprocessor will likely no longer calculate anything useful (because the pressure is already compensated by building a topography).

Hope that helps,

Best,

Rene

On 11/06/2016 01:58 PM, Payman Janbakhsh wrote:
Hi
When running a model, postprocessor outputs min and max topography at the end of each time step. In my case shows  values around + - 1.5m  (early steps).
Then when using dynamic topography postprocessor to plot dynamic topography vs X, with or without the option of Subtract mean of topography, my plot  shows values between -150m to 200m in some areas and zero(in the case of subtracted mean)  for the rest of the x dimension.
Why is there a discrepancy between Topography min/max  and dynamic topography at the same time step? Shouldn’t the topography min/max reflect the min /max on my dynamic topography plot?

Thank you

Payman




_______________________________________________

Aspect-devel mailing list

Aspect-devel at geodynamics.org<mailto:Aspect-devel at geodynamics.org>

http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel

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From egpuckett at ucdavis.edu  Wed Nov  9 07:44:31 2016
From: egpuckett at ucdavis.edu (Elbridge Gerry Puckett)
Date: Wed, 9 Nov 2016 16:44:31 +0100
Subject: [aspect-devel] Is it possible to prescribe a function F(R_0,
 theta) and F (R_1,
 theta) as the boundary conditions on the two boundaries r = R_0 and r= R_1
 of an annular domain?
Message-ID: <4f529f3d-ed56-0c63-2b7c-af9e4005b7b6@ucdavis.edu>

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From heister at clemson.edu  Wed Nov  9 08:15:34 2016
From: heister at clemson.edu (Timo Heister)
Date: Wed, 9 Nov 2016 11:15:34 -0500
Subject: [aspect-devel] Is it possible to prescribe a function F(R_0,
 theta) and F (R_1,
 theta) as the boundary conditions on the two boundaries r = R_0 and r= R_1
 of an annular domain?
In-Reply-To: <4f529f3d-ed56-0c63-2b7c-af9e4005b7b6@ucdavis.edu>
References: <4f529f3d-ed56-0c63-2b7c-af9e4005b7b6@ucdavis.edu>
Message-ID: <CAMRj59E7mUtgDR00BsTsuvBdG0wbOuDFumVr5iTai0KQe1MELA@mail.gmail.com>

Gerry,

of course this is possible. You can use atan2(y,x) which returns an
angle between -pi and pi and sqrt(x^2+y^2) to compute the radius. The
choice between inner and outer can be done using
if(sqrt(x^2+y^2)<(r0+r1)/2,r0,r1) or something similar.

At some point it might be easier to write a plugin and do this logic
inside a simple c++ function, though. You do this by defining and
registering a new boundary class. See
tests/prescribed_velocity_boundary.cc for an example.


On Wed, Nov 9, 2016 at 10:44 AM, Elbridge Gerry Puckett
<egpuckett at ucdavis.edu> wrote:
> Hi,
>
> We want to compute the solution of Stokes in the annular domain
>
> R_0 <= r <= R_1    and   0 <= theta <= 2 pi
>
> We would like to prescribe
>
> (u, v) = F(R_0, theta)  = ( f(R_0, theta),  g(R_0, theta) )   at r = R_0
>
> and
>
> (u, v) = F(R_1, theta) =  ( f(R_1, theta),  g(R_1, theta) )   at r = R_1
>
> Is this possible? Currently we know how to prescribe
>
> (u, v) = (-y,x) at both r = R_0 and r = R_1
>
> This is what we're currently doing ...
>
> ############### Parameters describing the model
>
> subsection Geometry model
>   set Model name = spherical shell
>
>   subsection Spherical shell
>     set Inner radius = .4
>     set Outer radius = 1
>     set Opening angle = 360
>
>    end
> end
>
> subsection Model settings
>
>
>   # Set to tangential velocity boundary conditions.
>   # Note that the function specified in "Boundary velocity model" has no
> influence unless the following line is uncommented
>   # and the parameter  "Tangential velocity boundary indicators" is reset.
>
>   set Prescribed velocity boundary indicators = 0: function, 1: function
>
>   #  set Prescribed velocity boundary indicators =
>
>   set Tangential velocity boundary indicators =
>   set Zero velocity boundary indicators       =
>
> end
>
>
> subsection Boundary velocity model
>   subsection Function
>     set Function constants   = pi=3.1415926
>     set Variable names        = x,y
>     set Function expression = -y;x
>   end
> end
>
> subsection Material model
>
>   set Model name = ...
>
>   subsection EGPHVL
>
>     # Do not change these set of parameters! EGP && HL
>
>       set Viscosity jump       = 1
>       set Reference density = 1
>    end
>
> end
>
> Thanks!
>
> - G
>
>
> _______________________________________________
> Aspect-devel mailing list
> Aspect-devel at geodynamics.org
> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.geodynamics.org_cgi-2Dbin_mailman_listinfo_aspect-2Ddevel&d=CwIGaQ&c=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4&r=R5lvg9JC99XvuTgScgbY_QFS80R7PEA2q0EPwDy7VQw&m=UxEweuniOSYML-OMWv5_ph03TZc_eyvDW4Y1WjnvWyI&s=Isbfz0YFq0MzOx27fWo_ZkXrIsjQXdpeTVlBJqLO_NU&e=



-- 
Timo Heister
http://www.math.clemson.edu/~heister/

From ljhwang at ucdavis.edu  Wed Nov  9 13:10:31 2016
From: ljhwang at ucdavis.edu (Lorraine Hwang)
Date: Wed, 9 Nov 2016 13:10:31 -0800
Subject: [aspect-devel] CIG Webinar: TOMRROW @ 2pm featuring Renee
	Gassmoeller
Message-ID: <9AB35B8D-4ABF-493C-89C8-69A7873FBAE0@ucdavis.edu>



Don’t miss a chance to learn from the expert...

Rene Gassmoeller will be delivering tomorrow’s CIG webinar  Thursday November 10 @ 2pm PT talking to us about a key feature of ASPECT - particle implementation. 

Intricacies of particle-in-cell methods in convection models with adaptive meshes: Using ASPECT's particle implementation
Rene Gassmoeller, CSU Fort Collins

Particle-in-cell methods have a long history in modeling of mantle convection, lithospheric deformation and crustal dynamics. However, their efficient parallel implementation and application in models - in particular combined with adaptive meshes - is involved due to the complex reassignment of particles to cells and frequent parallel communication.

In this webinar, I present the implementation of a flexible, scalable and efficient particle-in-cell method for the massively parallel finite-element code ASPECT. I discuss the complexity of the implemented algorithms, present scaling tests and discuss load-balancing strategies like balanced repartitioning for particles in adaptive meshes with their strengths and weaknesses. Additionally, I will show an application tutorial on how to convert a model with compositional fields into one using the particle advection scheme, and which consequences follow from this conversion for model runtime and accuracy.

Connect: http://uc-d.adobeconnect.com/r28i3av93ti/ <http://uc-d.adobeconnect.com/r28i3av93ti/>

Best,
-Lorraine

*****************************
Lorraine Hwang, Ph.D.
Associate Director, CIG
530.752.3656





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From rene.gassmoeller at mailbox.org  Wed Nov  9 18:37:02 2016
From: rene.gassmoeller at mailbox.org (Rene Gassmoeller)
Date: Wed, 9 Nov 2016 19:37:02 -0700
Subject: [aspect-devel] Dynamic Topography vs Topography
In-Reply-To: <CY1PR03MB15183F9604C68A2233770D0DADB90@CY1PR03MB1518.namprd03.prod.outlook.com>
References: <CY1PR03MB151850DB7C7A6869B0548BB3ADA40@CY1PR03MB1518.namprd03.prod.outlook.com>
 <e1ee9f21-63a0-b000-3d37-9b28feeba640@mailbox.org>
 <CY1PR03MB15183F9604C68A2233770D0DADB90@CY1PR03MB1518.namprd03.prod.outlook.com>
Message-ID: <6a7acae5-7d58-8bbc-7204-b8bbad6cb31e@mailbox.org>

Hi Payman,

surprisingly (also to me) ASPECT currently does not have a postprocessor
that outputs a map of the topography of a deformed mesh. The closest
thing is the visualization/depth postprocessor that will output the
depth of every point of the domain. However, the `depth()` function of
the geometry model is bounded to (0,maximal_depth), so it will not
output positive topography correctly. If you would be willing to spend
some time helping create a postprocessor for topography that would
certainly be a useful addition. Let us know if you would have the time
and willingness to do so, we could then discuss the details of the
implementation (always easier to discuss that first, before writing
something and then reworking it many times).

Depending on your intended purpose you would either need to create a
general postprocessor that outputs the topography into a separate file
(as for example postprocess/heat_flux_map), or a visualization
postprocessor that adds another field to the .vtu output of the solution
(as for example postprocess/visualization/depth). However, there might
be some challenges to make it work for arbitrary model geometries.

Let me know what you think about that,

Rene



On 11/09/2016 06:40 AM, Payman Janbakhsh wrote:
>
> Thanks Rene, sorry for late reply
>
> It was my misunderstanding that for a free surface I can use the
> generated dynamic topography text files and see the surface evolution
> across my model domain at any given time step.
>
> Is there an implemented option for it currently ?  (for a free surface).
>
> Not the Topography postprocessor since it gives the max(min)  vs
> time(run time) ,
>
>    Looking for a measure of surface mesh elevation(from its initial
> datum or a mean) vs X lateral dimension, at any given time step.
>
> Thanks
>
>  
>
> payman
>
> *From:*Aspect-devel [mailto:aspect-devel-bounces at geodynamics.org] *On
> Behalf Of *Rene Gassmoeller
> *Sent:* November 7, 2016 2:58 PM
> *To:* aspect-devel at geodynamics.org
> *Subject:* Re: [aspect-devel] Dynamic Topography vs Topography
>
>  
>
> Hi Payman,
>
> I guess the short answer is: They do different things. The topography
> postprocessor measures the actual deformation of the mesh (i.e. you
> will only see significant values, if you use a deforming mesh / free
> surface). The dynamic topography however is calculated as: How much
> topography would be here, if the pressure were to be balanced by
> overlying topography (for a longer explanation including formulas take
> a look at the postprocessor description in the manual or the source code).
>
> So as long as you do not use a free surface, the values of the
> 'topography' postprocessor will be close to zero (there might be a
> tiny value). And if you use a free surface the 'dynamic topography'
> postprocessor will likely no longer calculate anything useful (because
> the pressure is already compensated by building a topography).
>
> Hope that helps,
>
> Best,
>
> Rene
>
>  
>
> On 11/06/2016 01:58 PM, Payman Janbakhsh wrote:
>
>     Hi
>
>     When running a model, postprocessor outputs min and max topography
>     at the end of each time step. In my case shows  values around + -
>     1.5m  (early steps).
>
>     Then when using dynamic topography postprocessor to plot dynamic
>     topography vs X, with or without the option of Subtract mean of
>     topography, my plot  shows values between -150m to 200m in some
>     areas and zero(in the case of subtracted mean)  for the rest of
>     the x dimension.
>
>     Why is there a discrepancy between Topography min/max  and dynamic
>     topography at the same time step? Shouldn’t the topography min/max
>     reflect the min /max on my dynamic topography plot?
>
>      
>
>     Thank you
>
>      
>
>     Payman
>
>
>
>
>     _______________________________________________
>
>     Aspect-devel mailing list
>
>     Aspect-devel at geodynamics.org <mailto:Aspect-devel at geodynamics.org>
>
>     http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel
>
>  
>
>
>
> _______________________________________________
> Aspect-devel mailing list
> Aspect-devel at geodynamics.org
> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel

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From payman.janbakhsh at mail.utoronto.ca  Thu Nov 10 08:28:37 2016
From: payman.janbakhsh at mail.utoronto.ca (Payman Janbakhsh)
Date: Thu, 10 Nov 2016 16:28:37 +0000
Subject: [aspect-devel] Dynamic Topography vs Topography
In-Reply-To: <6a7acae5-7d58-8bbc-7204-b8bbad6cb31e@mailbox.org>
References: <CY1PR03MB151850DB7C7A6869B0548BB3ADA40@CY1PR03MB1518.namprd03.prod.outlook.com>
 <e1ee9f21-63a0-b000-3d37-9b28feeba640@mailbox.org>
 <CY1PR03MB15183F9604C68A2233770D0DADB90@CY1PR03MB1518.namprd03.prod.outlook.com>,
 <6a7acae5-7d58-8bbc-7204-b8bbad6cb31e@mailbox.org>
Message-ID: <hneep5eaw78xx8afbyl40f6s.1478795309892@email.android.com>

Hi Rene
That would be something I myself need for my research. so I would be glad to start working on it with the team's help and guidance, given the time frame and it being my first try at creating a plug-in .
I'll contact you via research gate to get more details .

Cheers

Payman


Sent from my Samsung Galaxy smartphone.


-------- Original message --------
From: Rene Gassmoeller <rene.gassmoeller at mailbox.org>
Date: 2016-11-09 9:37 PM (GMT-05:00)
To: aspect-devel at geodynamics.org
Subject: Re: [aspect-devel] Dynamic Topography vs Topography


Hi Payman,

surprisingly (also to me) ASPECT currently does not have a postprocessor that outputs a map of the topography of a deformed mesh. The closest thing is the visualization/depth postprocessor that will output the depth of every point of the domain. However, the `depth()` function of the geometry model is bounded to (0,maximal_depth), so it will not output positive topography correctly. If you would be willing to spend some time helping create a postprocessor for topography that would certainly be a useful addition. Let us know if you would have the time and willingness to do so, we could then discuss the details of the implementation (always easier to discuss that first, before writing something and then reworking it many times).

Depending on your intended purpose you would either need to create a general postprocessor that outputs the topography into a separate file (as for example postprocess/heat_flux_map), or a visualization postprocessor that adds another field to the .vtu output of the solution (as for example postprocess/visualization/depth). However, there might be some challenges to make it work for arbitrary model geometries.

Let me know what you think about that,

Rene


On 11/09/2016 06:40 AM, Payman Janbakhsh wrote:
Thanks Rene, sorry for late reply
It was my misunderstanding that for a free surface I can use the generated dynamic topography text files and see the surface evolution across my model domain at any given time step.
Is there an implemented option for it currently ?  (for a free surface).
Not the Topography postprocessor since it gives the max(min)  vs time(run time) ,
   Looking for a measure of surface mesh elevation(from its initial datum or a mean) vs X lateral dimension, at any given time step.
Thanks

payman
From: Aspect-devel [mailto:aspect-devel-bounces at geodynamics.org] On Behalf Of Rene Gassmoeller
Sent: November 7, 2016 2:58 PM
To: aspect-devel at geodynamics.org<mailto:aspect-devel at geodynamics.org>
Subject: Re: [aspect-devel] Dynamic Topography vs Topography


Hi Payman,

I guess the short answer is: They do different things. The topography postprocessor measures the actual deformation of the mesh (i.e. you will only see significant values, if you use a deforming mesh / free surface). The dynamic topography however is calculated as: How much topography would be here, if the pressure were to be balanced by overlying topography (for a longer explanation including formulas take a look at the postprocessor description in the manual or the source code).

So as long as you do not use a free surface, the values of the 'topography' postprocessor will be close to zero (there might be a tiny value). And if you use a free surface the 'dynamic topography' postprocessor will likely no longer calculate anything useful (because the pressure is already compensated by building a topography).

Hope that helps,

Best,

Rene

On 11/06/2016 01:58 PM, Payman Janbakhsh wrote:
Hi
When running a model, postprocessor outputs min and max topography at the end of each time step. In my case shows  values around + - 1.5m  (early steps).
Then when using dynamic topography postprocessor to plot dynamic topography vs X, with or without the option of Subtract mean of topography, my plot  shows values between -150m to 200m in some areas and zero(in the case of subtracted mean)  for the rest of the x dimension.
Why is there a discrepancy between Topography min/max  and dynamic topography at the same time step? Shouldn't the topography min/max reflect the min /max on my dynamic topography plot?

Thank you

Payman




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From bangerth at tamu.edu  Thu Nov 10 08:58:48 2016
From: bangerth at tamu.edu (Wolfgang Bangerth)
Date: Thu, 10 Nov 2016 09:58:48 -0700
Subject: [aspect-devel] Dynamic Topography vs Topography
In-Reply-To: <hneep5eaw78xx8afbyl40f6s.1478795309892@email.android.com>
References: <CY1PR03MB151850DB7C7A6869B0548BB3ADA40@CY1PR03MB1518.namprd03.prod.outlook.com>
 <e1ee9f21-63a0-b000-3d37-9b28feeba640@mailbox.org>
 <CY1PR03MB15183F9604C68A2233770D0DADB90@CY1PR03MB1518.namprd03.prod.outlook.com>
 <6a7acae5-7d58-8bbc-7204-b8bbad6cb31e@mailbox.org>
 <hneep5eaw78xx8afbyl40f6s.1478795309892@email.android.com>
Message-ID: <9dfd4f87-f798-8097-f490-cebb88d68f73@tamu.edu>

On 11/10/2016 09:28 AM, Payman Janbakhsh wrote:
> That would be something I myself need for my research. so I would be
> glad to start working on it with the team's help and guidance, given the
> time frame and it being my first try at creating a plug-in .
> I'll contact you via research gate to get more details .

It's generally best to have these sorts of technical discussions on the 
mailing list or other public forums, simply because it multiplies the 
number of people with knowledge who can chime in.

I've created an issue for your problem here:
   https://github.com/geodynamics/aspect/issues/1270
I think that's the right place to have the technical discussion of how 
to go about writing such a postprocessor.

Best
  W.

-- 
------------------------------------------------------------------------
Wolfgang Bangerth          email:                 bangerth at colostate.edu
                            www: http://www.math.colostate.edu/~bangerth/

From c.thieulot at uu.nl  Thu Nov 10 12:09:16 2016
From: c.thieulot at uu.nl (Thieulot, C.A.P. (Cedric))
Date: Thu, 10 Nov 2016 20:09:16 +0000
Subject: [aspect-devel] CIG Webinar: TOMRROW @ 2pm featuring
	Renee	Gassmoeller
In-Reply-To: <9AB35B8D-4ABF-493C-89C8-69A7873FBAE0@ucdavis.edu>
References: <9AB35B8D-4ABF-493C-89C8-69A7873FBAE0@ucdavis.edu>
Message-ID: <5B436DD2-0CBA-41C0-B04F-FA54DB9F610D@uu.nl>

Hi Lorraine,

is Rene’s talk recorded ? I am of course interested but his talk is at 11pm local time here  :(

Ce/


On 09 Nov 2016, at 22:10, Lorraine Hwang <ljhwang at ucdavis.edu<mailto:ljhwang at ucdavis.edu>> wrote:



Don’t miss a chance to learn from the expert...

Rene Gassmoeller will be delivering tomorrow’s CIG webinar  Thursday November 10 @ 2pm PT talking to us about a key feature of ASPECT - particle implementation.

Intricacies of particle-in-cell methods in convection models with adaptive meshes: Using ASPECT's particle implementation

Rene Gassmoeller, CSU Fort Collins

Particle-in-cell methods have a long history in modeling of mantle convection, lithospheric deformation and crustal dynamics. However, their efficient parallel implementation and application in models - in particular combined with adaptive meshes - is involved due to the complex reassignment of particles to cells and frequent parallel communication.

In this webinar, I present the implementation of a flexible, scalable and efficient particle-in-cell method for the massively parallel finite-element code ASPECT. I discuss the complexity of the implemented algorithms, present scaling tests and discuss load-balancing strategies like balanced repartitioning for particles in adaptive meshes with their strengths and weaknesses. Additionally, I will show an application tutorial on how to convert a model with compositional fields into one using the particle advection scheme, and which consequences follow from this conversion for model runtime and accuracy.

Connect: http://uc-d.adobeconnect.com/r28i3av93ti/


Best,
-Lorraine

*****************************
Lorraine Hwang, Ph.D.
Associate Director, CIG
530.752.3656

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From payman.janbakhsh at mail.utoronto.ca  Thu Nov 10 12:10:59 2016
From: payman.janbakhsh at mail.utoronto.ca (Payman Janbakhsh)
Date: Thu, 10 Nov 2016 20:10:59 +0000
Subject: [aspect-devel] Dynamic Topography vs Topography
In-Reply-To: <9dfd4f87-f798-8097-f490-cebb88d68f73@tamu.edu>
References: <CY1PR03MB151850DB7C7A6869B0548BB3ADA40@CY1PR03MB1518.namprd03.prod.outlook.com>
 <e1ee9f21-63a0-b000-3d37-9b28feeba640@mailbox.org>
 <CY1PR03MB15183F9604C68A2233770D0DADB90@CY1PR03MB1518.namprd03.prod.outlook.com>
 <6a7acae5-7d58-8bbc-7204-b8bbad6cb31e@mailbox.org>
 <hneep5eaw78xx8afbyl40f6s.1478795309892@email.android.com>
 <9dfd4f87-f798-8097-f490-cebb88d68f73@tamu.edu>
Message-ID: <CY1PR03MB1518201BFB4E7D42007E24F4ADB80@CY1PR03MB1518.namprd03.prod.outlook.com>

Thanks Wolfgang.

payman

-----Original Message-----
From: Aspect-devel [mailto:aspect-devel-bounces at geodynamics.org] On Behalf Of Wolfgang Bangerth
Sent: November 10, 2016 11:59 AM
To: aspect-devel at geodynamics.org
Subject: Re: [aspect-devel] Dynamic Topography vs Topography

On 11/10/2016 09:28 AM, Payman Janbakhsh wrote:
> That would be something I myself need for my research. so I would be 
> glad to start working on it with the team's help and guidance, given 
> the time frame and it being my first try at creating a plug-in .
> I'll contact you via research gate to get more details .

It's generally best to have these sorts of technical discussions on the mailing list or other public forums, simply because it multiplies the number of people with knowledge who can chime in.

I've created an issue for your problem here:
   https://github.com/geodynamics/aspect/issues/1270
I think that's the right place to have the technical discussion of how to go about writing such a postprocessor.

Best
  W.

--
------------------------------------------------------------------------
Wolfgang Bangerth          email:                 bangerth at colostate.edu
                            www: http://www.math.colostate.edu/~bangerth/
_______________________________________________
Aspect-devel mailing list
Aspect-devel at geodynamics.org
http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel

From jbnaliboff at ucdavis.edu  Thu Nov 10 12:10:38 2016
From: jbnaliboff at ucdavis.edu (John Naliboff)
Date: Thu, 10 Nov 2016 12:10:38 -0800
Subject: [aspect-devel] CIG Webinar: TOMRROW @ 2pm featuring Renee
 Gassmoeller
In-Reply-To: <5B436DD2-0CBA-41C0-B04F-FA54DB9F610D@uu.nl>
References: <9AB35B8D-4ABF-493C-89C8-69A7873FBAE0@ucdavis.edu>
 <5B436DD2-0CBA-41C0-B04F-FA54DB9F610D@uu.nl>
Message-ID: <6e8ce8e1-81a3-1e84-e9dd-9eb05532dec6@ucdavis.edu>

Hi Cedric,

Rene's talk will indeed be recorded.

Cheers,
John

*************************************************
John Naliboff
Assistant Project Scientist, CIG
Earth & Planetary Sciences Dept., UC Davis

On 11/10/2016 12:09 PM, Thieulot, C.A.P. (Cedric) wrote:
> Hi Lorraine,
>
> is Rene’s talk recorded ? I am of course interested but his talk is at 
> 11pm local time here  :(
>
> Ce/
>
>
> On 09 Nov 2016, at 22:10, Lorraine Hwang <ljhwang at ucdavis.edu 
> <mailto:ljhwang at ucdavis.edu>> wrote:
>
>>
>>
>> Don’t miss a chance to learn from the expert...
>>
>> Rene Gassmoeller will be delivering tomorrow’s CIG webinar *Thursday 
>> November 10 @ 2pm PT* talking to us about a key feature of ASPECT - 
>> particle implementation.
>>
>>     *Intricacies of particle-in-cell methods in convection models
>>     with adaptive meshes: Using ASPECT's particle *implementation
>>
>>     /Rene Gassmoeller, CSU Fort Collins/
>>
>>     Particle-in-cell methods have a long history in modeling of
>>     mantle convection, lithospheric deformation and crustal dynamics.
>>     However, their efficient parallel implementation and application
>>     in models - in particular combined with adaptive meshes - is
>>     involved due to the complex reassignment of particles to cells
>>     and frequent parallel communication.
>>
>>     In this webinar, I present the implementation of a flexible,
>>     scalable and efficient particle-in-cell method for the massively
>>     parallel finite-element code ASPECT. I discuss the complexity of
>>     the implemented algorithms, present scaling tests and discuss
>>     load-balancing strategies like balanced repartitioning for
>>     particles in adaptive meshes with their strengths and weaknesses.
>>     Additionally, I will show an application tutorial on how to
>>     convert a model with compositional fields into one using the
>>     particle advection scheme, and which consequences follow from
>>     this conversion for model runtime and accuracy.
>>
>>     *Connect: *http://uc-d.adobeconnect.com/r28i3av93ti/
>>
>>
>>
>> Best,
>> -Lorraine
>>
>> *****************************
>> Lorraine Hwang, Ph.D.
>> Associate Director, CIG
>> 530.752.3656
>
>
>
> _______________________________________________
> Aspect-devel mailing list
> Aspect-devel at geodynamics.org
> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel

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From rene.gassmoeller at mailbox.org  Thu Nov 10 16:56:06 2016
From: rene.gassmoeller at mailbox.org (Rene Gassmoeller)
Date: Thu, 10 Nov 2016 17:56:06 -0700
Subject: [aspect-devel] A follow question from the webinar ...
In-Reply-To: <2be31735-33f8-3648-0bb9-3a3c3fc9996e@ucdavis.edu>
References: <2be31735-33f8-3648-0bb9-3a3c3fc9996e@ucdavis.edu>
Message-ID: <7ba3382d-1ca7-6655-12f0-ddbc5c065505@mailbox.org>

Hi John,

let me copy this mail to the developer list, because it is a reasonable
question, and others might profit from the discussion as well.

What you propose is already possible, just not the default way. You can
access the particles from the outside (see
source/postprocess/visualization/particle_count.cc for an example), and
you can either implement your own averaging scheme, or ask the particle
world for the selected interpolator (World::get_interpolator()).

That being said, I am skeptical you can do better that way for two reasons:
- The memory requirement of ASPECT mainly comes from the space needed
for the matrices, but if you select to advect a compositional field by
particles then we do not assemble or reserve the space for this block of
the system matrix (that was a problem in the beginning but was fixed a
while back by @klass4kayaker in pull request #1155). The solution vector
itself should not need much memory.
- The reason we interpolate the properties once and then access them
like a compositional field is that the interpolation is expensive
compared to the evaluation of this field at a certain position. If you
directly access the particle data you will need to do the interpolation
many more times (e.g. once for the assembly of the Stokes system, once
for other advection systems, once for the postprocessors, ...). Maybe it
can be similar in speed if the interpolation is fast, but I doubt it can
be faster.

Feel free to give it a try, but I would not expect many benefits (except
you do not need to rely on the finite element discretization of the
compositional field, but then you introduce that again, because the
velocity you are solving for is discretized the same way).

Cheers,
Rene

On 11/10/2016 05:28 PM, John Naliboff wrote:
> Hi Rene,
>
> I actually have a follow up question from the talk.  To reduce memory
> requirements, would it be reasonable in the future to have material
> models that access particle information directly rather than through a
> compositional field?
>
> In this scenario, a particle interpolation scheme would be called
> every time the material model needs particle information interpolated
> to a quadrature point.
>
> I suppose this could noticeably increase the computational time if one
> has to do lots on non-linear iterations.   Trade-off between
> computational time and memory requirements.  For 3D models, I imagine
> the memory requirements may be a bigger issue.
>
> Gerry Puckett and I have been discussing this after running into
> memory issues with 3D models.
>
> Anyhow, thanks again for the great talk!
>
> Cheers,
> John
>


From jbnaliboff at ucdavis.edu  Fri Nov 11 10:33:43 2016
From: jbnaliboff at ucdavis.edu (John Naliboff)
Date: Fri, 11 Nov 2016 10:33:43 -0800
Subject: [aspect-devel] A follow question from the webinar ...
In-Reply-To: <7ba3382d-1ca7-6655-12f0-ddbc5c065505@mailbox.org>
References: <2be31735-33f8-3648-0bb9-3a3c3fc9996e@ucdavis.edu>
 <7ba3382d-1ca7-6655-12f0-ddbc5c065505@mailbox.org>
Message-ID: <D4476E93-DD81-4172-9F00-74BACA496B55@ucdavis.edu>

Hi Rene,

Thanks for the detailed reply and copying this to the developer list, definitely the right place for it. 

Everything you outlined below makes sense in terms of reasons for sticking with the current active particle method (i.e. interpolate once).  Many of the models I ran require a large number of non-linear iterations, which as you point out is likely to slow things down.

Admittedly, I have not compared the memory requirements between active particles and ‘regular’ compositional field method in a rigorous manner.  My experience was that for a 3D model the memory jumped noticeably, but it was long enough ago that I do not know if the version of ASPECT I used had pull request #1155 incorporated.  

Hopefully before AGU I will have the chance to do a rigorous comparison between the two methods. For the purposes of examining memory requirements , I think initial comparisons should have the same number of particles per cell as integration points.  Something to discuss in more detail later on.

Thanks again for the reply and for the webinar yesterday!

Cheers,
John

*************************************************
John Naliboff
Assistant Project Scientist, CIG
Earth & Planetary Sciences Dept., UC Davis


> On Nov 10, 2016, at 4:56 PM, Rene Gassmoeller <rene.gassmoeller at mailbox.org> wrote:
> 
> Hi John,
> 
> let me copy this mail to the developer list, because it is a reasonable
> question, and others might profit from the discussion as well.
> 
> What you propose is already possible, just not the default way. You can
> access the particles from the outside (see
> source/postprocess/visualization/particle_count.cc for an example), and
> you can either implement your own averaging scheme, or ask the particle
> world for the selected interpolator (World::get_interpolator()).
> 
> That being said, I am skeptical you can do better that way for two reasons:
> - The memory requirement of ASPECT mainly comes from the space needed
> for the matrices, but if you select to advect a compositional field by
> particles then we do not assemble or reserve the space for this block of
> the system matrix (that was a problem in the beginning but was fixed a
> while back by @klass4kayaker in pull request #1155). The solution vector
> itself should not need much memory.
> - The reason we interpolate the properties once and then access them
> like a compositional field is that the interpolation is expensive
> compared to the evaluation of this field at a certain position. If you
> directly access the particle data you will need to do the interpolation
> many more times (e.g. once for the assembly of the Stokes system, once
> for other advection systems, once for the postprocessors, ...). Maybe it
> can be similar in speed if the interpolation is fast, but I doubt it can
> be faster.
> 
> Feel free to give it a try, but I would not expect many benefits (except
> you do not need to rely on the finite element discretization of the
> compositional field, but then you introduce that again, because the
> velocity you are solving for is discretized the same way).
> 
> Cheers,
> Rene
> 
> On 11/10/2016 05:28 PM, John Naliboff wrote:
>> Hi Rene,
>> 
>> I actually have a follow up question from the talk.  To reduce memory
>> requirements, would it be reasonable in the future to have material
>> models that access particle information directly rather than through a
>> compositional field?
>> 
>> In this scenario, a particle interpolation scheme would be called
>> every time the material model needs particle information interpolated
>> to a quadrature point.
>> 
>> I suppose this could noticeably increase the computational time if one
>> has to do lots on non-linear iterations.   Trade-off between
>> computational time and memory requirements.  For 3D models, I imagine
>> the memory requirements may be a bigger issue.
>> 
>> Gerry Puckett and I have been discussing this after running into
>> memory issues with 3D models.
>> 
>> Anyhow, thanks again for the great talk!
>> 
>> Cheers,
>> John
>> 
> 

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From payman.janbakhsh at mail.utoronto.ca  Sat Nov 12 14:35:44 2016
From: payman.janbakhsh at mail.utoronto.ca (Payman Janbakhsh)
Date: Sat, 12 Nov 2016 22:35:44 +0000
Subject: [aspect-devel] Continental extension model
In-Reply-To: <AM5PR0301MB23566C3EC780F8D514942A2FD1D40@AM5PR0301MB2356.eurprd03.prod.outlook.com>
References: <AM5PR0301MB2356DD1EE380A0165856F5A7D1DB0@AM5PR0301MB2356.eurprd03.prod.outlook.com>
 <2938597d-312c-cea5-2b45-66617de140ad@ucdavis.edu>
 <AM5PR0301MB2356CCD6473B8270B4030CE0D1D50@AM5PR0301MB2356.eurprd03.prod.outlook.com>
 <387c7dd8-148e-86f3-8051-820a6930e32a@ucdavis.edu>
 <AM5PR0301MB23566C3EC780F8D514942A2FD1D40@AM5PR0301MB2356.eurprd03.prod.outlook.com>
Message-ID: <CY1PR03MB151835BC48D37E9E86ECE2F2ADBA0@CY1PR03MB1518.namprd03.prod.outlook.com>

Hi John,
In visco_plastic.cc file line 151 : std::pow(grain_size, -grain_size_exponents_diffusion[j]):
Shouldn’t the sign of grain size exponent be positive? Ie.
std::pow(grain_size, grain_size_exponents_diffusion[j]):
that way decrease in grain size decreases the diffusion viscosity.

Thanks
payman

From: Aspect-devel [mailto:aspect-devel-bounces at geodynamics.org] On Behalf Of Mohamed Gouiza
Sent: October 21, 2016 11:43 AM
To: aspect-devel at geodynamics.org
Subject: Re: [aspect-devel] Continental extension model

Hi John,

I added a couple of suggestions to the commit request of the continental_extension_cookbook

Thanks for the DG method. I am running the development versions of ASPECT and deal.ii but from a month ago or so.

On a different matter, is there a postprocessor that allows to visualize the dominant creep law (dislocation vs diffusion) if I choose composite flow in my material model?

Cheers,

From: Aspect-devel [mailto:aspect-devel-bounces at geodynamics.org] On Behalf Of John Naliboff
Sent: 20 October 2016 21:53
To: aspect-devel at geodynamics.org<mailto:aspect-devel at geodynamics.org>
Subject: Re: [aspect-devel] Continental extension model

Hi Mohamed,

The value is indeed related to the fact that there is inflow at the base.  Many months ago, I was seeing odd behavior in the compositional fields and I suspected not having the mantle layer extend well past the model base might be one of the reasons.

However, at the moment I can't recall if this alone fixed the issue.  In theory, the simulation should work fine as long as the mantle layer is defined as extending exactly to the model base.

Aside, one way to improve the accuracy of the compositional field advection is by using the DG method option for the compositional discretization.  In the input file I sent you, add the following lines:
    subsection Discretization
      set Use discontinuous composition discretization = true
      subsection Stabilization parameters
          set Use limiter for discontinuous composition solution = true # apply the limiter to the DG solutions
          set Global composition maximum = 1.0, 1.0, 1.0, 1.0
          set Global composition minimum =  0.0, 0.0, 0.0, 0.0
      end
    end

To use this option you will need to work of the development version of both ASPECT and deal.ii.  Let us know if you have any issues getting things installed on this front or with using the DG method.  If you see anything odd in the models, please do not hesitate to email the list!

Last, I just opened a pull request for a cookbook related to this input file.  You can check out my forked copy ASPECT (branch continental_extension_cookbook) if you want to take a look at it before it gets merged.  Even better, make some comments on the pull request!

Cheers,
John


*************************************************

John Naliboff

Assistant Project Scientist, CIG

Earth & Planetary Sciences Dept., UC Davis
On 10/20/2016 08:02 AM, Mohamed Gouiza wrote:
Hi John,

In the continental extension input file that you sent me, the mantle compositional field is defined as 70.e3 && y>-100.e3
Is the -100.e3 a typo or is it because of the prescribed inflow at the base of the model?

Mohamed

From: Aspect-devel [mailto:aspect-devel-bounces at geodynamics.org] On Behalf Of John Naliboff
Sent: 10 October 2016 17:12
To: aspect-devel at geodynamics.org<mailto:aspect-devel at geodynamics.org>
Subject: Re: [aspect-devel] Continental extension model

Hi Mohamed,

An example continental extension input file is attached, which will be submitted as a cookbook example in the next few days.

In this example, extension is driven by prescribed outflow on the sides and inflow at the base.  The rheology is dislocation creep with different flow laws for the upper/lower crust and mantle.  Internal friction angle (20 degrees) (20 MPa) are within the range of commonly used values.  No strain-weakening, but I have a pull request open that implements this.

Most extension problems include the asthenosphere, while this model only goes down to 100 km.  As such, I would only use this type of setup for studying early stage extension.  Any problems examining extension from start to breakup should extend to at least 150 km. In this case, one might alter the simple boundary conditions I've prescribed.

Hope this helps and let me know you if you have any questions about the input file.

Cheers,
John






*************************************************

John Naliboff

Assistant Project Scientist, CIG

Earth & Planetary Sciences Dept., UC Davis
On 10/10/2016 12:59 AM, Mohamed Gouiza wrote:
Hi John,

I looked for the continental extension model that you showed in the online workshop last month, but couldn’t find it in tests/ folder.
I’ve been running several extension models with the visco-plastic material model and I am interested in knowing the visco-plastic law parameters that you used and how do you prescribe the boundary conditions: is the extension rate defined the same way as in the crustal deformation example in the cookbook by Cedric?

Thank you

-------------------------------------------------
Mohamed Gouiza, Research Fellow
Basin Structure Group, Institute of Applied Geosciences
University of Leeds, School of Earth and Environment
Leeds,  LS2 9JT, UK
M.Gouiza at leeds.ac.uk<mailto:M.Gouiza at leeds.ac.uk>
+44 7985 782073
-------------------------------------------------





_______________________________________________

Aspect-devel mailing list

Aspect-devel at geodynamics.org<mailto:Aspect-devel at geodynamics.org>

http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel




_______________________________________________

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From M.Gouiza at leeds.ac.uk  Mon Nov 14 02:43:23 2016
From: M.Gouiza at leeds.ac.uk (Mohamed Gouiza)
Date: Mon, 14 Nov 2016 10:43:23 +0000
Subject: [aspect-devel] Compiling dealii
Message-ID: <AM5PR0301MB23565317B54F08941EF3775DD1BC0@AM5PR0301MB2356.eurprd03.prod.outlook.com>

Hi,

I am trying to compile the devl version of dealii (to compile the devl version of ASPECT) but the configuration fails with this message: Configuration incomplete, error occurred!
I am attaching the error log.

I know it is a dealii issue and not related to ASPECT but I thought I will start with you guys to see if you had the same problem.
Thank you for your help

-------------------------------------------------
Mohamed Gouiza, Research Fellow
Basin Structure Group, Institute of Applied Geosciences
University of Leeds, School of Earth and Environment
Leeds,  LS2 9JT, UK
M.Gouiza at leeds.ac.uk<mailto:M.Gouiza at leeds.ac.uk>
+44 7985 782073
-------------------------------------------------

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From heister at clemson.edu  Mon Nov 14 08:19:41 2016
From: heister at clemson.edu (Timo Heister)
Date: Mon, 14 Nov 2016 11:19:41 -0500
Subject: [aspect-devel] Compiling dealii
In-Reply-To: <AM5PR0301MB23565317B54F08941EF3775DD1BC0@AM5PR0301MB2356.eurprd03.prod.outlook.com>
References: <AM5PR0301MB23565317B54F08941EF3775DD1BC0@AM5PR0301MB2356.eurprd03.prod.outlook.com>
Message-ID: <CAMRj59HmTzd6Svj3_iCpNens=kQtds5hVGir5_PhUkNrkcFL_g@mail.gmail.com>

Mohamed,

please post the screen output from cmake. It should tell you what the issues is.

On Mon, Nov 14, 2016 at 5:43 AM, Mohamed Gouiza <M.Gouiza at leeds.ac.uk> wrote:
> Hi,
>
>
>
> I am trying to compile the devl version of dealii (to compile the devl
> version of ASPECT) but the configuration fails with this message:
> Configuration incomplete, error occurred!
>
> I am attaching the error log.
>
>
>
> I know it is a dealii issue and not related to ASPECT but I thought I will
> start with you guys to see if you had the same problem.
>
> Thank you for your help
>
>
>
> -------------------------------------------------
> Mohamed Gouiza, Research Fellow
> Basin Structure Group, Institute of Applied Geosciences
> University of Leeds, School of Earth and Environment
>
> Leeds,  LS2 9JT, UK
>
> M.Gouiza at leeds.ac.uk
> +44 7985 782073
> -------------------------------------------------
>
>
>
>
> _______________________________________________
> Aspect-devel mailing list
> Aspect-devel at geodynamics.org
> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.geodynamics.org_cgi-2Dbin_mailman_listinfo_aspect-2Ddevel&d=CwIGaQ&c=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4&r=R5lvg9JC99XvuTgScgbY_QFS80R7PEA2q0EPwDy7VQw&m=aL6z8oyWQbZ8siB9lZ-NXNymu2HK_6gY2XEOLZkJ0Pw&s=cXKlEr0Z7CDI39QCDMaikxGXfzKdnaO8nV6KGnk8maw&e=



-- 
Timo Heister
http://www.math.clemson.edu/~heister/

From M.Gouiza at leeds.ac.uk  Mon Nov 14 08:32:31 2016
From: M.Gouiza at leeds.ac.uk (Mohamed Gouiza)
Date: Mon, 14 Nov 2016 16:32:31 +0000
Subject: [aspect-devel] Compiling dealii
In-Reply-To: <CAMRj59HmTzd6Svj3_iCpNens=kQtds5hVGir5_PhUkNrkcFL_g@mail.gmail.com>
References: <AM5PR0301MB23565317B54F08941EF3775DD1BC0@AM5PR0301MB2356.eurprd03.prod.outlook.com>
 <CAMRj59HmTzd6Svj3_iCpNens=kQtds5hVGir5_PhUkNrkcFL_g@mail.gmail.com>
Message-ID: <AM5PR0301MB23567FB24BF55AA5A2B38E71D1BC0@AM5PR0301MB2356.eurprd03.prod.outlook.com>

Hi Timo,

There was a small typo in my configuration command (I forgot the D before CMAKE_INSTAL_PREFIX)! It took me a while before seeing it.

Mohamed

-----Original Message-----
From: Aspect-devel [mailto:aspect-devel-bounces at geodynamics.org] On Behalf Of Timo Heister
Sent: 14 November 2016 16:20
To: aspect-devel <aspect-devel at geodynamics.org>
Subject: Re: [aspect-devel] Compiling dealii

Mohamed,

please post the screen output from cmake. It should tell you what the issues is.

On Mon, Nov 14, 2016 at 5:43 AM, Mohamed Gouiza <M.Gouiza at leeds.ac.uk> wrote:
> Hi,
>
>
>
> I am trying to compile the devl version of dealii (to compile the devl 
> version of ASPECT) but the configuration fails with this message:
> Configuration incomplete, error occurred!
>
> I am attaching the error log.
>
>
>
> I know it is a dealii issue and not related to ASPECT but I thought I 
> will start with you guys to see if you had the same problem.
>
> Thank you for your help
>
>
>
> -------------------------------------------------
> Mohamed Gouiza, Research Fellow
> Basin Structure Group, Institute of Applied Geosciences University of 
> Leeds, School of Earth and Environment
>
> Leeds,  LS2 9JT, UK
>
> M.Gouiza at leeds.ac.uk
> +44 7985 782073
> -------------------------------------------------
>
>
>
>
> _______________________________________________
> Aspect-devel mailing list
> Aspect-devel at geodynamics.org
> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.geodynamics.
> org_cgi-2Dbin_mailman_listinfo_aspect-2Ddevel&d=CwIGaQ&c=Ngd-ta5yRYsqe
> UsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4&r=R5lvg9JC99XvuTgScgbY_QFS80R7PEA2q0EPw
> Dy7VQw&m=aL6z8oyWQbZ8siB9lZ-NXNymu2HK_6gY2XEOLZkJ0Pw&s=cXKlEr0Z7CDI39Q
> CDMaikxGXfzKdnaO8nV6KGnk8maw&e=



--
Timo Heister
http://www.math.clemson.edu/~heister/
_______________________________________________
Aspect-devel mailing list
Aspect-devel at geodynamics.org
http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel

From rene.gassmoeller at mailbox.org  Mon Nov 14 11:00:22 2016
From: rene.gassmoeller at mailbox.org (Rene Gassmoeller)
Date: Mon, 14 Nov 2016 19:00:22 -0000
Subject: [aspect-devel] ASPECT Newsletter #17
Message-ID: <20161114190017.69D36AC29C5@geodynamics.org>

Hello everyone!

This is ASPECT newsletter #17.
It automatically reports recently merged features and discussions about the ASPECT mantle convection code.


## Below you find a list of recently proposed or merged features:

#1267: fixes to compile without cxx11 (proposed by tjhei; merged) https://github.com/geodynamics/aspect/pull/1267

#1266: Added two particle generators (proposed by hlokavarapu; merged) https://github.com/geodynamics/aspect/pull/1266

#1265: Particle emplace cpp14 (proposed by gassmoeller; merged) https://github.com/geodynamics/aspect/pull/1265

#1264: Rename the variables in DataPostprocessor derived classes. (proposed by bangerth; merged) https://github.com/geodynamics/aspect/pull/1264

#1263: require cxx14 for emplace_hint (proposed by tjhei) https://github.com/geodynamics/aspect/pull/1263

#1262: Speedup cell id transport (proposed by gassmoeller; merged) https://github.com/geodynamics/aspect/pull/1262

#1261: Manual fixes and update (proposed by tjhei; merged) https://github.com/geodynamics/aspect/pull/1261

#1259: Avoid maps. Use vertex neighbors for sort. (proposed by gassmoeller; merged) https://github.com/geodynamics/aspect/pull/1259


## And this is a list of recently opened or closed discussions:

#1271: Issues compiling ASPECT on stampede (opened) https://github.com/geodynamics/aspect/issues/1271

#1270: Write a postprocessor that outputs the elevation from the dynamic topography/mesh movement scheme (opened) https://github.com/geodynamics/aspect/issues/1270

#1269: Run a static analyzer on the ASPECT code base (opened) https://github.com/geodynamics/aspect/issues/1269

#1268: [Post 1.5] Convert postprocessors to take DataPostprocessorInputs arguments (opened) https://github.com/geodynamics/aspect/issues/1268

#1260: emplace_hint missing in gcc 4.6 (opened) https://github.com/geodynamics/aspect/issues/1260


A list of all major changes since the last release can be found at https://aspect.dealii.org/doc/doxygen/changes_current.html.


Thanks for being part of the community!


Let us know about questions, problems, bugs or just share your experience by writing to aspect-devel at geodynamics.org, or by opening issues or pull requests at https://www.github.com/geodynamics/aspect.
Additional information can be found at https://aspect.dealii.org/, and https://geodynamics.org/cig/software/aspect/.
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From jbnaliboff at ucdavis.edu  Mon Nov 14 11:07:58 2016
From: jbnaliboff at ucdavis.edu (John Naliboff)
Date: Mon, 14 Nov 2016 11:07:58 -0800
Subject: [aspect-devel] Continental extension model
In-Reply-To: <CY1PR03MB151835BC48D37E9E86ECE2F2ADBA0@CY1PR03MB1518.namprd03.prod.outlook.com>
References: <AM5PR0301MB2356DD1EE380A0165856F5A7D1DB0@AM5PR0301MB2356.eurprd03.prod.outlook.com>
 <2938597d-312c-cea5-2b45-66617de140ad@ucdavis.edu>
 <AM5PR0301MB2356CCD6473B8270B4030CE0D1D50@AM5PR0301MB2356.eurprd03.prod.outlook.com>
 <387c7dd8-148e-86f3-8051-820a6930e32a@ucdavis.edu>
 <AM5PR0301MB23566C3EC780F8D514942A2FD1D40@AM5PR0301MB2356.eurprd03.prod.outlook.com>
 <CY1PR03MB151835BC48D37E9E86ECE2F2ADBA0@CY1PR03MB1518.namprd03.prod.outlook.com>
Message-ID: <66cfdd24-2466-52d4-d145-a4a68f61f342@ucdavis.edu>

Hi Payman,

That is indeed an error, thank you for catching it!  Not sure how that 
got in there, but I haven't run models with a diffusion flow law yet so 
the error did not pop up.  I will apply a fix this afternoon, but for 
now you can simply remove the minus sign and recompile.

Cheers,
John


*************************************************
John Naliboff
Assistant Project Scientist, CIG
Earth & Planetary Sciences Dept., UC Davis

On 11/12/2016 02:35 PM, Payman Janbakhsh wrote:
>
> Hi John,
>
> In visco_plastic.cc file line 151 : std::pow(grain_size, 
> -grain_size_exponents_diffusion[j]):
>
> Shouldn’t the sign of grain size exponent be positive? Ie.
>
> std::pow(grain_size, grain_size_exponents_diffusion[j]):
>
> that way decrease in grain size decreases the diffusion viscosity.
>
> Thanks
>
> payman
>
> *From:*Aspect-devel [mailto:aspect-devel-bounces at geodynamics.org] *On 
> Behalf Of *Mohamed Gouiza
> *Sent:* October 21, 2016 11:43 AM
> *To:* aspect-devel at geodynamics.org
> *Subject:* Re: [aspect-devel] Continental extension model
>
> Hi John,
>
> I added a couple of suggestions to the commit request of the 
> continental_extension_cookbook
>
> Thanks for the DG method. I am running the development versions of 
> ASPECT and deal.ii but from a month ago or so.
>
> On a different matter, is there a postprocessor that allows to 
> visualize the dominant creep law (dislocation vs diffusion) if I 
> choose composite flow in my material model?
>
> Cheers,
>
> *From:*Aspect-devel [mailto:aspect-devel-bounces at geodynamics.org] *On 
> Behalf Of *John Naliboff
> *Sent:* 20 October 2016 21:53
> *To:* aspect-devel at geodynamics.org <mailto:aspect-devel at geodynamics.org>
> *Subject:* Re: [aspect-devel] Continental extension model
>
> Hi Mohamed,
>
> The value is indeed related to the fact that there is inflow at the 
> base.  Many months ago, I was seeing odd behavior in the compositional 
> fields and I suspected not having the mantle layer extend well past 
> the model base might be one of the reasons.
>
> However, at the moment I can't recall if this alone fixed the issue.  
> In theory, the simulation should work fine as long as the mantle layer 
> is defined as extending exactly to the model base.
>
> Aside, one way to improve the accuracy of the compositional field 
> advection is by using the DG method option for the compositional 
> discretization.  In the input file I sent you, add the following lines:
>     subsection Discretization
>       set Use discontinuous composition discretization = true
>       subsection Stabilization parameters
>           set Use limiter for discontinuous composition solution = 
> true # apply the limiter to the DG solutions
>           set Global composition maximum = 1.0, 1.0, 1.0, 1.0
>           set Global composition minimum =  0.0, 0.0, 0.0, 0.0
>       end
>     end
>
> To use this option you will need to work of the development version of 
> both ASPECT and deal.ii.  Let us know if you have any issues getting 
> things installed on this front or with using the DG method.  If you 
> see anything odd in the models, please do not hesitate to email the list!
>
> Last, I just opened a pull request for a cookbook related to this 
> input file.  You can check out my forked copy ASPECT (branch 
> continental_extension_cookbook) if you want to take a look at it 
> before it gets merged.  Even better, make some comments on the pull 
> request!
>
> Cheers,
> John
>
> *************************************************
> John Naliboff
> Assistant Project Scientist, CIG
> Earth & Planetary Sciences Dept., UC Davis
>
> On 10/20/2016 08:02 AM, Mohamed Gouiza wrote:
>
>     Hi John,
>
>     In the continental extension input file that you sent me, the
>     mantle compositional field is defined as 70.e3 && y>*-100.e3*
>
>     Is the -100.e3 a typo or is it because of the prescribed inflow at
>     the base of the model?
>
>     Mohamed
>
>     *From:*Aspect-devel [mailto:aspect-devel-bounces at geodynamics.org]
>     *On Behalf Of *John Naliboff
>     *Sent:* 10 October 2016 17:12
>     *To:* aspect-devel at geodynamics.org
>     <mailto:aspect-devel at geodynamics.org>
>     *Subject:* Re: [aspect-devel] Continental extension model
>
>     Hi Mohamed,
>
>     An example continental extension input file is attached, which
>     will be submitted as a cookbook example in the next few days.
>
>     In this example, extension is driven by prescribed outflow on the
>     sides and inflow at the base.  The rheology is dislocation creep
>     with different flow laws for the upper/lower crust and mantle. 
>     Internal friction angle (20 degrees) (20 MPa) are within the range
>     of commonly used values.  No strain-weakening, but I have a pull
>     request open that implements this.
>
>     Most extension problems include the asthenosphere, while this
>     model only goes down to 100 km.  As such, I would only use this
>     type of setup for studying early stage extension.  Any problems
>     examining extension from start to breakup should extend to at
>     least 150 km. In this case, one might alter the simple boundary
>     conditions I've prescribed.
>
>     Hope this helps and let me know you if you have any questions
>     about the input file.
>
>     Cheers,
>     John
>
>
>
>
>
>     *************************************************
>
>     John Naliboff
>
>     Assistant Project Scientist, CIG
>
>     Earth & Planetary Sciences Dept., UC Davis
>
>     On 10/10/2016 12:59 AM, Mohamed Gouiza wrote:
>
>         Hi John,
>
>         I looked for the continental extension model that you showed
>         in the online workshop last month, but couldn’t find it in
>         tests/ folder.
>
>         I’ve been running several extension models with the
>         visco-plastic material model and I am interested in knowing
>         the visco-plastic law parameters that you used and how do you
>         prescribe the boundary conditions: is the extension rate
>         defined the same way as in the crustal deformation example in
>         the cookbook by Cedric?
>
>         Thank you
>
>         -------------------------------------------------
>         Mohamed Gouiza, Research Fellow
>         Basin Structure Group, Institute of Applied Geosciences
>         University of Leeds, School of Earth and Environment
>
>         Leeds,  LS2 9JT, UK
>
>         M.Gouiza at leeds.ac.uk <mailto:M.Gouiza at leeds.ac.uk>
>         +44 7985 782073
>         -------------------------------------------------
>
>
>
>
>         _______________________________________________
>
>         Aspect-devel mailing list
>
>         Aspect-devel at geodynamics.org <mailto:Aspect-devel at geodynamics.org>
>
>         http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel
>
>
>
>     _______________________________________________
>
>     Aspect-devel mailing list
>
>     Aspect-devel at geodynamics.org <mailto:Aspect-devel at geodynamics.org>
>
>     http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel
>
>
>
> _______________________________________________
> Aspect-devel mailing list
> Aspect-devel at geodynamics.org
> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel

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From payman.janbakhsh at mail.utoronto.ca  Mon Nov 14 18:31:49 2016
From: payman.janbakhsh at mail.utoronto.ca (Payman Janbakhsh)
Date: Tue, 15 Nov 2016 02:31:49 +0000
Subject: [aspect-devel] Continental extension model
In-Reply-To: <66cfdd24-2466-52d4-d145-a4a68f61f342@ucdavis.edu>
References: <AM5PR0301MB2356DD1EE380A0165856F5A7D1DB0@AM5PR0301MB2356.eurprd03.prod.outlook.com>
 <2938597d-312c-cea5-2b45-66617de140ad@ucdavis.edu>
 <AM5PR0301MB2356CCD6473B8270B4030CE0D1D50@AM5PR0301MB2356.eurprd03.prod.outlook.com>
 <387c7dd8-148e-86f3-8051-820a6930e32a@ucdavis.edu>
 <AM5PR0301MB23566C3EC780F8D514942A2FD1D40@AM5PR0301MB2356.eurprd03.prod.outlook.com>
 <CY1PR03MB151835BC48D37E9E86ECE2F2ADBA0@CY1PR03MB1518.namprd03.prod.outlook.com>,
 <66cfdd24-2466-52d4-d145-a4a68f61f342@ucdavis.edu>
Message-ID: <7a6qo2wxj6gxjos2rv471hml.1479177106947@email.android.com>

Cheers

Payman



Sent from my Samsung Galaxy smartphone.


-------- Original message --------
From: John Naliboff <jbnaliboff at ucdavis.edu>
Date: 2016-11-14 9:26 PM (GMT-05:00)
To: aspect-devel at geodynamics.org
Subject: Re: [aspect-devel] Continental extension model

Hi Payman,

That is indeed an error, thank you for catching it!  Not sure how that got in there, but I haven't run models with a diffusion flow law yet so the error did not pop up.  I will apply a fix this afternoon, but for now you can simply remove the minus sign and recompile.

Cheers,
John



*************************************************
John Naliboff
Assistant Project Scientist, CIG
Earth & Planetary Sciences Dept., UC Davis


On 11/12/2016 02:35 PM, Payman Janbakhsh wrote:
Hi John,
In visco_plastic.cc file line 151 : std::pow(grain_size, -grain_size_exponents_diffusion[j]):
Shouldn’t the sign of grain size exponent be positive? Ie.
std::pow(grain_size, grain_size_exponents_diffusion[j]):
that way decrease in grain size decreases the diffusion viscosity.

Thanks
payman

From: Aspect-devel [mailto:aspect-devel-bounces at geodynamics.org] On Behalf Of Mohamed Gouiza
Sent: October 21, 2016 11:43 AM
To: aspect-devel at geodynamics.org<mailto:aspect-devel at geodynamics.org>
Subject: Re: [aspect-devel] Continental extension model

Hi John,

I added a couple of suggestions to the commit request of the continental_extension_cookbook

Thanks for the DG method. I am running the development versions of ASPECT and deal.ii but from a month ago or so.

On a different matter, is there a postprocessor that allows to visualize the dominant creep law (dislocation vs diffusion) if I choose composite flow in my material model?

Cheers,

From: Aspect-devel [mailto:aspect-devel-bounces at geodynamics.org] On Behalf Of John Naliboff
Sent: 20 October 2016 21:53
To: aspect-devel at geodynamics.org<mailto:aspect-devel at geodynamics.org>
Subject: Re: [aspect-devel] Continental extension model

Hi Mohamed,

The value is indeed related to the fact that there is inflow at the base.  Many months ago, I was seeing odd behavior in the compositional fields and I suspected not having the mantle layer extend well past the model base might be one of the reasons.

However, at the moment I can't recall if this alone fixed the issue.  In theory, the simulation should work fine as long as the mantle layer is defined as extending exactly to the model base.

Aside, one way to improve the accuracy of the compositional field advection is by using the DG method option for the compositional discretization.  In the input file I sent you, add the following lines:
    subsection Discretization
      set Use discontinuous composition discretization = true
      subsection Stabilization parameters
          set Use limiter for discontinuous composition solution = true # apply the limiter to the DG solutions
          set Global composition maximum = 1.0, 1.0, 1.0, 1.0
          set Global composition minimum =  0.0, 0.0, 0.0, 0.0
      end
    end

To use this option you will need to work of the development version of both ASPECT and deal.ii.  Let us know if you have any issues getting things installed on this front or with using the DG method.  If you see anything odd in the models, please do not hesitate to email the list!

Last, I just opened a pull request for a cookbook related to this input file.  You can check out my forked copy ASPECT (branch continental_extension_cookbook) if you want to take a look at it before it gets merged.  Even better, make some comments on the pull request!

Cheers,
John


*************************************************

John Naliboff

Assistant Project Scientist, CIG

Earth & Planetary Sciences Dept., UC Davis
On 10/20/2016 08:02 AM, Mohamed Gouiza wrote:
Hi John,

In the continental extension input file that you sent me, the mantle compositional field is defined as 70.e3 && y>-100.e3
Is the -100.e3 a typo or is it because of the prescribed inflow at the base of the model?

Mohamed

From: Aspect-devel [mailto:aspect-devel-bounces at geodynamics.org] On Behalf Of John Naliboff
Sent: 10 October 2016 17:12
To: aspect-devel at geodynamics.org<mailto:aspect-devel at geodynamics.org>
Subject: Re: [aspect-devel] Continental extension model

Hi Mohamed,

An example continental extension input file is attached, which will be submitted as a cookbook example in the next few days.

In this example, extension is driven by prescribed outflow on the sides and inflow at the base.  The rheology is dislocation creep with different flow laws for the upper/lower crust and mantle.  Internal friction angle (20 degrees) (20 MPa) are within the range of commonly used values.  No strain-weakening, but I have a pull request open that implements this.

Most extension problems include the asthenosphere, while this model only goes down to 100 km.  As such, I would only use this type of setup for studying early stage extension.  Any problems examining extension from start to breakup should extend to at least 150 km. In this case, one might alter the simple boundary conditions I've prescribed.

Hope this helps and let me know you if you have any questions about the input file.

Cheers,
John






*************************************************

John Naliboff

Assistant Project Scientist, CIG

Earth & Planetary Sciences Dept., UC Davis
On 10/10/2016 12:59 AM, Mohamed Gouiza wrote:
Hi John,

I looked for the continental extension model that you showed in the online workshop last month, but couldn’t find it in tests/ folder.
I’ve been running several extension models with the visco-plastic material model and I am interested in knowing the visco-plastic law parameters that you used and how do you prescribe the boundary conditions: is the extension rate defined the same way as in the crustal deformation example in the cookbook by Cedric?

Thank you

-------------------------------------------------
Mohamed Gouiza, Research Fellow
Basin Structure Group, Institute of Applied Geosciences
University of Leeds, School of Earth and Environment
Leeds,  LS2 9JT, UK
M.Gouiza at leeds.ac.uk<mailto:M.Gouiza at leeds.ac.uk>
+44 7985 782073
-------------------------------------------------





_______________________________________________

Aspect-devel mailing list

Aspect-devel at geodynamics.org<mailto:Aspect-devel at geodynamics.org>

http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel




_______________________________________________

Aspect-devel mailing list

Aspect-devel at geodynamics.org<mailto:Aspect-devel at geodynamics.org>

http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel




_______________________________________________
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Aspect-devel at geodynamics.org<mailto:Aspect-devel at geodynamics.org>
http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel

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From lev.karatun at gmail.com  Wed Nov 16 12:50:36 2016
From: lev.karatun at gmail.com (Lev Karatun)
Date: Wed, 16 Nov 2016 15:50:36 -0500
Subject: [aspect-devel] Compilation error
Message-ID: <CAPGyz26ZuVJq+vzr-RHhC-=MH+kxp9ynREhJbesp0JMCBp_=Mw@mail.gmail.com>

Hi,

I'm getting an error when trying to compile aspect (both aspect and dealII
are latest development versions).

[  0%] Building CXX object CMakeFiles/aspect.dir/source/particle/world.cc.o
/home/r/russ/lkaratun/aspect/aspect/source/particle/world.cc: In member
function 'void aspect::Particle::World<dim>::send_recv_particles(const
std::vector<std::vector<std::pair<std::pair<int, int>,
aspect::Particle::Particle<dim> > > >&,
std::vector<std::pair<std::pair<int, int>, aspect::Particle::Particle<dim>
> >&)':
/home/r/russ/lkaratun/aspect/aspect/source/particle/world.cc:1035:47:
error: 'binary_type' is not a member of 'dealii::CellId'
       const unsigned int cellid_size = sizeof(CellId::binary_type);
                                               ^
/home/r/russ/lkaratun/aspect/aspect/source/particle/world.cc:1066:21:
error: 'binary_type' in 'class dealii::CellId' does not name a type
               const CellId::binary_type cellid = cell->id().template
to_binary<dim>();
                     ^
/home/r/russ/lkaratun/aspect/aspect/source/particle/world.cc:1067:29:
error: 'cellid' was not declared in this scope
               memcpy(data, &cellid, cellid_size);
                             ^
/home/r/russ/lkaratun/aspect/aspect/source/particle/world.cc:1129:11:
error: 'binary_type' is not a member of 'dealii::CellId'
           CellId::binary_type binary_cellid;
           ^
/home/r/russ/lkaratun/aspect/aspect/source/particle/world.cc:1129:31:
error: expected ';' before 'binary_cellid'
           CellId::binary_type binary_cellid;
                               ^
/home/r/russ/lkaratun/aspect/aspect/source/particle/world.cc:1130:19:
error: 'binary_cellid' was not declared in this scope
           memcpy(&binary_cellid, recv_data_it, cellid_size);
                   ^
make[2]: *** [CMakeFiles/aspect.dir/source/particle/world.cc.o] Error 1
make[1]: *** [CMakeFiles/aspect.dir/all] Error 2
make: *** [all] Error 2

Best regards,
Lev Karatun.
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From bangerth at tamu.edu  Wed Nov 16 13:58:30 2016
From: bangerth at tamu.edu (Wolfgang Bangerth)
Date: Wed, 16 Nov 2016 14:58:30 -0700
Subject: [aspect-devel] Compilation error
In-Reply-To: <CAPGyz26ZuVJq+vzr-RHhC-=MH+kxp9ynREhJbesp0JMCBp_=Mw@mail.gmail.com>
References: <CAPGyz26ZuVJq+vzr-RHhC-=MH+kxp9ynREhJbesp0JMCBp_=Mw@mail.gmail.com>
Message-ID: <a07d4350-60be-9bc7-7cce-deebab6d60c7@tamu.edu>


> I'm getting an error when trying to compile aspect (both aspect and
> dealII are latest development versions).

Lev - I think you're not using the latest deal.II version, or if you do 
you may have forgotten to not just compile, but also *install* it. Can 
you try to update your installation?

Best
  W.


-- 
------------------------------------------------------------------------
Wolfgang Bangerth          email:                 bangerth at colostate.edu
                            www: http://www.math.colostate.edu/~bangerth/

From jbnaliboff at ucdavis.edu  Wed Nov 16 13:26:54 2016
From: jbnaliboff at ucdavis.edu (John Naliboff)
Date: Wed, 16 Nov 2016 13:26:54 -0800
Subject: [aspect-devel] Compilation error
In-Reply-To: <CAPGyz26ZuVJq+vzr-RHhC-=MH+kxp9ynREhJbesp0JMCBp_=Mw@mail.gmail.com>
References: <CAPGyz26ZuVJq+vzr-RHhC-=MH+kxp9ynREhJbesp0JMCBp_=Mw@mail.gmail.com>
Message-ID: <614A862A-86F0-4C8B-BE51-A35F892ADBD0@ucdavis.edu>

Hi Lev,

When was the last commit for deal.II?  I just compiled the latest development version of ASPECT (as of today) with the development version of deal.II.  

The last commit for deal.II was November 8 (Introduce configuration variable CUDA_DIR to select CUDA installation).  

What is the last deal.ii commit on your version?  Did you build deal.II completely from scratch and do a ‘make distclean’ before compiling ASPECT?  I’ve been caught once or twice with ASPECT compiling issues when I had not fully rebuilt deal.II.

Cheers,
John

*************************************************
John Naliboff
Assistant Project Scientist, CIG
Earth & Planetary Sciences Dept., UC Davis






> On Nov 16, 2016, at 12:50 PM, Lev Karatun <lev.karatun at gmail.com> wrote:
> 
> Hi,
> 
> I'm getting an error when trying to compile aspect (both aspect and dealII are latest development versions).
> 
> [  0%] Building CXX object CMakeFiles/aspect.dir/source/particle/world.cc.o
> /home/r/russ/lkaratun/aspect/aspect/source/particle/world.cc: In member function 'void aspect::Particle::World<dim>::send_recv_particles(const std::vector<std::vector<std::pair<std::pair<int, int>, aspect::Particle::Particle<dim> > > >&, std::vector<std::pair<std::pair<int, int>, aspect::Particle::Particle<dim> > >&)':
> /home/r/russ/lkaratun/aspect/aspect/source/particle/world.cc:1035:47: error: 'binary_type' is not a member of 'dealii::CellId'
>        const unsigned int cellid_size = sizeof(CellId::binary_type);
>                                                ^
> /home/r/russ/lkaratun/aspect/aspect/source/particle/world.cc:1066:21: error: 'binary_type' in 'class dealii::CellId' does not name a type
>                const CellId::binary_type cellid = cell->id().template to_binary<dim>();
>                      ^
> /home/r/russ/lkaratun/aspect/aspect/source/particle/world.cc:1067:29: error: 'cellid' was not declared in this scope
>                memcpy(data, &cellid, cellid_size);
>                              ^
> /home/r/russ/lkaratun/aspect/aspect/source/particle/world.cc:1129:11: error: 'binary_type' is not a member of 'dealii::CellId'
>            CellId::binary_type binary_cellid;
>            ^
> /home/r/russ/lkaratun/aspect/aspect/source/particle/world.cc:1129:31: error: expected ';' before 'binary_cellid'
>            CellId::binary_type binary_cellid;
>                                ^
> /home/r/russ/lkaratun/aspect/aspect/source/particle/world.cc:1130:19: error: 'binary_cellid' was not declared in this scope
>            memcpy(&binary_cellid, recv_data_it, cellid_size);
>                    ^
> make[2]: *** [CMakeFiles/aspect.dir/source/particle/world.cc.o] Error 1
> make[1]: *** [CMakeFiles/aspect.dir/all] Error 2
> make: *** [all] Error 2
> 
> Best regards,
> Lev Karatun.
> _______________________________________________
> Aspect-devel mailing list
> Aspect-devel at geodynamics.org
> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel

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From lev.karatun at gmail.com  Wed Nov 16 18:43:30 2016
From: lev.karatun at gmail.com (Lev Karatun)
Date: Wed, 16 Nov 2016 21:43:30 -0500
Subject: [aspect-devel] Compilation error
In-Reply-To: <a07d4350-60be-9bc7-7cce-deebab6d60c7@tamu.edu>
References: <CAPGyz26ZuVJq+vzr-RHhC-=MH+kxp9ynREhJbesp0JMCBp_=Mw@mail.gmail.com>
 <a07d4350-60be-9bc7-7cce-deebab6d60c7@tamu.edu>
Message-ID: <CAPGyz257ez2E+nCeoFYRvXcjJ4XikJMje7ecUYygbG-RLGS8-g@mail.gmail.com>

Thanks Wolfgang,

you are right, I got lost in 4 different installations, my bad.

Best regards,
Lev Karatun.

2016-11-16 16:58 GMT-05:00 Wolfgang Bangerth <bangerth at tamu.edu>:

>
> I'm getting an error when trying to compile aspect (both aspect and
>> dealII are latest development versions).
>>
>
> Lev - I think you're not using the latest deal.II version, or if you do
> you may have forgotten to not just compile, but also *install* it. Can you
> try to update your installation?
>
> Best
>  W.
>
>
> --
> ------------------------------------------------------------------------
> Wolfgang Bangerth          email:                 bangerth at colostate.edu
>                            www: http://www.math.colostate.edu/~bangerth/
> _______________________________________________
> Aspect-devel mailing list
> Aspect-devel at geodynamics.org
> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel
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From cbranecky at ucsc.edu  Fri Nov 18 11:29:15 2016
From: cbranecky at ucsc.edu (Carolyn Branecky)
Date: Fri, 18 Nov 2016 11:29:15 -0800
Subject: [aspect-devel] free surface with non-zero surface pressure
Message-ID: <CAMe2WcpyGH+MpqqukibyeFarx+ym2WOFGssvf_hxRAkZgCHatg@mail.gmail.com>

Hi all,

I'm wondering whether is any reason why the free surface option could not
be run with a traction boundary condition at the free surface.  Here, I
have in mind applying a normal force at the surface, which could be due to
an ice sheet, sediment load, etc., and then the surface would be allowed to
deform under that load.

This could be framed as two questions:
1. Can surface pressure be combined with a free surface in principle in
ASPECT?
2. Are there any barriers to implementing these together in either the 1.4
release or the development version?

Looking forward to hearing your thoughts.
-Carolyn

-- 
Carolyn Branecky
Ph.D. candidate
University of California, Santa Cruz
Earth and Planetary Sciences
cbranecky at ucsc.edu
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From jbnaliboff at ucdavis.edu  Fri Nov 18 13:46:18 2016
From: jbnaliboff at ucdavis.edu (John Naliboff)
Date: Fri, 18 Nov 2016 13:46:18 -0800
Subject: [aspect-devel] free surface with non-zero surface pressure
In-Reply-To: <CAMe2WcpyGH+MpqqukibyeFarx+ym2WOFGssvf_hxRAkZgCHatg@mail.gmail.com>
References: <CAMe2WcpyGH+MpqqukibyeFarx+ym2WOFGssvf_hxRAkZgCHatg@mail.gmail.com>
Message-ID: <14ac9863-ecc4-5dfd-03f4-f10d91d98591@ucdavis.edu>

Hi Carolyn,

Great question!

Currently, it is not possible to mix a free surface and traction 
boundary condition.  However, as you pointed out this feature would be 
very useful for a number of applications and I do not see any reason why 
it can't be implemented.

I think this kind of feature would likely be implemented as an added 
option to the free surface portions of the code or as a new boundary 
condition model/option.  Others will have a much better idea of exactly 
how/where this should be done.

I imagine everyone is pretty busy gearing up for AGU, but this is a 
point one or more of us could return to next year.  Alternatively, If 
you would like to try the implementation please do so! You can always 
send questions to the mailing list as you go along.

Hope this helps and if you plan to attend AGU keep in mind there will be 
a whole suite of APSECT-related presentations 
(https://geodynamics.org/cig/events/calendar/agu-2016-week/abstracts/).

Cheers,
John

*************************************************
John Naliboff
Assistant Project Scientist, CIG
Earth & Planetary Sciences Dept., UC Davis

On 11/18/2016 11:29 AM, Carolyn Branecky wrote:
> Hi all,
>
> I'm wondering whether is any reason why the free surface option could 
> not be run with a traction boundary condition at the free surface.  
> Here, I have in mind applying a normal force at the surface, which 
> could be due to an ice sheet, sediment load, etc., and then the 
> surface would be allowed to deform under that load.
>
> This could be framed as two questions:
> 1. Can surface pressure be combined with a free surface in principle 
> in ASPECT?
> 2. Are there any barriers to implementing these together in either the 
> 1.4 release or the development version?
>
> Looking forward to hearing your thoughts.
> -Carolyn
>
> -- 
> Carolyn Branecky
> Ph.D. candidate
> University of California, Santa Cruz
> Earth and Planetary Sciences
> cbranecky at ucsc.edu <mailto:cbranecky at ucsc.edu>
>
>
> _______________________________________________
> Aspect-devel mailing list
> Aspect-devel at geodynamics.org
> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel

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From f_orellana at berkeley.edu  Sun Nov 20 20:34:57 2016
From: f_orellana at berkeley.edu (FELIPE ORELLANA ROVIROSA)
Date: Sun, 20 Nov 2016 20:34:57 -0800
Subject: [aspect-devel] Error from violated condition on parameters
Message-ID: <CANEUqvjDrmjy-E0bk5+SFOjBQxXQwJ2WUgv4z0pB+L8Vto=Qjg@mail.gmail.com>

 Hi all,

    I am running aspect 1.5.0-pre

    I have tried to run my job several times, and I get this awkward error

  -- This is ASPECT, the Advanced Solver for Problems in Earth's ConvecTion.
--     . version 1.5.0-pre
--     . running in DEBUG mode
--     . running with 32 MPI processes
--     . using Trilinos
-----------------------------------------------------------------------------


-----------------------------------------------------------------------------
The output directory </home1/04020/unfelipe/brickbic/> provided in the
input file appears not to exist.
ASPECT will create it for you.
-----------------------------------------------------------------------------


Number of active cells: 512 (on 4 levels)
Number of degrees of freedom: 20,381 (14,739+729+4,913)

*** Timestep 0:  t=0 years

--------------------------------------------------------
An error occurred in line <1152> of file
</home1/04020/unfelipe/packages/aspect/source/simulator/assembly.cc> in
function
    void
aspect::Assemblers::CompleteEquations<dim>::local_assemble_advection_system(const
typename aspect::Simulator<dim>::Adv
ectionField&, double,
aspect::internal::Assembly::Scratch::AdvectionSystem<dim>&,
aspect::internal::Assembly::CopyData::Advecti
onSystem<dim>&) const [with int dim = 3; typename
aspect::Simulator<dim>::AdvectionField =
aspect::Simulator<3>::AdvectionField
]
The violated condition was:
    density_c_P >= 0
The name and call sequence of the exception was:
    ExcMessage ("The product of density and c_P needs to be a "
"non-negative quantity.")
Additional Information:
The product of density and c_P needs to be a non-negative quantity.

Stacktrace:
-----------
#0  /home1/04020/unfelipe/packages/aspect/build/aspect:
aspect::Assemblers::CompleteEquations<3>::local_assemble_advection_syst
em(aspect::Simulator<3>::AdvectionField const&, double,
aspect::internal::Assembly::Scratch::AdvectionSystem<3>&, aspect::inter
nal::Assembly::CopyData::AdvectionSystem<3>&) const
#1  /home1/04020/unfelipe/packages/aspect/build/aspect: s...
..

of course, my parameters are positive numbers, so I don't know where the
error comes from.

I am attaching my parameter file.

any help would be appreciated,
thanks,

Felipe
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From M.Gouiza at leeds.ac.uk  Mon Nov 21 01:17:49 2016
From: M.Gouiza at leeds.ac.uk (Mohamed Gouiza)
Date: Mon, 21 Nov 2016 09:17:49 +0000
Subject: [aspect-devel] Error from violated condition on parameters
In-Reply-To: <CANEUqvjDrmjy-E0bk5+SFOjBQxXQwJ2WUgv4z0pB+L8Vto=Qjg@mail.gmail.com>
References: <CANEUqvjDrmjy-E0bk5+SFOjBQxXQwJ2WUgv4z0pB+L8Vto=Qjg@mail.gmail.com>
Message-ID: <AM5PR0301MB2356E3FF314BD1F34B2D9BB1D1B50@AM5PR0301MB2356.eurprd03.prod.outlook.com>

Hi Felipe,

Your prm file does run on my machine, see below.
Either your ASPECT didn’t compile correctly (Try to run an example from the cookbook), or try in optimized mode rather than debug mode.

Mohamed

[earmgo at login1.polaris test]$ aspect RR3Dbic.prm
-----------------------------------------------------------------------------
-- This is ASPECT, the Advanced Solver for Problems in Earth's ConvecTion.
--     . version 1.5.0-pre
--     . running in OPTIMIZED mode
--     . running with 1 MPI process
--     . using Trilinos
-----------------------------------------------------------------------------


-----------------------------------------------------------------------------
The output directory <output/> provided in the input file appears not to exist.
ASPECT will create it for you.
-----------------------------------------------------------------------------


Number of active cells: 512 (on 4 levels)
Number of degrees of freedom: 20,381 (14,739+729+4,913)

*** Timestep 0:  t=0 years
   Solving temperature system... 0 iterations.
   Rebuilding Stokes preconditioner...
   Solving Stokes system... 30+2 iterations.

Number of active cells: 1,296 (on 5 levels)
Number of degrees of freedom: 51,950 (37,617+1,794+12,539)

*** Timestep 0:  t=0 years
   Solving temperature system... 0 iterations.
   Rebuilding Stokes preconditioner...
   Solving Stokes system... 30+2 iterations.

Number of active cells: 4,544 (on 6 levels)
Number of degrees of freedom: 179,987 (130,407+6,111+43,469)

*** Timestep 0:  t=0 years
   Solving temperature system... 0 iterations.
   Rebuilding Stokes preconditioner...
   Solving Stokes system... 30+3 iterations.

Number of active cells: 10,368 (on 6 levels)
Number of degrees of freedom: 377,927 (274,239+12,275+91,413)

*** Timestep 0:  t=0 years
   Solving temperature system... 0 iterations.
   Rebuilding Stokes preconditioner...
   Solving Stokes system... 30+4 iterations.

   Postprocessing:
     RMS, max velocity:                  0.00454 m/year, 0.0155 m/year
     Temperature min/avg/max:            300 K, 2.474e+05 K, 4.922e+05 K
     Heat fluxes through boundary parts: 0.001263 W, 0.0006153 W, 0.005619 W, 0.002371 W, 1.895e+14 W, 1.971e+12 W
     Writing graphical output:           output/solution/solution-00000

*** Timestep 1:  t=1 years
   Solving temperature system... 3 iterations.
   Solving Stokes system... 8+0 iterations.

   Postprocessing:
     RMS, max velocity:                  0.00454 m/year, 0.0155 m/year
     Temperature min/avg/max:            300 K, 2.474e+05 K, 4.922e+05 K
     Heat fluxes through boundary parts: 91.23 W, 113.4 W, 363.3 W, 454.7 W, 1.895e+14 W, 1.971e+12 W

Termination requested by criterion: end time


+---------------------------------------------+------------+------------+
| Total wallclock time elapsed since start    |       107s |            |
|                                             |            |            |
| Section                         | no. calls |  wall time | % of total |
+---------------------------------+-----------+------------+------------+
| Assemble Stokes system          |         5 |      33.6s |        31% |
| Assemble temperature system     |         5 |      7.01s |       6.5% |
| Build Stokes preconditioner     |         4 |      17.4s |        16% |
| Build temperature preconditioner|         5 |      2.36s |       2.2% |
| Solve Stokes system             |         5 |      30.1s |        28% |
| Solve temperature system        |         5 |     0.158s |      0.15% |
| Initialization                  |         1 |     0.123s |      0.11% |
| Postprocessing                  |         2 |       1.6s |       1.5% |
| Refine mesh structure, part 1   |         3 |      2.17s |         2% |
| Refine mesh structure, part 2   |         3 |     0.451s |      0.42% |
| Setup dof systems               |         4 |      11.6s |        11% |
| Setup initial conditions        |         4 |     0.416s |      0.39% |
+---------------------------------+-----------+------------+------------+

From: Aspect-devel [mailto:aspect-devel-bounces at geodynamics.org] On Behalf Of FELIPE ORELLANA ROVIROSA
Sent: 21 November 2016 04:35
To: aspect-devel at geodynamics.org
Subject: [aspect-devel] Error from violated condition on parameters


 Hi all,
    I am running aspect 1.5.0-pre
    I have tried to run my job several times, and I get this awkward error

  -- This is ASPECT, the Advanced Solver for Problems in Earth's ConvecTion.
--     . version 1.5.0-pre
--     . running in DEBUG mode
--     . running with 32 MPI processes
--     . using Trilinos
-----------------------------------------------------------------------------


-----------------------------------------------------------------------------
The output directory </home1/04020/unfelipe/brickbic/> provided in the input file appears not to exist.
ASPECT will create it for you.
-----------------------------------------------------------------------------


Number of active cells: 512 (on 4 levels)
Number of degrees of freedom: 20,381 (14,739+729+4,913)

*** Timestep 0:  t=0 years

--------------------------------------------------------
An error occurred in line <1152> of file </home1/04020/unfelipe/packages/aspect/source/simulator/assembly.cc> in function
    void aspect::Assemblers::CompleteEquations<dim>::local_assemble_advection_system(const typename aspect::Simulator<dim>::Adv
ectionField&, double, aspect::internal::Assembly::Scratch::AdvectionSystem<dim>&, aspect::internal::Assembly::CopyData::Advecti
onSystem<dim>&) const [with int dim = 3; typename aspect::Simulator<dim>::AdvectionField = aspect::Simulator<3>::AdvectionField
]
The violated condition was:
    density_c_P >= 0
The name and call sequence of the exception was:
    ExcMessage ("The product of density and c_P needs to be a " "non-negative quantity.")
Additional Information:
The product of density and c_P needs to be a non-negative quantity.

Stacktrace:
-----------
#0  /home1/04020/unfelipe/packages/aspect/build/aspect: aspect::Assemblers::CompleteEquations<3>::local_assemble_advection_syst
em(aspect::Simulator<3>::AdvectionField const&, double, aspect::internal::Assembly::Scratch::AdvectionSystem<3>&, aspect::inter
nal::Assembly::CopyData::AdvectionSystem<3>&) const
#1  /home1/04020/unfelipe/packages/aspect/build/aspect: s...
..
of course, my parameters are positive numbers, so I don't know where the error comes from.
I am attaching my parameter file.
any help would be appreciated,
thanks,
Felipe
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From f_orellana at berkeley.edu  Mon Nov 21 22:56:55 2016
From: f_orellana at berkeley.edu (FELIPE ORELLANA ROVIROSA)
Date: Mon, 21 Nov 2016 22:56:55 -0800
Subject: [aspect-devel] Error from violated condition on parameters
In-Reply-To: <AM5PR0301MB2356E3FF314BD1F34B2D9BB1D1B50@AM5PR0301MB2356.eurprd03.prod.outlook.com>
References: <CANEUqvjDrmjy-E0bk5+SFOjBQxXQwJ2WUgv4z0pB+L8Vto=Qjg@mail.gmail.com>
 <AM5PR0301MB2356E3FF314BD1F34B2D9BB1D1B50@AM5PR0301MB2356.eurprd03.prod.outlook.com>
Message-ID: <CANEUqvihkggaDNUWm=rdruGWxK0pXVJ8B77kmbY9EEHjPBJYzQ@mail.gmail.com>

 Thanks Mohamed,

 I will check this thing.

tank you,

Felipe



On Mon, Nov 21, 2016 at 1:17 AM, Mohamed Gouiza <M.Gouiza at leeds.ac.uk>
wrote:

> Hi Felipe,
>
>
>
> Your prm file does run on my machine, see below.
>
> Either your ASPECT didn’t compile correctly (Try to run an example from
> the cookbook), or try in optimized mode rather than debug mode.
>
>
>
> Mohamed
>
>
>
> [earmgo at login1.polaris test]$ aspect RR3Dbic.prm
>
> ------------------------------------------------------------
> -----------------
>
> -- This is ASPECT, the Advanced Solver for Problems in Earth's ConvecTion.
>
> --     . version 1.5.0-pre
>
> --     . running in OPTIMIZED mode
>
> --     . running with 1 MPI process
>
> --     . using Trilinos
>
> ------------------------------------------------------------
> -----------------
>
>
>
>
>
> ------------------------------------------------------------
> -----------------
>
> The output directory <output/> provided in the input file appears not to
> exist.
>
> ASPECT will create it for you.
>
> ------------------------------------------------------------
> -----------------
>
>
>
>
>
> Number of active cells: 512 (on 4 levels)
>
> Number of degrees of freedom: 20,381 (14,739+729+4,913)
>
>
>
> *** Timestep 0:  t=0 years
>
>    Solving temperature system... 0 iterations.
>
>    Rebuilding Stokes preconditioner...
>
>    Solving Stokes system... 30+2 iterations.
>
>
>
> Number of active cells: 1,296 (on 5 levels)
>
> Number of degrees of freedom: 51,950 (37,617+1,794+12,539)
>
>
>
> *** Timestep 0:  t=0 years
>
>    Solving temperature system... 0 iterations.
>
>    Rebuilding Stokes preconditioner...
>
>    Solving Stokes system... 30+2 iterations.
>
>
>
> Number of active cells: 4,544 (on 6 levels)
>
> Number of degrees of freedom: 179,987 (130,407+6,111+43,469)
>
>
>
> *** Timestep 0:  t=0 years
>
>    Solving temperature system... 0 iterations.
>
>    Rebuilding Stokes preconditioner...
>
>    Solving Stokes system... 30+3 iterations.
>
>
>
> Number of active cells: 10,368 (on 6 levels)
>
> Number of degrees of freedom: 377,927 (274,239+12,275+91,413)
>
>
>
> *** Timestep 0:  t=0 years
>
>    Solving temperature system... 0 iterations.
>
>    Rebuilding Stokes preconditioner...
>
>    Solving Stokes system... 30+4 iterations.
>
>
>
>    Postprocessing:
>
>      RMS, max velocity:                  0.00454 m/year, 0.0155 m/year
>
>      Temperature min/avg/max:            300 K, 2.474e+05 K, 4.922e+05 K
>
>      Heat fluxes through boundary parts: 0.001263 W, 0.0006153 W, 0.005619
> W, 0.002371 W, 1.895e+14 W, 1.971e+12 W
>
>      Writing graphical output:           output/solution/solution-00000
>
>
>
> *** Timestep 1:  t=1 years
>
>    Solving temperature system... 3 iterations.
>
>    Solving Stokes system... 8+0 iterations.
>
>
>
>    Postprocessing:
>
>      RMS, max velocity:                  0.00454 m/year, 0.0155 m/year
>
>      Temperature min/avg/max:            300 K, 2.474e+05 K, 4.922e+05 K
>
>      Heat fluxes through boundary parts: 91.23 W, 113.4 W, 363.3 W, 454.7
> W, 1.895e+14 W, 1.971e+12 W
>
>
>
> Termination requested by criterion: end time
>
>
>
>
>
> +---------------------------------------------+------------+------------+
>
> | Total wallclock time elapsed since start    |       107s |            |
>
> |                                             |            |            |
>
> | Section                         | no. calls |  wall time | % of total |
>
> +---------------------------------+-----------+------------+------------+
>
> | Assemble Stokes system          |         5 |      33.6s |        31% |
>
> | Assemble temperature system     |         5 |      7.01s |       6.5% |
>
> | Build Stokes preconditioner     |         4 |      17.4s |        16% |
>
> | Build temperature preconditioner|         5 |      2.36s |       2.2% |
>
> | Solve Stokes system             |         5 |      30.1s |        28% |
>
> | Solve temperature system        |         5 |     0.158s |      0.15% |
>
> | Initialization                  |         1 |     0.123s |      0.11% |
>
> | Postprocessing                  |         2 |       1.6s |       1.5% |
>
> | Refine mesh structure, part 1   |         3 |      2.17s |         2% |
>
> | Refine mesh structure, part 2   |         3 |     0.451s |      0.42% |
>
> | Setup dof systems               |         4 |      11.6s |        11% |
>
> | Setup initial conditions        |         4 |     0.416s |      0.39% |
>
> +---------------------------------+-----------+------------+------------+
>
>
>
> *From:* Aspect-devel [mailto:aspect-devel-bounces at geodynamics.org] *On
> Behalf Of *FELIPE ORELLANA ROVIROSA
> *Sent:* 21 November 2016 04:35
> *To:* aspect-devel at geodynamics.org
> *Subject:* [aspect-devel] Error from violated condition on parameters
>
>
>
>
>
>  Hi all,
>
>     I am running aspect 1.5.0-pre
>
>     I have tried to run my job several times, and I get this awkward error
>
>   -- This is ASPECT, the Advanced Solver for Problems in Earth's
> ConvecTion.
> --     . version 1.5.0-pre
> --     . running in DEBUG mode
> --     . running with 32 MPI processes
> --     . using Trilinos
> ------------------------------------------------------------
> -----------------
>
>
> ------------------------------------------------------------
> -----------------
> The output directory </home1/04020/unfelipe/brickbic/> provided in the
> input file appears not to exist.
> ASPECT will create it for you.
> ------------------------------------------------------------
> -----------------
>
>
> Number of active cells: 512 (on 4 levels)
> Number of degrees of freedom: 20,381 (14,739+729+4,913)
>
> *** Timestep 0:  t=0 years
>
> --------------------------------------------------------
> An error occurred in line <1152> of file </home1/04020/unfelipe/
> packages/aspect/source/simulator/assembly.cc> in function
>     void aspect::Assemblers::CompleteEquations<dim>::local_
> assemble_advection_system(const typename aspect::Simulator<dim>::Adv
> ectionField&, double, aspect::internal::Assembly::
> Scratch::AdvectionSystem<dim>&, aspect::internal::Assembly::
> CopyData::Advecti
> onSystem<dim>&) const [with int dim = 3; typename aspect::Simulator<dim>::AdvectionField
> = aspect::Simulator<3>::AdvectionField
> ]
> The violated condition was:
>     density_c_P >= 0
> The name and call sequence of the exception was:
>     ExcMessage ("The product of density and c_P needs to be a "
> "non-negative quantity.")
> Additional Information:
> The product of density and c_P needs to be a non-negative quantity.
>
> Stacktrace:
> -----------
> #0  /home1/04020/unfelipe/packages/aspect/build/aspect:
> aspect::Assemblers::CompleteEquations<3>::local_assemble_advection_syst
> em(aspect::Simulator<3>::AdvectionField const&, double,
> aspect::internal::Assembly::Scratch::AdvectionSystem<3>&, aspect::inter
> nal::Assembly::CopyData::AdvectionSystem<3>&) const
> #1  /home1/04020/unfelipe/packages/aspect/build/aspect: s...
> ..
>
> of course, my parameters are positive numbers, so I don't know where the
> error comes from.
>
> I am attaching my parameter file.
>
> any help would be appreciated,
>
> thanks,
>
> Felipe
>
> _______________________________________________
> Aspect-devel mailing list
> Aspect-devel at geodynamics.org
> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel
>
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From dannberg at gfz-potsdam.de  Tue Nov 22 07:41:08 2016
From: dannberg at gfz-potsdam.de (Juliane Dannberg)
Date: Tue, 22 Nov 2016 10:41:08 -0500
Subject: [aspect-devel] Error from violated condition on parameters
In-Reply-To: <CANEUqvihkggaDNUWm=rdruGWxK0pXVJ8B77kmbY9EEHjPBJYzQ@mail.gmail.com>
References: <CANEUqvjDrmjy-E0bk5+SFOjBQxXQwJ2WUgv4z0pB+L8Vto=Qjg@mail.gmail.com>
 <AM5PR0301MB2356E3FF314BD1F34B2D9BB1D1B50@AM5PR0301MB2356.eurprd03.prod.outlook.com>
 <CANEUqvihkggaDNUWm=rdruGWxK0pXVJ8B77kmbY9EEHjPBJYzQ@mail.gmail.com>
Message-ID: <eff3bf1e-6e9d-12f8-f8fe-ec858d0252c7@gfz-potsdam.de>

Hi Felipe,

if you run your input file in optimized mode you will see that the 
density is indeed negative in a part of your model domain (probably 
because your temperature goes up to almost 5000 K), and that is exactly 
what the error message is telling you.

I would also like to add that normally it is not a good idea to just run 
your models in optimized mode if you get an error message in debug mode, 
because usually the error message tells you that something in your code 
or your model setup is not working as intended, and in these cases it 
helps to look at the setup again and fix these things.

Best,
Juliane


On 11/22/2016 01:56 AM, FELIPE ORELLANA ROVIROSA wrote:
>
>  Thanks Mohamed,
>
>  I will check this thing.
>
> tank you,
>
> Felipe
>
>
>
> On Mon, Nov 21, 2016 at 1:17 AM, Mohamed Gouiza <M.Gouiza at leeds.ac.uk 
> <mailto:M.Gouiza at leeds.ac.uk>> wrote:
>
>     Hi Felipe,
>
>     Your prm file does run on my machine, see below.
>
>     Either your ASPECT didn’t compile correctly (Try to run an example
>     from the cookbook), or try in optimized mode rather than debug mode.
>
>     Mohamed
>
>     [earmgo at login1.polaris test]$ aspect RR3Dbic.prm
>
>     -----------------------------------------------------------------------------
>
>     -- This is ASPECT, the Advanced Solver for Problems in Earth's
>     ConvecTion.
>
>     -- . version 1.5.0-pre
>
>     -- . running in OPTIMIZED mode
>
>     -- . running with 1 MPI process
>
>     -- . using Trilinos
>
>     -----------------------------------------------------------------------------
>
>     -----------------------------------------------------------------------------
>
>     The output directory <output/> provided in the input file appears
>     not to exist.
>
>     ASPECT will create it for you.
>
>     -----------------------------------------------------------------------------
>
>     Number of active cells: 512 (on 4 levels)
>
>     Number of degrees of freedom: 20,381 (14,739+729+4,913)
>
>     *** Timestep 0:  t=0 years
>
>     Solving temperature system... 0 iterations.
>
>     Rebuilding Stokes preconditioner...
>
>     Solving Stokes system... 30+2 iterations.
>
>     Number of active cells: 1,296 (on 5 levels)
>
>     Number of degrees of freedom: 51,950 (37,617+1,794+12,539)
>
>     *** Timestep 0:  t=0 years
>
>     Solving temperature system... 0 iterations.
>
>     Rebuilding Stokes preconditioner...
>
>     Solving Stokes system... 30+2 iterations.
>
>     Number of active cells: 4,544 (on 6 levels)
>
>     Number of degrees of freedom: 179,987 (130,407+6,111+43,469)
>
>     *** Timestep 0:  t=0 years
>
>     Solving temperature system... 0 iterations.
>
>     Rebuilding Stokes preconditioner...
>
>     Solving Stokes system... 30+3 iterations.
>
>     Number of active cells: 10,368 (on 6 levels)
>
>     Number of degrees of freedom: 377,927 (274,239+12,275+91,413)
>
>     *** Timestep 0:  t=0 years
>
>     Solving temperature system... 0 iterations.
>
>     Rebuilding Stokes preconditioner...
>
>     Solving Stokes system... 30+4 iterations.
>
>     Postprocessing:
>
>     RMS, max velocity:                  0.00454 m/year, 0.0155 m/year
>
>     Temperature min/avg/max:            300 K, 2.474e+05 K, 4.922e+05 K
>
>     Heat fluxes through boundary parts: 0.001263 W, 0.0006153 W,
>     0.005619 W, 0.002371 W, 1.895e+14 W, 1.971e+12 W
>
>     Writing graphical output: output/solution/solution-00000
>
>     *** Timestep 1:  t=1 years
>
>     Solving temperature system... 3 iterations.
>
>     Solving Stokes system... 8+0 iterations.
>
>     Postprocessing:
>
>     RMS, max velocity:                  0.00454 m/year, 0.0155 m/year
>
>     Temperature min/avg/max:            300 K, 2.474e+05 K, 4.922e+05 K
>
>     Heat fluxes through boundary parts: 91.23 W, 113.4 W, 363.3 W,
>     454.7 W, 1.895e+14 W, 1.971e+12 W
>
>     Termination requested by criterion: end time
>
>     +---------------------------------------------+------------+------------+
>
>     | Total wallclock time elapsed since start    | 107s |            |
>
>     | |            |            |
>
>     | Section   | no. calls | wall time | % of total |
>
>     +---------------------------------+-----------+------------+------------+
>
>     | Assemble Stokes system          |         5 | 33.6s |        31% |
>
>     | Assemble temperature system     |         5 | 7.01s |       6.5% |
>
>     | Build Stokes preconditioner     |         4 | 17.4s |        16% |
>
>     | Build temperature preconditioner|         5 | 2.36s |       2.2% |
>
>     | Solve Stokes system             |         5 | 30.1s |        28% |
>
>     | Solve temperature system        |         5 | 0.158s |      0.15% |
>
>     | Initialization   |         1 |     0.123s |      0.11% |
>
>     | Postprocessing   |         2 |       1.6s |       1.5% |
>
>     | Refine mesh structure, part 1   |         3 | 2.17s |         2% |
>
>     | Refine mesh structure, part 2   |         3 | 0.451s |      0.42% |
>
>     | Setup dof systems               |         4 | 11.6s |        11% |
>
>     | Setup initial conditions        |         4 | 0.416s |      0.39% |
>
>     +---------------------------------+-----------+------------+------------+
>
>     *From:*Aspect-devel [mailto:aspect-devel-bounces at geodynamics.org
>     <mailto:aspect-devel-bounces at geodynamics.org>] *On Behalf Of
>     *FELIPE ORELLANA ROVIROSA
>     *Sent:* 21 November 2016 04:35
>     *To:* aspect-devel at geodynamics.org
>     <mailto:aspect-devel at geodynamics.org>
>     *Subject:* [aspect-devel] Error from violated condition on parameters
>
>      Hi all,
>
>         I am running aspect 1.5.0-pre
>
>         I have tried to run my job several times, and I get this
>     awkward error
>
>       -- This is ASPECT, the Advanced Solver for Problems in Earth's
>     ConvecTion.
>     --     . version 1.5.0-pre
>     --     . running in DEBUG mode
>     --     . running with 32 MPI processes
>     --     . using Trilinos
>     -----------------------------------------------------------------------------
>
>
>     -----------------------------------------------------------------------------
>     The output directory </home1/04020/unfelipe/brickbic/> provided in
>     the input file appears not to exist.
>     ASPECT will create it for you.
>     -----------------------------------------------------------------------------
>
>
>     Number of active cells: 512 (on 4 levels)
>     Number of degrees of freedom: 20,381 (14,739+729+4,913)
>
>     *** Timestep 0:  t=0 years
>
>     --------------------------------------------------------
>     An error occurred in line <1152> of file
>     </home1/04020/unfelipe/packages/aspect/source/simulator/assembly.cc>
>     in function
>         void
>     aspect::Assemblers::CompleteEquations<dim>::local_assemble_advection_system(const
>     typename aspect::Simulator<dim>::Adv
>     ectionField&, double,
>     aspect::internal::Assembly::Scratch::AdvectionSystem<dim>&,
>     aspect::internal::Assembly::CopyData::Advecti
>     onSystem<dim>&) const [with int dim = 3; typename
>     aspect::Simulator<dim>::AdvectionField =
>     aspect::Simulator<3>::AdvectionField
>     ]
>     The violated condition was:
>         density_c_P >= 0
>     The name and call sequence of the exception was:
>         ExcMessage ("The product of density and c_P needs to be a "
>     "non-negative quantity.")
>     Additional Information:
>     The product of density and c_P needs to be a non-negative quantity.
>
>     Stacktrace:
>     -----------
>     #0  /home1/04020/unfelipe/packages/aspect/build/aspect:
>     aspect::Assemblers::CompleteEquations<3>::local_assemble_advection_syst
>     em(aspect::Simulator<3>::AdvectionField const&, double,
>     aspect::internal::Assembly::Scratch::AdvectionSystem<3>&,
>     aspect::inter
>     nal::Assembly::CopyData::AdvectionSystem<3>&) const
>     #1  /home1/04020/unfelipe/packages/aspect/build/aspect: s...
>     ..
>
>     of course, my parameters are positive numbers, so I don't know
>     where the error comes from.
>
>     I am attaching my parameter file.
>
>     any help would be appreciated,
>
>     thanks,
>
>     Felipe
>
>
>     _______________________________________________
>     Aspect-devel mailing list
>     Aspect-devel at geodynamics.org <mailto:Aspect-devel at geodynamics.org>
>     http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel
>     <http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel>
>
>
>
>
> _______________________________________________
> Aspect-devel mailing list
> Aspect-devel at geodynamics.org
> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel

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From bangerth at tamu.edu  Tue Nov 22 16:45:07 2016
From: bangerth at tamu.edu (Wolfgang Bangerth)
Date: Tue, 22 Nov 2016 17:45:07 -0700
Subject: [aspect-devel] Error from violated condition on parameters
In-Reply-To: <eff3bf1e-6e9d-12f8-f8fe-ec858d0252c7@gfz-potsdam.de>
References: <CANEUqvjDrmjy-E0bk5+SFOjBQxXQwJ2WUgv4z0pB+L8Vto=Qjg@mail.gmail.com>
 <AM5PR0301MB2356E3FF314BD1F34B2D9BB1D1B50@AM5PR0301MB2356.eurprd03.prod.outlook.com>
 <CANEUqvihkggaDNUWm=rdruGWxK0pXVJ8B77kmbY9EEHjPBJYzQ@mail.gmail.com>
 <eff3bf1e-6e9d-12f8-f8fe-ec858d0252c7@gfz-potsdam.de>
Message-ID: <4ca42fe1-3863-0652-e885-448922b9d046@tamu.edu>

On 11/22/2016 08:41 AM, Juliane Dannberg wrote:
>
> I would also like to add that normally it is not a good idea to just run your
> models in optimized mode if you get an error message in debug mode, because
> usually the error message tells you that something in your code or your model
> setup is not working as intended, and in these cases it helps to look at the
> setup again and fix these things.

Let me put this differently: It is a bad idea in general to run something in 
optimized mode if you haven't made sure that it runs without problem in debug 
mode -- you miss out on so many warnings and errors for bugs that are much 
easier to find in debug mode.

It is a *terrible* idea to run in optimized mode *if you know that there is an 
error in your code*. It is equivalent to seeing a warning light in your car 
that says that your brakes don't work, and to respond to it by disconnecting 
the light's power supply. Only bad things can happen to your car if you do 
this. Only bad results can happen if you purposefully ignore an error from 
ASPECT that you do not understand fully.

Best
  Wolfgang


-- 
------------------------------------------------------------------------
Wolfgang Bangerth          email:                 bangerth at colostate.edu
                            www: http://www.math.colostate.edu/~bangerth/


From M.Gouiza at leeds.ac.uk  Wed Nov 23 00:11:35 2016
From: M.Gouiza at leeds.ac.uk (Mohamed Gouiza)
Date: Wed, 23 Nov 2016 08:11:35 +0000
Subject: [aspect-devel] Error from violated condition on parameters
In-Reply-To: <4ca42fe1-3863-0652-e885-448922b9d046@tamu.edu>
References: <CANEUqvjDrmjy-E0bk5+SFOjBQxXQwJ2WUgv4z0pB+L8Vto=Qjg@mail.gmail.com>
 <AM5PR0301MB2356E3FF314BD1F34B2D9BB1D1B50@AM5PR0301MB2356.eurprd03.prod.outlook.com>
 <CANEUqvihkggaDNUWm=rdruGWxK0pXVJ8B77kmbY9EEHjPBJYzQ@mail.gmail.com>
 <eff3bf1e-6e9d-12f8-f8fe-ec858d0252c7@gfz-potsdam.de>
 <4ca42fe1-3863-0652-e885-448922b9d046@tamu.edu>
Message-ID: <AM5PR0301MB23565E1F18441F393188184CD1B70@AM5PR0301MB2356.eurprd03.prod.outlook.com>

Sorry for the bad advice.
I thought that DEBUG mode is useful to reveal errors in the code only, but not in a particular model setup...

Mohamed  

-----Original Message-----
From: Aspect-devel [mailto:aspect-devel-bounces at geodynamics.org] On Behalf Of Wolfgang Bangerth
Sent: 23 November 2016 00:45
To: aspect-devel at geodynamics.org
Subject: Re: [aspect-devel] Error from violated condition on parameters

On 11/22/2016 08:41 AM, Juliane Dannberg wrote:
>
> I would also like to add that normally it is not a good idea to just 
> run your models in optimized mode if you get an error message in debug 
> mode, because usually the error message tells you that something in 
> your code or your model setup is not working as intended, and in these 
> cases it helps to look at the setup again and fix these things.

Let me put this differently: It is a bad idea in general to run something in optimized mode if you haven't made sure that it runs without problem in debug mode -- you miss out on so many warnings and errors for bugs that are much easier to find in debug mode.

It is a *terrible* idea to run in optimized mode *if you know that there is an error in your code*. It is equivalent to seeing a warning light in your car that says that your brakes don't work, and to respond to it by disconnecting the light's power supply. Only bad things can happen to your car if you do this. Only bad results can happen if you purposefully ignore an error from ASPECT that you do not understand fully.

Best
  Wolfgang


-- 
------------------------------------------------------------------------
Wolfgang Bangerth          email:                 bangerth at colostate.edu
                            www: http://www.math.colostate.edu/~bangerth/

_______________________________________________
Aspect-devel mailing list
Aspect-devel at geodynamics.org
http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel

From M.Gouiza at leeds.ac.uk  Wed Nov 23 08:19:30 2016
From: M.Gouiza at leeds.ac.uk (Mohamed Gouiza)
Date: Wed, 23 Nov 2016 16:19:30 +0000
Subject: [aspect-devel] melt in the visco plastic model
Message-ID: <AM5PR0301MB2356D994595C519660BCF846D1B70@AM5PR0301MB2356.eurprd03.prod.outlook.com>

Hi All,

Is there a way to combine the visco plastic material model with the melt simple material model?

I want to set up a model that simulate lithospheric extension and induce melt generation and transport at various stages of the extension.

Thank you

-------------------------------------------------
Mohamed Gouiza, Research Fellow
Basin Structure Group, Institute of Applied Geosciences
University of Leeds, School of Earth and Environment
Leeds,  LS2 9JT, UK
M.Gouiza at leeds.ac.uk<mailto:M.Gouiza at leeds.ac.uk>
+44 7985 782073
-------------------------------------------------

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From payman.janbakhsh at mail.utoronto.ca  Wed Nov 23 10:17:48 2016
From: payman.janbakhsh at mail.utoronto.ca (Payman Janbakhsh)
Date: Wed, 23 Nov 2016 18:17:48 +0000
Subject: [aspect-devel] Nonlinear solver scheme
Message-ID: <CY1PR03MB15188B665FE0F9AFD351AE92ADB70@CY1PR03MB1518.namprd03.prod.outlook.com>

Hi
For visco-plastic material model with fixed top surface , which non linear solver scheme is recommended? Particularly in 3D where DOFs are very large.
To be more specific on where my doubts are I should say, to my understanding velocity, temperature and viscosity are very much influencing each other in this model. So I was thinking choosing a scheme that solves temperature and velocity equations simultaneously. Please correct me if I'm off the chart.

As a second question, I know increasing temperature polynomial degree increases accuracy. So is it recommended to have it at 3 or 2 is sufficient for a viscoplastic 3D model.
Thanks

payman
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From jbnaliboff at ucdavis.edu  Wed Nov 23 10:15:01 2016
From: jbnaliboff at ucdavis.edu (John Naliboff)
Date: Wed, 23 Nov 2016 10:15:01 -0800
Subject: [aspect-devel] melt in the visco plastic model
In-Reply-To: <AM5PR0301MB2356D994595C519660BCF846D1B70@AM5PR0301MB2356.eurprd03.prod.outlook.com>
References: <AM5PR0301MB2356D994595C519660BCF846D1B70@AM5PR0301MB2356.eurprd03.prod.outlook.com>
Message-ID: <c7205821-4aa6-700f-2d6d-7017b4863786@ucdavis.edu>

Hi Mohamed,

With some work it is certainly possible to combine the functionality of 
the visco plastic material model and 'melting' components of the code.

However, do note that the visco plastic model is incompressible and the 
melting material models are inherently compressible.  My suggestion is 
to use the 'melt simple' material model as a starting point and then add 
in the features in 'visco plastic'.

However, this seems like a good time to release a general cautionary 
note about moving to quickly on this front.  I am still in the process 
of doing sensitivity tests with the provided extension models and adding 
in melting is likely going to require a huge amount of additional 
testing to obtain robust convergence behavior and results.

I certainly encourage you to move forward with the idea, but just keep 
in mind that this is not a trivial numerical exercise in any way, shape 
or form.

Cheers,
John

*************************************************
John Naliboff
Assistant Project Scientist, CIG
Earth & Planetary Sciences Dept., UC Davis

On 11/23/2016 08:19 AM, Mohamed Gouiza wrote:
>
> Hi All,
>
> Is there a way to combine the visco plastic material model with the 
> melt simple material model?
>
> I want to set up a model that simulate lithospheric extension and 
> induce melt generation and transport at various stages of the extension.
>
> Thank you
>
> -------------------------------------------------
> Mohamed Gouiza, Research Fellow
> Basin Structure Group, Institute of Applied Geosciences
> University of Leeds, School of Earth and Environment
>
> Leeds,  LS2 9JT, UK
>
> M.Gouiza at leeds.ac.uk <mailto:M.Gouiza at leeds.ac.uk>
> +44 7985 782073
> -------------------------------------------------
>
>
>
> _______________________________________________
> Aspect-devel mailing list
> Aspect-devel at geodynamics.org
> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel

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From jbnaliboff at ucdavis.edu  Wed Nov 23 10:34:41 2016
From: jbnaliboff at ucdavis.edu (John Naliboff)
Date: Wed, 23 Nov 2016 10:34:41 -0800
Subject: [aspect-devel] Nonlinear solver scheme
In-Reply-To: <CY1PR03MB15188B665FE0F9AFD351AE92ADB70@CY1PR03MB1518.namprd03.prod.outlook.com>
References: <CY1PR03MB15188B665FE0F9AFD351AE92ADB70@CY1PR03MB1518.namprd03.prod.outlook.com>
Message-ID: <807c7022-b75b-fb55-2609-cbf340f8d3d9@ucdavis.edu>

Hi Payman,

Typically the non-linear solver scheme is chosen based on the rheology 
and general processes you are trying to model, independent of the 
boundary conditions.  When using the 'visco plastic' material model I 
typically use the 'iterated IMPES' or 'iterated Stokes' non-linear solvers.

Trying the same model with each solver can be considered a good addition 
to a broader suite of sensitivity tests.  Likewise, testing how your 
results vary with the temperature polynomial degree is a good 
sensitivity test.  However, by default I typically use high-order 
elements for temperature/velocity/pressure/composition.

Hope this helps and when in doubt do lots of tests (preferably in 2D) to 
see how your model results vary with different parameters!

Cheers,
John

*************************************************
John Naliboff
Assistant Project Scientist, CIG
Earth & Planetary Sciences Dept., UC Davis

On 11/23/2016 10:17 AM, Payman Janbakhsh wrote:
>
> Hi
>
> For visco-plastic material model with fixed top surface , which non 
> linear solver scheme is recommended? Particularly in 3D where DOFs are 
> very large.
>
> To be more specific on where my doubts are I should say, to my 
> understanding velocity, temperature and viscosity are very much 
> influencing each other in this model. So I was thinking choosing a 
> scheme that solves temperature and velocity equations simultaneously. 
> Please correct me if I’m off the chart.
>
> As a second question, I know increasing temperature polynomial degree 
> increases accuracy. So is it recommended to have it at 3 or 2 is 
> sufficient for a viscoplastic 3D model.
>
> Thanks
>
> payman
>
>
>
> _______________________________________________
> Aspect-devel mailing list
> Aspect-devel at geodynamics.org
> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel

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From dannberg at gfz-potsdam.de  Wed Nov 23 12:19:01 2016
From: dannberg at gfz-potsdam.de (Juliane Dannberg)
Date: Wed, 23 Nov 2016 15:19:01 -0500
Subject: [aspect-devel] melt in the visco plastic model
In-Reply-To: <c7205821-4aa6-700f-2d6d-7017b4863786@ucdavis.edu>
References: <AM5PR0301MB2356D994595C519660BCF846D1B70@AM5PR0301MB2356.eurprd03.prod.outlook.com>
 <c7205821-4aa6-700f-2d6d-7017b4863786@ucdavis.edu>
Message-ID: <7d1c4a72-11ee-2118-76d8-2aea91d94965@gfz-potsdam.de>

Hi Mohamed,

I would also like to add that combining melt migration and plasticity 
will make the problem strongly nonlinear, and probably very difficult 
for both the linear and the nonlinear solver. So if your viscosity 
contrast is high, you should expect a large number of linear iterations 
(this could be up to 1000) and a large number of nonlinear iterations.

We are working to make both parts faster, but at the moment you will 
probably need a lot of computational resources to run these kind of 
models, and we haven't tested ASPECT with this kind of models, so other 
problems might come up.

Cheers,
Juliane


On 11/23/2016 01:15 PM, John Naliboff wrote:
> Hi Mohamed,
>
> With some work it is certainly possible to combine the functionality 
> of the visco plastic material model and 'melting' components of the code.
>
> However, do note that the visco plastic model is incompressible and 
> the melting material models are inherently compressible.  My 
> suggestion is to use the 'melt simple' material model as a starting 
> point and then add in the features in 'visco plastic'.
>
> However, this seems like a good time to release a general cautionary 
> note about moving to quickly on this front.  I am still in the process 
> of doing sensitivity tests with the provided extension models and 
> adding in melting is likely going to require a huge amount of 
> additional testing to obtain robust convergence behavior and results.
>
> I certainly encourage you to move forward with the idea, but just keep 
> in mind that this is not a trivial numerical exercise in any way, 
> shape or form.
>
> Cheers,
> John
>
> *************************************************
> John Naliboff
> Assistant Project Scientist, CIG
> Earth & Planetary Sciences Dept., UC Davis
> On 11/23/2016 08:19 AM, Mohamed Gouiza wrote:
>>
>> Hi All,
>>
>> Is there a way to combine the visco plastic material model with the 
>> melt simple material model?
>>
>> I want to set up a model that simulate lithospheric extension and 
>> induce melt generation and transport at various stages of the extension.
>>
>> Thank you
>>
>> -------------------------------------------------
>> Mohamed Gouiza, Research Fellow
>> Basin Structure Group, Institute of Applied Geosciences
>> University of Leeds, School of Earth and Environment
>>
>> Leeds,  LS2 9JT, UK
>>
>> M.Gouiza at leeds.ac.uk <mailto:M.Gouiza at leeds.ac.uk>
>> +44 7985 782073
>> -------------------------------------------------
>>
>>
>>
>> _______________________________________________
>> Aspect-devel mailing list
>> Aspect-devel at geodynamics.org
>> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel
>
>
>
> _______________________________________________
> Aspect-devel mailing list
> Aspect-devel at geodynamics.org
> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel

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From M.Gouiza at leeds.ac.uk  Thu Nov 24 01:46:14 2016
From: M.Gouiza at leeds.ac.uk (Mohamed Gouiza)
Date: Thu, 24 Nov 2016 09:46:14 +0000
Subject: [aspect-devel] melt in the visco plastic model
In-Reply-To: <7d1c4a72-11ee-2118-76d8-2aea91d94965@gfz-potsdam.de>
References: <AM5PR0301MB2356D994595C519660BCF846D1B70@AM5PR0301MB2356.eurprd03.prod.outlook.com>
 <c7205821-4aa6-700f-2d6d-7017b4863786@ucdavis.edu>
 <7d1c4a72-11ee-2118-76d8-2aea91d94965@gfz-potsdam.de>
Message-ID: <DB6PR0301MB23587A8714BBB9D498F56410D1B60@DB6PR0301MB2358.eurprd03.prod.outlook.com>

Hi Juliane, John,

Thank you for the feedback.

Mohamed.

From: Aspect-devel [mailto:aspect-devel-bounces at geodynamics.org] On Behalf Of Juliane Dannberg
Sent: 23 November 2016 20:19
To: aspect-devel at geodynamics.org
Subject: Re: [aspect-devel] melt in the visco plastic model


Hi Mohamed,

I would also like to add that combining melt migration and plasticity will make the problem strongly nonlinear, and probably very difficult for both the linear and the nonlinear solver. So if your viscosity contrast is high, you should expect a large number of linear iterations (this could be up to 1000) and a large number of nonlinear iterations.

We are working to make both parts faster, but at the moment you will probably need a lot of computational resources to run these kind of models, and we haven't tested ASPECT with this kind of models, so other problems might come up.

Cheers,
Juliane

On 11/23/2016 01:15 PM, John Naliboff wrote:
Hi Mohamed,

With some work it is certainly possible to combine the functionality of the visco plastic material model and 'melting' components of the code.

However, do note that the visco plastic model is incompressible and the melting material models are inherently compressible.  My suggestion is to use the 'melt simple' material model as a starting point and then add in the features in 'visco plastic'.

However, this seems like a good time to release a general cautionary note about moving to quickly on this front.  I am still in the process of doing sensitivity tests with the provided extension models and adding in melting is likely going to require a huge amount of additional testing to obtain robust convergence behavior and results.

I certainly encourage you to move forward with the idea, but just keep in mind that this is not a trivial numerical exercise in any way, shape or form.

Cheers,
John



*************************************************

John Naliboff

Assistant Project Scientist, CIG

Earth & Planetary Sciences Dept., UC Davis
On 11/23/2016 08:19 AM, Mohamed Gouiza wrote:
Hi All,

Is there a way to combine the visco plastic material model with the melt simple material model?

I want to set up a model that simulate lithospheric extension and induce melt generation and transport at various stages of the extension.

Thank you

-------------------------------------------------
Mohamed Gouiza, Research Fellow
Basin Structure Group, Institute of Applied Geosciences
University of Leeds, School of Earth and Environment
Leeds,  LS2 9JT, UK
M.Gouiza at leeds.ac.uk<mailto:M.Gouiza at leeds.ac.uk>
+44 7985 782073
-------------------------------------------------





_______________________________________________

Aspect-devel mailing list

Aspect-devel at geodynamics.org<mailto:Aspect-devel at geodynamics.org>

http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel





_______________________________________________

Aspect-devel mailing list

Aspect-devel at geodynamics.org<mailto:Aspect-devel at geodynamics.org>

http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel

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From M.Gouiza at leeds.ac.uk  Thu Nov 24 03:35:06 2016
From: M.Gouiza at leeds.ac.uk (Mohamed Gouiza)
Date: Thu, 24 Nov 2016 11:35:06 +0000
Subject: [aspect-devel] Depletion density change
Message-ID: <DB6PR0301MB2358DC8EEC003E11726BC2D8D1B60@DB6PR0301MB2358.eurprd03.prod.outlook.com>

Hi,

In the Material model/Melt simple, the Depletion density change parameter takes only positive values (0 <= v <= MAX_DOUBLE).
It should take negative values too, as depleted material usually has lower densities.
The same parameter in the Material model/Melt global accepts negative value: -MAX_DOUBLE <= v <= MAX_DOUBLE

Cheers,
-------------------------------------------------
Mohamed Gouiza, Research Fellow
Basin Structure Group, Institute of Applied Geosciences
University of Leeds, School of Earth and Environment
Leeds,  LS2 9JT, UK
M.Gouiza at leeds.ac.uk<mailto:M.Gouiza at leeds.ac.uk>
+44 7985 782073
-------------------------------------------------

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From payman.janbakhsh at mail.utoronto.ca  Thu Nov 24 05:17:24 2016
From: payman.janbakhsh at mail.utoronto.ca (Payman Janbakhsh)
Date: Thu, 24 Nov 2016 13:17:24 +0000
Subject: [aspect-devel] Nonlinear solver scheme
In-Reply-To: <807c7022-b75b-fb55-2609-cbf340f8d3d9@ucdavis.edu>
References: <CY1PR03MB15188B665FE0F9AFD351AE92ADB70@CY1PR03MB1518.namprd03.prod.outlook.com>,
 <807c7022-b75b-fb55-2609-cbf340f8d3d9@ucdavis.edu>
Message-ID: <ba5g298vm7qqxuhlhljsbomo.1479993439663@email.android.com>

Thanks John



Sent from my Samsung Galaxy smartphone.


-------- Original message --------
From: John Naliboff <jbnaliboff at ucdavis.edu>
Date: 2016-11-23 3:16 PM (GMT-05:00)
To: aspect-devel at geodynamics.org
Subject: Re: [aspect-devel] Nonlinear solver scheme

Hi Payman,

Typically the non-linear solver scheme is chosen based on the rheology and general processes you are trying to model, independent of the boundary conditions.  When using the 'visco plastic' material model I typically use the 'iterated IMPES' or 'iterated Stokes' non-linear solvers.

Trying the same model with each solver can be considered a good addition to a broader suite of sensitivity tests.  Likewise, testing how your results vary with the temperature polynomial degree is a good sensitivity test.  However, by default I typically use high-order elements for temperature/velocity/pressure/composition.

Hope this helps and when in doubt do lots of tests (preferably in 2D) to see how your model results vary with different parameters!

Cheers,
John

*************************************************
John Naliboff
Assistant Project Scientist, CIG
Earth & Planetary Sciences Dept., UC Davis


On 11/23/2016 10:17 AM, Payman Janbakhsh wrote:
Hi
For visco-plastic material model with fixed top surface , which non linear solver scheme is recommended? Particularly in 3D where DOFs are very large.
To be more specific on where my doubts are I should say, to my understanding velocity, temperature and viscosity are very much influencing each other in this model. So I was thinking choosing a scheme that solves temperature and velocity equations simultaneously. Please correct me if I'm off the chart.

As a second question, I know increasing temperature polynomial degree increases accuracy. So is it recommended to have it at 3 or 2 is sufficient for a viscoplastic 3D model.
Thanks

payman



_______________________________________________
Aspect-devel mailing list
Aspect-devel at geodynamics.org<mailto:Aspect-devel at geodynamics.org>
http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel

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From rene.gassmoeller at mailbox.org  Fri Nov 25 14:43:23 2016
From: rene.gassmoeller at mailbox.org (Rene Gassmoeller)
Date: Fri, 25 Nov 2016 15:43:23 -0700
Subject: [aspect-devel] Open boundaries + tracers
In-Reply-To: <CAPGyz27j15AoLd4dOCjkLv3ibw3ABz_zvDfakHhA-OUSTcSPCw@mail.gmail.com>
References: <CAPGyz27j15AoLd4dOCjkLv3ibw3ABz_zvDfakHhA-OUSTcSPCw@mail.gmail.com>
Message-ID: <5fc49721-6085-de7d-e235-a60acf841d33@mailbox.org>

Hi Lev,

Let me cc this to the mailing list so that others hear about problems
and solutions as well.

Cool model! From what you describe it seems you are doing everything
right so far. What is the value for the 'Load balancing strategy' in the
Particles subsection? In order for the 'Minimum tracers per cell' option
to have an effect you need to at least select the option 'add tracers'
(possibly combine it with others like "set Load balancing strategy = add
tracers, remove tracers, repartition"). This should then generate new
tracers when many others have left that cell. However keep in mind that
the properties of these new particles will be interpolated from the
remaining existing particles in that cell. This might or might not be a
problem for your model.

Let me know about the parameter file option,

Best,

Rene

On 11/24/2016 10:36 PM, Lev Karatun wrote:
> Hi Rene,
>
> I recently added tracers to my models, they work great, thank you for
> adding them! I was trying to incorporate open boundaries (by Anne
> Glerum) into my models, they work just fine too. However, when I
> included both of them, I ran into a problem: the cells near the open
> boundary, through which constant inflow of material is happening end
> up not having enough tracers (and later not  having any tracers at
> all) (see attached screenshot). I decreased the CFL number from 0.5 to
> 0.1, but it didn't help. So I was wondering if you could tell me what
> the possible causes are? It happens both with and without adaptive
> refinement, and I have min tracers number set to 10. 
>
> Thanks in advance!
>
> Best regards,
> Lev Karatun.

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From lev.karatun at gmail.com  Mon Nov 28 18:22:48 2016
From: lev.karatun at gmail.com (Lev Karatun)
Date: Mon, 28 Nov 2016 21:22:48 -0500
Subject: [aspect-devel] Open boundaries + tracers
In-Reply-To: <5fc49721-6085-de7d-e235-a60acf841d33@mailbox.org>
References: <CAPGyz27j15AoLd4dOCjkLv3ibw3ABz_zvDfakHhA-OUSTcSPCw@mail.gmail.com>
 <5fc49721-6085-de7d-e235-a60acf841d33@mailbox.org>
Message-ID: <CAPGyz27jUekGYxfAHGRghZC-pn5BffpNzHz5R=+itArrTs_oNw@mail.gmail.com>

Hi Rene,

thanks a lot, I actually had the load balancing strategy set to
"repartition", changing it to "remove and add particles" solved the
problem. The manual only lists the possible choices, but doesn't explain
what they do, so I originally went with the default option.
Could you get into some more detail on the strategies, please? Do I
understand it correctly that the option "add particles" enforces the
minimum number of particles in the cell, generating them whenever needed?
What would be the difference between "set Load balancing strategy = add
particles, remove particles" and ""set Load balancing strategy = add
tracers, remove tracers"? And how will the "repartition" strategy work
together with the other listed algorithms? Speaking about the webinar on
particles, does "repartition" correspond to the "balanced repartitioning",
and the rest (except for none) - "particle management"? And for the
"Variable distribution" strategy (mentioned in the webinar), what option do
I have to choose to enable the mesh adjustment according to particles (and
how will it work together with the regular mesh refinement strategy?) ?

Best regards,
Lev Karatun.

2016-11-25 17:43 GMT-05:00 Rene Gassmoeller <rene.gassmoeller at mailbox.org>:

> Hi Lev,
>
> Let me cc this to the mailing list so that others hear about problems and
> solutions as well.
>
> Cool model! From what you describe it seems you are doing everything right
> so far. What is the value for the 'Load balancing strategy' in the
> Particles subsection? In order for the 'Minimum tracers per cell' option to
> have an effect you need to at least select the option 'add tracers'
> (possibly combine it with others like "set Load balancing strategy = add
> tracers, remove tracers, repartition"). This should then generate new
> tracers when many others have left that cell. However keep in mind that the
> properties of these new particles will be interpolated from the remaining
> existing particles in that cell. This might or might not be a problem for
> your model.
>
> Let me know about the parameter file option,
>
> Best,
>
> Rene
> On 11/24/2016 10:36 PM, Lev Karatun wrote:
>
> Hi Rene,
>
> I recently added tracers to my models, they work great, thank you for
> adding them! I was trying to incorporate open boundaries (by Anne Glerum)
> into my models, they work just fine too. However, when I included both of
> them, I ran into a problem: the cells near the open boundary, through
> which constant inflow of material is happening end up not having enough
> tracers (and later not  having any tracers at all) (see attached
> screenshot). I decreased the CFL number from 0.5 to 0.1, but it didn't
> help. So I was wondering if you could tell me what the possible causes are?
> It happens both with and without adaptive refinement, and I have min
> tracers number set to 10.
>
> Thanks in advance!
>
> Best regards,
> Lev Karatun.
>
>
>
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From jbnaliboff at ucdavis.edu  Tue Nov 29 09:07:40 2016
From: jbnaliboff at ucdavis.edu (John Naliboff)
Date: Tue, 29 Nov 2016 09:07:40 -0800
Subject: [aspect-devel] Open boundaries + tracers
In-Reply-To: <CAPGyz27jUekGYxfAHGRghZC-pn5BffpNzHz5R=+itArrTs_oNw@mail.gmail.com>
References: <CAPGyz27j15AoLd4dOCjkLv3ibw3ABz_zvDfakHhA-OUSTcSPCw@mail.gmail.com>
 <5fc49721-6085-de7d-e235-a60acf841d33@mailbox.org>
 <CAPGyz27jUekGYxfAHGRghZC-pn5BffpNzHz5R=+itArrTs_oNw@mail.gmail.com>
Message-ID: <BBB0C48D-942D-4968-B441-77CCCC8D009D@ucdavis.edu>

Hi Lev,

You should set your load balancing strategy to “remove and add particles, repartition”.  If you do not include the “repartition” option, the majority of your model time will likely be spent with particle sorting if you are using multiple processors.  

For example, in one case without the ‘repartition’ option the time spent in particle sorting is roughly 80-90% (16 processors, ~ 1e6 particles, fixed grid) as opposed to 20% with the ‘repartition’ option.

On a related note, I’ve found using ‘active tracers’ in replace of compositional fields increases the ’Solve Stokes system’ time by over an order of magnitude.  At least this is the case in the ‘extension’ models I’ve been running. 

I haven’t had time to track down where exactly in the "Stokes solve" this time is being eaten up or look at similar time increases in other models, but it will be interesting to see if this is the case in your models as well.  Certainly keep on eye on it before sending any large models off to a cluster.

Rene - Is this possibly due to re-interpolation of particle values during each stokes solve? 

Cheers,
John

*************************************************
John Naliboff
Assistant Project Scientist, CIG
Earth & Planetary Sciences Dept., UC Davis






> On Nov 28, 2016, at 6:22 PM, Lev Karatun <lev.karatun at gmail.com> wrote:
> 
> Hi Rene,
> 
> thanks a lot, I actually had the load balancing strategy set to "repartition", changing it to "remove and add particles" solved the problem. The manual only lists the possible choices, but doesn't explain what they do, so I originally went with the default option. 
> Could you get into some more detail on the strategies, please? Do I understand it correctly that the option "add particles" enforces the minimum number of particles in the cell, generating them whenever needed? What would be the difference between "set Load balancing strategy = add particles, remove particles" and ""set Load balancing strategy = add tracers, remove tracers"? And how will the "repartition" strategy work together with the other listed algorithms? Speaking about the webinar on particles, does "repartition" correspond to the "balanced repartitioning", and the rest (except for none) - "particle management"? And for the "Variable distribution" strategy (mentioned in the webinar), what option do I have to choose to enable the mesh adjustment according to particles (and how will it work together with the regular mesh refinement strategy?) ?
> 
> Best regards,
> Lev Karatun.
> 
> 2016-11-25 17:43 GMT-05:00 Rene Gassmoeller <rene.gassmoeller at mailbox.org <mailto:rene.gassmoeller at mailbox.org>>:
> Hi Lev,
> 
> Let me cc this to the mailing list so that others hear about problems and solutions as well.
> Cool model! From what you describe it seems you are doing everything right so far. What is the value for the 'Load balancing strategy' in the Particles subsection? In order for the 'Minimum tracers per cell' option to have an effect you need to at least select the option 'add tracers' (possibly combine it with others like "set Load balancing strategy = add tracers, remove tracers, repartition"). This should then generate new tracers when many others have left that cell. However keep in mind that the properties of these new particles will be interpolated from the remaining existing particles in that cell. This might or might not be a problem for your model.
> Let me know about the parameter file option,
> 
> Best,
> Rene
> On 11/24/2016 10:36 PM, Lev Karatun wrote:
>> Hi Rene,
>> 
>> I recently added tracers to my models, they work great, thank you for adding them! I was trying to incorporate open boundaries (by Anne Glerum) into my models, they work just fine too. However, when I included both of them, I ran into a problem: the cells near the open boundary, through which constant inflow of material is happening end up not having enough tracers (and later not  having any tracers at all) (see attached screenshot). I decreased the CFL number from 0.5 to 0.1, but it didn't help. So I was wondering if you could tell me what the possible causes are? It happens both with and without adaptive refinement, and I have min tracers number set to 10. 
>> 
>> Thanks in advance!
>> 
>> Best regards,
>> Lev Karatun.
> 
> 
> _______________________________________________
> Aspect-devel mailing list
> Aspect-devel at geodynamics.org
> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel

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From rene.gassmoeller at mailbox.org  Tue Nov 29 11:00:09 2016
From: rene.gassmoeller at mailbox.org (Rene Gassmoeller)
Date: Tue, 29 Nov 2016 19:00:09 -0000
Subject: [aspect-devel] ASPECT Newsletter #18
Message-ID: <20161129185959.D8C2BAC03AA@geodynamics.org>

Hello everyone!

This is ASPECT newsletter #18.
It automatically reports recently merged features and discussions about the ASPECT mantle convection code.


## Below you find a list of recently proposed or merged features:

#1280: Remove unused parameter (proposed by gassmoeller; merged) https://github.com/geodynamics/aspect/pull/1280

#1278: Fix memory postprocessor to output with types::global_dof_index. (proposed by spco; merged) https://github.com/geodynamics/aspect/pull/1278

#1276: Use nonlinear solver tolerance for "Stokes only" solver scheme (proposed by gassmoeller) https://github.com/geodynamics/aspect/pull/1276

#1275: [WIP] Rebase density approximations (proposed by gassmoeller) https://github.com/geodynamics/aspect/pull/1275

#1274: Adiabatic density profile (proposed by gassmoeller; merged) https://github.com/geodynamics/aspect/pull/1274

#1273: Fix doxygen errors and change title (proposed by tjhei; merged) https://github.com/geodynamics/aspect/pull/1273

#1272: Fix sign of grain size exponent term in visco_plastic material model (proposed by naliboff; merged) https://github.com/geodynamics/aspect/pull/1272

#1192: Add strain weakening option to the visco_plastic material model (proposed by naliboff; merged) https://github.com/geodynamics/aspect/pull/1192


## And this is a list of recently opened or closed discussions:

#1279: Contract nonlinear solvers code (opened) https://github.com/geodynamics/aspect/issues/1279

#1277: Adiabatic conditions: Function with separate expressions (opened) https://github.com/geodynamics/aspect/issues/1277


A list of all major changes since the last release can be found at https://aspect.dealii.org/doc/doxygen/changes_current.html.


Thanks for being part of the community!


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From rene.gassmoeller at mailbox.org  Wed Nov 30 15:19:41 2016
From: rene.gassmoeller at mailbox.org (Rene Gassmoeller)
Date: Wed, 30 Nov 2016 16:19:41 -0700
Subject: [aspect-devel] Open boundaries + tracers
In-Reply-To: <BBB0C48D-942D-4968-B441-77CCCC8D009D@ucdavis.edu>
References: <CAPGyz27j15AoLd4dOCjkLv3ibw3ABz_zvDfakHhA-OUSTcSPCw@mail.gmail.com>
 <5fc49721-6085-de7d-e235-a60acf841d33@mailbox.org>
 <CAPGyz27jUekGYxfAHGRghZC-pn5BffpNzHz5R=+itArrTs_oNw@mail.gmail.com>
 <BBB0C48D-942D-4968-B441-77CCCC8D009D@ucdavis.edu>
Message-ID: <61ad9a55-0cad-7763-c6f5-afdbb4ab54e8@mailbox.org>

Hi Lev, Hi John,

Sorry for the late reply. John's suggestion should be indeed the 
solution to your problem Lev.

Currently, the most reasonable setting for the load balancing strategy 
is 'repartition' (the 'balanced repartition' method I talked about in 
the webinar) if you do not need to generate new tracers / remove old 
ones, and 'repartition, add tracers, remove tracers' if you get empty 
cells, or so largely unbalanced particle numbers that the particle 
algorithm takes too much time. This happens for example if you have 
'many' different levels of cells, and 'many' particles, with the 
definition of 'many' depending on your model size and available 
computing time ;-).

The documentation of the particle load balancing schemes is currently 
not as detailed as I would like. I need extend that at some point.

About John's question: The tracer interpolation itself is not handled in 
the "Stokes solve" part, it is happening in the "Solve composition 
system" part of the timer and is only done once per nonlinear iteration. 
My guess would be that setting up your model with tracers creates 
sharper gradients in whatever property they track, and therefore the 
Stokes solution is harder to obtain. Does the number of Stokes 
iterations change between the two methods?

Best,

Rene


On 11/29/2016 10:07 AM, John Naliboff wrote:
> Hi Lev,
>
> You should set your load balancing strategy to “remove and add 
> particles, repartition”.  If you do not include the “repartition” 
> option, the majority of your model time will likely be spent with 
> particle sorting if you are using multiple processors.
>
> For example, in one case without the ‘repartition’ option the time 
> spent in particle sorting is roughly 80-90% (16 processors, ~ 1e6 
> particles, fixed grid) as opposed to 20% with the ‘repartition’ option.
>
> On a related note, I’ve found using ‘active tracers’ in replace of 
> compositional fields increases the ’Solve Stokes system’ time by over 
> an order of magnitude.  At least this is the case in the ‘extension’ 
> models I’ve been running.
>
> I haven’t had time to track down where exactly in the "Stokes solve" 
> this time is being eaten up or look at similar time increases in other 
> models, but it will be interesting to see if this is the case in your 
> models as well.  Certainly keep on eye on it before sending any large 
> models off to a cluster.
>
> Rene - Is this possibly due to re-interpolation of particle values 
> during each stokes solve?
>
> Cheers,
> John
>
> *************************************************
> John Naliboff
> Assistant Project Scientist, CIG
> Earth & Planetary Sciences Dept., UC Davis
>
>
>
>
>
>
>> On Nov 28, 2016, at 6:22 PM, Lev Karatun <lev.karatun at gmail.com 
>> <mailto:lev.karatun at gmail.com>> wrote:
>>
>> Hi Rene,
>>
>> thanks a lot, I actually had the load balancing strategy set to 
>> "repartition", changing it to "remove and add particles" solved the 
>> problem. The manual only lists the possible choices, but doesn't 
>> explain what they do, so I originally went with the default option.
>> Could you get into some more detail on the strategies, please? Do I 
>> understand it correctly that the option "add particles" enforces the 
>> minimum number of particles in the cell, generating them whenever 
>> needed? What would be the difference between "set Load balancing 
>> strategy = add particles, remove particles" and ""set Load balancing 
>> strategy = add tracers, remove tracers"? And how will the 
>> "repartition" strategy work together with the other listed 
>> algorithms? Speaking about the webinar on particles, does 
>> "repartition" correspond to the "balanced repartitioning", and the 
>> rest (except for none) - "particle management"? And for the "Variable 
>> distribution" strategy (mentioned in the webinar), what option do I 
>> have to choose to enable the mesh adjustment according to particles 
>> (and how will it work together with the regular mesh refinement 
>> strategy?) ?
>>
>> Best regards,
>> Lev Karatun.
>>
>> 2016-11-25 17:43 GMT-05:00 Rene Gassmoeller 
>> <rene.gassmoeller at mailbox.org <mailto:rene.gassmoeller at mailbox.org>>:
>>
>>     Hi Lev,
>>
>>     Let me cc this to the mailing list so that others hear about
>>     problems and solutions as well.
>>
>>     Cool model! From what you describe it seems you are doing
>>     everything right so far. What is the value for the 'Load
>>     balancing strategy' in the Particles subsection? In order for the
>>     'Minimum tracers per cell' option to have an effect you need to
>>     at least select the option 'add tracers' (possibly combine it
>>     with others like "set Load balancing strategy = add tracers,
>>     remove tracers, repartition"). This should then generate new
>>     tracers when many others have left that cell. However keep in
>>     mind that the properties of these new particles will be
>>     interpolated from the remaining existing particles in that cell.
>>     This might or might not be a problem for your model.
>>
>>     Let me know about the parameter file option,
>>
>>     Best,
>>
>>     Rene
>>
>>     On 11/24/2016 10:36 PM, Lev Karatun wrote:
>>>     Hi Rene,
>>>
>>>     I recently added tracers to my models, they work great, thank
>>>     you for adding them! I was trying to incorporate open boundaries
>>>     (by Anne Glerum) into my models, they work just fine too.
>>>     However, when I included both of them, I ran into a problem: the
>>>     cells near the open boundary, through which constant inflow of
>>>     material is happening end up not having enough tracers (and
>>>     later not  having any tracers at all) (see attached screenshot).
>>>     I decreased the CFL number from 0.5 to 0.1, but it didn't help.
>>>     So I was wondering if you could tell me what the possible causes
>>>     are? It happens both with and without adaptive refinement, and I
>>>     have min tracers number set to 10.
>>>
>>>     Thanks in advance!
>>>
>>>     Best regards,
>>>     Lev Karatun.
>>
>>
>> _______________________________________________
>> Aspect-devel mailing list
>> Aspect-devel at geodynamics.org <mailto:Aspect-devel at geodynamics.org>
>> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel
>
>
>
> _______________________________________________
> Aspect-devel mailing list
> Aspect-devel at geodynamics.org
> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel

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From dannberg at gfz-potsdam.de  Wed Nov 30 13:39:58 2016
From: dannberg at gfz-potsdam.de (Juliane Dannberg)
Date: Wed, 30 Nov 2016 16:39:58 -0500
Subject: [aspect-devel] Depletion density change
In-Reply-To: <DB6PR0301MB2358DC8EEC003E11726BC2D8D1B60@DB6PR0301MB2358.eurprd03.prod.outlook.com>
References: <DB6PR0301MB2358DC8EEC003E11726BC2D8D1B60@DB6PR0301MB2358.eurprd03.prod.outlook.com>
Message-ID: <27b007ef-b6d2-a74e-1374-0238b0fc5f74@gfz-potsdam.de>

Hi Mohamed,

sorry for the late reply.
You are right, we should allow negative density changes (and the 
documentation of the parameter already describes what happens in this 
case).
I have created a pull request here: 
https://github.com/geodynamics/aspect/pull/1281

Best,
Juliane


On 11/24/2016 06:35 AM, Mohamed Gouiza wrote:
>
> Hi,
>
> In the Material model/Melt simple, the Depletion density change 
> parameter takes only positive values (0 <= v <= MAX_DOUBLE).
>
> It should take negative values too, as depleted material usually has 
> lower densities.
>
> The same parameter in the Material model/Melt global accepts negative 
> value: -MAX_DOUBLE <= v <= MAX_DOUBLE
>
> Cheers,
>
> -------------------------------------------------
> Mohamed Gouiza, Research Fellow
> Basin Structure Group, Institute of Applied Geosciences
> University of Leeds, School of Earth and Environment
>
> Leeds,  LS2 9JT, UK
>
> M.Gouiza at leeds.ac.uk <mailto:M.Gouiza at leeds.ac.uk>
> +44 7985 782073
> -------------------------------------------------
>
>
>
> _______________________________________________
> Aspect-devel mailing list
> Aspect-devel at geodynamics.org
> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel

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From jbnaliboff at ucdavis.edu  Wed Nov 30 22:25:15 2016
From: jbnaliboff at ucdavis.edu (John Naliboff)
Date: Wed, 30 Nov 2016 22:25:15 -0800
Subject: [aspect-devel] Open boundaries + tracers
In-Reply-To: <61ad9a55-0cad-7763-c6f5-afdbb4ab54e8@mailbox.org>
References: <CAPGyz27j15AoLd4dOCjkLv3ibw3ABz_zvDfakHhA-OUSTcSPCw@mail.gmail.com>
 <5fc49721-6085-de7d-e235-a60acf841d33@mailbox.org>
 <CAPGyz27jUekGYxfAHGRghZC-pn5BffpNzHz5R=+itArrTs_oNw@mail.gmail.com>
 <BBB0C48D-942D-4968-B441-77CCCC8D009D@ucdavis.edu>
 <61ad9a55-0cad-7763-c6f5-afdbb4ab54e8@mailbox.org>
Message-ID: <33292F45-096F-4183-A993-EFAC95A10594@ucdavis.edu>

Hi Rene,

The number of iterations for the linear and non-linear iterations is actually very similar between the two methods.  

The apparent ‘time’ for each solve is seemingly taking significantly longer with active particles verse the compositional fields. The attached file illustrates one example of this for two models where the only difference is using compositional fields or active tracers.

I’ll take a look and see if this behavior is reproduced in other models as well.

Cheers,
John

*************************************************
John Naliboff
Assistant Project Scientist, CIG
Earth & Planetary Sciences Dept., UC Davis




> On Nov 30, 2016, at 3:19 PM, Rene Gassmoeller <rene.gassmoeller at mailbox.org> wrote:
> 
> Hi Lev, Hi John,
> 
> Sorry for the late reply. John's suggestion should be indeed the solution to your problem Lev.  
> Currently, the most reasonable setting for the load balancing strategy is 'repartition' (the 'balanced repartition' method I talked about in the webinar) if you do not need to generate new tracers / remove old ones, and 'repartition, add tracers, remove tracers' if you get empty cells, or so largely unbalanced particle numbers that the particle algorithm takes too much time. This happens for example if you have 'many' different levels of cells, and 'many' particles, with the definition of 'many' depending on your model size and available computing time ;-).
> The documentation of the particle load balancing schemes is currently not as detailed as I would like. I need extend that at some point.
> 
> About John's question: The tracer interpolation itself is not handled in the "Stokes solve" part, it is happening in the "Solve composition system" part of the timer and is only done once per nonlinear iteration. My guess would be that setting up your model with tracers creates sharper gradients in whatever property they track, and therefore the Stokes solution is harder to obtain. Does the number of Stokes iterations change between the two methods?
> 
> Best,
> 
> Rene
> 
> On 11/29/2016 10:07 AM, John Naliboff wrote:
>> Hi Lev,
>> 
>> You should set your load balancing strategy to “remove and add particles, repartition”.  If you do not include the “repartition” option, the majority of your model time will likely be spent with particle sorting if you are using multiple processors.  
>> 
>> For example, in one case without the ‘repartition’ option the time spent in particle sorting is roughly 80-90% (16 processors, ~ 1e6 particles, fixed grid) as opposed to 20% with the ‘repartition’ option.
>> 
>> On a related note, I’ve found using ‘active tracers’ in replace of compositional fields increases the ’Solve Stokes system’ time by over an order of magnitude.  At least this is the case in the ‘extension’ models I’ve been running. 
>> 
>> I haven’t had time to track down where exactly in the "Stokes solve" this time is being eaten up or look at similar time increases in other models, but it will be interesting to see if this is the case in your models as well.  Certainly keep on eye on it before sending any large models off to a cluster.
>> 
>> Rene - Is this possibly due to re-interpolation of particle values during each stokes solve? 
>> 
>> Cheers,
>> John
>> 
>> *************************************************
>> John Naliboff
>> Assistant Project Scientist, CIG
>> Earth & Planetary Sciences Dept., UC Davis
>> 
>> 
>> 
>> 
>> 
>> 
>>> On Nov 28, 2016, at 6:22 PM, Lev Karatun <lev.karatun at gmail.com <mailto:lev.karatun at gmail.com>> wrote:
>>> 
>>> Hi Rene,
>>> 
>>> thanks a lot, I actually had the load balancing strategy set to "repartition", changing it to "remove and add particles" solved the problem. The manual only lists the possible choices, but doesn't explain what they do, so I originally went with the default option. 
>>> Could you get into some more detail on the strategies, please? Do I understand it correctly that the option "add particles" enforces the minimum number of particles in the cell, generating them whenever needed? What would be the difference between "set Load balancing strategy = add particles, remove particles" and ""set Load balancing strategy = add tracers, remove tracers"? And how will the "repartition" strategy work together with the other listed algorithms? Speaking about the webinar on particles, does "repartition" correspond to the "balanced repartitioning", and the rest (except for none) - "particle management"? And for the "Variable distribution" strategy (mentioned in the webinar), what option do I have to choose to enable the mesh adjustment according to particles (and how will it work together with the regular mesh refinement strategy?) ?
>>> 
>>> Best regards,
>>> Lev Karatun.
>>> 
>>> 2016-11-25 17:43 GMT-05:00 Rene Gassmoeller <rene.gassmoeller at mailbox.org <mailto:rene.gassmoeller at mailbox.org>>:
>>> Hi Lev,
>>> 
>>> Let me cc this to the mailing list so that others hear about problems and solutions as well.
>>> Cool model! From what you describe it seems you are doing everything right so far. What is the value for the 'Load balancing strategy' in the Particles subsection? In order for the 'Minimum tracers per cell' option to have an effect you need to at least select the option 'add tracers' (possibly combine it with others like "set Load balancing strategy = add tracers, remove tracers, repartition"). This should then generate new tracers when many others have left that cell. However keep in mind that the properties of these new particles will be interpolated from the remaining existing particles in that cell. This might or might not be a problem for your model.
>>> Let me know about the parameter file option,
>>> 
>>> Best,
>>> Rene
>>> On 11/24/2016 10:36 PM, Lev Karatun wrote:
>>>> Hi Rene,
>>>> 
>>>> I recently added tracers to my models, they work great, thank you for adding them! I was trying to incorporate open boundaries (by Anne Glerum) into my models, they work just fine too. However, when I included both of them, I ran into a problem: the cells near the open boundary, through which constant inflow of material is happening end up not having enough tracers (and later not  having any tracers at all) (see attached screenshot). I decreased the CFL number from 0.5 to 0.1, but it didn't help. So I was wondering if you could tell me what the possible causes are? It happens both with and without adaptive refinement, and I have min tracers number set to 10. 
>>>> 
>>>> Thanks in advance!
>>>> 
>>>> Best regards,
>>>> Lev Karatun.
>>> 
>>> 
>>> _______________________________________________
>>> Aspect-devel mailing list
>>> Aspect-devel at geodynamics.org <mailto:Aspect-devel at geodynamics.org>
>>> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel <http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel>
>> 
>> 
>> _______________________________________________
>> Aspect-devel mailing list
>> Aspect-devel at geodynamics.org <mailto:Aspect-devel at geodynamics.org>
>> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel <http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel>
> _______________________________________________
> Aspect-devel mailing list
> Aspect-devel at geodynamics.org
> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel

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