[aspect-devel] Error on a depth dependent material model
John Naliboff
jbnaliboff at ucdavis.edu
Tue May 8 12:28:12 PDT 2018
Dear Eleonora,
Yes, the error messages below don't provide much more information.
Perhaps "[5]PETSC ERROR: #1 User provided function() line 0 in unknown
file" might be pointing to the underlying issue? Regardless, more
information is needed to pinpoint the problem. If you printed the
"screen output" to a file, could you pass that along as well?
An alternative is to run your model through a debugger. If you have gdb
installed on your machine (check with "which gdb") and you compiled
ASPECT in debug mode (highly recommended for all but production models),
you may be able to get a bit more information. The command to run ASPECT
in gdb is "gdb --args path_to_aspect/aspect parameter_file_name" then
once gdb starts up type "run". After doing this (if possible), could you
send over all of the error messages (or the entire output history)?
If you don't have gdb installed and there is no additional error
messages from your previous run, I think the best solution is to send us
the parameter file and any additional files.
Cheers,
John
On 05/08/2018 09:53 AM, Eleonora Ficini wrote:
> Dear Max and Wolfgang,
> thanks for the replies.
> The error does not seem to give any information about where the
> problem is. However, below you can find the error itself.
>
> I also already tried to run a version in which the base model is the
> simple one, and it worked.
>
> Let me know if the input parameters can help.
>
> Thanks a lot for your help!
>
> All the best,
> Eleonora
>
> 0]PETSC ERROR:
> ------------------------------------------------------------------------
>
> [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
> probably memory access out of range
>
> [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
>
> [0]PETSC ERROR: or see
> http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind
>
> [0]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac
> OS X to find memory corruption errors
>
> [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link,
> and run
>
> [0]PETSC ERROR: to get more information on the crash.
>
> [0]PETSC ERROR: --------------------- Error Message
> --------------------------------------------------------------
>
> [0]PETSC ERROR: Signal received
>
> [0]PETSC ERROR: See
> http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting.
>
> [0]PETSC ERROR: Petsc Release Version 3.7.6, Apr, 24, 2017
>
> [0]PETSC ERROR: ../aspect on a arch-linux2-c-opt named dell2017yz by
> aspect Tue May 8 18:39:33 2018
>
> [1]PETSC ERROR:
> ------------------------------------------------------------------------
>
> [1]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
> probably memory access out of range
>
> [1]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
>
> [1]PETSC ERROR: or see
> http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind
>
> [1]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac
> OS X to find memory corruption errors
>
> [1]PETSC ERROR: configure using --with-debugging=yes, recompile, link,
> and run
>
> [1]PETSC ERROR: to get more information on the crash.
>
> [1]PETSC ERROR: --------------------- Error Message
> --------------------------------------------------------------
>
> [1]PETSC ERROR: Signal received
>
> [1]PETSC ERROR: See
> http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting.
>
> [1]PETSC ERROR: Petsc Release Version 3.7.6, Apr, 24, 2017
>
> [1]PETSC ERROR: ../aspect on a arch-linux2-c-opt named dell2017yz by
> aspect Tue May 8 18:39:33 2018
>
> [1]PETSC ERROR: [0]PETSC ERROR: Configure options
> --prefix=/home/aspect/deal.ii-candi/petsc-3.7.6 --with-debugging=0
> --with-shared-libraries=1 --with-mpi=1 --with-x=0
> --with-64-bit-indices=0 --download-hypre=1 CC=mpicc CXX=mpicxx
> FC=mpif90
> --with-parmetis-dir=/home/aspect/deal.ii-candi/parmetis-4.0.3
> --with-metis-dir=/home/aspect/deal.ii-candi/parmetis-4.0.3
> --download-scalapack=1 --download-mumps=1
>
> [0]PETSC ERROR: #1 User provided function() line 0 in unknown file
>
> Configure options --prefix=/home/aspect/deal.ii-candi/petsc-3.7.6
> --with-debugging=0 --with-shared-libraries=1 --with-mpi=1 --with-x=0
> --with-64-bit-indices=0 --download-hypre=1 CC=mpicc CXX=mpicxx
> FC=mpif90
> --with-parmetis-dir=/home/aspect/deal.ii-candi/parmetis-4.0.3
> --with-metis-dir=/home/aspect/deal.ii-candi/parmetis-4.0.3
> --download-scalapack=1 --download-mumps=1
>
> [1]PETSC ERROR: #1 User provided function() line 0 in unknown file
>
> --------------------------------------------------------------------------
>
> MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
>
> with errorcode 59.
>
> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
>
> You may or may not see output from other processes, depending on
>
> exactly when Open MPI kills them.
>
> --------------------------------------------------------------------------
>
> [2]PETSC ERROR:
> ------------------------------------------------------------------------
>
> [2]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
> probably memory access out of range
>
> [2]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
>
> [2]PETSC ERROR: or see
> http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind
>
> [2]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac
> OS X to find memory corruption errors
>
> [2]PETSC ERROR: configure using --with-debugging=yes, recompile, link,
> and run
>
> [2]PETSC ERROR: to get more information on the crash.
>
> [2]PETSC ERROR: --------------------- Error Message
> --------------------------------------------------------------
>
> [2]PETSC ERROR: Signal received
>
> [2]PETSC ERROR: See
> http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting.
>
> [2]PETSC ERROR: Petsc Release Version 3.7.6, Apr, 24, 2017
>
> [2]PETSC ERROR: ../aspect on a arch-linux2-c-opt named dell2017yz by
> aspect Tue May 8 18:39:33 2018
>
> [2]PETSC ERROR: Configure options
> --prefix=/home/aspect/deal.ii-candi/petsc-3.7.6 --with-debugging=0
> --with-shared-libraries=1 --with-mpi=1 --with-x=0
> --with-64-bit-indices=0 --download-hypre=1 CC=mpicc CXX=mpicxx
> FC=mpif90
> --with-parmetis-dir=/home/aspect/deal.ii-candi/parmetis-4.0.3
> --with-metis-dir=/home/aspect/deal.ii-candi/parmetis-4.0.3
> --download-scalapack=1 --download-mumps=1
>
> [2]PETSC ERROR: #1 User provided function() line 0 in unknown file
>
> [3]PETSC ERROR:
> ------------------------------------------------------------------------
>
> [3]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
> probably memory access out of range
>
> [3]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
>
> [3]PETSC ERROR: or see
> http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind
>
> [3]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac
> OS X to find memory corruption errors
>
> [3]PETSC ERROR: configure using --with-debugging=yes, recompile, link,
> and run
>
> [3]PETSC ERROR: to get more information on the crash.
>
> [3]PETSC ERROR: --------------------- Error Message
> --------------------------------------------------------------
>
> [3]PETSC ERROR: Signal received
>
> [3]PETSC ERROR: See
> http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting.
>
> [3]PETSC ERROR: Petsc Release Version 3.7.6, Apr, 24, 2017
>
> [3]PETSC ERROR: ../aspect on a arch-linux2-c-opt named dell2017yz by
> aspect Tue May 8 18:39:33 2018
>
> [3]PETSC ERROR: Configure options
> --prefix=/home/aspect/deal.ii-candi/petsc-3.7.6 --with-debugging=0
> --with-shared-libraries=1 --with-mpi=1 --with-x=0
> --with-64-bit-indices=0 --download-hypre=1 CC=mpicc CXX=mpicxx
> FC=mpif90
> --with-parmetis-dir=/home/aspect/deal.ii-candi/parmetis-4.0.3
> --with-metis-dir=/home/aspect/deal.ii-candi/parmetis-4.0.3
> --download-scalapack=1 --download-mumps=1
>
> [3]PETSC ERROR: #1 User provided function() line 0 in unknown file
>
> [4]PETSC ERROR:
> ------------------------------------------------------------------------
>
> [4]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
> probably memory access out of range
>
> [4]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
>
> [4]PETSC ERROR: or see
> http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind
>
> [4]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac
> OS X to find memory corruption errors
>
> [4]PETSC ERROR: configure using --with-debugging=yes, recompile, link,
> and run
>
> [4]PETSC ERROR: to get more information on the crash.
>
> [4]PETSC ERROR: --------------------- Error Message
> --------------------------------------------------------------
>
> [4]PETSC ERROR: Signal received
>
> [4]PETSC ERROR: See
> http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting.
>
> [4]PETSC ERROR: Petsc Release Version 3.7.6, Apr, 24, 2017
>
> [4]PETSC ERROR: ../aspect on a arch-linux2-c-opt named dell2017yz by
> aspect Tue May 8 18:39:33 2018
>
> [4]PETSC ERROR: Configure options
> --prefix=/home/aspect/deal.ii-candi/petsc-3.7.6 --with-debugging=0
> --with-shared-libraries=1 --with-mpi=1 --with-x=0
> --with-64-bit-indices=0 --download-hypre=1 CC=mpicc CXX=mpicxx
> FC=mpif90
> --with-parmetis-dir=/home/aspect/deal.ii-candi/parmetis-4.0.3
> --with-metis-dir=/home/aspect/deal.ii-candi/parmetis-4.0.3
> --download-scalapack=1 --download-mumps=1
>
> [4]PETSC ERROR: #1 User provided function() line 0 in unknown file
>
> [5]PETSC ERROR:
> ------------------------------------------------------------------------
>
> [5]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
> probably memory access out of range
>
> [5]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
>
> [5]PETSC ERROR: or see
> http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind
>
> [5]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac
> OS X to find memory corruption errors
>
> [5]PETSC ERROR: configure using --with-debugging=yes, recompile, link,
> and run
>
> [5]PETSC ERROR: to get more information on the crash.
>
> [5]PETSC ERROR: --------------------- Error Message
> --------------------------------------------------------------
>
> [5]PETSC ERROR: Signal received
>
> [5]PETSC ERROR: See
> http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting.
>
> [5]PETSC ERROR: Petsc Release Version 3.7.6, Apr, 24, 2017
>
> [5]PETSC ERROR: ../aspect on a arch-linux2-c-opt named dell2017yz by
> aspect Tue May 8 18:39:33 2018
>
> [5]PETSC ERROR: Configure options
> --prefix=/home/aspect/deal.ii-candi/petsc-3.7.6 --with-debugging=0
> --with-shared-libraries=1 --with-mpi=1 --with-x=0
> --with-64-bit-indices=0 --download-hypre=1 CC=mpicc CXX=mpicxx
> FC=mpif90
> --with-parmetis-dir=/home/aspect/deal.ii-candi/parmetis-4.0.3
> --with-metis-dir=/home/aspect/deal.ii-candi/parmetis-4.0.3
> --download-scalapack=1 --download-mumps=1
>
> [5]PETSC ERROR: #1 User provided function() line 0 in unknown file
>
> [dell2017yz:21043] 4 more processes have sent help message
> help-mpi-api.txt / mpi-abort
>
> [dell2017yz:21043] Set MCA parameter "orte_base_help_aggregate" to 0
> to see all help / error messages
>
> 2018-05-07 18:53 GMT+02:00 <aspect-devel-request at geodynamics.org
> <mailto:aspect-devel-request at geodynamics.org>>:
>
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> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Aspect-devel digest..."
>
>
> Today's Topics:
>
> 1. Error on a depth dependent material model (Eleonora Ficini)
> 2. Re: Error on a depth dependent material model (Wolfgang
> Bangerth)
> 3. Re: Error on a depth dependent material model (Max Rudolph)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 7 May 2018 12:27:36 +0200
> From: Eleonora Ficini <eleonora.ficini at uniroma1.it
> <mailto:eleonora.ficini at uniroma1.it>>
> To: aspect-devel at geodynamics.org <mailto:aspect-devel at geodynamics.org>
> Subject: [aspect-devel] Error on a depth dependent material model
> Message-ID:
>
> <CACT2GZbZBms4kahKr5DY6uqLFJhtJSP1ED4p4rXkNR3edB0VjA at mail.gmail.com
> <mailto:CACT2GZbZBms4kahKr5DY6uqLFJhtJSP1ED4p4rXkNR3edB0VjA at mail.gmail.com>>
> Content-Type: text/plain; charset="utf-8"
>
> Dear all,
> I am trying to modify an Ascii reference profile model with a depth
> dependent viscosity. So, I am using a Depth dependent material
> model (that
> uses a File depth dependence method) with an Ascii reference
> profile as
> Base model.
> Unfortunately I got a never-met-before error:
>
> [3]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
> probably memory access out of range
>
> Below you can find the rows of my parameter files that involves
> the main
> changes: what am I missing? (I am using a burnman-type
> composition.txt file)
>
> subsection Material model
> set Model name =depth dependent
>
> subsection Depth dependent model
> set Base model = ascii reference profile
> set Depth dependence method = File
> set Data directory = $ASPECT_SOURCE_DIR/source/
> set Viscosity depth file = visc-depth.txt
> end
>
> subsection Ascii reference profile
> subsection Ascii data model
> set Data directory =
> $ASPECT_SOURCE_DIR/data/adiabatic-conditions/ascii-data/
> set Data file name = composition.txt
> end
> end
> end
>
> Thank you in advance.
>
> All the best,
> Eleonora
>
> --
> ___________________________________________
> *Il tuo 5 diventa 1000*
> Fai
> crescere la tua università
> Dona il 5 per mille alla Sapienza
> Codice
> fiscale: *80209930587*
>
> https://www.uniroma1.it/it/pagina/fai-crescere-la-tua-universita-con-il-cinque-mille
> <https://www.uniroma1.it/it/pagina/fai-crescere-la-tua-universita-con-il-cinque-mille>
>
> <https://www.uniroma1.it/it/pagina/fai-crescere-la-tua-universita-con-il-cinque-mille
> <https://www.uniroma1.it/it/pagina/fai-crescere-la-tua-universita-con-il-cinque-mille>>
>
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> ------------------------------
>
> Message: 2
> Date: Mon, 7 May 2018 22:26:31 +0800
> From: Wolfgang Bangerth <bangerth at colostate.edu
> <mailto:bangerth at colostate.edu>>
> To: aspect-devel at geodynamics.org <mailto:aspect-devel at geodynamics.org>
> Subject: Re: [aspect-devel] Error on a depth dependent material model
> Message-ID: <14182566-4029-1901-07c4-5634e154da72 at colostate.edu
> <mailto:14182566-4029-1901-07c4-5634e154da72 at colostate.edu>>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
>
> Eleonora,
>
> > [3]PETSC ERROR: Caught signal number 11 SEGV: Segmentation
> Violation, probably
> > memory access out of range
> A segmentation fault means that the code somewhere accesses memory
> that can't
> be accessed -- think of trying to read past the end of an array.
>
> In order to find out what the problem is, we need to find out
> *where* the
> problem is. Is there any more information that is printed along
> with the error
> above? For example, a "stack trace", i.e., a list of functions
> that were
> called before the error happened? Alternatively, can you send all
> necessary
> input files for someone to try and reproduce the issue?
>
> Best
> W.
>
> --
> ------------------------------------------------------------------------
> Wolfgang Bangerth email: bangerth at colostate.edu
> <mailto:bangerth at colostate.edu>
> www:
> http://www.math.colostate.edu/~bangerth/
> <http://www.math.colostate.edu/%7Ebangerth/>
>
>
>
> ------------------------------
>
> Message: 3
> Date: Mon, 7 May 2018 10:00:15 -0700
> From: Max Rudolph <maxrudolph at ucdavis.edu
> <mailto:maxrudolph at ucdavis.edu>>
> To: aspect-devel at geodynamics.org <mailto:aspect-devel at geodynamics.org>
> Subject: Re: [aspect-devel] Error on a depth dependent material model
> Message-ID:
>
> <CA+pU5655r7pJUx2prGJWwp0=OrnT-EY9xZVTgwAhrk+LqFrn6Q at mail.gmail.com
> <mailto:OrnT-EY9xZVTgwAhrk%2BLqFrn6Q at mail.gmail.com>>
> Content-Type: text/plain; charset="utf-8"
>
> I suggest that you first try to isolate whether the problem is
> with the
> depth dependent model or with the ascii reference profile. One way
> to do
> this is to temporarily switch to the simple material model for the
> base
> model. Sometimes segmentation faults can occur when a file is not
> found.
>
> On Mon, May 7, 2018 at 3:27 AM, Eleonora Ficini
> <eleonora.ficini at uniroma1.it <mailto:eleonora.ficini at uniroma1.it>
> > wrote:
>
> > Dear all,
> > I am trying to modify an Ascii reference profile model with a depth
> > dependent viscosity. So, I am using a Depth dependent material
> model (that
> > uses a File depth dependence method) with an Ascii reference
> profile as
> > Base model.
> > Unfortunately I got a never-met-before error:
> >
> > [3]PETSC ERROR: Caught signal number 11 SEGV: Segmentation
> Violation,
> > probably memory access out of range
> >
> > Below you can find the rows of my parameter files that involves
> the main
> > changes: what am I missing? (I am using a burnman-type
> composition.txt file)
> >
> > subsection Material model
> > set Model name =depth dependent
> >
> > subsection Depth dependent model
> > set Base model = ascii reference profile
> > set Depth dependence method = File
> > set Data directory = $ASPECT_SOURCE_DIR/source/
> > set Viscosity depth file = visc-depth.txt
> > end
> >
> > subsection Ascii reference profile
> > subsection Ascii data model
> > set Data directory = $ASPECT_SOURCE_DIR/data/
> > adiabatic-conditions/ascii-data/
> > set Data file name = composition.txt
> > end
> > end
> > end
> >
> > Thank you in advance.
> >
> > All the best,
> > Eleonora
> >
> > ___________________________________________
> > *Il tuo 5 diventa 1000*
> > Fai crescere la tua università
> > Dona il 5 per mille alla Sapienza
> > Codice fiscale: *80209930587*
> > https://www.uniroma1.it/it/pagina/fai-crescere-la-tua-univer
> <https://www.uniroma1.it/it/pagina/fai-crescere-la-tua-univer>
> > sita-con-il-cinque-mille
> >
> >
> > _______________________________________________
> > 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>
> >
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> End of Aspect-devel Digest, Vol 78, Issue 12
> ********************************************
>
>
>
>
> --
> Eleonora Ficini, PhD student
> Department of Earth Sciences
> Sapienza University of Rome
> P.le A. Moro, 5 - 00185, Rome, Italy
>
>
>
> ___________________________________________
> *Il tuo 5 diventa 1000*
> Fai crescere la tua università
> Dona il 5 per mille alla Sapienza
> Codice fiscale: *80209930587*
> https://www.uniroma1.it/it/pagina/fai-crescere-la-tua-universita-con-il-cinque-mille
> <https://www.uniroma1.it/it/pagina/fai-crescere-la-tua-universita-con-il-cinque-mille>
>
>
>
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