[aspect-devel] Error on a depth dependent material model
Eleonora Ficini
eleonora.ficini at uniroma1.it
Tue May 8 09:53:53 PDT 2018
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>:
> Send Aspect-devel mailing list submissions to
> aspect-devel at geodynamics.org
>
> To subscribe or unsubscribe via the World Wide Web, visit
> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel
> or, via email, send a message with subject or body 'help' to
> aspect-devel-request at geodynamics.org
>
> You can reach the person managing the list at
> aspect-devel-owner at geodynamics.org
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Aspect-devel digest..."
>
>
> Today's Topics:
>
> 1. 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>
> To: aspect-devel at geodynamics.org
> Subject: [aspect-devel] Error on a depth dependent material model
> Message-ID:
> <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>
>
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: <http://lists.geodynamics.org/pipermail/aspect-devel/
> attachments/20180507/86742871/attachment-0001.html>
>
> ------------------------------
>
> Message: 2
> Date: Mon, 7 May 2018 22:26:31 +0800
> From: Wolfgang Bangerth <bangerth at colostate.edu>
> To: 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>
> 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
> www: http://www.math.colostate.edu/~bangerth/
>
>
>
> ------------------------------
>
> Message: 3
> Date: Mon, 7 May 2018 10:00:15 -0700
> From: Max Rudolph <maxrudolph at ucdavis.edu>
> To: 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>
> 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
> > 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
> > sita-con-il-cinque-mille
> >
> >
> > _______________________________________________
> > Aspect-devel mailing list
> > Aspect-devel at geodynamics.org
> > http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel
> >
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: <http://lists.geodynamics.org/pipermail/aspect-devel/
> attachments/20180507/24cff724/attachment.html>
>
> ------------------------------
>
> Subject: Digest Footer
>
> _______________________________________________
> Aspect-devel mailing list
> Aspect-devel at geodynamics.org
> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel
>
> ------------------------------
>
> End of Aspect-devel Digest, Vol 78, Issue 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>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.geodynamics.org/pipermail/aspect-devel/attachments/20180508/e7ea350e/attachment-0001.html>
More information about the Aspect-devel
mailing list