[petsc-users] Segmentation faults: Derived types
Santiago Ospina De Los Rios
sospinar at unal.edu.co
Sun Aug 21 05:09:46 CDT 2016
wow, what a dumb mistake. thank you very much!
Since you've noticed me such error, I am taking the time to learn all of
your advice about management and debugging code
<https://www.mcs.anl.gov/petsc/documentation/codemanagement.html>. Then I'm
learning emacs and so... the matter is that you recommend to use PETSc tags
which it's supposed to be in ${PETSC_DIR}/TAGS, but it seems to be changed
or something because I wasn't able to find it.
So, how can I use the tags you are referring to?
2016-08-19 14:40 GMT-05:00 Barry Smith <bsmith at mcs.anl.gov>:
>
> You code has a bug right at the top:
>
> CALL PetscInitialize(PETSC_COMM_WORLD,ierr)
>
> should be
>
> CALL PetscInitialize(PETSC_NULL_CHARACTER,ierr)
>
> you were just lucky previously that the stack frame was different enough
> that it did not previously crash. Once I corrected the code the new version
> ran without crashing. I found the bug very easily by simply running the new
> version directly in the debugger
>
> lldb ./ANSIFLOW
>
> and seeing it crashed with a crazy stack in petscinitialize_
>
> Barry
>
>
> > On Aug 5, 2016, at 11:34 PM, Santiago Ospina De Los Rios <
> sospinar at unal.edu.co> wrote:
> >
> > Dear Barry,
> >
> > I tried to build a simple code with the same things I mentioned to you
> on last e-mail but it worked, which is more strange to me. So I built two
> branches on my git code to show you the problem:
> >
> > git code: https://github.com/SoilRos/ANISOFLOWPACK
> >
> > Branch: PETSc_debug_boolean_0
> > The first one is a simple code which is working for what was designed.
> Forget sample problems, just compile and run the ANISOFLOW executable on
> src folder, if there are some verbose messages then the program is working.
> >
> > Branch: PETSc_debug_boolean_1
> > The second one is just a modification of the first one adding the two
> booleans mentioned above in 01_Types.F90 file. I tried it in mac El Capitan
> and Ubuntu (with Valgrind) and PETSc 3.7.3 and 3.7.2 respectively, both
> with the same segmentation fault.
> >
> > PD: Although I already fixed it compressing the three booleans into one
> integer, I think is better if we try to figure out why there is a
> segmentation fault because I had similar problems before.
> > PD2: Please obviate the variable description because are pretty out of
> date. I'm trying to change it, so it can be confusing.
> >
> > Best wishes,
> > Santiago Ospina
> >
> > 2016-08-05 15:54 GMT-05:00 Barry Smith <bsmith at mcs.anl.gov>:
> >
> > > On Aug 1, 2016, at 4:41 PM, Santiago Ospina De Los Rios <
> sospinar at unal.edu.co> wrote:
> > >
> > > Hello there,
> > >
> > > I'm having problems defining some variables into derived types in
> Fortran. Before, I had a similar problems with an allocatable array
> "PetsInt" but I solved it just doing a non-collective Petsc Vec. Today I'm
> having troubles with "PetscBool" or "Logical":
> > >
> > > In a module which define the variables, I have the following:
> > >
> > > MODULE ANISOFLOW_Types
> > >
> > > IMPLICIT NONE
> > >
> > > #include <petsc/finclude/petscsys.h>
> > > #include <petsc/finclude/petscvec.h>
> > >
> > > ...
> > >
> > > TYPE ConductivityField
> > > PetscBool ::
> DefinedByCvtZones=.FALSE. ! It produces the segmentation fault.
> > > PetscBool ::
> DefinedByPptZones=.FALSE. ! It produces the segmentation fault.
> > > PetscBool ::
> DefinedByCell=.FALSE.
> > > ! Conductivity defined by zones (Local):
> > > Vec :: ZoneID
> > > TYPE(Tensor),ALLOCATABLE :: Zone(:)
> > > ! Conductivity defined on every cell (Local):
> > > Vec :: Cell
> > > END TYPE ConductivityField
> > >
> > >
> > > TYPE SpecificStorageField
> > > PetscBool ::
> DefinedByStoZones=.FALSE. ! It produces the segmentation fault.
> > > PetscBool ::
> DefinedByPptZones=.FALSE. ! It produces the segmentation fault.
> > > PetscBool ::
> DefinedByCell=.FALSE.
> > > ! Specific Storage defined by zones (Local):
> > > Vec :: ZoneID
> > > Vec :: Zone
> > > ! Specific Storage defined on every cell (Global).:
> > > Vec :: Cell
> > > END TYPE SpecificStorageField
> > >
> > > TYPE PropertiesField
> > > TYPE(ConductivityField) :: Cvt
> > > TYPE(SpecificStorageField) :: Sto
> > > ! Property defined by zones (Local):
> > > PetscBool :: DefinedByPptZones=.FALSE.
> > > Vec :: ZoneID
> > > END TYPE PropertiesField
> > >
> > > ...
> > >
> > > CONTAINS
> > >
> > > ...
> > >
> > > END MODULE ANISOFLOW_Types
> > >
> > >
> > > Later I use it in the main program, with something like this
> > >
> > > PROGRAM ANISOFLOW
> > >
> > > USE ANISOFLOW_Types, ONLY : ... ,PropertiesField,
> ...
> > > ...
> > >
> > > IMPLICIT NONE
> > >
> > > #include <petsc/finclude/petscsys.h>
> > >
> > > ...
> > > TYPE(PropertiesField) :: PptFld
> > > ...
> > >
> > > CALL PetscInitialize(PETSC_COMM_WORLD,ierr)
> > > ...
> > > CALL PetscFinalize(ierr)
> > >
> > > END PROGRAM
> > >
> > >
> > > When I run the program appears a Segmentation Fault, which disappears
> when I comment the booleans marked in the code. Because I need them, I used
> Valgrind to figure out what is happening but it is yet a mistery to me.
> > >
> > > Valgrind message:
> > > ==5160==
> > > ==5160== Invalid read of size 1
> >
> > It is curious that it says "of size 1" when we declare PetscBool to
> be a logical*4 I don't see anything obviously wrong.
> >
> > Please send a simple code we can compile and run that reproduces the
> problem.
> >
> > Barry
> > > ==5160== at 0x4FB2156: petscinitialize_ (zstart.c:433)
> > > ==5160== by 0x4030EA: MAIN__ (ANISOFLOW.F90:29) # line of petsc
> inizalitation
> > > ==5160== by 0x404380: main (ANISOFLOW.F90:3) # line of "USE
> ANISOFLOW_Types, ONLY : ... ,PropertiesField, ..."
> > > ==5160== Address 0xc54fff is not stack'd, malloc'd or (recently)
> free'd
> > > ==5160==
> > >
> > > Program received signal SIGSEGV: Segmentation fault - invalid memory
> reference.
> > >
> > > Backtrace for this error:
> > > #0 0x699E777
> > > #1 0x699ED7E
> > > #2 0x6F0BCAF
> > > #3 0x4FB2156
> > > #4 0x4030EA in anisoflow at ANISOFLOW.F90:29
> > >
> > > I think it is maybe related with petsc because the error popped out
> just in its initialization, so if you know what's going on, I would
> appreciate to tell me.
> > >
> > > Santiago Ospina
> > > --
> > >
> > > --
> > > Att:
> > >
> > > Santiago Ospina De Los Ríos
> > > National University of Colombia
> >
> >
> >
> >
> > --
> >
> > --
> > Att:
> >
> > Santiago Ospina De Los Ríos
> > National University of Colombia
>
>
--
--
Att:
Santiago Ospina De Los Ríos
National University of Colombia
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