[petsc-users] Vec is locked read only
Matthew Knepley
knepley at gmail.com
Sat Apr 2 08:22:37 CDT 2016
On Sat, Apr 2, 2016 at 8:18 AM, Rongliang Chen <rl.chen at siat.ac.cn> wrote:
> On 04/02/2016 09:08 PM, Matthew Knepley wrote:
>
> On Sat, Apr 2, 2016 at 8:03 AM, Rongliang Chen <rl.chen at siat.ac.cn> wrote:
>
>> Hi Matt,
>>
>> Many thanks for your helps. I will change the way that I used for the
>> boundary condition setup.
>>
>
> I will note that we (Barry, Jed, Mark, and I at least) have adopted the
> view that by and large
>
> a) global vectors are for solvers
>
> b) local vectors are for assembly
>
> For me, that means local vectors have ghost values and boundary
> conditions, but global vectors
> have them removed. This is how SNES ex12 and ex62 are organized.
>
> Does this means that if I want to use the local vector (obtained by
> DMGlobalToLocalBegin and DMGlobalToLocalEnd), I need to reset the boundary
> conditions for the local vector before I use it?
>
Yes, that is how PETSc is setup internally.
1) The solver generates a new initial guess
2) PETSc calls DMGlobalToLocal(). In Plex, this adds in ghosts and BC
3) The local guess is passed to FormFunctionLocal()
Thanks,
Matt
> Best regards,
> Rongliang
>
> Thanks,
>
> Matt
>
>
>> Best regards,
>> Rongliang
>>
>>
>>
>> On 04/02/2016 08:49 PM, Matthew Knepley wrote:
>>
>> On Sat, Apr 2, 2016 at 7:46 AM, Rongliang Chen <rl.chen at siat.ac.cn>
>> wrote:
>>
>>> But I need to setup the boundary conditions for the solution vector X,
>>> which is in FormMassTimeStep().
>>>
>>
>> Make a copy. The solution vector is used in the solver, and you have no
>> idea exactly what it is doing with it.
>> Or put your boundary conditions in the initial guess to SNESSolve().
>>
>> Matt
>>
>>
>>> Best regards,
>>> Rongliang
>>>
>>>
>>> On 04/02/2016 08:37 PM, Matthew Knepley wrote:
>>>
>>> On Sat, Apr 2, 2016 at 7:37 AM, Rongliang Chen <rl.chen at siat.ac.cn>
>>> wrote:
>>>
>>>> Hi Matt,
>>>>
>>>> How to check in the explicit method? This kind of errors does come out
>>>> in the explicit method.
>>>>
>>>
>>> You said "that is I use the explicit method with the same function
>>> FormMassTimeStep(), this error disappeared"
>>>
>>>
>>>> What do you mean "You should never be changing the input guess"? Do you
>>>> mean that the value of the solution vector X in FormFunction are not
>>>> allowed to be changed by the user defined function?
>>>>
>>>
>>> Yes.
>>>
>>> Matt
>>>
>>>
>>>> Best regards,
>>>> Rongliang
>>>>
>>>> On 04/02/2016 08:19 PM, Matthew Knepley wrote:
>>>>
>>>> On Sat, Apr 2, 2016 at 7:15 AM, Rongliang Chen <rl.chen at siat.ac.cn>
>>>> wrote:
>>>>
>>>>> Hi Matt,
>>>>>
>>>>> That's right. The FormMassTimeStep() is inside the FormFunction() and
>>>>> I call the FormFunction() in this way: SNESSetFunction(user->snes,
>>>>> algebra->f, FormFunction, (void*)user). How can I know the X is read-only
>>>>> or not?
>>>>>
>>>>
>>>> Exactly that you get this error message, and it should be in the
>>>> documentation.
>>>>
>>>>
>>>>> If I do not use the SNESSolve, that is I use the explicit method with
>>>>> the same function FormMassTimeStep(), this error disappeared. So it seems
>>>>> that the SNESSolve locked the vector X.
>>>>>
>>>>
>>>> Then we need to put that check in the explicit method as well. You
>>>> should never be changing the input guess.
>>>>
>>>> Thanks,
>>>>
>>>> Matt
>>>>
>>>>
>>>>> Best regards,
>>>>> Rongliang
>>>>>
>>>>> On 04/02/2016 07:59 PM, Matthew Knepley wrote:
>>>>>
>>>>> On Sat, Apr 2, 2016 at 6:49 AM, Rongliang Chen <rl.chen at siat.ac.cn>
>>>>> wrote:
>>>>>
>>>>>> Hi Dave,
>>>>>>
>>>>>> I did not call any VecGetArrary and VecGetArraryRead in function
>>>>>> FormMassTimeStepFunction().
>>>>>>
>>>>>
>>>>> It looks like you have a function FormMassTimeStep() inside your
>>>>> FormFunction() method. This
>>>>> has an argument X, the solution guess, which is read-only. However,
>>>>> you are calling DMLocalToGlobal()
>>>>> using that X, which is illegal, since its read-only. Is this right?
>>>>>
>>>>> Matt
>>>>>
>>>>>
>>>>>> Best regards,
>>>>>> Rongliang
>>>>>>
>>>>>> On 04/02/2016 06:20 PM, Dave May wrote:
>>>>>>
>>>>>>
>>>>>>
>>>>>> On 2 April 2016 at 11:18, Rongliang Chen <rl.chen at siat.ac.cn> wrote:
>>>>>>
>>>>>>> Hi Shri,
>>>>>>>
>>>>>>> Thanks for your reply.
>>>>>>>
>>>>>>> Do you mean that I need to change the VecGetArrary() in
>>>>>>> /home/rlchen/soft/petsc-3.6.3/src/dm/interface/dm.c to VecGetArrayRead()?
>>>>>>>
>>>>>>
>>>>>> No - you should change it in your function FormMassTimeStepFunction().
>>>>>> The input vector x passed into SNESComputeFunction() is read only.
>>>>>>
>>>>>>
>>>>>>
>>>>>>> I tried it and I got a warning when I make the petsc:
>>>>>>>
>>>>>>> /home/rlchen/soft/petsc-3.6.3/src/dm/interface/dm.c: In function
>>>>>>> ‘DMLocalToGlobalBegin’:
>>>>>>> /home/rlchen/soft/petsc-3.6.3/src/dm/interface/dm.c:1913:5: warning:
>>>>>>> passing argument 2 of ‘VecGetArrayRead’ from incompatible pointer type
>>>>>>> [enabled by default]
>>>>>>> In file included from
>>>>>>> /home/rlchen/soft/petsc-3.6.3/include/petscmat.h:6:0,
>>>>>>> from /home/rlchen/soft/petsc-3.6.3/include/petscdm.h:6,
>>>>>>> from /home/rlchen/soft/petsc-3.6.3/include/petsc/private/dmimpl.h:6,
>>>>>>> from /home/rlchen/soft/petsc-3.6.3/src/dm/interface/dm.c:1:
>>>>>>> /home/rlchen/soft/petsc-3.6.3/include/petscvec.h:420:29: note:
>>>>>>> expected ‘const PetscScalar **’ but argument is of type ‘PetscScalar **’
>>>>>>>
>>>>>>> Best regards,
>>>>>>> Rongliang
>>>>>>>
>>>>>>> ---------------------
>>>>>>> Rongliang Chen, PhD
>>>>>>> Associate Professor
>>>>>>>
>>>>>>> Laboratory for Engineering and Scientific Computing
>>>>>>> Shenzhen Institutes of Advanced Technology
>>>>>>> Chinese Academy of Sciences
>>>>>>> Address: 1068 Xueyuan Avenue, Shenzhen University Town, Shenzhen,
>>>>>>> Guangdong (518055), P. R. China
>>>>>>> E-mail: rl.chen at siat.ac.cn
>>>>>>> Phone: +86-755-86392312
>>>>>>>
>>>>>>>
>>>>>>> On 04/02/2016 05:03 PM, Abhyankar, Shrirang G. wrote:
>>>>>>>
>>>>>>>> Use VecGetArrayRead instead of VecGetArray
>>>>>>>>
>>>>>>>>
>>>>>>>> http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/Vec/VecGetArray
>>>>>>>> Read.html
>>>>>>>>
>>>>>>>>
>>>>>>>> Shri
>>>>>>>>
>>>>>>>> -----Original Message-----
>>>>>>>> From: Rongliang Chen <rl.chen at siat.ac.cn>
>>>>>>>> Date: Saturday, April 2, 2016 at 3:51 AM
>>>>>>>> To: PETSc users list <petsc-users at mcs.anl.gov>, "
>>>>>>>> rongliang.chan at gmail.com"
>>>>>>>> <rongliang.chan at gmail.com>
>>>>>>>> Subject: [petsc-users] Vec is locked read only
>>>>>>>>
>>>>>>>> Dear All,
>>>>>>>>>
>>>>>>>>> My code got the following error messages, but the code works well
>>>>>>>>> for
>>>>>>>>> the petsc optimized version (--with-debugging=0). Anyone can tell
>>>>>>>>> me how
>>>>>>>>> to fix this problem?
>>>>>>>>>
>>>>>>>>> Best regards,
>>>>>>>>> Rongliang
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> [0]PETSC ERROR: --------------------- Error Message
>>>>>>>>> --------------------------------------------------------------
>>>>>>>>> [0]PETSC ERROR: Object is in wrong state
>>>>>>>>> [0]PETSC ERROR: Vec is locked read only, argument # 1
>>>>>>>>> [0]PETSC ERROR: See
>>>>>>>>> http://www.mcs.anl.gov/petsc/documentation/faq.html
>>>>>>>>> for trouble shooting.
>>>>>>>>> [0]PETSC ERROR: Petsc Release Version 3.6.3, Dec, 03, 2015
>>>>>>>>> [0]PETSC ERROR: ./Nwtun on a 64bit-debug named rlchen by rlchen
>>>>>>>>> Sat Apr
>>>>>>>>> 2 15:40:32 2016
>>>>>>>>> [0]PETSC ERROR: Configure options --download-blacs
>>>>>>>>> --download-scalapack
>>>>>>>>> --download-metis --download-parmetis --download-exodusii
>>>>>>>>> --download-netcdf --download-hdf5
>>>>>>>>> --with-mpi-dir=/home/rlchen/soft/Program/mpich2-shared
>>>>>>>>> --with-debugging=1 --download-fblaslapack --download-chaco
>>>>>>>>> [0]PETSC ERROR: #1 VecGetArray() line 1646 in
>>>>>>>>> /home/rlchen/soft/petsc-3.6.3/src/vec/vec/interface/rvector.c
>>>>>>>>> [0]PETSC ERROR: #2 DMLocalToGlobalBegin() line 1913 in
>>>>>>>>> /home/rlchen/soft/petsc-3.6.3/src/dm/interface/dm.c
>>>>>>>>> [0]PETSC ERROR: #3 FormMassTimeStepFunction() line 191 in
>>>>>>>>>
>>>>>>>>> /home/rlchen/soft/3D_fluid/FiniteVolumeMethod/PETScCodes/codefor3.6/SetupF
>>>>>>>>> unctions.c
>>>>>>>>> [0]PETSC ERROR: #4 FormFunction() line 46 in
>>>>>>>>>
>>>>>>>>> /home/rlchen/soft/3D_fluid/FiniteVolumeMethod/PETScCodes/codefor3.6/SetupF
>>>>>>>>> unctions.c
>>>>>>>>> [0]PETSC ERROR: #5 SNESComputeFunction() line 2067 in
>>>>>>>>> /home/rlchen/soft/petsc-3.6.3/src/snes/interface/snes.c
>>>>>>>>> [0]PETSC ERROR: #6 SNESSolve_NEWTONLS() line 184 in
>>>>>>>>> /home/rlchen/soft/petsc-3.6.3/src/snes/impls/ls/ls.c
>>>>>>>>> [0]PETSC ERROR: #7 SNESSolve() line 3906 in
>>>>>>>>> /home/rlchen/soft/petsc-3.6.3/src/snes/interface/snes.c
>>>>>>>>> [0]PETSC ERROR: #8 SolveTimeDependent() line 843 in
>>>>>>>>>
>>>>>>>>> /home/rlchen/soft/3D_fluid/FiniteVolumeMethod/PETScCodes/codefor3.6/Nwtun.
>>>>>>>>> c
>>>>>>>>> [0]PETSC ERROR: #9 main() line 452 in
>>>>>>>>>
>>>>>>>>> /home/rlchen/soft/3D_fluid/FiniteVolumeMethod/PETScCodes/codefor3.6/Nwtun.
>>>>>>>>> c
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> What most experimenters take for granted before they begin their
>>>>> experiments is infinitely more interesting than any results to which their
>>>>> experiments lead.
>>>>> -- Norbert Wiener
>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>> --
>>>> What most experimenters take for granted before they begin their
>>>> experiments is infinitely more interesting than any results to which their
>>>> experiments lead.
>>>> -- Norbert Wiener
>>>>
>>>>
>>>>
>>>
>>>
>>> --
>>> What most experimenters take for granted before they begin their
>>> experiments is infinitely more interesting than any results to which their
>>> experiments lead.
>>> -- Norbert Wiener
>>>
>>>
>>>
>>
>>
>> --
>> What most experimenters take for granted before they begin their
>> experiments is infinitely more interesting than any results to which their
>> experiments lead.
>> -- Norbert Wiener
>>
>>
>>
>
>
> --
> What most experimenters take for granted before they begin their
> experiments is infinitely more interesting than any results to which their
> experiments lead.
> -- Norbert Wiener
>
>
>
--
What most experimenters take for granted before they begin their
experiments is infinitely more interesting than any results to which their
experiments lead.
-- Norbert Wiener
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