[petsc-users] DAGlobalToLocalBegin()
(Rebecca) Xuefei YUAN
xy2102 at columbia.edu
Wed Mar 24 19:50:36 CDT 2010
Dear Barry,
Thanks for pointing out this issue and my problem is solved with
-dmmg_is_coloring_type global. I will add FormJacobian() in my code,
so this won't be a problem for me later on.
Have a good night!
Rebecca
Quoting Barry Smith <bsmith at mcs.anl.gov>:
>
> Rebecca,
>
> I apologize, there is an error in our code. In DMMGCreate() is the
> line (including the comment)
>
> p[i]->isctype = IS_COLORING_GHOSTED; /* default to faster
> version, requires DMMGSetSNESLocal() */
>
> This code is fundamentally wrong, the only place we check that
> DMMGSetSNESLocal() is used is in the comment!!!
>
> These the default value doesn't work when you use DMMGSetSNES(), it
> only works as Matt points out when you change the value from the
> default.
>
> I have fixed this in the petsc-dev source.
>
> I apologize for the run-around on this and that it took us so long
> to deal with it properly.
>
> Barry
>
> PETSc developers, it is also disgraceful that we don't have a single
> test case that detects this problem!
>
> .
> On Mar 24, 2010, at 4:12 PM, (Rebecca) Xuefei YUAN wrote:
>
>> Dear Matt,
>>
>> Thanks a lot!
>>
>> Yes, when
>>
>> -dmmg_iscoloring_type global
>>
>> is applied, this is right now. But what is difference between
>> IS_COLORING_GHOSTED and IS_COLORING_GLOBAL?
>>
>> Cheers,
>>
>> Rebecca
>>
>>
>> Quoting Matthew Knepley <knepley at gmail.com>:
>>
>>> On Wed, Mar 24, 2010 at 3:01 PM, (Rebecca) Xuefei YUAN
>>> <xy2102 at columbia.edu>wrote:
>>>
>>>> Dear Jed and Matt,
>>>>
>>>
>>> This is a genuine bug. It is in DMMGComputeJacobianWithFD() and only occurs
>>> when
>>> IS_COLORING_GHOSTED is true. So, using IS_COLORING_GLOBAL would probably
>>> work here (can't look up the option right now).
>>>
>>> Barry, what is supposed to happen here? Clearly a local vector is being
>>> passed where
>>> a global vector is expected (at least part of the time).
>>>
>>> Matt
>>>
>>>
>>>> Yes, X and F are global and localFIELD is serial. I ran with np=2.
>>>>
>>>> The error I get is:
>>>>
>>>>
>>>> **************************************************
>>>> 0 SNES Function norm 1.095445115010e+01
>>>> [1]PETSC ERROR: VecScatterBegin() line 1538 in src/vec/vec/utils/vscat.c
>>>> Vector wrong size 100 for scatter 60 (scatter forward and vector
>>>> from != ctx
>>>> from size)
>>>> [0]PETSC ERROR: VecScatterBegin() line 1538 in src/vec/vec/utils/vscat.c
>>>> Vector wrong size 100 for scatter 60 (scatter forward and vector
>>>> from != ctx
>>>> from size)
>>>>
>>>>
>>>> from gdb, I get:
>>>>
>>>>
>>>> Program received signal SIGABRT, Aborted.
>>>> [Switching to Thread 0xb7c396b0 (LWP 6301)]
>>>> 0xb7f09410 in __kernel_vsyscall ()
>>>> (gdb) where
>>>> #0 0xb7f09410 in __kernel_vsyscall ()
>>>> #1 0xb7c89085 in raise () from /lib/tls/i686/cmov/libc.so.6
>>>> #2 0xb7c8aa01 in abort () from /lib/tls/i686/cmov/libc.so.6
>>>> #3 0x087d591d in PetscAbortErrorHandler (line=1538,
>>>> fun=0x88fe26d "VecScatterBegin", file=0x88fd9f7 "vscat.c",
>>>> dir=0x88fd9ff "src/vec/vec/utils/", n=60, p=1,
>>>> mess=0xbfd31124 "Vector wrong size 100 for scatter 60 (scatter forward
>>>> and v
>>>> ector from != ctx from size)", ctx=0x0) at errabort.c:62
>>>> #4 0x0874a88e in PetscError (line=1538, func=0x88fe26d "VecScatterBegin",
>>>> file=0x88fd9f7 "vscat.c", dir=0x88fd9ff "src/vec/vec/utils/", n=60, p=1,
>>>> mess=0x88fe3a0 "Vector wrong size %D for scatter %D (scatter forward and
>>>> vec
>>>> tor from != ctx from size)") at err.c:482
>>>> #5 0x086558cc in VecScatterBegin (inctx=0x8a393b0, x=0x8b39cc0,
>>>> y=0x8b3b310,
>>>> addv=INSERT_VALUES, mode=SCATTER_FORWARD) at vscat.c:1538
>>>> #6 0x0828b54c in DAGlobalToLocalBegin (da=0x8a2d360, g=0x8b39cc0,
>>>> mode=INSERT_VALUES, l=0x8b3b310) at dagtol.c:50
>>>> #7 0x080f1b25 in FormFunction (snes=0x8a47840, X=0x8b39cc0, F=0x8adb2f0,
>>>> dummg=0x8a2b810) at twgcqt2unffnictv.c:8382
>>>> #8 0x0860c63d in MatFDColoringApply_AIJ (J=0x8a6bbb0, coloring=0x8aa7b40,
>>>> x1=0x8b12a60, flag=0xbfd32164, sctx=0x8a47840) at fdmatrix.c:680
>>>> #9 0x0860abaf in MatFDColoringApply (J=0x8a6bbb0, coloring=0x8aa7b40,
>>>> x1=0x8b12a60, flag=0xbfd32164, sctx=0x8a47840) at fdmatrix.c:521
>>>> #10 0x08122e45 in SNESDefaultComputeJacobianColor (snes=0x8a47840,
>>>> ---Type <return> to continue, or q <return> to quit---
>>>> x1=0x8b12a60, J=0x8a47910, B=0x8a47914, flag=0xbfd32164, ctx=0x8aa7b40)
>>>> at snesj2.c:49
>>>> #11 0x0811c7cf in DMMGComputeJacobianWithFD (snes=0x8a47840, x1=0x8a39c20,
>>>> J=0x8a47910, B=0x8a47914, flag=0xbfd32164, ctx=0x8a2b810) at
>>>> damgsnes.c:365
>>>> #12 0x0811a883 in DMMGComputeJacobian_Multigrid (snes=0x8a47840,
>>>> X=0x8a39c20,
>>>> J=0x8a47910, B=0x8a47914, flag=0xbfd32164, ptr=0x8a2b6b0) at
>>>> damgsnes.c:60
>>>> #13 0x080fc610 in SNESComputeJacobian (snes=0x8a47840, X=0x8a39c20,
>>>> A=0x8a47910, B=0x8a47914, flg=0xbfd32164) at snes.c:1188
>>>> #14 0x08124471 in SNESSolve_LS (snes=0x8a47840) at ls.c:189
>>>> #15 0x08103fac in SNESSolve (snes=0x8a47840, b=0x0, x=0x8a39c20) at
>>>> snes.c:2242
>>>> #16 0x0811db31 in DMMGSolveSNES (dmmg=0x8a2b6b0, level=0) at
>>>> damgsnes.c:510
>>>> #17 0x08117029 in DMMGSolve (dmmg=0x8a2b6b0) at damg.c:313
>>>> #18 0x08052ecc in Solve (dmmg=0x8a2b6b0) at twgcqt2unffnictv.c:679
>>>> #19 0x0804def5 in main (argc=Cannot access memory at address 0x189d
>>>> ) at twgcqt2unffnictv.c:303
>>>>
>>>>
>>>> Same things happened to ex25.c from
>>>>
>>>>
>>>> http://www.mcs.anl.gov/petsc/petsc-as/snapshots/petsc-current/src/snes/examples/tutorials/ex25.c.html
>>>>
>>>>
>>>> with
>>>>
>>>> ierr = DMMGSetSNES(dmmg,FormFunction,0);CHKERRQ(ierr);
>>>> // ierr =
>>>> DMMGSetSNESLocal(dmmg,FormFunctionLocal,0,ad_FormFunctionLocal,0);CHKERRQ(ierr);
>>>>
>>>>
>>>> Thanks a lot!
>>>>
>>>> Rebecca
>>>>
>>>>
>>>>
>>>>
>>>> Quoting Jed Brown <jed at 59A2.org>:
>>>>
>>>> On Wed, 24 Mar 2010 15:41:38 -0400, "(Rebecca) Xuefei YUAN" <
>>>>> xy2102 at columbia.edu> wrote:
>>>>>
>>>>>> Hi,all,
>>>>>>
>>>>>> I have an error from
>>>>>>
>>>>>> ierr = DAGlobalToLocalBegin(dafield,X,INSERT_VALUES,localFIELD);
>>>>>> CHKERRQ(ierr);
>>>>>>
>>>>>> where
>>>>>>
>>>>>> ierr = DMMGSetSNES(dmmg, FormFunction,0);CHKERRQ(ierr); is used for
>>>>>> set up the SNES.
>>>>>>
>>>>>> So I check up the vector size of X, F, localFIELD where
>>>>>> ierr = DAGetLocalVector(dafield,&localFIELD);CHKERRQ(ierr);
>>>>>> PetscInt nlocalFIELD,nX,nF;
>>>>>> ierr = VecGetSize(localFIELD,&nlocalFIELD);CHKERRQ(ierr);
>>>>>> ierr = VecGetSize(X,&nX);CHKERRQ(ierr);
>>>>>> ierr = VecGetSize(F,&nF);CHKERRQ(ierr);
>>>>>> ierr = DAGlobalToLocalBegin(dafield,X,INSERT_VALUES,localFIELD);
>>>>>> CHKERRQ(ierr);
>>>>>> ierr =
>>>>>> DAGlobalToLocalEnd(dafield,X,INSERT_VALUES,localFIELD);CHKERRQ(ierr);
>>>>>> ierr =
>>>>>> DAVecGetArray(dafield,localFIELD,&localfield);CHKERRQ(ierr);
>>>>>>
>>>>>>
>>>>>> (gdb) disp nX
>>>>>> 1: nX = 120
>>>>>> (gdb) disp nF
>>>>>> 2: nF = 120
>>>>>> (gdb) disp nlocalFIELD
>>>>>> 3: nlocalFIELD = 100
>>>>>>
>>>>>
>>>>> Is this run in parallel? Note that the sizes of X and F are global,
>>>>> while localFIELD is serial. What error did you get?
>>>>>
>>>>>
>>>>> Matt, it's clearly FormFunction and not FormFunctionLocal because the
>>>>> function prototype has the SNES.
>>>>>
>>>>> Jed
>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>> --
>>>> (Rebecca) Xuefei YUAN
>>>> Department of Applied Physics and Applied Mathematics
>>>> Columbia University
>>>> Tel:917-399-8032
>>>> www.columbia.edu/~xy2102
>>>>
>>>>
>>>
>>>
>>> --
>>> 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
>>>
>>
>>
>>
>> --
>> (Rebecca) Xuefei YUAN
>> Department of Applied Physics and Applied Mathematics
>> Columbia University
>> Tel:917-399-8032
>> www.columbia.edu/~xy2102
>>
--
(Rebecca) Xuefei YUAN
Department of Applied Physics and Applied Mathematics
Columbia University
Tel:917-399-8032
www.columbia.edu/~xy2102
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