[petsc-users] A question of DMPlexGetAdjacency

[Matthew Knepley]

On Tue, Nov 15, 2016 at 6:07 AM, leejearl <leejearl at 126.com> wrote:

> Hi, Matt:
>     Thank you for your kind reply. Since it is a low level routine, is
> there any method which I can used for creating a
> dynamic array?
>

I am not sure what you are asking for?

  Thanks,

    Matt


>     Thanks
> leejearl
>
> On 2016年11月15日 16:20, Matthew Knepley wrote:
>
> On Tue, Nov 15, 2016 at 1:00 AM, leejearl <leejearl at 126.com> wrote:
>
>> Hi Lawrence:
>>
>>     Thank you for your prompt reply.  It works well, but I encounter
>> another problem.
>>
>>  The code is as follows:
>>
>>         PetscScalar *arrayConVar, *arrayDeltaX, *arrayDeltaY;
>>
>>         ierr = DMPlexGetAdjacency(dm, c, &adjSize, &adj); CHKERRQ(ierr);
>>
>>         /*PetscSynchronizedPrintf(PETSC_COMM_WORLD, "adjSize = %d\n",
>> adjSize);*/
>>         adjSizeInterior = -1;
>>         for(i = 0; i < adjSize; i++)
>>         {
>>             if(adj[i] < cEndInterior)
>>             {
>>                 adjSizeInterior++;
>>                 /*PetscSynchronizedPrintf(PETSC_COMM_WORLD, "adj[%d]=
>> %d\n", i, adj[i]);*/
>>             }
>>         }
>>         /*
>>         PetscSynchronizedPrintf(PETSC_COMM_WORLD, "adjSizeInterior =
>> %d\n", adjSizeInterior);
>>         PetscSynchronizedFlush(PETSC_COMM_WORLD,PETSC_STDOUT);
>>         */
>>
>>         ierr = PetscMalloc3(adjSizeInterior*4, &arrayConVar,
>> adjSizeInterior, &arrayDeltaX, adjSizeInterior, &arrayDeltaY);
>> CHKERRQ(ierr);
>>
>>         PetscFree3(arrayConVar, arrayDeltaX, arrayDeltaY); CHKERRQ(ierr);
>>         ierr = PetscFree(adj); CHKERRQ(ierr);
>>
>> The error messages are like as :
>>
>> [0]PETSC ERROR: --------------------- Error Message
>> --------------------------------------------------------------
>> [0]PETSC ERROR: Petsc has generated inconsistent data
>> [0]PETSC ERROR: Invalid mesh exceeded adjacency allocation (0)
>>
>
> You are resetting the size to 0 in your loop. It needs to be set to
> PETSC_DETERMINE.
>
> This is a very low level routine with complicated memory management for
> efficiency. It is not intended for
> most user code. However, here is an example:
>
>   https://bitbucket.org/petsc/petsc/src/f98bafe09724ec53686c21e51e969e
> 41f10d977b/src/dm/impls/plex/plexdistribute.c?at=master&
> fileviewer=file-view-default#plexdistribute.c-570
>
>   Thanks,
>
>      Matt
>
>
>> [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html
>> for trouble shooting.
>> [0]PETSC ERROR: Petsc Development GIT revision: v3.7.4-1864-ga10654c  GIT
>> Date: 2016-11-01 22:25:06 -0500
>> [0]PETSC ERROR: ./cavity on a arch-linux2-c-debug named leejearl by
>> leejearl Tue Nov 15 14:48:57 2016
>> [0]PETSC ERROR: Configure options --prefix=/home/leejearl/Install/Petsc
>> --with-mpi-dir=/home/leejearl/Install/openmpi/1.8.5_gnu
>> --download-exodusii=../externalpackages/exodus-5.24.tar.bz2
>> --download-netcdf=../externalpackages/netcdf-4.3.2.tar.gz
>> --download-hdf5=../externalpackages/hdf5-1.8.12.tar.gz
>> --download-triangle=../externalpackages/Triangle.tar.gz
>> --download-sowing=../externalpackages/git.sowing.tar.gz
>> [0]PETSC ERROR: #1 DMPlexGetAdjacency_Cone_Internal() line 193 in
>> /home/leejearl/Software/petsc/petsc/src/dm/impls/plex/plexdistribute.c
>> [0]PETSC ERROR: #2 DMPlexGetAdjacency_Internal() line 298 in
>> /home/leejearl/Software/petsc/petsc/src/dm/impls/plex/plexdistribute.c
>> [0]PETSC ERROR: #3 DMPlexGetAdjacency() line 372 in
>> /home/leejearl/Software/petsc/petsc/src/dm/impls/plex/plexdistribute.c
>> [0]PETSC ERROR: #4 CalcConVarGradient() line 126 in
>> /home/leejearl/Desktop/PETSc/GKSCavity_Petsc/cavity.c
>>
>> It is very strange that PetscMalloc3 can arouse such an error. If I
>> comment the statement relative with PetscMalloc3, it is ok! I can not
>> understand what happened.
>>
>> Can anyone figure me out the problems of my codes?
>>
>> I attach the code and the grid, so you can compile in your workstation.
>>
>> Thanks
>>
>> leejearl
>>
>>
>> On 2016年11月14日 23:09, Lawrence Mitchell wrote:
>>
>>> On 14 Nov 2016, at 14:59, leejearl <leejearl at 126.com> wrote:
>>>>
>>>> Hi all:
>>>>
>>>>     I am not sure the using of the function "DMPlexGetAdjacency".
>>>>
>>>>     My codes are as follows:
>>>>
>>>>     PetscInt adj, *adjSize=NULL;
>>>>
>>>>     ierr = DMPlexGetAdjacency(dm, p,  &adj, &adj);
>>>>
>>>
>>> Your calling sequence is wrong:
>>>
>>> PetscInt adjSize;
>>> PetscInt *adj = NULL;
>>>
>>> ierr = DMPlexGetAdjacency(dm, p, &adjSize, &adj); CHKERRQ(ierr);
>>>
>>> adjSize is now the size of the adj array.  You should remember to free
>>> it afterwards:
>>>
>>> /* use adj here *
>>> ...
>>>
>>> ierr = PetscFree(adj); CHKERRQ(ierr);
>>>
>>> Lawrence
>>>
>>
>>
>
>
> --
> 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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