[petsc-users] A question of DMPlexGetAdjacency

[leejearl]

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?
     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 
> <mailto: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/f98bafe09724ec53686c21e51e969e41f10d977b/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
>     <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
>             <mailto: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

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