[petsc-users] A question of DMPlexGetAdjacency

[leejearl]

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)
[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

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All: cavity
CFLAGS	        =
FFLAGS	        =
CPPFLAGS        =
FPPFLAGS        =
LOCDIR          = ./
EXAMPLESC       = cavity.c
MANSEC          = DM

include ${PETSC_DIR}/lib/petsc/conf/variables
include ${PETSC_DIR}/lib/petsc/conf/rules

cavity: cavity.o  chkopts
	-${CLINKER} -o cavity cavity.o ${PETSC_DM_LIB}
	${RM} -f cavity.o

#--------------------------------------------------------------------------

include ${PETSC_DIR}/lib/petsc/conf/test