valgrind question

[Satish Balay]

On Thu, 22 Jan 2009, Boyce Griffith wrote:

> Hi, Folks --
> 
> I am trying to track down a bug in some of my code using Valgrind 3.4.0.  I'm
> using OpenMPI 1.3, which directly integrates with Valgrind. Unfortunately, I
> have not completed the process of transitioning my code from PETSc 2.3.3 to
> 3.0.0, so these runs are using PETSc 2.3.3-p15.
> 
> Running my code with Valgrind, I get a number of errors like the following:
> 
> Invalid read of size 8
>    at 0x6104C8F: UnPack_1 (vpscat.c:421)
>    by 0x61047A4: VecScatterEnd_1 (vpscat.h:150)
>    by 0x6133B2B: VecScatterEnd (vscat.c:1564)
>    by 0xC6A258: IBTK::LDataManager::endDataRedistribution(int, int)
> (LDataManager.C:1200)
>    by 0xA0AEF2: IBAMR::IBStaggeredHierarchyIntegrator::regridHierarchy()
> (IBStaggeredHierarchyIntegrator.C:1196)
>    by 0xA0CF53:
> IBAMR::IBStaggeredHierarchyIntegrator::advanceHierarchy(double)
> (IBStaggeredHierarchyIntegrator.C:653)
>    by 0x7308C4: main (main.C:798)
>  Address 0xa66bfd0 is 496 bytes inside a block of size 528 alloc'd
>    at 0x4A05FBB: malloc (vg_replace_malloc.c:207)
>    by 0x63DCFAF: PetscMallocAlign (mal.c:40)
>    by 0x63EA8A0: PetscTrMallocDefault (mtr.c:194)
>    by 0x611BDB2: VecScatterCreate_PtoS (vpscat.c:1570)
>    by 0x6121252: VecScatterCreate_StoP (vpscat.c:1946)
>    by 0x6122D2D: VecScatterCreate_PtoP (vpscat.c:2123)
>    by 0x6131B08: VecScatterCreate (vscat.c:1380)
>    by 0xC6960F: IBTK::LDataManager::endDataRedistribution(int, int)
> (LDataManager.C:1158)
>    by 0xA0AEF2: IBAMR::IBStaggeredHierarchyIntegrator::regridHierarchy()
> (IBStaggeredHierarchyIntegrator.C:1196)
>    by 0xA0CF53:
> IBAMR::IBStaggeredHierarchyIntegrator::advanceHierarchy(double)
> (IBStaggeredHierarchyIntegrator.C:653)
>    by 0x7308C4: main (main.C:798)
> 
> Has anyone seen this kind of error crop up before?  Does it indicate that I am
> messing up the call to VecScatterCreate?  (This VecScatter is being used to
> scatter data between ghosted Vecs, and I wouldn't be shocked if I have made a
> dumb mistake.)  Could Valgrind be returning a false positive?

Most likely valgrind is correct here. However its a challenge
determining where exactly the bug is - that is causing this behavior..

Checking ScatterCreate() and ScatterBegin() - and making sure that
same vector [or dupes] are specified to these routines is a start...

It is also possible that there was some other memory corruption much
earlier than this piece of code that valgrind couldn't detect [so
there is some garage already in some arrays]. And this garbage is now
causing bad memory access - thus this error.

Satish

> 
> Again, this is with PETSc 2.3.3-p15.  I am working on getting things up and
> running with PETSc 3.0.0.
> 
> Thanks!
> 
> -- Boyce
>