[petsc-users] valgrind errors.

[(Rebecca) Xuefei YUAN]

Dear Jed,

I found the source of these uninitialised values.

In my FormFunction(), there is a user-defined structure called  
FieldOther and I will use this as a temp values to build up my  
residual function. The main loop is like:


typedef struct {
	PetscReal	x1,x2,x3,x4;
} FieldOther;

#undef __FUNCT__
#define __FUNCT__ "FormFunction"
PetscErrorCode FormFunction(SNES snes,Vec X,Vec F,void*dummg)
{
// ...
	FieldOther		*fieldother;
// ...
	PetscFunctionBegin;
// ...
	ierr =  
PetscMalloc(sizeof(PetscReal)*(info.mx)*(info.my)*sizeof(FieldOther),  
&fieldother);CHKERRQ(ierr);
// ...
     for (j = jFirst; j <= jLast; j++){
         for (i = iFirst; i <= iLast; i++){
                 fieldother[(i)+(j)*(info.mx)].x1 = 0;
                 fieldother[(i)+(j)*(info.mx)].x2 = 0;
                 fieldother[(i)+(j)*(info.mx)].x3 = 0;
                 fieldother[(i)+(j)*(info.mx)].x4 = 0;
		}
	}
// ...
     for (j = jFirst; j <= jLast; j++){
         for (i = iFirst; i <= iLast; i++){
// errors coming out from valgrind if fieldother[] is used in residual  
function evaluation.
//			ffield[j][i].x1 = fieldother[(i)+(j)*(info.mx)].x1;
// everything looks fine from valgrind if fieldother[] is not used in  
residual function evaluation.
			ffield[j][i].x1 = field[j][i].x1;
		}
	}
// ...
	ierr = PetscFree(fieldother);CHKERRQ(ierr);
// ...
	PetscFunctionReturn(0);

}

If I will use those fieldother[] in my residual evaluation functions,  
errors from valgrind come out like:

==24486==
==24486== Conditional jump or move depends on uninitialised value(s)
==24486==    at 0x4024D9B: memcpy (mc_replace_strmem.c:482)
==24486==    by 0x41F6387: __printf_fp (in /lib/tls/i686/cmov/libc-2.7.so)
==24486==    by 0x41F1563: vfprintf (in /lib/tls/i686/cmov/libc-2.7.so)
==24486==    by 0x41F5581: ??? (in /lib/tls/i686/cmov/libc-2.7.so)
==24486==    by 0x41F1229: vfprintf (in /lib/tls/i686/cmov/libc-2.7.so)
==24486==    by 0x8643996: PetscVFPrintfDefault (mprint.c:193)
==24486==    by 0x85F3F00: PetscViewerASCIIMonitorPrintf (filev.c:988)
==24486==    by 0x80C814A: SNESMonitorDefault (snesut.c:150)
==24486==    by 0x80E0450: SNESSolve_LS (ls.c:173)
==24486==    by 0x80C199F: SNESSolve (snes.c:2221)
==24486==    by 0x80DA4A0: DMMGSolveSNES (damgsnes.c:510)
==24486==    by 0x80D3CDF: DMMGSolve (damg.c:372)
==24486==  Uninitialised value was created by a heap allocation
==24486==    at 0x4022BF3: malloc (vg_replace_malloc.c:195)
==24486==    by 0x864BAFC: PetscMallocAlign (mal.c:40)
==24486==    by 0x864CBEB: PetscTrMallocDefault (mtr.c:194)
==24486==    by 0x8055FB8: FormFunction (twgcqt2unff.c:941)
==24486==    by 0x80B86A4: SNESComputeFunction (snes.c:1016)
==24486==    by 0x80DFFC2: SNESSolve_LS (ls.c:159)
==24486==    by 0x80C199F: SNESSolve (snes.c:2221)
==24486==    by 0x80DA4A0: DMMGSolveSNES (damgsnes.c:510)
==24486==    by 0x80D3CDF: DMMGSolve (damg.c:372)
==24486==    by 0x804F539: Solve (twgcqt2unff.c:437)
==24486==    by 0x804DC92: main (twgcqt2unff.c:283)

FormFunction (twgcqt2unff.c:941) is located at the line of

	ierr =  
PetscMalloc(sizeof(PetscReal)*(info.mx)*(info.my)*sizeof(FieldOther),  
&fieldother);CHKERRQ(ierr);

I think I did give values of those fieldother and free them after  
usage, but why this uninitialised message comes out all the time?

Thanks very much!

Rebecca


Quoting Jed Brown <jed at 59A2.org>:

> On Mon, 18 Jan 2010 16:32:22 -0500, "(Rebecca) Xuefei YUAN"   
> <xy2102 at columbia.edu> wrote:
>> Dear Jed,
>>
>> I got some origins, but I still do not understand what is going on here?
>>
>> Here is a piece of uninitialised value from
>
> I think you have an indexing error while reading from this local vector
> in your residual evaluation.  The contents of the array are explicitly
> initialized to zero in VecCreate_Seq, but when memalign is not available
> (your trace indicates this is so) PetscMallocAlign allocate a little
> extra space and aligns the result, leaving a few bytes uninitialized
> (memory further away may also be uninitialized, but this error isn't
> saying complaining about those places).
>
> Jed
>
>



-- 
(Rebecca) Xuefei YUAN
Department of Applied Physics and Applied Mathematics
Columbia University
Tel:917-399-8032
www.columbia.edu/~xy2102