[petsc-users] valgrind errors.

[Barry Smith]

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

     This line is wrong, but is not the cause of the problem.  
sizeof(FieldOther) takes into account the size of the real values  
inside so you do not need the sizeof(PetscReal)*

   What are iFirst and iLast? If they are not 0 then you indexing into  
fieldother[] wrong since that array starts at 0.

    Barry

On Jan 19, 2010, at 11:24 AM, (Rebecca) Xuefei YUAN wrote:

> 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
>