[gmx-developers] uninitialized data

[David van der Spoel]

Alexander Herz wrote:
> of course it must be
> 
>  memset(fr,0,sizeof(t_forcerec)); 
> 
> as fr is a pointer

snew does this.

> 
> Alex
> 
> Alexander Herz schrieb:
>> There appears to be a problem with uninitialized data that might affact
>> the shifted virial and other things:
>>
>> in md.c the following code creates the forcerec:
>>
>>     fr = mk_forcerec();
>>     init_forcerec(fplog,fr,fcd,inputrec,mtop,cr,box,FALSE,
>>           opt2fn("-table",nfile,fnm),opt2fn("-tablep",nfile,fnm),
>>           opt2fn("-tableb",nfile,fnm),FALSE,pforce);
>>     fr->bSepDVDL = ((Flags & MD_SEPPOT) == MD_SEPPOT);
>>
>>
>> where mk_forcerec() contains:
>>
>> t_forcerec *mk_forcerec(void)
>> {
>>   t_forcerec *fr;
>>  
>>   snew(fr,1);
>>
>>     //!!!!!!missing :     memset(fr,0,sizeof(fr));
>>   return fr;
>> }
>>
>> and init_forcerec() contains:
>> ...
>>     if (fr->fshift == NULL)
>>         snew(fr->fshift,SHIFTS);
>>    
>>     if (fr->nbfp == NULL) {
>>         fr->ntype = mtop->ffparams.atnr;
>>         fr->bBHAM = (mtop->ffparams.functype[0] == F_BHAM);
>>         fr->nbfp  = mk_nbfp(&mtop->ffparams,fr->bBHAM);
>>     }
>> ...
>>
>> Without the missing memset I added as a comment to mk_forcerec,
>> fr->fshift may contain anything
>> and might therefore not be initialized. Valgrind also complains about this.
>>
>> I have not yet had the time to see if this affects the shifted virial
>> problems I reported the other day.
>> I'll look at that tomorrow!
>>
>> Alex
>>
>>
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> 
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-- 
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se