[petsc-users] configure error with netcdf

[fdkong]

>On Sep 9, 2012, at 12:02 PM, Satish Balay <balay at mcs.anl.gov> wrote:


>> On Sun, 9 Sep 2012, Barry Smith wrote:
> >
>> >
>> >On Sep 9, 2012, at 7:55 AM, Matthew Knepley <knepley at gmail.com> wrote:
>>> 
>>> >On Sun, Sep 9, 2012 at 12:31 AM, Satish Balay <balay at mcs.anl.gov> wrote:
>>>>> ncgentab.c:(.text+0x1e2): undefined reference to `yyunput'
>> >
>>  > Satish,
>>> 
>> >  Weird undefined symbols like yyunput are always a result of flex issues. 
>> >
>>   > Could you please make the same changes to netcdf.py that you made to the other package that used flex (which resolved the problem there).
>> 
> >In this case netcdf has its own configure - and does its own search for flex etc.
> >
>>>> >
> >checking for flex... flex
> >checking lex output file root... lex.yy
> >checking lex library... -lfl
> ><<<
> >
>> So the tools appear to be found. And I don't see them being used
> >further down [in configure.log].


  > Agreed. It seems some of the processing is lost; perhaps netcdf build tools do not properly display everything >they are doing


  > Note the use of .l files and the symbol yyunput which is very specific to flex. 
> 
> > So its not clear if 'missing flex'
> >is the cause of this error.


 >  Yes, it may not be a "missing" flex that is causing the problem but the problem is related flex, bison and all that >crap. Unfortunately if we cannot reproduce on a machine we have access to there is no way we can debug it.


I am not sure if  the error is the result of the "missing" flex, but when I used netcdf-4.1.3, instead of netcdf-4.1.1, the petsc worked well. Thus, Maybe there is a bug in the netcdf itself.


 >   Barry


> >
> 
> >And after my patch [with netcdf upgrade] - I have a successful build
> >of netcdf on rhel5 - even without flex/bison.
> >
> >However flex is needed for ptscotch anyway [so one would get an error
> >from ptscotch if flex is missing]
>> 
> >Satish







------------------
Fande Kong
ShenZhen Institutes of Advanced Technology
Chinese Academy of Sciences
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