[FLASH-USERS] Big Problem??

[Carlo Graziani]

Hi Seyit.

Nathan's suggestion of investigating un-initialized variables use
and erratically allocated/deallocated memory is very sensible for
tracking down a problem that manifests itself as unpredictable behavior.

There is actually an open-source tool for doing this called valgrind.
It may already be installed on your local linux systems, and if not it
is easy enough to obtain.

One runs a program under valgrind very simply (the documentation gives
more options):

Prompt> valgrind <program-name> <program arguments>

Then one sits back and digests the potentially-voluminous output.

Valgrind will flag any access to uninitialized memory and memory-management
screw-ups.

Caveats are:  

(1) It's slow;

(2) You'd be amazed at how much valgrind finds distasteful in system
libraries.  You'll probably have to filter away a bunch of uninteresting
warnings about libc/mpi/hdf5 and so on (which are probably harmless,
and which you can't do much about anyway).  Valgrind has some facilities
for suppressing certain types of warnings, which you can use to cut down
the noise.

If you can make a small version of the problem, running on one processor, that
exhibits the erratic behavior, this would probably be an ideal case to
feed to valgrind.  There's some support for parallel debugging, but you'd probably
have to spend some quality time with documentation and haunt some other
mailing lists to get that running.

Cheers,

Carlo

Nathan Hearn wrote:
> Hi Seyit,
> 
>     An uninitialized variable is one that is declared (specified as
> integer, real, etc.), but not assigned a value.  Thus, an
> uninitialized variable usually has whatever value was in its memory
> location before it was declared.  (It could be a random number,
> "infinity," or just garbage.)  If this variable gets used before a
> value is assigned to it, strange behavior may result, which would be
> very compiler- and architecture-specific).  If you are using
> uninitialized pointer or allocatable variables, the effects can be
> quite drastic and hard to identify.
> 
>     Generally speaking, it is a good idea to assign a value to every
> variable soon after it is declared, even if it is only a temporary
> value that is not actually used.  (As I recall, there is a way to
> assign a null value to pointers, which is also a very useful
> practice.)
> 
> 
> - Nathan
> 
> 
> On 8/4/08, Seyit Hocuk <seyit at astro.rug.nl> wrote:
>> Hi Paul, hi Nathan,
>>
>> First of all; using --with-default-api-version=v16 when configuring
>> hdf5-1.8.1 works fine. Thanks for that Paul.
>>
>> Nathan, if you mean by uninitialized that the types are not defined
>> (like in config file REAL or INTEGER or whatever), then no because I
>> define them all. But if you mean I have included modules or parameters
>> which I don't use, that's correct and I am no expert in programming so
>> it might indeed be good to check this.
>>
>> Greetz,
>> Seyit


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Carlo Graziani                                 (773) 702-7973 (Voice)
Department of Astronomy and Astrophysics       (773) 702-6645 (FAX)
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