Hi Dominik,
On Wed, Sep 14, 2011 at 07:55:55PM +0200, Dominik Szczerba wrote:
> I am reproducibly getting the following message from valgrind:
>
> ==20888== Conditional jump or move depends on uninitialised value(s)
> ==20888== at 0x52C7510: inflateReset2 (in
> /lib/x86_64-linux-gnu/libz.so.1.2.3.4)
> ==20888== by 0x52C7605: inflateInit2_ (in
> /lib/x86_64-linux-gnu/libz.so.1.2.3.4)
> ==20888== by 0x5019C13: H5Z_filter_deflate (H5Zdeflate.c:110)
> ==20888== by 0x5019170: H5Z_pipeline (H5Z.c:1103)
> ==20888== by 0x4E9CB69: H5D_chunk_lock (H5Dchunk.c:2758)
> ==20888== by 0x4E9DB20: H5D_chunk_read (H5Dchunk.c:1728)
> ==20888== by 0x4EACDDA: H5D_read (H5Dio.c:447)
> ==20888== by 0x4EAD248: H5Dread (H5Dio.c:173)
> ==20888== by 0x4CAD1D: HDF5::HDF5Reader::readData(std::string
> const&) (HDF5Reader.cxx:634)
> ==20888== by 0x4CA489: HDF5::HDF5Reader::read(std::vector<int,
> std::allocator<int> >&, std::string const&) (HDF5Reader.cxx:527)
> ==20888== by 0x4C379E: CD3T10_USER::SetupConstraints()
> (cd3t10mpi_main.cxx:404)
> ==20888== by 0x4B6B7A: CD3T10::Solve() (CD3T10mpi.cxx:692)
> ==20888== by 0x4C0095: main (cd3t10mpi_main.cxx:589)
>
> My own code HDF5Reader.cxx:634 reads:
>
> status = H5Dread(dataset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL,
> H5P_DEFAULT, (int*)data);
>
> I write my arrays several times, the message comes up only at the first use.
>
> Any hints how to fix are highly appreciated.
According to the top-most lines this looks to me as if it's
coming from libz, which in turn is used by HDF5. Thus the
people to fix it would be the libz maintainers. I just down-
loaded the newest version (1.25, you seem to still be using
1.2.3.4) and there's an entry in the ChangeLog file for the
version 1.2.3.7:
Avoid access of uninitialized data for first inflateReset2
call [Gomes]
This sounds quite a bit as if it may be the fix for the prob-
lem you encountered. So I would recomment that you update to
at least version 1.2.3.7 and test if valgrind's complaint goes
away if you use the newer libz version instead.
Regards, Jens
--
\ Jens Thoms Toerring ________ [email protected]
\_______________________________ http://toerring.de
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