Hi Bojan --
The crash is not happening in DataSet::p_read_fixed_len. I tried a
bunch of things with Binh-Minh Ribler, but we were unable to resolve
it, but here's a summary. The crash is in DataSet::p_read_variable_len
on the line with:
strg = strg_C;
The error is a double free on strg:
Python(10981) malloc: *** error for object 0x104010820: pointer being
freed was not allocated
*** set a breakpoint in malloc_error_break to debug
[amosa:10981] *** Process received signal ***
[amosa:10981] Signal: Abort trap: 6 (6)
[amosa:10981] Signal code: (0)
[amosa:10981] [ 0] 2 libsystem_c.dylib
0x00007fff8ce3bcfa _sigtramp + 26
[amosa:10981] [ 1] 3 libhdf5.7.dylib
0x00000001042ec3f1 H5S_select_hyperslab + 1393
[amosa:10981] [ 2] 4 libsystem_c.dylib
0x00007fff8ce3984c free + 389
[amosa:10981] [ 3] 5 libstdc++.6.dylib
0x00007fff8c8f3702 _ZNSs4_Rep10_M_disposeERKSaIcE + 60
[amosa:10981] [ 4] 6 libstdc++.6.dylib
0x00007fff8c8f4aab _ZNSs9_M_mutateEmmm + 281
[amosa:10981] [ 5] 7 libstdc++.6.dylib
0x00007fff8c8f4b2d _ZNSs15_M_replace_safeEmmPKcm + 37
[amosa:10981] [ 6] 8 libhdf5_cpp.7.dylib
0x000000010414af90 _ZNK2H57DataSet19p_read_variable_lenEiiiiRSs + 1316
[amosa:10981] [ 7] 9 libhdf5_cpp.7.dylib
0x000000010414d5ea
_ZNK2H57DataSet4readERSsRKNS_8DataTypeERKNS_9DataSpaceES7_RKNS_19DSetMemXferPropListE
+ 1286
The problem does not occur in a standalone unit test I made (and there
is no problem on linux or osx 10.6). This implies the problem could be
somewhere else in the rest of my code, but unfortunately valgrind
doesn't work on osx 10.7 yet (and no problems have been detected on
other machines). However, I can make the problem go away if I
initialize the std::string in my code before calling DataSet::read:
H5::StrType st(H5::PredType::C_S1, H5T_VARIABLE);
H5::DataSet dataset;
Vector_string conf(dims[0]);
#if __ENVIRONMENT_MAC_OS_X_VERSION_MIN_REQUIRED__ >= 1070
conf[j] = "hack to avoid crash";
#endif
dataset.read(conf[j],st,mem_space,file_space);
Doing a google search on the error message itself along with a few
keywords revealed this:
http://stackoverflow.com/questions/1962685/xcode-stl-c-debug-compile-error
and other similar posts, problems which I am able to replicate, and
sets a precedent for the problem being with the compiler itself. OSX
10.7 in general has seemed somewhat buggy too...
Amos.
On Wed, Sep 28, 2011 at 3:48 AM, Bojan Nikolic <[email protected]> wrote:
>
> I haven't had the time to test this hypothesis but looking at the HDF5
> C++ wrapping code it looks like it may not be terminating the string
> before converting to C++ std::string if the H5Dread doesn't do that by
> itself for some reason. Maybe worth trying this patch?
>
>
> *** hdf5-1.8.7/c++/src/H5DataSet-fix.cpp 2011-09-28 11:44:09.000000000
> +0100
> --- hdf5-1.8.7/c++/src/H5DataSet.cpp 2011-04-20 22:23:08.000000000
> +0100
> ***************
> *** 721,729 ****
> throw DataSetIException("DataSet::read", "H5Dread failed for fixed
> length string");
> }
>
> - // Terminate the string
> - strg_C[attr_size]=0;
> -
> // Get string from the C char* and release resource allocated locally
> strg = strg_C;
> delete []strg_C;
> --- 721,726 ----
>
>
> --
> Bojan Nikolic || http://www.bnikolic.co.uk
>
>
> _______________________________________________
> Hdf-forum is for HDF software users discussion.
> [email protected]
> http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
>
--
~<>~<>~<>~<>~<>~<>~<>~<>~
Amos G. Anderson
+1-626-399-8958 (cell)
_______________________________________________
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