H5Part development and discussion

[Quincey Koziol <qkoziol AT gmail.com>]

Hi Mohamad,

On May 9, 2012, at 9:26 AM, Mohamad Chaarawi wrote:

> Hi All,
> 
>> I'm guessing that H5MM_xstrdup is returning a malloc'd string to 
>> H5P_remove that isn't being free'd.
> 
> The string is free'd again in H5P_close, so I don't see why a memory leak 
> would be possible there.

        Maybe the property list is internal to the h5part code and isn't 
being freed there?

        Mark, is that possible?

> Is there a short version of the code that I could use to work with and 
> replicate the problem, because just looking at the internal HDF5 library 
> doesn't get me anywhere :-)
> 
> Quincey,
> Could this be related to the memory leak discovered in the derived datatype 
> construction which you fixed and checked in the trunk and the 1_8_9 release 
> branch?

        Hmm, probably not...

        Quincey

> Thanks,
> Mohamad
> 
>> Thanks, Mark On May 2, 2012, at 7:47 AM, Stefan Adami wrote:
>>>> Dear H5Part-Developers,
>>>> 
>>>> I am using H5Part for my SPH simulation output and found recently a
>>>> problem when writing in parallel. To be more precise, I get a memory
>>>> leak when writing things in parallel. I checked the test-code you
>>>> provide in the test-folder and when adding the preproc-flag
>>>> -DPARALLEL_IO to the Makefile (by default --enable-parallel does not set
>>>> this correctly, the testf.f90 is actually compiled in serial version) I
>>>> can reproduce this memory leak:
>>>> 
>>>> 23 bytes in 1 blocks are definitely lost in loss record 13 of 20
>>>> ==9990==    at 0x4024F20: malloc (vg_replace_malloc.c:236)
>>>> ==9990==    by 0x811770C: H5MM_xstrdup (H5MM.c:170)
>>>> ==9990==    by 0x8153A47: H5P_remove (H5Pint.c:3932)
>>>> ==9990==    by 0x80BB1E3: H5FD_mpi_teardown_collective (H5FDmpi.c:525)
>>>> ==9990==    by 0x808F664: H5D_inter_collective_io (H5Dmpio.c:1511)
>>>> ==9990==    by 0x808DBA6: H5D_contig_collective_write (H5Dmpio.c:532)
>>>> ==9990==    by 0x808C06E: H5Dwrite (H5Dio.c:265)
>>>> ==9990==    by 0x804EF03: H5PartWriteDataFloat64 (H5Part.c:1134)
>>>> ==9990==    by 0x804C9F8: h5pt_writedata_r8_ (H5PartF.c:501)
>>>> ==9990==    by 0x804C196: MAIN__ (testf.F90:63)
>>>> ==9990==    by 0x804B563: main
>>>> (in /scratch/adami/source/ppm/work/H5Part-1.6.6/test/test
>>>> 
>>>> ==9990== LEAK SUMMARY:
>>>> ==9990==    definitely lost: 270 bytes in 12 blocks
>>>> ==9990==    indirectly lost: 0 bytes in 0 blocks
>>>> ==9990==      possibly lost: 0 bytes in 0 blocks
>>>> ==9990==    still reachable: 5,564 bytes in 8 blocks
>>>> ==9990==         suppressed: 0 bytes in 0 blocks
>>>> ==9990==
>>>> ==9990== For counts of detected and suppressed errors, rerun with: -v
>>>> ==9990== Use --track-origins=yes to see where uninitialised values come
>>>> from
>>>> ==9990== ERROR SUMMARY: 1060 errors from 191 contexts (suppressed: 29
>>>> from 10)
>>>> 
>>>> Is there a special compiler-adjustment required or anything else the
>>>> user should take care of? I tested this test-code on two different
>>>> machines with a 32 and 64bit system with the same result...
>>>> Do you have any ideas or are you aware of this leak?
>>>> 
>>>> Thank you very much for any help,
>>>> 
>>>> Stefan
>>>> 
>>>> -- 
>>>> ________________________________________
>>>> Dipl.-Ing. Stefan Adami
>>>> Lehrstuhl für Aerodynamik und Strömungsmechanik
>>>> Technische Universität München
>>>> Boltzmannstr. 15, 85748 Garching
>>>> Tel.: +49-89-289-16122
>>>> Fax.: +49-89-289-16139
>>>> http://www.aer.mw.tum.de
>>>> 
>>>> _______________________________________________
>>>> H5Part mailing list
>>>> H5Part AT lists.psi.ch
>>>> https://lists.web.psi.ch/mailman/listinfo/h5part
>