H5Part development and discussion

[Quincey Koziol <koziol AT hdfgroup.org>]

Hi Mark,
        Sorry for the delay on this, I've been busy with a proposal.

        Mohamad, can you take a look into this and see about addressing it, 
if its an actual memory leak?

        Thanks,
                Quincey

On May 2, 2012, at 7:05 AM, Mark Howison wrote:

> Hi Stefan, sorry I didn't get back to you sooner about this. I did take a 
> look at the H5PartWriteDataFloat64 call, and as far as I can tell, the leak 
> you are seeing is coming from deeper in the HDF5 library. I've cc'ed 
> Quincey, who can hopefully have someone at the HDF Group look into this. 
> I'm guessing that H5MM_xstrdup is returning a malloc'd string to H5P_remove 
> that isn't being free'd. 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
>> 
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>