H5Part development and discussion

[Mark Howison <mhowison AT brown.edu>]

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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