Hi Anton,
On Mar 17, 2010, at 6:37 PM, Anton Kulchitsky wrote:
>
> I have got the following diagnostics when run my program with
> valgrind. This was generated by H5Dwrite call on array of compound
> types. Maybe somebody is familiar with this? It does not seem right!
> When I remove writing call, everything is fine.
If you are going to use valgrind (or another memory checking tool, like
Purify), you should configure the HDF5 distribution with the
--enable-using-memchecker flag.
Quincey
> Anton
>
>
> ==15272== Memcheck, a memory error detector.
> ==15272== Copyright (C) 2002-2007, and GNU GPL'd, by Julian Seward et al.
> ==15272== Using LibVEX rev 1732, a library for dynamic binary translation.
> ==15272== Copyright (C) 2004-2007, and GNU GPL'd, by OpenWorks LLP.
> ==15272== Using valgrind-3.2.3, a dynamic binary instrumentation framework.
> ==15272== Copyright (C) 2000-2007, and GNU GPL'd, by Julian Seward et al.
> ==15272== For more details, rerun with: -v
> ==15272==
> filename: haha003.h5
> ==15272== Syscall param write(buf) points to uninitialised byte(s)
> ==15272== at 0x5607420: __write_nocancel (in /lib64/libc-2.6.so)
> ==15272== by 0x5164FDC: H5FD_sec2_write (in
> /export/staffdata/kulchits/usr/lib/libhdf5.so.6.0.3)
> ==15272== by 0x515EA82: H5FD_write (in
> /export/staffdata/kulchits/usr/lib/libhdf5.so.6.0.3)
> ==15272== by 0x514DEE8: H5F_block_write (in
> /export/staffdata/kulchits/usr/lib/libhdf5.so.6.0.3)
> ==15272== by 0x5126BDC: H5D_flush_sieve_buf (in
> /export/staffdata/kulchits/usr/lib/libhdf5.so.6.0.3)
> ==15272== by 0x511F8E1: H5D_contig_flush (in
> /export/staffdata/kulchits/usr/lib/libhdf5.so.6.0.3)
> ==15272== by 0x5126A49: H5D_flush_real (in
> /export/staffdata/kulchits/usr/lib/libhdf5.so.6.0.3)
> ==15272== by 0x5127E89: H5D_close (in
> /export/staffdata/kulchits/usr/lib/libhdf5.so.6.0.3)
> ==15272== by 0x51B3EC8: H5I_dec_ref (in
> /export/staffdata/kulchits/usr/lib/libhdf5.so.6.0.3)
> ==15272== by 0x5112B5D: H5Dclose (in
> /export/staffdata/kulchits/usr/lib/libhdf5.so.6.0.3)
> ==15272== by 0x400FE1: dsio_save_astruct_1d (dsio.nw:235)
> ==15272== by 0x40138F: main (dsio.nw:501)
> ==15272== Address 0x412830C is 12 bytes inside a block of size 65,544 alloc'd
> ==15272== at 0x4C1F996: malloc (vg_replace_malloc.c:149)
> ==15272== by 0x516840B: H5FL_malloc (in
> /export/staffdata/kulchits/usr/lib/libhdf5.so.6.0.3)
> ==15272== by 0x5168B6C: H5FL_blk_malloc (in
> /export/staffdata/kulchits/usr/lib/libhdf5.so.6.0.3)
> ==15272== by 0x51207A7: H5D_contig_writevv (in
> /export/staffdata/kulchits/usr/lib/libhdf5.so.6.0.3)
> ==15272== by 0x5130C24: H5D_select_io (in
> /export/staffdata/kulchits/usr/lib/libhdf5.so.6.0.3)
> ==15272== by 0x5130EEC: H5D_select_write (in
> /export/staffdata/kulchits/usr/lib/libhdf5.so.6.0.3)
> ==15272== by 0x511F94C: H5D_contig_write (in
> /export/staffdata/kulchits/usr/lib/libhdf5.so.6.0.3)
> ==15272== by 0x512CD20: H5Dwrite (in
> /export/staffdata/kulchits/usr/lib/libhdf5.so.6.0.3)
> ==15272== by 0x400F6C: dsio_save_astruct_1d (dsio.nw:212)
> ==15272== by 0x40138F: main (dsio.nw:501)
> ==15272==
> ==15272== ERROR SUMMARY: 1 errors from 1 contexts (suppressed: 5 from 1)
> ==15272== malloc/free: in use at exit: 0 bytes in 0 blocks.
> ==15272== malloc/free: 2,199 allocs, 2,199 frees, 821,653 bytes allocated.
> ==15272== For counts of detected errors, rerun with: -v
> ==15272== All heap blocks were freed -- no leaks are possible.
>
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