h5repack pointer being freed was not allocated

[BinDong314]

Hello SZ, When to run the h5repack code and it failed with below error. Could anyone help to look it?

Thanks. Bin

h5repack(11138,0x10bd43e00) malloc: error for object 0x7f926e922030: pointer being freed was not allocated h5repack(11138,0x10bd43e00) malloc: set a breakpoint in malloc_error_break to debug ./h5repack.sh: line 12: 11138 Abort trap: 6 h5repack -f UD=32017,0 -i $inputFile -o $outputFile

When running it via lldb, it has below info.

% lldb h5repack (lldb) run -f UD=32017,0 -i testfloat_8_8_128.h5 -o testfloat_8_8_128_sz.h5 Process 11129 launched: '/Users/dbin/work/soft/hdf5-1.12.0/build/bin/h5repack' (x86_64) h5repack(11129,0x10013be00) malloc: error for object 0x101fbd030: pointer being freed was not allocated h5repack(11129,0x10013be00) malloc: set a breakpoint in malloc_error_break to debug Process 11129 stopped

• thread #1, queue = 'com.apple.main-thread', stop reason = signal SIGABRT frame #0: 0x00007fff203c1462 libsystem_kernel.dylib__pthread_kill + 10 libsystem_kernel.dylib__pthread_kill: -> 0x7fff203c1462 <+10>: jae 0x7fff203c146c ; <+20> 0x7fff203c1464 <+12>: movq %rax, %rdi 0x7fff203c1467 <+15>: jmp 0x7fff203bb6a1 ; cerror_nocancel 0x7fff203c146c <+20>: retq Target 0: (h5repack) stopped. (lldb) bt
• thread #1, queue = 'com.apple.main-thread', stop reason = signal SIGABRT
  • frame #0: 0x00007fff203c1462 libsystem_kernel.dylib__pthread_kill + 10 frame #1: 0x00007fff203ef610 libsystem_pthread.dylibpthread_kill + 263 frame #2: 0x00007fff20342720 libsystem_c.dylibabort + 120 frame #3: 0x00007fff20223430 libsystem_malloc.dylibmalloc_vreport + 548 frame #4: 0x00007fff202264c8 libsystem_malloc.dylibmalloc_report + 151 frame #5: 0x0000000101e861b2 libhdf5sz.soH5Z_filter_sz(flags=0, cd_nelmts=, cd_values=, nbytes=32768, buf_size=0x00007ffeefbfe378, buf=0x00007ffeefbfe420) at H5Z_SZ.c:0 [opt] frame #6: 0x00000001008b79dd libhdf5.200.dylibH5Z_pipeline + 2797 frame #7: 0x00000001002a07f2 libhdf5.200.dylibH5Dchunk_flush_entry + 1922 frame #8: 0x0000000100298da8 libhdf5.200.dylib`H5Dchunk_flush + 536 frame #9: 0x00000001002e7ea8 libhdf5.200.dylibH5D__flush_real + 616 frame #10: 0x00000001002e6c96 libhdf5.200.dylibH5D_close + 502 frame #11: 0x0000000100897bd7 libhdf5.200.dylibH5VL__native_dataset_close + 391 frame #12: 0x0000000100862ecf libhdf5.200.dylibH5VL__dataset_close + 703 frame #13: 0x0000000100862af0 libhdf5.200.dylibH5VL_dataset_close + 832 frame #14: 0x00000001002f297b libhdf5.200.dylibH5D__close_cb + 475 frame #15: 0x00000001004c1911 libhdf5.200.dylibH5I_dec_ref + 401 frame #16: 0x00000001004c15f5 libhdf5.200.dylibH5I_dec_app_ref + 181 frame #17: 0x00000001004c1aa5 libhdf5.200.dylibH5I_dec_app_ref_always_close + 181 frame #18: 0x000000010028052d libhdf5.200.dylibH5Dclose + 877 frame #19: 0x000000010000fa9e h5repackdo_copy_objects + 14510 frame #20: 0x000000010000b5d0 h5repackcopy_objects + 8416 frame #21: 0x0000000100004685 h5repackh5repack + 101 frame #22: 0x000000010000191d h5repackmain + 413 frame #23: 0x00007fff2040a621 libdyld.dylib`start + 1

[disheng222]

Hi, I noted that H5Z-SZ cannot work normally with hdf5-1.12.0. I tested other filters with hdf5-1.12.0, and they all work abnormally. For other filters, the compressed data have exactly the same size as the original .h5 data file, which obviously means that the filter was not called correctly. If I use the hdf5-1.10.x version, all filters (including H5Z-SZ) work very well. Could you use hdf5-1.10.x to try it again?

Best, Sheng

On Mon, Jul 26, 2021 at 4:47 PM dbinlbl @.***> wrote:

Hello SZ, When to run the h5repack code and it failed with below error. Could anyone help to look it? Thanks. Bin

h5repack(11138,0x10bd43e00) malloc: error for object 0x7f926e922030: pointer being freed was not allocated h5repack(11138,0x10bd43e00) malloc: set a breakpoint in malloc_error_break to debug ./h5repack.sh: line 12: 11138 Abort trap: 6 h5repack -f UD=32017,0 -i $inputFile -o $outputFile When running it via lldb, it has below info.

% lldb h5repack (lldb) run -f UD=32017,0 -i testfloat_8_8_128.h5 -o testfloat_8_8_128_sz.h5 Process 11129 launched: '/Users/dbin/work/soft/hdf5-1.12.0/build/bin/h5repack' (x86_64) h5repack(11129,0x10013be00) malloc: error for object 0x101fbd030: pointer being freed was not allocated h5repack(11129,0x10013be00) malloc: set a breakpoint in malloc_error_break to debug Process 11129 stopped

• thread #1 https://github.com/szcompressor/SZ/issues/1, queue = 'com.apple.main-thread', stop reason = signal SIGABRT frame #0: 0x00007fff203c1462 libsystem_kernel.dylibpthread_kill + 10 libsystem_kernel.dylibpthread_kill: -> 0x7fff203c1462 <+10>: jae 0x7fff203c146c ; <+20> 0x7fff203c1464 <+12>: movq %rax, %rdi 0x7fff203c1467 <+15>: jmp 0x7fff203bb6a1 ; cerror_nocancel 0x7fff203c146c <+20>: retq Target 0: (h5repack) stopped. (lldb) bt
• thread #1 https://github.com/szcompressor/SZ/issues/1, queue = 'com.apple.main-thread', stop reason = signal SIGABRT
  • frame #0: 0x00007fff203c1462 libsystem_kernel.dylib__pthread_kill
  • 10 frame #1: 0x00007fff203ef610 libsystem_pthread.dylibpthread_kill
  • 263 frame #2 https://github.com/szcompressor/SZ/issues/2: 0x00007fff20342720 libsystem_c.dylibabort + 120 frame #3: 0x00007fff20223430 libsystem_malloc.dylibmalloc_vreport + 548 frame #4 https://github.com/szcompressor/SZ/issues/4: 0x00007fff202264c8 libsystem_malloc.dylibmalloc_report + 151 frame

    5: 0x0000000101e861b2 libhdf5sz.soH5Z_filter_sz(flags=0,

    cd_nelmts=, cd_values=, nbytes=32768, buf_size=0x00007ffeefbfe378, buf=0x00007ffeefbfe420) at H5Z_SZ.c:0 [opt] frame #6 https://github.com/szcompressor/SZ/issues/6: 0x00000001008b79dd libhdf5.200.dylibH5Z_pipeline + 2797 frame #7: 0x00000001002a07f2 libhdf5.200.dylibH5Dchunk_flush_entry + 1922 frame #8 https://github.com/szcompressor/SZ/issues/8: 0x0000000100298da8 libhdf5.200.dylibH5Dchunk_flush + 536 frame

    9: 0x00000001002e7ea8 libhdf5.200.dylibH5D__flush_real + 616

    frame #10 https://github.com/szcompressor/SZ/issues/10: 0x00000001002e6c96 libhdf5.200.dylibH5D_close + 502 frame #11: 0x0000000100897bd7 libhdf5.200.dylibH5VLnative_dataset_close + 391 frame #12 https://github.com/szcompressor/SZ/issues/12: 0x0000000100862ecf libhdf5.200.dylibH5VLdataset_close + 703 frame

    13: 0x0000000100862af0 libhdf5.200.dylibH5VL_dataset_close + 832

    frame #14 https://github.com/szcompressor/SZ/pull/14: 0x00000001002f297b libhdf5.200.dylibH5D__close_cb + 475 frame #15: 0x00000001004c1911 libhdf5.200.dylibH5I_dec_ref + 401 frame #16 https://github.com/szcompressor/SZ/issues/16: 0x00000001004c15f5 libhdf5.200.dylibH5I_dec_app_ref + 181 frame

    17: 0x00000001004c1aa5 libhdf5.200.dylibH5I_dec_app_ref_always_close

  • 181 frame #18 https://github.com/szcompressor/SZ/pull/18: 0x000000010028052d libhdf5.200.dylibH5Dclose + 877 frame #19: 0x000000010000fa9e h5repackdo_copy_objects + 14510 frame #20 https://github.com/szcompressor/SZ/pull/20: 0x000000010000b5d0 h5repackcopy_objects + 8416 frame #21: 0x0000000100004685 h5repackh5repack + 101 frame #22 https://github.com/szcompressor/SZ/issues/22: 0x000000010000191d h5repackmain + 413 frame #23: 0x00007fff2040a621 libdyld.dylibstart + 1

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