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 SZ 1.4.6-beta #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 SZ 1.4.6-beta #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 SZ 1.4.8-beta #2: 0x00007fff20342720 libsystem_c.dylibabort + 120 frame #3: 0x00007fff20223430 libsystem_malloc.dylibmalloc_vreport + 548
    frame confusing libtool error when fortran compiler is not present #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 unable to build from github checkout #6: 0x00000001008b79dd libhdf5.200.dylibH5Z_pipeline + 2797 frame #7: 0x00000001002a07f2 libhdf5.200.dylibH5D__chunk_flush_entry + 1922
    frame user manual: 2d array dimension example error? #8: 0x0000000100298da8 libhdf5.200.dylibH5D__chunk_flush + 536 frame #9: 0x00000001002e7ea8 libhdf5.200.dylibH5D__flush_real + 616
    frame error larger than abs error param on linear data #10: 0x00000001002e6c96 libhdf5.200.dylibH5D_close + 502 frame #11: 0x0000000100897bd7 libhdf5.200.dylibH5VL__native_dataset_close + 391
    frame fortran build no longer works #12: 0x0000000100862ecf libhdf5.200.dylibH5VL__dataset_close + 703 frame #13: 0x0000000100862af0 libhdf5.200.dylibH5VL_dataset_close + 832
    frame Fix for very pedantic compiler in external build #14: 0x00000001002f297b libhdf5.200.dylibH5D__close_cb + 475 frame #15: 0x00000001004c1911 libhdf5.200.dylibH5I_dec_ref + 401
    frame Possible to have incorrect numbers with PW_REL? #16: 0x00000001004c15f5 libhdf5.200.dylibH5I_dec_app_ref + 181 frame #17: 0x00000001004c1aa5 libhdf5.200.dylibH5I_dec_app_ref_always_close + 181
    frame C++ compatibility for TightDataPointStorageI.h #18: 0x000000010028052d libhdf5.200.dylibH5Dclose + 877 frame #19: 0x000000010000fa9e h5repackdo_copy_objects + 14510
    frame various cleanups and GPU code. #20: 0x000000010000b5d0 h5repackcopy_objects + 8416 frame #21: 0x0000000100004685 h5repackh5repack + 101
    frame Seg fault when calling SZ_Init_Params #22: 0x000000010000191d h5repackmain + 413 frame #23: 0x00007fff2040a621 libdyld.dylibstart + 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 <#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 <#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 <#2>: 0x00007fff20342720 libsystem_c.dylibabort + 120 frame #3: 0x00007fff20223430 libsystem_malloc.dylibmalloc_vreport + 548 frame #4 <#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 <#6>: 0x00000001008b79dd libhdf5.200.dylibH5Z_pipeline + 2797 frame #7: 0x00000001002a07f2 libhdf5.200.dylibH5D__chunk_flush_entry + 1922 frame #8 <#8>: 0x0000000100298da8 libhdf5.200.dylibH5D__chunk_flush + 536 frame #9: 0x00000001002e7ea8 libhdf5.200.dylibH5D__flush_real + 616 frame #10 <#10>: 0x00000001002e6c96 libhdf5.200.dylibH5D_close + 502 frame #11: 0x0000000100897bd7 libhdf5.200.dylibH5VL__native_dataset_close + 391 frame #12 <#12>: 0x0000000100862ecf libhdf5.200.dylibH5VL__dataset_close + 703 frame #13: 0x0000000100862af0 libhdf5.200.dylibH5VL_dataset_close + 832 frame #14 <#14>: 0x00000001002f297b libhdf5.200.dylibH5D__close_cb + 475 frame #15: 0x00000001004c1911 libhdf5.200.dylibH5I_dec_ref + 401 frame #16 <#16>: 0x00000001004c15f5 libhdf5.200.dylibH5I_dec_app_ref + 181 frame #17: 0x00000001004c1aa5 libhdf5.200.dylibH5I_dec_app_ref_always_close + 181 frame #18 <#18>: 0x000000010028052d libhdf5.200.dylibH5Dclose + 877 frame #19: 0x000000010000fa9e h5repackdo_copy_objects + 14510 frame #20 <#20>: 0x000000010000b5d0 h5repackcopy_objects + 8416 frame #21: 0x0000000100004685 h5repackh5repack + 101 frame #22 <#22>: 0x000000010000191d h5repackmain + 413 frame #23: 0x00007fff2040a621 libdyld.dylibstart + 1 — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#73>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACK3KSPWHCS533O2BYUEFRDTZXJWFANCNFSM5BA6L2YA> .