[Hdf-forum] User-defined filter parameter parsing broken in h5repack?

Elvis Stansvik elvis.stansvik at orexplore.com
Mon Aug 22 08:47:16 CDT 2016


2016-08-22 15:09 GMT+02:00 Bálint Balázs <bluqesh at gmail.com>:

> Hi Elvis,
>
> I also had this problem a few weeks ago on Windows 7, both version 1.8.15
> and 1.8.17. I managed to fix it in version 1.8.17, it was indeed in
> h5repack_parse.c, as you suspected. Please find attached the corrected
> file, hopefully if will work with 1.8.16 as well.
>

Thanks a lot for sharing Balint.

I haven't built HDF5 myself, but using the Ubuntu package, and it seems
it's not so easy to just recompile the h5repack tool. But I might try a
full build of HDF5 at some point. Your corrected h5repack_parse.c will most
probably work fine.

Did you report the issue to the HDF5 maintainers, and do you know if it
will be fixed in a future version?

Elvis


>
> Balint
>
>
>
> 2016-08-22 14:43 GMT+02:00 <hdf-forum-request at lists.hdfgroup.org>:
>
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>>    1. Re: HDF5 running on ARM V 7 (Gerd Heber)
>>    2. Re: User-defined filter parameter parsing broken in h5repack?
>>       (Elvis Stansvik)
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>> Message: 2
>> Date: Mon, 22 Aug 2016 14:42:21 +0200
>> From: Elvis Stansvik <elvis.stansvik at orexplore.com>
>> To: HDF Users Discussion List <hdf-forum at lists.hdfgroup.org>
>> Subject: Re: [Hdf-forum] User-defined filter parameter parsing broken
>>         in h5repack?
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>> 2016-08-22 14:21 GMT+02:00 Andrea Bedini <andrea at andreabedini.com>:
>>
>> > I can reproduce on OS X, same version of HDF5. Compiling the library
>> with
>> > --enable-debug and getting the trace (HDF5_DEBUG=?trace?) shows the
>>
>> > following call:
>> >
>> > H5Pset_filter(plist=167772178 (genprop list), filter=42, flags=0,
>> > cd_nelmts=2, cd_values=0x7fff50f2b10c {2, 2}) = SUCCEED;
>> >
>> > So I bet it's a bug in h5repack.
>> >
>>
>> Thanks for testing Andrea. Yes I'm pretty sure it's a parsing bug. The
>> parsing code in tools/h5repack/h5repack_parse.c looks pretty gnarly and I
>> haven't fully understood it yet. But I suspect it might be ignoring
>> anything past the first user parameter, so anything I'm seeing past that
>> is
>> just uninialized memory.. not sure though.
>>
>> Elvis
>>
>>
>> > Andrea
>> >
>> >
>> > > On 22 Aug 2016, at 4:18 PM, Elvis Stansvik <
>> elvis.stansvik at orexplore.com>
>> > wrote:
>> > >
>> > > 2016-08-22 10:16 GMT+02:00 Elvis Stansvik <
>> elvis.stansvik at orexplore.com>
>> > :
>> > > Consider the attached noop_plugin.c. It contains a dynamically loaded
>> > filter plugin, with filter number 42, which does nothing except print
>> out
>> > the received `cd_values` array in the filter function.
>> > >
>> > > Build the test plugin (on *NIX) with `make`.
>> > >
>> > > Then test the following:
>> > >
>> > > estan at newton:~/noop_plugin$ HDF5_PLUGIN_PATH=. h5repack -f UD=42,1,1
>> > input.hdf5 output.hdf5
>> > > 1
>> > > estan at newton:~/noop_plugin$ HDF5_PLUGIN_PATH=. h5repack -f
>> UD=42,2,1,2
>> > input.hdf5 output.hdf5
>> > > 2 2
>> > > estan at newton:~/noop_plugin$
>> > >
>> > > Notice how in the second invokation (with UD=42,2,1,2), the cd_values
>> > contains { 2, 2 }, despite { 1, 2 } being passed on the command line.
>> > >
>> > > I forgot to say: This was with HDF5 1.8.16 on Ubuntu 16.04.
>> > >
>> > > Elvis
>> > >
>> > >
>> > > Has anyone seen this strangeness before, or can reproduce?
>> > >
>> > > Thanks in advance,
>> > > Elvis Stansvik
>> > >
>> > > _______________________________________________
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>> >
>> > --
>> > Andrea Bedini
>> > @andreabedini, http://www.andreabedini.com
>> >
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>> >
>> >
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