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Subject: Re: Octave/HDF5 library/header mismatch
To: cygwin AT cygwin DOT com
References: <93d9b19e-d234-b2db-65be-e65f828a9df6 AT photonicinnovations DOT com> <6d5164b3-75e6-e7c0-1095-3e61363bd9fa AT gmail DOT com>
From: Gavin King <gavin DOT king AT photonicinnovations DOT com>
Message-ID: <391d5f0b-aebc-71a0-2287-8010dd4f108b@photonicinnovations.com>
Date: Thu, 23 Jun 2016 11:11:18 +1200
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On 21/06/2016 9:03 p.m., Marco Atzeri wrote:
> On 21/06/2016 06:20, Gavin King wrote:

>> Reverting the package libhdf5_10 from the current version 1.8.17-1 to
>> the previous version 1.8.16-1 means that octave 4.0.1-1 can save the
>> workspace.
>>
>> So: workaround: revert libhdf5_10 to 1.8.16-1. Presumably, the current
>> version of octave was compiled at an inopportune point; I don't think
>> this is something that I can remedy myself, is it?
>
> the official workaround is mentioned on the warning message
>
> "You can, at your own risk, disable this warning by setting the
> environment variable 'HDF5_DISABLE_VERSION_CHECK' to a value of '1'.
> Setting it to 2 or higher will suppress the warning messages totally.
> Headers are 1.8.16, library is 1.8.17"
>
> so if you use, before running octave
>
>   export HDF5_DISABLE_VERSION_CHECK=1
>
> you will still see the warning but the action will be completed
>
>   export HDF5_DISABLE_VERSION_CHECK=2
>
> will suppress also the warning.
>

That is slightly scary, since the warning says "Data corruption or 
segmentation faults may occur if the application continues." Segfaults 
aside, the prospect of data corruption is unpleasant.

>
>> I think this is the correct place to report this to; it isn't a problem
>> per se with the individual programs, but with the way they're packed
>> together. I think. Do correct me if I am wrong; I'm a bit new to this
>> whole business.
>>
>
> It is the right place.
> This problem is clearly a hdf5 upstream problem and a questionable
> design choice.
>
> I am following with them
>
> https://lists.hdfgroup.org/pipermail/hdf-forum_lists.hdfgroup.org/2016-June/009564.html
>
Thanks for looking further into it, and for you advice. I'll follow this 
progress with interest, since I use octave and cygwin rather extensively.

yours

Gavin

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