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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> <391d5f0b-aebc-71a0-2287-8010dd4f108b AT photonicinnovations DOT com>
From:	Marco Atzeri <marco DOT atzeri AT gmail DOT com>
Message-ID:	<2b6a50ba-826c-1adc-fdad-d63bed58e084@gmail.com>
Date:	Thu, 23 Jun 2016 12:29:13 +0200
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On 23/06/2016 01:11, Gavin King wrote:
>
>
> 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 agree, but I suspect that the risk is strongly exagerated
in the warning.
hdf5 have a very poor policy on the matter.


>>> 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.

Nice to see I am not the only one using my packages.

As soon next netcdf is out, I will rebuild also octave
so that both are built with 1.8.17.


>
> yours
>
> Gavin

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