X-Recipient: archive-cygwin AT delorie DOT com
DomainKey-Signature: a=rsa-sha1; c=nofws; d=sourceware.org; h=list-id
	:list-unsubscribe:list-subscribe:list-archive:list-post
	:list-help:sender:subject:to:references:from:message-id:date
	:mime-version:in-reply-to:content-type
	:content-transfer-encoding; q=dns; s=default; b=NkVd2Jkq3+hcMTkM
	7lfxgj06m7jdA0fyvSI+w1H3uJMjhIL61Dzgc0DP/sbeiNjQ1OV0MB3Qnhr0uDfe
	Wm3cDd+Kue4GYG6+o254fFIQXvWwLSXxIER+5XfuvNqcrdB162stYg/jTR+vjnXz
	GER5Eo2rSWpS8B/d59d5iSNnBbk=
DKIM-Signature: v=1; a=rsa-sha1; c=relaxed; d=sourceware.org; h=list-id
	:list-unsubscribe:list-subscribe:list-archive:list-post
	:list-help:sender:subject:to:references:from:message-id:date
	:mime-version:in-reply-to:content-type
	:content-transfer-encoding; s=default; bh=PsHTBD94unxZM4qp5HdFqf
	PLEuk=; b=eDDzKid706VGCLbb/NSmaeQqPrihSir22DXuJkMRpxXmtR6Wx/Hhfl
	tspvHO2VNPijoY8uJDOzNEcQGnUEPvP03gVI6ghaAwVCfjHtkdueP6UxS/iMyPU7
	ft5OvUab0L6r13wbhknrlp1oxYipwWyA5VgFt1eFnsNslYH/UC2UA=
Mailing-List: contact cygwin-help AT cygwin DOT com; run by ezmlm
List-Id: <cygwin.cygwin.com>
List-Subscribe: <mailto:cygwin-subscribe AT cygwin DOT com>
List-Archive: <http://sourceware.org/ml/cygwin/>
List-Post: <mailto:cygwin AT cygwin DOT com>
List-Help: <mailto:cygwin-help AT cygwin DOT com>, <http://sourceware.org/ml/#faqs>
Sender: cygwin-owner AT cygwin DOT com
Mail-Followup-To: cygwin AT cygwin DOT com
Delivered-To: mailing list cygwin AT cygwin DOT com
Authentication-Results: sourceware.org; auth=none
X-Virus-Found: No
X-Spam-SWARE-Status: No, score=-2.3 required=5.0 tests=AWL,BAYES_00,FREEMAIL_FROM,RCVD_IN_DNSWL_LOW,SPF_PASS autolearn=ham version=3.3.2 spammy=Hx-languages-length:2241, H*MI:sk:391d5f0, H*f:sk:391d5f0, H*i:sk:391d5f0
X-HELO: mail-wm0-f52.google.com
X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed;        d=1e100.net; s=20130820;        h=x-gm-message-state:subject:to:references:from:message-id:date         :user-agent:mime-version:in-reply-to:content-transfer-encoding;        bh=j91d35UXQtSuglv9viAud5YcyObfL+h30kczNXlne8E=;        b=g+nqWmyq0JMZdBeDNAMeLZcxitC8e4pcQ/+f//lijREwXmEzG4J9xFGouzdgj4T1nj         osTsNb78YCVWh1SjQm+SpJjJGVg6+j5sfTW4BWkng00uTHzGnwx+Chm3yjZTH+g/knrE         r6eBXdFeIEFe2TmHu3SbKi7HgDbZwzbN/0998acRGJhbAu02NOBXnVMGYs8KBIGOUrVj         YNll/Q7NcjtJItMbX9tUxJSzN0dO4503hsKKembp9pVgdSoS1VyhFFfeJm7AdiGkqjmJ         aKTSJ6J16yYt/sJOInDsJCy9bQq/3JJJr/fwrRw+NgKs/FsoNrmfqmbQhDWvNPho86qq         Ym8Q==
X-Gm-Message-State: ALyK8tJjT45WGvR4hvSDt4EdK0nIUaask+N9vBo6aDhjHXoyGCWSPgQD0qeqEGJS535/Fw==
X-Received: by 10.28.141.4 with SMTP id p4mr13245828wmd.46.1466677758435;        Thu, 23 Jun 2016 03:29:18 -0700 (PDT)
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
User-Agent: Mozilla/5.0 (Windows NT 6.1; WOW64; rv:45.0) Gecko/20100101 Thunderbird/45.1.1
MIME-Version: 1.0
In-Reply-To: <391d5f0b-aebc-71a0-2287-8010dd4f108b@photonicinnovations.com>
Content-Type: text/plain; charset=windows-1252; format=flowed
Content-Transfer-Encoding: 7bit
X-IsSubscribed: yes

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

--
Problem reports:       http://cygwin.com/problems.html
FAQ:                   http://cygwin.com/faq/
Documentation:         http://cygwin.com/docs.html
Unsubscribe info:      http://cygwin.com/ml/#unsubscribe-simple