[CIG-SHORT] hdf5 issue while compiling
Romain Jolivet
rjolivet at caltech.edu
Wed Nov 5 01:40:50 PST 2014
Please find the config.log file attached.
Does not work with lines removed/correclty commented…
R
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On 4 Nov 2014, at 22:34, cig-short-request at geodynamics.org wrote:
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> Today's Topics:
>
> 1. Re: hdf5 issue while compiling (Matthew Knepley)
> 2. Re: CIG-SHORT Digest, Vol 98, Issue 3 (Romain Jolivet)
> 3. Re: CIG-SHORT Digest, Vol 98, Issue 3 (Brad Aagaard)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 4 Nov 2014 21:41:15 +0000
> From: Matthew Knepley <knepley at mcs.anl.gov>
> To: "cig-short at geodynamics.org" <cig-short at geodynamics.org>
> Subject: Re: [CIG-SHORT] hdf5 issue while compiling
> Message-ID:
> <CAMYG4GmDZAUYCAygb02++3Tr80pwWA7Cbr_AdQVEbnxJH8PfCw at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> On Tue, Nov 4, 2014 at 2:45 PM, Romain Jolivet <rjolivet at caltech.edu> wrote:
>
>> Dear Brad et al.,
>>
>> I compiled pylith using the installer on an iMac (brand new), running Mac
>> os X 10.9 (not Yosemite, Mavericks).
>> As things were not going that smoothly, I decided to enable every options
>> available with the installer, but not gcc (I have gcc4.9 from macports).
>>
>> When compiling hdf5, it stops, saying:
>>
>> ../../../hdf5-1.8.11/tools/lib/h5tools_dump.c:635:9: error: expected
>> expression before '/' token
>> //HGOTO_ERROR(dimension_break, H5E_tools_min_id_g, "Could not
>> allocate buffer for ptdata?);
>>
>
> It looks like they used a C99 comment, but your compiler does not like it.
> Delete the line and try again is the
> easiest option.
>
> Thanks,
>
> Matt
>
>
>> The compiler used is mpicc (given what the Makefile says) that has been
>> compiled using the pylith installer.
>>
>> Any idea?
>> Cheers,
>> Romain
>>
>>
>> ?????????????????????????????????????
>> ?????????????????????????????????????
>> Romain Jolivet
>> Postdoctoral Fellow
>>
>> University of Cambridge
>> Department of Earth Sciences
>> Bullard Labs
>> Madingley Rise
>> Madingley Road
>> Cambridge CB3 0EZ
>> United Kingdom
>>
>> email: rpj29 at cam.ac.uk
>> Phone: +44 1223 748 938
>> Mobile: +44 7596 703 148
>>
>> France: +33 6 52 91 76 39
>> US: +1 (626) 560 6356
>> ?????????????????????????????????????
>> ?????????????????????????????????????
>>
>>
>>
>>
>>
>> _______________________________________________
>> CIG-SHORT mailing list
>> CIG-SHORT at geodynamics.org
>> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
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>
>
>
> --
> What most experimenters take for granted before they begin their
> experiments is infinitely more interesting than any results to which their
> experiments lead.
> -- Norbert Wiener
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> ------------------------------
>
> Message: 2
> Date: Tue, 4 Nov 2014 22:32:00 +0000
> From: Romain Jolivet <rjolivet at caltech.edu>
> To: cig-short at geodynamics.org
> Subject: Re: [CIG-SHORT] CIG-SHORT Digest, Vol 98, Issue 3
> Message-ID: <55DDBBFB-7A56-4FF9-908D-C5612D1BB659 at caltech.edu>
> Content-Type: text/plain; charset="us-ascii"
>
> Using gcc4.7 does not change anything, although it does accept the // way of commenting (must be a change in standards between 4.8 and 4.9).
> I am using the git version of pylith (main branch, nothing fancy).
> I will send you the config.log file tomorrow, but I did not specify anything more than enabling all options for configure.
> Also, I can try with the tarballs tomorrow morning.
>
> Cheers,
> R
>
> ----------------------------------------------------------------
> !!!!!! ADDRESS CHANGED!!!!!!
> ----------------------------------------------------------------
> Romain Jolivet
> Postdoctoral Fellow
>
> University of Cambridge
> Department of Earth Sciences
> Bullard Laboratories
> Madingley Road,
> Cambridge, CB3 0EZ,
> United Kingdom
>
> email: rpj29 at cam.ac.uk
> Phone: +44 7 596 703 148
> Phone (Fr): +33 7 52 91 76 39
> ----------------------------------------------------------------
> ----------------------------------------------------------------
>
> On Nov 4, 2014, at 20: 00, cig-short-request at geodynamics.org wrote:
>
>> Send CIG-SHORT mailing list submissions to
>> cig-short at geodynamics.org
>>
>> To subscribe or unsubscribe via the World Wide Web, visit
>> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>> or, via email, send a message with subject or body 'help' to
>> cig-short-request at geodynamics.org
>>
>> You can reach the person managing the list at
>> cig-short-owner at geodynamics.org
>>
>> When replying, please edit your Subject line so it is more specific
>> than "Re: Contents of CIG-SHORT digest..."
>>
>>
>> Today's Topics:
>>
>> 1. Re: Follow up on hdf5 issue while compiling (Brad Aagaard)
>>
>>
>> ----------------------------------------------------------------------
>>
>> Message: 1
>> Date: Tue, 4 Nov 2014 08:17:05 -0800
>> From: Brad Aagaard <baagaard at usgs.gov>
>> To: <cig-short at geodynamics.org>
>> Subject: Re: [CIG-SHORT] Follow up on hdf5 issue while compiling
>> Message-ID: <5458FC01.2080108 at usgs.gov>
>> Content-Type: text/plain; charset="windows-1252"; format=flowed
>>
>> On 11/04/2014 07:52 AM, Romain Jolivet wrote:
>>> Dear Brad et al.,
>>>
>>> Following my previous email:
>>> I compiled pylith using the installer on an iMac (brand new), running Mac os X
>>> 10.9 (not Yosemite, Mavericks).
>>> As things were not going that smoothly, I decided to enable every options
>>> available with the installer, but not gcc (I have gcc4.9 from macports).
>>>
>>> When compiling hdf5, it stops, saying:
>>>
>>> ../../../hdf5-1.8.11/tools/lib/h5tools_dump.c:635:9: error: expected expression
>>> before '/' token
>>> //HGOTO_ERROR(dimension_break, H5E_tools_min_id_g, "Could not allocate
>>> buffer for ptdata?);
>>>
>>> The compiler used is mpicc (given what the Makefile says) that has been compiled
>>> using the pylith installer.
>>>
>>> I went inside the hdf5 code and modified the way comment were implemented at a
>>> few places, replacing // by the classic /* */.
>>> It compiled, but this small issue must hide something bigger because the tests
>>> fail in pylith due to some hdf5 opening problem in pets (see testmeshio.log file
>>> attached).
>>
>>
>> This is a clear HDF5 bug. C files should use C style comments /* */, not
>> C++ style comments //. Your fix is correct. I am not sure why gcc 4.8.2
>> let this pass when I built HDF5.
>>
>>> The tests that fail are in unittests/libtests/meshio
>>> It also fails when running the 2d subduction examples and any other example that
>>> writes hdf5 outputs.
>>>
>>> Any idea? In the mean time, I will try with the 4.7 version of gcc from MacPorts
>>> (faster to install than the one from the installer),
>>
>> What are the config arguments to the PyLith installer? I want to know if
>> you are using the tarballs or repositories for PETSc and PyLith. If
>> using the repositories, what branches are you using?
>>
>> Brad
>>
>>
>>
>>
>> ------------------------------
>>
>> _______________________________________________
>> CIG-SHORT mailing list
>> CIG-SHORT at geodynamics.org
>> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>>
>> End of CIG-SHORT Digest, Vol 98, Issue 3
>> ****************************************
>
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> ------------------------------
>
> Message: 3
> Date: Tue, 4 Nov 2014 14:34:35 -0800
> From: Brad Aagaard <baagaard at usgs.gov>
> To: <cig-short at geodynamics.org>
> Subject: Re: [CIG-SHORT] CIG-SHORT Digest, Vol 98, Issue 3
> Message-ID: <5459547B.5010705 at usgs.gov>
> Content-Type: text/plain; charset="ISO-8859-1"; format=flowed
>
> Romain,
>
> Yes, please send your complete configure arguments, so I can try to
> replicate the error.
>
> Brad
>
>
> On 11/4/14, 2:32 PM, Romain Jolivet wrote:
>> Using gcc4.7 does not change anything, although it does accept the //
>> way of commenting (must be a change in standards between 4.8 and 4.9).
>> I am using the git version of pylith (main branch, nothing fancy).
>> I will send you the config.log file tomorrow, but I did not specify
>> anything more than enabling all options for configure.
>> Also, I can try with the tarballs tomorrow morning.
>>
>> Cheers,
>> R
>>
>> ----------------------------------------------------------------
>> !!!!!! ADDRESS CHANGED!!!!!!
>> ----------------------------------------------------------------
>> Romain Jolivet
>> Postdoctoral Fellow
>>
>> University of Cambridge
>> Department of Earth Sciences
>> Bullard Laboratories
>> Madingley Road,
>> Cambridge, CB3 0EZ,
>> United Kingdom
>>
>> email: rpj29 at cam.ac.uk <mailto:rpj29 at cam.ac.uk>
>> Phone: +44 7 596 703 148
>> Phone (Fr): +33 7 52 91 76 39
>> ----------------------------------------------------------------
>> ----------------------------------------------------------------
>>
>> On Nov 4, 2014, at 20: 00, cig-short-request at geodynamics.org
>> <mailto:cig-short-request at geodynamics.org> wrote:
>>
>>> Send CIG-SHORT mailing list submissions to
>>> cig-short at geodynamics.org <mailto:cig-short at geodynamics.org>
>>>
>>> To subscribe or unsubscribe via the World Wide Web, visit
>>> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>>> or, via email, send a message with subject or body 'help' to
>>> cig-short-request at geodynamics.org
>>>
>>> You can reach the person managing the list at
>>> cig-short-owner at geodynamics.org
>>>
>>> When replying, please edit your Subject line so it is more specific
>>> than "Re: Contents of CIG-SHORT digest..."
>>>
>>>
>>> Today's Topics:
>>>
>>> 1. Re: Follow up on hdf5 issue while compiling (Brad Aagaard)
>>>
>>>
>>> ----------------------------------------------------------------------
>>>
>>> Message: 1
>>> Date: Tue, 4 Nov 2014 08:17:05 -0800
>>> From: Brad Aagaard <baagaard at usgs.gov>
>>> To: <cig-short at geodynamics.org>
>>> Subject: Re: [CIG-SHORT] Follow up on hdf5 issue while compiling
>>> Message-ID: <5458FC01.2080108 at usgs.gov>
>>> Content-Type: text/plain; charset="windows-1252"; format=flowed
>>>
>>> On 11/04/2014 07:52 AM, Romain Jolivet wrote:
>>>> Dear Brad et al.,
>>>>
>>>> Following my previous email:
>>>> I compiled pylith using the installer on an iMac (brand new), running
>>>> Mac os X
>>>> 10.9 (not Yosemite, Mavericks).
>>>> As things were not going that smoothly, I decided to enable every options
>>>> available with the installer, but not gcc (I have gcc4.9 from macports).
>>>>
>>>> When compiling hdf5, it stops, saying:
>>>>
>>>> ../../../hdf5-1.8.11/tools/lib/h5tools_dump.c:635:9: error: expected
>>>> expression
>>>> before '/' token
>>>> //HGOTO_ERROR(dimension_break, H5E_tools_min_id_g, "Could
>>>> not allocate
>>>> buffer for ptdata?);
>>>>
>>>> The compiler used is mpicc (given what the Makefile says) that has
>>>> been compiled
>>>> using the pylith installer.
>>>>
>>>> I went inside the hdf5 code and modified the way comment were
>>>> implemented at a
>>>> few places, replacing // by the classic /* */.
>>>> It compiled, but this small issue must hide something bigger because
>>>> the tests
>>>> fail in pylith due to some hdf5 opening problem in pets (see
>>>> testmeshio.log file
>>>> attached).
>>>
>>>
>>> This is a clear HDF5 bug. C files should use C style comments /* */, not
>>> C++ style comments //. Your fix is correct. I am not sure why gcc 4.8.2
>>> let this pass when I built HDF5.
>>>
>>>> The tests that fail are in unittests/libtests/meshio
>>>> It also fails when running the 2d subduction examples and any other
>>>> example that
>>>> writes hdf5 outputs.
>>>>
>>>> Any idea? In the mean time, I will try with the 4.7 version of gcc
>>>> from MacPorts
>>>> (faster to install than the one from the installer),
>>>
>>> What are the config arguments to the PyLith installer? I want to know if
>>> you are using the tarballs or repositories for PETSc and PyLith. If
>>> using the repositories, what branches are you using?
>>>
>>> Brad
>>>
>>>
>>>
>>>
>>> ------------------------------
>>>
>>> _______________________________________________
>>> CIG-SHORT mailing list
>>> CIG-SHORT at geodynamics.org
>>> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>>>
>>> End of CIG-SHORT Digest, Vol 98, Issue 3
>>> ****************************************
>>
>>
>>
>> _______________________________________________
>> CIG-SHORT mailing list
>> CIG-SHORT at geodynamics.org
>> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>>
>
>
>
> ------------------------------
>
> _______________________________________________
> CIG-SHORT mailing list
> CIG-SHORT at geodynamics.org
> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>
> End of CIG-SHORT Digest, Vol 98, Issue 4
> ****************************************
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