[CIG-SHORT] CIG-SHORT Digest, Vol 98, Issue 3

[Brad Aagaard]

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:
>
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>> 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
>>
>>
>>
>>
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>> End of CIG-SHORT Digest, Vol 98, Issue 3
>> ****************************************
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