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

[Romain Jolivet]

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

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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
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On Nov 4, 2014, at 20: 00, cig-short-request at geodynamics.org wrote:

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>   1. Re: Follow up on hdf5 issue while compiling (Brad Aagaard)
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> ----------------------------------------------------------------------
> 
> 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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