[Python-cgns-main] Fwd: Re: PythonCGNS

[Oliver B. <oli...@we...>]

-------- Original-Nachricht --------
Betreff: 	Re: [Python-cgns-main] PythonCGNS
Datum: 	Tue, 29 Jan 2013 09:18:28 +0100
Von: 	Lionel Gamet <Lio...@fl...>
An: 	Jorge Sancho Ponce <j.s...@uq...>
Kopie (CC): 	Oliver Borm <oli...@we...>



On 01/29/2013 01:28 AM, Jorge Sancho Ponce wrote:
> Hello Lionel,
>
> Sorry for my late replay and thank you for your kind attention. 
> Following your indications I definitely think is a problem of linking 
> to my hdf5 library. I will investigate why it did not link it properly.
> I have opensuse in this machine, so certainly rpms for that will help.

Dear Jorge,

Here are some rpms for SLES11 SP2 that should work on OpenSuse (not 
tested !!).
Otherwise, just recompile them for your machine. I have joined our RPMS 
public key
(rpm --import RPM-GPG-KEY-FLUOREM) as our packages are signed.

You will need to have HDF5 installed on your machine. We have used HDF5 
1.8.9
on our SLES11 SP2 machine (so that you need exactly the same HDF5 
version if you
want to install our binary packages).

The cgns source package (cgns-3.1.3-4.2.sles11.fluorem.src.rpm) can 
create both
HDF5 or ADF versions of the binary cgns package. Same thing for the 
python bind.

To re-compile on your machine, say you want the HDF5 version, you can 
type :

rpmbuild --rebuild --define "dist .opensuse12" --with hdf5 
cgns-3.1.3-4.2.sles11.fluorem.src.rpm

You need to install the generated cgns packages in order to recompile 
the python binding :

rpm -Uv /usr/src/packages/RPMS/x86_64/cgns-hdf5-*

Then you can recompile the python binding (requires swig) :

rpmbuild --rebuild --define "dist .opensuse12" --with hdf5 
python-cgns-0.3-3.sles11.fluorem.src.rpm

And install the generated package.

That's it,
"Have fun"

Best regards

Lionel


>
> again thank you and best regards
> jorge
> ------------------------------------------------------------------------
> *From:* Lionel Gamet [Lio...@fl...]
> *Sent:* Tuesday, January 22, 2013 6:17 PM
> *To:* Jorge Sancho Ponce
> *Cc:* Oliver Borm
> *Subject:* Re: [Python-cgns-main] PythonCGNS
>
> On 01/21/2013 06:50 PM, Oliver Borm wrote:
>> Hi,
>>
>> well I have not yet used the pythonCGNS module with cgns v3.0. So I 
>> can only guess, that the cgns library (so file) is compiled with hdf5 
>> support but not linked to the hdf5 library itself. Thus there are 
>> missing symbols.  So either you link the cgns library itself to the 
>> hdf5 library, or you link the pythonCGNS module library additionally 
>> against the hdf5 library. Therefore you'll need to adapt the setup.py 
>> file. Try to change the following item in line 48
>>
>> libraries=["cgns","hdf5"]
>>
>> This is not tested, so maybe the syntax or the library is different. 
>> Please report any success or failure to the mailing list.
>
>
> Hi
>
> Thanks for reporting the problem.
>
> Are you using RPM based distributions ? If yes, I could provide
> you with CGNS and python-CGNS rpms if you are interested.
> We have been using python-CGNS with CGNS 3 without any problem
> for quite a while.
> I never took some time to communicate these rpms to the Web...
> (and CGNS spec file is not included in the python-CGNS sourceforge)
> but I know I should !
>
> But, as it has been mentioned by Oliver, you have to compile the CGNS
> library with linking against HDF5. So, if you type "ldd libcgns.so",
> you should see a dependence against HDF5, like this :
>
> >ldd /usr/lib64/cgns/lib/libcgns.so
>         linux-vdso.so.1 =>  (0x00007fffbeb7c000)
>         libhdf5.so.7 => /usr/lib64/libhdf5.so.7 (0x00007f31cb315000)
>         libc.so.6 => /lib64/libc.so.6 (0x00007f31caf82000)
>         libz.so.1 => /lib64/libz.so.1 (0x00007f31cad6c000)
>         libm.so.6 => /lib64/libm.so.6 (0x00007f31caae7000)
>         /lib64/ld-linux-x86-64.so.2 (0x000000395fe00000)
>
> Best regards
>
> Lionel
>
>>
>> Thx,
>> Oliver
>>
>> Am 15.01.2013 03:28, schrieb Jorge Sancho Ponce:
>>> Hello Oliver,
>>>
>>> First thank you for leading python-cgns code, which is very useful 
>>> for us to import our meshes into 
>>> Eilmer3(http://www.mech.uq.edu.au/cfcfd/eilmer3.html).
>>>
>>> Python-cgnslinked with cgns version 2.5 worked correctly, but now 
>>> with 3.1 and hdf5 give us this error when executing the tutorials:
>>>
>>> "ImportError: /usr/local/lib/libcgns.so.3.1: undefined symbol: 
>>> H5T_NATIVE_SCHAR_g"
>>>
>>> Seems that cgns library works ok by itself, since runs tests in hdf5 
>>> format. Sorry for our lack of knowledge, do you know where this 
>>> error may be pointing?
>>>
>>>
>>> thank you very much
>>> jorge sancho
>>> postgraduate student
>>> Centre for hypersonics, UQ
>>
>>
>>
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>