Re: [Python-cgns-main] PythonCGNS

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Dear Lionel,

I had a modification of the LD_LIBRARY_PATH in my .bashrc that prevent python-cgns from finding the library. Now works perfecty!
Thank you very much, no doubt I could not be able to solve it without your and Oliver kind advice.

Best Regards
Jorge Sancho
________________________________
From: Lionel Gamet [Lio...@fl...]
Sent: Wednesday, January 30, 2013 6:08 PM
To: Jorge Sancho Ponce
Cc: Oliver Borm; pyt...@li...
Subject: Re: [Python-cgns-main] PythonCGNS

On 01/30/2013 08:47 AM, Jorge Sancho Ponce wrote:
Hello Lionel,

Thank you so much for the rpms, It is much more easy! .
Unfortunately the first try did not work since when doing (import CGNS) in python still complains with "ImportError: libcgns.so.3.1: cannot open shared object file: No such file or directory".

It is weird since the recompiling and installing process did not show any error or significant warning, and also the libcgns.so.3.1 exists in /usr/lib64/cgns as it should. I will investigate it tomorrow.

Dear Jorge,

Have you logged out of the shell where you typed the commands ?

For CGNS to be in your LD_LIBRARY_PATH, you need to source the file /etc/profile.d/cgns.sh.
This is automatically done when you exit your bash shell and re-login to a new bash shell.

Regards

Lionel

thank you very much!
jorge

________________________________
From: Lionel Gamet [Lio...@fl...<mailto:Lio...@fl...>]
Sent: Tuesday, January 29, 2013 6:18 PM
To: Jorge Sancho Ponce
Cc: Oliver Borm
Subject: Re: [Python-cgns-main] PythonCGNS

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...<mailto: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-cgns linked 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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