Syrthès installation issue with med

[Rodolphe]

Hi,

I'm trying to do the coupling between Code Saturne and Syrthès with the tuto uploaded years ago on this forum (viewtopic.php?p=7724#p7724). But when I try to install Syrthès first, I have an error with med library :

checking consistency of all components of python development environment... no
configure: error: in `/home/rodolphe/S4.3/syrthes-linux-4.3.0/syrthes4.3.0/extern-libraries/src/TMP/med-3.0.7.build/Linux_x86_64':
configure: error:
Could not link test program to Python. Maybe the main Python library has been
installed in some non-standard library path. If so, pass it to configure,
via the LDFLAGS environment variable.
Example: ./configure LDFLAGS="-L/usr/non-standard-path/python/lib"
============================================================================
ERROR!
You probably have to install the development version of the Python package
for your distribution. The exact name of this package varies among them.
============================================================================

See `config.log' for more details
make: *** Aucune règle pour fabriquer la cible « install ». Arrêt.
Error during make install of med-3.0.7


Note that i had an issue with the python path when installing CS few months ago and i had to do alias python/export python in the .bashrc file to make it work.

I'm running on Ubuntu 20.04 LTS.

Sorry, I did not find the config.log file (I'm new on Linux).

Best regards,


Rodolphe Vancoillie

[Yvan Fournier]

Hello,

You seem to have downloaded the old release of Syrthes and not the one available on this website (https://www.code-saturne.org/cms/download/prerequisites). That version includes obsolete precompiled binaries, so when searching for posts on this forum, you will have more luck with recent posts than very old tutorials.

Best regards,

Yvan

[Rodolphe]

Hello,

Thanks a lot for your quick answer. I did download the latest version of Syrthès as you advised but nevertheless I still have some issues. I join the setup and error files.

Thanks for your help !

Rodolphe

[Yvan Fournier]

Hello,

Are you sure there are *.h files under /home/rodolphe/Salome/SALOME-9.5.0/BINARIES-CO7/hdf5/include ? This seems to be a "salome-platform.org" binary SALOME installation, and I do not remember if headers are included or not.

Best regards,

Yvan

[Rodolphe]

Hello,

Yes there are .h files in /home/rodolphe/Salome/SALOME-9.5.0/BINARIES-CO7/hdf5/include.
I also tried with hdf5 that I've downloaded from Code Saturne prerequisites (which worked when I've installed Code Saturne) but I still have errors. Here are the error and setup files with also the syrthescfd.log file since the error file seems to point out this file.

Thanks,

Best regards,

Rodolphe

[Yvan Fournier]

Hello,

If the libraries work with code_saturne, it means it is probably the Syrthes installer which does not pass the correct compile or link options.

I am not very familiar with the Syrthes install scripts (or rather, each time I need to solve an issue with them, I basically need to restart from 0), so simply letting those scripts install another version of HDF5 and MED might be the the fastest solution.

Best regards,

Yvan

[niuniuaba]

It seems there is a 'dedicated' syrthes site online now https://www.syrthes-software.org/
After downloading ver. 5.0 and taking a look at the 'VERSION.md' file (which is not included in ver 4.3.5), as far as I understand, syrthes 4.3.5 is NOT compatible with med-4.1.0. If you want it with med-4.1.0 you can try syrthes 5.0.

Best regards,

niuniuaba

[Yvan Fournier]

Hello,

Actually, I would be surprised if you cannot compile Syrthes 4.3 with MED 4.1, though it was tested and released with older versions.

So I believe the issue is different. In any case, the new Syrthes version should also be compatible with code_saturne, but it's installer contains some binary files, which may work better on some systems than others.

So you can try both ans see what works best.

Best regards,

Yvan

[niuniuaba]

I would be surprised if you cannot compile Syrthes 4.3 with MED 4.1

Sorry I confused this thread with another one viewtopic.php?f=11&t=2794.
Back to this one, I think the issue is that hdf5 and med are from different 'pairs'. For example if you use hdf5 from CO7 binaries package it's a better idea to use med from the same package.

Code: Select all

hdf5  USE=yes  PATH=/home/rodolphe/Salome/SALOME-9.5.0/BINARIES-CO7/hdf5
med   USE=yes  PATH=/home/rodolphe/Salome/SALOME-9.5.0/BINARIES-CO7/medfile

Another thing I noticed is the path of ple.

Code: Select all

ple USE=yes    PATH=/home/rodolphe/CS6.0/code_saturne-6.0.6(1)/code_saturne-6.0.6/libple

should be

Code: Select all

ple USE=yes    PATH=/home/rodolphe/CS6.0/code_saturne-6.0.6(1)/code_saturne-6.0.6

isn't it?

[Yvan Fournier]

Hello,

Yes, you should use the same HDF5 that MED was built with, so using the 2 from the same package is the most reliable way to do this.

And for PLE, yes, the path should match the top-level directory, not one of its subdirectories, and when PLE is built along with code_saturne, it's installation path is the same as for all of code_saturne. So the second version seems right.

Best regards,

Yvan