coupling Code_Saturne with Syrthes on mint 20.1

This forum is dedicated to Syrthes related issues, as the Syrthes tool does not have its own forum.
michal777
Posts: 9
Joined: Thu Feb 25, 2021 9:58 pm

coupling Code_Saturne with Syrthes on mint 20.1

Post by michal777 »

Hi

I'd like to start with thermal simulations using Code_Saturne+Syrthes. When trying to do example simulations according to tutorial "Code Saturne version 6.0 tutorial: three 2D disks" I had some problems with the software.

1. I downloaded Salome-CFD (Qualified version based on Code_Saturne 5.0 and SALOME 8.3). I tried development version too but it crashed.
2. I did extra steps acc. https://www.code-aster.org/forum2/viewt ... p?id=24883 (post by sb1966 2020-06-25), including the necessary change of python to python2 in installer and removing libstdc++.so
3. The salome was working (except GUI bugs) OK, so I started with the three 2D disks. I couldn't find the mentioned "syrthes.profile" file and even though syrthes is not installed, so I installed it from mint20.1 repo. Later found out it wasn't necessary (the file exist but it's burried deep in the Salome_CFD-SCFD_V8_5_0-Code_Saturne-5_2-univ_d54f597c). I removed the unnecessary syrthes, hope it didn't cause future issues.
4. I don't understand the step with editing "vim <install-prefix>/etc/code_saturne.cfg" to add "SYRTHES installation directory" - I don't know what's the directory, anyway it seems unnecessary to run syrthes.
5. I entered all the input to syrthes in salome and tried to start simulation. It failed because it couldn't find python. I installed python-is-python2. Got another error "No module named builtins ubuntu", found solution - install library "future" (https://stackoverflow.com/questions/274 ... d-builtins) from mint repo (python3-future if I recall correctly).
6. Syrthes still not running. The solution was to manually edit makefile in SOLID directory and add option -no-pie (https://nanxiao.me/en/gccs-enable-enabl ... nst-error/). It runs!
7. Next step is fluid symulation with code_saturne. No major issues (if I recall correctly) except different GUI and apparently wrong formula describing density (with Figure III.22 I got pointless results, correction acc. formula II.1 helped).
8. Next step was coupled simulations. At the beginning it failed because I set number of processes to 1 which I didn't expect to cause error, but that was easy to fix. Next, I got warning that syrthes and code_saturne use different libraries: libmpi.so.1 and libmpi.so.40.
So here's the question: can this be fixed in the version that is installed from Salome_CFD-SCFD_V8_5_0-Code_Saturne-5_2-univ_d54f597c.run or I need to compile the software instead of using this installer, to get the right libraries?

9. For further attempts I tried to install newer version of Salome and Code_Saturne. I downloaded salome 9.3 installer (http://files.salome-platform.org/Salome ... withOT.run).
10. After installing salome I tried to separately install code_saturne-6.1.3 with option to integrate with salome. It's not working because of missing pyqt5. The reason is in point 5. - for the newer version I need python-is-python3 instead of python-is-python2. I reinstalled also salome after this.
11. Still couldn't compile - got error "failed to get the Python codec of the filesystem encoding compilation". Maybe because salome installer has python3.6 and my linux uses 3.8. I found solution for this (viewtopic.php?p=15031) - run "salome shell" and then compile. I had to use ./configure... instead of the installer script "install_saturne.py", fortunately the "install_saturne.py" generated config.log before crash so I got the options ready to copy:

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"configure --prefix=/home/michal/Code_Saturne/6.1.3/code_saturne-6.1.3/arch/Linux_x86_64 --with-hdf5=salome --with-cgns=salome --with-med=salome --without-metis --without-scotch PYTHON=/usr/bin/python --with-salome=/home/michal/salome/Salome-V9_3_0-x86_64 --disable-static CXX=/usr/bin/mpicxx CC=/usr/bin/mpicc FC=/usr/bin/f95"
(except I removed "PYTHON=/usr/bin/python" as I want to use python from Salome).
12. More errors while making - some libraries can't be linked. In log I found that compiler looks for some libraries in some weird locations that have never existed on my computer, e.g.
[/code]"/home/rd-ap-palmco/salome/edf/V9_3_0_univ_yamm_test/prerequisites/install/Gcc-630-bin227-cloog0184-gmp513-mpc102-mpfr312/lib64/libstdc++.la"[/code]
I'm not rd-ap-palmco and directories in my salome versions have different names.
So the question: How could it happen and how to fix the pathes?
In config.log it appears the first time here:

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configure:4754: $? = 0
configure:4743: /usr/bin/mpicc -v >&5
Using built-in specs.
COLLECT_GCC=/home/michal/salome/Salome-V9_3_0-x86_64/prerequisites/Gcc-630/bin/gcc
COLLECT_LTO_WRAPPER=/home/michal/salome/Salome-V9_3_0-x86_64/prerequisites/Gcc-630/bin/../libexec/gcc/x86_64-pc-linux-gnu/6.3.0/lto-wrapper
Target: x86_64-pc-linux-gnu
Configured with: /home/rd-ap-palmco/salome/edf/V9_3_0_univ_yamm_test/prerequisites/src/Gcc-630-bin227-cloog0184-gmp513-mpc102-mpfr312/configure --prefix=/home/rd-ap-palmco/salome/edf/V9_3_0_univ_yamm_test/prerequisites/install/Gcc-630-bin227-cloog0184-gmp513-mpc102-mpfr312 --with-binutils=/home/rd-ap-palmco/salome/edf/V9_3_0_univ_yamm_test/prerequisites/install/Binutils-227-cloog0184-gmp513-mpc102-mpfr312 --with-cloog=/home/rd-ap-palmco/salome/edf/V9_3_0_univ_yamm_test/prerequisites/install/Cloog-0184-gmp513-mpfr312 --with-gmp=/home/rd-ap-palmco/salome/edf/V9_3_0_univ_yamm_test/prerequisites/install/Gmp-513 --with-mpc=/home/rd-ap-palmco/salome/edf/V9_3_0_univ_yamm_test/prerequisites/install/Mpc-102-gmp513-mpfr312 --with-mpfr=/home/rd-ap-palmco/salome/edf/V9_3_0_univ_yamm_test/prerequisites/install/Mpfr-312-gmp513 -v --enable-languages=c,c++,fortran --enable-shared --enable-threads=posix --enable-bootstrap --enable-nls --enable-__cxa_atexit --enable-checking=release --with-pkgversion='GCC 6.3.0 PR-2015/02/04'
13. Tried to fixed the missing libraries in ugly way - I added new directory "rd-ap-palmco" to my /home and created all necessary directories where I copied missing libraries from my salome installation. This allowed to complete make but make install failed.

14. I tried the newest salome - salome 9.6 for ubuntu 20.04. It installs differently than the previous .run installers, with "sat" tool. The "sat" didn't work because it coudn't find linux distro name. I hardcoded mint (distrib="LM") in ./salomeTools/src/architecture.py - it worked.
15. Trying to compile using sat - compilation failed because openssl-dev, libtbb, libtbb-dev are missing but actually I've got libssl-dev, libtbb2, libtbb-dev which should be fine.
16. According to readme in salome 9.6 I tried "compilation based on the binaries used as prerequisites". It worked, except I didn't know how should I understand

Code: Select all

Use SalomeTool (as explained in Sources section) and compile only the 
    modules you need to (with -p option)
I don't know what are the options I could specify so probably installed all.
17. The newest salome works but compilation of code_saturne fails. Problems like:

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/home/michal/build/code_saturne-6.1.3/src/fvm/fvm_to_medcoupling.cxx:637:48: error: cannot convert ‘int [8]’ to ‘const mcIdType*’ {aka ‘const long int*’}
  637 |     med_mesh->insertNextCell(med_type, stride, elt_buf);
      |                                                ^~~~~~~
      |                                                |
      |                                                int [8]
 
Question: Does it mean the code_saturne-6.1.3 is incompatible with salome 9.6? If yes, what versions of salome and cs should I choose on mint 20.1? Sould I compile salome or I can use installer


All that is a little mess. Has someone managed to install coupled CS+Syrthes, with consistent libmpi on mint 20.1? Where to start?
Yvan Fournier
Posts: 4164
Joined: Mon Feb 20, 2012 3:25 pm

Re: coupling Code_Saturne with Syrthes on mint 20.1

Post by Yvan Fournier »

Hello,

Sorry to see you needed to go through so many hoops to try to get it working.

My recommendations are:

1) try salome_cfd it an available version matches your system. If it works, fine. If it does not, do not insist, as you can need to solve an endles sseries of subtle issues. Got to 2)

2) install code_saturne and Syrthes from sources.
Before installing code_saturne, check https://github.com/code-saturne/code_sa ... n-packages (Mint being Ubuntu or Debian-based, the entry for those should be fine).
Then install code_saturne from sources (https://github.com/code-saturne/code_sa ... INSTALL.md ; you mainly need to read the introduction ; the rest is additional examples and details, you probably can skip those).
Than install Syrthes (using the link from this page https://www.code-saturne.org/cms/download/prerequisites, not the general EDF website link, which is an old version including obsolete binary libraries).

This should probably take less time and effort than you already spent trying to get the pre-compiled binaries working.

Do not hesitate to post again as you make progress or have questions.

Also, prefer code_saturne v6.0 to v5.0: we are working on the v7 release, which should be released May 2021 and maintained up to 2025 (when v9 is released), while v6 was released in 2019 and should be maintained until 2023 (when v8 is released). Version 5.0 is nearing end of life, as it will be retired next May upon v7.0 release. If you are interested in a v7.0 beta to avoid needing to upgrade again too soon, we can help you install that version from GitHub.

Regards,

Yvan
michal777
Posts: 9
Joined: Thu Feb 25, 2021 9:58 pm

Re: coupling Code_Saturne with Syrthes on mint 20.1

Post by michal777 »

Thanks, I will try with these.
I've got a question regarding 2): What about Salome? Compile it? What version? Should code_saturne be compiled from salome shell and with option to build for integration with Salome? Or Salome and code_saturne+syrthes can be independent, which maybe could save some troubles? Is there an easy workflow with separate tools instead of salome with all the modules?
Yvan Fournier
Posts: 4164
Joined: Mon Feb 20, 2012 3:25 pm

Re: coupling Code_Saturne with Syrthes on mint 20.1

Post by Yvan Fournier »

Hello,

Salome can be independent from code_saturne + Syrthes. Compiling Salome is very complex (which is why you won'f find up to date binaries for more systems), as it is a software stack distribution in itself.

So what I usually do is use a separate Salome binary for CAD and mesh generation, and my ow compiled versons of code_saturne and SYRTHES. For postprocessing, either the version of ParaView provided with Salome or an external version are fine.

You only need to make sure you compile code_saturne and Syrthes with a MED file library version at least as recent as the one used in salome (and can use that one) to avoid file compatibility issues.

Best regards,

Yvan
michal777
Posts: 9
Joined: Thu Feb 25, 2021 9:58 pm

Re: coupling Code_Saturne with Syrthes on mint 20.1

Post by michal777 »

I installed SALOME-9.6.0-UB20.04-SRC.

Next I installed code_saturne-6.1.3. To have compatible med format I've set setup file as below.

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#  Name    Use   Install  Path
#
hdf5       yes   no       /home/michal/salome/SALOME-9.6.0-UB20.04-SRC/INSTALL/hdf5
cgns       yes   no       /home/michal/salome/SALOME-9.6.0-UB20.04-SRC/INSTALL/cgns
med        yes   no       /home/michal/salome/SALOME-9.6.0-UB20.04-SRC/INSTALL/medfile
scotch     yes   no       /home/michal/salome/SALOME-9.6.0-UB20.04-SRC/INSTALL/scotch
parmetis   yes   no       /home/michal/salome/SALOME-9.6.0-UB20.04-SRC/INSTALL/metis
Code_Saturne was not working after installation:

Code: Select all

/home/michal/Code_Saturne/6.1.3/code_saturne-6.1.3/arch/Linux_x86_64/libexec/code_saturne/cs_preprocess: error while loading shared libraries: libhdf5.so.103: cannot open shared object file: No such file or directory
To fix: load the library before running Code_Saturne (viewtopic.php?t=2185)

Code: Select all

/home/michal/salome/SALOME-9.6.0-UB20.04-SRC/INSTALL/hdf5
Next, installation of saturne. For med compatibility, paths for med and hdf in setup.ini are specified to use the libraries from salome installation (as in code_saturne)

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# for MED format conversion : choose to istall or the path to the libraries
#hdf5  USE=no   INSTALL=no
hdf5   USE=yes  PATH=/home/michal/salome/SALOME-9.6.0-UB20.04-SRC/INSTALL/hdf5
#
#
#med   USE=no   INSTALL=no
med    USE=yes  PATH=/home/michal/salome/SALOME-9.6.0-UB20.04-SRC/INSTALL/medfile
also (not sure if needed):

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#metis USE=no  INSTALL=no
metis   USE=yes  PATH=/home/michal/salome/SALOME-9.6.0-UB20.04-SRC/INSTALL/metis
#
#scotch USE=no  INSTALL=no
scotch   USE=yes   PATH=/home/michal/salome/SALOME-9.6.0-UB20.04-SRC/INSTALL/scotch
and:

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#ple USE=no
ple USE=yes    PATH=/home/michal/Code_Saturne/6.1.3/code_saturne-6.1.3/arch/Linux_x86_64
#
# Answer by yes or no (if yes, ple_USE must be set to yes)
#
syrthescfd INSTALL=yes
#
10. There was a warning at the end of the installation:

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---------------------------------------------------------
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Warning : installation of some components failed
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Check log files for more information....
but I couldn't find the error in log files and apparently syrthes works (attached log from installation, can't see errors there).

After this I was able to run 3_2D_DISKS example with syrthes and code_saturne, with mesh files provided.
Unfortunately something went wrong when I tried to import mesh from salome to syrthes (didn't try cs yet, I'm not even sure my mesh is ok, but it's a simple sphere meshed in salome)

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commande ---> /home/michal/syrthes4.3.5/arch/Linux_x86_64/bin/convert2syrthes4 -m "/home/michal/therm/tmp1/zxcv.med"

***************************************************************
  convert2syrthes : convert mesh file to SYRTHES format     
**************************************************************

SYRTHES file opened : /home/michal/therm/tmp1/zxcv.syr

- MED version used to read the file : 4.1.0 
   WARNING : HDF format of the MED file not in accordance with HDF format now used
   WARNING : MED version of the file not in accordance with MED version used now 
   This file has been created with MED 4.1.0 

Name of the MED file : /home/michal/therm/tmp1/zxcv.med
Name of the MED-SYRTHES correspondance file : /home/michal/therm/tmp1/zxcv.syr_desc

Reading mesh information...
   Mesh name : Mesh_1 - dimension : 3 - espace : 3
   Number of nodes : 63 
   Number of tetrahedra P1 : 132
   Number of triangles P1 : 118

Writing the head of the file..

WARNING : make sure your mesh is using the meter unit.

Building entity and family association for Nodes... 

Writing coordinates...
Reading elements...
Reading zones ...
Building entity and family association for elements... 
Writing elements...
free(): invalid pointer
Aborted (core dumped)
zxcv.syr
I tried to specify med and hdf paths so that they should be taken from salome installation but it seems it didn't work like that?:

Code: Select all

michal@michal-X555LJ:~/syrthes4.3.5/arch/Linux_x86_64/bin$ ldd convert2syrthes4
	...
	libmedC.so.11 => /lib/x86_64-linux-gnu/libmedC.so.11 (0x00007fccf0ac9000)
	...
	libhdf5_openmpi.so.103 => /lib/x86_64-linux-gnu/libhdf5_openmpi.so.103 (0x00007fccf053a000)
	...
Attachments
from terminal log.txt
(484.91 KiB) Downloaded 1224 times
Yvan Fournier
Posts: 4164
Joined: Mon Feb 20, 2012 3:25 pm

Re: coupling Code_Saturne with Syrthes on mint 20.1

Post by Yvan Fournier »

Hello,

Could you also post your /home/michal/syrthes4.3.5/arch/Linux_x86_64/bin/syrthes.profile file ?

I do not know why the paths found are not good (maybe a priority aspect).

Did you source the "syrthes.profile" before converting the mesh ? Doing so at least before running Syrthes tools may be necessary (in the course of a coupled computation, code_saturne should handle that, but for Syrthes-only tasks, you need to do so).

If it contains the LD_LIBRARY_PATH settings needed, sourcing it should solve the issue. Otherwise, adding the LD_LIBRARY_PATH settings in it should be OK.

Best regards,

Yvan
michal777
Posts: 9
Joined: Thu Feb 25, 2021 9:58 pm

Re: coupling Code_Saturne with Syrthes on mint 20.1

Post by michal777 »

I tried:
- source syrthes.profile,
- make a mesh in salome (open salome, create 1x1x1 face with geometry module, add mesh from this face, export it as med 4.1 file),
- check ldd convert2syrthes4 - it looks like med and hdf paths are good (or should I care about more libraries?)
- run convert2syrthes4

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michal@michal-X555LJ:~$ source syrthes.profile
 
SYRTHES4_HOME= /home/michal/syrthes4.3.5/arch/Linux_x86_64
NOM_ARCH=      Linux_x86_64
PATH=          /home/michal/syrthes4.3.5/arch/Linux_x86_64/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin
LD_LIBRARY_PATH=/home/michal/Code_Saturne/6.1.3/code_saturne-6.1.3/arch/Linux_x86_64/lib:/home/michal/salome/SALOME-9.6.0-UB20.04-SRC/INSTALL/scotch/lib:/home/michal/salome/SALOME-9.6.0-UB20.04-SRC/INSTALL/metis/lib:/usr/lib:/home/michal/salome/SALOME-9.6.0-UB20.04-SRC/INSTALL/medfile/lib:/home/michal/salome/SALOME-9.6.0-UB20.04-SRC/INSTALL/hdf5/lib:
 
michal@michal-X555LJ:~$ ./salome/SALOME-9.6.0-UB20.04-SRC/salome
runSalome running on michal-X555LJ
Searching for a free port for naming service: 2810 - OK
Searching Naming Service  + found in 0.1 seconds 
Searching /Kernel/Session in Naming Service  ++Warning, no type found for resource "localhost", using default value "single_machine"
++ found in 2.0 seconds 
Start SALOME, elapsed time :   2.3 seconds
michal@michal-X555LJ:~$ ldd ./syrthes4.3.5/arch/Linux_x86_64/bin/convert2syrthes4
	linux-vdso.so.1 (0x00007ffe9e995000)
	libmedC.so.11 => /home/michal/salome/SALOME-9.6.0-UB20.04-SRC/INSTALL/medfile/lib/libmedC.so.11 (0x00007f5abd3c6000)
	libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f5abd18b000)
	libhdf5.so.103 => /home/michal/salome/SALOME-9.6.0-UB20.04-SRC/INSTALL/hdf5/lib/libhdf5.so.103 (0x00007f5abcdc1000)
	libstdc++.so.6 => /lib/x86_64-linux-gnu/libstdc++.so.6 (0x00007f5abcbe0000)
	libgcc_s.so.1 => /usr/lib/libgcc_s.so.1 (0x00007f5abcbc5000)
	/lib64/ld-linux-x86-64.so.2 (0x00007f5abd5ec000)
	libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f5abca74000)
	libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f5abca6e000)
	libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f5abca4b000)
michal@michal-X555LJ:~$ ./syrthes4.3.5/arch/Linux_x86_64/bin/convert2syrthes4 -m ~/Desktop/asdfasdfasdf/me/Mesh_1.med

***************************************************************
  convert2syrthes : convert mesh file to SYRTHES format     
**************************************************************

SYRTHES file opened : /home/michal/Desktop/asdfasdfasdf/me/Mesh_1.syr

- MED version used to read the file : 4.1.0 
   WARNING : HDF format of the MED file not in accordance with HDF format now used
   WARNING : MED version of the file not in accordance with MED version used now 
   This file has been created with MED 4.1.0 

Name of the MED file : /home/michal/Desktop/asdfasdfasdf/me/Mesh_1.med
Name of the MED-SYRTHES correspondance file : /home/michal/Desktop/asdfasdfasdf/me/Mesh_1.syr_desc

Reading mesh information...
   Mesh name : Mesh_1 - dimension : 2 - espace : 2
   Number of nodes : 511 
   Number of triangles P1 : 940
   Number of bars P1 : 80

Writing the head of the file..

WARNING : make sure your mesh is using the meter unit.
free(): invalid pointer
Aborted (core dumped)
It complains about difference of version of med but in the same place it shows both file and reader are med 4.1.0.
The converter is able to create .syr file, with properly recognized number of elements etc. but then crashes (invalid pointer).
In ERREUR.log I got this

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../syrthesconvert.log: 1224 |               printf("ERROR : allocation error for face references, needed size : %i \n", sizeof(int *) * ((*maillage).nbelem));
It also complains about unit (meter) - I didn't set any units in salome (is it possible?).
Attachments
Mesh_1.med
(63.32 KiB) Downloaded 1173 times
syrthes.profile.txt
(2.98 KiB) Downloaded 1240 times
Yvan Fournier
Posts: 4164
Joined: Mon Feb 20, 2012 3:25 pm

Re: coupling Code_Saturne with Syrthes on mint 20.1

Post by Yvan Fournier »

Hello,

I think the MED format can handle strings defining coordinate units, but do not know how to set them from SALOME, and the message about units probably means that Syrthes ignores the unit info, so it the mesh should be in meters to remain consistent.

I guess the crash is due to some remaining issue with mixed library versions, but do not understand where some other version might be found since you seem to have used the same definition everywhere.

Is it possible you might have a trace of an older install of MED files in your environment ? Or in your base Linux installation ?

One option might be to install Syrthes from a "salome shell" environment. In this case, it is possible you may not run it outside of at least the SALOME shell environment (to load the Python interpreter), but it might at least help ensure there is no library inconsistency here. If you still have the problem, it may be useful to go through Syrthes compile logs to see what happens (I am not so familiar with them, so can't list them from memory).

Best regards,

Yvan
niuniuaba
Posts: 18
Joined: Mon May 17, 2021 10:22 am

Re: coupling Code_Saturne with Syrthes on mint 20.1

Post by niuniuaba »

Quote from syrthes-5.0/VERSION.md
SYRTHES : Compatibilite des versions
====================================

Compatibilite des couplage SYRTHES / Code_Saturne / SALOME
---------------------------------------------------------------------------------
| SYRTHES | Code_Saturne (PLE) | Salome/Med |
---------------------------------------------------------------------------------
| SYRTHES 4.0 | 3.x (1.0) | |
| SYRTHES 4.1 | 3.x (1.0) | |
| SYRTHES 4.2 | 3.x (1.0) | |
| | | |
| SYRTHES 4.3 | 4.x (2.0) | Salome ??? - med 3.0.7 |
| 4.3.2 | 4.x (2.0) | Salome 7.6 - med 3.1 |
| 4.3.3 | 4.x (2.0) | Salome 7.8 - med 3.2.0 |
| 4.3.4 | 4.x (2.0) | Salome 7.8 - med 3.2.0 |
| 4.3.5 | 4.x 5.x 6.x (2.0) | Salome 9. - med 4 |
| 5.0. | 6.x (2.0) | Salome 9.6 - med 4.1 |
--------------------------------------------------------------------------------
So as far as I understand syrthes-4.3.5 is NOT compatible with med-4.1.0 (even though it compiled). Could this be the reason of 'MED version of the file not in accordance with MED version used now' problem?
Yvan Fournier
Posts: 4164
Joined: Mon Feb 20, 2012 3:25 pm

Re: coupling Code_Saturne with Syrthes on mint 20.1

Post by Yvan Fournier »

Hello,

This file describes the tested combinations, but does not imply non-tested combinations do not work.

The message you mention should happen when you try reading a MED 4.1 file with a code built with MED 4.0 for example, but not the other way around. Unless the code is stricter than necessary (I know code_saturne use that logic, but have not checked for Syrthes).

Again, you can also encounter issues if you have multiple installed versions with some mixing between library search paths, so it is important to use a clean directory hierarchy to avoid that, and avoid installs in /usr/local which often has priority in the search path an can contribute to the mess. Some environment modules or CONDA environments can also mess things up if they are used and contain HDF5 or MED libraries.

Regards,

Yvan
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