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CS_4.0.2 and syrthes4.3.0 coupling issues

https://www.code-saturne.org/forum/viewtopic.php?t=1786

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CS_4.0.2 and syrthes4.3.0 coupling issues

Posted: Tue Dec 08, 2015 4:27 pm
by ROLLAND
Hi,

I recently followed the "Guide to couple Saturne & SYRTHES" for installing and coupling Code_Saturne and Syrthes in a forum. To check their installation, I just run the test case 3disks2D (Three-2D-disks.pdf).
It turns out that each domain (fluid and solid) without coupling is working. However, when coupling by both adding a term in "Conjugate heat exchange" in the saturne gui and syrthes gui, I have an error message.

Code: Select all

 ****************************
  Preparing calculation data
 ****************************

 SYRTHES4 home directory: /home/rolland/syrthes4.3.0/arch/Linux_x86_64
 MPI home directory: /usr
 Building the executable file syrthes..                                                                                                                                                                                                      
/home/rolland/syrthes4.3.0/arch/Linux_x86_64/lib/libsyrthes_cfd.a(syr_cfd_coupling.o): dans la fonction « _interpolation_init »:                                                                                                             
syr_cfd_coupling.c:(.text+0xfcf): référence indéfinie vers « ple_locator_extend_search »                                                                                                                                                     
collect2: error: ld returned 1 exit status                                                                                                                                                                                                   
make: *** [exe] Erreur 1
I changed in fluid/src/cs_user_coupling.c the value of allow_non_matching (according to the tutorial) for true instead of false but nothing has changed.
I check the file syr_cfd_coupling.c and the function ple_locator_extend_search actually do exist.
I don't know if I miss something during the installation process (PLE library ?) or a put a wrong parameter somewhere (the two different meshes not matching?).

Can someone help me?

Thanks!

Regards,

QR

Re: CS_4.0.2 and syrthes4.3.0 coupling issues

Posted: Tue Dec 08, 2015 5:54 pm
by Yvan Fournier
Hello,

Which version of Code_Saturne did you install with Syrthes 4.3 ?

Did you use the PLE sublibrary from Code_Saturne, or a separate build ?

"ple_locator_extend_search" is a function which exists in Code_Saturne 4.0 / PLE 2.0 / Syrthes 4.3, but not in older versions, so I suspect an installation issue or a mix with older versions.

Regards,

Yvan

Re: CS_4.0.2 and syrthes4.3.0 coupling issues

Posted: Thu Dec 10, 2015 1:59 pm
by ROLLAND
Hi,

Thanks for your quick reply!
I have installed Code_Saturne version 4.0.2. I pre-installed Syrthes 4.3.0 before installing CS.
I located the PLE path from CS in the code_saturne_build folder, from which I installed CS. You can find the setup.ini and lauch.config for your consideration. I didn't install external library of PLE, assuming that CS already got the last version of it.
The PLE version is 2.0.1.
I hope I answered your question.


Regards,

QR

Re: CS_4.0.2 and syrthes4.3.0 coupling issues

Posted: Thu Dec 10, 2015 4:35 pm
by Yvan Fournier
Hello,

In your syrthes.ini, you should not use libple from code_saturne_build (which may contain a different directory hierarchy), but from the main installation (destination) prefix, so in your case:
ple USE=yes /home/rolland/Code_Saturne_4.0.2
Best regards,

Yvan

Re: CS_4.0.2 and syrthes4.3.0 coupling issues

Posted: Fri Dec 11, 2015 2:02 pm
by ROLLAND
Hi,

Thank you! It's working!
The code compiles properly now. However in the calculation process (Starting calculation
), another library problem showed up:

Code: Select all

 Coupling execution between: 
   o Code_Saturne [1 domain(s)];
   o SYRTHES      [1 domain(s)];


                      Code_Saturne is running
                      ***********************

 Version: 4.0
 Path:    /home/rolland/Code_Saturne_4.0.2

 Result directory:
   /home/rolland/Documents/EXEMPLE3/3disks2D/RESU_COUPLING/20151211-1123


 Single processor Code_Saturne simulation.
 Single processor SYRTHES simulation.

 ****************************************
  Compiling user subroutines and linking
 ****************************************


 ****************************
  Preparing calculation data
 ****************************

 SYRTHES4 home directory: /home/rolland/syrthes4.3.0/arch/Linux_x86_64
 MPI home directory: /usr
 Building the executable file syrthes.. 

  *****  SYRTHES compilation and link completed *****

 ***************************
  Preprocessing calculation
 ***************************


  SyrthesCase summary:

    Name =                         solid
    Data file =                    solidcoupling.syd
    Update Data file =             True
    Do preprocessing =             True
    Debug =                        False
    Case dir. =                    /home/rolland/Documents/EXEMPLE3/3disks2D/solid
    Execution dir. =               /home/rolland/Documents/EXEMPLE3/3disks2D/RESU_COUPLING/20151211-1123/solid
    Data dir. =                    /home/rolland/Documents/EXEMPLE3/3disks2D/RESU_COUPLING/20151211-1123/solid
    Source dir. =                  /home/rolland/Documents/EXEMPLE3/3disks2D/RESU_COUPLING/20151211-1123/solid/src
    Post dir. =                    /home/rolland/Documents/EXEMPLE3/3disks2D/RESU_COUPLING/20151211-1123/solid/POST

    Conduction mesh dir. =         /home/rolland/Documents/EXEMPLE3/3disks2D/solid/
    Conduction mesh name =         3rond2d.syr

    Total num. of processes =      1
    Logfile name            =      syrthes.log
    Echo =                         True
    Parallel run =                 False
    Do preprocessing =             True

   SyrthesParam summary
    Param file name =            solidcoupling.syd
    Conduction mesh name =       3rond2d.syr
    Radiation mesh name =        None
    Result prefix. =             resu1
    Restart =                    False
    Coupling =                   True
    Interpreted functions =      False


  ---------------------------
  Start SYRTHES preprocessing
  ---------------------------

Updating the mesh file name.. 
   -> OK


 **********************
  Starting calculation
 **********************

--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 in communicator MPI COMMUNICATOR 3 SPLIT FROM 0 
with errorcode 1.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
mpiexec has exited due to process rank 1 with PID 837 on
node rolland-Precision-WorkStation-T7400 exiting improperly. There are two reasons this could occur:

1. this process did not call "init" before exiting, but others in
the job did. This can cause a job to hang indefinitely while it waits
for all processes to call "init". By rule, if one process calls "init",
then ALL processes must call "init" prior to termination.

2. this process called "init", but exited without calling "finalize".
By rule, all processes that call "init" MUST call "finalize" prior to
exiting or it will be considered an "abnormal termination"

This may have caused other processes in the application to be
terminated by signals sent by mpiexec (as reported here).
--------------------------------------------------------------------------
 solver script exited with status 1.

Error running the coupled calculation.

Either Code_Saturne or SYRTHES may have failed.

Check Code_Saturne log (listing) and SYRTHES log (syrthes.log)
for details, as well as error* files.


 ****************************
  Saving calculation results
 ****************************

 Error in calculation stage.
Even by lowering down the n_procs_max and n_procs_min to one processor in the coupling_parameters.py file, as well as in the CS GUI (Number of processes) and Syrthes (Scalar/Parallel calculation) GUI, the Starting calculation step still fails.
I decided to overcome this problem by writing mpi USE=yes PATH=/usr/bin instead of mpi USE=yes PATH=/usr in the setup.ini file to have a direct match in the path given in the lauch.config file. And the problem got worst:

Code: Select all

 Coupling execution between: 
   o Code_Saturne [1 domain(s)];
   o SYRTHES      [1 domain(s)];


                      Code_Saturne is running
                      ***********************

 Version: 4.0
 Path:    /home/rolland/Code_Saturne_4.0.2

 Result directory:
   /home/rolland/Documents/EXEMPLE3/3disks2D/RESU_COUPLING/20151211-1203


 Single processor Code_Saturne simulation.
 Single processor SYRTHES simulation.

 ****************************************
  Compiling user subroutines and linking
 ****************************************


 ****************************
  Preparing calculation data
 ****************************

 SYRTHES4 home directory: /home/rolland/syrthes4.3.0/arch/Linux_x86_64
 MPI home directory: /usr/bin
 Building the executable file syrthes.. 
ar: /home/rolland/syrthes4.3.0/arch/Linux_x86_64/lib/libsyrthes_cfd.a: Aucun fichier ou dossier de ce type
make: *** [exe] Erreur 9

  Error during the compilation stage
Traceback (most recent call last):
  File "/home/rolland/Code_Saturne_4.0.2/bin/code_saturne", line 76, in <module>
    retcode = cs.execute()
  File "/home/rolland/Code_Saturne_4.0.2/lib/python2.7/site-packages/code_saturne/cs_script.py", line 88, in execute
    return self.commands[command](options)
  File "/home/rolland/Code_Saturne_4.0.2/lib/python2.7/site-packages/code_saturne/cs_script.py", line 150, in run
    return cs_run.main(options, self.package)
  File "/home/rolland/Code_Saturne_4.0.2/lib/python2.7/site-packages/code_saturne/cs_run.py", line 304, in main
    save_results=save_results)
  File "/home/rolland/Code_Saturne_4.0.2/lib/python2.7/site-packages/code_saturne/cs_case.py", line 1764, in run
    force_id)
  File "/home/rolland/Code_Saturne_4.0.2/lib/python2.7/site-packages/code_saturne/cs_case.py", line 1491, in prepare_data
    d.prepare_data()
  File "/home/rolland/Code_Saturne_4.0.2/lib/python2.7/site-packages/code_saturne/cs_case_domain.py", line 1139, in prepare_data
    retval = self.syrthes_case.prepare_run(exec_srcdir, compile_logname)
  File "/home/rolland/syrthes4.3.0/arch/Linux_x86_64/share/syrthes/syrthes.py", line 417, in prepare_run
    destdir = self.exec_dir)
  File "/home/rolland/syrthes4.3.0/arch/Linux_x86_64/share/syrthes/syrthes.py", line 1348, in build_syrthes
    shutil.move(os.path.abspath("syrthes"), exec_name)
  File "/usr/lib/python2.7/shutil.py", line 302, in move
    copy2(src, real_dst)
  File "/usr/lib/python2.7/shutil.py", line 130, in copy2
    copyfile(src, dst)
  File "/usr/lib/python2.7/shutil.py", line 82, in copyfile
    with open(src, 'rb') as fsrc:
IOError: [Errno 2] No such file or directory: '/home/rolland/Documents/EXEMPLE3/3disks2D/RESU_COUPLING/20151211-1203/solid/src/syrthes'
That's weird as MPI library is installed in /usr/bin not in /usr unless Syrthes recognize the path to follow from /usr.
Or did I miss something in the configuration/parameters of the fluid/solid domains?

Sorry for this long answer,

Regards,

QR

Re: CS_4.0.2 and syrthes4.3.0 coupling issues

Posted: Sat Dec 12, 2015 6:37 pm
by Yvan Fournier
Hello,

Now that the code seems installed correctly, could you move future usage questions to the "general usage" section of the forum (and adapt the info/logs to that section's recommendations) ?

Did you create the tutorial coupling directory structure using "code_saturne create -c fluid --syrthes solid" ? You do not seem to have the correct directory structure for a coupled case.

Regards,

Yvan
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