installation Salome+CS+Syrthes via VM on ubuntu 15.10

[jgd23]

Hello Yvan,

Thank you for your file, but where can I put it exactly in the source folder? I recompile Syrthes with the file in syrthes4.3.0/src

I have install Debian 8.5 on my laptop because of holidays. setup files are exactly the same and CS4.0.5 and Syrthes 4.3 runs in serial and parallel.
I create a new very simple 3D case in which I can check the boundaries ID for a correct coupling.

I have the following error during coupling (the case run without error with CS alone on fluid and syrthes alone on solid domains).

julien@debian:~/couplage$ ./runcase
Coupling execution between:
o Code_Saturne [1 domain(s)];
o SYRTHES [1 domain(s)];


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

Version: 4.0
Path: /home/julien/Code_Saturne/4.0.5/code_saturne-4.0.5/arch/Linux_x86_64

Result directory:
/home/julien/couplage/RESU_COUPLING/20160729-1029


Single processor Code_Saturne simulation.
Single processor SYRTHES simulation.


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

SYRTHES4 home directory: /home/julien/syrthes43/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 = solid_couple.syd
Update Data file = True
Do preprocessing = True
Debug = False
Case dir. = /home/julien/couplage/solid
Execution dir. = /home/julien/couplage/RESU_COUPLING/20160729-1029/solid
Data dir. = /home/julien/couplage/RESU_COUPLING/20160729-1029/solid
Source dir. = /home/julien/couplage/RESU_COUPLING/20160729-1029/solid/src
Post dir. = /home/julien/couplage/RESU_COUPLING/20160729-1029/solid/POST

Conduction mesh dir. = /home/julien/couplage
Conduction mesh name = solid.syr

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

SyrthesParam summary
Param file name = solid_couple.syd
Conduction mesh name = /home/julien/couplage/solid.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.openmpi has exited due to process rank 1 with PID 6428 on
node debian 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.openmpi (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
****************************

Post-processing..
.syrthes --> med..
--> /home/julien/syrthes43/syrthes4.3.0/arch/Linux_x86_64/bin/syrthes4med30 -m "/home/julien/couplage/solid.syr" -r "/home/julien/couplage/RESU_COUPLING/20160729-1029/solid/resu1.res" -o "resu1.med"
.syrthes --> med..
--> /home/julien/syrthes43/syrthes4.3.0/arch/Linux_x86_64/bin/syrthes4med30 -m "/home/julien/couplage/solid.syr" -r "/home/julien/couplage/RESU_COUPLING/20160729-1029/solid/resu1.rdt" -o "resu1_rdt.med"
Error in calculation stage.

See log files

Best regards

Julien

[Yvan Fournier]

Hello,

The error appears in the Code_Saturne log:

Code_Saturne : /home/julien/code_saturne/code_saturne-4.0.5/src/base/cs_syr4_coupling.c:965 : Avertissement
Couplage avec SYRTHES impossible :
220 centres d'éléments du maillage "Faces SYRTHES solid"
non localisés sur le maillage SYRTHES.

So you are probably missing a reference on the Syrthes side. Could you check or post your Syrthes ".syd" file to verify this ? (though your data I tested last week seemed OK) ?

Regards,

Yvan

[gbenefice]

Hello,

I had the same error but I re install the syrthes codes taking into account the Yvan post (Jeu Jan 07, 2016 9:53 am ):
http://code-saturne.org/forum/viewtopic ... D&start=10
To path files, I use the command:

Code: Select all

find /home -type f -name "ecrire_fichier.c"

And the tutorial is OK with the file in /code_saturne-4.0.5/examples/4-2Ddisks directory

Thanks

Best regard
Guillaume
PS: I can go on holiday !

[jgd23]

Hello,

I am in holidays so I can't post data of last week.
My mesh is non conformal between fluid surface and solid surface, maybe it's an issue for the computation, I think that it wasn't?
I have done exactly the same case than the tutorial than the last week without already existing files 3rond2d. I have just change to 0 (flux) a bad BC leaving a value of heat transfert coeff on the coupled boundary.
I have always errors, I post listing and syrthes log and also the .syd file of my case (you talk about the syd file that I save before computation isn't it?)

Best regards

Julien

[jgd23]

Hello Yvan,

Can you try to reproduce my simple coupling case please?

Salome 7.6.0, CS 4.0.5, syrthes 4.3 on debian 8.5.0.

I join the whole case with geometry.

Best regards,

Julien

[Yvan Fournier]

Hello,

I recommend testing your installation with the tutorial case instead of a new case. Your mesh is coarse, so you might have mesh location issues, requiring a specific option available only through user subroutines (not the GUI).

In any case, you selected all[] for fluid faces coupled with Syrthes, while you should only have selected wall_fluid.

This is not an installation issue, it is incorrect data (or if there is an installation issue, it is "masked" by the incorrect data setup).

Regards,

Yvan

[jgd23]

Hello,

How can I quantify if the mesh is fine enough for the coupling between CS and syrthes? Is there some general rules or some special error message when the mesh is too coarse?

Guillaume, can you post please your setup and setuini files for the CS and Syrthes installation for your ubuntu 16.04 installation?

Best regards

Julien

[Yvan Fournier]

Hello,

The mesh coarseness issue arises when the fluid and solid meshes are not conforming, and at least one of the two is coarse on a curved surface section. In this case, you have messages in the listing and syrthes.log files mentioning that, and you may have additional postprocessing output.

But this does not relate to code installation: you can test the installation with the tutorial case, which does not have any location issues (assuming you start from the included file).

Regards,

Yvan

[jgd23]

Hello,

Finally it works!!!!! But on ubuntu 16.04 LTS. I had too much problem with debian for visualization with 3d acceleraion feature of my virtual machine...

Thanks again for your time Yvan. I can work with this beautiful tool.

One last question: when the CS5.0 is planed to be released? Is there some transparent radiation between surfaces calculations like in syrthes?

Best regards

thank you again

Julien

[jgd23]

Hello,

i have checked for a parallel coupling for the 3disks2d calculation and it doesn't work...

Serial is working.

what's wrong?

best regards

julien