medCoupling for saturne-aster coupling

vshinde · August 22, 2016, 10:07am

Hello,

I am trying to configure code_saturne (v4.3.0) for aster (v12.6) external coupling using salome_meca (v2016) platform. I use following options for configuration: --with-prefix=, --with-hdf5=, --with-cgns=, --with-med=, --with-salome=.

The configuration is done as below:

===========================================
Configuration options:
use debugging code: no
use malloc hooks: no
use graphical user interface: yes
use long global numbers: yes
Zlib (gzipped file) support: yes
MPI (Message Passing Interface) support: yes
MPI I/O support: yes
MPI2 one-sided communication support: yes
MPI3 neighborhood collectives support: yes
MPI3 nonblocking barrier support: no
OpenMP support: yes
OpenMP Fortran support: yes
BLAS (Basic Linear Algebra Subprograms) support: no
Libxml2 (XML Reader) support: yes
ParMETIS (Parallel Graph Partitioning) support: no
METIS (Graph Partitioning) support: no
PT-SCOTCH (Parallel Graph Partitioning) support: no
SCOTCH (Graph Partitioning) support: no
CCM support: no
HDF (Hierarchical Data Format) support: yes
CGNS (CFD General Notation System) support: yes
MED (Model for Exchange of Data) support: yes
MED MPI I/O support: no
MEDCoupling support: no
Catalyst (ParaView co-processing) support: no
EOS support: no
freesteam support: no
CoolProp support: no
PETSc support: no
SALOME GUI support: yes
SALOME Kernel support: yes
Dynamic loader support: dlopen

The package has been configured. Type:
make
make install

To generate and install the Code_Saturne kernel

Am I missing something related to MEDCoupling support ?

Many thanks in advance for your time.

Vilas

Yvan_Fournier · August 22, 2016, 1:18pm

Hello,

MEDCoupling is a specific module, which has changed a bit (so Code_Saturne 4.3 is compatible only with MEDCoupling 8), but you do not need it for the coupling which Code_Aster, which uses only an older subset of the Salome Kernel and YACS.

Regards,

Yvan

vshinde · August 23, 2016, 10:13am

Hello Yvan,

Thank you for your reply.
I get below output when I run a testcase. (Sorry for the bulk message, but it is as it is.)

=====================================================================================
./runcase
Coupling execution between:
o Code_Saturne [1 domain(s)];
o Code_Aster [1 domain(s)];
[1 coupler(s)];

Code_Saturne is running

Version: 4.0
Path: /home/vilas/saturne/4.0.5

Result directory:
/home/vilas/Desktop/PostDoc/NS/FSI/new/RESU_COUPLING/20160823-1152

Single processor Code_Saturne simulation.
Single processor Code_Aster simulation.

Compiling user subroutines and linking

\

Preparing calculation data

\

Preprocessing calculation

Creating YACS coupling scheme.
Configure parser: processing /home/vilas/saturne/4.0.5/etc/salome/fsi_appli_config.xml …
— add module KERNEL /home/vilas/salome_meca/V2015_2/modules/KERNEL_V7_6_0
link /home/vilas/Desktop/PostDoc/NS/FSI/new/RESU_COUPLING/20160823-1152/appli/bin/salome/test/KERNEL → /home/vilas/salome_meca/V2015_2/modules/KERNEL_V7_6_0/bin/salome/test
— add module GUI /home/vilas/salome_meca/V2015_2/modules/GUI_V7_6_0
— add module YACS /home/vilas/salome_meca/V2015_2/modules/YACS_V7_6_0
— add module FSI /home/vilas/saturne/4.0.5
WARNING: context file does not exist

Starting calculation

th. 140118542313216 - Trace /home/I27518/TRAV/C3/V2015_2_public/modules/src/KERNEL/src/NamingService/SALOME_NamingService.cxx [1488] : CORBA::SystemException: unable to contact the naming service
runSalome running on vilas-namrata
Searching for a free port for naming service: 2810 - OK
Searching Naming Service + found in 0.1 seconds
Searching /Registry in Naming Service + found in 0.5 seconds
Searching /Kernel/ModulCatalog in Naming Service +th. 139986930640704 - Trace /home/I27518/TRAV/C3/V2015_2_public/modules/src/KERNEL/src/ModuleCatalog/SALOME_ModuleCatalog_Server.cxx [101] : Module Catalog Server: Naming Service was found
found in 0.5 seconds
RunStudy
Searching /myStudyManager in Naming Service + found in 0.5 seconds
Searching /Containers/vilas-namrata/FactoryServer in Naming Service ++ found in 1.0 seconds
Start SALOME, elapsed time : 2.7 seconds
graph = fsi_yacs_scheme.xml options: display=0 verbose=0 stop-on-error=1 shutdown=1 reset=0 dumpErrorFile=dumpErrorState.xml
Starting 0 ms
Elapsed time before load: 210 ms
Elapsed time after load: 214 ms
Elapsed time after validation: 214 ms
Elapsed time after check consistency: 214 ms
+++++++++++++++++++ start calculation +++++++++++++++++++
th. 139814500787968 - Trace /home/I27518/TRAV/C3/V2015_2_public/modules/src/KERNEL/src/Container/SALOME_ContainerManager.cxx [620] : [GiveContainer] waiting 60 second steps container /Containers/vilas-namrata/1856_FSI_MILIEU_0x23dca00
th. 139814484002560 - Trace /home/I27518/TRAV/C3/V2015_2_public/modules/src/KERNEL/src/Container/SALOME_ContainerManager.cxx [620] : [GiveContainer] waiting 60 second steps container /Containers/vilas-namrata/1856_FSI_SATURNE_0x23dcd10
th. 139814492395264 - Trace /home/I27518/TRAV/C3/V2015_2_public/modules/src/KERNEL/src/Container/SALOME_ContainerManager.cxx [620] : [GiveContainer] waiting 60 second steps container /Containers/vilas-namrata/1856_FSI_ASTER_0x23dc700
th. 139814492395264 - Trace /home/I27518/TRAV/C3/V2015_2_public/modules/src/KERNEL/src/Container/SALOME_ContainerManager.cxx [432] : [GiveContainer] container /Containers/vilas-namrata/1856_FSI_ASTER_0x23dc700 launched
SalomeContainer launched : /Containers/vilas-namrata/1856_FSI_ASTER_0x23dc700 vilas-namrata 1887
th. 139814484002560 - Trace /home/I27518/TRAV/C3/V2015_2_public/modules/src/KERNEL/src/Container/SALOME_ContainerManager.cxx [432] : [GiveContainer] container /Containers/vilas-namrata/1856_FSI_SATURNE_0x23dcd10 launched
SalomeContainer launched : /Containers/vilas-namrata/1856_FSI_SATURNE_0x23dcd10 vilas-namrata 1886
th. 139814500787968 - Trace /home/I27518/TRAV/C3/V2015_2_public/modules/src/KERNEL/src/Container/SALOME_ContainerManager.cxx [432] : [GiveContainer] container /Containers/vilas-namrata/1856_FSI_MILIEU_0x23dca00 launched
SalomeContainer launched : /Containers/vilas-namrata/1856_FSI_MILIEU_0x23dca00 vilas-namrata 1881
Can’t get reference to DSC object (or it was nil).
Error while trying to create a new component: component ‘FSI_ASTER’ is not installed or it’s a wrong name
SALOME_Container::create_component_instance failed
Error while trying to create a new component: component ‘FSI_SATURNE’ is not installed or it’s a wrong name
SALOME_Container::create_component_instance failed
+++++++++++++++++++ end calculation +++++++++++++++++++
Proc state : FAILED
Elapsed time after execution: 21284 ms
Execution has ended in error

Can’t get reference to DSC object (or it was nil).

Error while trying to create a new component: component ‘FSI_SATURNE’ is not installed or it’s a wrong name
SALOME_Container::create_component_instance failed

Error while trying to create a new component: component ‘FSI_ASTER’ is not installed or it’s a wrong name
SALOME_Container::create_component_instance failed

shutdown SALOME container: /Containers/vilas-namrata/1856_FSI_MILIEU_0x23dca00
shutdown SALOME container: /Containers/vilas-namrata/1856_FSI_SATURNE_0x23dcd10
shutdown SALOME container: /Containers/vilas-namrata/1856_FSI_ASTER_0x23dc700
/home/vilas/Desktop/PostDoc/NS/FSI/new/RESU_COUPLING/20160823-1152/run_solver: line 13: $localexec: ambiguous redirect
solver script exited with status 1.

Error running the calculation.

Check Code_Saturne log (listing) and error* files for details.

\

Saving calculation results

Error in calculation stage.

I am trying out different versions of the codes (saturne and salome meca) for the coupling. Am I missing something?
Please suggest. Many thanks for your time and concern.

Vilas

Yvan_Fournier · August 23, 2016, 1:56pm

Hello,

Actually, the SALOME detection report for the install might be wrong, or you may have subtle environment aspects. When running configure, for --with-salome= you need to add the full path to your SALOME installation (not application).

Regards,

Yvan

vshinde · September 7, 2016, 1:30pm

Hello,
In a recent attempt to run a coupled case, I have an error (from code_saturne listing) that says:

=====================================================================================
command:
./cs_solver --param param.xml --mpi --app-name fluid --yacs-module=/home/vilas/saturne/4.2.1/lib/salome/libFSI_SATURNEExelib.so

(R)
Code_Saturne

revision 4.2.1
build Wed 07 Sep 2016 11:19:08 AM CEST
MPI version 3.0 (Open MPI 1.10.2)

The Code_Saturne CFD tool is free software;
you can redistribute it and/or modify it under the terms
of the GNU General Public License as published by the
Free Software Foundation; either version 2 of the License,
or (at your option) any later version.

The Code_Saturne CFD tool is distributed in the hope that
it will be useful, but WITHOUT ANY WARRANTY; without even
the implied warranty of MERCHANTABILITY or FITNESS FOR A
PARTICULAR PURPOSE. See the GNU General Public License
for more details.

../.././../code_saturne-4.2.1/src/base/cs_calcium.c:949: Fatal error.

Error loading /home/vilas/saturne/4.2.1/lib/salome/libFSI_SATURNEExelib.so: /home/vilas/saturne/4.2.1/lib/salome/libFSI_SATURNEExelib.so: undefined symbol: _ZN19Engines_Component_i20configureSalome_fileENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES5_P13Salome_file_i.

Call stack:
1: 0x7f7db771be8e <cs_calcium_load_yacs+0x17e> (libsaturne.so.0)
2: 0x7f7db76ab922 <main+0xe2> (libsaturne.so.0)
3: 0x7f7db6e2b780 <__libc_start_main+0xf0> (libc.so.6)
4: 0x4013e9 <_start+0x29> (cs_solver)
End of stack

Any suggestions?

Many thanks in advance for your time.

Vilas

Yvan_Fournier · September 7, 2016, 11:42pm

Hello Vilas,

Could you post your config.log file for the Code_Saturne build, as well as the cs_config.h file ?

Regards,

Yvan

vshinde · September 8, 2016, 11:50am

Hello Yvan,
Please find the files attached.
Many thanks for your time.

Vilas
cs_config.h (10.6 KB)
config.log (274 KB)

Yvan_Fournier · September 8, 2016, 4:01pm

Hello Vilas,

Your install seems OK. I do not have exactly the same symbols in my case as as one which does not load in your case, but this is probably due to using different versions of gcc.

Could you post the output of the following command ?

nm /home/vilas/saturne/4.2.1/lib/salome/libFSI_SATURNEExelib.so

The problem might still be due to different compilers being used for the SALOME build and for Code_Saturne, but I am not sure.

I guess we’ll have to solve this step by step…

Regards,

Yvan

vshinde · September 9, 2016, 4:07pm

Many thanks Yvan,

Please find the output of the command you asked in a file (output.txt) attached.

BW
Vilas
output.txt (33 KB)

Yvan_Fournier · September 12, 2016, 11:54am

Hello,

Ok, could you also send the output of:

ldd /home/vilas/saturne/4.2.1/lib/salome/libFSI_SATURNEExelib.so

and:

nm /home/vilas/salome_meca/V2015_2/modules/KERNEL_V7_6_0/lib/salome/libSalomeContainer.so

On a “calibre7” (Debian 6) workstation, the symbol: _ZN19Engines_Component_i20configureSalome_fileENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES5_P13Salome_file_i
is the one which matches your: _ZN19Engines_Component_i20configureSalome_fileENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES5_P13Salome_file_i.

I suspect the difference is probably due to different name mangling by a different version of the g++ compiler, but I would like to confirm this with the actual output..

Regards,

Yvan

vshinde · September 14, 2016, 12:17pm

Hello,

Please find attached the outputs of the commands.
Many thanks for your time.

Vilas
output1.txt (689 Bytes)
output2.txt (69.9 KB)

Yvan_Fournier · September 14, 2016, 4:05pm

Hello,

This is strange: your error message mentioned:

Error loading /home/vilas/saturne/4.2.1/lib/salome/libFSI_SATURNEExelib.so: /home/vilas/saturne/4.2.1/lib/salome/libFSI_SATURNEExelib.so: undefined symbol: _ZN19Engines_Component_i20configureSalome_fileENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES5_P13Salome_file_i.

While your “nm /home/vilas/saturne/4.2.1/lib/salome/libSalomeIDLFSI.so.0” command does not seem to mention this symbol (but only _ZN19Engines_Component_i20configureSalome_fileESsSsP13Salome_file_i, which exists in the libSalomeContainer.so library).

Also (probably an independent issue), I was able to get the coupling running (10 iterations) using Code_Saturne 4.0 or trunk with SALOME-MECA 1015.1, but not with SALOME-MECA 1015.2…

Regards,

Yvan