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Installing Code Saturne with Salome-Meca 2014.1
Posted: Thu Feb 27, 2014 11:32 am
by flujo
Hi,
I am trying to install Code Saturne with links to Salome. My version of Salome is the installation wizard version of Salome-Meca 2014.1. My first issue was the Code Saturne make failing because of issues with paraMEDMEM, but looking
here it seems that installing without it will be ok. Is this still true if I am hoping to run coupled simulations?
The second issue is that once the make and install with "--without-salome-med" runs and succeeds, upon trying to launch with the command "code_saturne salome" the error
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/bin/bash: line 4: /bin/salome/envSalome.py: No such file or directory
appears. Sourcing salome.sh and envSalome.sh temporarily fix it, but then there is no CFDSTUDY in SalomeMeca.
If instead I create a symbolic link to envSalome.py in /bin/salome, then
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Traceback (most recent call last):
File "/bin/salome/envSalome.py", line 36, in <module>
import setenv
File "/home/kwasi/salome/V7_3_0/modules/KERNEL_V7_3_0/bin/salome/setenv.py", line 26, in <module>
import orbmodule
File "/home/kwasi/salome/V7_3_0/modules/KERNEL_V7_3_0/bin/salome/orbmodule.py", line 31, in <module>
from omniORB import CORBA
ImportError: No module named omniORB
appears. The documentation online suggests that omniORB is no longer used, so I'm not sure what to do.
Many thanks for your help.
Re: Installing Code Saturne with Salome-Meca 2014.1
Posted: Thu Feb 27, 2014 3:20 pm
by Yvan Fournier
Hello,
Could you post additional information as per the forum recommendations (especially Code_Saturne version, config.log, and config.status may be useful) ?
I do not reproduce your issue with the SALOME-MECA-2014.1-LGPL installer and Code_Saturne version 3.0.3. Without your config.log or configure command, I can't check if you followed th "build outside source tree" recommendation.
Regards,
Yvan
Re: Installing Code Saturne with Salome-Meca 2014.1
Posted: Thu Feb 27, 2014 3:42 pm
by flujo
Sorry for not including that information.
The Code Saturne version was 3.2.1
I have attached the files, though I was nt able to attach the config.status as the forum thinks .status is an unpermitted extension.
I am quite new to Linux, so am not entirely sure what building outside the source tree means. Does that mean specifying a separate folder for the compiled products to be put into?
Re: Installing Code Saturne with Salome-Meca 2014.1
Posted: Thu Feb 27, 2014 5:22 pm
by flujo
I believe I have now tried building outside source. The envSalome error no longer appears, but the omniORB error still does.
Again, Code Saturne 3.2.1 with Salome Meca 2014.1.
Error is
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Traceback (most recent call last):
File "/bin/salome/envSalome.py", line 36, in <module>
import setenv
File "/home/kwasi/salome/V7_3_0/modules/KERNEL_V7_3_0/bin/salome/setenv.py", line 26, in <module>
import orbmodule
File "/home/kwasi/salome/V7_3_0/modules/KERNEL_V7_3_0/bin/salome/orbmodule.py", line 31, in <module>
from omniORB import CORBA
Re: Installing Code Saturne with Salome-Meca 2014.1
Posted: Thu Feb 27, 2014 5:26 pm
by Yvan Fournier
Hello,
To post config.status, you would need to rename it to config.status.txt for example (sorry, the options for the forum attachment filters are limited).
Building outside the source tree means creating a separate directory for "configure, make, make install". The installation manual explains how to do this (in the very first sections; you don't need to go through the advanced stuff).
Regards,
Yvan
Re: Installing Code Saturne with Salome-Meca 2014.1
Posted: Mon Mar 03, 2014 11:41 am
by flujo
Thank you for getting back to me.
Now separating the build directory from install, when I run configure, the result says I have MEDCoupling support but not ParaMEDMEM support. When running make, the compile fails around med coupling with errors like this:
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/home/kwasi/salome/V7_3_0/modules/MED_V7_3_0/include/salome/MEDCouplingMemArray.txx:90:43: required from 'void ParaMEDMEM::MemArray<T>::writeOnPlace(std::size_t, T, const T*, std::size_t) [with T = int; std::size_t = long unsigned int]'
/home/kwasi/salome/V7_3_0/modules/MED_V7_3_0/include/salome/MEDCouplingMemArray.hxx:598:160: required from here
/home/kwasi/salome/V7_3_0/modules/MED_V7_3_0/include/salome/MEDCouplingMemArray.txx:403:8: warning: unused parameter 'param' [-Wunused-parameter]
make[3]: *** [fvm_medcoupling_la-fvm_to_medcoupling.lo] Error 1
make[3]: Leaving directory `/home/kwasi/Code_Saturne/3.2/src/build/src/fvm'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/home/kwasi/Code_Saturne/3.2/src/build/src'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/kwasi/Code_Saturne/3.2/src/build'
make: *** [all] Error 2
kwasi@IBEC-Ubuntu:~/Code_Saturne/3.2/src/build$
Re: Installing Code Saturne with Salome-Meca 2014.1
Posted: Mon Mar 03, 2014 11:49 am
by flujo
Just in case the error is not one critical to the coupling properly functioning, I tried running configure with the --without-salome-med flag as suggested
here.
That also results in errors but this time directly with the CFDStudy creation:
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make[3]: Leaving directory `/home/kwasi/Code_Saturne/3.2/src/build/src/apps'
make[2]: Leaving directory `/home/kwasi/Code_Saturne/3.2/src/build/src'
Making all in salome
make[2]: Entering directory `/home/kwasi/Code_Saturne/3.2/src/build/salome'
Making all in cfd_study
make[3]: Entering directory `/home/kwasi/Code_Saturne/3.2/src/build/salome/cfd_study'
Making all in idl
make[4]: Entering directory `/home/kwasi/Code_Saturne/3.2/src/build/salome/cfd_study/idl'
PYTHONPATH=/home/kwasi/salome/V7_3_0/prerequisites/Omniorb_416/lib/python2.7/site-packages:/home/kwasi/salome/V7_3_0/prerequisites/Omniorb_416/lib/python2.7/site-packages${PYTHONPATH:+:$PYTHONPATH} \
LD_LIBRARY_PATH=/home/kwasi/salome/V7_3_0/prerequisites/Python_273/lib${LD_LIBRARY_PATH:+:$LD_LIBRARY_PATH} \
/home/kwasi/salome/V7_3_0/prerequisites/Omniorb_416/bin/omniidl -bcxx -Wba -nf -I/home/kwasi/salome/V7_3_0/prerequisites/Omniorb_416/idl -I/home/kwasi/salome/V7_3_0/modules/KERNELV_7_3_0/idl/salome -I/home/kwasi/salome/V7_3_0/modules/GUIV_7_3_0/idl/salome /home/kwasi/Code_Saturne/3.2/code_saturne-3.2.1/salome/cfd_study/idl/CFDSTUDY_Gen.idl
/home/kwasi/Code_Saturne/3.2/code_saturne-3.2.1/salome/cfd_study/idl/CFDSTUDY_Gen.idl:26: SALOME_Component.idl: No such file or directory
/home/kwasi/Code_Saturne/3.2/code_saturne-3.2.1/salome/cfd_study/idl/CFDSTUDY_Gen.idl:27: SALOMEDS.idl: No such file or directory
/home/kwasi/Code_Saturne/3.2/code_saturne-3.2.1/salome/cfd_study/idl/CFDSTUDY_Gen.idl:32: Error in look-up of 'Engines::EngineComponent': 'Engines' not found
/home/kwasi/Code_Saturne/3.2/code_saturne-3.2.1/salome/cfd_study/idl/CFDSTUDY_Gen.idl:33: Error in look-up of 'SALOMEDS::Driver': 'SALOMEDS' not found
omniidl: 2 errors.
omniidl: Error running preprocessor
make[4]: *** [CFDSTUDY_GenSK.cc] Error 1
make[4]: Leaving directory `/home/kwasi/Code_Saturne/3.2/src/build/salome/cfd_study/idl'
make[3]: *** [all-recursive] Error 1
make[3]: Leaving directory `/home/kwasi/Code_Saturne/3.2/src/build/salome/cfd_study'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/home/kwasi/Code_Saturne/3.2/src/build/salome'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/kwasi/Code_Saturne/3.2/src/build'
make: *** [all] Error 2
Re: Installing Code Saturne with Salome-Meca 2014.1
Posted: Tue Mar 04, 2014 6:34 pm
by Yvan Fournier
Hello,
We'd need to look in detail why, but I was able to reproduce your problem, and things work better with a simpler configuration command:
Replacing:
./configure --srcdir=/home/kwasi/Code_Saturne/3.2/code_saturne-3.2.1 --prefix=/home/kwasi/Code_Saturne/Saturne3.2 --with-salome=/home/kwasi/salome/V7_3_0 --with-mpi=/usr/lib/openmpi --with-salome-kernel=/home/kwasi/salome/V7_3_0/modules/KERNELV_7_3_0 --with-salome-gui=/home/kwasi/salome/V7_3_0/modules/GUIV_7_3_0 --with-salome-yacs=/home/kwasi/salome/V7_3_0/modules/YACSV_7_3_0 --enable-openmp --without-salome-med
With:
/home/kwasi/Code_Saturne/3.2/code_saturne-3.2.1/configure --prefix=/home/kwasi/Code_Saturne/Saturne3.2 --with-salome=/home/kwasi/salome/V7_3_0 --with-mpi=/usr/lib/openmpi --enable-openmp --without-salome-med
should do the trick. Also, --with-mpi=/usr/lib/openmpi should not be necessary, unless you have multiple MPI versions as MPI will be autodetected when in standard system libraries (you would actually need --without-mpi to disable it).
OpenMP is not much tested in this version, performance increases are hard to get except when running on a high number of cores (for example, 256 MPI tasks x4 threads vs. 1024 MPI tasks for a medium sized mesh), so it is not enabled by default.
Regards,
Yvan
Re: Installing Code Saturne with Salome-Meca 2014.1
Posted: Wed Mar 05, 2014 1:27 pm
by flujo
Thanks again!
In the VM on my laptop, the install works and I am able to bring up Salome with the CFDSTUDY module with the "code_saturne salome" command, though Aster is not included. What would I need to do to be able to have the CFDSTUDY module appear with the runAppli command, or have Aster within the Saturne instance of Salome?
On my other PC, the make works, though the install does not. I am presented with an install ending with:
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/usr/bin/install: cannot create regular file ‘/home/kwasi/Code_Saturne/Saturne3.2/lib/python2.7/site-packages/salome//home/kwasi/Code_Saturne/3.2/code_saturne-3.2.1/salome/cfd_study/src/CFDSTUDYGUI/ui_EnvSettingsDialog.py’: No such file or directory
/usr/bin/install: cannot create regular file ‘/home/kwasi/Code_Saturne/Saturne3.2/lib/python2.7/site-packages/salome//home/kwasi/Code_Saturne/3.2/code_saturne-3.2.1/salome/cfd_study/src/CFDSTUDYGUI/ui_GUIActivationDialog.py’: No such file or directory
/usr/bin/install: cannot create regular file ‘/home/kwasi/Code_Saturne/Saturne3.2/lib/python2.7/site-packages/salome//home/kwasi/Code_Saturne/3.2/code_saturne-3.2.1/salome/cfd_study/src/CFDSTUDYGUI/ui_InfoDialog.py’: No such file or directory
/usr/bin/install: cannot create regular file ‘/home/kwasi/Code_Saturne/Saturne3.2/lib/python2.7/site-packages/salome//home/kwasi/Code_Saturne/3.2/code_saturne-3.2.1/salome/cfd_study/src/CFDSTUDYGUI/ui_RunCaseDialog.py’: No such file or directory
/usr/bin/install: cannot create regular file ‘/home/kwasi/Code_Saturne/Saturne3.2/lib/python2.7/site-packages/salome//home/kwasi/Code_Saturne/3.2/code_saturne-3.2.1/salome/cfd_study/src/CFDSTUDYGUI/ui_SetTreeLocationDialog.py’: No such file or directory
make[5]: *** [install-exec-local] Error 1
I assume this is because the CFDSTUDY was not created for some reason during the compilation. Iǘe attached the config files below.
One question regarding ParaMEDMEM and MEDCoupling support - are they necessary for running a FSI routine with Aster, and if so, which steps would I need to take/prerequisites do I need installed to ensure support? My end goal is to run an implicit FSI routine.
Re: Installing Code Saturne with Salome-Meca 2014.1
Posted: Wed Mar 05, 2014 5:34 pm
by Yvan Fournier
Hello,
ParaMEDMEM and Medcoupling are not used for the Code_Saturne/Code_Aster coupling which is based only an YACS and its old Calcium layer, so you won't have any issues there.
I'm not sure whether vanilla Code_Aster includes the coupling functionality for Code_Saturne (as this has been debugged quite recently), and coupling has not been tested in parallel yet (not a huge amount of work to get working, but this coupling is not a current priority on our side).
In any case, a coupled case is defined as any other ("code_saturne create --case <code_saturne_case> --aster <code_aster_case>"), and the runcase_coupling the creates a (non graphical) SALOME virtual application which it uses while running.
For your data setup, you'll need to run SalomeMeca and "code_saturne salome" or "code_saturne gui" separately for now (in the future, both may be available in the same package, but this is work in progress, so don't expect if before the end of this year).
Regards,
Yvan