Installing CS 4.2.1 and Syrthes 4.3.0 on Xubuntu 15.10
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Re: Installing CS 4.2.1 and Syrthes 4.3.0 on Xubuntu 15.10
I was thinging that compiling CS was mandatory for using with Syrthes...
Was I wrong???
I'm going to install CS using the automated installer script.
Was I wrong???
I'm going to install CS using the automated installer script.
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- Posts: 4206
- Joined: Mon Feb 20, 2012 3:25 pm
Re: Installing CS 4.2.1 and Syrthes 4.3.0 on Xubuntu 15.10
Hello,
No, CS and Syrthes are independent. The only real requirement if you want to run coupled calculations are that both codes use the same MPI library. All other libraries are independent.
Regards,
Yvan
No, CS and Syrthes are independent. The only real requirement if you want to run coupled calculations are that both codes use the same MPI library. All other libraries are independent.
Regards,
Yvan
Re: Installing CS 4.2.1 and Syrthes 4.3.0 on Xubuntu 15.10
So, I've try to install CS using the automated script.
But things go wrong in the compilation stage.
In the setup file, the script detect the MPI from syrthes :
Any idea of what's wrong?
Do I give the path to MPI in the good way?
please find enclosed the setup and the install_saturne.log files
Thanks... a lot!
JB
But things go wrong in the compilation stage.

Code: Select all
In file included from /home/jbl/code_saturne-4.2.1/src/fvm/fvm_to_medcoupling.cxx:28:0:
/home/jbl/code_saturne-4.2.1/src/base/cs_defs.h:81:19: fatal error: mpi.h: Aucun fichier ou dossier de ce type
compilation terminated.
Makefile:1025: recipe for target 'fvm_medcoupling_la-fvm_to_medcoupling.lo' failed
make[3]: *** [fvm_medcoupling_la-fvm_to_medcoupling.lo] Error 1
make[3]: Leaving directory '/home/jbl/code_saturne-4.2.1.build/src/fvm'
Makefile:895: recipe for target 'all-recursive' failed
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory '/home/jbl/code_saturne-4.2.1.build/src'
Makefile:1286: recipe for target 'all-recursive' failed
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory '/home/jbl/code_saturne-4.2.1.build'
Makefile:820: recipe for target 'all' failed
make: *** [all] Error 2
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# C compiler and optional MPI wrapper
#--------------------------------------------------------
compC /usr/bin/cc
mpiCompC /home/jbl/syrthes4.3.0/extern-libraries/opt/openmpi-1.8.3/arch/Linux_x86_64/bin/mpicc
#
#--------------------------------------------------------
# Fortran compiler
#--------------------------------------------------------
compF /usr/bin/f95
#
#--------------------------------------------------------
# C++ compiler and MPI wrapper for optional packages
#
# Required only for static builds using the MED library
# or for build of optional modules such as MEDCoupling
# support.
#--------------------------------------------------------
compCxx /usr/bin/c++
mpiCompCxx /home/jbl/syrthes4.3.0/extern-libraries/opt/openmpi-1.8.3/arch/Linux_x86_64/bin/mpicxx
Do I give the path to MPI in the good way?
please find enclosed the setup and the install_saturne.log files
Thanks... a lot!
JB
- Attachments
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- install_saturne.log
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Re: Installing CS 4.2.1 and Syrthes 4.3.0 on Xubuntu 15.10
here is the setup file
- Attachments
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- setup.txt
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- Posts: 4206
- Joined: Mon Feb 20, 2012 3:25 pm
Re: Installing CS 4.2.1 and Syrthes 4.3.0 on Xubuntu 15.10
Hello,
There seems to be a bug in the handling of mpicxx by the installer, which impacts compilation when you use SALOME (and Code_Saturne tries to build the MEDCoupling interface).
The attached fix should solve the issue (don't forget to make the file executable using "chmod +x", then replace the previous one with this one)
Regards,
Yvan
There seems to be a bug in the handling of mpicxx by the installer, which impacts compilation when you use SALOME (and Code_Saturne tries to build the MEDCoupling interface).
The attached fix should solve the issue (don't forget to make the file executable using "chmod +x", then replace the previous one with this one)
Regards,
Yvan
- Attachments
-
- install_saturne.py
- (46.71 KiB) Downloaded 520 times
Re: Installing CS 4.2.1 and Syrthes 4.3.0 on Xubuntu 15.10
Hello,
Thanks a lot for the updated installer.
The compilation and installation go to the end stage and seem to finish correctly.
However, the installation doesn't work :
When typing :
the answer is
when trying
the answer is:
I'm a bit disapointed...
What did I do wrong?
Please find the install.log and the setup file
If anybody has any idea...
Thanks a lot for the updated installer.
The compilation and installation go to the end stage and seem to finish correctly.
However, the installation doesn't work :
When typing :
Code: Select all
jbl@VM-CAO-S81-BA:~/Documents/Test_saturne$ code_saturne create --study test1
Code: Select all
bash: /home/jbl/Code_Saturne/4.2.1/code_saturne-4.2.1/arch/Linux_x86_64/bin/bin: Aucun fichier ou dossier de ce type
Code: Select all
jbl@VM-CAO-S81-BA:~/CS4.2.1$ code_saturne gui
Code: Select all
Traceback (most recent call last):
File "/usr/local/bin/code_saturne", line 76, in <module>
retcode = cs.execute()
File "/usr/local/lib/python2.7/dist-packages/code_saturne/cs_script.py", line 89, in execute
return self.commands[command](options)
File "/usr/local/lib/python2.7/dist-packages/code_saturne/cs_script.py", line 144, in gui
return cs_gui.main(options, self.package)
File "/usr/local/lib/python2.7/dist-packages/code_saturne/cs_gui.py", line 194, in main
from code_saturne.Base.MainView import MainView
ImportError: No module named Base.MainView
What did I do wrong?
Please find the install.log and the setup file
If anybody has any idea...
- Attachments
-
- setup.txt
- (4.39 KiB) Downloaded 510 times
-
- install_saturne.log
- (2.19 MiB) Downloaded 514 times
Re: Installing CS 4.2.1 and Syrthes 4.3.0 on Xubuntu 15.10
Ok,
the mistakes was in the .bashrc file during the shell configuration step.
I've past and copy the data from the end of the console utput at the end of the install process.
instead of this, indications in the installation guide (chapter 10, shell configuration) has to be followed...
Anyway, there is still some errors :
the mistake seems to be in the code_saturne.cfg, about the syrthes path...
What should it be?
is the following not correct?
JB
the mistakes was in the .bashrc file during the shell configuration step.
I've past and copy the data from the end of the console utput at the end of the install process.

instead of this, indications in the installation guide (chapter 10, shell configuration) has to be followed...
Anyway, there is still some errors :
Code: Select all
jbl@VM-CAO-S81-BA:~/Documents/Test_saturne$ code_saturne create --study test1
code_saturne 4.2 study/case generation
o Creating study 'test1'...
o Creating case 'CASE1'...
Traceback (most recent call last):
File "/home/jbl/Code_Saturne/4.2.1/code_saturne-4.2.1/arch/Linux_x86_64/bin/code_saturne", line 76, in <module>
retcode = cs.execute()
File "/home/jbl/Code_Saturne/4.2.1/code_saturne-4.2.1/arch/Linux_x86_64/lib/python2.7/site-packages/code_saturne/cs_script.py", line 89, in execute
return self.commands[command](options)
File "/home/jbl/Code_Saturne/4.2.1/code_saturne-4.2.1/arch/Linux_x86_64/lib/python2.7/site-packages/code_saturne/cs_script.py", line 140, in create
return cs_create.main(options, self.package)
File "/home/jbl/Code_Saturne/4.2.1/code_saturne-4.2.1/arch/Linux_x86_64/lib/python2.7/site-packages/code_saturne/cs_create.py", line 650, in main
study.create()
File "/home/jbl/Code_Saturne/4.2.1/code_saturne-4.2.1/arch/Linux_x86_64/lib/python2.7/site-packages/code_saturne/cs_create.py", line 244, in create
self.create_case(c)
File "/home/jbl/Code_Saturne/4.2.1/code_saturne-4.2.1/arch/Linux_x86_64/lib/python2.7/site-packages/code_saturne/cs_create.py", line 574, in create_case
casename = casename)
File "/home/jbl/Code_Saturne/4.2.1/code_saturne-4.2.1/arch/Linux_x86_64/lib/python2.7/site-packages/code_saturne/cs_create.py", line 602, in build_batch_file
case_name=casename)
File "/home/jbl/Code_Saturne/4.2.1/code_saturne-4.2.1/arch/Linux_x86_64/lib/python2.7/site-packages/code_saturne/cs_runcase.py", line 69, in __init__
self.build_template(package, study_name, case_name)
File "/home/jbl/Code_Saturne/4.2.1/code_saturne-4.2.1/arch/Linux_x86_64/lib/python2.7/site-packages/code_saturne/cs_runcase.py", line 187, in build_template
config.read(package.get_configfiles())
File "/usr/lib/python2.7/ConfigParser.py", line 305, in read
self._read(fp, filename)
File "/usr/lib/python2.7/ConfigParser.py", line 546, in _read
raise e
ConfigParser.ParsingError: File contains parsing errors: /home/jbl/Code_Saturne/4.2.1/code_saturne-4.2.1/arch/Linux_x86_64/etc/code_saturne.cfg
[line 20]: ' syrthes = /home/jbl/syrthes4.3.0/arch/Linux_x86_64/\n'
jbl@VM-CAO-S81-BA:~/Documents/Test_saturne$ code_saturne gui
Traceback (most recent call last):
File "/home/jbl/Code_Saturne/4.2.1/code_saturne-4.2.1/arch/Linux_x86_64/bin/code_saturne", line 76, in <module>
retcode = cs.execute()
File "/home/jbl/Code_Saturne/4.2.1/code_saturne-4.2.1/arch/Linux_x86_64/lib/python2.7/site-packages/code_saturne/cs_script.py", line 89, in execute
return self.commands[command](options)
File "/home/jbl/Code_Saturne/4.2.1/code_saturne-4.2.1/arch/Linux_x86_64/lib/python2.7/site-packages/code_saturne/cs_script.py", line 144, in gui
return cs_gui.main(options, self.package)
File "/home/jbl/Code_Saturne/4.2.1/code_saturne-4.2.1/arch/Linux_x86_64/lib/python2.7/site-packages/code_saturne/cs_gui.py", line 135, in main
source_rcfile(pkg)
File "/home/jbl/Code_Saturne/4.2.1/code_saturne-4.2.1/arch/Linux_x86_64/lib/python2.7/site-packages/code_saturne/cs_exec_environment.py", line 661, in source_rcfile
rcfile = get_rcfile(pkg)
File "/home/jbl/Code_Saturne/4.2.1/code_saturne-4.2.1/arch/Linux_x86_64/lib/python2.7/site-packages/code_saturne/cs_exec_environment.py", line 644, in get_rcfile
config.read(pkg.get_configfiles())
File "/usr/lib/python2.7/ConfigParser.py", line 305, in read
self._read(fp, filename)
File "/usr/lib/python2.7/ConfigParser.py", line 546, in _read
raise e
ConfigParser.ParsingError: File contains parsing errors: /home/jbl/Code_Saturne/4.2.1/code_saturne-4.2.1/arch/Linux_x86_64/etc/code_saturne.cfg
[line 20]: ' syrthes = /home/jbl/syrthes4.3.0/arch/Linux_x86_64/\n'
What should it be?
is the following not correct?
Code: Select all
### Set the location to the SYRTHES installation directory.
syrthes = /home/jbl/syrthes4.3.0/arch/Linux_x86_64/
Re: Installing CS 4.2.1 and Syrthes 4.3.0 on Xubuntu 15.10
The problem was in the code_saturne.config file.
Solved with :
blankspace removed...
Now, let's test Code_saturne install by doing some tutorials cases...
Solved with :
Code: Select all
### Set the location to the SYRTHES installation directory.
syrthes =/home/jbl/syrthes4.3.0/arch/Linux_x86_64/bin
Now, let's test Code_saturne install by doing some tutorials cases...
Re: Installing CS 4.2.1 and Syrthes 4.3.0 on Xubuntu 15.10
The preprocessing stage of the lid driven cavity fails :
Looking in the preprocessor.log gives :
and a litlle bit after :
This means that the Salome version of MED is 3.1.0 and the Saturne version is 3.0.7.
The aren't compatible.
But in this install, the Saturne MED was set to be the Syrthes Med in the setup file.
So, Syrthes has to be reinstalled with pointing MED library to the Salome one, with in the setup.ini :
Then Saturne has to be reinstalled, alos pointing to the Salome MED library, with in the setup file :
the HDF5 library has also been changed to be linked with the salome one... even if it's the same version as Syrthes.
By the way, how should be "cleanly" uninstalled Saturne and Syrthes?
Typing "make uninstall" in the build directory is enough?
Code: Select all
***************************
Preprocessing calculation
***************************
Error running the preprocessor.
Check the preprocessor.log file for details.
****************************
Saving calculation results
****************************
Error in preprocessing stage.
Error in preprocessing stage.
Code: Select all
code_saturne version 4.2.1 (compilée le ven. 25 mars 2016 08:21:48 CET)
Support du format de fichiers CGNS 3.1.4
Support du format de fichiers MED 3.0.7 (HDF5 1.8.14)
Lecture de fichiers compressés ('.gz') avec Zlib 1.2.8
Code: Select all
Lecture du fichier de maillage au format MED (EDF/CEA)
------------------------------
Fichier de maillage : /home/jbl/Documents/Test_saturne/DrivenCavity/MESH/cavity_mesh.med
MEDversionedApi3C.c [50] : Cette bibliothèque MED n'est pas capable de lire un fichier MED dont le mineur de la versionexcède celui de la bibliothèque.
MEDversionedApi3C.c [51] : La version demandée est :
MEDversionedApi3C.c [51] : _fversionMMR = 310
MEDversionedApi3C.c [116] : Impossible d'obtenir une implémentation de :
MEDversionedApi3C.c [117] : key = "_MEDmeshInfoByName"
MEDversionedApi3C.c [118] : en version :
MEDversionedApi3C.c [119] : _fversionMMR = 310
MEDversionedApi3C.c [120] : Vérifiez votre fichier .med
MEDmeshInfo.c [83] : Erreur d'appel de l'API
MEDmeshInfo.c [83] : du maillage
MEDmeshInfo.c [84] : meshname = "cavity_mesh"
MEDmeshInfo.c [84] : _meshpath = "/ENS_MAA/cavity_mesh"
MEDmeshInfo.c [84] : "MEDmeshInfoByName" = "MEDmeshInfoByName"
The aren't compatible.
But in this install, the Saturne MED was set to be the Syrthes Med in the setup file.
So, Syrthes has to be reinstalled with pointing MED library to the Salome one, with in the setup.ini :
Code: Select all
#med USE=yes INSTALL=yes
#med USE=no INSTALL=no
med USE=yes PATH=/home/jbl/salome/Salome-V7_7_1-x86_64/tools/Medfichier-310/
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# Name Use Install Path
#
hdf5 yes no /home/jbl/salome/Salome-V7_7_1-x86_64/prerequisites/Hdf5-1814/
cgns auto no /usr
med yes no /home/jbl/salome/Salome-V7_7_1-x86_64/tools/Medfichier-310
scotch yes no /home/jbl/Code_Saturne/4.2.1/scotch-6.0.4/arch/Linux_x86_64
parmetis yes no /home/jbl/Code_Saturne/4.2.1/parmetis-4.0.3/arch/Linux_x86_64
libxml2 auto no None
#
By the way, how should be "cleanly" uninstalled Saturne and Syrthes?
Typing "make uninstall" in the build directory is enough?
Re: Installing CS 4.2.1 and Syrthes 4.3.0 on Xubuntu 15.10
Ok,
Syrthes and Saturne have been rebuild and installed and now are working both in serial and parallel.
Next step, the 3disks 2D tutorial for coupled calculation.
See you after the Eastern Week End for that...
Syrthes and Saturne have been rebuild and installed and now are working both in serial and parallel.
Next step, the 3disks 2D tutorial for coupled calculation.
See you after the Eastern Week End for that...