Installing CS 4.2.1 and Syrthes 4.3.0 on Xubuntu 15.10

[jb_l]

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.

[Yvan Fournier]

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

[jb_l]

So, I've try to install CS using the automated script.

But things go wrong in the compilation stage.

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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

In the setup file, the script detect the MPI from syrthes :

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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

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

[jb_l]

here is the setup file

[Yvan Fournier]

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

[jb_l]

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 :

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jbl@VM-CAO-S81-BA:~/Documents/Test_saturne$ code_saturne create --study test1

the answer is

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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

when trying

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jbl@VM-CAO-S81-BA:~/CS4.2.1$ code_saturne gui

the answer is:

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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

I'm a bit disapointed...
What did I do wrong?

Please find the install.log and the setup file

If anybody has any idea...

[jb_l]

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 :

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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'

the mistake seems to be in the code_saturne.cfg, about the syrthes path...

What should it be?
is the following not correct?

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### Set the location to the SYRTHES installation directory.
 syrthes = /home/jbl/syrthes4.3.0/arch/Linux_x86_64/

JB

[jb_l]

The problem was in the code_saturne.config file.
Solved with :

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### Set the location to the SYRTHES installation directory.
syrthes =/home/jbl/syrthes4.3.0/arch/Linux_x86_64/bin

blankspace removed...

Now, let's test Code_saturne install by doing some tutorials cases...

[jb_l]

The preprocessing stage of the lid driven cavity fails :

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

Error running the preprocessor.
Check the preprocessor.log file for details.


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

Error in preprocessing stage.

Error in preprocessing stage.

Looking in the preprocessor.log gives :

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  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

and a litlle bit after :

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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"

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 :

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#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/

Then Saturne has to be reinstalled, alos pointing to the Salome MED library, with in the setup file :

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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
#

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?

[jb_l]

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...