installation Salome+CS+Syrthes via VM on ubuntu 15.10

[jgd23]

To couple Code saturne with Syrthes I need to link the PLE library of code saturne in the set up.ini of Syrthes. I find several ple files which path have I to specify?

Best regards

Julien

[Yvan Fournier]

Hello,

If you used the defaults for Code_Saturne (i.e. did not use any "--with-ple" configure option), the path for PLE is the same as the Code_Saturne installation prefix.

Best regards,

Yvan

[jgd23]

Hello Yvan,

1.Can you please tell me how can I run code saturne with salome with the command "code_saturne salome"?
I need a created salome case before?
2. I try to install Syrthes with the ple file associated with code saturne. Sorry I don't understand very well your previous post, this is my set up.ini file:
#--------------------------------------------------------
# Architecture Name
#--------------------------------------------------------
#nom_arch Linux_x86_64 <- for specific architecture
#nom_arch <- leave empty for automatic default
# value (based on uname)
nom_arch
#
#--------------------------------------------------------
# C compiler (sequential)
#--------------------------------------------------------
#compC /home/toto/gcc-x.y.z/gcc <- for specific C compiler
#compCX /home/toto/gcc-x.y.z/g++ <- for specific C++ compiler (only needed for MPI installation)
#compC gcc <- leave gcc for automatic default
#compCX g++ <- leave g++ for automatic default
#
compC gcc
compCX g++
#
# C wrapper
#wrapperC mpicc <- for specific C wrapper without path (only needed for MPI installation)
# leave mpicc for automatic default
wrapperC mpicc
#
# Specific options for compiler
#specific_inc= -I /myinclude/inc -I /myinclude2/inc
#specific_lib= -L /mylib/lib1 -L /mylib/lib2
#specific_debug= -g
#specific_option= -D _SYRTHES_MPI_IO_
#
# parallel compilation
#specific_makej= -j8
#
#--------------------------------------------------------
# Graphical user Interface
#--------------------------------------------------------
gui INSTALL=yes
#
#--------------------------------------------------------
# Interpreted functions
#--------------------------------------------------------
# Answer by yes or no
#
# interpreted function module - SYRTHES - sequential version
syrthesppfunc INSTALL=yes
#
#--------------------------------------------------------
# SYRTHES4 - kernel - sequential version
#--------------------------------------------------------
# Answer by yes or no
#
# SYRTHES - sequential version
syrthesseq INSTALL=yes
#
#
#--------------------------------------------------------
# SYRTHES4 - tools for meshes and results conversions
#--------------------------------------------------------
# Choose your type of installation and answer by yes or no
# Select the line corresponding to your choice
#
# for MED format conversion : choose to istall or the path to the libraries
hdf5 USE=yes INSTALL=yes
#hdf5 USE=no INSTALL=no
#hdf5 USE=yes PATH=/.../syrthes4.2/extern-libraries/opt/hdf5-1.8.8/arch/MY_ARCH
#
#
med USE=yes INSTALL=yes
#med USE=no INSTALL=no
#med USE=yes PATH=/.../syrthes4.2/extern-libraries/opt/med-3.0.6/arch/MY_ARCH
#
#
# Answer by yes or no
#
# mesh format conversion tool
syrthesconvert INSTALL=yes
#
# results file format conversion tool SYRTHES --> Paraview/Ensight
syrthesensight INSTALL=yes
#
# results file format conversion tool SYRTHES --> SALOME-MED
syrthesmed INSTALL=yes
#
#--------------------------------------------------------
# SYRTHES4 - parall version (optional)
#--------------------------------------------------------
# Choose your type of installation and answer by yes or no
# Select the line corresponding to your choice
# mpi is required, metis AND/OR scotch are required
#
mpi USE=yes INSTALL=yes
#mpi USE=no INSTALL=no
#mpi USE=yes PATH=/.../syrthes4.2/extern-libraries/opt/openmpi-1.4.3/arch/MY_ARCH
#
metis USE=no INSTALL=no
#metis USE=no INSTALL=no
#metis USE=yes PATH=/.../syrthes4.2/extern-libraries/opt/metis-5.0.2/arch/MY_ARCH
#
scotch USE=yes INSTALL=yes
#scotch USE=no INSTALL=no
#scotch USE=yes PATH=/.../syrthes4.2/extern-libraries/opt/scotch_5.1.12b/arch/MY_ARCH
#
# Answer by yes or no
#
# mesh partitionning - SYRTHES parallel version - rebuilding results file
syrthespp INSTALL=yes
syrthesmpi INSTALL=yes
syrthespost INSTALL=yes
#
#--------------------------------------------------------
# Optional extern libraries
#--------------------------------------------------------
# Choose your type of installation and answer by yes or no
# Select the line corresponding to your choice
#
# BLAS Linear algebra library
blas USE=no INSTALL=no
#blas USE=yes PATH=/home/...
#
#--------------------------------------------------------
# SYRTHES for coupling with Code-Saturne (optional)
#--------------------------------------------------------
# Warning : MPI installation must be defined before
#
# ple USE=no
ple USE=yes PATH=/home/julien/code_saturne-4.0.5/libple
#
#PATH=/.../saturne/opt/libple-1.0/arch/MY_ARCH
#
# answer by yes or no
syrthescfd INSTALL=yes
#
#

I have a new error during the installation of med in Syrthes
Installation of med-3.0.7 on architecture Linux_x86_64, see the terminal:

Unzip med-3.0.7

***************************************************
* Installation MED *
***************************************************


cat: med.log: Aucun fichier ou dossier de ce type
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... no
checking for mawk... mawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking how to create a ustar tar archive... gnutar
checking whether to compile using MPI... no
checking for style of include used by make... GNU
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking dependency style of gcc... gcc3
checking for gcc option to accept ISO C99... none needed
checking whether to compile using MPI... no
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
configure: Can't find a parallel version of HDF.
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking absolute name of <H5public.h>... checking H5public.h usability... yes
checking H5public.h presence... yes
checking for H5public.h... yes
///home/julien/Syrthes/syrthes4.3.0/extern-libraries/opt/hdf5-1.8.14/arch/Linux_x86_64/include/H5public.h
checking absolute name of <H5Ipublic.h>... checking H5Ipublic.h usability... yes
checking H5Ipublic.h presence... yes
checking for H5Ipublic.h... yes
///home/julien/Syrthes/syrthes4.3.0/extern-libraries/opt/hdf5-1.8.14/arch/Linux_x86_64/include/H5Ipublic.h
checking for H5open in -lhdf5... no
configure: error: either use HDF5HOME env. var. or --with-hdf5=<path>
make: *** No rule to make target 'install'. Arrêt.
Error during make install of med-3.0.7

Best regards

Julien

[Yvan Fournier]

Hello,

For code_saturne / salome, juste type "code_saturne salome" or $install_prefix code_saturne salome" instead of code_saturne to have a SALOME session with CFDSTUDY available.

I'll be mostly offline for the next 3 days, so i'll check the rest next wek.

Regards,

Yvan

[jgd23]

Hello,

I didn't suceed to launch code saturn via salome... I don't understand what you mean with "$install_prefix code_saturne salome instead of code_saturne".

When I type in a terminal in the folder where I can execute code_saturne:
./code_saturne salome
/bin /bash: ligne 4: /bin/salome/envSalome.py: Aucun fichierou dossier de ce type.

My set up file is in the previous mail.

Best regards

Julien

[Yvan Fournier]

Hello,

I noticed that the PLE path in your syrthes.ini configuration seems incorrect (it must point to the installation, not the sources).
Also, in your Code_Saturne setup, you have:

salome /home/julien/salome

which is probably incorrect (you need the path of the salome directory (not application) inside that directory (probably something similar to: /home/julien/salome/Salome-V7_7_1-x86_6)

Regards,

Yvan

[jgd23]

Hello Yvan,

I change as you said the path for salome in the set up file of code saturne.
"salome /home/julien/salome/Salome-V7_6_0-x86_64"

I have a new error during compilation, with another path there is no error in compilation.

The log is attached

For Syrthes, I try the set up.ini for ple

ple USE=yes PATH=/home/julien/Code_Saturne/4.0.5/code_saturne-4.0.5/arch/code_saturne/lib

I don't know exactly where I have to point...

I have the same error during the med installation.

Best regards

Julien

[Yvan Fournier]

Hello,

It seems you are missing the "lrelease" tool which is part of the Qt development environment.

Make sure you have all Qt development packages installed.

For the PLE path, try /home/julien/Code_Saturne/4.0.5/code_saturne-4.0.5/arch/Linux_x86_64

Regards,

Yvan

[jgd23]

Hello,

I download others Qt4 dev tools. I can launch code saturne salome now!
I try a tutorial: http://code-saturne.org/cms/sites/defau ... _Study.pdf

It works until the time I launch the calcul, I have the error: version 'GFORTRAN_1.4' not found
See log attached

In the tutorial the temperature is coupled with the fluid motion, the variable TempC is used but in my file TempC is not recognized... Any suggestion?

Best regards

Julien

[jgd23]

I tried to specify the gfortran path for code saturne as you told in
http://code-saturne.org/forum/viewtopic ... 6&start=10

when I install code saturn I do:
./install_saturne.py LDFLAGS="-Wl,-rpath -Wl,/usr/lib"

Code saturne is installed withour error but when I launc a calculation I have the same error with Gfortan_1.4 missing...

Best regards

Julien