installation Salome+CS+Syrthes via VM on ubuntu 15.10

[Yvan Fournier]

Hello,

Yes, to have the CFDSTUDY module, you need to set the salome = line (and then run SALOME using "code_saturne salome", not directly run the main SALOME application).

If you have an error when you do this, could you post it ?

For Syrthes, you can use Scotch instead of Metis 5.1 if you prefer. You do not need to use the same version of HDF5 or MED, so you can use the ones included (but be careful if you use SALOME 7.7, which generates MED 3.1 files, which are not readable by MED 3.0).

You'll also have to provide the path for PLE (the same as Code_Saturne).

Regards,

Yvan

[jgd23]

Hello Yvan,

I have restart from the beginning with a fresh version of linux 15.10
I have installed Salome 7.6.0 to have the MED.3.0
I have modify the set up file of Code Saturne like this:

#===============================....
# Setup file for Code_Saturne installation
#========================================================
#
#--------------------------------------------------------
# Download packages ?
#--------------------------------------------------------
download no
#
#--------------------------------------------------------
# Language
# default: "en" english
# others: "fr" french
#--------------------------------------------------------
language fr
#
#--------------------------------------------------------
# Install Code_Saturne with debugging symbols
#--------------------------------------------------------
debug no
#
#--------------------------------------------------------
# Installation directory
#--------------------------------------------------------
prefix /home/julien/Code_Saturne/4.0.5
#
#--------------------------------------------------------
# Optional architecture Name (installation subdirectory)
#--------------------------------------------------------
use_arch no
arch Linux_x86_64
#
#--------------------------------------------------------
# C compiler and optional MPI wrapper
#--------------------------------------------------------
compC /usr/bin/cc
mpiCompC /usr/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 /usr/bin/mpicxx
#
#--------------------------------------------------------
# Python interpreter.
#--------------------------------------------------------
python /usr/bin/python
#
#--------------------------------------------------------
# Disable the Graphical user Interface ?
#--------------------------------------------------------
disable_gui no
#
#--------------------------------------------------------
# Disable frontend (also disables GUI) ?
# May be useful for debug builds and HPC cluster builds
# installed side-by side with a full build.
#--------------------------------------------------------
disable_frontend no
#
#--------------------------------------------------------
# Optional SALOME platform install path.
#
# This is the path for the main SALOME directory,
# not the application directory.
#
# If Code_Saturne is built with SALOME support,
# running "code_saturne salome" will launch the
# associated application, containing the CFDSTUDY module.
#--------------------------------------------------------
salome /home/julien/salome
#
#--------------------------------------------------------
# Optional packages:
# ------------------
#
# MED / HDF5 For MED file format support
# (used by SALOME and by Gmsh)
#
# CGNS / HDF5 For CGNS file support
# (used by many meshing tools)
#
# Scotch (includes PT-Scotch) and/or ParMetis
# for parallel partitioning
#
# For Linux workstations, HDF5, CGNS, and even MED
# packages may be available through the package manager.
# HDF5 is also often available on large systems such as
# IBM Blue Gene or Cray XT/XE/XC/XK.
#
# Scotch and Pt-Scotch are available in some Linux
# distributtions, but may be built with options
# incompatible with non-threaded Code_Saturne runs.
#
# To install CGNS or ParMetis, the CMake
# configuration/installation tool is required
# (it is available in most Linux distributions)
#
# Libxml2 is needed to read XML files output by the
# Graphical User Interface. It is generally available
# through the package manager.
#--------------------------------------------------------
#
# Name Use Install Path
#
hdf5 yes no /home/julien/salome/Salome-V7_6_0-x86_64/prerequisites/Hdf5-1810
cgns no no None
med yes no /home/julien/salome/Salome-V7_6_0-x86_64/modules/MED_V7_6_0
scotch no no None
parmetis no no None
libxml2 no no None
#
#========================================================

I run install_saturne.py and I have a new error message:

"o Configure...
Error during configure stage of Code_Saturne.
See install_saturne.log for more information."

The log is here:

"checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking target system type... x86_64-unknown-linux-gnu
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 how to create a pax tar archive... gnutar
checking whether to enable maintainer-specific portions of Makefiles... no
checking for modulecmd... no
checking for gcc... /usr/bin/mpicc
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 /usr/bin/mpicc accepts -g... yes
checking for /usr/bin/mpicc option to accept ISO C89... none needed
checking for style of include used by make... GNU
checking dependency style of /usr/bin/mpicc... gcc3
checking whether we are using the GNU C++ compiler... yes
checking whether /usr/bin/mpicxx accepts -g... yes
checking dependency style of /usr/bin/mpicxx... gcc3
checking whether we are using the GNU Fortran compiler... yes
checking whether /usr/bin/f95 accepts -g... yes
checking whether ln -s works... yes
checking whether /usr/bin/mpicc and cc understand -c and -o together... yes
checking for a sed that does not truncate output... /bin/sed
checking for flex... no
checking for lex... no
checking for bison... no
checking for byacc... no
configure: sourcing config/cs_auto_flags.sh (test for known compilers)
compiler '/usr/bin/mpicc' is GNU gcc-5.2.1
compiler '/usr/bin/mpicxx' is GNU g++-5.2.1
compiler '/usr/bin/f95' is GNU gfortran-5.2.1
checking for a sed that does not truncate output... (cached) /bin/sed
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for fgrep... /bin/grep -F
checking for ld used by /usr/bin/mpicc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking the maximum length of command line arguments... 1572864
checking whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... yes
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for ar... ar
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from /usr/bin/mpicc object... ok
checking how to run the C preprocessor... /usr/bin/mpicc -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 for dlfcn.h... yes
checking whether we are using the GNU C++ compiler... (cached) yes
checking whether /usr/bin/mpicxx accepts -g... (cached) yes
checking dependency style of /usr/bin/mpicxx... (cached) gcc3
checking how to run the C++ preprocessor... /usr/bin/mpicxx -E
checking whether we are using the GNU Fortran compiler... (cached) yes
checking whether /usr/bin/f95 accepts -g... (cached) yes
checking for objdir... .libs
checking if /usr/bin/mpicc supports -fno-rtti -fno-exceptions... no
checking for /usr/bin/mpicc option to produce PIC... -fPIC -DPIC
checking if /usr/bin/mpicc PIC flag -fPIC -DPIC works... yes
checking if /usr/bin/mpicc static flag -static works... no
checking if /usr/bin/mpicc supports -c -o file.o... yes
checking if /usr/bin/mpicc supports -c -o file.o... (cached) yes
checking whether the /usr/bin/mpicc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... no
checking for ld used by /usr/bin/mpicxx... /usr/bin/ld -m elf_x86_64
checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes
checking whether the /usr/bin/mpicxx linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking for /usr/bin/mpicxx option to produce PIC... -fPIC -DPIC
checking if /usr/bin/mpicxx PIC flag -fPIC -DPIC works... yes
checking if /usr/bin/mpicxx static flag -static works... no
checking if /usr/bin/mpicxx supports -c -o file.o... yes
checking if /usr/bin/mpicxx supports -c -o file.o... (cached) yes
checking whether the /usr/bin/mpicxx linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... no
checking for /usr/bin/f95 option to produce PIC... -fPIC
checking if /usr/bin/f95 PIC flag -fPIC works... yes
checking if /usr/bin/f95 static flag -static works... yes
checking if /usr/bin/f95 supports -c -o file.o... yes
checking if /usr/bin/f95 supports -c -o file.o... (cached) yes
checking whether the /usr/bin/f95 linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking for an ANSI C-conforming const... yes
checking for inline... inline
checking for size_t... yes
checking for pid_t... yes
checking whether time.h and sys/time.h may both be included... yes
checking for stdbool.h that conforms to C99... yes
checking for _Bool... yes
checking for long long... yes
checking for unsigned long long... yes
checking for int32_t... yes
checking for int64_t... yes
checking for uint32_t... yes
checking for uint64_t... yes
checking for ptrdiff_t... yes
checking size of void *... 8
checking size of short... 2
checking size of int... 4
checking size of long... 8
checking size of long long... 8
checking size of float... 4
checking size of double... 8
checking whether /usr/bin/python version >= "2.4"... yes
checking for /usr/bin/python version... 2.7
checking for /usr/bin/python platform... linux2
checking for /usr/bin/python script directory... ${prefix}/lib/python2.7/site-packages
checking for /usr/bin/python extension module directory... ${exec_prefix}/lib/python2.7/site-packages
checking how to get verbose linking output from /usr/bin/f95... -v
checking for Fortran libraries of /usr/bin/f95... -L/usr/lib/gcc/x86_64-linux-gnu/5 -L/usr/lib/gcc/x86_64-linux-gnu/5/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/5/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/5/../../.. -lgfortran -lm -lquadmath
checking for ESSL BLAS headers... no
checking for threaded MKL BLAS... no
checking for MKL BLAS... no
checking for threaded ATLAS BLAS... no
checking for ATLAS BLAS... no
checking for threaded ACML BLAS... no
checking for ACML BLAS... no
checking for legacy C BLAS... no
configure: WARNING: no BLAS support
checking for MPI (MPI compiler wrapper test)... yes
checking for MPI I/O... yes
checking for MPI2 one-sided communication... yes
checking for MPI2 features... yes
checking hdf5.h usability... yes
checking hdf5.h presence... yes
checking for hdf5.h... yes
checking for H5Fopen in -lhdf5... yes
MED >= 3.0 headers not found
configure: error: in `/home/julien/code_saturne/code_saturne-4.0.5.build':
configure: error: MED support is requested, but test for MED failed!
See `config.log' for more details"

And the config log is attached.

What's wrong this time?

Best regards

Julien

[Yvan Fournier]

Hello,

The MED SALOME module is a higher-level tool than the MED I/O library, which is in a separate path... ):

So you should replace (in your setup file):

med yes no /home/julien/salome/Salome-V7_6_0-x86_64/modules/MED_V7_6_0

with:

med yes no /home/julien/salome/Salome-V7_6_0-x86_64/tools/Medfichier-308

Best regards,

Yvan

[jgd23]

Thank you, it works now after the install_saturne.py without errors.

I update environment as it says with "cspath=..." and "alias code_saturne="cspath/bin".
When I make the command code_saturne, it says that code saturne is not installed and that I have to do:
sudo apt-get install code-saturne-bin

to install code saturne

I thank that code saturne was installed in the step juste before... Do I have to execute this command?

Best regards

Julien

[Yvan Fournier]

Hello,

For the alias, did you use cspath/bin, or $cspath/bin ?

Did you try using the absolute path (that should always work) ?

Regards,

Yvan

[jgd23]

Hello,

After the command line: install_saturne.py, I follow instructions written in the terminal:

cspath=/home/julien/Code_Saturne/4.0.5/code_saturne-4.0.5/arch/Linux_x86_64/bin
alias code_saturne="$cspath/bin"

Best regards

Julien

[Yvan Fournier]

Hello,

Your alias should be:

alias code_saturne="$cspath/bin/code_saturne"

Regards,

Yvan

[jgd23]

I change the alias.

It gives me the same message, that code saturne is not yet installed and that I have to do:

sudo apt-get install code-saturne-bin

Best regards

Julien

[Yvan Fournier]

Hello,

Did you try using the full path instead or the alias:
/home/julien/Code_Saturne/4.0.5/code_saturne-4.0.5/arch/Linux_x86_64/bin/code_saturne

?

Regards,

Yvan

[jgd23]

It works! I can launch the GUI! I can create a case also.
I see all the different options associated, also salome, but I can't launch with the command salome with code_saturne salome...

May I need an existing salome file?

Best regards