HDF5 library not found

[siden]

Hi All,

I try to run code_saturne 5.0.4 from a compilation
when I want to run a case I have the following error when doing the preprocessing:

/home/denis/Code_Saturne/5.0.4/code_saturne-5.0.4/arch/Linux_x86_64/libexec/code_saturne/cs_preprocess: error while loading shared libraries: libhdf5.so.9.0.0: cannot open shared object file: No such file or directory
Error running the preprocessor.
Check the preprocessor.log file for details.

The prepcocessor doesn't give me more information.

I compiled code_saturne with the salome_meca 2017 libraries by using the setup config as follow

#========================================================
# 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/denis/Code_Saturne/5.0.4
#
#--------------------------------------------------------
# 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/denis/salome_meca/V2017
#
#--------------------------------------------------------
# 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.
# When building with SALOME, the platform distribution's
# packages may be used, by setting 'salome' in the
# matching entry under the "Use" column.
#
# Scotch and Pt-Scotch are available in some Linux
# distributions, 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 auto no /home/denis/salome_meca/V2017/prerequisites/Hdf5-1814
cgns yes no /home/denis/salome_meca/V2017/prerequisites/Cgnslib-3134
med yes no /home/denis/salome_meca/V2017/tools/Medfichier-321
scotch yes no /home/denis/salome_meca/V2017/prerequisites/Scotch-5111
parmetis yes no /home/denis/salome_meca/V2017/prerequisites/Metis_aster-510_aster1
libxml2 auto no /home/denis/salome_meca/V2017/prerequisites/Libxml2-290
#
#========================================================

the compilation is running ok
I tried to use the system HDF5 libraries but the compilation fails to find it

does anyone knows how to solve that?

[Yvan Fournier]

Hello,

What type of system are you trying to run on ?

Could you run "/usr/bin/mpicc --version" and "/usr/bin/mpicc -show ?" and indicate the output ?

If your system adds "--enable-new-dtags" to the compile wrapper (this is the case on some types of systems, not Debian or Ubuntu to my knowledge), the issue is described in the install manual, and you may have no easy solution, except defining LD_LIBRARY_PATH). Otherwise, this is surprising.

In any case if you run "salome context" before running Code_Saturne commands, you should have a workaround solution.

Regards,

Yvan

[siden]

Hello,

I'm running on linux mint 18.2

/usr/bin/mpicc --version

gcc (Ubuntu 5.4.0-6ubuntu1~16.04.4) 5.4.0 20160609
Copyright (C) 2015 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

/usr/bin/mpicc -show

gcc -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2021/libevent -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2021/libevent/include -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -pthread -Wl,-rpath -Wl,/usr/lib/openmpi/lib -Wl,--enable-new-dtags -L/usr/lib/openmpi/lib -lmpi

I still have the issue after executing " salome context"

[Yvan Fournier]

Hello,

Your system uses the --enable-new-dtags option I mentioned (explained in more detail at the end of the installation manual). This is a stupid standard, but we'll have to adapt to it someway in the future if it becomes more common...

In the meantime, could you try "salome shell" instead of "salome context" ? (be careful, other aliases will be ignored under that subshell).

Best regards,

Yvan

[siden]

Hi,

with "salome shell" I have no Gui ( Qt is missing)
how can i define the LD_LIBRARY_PATH ?

If i add it with

Code: Select all

export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:"/home/denis/salome_meca/V2017/prerequisites/Hdf5-1814"

it still doesn't work

[Yvan Fournier]

Hello,

Can you try:

export LD_LIBRARY_PATH="/home/denis/salome_meca/V2017/prerequisites/Hdf5-1814/lib:$LD_LIBRARY_PATH"

Regards,

Yvan