code_saturne User's Forum

Hi all,
i'm trying to install cs 4.2.0 manually but when I run ./configure the installation program is not able to detect BLAS Scotch CGNS , MED, HDF... and so on despite I have them installed via synaptic.
What can i do to make configure file recognise them directly ?

Thanks in advance

bindir='${exec_prefix}/bin'
build='x86_64-unknown-linux-gnu'
build_alias=''
build_cpu='x86_64'
build_os='linux-gnu'
build_vendor='unknown'
ccversion='5.2.1'
cgns_prefix=''
coolprop_prefix='check'
cs_env_modules='no'
cs_have_blas='no'
cs_have_calcium='no'
cs_have_catalyst='no'
cs_have_ccm='no'
cs_have_cgns='no'
cs_have_coolprop='no'
cs_have_doxygen='no'
cs_have_eos='no'
cs_have_freesteam='no'
cs_have_frontend='yes'
cs_have_gui='yes'
cs_have_hdf5='no'
cs_have_latex='no'
cs_have_libxml2='yes'
cs_have_long_gnum='yes'
cs_have_med='no'
cs_have_medcoupling='no'
cs_have_metis='no'
cs_have_mpi='yes'
cs_have_openmp='yes'
cs_have_paramedmem='no'
cs_have_petsc='no'
cs_have_salome_gui='yes'
cs_have_salome_kernel='yes'
cs_have_salome_yacs='yes'
cs_have_scotch='no'
cs_have_sphinx='no'
cs_py_have_plugins='False'
cs_special_user_link=''
cs_src_revision='4.2.0'
cs_tex_path_end=':'
cs_tex_path_sep=':'
cs_version='4.2'
cs_version_full='4.2.0'
cs_version_short='4.2'

Hello,

Could you post the details as listed in this Forum section's recommendations ?

Also, avoid running "configure" in the source directory (using a separate build directory is strongly recommended).

Regards,

Yvan

Hello Yvan, thank you for the fast reply and sorry for not attaching config.log
I run configure in another separate directory but the error is still there. this time I have attached the log file.

Thanks in advance.

Andrea

Hello,

At least for HDF5 (required by MED), the med.h file is not installed. Did you install the associated "-dev" package series as described in the installation manual ?

Regards,

Yvan

Yes, i checked from synaptic and i have installed:
Hierarchical Data Format 5 (HDF5) - development files - serial version
Hierarchical Data Format 5 (HDF5) - development files - OpenMPI version
Hierarchical Data Format 5 (HDF5) - development files - default MPI version

Development files for libmed
Development files for libmedc

libcgns-dev

libmetis-dev
libmetis-edf-dev

...and so on
but still configure won't display me

Hello,

Due to the multiple builds of HDF5 (with and without MPI), the files may not be directly in /usr/include and /usr/lib; but under a subdirectory. You might need to check the file paths by listing files associated with the packages under Synaptic to adapt them to Ubuntu, but on some of our Debian machines, for HDF5, we need to add:
--with-hdf5=/usr/lib/x86_64-linux-gnu/hdf5/serial

Best regards,

Yvan

really thank you !
directly linking the libraries is working. I'm wondering why it can't find, for example, BLAS by himself but it's ok with --with-blas=/usr/lib/libblas

Is there any way to check if the software is able to browse usr/lib folder in search of pre-requisites? if not i'll manually provide all the libraries.

Another question, if you can answer me, since i want to use multiple processors during simulations i have to choose hdf5 openmpi instead of serial, right ?

Thanks

Andrea

Hello,

No, we currently only use MPI-IO for EnSight format output and checkpoint/restart files.

MED and CGNS still use serialized I/O, so serial HDF5 is fine.

The code should look in /usr by itself, but BLAS might be only linked if forced. BLAS are only used for some unit performance comparison tests in the code (except for the Intel MKL, whose sparse matrix-vector multiplication functions can be used during computation, and then still only if forced through tuning defined in user subroutines), so I would not bother with them.

Regards,

Yvan