code_saturne User's Forum

Hello everyone,

I use ./configure make and make install to install code_saturne 4.0.7, but after installation I find that the mesh can not be checked, so i think the MED is not successfully installed, then I try to install it but meet a problem:

Problem of MED installation: ERROR "configure: error: either use HDF5HOME env. var. or --with-hdf5=<path>"

Is there anyone who has met this problem?

best regards

Hello,

Which version of MED did you try to install ? It seems you tried version 3.0.8, while 3.2 whould be better (and the installer downloads 3.2, which would need to be updated to 3.2.1).

Best regards,

Yvan

Hello Yvan,

I am trying to install code_saturne-4.2.3 by using installer. But there is an error when the installation process comes to scotch.

Originally, the error shown in install_saturne.log is "fatal error: mpi.h: No such file or directory", so I copy the mpi.h from file mpi into file /usr/include/, is it right? Then this error disappearred.

however a new error occurred which is shown as "collect2: error: ld returned 1 exit status", the install_saturne.log is attached.

Best regars
Jiawei

Hello,

You should not need to copy mpi.h to another place if your MPI library is installed correctly (and completely; there may be several packages).

Doing so risks messing up you system if you do not know exactly what you are doing.

You should check your MPI installation/reinstall packages.

I can't tell you which packages you may need since you did not provide the recommended info on your system, but the install manual has some info.

Regards,

Yvan

Hello yvan,

I reinstall code_saturne_4.0.7 with installer. And I met the original problem, there is an error "error: either use HDF5HOME env. var. or --with-hd" for the installation of MED.

Moreover, I tried to install libz1g-dev and install python-dev, and I also tried to change my environment, but the outcome is still negative.

The install_saturne.log and MED config are attached, would you please take a look and give me some advice?

Best regards,
Jiawei

Hello,

Try to check if there is an hdf5-tools or similar package which is available but not installed on your system. If this is the case, install it.

Otherwise, try also to install HDF5 using the installer (even if you already have an installed package). This may help if hdf5 does not contain the "bin" directory due to missing tools.

Regards,

Yvan

Hello Yvan,

Thanks for your suggestion. The problem about MED has been solved, but there is still an error when installing code_saturne.

PyQT4 has been installed in my ubuntu 16.04, but It seems that pyqt4 connot be detected. By the way, I use installer to install CS and all the prepackages automatically. Would you please give me some advice?

PS: installer_saturne.log is shown as follows:
" unknown orb
checking for pdflatex... no
configure: WARNING: pdflatex not found
checking for bibtex... no
configure: WARNING: bibtex not found
checking for makeindex... no
configure: WARNING: makeindex not found
checking for fig2dev... no
configure: WARNING: fig2dev not found
checking for doxygen... no
configure: WARNING: doxygen not found
checking for dot... no
configure: WARNING: dot not found
checking for sphinx-build... no
configure: WARNING: sphinx-build not found
checking for PyQt4 version >= 4.3... /home/liu/Desktop/packages/folder/code_saturne-4.0.7/configure: line 26898: 26189 Segmentation fault (core dumped) ${PYTHON} -c "${prog}"
no
configure: error: in `/home/liu/Desktop/packages/folder/code_saturne-4.0.7.build':
configure: error: cannot find PyQt4 support (>= 4.3), Graphical User Interface cannot be installed
See `config.log' for more details"

Best regards,
Jiawei

Hello,

You may need (and be missing) pyqt4-dev or pyqt4-tools (or similarly named packages).

Regards,

Yvan

Hello Yvan,

I am very grateful for your help, all the prepackages and CS have been successfully installed. Then i created a simple case to test the functions I need. However, the code_saturne cannot check mesh in the format MED, I don't understand the reason, do I need link manually CS and MED, HDF5 and so on? The error is shown as follows.

Regards,

Jiawei

Error in preprocessor execution
===============================

/home/liu/Desktop/Installation/code_saturne-4.0.7/preprocessor/pre-post/ecs_pre.c:486: Fatal error.

File format "MED" support not available in this
installation (file "/home/liu/Desktop/work/projet/MESH/core-mesh.med").


Call stack
1: 0x40b871 (cs_preprocess)
2: 0x407293 (cs_preprocess)
3: 0x404bdf (cs_preprocess)
4: 0x7f3cb99c1830 (libc.so.6)
5: 0x4054c9 (cs_preprocess)
End of stack

Hello,

It seems your MED installation was not detected. Could you provide the info and files detailed in this forum's usage guidelines ?

Regards,

Yvan