TELEMAC-MASCARET Forum: Compatibility problems, installation HDF5 and MED (1/1)

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TOPIC: Compatibility problems, installation HDF5 and MED

Compatibility problems, installation HDF5 and MED 2 years 8 months ago #39985

CFDavatar
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Junior Boarder
Posts: 31

Dear all,

I have succesfully compiled telemac without the additional libraries, I am trying to install HDF5 and MED. However, there is an issue with the compatibility between them.

This is a error I have when running ./configure --with-hdf5=<Path-to-installation>:

///opt/hdf5-1.8.13/hdf5//include/H5public.h
configure: error: 
This HDF5 version 1.8.13 must not be used with med-fichier4.1.0.
The HDF5 library version used by med-fichier4.y.z MUST NOT be > 1.10 and have to be at least HDF5-1.10.2.
DO NOT TRY TO COMPILE med-fichier4.1.0 version with an HDF5 library which would generate an hdf5 file not compliant with HDF5-1.10.z library.
This would BREAK med-fichier compatibility between files with the same revision number !

I have tried with different distributions of hdf5: 1.12.0, 1.8.14, 1.8.13

Does anyone of you know how to solve this issue?

Kind regards,

Marcelo

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Compatibility problems, installation HDF5 and MED 2 years 8 months ago #39986

pham
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Administrator
Posts: 1559
Thank you received: 602

Hello Marcello,

I use MED 4.1.0 with HDF5 1.10.3 and it works. You should try this release of HDF5. For sure with version 1.8, the error message you have will be written. Perhaps version 1.12.0 is too recent or there is a bug with this version (I am not a specialist to install MED).

Anyway, if you only use serafin format rather than MED for your computations, you do not need to install MED.

Hope this helps,

Chi-Tuan

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Compatibility problems, installation HDF5 and MED 2 years 8 months ago #39999

CFDavatar
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Junior Boarder
Posts: 31

Dear Chi-Tuan

I am trying to compile Telemac to use TelApy as described in the installation linkinstallation link:

[C9.gfortran.dyn]
brief: Gfortran compiler 4.9.2 with open_mpi for a debian 8 all libraries are compiled in dynamic
#
options: api
#
sfx_lib:    .so
#
mpi_cmdexec: mpirun -machinefile MPI_HOSTFILE -np <ncsize> <exename>
#
cmd_obj:    mpif90 -c -cpp -fPIC -O2 -fconvert=big-endian -frecord-marker=4 -DHAVE_MPI -DHAVE_MUMPS -DHAVE_MED -DHAVE_VTK <mods> <incs> <f95name>
cmd_lib:    mpif90 -fPIC -shared -fconvert=big-endian -frecord-marker=4 -lpthread -lm -o <libname> <objs>
cmd_exe:    mpif90 -fPIC -fconvert=big-endian -frecord-marker=4 -lpthread -lm -o <exename> <objs> <libs>
#
libs_all: -L$MUMPSHOME/lib -ldmumps -lmumps_common -lpord
          -L$SCALAPACKHOME/lib -lscalapack
          -lblas
          -lm -L$MEDHOME/lib -lmed -L$HDF5HOME/lib -lhdf5 -ldl -lstdc++ -lz
          -L$METISHOME/lib -lmetis
 
cmd_obj_c: gcc -c -fPIC <srcName> -o <objName>

In this section it is specified HDF5 and MED in the libraries. I already changed the version of HDF5, and it solved it. Now, I am facing another issue. The ./ configuration in med 4.1.0 displays this error:

checking for python... no
configure: error: Cannot find python in your system path

I have added /usr/bin/python3.4 to the PATH in .bashrc
I also have set PYTHONPATH in the .bashrc file.

I have been looking for some support online but not succeeding. I cannot find another version to try.

I will appreciate any support.

Kind regards,

Marcelo

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Compatibility problems, installation HDF5 and MED 2 years 8 months ago #40019

CFDavatar
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Junior Boarder
Posts: 31

Dear all I have solved the issue.

If the command ./configuration cannot find a python library it is most likely you don't have the directory "/usr/bin/python". Make this directory available and link it with Python 3.# with the following command

$ update-alternatives --config python

I installed python2:

$ sudo apt-get install python2

and then change it to python3.

I hope this help someone who is facing the same issue,

Regards,

Marcelo

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Compatibility problems, installation HDF5 and MED 2 years 8 months ago #40062

pham OFFLINE Administrator Posts: 1559 Thank you received: 602	Hello Marcelo, Good news if you have solved the issue. Thanks for sharing your solution, it may help other users. Chi-Tuan
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Compatibility problems, installation HDF5 and MED 2 years 8 months ago #40065

nicogodet OFFLINE Expert Boarder Posts: 157 Thank you received: 39	Installing the package python-is-python3 should solve this issue without the need to install python2. Anyway, MED compilation should be fixed by looking for python3 instead of python.
	The administrator has disabled public write access. The following user(s) said Thank You: CFDavatar