Hdf5 linking not working

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CTrinca
Posts: 32
Joined: Mon Mar 30, 2015 9:19 am

Hdf5 linking not working

Post by CTrinca »

Hello everyone,

I am trying to install the triplet Salome + Saturne + Syrthes on a new workstation, but I encounter a problem I never had in my previous installation.
I make use of Salome's libraries, and nothing seems to go wrong during the compilation: in particular, at the end of the configure run, Hdf5 seems to be supported:

Code: Select all

 HDF (Hierarchical Data Format) support: yes
Also, make and make install do not seem to protest (I attach their output to this post, in case it could help)
However, when I try a test run, Saturne complains that it cannot find libhdf5:

Code: Select all

/opt/Code_Saturne/4.0.7/prod/libexec/code_saturne/cs_solver: error while loading shared libraries: libhdf5.so.9: cannot open shared object file: No such file or directory
solver script exited with status 127.
Indeed, ldd confirms that there is a problem:

Code: Select all

[...]
libhdf5.so.9 => not found
I tried to fix it by adding /opt/Salome/BINARIES-UB16.04/hdf5/lib/ to LD_LIBRARY_PATH but that did not solve the issue.
Is there a known cause for this problem, or a workaround I can try?
Thanks in advance and regards,

Cosimo
Attachments
configure.log
Output of configure
(21.73 KiB) Downloaded 276 times
make_install.log
Output of make install
(88.88 KiB) Downloaded 283 times
make.log
Output of make
(15.04 KiB) Downloaded 262 times
Yvan Fournier
Posts: 4070
Joined: Mon Feb 20, 2012 3:25 pm

Re: Hdf5 linking not working

Post by Yvan Fournier »

Hello,

What system is running on your workstation ?

The configure.log seems to be different from the usual config.log (actually, it is the one from the installer; the lower-lever install adds a config.log in the build directory, which could be useful).

Which version of SALOME are you using ? How was it installed ?

More importantly, did you source the Syrthes environment when installing or running Code_Saturne ? If yes, could you try not sourcing it ? IF Syrthes uses a different version of HDF5, it might generate a conflict on some systems (especially on systems such as OpenSUSE, which add --enable-new-dtags to GCC's linker options).

Best regards,

Yvan
CTrinca
Posts: 32
Joined: Mon Mar 30, 2015 9:19 am

Re: Hdf5 linking not working

Post by CTrinca »

Hi Yvan,

Many thanks for your answer. I am running Ubuntu 16.04.1, 64 bit.
The configure.log I posted is just what the configure command printed on the standard output, I did not use the installer. I am attaching config.log in the hope it is more helpful.
I am using Salome 8.2.0, the pre-compiled version for Ubuntu. I just unpacked it in a folder in /opt. Saturne's version is 4.0.7.
I did not source syrthes.profile, because I have two different versions of Syrthes installed and I was worried it could raise confusion. I compiled them using Salome's libraries, so I do not think they should conflict.
Thanks again, and please let me know what other information I can give you to help identify the problem.
Best regards,

Cosimo
Attachments
config.log
(246.81 KiB) Downloaded 268 times
Yvan Fournier
Posts: 4070
Joined: Mon Feb 20, 2012 3:25 pm

Re: Hdf5 linking not working

Post by Yvan Fournier »

Hello,

This may be due to a lack of robustness for some cases in the install system.

Could you try:
export LD_LIBRARY_PATH=/opt/Salome/BINARIES-UB16.04/hdf5:$LD_LIBRARY_PATH

before running Code_Saturne ?

If this works, we'll need a small addition in the install scripts.

Regards,

Yvan
CTrinca
Posts: 32
Joined: Mon Mar 30, 2015 9:19 am

Re: Hdf5 linking not working

Post by CTrinca »

Hi,

It worked when I added /opt/Salome/BINARIES-UB16.04/hdf5/lib, which I had already tried but I did not think of restarting the GUI.
Thanks for that. Can you suggest me the modification to the script?
Regards,

Cosimo
Yvan Fournier
Posts: 4070
Joined: Mon Feb 20, 2012 3:25 pm

Re: Hdf5 linking not working

Post by Yvan Fournier »

Hello,

Actually, the code already includes the patches I was thinking about (handling HDF5RUNPATH), so Im not sure why you have that behavior.

Could you also post your config.status and top-level generated Makefile ?

Best regards,

Yvan
CTrinca
Posts: 32
Joined: Mon Mar 30, 2015 9:19 am

Re: Hdf5 linking not working

Post by CTrinca »

Hello,

Sorry for the late reply, I attached config.status and the Makefile in my build directory (hope is the one you meant). I had a glance at them and the variables concerning hdf5 seem reasonable. Hopefully you can get more from them.
Thank you again and regards,

Cosimo
Attachments
makefile_config.tar.gz
(40.51 KiB) Downloaded 274 times
Yvan Fournier
Posts: 4070
Joined: Mon Feb 20, 2012 3:25 pm

Re: Hdf5 linking not working

Post by Yvan Fournier »

Hello,

I doubt it should make a difference, but could you try configurin with "--with-hdf5=/opt/Salome/BINARIES-UB16.04/hdf5" instead of "--with-hdf5=/opt/Salome/BINARIES-UB16.04/hdf5/" (removind the last "/" character) ?

Otherwise it that has not impact, I assume there may be other HDF5 installations, but am not sure which. Could you post the output of "echo $LD_LIBRARY_PATH" or env "env" ?

Regards,

Yvan
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