Problems setting up Salome/Saturne/Syrthes on ubuntu 16.04.3

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maciej barwicki
Posts: 6
Joined: Sun Oct 01, 2017 11:03 pm

Problems setting up Salome/Saturne/Syrthes on ubuntu 16.04.3

Post by maciej barwicki »

Hello Everyone.

im trying to set up Saturne/Syrthes for cosimulation and possibly my next step would be to integrate Syrthes with Aster for thermal structural problems (but thats far future for now)

I started with installing Salome v2016 counting that some of the libraries will get installed for me by Salome.

For Syrthes i picked 4.1.1 and for Saturne 3.2.5 because from previous experiences i know that these versions can cooperate (last time the installation and setup was done for me by someone else)

Then, following the Syrthes/Saturne/Syrthes methodology i started with Syrthes. I was expecting that the first Syrthes installation will end with errors since the ple library is missing, so i tried to eliminate as much errors as i could and proceeded to Saturne.

The Saturne installation, with some tweeking of the library paths went quite well. If its necessary i will provide the log but i think that, at least for now the bigger concern is Syrthes.

When i tried to install Syrthes again, pointing at the ple libraries, there are errors - from what i can see coming from ple and metis as well. For Metis libraries i pointed Metis-40 that was in Salome prerequisites folder.

I am attaching my setup.ini for syrthes and erreurs

I cant really understand the problem that takes the few lines in the beggining "allocation, coordinate etc.."
Next i see that metis is named a few times , then ple. Since metis is a prerequisite i think it is important to focus on it first.

I would greatly appreciate any help - concerning my errors and general advice on the installation process. Maybe there is another way for the setup? Maybe i'm using wrong versions of the libraries? My first attempt was to install all the latest versions of salome/syrthes and saturne, but after a few tries, i reverted to the versions that i know worked for me 3 years ago - that was built on caelinux2013.

Excuse me if there is a similar subject already on the forum but i haven't found anything close. If there is, please let me know and ill try with it first.

Best Regards
Attachments
ERREUR.log
(9.74 KiB) Downloaded 294 times
setup.ini
(4.1 KiB) Downloaded 304 times
Yvan Fournier
Posts: 4070
Joined: Mon Feb 20, 2012 3:25 pm

Re: Problems setting up Salome/Saturne/Syrthes on ubuntu 16.

Post by Yvan Fournier »

Hello,

Most of the errors can be ignored (the printf / allocation errors look like a "grep" of the sources mixed with the real errors; ugly Syrthes build script, example of how not to code, but false positives).

The real errors mixed in the ERREUR.log are the Metis errors. I assume this is due to using Metis 4.0. You need either Metis 5.0 or 5.1 or Scotch 6.0.x (5.11 might work, not sure). More recent versions of Salome use more recent versions of Metis (Salome-Meca 2017 or Salome 8.2 or 8.3).

In any case, Code_Saturne 3.x and Syrthes versions prior to 4.3 are unmaintained, so I suggest upgrading.

Regards,

Yvan
maciej barwicki
Posts: 6
Joined: Sun Oct 01, 2017 11:03 pm

Re: Problems setting up Salome/Saturne/Syrthes on ubuntu 16.

Post by maciej barwicki »

Thank you Yvan for such a quick response.

Following youre advice i will now try to reinstall ubuntu and start again clean.
From what i recall, salome v2017 had Metis-40 as well in the prerequisites folder. I may be wrong ill check this later.
My general attitude to the whole installation process of my working environment with EDF software is that i am very cautious to get as good cooperation between different codes and post-pre processors as possible. As i said before, my goal is to be able to perform thermal-structural analysis as well as cfd-thermal. Considering this, and the poor level of knowledge about linux that i have, my priority was to always use the libraries that are installed alongside the bigger installations of programs. My uderstanding is that to get good cooperation , the libraries used by different programs need to be in the same versions. For example to read a mesh prepared with salome, aster or saturne needs to be built with the same library as salome. Once again, i may be wrong , please correct me if i am.

Now as you advise me to install a newer version of metis for syrthes and saturne i am wondering , what about intergration of the newer version with salome? Can i substitute the newer metis version in salome settings? Do i even need to? Im quite confused with what types of libraries are required for which program. Is there maybe a document that describes what libraries are used by what program and for what purpose?

Thank You once again
Yvan Fournier
Posts: 4070
Joined: Mon Feb 20, 2012 3:25 pm

Re: Problems setting up Salome/Saturne/Syrthes on ubuntu 16.

Post by Yvan Fournier »

Hello,

As Salome-Meca may have a modified Metis, they might still have the old version. In this case, do not use Metis but use Scotch for the Syrthes (and optionally Code_Saturne) installs.

Regards,

Yvan
maciej barwicki
Posts: 6
Joined: Sun Oct 01, 2017 11:03 pm

Re: Problems setting up Salome/Saturne/Syrthes on ubuntu 16.

Post by maciej barwicki »

Hello,

since last time, i've managed to make some progress.

So i reinstalled Ubuntu. Then i installed Salome v2017. Then started working on Syrthes. This time Syrthes 4.3.0, and i've setup the build to install Metis as advised (setup.ini attached - this is the version updated with ple and syrthescfd, for the second installation of syrthes). Now i have errors with syrthesensight (erreur.log attached) and i am not sure what to do with this because it was supposed to be installed with syrthes by the script. I can see some files named syrthes4ensight in the src folders, but if they are not working then what can i do?

At this point i decided to carry on with the process to check if Saturne installs and maybe cosimulation would even work after all. I also never reached the final part of the process, up to sourcing syrthes and adding aliases, so i thought that ill try to do this and if i brake something then im not losing much anyway.

Code-saturne-4.3.4installation went quite well, i had to install some libraries "by hand" using Synaptic. I think i have a problem with pt-scotch (conftest.c:59:22: fatal error: ptscotch.h: No such file or directory) - the config.log is attached as well. There may be more problems that i am not aware of. I have installed pt-scotch with synaptic. What should i do about it? add another line "--with-ptscotch..." to the configure file? (my configure is attached as well)
If you can see any other problems please let me know.

After saturne i ran syrthes installation pointig ple etc - no problems with this i think.

Finally i tried the post installation setup. I have some instructions from the person who was doing the installation for me back in 2015 , but it was made on caelinux so some entries where already present in bashrc and they were not present this time in ubuntu so i added them. I would appreciate some advice if those steps are necessary and if they should be different with ubuntu now.

So the steps were:
1
# cd /opt/saturne-3.2.5/etc/
# sudo bash
[pass]
# cp code_saturne.cfg.template code_saturne.cfg
# nano code_saturne.cfg

and put the curent syrthes path in the file

syrthes = /opt/syrthes4.1.1-ubuntu/arch/Linux_x86_64

2 edit bashrc
Find salome section and insert the correct path:
# SALOME
if [ -e /opt/SALOME-MECA-2013.1 ]; then
export PATH=$PATH:/opt/SALOME-MECA-2013.1/appli_V6_6_0/
fi

There was no salome path in my bashrc so i made it (bashrc attached)

3 edit bashrc
# Saturne
if [ -e /opt/saturne-3.0/bin/ ]; then
export PATH=$PATH:/opt/saturne-3.0/bin/
fi

and add

source /opt/syrthes4.1.1-ubuntu/arch/Linux_x86_64/bin/syrthes.profile > /dev/null

I also added an alias for code saturne

I sorced syrthes differenly but it works. When followed the 2D tutorial for cosimulation, the first command works


root@maciek-P5K:~# code_saturne create -s example -c fluid --syrthes solid
code_saturne 4.3 study/case generation
o Creating study 'example'...
o Creating case 'fluid'...
SYRTHES4 home directory: /home/maciek/syrthes4.3.0/arch/Linux_x86_64
MPI home directory: /home/maciek/syrthes4.3.0/extern-libraries/opt/openmpi-1.8.3/arch/Linux_x86_64

*****************************************
solid : creating SYRTHES case...
/home/maciek/syrthes4.3.0/arch/Linux_x86_64
Linux_x86_64
OK !
*****************************************

o Creating coupling features ...
root@maciek-P5K:~#


The folders are created. Then there is the step wherew i need to run syrthes gui and:

root@maciek-P5K:~/Desktop/Tutek_syr_CS/4_disk2D/solid# syrthes.gui
/home/maciek/syrthes4.3.0/arch/Linux_x86_64/lib/syrthes-GUI_exe/SyrthesMain: error while loading shared libraries: libssl.so.0.9.8: cannot open shared object file: No such file or directory


Now im stuck here. I request assistance with the last (i hope) problems with the installation and the one above. I think im geting close to success but still have some issues :/

Best Regards
Attachments
config.log
(218.16 KiB) Downloaded 297 times
ERREUR.log
(7.72 KiB) Downloaded 280 times
setup.ini
(4.41 KiB) Downloaded 282 times
maciej barwicki
Posts: 6
Joined: Sun Oct 01, 2017 11:03 pm

Re: Problems setting up Salome/Saturne/Syrthes on ubuntu 16.

Post by maciej barwicki »

I managed to shake of some of the frustration, and tried to find a solution for the libssl problem.

What i have found is that i have a newer version of this library and possibly the 9.8.0 wouldnt work on ubuntu 16.04 anyway.

I have found some trick. I created symlinks for libssl and then libcrypto but another error pops up:

root@maciek-P5K:~/Desktop/Tutek_syr_CS/4_disk2D/solid# syrthes.gui
/home/maciek/syrthes4.3.0/arch/Linux_x86_64/lib/syrthes-GUI_exe/SyrthesMain: /lib/x86_64-linux-gnu/libcrypto.so.0.9.8: version `OPENSSL_0.9.8' not found (required by /home/maciek/syrthes4.3.0/arch/Linux_x86_64/lib/syrthes-GUI_exe/libpython2.6.so.1.0)
/home/maciek/syrthes4.3.0/arch/Linux_x86_64/lib/syrthes-GUI_exe/SyrthesMain: /lib/x86_64-linux-gnu/libssl.so.0.9.8: version `OPENSSL_0.9.8' not found (required by /home/maciek/syrthes4.3.0/arch/Linux_x86_64/lib/syrthes-GUI_exe/libpython2.6.so.1.0)


I could try to go on with creating these symlinks but im kind of suspicious that this is not the best way. Maybe it is?

Im wondering, maybe i should try with an older version of Ubyntu? (14..)

Best Regards
maciej barwicki
Posts: 6
Joined: Sun Oct 01, 2017 11:03 pm

Re: Problems setting up Salome/Saturne/Syrthes on ubuntu 16.

Post by maciej barwicki »

Oh and the files from previous post.
Attachments
Saturne_config.txt
(873 Bytes) Downloaded 302 times
bashrc.txt
(3.97 KiB) Downloaded 289 times
Yvan Fournier
Posts: 4070
Joined: Mon Feb 20, 2012 3:25 pm

Re: Problems setting up Salome/Saturne/Syrthes on ubuntu 16.

Post by Yvan Fournier »

Hello,

The issue with the Syrthes GUI on more recent systems is due to precompiled binaries. To recompile them, you need to go into the detailed instructions in the GUI directory, and might get things to work. A simpler solution I think is to simply run ./install.sh inside Syrthes's src/syrthes-gui/src/ directory, then replace "python SyrthesMain.py" instead of the SyrthesMain in the arch/<name>/bins/yrthes.gui file.

I usually grow frustrated each time I try to install the Syrthes GUI, and do it rarely, so my instructions might not be exact, but should be close...

I may move this post in the future to the Syrthes section, as most of you issues are related to Syrthes.

Regards,

Yvan
maciej barwicki
Posts: 6
Joined: Sun Oct 01, 2017 11:03 pm

Re: Problems setting up Salome/Saturne/Syrthes on ubuntu 16.

Post by maciej barwicki »

Thank you Yvan.

Do you have any info about syrthes support? Is it working? I have found some post from 2016 that support-syrthes@edf.fr was not responding. Has the situation changed or any other way to contact support was established?

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

Re: Problems setting up Salome/Saturne/Syrthes on ubuntu 16.

Post by Yvan Fournier »

Hello,

No, there is no change, which is why I added a Syrthes section in this forum (but users need to animate it).

I will need to check with the Surges team if they are ok if we place new releases on this web site.

Regards,

Yvan

PS: I will have limited connectivity this week an d next week so I won't much be on this forum
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