Help needed, in ubuntu 14.10

Discussion about building and installing Elmer
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mechpanos
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Joined: 24 Sep 2015, 10:24
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Help needed, in ubuntu 14.10

Post by mechpanos »

Hi, I am a new wanna-be user, but I have trouble installing Elmer & ElmerGUI correctly!
Firstly I tried using the packages in the ubuntu repository, and installing the GUI with the cmake method. It installed, but couldn't open any of the examples!
Then, I removed all the packages, deleted the ElmerGUI folders, and followed the guide here viewtopic.php?f=2&t=3742
step - by - step, with the graphical interface solution.
After I performed the ctest, 91% were passed, so I proceeded to Getting started, section...
Then, when i give

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$ElmerGrid 1 2 square.grd
, I get a result of "Elmergrid is not installed, you can install it using sudo apt-get install elmer".
I think it has to do with variables, any help?

Then, I skipped this and tried to run the GUI examples...
First, I realized that the /elmer/install/ directory, hasn't been created...

Then, I give the command ElmerGUI...The GUI starts, with some warnings:
Load /usr/local/bin/../share/ElmerGUI/edf/egini.xml... done
Load tetgen plugin... not found
Tetgen functionality unavailable
Constructing ElmergridAPI... done
Load /usr/local/bin/../share/ElmerGUI/edf/edf.xml... done
Load /usr/local/bin/../share/ElmerGUI/edf/linearelasticity.xml... done
Load /usr/local/bin/../share/ElmerGUI/edf/helmholtz.xml... done
Load /usr/local/bin/../share/ElmerGUI/edf/electrostatics.xml... done
Load /usr/local/bin/../share/ElmerGUI/edf/navier-stokes.xml... done
Load /usr/local/bin/../share/ElmerGUI/edf/meshdeform.xml... done
Load /usr/local/bin/../share/ElmerGUI/edf/heatequation.xml... done
Load /usr/local/bin/../share/ElmerGUI/edf/resultoutput.xml... done
Initialize GL
Vendor: ATI Technologies Inc.
Renderer: AMD Radeon HD 5450
Version: 4.4.13374 Compatibility Profile Context 15.20.1013
Then, I am not able to open the examples of the ElmerGUI tutorials (i.e. the elastic beam)...

Do you have any clue, what might I be doing wrong?

Regards,
Panos from Greece
annier
Posts: 1168
Joined: 27 Aug 2013, 13:51
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Re: Help needed, in ubuntu 14.10

Post by annier »

Hi Panos,
Did you set up the environment variables in bash shell?

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export ELMER_HOME=$HOME/elmer/install/
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$ELMER_HOME/lib
export PATH=$PATH:$ELMER_HOME/bin
Is your installation directory structure similar to the one mentioned in viewtopic.php?f=2&t=4049 ?



Yours Sincerely
Anil Kunwar
Anil Kunwar
Faculty of Mechanical Engineering, Silesian University of Technology, Gliwice
kataja
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Joined: 09 May 2014, 16:06
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Re: Help needed, in ubuntu 14.10

Post by kataja »

Hi!

Have you tried the upstream build at launchpad?

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$ sudo apt-add-repository ppa:elmer-csc-ubuntu/elmer-csc-ppa
$ sudo apt-get update
$ sudo apt-get install elmerfem-csc
Using this method, you should not set ELMER_HOME environment variable.

For other ways to obtain elmer, see viewtopic.php?f=11&t=3725

Cheers,
Juhani
mechpanos
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Joined: 24 Sep 2015, 10:24
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Re: Help needed, in ubuntu 14.10

Post by mechpanos »

Hi guys!
1.Anil
I have added, in .bashrc, the following lines:
#Elmer
export ELMER_HOME=$HOME/elmer/install/
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$ELMER_HOME/lib
export PATH=$PATH:$ELMER_HOME/bin

However, as I said, I realized that /install directory, hasn't been created!
Here is my elmer folder:

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~/elmer$ ls
build  elmerfem
So, should I probably change /install/ folder, to /elmerfem/ ? Or should I perform the installation process, to have it create the /install folder and its contents, correctly this time?
...(i.e. there is no /bin/ folder instide /elmerfem/)

2. Juhani,
I have not been aware of the ppa!
I followed the step by step guide that I mentioned above...Do you think I should try the PPA?

Thank you both for your answers and your help!
annier
Posts: 1168
Joined: 27 Aug 2013, 13:51
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Re: Help needed, in ubuntu 14.10

Post by annier »

Hi Panos,
1. You need to delete the build directory and reinstall the Elmer from step 3 of viewtopic.php?f=2&t=3742 .
Before doing that, try to manually create the \install directory within ~\elmer alongside \elmerfem directory so that this time all the installations will be placed within the \install directory.

And, for step 4, make sure that you perform the following task in cmake-gui
Some user settings for destination install folder are:
**(A) Either : User setiings for installation path
The prefix of install directory can be changed to the desired path by clicking at the corresponding rows of the "Value" column:

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    CMAKE _INSTALL_PREFIX                   home/username/elmer/install
    ELMER_SOLVER_HOME                                 home/username/elmer/install/share/elmersolver


**(B) Or: Default settings (Has to be proceeded as root user during installation i.e. $sudo -s)
By default, the install destination for Elmer will appear as following during the configuration process in the gui of cmake-gui:

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    CMAKE_INSTALL_PREFIX                                  /usr/local
    ELMER_SOLVER_HOME                                     /usr/local/share/elmersolver
If you proceed through (A) , the environment variables would be

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export ELMER_HOME=$HOME/elmer/install/
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$ELMER_HOME/lib
export PATH=$PATH:$ELMER_HOME/bin
If you don't proceed through (A), which means your installation will be made in /usr/local/ directory by default i.e. (B), then you need to set the environment variables as

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export ELMER_HOME= /usr/local/
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$ELMER_HOME/lib
export PATH=$PATH:$ELMER_HOME/bin
2. In addition to the reference note made by Juhani , the different ways how Elmer can be installed in Ubuntu are also listed in viewtopic.php?f=2&t=3653 .


If the installation can be done through Cmake, you don't need to install through PPA or vice versa. Or, in other words, when you install via PPA, you don't need to do the Cmake based installation. Installing Elmer through PPA in Ubuntu is a few lines of code and is substantially easier than the Cmake based installation. The installation through PPA is readily available for Ubuntu versions 14.04 or later and so you can do whenever you like to try it. On the basis of recent Elmer features, both options are equally recommended for the users. Personally, i would recommend you to try first in installing via Cmake. Installing through Cmake can enable the users to be motivated in knowing the different components of Elmer multiphysics they are using and moreover they can choose between the wide range of features provided by the developers. Whereas the features and components of PPA version is specified by the developers for the users. If you cannot do it (Cmake based Elmer installation) for some unknown reasons, the option of installing through PPA is always there for you.
Cheers

Yours Sincerely
Anil Kunwar
Anil Kunwar
Faculty of Mechanical Engineering, Silesian University of Technology, Gliwice
mechpanos
Posts: 4
Joined: 24 Sep 2015, 10:24
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Re: Help needed, in ubuntu 14.10

Post by mechpanos »

Anil,

Thank you for giving me all this explanation! I think the solution was much simpler, since I hadn't noticed the meaning of the nproc command, so I just used the make -j4 install command, instead of using -j2 for my case...Now it worked, and I have a working installation (I am wondering, why it hadn't caused any errors, and how it passed all those tests, with my previous attempt??!!!)...
So, I managed to perform the square cavity example and open it in Paraview!
I am having some issues with the GUI, it doesn't show me the complete mesh...
For example, the reference tutorial of a curved pipe, looks something like this in ElmerGUI:
Image

And the result in ParaView, looks like this:
Image


What do you think?

(another interesting thing, is that, from what I manage to catch while loading ElmerGUI, it loads from /usr/local/bin/....share/elmergui..... something...
even if I have installed it in /elmer/install/bin, and updated the values in bashrc...strange!)
mzenker
Posts: 1999
Joined: 07 Dec 2009, 11:49
Location: Germany

Re: Help needed, in ubuntu 14.10

Post by mzenker »

Hi,

just a guess: View->Volume Mesh?

HTH,

Matthias
mechpanos
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Re: Help needed, in ubuntu 14.10

Post by mechpanos »

Good morning!
After the helm of ElmerGUITester utility and some google search, I solved ElmerGUI trying to load from usr/local/bin/....share/elmergui.
I have put all necessary variables in the file .profile, so the only thing I miss now, is ElmerPost.

I don't understand, why my ElmerGUI cant show the mesh, I tried Matthias' suggestion but no luck...

[EDIT] I figured that, if I open a file (grd for example) and it doesn't show the mesh, if I perform Load Mesh and select the folder containing the Mesh, it shows it...
It worked on my previous example, with the curved pipe.

So now, as a new user, I have to figure how to configure the mesh outside of ElmerGUI with another tool (is Gmsh the correct one? or should I use other tool?), and then load my geometry and the mesh in ElmerGUI to set the boundary conditions and the equations for the problem I want to solve...
[/EDIT]

[EDIT2]Just understood that I had to "Load Project", not "Open File"...While I live, I learn (Socrates)[/EDIT2]
annier
Posts: 1168
Joined: 27 Aug 2013, 13:51
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Re: Help needed, in ubuntu 14.10

Post by annier »

Hi Panos,
I loaded ElmerGUI for the ELmer8 installed via Cmake and it presented the following log:

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username@username-AOD271:~$ elmer8
username@username-AOD271:~$ ElmerGUI
Load /home/username/elmer_8/install/bin/../share/ElmerGUI/edf/egini.xml... done
Load tetgen plugin... not found
Tetgen functionality unavailable
Constructing ElmergridAPI... done
Load /home/username/elmer_8/install/bin/../share/ElmerGUI/edf/edf.xml... done
Load /home/username/elmer_8/install/bin/../share/ElmerGUI/edf/heatequation.xml... done
Load /home/username/elmer_8/install/bin/../share/ElmerGUI/edf/helmholtz.xml... done
Load /home/username/elmer_8/install/bin/../share/ElmerGUI/edf/linearelasticity.xml... done
Load /home/username/elmer_8/install/bin/../share/ElmerGUI/edf/navier-stokes.xml... done
Load /home/username/elmer_8/install/bin/../share/ElmerGUI/edf/resultoutput.xml... done
Load /home/username/elmer_8/install/bin/../share/ElmerGUI/edf/meshdeform.xml... done
Load /home/username/elmer_8/install/bin/../share/ElmerGUI/edf/electrostatics.xml... done
Initialize GL
Vendor: VMware, Inc.
Renderer: Gallium 0.4 on llvmpipe (LLVM 3.4, 128 bits)
Version: 2.1 Mesa 10.1.3
And, the File > Open procedure for curved_pipe.grd in ~/elmer_8/elmerfem/ElmerGUI/samples/grd/ led to the following outcome:
ElmerGUI opens the grd file through file > open option
ElmerGUI opens the grd file through file > open option
curved_pipe.png (50.74 KiB) Viewed 8671 times
You need to make sure what exactly did you place in the installation location via the cmake-gui .

Yours Sincerely
Anil Kunwar
Anil Kunwar
Faculty of Mechanical Engineering, Silesian University of Technology, Gliwice
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