Installing, Compiling & Running ElmerNonGUI in Ubuntu 12.04

[annier]

The following links have been referred for installation and compilation of elmer in Ubuntu 12.04
http://www.elmerfem.org/elmerwiki/index ... r_on_Linux
http://ascend4.org/Building_Elmer_on_Ubuntu_12.04
https://subversion.apache.org/packages.html#debian
viewtopic.php?f=2&t=3653&sid=be626f5ee2 ... b11186abeb

Steps:
Note:
For the context of here , the scripts with "$" in their front mean that they are to be typed in the terminal and if they are without it "they are to be pasted in a file" and then will be implemented.

1. Check out for the subversion

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$ sudo apt-get install subversion
$ sudo apt-get install libapache2-svn

Also, one can get the rabbitvcs subversion in the Ubuntu software centre.

2. Get the elmerfem source via the subversion

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$ svn checkout http://svn.code.sf.net/p/elmerfem/code/trunk elmerfem

or

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$ svn checkout https://svn.code.sf.net/p/elmerfem/code/trunk elmerfem

3. Jump into the elmerfem directory

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$ cd elmerfem

4. Create the compile script with the filename compile.sh inside the elmerfem directory.The following script should be added to the compile.sh file. Note that the module fem has been dealt separately from other modules to include the "mpi" related aspect.

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#!/bin/sh -f
#the compiler (here the gcc 4.X suite)
export CC=gcc
export CXX=g++
export FC=gfortran
export F77=gfortran
#the compiler flags
export CFLAGS=""
export FCFLAGS=""
export F77FLAGS=""
export FFLAGS=""
#linking
export LDFLAGS=""
#paths
#export ELMER_HOME="/path/to/Elmerdir"
export ELMER_HOME="$HOME/elmerinst"
# modules
modules="matc umfpack mathlibs elmergrid meshgen2d eio hutiter  post"
# configure and build
for m in $modules; do
   cd $m ; ./configure --prefix=$ELMER_HOME && make clean && make && make install && cd ..
# configure and build the module fem using mpi related aspect
cd fem; ./configure --prefix=$ELMER_HOME --with-mpi-inc-dir=/usr/include/mpich2 && make clean && make && make install && cd ..
done

5. Run the script as follows. This will make an installation directory "elmerinst" within the Home directory and it is the path to elmer.

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$ chmod u+x compile.sh
$ ./compile.sh

6. Set the environment variables in the bashrc file for defining the path of Elmer
- In the terminal, type the following;

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$ gedit ~/.bashrc

-Add the following scripts at the end of the bashrc file

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export ELMER_HOME=$HOME/elmerinst
export ELMER_POST_HOME=$ELMER_HOME/share/elmerpost
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$ELMER_HOME/lib
export PATH=$PATH:$ELMER_HOME/bin

The installation and compilation of elmer in nonGui form is completed.

Steps for Testing of the ElmerNonGui
It is assumed that the elmerfem and elmerinst folders are in the home directory.
1. Make an elmer project directory

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$mkdir elmer_project

2. Copy a test from elmerfem directory (e.g.CavityLid) to the elmer_project directory.

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$cp -r $HOME/elmerfem/fem/tests/CavityLid/ $HOME/elmer_project/CavityLid

3. Jump into the CavityLid tutorial.

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$cd ~/elmer_project/CavityLid/

4.Convert mesh file in .grd format [1] to .mesh.*(ElmerSolver) format [2] [Please refer chapter 1 of Elmer Grid Manual (http://www.nic.funet.fi/pub/sci/physics ... Manual.pdf) to find the corresponding number of Different File Formats]

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$ElmerGrid 1 2 square.grd

5. For users of Paraview, open the case.sif file via

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$gedit case.sif

and replace post file = case.ep (in simulation section) with

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Post File = case.vtu

Save the edited file.

6. Run the ElmerSolver command

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$ElmerSolver > anyname.log 2>&1

7.Open paraview by typing in terminal

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$paraview

Note: paraview can be installed in ubuntu by typing

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$sudo apt-get install paraview

The file>open>... can lead us to opening the case.vtu file located within the $HOME/emer_project/CavityLid/square/ directory.


The following reply to this post describes the steps for running ElmerNonGUI in Ubuntu 12.04.

Yours
Anil Kunwar

[annier]

Steps for Running ElmerNonGUI in Ubuntu 12.04
1. We need to write all the input information (Header, Body, Solver, Simulation, Equation, Material ,Boundary Conditions) in a text file and make it a SIF (ending with .sif). Let it be named as abcd.sif. ( A sample Solver Input File for learning about the structure of .sif file can be found at different test examples in the downloaded elmer directory => $HOME/elmerfem/fem/tests or in general /path/ to elmer directory/fem/tests .)
Additionally, we need to create an empty text file with the file name ELMERSOLVER_STARTINFO and inside it we write the following thing:

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abcd.sif
1

The ELMERSOLVER_STARTINFO file should be in the same directory with the abcd.sif file.

2. We draw the geometry and mesh in some other preprocessors and convert it into Elmer format with ElmerGrid command in the terminal by jumping into the directory where the geometry/mesh files are located.
If the file exported by the preprocessor in .unv format has the name abcdwxyz.unv, then the following command converts the .unv file into Elmer format:

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$ ElmerGrid 8 2 abcdwxyz.unv -autoclean

3. Then we put the folder with mesh files (in elmer grid format) in the directory where the SIF file is located. If the folder having mesh files (in Elmer Format) is named mymesh, then Header in abcd.sif should be like:

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Header
Mesh DB "." "mymesh"
End

4. In the terminal, we jump into the directory containing abcd.sif and type:

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$ ElmerSolver

or, in case we need to see the solver logfile

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$ ElmerSolver > anyname.log  2>&1

This will run the Elmer Solver.

5. In order to see the result, we can open postprocessor (example : Paraview) and browse the .vtu files located within the mymesh directory.
For this, there should have been written the following command in the simulation section of abcd.sif:

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Simulation
...
Post File = "case.vtu"
...
End

Yours
Anil Kunwar

[annier]

Hi All,
Now, Elmer can be installed (1) using cmake as described in this post(elmer installation using cmake) or (2) with launchpad as described in post(related with installation of Elmer in Ubuntu 14.04).

Yours
Anil Kunwar