Elmer

Elmer is an open source multiphysical simulation software developed by CSC - IT (Finland).

From their Github README:

Elmer is a finite element software for numerical solution of partial
differential equations. Elmer is capable of handling any number of equations
and is therefore ideally suited for the simulation of multiphysical problems.
It includes models, for example, of structural mechanics, fluid dynamics, heat
transfer and electromagnetics. Users can also write their own equations that
can be dynamically linked with the main program.
Elmer consists of several parts. The most important ones are ElmerSolver, the
finite element solver, ElmerGUI, the graphical user interface, and ElmerGrid,
the mesh creation and manipulation tool. Also a visualization tool, ElmerPost,
is included in the package but it is no longer developed.  
Elmer software is licensed under GPL except for the ElmerSolver library which
is licensed under LGPL license. 
Elmer is mainly developed at CSC - IT Center for Science, Finland. However,
there have been numerous contributions from other organizations and developers
as well, and the project is open for new contributions.

Availability and Restrictions

Versions

The following versions of Elmer are available on OSC clusters:

version oakley Ruby
8.1 X X

 

The current versions of Elmer are compiled with GNU 4.8.4 (requirement > 4.8) and BLAS libraries from MKL/11.2.3.

Feel free to contact OSC Help if you need other versions for your work.

Access 

Elmer is available to all OSC users without restriction.

Usage

Usage on Oakley or Ruby

Setup on Oakley or Ruby

To configure the Oakley or Ruby cluster for the use of Elmer 8.1, use the following commands:

module load gnu/4.8.4
module load mkl/11.2.3
module load elmer

Batch Usage on Oakley or Ruby

Batch jobs can request mutiple nodes/cores and compute time up to the limits of the OSC systems. Refer to Queues and Reservations for OakleyQueues and Reservations for Ruby, and Scheduling Policies and Limits for more info.

Converting Mesh with ElmerGrid and Running ElmerSolver

Below is an example batch script ( job.txt ) for using Elmer:

#PBS -N Elmer
#PBS -l nodes=1:ppn=1 
#PBS -l walltime=30:00
#PBS -j oe 
#PBS -S /bin/bash 
# Load the modules for Elmer
module load gnu/4.8.4
module load mkl/11.2.3
module load elmer
# Move to the problem directory
cd $PBS_O_WORKDIR
# Copy files to $TMPDIR and move there to execute the program
cp -r * $TMPDIR
cd $TMPDIR
# Convert the mesh - see Elmer webpage for more examples of 'ElmerGrid'
ElmerGrid 14 2 beam.msh -autoclean
# Run the solver 
ElmerSolver beam.sif
# Finally, copy files back to your home directory 
cp -r * $PBS_O_WORKDIR

In order to run it via the batch system, submit the job.txt   file with the following command:

qsub job.txt

Further Reading

https://www.csc.fi/web/elmer/

https://github.com/ElmerCSC/elmerfem

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