Before beginning to use Nek5000, it is recommended that the user have basic familiarity with Linux or another Unix-based OS. The instructions provided in the quickstart guide and the tutorials use basic bash commands and assume the user has this knowledge.
Here’s a brief description of each top-level directory:
contains the Nek5000 application sources.
contains scripts for running nek5000 and manipulating its output.
contains the sources for the pre- and post-processing tools which are stand-alone.
contains light-weight regression tests for verification.
consistent place for users to place their problem cases.
contains example problems. Note: NOT included in the master branch on the GitHub repo.
contains the user documentation. Note: NOT included in the master branch on the GitHub repo.
its purpose it to provide a consistent place for 3rd party code.
contains some hardwired runtime parameters to dimension static arrays.
contains runtime parameters.
contains mesh and boundary data.
contains partioning data.
contains user specific code to initialize solver, set source terms and boundary conditions or to manipulate solver internals.
contains probing points.
contains checkpoint data.
contains metadata for VisIt or ParaView.
contains runtime parameters and mesh in ASCII. Replaced by .par and .re2 file.
contains partioning data in ASCII.
Note: The old legacy files (.rea & .map) are recommended for debugging purposes only.
Let’s walk through some useful batch scripts:
makenek <case>compiles your case
nek/nekb <case>runs a serial job in foreground or background
nekmpi/nekbmpi <case> <number of ranks>runs a parallel job
neknek <case1> <cas2> <ranks 1> <ranks 2>runs Nek5000 with two overlapping component grids
visnek <case>creates metadata file required by VisIt and ParaView.
mvn <old name> <new name>renames all case files
cpn <old name> <new name>copies all case files
Running your very first simulation¶
Hold your horses, this needs less than 5 min. Begin by downloading the latest release tarball from here. Then follow the instructions below
cd ~ tar -xvzf Nek5000_X.Y.tar.gz export PATH=$HOME/Nek5000/bin:$PATH cd ~/Nek5000/tools ./maketools genmap cd ~/Nek5000/run cp -r ../examples/eddy_uv . cd eddy_uv genmap # run partioner, on input type eddy_uv makenek eddy_uv # build case, edit script to change settings nekbmpi eddy_uv 2 # run Nek5000 on 2 ranks in the background tail logfile # view solver output visnek eddy_uv # produces the eddy_uv.nek5000 file
As the case runs, it will generate multiple
These are the restart checkpoint and visualization data files.
The metadata file,
eddy_uv.nek5000, can be opened with either VisIt or ParaView, which will look for the data files in the same directory as the
Note that this will not work if you clone the master branch from GitHub, as the
examples folder is NOT included.
To obtain the examples using git, clone the
Nek5000 is mainly a solver.
However, simple box type meshes can be generated with the
For more complex meshes please consider using
PRENEK and the meshing tools
We provide mesh converters like
msh2nek which are quite handy if you want to use your favorite mesh generator.