Quickstart

Downloading the code

All release tarballs can be found here. We do not recommend using the master branch on GitHub in a production environment!

If you use our software, please cite the following:

NEK5000 Version X.Y. Release date. Argonne National Laboratory, Illinois.
Available: https://nek5000.mcs.anl.gov.

Directory structure

Here’s a brief description of each top-level directory:

/core

contains the Nek5000 application sources.

/bin

contains scripts for running nek5000 and manipulating its output.

/tools

contains the sources for the pre- and post-processing tools which are stand-alone.

/short-tests

contains light-weight regression tests for verification.

/run

consistent place for users to place their problem cases.

/examples

contains example problems.

/doc

contains the user documentation.

/3rd_party

its purpose it to provide a consistent place for 3rd party code.

Case files

SIZE

contains some hardwired runtime parameters to dimension static arrays.

foo.par

contains runtime parameters.

foo.re2

contains mesh and boundary data.

foo.ma2

contains partioning data.

foo.usr

contains user specific code to initialize solver, set source terms and boundary conditions or to manipulate solver internals.

foo.his

contains probing points.

foo.f00000

contains checkpoint data.

foo.nek5000

contains metadata for VisIt or ParaView.

foo.rea (legacy)

contains runtime parameters and mesh in ASCII. Replaced by .par and .re2 file.

foo.map (legacy)

contains partioning data in ASCII.

Note: The old legacy files (.rea & .map) are recommended for debugging purposes only.

Scripts

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.
  • 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.

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 .
cd eddy
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; visit -o eddy_uv.nek5000 # requires a VisIt/Paraview installation

Meshing

Nek5000 is mainly a solver. However, simple box type meshes can be generated with the genbox tool. For more complex meshes please consider using PRENEK and the meshing tools nekmerge and n2to3. We provide mesh converters like exo2nek and msh2nek which are quite handy if you want to use your favorite mesh generator. Also check our Bazaar for 3rd party meshing tools.

Visualization

Nek5000 output (fld) files can be read by VisIt or ParaView. There is also an build-in X-Window based postprocessor called POSTNEK located in tools.

Troubleshooting

If you run into problems compiling, installing, or running Nek5000, first check the User’s Guide. If you are not able to find a solution to your problem there, please send a message to the User’s Group mailing list.

Reporting Bugs

Nek5000 is hosted on GitHub and all bugs are reported and tracked through the Issues feature on GitHub. However, GitHub Issues should not be used for common troubleshooting purposes. If you are having trouble installing the code or getting your model to run properly, you should first send a message to the User’s Group mailing list. If it turns out your issue really is a bug in the code, an issue will then be created on GitHub. If you want to request that a feature be added to the code, you may create an Issue on GitHub.

Contributing

Our project is hosted on GitHub. Here are the most important things you need to know:

  • follow the usual “fork-and-pull” Git workflow
  • all development happens on the master branch
  • anything in master is always deployable
  • upcoming releases get their own tags out of master

If you are planning a large contribution, we encourage you to discuss the concept here on GitHub and interact with us frequently to ensure that your effort is well-directed.