Quickstart¶
Before You Begin…¶
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.
At an absolute minimum, to successfully build and run Nek5000 will require compatible C and Fortran compilers, such as gcc and gfortran, and GNU Make.
To successfully build and run Nek5000 in parallel will additionally require a compatible MPI wrapper, such as OpenMPI or MPICH.
Some of the tools and advanced features will have additional dependencies, such as CMake.
On Ubuntu, the following packages will provide the necessary compilers and wrappers to run Nek5000 in parallel.
$ sudo apt-get update
$ sudo apt install build-essential #provides gcc
$ sudo apt install gfortran #provides gfortran
$ sudo apt install libopenmpi-dev #provides openmpi
Additionally, to install all of the NekTools, the following packages are necessary
$ sudo apt install cmake #provides cmake
$ sudo apt install libx11-dev #provides X11
$ sudo apt install libxt-dev #provides X11
Note
These package lists also work for Ubuntu on the Windows Subsystem for Linux
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 # prints the last few lines of the solver output to the terminal
$ visnek eddy_uv # produces the eddy_uv.nek5000 file
Note
The eddy_uv case will not be available if you cloned the master branch from GitHub, as the examples folder is NOT included.
To obtain the examples using git, clone the Nek5000/NekExamples.git repository.
As the case runs, it will generate multiple eddy_uv0.fXXXXX files.
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 eddy_uv.nek5000 file.
Assuming all went well, congratulations! You have now run your first simulation with Nek5000.
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, and binaries for the tools. This directory should be added to your environment PATH (see below).
/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
A place for users to keep their problem cases. Note that many HPC systems recommend keeping source code and output on separate file systems, in which case this directory should not be used. Consult your system administrator for best practices.
/examples
Contains example problems. Note that this directory is NOT included in the master branch on the GitHub repo. The NekExamples repository can be found here.
/3rd_party
Contains third party software not part of the Nek5000 core, e.g. gslib, HYPRE, and CVODE.
Setting up your PATH¶
We recommend adding the bin directory to your shell’s execution PATH.
In the bash shell, this can be done temporarily (only for your active session) with the command
$ export PATH+=:$HOME/Nek5000/bin
To do this more permanently, this line can be added to your .bashrc file in your $HOME directory.
This will require you to restart your current session, i.e. log out and log back in, to become active.
You can check your current execution PATH with
$ echo $PATH
This will print a colon-separated list of the directories searched by Linux for the commands typed into the command line to the terminal.
If you used the above command, the Nek5000/bin entry should be the last value in this list.
Other common setups may add it as the first entry in this list.
Your particular setup depends on your environment.
For more information on the execution PATH in Linux, see here (warning: links to a 3rd party website).
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. For more information see the User Routines File (.usr).
foo.his
Contains probing points. For more information see History 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 casenek/nekb <case>runs a serial job in foreground or backgroundnekmpi/nekbmpi <case> <number of ranks>runs a parallel jobneknek <case1> <cas2> <ranks 1> <ranks 2>runs Nek5000 with two overlapping component gridsvisnek <case>creates metadata file required by VisIt and ParaView.mvn <old name> <new name>renames all case filescpn <old name> <new name>copies all case files
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 gmsh2nek which are quite handy if you want to use your favorite mesh generator.