Downloading the code
Just click on the button below, untar the file into your home directory and your all set.
Note: If you are a developer, please follow the
Contributing section below to download the code.
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.
reserved for the Nek5000 example problems.
contains the user documentation in HTML and PDF.
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
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 us 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_17.0.0.tar.gz export PATH=$HOME/Nek5000/bin:$PATH cd ~/Nek5000/tools; ./maketools genmap cd ~/Nek5000/run cp -r ../examples/turbChannel . cd turbChannel genmap # run partioner, on input type ethier makenek turbChannel # build case, edit script to change settings nekbmpi turbChannel 2 # run Nek5000 on 2 ranks in the background echo -2 >ioinfo # stop Nek5000 run and dump checkpoint visnek turbChannel; visit -o turbChannel.nek5000 # requires a VisIt installation
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
n2to3. We provide mesh converters like
msh2nek which are quite handy if you want to use your favorite mesh generator. Also check our Bazaar for 3rd party meshing tools.
Visit our online documentation.
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.
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.
Our project is hosted on GitHub. 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.
How we do it
- Anything in master is always deployable
- Upcoming feature release get their own tags or branch that are branched out of master
- All development happens on the master branch.
- To work on something new, create a short lived local branch off of master
- When you need feedback or help, or your change is ready for merging, open a pull request.
- Fork our repo Nek5000 on GitHub
- Download fork with
git clone -o myfork https://github.com/<username>/Nek5000.git ~/Nek5000
- Add our repo
cd ~/Nek5000; git remote add origin https://github.com/Nek5000/Nek5000.git
- Download our repo
git fetch origin
- Set upstream for local master branch
git branch --set-upstream master remotes/origin/master
~/Nek5000/bin/git-hub setup —u <your username on GitHub> --global
- Add this to your [hub] section in
[hub] ... upstream = Nek5000/Nek5000 forkremote = myfork
- Create a feature branch hosting your change with
nekgit_co <descriptive name>. Using a dedicated branch for every feature helps you to move between different developments while some are work in progress or under review.
- Implement your code changes. To reset your branch and discard any changes run
git reset --hard origin/master. To revert a set of files run
git checkout file1 file2 ...
- Commit your changes to your local repo using e.g.
git commit file1 file2 .... Do this frequently to save your work.
- Periodically, changes made in our master should be pulled back into your local branch by
git pull -r. This ensures that we do not end up in integration hell that will happen when many feature branches need to be combined at once.
- If there are no merge conflicts, go to the next step. In case of conflicts edit the unmerged files in question. Merge conflicts are indicated by the conflict marker
<<<<<<<in your file.
- Assuming you are happy run
nekgit_push. This will create a pull request on GitHub. You can check with
git diff origin/masterwhat your push will do. When your pull request was merged, run
git pullon your local master branch to see your change. You can delete the branch created in step (1) with
nekgit_rm <my branch name>.