Nek5000

| Short Tests | Examples | |-----------------|---------------------|------------------|-------------------|---------------| | | |

Nek5000 is an open source, fast and scalable spectral element code designed to simulate:

• unsteady incompressible Navier-Stokes flows and magnetohydrodynamics (MHD)
• low Mach-number flows
• heat transfer and scalar transport

Highlights

• Written in Fortran 77 and C
• Pure MPI for parallelization
• Proven scalability to over a million processes
• Easy-to-build and easy-to-use
• High-order conforming curved quadrilateral/hexahedral meshes
• 3rd order CFL adaptive semi-implicit timestepping
• Efficient preconditioners
• Parallel I/O
• Moving meshes and free surface flow
• Lagrangian particle tracking
• Conjugate fluid-solid heat transfer
• uRANS and LES turbulence models
• Interface to VisIt for parallel data analysis and visualization

Download

You can download the latest release of Nek5000 here.

Getting Started

1. Unpack the tarball to ~/Nek5000
2. Add ~/Nek5000/bin to your shell search path
3. Copy ~/Nek5000/short-tests/eddy to ~/nekcases/eddy
4. Copy ~/Nek5000/core/makenek to ~/nekcases/eddy
5. Go to ~/nekcases/eddy and run ./makenek eddy (see makenek for build options)
6. You can run the case using two processes with nekmpi eddy 2

Note: For more information see here

Documentation

Visit our website

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

If you have improvements to Nek5000, send us your pull requests! If you are planning a large contribution, we encourage you to discuss the concept here on GitHub (just open a pull-reqest) and interact with us frequently to ensure that your effort is well-directed. Our project is hosted on GibHub. The main repository will always hold two evergreen branches:

• develop
• master

The main branch should be considered develop and will be the main branch where the source code of HEAD always reflects a state with the latest delivered development changes for the next release. As a developer, you will you typically be branching and merging from develop.

Consider master to always represent the latest code deployed to production. During day to day development, the master branch will not be interacted with. When the source code in the develop branch is stable and has been deployed, all of the changes will be merged into master and tagged with a release number.

For those just getting started with GitHub, here a short how-to:

One-time Setup

1. Sign up on GibHub
2. Fork our project on GitHub
3. Download fork with git clone -o myfork https://github.com/<username>/Nek5000.git ~/Nek5000
4. Add our repo cd ~/Nek5000; git remote add origin https://github.com/Nek5000/Nek5000.git
5. Download our repo git fetch origin
6. Set upstream for local develop branch git branch --set-upstream develop remotes/origin/develop
7. Run ~/Nek5000/bin/git-hub setup —u <your username on GitHub> --global
8. Add this to your [hub] section in ~/.gitconfig:

[hub]
        ...
        upstream = Nek5000/Nek5000
        forkremote = myfork 

Typical Workflow

1. Create a branch hosting your changes with nekgit_co <my branch name> develop. The core idea is that all development should take place in a dedicated branch instead of the local development branch.
2. Implement your changes. Make sure your change is atomic and consistent. You can work on multiple branches simultaneously. Just do a git checkout <your branch name> to change the branch. Note, this will update the files in your working directory (~/Nek5000). To compare your files with our develop repo use git diff origin/develop.
3. Commit the changes to your local repo using git commit -a -m 'a descriptive comment'. Do this frequently to save your work (otherwise you cannot switch branches).
4. Periodically, changes made in our Nek5000 repo should be pulled back into your branch by git pull.
5. 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. If you are done with all files, run git add . and do a git commit to indicate that all conflicts have been resolved.
6. Assuming you are happy with your change, run nekgit_push. Now you should be able to see your pull request on GitHub. The core developers will review your change and discuss potential modifications. We cannot consider your merge request if it is outdated or does not pass the regression tests. Please include a short-test in case of a new feature. When your pull request was merged or closed, you can delete your branch (created in step 1) with nekgit_rm <my branch name>.
7. You may want to set your working directory back to our latest develop branch. To do this just run git checkout develop; git pull. After your pull reqest was merged, you have to update your local develop branch again (git pull) to see your change.

Code Structure

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

####core contains the majority of the Nek5000 application sources.

####jl contains gather/scatter communication (gslib), interpolation, and preconditioners written in highly general C code.

####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 validation.

3rd_party

contains nothing. Its purpose it to provide a consistent place for 3rd part plugin/toolbox developers to place their code.