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NekCEM

NekCEM is a discontinous-Galerkin, spectral-element solver for Maxwell's equations and the drift-diffusion equations written in Fortran and C. It runs efficiently in parallel on a wide variety of systems, from laptops to the supercomputers at the Argonne Leadership Computing Facility (ALCF) and the Oak Ridge Leadership Computing Facility (OLCF). Its core is based on the computational fluid dynamics code Nek5000.

Installing

Dependencies

To run simulations with NekCEM you will need the following things.

  • An MPI implementation.
  • Python 2.7 or higher (including all versions of Python 3).
  • BLAS and Lapack.

Some notes on the dependencies:

  • To keep things simple, make sure the compiler wrappers mpif77 (or mpifort) and mpicc are on your path. This isn't strictly necessary, but without them you will have to do more work when compiling simulations.
  • Python is only used in the build process.
  • The system version of Python on some ALCF and OLCF systems is 2.6; use softenv or modules to switch to a more recent version. Run soft add +python on a softenv system and module load python on a modules system.
  • Again to keep things simple, make sure you can link to BLAS and Lapack using -lblas and -llapack.

Standard install

To install NekCEM run

git clone https://github.com/NekCEM/NekCEM
cd NekCEM
sudo make install

The command make install does a couple of things.

  • It copies NekCEM/src and NekCEM/bin to /usr/local.
  • It symlinks some scripts to /usr/local/bin.

Note that installing to /usr/local is simply the default option; the install directory can be controlled in the standard way using the variables DESTDIR, prefix, and bindir.

Development install

If you want to help develop the NekCEM source code, first fork the NekCEM repo on Github. Then do

git clone https://github.com/<github-username>/NekCEM
cd NekCEM
git remote add upstream https://github.com/NekCEM/NekCEM
sudo make install_inplace

The command sudo make install_inplace only symlinks scripts to /usr/local/bin, allowing a developer to edit the source in their local clone while still having the necessary scripts on their path.

Running simulations with NekCEM

Setting up a simulation with NekCEM requires creating four files.

  • A user file. This is a Fortran file which contains various subroutines used to control the solvers. Its file extension should be usr.
  • A size file. This file contains compile-time parameters. It should be called SIZE.
  • A read file. This file contains parameters which are read at runtime. Its file extension should be rea.
  • A map file. This file contains the mapping between processors and elements. Its file extension should be map, and it must have the same stem as the read file.

A typical NekCEM simulation will be set up like this

example
├── readfile.map
├── readfile.rea
├── userfile.usr
└── SIZE

To build and run the code do the following from the example directory.

configurenek <solver> userfile
make
mpirun -np <number-of-processors> ./nekcem readfile &> log

Let's break down what's going on.

  • In the first step configurenek creates a makefile. The <solver> option determines which equations the application is targeting; it should be one of maxwell, drift, or shrod.
  • In the second step the makefile builds the code in the normal way; it produces an executable nekcem.
  • In the third step the code is run in the normal way for MPI applications.

The third step can be replaced with nek readfile <number-of-processors>. On a typical system this will do the exact same thing as mpirun, but on ALCF and OLCF machines it will also queue your job correctly.

Running the Tests

The tests can be run with bin/runtests [options]. For a complete list of options use the -h flag.