Foreword

• MagIC is a numerical code that can simulate fluid dynamics in spherical geometry. MagIC solves for the Navier-Stokes equation including Coriolis force, optionally coupled with an induction equation for Magneto-Hydro Dynamics (MHD), a temperature (or entropy) equation and an equation for chemical composition under both the anelastic and the Boussinesq approximations.

• MagIC uses either Chebyshev polynomials or finite differences in the radial direction and spherical harmonic decomposition in the azimuthal and latitudinal directions. MagIC supports several Implicit-Explicit time schemes where the nonlinear terms and the Coriolis force are treated explicitly, while the remaining linear terms are treated implicitly.

• MagIC is written in Fortran and designed to be used on supercomputing clusters. It thus relies on a hybrid parallelisation scheme using both OpenMP and MPI. Postprocessing functions written in python (requiring matplotlib and scipy are also provided to allow a useful data analysis.

• MagIC is a free software. It can be used, modified and redistributed under the terms of the GNU GPL v3 licence.

Quickly start using MagIC

1) In order to check out the code, use the command

$ git clone https://github.com/magic-sph/magic.git

or via SSH (it requires a public key):

$ git clone ssh://[email protected]/magic-sph/magic.git

2) Go to the root directory and source the environment variables (useful for python and auto-tests)

$ cd magic

If you are using sh, bash or zsh as default shell (echo $SHELL), just use the command

$ source sourceme.sh

If you are using csh or tcsh, then use the following command

$ source sourceme.csh

3) Install SHTns (recommended)

SHTns is a an open-source library for the Spherical Harmonics transforms. It is significantly faster than the native transforms implemented in MagIC, and it is hence recommended (though not mandatory) to install it. To install the library, first define a C compiler:

$ export CC=gcc

or

$ export CC=icc

Then make sure a FFT library such FFTW or the MKL is installed on the target machine. Then make use of the install script

$ cd $MAGIC_HOME/bin
$ ./install-shtns.sh

or install it manually after downloading and extracting the latest version here

$ ./configure --enable-openmp --prefix=$HOME/local

if FFTW is used or

$ ./configure --enable-openmp --enable-ishioka --enable-magic-layout --prefix=$HOME/local --enable-mkl

if the MKL is used. Possible additional options may be required depending on the machine (check the website). Then compile and install the library

$ make
$ make install

4) Set up your compiler and compile the code

a) Using CMake (recommended)

Create a directory where the sources will be built

$ mkdir $MAGIC_HOME/build
$ cd $MAGIC_HOME/build

Set up your Fortran compiler

$ export FC=mpiifort

or

$ export FC=mpif90

Compile and produce the executable (options can be passed to cmake using -DOPTION=value)

$ cmake .. -DUSE_SHTNS=yes
$ make -j

The executable magic.exe has been produced!

b) Using make (backup solution)

Go to the source directory

$ cd $MAGIC_HOME/src

Edit the Makefile with your favourite editor and specify your compiler (intel, gnu, portland) and additional compiler options (SHTns, production run or not, debug mode, MKL library, ...)

$ make -j

The executable magic.exe has been produced!

5) Go to the samples directory and check that everything is fine

$ cd $MAGIC_HOME/samples
$ ./magic_wizard.py --use-mpi --nranks 4 --mpicmd mpiexec

If everything is correctly set, all auto-tests should pass!

6) You're ready for a production run

$ cd $SCRATCHDIR/run
$ cp $MAGIC_HOME/build/magic.exe .
$ cp $MAGIC_HOME/samples/hydro_bench_anel/input.nml .

Then change the input namelist to the setup you want and run the code:

$ export OMP_NUM_THREADS=2
$ export KMP_AFFINITY=verbose,granularity=core,compact,1
$ mpiexec -n 4 ./magic.exe input.nml

7) Data visualisation and postprocessing

a) Set-up your PYTHON environment (ipython, scipy and matplotlib are needed)

b) Modify magic.cfg according to your machine in case the auto-configuration didn't work

$ vi $MAGIC_HOME/python/magic/magic.cfg

c) You can now import the python classes:

python> from magic import *

and use them to read time series, graphic files, movies, ...

python> ts = MagicTs(field='e_kin', all=True)
python> s = Surf()
python> s.equat(field='vr')
python> ...

8) Modify the code and submit your modifications

a) Before commiting your modifications always make sure that the auto-tests pass correctly.

b) Try to follow the same coding style rules as in the rest of the code:

1. Never use TABS but always SPACES instead
2. Use 3 spaces for indentation
3. Never use capital letters for variable declaration or Fortran keywords
4. Never use dimension(len) for declaring array but rather real(cp) :: data(len)
5. Always use the default precisions when introducing new variables (cp)

More on that topic here

9) Make sure you cite the following papers if you intend to publish scientific results using MagIC:

• Boussinesq equations: Wicht (2002, PEPI, 132, 281-302)
• Anelastic equations: Gastine & Wicht (2012, Icarus, 219, 428-442)
• In case you use the SHTns library for the spherical harmonics transforms (MagIC 5.3 or later), please also cite: Schaeffer (2013, GGG, 14, 751-758)

MagIC has been tested and validated against several international dynamo benchmarks:

• Christensen et al. (2001, PEPI, 128, 25-34)
• Breuer et al. (2010, GJI, 183, 150-162)
• Jones et al. (2011, Icarus, 216, 120-135)