How to compile the SWMF model

SWMF

Pre-requisites

• Start by updating the packages list:

sudo apt update

• Install the build-essential package by typing:

sudo apt install build-essential

The command installs a bunch of new packages including gcc, g++ and make.

• To validate that the GCC compiler is successfully installed, use the gcc --version command which prints the GCC version:

gcc --version

Then we need an MPI support. We choose OpenMPI:

sudo apt-get update && sudo apt-get install infiniband-diags ibverbs-utils \
     libibverbs-dev libfabric1 libfabric-dev libpsm2-dev -y
sudo apt-get install openmpi-bin openmpi-common libopenmpi-dev libgtk2.0-dev
sudo apt-get install librdmacm-dev libpsm2-dev

The command installs a bunch of new programs including mpiexec, mpif90, and mpicxx.

Downloading

The source code locates at: https://github.com/SWMFsoftware/SWMF

To download the code, we choose to clone through SSH:

git clone git@github.com:SWMFsoftware/SWMF.git

If you use HTTPS, you will encounter errors during installation. SSH connection requires setup in the terminal. Checkout this GitHub post.

Compilation

./Config.pl

./Config.pl -install

Checkout the usage of Config.pl for switching compilers etc.

On Perlmutter, we need to manually add -pthread to the linking stage. Identify the following line in Makefile.conf:

LINK.f90         = ${CUSTOMPATH_MPI}mpif90

Append -pthread to the end:

LINK.f90         = ${CUSTOMPATH_MPI}mpif90 -pthread

Testing

make -j test16_2d

BATSRUS

git clone git@github.com:SWMFsoftware/BATSRUS.git
cd BATSRUS
./Config.pl -install

Here we try a simple KHI demo on Perlmutter.

/Config.pl -e=Hd -g=8,8,1 -u=KelvinHelmholtz
make -j
make PIDL
make rundir
cp Param/SHOCKTUBE/PARAM.in.kelvin_helmholtz run/PARAM.in

mv run ~/scratch # move the run folder to your workspace

Next we ask for an interactive job:

salloc --nodes 1 --qos interactive --time 00:10:00 --constraint cpu

After entering the interactive job, we go to the copied run directory.

srun -n 1 ./BATSRUS.exe | tee runlog

Then we postprocess the data into a new folder:

./PostProc RESULT/run1

The actual data is stored under RESULT/run1/GM/. For plotting with Python, checkout flekspy demos here.

import flekspy as fs
import matplotlib.pyplot as plt

file = 'z=0_hd_1_t00000320_n00001016.out'
ds = fs.load(file)
ds.Rho.plot.pcolormesh(x="x", y="y")

plt.savefig("test.png")