pkdgrav3 compilation

example.py

import pynbody
import matplotlib.pyplot as plt
import numpy as np

s = pynbody.load("./pkdgrav3/examples/example.00140")
plt.figure(figsize=(6,5))
b = np.linspace(-0.5, 0.5, 256)
plt.hist2d(s["pos"][:, 0], s["pos"][:, 1], bins=(b, b), cmap="Blues");
plt.colorbar()

gistfile1.txt

#build the software
rm -Rf build
mkdir build
cd build
singularity exec base.simg cmake -DFFTW_INCLUDES=/usr/include/ .. &> log
singularity exec base.simg make -j16

#Run the simulation on GPU
chmod +x run_sim.sh
singularity exec --nv base.simg ./run_sim.sh

#Check the output
singularity exec --nv python3 example.py

run_sim.sh

#!/bin/bash

#https://github.com/open-mpi/ompi/issues/7701#issuecomment-932587086
export HWLOC_COMPONENTS=-gl
lstopo
cd examples
mpirun --display-topo ../build/pkdgrav3 cosmology.par