pynx¶

Summary

Source: http://ftp.esrf.fr/pub/scisoft/PyNX/doc/

License: http://ftp.esrf.fr/pub/scisoft/PyNX/doc/#license

Path: /software/pynx

Documentation: http://ftp.esrf.fr/pub/scisoft/PyNX/doc/

PyNX stands for Python tools for Nano-structures Xtallography.It can be used for:

Coherent X-ray imaging simulation and analysis: coherent diffraction imaging (CDI), Ptychography, Wavefront propagation, near field and far field techniques…
Fast scattering calculations from large number of atoms and reciprocal space positions.

Using pynx¶

pynx is installed as a python 3.9 virtual environment. Use modules to setup the environment:

xwhich pynx

# Provided by module(s)
#  ... module load maxwell pynx/2020.2.2                        which pynx: /software/pynx/2020.2.2/bin/pynx 
#  ... module load maxwell pynx/2022.1                          which pynx: /software/pynx/2022.1/bin/pynx 
#
# Documentation: https://docs.desy.de/maxwell/applications/pynx

module load pynx/2022.1

# note: the pynx command is just a dummy

Installation¶

the procedure used to install pynx v2022.1:

# setup
module purge
module load maxwell openmpi/3.1.6 cuda/11.3 python/3.9
unset PYTHONPATH
unset MPI_PYTHON3_SITEARCH
unset MPI_PYTHON_SITEARCH

# create the virtual environment
cd /software/pynx/
mkdir 2022.1
cd 2022.1/
virtualenv -p python3.9 ./
source bin/activate

# install python packages
python3.9 -m pip install --upgrade pip
python3.9 -m pip install setuptools wheel --upgrade
python3.9 -m pip install numpy cython scipy matplotlib ipython notebook h5py psutil pyvkfft --upgrade
python3.9 -m pip install scikit-image hdf5plugin h5glance silx fabio ipywidgets ipympl scikit-learn --upgrade
python3.9 -m pip install mpi4py --upgrade 
python3.9 -m pip install pybind11 mako
python3.9 -m pip install pyopencl --upgrade
has_pyopencl=1
python3.9 -m pip install pyqt5 pyopengl
python3.9 -m pip install scikit-cuda

# install pycuda
mkdir dev
cd dev
wget https://files.pythonhosted.org/packages/5a/56/4682a5118a234d15aa1c8768a528aac4858c7b04d2674e18d586d3dfda04/pycuda-2021.1.tar.gz
tar xf pycuda-2021.1.tar.gz 
cd pycuda-2021.1/
python configure.py --cuda-root=$CUDA_PATH --cxxflags="-std=c++11"
make
make install
cd ..

# install pynx
curl -O http://ftp.esrf.fr/pub/scisoft/PyNX/pynx-latest.tar.bz2 
tar xf pynx-latest.tar.bz2 
cd pynx/
pip install .