5. Python on expanse¶
5.1. Installing python and jupyter notebooks on expanse¶
python is installed on a user basis. Follow the directions here, under the section “Software Prerequisites”: https://hpc-training.sdsc.edu/notebooks-101/notebook-101.html#software-prerequisites
Note
You may want to change the install directory to your projects directory:
/expanse/lustre/projects/uic406/$USER/miniconda3
5.2. Installing reverse-proxy for accessing jupyter notebooks¶
We’ll follow the directions here: https://hpc-training.sdsc.edu/notebooks-101/notebook-101.html#security-with-reverse-proxy-service
5.3. Installing required python packages matplotlib, netcdf4, and wrf-python on expanse¶
conda install -c conda-forge matplotlib netcdf4 wrf-python
5.4. Starting up a jupyter notebook¶
(base) [snesbitt@login02 reverse-proxy]$ ./start-jupyter -A uic406
Your notebook is here:
https://census-dragging-repent.expanse-user-content.sdsc.edu?token=fef373e07c8b0736c2ecc3219fd962e9
If you encounter any issues, please email help@xsede.org and mention the Reverse Proxy Service.
No time given. Default is 30 mins
Using ./slurm_expanse/notebook.sh
Your job id is 1199869
You may occasionally run the command 'squeue -j 1199869' to check the status of your job
5.5. Basic notebook for wrf-analysis¶
Paste the text into the notebook cells, press Control-Enter (PC) or Command-Return (Mac)
# set up plotting and matplotlib
%pylab inline
# load modules
from netCDF4 import Dataset
from wrf import getvar
# define path to file
ncfile = Dataset("/expanse/lustre/scratch/snesbitt/temp_project/WRF/test/em_quarter_ss/wrfout_d01_0001-01-01_00:00:00")
# Load a variable
p = getvar(ncfile, "P")
p
Basic plotting:
# select the lowest model level and plot a plan view
p.sel(bottom_top=0).plot()