Author: Ezhilsabareesh Kannadasan (edits by Christopher Bull)
Version: v0.2
Purpose: A reusable single-prompt workflow for preliminary optimisation of any ACCESS-OM3-style Payu configuration, with continuous progress tracking after every Codex interaction, machine-readable performance summaries, a shareable, re-runnable Jupyter notebook with plots, and MOM6 mask-table/layout safety for finer-resolution configs.
This version is designed for configs such as:
This is a lesson by way of a sandbox repository. We have a file at commit A that looks like:
# double-triple-dot-git
This line will be used for commit B: I am adding some text for commit B
This line will be used for commit C: I am adding some text for commit C
This line will be used for commit D: I am adding some text for commit D
| #https://stackoverflow.com/questions/1767384/how-can-i-get-a-recursive-full-path-listing-one-line-per-file | |
| SRCEPATH=/g/data/ol01/access-om3-output | |
| DESTPATH=/g/data/ol01/outputs/access-om3 | |
| ln -s ${DESTPATH}/access-om3-025/MC_25km_jra_ryf-1.0-beta-cdfb3543/output018/access-om3.mom6.2d.zossq.1mon.mean.1951.nc ${SRCEPATH}/access-om3-025/MC_25km_jra_ryf-1.0-beta-cdfb3543/output018/access-om3.mom6.2d.zossq.1mon.mean.1951.nc | |
| ln -s ${DESTPATH}/access-om3-025/MC_25km_jra_ryf-1.0-beta-cdfb3543/output018/Vertical_coordinate.nc ${SRCEPATH}/access-om3-025/MC_25km_jra_ryf-1.0-beta-cdfb3543/output018/Vertical_coordinate.nc | |
| ln -s ${DESTPATH}/access-om3-025/MC_25km_jra_ryf-1.0-beta-cdfb3543/output018/access-om3.mom6.2d.sos.1mon.max.1950.nc ${SRCEPATH}/access-om3-025/MC_25km_jra_ryf-1.0-beta-cdfb3543/output018/access-om3.mom6.2d.sos.1mon.max.1950.nc | |
| ln -s ${DESTPATH}/access-om3-025/MC_25km_jra_ryf-1.0-beta-cdfb3543/output018/access-om3 |
| import requests | |
| import csv | |
| # GitHub API URL for the COSIMA organization repositories | |
| url = "https://api.github.com/orgs/cosima/repos" | |
| # Function to fetch all repositories with pagination | |
| def fetch_all_repos(url): | |
| repos = [] | |
| while url: |
| if paper_case=='20170113_EACnowClimateChange01': | |
| section_description_dict=collections.OrderedDict() | |
| section_description_dict['AB']=[ 60, 61,217,226,0,54,'zonal' ] | |
| section_description_dict['BC']=[ 60, 61,226,303,0,54,'zonal' ] | |
| section_description_dict['GD']=[ 85,128,311,312,0,54,'meridional' ] | |
| section_description_dict['FE']=[127,128,239,247,0,54,'zonal' ] | |
| section_description_dict['ED']=[127,128,247,311,0,54,'zonal' ] | |
| section_description_dict['IH']=[ 46,58 ,212,213,0,54,'meridional' ] | |
| section_description_dict['JK']=[ 85,86 ,224,231,0,54,'zonal' ] | |
| section_description_dict['PQ']=[ 68,80 ,212,213,0,54,'meridional' ] |
| lg.info("") | |
| lg.info("Running check to see if changes found in "+cfgf+" are now in: "+ofile) | |
| #run quick check to make sure all diff'd parameters were inserted | |
| #(still uses f90nml, so not exactly independent) | |
| with open(ofile) as nml_file: | |
| new_nml = f90nml.read(nml_file) | |
| for top_key in diff[cfgf].keys(): | |
| for bot_key in diff[cfgf][top_key].keys(): | |
| # assert(new_nml[top_key][bot_key]==diff[cfgf][top_key][bot_key]),ofile + " did not get created correctly" | |
| # print(top_key,bot_key,new_nml[top_key][bot_key],diff[cfgf][top_key][bot_key]) |
| # hacked up from: http://www.trondkristiansen.com/?page_id=846 | |
| import os | |
| from netCDF4 import Dataset | |
| import matplotlib.pyplot as plt | |
| import matplotlib.cm | |
| import numpy as np | |
| def LevelColormap(levels, cmap=None): | |
| """ |
| function vimnci() | |
| { | |
| if [[ ( $# -eq 0 ) || ( $1 == "--help" ) || ( $1 == "-h" ) ]] ; then | |
| echo "Usage: vimnci PATH_TO." | |
| echo "Purpose: Allows remote editing of files on nci servers..." | |
| echo " " | |
| echo "Mandatory arguments: " | |
| echo "path or file: vim will either edit or open file passed" | |
| echo " " | |
| echo "Example." |
| snippet cdo | |
| ########################################################################### | |
| # CDO # | |
| ########################################################################### | |
| #extract a time | |
| cdo seltimestep,1,2,5 cordex24_CURLFX-FLUXFCE_3h_20040101_20041231_grid_U_2D.nc test.nc | |
| #do simple arithmatic | |
| cdo expr,'sum=qsr+qns-qt' cordex24_CURLFX-FLUXFCE_3h_19980101_19981231_grid_T_2D.nc ofile.nc |
| import matplotlib | |
| import matplotlib.pyplot as plt | |
| #nb requires latex installed on the machine, see http://matplotlib.org/users/usetex.html | |
| from matplotlib import rc | |
| import numpy as np | |
| rc('text', usetex=True) | |
| matplotlib.rcParams['mathtext.fontset'] = 'custom' | |
| matplotlib.rcParams['mathtext.rm'] = 'Bitstream Vera Sans' | |
| matplotlib.rcParams['mathtext.it'] = 'Bitstream Vera Sans:italic' |