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Common commands

Command line

Task Command
Remove directory rm -r -f
-r recursive (do all directories underneath)
-f supresses prompt for write protected files (useful for deleting a git repo)
Git git filter-branch --force --index-filter 'git rm --cached --ignore-unmatch file.py' --prune-empty --tag-name-filter cat -- --all then git push origin --force --all to remove history of sensitive files
Checking jobs top
-u STUDENT\\dbirving (shows just my jobs)
-r (renice the job)
-k (kill the job)
Run in background nohup nice myscript.py &
Check data size du -B GB -c -s
-B (units: GB, MB, etc)
-c (display grand total)
-s (don't display sub directory totals)
ls -lah
Search for patterns in file grep -r 'word' *
-r (look through all directories under the current
Search for file names find . -name *.txt
Cygwin startx
ssh -Y STUDENT\\dbirving@abyss
Secure copy scp {remote file} {local file destination}
e.g. scp STUDENT\\dbirving@abyss:~/directory/script.py .
Remove netCDF attribute ncatted -O -a missing_value,var,d,,
Check netCDF type ncdump -k (see details)

Python

Task Command
Python debugger python -m pdb script.py
c continue until crash
s step
n next
Expand dimension old_array = old_array[numpy.newaxis, ...]
numpy.repeat(old_array, x_times, axis=0)

Installing Python stuff

There are essentially 3 ways to install things (see this blog post for details):

  1. Use apt-get to install packages in the Ubuntu repositories
    e.g. sudo apt-get install python-scientific
  2. Use pip (tool for installing and managing Python packages)
    e.g. sudo pip install ipython
  3. Manually install by downloading the source code
    e.g. cd ~/gitLocal (i.e. directory where you want the code)
    git clone https://github.com/DamienIrving/example.git
    cd example
    sudo python setup.py install -cython

Textwrangler

  • Change font size (zoom doesn't work): View => text display => show fonts
  • Replace tabs with spaces: Text => Detab
  • Block indentation: [command] and [ or ]

CMIP tos data

Some of this data are on a triangulated grid. To get them onto a regular lat/lon grid, you need to use the following cdo command (at least that's what they've done at CSIRO)

cdo remapbil,sftlf.nc tos.nc out.nc

Note that sftlf.nc is the file that it copies the new grid from.