postprocessing with python -...

Postprocessing with Python

Boris Dintrans (CNRS & University of Toulouse)[email protected]

Collaborator: Thomas Gastine (PhD)

mailto:[email protected]

mailto:[email protected]

Outline

• Introduction- what’s Python and why using it?- Installation procedure

Outline


Outline

• Python and the Pencil Code- the Python repository and initialization- Migrating from IDL to Python- Some examples & tricks- Parallel Python with Pypar- Doing widgets with PyQt


Outline

• Python and the Pencil Code- the Python repository and initialization- Migrating from IDL to Python- Some examples & tricks- Parallel Python with Pypar- Doing widgets with PyQt

• Conclusion/Outlook

What’s Python?

What’s Python?

Python was created in 1991 by Guido van

Rossum (CWI, Centrum voor Wiskunde en Informatica, Amsterdam)

Benevolent Dictatorfor Life (BDFL)

The first release in 1991 on alt.sources

DARPA funding proposal “Computer Programming for Everybody” (1999):

•an easy and intuitive language just as powerful as major competitors

•open source, so anyone can contribute to its development•code that is as understandable as plain English•suitability for everyday tasks, allowing for short development times





year 1991 1994 1995 2001 2003 2007 2009

version 0.9 1.0 1.2 2.0 2.2 2.5 3.0




year 1991 1994 1995 2001 2003 2007 2009

version 0.9 1.0 1.2 2.0 2.2 2.5 3.0

• Why Python?- it’s free! ;-)- quite easy to use; object-oriented; highly modular, etc...- much more rapid than IDL and even PARALLEL

The main Python website: www.python.org

http://www.python.org




The SciPy website: www.scipy.org

http://www.scipy.org

http://www.scipy.org



How to install Python?

How to install Python?Required: • python 2.5: the engine• numpy: the scientific computing package (arrays, linear algebra, FFT, random numbers, etc...); [replaces old numarray and numeric]• scipy: modules for integrating ODEs, optimizing functions, etc... [tends to federate all of Python scientific modules]• matplotlib: MATLAB-inspired mostly-2D plotting modules

How to install Python?Required: • python 2.5: the engine• numpy: the scientific computing package (arrays, linear algebra, FFT, random numbers, etc...); [replaces old numarray and numeric]• scipy: modules for integrating ODEs, optimizing functions, etc... [tends to federate all of Python scientific modules]• matplotlib: MATLAB-inspired mostly-2D plotting modules

Optional:• ipython: convenient shell to develop and run Python• basemap: map projections• Pypar: parallel Python (interface with MPI libraries)• PyQt: to do Qt-like widgets VERY easily under Python• MayaVi: 3D plotting

http://python.org/download/





From sources or binary packages?

• For all platforms: everything can be compiled from sources• For Linux, Windows & Mac (at least): binaries are provided (Linux: yum, apt-get, dpkg; Mac: Fink, MacPorts, dmg)


• For all platforms: everything can be compiled from sources• For Linux, Windows & Mac (at least): binaries are provided (Linux: yum, apt-get, dpkg; Mac: Fink, MacPorts, dmg)


Linux (FedoraCore 7) Mac OS X 10.4 (Tiger)Python 2.5.12 2.5.2Numpy 1.0.3 1.0.4Scipy 0.6.0 0.7.0

Matplotlib 0.90.0 0.90.1ipython 0.8.1 0.8.2

Typical installation on a Linux box

Python on Mac OSX: www.pythonmac.org/packages/py25-fat

http://www.pythonmac.org/packages


http://www.pythonmac.org/packages/py25-fat/index.html

http://www.pythonmac.org/packages/py25-fat/index.html

Scipy Superpack for OS X: http://macinscience.org/?page_id=6



http://macinscience.org/?page_id=6

http://macinscience.org/?page_id=6

Python packages on my Macbook Pro

(SciPy Superpack)

Python in the Pencil Code repository:f90/pencil-code/numpy commited by Jeff in fall of 2007

revision 1.1date: 2007-11-16 13:57:04 +0000; author: joishi; state: Exp;* added python scripts for reading pencil code data. they require only the numpy package, but matplotlib is useful for plotting. almost all of these routines are simplified clones of their idl counterparts. i'd love to make a more OO pencil-code package, but my current occupational constraints make that unlikely in the near term. NB: the byte ordering in python is C, not fortran, so these routines return an f array with shape f[nvar,nz,ny,nx]--the reverse of pencil.

* added nl2python to take advantage of the amazing perl F90Namelist.pm

* modified F90Namelist.pm to output python

* i hope these are moderately useful to people!

The actual Python tree: 3 directories

numpy/pencil/files__init__.pyyzaver.pyyaver.pyxyaver.pynpfile.pydim.py

param.pygrid.pyslices.pyzprof.pyindex.pyvar.pyts.py

The reading stuff

The actual Python tree: 3 directories

numpy/pencil/files__init__.pyyzaver.pyyaver.pyxyaver.pynpfile.pydim.py

param.pygrid.pyslices.pyzprof.pyindex.pyvar.pyts.py

The reading stuffnumpy/pencil/math

__init__.pyvector_multiplication.py

derivatives/

numpy/pencil/math/derivatives__init__.py

der.pydiv_grad_curl.py

der_6th_order_w_ghosts.py

The math stuff

# Set PYTHON path if ($?PYTHONPATH) then setenv PYTHONPATH "${PYTHONPATH}:${PENCIL_HOME}/numpy" else setenv PYTHONPATH "${PENCIL_HOME}/numpy" endif

...and the initialization of $PYTHONPATH in f90/pencil-code/sourceme.csh

# Set PYTHON path if ($?PYTHONPATH) then setenv PYTHONPATH "${PYTHONPATH}:${PENCIL_HOME}/numpy" else setenv PYTHONPATH "${PENCIL_HOME}/numpy" endif

...and the initialization of $PYTHONPATH in f90/pencil-code/sourceme.csh

These modules are loaded when importing the whole pencil directory due to the __init__.py file

cat numpy/pencil/__init__.py

cat numpy/pencil/__init__.py

In [1]: import pencil as pcIn [2]: pc.read_ts()

An important point: Python’s classes• Python is an object-oriented interpreted language:

instead of doing pc.read_ts(),it is better to do a=pc.read_ts()

An important point: Python’s classes• Python is an object-oriented interpreted language:

instead of doing pc.read_ts(),it is better to do a=pc.read_ts()

... and we can plot the other variables read in time_series.dat and embedded in object ‘a’

Another example when using pc.read_var()

Another example when using pc.read_var()

...and we plot the entropy at the top of

the 32^3 box

Another examples of postprocesing with Python

Basemap: various kind of map projections

MayaVi:3D plots

http://code.enthought.com/projects/mayavi/





Be careful: Python’s arrays are ordered like

i.e. REVERSED ORDER COMPARED TO PENCIL-

CODE OR IDL!!!

f[nvar,mz,my,mx]

Migrating from IDL to Python: some useful Web Guideshttp://www.stsci.edu/resources/software_hardware/numarray/idl2numarray

http://www.stsci.edu/resources/software_hardware/numarray/idl2numarray




http://mathesaurus.sourceforge.net/idl-numpy.html





http://code.google.com/p/i2py/For lazy guys: the i2py converter

http://code.google.com/p/i2py/





Some tricks when using Python...


• plays with ~/.ipython/ipythonrc to load modules by default (import_all pencil) and thus use ‘read_var’ instead of ‘pc.read_var()’, etc...



• import just what you need! (a cleaning is certainly needed in that respect in the PC tree...)




• launch ipython with the ‘-pylab’ option to call directly plot, contour, imshow, etc...





• accelerate the VAR* reading by passing param, grid, index, etc... [tricks.py]






• accelerate the graphics by using an handle [tricks.py]


• take advantage of class and objects (a.shape instead of shape(a))





• accelerate the graphics by using an handle [tricks.py]

Parallel Python using the Pypar modulehttp://sourceforge.net/projects/pypar

http://sourceforge.net/projects/pypar





Pypar example 1: compute a vertical profile in parallel

Pypar example 2: write PNG files in parallel for a movie

Widgets using Qt Designer + PyQt

Conclusion/Outlook

Conclusion/Outlook• Python can do a very good job in the Pencil Code post-processing• Its using is rapidly increasing in astrophysics (NASA, ESA, ESO, labs,...)• More in the Pencil Code philosophy (i.e. under GPL) compared to IDL

Conclusion/Outlook

• the actual Python subroutines must be rewritten in a more oriented-object form (class inheritance) •the Python tree shall maybe be re-organized in something like f90/pencil-code/python or???• what’s about the calling of Fortran or C subroutines to increase the speed?

• Python can do a very good job in the Pencil Code post-processing• Its using is rapidly increasing in astrophysics (NASA, ESA, ESO, labs,...)• More in the Pencil Code philosophy (i.e. under GPL) compared to IDL

postprocessing with python -...

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