Monday, November 20, 2006

WaveMetrics - scientific graphing, data analysis, curve fitting & image processing software

From the scipy mailing list:

It's hard to describe what this amazing program does because it does
so much. I have a few personal dislikes about it but by comparison,
Matlab "isn't even wrong," to misuse a quote from Wolfgang Pauli.


WaveMetrics - scientific graphing, data analysis, curve fitting & image processing software

pydap and pupynere

pydap is a python module that will allow you to read (and serve?) netcdf files over the internet. This is very useful if you don't want to have an entire model run on your laptop. John Evans and I are working on prslice that uses this package.

Even more cool, however, is pupynere (PUre PYthon NEtcdf REader) that can read (only, for now) NetCDF files with only builtin python packages and nympy.

Sunday, July 16, 2006

Tuesday, June 20, 2006

Test post from TextMate

This is my first test post from textmate. Let me try to edit it a bit more.. How about a link in [markdown][].

Friday, June 16, 2006

Compiling netcdf with ifort 9.1 on an Intel Mac

First, if you haven't already done so, you need to do this if you are runing Xcode 2.3, like I am. Otherwise, ifort will not make it through configure.


cd /usr/lib
sudo ln -s gcc/darwin/3.3/crt2.o .


Then, you can set up your environmental variables just like you would using ifort in Linux. For example:


export FC=ifort
export F90=ifort
export FFLAGS="-O -mp"
export CPPFLAGS="-DNDEBUG -DpgiFortran"


Then, like always, run


./configure --prefix=/usr/local
make

Thursday, June 15, 2006

Shed Skin -- python to C++ compiler

Shed Skin - Shed Skin is a compiler that takes pure python code, and coverts it to annotated C++ code. Speedup is (suposedly) much higher than other similar methods.

Wednesday, June 14, 2006

Creating an SVN repository.

First, make sure you have a WebDAV module turned on in you apache server. You need to configure your apache server as described [here](http://www.csoft.net/docs/micro/svndav.html) or [here](href="http://svnbook.red-bean.com/en/1.1/ch06s04.html), for example. Of particular note allowing anonymous access through LimitExcept, and creating a root svn directory for numerous repositories by using SVNParentPath. You can then access this server using svn, a web browser, or mount it like a networked disk. Very cool.

After you set up the WebDAV server, you need to create a snv repository. Here is how I made a repository for my python modules:

# cd /home/svn
# svnadmin create python
# svn mkdir file:///home/svn/python/trunk file:///home/svn/python/branches file:///home/svn/python/tags -m "creating initial repository layout"

You may need to change permissions so that httpd can read this directory. Now, as a user, you can start to populate the reposatory. I will add a directory 'gridgen' and the file 'gridgen.py'. There are some other things in this directory that I don't want to add, so I won't just add the whole thing, but rather I will do it piece by piece. Note, I will log in as a registered user, so that I can write to the repository later.

$ svn co http://rob@pong.tamu.edu/svn/python/trunk python
$ svn add gridgen --non-recursive
$ svn add gridgen/gridgen.py
$ svn commit -m "Initial commit of gridgen module"

Sunday, June 11, 2006

stack size limits using ifort

I use ifort on both Linux and Intel Macs. I have come across some strange behaviors that make me think that the stack is not really unlimited. This post on automatic array stack size limit bug - Intel Fortran Compiler for Linux and Mac OS - Intel Software Network Forumsto the ifort message boards seems to suggest this is a bug in ifort.

This seems to be less of an issue on my Linux machines, where I can set ulimit to unlimited (particularly the stack). On my Mac, I can't set ulimit to unlimited (and if you want to increase it at all, you need to add a flag that lets you use the 'soft' limit). As far as I can tell, partitioning through MPI does not seem to help, but I will look into it more.


Thursday, June 8, 2006

Map Projections Poster

Although 'poster' seems a bit of an exageration, the Map Projections Poster is the best source I have found so far for describing the different mapping projections.

Friday, May 12, 2006

Merrimack river discharge

Here is a python script (merrimack_discharge.py) that downloads river discharge based on the USGS station code. The class provides time-dependent dischrge data and a few simple methods for deriving anual statistics. Running the script creates a plot of the historical (for statistics) and recent disharge of the Merrimack river in New England. This was developed for my near-field plume study with Dan Macdonald.

UPDATED: script now includes real-time data from the USGS, and the figure has been updated to look at the recent flood as compared to historical floods.



Thursday, May 11, 2006

Real-time stream flow data in Google Earth.

The USGS has released two kml files for Google Earth that show real time river guage data relative to climatologies. You can click on the colored points and get information about the station. A sample screen grab from New England today shows the rain New England has been getting recently.



Dvorak-ing

I've been wondering when I should make the leap over to Dvorak. The new sleves for the TypeMatrix 2030 seems to be a good way to switch without much pain..

Monday, March 6, 2006

OpenCFD

OpenCFD is an open source utility for finite volume computational fluid dynamics.

Thursday, February 16, 2006

Test post from deepest sender

Here is a draft post from Deepest Sender, a Firefox extension for working with blogs.  The editor seems fairly easy to use, and has a Word-like editor, a source editor, and a rendered preview.  Pretty cool.  Firefox has come a long way, and has definately surpassed Safari.  The single feature of Safari that is still better is the built-in RSS viewer.  Fortunately, the Sage extension for Firefox has different advantages, and mitigates this difference some.

Thursday, February 9, 2006

Tuesday, February 7, 2006

PyDSTool

PyDSTool is a python module for dealing with dynamical systems. For when the SciPy ode solver is just not good enough..

Thursday, January 26, 2006

PyNGL and PyNIO

There is an effort at UCAR to translate NGL (the NCAR Graphics Language) to python: PyNGL. Also, as part of this project, there is PyNIO, and input/output module that reads and writes in many different formats supported by NGL.

Thursday, January 5, 2006

TVTK

Although matplotlib supports 2D graphics (and quite well, I might add), there is no support for 3D graphics. VTK is clearly the way to go, but there has been no 'pythonic' interface... until TVTK.

Also of interest might be NCVTK, which provides another interface for visualization of NetCDF files using VTK.