Does anybody use Fedora for scientific use?

Optimal Aurora · #1 6th July 2005, 09:53 PM

I mean anything like Astronomy, Chemistry, Computer Science, Physics, etc... This goes out to amateurs and professionals alike. Please also list what programs you use.

BandC · #2 6th July 2005, 10:05 PM

KStars is cool. It shows you celestial objects on a star map. I also had something Celestica called in FC3. It renders planets and stars for you in 3D. Gets old fairly quick but still neat.

I also like the KDE application that shows you the table of elements. I think it's called Kalzium.

bryancole · #3 6th July 2005, 10:23 PM

Yup. We develop data acquisitions and data analysis applications using FC and Python for advanced terahertz imaging instruments. The Python apps are easily ported over to windows (customers seem to want Windows for some reason...).

Data acquisition is based on the Comedi framework (www.comedi.org). The Comedi API is much easier to work with (and more stable) than the typical SDKs provided by the I/O DAQ board manufacturers. It also has Python bindings (although almost any library can easily be wrapped with python, using SWIG).

Data analysis is handled by Python + various python extensions:
Numarray (http://www.stsci.edu/resources/softw...dware/numarray) - for efficient multidimensional array handling, FFTs
SciPy (www.scipy.org) - for fast linear algebra, interpolation, fitting and much more
Matplotlib (http://matplotlib.sourceforge.net/) - for fabulous quality 2D plots
VTK (www.vtk.org) - for advanced 3D visualisation
wxPython + wxGlade - for easy, cross-platform GUI design

I usually use SciTE as my favorite Python editor but since FC4 I've become a big fan of Eclipse for developing code (it's python plugin is excellent).

Previously we've also tried:
Grace - good for 2D plots and analysis but the Motif UI sucks
SciGraphica - nearly a great clone of Microcal Origin. A new version has recently been released but I couldn't get it to work
SciLab - a matlab-clone without matlabs' nice GUI and without python's nice language, or nice quality plots
Maxima - symbolic computation, but GUI now very dated
OpenDX - similar capabilities to VTK but with a nasty Motif GUI. Harder to learn IMHO
Octave - similar to SciLab but without it's own plotting capabilities
kmatplot - 2D/3D plotting but *very* confusing UI
gnuplot - yea olde plotting program ...

that about covers it.

Optimal Aurora · #4 8th July 2005, 03:43 AM

Thanks because I am thinking about using Fedora for just that, Astronomy and helping with Chemistry and Computer Science usage. Thanks you two...

mluntz · #5 19th July 2005, 01:49 AM

Quote:

Originally Posted by bryancole

Previously we've also tried:
Grace - good for 2D plots and analysis but the Motif UI sucks
SciGraphica - nearly a great clone of Microcal Origin. A new version has recently been released but I couldn't get it to work
SciLab - a matlab-clone without matlabs' nice GUI and without python's nice language, or nice quality plots
Maxima - symbolic computation, but GUI now very dated
OpenDX - similar capabilities to VTK but with a nasty Motif GUI. Harder to learn IMHO
Octave - similar to SciLab but without it's own plotting capabilities
kmatplot - 2D/3D plotting but *very* confusing UI
gnuplot - yea olde plotting program ...

that about covers it.

I have used Matlab extensively on windows and Unix systems and would like to use Octave on a linux system. But I have yet to find decent graphics for Octave. I could not get kmatplot to compile on an FC3 system (lots of compile errors and I'm not a c++ programmer). Were you able to get kmatplot to compile on an FC system? Also, have you tried Octaviz? It claims to be a replacement for gnuplot in Octave, but I don't have a feel for how complete it is at this point.

BandC · #6 19th July 2005, 05:37 PM

I installed a program called Stellarium. It's really neat. It's akin to KStars. KStars has more features but Stellarium is prettier.

**Finalzone** · #7 19th July 2005, 07:15 PM

If you like Celestia, you will be interested at this website that has a lot of theme dedicated for Celestia including your favorite fictious universe like Star Wars.

icthy · #8 21st July 2005, 05:58 PM

I and several folks I know use FC3 for geophysics and seismology. Mostly we write shell-scripts in perl or bash, run Matlab, and write our own code in Fortran. I've been running WinXP on VMware so I can collaborate with colleagues on Word documents, and make figures on Adobe Illustrator.

***Firewing1*** · #9 21st July 2005, 06:24 PM

Quote:

computer science

Well, Linux is that...
But yes, I use it for programming. PHP, MySQL, Java, JavaScript, HTML, I know a bit of BASH and I can't program Python, but if I read the code I can understand it pretty well...
And, if you wanted to, I'm sure you could find a way to put Linux to all the uses you listed above. It's very versitile, stable and secure.
It's not really me, but I remember at somepoint reading the history of Linux. I remember that amazon.com/ca switched to Linux long ago. A web hosting company I know uses FC4 for it's servers... Linux has been put to many professional uses...
Firewing1

Jman · #10 22nd July 2005, 03:31 AM

I did have Mathematica working on Fedora, before the license expired.

#11 4th August 2005, 12:55 PM

I use FC4 for fortran 90 programming and mathematica, both applied to univ. physics. Apart from that I enjoy the fact that latex, emacs, vim etc. come standard, so I don't have to mess with cygwin or miktex as I had to under WinXP.

FC4 is just right for these things. It has good support, it's not as rigid as distributions like Gentoo or Debian. Gnome looks great. I can do the things I need to do without playing part-time sysadmin.

ucfagls · #12 4th August 2005, 01:28 PM

I'm a freshwater ecologist and also study the history of aquatic systems using lake sediment archives. I deal with large multivariate datasets pretty much everyday at work(university). I use R (an open source implementation of the S language for data analysis, better known (in the past at least) as the basis for the commercial app S-Plus) for almost all my data analysis needs, including coding up new analysis routines.

I used Xemacs/emacs and the ESS package to link R to (X)emacs to write my R code and for running analyses. I write reports in LaTeX using the Kile editor and embed R code within LaTeX documents using the Sweave tool for R, making my report text and data analysis self contained within one file.

I also use Fedora on our group's webservers with apache, mysql, php etc, that support our project websites and data holdings. These servers used to run Windows but I got sick of all the admin I had to do on them so scrub them and install Fedora instead.

sailor · #13 7th August 2005, 05:17 PM

I really love Stellarium (requires 3d video card for opengl effects) or Kstars, both for astronomy and stargazing.

asun · #14 6th August 2006, 12:05 AM

Quote:

Originally Posted by mluntz

I have used Matlab extensively on windows and Unix systems and would like to use Octave on a linux system. But I have yet to find decent graphics for Octave. I could not get kmatplot to compile on an FC3 system (lots of compile errors and I'm not a c++ programmer). Were you able to get kmatplot to compile on an FC system? Also, have you tried Octaviz? It claims to be a replacement for gnuplot in Octave, but I don't have a feel for how complete it is at this point.

There is also plplot for octave, however I'm having problem to get it running. The command toggle_plplot_use seems to run into many problems. Is there anyone who has successfully use plplot with octave in FC5?

mluntz · #15 15th August 2006, 01:29 AM

Quote:

Originally Posted by asun

There is also plplot for octave, however I'm having problem to get it running. The command toggle_plplot_use seems to run into many problems. Is there anyone who has successfully use plplot with octave in FC5?

Thanks for the tip about plplot. It runs fine on fc4. I downloaded and installed the executable rpms for plplot and plplot_octave from fedora extras. Tried building from the source but wasn't able to get config to recognize the presence of octave. Gave up and then found the executable. I think there is a version for fc5 as well. It did take a little experimentation to get everything working the way I wanted, but the file USAGE.octave was quite helpful.

Mike