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 Forum index » Advanced Topics » Additional Software (PETs, n' stuff) » Engineering/Science/Simulation
Math Base - Basic Free Mathematic Software for Puppy Linux
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emil

Joined: 10 Nov 2009
Posts: 612
Location: Austria

PostPosted: Sun 10 Jan 2010, 13:45    Post subject:  Math Base - Basic Free Mathematic Software for Puppy Linux
Subject description: Octave, R, Maxima, Gretl, Yacas, GeoGebra, Sage, Numpy, Scipy, Sympy, Scilab
 

Hello math-lovers,







Over the last weeks I have spent some time to get Basic Mathematic Packages working in Puppy Linux 431.

Those are:
GNU OCTAVE - For engineering and numerics (strong side matrix calculations). Mostly compatible to Matlab.
GNU R - standard package for statistics
MAXIMA - Computer Algebra System, also with GUI Frontend wxmaxima (similar to Mathematica and Maple)
GNU GRETL - econometrics and time series analysis
GEOGEBRA - interactive educational math package (high school level)
YACAS - tiny and efficient Computer Algebra
Sage - Huge, comprehsive and (all?)mighty package
NumPy, SciPy, SymPy - Python math modules
SciLab - Numeric package, similar to Matlab but not as compatible than Octave

the pet files also include amongs others gnuplot, GNU Lisp (glc), GNU Fortran (gfortran), GNU scientific Library and LAPACK libraries.

Beside beeing strong command line interpreters, most of these packages can be used as scripting languages.
I have packed the necessary pet files into tarballs.

Old Download links are not working any more, I have moved most packages to

DOWNLOAD
http://boxen.math.washington.edu/home/emil/MathSoftware/Puppy4


Download Sage
at official Sage mirrors (choose your mirror, Linux binaries, 32 bit)

Scilab
forum member Q5sys postet this link: http://lhpup.org/team/Q5sys/scilab-5.2.2.sfs and this md5sum: http://lhpup.org/team/Q5sys/scilab-5.2.2.sfs-md5.txt

File List MathBasePup431.tar (Octave, R, Maxima):
gcl-2.6.7-i486.pet - Lisp (needed for Maxima)
gfortran-4.2.2.pet - Fortran (needed for Octave and R)
glpk-4.10-i486.pet - Numeric package needed for Octave
gnuplot-4.2.5-i486.pet - gnuplot for graphics of Octave and maxima (command line)
libiconv-2.5.0.pet - R needs the library and symlinks
maxima-5.2.0-i486.pet - CAS
octave-3.2.3-i486.pet - Numerics
R-2.10.1-i686.pet - Statistics
wxGTK-2.8.9-unicode.pet - GTK for the wxMaxima frontend, custoz to disciple
wxMaxima-0.8.2-i386.pet - Maxima GUI, courtesy disciple

File list gretl_for_puppy:
fftw-3.3.3.pet (Fast Fourier transform)
gfortran-4.2.2pet (fortran compiler - same as in octave package)
gnuplot-4.2.5-i486.pet (gnuplot - same as in octave package)
gsl-1.13-i486.pet - (GNU scientific library)
lapack-3.2.1-i686.pet -(Linear Algebra Package)
libxml2-2.7.2-i486.pet - (XML Library)

File list for Python modules
gfortran-4.2.2.pet
gnuplot-4.2.5-i486.pet
gnuplot-py-1.8-i686.pet
ipython-0.1.0-i686.pet
numpy-1.4.0-i686.pet
python-2.6.4-i386.pet
scipy-0.7.1-i686.pet
sympy-0.6.6-i686.pet


Yacas is a single pet and Geogebra is a Java Package (need Java installed), sage is packaged to an sfs

How to install
Unpack the tarballs and install all pets (Or just those you need).
Geogebra: install Java, more Information GeoGebra Threat
Sage: install sfs files (see this thread page 2 for details)

How to run
Open a console and type octave, R, maxima, gretl, yacas, sage, ipython (case sensitive).
wxmaxima can be run from Menu/Utility
To run Geogebra unzip it and run the script geogebra.sh in its base directory.
For R there are also 2 GUI's (PMG and Rcmdr) working, more info at the R -thread

This software packages are powerful tools for education and studies. I like the idea that you can put it on a pendrive and use your Puppy at home and at school/university.

I think these are the basic free and open source Math packages (I didn't add scilab yet because it doesn't offer much more than octave, which in turn is more compatible to the Matlab, the industry standard).

Misc:
I must admit I am a new user, and probably those packages could be smaller. I have just skipped some documentation, since this is easily found on the net. I haven't tested the programs very much, feel free to notify me if there are problems.
I also tried to put everything together in a sfs File but failed (it is not working properly) maybe someone with a clue can do it if need arises.

I sincerly hope more people come up with science and math software for puppy linux!

Servus
emil

21.01.2010: edited to include gretl, yacas and geogebra
22.01.2010: edited to include sage
26.01.2010: edited the link to R GUI's PMG and Rcmdr
29.01.2010: edited to include Python packages
13.05.2010: edited to include Scilab package

---
5.474 The number of fundamental operations that are necessary depends solely on our notation. - Tractatus
my place

Last edited by emil on Thu 25 Nov 2010, 06:07; edited 11 times in total
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DMcCunney

Joined: 02 Feb 2009
Posts: 894

PostPosted: Sun 10 Jan 2010, 16:36    Post subject:  

This is a nice attempt, but has issues.

FileHost.org wants you to provide an email address, and they email you a link to grab the file. I did so, but the tar.gz file I got was broken. I get an unexpected EOF error from tar trying to extract it.

I'm not sure whether the archive you uploaded was bad or it got garbled in transit. Attempts to re-download time out, as though the hosting site went off the air.

It doesn't appear possible to use the direct link in your post.
______
Dennis
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Dingo


Joined: 11 Dec 2007
Posts: 1411
Location: somewhere at the end of rainbow...

PostPosted: Sun 10 Jan 2010, 17:26    Post subject:  

Woof Woof

I mirrored (and organized separately, with respective dependencies) math apps by emil, here:

http://puppylover.netsons.org/dokupuppy/programs:math_apps

The goal of Dokupuppy is avoid vanishing of useful software, I have ever a copy of files on my local hard drive, if any file disappears (but I check from time in time in orderto avoid this) you can e-mail me at address on this dokupuppy front page

http://puppylover.netsons.org/dokupuppy

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emil

Joined: 10 Nov 2009
Posts: 612
Location: Austria

PostPosted: Sun 10 Jan 2010, 18:34    Post subject: Broken files?  

Hello,

@DMcCunney: Thank you for testing, you are probably right.

@dingo: Thank you for the mirror - Did you experience any problems with the download?

I tested the original link and must admit I also had problems with the download. So I removed the file (maybe to quick?), before I saw dingos post.

I uploaded again with a new link
http://www.filehosting.org/file/details/98968/MathBase-Pup431.tar

I will also edit the original post and provide a md5 checksum.

dingo, could you please also correct the link in the mirror, sorry for the hazzle.

Most of this files were already available on this forum, only maxima and lisp are new. If the problem with the large file persists I can post those seperatly. (I will not be online the next few days, so please be patient).

Maybe I have still time to check if dingos links are working.
All the best
emil
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Dingo


Joined: 11 Dec 2007
Posts: 1411
Location: somewhere at the end of rainbow...

PostPosted: Sun 10 Jan 2010, 20:01    Post subject:  

I downloaded from original link you have posted, without any pain anyway next days I'll add another mirror also meantime I'll update links for all-in-one-tar.gz package
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charlie6

Joined: 30 Jun 2008
Posts: 937
Location: South of Belgium

PostPosted: Mon 11 Jan 2010, 01:32    Post subject:
Subject description: compatibility with other Puppies than 4.3.1 or kernels ?
 

Hi emil,
many thanks for this !
Just wanted to know if this package could run on puppies (4.1.2; 4.20...) with k.2.6.25.16 or older kernels?
Thanks for your answer
Cheers, Charlie
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emil

Joined: 10 Nov 2009
Posts: 612
Location: Austria

PostPosted: Mon 11 Jan 2010, 02:03    Post subject: older kernals  

Hi charly

To be honest, I haven't tried. I just have puppy 4.31 running.
Could anybody try and tell us if it works?
emil
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disciple

Joined: 20 May 2006
Posts: 6378
Location: Auckland, New Zealand

PostPosted: Mon 11 Jan 2010, 04:44    Post subject:  

The R package (and dependencies) runs on Puppy 2.16 (k2.6.18.1). I haven't downloaded the others, but I think it is extremely likely that they will work... apart from things like kernel modules it is pretty rare for anything to care about the kernel version.

Thanks for these Emil, and for splitting them up Dingo. It is good to keep packages of libraries and separate programs separate, so people can also use them with other programs or newer versions, without downloading big things they don't need.

This is just what Puppy needed Smile

Quote:
Misc:
I must admit I am a new user, and probably those packages could be smaller.

Yes, there are a couple of basic things to keep in mind in future:
- before running dir2pet check that binaries and libraries are stripped (right-click on them in rox and look at the properties). e.g. the R binary was stripped, but the libraries weren't. You can run `strip --strip-unneeded /usr/local/lib/R/lib/libRblas.so /usr/local/lib/R/lib/libRlapack.so` to strip them.
- you can compress binaries with upx (search for it on the forum). This doesn't really make the .pet smaller (as it is compressed anyway), but it does make it take up less space when it is installed. Space in a save file is important in Puppy Smile
Often a lot more space can be saved by deleting other stuff that isn't usually needed, but that takes a bit more time and knowledge about what you are packaging.
There is also a forum thread somewhere about compilation options to make things smaller, but I've never spent the time to get into that stuff.

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MinHundHettePerro


Joined: 05 Feb 2009
Posts: 844
Location: SE

PostPosted: Mon 11 Jan 2010, 18:13    Post subject: Re: MathBase - Octave, R, Maxima
Subject description: Basic Free Mathematic Software for Puppy 431
 

emil wrote:
Hello math-lovers,
...
GNU OCTAVE - For engineering and numerics (strong side matrix calculations). Mostly compatible to Matlab.
...
Just downloaded, if this means I can run Matlab-scripts in puppy (without installing the Linux version of MatLab, which is Huge) it'd make me a very happy puppy user Smile . If not, I would probably be happy anyway (re-writing, adapting Sad Smile) Smile. Have used Gnuplot before (long ago and in a cygwin environment, though) and found it rather versatile Cool.
Will install and try it out within the week (to much work at the mo. Sad) Smile .

Cheers Smile/
MHHP

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disciple

Joined: 20 May 2006
Posts: 6378
Location: Auckland, New Zealand

PostPosted: Tue 12 Jan 2010, 07:40    Post subject:  

Just to help people get started, after installing R and its dependencies I:
- ran
Code:
R

- added a couple of numbers together to check that it was working
- ran
Code:
help(chooseCRANmirror)
(because I read the manual about how to install packages)
N.B. you can get a general help just by running help(), and when you are in a help you can get help on using the help() by pressing h. And you exit a help by pressing q.
- ran
Code:
chooseCRANmirror(graphics=false)
because chooseCRANmirror otherwise wanted to use a dialogue, but I don't have tcl/tk installed, and if there is an xlib gui I don't know how to tell it to use it.
- ran
Code:
chooseCRANmirror(graphics=false)
and told it the number of the mirror I wanted to use.
- ran
Code:
install.packages("s20x")
to install the s20x library. I have the devx, but I don't think it did any compiling or anything, so it would be good if someone without the devx could try installing a package and report back. I imagine some packages would require compiling, but not others. I think all it did was create /usr/local/lib/R/library/s20x, so I have made a .pet of that; please report if it works.

I imagine there is lots of information on the internet about using R... the trouble is finding it, since it has such a useless name Smile!

BTW you exit R with
Code:
quit()

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Last edited by disciple on Tue 12 Jan 2010, 08:02; edited 1 time in total
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disciple

Joined: 20 May 2006
Posts: 6378
Location: Auckland, New Zealand

PostPosted: Tue 12 Jan 2010, 07:57    Post subject:  

They like to use s20x in engineering maths classes.
You need to load libraries like this:
Code:
library(s20x)

I think you can check if what is in my .pet is all that is needed to install s20x just by trying to run an s20x command - say
Code:
interactionPlots()
, even though that just produces an error message because you didn't provide the right input arguments.

N.B. for some reason the file paths in /root/.packages/s20x.files are showing up missing the y in library for me... does anyone know why that is? Seems like a bug in petget.[/code]
s20x.pet
Description 
pet

 Download 
Filename  s20x.pet 
Filesize  162.77 KB 
Downloaded  1029 Time(s) 

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emil

Joined: 10 Nov 2009
Posts: 612
Location: Austria

PostPosted: Thu 14 Jan 2010, 06:29    Post subject: Getting startet
Subject description: some useful links and setting
 

Hello math-lovers,

I am glad that the packages seem to work and you like them.
I thought I add some links to get startet.

OCTAVE Homepage - Packages - Tutorial try also Matlab Tutorials and Examples
R Homepage with tons of Links Edit: http://rseek.org/ thanks @ carolus
MAXIMA Homepage - Tutorial - Wiki

@disciple
thanks for testing the older kernel and also your advice on pet stripping. Do you think compile options --enable static --disable shared would help? I read something about those options but cant remember where.
Thank you also on the short intro to R and your link to the s20x library.
Why do you think R is a useless name for a programing language? Just as compared to e.g. C Very Happy ???

@MinHundHettePerro OCTAVE/MATLAB Compatibility
Good news is that for basic work and scripts Octave will run Matlab scripts fine without changes, or they will only need really minor tweaking. In my "main" side-project I try to get a Chemical package running (CANTERA, C++) which has Library Wrappers for Matlab and Fortran. I changed the source to use Octave instead of Matlab. Most demos and examples of this package run without change, I just have problems with a few who use Matlabs implementation of Class-Inheritance (which is still a rather exotic feature). Advanced features (e.g. specialised functions, GUI Interfaces) will need more work and patience if you intend to port them.

Some Links on this topic:
Octave <-> Matlab Compatibility Database
Wiki
Homepage FAQ

Geany is a perfect little IDE for Octave scripting. You can set the proper format in the Menu Document->Set Filetype->Scripting Langugage. It will autodetect the format for all .m file extensions.
I use Menu Build->Set Includes and Arguments Compile:<blank> Execute: octave -q --traditional "%f"
the option -traditional will help with Matlab compatibiliy.
And of course put this in
Menu Edit->Preferences->Tools: /usr/bin/xterm -e bash -c

Ok, have fun, Christmas/Newyear time is over, back to some serious work.
emil

Last edited by emil on Wed 20 Jan 2010, 15:06; edited 2 times in total
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disciple

Joined: 20 May 2006
Posts: 6378
Location: Auckland, New Zealand

PostPosted: Thu 14 Jan 2010, 15:07    Post subject:  

Quote:
Why do you think R is a useless name for a programing language? Just as compared to e.g. C

Yes, it is even harder to find information on C, as I can't search for "r statistics" or add "CRAN" to the search

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carolus

Joined: 14 Feb 2007
Posts: 129

PostPosted: Fri 15 Jan 2010, 20:22    Post subject:  

disciple wrote:

I imagine there is lots of information on the internet about using R... the trouble is finding it, since it has such a useless name Smile!


Supposedly the following search engine gets around that problem, but I haven't tried it:

http://rseek.org/
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disciple

Joined: 20 May 2006
Posts: 6378
Location: Auckland, New Zealand

PostPosted: Fri 15 Jan 2010, 20:49    Post subject:  

Great! Thanks for that.
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