Math Base - Basic Free Mathematic Software for Puppy Linux

Mathematical tools, physics simulators, CAD, CNC, etc.
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emil
Posts: 633
Joined: Tue 10 Nov 2009, 08:36
Location: Austria
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gretl

#21 Post by emil »

Hello!
Image

As you have suspected I couldn't resist to compile gretl ( :wink: @ Minimatter).
It comes as a tar - package (21 MB) which consists of

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 - some functions are needed)
lapack-3.2.1-i686.pet -(Linear Algebra Package)
libxml2-2.7.2-i486.pet - (XML Library)

please try it, hope it works for you
I will also edit the original post.

emil

Comments on the build:
Lapack is machine specific, just run make. Two static Libraries are created in the directory Lapack_LINUX.a and BLAS_Linux.a. Those have to go to /usr/lib and must be renamed to liblapack.a and libblas.a to be found by gretl.
(I had put them in a pet with the correct directories).

gretl:
Although I had lapack and blas installed and the configure ran without error gretl complained at missing dependencies while linking (something about the blas c interface). I googled and then I added the GNU Scientific Library.
Then it worked.

other packages were ./configure make make install type.

Minimatter
Posts: 33
Joined: Sun 08 Feb 2009, 21:50
Location: Massachusetts

#22 Post by Minimatter »

emil,

Thank you again!

I hope these will all be available in the usual pet repositories soon.

Everyone should be aware that with:

R and Octave as high-powered numerical interpreters,
gnuplot for graphics (used by Octave and gretl; R has its own graphics),
gretl as a good regression/time series system in its own right, and also useful as a front-end preparing data for R (even from the gnumeric spreadsheet),
maxima and/or yacas symbolic manipulation programs

we now have a good selection of the most important available mathematical software.

Minimatter

ps. Yes indeed emil, yacas misuses the del-key showing me 3 followed by a raised ~ ; similar behavior for page-up, page-down, insert, and keys on the numeric keypad. Seems to be in their own mini-readline.

emil
Posts: 633
Joined: Tue 10 Nov 2009, 08:36
Location: Austria
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Sage

#23 Post by emil »

Hello,
Image

Sage is the most comprehensive open source math suite, really huge.
It is based on numerous existing packages (e.g. Maxima and R are contained inside) and it uses python. The webbrouser can be used to create a notebook (Mathematica style).
It seems there are tutorials and good dokumentation available at http://www.sagemath.org

I have made an sfs file, it is big (390 MB) but if you want to do serious maths this should be the ultimate open source package.

download
405022d49a388969fb65276261ff4e63 sage-4.3.1.sfs

Frugal install:
copy it to your /mnt/home/ directory and add it to the list in your Bootmanager (Menu/System/Bootmanager configure bootup) then reboot.

Full install (from puppy homepage):
1. Click on the sage-4.3.1.sfs in a ROX-Filer window to mount it.
2. Open a terminal in the mounted directory.
3. # cp -a --remove-destination ./* /mnt/hda2/
4. # sync
5. Close the terminal.
6. Click on the sage-4.3.1.sfs file to unmount it
Note, the '--remove-destination' option is essential. If you only use '-f' to force overwrite, it will follow (dereference) a symlink, that can cause unexpected overwrites.


open terminal and start it with sage

As the other packages this is not tested much, basics seemed OK. I had troubles with command plot3d, obviously this uses the webbrouser and a package which needs Java. I had java installed and enabled in Seamonkey - I dont know whats wrong.

Sage is huge and heavy, not really puppy Linux like, but there is definitly power in it. I am a bit ashamed about the size but I didn't dare to remove anything.

comment on the build:
In the sage mission statement the goal of an easy build is expressed. Although by far the biggest of those math packages it was the easiest to build, perfect scripts and foolproof readme! It needed 2 hours to compile though on my box.
This was compiled on a Intel Pentium III, since sage uses the opimizing Atlas packages for building BLAS it may be worth to recompile from source on other machines - it is easy.
Edit: This package is compiled without Latex, if you have Latex installed and want to recompile Sage: it is looking for "Latex" ("latex" wont work) so put a Symlink if necessary.

This will be the last one about math for some time,
Goodbye
emil
Last edited by emil on Fri 22 Jan 2010, 14:35, edited 2 times in total.

aarf

#24 Post by aarf »

thanks for your efforts here emil but do you really need to use that webhost? i would prefer not to make more email address to give out to collect spam. host for large files

emil
Posts: 633
Joined: Tue 10 Nov 2009, 08:36
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webhost

#25 Post by emil »

Sorry for the inconvenience with the download. I was not aware of that possibility. Thank you for the information aarf.
For sage there is a mirror at http://boxen.math.washington.edu/home/wstein/binaries/
and also at at official Sage mirrors (choose your mirror, Linux binaries, 32 bit) now!
405022d49a388969fb65276261ff4e63 sage-4.3.1.sfs

I will do better in future
Last edited by emil on Sat 23 Jan 2010, 09:54, edited 1 time in total.

aarf

Re: webhost

#26 Post by aarf »

emil wrote: For sage there is a mirror at http://boxen.math.washington.edu/home/wstein/binaries/
thank you

emil
Posts: 633
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Location: Austria
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Rcmdr

#27 Post by emil »

I just want to add a link, how it is possible to get Rcmdr and PMG, GUI's for R in Puppy Linux.
R - thread
Last edited by emil on Tue 26 Jan 2010, 09:33, edited 1 time in total.

brad_chuck
Posts: 286
Joined: Tue 16 Aug 2005, 03:47
Location: Appalachian Mountains

#28 Post by brad_chuck »

Don't count out Python for math. With SciPy / NumPy it is an extremely robust mathematical application.

http://www.scipy.org/

You also have Matplotlib for graphics / charts. Even embed in GUI's...

http://matplotlib.sourceforge.net/

and pyGTK for GUI

http://www.pygtk.org/

And if you need symbolics theres a module for that too but I have found Yacas to be a nice program. Quick, Dirty and Light...

emil
Posts: 633
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Location: Austria
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Math Python Modules

#29 Post by emil »

Hello,

brad_chuck thanks for your comment and hint. I have packaged

Download: Math_Python.tar
Filelist:

gfortran-4.2.2.pet - gfortran compiler and library
gnuplot-4.2.5-i486.pet - gnuplot for graphics
gnuplot-py-1.8-i686.pet - Python / gnuplot interface
ipython-0.1.0-i686.pet - ipython (improved python shell)
numpy-1.4.0-i686.pet - NumPy python numeric module
python-2.6.4-i386.pet - python interpreter
scipy-0.7.1-i686.pet - SciPy python scientific module
sympy-0.6.6-i686.pet - SymPy python Symbolic math module

installing those pets should give you a working Python Math environment.

Together with Python 2.6.4 I included also the complete gfortran.pet, probably you would only need the dynamic library (gfortran.so or similar). For plotting graphs I have included the gnuplot-py Library and gnuplot.- this works reasonable well.

How to start:
There is an entry in the menu/utilities for ipython. Or type ipython or python2.6 in terminal window. For convenience it is possible to
symlink python2.6 with python in the usr/bin directory.

How to work:
start ipython (Menu/utilities), then import the libraries e.g. like this (there are different possibilites to import them - it influences your python namespace):

Code: Select all

In [1]: import numpy
In [2]: import scipy
In [3]: import sympy
In [4]: import Gnuplot
For scripting Geany offers a very good and lightweight "IDE"
recomended settings:
Menu Edit -> preferences ->Tools->
Terminal: xterm -e bash -c
Menu Build ->Set Includes and arguments
Compile: ipython -c "import py_compile; py_compile.compile('%f')"
Execute: ipython "%f"

First help and documentation:
The homepages of the projects offer pretty good starting points (just google). Exception is Gnuplot-py. You find very little usefull information - best is to study the demo.py in the
/usr/lib/python2.6/site-packages/Gnuplot directory.

Maybe it is noteworthy that SAGE contains and uses all of those python packages.

This was made on Puppy 431, probably it works on all 4xx versions. I had no time on extensive tests though, please report any problems.

cheers
emil

PS:

About Gtk & matplotlib
I couldnt include the gtk Libraries and matplotlib as you suggested. I had some conflicts with different Libraries header files (compiled ok, but gave errors at runtime). I also tried these existing pets but somhow it didn't work for me. So if anybody get gtk and matplotlib going please share it.

About installing
NumPy, SciPy and Sympy are easy to install from source. They use
a python install script. After download it can be done with: installwatch -o logfile.txt python setup.py install
do install the package. If there are more than 1 python environemts present, the packages will be installed in every python version (E.g. Sage uses Python 2.5). For each package a subdirectory in the
/usr/lib/python2.x/site-packages/ is created. For the creation of the pets I basically used those subdirectories.

aarf

#30 Post by aarf »

after 15 hours over my wget gprs connection in puppy421 i have it down and md5sum is correct 8)

emil
Posts: 633
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SageLivePup

#31 Post by emil »

I made a puplet which includes sage. Link to Post in the Puppy Derivative section.

jamesbond
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Joined: Mon 26 Feb 2007, 05:02
Location: The Blue Marble

#32 Post by jamesbond »

Emil,

Thank you. This is excellent effort.

cheers!
Fatdog64 forum links: [url=http://murga-linux.com/puppy/viewtopic.php?t=117546]Latest version[/url] | [url=https://cutt.ly/ke8sn5H]Contributed packages[/url] | [url=https://cutt.ly/se8scrb]ISO builder[/url]

emil
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Scilab

#33 Post by emil »

Scilab is a mostly nummerical package which can be used in science and engineering as an alternative to Matlab (and the free Octave). It has a similar, but not compatibel syntax and it is developed in france.

Forum member Q5sys has posted on the SageLive thread and offers a sfs of the package:
got something you might want to test to see if it works with your puplet.

I made it originally for LightHousePup, but it seems to fit right in with what you are doing.
The SciLab suite
I already packaged it as an SFS.
http://lhpup.org/team/Q5sys/scilab-5.2.2.sfs
http://lhpup.org/team/Q5sys/scilab-5.2.2.sfs-md5.txt

Might duplicate the functionatlity you already have, but it also might offer a bit more. I made it a SFS because its 118MB, and figured I could load and unload that whenever I needed.
If it works for you, feel free to bundle it with your setup.
I cannot test at the moment due to limited time and bandwith, but maybe somebody can and send short feedback.

kind regards
emil

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neurino
Posts: 362
Joined: Thu 15 Oct 2009, 13:08

Re: Math Python Modules

#34 Post by neurino »

emil wrote:About installing
NumPy, SciPy and Sympy are easy to install from source. They use
a python install script
emil I had no problems compiling numpy (also can be done simply by pypi easy_install) but scipy needs lapack and(or) blas.

I see you already compiled lapack but filehosting.org has a very bad policy asking email addresses I don't want to accept, any alternatives?
And since you already did it: isn't lapack machine dependant? Will it work on any computer running puppy?

I made myself a (not shrinked tho) python sfs with python2.6, wxpython2.8, reportlab, numpy, PIL, lxml, matplotlib I use for work but since I encounter errors sometime I don't feel about sharing an imperfect solution.

Could you please make available your packages for example on drop.io like jemimah used to distribute puppeee?

Thank you very much

edit: don't bother, I found this mirror on my forum search: http://dokupuppylinux.co.cc/programs:ma ... :math_apps

emil
Posts: 633
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Some packages

#35 Post by emil »

Hi neurino,
Various people disliked the filhosting.org server. Also many links in this thread are not working any more. Thanks to dingo we have dokupuppy
http://puppylover.netsons.org/dokupuppy ... :math_apps
Myself I have moved some packages for download to
http://boxen.math.washington.edu/home/emil

I will gradually try to complete/extend them.
emil

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prehistoric
Posts: 1744
Joined: Tue 23 Oct 2007, 17:34

problems with Sage, geogebra

#36 Post by prehistoric »

Well, I spoke too soon. I got the version of Puppy 431 with Sage on CD, and booted it. Everything looked good, but when I tried to start a Sage console it crashed immediately. I suspect I need to configure something.

As per your suggestion, I tried www.sagenb.org. After I got an account set up and tried to create a notebook, it told me it failed to set up jsMath, and warned things could get ugly. (They did.) Basically, nothing worked. Sigh.

Lastly, while I have been able to run geogebra on-line, the sfs file at http://boxen.math.washington.edu/home/emil failed to download more than 431 bytes. (Tried two methods of download.) The file contains over 40 MB. Could something be picking up that version number?

Must not be my day for symbolic math.

emil
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crash

#37 Post by emil »

prehistoric,
how is your memory configuration?
what does the "free" command give?
emil

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neurino
Posts: 362
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#38 Post by neurino »

thanks emil,

in the meanwhile I hand-joined you pets in an unique sfs and added wxPython and setuptools and so, via easy_install, cython, lxml, PIL, reportlab, and matplotlib (and maybe some other I don't remember).

The global sfs is about 93Mb, I did not shrinked anything because, as a developer, I prefer full features despite minor size, just an exception for wxPython demos I keep on an sd card and can be simply tar.gz'd

I will share them if some puppy place to upload suggested.

Only one note: I used puppeee to compile, using its OpenGL for wxpython (should affect only wxGLCanvas) I guess it's full puppy compatible anyway.

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prehistoric
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Re: crash

#39 Post by prehistoric »

emil wrote:prehistoric,
how is your memory configuration?
what does the "free" command give?
emil
Here's the result of free in your SageLive puplet, which is showing 1.2G in the tray as I write.

Code: Select all

# free
              total                used          free           shared      buffers
Mem:      1943316       227464      1715852            0        37120
Swap:     4192956                 0      4192956
Total:      6136272       227464      5908808
# 
The Puppy I normally run (Luci204) also uses those swap partitions. It is, however, a frugal install with only 840 MB of save file shown. Could this result in the error with jsMath and www.sagenb.org? I didn't think the on-line version used much memory.

With so much RAM and swap, I haven't been worrying about space in the save file.

emil
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#40 Post by emil »

Hi prehistoric,
thats lots of memory :). Can't be an issue you are right.

Check error message (sage >> error.log) - look in error.log
Delete sage-flags.txt in the /local/lib directory as maybe suggested.
I will have a closer look on it.

hi neurino,
maybe send a private mail to one of the site admins of Puppy servers how to upload the package. If you put it somewhere on a webhost I could upload it also to my (slow) boxen.math server space, but would be better if it is on an official puppy server.

kind regards
emil

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