Sage Live - 511 -53

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emil
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Next version out

#21 Post by emil »

Hi ICPUG,

In the meantime I have been busy and pulled together the next version of my sage live puppy. I have included Java, so even 3d Plotting should work out of the box.

sagelive-511-46.iso (normal iso file)
sagelive-511-46.exe (Windows exe installer)
sagelive-511-46.tar.gz (just vmlinu. initrd.gz and lupq-511.sfs for frugal inst)

I already uploaded them to
http://www.mydrive.ch
Username: download@sagelive
Password: mathematics

Beside that I had some other fixes:
added swapfilemanager (to autocreate swapspace)
added scratchfiletool (to give paranoid windows NTFS users a possibility for quarantine disk storage)
added Samba-TNG
fix for xgamma-gui (I didn't even knew that xgamma existet, but after my first sagelive version a year ago one of the first responses was that this in not working, so I feel responsible)

I will update also the top Post.


Regarding modularity:
Yes I think the SFS-TXZ linker seems a very interesting project. But I also had a look inside the initrd.gz, there seems a possibility that at least 1 sfs package is loaded "hard wired" by default. This would make production and maintainance of thematic live CD's much easier (Split of Base OS and Addons).

Regarding how to classify "beginner programs"
It all depends on the viewpoint and you are right, my intended target audience is not primarily on this forum, but outside - not even on the sage forum, because there it's rather about big workstations with 16+ cores, and how to compile on solaris etc... . As a fact I think it can be very useful to students of technical/scientific branches, who want to use a powerful software and who don't want to mess to much with the system behind it. Or for the math-prof who want to walk around with his sage puppy on usb stick, or want to install it quickly on some laptop. And personally I like the application mix of puppy very much. I have the feeling if taking them away and have just sage running on a barebone puppy would feel much too dry and no fun anymore.

About criteria
Other aspects, like being open source and free are secondary (thinking of the usual habbit of allowing those extra free copies of 1000$+ priced software to stay in business). In so far, userfriendly-wise we are doing good, especially I must say the windows exe installer makes it easier to install sagelive into a windows system, than any other variant (even easier than a frugal install on linux). With a decent download an inexperienced user can install and test the system in less then 15 minutes. Although it seems huge and bloated to puppy users it will seem lean for windows users and also regular sage users. Packages in the scope of sage usually take up far more than 1 GB of diskspace, so the 630 MB including OS (+Java..) will not scare them away.

So its about providing information and infrastructure, thats why I also set up some webpages with help and info about sagelive (puppy).

http://boxen.math.washington.edu/home/emil/doc/html/en

I noticed that I learned so much during the last year that many things that seem natural from my viewpoint, may seem arcane and quirky for somebody not introduced to the puppy way of doing things.

As always, there is much room for improvements!

emil

ICPUG
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#22 Post by ICPUG »

Thanks emil - another big download session coming up! I get around 220k max download speed so it's a 40-50 minute job for me.

You have spent a lot of time on your web site for Sage Live. Well done.

I'm trying to arrange for somebody at my place of work to give me a run through of Matlab so I can compare.

I like the idea of the prof going around with Sage Live on a USB stick! Then make it available to the students and then they take it to work ...

emil
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compare to matlab and a very nice feature :-)

#23 Post by emil »

Hi, sure I spent a lot of time with the homepage :wink: , but its still bug ridden, lots of typos. But I think I gathered lots of useful information, especially on getting things installed. I hope I can improve it gradually ...

Well I came across one very interesting possibility of sage today :D .

Most of the packages that are bundled inside can be made available "outside".
This was a feature absolutly top on my wishlist, and I just missed that the possibility was always there!

you can do the following:
start sage, then type:

Code: Select all

install_scripts('/usr/bin/') 
Sage creates a couple of scripts: gap
gp hg ipython maxima mwrank R singular

There is not much magic in the scripts. For example, the "gap" script
is

Code: Select all

#!/bin/sh
sage -gap $*
Hence, if I do
gap
in a shell, then in fact "sage -gap" is executed; so, it uses the gap
shipped by Sage, but it doesn't start Sage.

So you can use R, maxima, ipython like normal.

I noticed that there is no script created for python,, but you can create on yourself and you have a working python and access to all libraries (numpy, sympy, pylab).

Code: Select all

#!/bin/sh
sage -python $* 
I missed that possibility, so I just made a symlink. But then it is not possible to import the libraries - so creating that script is preferable

About matlab - well its about numeric. Its main application is in the engineering sector, and they have a great set of extensions (toolboxes).

I compiled octave, which is an open source project which keeps very close to the matlab syntax. I had it compiled and you can download it from
//http:boxen.math.washington.edu/MathSoftware/Puppy4/Octave

I think best is you install all pets (with the exception of fortran, thats already included in sagelive). From the sage notebook therre is an interface to octave (and I guess even to matlab) so you have an integrating workbench.

8) emil

ICPUG
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#24 Post by ICPUG »

Just thought I would report back to say I frugally installed the latest update on my laptop with 512K RAM. I then used the pfix=nocopy boot code and everything worked fine.

There was a little delay when complex calcs were done but it was acceptable.

I also got Sage running in the browser rather than the command line. Still need to understand fully this mode - how to print things etc. and how to correct things when you make a mistake in entry and the wrong result comes out. You don't want errors to print out!

Your link:
http://boxen.math.washington.edu/MathSo ... py4/Octave

gave me a not found on server error

I went to:
http://boxen.math.washington.edu/home/e ... ctave.html

but the download link to octave seemed to point to gnuplot

emil
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#25 Post by emil »

Correct Link
http://boxen.math.washington.edu/home/e ... py4/Octave

I was updating the page yesterday, maybe it was just a crossover.
it should work now

emil

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Lobster
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#26 Post by Lobster »

This would seem the ideal sort of Puplet to run on a Puppy cluster?
Any interest in porting this software?
http://www.murga-linux.com/puppy/viewto ... 243#479243
Puppy Raspup 8.2Final 8)
Puppy Links Page http://www.smokey01.com/bruceb/puppy.html :D

emil
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supercomputer

#27 Post by emil »

Hi Lobster,
welcome on this thread :D .

Hey this sounds fun, I will give it a try. But this gets way out of hand, all I wanted to do was a quick and dirty update on the sage live CD and what have I got now

Windows exe installer
Project Homepage
Update additional packages
Play around with virtual machines
+ Supercomputer project

LOL,
Anyway, I will better go skiing some
Merry christmas

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Lobster
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Re: supercomputer

#28 Post by Lobster »

emil wrote:But this gets way out of hand
. . .

LOL,
Anyway, I will better go skiing some
Merry Christmas
Merry Christmas Emil :)
Once you realise Puppy could power your own
mathematical supercomputer there will be no escape on skis
or some other formula . . .

I have just taken up running (this morning in wellies
because of snowfall)
Just finished week 2 of this:
http://www.coolrunning.com/engine/2/2_3/181.shtml
I won't be running as far as Cliff Young that is for sure . . .
http://www.elitefeet.com/the-legend-of-cliff-young
. . . but what an inspiration . . .

I used to do running when doing a harder style of martial art
but have gone soft (style) in my old age

Anyways . . . look forward to running that Puppy Super Computer . . .

Puppy Linux
May be addictive, always read the license
Puppy Raspup 8.2Final 8)
Puppy Links Page http://www.smokey01.com/bruceb/puppy.html :D

nickdobrinich
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bad octave link

#29 Post by nickdobrinich »

The download link for Octave:

http://boxen.math.washington.edu/home/e ... ctave.html

is linked to gnuplot download.

Is it possible to get Octave?
Thanks.

emil
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#30 Post by emil »

Link should work now,
Thanks for reporting the error.

NOTE: you can access via
http://boxen.math.washington.edu/home/emil

then you access to all packages
emil

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hayden
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R in Sage

#31 Post by hayden »

I send this from a running CD of sagelive--511-46.iso which I downloaded yesterday. Hardware is a Dell GX-270, 1.5 Gb RAM. I know there is a Linux swap file in there but I cannot find the tools I usually use to see how big it is or whether it is in use. Lower right corner of my screen says "1.7Gb free".

Sage starts and computes 1+1;-) My main interest is in R. To run R you need to pull down a menu under the name of your Sage Notebook (top left of screen) that initially says Sage but needs to say "r" (small r!) I then did some basic stats with R. Number crunching seems to work but trying to plot data gives me an error message that X11 is not available. Since I am running Sage in X11, this seems odd. Googling around it appears I need devleopment libraries for X11, not just a functioning GUI. Here is simple R code to reproduce this:

Code: Select all

x <- c(1,2,3)
plot(x)
I ran the script to make R available from the command line. This works but again no plots are available.

With some mesing around I was able to use the R packages already included with Sage, but attempts to install those not included gave no reposnse in Sage. Strangely, in the command-line version of R that Sage installed, I could start downloading packages. I tried Rcmdr first because it has a zillion dependencies. Looks like it may not finish today so I'll move on;-)

Let me interrupt this post to explain my interest in this project. It would be nice for professors in math/sci to hand out to students a CD with the tools they will need in their courses. In the place where I last taught this would mean R, any matrix package (such as Octave), a computer algebra system (such as Maxima) and the ability to compile C and/or Java code. Still we do not want it to get too big because student machines may not have a DVD drive or a lot of memory.

The Sage Live CD provides a lot of this. I have mixed feelings about Sage itself. The common interface is nice if you use multiple tools at once but for me it just got in the way of using R. To use regular R you just click on Console and type "R". Even a Mac user could do it;-) Sage makes you jump through a lot of hoops to get the same effect. And though you end up in a pretier terminal you still ahve to type the same text comands as in regular R. So it's a GUI only on the appearance level -- there are no menus for stats. as in Minitab or SPSS.

So, for my use I would definitely want the individual applications ready on boot up (without the student having to run a script from inside Sage). I am curious as to whether Sage takes up more or less space than jsut command-line versions or R, Octave and Maxima. (Some of those other tools are only for a very specialist minority.)

So MANY thanks to emil for his work on this. Even if the entire Sage turns out to be overkill, the process had produced all the individual pieces for us to play with!

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hayden
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PS

#32 Post by hayden »

It looks like the packages all downloaded but few if any installed. Probably the most common error was failure to find "make" so it looks like most of these DO require real compilation on the local machine.

emil
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about using R and other packages

#33 Post by emil »

Hello Hayden,

thank you for your interest. To make the included packages available outside of sage there is the following *very* useful command:

start sage from commandline then type

Code: Select all

install_scripts('/usr/bin/')
this writes some start scripts for the most common components like maxima or R to /usr/bin. So you can expose most of the internal packages to the user. (start R with R from terminal)

This is one of the best features of sage which I was totally ignorant for more than a year. I also think the sage developers underestimate that this could be the the real "killer" feature of the sage package.

There is no such script for python created, only for ipython (somewhat improved interface for python), but if you want to have python work from commandline e.g. make a script like

Code: Select all

#!/bin/sh 
sage -python $*
and put it in /usr/bin

The advantage is that dependecies are correct, so you can import all installed libraries (numpy, scipy, sympy).

About the installation of R-packages:
There are no compilers etc included in the base distribution of sage live. You will probably have to install the lupq_devx_511.sfs (compile environment) to install additional packages for R. To have R commander and wxmaxima working would be a nice feature! I have to admit I didn't tried to do this yet, but I am a bit short of time atm.

I would be glad if you or anybody else could try to get RCMDR or other packages working, I know this can take some time, patience and commitment so I am just asking and share a few hints:

Install the Developer package
http://boxen.math.washington.edu/home/e ... E_devx.htm

then try to follow steps from this thread
http://www.murga-linux.com/puppy/viewtopic.php?t=51141

about the swap:

at startup a script is running, it is called swapwizard.sh (it is placed in /root/Startup).

It will allocate swapspace if needed, but it will just create a swapfile (no deticated linux swap partition). The swapfile is probably called pupswap.swp. There is an option to use a windows pagefile.sys if one is found.

more info about size of swapspace, from commandline

Code: Select all

free
or even more detailled (filename)

Code: Select all

cat /proc/swaps
Thanks for your interest in this project! I think most of your demands could be met by installing the Developement package, gnuplot and the octave package.

I agree with you that sage might be overkill, but it provides a coherent package of all tools, and the browser notebook interface is a good approach (setting up servers to use in a network is not difficult).

kind regards
emil

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hayden
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more on R

#34 Post by hayden »

OK, thanks for the tip re swap space. It looks like my swap file is 2Gb and in use. I mention that only as info on what hardware configuration can run SageLive.

A separate issue is how to set up a swap for students who walk away with a CD. I think I will leave that for when all other problems are solved!-)

I did use the script to make R accessible on the command line. I think I reported data on how it worked both in Sage and from the command line.
BTW, R did eventually download packages from within Sage but this took hours with no indication anything was happening. I did mean to suggest that the iso have that script already run so the user does not have to figure that out. I remastered SageLive and the results of running the script were preserved (as was yacas -- thanks for that).

I will look at the development sfs. However, it looks like Rcmdr would not be a suitable first project!-) Rcmdr downloaded 146 files (105Mb) as dependencies! Of those, four installed and one worked. That's in resposne to a post somewhere that was hoping only a few R packages would actually require compiling;-( I think the only exceptions are packages that contain only data, say all the datasets for an R textbook.

To make a Puppy that includes R with Rcmdr seems to require an additional 100Mb for dependencies. Then if you want the user to be able to add other packages the development sfs has to be built into the iso. I am starting to think that will fill up the whole CD even without Sage or any other programs!

Then there is the issue that graphics do not work in R. I have no idea what it would take to fix that. The graphics in R are fabulous so it would be a waste to not have them. And it would make R unable to do even the tasks in an intro. stats. course.

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Re: more on R

#35 Post by shinobar »

hayden wrote:A separate issue is how to set up a swap for students who walk away with a CD.
If the PC has Windows, follow Menu>System>System memory>Winfonts
Downloads for Puppy Linux [url]http://shino.pos.to/linux/downloads.html[/url]

emil
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swap space

#36 Post by emil »

Hi shinobar and hayden,

swapspace:
My original indent was to have it handled "automagically".

well, there is this script (my first), swapwizard.sh :oops: . It is called at startup (placed in /root/Startup). I originally wrote it because my first versions of sagelive were not pfix=nocopy and people had real memory problems.

It will detect if swapspace is present, and also check the available RAM. There are variables which control the limits.

Currently those are:

Code: Select all

LOWRAM=700000     # Gives Warning if lower RAM
BIGRAM=1500000    # Don't make Swapspace if more RAM than this
MINDISK=4194304   # Only makes a Swapfile if more Space on Disk than this
MINSWAP=1048576  # Size of Swapfile
swapfiles will only be created on linux partitions by default. The Windows swapfile pagefile.sys will not be used by default. You can use it if you start swapwizard.sh with parameter -win (edit script around line 188 to change this).
There is another peculiarity, swapwizard mounts all partitions at startup, but NTFS partitions are mounted read only. If you want to write you have to unmount/remount them.

So you can adjust swapwizard to use pagefile.sys or other memory configurations, but maybe its better to handle swapspace manually and use shinobars gui for it. In that case just delete swapwizard.sh from the startup menu.

Shinobar, would it be an idea to move the swapfile settings to the first start menus? Having it under Desktop/Desktop Applets/Windows fonts is at least a bit counter intuitiv. Maybe it would fit somewhere into the gui for savefile creation?

About CD for students:
Have you ever thought to offer them an USB install - I mean it is even possible to load a bootable system on an I-pod :D .

About the R plotting:
if you type r.capabilities() into the notebook it will tell that no X11 and no graphics support is present. Thats definitely bad. I also checked the official vmware image, it has the same problem.

I posted a question about the topic on http://groups.google.com/group/sage-support.
Maybe there is a reasonable fix. In the meantime It is possible to make a seperate R package which has the necessary dependencies. Since the resulting package is zipped or squashed it is possible that it still fits on CD (I guess 68 MB are free).

Actually I think the plotting difficulties are not restricted to R. Recently I tried to get TexMacs working and make a package, it worked but plotting was broken too. Do you have similar issues with maxima?

You could try to build the R package yourself, the basic R is easy to compile. The problem is to make the package with Rcmdr included, since those dependencies are installed from inside R. So it is probably necessary to make a R installation in a seperated, non default location, then install the packages you want, and at last package the whole directory tree.

If you have some days time, I would probably try it and I am especially interested if this package would also work under the new wary. But atm I am deep in making a working VM image (it's a bit tricky but I am almost there :D ).

Hayeden I hope you will stay tuned and keep an eye on sagelive, I am sure there will be a solution.

8) emil

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shinobar
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Re: swap space

#37 Post by shinobar »

emil wrote:Shinobar, would it be an idea to move the swapfile settings to the first start menus? Having it under Desktop/Desktop Applets/Windows fonts is at least a bit counter intuitiv. Maybe it would fit somewhere into the gui for savefile creation?
Do you know that the SageLive automatically creates swap file, 'pupswap.swp', when the session is saved? It will be used at next boot.
This mechanism is what Barry built in recent woof.
But it doesn't work without pupsave. Barry's idea is nothing touch on HDD at Live CD mode.

Offering to create swap file at the boot up is a good idea. The user can choose touch the HDD or not.

One of my attempt is the firstrun and pupsaveconfig.
The firstrun calls the pupsaveconfig, and the pupsaveconfig offers swap file.
If you choose to make swap file, it is activated right away and in use for the session even before reboot.

There are another approaches, your swapwizard.sh, my winfonts, jpeps's swapfile manager, and etc..
Last edited by shinobar on Wed 29 Dec 2010, 22:35, edited 1 time in total.
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emil
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swapfile

#38 Post by emil »

Hi shinobar,

I think a gui supported possibility to manage and create swapspace would fit well into the first run dialogs, maybe in an advanced section so that it doesn't scare inexperienced users. It would also fit well into a Menu/System or even Menu/Filesystem.

I also second the idea that it is better not to touch harddisks without express consent of the user. I just made the suggestion of moving the gui because I felt this is the right adress :D . You did enourmous work to improve and ease startup recently and also all the work with the improved localisation support which I am very grateful to have in lupq. Thanks for all this work!!

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Interim: R + Rcmdr available as pet

#39 Post by emil »

I tested the R functionality in sage and it is, well, inclomplete ...
It is possible to test enabled features from the R prompt with

Code: Select all

capabilities()
The R which is included in the current ubuntu binaries fails in lots of those (especially no graphic support). I asked about it in the sage support forum and the answer was that it should basically work (but it doesn't), so I will investigate further with them. I think it is a bug that it doesn't work, and it is an additional bug that it doesn't work and sage -testall gives no error (not even a warning).

I will also recompile sage from source in lupq and see if I can get the missing functionality in. If I manage it there will be an upgraded version of sagelive

In the meantime I dived into it and made pets for R, and R+ R Commander (Gui). Read about it here.

However I also found a bug in sagelive's gfortran :( ,
please install gfortran-4.4.3.pet to fix it.

Happy new year 8)
emil

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sagelive-511-46-r3 released

#40 Post by emil »

sagelive-511-46-r3 released
Image


Release announcment (first post of this thread)

I made a complete recompile of sage to address the fact that R is incomplete (Plotting disabled) in the official Sage binaries. Beside that there were some other bugfixes and an upgrade of gfortran.
@ hayden: problem with R plotting is solved, you can install Rcmdr in that version. It includes also shinobars new pupsaveconfig GUI(credits and thanks). Together with all the other Quickset goodies this is a "GUI only puppy".

In the short term I will work on a Virtual machine version and try to make some additional packages. In the long term I think about to make it more modular, i.e. I think about to make something like goingnuts OTF_SFS loader work and have additional sfs loaded at first boot.

8) emil
Last edited by emil on Wed 26 Jan 2011, 21:07, edited 1 time in total.

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