date:20100528

Aha!  I did some further investigation and found that I had the
following line in my ~/.bash_profile file

MAGMAPASSFILE=.magmapass

However, it should have been

MAGMAPASSFILE=~/.magmapass

so that's why it couldn't find it because it was running in a
directory not my home directory.

Victor

On May 28, 9:24 pm, VictorMiller  wrote:
> Ah, that's it.  I had put the .magmapass file in my home directory,
> but never set up MAGMAPASSFILE as an environment variable.  For some
> reason when I started magma from the command line, or with !magma this
> didn't bother it, but from the notebook it did.   I added something to
> set MAGMAPASSFILE in the magma script and now everything works ok.
>
> Victor
>
> On May 28, 9:09 pm, William Stein  wrote:
>
>
>
> > On Fri, May 28, 2010 at 5:46 PM, Jason Grout
>
> >  wrote:
> > > On 5/28/10 7:10 PM, William Stein wrote:
>
> > >> On Fri, May 28, 2010 at 5:07 PM, VictorMiller
> > >>  wrote:
>
> > >>> After 1/2 hour (!) I decided to interrupt the worksheet, quite the
> > >>> notebook, quite sage, and then restart sage.  Now when I try
>
> > >>> os.system('mamga') it comes back right away with
>
> > >>> Can't open Magma password file
> > >>> .magmapass
>
> > >>> 256
>
> > > I wonder if it just can't find the magma password file.  After skimming
>
> > >http://magma.maths.usyd.edu.au/magma/prot/prot.html
>
> > > it looks like you can (must?) set the MAGMAPASSFILE environment variable.
> > >  Can you try:
>
> > > os.system('export MAGMAPASSFILE= && magma')
>
> > No, do
>
> > os.system('export MAGMAPASSFILE= && magma < /dev/null')
>
> > so you don't just hang things.
>
> > > or
>
> > > import os
> > > os.environ['MAGMAPASSFILE']
>
> > > Jason
>
> > > --
> > > To post to this group, send email to sage-support@googlegroups.com
> > > To unsubscribe from this group, send email to
> > > sage-support+unsubscr...@googlegroups.com
> > > For more options, visit this group at
> > >http://groups.google.com/group/sage-support
> > > URL:http://www.sagemath.org
>
> > --
> > William Stein
> > Professor of Mathematics
> > University of Washingtonhttp://wstein.org

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Re: [sage-support] Re: Sage Server - displaying Matlab plots

On Fri, May 28, 2010 at 6:24 PM, Jason Grout
 wrote:
> On 5/28/10 8:08 PM, William Stein wrote:
>>
>> On Fri, May 28, 2010 at 5:52 PM, Jason Grout
>>   wrote:
>>>
>>> On 5/28/10 7:47 PM, Vinod wrote:
>>>
 X11 connection rejected because of wrong authentication.
 Warning: Unable to open display 'localhost:12.0'.  You will not be
 able to display graphics on the screen.

>>>
>>> So now it's not a Sage question, but a question of how to run Matlab over
>>> an
>>> ssh session.  That's something that should have an answer somewhere,
>>> either
>>> through a google search or asking MathWorks.
>>
>> No, that is not the problem at all.
>> What's happening is that he's giving code to Matlab that asks it to
>> pop up a plot.  Matlab
>> is then trying to make the plot appear on the screen using *XWindows*.
>>  Naturally, this fails
>> in the notebook -- it simply doesn't make any sense to do this.
>>
>
> Right.  Thanks for reminding me the context of this conversation.  The same
> problem (needing to pop up a window) appears when trying to render an image
> using OpenGL without X.  In the OpenGL case, I believe there are ways of
> getting an opengl context to work without trying to pop up an XWindows
> window.  I believe the typical way to do this is to use a framebuffer.  A
> google search "opengl without x11" turns up lots of hits for doing such a
> thing.  Instructions for doing such a thing are also in the Mayavi manual:
> http://code.enthought.com/projects/mayavi/docs/development/html/mayavi/tips.html#rendering-using-the-virtual-framebuffer
>
> I've never done this, though.  Whether or not OpenGL is the problem here,
> using a framebuffer might solve the problem.  Maybe.  Assuming you are using
> Ubuntu, can you try following the instructions in the Mayavi manual?

I don't think this makes any sense.  Matlab is fully capable of
saving images to file using the "saveas" command, as explained in
detail I think earlier in this very thread.

 -- William

>
> $ sudo apt-get install xvfb
> ssh in as the sage worksheet user
> $ xvfb-run matlab
>
> then try the plotting command
>
> Jason
>
> --
> To post to this group, send email to sage-support@googlegroups.com
> To unsubscribe from this group, send email to
> sage-support+unsubscr...@googlegroups.com
> For more options, visit this group at
> http://groups.google.com/group/sage-support
> URL: http://www.sagemath.org
>



-- 
William Stein
Professor of Mathematics
University of Washington
http://wstein.org

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[sage-support] Re: Sage Server - displaying Matlab plots

On 5/28/10 8:08 PM, William Stein wrote:

On Fri, May 28, 2010 at 5:52 PM, Jason Grout
wrote:

On 5/28/10 7:47 PM, Vinod wrote:

X11 connection rejected because of wrong authentication.
Warning: Unable to open display 'localhost:12.0'. You will not be
able to display graphics on the screen.

So now it's not a Sage question, but a question of how to run Matlab over an
ssh session. That's something that should have an answer somewhere, either
through a google search or asking MathWorks.

No, that is not the problem at all.
What's happening is that he's giving code to Matlab that asks it to
pop up a plot. Matlab
is then trying to make the plot appear on the screen using *XWindows*.
Naturally, this fails
in the notebook -- it simply doesn't make any sense to do this.

Right. Thanks for reminding me the context of this conversation. The
same problem (needing to pop up a window) appears when trying to render
an image using OpenGL without X. In the OpenGL case, I believe there
are ways of getting an opengl context to work without trying to pop up
an XWindows window. I believe the typical way to do this is to use a
framebuffer. A google search "opengl without x11" turns up lots of hits
for doing such a thing. Instructions for doing such a thing are also in
the Mayavi manual:
http://code.enthought.com/projects/mayavi/docs/development/html/mayavi/tips.html#rendering-using-the-virtual-framebuffer

I've never done this, though. Whether or not OpenGL is the problem
here, using a framebuffer might solve the problem. Maybe. Assuming you
are using Ubuntu, can you try following the instructions in the Mayavi
manual?

$ sudo apt-get install xvfb
ssh in as the sage worksheet user
$ xvfb-run matlab

then try the plotting command

Jason

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[sage-support] Re: Magma on a mac

Ah, that's it.  I had put the .magmapass file in my home directory,
but never set up MAGMAPASSFILE as an environment variable.  For some
reason when I started magma from the command line, or with !magma this
didn't bother it, but from the notebook it did.   I added something to
set MAGMAPASSFILE in the magma script and now everything works ok.

Victor

On May 28, 9:09 pm, William Stein  wrote:
> On Fri, May 28, 2010 at 5:46 PM, Jason Grout
>
>
>
>
>
>  wrote:
> > On 5/28/10 7:10 PM, William Stein wrote:
>
> >> On Fri, May 28, 2010 at 5:07 PM, VictorMiller
> >>  wrote:
>
> >>> After 1/2 hour (!) I decided to interrupt the worksheet, quite the
> >>> notebook, quite sage, and then restart sage.  Now when I try
>
> >>> os.system('mamga') it comes back right away with
>
> >>> Can't open Magma password file
> >>> .magmapass
>
> >>> 256
>
> > I wonder if it just can't find the magma password file.  After skimming
>
> >http://magma.maths.usyd.edu.au/magma/prot/prot.html
>
> > it looks like you can (must?) set the MAGMAPASSFILE environment variable.
> >  Can you try:
>
> > os.system('export MAGMAPASSFILE= && magma')
>
> No, do
>
> os.system('export MAGMAPASSFILE= && magma < /dev/null')
>
> so you don't just hang things.
>
>
>
>
>
>
>
> > or
>
> > import os
> > os.environ['MAGMAPASSFILE']
>
> > Jason
>
> > --
> > To post to this group, send email to sage-support@googlegroups.com
> > To unsubscribe from this group, send email to
> > sage-support+unsubscr...@googlegroups.com
> > For more options, visit this group at
> >http://groups.google.com/group/sage-support
> > URL:http://www.sagemath.org
>
> --
> William Stein
> Professor of Mathematics
> University of Washingtonhttp://wstein.org

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Re: [sage-support] Re: Magma on a mac

On Fri, May 28, 2010 at 5:46 PM, Jason Grout
 wrote:
> On 5/28/10 7:10 PM, William Stein wrote:
>>
>> On Fri, May 28, 2010 at 5:07 PM, VictorMiller
>>  wrote:
>>>
>>> After 1/2 hour (!) I decided to interrupt the worksheet, quite the
>>> notebook, quite sage, and then restart sage.  Now when I try
>>>
>>> os.system('mamga') it comes back right away with
>>>
>>> Can't open Magma password file
>>> .magmapass
>>>
>>> 256
>>
>
> I wonder if it just can't find the magma password file.  After skimming
>
> http://magma.maths.usyd.edu.au/magma/prot/prot.html
>
> it looks like you can (must?) set the MAGMAPASSFILE environment variable.
>  Can you try:
>
> os.system('export MAGMAPASSFILE= && magma')

No, do

os.system('export MAGMAPASSFILE= && magma < /dev/null')

so you don't just hang things.



>
> or
>
> import os
> os.environ['MAGMAPASSFILE']
>
> Jason
>
> --
> To post to this group, send email to sage-support@googlegroups.com
> To unsubscribe from this group, send email to
> sage-support+unsubscr...@googlegroups.com
> For more options, visit this group at
> http://groups.google.com/group/sage-support
> URL: http://www.sagemath.org
>



-- 
William Stein
Professor of Mathematics
University of Washington
http://wstein.org

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Re: [sage-support] Re: Sage Server - displaying Matlab plots

On Fri, May 28, 2010 at 5:52 PM, Jason Grout
 wrote:
> On 5/28/10 7:47 PM, Vinod wrote:
>
>> X11 connection rejected because of wrong authentication.
>> Warning: Unable to open display 'localhost:12.0'.  You will not be
>> able to display graphics on the screen.
>>
>
> So now it's not a Sage question, but a question of how to run Matlab over an
> ssh session.  That's something that should have an answer somewhere, either
> through a google search or asking MathWorks.

No, that is not the problem at all.
What's happening is that he's giving code to Matlab that asks it to
pop up a plot.  Matlab
is then trying to make the plot appear on the screen using *XWindows*.
 Naturally, this fails
in the notebook -- it simply doesn't make any sense to do this.

>
>
>> So if we get this working, I can make other softwares like octave
>> working too.
>
>
> Does Octave not work right now?
>
>
> Jason
>
> --
> To post to this group, send email to sage-support@googlegroups.com
> To unsubscribe from this group, send email to
> sage-support+unsubscr...@googlegroups.com
> For more options, visit this group at
> http://groups.google.com/group/sage-support
> URL: http://www.sagemath.org
>



-- 
William Stein
Professor of Mathematics
University of Washington
http://wstein.org

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[sage-support] Re: Sage Server - displaying Matlab plots


On 5/28/10 7:47 PM, Vinod wrote:


X11 connection rejected because of wrong authentication.
Warning: Unable to open display 'localhost:12.0'.  You will not be
able to display graphics on the screen.



So now it's not a Sage question, but a question of how to run Matlab 
over an ssh session.  That's something that should have an answer 
somewhere, either through a google search or asking MathWorks.




So if we get this working, I can make other softwares like octave
working too.



Does Octave not work right now?


Jason

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[sage-support] Re: Sage Server - displaying Matlab plots

2010-05-28 Thread Vinod




On May 28, 12:38 pm, Jason Grout  wrote:
> On 5/28/10 1:53 AM, Vinod wrote:
>
>
>
> > Now I have a different error message in the terminal when I try to
> > execute the matlab code involving plots in the webserver
> > " X11 connection rejected because of wrong authentication."
>
> > I verified all the X11 settings and it looks fine.
> > The link lists all the check points one should look for:
> >http://www.cyberciti.biz/faq/x11-connection-rejected-because-of-wrong...
>
> > The sage server was setup using the method discussed under the  last
> > section " Other Instructions -from JasonGrout" in the below link.
> >http://wiki.sagemath.org/DanDrake/JustEnoughSageServer
>
> I wonder if you'll have to do something to the Sage worksheet process
> users.  See, for example,http://umdmath.blogspot.com/
>
> What happens if you ssh into a Sage worksheet account and try running
> matlab?
>
> ssh sageus...@localhost
>
> then try running matlab from the command line.
>
> My guess is that if you get that working, then Sage will be able to get
> matlab to work.


I tried all this and it displays the following error message when the
matlab is started from the command line.

X11 connection rejected because of wrong authentication.
Warning: Unable to open display 'localhost:12.0'.  You will not be
able to display graphics on the screen.

So if we get this working, I can make other softwares like octave
working too.

>
> Note that there might be legal issues with providing access to matlab
> via a webserver (whether or not it is a private webserver).  I don't
> know, but it would be something to be aware of if it is an issue.
>

Yes, We are planning to have a word with matlab before we bring this
to our students.

> Thanks,
>
> Jason

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[sage-support] Re: Magma on a mac


On 5/28/10 7:10 PM, William Stein wrote:

On Fri, May 28, 2010 at 5:07 PM, VictorMiller  wrote:

After 1/2 hour (!) I decided to interrupt the worksheet, quite the
notebook, quite sage, and then restart sage.  Now when I try

os.system('mamga') it comes back right away with

Can't open Magma password file
.magmapass

256




I wonder if it just can't find the magma password file.  After skimming

http://magma.maths.usyd.edu.au/magma/prot/prot.html

it looks like you can (must?) set the MAGMAPASSFILE environment 
variable.  Can you try:


os.system('export MAGMAPASSFILE= && magma')

or

import os
os.environ['MAGMAPASSFILE']

Jason

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Re: [sage-support] Re: Magma on a mac

On Fri, May 28, 2010 at 5:07 PM, VictorMiller  wrote:
> After 1/2 hour (!) I decided to interrupt the worksheet, quite the
> notebook, quite sage, and then restart sage.  Now when I try
>
> os.system('mamga') it comes back right away with
>
> Can't open Magma password file
> .magmapass
>
> 256

OK, then I'm stumped.I don't understand the mysteries of Magma's
proprietary copy protection.

William

>
> However, I have no trouble starting magma from a terminal or from sage
> in command line mode.
>
> Victor
>
> On May 28, 7:27 pm, William Stein  wrote:
>> On Fri, May 28, 2010 at 4:15 PM, VictorMiller  
>> wrote:
>> > I'm in the notebook and I typed
>>
>> > os.system('magma')
>>
>> > It's now over 5 minutes, and it still hasn't come back!  While I was
>> > waiting I went a terminal and typed magma and it started within less
>> > than a second.
>> > Something weird.
>>
>> What about
>>
>>  os.system('magma < /dev/null')
>>
>> William
>>
>>
>>
>>
>>
>>
>>
>> > Victor
>>
>> > On May 28, 6:55 pm, William Stein  wrote:
>> >> On Fri, May 28, 2010 at 3:33 PM, VictorMiller  
>> >> wrote:
>> >> > More data:  If I start sage and then type
>>
>> >> > !magma
>>
>> >> > it starts up Magma.  I then exit from it (by typing "exit;") and start
>> >> > the notebook.
>>
>> >> > However, if I try to run magma from the notebook, I get the message
>>
>> >> > "Type Error: unable to start magma"
>>
>> >> > What's going on?
>>
>> >> What happens if you do this on the command line:
>>
>> >>   sage: magma.eval('2+2')
>>
>> >> What happens if you type this in a notebook cell:
>>
>> >>   sage: os.system('magma')
>>
>> >> William
>>
>> >> > Victor
>>
>> >> > On May 28, 2:11 pm, William Stein  wrote:
>> >> >> On Fri, May 28, 2010 at 11:03 AM, VictorMiller 
>> >> >>  wrote:
>> >> >> > I have magma and sage 4.4.1 installed on my macbook pro.  I've made
>> >> >> > sure that the magma command is on my PATH.  Yet when I run sage, and 
>> >> >> > I
>> >> >> > try and call to magma.eval, it says that it can't find magma.  This
>> >> >> > has worked without problem on my linux workstation at work.  So what
>> >> >> > needs to be done to have sage find my installation of magma?  The 
>> >> >> > page
>> >> >> >http://www.sagemath.org/doc/reference/sage/interfaces/magma.html
>> >> >> > doesn't say anything about this.
>>
>> >> >> > Victor
>>
>> >> >> Start sage and type
>>
>> >> >>    sage: !magma
>>
>> >> >> What happens?
>>
>> >> >> > --
>> >> >> > To post to this group, send email to sage-support@googlegroups.com
>> >> >> > To unsubscribe from this group, send email to 
>> >> >> > sage-support+unsubscr...@googlegroups.com
>> >> >> > For more options, visit this group 
>> >> >> > athttp://groups.google.com/group/sage-support
>> >> >> > URL:http://www.sagemath.org
>>
>> >> >> --
>> >> >> William Stein
>> >> >> Professor of Mathematics
>> >> >> University of Washingtonhttp://wstein.org
>>
>> >> > --
>> >> > To post to this group, send email to sage-support@googlegroups.com
>> >> > To unsubscribe from this group, send email to 
>> >> > sage-support+unsubscr...@googlegroups.com
>> >> > For more options, visit this group 
>> >> > athttp://groups.google.com/group/sage-support
>> >> > URL:http://www.sagemath.org
>>
>> >> --
>> >> William Stein
>> >> Professor of Mathematics
>> >> University of Washingtonhttp://wstein.org
>>
>> > --
>> > To post to this group, send email to sage-support@googlegroups.com
>> > To unsubscribe from this group, send email to 
>> > sage-support+unsubscr...@googlegroups.com
>> > For more options, visit this group 
>> > athttp://groups.google.com/group/sage-support
>> > URL:http://www.sagemath.org
>>
>> --
>> William Stein
>> Professor of Mathematics
>> University of Washingtonhttp://wstein.org
>
> --
> To post to this group, send email to sage-support@googlegroups.com
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>



-- 
William Stein
Professor of Mathematics
University of Washington
http://wstein.org

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[sage-support] Re: Magma on a mac

After 1/2 hour (!) I decided to interrupt the worksheet, quite the
notebook, quite sage, and then restart sage.  Now when I try

os.system('mamga') it comes back right away with

Can't open Magma password file
.magmapass

256

However, I have no trouble starting magma from a terminal or from sage
in command line mode.

Victor

On May 28, 7:27 pm, William Stein  wrote:
> On Fri, May 28, 2010 at 4:15 PM, VictorMiller  wrote:
> > I'm in the notebook and I typed
>
> > os.system('magma')
>
> > It's now over 5 minutes, and it still hasn't come back!  While I was
> > waiting I went a terminal and typed magma and it started within less
> > than a second.
> > Something weird.
>
> What about
>
>  os.system('magma < /dev/null')
>
> William
>
>
>
>
>
>
>
> > Victor
>
> > On May 28, 6:55 pm, William Stein  wrote:
> >> On Fri, May 28, 2010 at 3:33 PM, VictorMiller  
> >> wrote:
> >> > More data:  If I start sage and then type
>
> >> > !magma
>
> >> > it starts up Magma.  I then exit from it (by typing "exit;") and start
> >> > the notebook.
>
> >> > However, if I try to run magma from the notebook, I get the message
>
> >> > "Type Error: unable to start magma"
>
> >> > What's going on?
>
> >> What happens if you do this on the command line:
>
> >>   sage: magma.eval('2+2')
>
> >> What happens if you type this in a notebook cell:
>
> >>   sage: os.system('magma')
>
> >> William
>
> >> > Victor
>
> >> > On May 28, 2:11 pm, William Stein  wrote:
> >> >> On Fri, May 28, 2010 at 11:03 AM, VictorMiller 
> >> >>  wrote:
> >> >> > I have magma and sage 4.4.1 installed on my macbook pro.  I've made
> >> >> > sure that the magma command is on my PATH.  Yet when I run sage, and I
> >> >> > try and call to magma.eval, it says that it can't find magma.  This
> >> >> > has worked without problem on my linux workstation at work.  So what
> >> >> > needs to be done to have sage find my installation of magma?  The page
> >> >> >http://www.sagemath.org/doc/reference/sage/interfaces/magma.html
> >> >> > doesn't say anything about this.
>
> >> >> > Victor
>
> >> >> Start sage and type
>
> >> >>    sage: !magma
>
> >> >> What happens?
>
> >> >> > --
> >> >> > To post to this group, send email to sage-support@googlegroups.com
> >> >> > To unsubscribe from this group, send email to 
> >> >> > sage-support+unsubscr...@googlegroups.com
> >> >> > For more options, visit this group 
> >> >> > athttp://groups.google.com/group/sage-support
> >> >> > URL:http://www.sagemath.org
>
> >> >> --
> >> >> William Stein
> >> >> Professor of Mathematics
> >> >> University of Washingtonhttp://wstein.org
>
> >> > --
> >> > To post to this group, send email to sage-support@googlegroups.com
> >> > To unsubscribe from this group, send email to 
> >> > sage-support+unsubscr...@googlegroups.com
> >> > For more options, visit this group 
> >> > athttp://groups.google.com/group/sage-support
> >> > URL:http://www.sagemath.org
>
> >> --
> >> William Stein
> >> Professor of Mathematics
> >> University of Washingtonhttp://wstein.org
>
> > --
> > To post to this group, send email to sage-support@googlegroups.com
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> --
> William Stein
> Professor of Mathematics
> University of Washingtonhttp://wstein.org

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Re: [sage-support] Re: Magma on a mac

On Fri, May 28, 2010 at 4:15 PM, VictorMiller  wrote:
> I'm in the notebook and I typed
>
> os.system('magma')
>
> It's now over 5 minutes, and it still hasn't come back!  While I was
> waiting I went a terminal and typed magma and it started within less
> than a second.
> Something weird.

What about

 os.system('magma < /dev/null')

William

>
> Victor
>
> On May 28, 6:55 pm, William Stein  wrote:
>> On Fri, May 28, 2010 at 3:33 PM, VictorMiller  
>> wrote:
>> > More data:  If I start sage and then type
>>
>> > !magma
>>
>> > it starts up Magma.  I then exit from it (by typing "exit;") and start
>> > the notebook.
>>
>> > However, if I try to run magma from the notebook, I get the message
>>
>> > "Type Error: unable to start magma"
>>
>> > What's going on?
>>
>> What happens if you do this on the command line:
>>
>>   sage: magma.eval('2+2')
>>
>> What happens if you type this in a notebook cell:
>>
>>   sage: os.system('magma')
>>
>> William
>>
>>
>>
>>
>>
>>
>>
>> > Victor
>>
>> > On May 28, 2:11 pm, William Stein  wrote:
>> >> On Fri, May 28, 2010 at 11:03 AM, VictorMiller  
>> >> wrote:
>> >> > I have magma and sage 4.4.1 installed on my macbook pro.  I've made
>> >> > sure that the magma command is on my PATH.  Yet when I run sage, and I
>> >> > try and call to magma.eval, it says that it can't find magma.  This
>> >> > has worked without problem on my linux workstation at work.  So what
>> >> > needs to be done to have sage find my installation of magma?  The page
>> >> >http://www.sagemath.org/doc/reference/sage/interfaces/magma.html
>> >> > doesn't say anything about this.
>>
>> >> > Victor
>>
>> >> Start sage and type
>>
>> >>    sage: !magma
>>
>> >> What happens?
>>
>> >> > --
>> >> > To post to this group, send email to sage-support@googlegroups.com
>> >> > To unsubscribe from this group, send email to 
>> >> > sage-support+unsubscr...@googlegroups.com
>> >> > For more options, visit this group 
>> >> > athttp://groups.google.com/group/sage-support
>> >> > URL:http://www.sagemath.org
>>
>> >> --
>> >> William Stein
>> >> Professor of Mathematics
>> >> University of Washingtonhttp://wstein.org
>>
>> > --
>> > To post to this group, send email to sage-support@googlegroups.com
>> > To unsubscribe from this group, send email to 
>> > sage-support+unsubscr...@googlegroups.com
>> > For more options, visit this group 
>> > athttp://groups.google.com/group/sage-support
>> > URL:http://www.sagemath.org
>>
>> --
>> William Stein
>> Professor of Mathematics
>> University of Washingtonhttp://wstein.org
>
> --
> To post to this group, send email to sage-support@googlegroups.com
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>



-- 
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Professor of Mathematics
University of Washington
http://wstein.org

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[sage-support] Re: Magma on a mac


On 5/28/10 6:15 PM, VictorMiller wrote:

I'm in the notebook and I typed

os.system('magma')

It's now over 5 minutes, and it still hasn't come back!  While I was
waiting I went a terminal and typed magma and it started within less
than a second.
Something weird.



Does it say anything in the notebook log (i.e., the screen you 
originally launched the notebook from)?


Jason

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[sage-support] Re: Magma on a mac

I'm in the notebook and I typed

os.system('magma')

It's now over 5 minutes, and it still hasn't come back!  While I was
waiting I went a terminal and typed magma and it started within less
than a second.
Something weird.

Victor

On May 28, 6:55 pm, William Stein  wrote:
> On Fri, May 28, 2010 at 3:33 PM, VictorMiller  wrote:
> > More data:  If I start sage and then type
>
> > !magma
>
> > it starts up Magma.  I then exit from it (by typing "exit;") and start
> > the notebook.
>
> > However, if I try to run magma from the notebook, I get the message
>
> > "Type Error: unable to start magma"
>
> > What's going on?
>
> What happens if you do this on the command line:
>
>   sage: magma.eval('2+2')
>
> What happens if you type this in a notebook cell:
>
>   sage: os.system('magma')
>
> William
>
>
>
>
>
>
>
> > Victor
>
> > On May 28, 2:11 pm, William Stein  wrote:
> >> On Fri, May 28, 2010 at 11:03 AM, VictorMiller  
> >> wrote:
> >> > I have magma and sage 4.4.1 installed on my macbook pro.  I've made
> >> > sure that the magma command is on my PATH.  Yet when I run sage, and I
> >> > try and call to magma.eval, it says that it can't find magma.  This
> >> > has worked without problem on my linux workstation at work.  So what
> >> > needs to be done to have sage find my installation of magma?  The page
> >> >http://www.sagemath.org/doc/reference/sage/interfaces/magma.html
> >> > doesn't say anything about this.
>
> >> > Victor
>
> >> Start sage and type
>
> >>    sage: !magma
>
> >> What happens?
>
> >> > --
> >> > To post to this group, send email to sage-support@googlegroups.com
> >> > To unsubscribe from this group, send email to 
> >> > sage-support+unsubscr...@googlegroups.com
> >> > For more options, visit this group 
> >> > athttp://groups.google.com/group/sage-support
> >> > URL:http://www.sagemath.org
>
> >> --
> >> William Stein
> >> Professor of Mathematics
> >> University of Washingtonhttp://wstein.org
>
> > --
> > To post to this group, send email to sage-support@googlegroups.com
> > To unsubscribe from this group, send email to 
> > sage-support+unsubscr...@googlegroups.com
> > For more options, visit this group 
> > athttp://groups.google.com/group/sage-support
> > URL:http://www.sagemath.org
>
> --
> William Stein
> Professor of Mathematics
> University of Washingtonhttp://wstein.org

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Re: [sage-support] Re: Magma on a mac

On Fri, May 28, 2010 at 3:33 PM, VictorMiller  wrote:
> More data:  If I start sage and then type
>
> !magma
>
> it starts up Magma.  I then exit from it (by typing "exit;") and start
> the notebook.
>
> However, if I try to run magma from the notebook, I get the message
>
> "Type Error: unable to start magma"
>
> What's going on?

What happens if you do this on the command line:

  sage: magma.eval('2+2')

What happens if you type this in a notebook cell:

  sage: os.system('magma')

William

>
> Victor
>
> On May 28, 2:11 pm, William Stein  wrote:
>> On Fri, May 28, 2010 at 11:03 AM, VictorMiller  
>> wrote:
>> > I have magma and sage 4.4.1 installed on my macbook pro.  I've made
>> > sure that the magma command is on my PATH.  Yet when I run sage, and I
>> > try and call to magma.eval, it says that it can't find magma.  This
>> > has worked without problem on my linux workstation at work.  So what
>> > needs to be done to have sage find my installation of magma?  The page
>> >http://www.sagemath.org/doc/reference/sage/interfaces/magma.html
>> > doesn't say anything about this.
>>
>> > Victor
>>
>> Start sage and type
>>
>>    sage: !magma
>>
>> What happens?
>>
>>
>>
>> > --
>> > To post to this group, send email to sage-support@googlegroups.com
>> > To unsubscribe from this group, send email to 
>> > sage-support+unsubscr...@googlegroups.com
>> > For more options, visit this group 
>> > athttp://groups.google.com/group/sage-support
>> > URL:http://www.sagemath.org
>>
>> --
>> William Stein
>> Professor of Mathematics
>> University of Washingtonhttp://wstein.org
>
> --
> To post to this group, send email to sage-support@googlegroups.com
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> URL: http://www.sagemath.org
>



-- 
William Stein
Professor of Mathematics
University of Washington
http://wstein.org

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[sage-support] Re: Magma on a mac

More data:  If I start sage and then type

!magma

it starts up Magma.  I then exit from it (by typing "exit;") and start
the notebook.

However, if I try to run magma from the notebook, I get the message

"Type Error: unable to start magma"

What's going on?

Victor

On May 28, 2:11 pm, William Stein  wrote:
> On Fri, May 28, 2010 at 11:03 AM, VictorMiller  
> wrote:
> > I have magma and sage 4.4.1 installed on my macbook pro.  I've made
> > sure that the magma command is on my PATH.  Yet when I run sage, and I
> > try and call to magma.eval, it says that it can't find magma.  This
> > has worked without problem on my linux workstation at work.  So what
> > needs to be done to have sage find my installation of magma?  The page
> >http://www.sagemath.org/doc/reference/sage/interfaces/magma.html
> > doesn't say anything about this.
>
> > Victor
>
> Start sage and type
>
>    sage: !magma
>
> What happens?
>
>
>
> > --
> > To post to this group, send email to sage-support@googlegroups.com
> > To unsubscribe from this group, send email to 
> > sage-support+unsubscr...@googlegroups.com
> > For more options, visit this group 
> > athttp://groups.google.com/group/sage-support
> > URL:http://www.sagemath.org
>
> --
> William Stein
> Professor of Mathematics
> University of Washingtonhttp://wstein.org

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[sage-support] typesetting arrays

2010-05-28 Thread Jim Ragsdale

System info:

'Sage Version 4.4.2, Release Date: 2010-05-19'
Compiled from source on Gentoo Linux.

All,
I am trying to get an array to show show properly in the notebook.
if I execute the following code:
input:
a=np.ones((3,3))
a

output:
array([[ 1.,  1.,  1.],
   [ 1.,  1.,  1.],
   [ 1.,  1.,  1.]])
which looks right to me.
However, if I use the show(a) command, I get:

[[ 1. 1. 1.] [ 1. 1. 1.] [ 1. 1. 1.]]


Shouldn't that show up as a 3x3?

Thanks,
Jim

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Re: [sage-support] error occurred while installing libgcrypt-1.4.4.p2: undefined reference to symbol 'gpg_strerror'

2010-05-28 Thread Mike Hansen

On Fri, May 28, 2010 at 12:36 AM, domingo.domingogo...@gmail.com
 wrote:
> I have all the necessary packages and additionally libgpg-error and
> libgpg-error-devel, could someone point
> what I am doing wrong?

There seems to be a problem with libgcrypt on Fedora 13.  It looks
like someone found a fix at
http://forum.videolan.org/viewtopic.php?f=13&t=33860#p121003 .  We
will try to get this fixed for the next release of Sage.

--Mike

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[sage-support] Weird error message from random_element

Here's something a bit odd:

sage: F = GF(2)
sage: A = CartesianProduct(F,F)
sage: print A.random_element()

This gets a trace back and the message

TypeError: You must specify the names of the variables



Victor

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[sage-support] Testing if something is an instance of FreeModule

I'm writing some code, and I'd like to test if a the value of a
variable, say M, is an instance of an element of a FreeModule(F,n) for
some F and n.  If this weren't a parametrized class I could write

if isinstance(M,C):
   # do stuff here

However doing

if isinstance(M,FreeModule):
   # do stuff here

doesn't work because FreeModule isn't a class or a type.  So how do I
do this?  And, then if it passes that test, how do I extract the F and
n (the two arguments to FreeModule)?

Victor

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[sage-support] Re: Sage Server - displaying Matlab plots


On 5/28/10 1:53 AM, Vinod wrote:



Now I have a different error message in the terminal when I try to
execute the matlab code involving plots in the webserver
" X11 connection rejected because of wrong authentication."

I verified all the X11 settings and it looks fine.
The link lists all the check points one should look for:
http://www.cyberciti.biz/faq/x11-connection-rejected-because-of-wrong-authentication/

The sage server was setup using the method discussed under the  last
section " Other Instructions -from JasonGrout" in the below link.
http://wiki.sagemath.org/DanDrake/JustEnoughSageServer



I wonder if you'll have to do something to the Sage worksheet process 
users.  See, for example, http://umdmath.blogspot.com/


What happens if you ssh into a Sage worksheet account and try running 
matlab?


ssh sageus...@localhost

then try running matlab from the command line.

My guess is that if you get that working, then Sage will be able to get 
matlab to work.


Note that there might be legal issues with providing access to matlab 
via a webserver (whether or not it is a private webserver).  I don't 
know, but it would be something to be aware of if it is an issue.


Thanks,

Jason

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[sage-support] Re: Sage Server - displaying Matlab plots

2010-05-28 Thread Vinod



On May 28, 12:08 am, William Stein  wrote:
> On Thu, May 27, 2010 at 11:53 PM, Vinod  wrote:
>
> > On May 27, 6:40 pm, William Stein  wrote:
> >> On Thu, May 27, 2010 at 6:39 PM, Vinod  wrote:
> >> > That's Awesome! Thanks for the help.
> >> > When would the sage4.4.3 release? Should I wait till then or is it
> >> > possible for you guys to post the patch here in the forum?
>
> >> > Vinod
>
> >> Just type
>
> >>   sage:   
> >> hg_sage.apply('http://trac.sagemath.org/sage_trac/attachment/ticket/9070/trac_9070.p...)
>
> >> exit sage, then type
>
> >>   sage -br
>
> >> And you should have the patch installed into your copy of Sage.
>
> >> William
>
> > Thank you William and Mike. I installed the patch and tried with the
> > matlab again.
>
> > Now I have a different error message in the terminal when I try to
> > execute the matlab code involving plots in the webserver
>
> What code are you executing.  What if you try:
>
> h = figure('Visible', 'off')
> plot(1:.1:10, sin(1:.1:10))
> saveas(h,'foo.png')
>
>  -- William
>
>


Even this doesn't display the plot.

Here is the snapshot of what I tried.
http://math.asu.edu/~scimm/images/screenshot_code1.png

Below is the snapshot with the other matlab code that I tried earlier
http://math.asu.edu/~scimm/images/screenshot_code2.png

In both  cases, the image is created in the directory.

Vinod


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Re: [sage-support] Magma on a mac

On Fri, May 28, 2010 at 11:03 AM, VictorMiller  wrote:
> I have magma and sage 4.4.1 installed on my macbook pro.  I've made
> sure that the magma command is on my PATH.  Yet when I run sage, and I
> try and call to magma.eval, it says that it can't find magma.  This
> has worked without problem on my linux workstation at work.  So what
> needs to be done to have sage find my installation of magma?  The page
> http://www.sagemath.org/doc/reference/sage/interfaces/magma.html
> doesn't say anything about this.
>
> Victor

Start sage and type

   sage: !magma

What happens?

>
> --
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>



-- 
William Stein
Professor of Mathematics
University of Washington
http://wstein.org

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[sage-support] Magma on a mac

I have magma and sage 4.4.1 installed on my macbook pro.  I've made
sure that the magma command is on my PATH.  Yet when I run sage, and I
try and call to magma.eval, it says that it can't find magma.  This
has worked without problem on my linux workstation at work.  So what
needs to be done to have sage find my installation of magma?  The page
http://www.sagemath.org/doc/reference/sage/interfaces/magma.html
doesn't say anything about this.

Victor

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Re: [sage-support] How can I get a PDF from a .show() acting on an expression, from within the notebook ?

2010-05-28 Thread Robert Bradshaw


On May 28, 2010, at 6:13 AM, Nicolas wrote:


Hi all,

I am trying to get, from within the notebook, a PDF from the show
method acting on an expression, just like sage does when used on the
command line. It works very nicely for graphics objects but I have not
figured out either how to get a graphics object from a nicely typeset
expression of just get the pdf that is produced by the command line.

Has this been thought of ? Is this possible ?


Oh, I didn't see that you were talking about an expression. Try

sage: view(expr, viewer='pdf')

- Robert


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Re: [sage-support] How can I get a PDF from a .show() acting on an expression, from within the notebook ?

2010-05-28 Thread Robert Bradshaw


On May 28, 2010, at 6:13 AM, Nicolas wrote:


Hi all,

I am trying to get, from within the notebook, a PDF from the show
method acting on an expression, just like sage does when used on the
command line. It works very nicely for graphics objects but I have not
figured out either how to get a graphics object from a nicely typeset
expression of just get the pdf that is produced by the command line.

Has this been thought of ? Is this possible ?

Thanks to all

Nicolas


Do

whatever.save(filename="foo.pdf")

- Robert


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[sage-support] Re: bug in maxima solve?

2010-05-28 Thread kcrisman



On May 28, 9:00 am, Nils Bruin  wrote:
> I have not been able to get the following behaviour out of maxima
> directly, but the following code illustrates that maxima's solve
> forgets about some solutions:
>
> def realzeros(f,g):
>     t = polygen(QQbar)
>     P = parent(f)
>     R = f.resultant(g,P.0)
>     yvals = [yval[0] for yval in R(0,t).roots() if yval[0] in RR]
>     result = []
>     for yval in yvals:
>         xpol = GCD(f(t,yval),g(t,yval))
>         result += [(xval[0],yval) for xval in xpol.roots() if xval[0]
> in RR]
>     return result
> var("x,y")
> f=(x^2-y^2+y^4)*(x^2+y^2-1)
> g=diff(f,x)+2*diff(f,y)
> temp=solve([f,g],x,y)
> S1 = [ (RR(p[0]),RR(p[1])) for p in [(x.subs(s[0]),y.subs(s[1])) for s
> in temp] if p[0] in RR and p[1] in RR]
> S2 = realzeros(f.polynomial(QQ),g.polynomial(QQ))
> implicit_plot(g,(x,-2,2),(y,-2,2))+implicit_plot(f,(x,-2,2),(y,-2,2))
> +points(S1,color="red",pointsize=40)+points(S2,color="blue",pointsize=20)
>
> This code produces a picture that clearly shows that maxima's solve
> misses some of the intersection points that a straightforward
> resultant-and-roots-of-univariate-polynomials does find.
>
> Perhaps someone more expert in using maxima can get this problem to
> happen directly in maxima so that it can be reported upstream?

I'm too lazy to see what roots you actually want :) but here is the
appropriate Maxima session:

(%i15) f:(x^2-y^2+y^4)*(x^2+y^2-1);
   22422
(%o15)   (y  + x  - 1) (y  - y  + x )
(%i16) g:diff(f,x)+2*diff(f,y);
422  22  3
422
(%o16) 2 (2 y (y  - y  + x ) + (y  + x  - 1) (4 y  - 2 y)) + 2 x (y  -
y  + x )
 
22
+ 2 x (y
+ x  - 1)
(%i17) solve([f,g],[x,y]);
  21  2  1
(%o17) [[x = - ---, y = ---], [x = ---, y = - ---],
   sqrt(5)  sqrt(5)sqrt(5)sqrt(5)
  [x = 0, y = - 1], [x = 0, y = 1], [x =
0, y = 0]]

So it gets five intersection points, including three on the x-axis and
two other conjugate ones on the unit circle.  Which ones is it
missing?  (to_poly_solve gets the same roots, by the way, in the Sage
Maxima.)

- kcrisman

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[sage-support] How can I get a PDF from a .show() acting on an expression, from within the notebook ?

2010-05-28 Thread Nicolas

Hi all,

I am trying to get, from within the notebook, a PDF from the show
method acting on an expression, just like sage does when used on the
command line. It works very nicely for graphics objects but I have not
figured out either how to get a graphics object from a nicely typeset
expression of just get the pdf that is produced by the command line.

Has this been thought of ? Is this possible ?

Thanks to all

Nicolas

PS: the reason I would like to get this PDF is to just save it from
the notebook and send it to a friend ! I am terribly lazy but I do not
want to retype all using the command line ;)

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[sage-support] bug in maxima solve?

2010-05-28 Thread Nils Bruin

I have not been able to get the following behaviour out of maxima
directly, but the following code illustrates that maxima's solve
forgets about some solutions:

def realzeros(f,g):
t = polygen(QQbar)
P = parent(f)
R = f.resultant(g,P.0)
yvals = [yval[0] for yval in R(0,t).roots() if yval[0] in RR]
result = []
for yval in yvals:
xpol = GCD(f(t,yval),g(t,yval))
result += [(xval[0],yval) for xval in xpol.roots() if xval[0]
in RR]
return result
var("x,y")
f=(x^2-y^2+y^4)*(x^2+y^2-1)
g=diff(f,x)+2*diff(f,y)
temp=solve([f,g],x,y)
S1 = [ (RR(p[0]),RR(p[1])) for p in [(x.subs(s[0]),y.subs(s[1])) for s
in temp] if p[0] in RR and p[1] in RR]
S2 = realzeros(f.polynomial(QQ),g.polynomial(QQ))
implicit_plot(g,(x,-2,2),(y,-2,2))+implicit_plot(f,(x,-2,2),(y,-2,2))
+points(S1,color="red",pointsize=40)+points(S2,color="blue",pointsize=20)

This code produces a picture that clearly shows that maxima's solve
misses some of the intersection points that a straightforward
resultant-and-roots-of-univariate-polynomials does find.

Perhaps someone more expert in using maxima can get this problem to
happen directly in maxima so that it can be reported upstream?

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[sage-support] Integrate dirichlet distribution problem

2010-05-28 Thread John Reid

Hi, I'm new to sage and am trying to work out how to use it to do some 
calculus on various probability distributions I have. It seems to 
integrate a beta distribution well but I can't get it to manage a 
Dirichlet distribution. Am I missing something or is this beyond its scope?


Here's my code:

a, b, c = var('a b c')
assume(a > 0)
assume(b > 0)
assume(c > 0)

#
# Beta
#
x = var('x')
beta_dist = x**(a-1) * (1 - x)**(b-1)
c = integral(beta_dist, x, 0, 1)

#
# Dirichlet
#
x_1, x_2, x_3 = var('x_1, x_2, x_3')
dirichlet_dist = x_1**(a-1) * x_2**(b-1) * (1-x_2-x_1)**(c-1)
e = integral(dirichlet_dist, x_1, 0, 1)
f = integral(e, x_2, 0, 1)


Then in my sage session I attach this and get:
--
| Sage Version 4.4.2, Release Date: 2010-05-19   |
| Type notebook() for the GUI, and license() for information.|
--
sage: attach('hdpm.py')
sage: c
beta(a, b)
sage: f
integrate(x_2^(b - 1)*integrate((-x_1 - x_2 + 1)^(beta(a, b) - 1)*x_1^(a 
- 1), x_1, 0, 1), x_2, 0, 1)


Presumably it left the integrals alone because it couldn't do them. Is 
there any way to help it along?


Thanks,
John.

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[sage-support] error occurred while installing libgcrypt-1.4.4.p2: undefined reference to symbol 'gpg_strerror'

2010-05-28 Thread domingo.domingogo...@gmail.com

Hi to all,
I have installed the latest Fedora 13 with the latest sage 4.4.2 from
source. The computer architecture is 32 bits
and I install all the necessary compilers and libgpg-error-devel using
yum.
When I tried to build from source, it appears this message error:

gcc -I/home/Rohan/Software/sage/sage-4.4.2/local/include -O2 -g -Wall -
fvisibility=hidden -Wall -o .libs/register register.o  ../src/.libs/
libgcrypt.so -Wl,--rpath -Wl,/home/Rohan/Software/sage/sage-4.4.2/
local/lib
/usr/bin/ld: register.o: undefined reference to symbol 'gpg_strerror'
/usr/bin/ld: note: 'gpg_strerror' is defined in DSO /home/Rohan/
Software/sage/sage-4.4.2/local/lib/libgpg-error.so.0 so try adding it
to the linker command line
/home/Rohan/Software/sage/sage-4.4.2/local/lib/libgpg-error.so.0:
could not read symbols: Invalid operation
collect2: ld returned 1 exit status
make[4]: *** [register] Error 1
make[4]: se sale del directorio `/home/Rohan/Software/sage/sage-4.4.2/
spkg/build/libgcrypt-1.4.4.p2/src/tests'
make[3]: *** [all-recursive] Error 1
make[3]: se sale del directorio `/home/Rohan/Software/sage/sage-4.4.2/
spkg/build/libgcrypt-1.4.4.p2/src'
make[2]: *** [all] Error 2
make[2]: se sale del directorio `/home/Rohan/Software/sage/sage-4.4.2/
spkg/build/libgcrypt-1.4.4.p2/src'
failed to build libgcrypt

real0m29.726s
user0m10.521s
sys 0m8.435s
sage: An error occurred while installing libgcrypt-1.4.4.p2

I have all the necessary packages and additionally libgpg-error and
libgpg-error-devel, could someone point
what I am doing wrong?
Cheers,
Domingo

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Re: [sage-support] Re: Sage Server - displaying Matlab plots