date:20090925


On Fri, Sep 25, 2009 at 5:19 PM, Dr. David Kirkby
david.kir...@onetel.net wrote:

SNIP

 I'm not so convinced of this. It is fine on workstations, but not on big
 multi-user servers. I would have stuck a maximum limit of 8 by default.

A default of 1 would work for any (probably most) machine.

-- 
Regards
Minh Van Nguyen

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[sage-devel] Re: new jmol

2009-09-25 Thread Jonathan


Bug fixes and code changes are documented with some more detail in the
file jmol.properties that can be found in the source code in the
directory src/org/jmol/viewer.

We try pretty hard not to change historical behavior unless it is
determined to be erroneous, so new versions usually work as drop-in
replacements for older versions, unless you are relying on erroneous
behavior.  An example I encountered was that I was depending on Jmol
loading molecular orbitals and associating them with the wrong
molecular structure from a particular data file type.  When that was
fixed, I had to rewrite my  web page that used those orbitals.

What problem were people having with Jmol on Windows?  Can you
describe it in detail?  The only failure problem I was aware of was
that it didn't work well with the non-Sun versions of the JavaVM on
some Linux ditros.  At this point we don't have the manpower to
support other virtual machines.

There are a number of things I would like to see about the way Jmol
shows up in SAGE.  It would be nice to have some buttons next to the
window that do things like turn on spinning and allow some zoom
facility (ideally smart enough to recalculate if necessary).  These
wouldn't be too hard to do, but I don't really understand how (or
where) in the notebook code the Jmol stuff is fed to the web browser.
After the notebook is separated out, if somebody can give me some
direction, I'd be willing to look at the generation of the div that
contains Jmol.

Jonathan


On Sep 24, 4:42 pm, Bill Page bill.p...@newsynthesis.org wrote:
 Jason,

 What are the Sage version prerequisites for this package (if any)?
 Besides new features is there a list of bug fixes? In particular, do
 you know if this version solves the problem with jmol on some Windows
 XP systems that has been mentioned occasionally here on this list?

 Regards,
 Bill Page.

 On Thu, Sep 24, 2009 at 3:52 PM, Jason Grout wrote:

  I updated the jmol spkg to 11.8.6 at #7003 (ready for review!).  Here
  are some new things since the current version of jmol we have in Sage.
  I post this here because some people might be interested in
  exposing/using some of these in Sage:

  These come from:http://chemapps.stolaf.edu/jmol/docs/examples-11/new8.htm
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[sage-devel] Re: Graph layout, graphviz, and dot2tex


Nicolas M. Thiery wrote:
 Ah, by the way, a question for spkg experts: the current dot2tex spkg
 I built contains two separate python modules, pyparsing and dot2tex,
 the later depending on the former. Should there be two spkg's instead?
 Is it possible to state the dependency so that users could just do
 sage -i dot2tex... and get both installed, or at leave have a useful
 error message?

I'm not an expert, but in case it helps:  It seems that pyparsing is
already included with matplotlib.  However, the import statement needs
to be qualified:

sage: import matplotlib.pyparsing


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[sage-devel] Re: Graph layout, graphviz, and dot2tex

2009-09-25 Thread Dan Drake

On Fri, 25 Sep 2009 at 09:12AM +0200, Nicolas M. Thiery wrote:
 Ah, by the way, a question for spkg experts: the current dot2tex spkg
 I built contains two separate python modules, pyparsing and dot2tex,
 the later depending on the former. Should there be two spkg's instead?

I'm not a spkg expert, but I believe there's already a pyparsing
somewhere in Sage...somewhere in matplotlib, I think. I'd look around
and see if you could just use that instead of shipping your own.

Dan

-- 
---  Dan Drake
-  http://mathsci.kaist.ac.kr/~drake
---


signature.asc
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[sage-devel] Re: survey: how many cpus do you have?

2009-09-25 Thread Dr. David Kirkby


William Stein wrote:

 SUN specifically donated that box to us for creating an optimized Sage
 *notebook* server system.   It was not for doing research
 compute-bound work.  It may well still turn out to be the case that T2
 is a good choice for running a notebook server with many simultaneous
 connections.  I don't know yet.  It's not inconceivable since i/o,
 many threads, etc., are all important for having say hundreds of
 clients at once all doing basic calculus (which isn't CPU bound).

Yes, that could certainly be so.

 The main concern I have so far is security -- I don't quite understand
 how to 100% safely sandbox processes on T2.  However, my understanding
 is that Solaris Zones are supposed to do exactly this in an elegant
 way.

Zones work well. I am going to try to find out how secure it would be to 
share an NFS file system into a zone. The fact 'disk' is a file server, 
I don't know if there would be any security issues in sharing that 
read/write to a zone.

There's no disk space on 't2' that is local, which  think might be 
advantageous for a machine designed to run multiple Sage instances from 
untrusted users. I'm just a bit concerned someone who managed to hack a 
zone might be able to do a bit more damage, the fact a NFS share is 
available to them too.

Perhaps my fears are unfounded.


Dave



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[sage-devel] Re: survey: how many cpus do you have?


On Fri, Sep 25, 2009 at 8:01 AM, Dr. David Kirkby
david.kir...@onetel.net wrote:

 William Stein wrote:

 SUN specifically donated that box to us for creating an optimized Sage
 *notebook* server system.   It was not for doing research
 compute-bound work.  It may well still turn out to be the case that T2
 is a good choice for running a notebook server with many simultaneous
 connections.  I don't know yet.  It's not inconceivable since i/o,
 many threads, etc., are all important for having say hundreds of
 clients at once all doing basic calculus (which isn't CPU bound).

 Yes, that could certainly be so.

 The main concern I have so far is security -- I don't quite understand
 how to 100% safely sandbox processes on T2.  However, my understanding
 is that Solaris Zones are supposed to do exactly this in an elegant
 way.

 Zones work well. I am going to try to find out how secure it would be to
 share an NFS file system into a zone. The fact 'disk' is a file server,
 I don't know if there would be any security issues in sharing that
 read/write to a zone.

 There's no disk space on 't2' that is local, which  think might be

Isn't this 22GB of unused local disk space:

$ df
...
rootpool2/scratch   30G   8.4G22G29%/scratch

22GB is plenty of local disk space for running something like a notebook server.
For performance and security reasons one would probably want to use
local disk space.


William

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[sage-devel] Re: new jmol


Jonathan wrote:
 Bug fixes and code changes are documented with some more detail in the
 file jmol.properties that can be found in the source code in the
 directory src/org/jmol/viewer.
 
 We try pretty hard not to change historical behavior unless it is
 determined to be erroneous, so new versions usually work as drop-in
 replacements for older versions, unless you are relying on erroneous
 behavior.  An example I encountered was that I was depending on Jmol
 loading molecular orbitals and associating them with the wrong
 molecular structure from a particular data file type.  When that was
 fixed, I had to rewrite my  web page that used those orbitals.


Thanks for your input!



 There are a number of things I would like to see about the way Jmol
 shows up in SAGE.  It would be nice to have some buttons next to the
 window that do things like turn on spinning and allow some zoom
 facility (ideally smart enough to recalculate if necessary).  These
 wouldn't be too hard to do, but I don't really understand how (or
 where) in the notebook code the Jmol stuff is fed to the web browser.
 After the notebook is separated out, if somebody can give me some
 direction, I'd be willing to look at the generation of the div that
 contains Jmol.

I tried messing with this briefly, trying to up the memory allocated so 
that I could get more than 11 plots on a screen.  Only having 11 is a 
pretty bad limitation for a calculus 3 worksheet on 3d functions :).  I 
didn't have any success, though; I still have a 64Mb limitation that 
quickly runs out.

For now, the code is in 
$SAGE_ROOT/devel/sage/sage/server/notebook/js.py.  I don't know where it 
will be in William's new notebook.

It would be *fantastic* if we could have better interaction with the 3d 
plots.  You can turn on spinning by the right-click menu, and zooming 
with the mouse works too.  I think it would be really fun to be able to 
pick points out in the 3d plot and have it do something (like talk back 
to the server in an interact, giving the coordinates of what you picked).

I was looking at the contour lines/planes.  I wish we could employ that 
to get contour cut planes for a scalar field.

Also, I'd really, really like to get some sort of mesh for 
pmesh/isosurfaces that looks like the black lines on contour plots 
rather than the light blue lines that currently show when the mesh is 
on.  In fact, what I'd really love to see is arbitrary mesh functions, 
similar to what is implemented in a worksheet here: 
http://trac.sagemath.org/sage_trac/ticket/5511 (see 
http://trac.sagemath.org/sage_trac/attachment/ticket/5511/mesh_function.jpeg 
for a picture).  I think Mathematica has a nice interface to these sorts 
of things: http://reference.wolfram.com/mathematica/ref/MeshFunctions.html

We (Sage) can take care of the interface to draw meshes.  What we'd need 
from jmol is the ability to draw a line *on* a surface and have it look 
like the contour lines look like on a plane (maybe by somehow specifying 
the edges of triangles that the line crosses, and at what place to put 
the point of the edge?)  The problem now is that we need to draw really 
thick lines so that the surface doesn't mask the line on one side or the 
other.

Jason


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[sage-devel] Re: new jmol

2009-09-25 Thread Bill Page

On Fri, Sep 25, 2009 at 9:20 AM, Jonathan wrote:

Bug fixes and code changes are documented with some more detail in the
file jmol.properties that can be found in the source code in the
directory src/org/jmol/viewer.

We try pretty hard not to change historical behavior unless it is
determined to be erroneous, so new versions usually work as drop-in
replacements for older versions, unless you are relying on erroneous
behavior. An example I encountered was that I was depending on Jmol
loading molecular orbitals and associating them with the wrong
molecular structure from a particular data file type. When that was
fixed, I had to rewrite my web page that used those orbitals.

I just dropped it into an older Sage release 3.4 and had no problems. Thanks.

What problem were people having with Jmol on Windows? Can you
describe it in detail? The only failure problem I was aware of was
that it didn't work well with the non-Sun versions of the JavaVM on
some Linux ditros. At this point we don't have the manpower to
support other virtual machines.

See this thread:

Jmol will not display graphics

http://groups.google.com/group/sage-support/browse_thread/thread/d3e59fd3cca25bb2/60546d2ec8041ebc?lnk=gstq=Jmol+will+not+display+graphics#60546d2ec8041ebc

Unfortunately there is no change in behavior with this update. It
still works fine for me on my Linux clients and when using Windows
Vista, but on a slightly older laptop running Windows XP (up-to-date
with SP2) it still fails. In Sage notebook jmol appears to load and
the graphics window appears but it is blank. I cannot see any object
but the window is otherwise responsive. I can right click and change
background color, axes and other options and I do see these displayed
but no graphic! This same page on the same server when viewed from
the other clients works fine.

Regards,
Bill Page.

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[sage-devel] Re: new jmol


On Fri, Sep 25, 2009 at 9:30 AM, Jason Grout
jason-s...@creativetrax.com wrote:

 Jonathan wrote:
 Bug fixes and code changes are documented with some more detail in the
 file jmol.properties that can be found in the source code in the
 directory src/org/jmol/viewer.

 We try pretty hard not to change historical behavior unless it is
 determined to be erroneous, so new versions usually work as drop-in
 replacements for older versions, unless you are relying on erroneous
 behavior.  An example I encountered was that I was depending on Jmol
 loading molecular orbitals and associating them with the wrong
 molecular structure from a particular data file type.  When that was
 fixed, I had to rewrite my  web page that used those orbitals.


 Thanks for your input!



 There are a number of things I would like to see about the way Jmol
 shows up in SAGE.  It would be nice to have some buttons next to the
 window that do things like turn on spinning and allow some zoom
 facility (ideally smart enough to recalculate if necessary).  These
 wouldn't be too hard to do, but I don't really understand how (or
 where) in the notebook code the Jmol stuff is fed to the web browser.
 After the notebook is separated out, if somebody can give me some
 direction, I'd be willing to look at the generation of the div that
 contains Jmol.

 I tried messing with this briefly, trying to up the memory allocated so
 that I could get more than 11 plots on a screen.  Only having 11 is a
 pretty bad limitation for a calculus 3 worksheet on 3d functions :).

We could try changing how jmol is used in Sage as follows:  when the
user isn't actively using the 3d image, it is replaced by a static
png.  Then there would be at most 1 jmol applet per page.

william

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[sage-devel] Re: new jmol


William Stein wrote:

 We could try changing how jmol is used in Sage as follows:  when the
 user isn't actively using the 3d image, it is replaced by a static
 png.  Then there would be at most 1 jmol applet per page.
 

That seems to be how mathematica does things.  At least, when I have 
compiz turned on, I physically see the static figure be replaced (with a 
window swooping in) by a window that lets me rotate, and when I let go, 
the figure is redrawn as a static image.  Sometimes this is really 
annoying, as I have to wait for the figure to be changed.

In our case, it sounds like we would have to wait for a round trip to 
the server every time we tried rotating things? (or maybe we'd wait a 
few seconds, and then replaced it?)

Is there any chance of making a lite jmol that was took much less than 
around 64/10=6.4M of memory?  Surely there is a lot in jmol that we 
don't use or need at the moment.

Thanks,

Jason


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[sage-devel] Re: new jmol

2009-09-25 Thread Alfredo Portes


Hi Bill,

On Fri, Sep 25, 2009 at 1:14 PM, Bill Page bill.p...@newsynthesis.org wrote:

 Unfortunately there is no change in behavior with this update. It
 still works fine for me on my Linux clients and when using Windows
 Vista, but on a slightly older laptop running  Windows XP (up-to-date
 with SP2) it still fails. In Sage notebook jmol appears to load and
 the graphics window appears but it is blank. I cannot see any object
 but the window is otherwise responsive. I can right click and change
 background color, axes and other options and I do see these displayed
 but no graphic!  This same page on the same server when viewed from
 the other clients works fine.

var('x y z')
implicit_plot3d(x^2+y^2+z^2==4, (x, -3, 3), (y, -3,3), (z, -3,3))

With XP/SP3 here works fine. What JRE (version) are you using?

JRE 6 Update 15
Firefox 3.5.1
Chrome 3.0.195

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[sage-devel] Re: new jmol

2009-09-25 Thread Bill Page


On Fri, Sep 25, 2009 at 2:35 PM, Alfredo Portes wrote:

 On Fri, Sep 25, 2009 at 1:14 PM, Bill Page wrote:

 Unfortunately there is no change in behavior with this update. It
 still works fine for me on my Linux clients and when using Windows
 Vista, but on a slightly older laptop running  Windows XP (up-to-date
 with SP2) it still fails. In Sage notebook jmol appears to load and
 the graphics window appears but it is blank. I cannot see any object
 but the window is otherwise responsive. I can right click and change
 background color, axes and other options and I do see these displayed
 but no graphic!  This same page on the same server when viewed from
 the other clients works fine.

 var('x y z')
 implicit_plot3d(x^2+y^2+z^2==4, (x, -3, 3), (y, -3,3), (z, -3,3))


That command is not in Sage-3.4. Try this:

  plot3d(b2+b1,(b1,-2,2),(b2,-2,2))

 With XP/SP3 here works fine. What JRE (version) are you using?

 JRE 6 Update 15
 Firefox 3.5.1
 Chrome 3.0.195


Same Windows. I've got same JRE, Firefox 3.5.2 (same problem with
older Firefox). What's Chrome?

Regards,
Bill Page

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[sage-devel] strange message from hg_sage.commit()

2009-09-25 Thread John Cremona


Can anyone tell me what this message means, in response to hg_sage.commit():

cd /home/jcooley/sage-4.1.1/devel/sage  hg diff  | less
cd /home/jcooley/sage-4.1.1/devel/sage  hg commit
abort: journal already exists - run hg recover!

And what to do about it?

This is in a clone on which lots of edits have been made:
hg_sage.status() shows 8 modified files.

John

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[sage-devel] sage -sh question and possible patch

2009-09-25 Thread Mariah Lenox


The open trac tickets #4644 and #5507 discuss
problems with sage -sh, specifically

#4644  - No new prompt when doing a ./sage -sh

#5507 - $ sage -sh -c echo hi there  # does not work, but should
  $ sage -sh -c -c echo hi there # works, but shouldn't

There is also a problem that sage -sh may pick up the user's
$PATH rather than the one defined in sage-env (which
is how I got into this issue).

The patch below fixes these three problems - but it may
not be what developers want.  Specifically, it will set the
prompt to be sage $ for all shells (with the exception of
csh which does not have a prompt environment variable and
so the prompt gets set to %).   Note that with the patch
the prompt is NOT listing the current directory.

Do developers prefer that a sage-sub-shell prompt list
the current directory?

If so, I will have another think about this.  If not, would
a kind person please check in the patch.

Mariah

--- sage-sage.old   2009-09-25 10:52:08.278703000 -0400
+++ sage-sage.new   2009-09-25 15:11:21.214214000 -0400
@@ -374,41 +374,37 @@
 echo with other copies of Sage!
 echo 
 SHELL_NAME=`basename $SHELL`
-if [ $# -eq 0 ]; then
-   SHELL_OPTS=
-else
-shift
-echo Bypassing shell configuration files ...
-echo
-# We must start a new shell with no .profile or .bashrc files
-# processed, so that we know our path is correct
-   PS1=sage$ 
-   export PS1
-   case $SHELL_NAME in
-   bash)
-   SHELL_OPTS= --norc
-   ;;
-   csh)
-   SHELL_OPTS= -f
-   ;;
-   ksh)
-   SHELL_OPTS= -p
-   ;;
-   sh)
-   SHELL_OPTS= --norc
-   ;;
-   tcsh)
-   SHELL_OPTS= -f
-   ;;
-   zsh)
-   SHELL_OPTS= -f -d
-   ;;
-   *)
-   echo Unknown shell: $SHELL!
-   echo Exiting Sage.
-   exit 1
-   esac
-fi
+
+echo Bypassing shell configuration files ...
+echo
+# We must start a new shell with no .profile or .bashrc files
+# processed, so that we know our path is correct
+PS1=sage$ 
+export PS1
+case $SHELL_NAME in
+bash)
+SHELL_OPTS= --norc
+;;
+csh)
+SHELL_OPTS= -f
+;;
+ksh)
+SHELL_OPTS= -p
+;;
+sh)
+SHELL_OPTS= --norc
+;;
+tcsh)
+SHELL_OPTS= -f
+;;
+zsh)
+SHELL_OPTS= -f -d
+;;
+*)
+echo Unknown shell: $SHELL!
+echo Exiting Sage.
+exit 1
+esac
 $SHELL_NAME $SHELL_OPTS $@

 echo Exited Sage subshell.

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[sage-devel] Re: Graph layout, graphviz, and dot2tex

2009-09-25 Thread Nicolas M. Thiery


On Fri, Sep 25, 2009 at 06:22:07AM -0700, Pat LeSmithe wrote:
 
 Nicolas M. Thiery wrote:
  Ah, by the way, a question for spkg experts: the current dot2tex spkg
  I built contains two separate python modules, pyparsing and dot2tex,
  the later depending on the former. Should there be two spkg's instead?
  Is it possible to state the dependency so that users could just do
  sage -i dot2tex... and get both installed, or at leave have a useful
  error message?
 
 I'm not an expert, but in case it helps:  It seems that pyparsing is
 already included with matplotlib.  However, the import statement needs
 to be qualified:
 
 sage: import matplotlib.pyparsing

Ah ah, thanks much for the pointer! That will make things simpler
indeed.

Any better suggestion than to include a patch in dot2tex's spkg to fix
the imports?

Best,
Nicolas
--
Nicolas M. Thiéry Isil nthi...@users.sf.net
http://Nicolas.Thiery.name/

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[sage-devel] Re: sage -sh question and possible patch


Hi Mariah,

On Sat, Sep 26, 2009 at 6:04 AM, Mariah Lenox mariah.le...@gmail.com wrote:

 The open trac tickets #4644 and #5507 discuss
 problems with sage -sh, specifically

 #4644  - No new prompt when doing a ./sage -sh

I can confirm that your patch fixes this issue:

{{{
[mv...@sage sage-4.1.1]$ ./sage -sh

Starting subshell with Sage environment variables set.
Be sure to exit when you are done and do not do anything
with other copies of Sage!

Bypassing shell configuration files ...

sage$ exit
exit
Exited Sage subshell.
}}}


 #5507 - $ sage -sh -c echo hi there  # does not work, but should

It also fixes this one as well:

{{{
[mv...@sage sage-4.1.1]$ ./sage -sh -c echo hi there

Starting subshell with Sage environment variables set.
Be sure to exit when you are done and do not do anything
with other copies of Sage!

Bypassing shell configuration files ...

hi there
Exited Sage subshell.
}}}



  $ sage -sh -c -c echo hi there # works, but shouldn't

This one still works:

{{{
[mv...@sage sage-4.1.1]$ ./sage -sh -c -c echo hi there

Starting subshell with Sage environment variables set.
Be sure to exit when you are done and do not do anything
with other copies of Sage!

Bypassing shell configuration files ...

hi there
Exited Sage subshell.
}}}



 There is also a problem that sage -sh may pick up the user's
 $PATH rather than the one defined in sage-env (which
 is how I got into this issue).

With the patch, the user's $PATH is picked up, but variables in
sage-env are prepended to it:

{{{
[mv...@sage sage-4.1.1]$ echo $PATH
/home/mvngu/usr:/home/mvngu/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
[mv...@sage sage-4.1.1]$
[mv...@sage sage-4.1.1]$ ./sage -sh

Starting subshell with Sage environment variables set.
Be sure to exit when you are done and do not do anything
with other copies of Sage!

Bypassing shell configuration files ...

sage$ echo $PATH
/scratch/mvngu/build/sage-4.1.1:/scratch/mvngu/build/sage-4.1.1/local/bin:/home/mvngu/usr:/home/mvngu/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
sage$ exit
exit
Exited Sage subshell.
}}}


 The patch below fixes these three problems - but it may
 not be what developers want.  Specifically, it will set the
 prompt to be sage $ for all shells (with the exception of
 csh which does not have a prompt environment variable and
 so the prompt gets set to %).   Note that with the patch
 the prompt is NOT listing the current directory.

 Do developers prefer that a sage-sub-shell prompt list
 the current directory?

Yes, that would be nice.

-- 
Regards
Minh Van Nguyen

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[sage-devel] Re: sage -sh question and possible patch

2009-09-25 Thread Paulo César Pereira de Andrade


2009/9/25 Minh Nguyen nguyenmi...@gmail.com:

 Hi Mariah,

 On Sat, Sep 26, 2009 at 6:04 AM, Mariah Lenox mariah.le...@gmail.com wrote:

 The open trac tickets #4644 and #5507 discuss
 problems with sage -sh, specifically

 #4644  - No new prompt when doing a ./sage -sh

 I can confirm that your patch fixes this issue:

 {{{
 [mv...@sage sage-4.1.1]$ ./sage -sh

 Starting subshell with Sage environment variables set.
 Be sure to exit when you are done and do not do anything
 with other copies of Sage!

 Bypassing shell configuration files ...

 sage$ exit
 exit
 Exited Sage subshell.
 }}}


 #5507 - $ sage -sh -c echo hi there  # does not work, but should

 It also fixes this one as well:

 {{{
 [mv...@sage sage-4.1.1]$ ./sage -sh -c echo hi there

 Starting subshell with Sage environment variables set.
 Be sure to exit when you are done and do not do anything
 with other copies of Sage!

 Bypassing shell configuration files ...

 hi there
 Exited Sage subshell.
 }}}



              $ sage -sh -c -c echo hi there # works, but shouldn't

 This one still works:

 {{{
 [mv...@sage sage-4.1.1]$ ./sage -sh -c -c echo hi there

 Starting subshell with Sage environment variables set.
 Be sure to exit when you are done and do not do anything
 with other copies of Sage!

 Bypassing shell configuration files ...

 hi there
 Exited Sage subshell.
 }}}



 There is also a problem that sage -sh may pick up the user's
 $PATH rather than the one defined in sage-env (which
 is how I got into this issue).

 With the patch, the user's $PATH is picked up, but variables in
 sage-env are prepended to it:

 {{{
 [mv...@sage sage-4.1.1]$ echo $PATH
 /home/mvngu/usr:/home/mvngu/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
 [mv...@sage sage-4.1.1]$
 [mv...@sage sage-4.1.1]$ ./sage -sh

 Starting subshell with Sage environment variables set.
 Be sure to exit when you are done and do not do anything
 with other copies of Sage!

 Bypassing shell configuration files ...

 sage$ echo $PATH
 /scratch/mvngu/build/sage-4.1.1:/scratch/mvngu/build/sage-4.1.1/local/bin:/home/mvngu/usr:/home/mvngu/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
 sage$ exit
 exit
 Exited Sage subshell.
 }}}


 The patch below fixes these three problems - but it may
 not be what developers want.  Specifically, it will set the
 prompt to be sage $ for all shells (with the exception of
 csh which does not have a prompt environment variable and
 so the prompt gets set to %).   Note that with the patch
 the prompt is NOT listing the current directory.

 Do developers prefer that a sage-sub-shell prompt list
 the current directory?

 Yes, that would be nice.

 --
 Regards
 Minh Van Nguyen

  Possibly a bit out of context. But I was hit by sage -sh
yesterday. I run ./sage -sh to make some tests, and gone do other
duties in the meantime.  Then, I forgot I was under a sage 4.1.1 shell
in that xterm, and things started working incorrectly.
  Curiously, I had been debugging a problem with
java-1.6-openjdk-plugin and java-1.6-sun-plugin, where only the sun
plugin works in my Mandriva setup, when loading the jmol plugin. (I
was testing/comparing both, the mandriva rpm package, and sage-4.1.1
binary downloaded from a sagemath mirror).
  Then, after playing with install/uninstall of several packages, I
ended up in a state where firefox would always refuse to start, and
the reason was LD_LIBRARY_PATH, because I was starting firefox from
the xterm that was running sage -sh.

Paulo

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[sage-devel] Re: strange message from hg_sage.commit()


On Fri, Sep 25, 2009 at 12:27 PM, John Cremona john.crem...@gmail.com wrote:

 Can anyone tell me what this message means, in response to hg_sage.commit():

 cd /home/jcooley/sage-4.1.1/devel/sage  hg diff  | less
 cd /home/jcooley/sage-4.1.1/devel/sage  hg commit
 abort: journal already exists - run hg recover!

 And what to do about it?

 This is in a clone on which lots of edits have been made:
 hg_sage.status() shows 8 modified files.

I don't know what it means.  But you might try doing what it says,
name - run hg recover!.
I.e.,

   cd /home/jcooley/sage-4.1.1/devel/sage
   hg recover

and see what happens.

William

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[sage-devel] Re: new jmol


On Fri, Sep 25, 2009 at 10:30 AM, Jason Grout
jason-s...@creativetrax.com wrote:

 William Stein wrote:

 We could try changing how jmol is used in Sage as follows:  when the
 user isn't actively using the 3d image, it is replaced by a static
 png.  Then there would be at most 1 jmol applet per page.


 That seems to be how mathematica does things.

Yes.  I should have acknowledged that this is where I got the idea.

 At least, when I have
 compiz turned on, I physically see the static figure be replaced (with a
 window swooping in) by a window that lets me rotate, and when I let go,
 the figure is redrawn as a static image.  Sometimes this is really
 annoying, as I have to wait for the figure to be changed.

True.  But it scales.

 In our case, it sounds like we would have to wait for a round trip to
 the server every time we tried rotating things? (or maybe we'd wait a
 few seconds, and then replaced it?)

I can't see why a roundtrip to the server would be needed.


 Is there any chance of making a lite jmol that was took much less than
 around 64/10=6.4M of memory?  Surely there is a lot in jmol that we
 don't use or need at the moment.

 Thanks,

 Jason


 




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

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[sage-devel] testing packages on OS X 10.5


Hi folks,

There are some updated packages that would be really cool to get into
Sage 4.1.2. These include:

* #6969 boehm_gc-7.1.p2.spkg
* #6971 ecl-9.8.4-20090913cvs.p1.spkg
* #7006 mpir-1.2.p6.spkg
* #6919 flint-1.5.0.p0.spkg
* #6990 python-2.6.2.p2.spkg
* #6951 singular-3-1-0-4-20090818.p0.spkg
* #6758 libgcrypt-1.4.3.p2.spkg
* #6681 cliquer-1.2.p0.spkg

I have been testing these under various 32- and 64-bit Linux machines,
including

* 64-bit Ubuntu 8.04.3 LTS (sage.math)
* 64-bit RHEL 5.4 (rosemary.math)
* 32-bit Fedora 9 (cicero on SkyNet)
* 64-bit Fedora 9 (eno on SkyNet)
* 64-bit RHEL 5.3 (lena on SkyNet)
* 64-bit openSUSE 11.1

As for Mac OS X, I only have access to bsd.math, which was recently
upgraded to OS X 10.6. Is there anyone with access to OS X 10.5 who
could build the above packages on that platform, both in 32- and
64-bit mode?

-- 
Regards
Minh Van Nguyen

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[sage-devel] Re: testing packages on OS X 10.5

2009-09-25 Thread John H Palmieri


On Sep 25, 4:50 pm, Minh Nguyen nguyenmi...@gmail.com wrote:
 Hi folks,

 There are some updated packages that would be really cool to get into
 Sage 4.1.2. These include:

 * #6969 boehm_gc-7.1.p2.spkg
 * #6971 ecl-9.8.4-20090913cvs.p1.spkg
 * #7006 mpir-1.2.p6.spkg

I'm making builds with these right now; I'll post results when they're
done.

 * #6681 cliquer-1.2.p0.spkg

This one I did already on OS X 10.5: see the ticket (from a few days
ago).

  John

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[sage-devel] Re: new jmol


William Stein wrote:

 In our case, it sounds like we would have to wait for a round trip to
 the server every time we tried rotating things? (or maybe we'd wait a
 few seconds, and then replaced it?)
 
 I can't see why a roundtrip to the server would be needed.


Can you unload a java applet and then reload it later, but still keep 
the applet around?  Or are you saying that the browser would have it in 
cache, so a roundtrip probably wouldn't happen?

Jason


-- 
Jason Grout


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[sage-devel] Re: new jmol


On Fri, Sep 25, 2009 at 5:15 PM, Jason Grout
jason-s...@creativetrax.com wrote:

 William Stein wrote:

 In our case, it sounds like we would have to wait for a round trip to
 the server every time we tried rotating things? (or maybe we'd wait a
 few seconds, and then replaced it?)

 I can't see why a roundtrip to the server would be needed.


 Can you unload a java applet and then reload it later, but still keep
 the applet around?  Or are you saying that the browser would have it in
 cache, so a roundtrip probably wouldn't happen?

One possibility might be that we have just one applet, but using
javascript we *move* it.

William

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[sage-devel] canvas3d_lib.js extended to work on iPhone, IE

2009-09-25 Thread Peter


Hi,

I really like the canvas3d plot option in 4.1.2 since it will make it
easier to implement interactive 3d scenes in Sage and make them also
display in browsers that do not support java. I modified the
canvas3d_lib.js file so that it can also be used in a plain html page
and works on the iPhone and in IE.

A small hack also makes the view angle similar to the one for jmol
(and the parameters have been adjusted to reduce the fisheye effect).

A demo is at http://mathcs.chapman.edu/~jipsen/canvas/sage/

and the js file can be downloaded from that page (put it in devel/sage/
sage/server/notebook/templates and restart the server to try it out
with sage-4.1.2.alpha).

Is anyone working on rendering surfaces with shading over the
wireframe?

Also I noticed that the line(...) command does not seem to work with
the canvas3d option.

--Peter
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[sage-devel] trac ticket 7013 is ready for review prime_pi and nth_prime (my first Sage contribution)

2009-09-25 Thread kstueve


Uses a hybrid table lookup and sieving algorithm.  Also provides the
option of using PARI's sieving algorithm, Andrew Ohana's optimized
Legendre algorithm, or Victor Miller's Lagarias Miller Odlyzko (LMO)
combinatorial algorithm.

Be sure to use the -m32 option when compiling the c code, and if
necessary, download the required libraries to run 32 bit code on your
computer.  Macbook pros should be the easiest to work.

The table of values of the prime counting function comes from
http://www.primefan.ru/stuff/primes/table.html  The gap between values
in the table is the same for each decade, and then jumps to a larger
value.  The performance of my prime_pi(x) is best near values of x in
the table, and worst for values halfway between.  The performance
decreases  after each power of 10, where the gap between table entries
increases.

I would like my code to be run against Mathematica on the same
machine.  It would be appropriate to create a random set of values in
each decade (i.e. values all with some number of digits) for
prime_pi.  For nth_prime, this would work, but for a better picture of
the performance of my code, it would be appropriate to make a random
set of values of n (to give to the nth_prime function) such that
nth_prime is between two successive powers of 10 (i.e. nth_prime is
some number of digits long) for each number of digits.

See 
http://en.wikipedia.org/wiki/Prime-counting_function#Table_of_.CF.80.28x.29.2C_x_.2F_ln_x.2C_and_li.28x.29
for a table of prime_pi.

Kevin Stueve
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[sage-devel] prime_range problem

2009-09-25 Thread kstueve


I am having trouble with the following lines.  Should I make a new
trac ticket for this or am I just doing something wrong?  I am on a
MacBook pro.

from sage.rings.fast_arith import prime_range
print prime_range(10^16,10^16+100)

Traceback (most recent call last):
 File stdin, line 1, in module
 File /Users/guestadmin/.sage/sage_notebook/worksheets/admin/3/code/
22.py,
line 8, in module
   print prime_range(_sage_const_10 **_sage_const_16 ,_sage_const_10
**_sage_const_16 +_sage_const_100 )
 File , line 1, in module

 File fast_arith.pyx, line 56, in sage.rings.fast_arith.prime_range
(sage/rings/fast_arith.c:3813)
 File fast_arith.pyx, line 105, in
sage.rings.fast_arith.prime_range (sage/rings/fast_arith.c:3580)
 File gen.pyx, line 8629, in
sage.libs.pari.gen.PariInstance.primes_up_to_n
(sage/libs/pari/gen.c:40808)
OverflowError: long int too large to convert to int
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[sage-devel] Re: canvas3d_lib.js extended to work on iPhone, IE


On Fri, Sep 25, 2009 at 6:01 PM, Peter peter.jip...@gmail.com wrote:

 Hi,

 I really like the canvas3d plot option in 4.1.2 since it will make it
 easier to implement interactive 3d scenes in Sage and make them also
 display in browsers that do not support java. I modified the
 canvas3d_lib.js file so that it can also be used in a plain html page
 and works on the iPhone and in IE.

 A small hack also makes the view angle similar to the one for jmol
 (and the parameters have been adjusted to reduce the fisheye effect).

 A demo is at http://mathcs.chapman.edu/~jipsen/canvas/sage/

WOW!  I just tried that with my iPhone, and it is extremely impressive
seeing interactive 3d Sage graphics on the iPhone.  Very cool.


 and the js file can be downloaded from that page (put it in devel/sage/
 sage/server/notebook/templates and restart the server to try it out
 with sage-4.1.2.alpha).

 Is anyone working on rendering surfaces with shading over the
 wireframe?

No.  Is it possible?

 Also I noticed that the line(...) command does not seem to work with
 the canvas3d option.

Can you implement it?   It would be great if more work could be done
on this.   Bill Cauchois -- a UW undergrad -- did a short summer
project with me in which he implemented the current canvas rendering,
but I don't think he plans to do much more on it.

William

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[sage-devel] Sage component manuals

2009-09-25 Thread Kwankyu


Hi,

I thought of this idea. How about including the manuals (and/or
tutorials and/or references) of all (perhaps not all but almost all)
the (enduser) components of Sage into Sage? Or maintain a repository
site of all the manuals such that the user can access them easily from
the Sage notebook? If this is to violate the licenses of those
components, how about keeping all the links to the manuals along with
the Sage reference manual?

For example, I may use the Sage notebook to teach how to use latex to
students. Then it will be very convenient if I can bring up the latex
manual (or reference) right away.

This is a quick thought, so might be a crazy idea... Then please tell
me why it is not feasible.


Kwankyu
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[sage-devel] Re: prime_range problem


Hi,

On Sat, Sep 26, 2009 at 11:28 AM, kstueve kevin.stu...@gmail.com wrote:

SNIP

 from sage.rings.fast_arith import prime_range
 print prime_range(10^16,10^16+100)

Those two lines gave me a segfault on sage.math:

{{{[mv...@sage ~]$ sage
--
| Sage Version 4.1.1, Release Date: 2009-08-14   |
| Type notebook() for the GUI, and license() for information.|
--
sage: from sage.rings.fast_arith import prime_range
sage: print prime_range(10^16,10^16+100)
/usr/local/sage/local/bin/sage-sage: line 199:  9892 Segmentation
fault  sage-ipython $@ -i
}}}

By all means, please open a ticket to address this issue.

-- 
Regards
Minh Van Nguyen

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[sage-devel] Re: Sage component manuals


On Fri, Sep 25, 2009 at 6:45 PM, Kwankyu ekwan...@gmail.com wrote:

 Hi,

 I thought of this idea. How about including the manuals (and/or
 tutorials and/or references) of all (perhaps not all but almost all)
 the (enduser) components of Sage into Sage? Or maintain a repository
 site of all the manuals such that the user can access them easily from
 the Sage notebook? If this is to violate the licenses of those
 components, how about keeping all the links to the manuals along with
 the Sage reference manual?

 For example, I may use the Sage notebook to teach how to use latex to
 students. Then it will be very convenient if I can bring up the latex
 manual (or reference) right away.

 This is a quick thought, so might be a crazy idea... Then please tell
 me why it is not feasible.

It is totally feasible.  It hasn't happened only because nobody has
done it.   I think the only good reasonable longterm way to do this
would be to modify the spkg-install for each and every package so that
it installs documentation for that package into
$SAGE_LOCAL/doc/pkgname.   This way when one upgrades a package, one
will also upgrade the corresponding docs.   We would not require that
doc be built from source though.   An extra advantage of this approach
is that you can start small -- just start with a single spkg and work
your way to others over time.

The other approach is for one person to just try to download random
docs from all over the web for every component of Sage.  This has
happened before, and it results in a massive spkg, which is
immediately out of date, and nobody maintains.  Here's the last such
instance:

http://sagemath.org/packages/optional/extra_docs-20070208.spkg

 -- William

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[sage-devel] Re: canvas3d_lib.js extended to work on iPhone, IE


Peter wrote:
 Hi,
 
 I really like the canvas3d plot option in 4.1.2 since it will make it
 easier to implement interactive 3d scenes in Sage and make them also
 display in browsers that do not support java. I modified the
 canvas3d_lib.js file so that it can also be used in a plain html page
 and works on the iPhone and in IE.
 
 A small hack also makes the view angle similar to the one for jmol
 (and the parameters have been adjusted to reduce the fisheye effect).
 
 A demo is at http://mathcs.chapman.edu/~jipsen/canvas/sage/


I am curious about how smooth it is on the iPhone.  For me (Firefox 3.5, 
ubuntu 9.04, with a P4 3.2Ghz), it's pretty jerky, often lagging by at 
around half a second.

That said, this is *very* impressive.  I'm really excited about the 
possibilities!

Thanks,

Jason

-- 
Jason Grout


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[sage-devel] Re: canvas3d_lib.js extended to work on iPhone, IE

2009-09-25 Thread Tim Lahey



On Sep 25, 2009, at 10:20 PM, Jason Grout wrote:

 I am curious about how smooth it is on the iPhone.  For me (Firefox  
 3.5,
 ubuntu 9.04, with a P4 3.2Ghz), it's pretty jerky, often lagging by at
 around half a second.

 That said, this is *very* impressive.  I'm really excited about the
 possibilities!


On my 2.1GHz MacBook it is perfectly smooth in Safari. Maybe it's a  
difference
of Javascript engines?

---
Tim Lahey
PhD Candidate, Systems Design Engineering
University of Waterloo
http://www.linkedin.com/in/timlahey


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[sage-devel] svg


When browsing through the abstracts here:

http://www.svgopen.org/2009/registration.php?section=abstracts_and_proceedings

I found a couple of cool things that people might be interested in:

  * A web-based interactive SVG geometry editor: 
http://boar.cs.kent.edu/geosite/

  * jsxgraph (I believe this may have come up before): which may allow 
us support @interact-like sliders and things in the svg graph: 
http://jsxgraph.uni-bayreuth.de/wiki/index.php/Lissajous_curves

   (jsxgraph also does geometry, apparently)

Jason


-- 
Jason Grout


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[sage-devel] Re: canvas3d_lib.js extended to work on iPhone, IE


Tim Lahey wrote:
 
 On Sep 25, 2009, at 10:20 PM, Jason Grout wrote:
 
 I am curious about how smooth it is on the iPhone.  For me (Firefox  
 3.5,
 ubuntu 9.04, with a P4 3.2Ghz), it's pretty jerky, often lagging by at
 around half a second.

 That said, this is *very* impressive.  I'm really excited about the
 possibilities!
 
 
 On my 2.1GHz MacBook it is perfectly smooth in Safari. Maybe it's a  
 difference
 of Javascript engines?
 

I just tried it in the Chromium daily build for ubuntu and it's as 
smooth as butter, so I guess you're right.

Jason



-- 
Jason Grout


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[sage-devel] Re: Sage component manuals

2009-09-25 Thread Kwankyu



 It is totally feasible.  It hasn't happened only because nobody has
 done it.   I think the only good reasonable longterm way to do this
 would be to modify the spkg-install for each and every package so that
 it installs documentation for that package into
 $SAGE_LOCAL/doc/pkgname.   This way when one upgrades a package, one
 will also upgrade the corresponding docs.   We would not require that
 doc be built from source though.   An extra advantage of this approach
 is that you can start small -- just start with a single spkg and work
 your way to others over time.


+1 to this approach. First thing to do will be to modify the developer
manual to insist the spkg maintainers to install the documentation as
well as the package itself.
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[sage-devel] Re: prime_range problem

2009-09-25 Thread kstueve


I opened ticket #7017.
Kevin Stueve

On Sep 25, 7:05 pm, Minh Nguyen nguyenmi...@gmail.com wrote:
 Hi,

 On Sat, Sep 26, 2009 at 11:28 AM, kstueve kevin.stu...@gmail.com wrote:

 SNIP

  from sage.rings.fast_arith import prime_range
  print prime_range(10^16,10^16+100)

 Those two lines gave me a segfault on sage.math:

 {{{[mv...@sage ~]$ sage
 --
 | Sage Version 4.1.1, Release Date: 2009-08-14                       |
 | Type notebook() for the GUI, and license() for information.        |
 --
 sage: from sage.rings.fast_arith import prime_range
 sage: print prime_range(10^16,10^16+100)
 /usr/local/sage/local/bin/sage-sage: line 199:  9892 Segmentation
 fault      sage-ipython $@ -i

 }}}

 By all means, please open a ticket to address this issue.

 --
 Regards
 Minh Van Nguyen
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[sage-devel] Re: canvas3d_lib.js extended to work on iPhone, IE


Peter wrote:
 Is anyone working on rendering surfaces with shading over the
 wireframe?

Is it practical to adapt the Pre3d library

http://deanm.github.com/pre3d/

?  For what it's worth, I've usually found that Chromium 4 renders more
quickly than Firefox 3.5.3.  But this is purely subjective.


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[sage-devel] Re: Graph layout, graphviz, and dot2tex


Nicolas M. Thiery wrote:
 On Fri, Sep 25, 2009 at 06:22:07AM -0700, Pat LeSmithe wrote:
 Nicolas M. Thiery wrote:
 Ah, by the way, a question for spkg experts: the current dot2tex spkg
 I built contains two separate python modules, pyparsing and dot2tex,
 the later depending on the former. Should there be two spkg's instead?
 Is it possible to state the dependency so that users could just do
 sage -i dot2tex... and get both installed, or at leave have a useful
 error message?
 I'm not an expert, but in case it helps:  It seems that pyparsing is
 already included with matplotlib.  However, the import statement needs
 to be qualified:

 sage: import matplotlib.pyparsing
 
 Ah ah, thanks much for the pointer! That will make things simpler
 indeed.
 
 Any better suggestion than to include a patch in dot2tex's spkg to fix
 the imports?

That may be simplest.  There appear to be just three lines to modify, in

dot2tex/dotparsing.py

But I'm not sure about setup.py.  Perhaps an expert can clarify?


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[sage-devel] Re: canvas3d_lib.js extended to work on iPhone, IE

2009-09-25 Thread Tim Lahey


On 2009-09-25, at 11:36 PM, Pat LeSmithe qed...@gmail.com wrote:


 Peter wrote:
 Is anyone working on rendering surfaces with shading over the
 wireframe?

 Is it practical to adapt the Pre3d library

 http://deanm.github.com/pre3d/


It doesn't seem to work on the iPod, though which is a nice advantage  
to this Canvas version.

Cheers,

Tim.

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[sage-devel] parametric_plot and variable ranges


Currently, the following works:

var('t')
parametric_plot((t,t^2), 0, 2)

since things are just passed to plot, and plot accepts a variable range 
as just two arguments, rather insisting that they be in a tuple.

However, the following doesn't work:

parametric_plot((t,t^2,t^3), 0, 2)

since parametric_plot3d insists that its variable ranges be specified as 
tuples, like (0, 2).

In a refactoring of some of the plotting code on #7008, I made it so 
that the first example is deprecated, so now someone would instead have 
to do:

parametric_plot((t,t^2), (0,2))

or

parametric_plot((t,t^2), (t,0,2))

Is there anyone opposed to this deprecation?


Thanks,

Jason

-- 
Jason Grout


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[sage-devel] Re: #sage-devel log