[sage-support] Re: how to use the Sage interface to CoCoA?

[mabshoff]

On Nov 7, 3:47 pm, Sébastien Labbé [EMAIL PROTECTED] wrote:
 Bonjour,

Hi Sébastien,

 This semester, I have a course on Computative Algebra and we are given
 exercices using CoCoA. I installed it and I don't really like the interface.
 Although, cocoa is not mentionned in 14. Interpreter
 Interfaceshttp://www.sagemath.org/doc/ref/node95.htmlof the
 *Sage* Reference Manual, I have seen that the file
 sage/interfaces/cocoa.py
 exists. But nothing of cocoa.py is imported in the file
 sage/interfaces/all.py .
 What should I do so that I can open a cocoa console in sage ? I would be
 happy to have an answer before November 11th, because I will give a
 presentation on sage that day to the teacher and the other students in the
 course mentionned above.

Unfortunately there interface never worked and it has actually been
discussed removing that file since it is non-functional for now. One
issue is that the separator in CoCoA does not work very well and that
there is no input prompt.

 Merci beaucoup,

 Sébastien, UQAM

Cheers,

Michael
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[sage-support] Re: Porting Sage to AIX

[mabshoff]

On Nov 6, 3:18 pm, Sameer [EMAIL PROTECTED] wrote:
 Hi Michael,

Hi Sameer,

    ParaTools, Inc. has ported SAGE successfully to AIX! We had to
 rebuild the library and debug it further
 but now I can say: set path=($PET_HOME/pkgs/sage-3.1.1 $path)
  sage

 --
 | SAGE Version 3.1.1, Release Date: 2008-08-17                       |
 | Type notebook() for the GUI, and license() for information.        |
 --

Excellent!

 sage: import numpy
 sage: numpy.test()
 Numpy is installed in /usr/local/PET/pkgs/sage-3.1.1/local/lib/
 python2.5/site-packages/numpy
 Numpy version 1.0.4
 Python version 2.5.2 (r252:60911, Oct 18 2008, 03:31:49) [GCC 4.2.1]
   Found 10/10 tests for numpy.core.defmatrix
   Found 36/36 tests for numpy.core.ma
   Found 223/223 tests for numpy.core.multiarray
   Found 65/65 tests for numpy.core.numeric
   Found 31/31 tests for numpy.core.numerictypes
   Found 12/12 tests for numpy.core.records
   Found 6/6 tests for numpy.core.scalarmath
   Found 14/14 tests for numpy.core.umath
   Found 4/4 tests for numpy.ctypeslib
   Found 5/5 tests for numpy.distutils.misc_util
   Found 1/1 tests for numpy.fft.fftpack
   Found 3/3 tests for numpy.fft.helper
   Found 9/9 tests for numpy.lib.arraysetops
   Found 46/46 tests for numpy.lib.function_base
   Found 5/5 tests for numpy.lib.getlimits
   Found 4/4 tests for numpy.lib.index_tricks
   Found 3/3 tests for numpy.lib.polynomial
   Found 49/49 tests for numpy.lib.shape_base
   Found 15/15 tests for numpy.lib.twodim_base
   Found 43/43 tests for numpy.lib.type_check
   Found 1/1 tests for numpy.lib.ufunclike
   Found 40/40 tests for numpy.linalg
   Found 2/2 tests for numpy.random
   Found 0/0 tests for __main__
 ... 
 ... 
 ... 
 ... 
 ... 
 ... 
 ... 
 ... 
 ... 
 .
 --
 Ran 680 tests in 1.228s

 OK
 unittest._TextTestResult run=680 errors=0 failures=0
 sage: integrate(tan(x),x)
 log(sec(x))
 sage: a = matrix(ZZ, 10, 4, [randint(0,1) for _ in xrange(40)]); a

 [0 1 1 0]
 [1 0 0 0]
 [0 0 1 1]
 [0 0 0 0]
 [1 0 1 1]
 [1 0 1 1]
 [1 1 0 1]
 [1 1 0 0]
 [0 1 0 1]
 [0 1 0 0]
 sage: list(AllExactCovers(a))

 [[(0, 0, 1, 1), (1, 0, 0, 0), (0, 1, 0, 0)],
  [(0, 0, 1, 1), (1, 1, 0, 0)],
  [(1, 0, 1, 1), (0, 1, 0, 0)],
  [(1, 0, 1, 1), (0, 1, 0, 0)]]
 sage: 22+32
 54
 sage: 3/4+1/6
 11/12
 sage:
 Exiting SAGE (CPU time 0m1.86s, Wall time 1m28.08s).
 Exiting spawned Maxima process.

  uname -a

 AIX  3 5 002B912C4C00

 The last error was resolved by printing the type of the object that
 was of type pari.gen. When we
 rebuilt that library by hand and the dependencies, it worked.

Interesting.

  I should
 also add (for the list) that we had to
 build clisp and gap in 32 bits

Ok, that should not be a problem. It would be nice to have GAP work in
64 bit mode, but that can be sorted out later. We will dumb clisp for
ecl in the future anyway, so I would not worry too much there. The ecl
maintainer does not support AIX yet due to lack of access, but a port
should be little work since it practically runs on everything.

  and change gap.py to use a fixed big
 number for the file descriptors as the max
 fileno from getrusage was not working properly in AIX. This change
 fixed pexpect.

Nice.

 Thanks a lot for your help! I look forward to discussing these issues
 and help with
 documenting this at the SD 11 with you.

Cool. Hopefully William will get access to that AIX cluster soon so
that we can start merging back fixes sooner than that.

It would be very helpful if you could post patches and notes to the
Wiki page. The output from make check would also be helpful. It
might happen that it hangs at some point in which case a CTRL-C or a
manual kill of the current doctest would get you past that. I would be
*very* interested in how that works out.

One bug you certainly have to fix is get_memory_usage() since that one
requires support for AIX to be added. There are likely other places
where you might run into trouble. Unfortunately getting Sage to build
up and start is only half of the battle since making it pass its test
suite can be a lot of work. For example the Solaris port has been
building more or less out of the box for 

[sage-support] Re: Error with LinearCode()

[mabshoff]

On Nov 5, 1:40 pm, cesarnda [EMAIL PROTECTED] wrote:
 I do the following:

 sage: MS = MatrixSpace(GF(2), 4,7)
 sage: G = MS([[1,1,1,0,0,0,0], [1,0,0,1,1,0,0], [0,1,0,1,0,1,0],
 [1,1,0,1,0,0,1]])
 sage: C = LinearCode(G)

 and I get:

 /home/carlos/sage-3.0.2-ubuntu32-intel-i686-Linux/local/bin/sage-sage:
 line 348:  1703 Instrucción ilegal     python $@

 and then it stops working.

 I have already upgraded to 3.1.4 and I didn't have that problem
 before :-s

 is there a way to solve this or do I have to upgrade again??

Hi,

see http://wiki.sagemath.org/faq and search for illegal instruction.
I would guess you are running a binary - or at least upgraded from
one.

Cheers,

Michael
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[sage-support] Re: Memory overflow workaround?

[mabshoff]

On Nov 3, 9:13 am, John Cremona [EMAIL PROTECTED] wrote:
 Does this help you:

 Suppose (for a toy example) I have defined a Python function like this:
 sage: def f(M):
 :         d = M.det()
 :     return d

 And I have a file called testin.sage containing a large number of
 lines like this:

 [[1,2],[3,4]]
 [[5,6],[7,8]]
 [[1,2],[3,4]]
 [[5,6],[7,8]]
 [[1,2],[3,4]]
 [[5,6],[7,8]]

 Then from the command line I can do this:

 sage: for l in open(/home/masgaj/testin.sage):
     print(f(Matrix(eval(l

 and what I see is this:
 -2
 -2
 -2
 -2
 -2
 -2

 As far as I know Python only reads the lines in the file one at at
 time, and returns each as a string (hence the eval()), which you can
 do what you like with.

 I did something similar when I wanted to process a million elliptic
 curves without reading them all in at once.

 John

Yep, the load is the expensive operation:

[EMAIL PROTECTED]:/scratch/mabshoff/release-cycle/sage-3.1.3.final$ ./sage
--
| Sage Version 3.2.alpha2, Release Date: 2008-10-31  |
| Type notebook() for the GUI, and license() for information.|
--

sage: time load SPOCs.sage
 CPU times: user 67.46 s, sys: 8.94 s, total: 76.40 s
Wall time: 76.59 s
sage:  get_memory_usage()
3700.5625
sage: time save (SPOC,'SPOCs.sobj')
CPU times: user 17.63 s, sys: 0.08 s, total: 17.71 s
Wall time: 17.71 s
sage:  get_memory_usage()
3700.5625
sage:
Exiting SAGE (CPU time 7m27.07s, Wall time 18m2.26s).


[EMAIL PROTECTED]:/scratch/mabshoff/release-cycle/sage-3.1.3.final$ ./sage
--
| Sage Version 3.2.alpha2, Release Date: 2008-10-31  |
| Type notebook() for the GUI, and license() for information.|
--

sage: time load('SPOCs.sobj')

CPU times: user 7.10 s, sys: 0.60 s, total: 7.70 s
Wall time: 7.70 s

What is off is that according to top the load operation took about 600
seconds CPU time, so where is the time going?

Cheers,

Michael
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[sage-support] Re: Memory overflow workaround?

[mabshoff]

On Nov 3, 9:35 am, mabshoff [EMAIL PROTECTED]
dortmund.de wrote:
 On Nov 3, 9:13 am, John Cremona [EMAIL PROTECTED] wrote:



  Does this help you:

  Suppose (for a toy example) I have defined a Python function like this:
  sage: def f(M):
  :         d = M.det()
  :     return d

  And I have a file called testin.sage containing a large number of
  lines like this:

  [[1,2],[3,4]]
  [[5,6],[7,8]]
  [[1,2],[3,4]]
  [[5,6],[7,8]]
  [[1,2],[3,4]]
  [[5,6],[7,8]]

  Then from the command line I can do this:

  sage: for l in open(/home/masgaj/testin.sage):
      print(f(Matrix(eval(l

  and what I see is this:
  -2
  -2
  -2
  -2
  -2
  -2

  As far as I know Python only reads the lines in the file one at at
  time, and returns each as a string (hence the eval()), which you can
  do what you like with.

  I did something similar when I wanted to process a million elliptic
  curves without reading them all in at once.

  John

 Yep, the load is the expensive operation:

 [EMAIL PROTECTED]:/scratch/mabshoff/release-cycle/sage-3.1.3.final$ ./sage
 --
 | Sage Version 3.2.alpha2, Release Date: 2008-10-31                  |
 | Type notebook() for the GUI, and license() for information.        |
 --

 sage: time load SPOCs.sage
  CPU times: user 67.46 s, sys: 8.94 s, total: 76.40 s
 Wall time: 76.59 s
 sage:  get_memory_usage()
 3700.5625
 sage: time save (SPOC,'SPOCs.sobj')
 CPU times: user 17.63 s, sys: 0.08 s, total: 17.71 s
 Wall time: 17.71 s
 sage:  get_memory_usage()
 3700.5625
 sage:
 Exiting SAGE (CPU time 7m27.07s, Wall time 18m2.26s).

 [EMAIL PROTECTED]:/scratch/mabshoff/release-cycle/sage-3.1.3.final$ ./sage
 --
 | Sage Version 3.2.alpha2, Release Date: 2008-10-31                  |
 | Type notebook() for the GUI, and license() for information.        |
 --

 sage: time load('SPOCs.sobj')

 CPU times: user 7.10 s, sys: 0.60 s, total: 7.70 s
 Wall time: 7.70 s

 What is off is that according to top the load operation took about 600
 seconds CPU time, so where is the time going?

Since the above is ambiguous I meant the first load, i.e. the time
load SPOCs.sage.

When one does load the SPOCs.sobj one should also assign the result to
some variable to be not treated to all the matrixes just read in
scrolling by on the scree :)

Cheers,

Michael
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[sage-support] Re: running sage on port 80 - is it possible?

[mabshoff]

On Nov 3, 3:10 am, [EMAIL PROTECTED] [EMAIL PROTECTED] wrote:
 Dear sage gurus, I am trying to run sage on port 80 instead of default
 8000 (I have a virtual server with sage for our PC lab which is behind
 firewall and we cannot forward ports 8000)

 apache, which has default 80 is at 81 or not running.

 If I start notebook by
 notebook(address='', port=8000, accounts=True)
 notebook starts, but when trying
 notebook(address='', port=80, accounts=True)
 I get the following error (se below)

 The same if I try ports like 800, 98 etc. On the other hand, ports
 like 8001 or 8005 work fine. I think that the problem is with
 permissions. Is there any chance to run sage under user account on
 port 80?

Any port up to and including port 1000 requires root privileges to
open on Linux (same on OSX and Unix by the way). So in order to work
you either need to sudo or run Sage as root - both options I would
highly discourage.

 Thank you. Robert Marik.

Cheers,

Michael
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[sage-support] Re: Porting Sage to AIX

[mabshoff]

On Nov 3, 6:39 pm, Sameer [EMAIL PROTECTED] wrote:
 Michael, William,

Hi Sameer,

good that we are back on the list again.

    Here is an update on AIX. I found why sage startup was crashing in
 real_mpfi.so. I rebuilt libmpfi.so and recompiled real_mpfi.pyx and
 complex_double.pyx. The illegal instruction error was due to an error
 in building libmpfi.so caused by arguments given by libtool. By
 testing with the supplied testcases I was able to narrow it down.

Ok, can you give some details what had to be changed?

 Also, for the list, I edited sage/rings/polynomial/
 mult_polynomial_libsingular.pyx and replaced the arguments to dlopen
 call to

 handle = dlopen(lib, 65536+4);

 It was using 256+1 earlier (RTLD_GLOBAL  | RTLD_LAZY). These values
 are defined differently in AIX's dlfcn.h as shown above.

This will be fixed in Sage 3.2 and a patch is at
http://trac.sagemath.org/sage_trac/ticket/4427

 Now I am running into another error: 
 /usr/local/PET/src/build/sage-3.1.1/local/lib/python2.5/site-packages/sage/ 
 matrix/matrix_space.py(38)module()

 - import matrix_modn_dense
 (Pdb) s
 --Call-- 
 /usr/local/PET/src/build/sage-3.1.1/local/lib/python2.5/site-packages/sage/ 
 libs/linbox/__init__.py(1)module()
 (Pdb) s
  /usr/local/PET/src/build/sage-3.1.1/local/lib/python2.5/site-packages/sage/ 
  libs/linbox/__init__.py(1)module()

 (Pdb) s
 --Return-- 
 /usr/local/PET/src/build/sage-3.1.1/local/lib/python2.5/site-packages/sage/ 
 libs/linbox/__init__.py(1)module()-None

 (Pdb) s
 /usr/local/PET/src/build/sage-3.1.1/local/bin/sage-sage: line 226:
 28756 Illegal instruction     (core dumped) sage-ipython $@ -c
 $SAGE_STARTUP_COMMAND;

Ok, that could be the BLAS or something in LinBox itself.  How did you
build ATLAS?

 I checked the __init__.py file and it has 0 bytes: ls -lt /usr/local/
 PET/src/build/sage-3.1.1/local/lib/python2.5/site-packages/sage/libs/
 linbox/__init__.py
 -rw-r-    1 sameer                 0 Dec 20 2007  /usr/local/PET/
 src/build/sage-3.1.1/local/lib/python2.5/site-packages/sage/libs/
 linbox/__init__.py

 Is this normal?

That should be ok, all that is required is that file to exist IRC.

  I think there may be another library (linbox) that
 probably needs to be rebuilt, but what I was wondering if this null
 init.py file is designed to be this way or if it is just an error in
 my installation. I think the illegal instruction probably points to an
 incorrectly installed liblinbox.so on which linbox.so is based, but I
 thought I would check with you.

You should get a svn checkout of LinBox and run make check - in Sage
we patch the commentator and that breaks make check. Should LinBox
pass its make check we can keep on digging.

 Thanks!
 - Sameer

Cheers,

Michael
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[sage-support] Re: Porting Sage to AIX

[mabshoff]

On Nov 3, 7:04 pm, Sameer [EMAIL PROTECTED] wrote:
 Hi Michael,     Here is an update on AIX. I found why sage startup was 
 crashing in
   real_mpfi.so. I rebuilt libmpfi.so and recompiled real_mpfi.pyx and
   complex_double.pyx. The illegal instruction error was due to an error
   in building libmpfi.so caused by arguments given by libtool. By
   testing with the supplied testcases I was able to narrow it down.

  Ok, can you give some details what had to be changed?

 I just did a manual:

 % cd spkg/build; cp -r mpfi* mympfi (the package builds without error
 and deletes the sources, so it is important to copy it midway while it
 is building);

Yes. Just run ./sage -sh, then cd into spkg/standard, tar xjf
foo.spkg, cd into foo and run ./spkg-install.

 % cd mympfi; make;
 % gcc -shared -o libmpfi.so ../src/.libs/*.o -L/usr/local/PET/src/
 build/sage-3.1.1/local/lib -lmpfr -lgmp
 cp libmpfi $SAGE_LOCAL/lib

 and tested with the tests/test_mpfi to make sure it didn't crash with
 the illegal instruction.

Ok, but why would a static library crash?

SNIP

 Thanks I will rebuild it!
 - Sameer

Cheers,

Michael
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[sage-support] Re: permissions in sage

[mabshoff]

On Nov 2, 9:24 am, William Stein [EMAIL PROTECTED] wrote:
 On Sun, Nov 2, 2008 at 10:23 AM, William Stein [EMAIL PROTECTED] wrote:
  On Sun, Nov 2, 2008 at 7:38 AM, Kevin Buzzard [EMAIL PROTECTED] wrote:
  I'm still unclear about the philosophy of permissions.

  I downloaded sage 3.1.4 source and compiled from source. As root. Into
  /usr/local. Because I wasn't sure how to make the installation global.

  And today I tried (as a non-root user)

  sage: magma('sqrt(2)')

  [yes, I know it should be Sqrt but I'm guessing that isn't the problem]

 I've made this trac ticket #4424:

 http://trac.sagemath.org/sage_trac/ticket/4424

Are you talking about the sig files? They seem to be ASCII, so the
issue is easy enough to fix, but I consider it ridiculous that a 15+
year old software package needs write permissions in the same
directory as a source file to read it.

SNIP

Cheers,

Michael

  William

 --
 William Stein
 Associate Professor of Mathematics
 University of Washingtonhttp://wstein.org
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[sage-support] Re: permissions in sage

[mabshoff]

On Nov 2, 9:45 am, William Stein [EMAIL PROTECTED] wrote:
 On Sun, Nov 2, 2008 at 9:32 AM, mabshoff

SNIP

  Are you talking about the sig files? They seem to be ASCII, so the
  issue is easy enough to fix,

 Yes, and that's the fix.

Ok, I attached each .m file into Magma and then checked all .sig files
into the extcode repo. Patch is up at #4424 for someone's reviewing
pleasure :)

  but I consider it ridiculous that a 15+
  year old software package needs write permissions in the same
  directory as a source file to read it.

 True.  Fix it and send them a patch...  Oh wait, they currently have a
 lame development model that makes that impossible.

:)

Cheers,

Michael
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[sage-support] Re: permissions in sage

[mabshoff]

On Nov 2, 11:35 am, William Stein [EMAIL PROTECTED] wrote:
 On Sun, Nov 2, 2008 at 10:02 AM, mabshoff



 [EMAIL PROTECTED] wrote:

  On Nov 2, 9:45 am, William Stein [EMAIL PROTECTED] wrote:
  On Sun, Nov 2, 2008 at 9:32 AM, mabshoff

  SNIP

   Are you talking about the sig files? They seem to be ASCII, so the
   issue is easy enough to fix,

  Yes, and that's the fix.

  Ok, I attached each .m file into Magma and then checked all .sig files
  into the extcode repo. Patch is up at #4424 for someone's reviewing
  pleasure :)

 Unfortunately, this doesn't work.  I have changed it to wontfix, and
 posted the following message on the ticket:

 Unfortunately, this doesn't work.  Probably the .sig files depend on
 the version of Magma.

Sigh, I was afraid that that might happen.

  I tried applying your patch and got then using
 it as a different user and got:

 {{{
 Runtime error in 'AttachSpec': Could not remove the invalid signature
 file /Users/wstein/sage/data/extcode//magma/latex/latex.sig

 }}}

 Since there are dozens of Magma versions out there, and we can't know
 which one people are using, there is literally *no possible way* to
 solve this problem without the user running a command such as
 {{{
 sage: magma('2')}}}

 as a user with write permissions to the extcode/magma directory.

 Since the error message clearly states that this is a permissions
 problem, there is nothing further to do really (i.e., nothing on the
 sage side).  This is just the way Magma works.


Ok, how about a script for the extcode.spkg that attaches each file to
a Magma session in case Magma is installed on the system?


   but I consider it ridiculous that a 15+
   year old software package needs write permissions in the same
   directory as a source file to read it.

  True.  Fix it and send them a patch...  Oh wait, they currently have a
  lame development model that makes that impossible.

  :)

  Cheers,

  Michael

 --
 William Stein
 Associate Professor of Mathematics
 University of Washingtonhttp://wstein.org
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[sage-support] Re: permissions in sage

[mabshoff]

On Nov 2, 11:46 am, William Stein [EMAIL PROTECTED] wrote:
 On Sun, Nov 2, 2008 at 11:39 AM, mabshoff

SNIP

  Ok, how about a script for the extcode.spkg that attaches each file to
  a Magma session in case Magma is installed on the system?

 If we do that, somebody else will complain just as much or more
 about Sage starting up and running Magma as root, or something.

We can't make everybody happy I guess :)

 It could be done though.  And it wouldn't require attaching each file -- all
 you have to do is put this line in the spkg-install:

   sage -c magma('1')

 That will run magma, which automatically attaches *all* of the
 magma code and generates the sig files, or it will go boom
 and give an error if there is no magma installed.

Nope, it doesn't:

[EMAIL PROTECTED]:/scratch/mabshoff/release-cycle/sage-3.2.alpha3$ ./sage -
c magma('1')
[EMAIL PROTECTED]:/scratch/mabshoff/release-cycle/sage-3.2.alpha3$ find
data/extcode/ -name *.sig
data/extcode/magma/sage/basic.sig
data/extcode/magma/latex/latex.sig
[EMAIL PROTECTED]:/scratch/mabshoff/release-cycle/sage-3.2.alpha3

Only two out of the 12 Magma files in the data/extcode/magma directory
were loaded. Even when running all optional doctest only four or five
Magma files out of 12 are loaded.

 I'm not sure if we should do this though, since I recall getting numerous
 complaints over the years from people about Sage starting up and
 running as root do stuff during the install process, but I've never
 once before seen the complaint about magma and permissions that
 resulted in #4424.  I'm guessing that people typically know precisely
 what to do in the situation of #4424 so that's what it isn't a problem
 (in fact, the reporter of #4424 knew precisely what to do).

 It's your call whether to add

      sage -c magma('1')

 to the spkg-install for extcode.

I don't care either way. Easiest would probably be to add an entry in
the FAQ for now and if people hit this problem regularly maybe we
should attempt to solve this problem again.

  -- William

Cheers,

Michael
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[sage-support] Re: permissions in sage

[mabshoff]

On Nov 2, 12:03 pm, William Stein [EMAIL PROTECTED] wrote:
 On Sun, Nov 2, 2008 at 11:52 AM, mabshoff

SNIP

  Only two out of the 12 Magma files in the data/extcode/magma directory
  were loaded. Even when running all optional doctest only four or five
  Magma files out of 12 are loaded.

 Intriguing. So there must be a lot of cruft in data/extcode/magma.
 I'll look into it.

I guess we are then in for a crapectomy:

data/extcode/magma/ell_padic/padic_height.m
data/extcode/magma/ell_padic/gl2.m
data/extcode/magma/ell_padic/examples.m
data/extcode/magma/ell_padic/kedlaya.m
data/extcode/magma/ell_padic/shark.m
data/extcode/magma/ell_padic/myl.m
data/extcode/magma/padic_height/padic_height.m
data/extcode/magma/padic_height/kedlaya.m
data/extcode/magma/stoll/3descent.m
data/extcode/magma/sage/basic.m
data/extcode/magma/user/foo.m
data/extcode/magma/latex/latex.m


  I don't care either way. Easiest would probably be to add an entry in
  the FAQ for now and if people hit this problem regularly maybe we
  should attempt to solve this problem again.

 That's an excellent suggestion.  If it comes up more, we'll make the
 change you suggested.

+1

 William

Since we are talking about Magma and Sage: I am still waiting on the
mistakenly not attached patch for #4395 - it fixes two file when
optional doctests are run :)

Cheers,

Michael
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[sage-support] Re: Memory overflow workaround?

[mabshoff]

On Nov 2, 2:12 pm, Daniel Allcock [EMAIL PROTECTED] wrote:

Hi Daniel,

 Hi all, just got started with SAGE and I hope someone has a suggestion
 for me.  I have a .sage file defining a big list of approx 170,000 4x4
 matrices with rational number entries, which I will want SAGE to do
 various things to.  It takes SAGE 4-5 minutes to read in the file
 (which was produced by a C++ program), and surely this can be
 improved.

Probably.

 I assumed that loading it into memory and then writing it to a .sobj
 file would give me something more manageable.  But I get memory
 allocation errors:

 python(2102) malloc: *** vm_allocate(size=8421376) failed (error
 code=3)
 python(2102) malloc: *** error: can't allocate region
 python(2102) malloc: *** set a breakpoint in szone_error to debug

 Presumably the system has just run out of memory.  This surprises me
 since the .sage file is only 12MB, and the .py file it creates is
 37MB.  The matrix entries are all small, numerators 10,000 and
 denominators  200 or so. I'm working on a MacBook Pro with 2GB RAM,
 and the machine didn't have any other substantial load.

 I will need only one matrix at a time, so there should be no need to
 load in all of them at once.  But poking around in SAGE and python
 docs hasn't shown me any simple way to, say, read in and execute a
 single line from some file.

 Thanks for your help,
 Daniel

Which version of Sage do you run?

Can you post the code so I can attempt to reproduce the problem?

Cheers,

Michael
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[sage-support] Re: Ubuntu 8.10

[mabshoff]

On Oct 30, 10:00 am, davedo2 [EMAIL PROTECTED] wrote:
 The install doc says that install from source isn't yet working with
 gcc 4.3.0.
 However, the version of gcc installed with Ubuntu 8.10 is 4.3.1 - is
 this still a problem?

Nope, gcc 4.3.x works and I will fix the README.txt or where ever that
info is today.

gcc 4.4.CVS doesn't work yet, but I have the eight spkg fixes ready to
go at some point.

Cheers,

Michael
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[sage-support] Re: Ubuntu 8.10

[mabshoff]

On Oct 30, 10:02 am, mabshoff [EMAIL PROTECTED]
dortmund.de wrote:
 On Oct 30, 10:00 am, davedo2 [EMAIL PROTECTED] wrote:

  The install doc says that install from source isn't yet working with
  gcc 4.3.0.
  However, the version of gcc installed with Ubuntu 8.10 is 4.3.1 - is
  this still a problem?

 Nope, gcc 4.3.x works and I will fix the README.txt or where ever that
 info is today.

Can someone point me toward the place in the documentation where such
a claim is made?

Cheers,

Michael
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[sage-support] Re: Ubuntu 8.10

[mabshoff]

On Oct 30, 10:56 am, Jaap Spies [EMAIL PROTECTED] wrote:
 mabshoff wrote:

SNIP

  Can someone point me toward the place in the documentation where such
  a claim is made?

 http://www.sagemath.org/doc/inst/node5.html

 Almost at the bottom of the page.

Thanks Jaap, this is now #4403.

 Jaap

Cheers,

Michael
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[sage-support] Re: How to detect memory leaks?

[mabshoff]

On Oct 29, 2:28 am, Simon King [EMAIL PROTECTED] wrote:
 Dear Michael,

 On 28 Okt., 15:27, mabshoff [EMAIL PROTECTED]

 dortmund.de wrote:
  Can you come up with some simple Cython code using libSingular that
  shows the same behavior, i.e. the more simple the better. This would
  help me potentially hunt down the cause.

Hi Simon,

 Your wish is my command...

:)

 It is ticket #4380. It seems to me that the leak will be located in
 the `reduce` method of MPolynomial_libsingular.

*really* nice catch. I am testing the patch right now and it looks
like a positive review. Interestingly Guppy would not have caught the
memleak either since it is inside Singular, i.e. omalloc screws us
here. Hans once showed me some debug tricks to hunt for leaks via
omalloc, so if this turns out to be a harder problems than we thought
we might want to go that way. Just as I mentioned on the ticket if you
find anything else please open a new ticket since I want this patch to
go in and it seems to resolve the vast majority of the problem in your
code.

 Cheers
         Simon

Cheers,

Michael
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[sage-support] Re: newbie: latex and czech text

[mabshoff]

On Oct 29, 3:35 am, [EMAIL PROTECTED] [EMAIL PROTECTED] wrote:
 On 29 Říj, 11:31, [EMAIL PROTECTED] [EMAIL PROTECTED] wrote:


Hi R.M.,


  Is there any way to use accented letters in maxima Notebook?

 sorry, sage notebook, of course :)

We figured :)

 R.M.

Unfortunately this is a known and yet to be solved problem - see
http://trac.sagemath.org/sage_trac/ticket/1477

Cheers,

Michael
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[sage-support] Re: Porting Sage to AIX

[mabshoff]

On Oct 27, 10:42 pm, William Stein [EMAIL PROTECTED] wrote:
 On Mon, Oct 27, 2008 at 9:15 PM, Sameer [EMAIL PROTECTED] wrote:
  Hi,
     I am trying to port sage 3.1.1 to an IBM Power5 AIX system. After
  I install gap (in 32 bits), I get:

So how far did you get building Sage? If GAP is the problem it sounds
like you get next to the end.

From the error messages above it also seems like it could be a pexpect
issue. If GAP by itself starts up cleanly I would assume that the
problem is in pexpect.

 Just out of curiosity, is this a machine you could give some (any?)
 of the Sage developers accounts on?  We would love to officially
 support AIX.  So far, none of us have ever been able to get access to
 an AIX box.

+1

 William

Cheers,

Michael
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[sage-support] Re: problems with FriCAS interface

[mabshoff]

On Oct 28, 9:31 am, Martin Rubey [EMAIL PROTECTED] wrote:

Hi Martin,

 Bill Page [EMAIL PROTECTED] writes:
        Expect.__init__(self,
                        name = 'axiom',
                        prompt = '\([0-9]+\) - ',
                        command = sh -c 'axiom -nox -noclef | cat',

 Apart from modifying axiom.py, do I have to do anything else?  Compiling, 
 installing?

After changing axiom.py in the $SAGE_ROOT/devel/sage tree run ./sage -
b from $SAGE_ROOT. Note that you are changing the main Sage library
and that the repo then has outstanding uncommitted changes. Upgrading
such an install requires some understanding on hg.

 Martin

Cheers,

Michael
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[sage-support] Re: problems with FriCAS interface

[mabshoff]

On Oct 28, 9:55 am, Martin Rubey [EMAIL PROTECTED] wrote:

SNIP

  After changing axiom.py in the $SAGE_ROOT/devel/sage tree run ./sage -
  b from $SAGE_ROOT. Note that you are changing the main Sage library
  and that the repo then has outstanding uncommitted changes. Upgrading
  such an install requires some understanding on hg.

 Tried, doesn't fix the problem.

 thanks anyway.  Oh dear, there will be some more chaos tomorrow.

Judging from your post on fricas-devel you are using not the
fricas-1.0.3.spkg. Can you try installing it and see if that fixes the
problem? In my experience changing underlying lisps for example for
Maxima changes the behavior of Maxima enough to make certain doctests
fail.

 Martin

Cheers,

Michael
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[sage-support] Re: problems with FriCAS interface

[mabshoff]

On Oct 28, 10:06 am, Martin Rubey [EMAIL PROTECTED] wrote:
 mabshoff [EMAIL PROTECTED] writes:
  On Oct 28, 9:55 am, Martin Rubey [EMAIL PROTECTED] wrote:

  SNIP

After changing axiom.py in the $SAGE_ROOT/devel/sage tree run ./sage -
b from $SAGE_ROOT. Note that you are changing the main Sage library
and that the repo then has outstanding uncommitted changes. Upgrading
such an install requires some understanding on hg.

   Tried, doesn't fix the problem.

   thanks anyway.  Oh dear, there will be some more chaos tomorrow.

  Judging from your post on fricas-devel you are using not the
  fricas-1.0.3.spkg. Can you try installing it and see if that fixes the
  problem?

 Hm, not really.  For my students, it's a site wide installation (and I'm not
 root) and it was already quite an effort to get sage running in the first
 place.

All you need to do is

 ./sage -i fricas-1.0.3.p0

This doesn't touch anything outside $SAGE_ROOT. I really hope that you
aren't running sage as the root user, too.

  On my laptop, it's actually better to be close to my students
 installation.

Ok. As stated above the optinal fricas.spkg touches nothing and does
not interfere with any other FriCAS installed on the system.

 I guess I should have tested sage more thoroughly before embarking on this
 adventure.

 Still, many many thanks for your support,

No problem. Let us know if you run into any trouble.

 Martin

Cheers,

Michael
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[sage-support] Re: problems with FriCAS interface

[mabshoff]

On Oct 28, 10:23 am, Martin Rubey [EMAIL PROTECTED] wrote:
 mabshoff [EMAIL PROTECTED] writes:
   Hm, not really.  For my students, it's a site wide installation (and I'm 
   not
   root) and it was already quite an effort to get sage running in the first
   place.

  All you need to do is

   ./sage -i fricas-1.0.3.p0

  This doesn't touch anything outside $SAGE_ROOT. I really hope that you
  aren't running sage as the root user, too.

 Huh?  I said I'm not root.

Well, your above statement could be interpreted that you cannot change
anything about the Sage install since you are not root. Hence my
remark.

 [EMAIL PROTECTED]:~ sage -i fricas-1.0.3.p0
 Installing fricas-1.0.3.p0
 Calling sage-spkg on fricas-1.0.3.p0
 tee: ../install.log: Keine Berechtigung
 You must set the SAGE_ROOT environment variable or
 run this script from the SAGE_ROOT or
 SAGE_ROOT/local/bin/ directory.
 fricas-1.0.3.p0
 Machine:
 Linux rp17 2.6.18.8-0.10-default #1 SMP Wed Jun 4 15:46:34 UTC 2008 x86_64
 x86_64 x86_64 GNU/Linux
 Deleting directories from past builds of previous/current versions of
 fricas-1.0.3.p0
 /opt/local/sage-3.1.2/local/bin/sage-spkg: file fricas-1.0.3.p0 does not exist
 Attempting to download it.
 mkdir: kann Verzeichnis „optional“ nicht anlegen: Keine Berechtigung
 /opt/local/sage-3.1.2/local/bin/sage-spkg: line 164: cd: optional: Datei oder
 Verzeichnis nicht gefunden

You need to have write permission to the $SAGE_ROOT tree to install
any spkg.

 Martin

Cheers,

Michael
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[sage-support] Re: problems with FriCAS interface

[mabshoff]

On Oct 28, 10:44 am, Martin Rubey [EMAIL PROTECTED] wrote:
 mabshoff [EMAIL PROTECTED] writes:
  You need to have write permission to the $SAGE_ROOT tree to install
  any spkg.

 Would be really nice, if this could be changed in future.  Suppose university
 provides sage, but without package SupiDupi, which is really super trooper.
 Then I need to install all of sage again

Yep, it would be nice and has been suggested and discussed before. But
it can introduce a number of subtle bugs when several user install
various versions of the same package and so on. As is one cannot
develop with the Sage library in a multi user setting either [at
least not in an elegant way].

 Martin

Cheers,

Michael
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[sage-support] Re: radius of convergence and inequalities

[mabshoff]

On Oct 27, 9:19 am, Stan Schymanski [EMAIL PROTECTED] wrote:
 Actually, the qepcad distro is only made for Linux and Solaris, so I
 suppose we would need to put more effort into getting it compiled on a
 mac.
 mksysdep.pl only tries to get the architecture of the computer in
 order to call the appropriate install script, but there is no install
 script for a Mac, anyway. I saw that there are people that got it
 compiled on a mac, but only the older version of qepcad 
 (e.g.http://www.cl.cam.ac.uk/~lp15/papers/Arith/qepcad-for-mac.html).

 I think this is becoming way too complicated for me. Sorry!

This should be fairly trivial to fix - at least to make it compile. I
am curious why the above web page states that the code cannot work on
MacOSX/PPC.

 Stan

Cheers,

Michael
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[sage-support] Re: problem with installing packages

[mabshoff]

On Oct 27, 5:44 pm, nostart [EMAIL PROTECTED] wrote:
 Hello,

Hi,

 when I am trying to perform the commands
 sage -standard or -optional
 I get the error message

 Using SAGE 
 Serverhttp://www.sagemath.org//packageshttp://www.sagemath.org//packages/standard/list--
  /opt/sage-3.1.4-
 debian32-IntelXeon-x86-i686-Linux/tmp/list
 [Errno socket error] (-2, 'Name or service not known')

This looks like a name resolution error when Sage attempts to download
the current list of standard or optional packages. Can you resolve
www.sagemath.org from that computer? Are you using any http proxy or
anything like that?

 *** 
 *

 Error contactinghttp://www.sagemath.org//packages/standard/list. Try
 using an alternative server.
 For example, from the bash prompt try typing

    export SAGE_SERVER=http://sage.scipy.org/sage/

 then try again.

 *** 
 *

 I am using SAGE Version 3.1.4, Release Date: 2008-10-20
 on linux from binary.

 Any help would be appreciated.

Cheers,

Michael
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[sage-support] Re: Compile prblem on my laptop

[mabshoff]

Hi,

please don't post logs or excerpts from logs on the list, but put them
up somewhere and post a link.

In your case the problem is a known issue with ArchLinux and the g95
we ship. You need to use the gfortran compiler provided by the system.
README.txt tells you the details:

NOTE: If you're using Fortran on a platform without g95 binaries
included
  with Sage, e.g., Itanium, you must use a system-wide gfortran.
You
  have to explicitly tell the build process about the fortran
  compiler and library location.  Do this by typing

  export SAGE_FORTRAN=/exact/path/to/gfortran
  export SAGE_FORTRAN_LIB=/path/to/fortran/libs/libgfortran.so

Unfortunately I would recommend for you to start the Sage build
process over in your case since otherwise you would need to force a
rebuild of all components using FORTAN manually.

Cheers,

Michael
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[sage-support] Re: How to detect memory leaks?

[mabshoff]

On Oct 25, 12:46 pm, Simon King [EMAIL PROTECTED] wrote:
 Dear Michael and all others,

Hi Simon,

 I tried 3 approaches to trac my problem down. Summary: It seems that
 my extension class is deallocated (__dealloc__ is called) but not
 deleted (__del__ is not called), see approach 3 below.

 1.
 On Oct 24, 6:03 pm, mabshoff [EMAIL PROTECTED]

 dortmund.de wrote:

  You need to rebuild Python after exporting SAGE_VALGRIND=yes -
  otherwise pymalloc is used and as is the valgrind log is useless in
  some regards.

 Thanks.
 I did rebuild sage 3.1.4 with SAGE_VALGRIND=yes, installed the
 optional valgrind spkg, and tried again.

 After computing F=F5(); G=F(I) I had
 sage: get_memory_usage()
 1125.95703125

 and after repeating the same computation 10 more times in a loop, it
 was
 sage: get_memory_usage()
 1197.0703125

 This time, valgrind found a tiny bit of unreachable memory, 
 seehttp://sage.math.washington.edu/home/SimonKing/f5/sage-memcheck.25789
 ==25789== LEAK SUMMARY:
 ==25789==    definitely lost: 697 bytes in 17 blocks.
 ==25789==      possibly lost: 399,844 bytes in 1,033 blocks.
 ==25789==    still reachable: 38,600,299 bytes in 332,837 blocks.
 ==25789==         suppressed: 337,860 bytes in 5,348 blocks.

 However, this still does not explain the loss of 71 MB reported by
 get_memory_usage

This is pretty much as expected, but now that pymalloc is no longer
used the log is likely much more readable, since a lot of false
positives are gone.

 2.

  Debugging these is hard and
  valgrind will not help much in that case. Much more useful could be
  Guppy.

 I installed guppy. hpy told me that after the first round of my
 computation I had (only indicating those items that increased)
 Index  Count   %     Size   % Cumulative  % Kind (class / dict of
 class)
     1     42  15     4264  16     13480  50 tuple
     4     19   7     2280   8     21416  79 unicode
     5      3   1     1608   6     23024  85 dict (no owner)
     9     11   4      560   2     26312  97 str

 But after 10 more runs I got
      1     55  15     7424  20     16640  45 unicode
      2      4   1     4960  13     21600  59 dict (no owner)
      3     44  12     4408  12     26008  71 tuple
      7     46  13     1104   3     34208  93 int
      8     14   4      704   2     34912  95 str

 Unfortunately I did not find a guppy tutorial. In particular, I don't
 know how to find out where the increased size of the dicts and
 unicodes comes from.

Yep, that is somewhat of a black art. I am planning to do a talk at SD
11 about Guppy since my project there involves debugging a similar
problem, but I have nothing obvious to contribute here. Is the latest
version of f5.pyx in the wiki so I can play around with it?

 3.
 Is the following method a correct way of testing whether instances of
 my extension classes are deleted at all?
   - In the init method of my class DecoratedPolynomial, I increased
 two globally defined counters by one.
   - I provided a custom __del__ method, that did nothing but to reduce
 the first counter by one.
   - I provided a custom __dealloc__ method, that simply reduced the
 second counter by one.

 Result:
 The init method was called 429 times (in 11 runs of the computation
 and deleting everything in the end), and so was the __dealloc__
 method.
 But the __del__ method was not called *at all*!

Mhh, some Python god need to comment here. But once any python element
goes out of scope and the reference count is zero it gets deallocated.
You could sprinkle your code with manual reference count checks and
see if any one of them is going up and is never decremented when it
should. But that is also a black art IMHO :)

 So, could this be at the core of the problem? I thought that a
 __dealloc__ method is called only after the __del__ method has done,
 or am I mistaken?
 To avoid misunderstanding: In my original code I did not provide
 custom __del__ or __dealloc__, but expected Cython to do the job.

 Cheers
         Simon

Cheers,

Michael
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[sage-support] Re: How to detect memory leaks?

[mabshoff]

On Oct 24, 8:52 am, Simon King [EMAIL PROTECTED] wrote:
 Dear Carlo and all others,

 On Oct 23, 5:11 pm, Carlo Hamalainen [EMAIL PROTECTED]
 wrote:

  Valgrind is the thing to try:http://wiki.sagemath.org/ValgrindingSage

 Sorry, when I read the first lines of that page I thought I had to re-
 build Sage from scratch. But later it says that there is an optional
 valgrind package for Sage. I installed it and tried sage -valgrind.

You need to rebuild Python after exporting SAGE_VALGRIND=yes -
otherwise pymalloc is used and as is the valgrind log is useless in
some regards.

 Then I did
 sage: attach f5.pyx
 Compiling /home/king/Projekte/f5/f5.pyx...
 sage: from sage.rings.ideal import Cyclic
 sage: R=PolynomialRing(QQ,'x',5)
 sage: I=Cyclic(R).homogenize()
 sage: get_memory_usage()
 1013.09765625
 sage: F=F5()
 sage: G1=F(I)
 sage: del F
 sage: del G1
 sage: get_memory_usage()
 1035.59765625
 sage: F=F5()
 sage: G1=F(I)
 sage: del F
 sage: del G1
 sage: get_memory_usage()
 1053.04296875
 sage: quit

 However, it didn't help much.

 The valgrind output available 
 athttp://sage.math.washington.edu/home/SimonKing/f5/sage-memcheck.18590
 says in the summary that ~386kB are possibly lost and nothing is
 definitely lost.

 I think this doesn't fit to the output of get_memory_usage() above.
 Running F=F5()    G=F(I) in a loop is soon eating all memory.

 Moreover, most of the valgrind output does not refer to my code, as
 much as I understand. Hence, there is only  a handful of references to
 _home_king_Projekte_f5_f5_pyx_0.c

 Can you help me with interpreting the valgrind findings?

The key thing here is that the still reachable amount of memory is
growing which indicates a problem with objects from the python heap
not getting properly deallocated, i.e. a potential reference count
issue when using Cython for example. Debugging these is hard and
valgrind will not help much in that case. Much more useful could be
Guppy.

 Thank you very much
       Simon

Cheers,

Michael
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[sage-support] Re: again problem with plotting

[mabshoff]

On Oct 23, 1:24 am, Martin Rubey [EMAIL PROTECTED] wrote:

Hi Martin,

 I tried to compile Sage from source, but it ran out of memory compiling
 linbox.  Is there a workaround?

Unfortunately not. gcc is an absolute pig when instantiating templates
and with LinBox you need anywhere from 350 to 700MB memory. You can
add swap space which will make the compilation work, but slow it down
by quiet a lot, i.e. I have build LinBox on a G4 with 256 MB physical
RAM, it just took a while.  Which hardware are you using?

 Martin

Cheers,

Michael
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[sage-support] Re: How to detect memory leaks?

[mabshoff]

On Oct 23, 7:57 am, Simon King [EMAIL PROTECTED] wrote:
 Dear Sage team,

 I have two cdef'd classes (lets call them A and B). They have some
 cdef'd attributes that should be harmless, namely of type int or list
 or dict. The entries of these lists/dicts may be objects of class A
 though.

 Let me emphasize that A and B do not rely on any external (wrapped) C-
 Types. They are entirely built from int, list, dict, object. In
 particular, I am not doing any nasty memory allocation.

 I understood that Cython knows how to allocate and deallocate cdef'd
 attributes of type int, list, dict, object etc. Hence, I expected that
 I do not need to provide __del__ or __dealloc__ methods for A and B.
 And I expected that it is virtually impossible to produce a memory
 leak in such setting.

Famous last words.

 Nevertheless, get_memory_usage() shows that
    creating an object of class B,
    doing a computation Result = B(...), and
    deleting B
 results in an increased memory usage of 2.57MB per run.

Do you also delete Result

 What tools do you recommend to tracking that memory leak down?

 Yours
        Simon

Depending on the situation it can either be guppy or valgrind. I can't
say anything without seeing the code, but I don't really have time to
take a closer look for the next couple days anyway.

Cheers,

Michael
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[sage-support] Re: again problem with plotting

[mabshoff]

On Oct 21, 2:14 pm, Jason Grout [EMAIL PROTECTED] wrote:
 William Stein wrote:

SNIP

  When I have Pentium M binaries, you'll be set to use those, and this
  will be soon, given my new hardware.

 Wow, what sort of new hardware are you getting that are Pentium M's?

It isn't new, it is an old laptop that William used to build Sage
binaries with until one day compiling ATLAS killed it :)

 Jason

Cheers,

Michael
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[sage-support] Re: Upgrade failed in Givaro

[mabshoff]

On Oct 20, 9:01 am, Simon King [EMAIL PROTECTED] wrote:
 Dear Team,

 after William's recent post that an upgrade to 3.1.4 should now be
 possible.

 I tried, but it failed.

 Strange: There was no new install.log (AFAIK, an upgrade should
 produce a new one).

 Last words on the screen:
 /home/king/SAGE/devel/sage-3.1.1/local/lib/../lib/libstdc++.so: could
 not read symbols: File in wrong format

This looks like a problem with your toolchain since we don't ship any
libstdc++.so since it is provided by the C++ compiler.

SNIP

 I tried to remove the givaro spkg and do upgrade again, but the same
 problem occured.

 What can I do?

 Cheers
      Simon

Cheers,

Michael
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[sage-support] Re: Upgrade failed in Givaro

[mabshoff]

On Oct 20, 2:01 pm, Simon King [EMAIL PROTECTED] wrote:
 Dear Michael,

 On Oct 20, 7:05 pm, Simon King [EMAIL PROTECTED] wrote:

  I think it'll be better to try from scratch (i.e., from sources).

 ... and that worked.

As long as you copy libstc++.so into $SAGE_LOCAL/lib Sage will likely
break on upgrade unless you use the same gcc you build Sage with. That
means setting PATH as well as LD_LIBRARY_PATH correctly.

 However, is it normal that the attempt to upgrade did *not* result in
 an install.log?

I have no clue what is going on with your build, but something is
FUBAR. I get an updated install.log every time I do an upgrade on one
of my test installs.

 Yours
      Simon

Cheers,

Michael
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[sage-support] Re: no plotting

[mabshoff]

On Oct 18, 12:56 am, Alex Ghitza [EMAIL PROTECTED] wrote:
 Sorry Martin, I completely missed the second sage: prompt in your original
 email.

 It's very likely that the problem is due to sage -upgrade.  I don't know
 enough about these things to give you better advice than start over with a
 fresh download of Sage, and you've mentioned that this might not be an
 option for a while.  Hopefully someone else on this list will know some
 magic to fix this.

This is likely a gonner. Downgrades don't work too well :(

 Note, however, that sage -upgrade is *not* recommended practice, precisely
 because this sort of problem keeps popping up over and over again.
 The recommended way of getting a new version is downloading the new binaries
 or source.


Right now since the 3.1.4 spkgs have not been pushed out -upgrade
downgrades and likely breaks your build.

If you want to upgrade a build when the online repo is not pushed out
yet download the tar.gz and copy the new spkgs over the old ones in
spkg/standard - then run make again. But I agree with Alex that one
should only use upgrade when one is familiar enough with the Sage
build system to fix bugs :)

 Good luck,
 Alex

Cheers,

Michael

Michael
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[sage-support] Re: calling a C program in sage with terminal output

[mabshoff]

On Oct 16, 4:51 pm, David Joyner [EMAIL PROTECTED] wrote:
 Hi:
SNIP

As pointed out popen is the easy way to go.

 Also, what is the proper way to do this? I'm guessing one should
 write wrapper classes as in the interfaces directory but is swig better?

I would suggest Cython :)

 - David Joyner

Cheers,

Michael
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[sage-support] Re: german keybord in vmware image

[mabshoff]

On Oct 16, 7:33 pm, Burcin Erocal [EMAIL PROTECTED] wrote:
 On 16 Oct 2008 20:21:55 +0200

Hi Martin,

 Martin Rubey [EMAIL PROTECTED] wrote:

  Some of my students complain that the vmware image of sage seems to
  use english keyboard.  Is there a way to configure this?

  (I do not own a windows machine, so I cannot try it...)

The VMware image does run on any platform where there is a VMWare
player, i.e. Linux and OSX would be a possible test bed for you in
case you want to play with the VMWare image.

 As far as I know the vmware image runs ubuntu, so one can just follow
 the instructions on the ubuntu community website:

 https://help.ubuntu.com/community/LocaleConf
 (scroll down for Keyboard configuration - console)

Exactly. This has come up before and does solve the problem.

 (I do not run ubuntu, so I cannot try it...) :)

:)


 Cheers,

 Burcin

Cheers,

Michael
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[sage-support] Re: Final Sage 3.1.3 sources are out

[mabshoff]

Note that a critical bug when using init.sage has been fixed in Sage
3.1.4 available in

http://sage.math.washington.edu/home/mabshoff/release-cycles-3.1.4/

Upgrades are not yet working and binaries are being build.

Cheers,

Michael



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[sage-support] Final Sage 3.1.3 sources are out

[mabshoff]

Hello folks,

here are the minimal fixes for the final 3.1.3:

#4271: Paul Zimmermann: improve coverage test of ell_generic.py to
100%, and fix typos [Reviewed by John Cremona]
#4272: Michael Abshoff: add the files from new coercion to the
reference manual [Reviewed by Mike Hansen]
#4279: Michael Abshoff: Sage 3.1.3.rc0: numerical noise in rings/
real_lazy.pyx [Reviewed by Mike Hansen]

Sources and a sage.math binary are at

http://sage.math.washington.edu/home/mabshoff/release-cycles-3.1.3/

The upgrade does not work yet, but hopefully should be done later on
tonight.

Cheers,

Michael


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[sage-support] Re: numeric approximations for symbolic expressions

[mabshoff]

On Oct 10, 10:02 am, Jason Grout [EMAIL PROTECTED] wrote:
 Burcin Erocal wrote:
  On Fri, 10 Oct 2008 10:35:16 -0500
  Jason Grout [EMAIL PROTECTED] wrote:

  The general request still stands, though: is there a way to
  numerically approximate all the constants in a symbolic expression,
  but keep the variables as variables?

  The pynac based symbolics code does the following:

  sage: x,y,z = var(x y z, ns=1)
  sage: t = 1 + sqrt(2)*x + sin(x)
  sage: t.n()
  sin(x) + (1.4142135623730951)*x + 1.0

  This is with the bundle at #3872 and patches at #4244 applied, and the
  package at #4243.

 Nice.  That's exactly what I was wanting.  Chalk me up as one more
 person eager to get this in shape and into Sage.

Yep, it is certainly the highest priority ticket for 3.2 and 3.1.3 has
unfortunately delayed longer than planned. I plan to do 3.1.3.rc0
tonight and unless something major happens it should be very close to
final. Then we can open 3.2 during the coding sprint at SD 10 here at
Loria.

 Thanks,

 Jason

Cheers,

Michael
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[sage-support] Re: jsMath issue and solution with error code -7

[mabshoff]

On Oct 10, 1:55 pm, Jason Grout [EMAIL PROTECTED] wrote:

SNIP

 We really ought to include these fonts with Sage and have the error
 message say: Here are some fonts.  Install them.  If you want darker or
 lighter variations, go here (link to the website)

#1608 :)

 Jason

Cheers,

Michael
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[sage-support] Re: numeric approximations for symbolic expressions

[mabshoff]

On Oct 10, 3:48 pm, Jason Grout [EMAIL PROTECTED] wrote:

SNIP

 Is there any chance this could be merged into 3.1.3 to get wider
 testing?  That is, if it's a purely optional framework.  Barring that,
 is there a chance we could get a single huge patch that consolidates all
 of this, or even just a single patch that contains the changes in the
 bundle?

Nope, I don't see this happening until I

 a) valgrind the new doctests
 b) build it on Cygwin, Solaris, Linux/Itanium and G4/G5 on OSX 10.4
and 10.5 and have all doctests pass

and the doctests pass. ghmm has taught me that just because it mostly
works and there is only a couple allegedly easy bugs to fix a patch
like that can still hold up a release for an extended amount of time
(2 weeks in 3.1.2 in my guesstimation). And those bugs in ghmm on
Itanium are still not fixed, but we did disable doctests globally in
those two files in order to make the doctests pass. 3.1.3 is supposed
to be out soon, i.e. before the SD 10 coding sprint, and I am not
willing to take the risk of pynac's integration bundle.

 Thanks,

 Jason

Cheers,

Michael
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[sage-support] Re: math range error on sqrt()

[mabshoff]

On Oct 10, 4:04 pm, john_perry_usm [EMAIL PROTECTED] wrote:
 Try adding another 1. Apparently I copied  pasted the wrong one.


I can reproduce it on a 64 bit box:

sage:
round(sqrt(1
))
1.05409255339e+154
sage:
round(sqrt(1
1))
---
OverflowError Traceback (most recent call
last)

/scratch/mabshoff/release-cycle/sage-3.1.3.rc0/ipython console in
module()

/scratch/mabshoff/release-cycle/sage-3.1.3.rc0/local/lib/python2.5/
site-packages/sage/misc/functional.pyc in round(x, ndigits)
845 else:
846 try: return x.round()
-- 847 except AttributeError: return
RealDoubleElement(__builtin__.round(x, 0))
848
849 def quotient(x, y, *args, **kwds):

/scratch/mabshoff/release-cycle/sage-3.1.3.rc0/local/lib/python2.5/
site-packages/sage/calculus/calculus.pyc in __float__(self)
   6201 f = self._operands[0]
   6202 g = self._operands[1]
- 6203 return float(f._approx_(float(g)))
   6204
   6205 def _fast_float_(self, *vars):

/scratch/mabshoff/release-cycle/sage-3.1.3.rc0/local/lib/python2.5/
site-packages/sage/calculus/calculus.pyc in _approx_(self, x)
   7978
   7979 def _approx_(self, x):
- 7980 return math.sqrt(x)
   7981
   7982 sqrt = Function_sqrt()

OverflowError: math range error

The issue seems to be that RealDoubleElement() cannot deal with a
value that large since it overflows the range that float provides.

Cheers,

Michael
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[sage-support] Re: Sage server incredibly slow

[mabshoff]

On Oct 9, 1:20 pm, Maike [EMAIL PROTECTED] wrote:
 Hello,

Hii Maike,

 I tried using the sage server at sagenb.org. Generally, it's great,
 but sometimes it's just incredibly slow. I'm having to wait about a
 minute for cells to be executed or worksheets to be loaded or saved
 sometimes.

 Is everyone having these problems or am I doing something wrong?

Every so often Sage backs up all the data and that takes a while.
William did optimize a bunch of the backup code, but there is
certainly still work to do.


 Thanks for any help!
 Maike

Cheers,

Michael
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[sage-support] Re: Using Sage with a large number of undergraduate students.

[mabshoff]

On Oct 8, 5:48 am, Pierre [EMAIL PROTECTED] wrote:
  Ironically pretty much everything works under Solaris now but the
  notebook. I think that issue is easy to fix (RAND_MAX related

 incidentally, is it possible to get knoboo to work on solaris instead
 of the notebook ?

 (sorry if this question is somewhat besides the point)

No problem, but I think it could work. The issue right now with the
notebook on Solaris is that the key generation takes forever due to
sucky entropy caused by RANDMAX issues. I can fix that, but I want to
make sure that I do not open a gaping security issue.

Cheers,

Michael
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[sage-support] Re: Sage compile fails on Fedora Core 2

[mabshoff]

On Oct 7, 10:01 am, Venkat [EMAIL PROTECTED] wrote:
 Hi all,

Hi,

 I'm using a Fedora Core2 based system, which I can't upgrade.

 Compilation fails for the latest Sage (3.1.2). I'm not sure how to fix
 this error. Any help is appreciated. I'm pasting the relevant lines
 below.

It looks like you are using gcc 3.3.3. To build Sage you need gcc 3.4
or higher since we need C99 capabilities. Even if you update the
compiler I doubt Sage will build corrrectly. FC 2 was released in 2004
and is way out of date.

 Thanks,
 Venkat.

Cheers,

Michael
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[sage-support] Re: Using Sage with a large number of undergraduate students.

[mabshoff]

On Oct 7, 1:27 pm, Mike Hansen [EMAIL PROTECTED] wrote:
 Hello,

 On Tue, Oct 7, 2008 at 1:15 PM, Jason Grout [EMAIL PROTECTED] wrote:
  To sum up the discussion about what makes things slow, is it a
  file-locking bottleneck with the sage server?

 I don't think anyone has done any serious profiling of the notebook so
 I think that conclusion is quite a bit premature.  One thing that
 might be helpful would be to run the notebook under Solaris with
 DTrace.

Ironically pretty much everything works under Solaris now but the
notebook. I think that issue is easy to fix (RAND_MAX related
probably), but the even shorter way to profile here is either using
VTune (which is proprietary) or Systemtap (which is free).

If we can get Mike's notebook testing code to do some larger number of
operations in automated mode we could probably easily determine where
the bottlenecks are.

 --Mike

Cheers,

Michael
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[sage-support] Re: URGENT - Problem with installing sage on suse10.1

[mabshoff]

On Oct 3, 5:30 am, Ines [EMAIL PROTECTED] wrote:
 Hi !
 I tried to insatll a last version of sage : sage-3.1.2.tar with no
 sucess. How can I send you the insall.log file ?

 Ines.

Hi Ines,

please send it compressed to me off list per email.

Cheers,

Michael
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[sage-support] Re: URGENT - Problem with installing sage on suse10.1

[mabshoff]

On Oct 3, 3:29 pm, William Stein [EMAIL PROTECTED] wrote:
 On Fri, Oct 3, 2008 at 1:25 PM, Ines Abdeljaoued-TEJ [EMAIL PROTECTED] 
 wrote:
  I'll be to the office tomorrow; do you understand french ?

I suggested sending the install log *off list* since most people on
this list did not want to receive a large attachment they will never
look at.

 You get an internal compiler error when installing the Cython
 spkg.  You're using gcc version 4.1.0 (SUSE Linux) and the
 error is copied below and is, in short internal compiler error.
 This always indicates either a serious bug in your compiler
 or your hardware is defective.

That gcc is a know bad compiler for Sage (and many other software
packages) - see #3123 blacklist gcc version 4.1.0 (SUSE Linux)

 You should definitely upgrade to a newer version of GCC
 and try building Sage again from scratch.

There are upgrades for OpenSuSE's 10.1 gcc rpms. They might be hard to
get hold of since OpenSuSE 10.1 is no longer supported.

SNIP

Cheers,

Michael

 --
 William Stein
 Associate Professor of Mathematics
 University of Washingtonhttp://wstein.org
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[sage-support] Re: URGENT - Problem with installing sage on suse10.1

[mabshoff]

On Sep 30, 12:56 am, Ines [EMAIL PROTECTED] wrote:

Hi Ines,

 I am trying to install sage on 14 pc for educational's need. the
 command make
 return three type of error's message (depending on the pc and after
 65min of
 compil) :

 error while installing cython-0.9.8
 error while installing atlas-3.8.1
 error while installing givaro-3.2.11

 and the same instruction (I replace the package's name by ... ):

 If you want to try to fix the problem, yourself *don't* just cd to
 /home/essai/Desktop/SAGEmath/sage-3.0.5/... and type 'make'.
 Instead type /home/essai/Desktop/SAGEmath/sage-3.0.5/sage -sh
 in order to set all environment variables correctly, then cd to
 /home/essai/Desktop/SAGEmath/sage-3.0.5/spkg/build/...
 (When you are done debugging, you can type exit to leave the
 subshell.)

 It is very urgent. I hope I'll can teach numerical analysis and
 operational
 research with sage to my students.

There is a file call install.log in the Sage base directory. Can you
upload it somewhere and post a link?

There are also x86 and x86-64 binaries for OpenSuSE 10.2 I believe, so
you might want to give them a try.

 Regards, Ines.

Cheers,

Michael
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[sage-support] Re: Is readline a prerequisite to build Sage?

[mabshoff]

On Sep 30, 5:42 am, Simon King [EMAIL PROTECTED] wrote:
 Dear Team,

Hi Simon,

 currently I try to build Sage from source on a laptop (GNU/Linux
 i686). The built of R failed, and the complaint is
   sys-std.c:401:33: error: readline/readline.h: No such file or
 directory
   sys-std.c:431:32: error: readline/history.h: No such file or
 directory

 Is readline required to build Sage?

No.

 Note that it is not mentioned in
 the README.txt (it only lists gcc, g++, m4, ranlib, and make).

 Or what else might be gone wrong?

It is a bug in R when doing processing on .d files. I have hit the
problem, too, but not fixed it yet. Feel free to open a ticket and I
will attempt to fix it in 3.1.3.

 I'll try to upload the install.log, but this will certainly take a
 while, and perhaps you already have a hint for me...

No need for the log :)

 Yours
       Simon

Cheers,

Michael
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[sage-support] Re: Is readline a prerequisite to build Sage?

[mabshoff]

On Sep 30, 6:32 am, Simon King [EMAIL PROTECTED] wrote:
 Dear Michael,

 On Sep 30, 3:21 pm, mabshoff [EMAIL PROTECTED]

 dortmund.de wrote:
  Please test the spkg at #4222. I am 99% sure it will solve your
  problem.

 I just did:
 * removed r-2.6.1... from build/ and from standard/,
 * downloaded your package
 * make

 Unfortunately, I belong to the 1%. It is the same error as before. Or
 did I do a mistake in the above steps?

Did you drop the spkg in $SAGE_ROOT/standard/spkg?

  It would make Sage compile, but it would potentially cause subtle
  issues with tab completion for example if the system's readline is
  old.

 Is there a system's readline? which readline shows nothing!

Well, your likely have to install the readline development package
from your package manager. You can also likely copy the readline
headers from Sage into /usr/include and then R should compile, but
that is not very clean. Note that the readline headers are in a
readline directory.

 Yours
      Simon

Cheers,

Michael
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[sage-support] Re: Is readline a prerequisite to build Sage?

[mabshoff]

On Sep 30, 6:42 am, Simon King [EMAIL PROTECTED] wrote:
 Hi,

 On Sep 30, 3:37 pm, mabshoff [EMAIL PROTECTED]

 dortmund.de wrote:
   I just did:
   * removed r-2.6.1... from build/ and from standard/,
   * downloaded your package
   * make

  Did you drop the spkg in $SAGE_ROOT/standard/spkg?

 Do you mean in $SAGE_ROOR/spkg/standard? Yes.
 Cheers
      Simon

Ok, please send me the complete output from a full build of the new
r-2.6.1.p20.spkg offlist. I found a potential issue, but have so far
failed to force a successful rebuild of the damn autohell buildsystem
of R.

Cheers,

Michael
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[sage-support] Re: Is readline a prerequisite to build Sage?

[mabshoff]

On Sep 30, 7:11 am, Simon King [EMAIL PROTECTED] wrote:
 On Sep 30, 4:02 pm, mabshoff [EMAIL PROTECTED]

 dortmund.de wrote:
  Ok, please send me the complete output from a full build of the new
  r-2.6.1.p20.spkg offlist.

 Sorry, this will take a couple of hours, because I tried the quick
 and dirty method (copy the headers into /usr/include/), which seems
 to work.

 Hence, I will
 * wait for the current built to finish
 * move the headers out of the way
 * start a new built in a different folder, using your spkg
 * wait until it fails
 * send you the log file off list
 * move the headers in place, so that I can use Sage.

No need to wait. Move the headers out of the way, download

http://sage.math.washington.edu/home/mabshoff/release-cycles-3.1.3/alpha2/r-2.6.1.p20.spkg

(it is an updated version). Then run ./sage -f path/to/spkg/
r-2.6.1.p20.spkg - that can be done in parallel to the build and if it
fails the currently installed r.spkg will not be affected.

 Cheers
        Simon

Cheers,

Michael
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[sage-support] Re: Is readline a prerequisite to build Sage?

[mabshoff]

On Sep 30, 7:19 am, mabshoff [EMAIL PROTECTED]
dortmund.de wrote:
 On Sep 30, 7:11 am, Simon King [EMAIL PROTECTED] wrote:



  On Sep 30, 4:02 pm, mabshoff [EMAIL PROTECTED]

  dortmund.de wrote:
   Ok, please send me the complete output from a full build of the new
   r-2.6.1.p20.spkg offlist.

  Sorry, this will take a couple of hours, because I tried the quick
  and dirty method (copy the headers into /usr/include/), which seems
  to work.

  Hence, I will
  * wait for the current built to finish
  * move the headers out of the way
  * start a new built in a different folder, using your spkg
  * wait until it fails
  * send you the log file off list
  * move the headers in place, so that I can use Sage.

 No need to wait. Move the headers out of the way, download

 http://sage.math.washington.edu/home/mabshoff/release-cycles-3.1.3/al...

 (it is an updated version). Then run ./sage -f path/to/spkg/
 r-2.6.1.p20.spkg - that can be done in parallel to the build and if it
 fails the currently installed r.spkg will not be affected.

Ironically now I am hitting the same problem as you since I touched
the .d file, so I can now actually debug this :)

Cheers,

Michael
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[sage-support] Re: Is readline a prerequisite to build Sage?

[mabshoff]

On Sep 30, 7:23 am, mabshoff [EMAIL PROTECTED]
dortmund.de wrote:

SNIP

 Ironically now I am hitting the same problem as you since I touched
 the .d file, so I can now actually debug this :)

And the problem is fixed in the thrid update of
http://sage.math.washington.edu/home/mabshoff/release-cycles-3.1.3/alpha2/r-2.6.1.p20.spkg

please try it out and let me know how it works. It does build on
sage.math without readline headers present, so it should work for you,
too. If it does not I am more than sure that NFS or some other crap
file system is to blame since as is the dependency creation code of R
is broken.

 Cheers,

 Michael

Cheers,

Michael
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[sage-support] Re: URGENT - Problem with installing sage on suse10.1

[mabshoff]

Ines Abdeljaoued-TEJ wrote:
 Hi !

Hi Ines,

please don't take discussions off list.

SNIP

 There is a file call install.log in the Sage base directory. Can you
 upload it somewhere and post a link?


 I'll try to upload the install.log, but this will take a while (I'm not in the
 office until friday).

Ok.

 There are also x86 and x86-64 binaries for OpenSuSE 10.2 I believe, so
 you might want to give them a try.


 Should Iinstall OpenSuse10.2 in place of suse 10.1 ?
 Thanks, Ines.

It is worth a try, but it might not work. I don't know a reason why
compiling Sage on OpenSuSE 10.1 should not work, but I guess we will
find out.

Cheers,

Michael
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[sage-support] Re: Is readline a prerequisite to build Sage?

[mabshoff]

On Sep 30, 6:07 am, Simon King [EMAIL PROTECTED] wrote:
 Dear Michael

 On Sep 30, 2:49 pm, mabshoff [EMAIL PROTECTED]

 dortmund.de wrote:
  It is a bug in R when doing processing on .d files. I have hit the
  problem, too, but not fixed it yet. Feel free to open a ticket and I
  will attempt to fix it in 3.1.3.

 It is #4222. I made it critical -- feel free to reduce the priority.

Please test the spkg at #4222. I am 99% sure it will solve your
problem.

 But would it solve my problem to install readline on that laptop?

It would make Sage compile, but it would potentially cause subtle
issues with tab completion for example if the system's readline is
old. Don't install readline for now to make sure the above spkg fixes
the problem.

 Cheers
       Simon

Cheers,

Michael
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[sage-support] Re: Is readline a prerequisite to build Sage?

[mabshoff]

SNIP

 Sorry, it does not work. Same error as before.

Yeah, considering I screwed up and did not replace the one r.spkg to
download this does not surprise me. Please try again and check that
the md5sum matches:

de0de83b25ca7b9e0a65246c067f0afa  /home/mabshoff/release-cycles-3.1.3/
alpha2/r-2.6.1.p20.spkg

Hopefully this will put this problem to rest once and for all.

 Cheers
         Simon

Cheers,

Michael
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[sage-support] Re: formatting not saved in notebooks

[mabshoff]

On Sep 29, 10:17 am, William Stein [EMAIL PROTECTED] wrote:
 On Mon, Sep 29, 2008 at 7:00 AM, Stan Schymanski [EMAIL PROTECTED] wrote:

  Dear all,

  As of version 3.1.2, plots are saved correctly in notebooks. Thanks to
  those that fixed it. However, I noticed that the formatting of cells
  beginning with %hide %html is not saved. I need to re-evaluate all
  of those cells to get the formatting back. Is this a bug in SAGE or
  does it have something to do with the web browser (Firefox 3.0.3 on
  Mac OS X 10.4)?

  Thanks again for the great effort!

 This is definitely a bug.  If it isn't listed at trac.sagemath.org somewhere,
 I hope somebody adds it, so it will get fixed.

This does not seem to be in trac, so I made this #4217.

 William

Cheers,

Michael
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[sage-support] Re: problem with animate on OS X 10.5, Sage 3.1.2

[mabshoff]

On Sep 29, 11:15 am, John H Palmieri [EMAIL PROTECTED] wrote:
 On Sep 29, 7:40 am, Jason Grout [EMAIL PROTECTED] wrote:



  Seehttp://trac.sagemath.org/sage_trac/ticket/975fora solution that is
  already put in place.  Basically, use
  $SAGE_ROOT/local/bin/sage-native-execute, which does exactly what
  mabshoff says above.

 So like the following?

 http://trac.sagemath.org/sage_trac/ticket/4216

Yep, pretty much.

 By the way, is there a way to tell which calls to os.system should use
 sage-native-execute, or should we just deal with case-by-case?

sage-native-execute sets [DY]LD_LIBRARY_PATH depending if the binary
is in $SAGE_LOCAL/bin or not and avoids the kind of missing or
incorrect symbol problem. I would always prefer sage-native-execute
over os.system.

   John

Cheers,

Michael
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[sage-support] Re: Lost notebook worksheets after updating

[mabshoff]

On Sep 29, 3:33 pm, William Stein [EMAIL PROTECTED] wrote:
 On Mon, Sep 29, 2008 at 2:27 PM, Rolandb [EMAIL PROTECTED] wrote:

  Several times I indicated the same problem but until now no action.

 It's definitely not due to lack of desire on our part.  It's just that there
 are so many things to do, and so little time.

 The simplest solution would be to add a link to the notebook that
 allows one to download all the files for that notebook into a single
 file (a tarball), and another link in the notebook that allows one to
 upload all worksheets in such an archive.   I think this could
 be implemented in a few hours.  What do people think of
 this?  It would beat doing this:

  I just save my worksheets (around 30) manually and recover the *.sws
  files one by one in the new SAGE version.

Yep, the feature request to do this is #2740.

Cheers,

Michael

 --
 William Stein
 Associate Professor of Mathematics
 University of Washingtonhttp://wstein.org
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[sage-support] Re: problem with wiki.sagemath.org

[mabshoff]

On Sep 27, 9:03 pm, pong [EMAIL PROTECTED] wrote:

Hi Pong,

 I apologize in advance that if this is not a right place to ask this
 question.

 I have some problem in using wiki.sagemath.org. I created an account
 but when I tried to re-login sometime later it compliant that my
 password is wrong. (I'm pretty sure I remember my password
 correctly).When I tried to create an account again using the same
 name, wiki compliant that the username has already been taken (so
 obviously it remember something).

 Now the only explanation that I could think of is that I choose not
 to remember something (sorry I forgot what the something is) by
 unchecking a box at some point. Could it be the reason?

 PS. I also tried to recover my password by providing wiki my email
 however it complaint that no info associate with my email address
 (again I'm pretty sure the email that I gave was correct, it simply my
 gmail account)

Please recreate your account, I did some spammer cleanup and might
have inadvertently delete it :(

 Please help.

Cheers,

Michael
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[sage-support] Re: problem with animate on OS X 10.5, Sage 3.1.2

[mabshoff]

On Sep 27, 5:41 pm, John H Palmieri [EMAIL PROTECTED] wrote:
 Can anyone else reproduce this?

I can't since I do not have convert on a Mac, but the problem is that
we switched to a dynamic libpng. The solution is:

 * create a convert script in $SAGE_LOCAL/bin
 * set DYLD_LIBRARY_PATH to SAGE_ORIG_DYLD_LIBRARY_PATH
 * call convert with an absolute path (use which convert from
outside Sage) and pass on all parameters (i.e. /use/local/foo/convert
$@)

We should probably do that automatically on OSX for convert, emacs and
the other usual suspects. The problem boils down to Apple renaming
some of the symbols in libpng and creating libPng.dylib in the
process.

Cheers,

Michael
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[sage-support] Re: How to do: is_Integer(sqrt(a^2+b^2))

[mabshoff]

On Sep 26, 12:06 am, Robert Bradshaw [EMAIL PROTECTED]
wrote:

SNIP

  Indeed!  I like Mike Hansen's (or your) proposal to get
  rid of them all from the global namespace, and replace
  them only by is_lowercase_method_name functions
  that are all conceptually meaningful.   Of course leave
  the type-checking is_Uppercase's around, but don't
  put them in all.py's.

  What do you guys think?

 +1 for sure.

The patch is up at #4192 and will be merge shortly unless there is
some last minute breakage.

SNIP

 - Robert

Cheers,

Michael
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[sage-support] Re: a problem starting the notebook

[mabshoff]

On Sep 25, 10:09 am, cesarnda [EMAIL PROTECTED] wrote:
 I am using Kubuntu 8.04

 On 25 sep, 07:39, cesarnda [EMAIL PROTECTED] wrote:

  --
  | SAGE Version 3.1.2, Release Date: 2008-09-19                       |
  | Typenotebook() for the GUI, and license() for information.        |
  --

  sage:notebook()
  Thenotebookfiles are stored in: /home/cesarnda/.sage//sage_notebook
  **
  *                                                *
  * Open your web browser tohttp://localhost:8000*
  *                                                *
  **
  2008-09-25 07:38:53-0500 [-] Log opened.
  2008-09-25 07:38:53-0500 [-] twistd 8.1.0 (/home/cesarnda/Sage/
  sage-3.0.6-i686-Linux/local/bin/python 2.5.2)startingup
  2008-09-25 07:38:53-0500 [-] reactor class: class
  'twisted.internet.selectreactor.SelectReactor'
  2008-09-25 07:38:53-0500 [-] 
  twisted.web2.channel.http.HTTPFactorystartingon 8000
  2008-09-25 07:38:53-0500 [-]Startingfactory
  twisted.web2.channel.http.HTTPFactory instance at 0x8c274ac
  2008-09-25 07:38:57-0500 [HTTPChannel,1,127.0.0.1] /home/cesarnda/Sage/
  sage-3.0.6-i686-Linux/local/lib/python2.5/site-packages/Twisted-8.1.0-
  py2.5-linux-i686.egg/twisted/internet/defer.py:267:
  exceptions.DeprecationWarning: Don't pass strings (like 'Bad token')
  to failure.Failure (replacing with a DefaultException).
  2008-09-25 07:38:57-0500 [HTTPChannel,1,127.0.0.1] Exception
  rendering:
  2008-09-25 07:38:57-0500 [HTTPChannel,1,127.0.0.1] Unhandled Error
          Traceback (most recent call last):
          Failure: twisted.python.failure.DefaultException: Bad token


Hmm, nothing obvious pops out. Can you move the .sage directory in
$HOME and see if the problem goes away?

Cheers,

Michael
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[sage-support] Re: Windows: Where are worksheets stored?

[mabshoff]

On Sep 24, 1:27 pm, Jannick Asmus [EMAIL PROTECTED] wrote:
 Hi,

 switching to the latest release 3.1.2 on windows machines I would like
 to save my workbooks. but where are they stored?

 Sorry for my ignorance since my question seems to be a FAQ.

 As always, thanks for your help.

 Best wishes,
 J.

Hi,

the VMware application of Sage on Windows stores the worksheets just
like the native OSX and Linux versions in $HOME/.sage. Unfortunately
it is not possible yet to do a one step download and re-upload of all
worksheets, but that is an open issue to be fixed in the future. So
you can either down and upload them one by one (tedious for obvious
reasons) or use a tool like WinSCP to log into the running VMware
seesion and copy the .sage directory from the old to the new image.

Let us know if you have any more trouble.

Cheers,

Michael
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[sage-support] Re: saving worksheets?

[mabshoff]

On Sep 25, 3:19 pm, RayKiddy [EMAIL PROTECTED] wrote:

Hi,

 This seems pretty basic, but I am having issues with deleting
 worksheets and then not having them pop up again.

 Yes, I could read a few hundred pages of manuals, but how hard should
 this be. I followed the instructions for installing sage on Mac OS X
 (10.4.11) and that works. So I do:

 % ./sage
 --
 | SAGE Version 3.1.1, Release Date: 2008-08-17                       |
 | Type notebook() for the GUI, and license() for information.        |
 --
 sage: notebook()
 The notebook files are stored in: /Users/ray/.sage//sage_notebook
 **
 *                                                *
 * Open your web browser tohttp://localhost:8000*
 *                                                *
 **

 So, I click on the checkbox next to one of the worksheets and hit the
 Delete button. I click on the Log out link. Now, I see this on
 sage's console:

 2008-09-25 15:06:15-0700 [-] Log opened.
 2008-09-25 15:06:15-0700 [-] twistd 8.0.1 (/Users/ray/Applications/
 sage/local/bin/python 2.5.2) starting up
 2008-09-25 15:06:15-0700 [-] reactor class: class
 'twisted.internet.selectreactor.SelectReactor'
 2008-09-25 15:06:15-0700 [-] twisted.web2.channel.http.HTTPFactory
 starting on 8000
 2008-09-25 15:06:15-0700 [-] Starting factory
 twisted.web2.channel.http.HTTPFactory instance at 0x38234b8
 2008-09-25 15:08:05-0700 [HTTPChannel,1,127.0.0.1]

 I never get back to a prompt? How do I? The only way I have found is
 to type a ^C.

 ^C2008-09-25 15:15:15-0700 [-] Saving notebook...
 2008-09-25 15:15:15-0700 [-] Saving notebook...
 2008-09-25 15:15:15-0700 [-] Notebook cleanly saved.
 2008-09-25 15:15:15-0700 [-] Notebook cleanly saved.
 2008-09-25 15:15:15-0700 [-] Main loop terminated.
 2008-09-25 15:15:15-0700 [-] Server Shut Down.
 True
 sage: quit
 Exiting SAGE (CPU time 0m0.03s, Wall time 9m15.28s).
 %

 Hm. Looks as though it saved. I re-start sage and there it is. The
 worksheet I thought I deleted is back.

This was a bug fixed in the 3.1.2 release. There is no 3.1.2 binary
for OSX 10.4 PPC yet, but there should be in the not too distant
future.

 So, I see a Delete button, a Save button, a Save  Quit button.
 I have tried all of these. No effect. Is there a Delete Really
 button? Where is it? I tried to get back to the sage: prompt with a
 ^D. What else should I try? ^X-elbow-Z? What is the magic word for
 getting it to do this rather obvious thing?

 If someone can explain it, I can find a rather obvious place to put
 this info in the documentation. I found several obvious places, and no
 documentation. Thanks.

Cheers,

Michael
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[sage-support] Re: saving worksheets?

[mabshoff]

On Sep 25, 3:35 pm, mabshoff [EMAIL PROTECTED]
dortmund.de wrote:
 On Sep 25, 3:19 pm, RayKiddy [EMAIL PROTECTED] wrote:

 Hi,



  This seems pretty basic, but I am having issues with deleting
  worksheets and then not having them pop up again.

  Yes, I could read a few hundred pages of manuals, but how hard should
  this be. I followed the instructions for installing sage on Mac OS X
  (10.4.11) and that works. So I do:

  % ./sage
  --
  | SAGE Version 3.1.1, Release Date: 2008-08-17                       |
  | Type notebook() for the GUI, and license() for information.        |
  --
  sage: notebook()
  The notebook files are stored in: /Users/ray/.sage//sage_notebook
  **
  *                                                *
  * Open your web browser tohttp://localhost:8000*
  *                                                *
  **

  So, I click on the checkbox next to one of the worksheets and hit the
  Delete button. I click on the Log out link. Now, I see this on
  sage's console:

  2008-09-25 15:06:15-0700 [-] Log opened.
  2008-09-25 15:06:15-0700 [-] twistd 8.0.1 (/Users/ray/Applications/
  sage/local/bin/python 2.5.2) starting up
  2008-09-25 15:06:15-0700 [-] reactor class: class
  'twisted.internet.selectreactor.SelectReactor'
  2008-09-25 15:06:15-0700 [-] twisted.web2.channel.http.HTTPFactory
  starting on 8000
  2008-09-25 15:06:15-0700 [-] Starting factory
  twisted.web2.channel.http.HTTPFactory instance at 0x38234b8
  2008-09-25 15:08:05-0700 [HTTPChannel,1,127.0.0.1]

  I never get back to a prompt? How do I? The only way I have found is
  to type a ^C.

[Sorry for the double post, but I missed to answer this one]

When you start the notebook you do not get back the prompt. I do not
know why, but I guess there is a good reason :)

  ^C2008-09-25 15:15:15-0700 [-] Saving notebook...
  2008-09-25 15:15:15-0700 [-] Saving notebook...
  2008-09-25 15:15:15-0700 [-] Notebook cleanly saved.
  2008-09-25 15:15:15-0700 [-] Notebook cleanly saved.
  2008-09-25 15:15:15-0700 [-] Main loop terminated.
  2008-09-25 15:15:15-0700 [-] Server Shut Down.
  True
  sage: quit
  Exiting SAGE (CPU time 0m0.03s, Wall time 9m15.28s).
  %

  Hm. Looks as though it saved. I re-start sage and there it is. The
  worksheet I thought I deleted is back.

 This was a bug fixed in the 3.1.2 release. There is no 3.1.2 binary
 for OSX 10.4 PPC yet, but there should be in the not too distant
 future.

  So, I see a Delete button, a Save button, a Save  Quit button.
  I have tried all of these. No effect. Is there a Delete Really
  button? Where is it? I tried to get back to the sage: prompt with a
  ^D. What else should I try? ^X-elbow-Z? What is the magic word for
  getting it to do this rather obvious thing?

  If someone can explain it, I can find a rather obvious place to put
  this info in the documentation. I found several obvious places, and no
  documentation. Thanks.

 Cheers,

 Michael
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[sage-support] Re: Seg fault with determinant calculation

[mabshoff]

On Sep 25, 12:34 pm, phil [EMAIL PROTECTED] wrote:

Hi,

I did valgrind a couple of the example sessions you gave for various n
(n=4,5 and 8 IIRC) and the good news is that there are no leaks going
on and Singular does not seem to do anything  naughty.

 One more thing I've noticed is that loading the saved result either
 doesn't work is is extremely inefficient.  On Monday, I started up
 3.1.2 final and ran load detMp.sobj.   It's been rough 3 days and
 it's still going.  This means loading takes longer than the original
 computation.

Yeah, pickling for those matrices over the mv polynomial ring probably
uses generic code and hence sucks speed wise. If malb or anyone else
familiar with that are of the code agrees please open a ticket so we
remember to fix this.

 Phil

Cheers,

Michael
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[sage-support] Re: Secure Sage Server

[mabshoff]

On Sep 24, 12:22 am, Maike [EMAIL PROTECTED] wrote:

Hi Maike,

 We'd like to set up a sage server allowing different users to see,
 copy and edit our published worksheets. However, this allows users to
 execute arbitrary system calls, e.g. os.popen(ps auxw).read()

Yes, any account on a Notebook server hands the user a shell, so you
either trust them or you secure the server itself.

 The formatting of the output is not perfect, but still, this is a
 problem!

 I'd be grateful for any suggestions on how to set up a SECURE sage
 server. If this has been covered elsewhere, just post the link...

There are a couple possibilities:

 a) a chroot jail
 b) a VMWare image (or some other kind of virtualization)
 c) SELinux, potentially in combination with (a)

None of the above is simple and securing a server so that it runs with
SELinux is difficult. There is no documentation on how to do this yet.
I would favor (b), frequent backups of the Sage notebook data and some
intrusion detection system in the notebook in addition to keeping
kernel and all the other components current to avoid break ins. Since
you are running a VMware image it is easily resettable and the
likelyhood of breaking out of the VMWare image is relatively small. So
should you have somebody break into your box it is much easier to
reset an image than the server. If you come up with something we would
definitely like to hear about it.

 Thanks!

 Maike

Cheers,

Michael
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[sage-support] Re: Numerical evaluate of the Dirichlet character value

[mabshoff]

On Sep 24, 4:15 am, Raouf [EMAIL PROTECTED] wrote:
 Hi,
 I want to have a numerical value of a  Dirichlet character :

 I have this line code in my notebook:

 sage:
 G = DirichletGroup(21)
 chi = G.1;
 chi(23)

 evaluate:
 zeta6 - 1

 And when i want to use this value: zeta6 - 1 i have the error message:

 G = DirichletGroup(21)
 chi = G.1;
 chi(23)
 B=13*chi(23)
 print float(B)

 error message:

 Traceback (most recent call last):
   File stdin, line 1, in module
   File /home/server2/nb1/sage_notebook/worksheets/fstthese/0/code/
 6.py, line 10, in module
     print float(B)
   File /home/server2/sage/local/lib/python2.5/site-packages/
 SQLAlchemy-0.4.6-py2.5.egg/, line 1, in module

 TypeError: float() argument must be a string or a number.

Looks like a bug to me. The usual trick (at least in my book of using
n() does also not work):

[EMAIL PROTECTED]:/scratch/mabshoff/release-cycle/sage-3.1.3.alpha1$ ./
sage
--
| SAGE Version 3.1.3.alpha1, Release Date: 2008-09-24|
| Type notebook() for the GUI, and license() for information.|
--

sage: G = DirichletGroup(21)
sage: chi = G.1;
sage: chi(23)
zeta6 - 1
sage: B=13*chi(23)
sage: print float(B)
---
TypeError Traceback (most recent call
last)

/scratch/mabshoff/release-cycle/sage-3.1.3.alpha1/ipython console in
module()

TypeError: float() argument must be a string or a number
sage: type(B)
type
'sage.rings.number_field.number_field_element_quadratic.NumberFieldElement_quadratic'
sage: n(B)
---
TypeError Traceback (most recent call
last)

/scratch/mabshoff/release-cycle/sage-3.1.3.alpha1/ipython console in
module()

/scratch/mabshoff/release-cycle/sage-3.1.3.alpha1/local/lib/python/
site-packages/sage/misc/functional.py in numerical_approx(x, prec,
digits)
716 return
sage.rings.real_mpfr.RealField_constructor(prec)(x)
717 except TypeError:
-- 718 return sage.rings.complex_field.ComplexField(prec)
(x)
719
720 n = numerical_approx

/scratch/mabshoff/release-cycle/sage-3.1.3.alpha1/local/lib/python2.5/
site-packages/sage/rings/complex_field.py in __call__(self, x, im)
212 except AttributeError:
213 pass
-- 214 return complex_number.ComplexNumber(self, x, im)
215
216 def _coerce_impl(self, x):

/scratch/mabshoff/release-cycle/sage-3.1.3.alpha1/complex_number.pyx
in sage.rings.complex_number.ComplexNumber.__init__ (sage/rings/
complex_number.c:2519)()

TypeError: unable to coerce to a ComplexNumber
sage:


Can someone more knowledgeable in the area open a ticket?

Cheers,

Michael
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[sage-support] Re: Sage runs amok when killing a sub process

[mabshoff]

On Sep 24, 5:18 am, Simon King [EMAIL PROTECTED] wrote:
 Dear Team,

Hi Simon,

 on a linux machine with 4 Dual Core AMD Opteron(tm) Processor 270, I
 had some computations with Sage 3.1.1.

 One of them had a very long Singular sub process, and eventually I
 killed the sub process.

 By consequence, a massive amount (more than 20) of new Python
 processes popped up (see below for a small part of what top shows).

I don't see why 20 of those python jobs would pop up. Can you
reproduce it?

 Fortunately the other Sage processes on that machine have not been
 affected. Nonetheless, I wonder if this is a bug.

The output from top as is is useless since there is no information to
gain. One would at least need PPID and the command line option used to
start the python jobs. It looks like you are ending up with something
that could turn into a zombie, but since it is unclear what exactly
you did this is undebuggable as is.

 Cheers
       Simon


Cheers,

Michael
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[sage-support] Re: maple from sage on mac os

[mabshoff]

On Sep 24, 3:20 pm, Alex Raichev [EMAIL PROTECTED] wrote:
 Hi William:

 The same thing happens to me on Mac OS X.  How do i fix this?

 Alex

Hi Alex,

I don't know how handy you are with patches and so on, but applying
the patch from #4180 followed by a sage -b would enable us to easily
see the pexpect logs. If you get the patch applied and so on do the
following:

export SAGE_PEXPECT_LOG=yes, then start sage from that console, do
some examples that break. Then check out $DOT_SAGE/pexpect_logs/ (that
is usually $HOME/.sage/pexpect_logs/) and send us the logs. That will
likely allow us to pinpoint what is going wrong.

If you do not want to or cannot do the patching just wait for 3.1.3
and it will have everything build in.

Cheers,

Michael
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[sage-support] Re: sage -wiki not starting

[mabshoff]

On Sep 22, 11:32 pm, Adam Webb [EMAIL PROTECTED] wrote:
   ^^^ This is some sort of permission error. Are you running SELinux or
   something like that?

Hi Adam,

 Just to confirm. SELinux was added to the computer. I am now
 'negotiating' with IT. :-)

good luck negotiating :). You can relabel all the files so that Sage
and SELinux can play well together, but adding new pages to the wiki
might prove difficult since those new files need to inherit the right
ACLs.

 cheers,
 Adam

Cheers,

Michael
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[sage-support] Re: Mercurial problems in 3.1.2

[mabshoff]

On Sep 22, 11:39 pm, Justin C. Walker [EMAIL PROTECTED] wrote:
 On Sep 22, 2008, at 22:24 , mabshoff wrote:

  Nope, none of those fixes is in alpha0, but I hope that at least some
  of them will make it into alpha1, due out late tomorrow. I still don't
  see how parallel make impacts numpy, so if you could send me the
  portion of the blown up numpy build with parallel make I could attempt
  to figure out what is wrong.

 See
    sage.math.washington.edu:~justin/logs/sage-numpy.log
 (the whole shebang; maybe something early on triggered it :-}).

Thanks. Numpy is complaining about a missing math module, but I think
that is more likely caused by the libpng.dylib disaster than anything
else. I just checked the python.spkg and we are running make install
with parallel make, which I would guess is not a good idea :)

The ticket for that issue is #4174 and there should be an spkg
shortly.

 Justin


Cheers,

Michael
 --
 Justin C. Walker, Curmudgeon-At-Large
 Institute for the Enhancement of the Director's Income
 
 When LuteFisk is outlawed,
 Only outlaws will have LuteFisk
 
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[sage-support] Re: Mercurial problems in 3.1.2

[mabshoff]

On Sep 21, 11:27 pm, Justin C. Walker [EMAIL PROTECTED] wrote:
 Hi, all,

 I'm on Mac OS X, 10.5.4 (dual quad xeon), and when I run sage -hg  
 commit, I get this


SNIP


 Anyone seen this?

This is the same crap issue you hit when building 3.1.2.rc-something,
i.e. emacs is linked against Apple's libnpng while launching it from
hg causes it to pick up out linpng. Results in *boom*. You can work
around this by writing an emacs script in SAGE_LOCAL/bin that sets
DYLD_LIBRARY_PATH to the old DYLD_LIBRARY_PATH and then launches
emacs.

Is someone can find out where Apple has its modifications to libpng
this issue can be resolved.

 Justin

Cheers,

Michael

 --
 Justin C. Walker, Curmudgeon-At-Large, Director
 Institute for the Enhancement of the Director's Income
 
 The path of least resistance:
 it's not just for electricity any more.
 
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[sage-support] Re: problems with install path

[mabshoff]

On Sep 22, 5:38 am, arnold [EMAIL PROTECTED] wrote:
 L.S.

Hi,

 When updating to Sage 3.1.2 I run into the following problem:

 Am using a Mac G4 dual core, OSX 10.4.11.
 Used a previous version of Sage without apparent problems. Updating to
 3.1.2 however was not without hickups: copying Sage with the finder
 resulted in error messages that duplicate names were not allowed.
 Removing all visible traces of Sage from /Applications and then
 installing with Terminal (sudo cp -R -P /Volumes/sage-3.1.2-osx10.4-
 ppc-PowerMacintosh-Darwin/ . inside the Applications folder) appeared
 to work fine. Starting Sage however resulted in the following:

 /Users/arnoldcd /Applications/sage ; /Applications/sage/sage
 --
 | SAGE Version 3.1.2, Release Date: 2008-09-19                       |
 | Type notebook() for the GUI, and license() for information.        |
 --
 The SAGE install tree may have moved.
 Regenerating Python.pyo and .pyc files that hardcode the install PATH
 (please wait at most a few minutes)...
 Please do not interrupt this.
 Traceback (most recent call last):
   File /Applications/sage/local/bin/sage-location, line 71, in
 module
     update_library_files(R)
   File /Applications/sage/local/bin/sage-location, line 39, in
 update_library_files
     open(LIB + F,'w').write(H)
 IOError: [Errno 13] Permission denied: '/Applications/sage/local/lib/
 libfplll.la'

Since you installed via sudo you do not own the Sage files. If you
start sage once under sudo this will likely fix those issues.

 sage:

 Typing notebook() gives me a list of previous notebooks; when I open
 one, type a new line and ask to evaluate nothing happens.

 The error message at startup never occurred before.
 What am I doing wrong?

 Regards,
 arnold

Cheers,

Michael
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[sage-support] Re: Seg fault with determinant calculation

[mabshoff]

On Sep 22, 4:23 pm, phil [EMAIL PROTECTED] wrote:
 On Sep 15, 10:26 am, Martin Albrecht [EMAIL PROTECTED]
 wrote:

SNIP

  I'll try to reproduce the crash and see what I can do about it. You could 
  help
  by running sage -gdb (if you have gdb installed) and send me the backtrace
  off list. Thanks.

   The original machine I was using was needed for other things.  So, I
 ran it on sage 3.1.2rc4 on sage.math.washington.edu and it completed
 successfully after 169446 seconds.  So, the problem was specific to
 the setup I was using or it was fixed in 3.1.2rc4.
   The scaling of the problem seems worse than it should be though.
 The 9x9 problem takes 40 seconds while the 10x0 problem takes 4236
 times longer.  That's worse than O(n!) let along O(n^3).
   If your curious, the test problem is 
 athttp://sage.math.washington.edu/home/fongpwf/sage_work/determinant_10...

It would be worth it to check foe either memory leaks or something
else fishy going on here via valgrind. Let me poke around to see if I
can find anything either in Sage or in libSingular.

 Phil

Cheers,

Michael
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[sage-support] Re: long arithmetic

[mabshoff]

On Sep 22, 6:17 pm, William Stein [EMAIL PROTECTED] wrote:
 On Mon, Sep 22, 2008 at 6:12 PM, Robert Bradshaw

SNIP

  This is a bug, so I've added it to trac:

 http://trac.sagemath.org/sage_trac/ticket/4171

  ... just after I added the ticket here:http://trac.sagemath.org/
  sage_trac/ticket/4170

 What's the rule about whose is a dupe then?  I posted on sage-support
 first, but you hit new ticket first.    I'll let you have the ticket; please
 mark mine a dupe.

 William

Well, my personal rule is this:

 * ticket with a patch closes other tickets as dupe
 * no patches: earlier ticket stays open *unless* the later ticket has
a much better description

In this case Robert's ticket with patch (that I am currently
doctesting and likely to merge in 10 minutes) wins :)

Cheers,

Michael
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[sage-support] Re: Mercurial problems in 3.1.2

[mabshoff]

On Sep 22, 8:41 pm, Justin C. Walker [EMAIL PROTECTED] wrote:
 On Sep 21, 2008, at 23:35 , mabshoff wrote:

Hi Justin,

  On Sep 21, 11:27 pm, Justin C. Walker [EMAIL PROTECTED] wrote:
  This is the same crap issue you hit when building 3.1.2.rc-something,
  i.e. emacs is linked against Apple's libnpng while launching it from
  hg causes it to pick up out linpng. Results in *boom*. You can work
  around this by writing an emacs script in SAGE_LOCAL/bin that sets
  DYLD_LIBRARY_PATH to the old DYLD_LIBRARY_PATH and then launches
  emacs.

 Well, that worked.  I actually used SAGE_ORIG_{LD,DYLD}_LIBRARY_PATH  
 to get it to work in all the cases I tried (and had to check the  
 $XXX_SET variables as well).  Thanks for the work-around.

No problem, good that it works for you.

  Is someone can find out where Apple has its modifications to libpng
  this issue can be resolved.

 I'll guess that it's a difference between versions (1.2.22 vs.  
 1.2.24), but I can't find old source on the libpng site, and it  
 doesn't show up on the Darwin site (which I infer means that they did  
 not change anything).  I'll poke further, but if anyone has a better  
 idea, speak up!

I am playing with libpng-1.2.32 since that is the latest release and
also has a boatload of security updates since the lowly 1.2.22 that we
ship. Hopefully this will resolve the symbol missing issues. I am
testing 3.1.3.alpha0 on OSX 10.5 to see if I can hit any of those
problems.

 Justin

Cheers,

Michael

 --
 Justin C. Walker, Curmudgeon at Large
 Institute for the Absorption of Federal Funds
 ---
 My wife 'n kids 'n dogs are gone,
 I can't get Jesus on the phone,
 But Ol' Milwaukee's Best is my best friend.
 ---
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[sage-support] Re: Mercurial problems in 3.1.2

[mabshoff]

On Sep 22, 10:16 pm, Justin C. Walker [EMAIL PROTECTED] wrote:
 On Sep 22, 2008, at 21:33 , mabshoff wrote:
[snip]

Hi Justin,

  I am playing with libpng-1.2.32 since that is the latest release and
  also has a boatload of security updates since the lowly 1.2.22 that we
  ship. Hopefully this will resolve the symbol missing issues. I am
  testing 3.1.3.alpha0 on OSX 10.5 to see if I can hit any of those
  problems.

 Is 1.2.32 in alpha0?  As well as the md5 and numpy fixes (for parallel  
 building)?

Nope, none of those fixes is in alpha0, but I hope that at least some
of them will make it into alpha1, due out late tomorrow. I still don't
see how parallel make impacts numpy, so if you could send me the
portion of the blown up numpy build with parallel make I could attempt
to figure out what is wrong.

 Justin

Cheers,

Michael

 --
 Justin C. Walker, Curmudgeon-At-Large
 Institute for the Absorption of Federal Funds
 
 Men are from Earth.
 Women are from Earth.
     Deal with it.
 
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[sage-support] Sage 3.1.2 released (i.e. binaries are available)

[mabshoff]

[Due to three security critical notebook bugs it is *highly*
recommended that you upgrade from all previous versions of Sage.
Binaries for all platforms are available at sagemath.org. The mirrors
are hopefully catching up soon.]

Hello folks,

Sage 3.1.2 was released on September 19th, 2008. It is available at

   http://sagemath.org/download.html

* About Sage (http://www.sagemath.org)

Sage is developed by volunteers and combines 71 open source packages.
It is available for download from sagemath.org and its mirrors in
source or binary form. If you have any questions and/or problems
please report them to the Google groups sage-devel or sage-support.
You can also drop by in #sage-devel or #sage-support in freenode.

-

The following 42 people contributed to this release:

 * Tim Abbott
 * Michael Abshoff
 * Martin Albrecht
 * Robert Bradshaw
 * Arnaud Bergeron [first contribution]
 * C. Boncelet [first contribution]
 * Tom Boothby
 * Michael Brickenstein
 * Ondrej Certik
 * Craig Citro
 * Timothy Clemans
 * John Cremona
 * Karl-Dieter Crisman
 * Burcin Erocal
 * Gary Furnish
 * Alex Ghitza
 * Andrzej Giniewicz
 * Jason Grout
 * Mike Hansen
 * Marshall Hampton
 * Chris Holdsworth [first contribution]
 * Hamish Ivey-Law [first contribution]
 * David Joyner
 * Josh Kantor
 * Simon King
 * Steve Linton
 * Jason Merrill [first contribution]
 * Robert Miller
 * Minh Nguyen
 * Willem Jan Palenstijn
 * John Palmieri
 * David Philp [first contribution]
 * Yi Qiang
 * Nils-Peter Skoruppa [first contribution]
 * Franco Saliola
 * William Stein
 * Griffen Thoma [first contribution]
 * Igor Tolkov
 * Ralf-Philipp Weinmann
 * Georg Weber [first contribution]
 * Carl Witty
 * Chris Wuthrich

Cheers,

Michael Abshoff (release chair), William Stein

* Major Features, New Spkgs and Bugfixes

 * Doctest Coverage Hits 60% (Mike Hansen and others)
 * Hidden Markov Models (William Stein)
 * Fix various Notebook Bugs (Timothy Clemans, Mike Hansen)
 * New Structures for Partition Refinement (Robert Miller)
 * Improved Dense Linear Algebra over GF(2) (Martin Albrecht)
 * Update to new PolyBoRi Version (0.5) and Improved Interface (Tim
Abbott, Michael Abshoff, Martin Albrecht)
 * QEPCAD Interface (Carl Witty)
 * Update Developer's Handbook (John Palmieri)
 * Improved 64-bit OSX Support (Michael Abshoff)
 * GAP Meataxe Interface (Simon King, David Joyner)
 * Better SymPy Integration (Ondrej Certik)
 * Real Number Inputs Improved (Robert Bradshaw)
 * Faster Determinants of Dense Matrices over Multivariate Polynomial
Rings (Martin Albrecht)
 * Arrow drawing improved (Jason Grout)
 * Eigen functions for matrices (Jason Grout)
 * Memory Leak fixes (Michael Abshoff, Craig Citro)

For details see the Sage 3.1.2 Release Tour at

  http://wiki.sagemath.org/sage-3.1.2

* Known Issues with 3.1.2:

 * RHEL 5 clisp build issue: the latest clisp.spkg does not build
   so please use the clisp.spkg from Sage 3.0.3.

* Bug Statistics

We closed 251 tickets. For details see

   http://trac.sagemath.org/sage_trac/milestone/sage-3.1.2

or check out the closed ticket section at the end of the
announcement.

* Upcoming Releases

The next release will be 3.1.3, chaired by Michael Abshoff. It will
be a mix of new features and bug fixes.

* Doctesting Coverage

For 3.1.1 we had:

Overall weighted coverage score:  56.5%
Total number of functions:  20920

We increased coverage by 4.0% in 3.1.2 while removing 336 functions:

Overall weighted coverage score:  60.5%
Total number of functions:  20584

* Closed Tickets:

Merged in Sage 3.1.2.rc5:

#3534: William Stein, John Palmieri: plot -- fix circle example in the
documentation [Reviewed by Mike Hansen]
#3894: John Palmieri: in tutorial, live version, triple dots are not
visible [Reviewed by Mike Hansen]
#4063: Timothy Clemans: properly escape the titles of worksheets
[Reviewed by Mike Hansen]
#4133: Mike Hansen, Michael Abshoff: sage.math - sage 3.1.2.rc4
doctest failure in interfaces/maxima.py [Reviewed By Robert Miller]
#4130: Michael Abshoff: #4125 does not work on OS X 10.4 [Reviewed by
Robert Miller]
#4131: Michael Abshoff: unbreak sage-clone [Reviewed by Mike Hansen]
#4137: William Stein: add doctests for user_type() in avatar.py
[Reviewed by Mike Hansen]
#4138: Michael Abshoff: Sage 3.1.2.rc5: fix documentation build issues
[Reviewed by Mike Hansen]

Merged in Sage 3.1.2.rc4:

#925: Michael Abshoff: valgrind options to sage (sage -valgrind, sage
-
callgrind, etc.) should be more customizable [Reviewed by Robert
Miller]
#1915: Alex Ghitza: infinity doesn't behave well [Reviewed by John
Cremona]
#3563: Michael Abshoff: make def atlas() deal with the Accelerate
Framework on OSX [Reviewed by Robert Miller]
#3675: Michael Abshoff: upgrade optinal valgrind.spkg to the 3.3.1
release [Reviewed by Robert Miller]
#3847: Alex Ghitza: can't make vector of ints [Reviewed by John
Cremona]
#4097: Robert Miller: matrix automorphism groups 

[sage-support] Re: problem of using surf in SAGE online server 2

[mabshoff]

On Sep 20, 11:37 am, pong [EMAIL PROTECTED] wrote:

Hi Pong,

 I tried the example

 sage: s = singular.eval
 sage: s('LIB surf.lib;')
       ...
 sage: s(ring rr0 = 0,(x1,x2),dp;)
       ...
 sage: s(ideal I = x1^3 - x2^2;)
       ''
 sage: s(plot(I);)

 inhttp://www.dms.umontreal.ca/~math/logiciels/Sage/const/node18.html#ch:AG

 Looks like surf has been loaded and everything is fine but at the end
 I got:

 Traceback (click to the left for traceback)
 ...
    skipping text from `;` error at token `)`

 Any help?

IIRC surf does depend on some Java binary code shipped with Singular
and we have removed it. I am also pretty sure surf is broken when used
via the notebook server.

Cheers,

Michael
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[sage-support] Re: Raising an Error resulted in a crash

[mabshoff]

On Sep 15, 4:07 pm, Robert Bradshaw [EMAIL PROTECTED]
wrote:
 On Sep 15, 2008, at 3:56 PM, Simon King wrote:



  Dear Robert,

  On Sep 16, 12:46 am, Robert Bradshaw [EMAIL PROTECTED]
  wrote:
  Try running as sage -gdb , which will catch the error. Then you can
  type bt at the prompt to get a c traceback.

  I don't understand what the following tells me.
  When there should be an error raised, instead i get:

  Program received signal SIGSEGV, Segmentation fault.
  [Switching to Thread 46922761735376 (LWP 26484)]
  0x0041befe in instancemethod_call (func=0x34ba680,
  arg=0x36ebab8,
      kw=0x0) at Objects/classobject.c:2477
  2477    Objects/classobject.c: Datei oder Verzeichnis nicht gefunden.
          in Objects/classobject.c
  (gdb) bt
  #0  0x0041befe in instancemethod_call (func=0x34ba680,
  arg=0x36ebab8,
      kw=0x0) at Objects/classobject.c:2477
  #1  0x00415913 in PyObject_Call (func=0x36ebab8,
  arg=0x36ebab8, kw=0x0)
      at Objects/abstract.c:1861
  #2  0x0047efd2 in PyEval_CallObjectWithKeywords
  (func=0x35a4f00,
      arg=0x36ebab8, kw=0x0) at Python/ceval.c:3442
  #3  0x0041dd68 in instance_getattr (inst=value optimized
  out,
      name=0x99a840) at Objects/classobject.c:755
  #4  0x2aad32fd7298 in ?? ()
  #5  0x in ?? ()

  That's all. But what does it mean?

 Hmm... that's not a very informative traceback (just generic Python  
 calls). I would try putting some print statements in. What is the  
 return type of the function you're raising an error from?

 - Robert

There are a couple things you can do:

a) boil it down to a simple patch against some recent 3.1.x and I can
take a look.
b) Build the Sage library with -O0. To do so edit $SAGE_ROOT/local/
lib/python2.5/config/Makefile and change

# Compiler options
OPT=-DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes

to

# Compiler options
OPT=-DNDEBUG -g -fwrapv -O0 -Wall -Wstrict-prototypes

Maybe that will help. Then do a sage -ba to rebuild the whole Sage
library

If that still does not help you can also build Python with -O0, but
we can do that later.

Cheers,

Michael
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[sage-support] Re: Raising an Error resulted in a crash

[mabshoff]

On Sep 15, 4:25 pm, Robert Bradshaw [EMAIL PROTECTED]
wrote:
 On Sep 15, 2008, at 4:22 PM, Simon King wrote:





  Dear Robert,

  simply for testing, i raise an error as soon as the init-method of my
  class is called. So, for the moment the code looks like this:
  class COHO:
      
      Docstring
      
      def __init__(self, *args, **kwds):
          raise ValueError, fooBAR...
          # followed by a lots of more code

  And now the reason why i am puzzled.
  If i write a .pyx file with the above content, then everything is fine
  (i.e., an error is raised, but no crash occurs). But with my module
  (although the relevant (?) part of it has exactly the above form), it
  fails:
  sage: from cohomology import *
  sage: H=COHO()
  /home/king/SAGE/devel/sage-3.1.1/local/bin/sage-sage: line 216: 27343
  Speicherzugriffsfehler  sage-ipython $@ -c $SAGE_STARTUP_COMMAND;

  Note that my class also has a __del__ method.
  Could that be the reason for the Speicherzugriffsfehler (what is it
  in english?)?
  I mean, would __del__ be called if __init__ fails?

 No idea what Speicherzugriffsfehler means (never heard of that  
 before) but __del__ might be called on a failing __init__.

invalid memory access :)

 For Cython, you might want to use __cinit__ and __dealloc__ (which  
 are guaranteed to be called exactly once in pairs).

 - Robert

Cheers,

Michael
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[sage-support] Re: bug in sage -clone for 3.1.2.rc4?

[mabshoff]

On Sep 15, 6:27 pm, David Joyner [EMAIL PROTECTED] wrote:
 Hi:

 After building 3.1.2.rc4 I got the following error when I tried to create a
 clone:

 snip

 SAGE build/upgrade complete!
 [EMAIL PROTECTED]:~/sagefiles/sage-3.1.2.rc4$ ./sage -clone dbl-coset
   File /home/wdj/sagefiles/sage-3.1.2.rc4/local/bin/sage-clone, line 71
     echo 'Pbuild is currently broken -- defaulting to serial build.'
                                                                    ^
 SyntaxError: invalid syntax

 real    0m0.043s
 user    0m0.018s
 sys     0m0.006s

 Does this make any sense?

Yes, it is a stupid buglet that we just fixed. It slipped by during
the review process since it was 5 am :(

 - David Joyner

Patch is up at #4131 that fixes the issue.

Cheers,

Michael
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[sage-support] Re: gmp.h again?

[mabshoff]

On Sep 11, 9:27 pm, TMichel [EMAIL PROTECTED] wrote:


Hi,

 Having a problem while building 3.1.1 on ia64 IRIX with gcc 4.4.  I
 donnot know what I am doing.  Info:

  uname -a

 Linux  2.6.5-7.244-sn2 #1 SMP Mon Dec 12 18:32:25 UTC 2005 ia64 GNU/
 Linux gcc --v

 Using built-in specs.
 Target: ia64-unknown-linux-gnu
 Configured with: ../gcc/configure --prefix=/home/me --enable-
 languages=c,c++,fortran --with-mpfr=/home/trm/
 Thread model: posix
 gcc version 4.4.0 20080911 (experimental) (GCC)
 ---
 mkdir .libs
  g++ -DHAVE_CONFIG_H -I. -I. -I.. -D__GMP_WITHIN_GMPXX -I.. -O3 -
 mtune=itanium2 -c isfuns.cc  -fPIC -DPIC -o .libs/isfuns.o
 In file included from isfuns.cc:25:
 ../gmp.h:516: error: 'std::FILE' has not been declared
 make[4]: *** [isfuns.lo] Error 1
 make[4]: Leaving directory `/mnt/uav-r0/trm/src/sage-3.1.1/spkg/build/
 gmp-4.2.2.p1.fake/src/cxx'
 make[3]: *** [all-recursive] Error 1
 make[3]: Leaving directory `/mnt/uav-r0/trm/src/sage-3.1.1/spkg/build/
 gmp-4.2.2.p1.fake/src'
 make[2]: *** [all] Error 2
 make[2]: Leaving directory `/mnt/uav-r0/trm/src/sage-3.1.1/spkg/build/
 gmp-4.2.2.p1.fake/src'
 Error building GMP.

 sage: An error occurred while installing gmp-4.2.2.p1.fake
 ---

 As noted in previous posts with similar problem
 commenting out the declarationstd::file in mpg.h
 enable compilation... but I have no idea how to
 fix the package.

 Apologies if this is a re-hash.

Nope, it isn't. I have a bunch of fixes to build Sage with gcc
4.4.CVS, but since that compiler is at Stage 3 they will not be in
3.1.2.  You need the following fixes which will likely make it into
the next release after 3.1.2.

Cheers,

Michael

Sage 3.1.2.rc0 vs. gcc 4.4-20080905

## gmp ## [clean fix]

 *  include cstdio in gmp-in.h

## ntl ## [clean fix]

 *  in src/WizardAux - add $|++; in the function to force autoflush
this might be broken: CFILEOUT-flush();, but seems to be the
recommended way to do things

 *  In tools.h add include cstdio for EOF

## matplotlib ## [clean fix]

 * add #include cstdio in src/mplutils.cpp

## libfplll ## [dirty fix]

 * src/nr.cpp - scope issues with gmp's and mpfr's string functions in
some templates

## polybori ## [clean fix?]

 * boost busted +138 boost_1_34_1.cropped/boost/mpl/apply.hpp and
others: problem might be extra () in a bunch of places

## clisp ##

 * internal compiler error - http://gcc.gnu.org/bugzilla/show_bug.cgi?id=37418

gcc -Igllib -O0 -g -I/home/mabshoff/build-3.1.2.rc0/sage-3.1.2.rc0-eno-
gccc-4.4-2008-09-5/local/include/ -L/home/mabshoff/build-3.1.2.rc0/
sage-3.1.2.rc0-eno-gccc-4.4-2008-09-5/local/lib/ -W -Wswitch -Wcomment
-Wpointer-arith -Wimplicit -Wreturn-type -Wmissing-declarations -Wno-
sign-compare -O -falign-functions=4 -DUNICODE -DNO_SIGSEGV -I. -c
eval.c
eval.d: In function ‘unwind_upto’:
eval.d:656: error: type mismatch in address expression
void (*restartf_t) (void * *)

void (*T14ab) (void * *)

unwind_protect_to_save.fun = unwind_upto;

eval.d:656: internal compiler error: verify_gimple failed
Please submit a full bug report,
with preprocessed source if appropriate.
See http://gcc.gnu.org/bugs.html for instructions.
make: *** [eval.o] Error 1
Error building clisp

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[sage-support] Re: PIL and jpeg on OS X workaround

[mabshoff]

On Sep 10, 7:11 pm, Jason Merrill [EMAIL PROTECTED] wrote:

Hi Jason,

 I had been having trouble for a while figuring out how to load jpgs
 into a usable form on OS X.  The optional PIL spkg that gets installed
 through sage -i PIL-1.1.5.spkg would throw an IOError when I tried to
 load in a jpeg, complaining that the jpeg decoder wasn't available.

 I found a work around tonight, which was to install PIL through
 macports (py25-pil is the package name).  I already had libjpeg
 installed through macports (jpeg is the package name).  Then I just
 went into the directory where PIL got installed, /opt/local/lib/
 python2.5/site-packages/, and then copied the PIL folder and PIL.pth
 into sage's python: /Applications/sage/local/lib/python/site-packages/

Sage 3.1.2 will have the fixes so we no longer end up using Apple's
IOKit. This caused a bunch of issues with libpng.dylib similar to the
above. There is an spkg for libjpeg, but it is not merged yet. Once
that is merged the above problem will go away.

 With that stuff there, I can now do

 sage: import pylab
 sage: imjpg = pylab.imread(DATA+'aarts02.jpg')
 sage: pylab.imshow(imjpg)
 sage: pylab.savefig('imjpg')

 and I actually see an image.

 If I can provide information or anything else helpful for turning this
 hack into something that works the way sage is supposed to, please let
 me know.

 Regards,

 JM

Cheers,

Michael
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[sage-support] Re: sage on eeepc

[mabshoff]

On Sep 10, 12:20 pm, hypermonkey2 [EMAIL PROTECTED] wrote:

Hi,

 OK! so ive managed to extract sage onto an SD card (ext2 formatted).
 when i run sage, i get this:
 --
 | SAGE Version 3.1.1, Release Date: 2008-08-17                       |
 | Type notebook() for the GUI, and license() for information.        |
 --
 /usr/bin/env: sage.bin: No such file or directory
 /home/user/E:/sage/local/bin/sage-sage: line 171: sage-cleaner:
 command not found
 /home/user/E:/sage/local/bin/sage-sage: line 218: sage-ipython:
 command not found

 any ideas??

Did you mount the disk to /home/user/E:? The colon, i.e. : is a
path separation character under Linux/Unix, so this cannot work.
Moving Sage to some place where the path has no colon should work.

 Thanks!
 Jon

Cheers,

Michael
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[sage-support] Re: Trace of Hecke Operator with large integer

[mabshoff]

Hi,

even  with what will become 3.1.2.rc2 this blows up on a 32 bit build:

varro:~/sage-3.1.2.rc1 mabshoff$ ./sage
--
| SAGE Version 3.1.2.rc1, Release Date: 2008-09-08   |
| Type notebook() for the GUI, and license() for information.|
--

sage: M1 =  ModularSymbols(21,2)
sage: T1 =  M1.hecke_operator(13^8)
sage: trace1=T1.trace()
sage: print trace1
2651076189
sage: M1 =  ModularSymbols(21,2)
sage: T1 =  M1.hecke_operator(13^9)
---
TypeError Traceback (most recent call
last)

/Users/mabshoff/sage-3.1.2.rc1/ipython console in module()

/Users/mabshoff/sage-3.1.2.rc1/local/lib/python2.5/site-packages/sage/
modular/hecke/module.py in hecke_operator(self, n)
858int n -- an integer at least 1.
859 
-- 860 return self.hecke_algebra().hecke_operator(n)
861
862 def T(self, n):

/Users/mabshoff/sage-3.1.2.rc1/local/lib/python2.5/site-packages/sage/
modular/hecke/algebra.py in hecke_operator(self, n)
184 pass
185 n = int(n)
-- 186 T = hecke_operator.HeckeOperator(self, n)
187 self.__hecke_operator[n] = T
188 return T

/Users/mabshoff/sage-3.1.2.rc1/local/lib/python2.5/site-packages/sage/
modular/hecke/hecke_operator.py in __init__(self, parent, n)
360 HeckeAlgebraElement.__init__(self, parent)
361 if not isinstance(n, int):
-- 362 raise TypeError, n must be an int
363 self.__n = n
364

TypeError: n must be an int

Ticket time: we are tracking the problem at 
http://trac.sagemath.org/sage_trac/ticket/4098

Cheers,

Michael
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[sage-support] Re: Trace of Hecke Operator with large integer

[mabshoff]

On Sep 10, 2:09 pm, Raouf [EMAIL PROTECTED] wrote:
 i have windows Xp Os and i use sage 3.1.1 vmware with notebook.

Ok, then you are using a 32 bit build. At

http://trac.sagemath.org/sage_trac/attachment/ticket/4098/trac-4098.patch

you can find a patch that fixes the issue and should cleanly apply
against 3.1.1. It will be in 3.1.2 which should be out in a few days.

Cheers,

Michael
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[sage-support] Re: problems with sage notebook and folder sharing on windows

[mabshoff]

On Sep 4, 7:28 pm, david [EMAIL PROTECTED] wrote:

Hi David,

 I just installed the VMWare  player and SAGE on my Windows XP
 machine.  The sage notebook does not come up, a slew of error messages
 are given, and the VMWare folder sharing does not seem to work.  I
 would post the error messages but there does not seem to be a way to
 copy data out of the VMWare player, nor to scroll upward in the
 window.  I also tried to run a browser outside of VMWare and open the
 localhost address given, but it did not work.  Any tips?  The sage
 version is 3.0.1 release data 2008-05-05, the VMWare is current as of
 9-04-08.

That is rather old. Where did you get the VMWare image? The current
download version is 3.0.6 (Sage 3.1.1 is out, but the VMWare image has
not been updated yet).

I suspect your download is either corrupted or incomplete. What size
is it?

 Also the VMWare only uses about a 1/4 of the screen, even in full
 screen mode, is there a way to enlarge the font in the shell?

Hmm, VMWare might have some settings, but there is not many knobs to
tweak.

 best regards,

 David

Cheers,

Michael
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[sage-support] Re: Copying/moving worksheets

[mabshoff]

On Sep 2, 2:44 pm, Marshall Hampton [EMAIL PROTECTED] wrote:
 I'm a little confused - I upgrade my sage version often in the middle
 of semesters.  Since the notebook lives in a seperate directory it
 shouldn't be a problem.

 Perhaps my confusion is related to the VMWare server, because I don't
 use that.  I thought you could upgrade those though.

 -M. Hampton


Odd, this discussion ended somehow on sage-devel, too.

Anyway: in this context upgrade == download new VMWare image of Sage.

As Marshall pointed out: the in-place upgrade should work and as I
mentioned in the sage-devel thread one should make a copy of the
VMWare image with the data before attempting to do so since if one has
backups fewer things tend to go wrong due to Murphy's law :)

Cheers,

Michael
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[sage-support] Re: failed to download cddlib-094b.p1

[mabshoff]

On Aug 29, 7:33 am, Thierry Dumont [EMAIL PROTECTED] wrote:
 Trying to install polymake in sage 3.1, I got the message:


Hi Thierry,

this is a known issue and I have a fixed spkg-install that should once
and for all resolve the issue. We are tracking this at #3640 and I
need to put up a spkg and get it reviewed since I have been sitting on
this for a while.

Sorry that this is taking so long :(

 **
 * Unable to download cddlib-094b.p1
 * Please seehttp://www.sagemath.org//packagesfor a list of valid
 * packages or check the package name.
 **
 sage: Failed to download package cddlib-094b.p1 fromhttp://www.sagemath.org/

 yours
 t.d.

Cheers,

Michael

  tdumont.vcf
  1KViewDownload

  smime.p7s
 5KViewDownload
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[sage-support] Re: numerically solving a polynomial system of equations

[mabshoff]

On Aug 25, 1:21 am, iSAGE [EMAIL PROTECTED] wrote:
 There is a matlab/octave interface to it. Look at the following
 reference onhttp://www.math.uic.edu/~jan/
 I don't know more about this since I am also at the moment collecting
 information on how to solve a large system of polynomial equations.

 Yun Guan and Jan Verschelde: PHClab: A MATLAB/Octave interface to
 PHCpack. The abstract and  paper . Take a look at the  Poster. In IMA
 Volume 148: Software for Algebraic Geometry, edited by Michael E.
 Stillman, Nobuki Takayama, and Jan Verschelde. Pages 15-32, Springer-
 Verlag, 2008.

 Bhalchandra Thatte

There is also a quite sophisticated interface in Sage, but as long as
the code is written in Ada there is a zero percent chance that that
code will become standard in Sage. The optional package we have is a
bunch of binaries since Ada support is usually not available. Note
that at least until recently there was not even a 64 bit x86-64 ot
Itanium binary on Verschelde's website.

Cheers,

Michael
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[sage-support] Re: numerically solving a polynomial system of equations

[mabshoff]

On Aug 24, 2:22 pm, William Stein [EMAIL PROTECTED] wrote:
 On Sun, Aug 24, 2008 at 2:03 PM, Joshua Kantor [EMAIL PROTECTED] wrote:

  1. I would recommend looking at phcpack, it is designed to exploit the
  special nature of large polynomial systems, however, supposedly I
  believe it is sometimes difficult to compile, I've never used it but

           ^

 It is written in ADA.

And building the GNU Ada compiler from sources is a giant pain unless
you have the GNU Ada compiler to bootstrap. I did build some phcpack
binaries for x86-64 Linux and it has a tendency to segfault when run
on say Debian if the binary was build on a FC8 box and vice versa. I
mainly wanted an Itanium binary, but cross compiling the ada toolchain
was just plainly not worth it for it.

So in conclusion: great code if you can use a binary that works, if
you need to build from sources it plainly sucks. The lesson learned
here is not to use exotic languages since the (alleged) benefit from
using Ada is far outweight by the fact that the practicality of
building the code :)

SNIP

 William Stein

Cheers,

Michael

 Associate Professor of Mathematics
 University of Washingtonhttp://wstein.org

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[sage-support] Re: polymake

[mabshoff]

On Aug 18, 2:37 pm, Alec Mihailovs [EMAIL PROTECTED] wrote:

Hi Alec,

 I just tried to install polymake (an optional package) in Sage 3.1.1 and it
 failed because it tried to find cddlib-094b.p1 while the next patch,
 cddlib-094b.p2 is included in standard packages.

 Alec

I have an updates spkg that fixes those issues once and for all. I
need to polish it and have it reviewed so that I can push it into the
repo.

Cheers,

Michael
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[sage-support] Re: Plans for a Sage port to Solaris ??

[mabshoff]

On Jul 22, 1:46 am, Pierre [EMAIL PROTECTED] wrote:
  Did the 32 bit binary work for you, i.e. did it at least start up?

 er... which one ? i keep having a look at the following page:

 http://wiki.sagemath.org/solaris

Oops, I did not mention it there, but only in a similar thread on sage-
devel.

 and i'm waiting for a 'download' link to pop up one day. Obviously i'm
 confused ! how does one get a binary ??

Check out

http://sage.math.washington.edu/home/mabshoff/release-cycles-3.0.5/

 i sort of feel like a charlie !

 cheers
 pierre

I will likely do a custom 3.0.6 binary in a day or two with numpy 1.1
that is supposed to fix a number of Solaris specific issues with numpy
that cause the root finding code to segfault. The binary is not ready
for prime time, but should at least start up and lets you play around.
Note that the (secure) notebook is broken, but I have a good lead how
to fix it.

Cheers,

Michael

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