Sage 3.4.1.rc4 released

[mabshoff]

Hello folks,

here goes rc4, only slightly later than planned :)

Anyway, we fixed nearly every blocker and postponed the the fixing of
the failing doc doctests, i.e. #5806 for now.

Aside from that we had the update to the latest MPIR 1.1, downgrade of
GAP to 4.4.10 and the update of clisp 2.47/maxima with a special no-
readline mode. This will not fix all observed strange Maxima hangs,
but at least some of the rather strange random ones. Gentoo users
should rejoice since this clisp release should build on more Gentoo
boxen, but it is broken on SLES 10/Itanium. Since the previous clisp
release was broken on RHEL 5.2/Itanium it seems to be business as
usual. Oh well, clisp's presence in Sage should be short lived at this
stage anyway since Sage 4.0 is supposed to work on Solaris/Sparc and
that mandates the ecl switch. Couple that with pynac being default for
Symbolics and a lot of the calls to Maxima should disappear
shortly :).

Another long standing problem were some issues with ATLAS, i.e.
building on Atom would take forever (this is now fixed) and Sage
binaries would require SSE3. Now we have the infrastructure in place
to create SSE2 only binaries, but the penalty for that is a decrease
in speed for certain LA problems for example. We have not done any
benchmarking, but it would be nice to do so before release.

As usual sources, the update bits and a sage.math binary can be found
at

http://sage.math.washington.edu/home/mabshoff/release-cycles-3.4.1/

Please build, test and report any issues. Unless something goes
terribly wrong this should be identical with the final 3.4.1 release
aside from two tickets affecting only the -bdist code and potential
last minute doctest fixes.

Cheers,

Michael

Merged in Sage 3.4.1.rc4:

#4933: John Cremona: lots of files in sage.schemes.elliptic_curves are
not included in the reference manual [Reviewed by John Palmieri]
#5219: Michael Abshoff: Build ATLAS in dist mode with SSE2 only
[Reviewed by William Stein]
#5378: Michael Abshoff: Sage 3.3: numerical noise in rings/polynomial/
complex_roots.py on cicero & fulvia [Reviewed by Rob Beezer]
#5541: Minh Van Nguyen, John Palmieri: more formatting fixes for
quaternion_algebra.py docstring [Reviewed by John Palmieri, Minh Van
Nguyen]
#5662: Gonzalo Tornaria: Fix timing issue in clisp-readline in maxima
pexpect [Reviewed by Dan Drake, Michael Abshoff]
#5697: Michael Abshoff: Sage 3.4.1.rc1: Downgrade GAP to 4.4.10
[Reviewed by William Stein]
#5741: Michael Abshoff: Detect Atom CPUs as Core2 in the ATLAS
detection script [Reviewed by William Stein]
#5742: Michael Abshoff: ATLAS.spkg: parallel make breaks on system
with "real" sh [Reviewed by William Stein]
#5785: Robert Bradshaw: RDF(0)^(1/2) is NaN [Reviewed by Michael
Abshoff]
#5788: Michael Abshoff: Fix MPIR build problem on OSX 10.4 exposed by
linbox, update to latest upstream [Reviewed by Georg Weber]
#5805: Michael Abshoff: Sage 3.4.1.rc3: numerical noise in "devel/sage/
sage/modular/dirichlet.py" [Reviewed by John Cremona]
#5808: John Cremona, John Palmieri: fix most warnings when building
the reference manual [Reviewed by John Palmieri, John Cremona]
#5816: William Stein: doctesting -- make it possible run doctests in
order from file, in random order, and in random seeded order [Reviewed
by Carl Witty]
#5823: Gonzalo Tornaria, Michael Abshoff: Update clisp to 2.47 and
introduce noreadline mode dynammically for clisp and maxima [Reviewed
by Michael Abshoff, Gonzalo Tornaria]
#5826: Dan Drake: add nodoctest to sagedoc.py and sageinspect.py to
work around #5806 [Reviewed by Michael Abshoff]

[mabshoff]

Oh well, there is one known build issues on OSX when SAGE64 is set to
"yes" - not that too many people will run into this. The workaround
fix is at #5817 and will be in 3.4.2.

Cheers,

Michael

[John Cremona]

Built fine and all tests pass on 32-bit Suse and 64-bit kubuntu.

John

2009/4/20 mabshoff <mabs...@googlemail.com>:

[Jaap Spies]

mabshoff wrote:
> Hello folks,
>
> here goes rc4, only slightly later than planned :)
>

[...]

>
> As usual sources, the update bits and a sage.math binary can be found
> at
>
> http://sage.math.washington.edu/home/mabshoff/release-cycles-3.4.1/
>
> Please build, test and report any issues. Unless something goes
> terribly wrong this should be identical with the final 3.4.1 release
> aside from two tickets affecting only the -bdist code and potential
> last minute doctest fixes.
>

On Fedora 9, 32 bit all tests passed!

Jaap

[John H Palmieri]

I have the same problem I reported with 3.4.1.rc3: on an ubuntu box
(perhaps ubuntu 8.04?), Sage() seems broken, leading to failures in
randstate.pyx and sage0.py.

$ uname -a
Linux jpalmieri538 2.6.24-23-generic #1 SMP Wed Apr 1 21:47:28 UTC
2009 i686 GNU/Linux

I'm appending logs from the failures, plus a sample sage session
displaying some problems. What other information would help to track
this down?

John


sage -t "devel/sage/sage/misc/randstate.pyx"
**********************************************************************
File "/home/palmieri/Documents/sage-3.4.1.rc4-upgrade/devel/sage/sage/
misc/randstate.pyx", line 124:
: s = ZZ(subsage('initial_seed()'))
Exception raised:
Traceback (most recent call last):
File "/home/palmieri/Documents/sage-3.4.1.rc3/local/bin/
ncadoctest.py", line 1231, in run_one_test
self.run_one_example(test, example, filename, compileflags)
File "/home/palmieri/Documents/sage-3.4.1.rc3/local/bin/
sagedoctest.py", line 38, in run_one_example
OrigDocTestRunner.run_one_example(self, test, example,
filename, compileflags)
File "/home/palmieri/Documents/sage-3.4.1.rc3/local/bin/
ncadoctest.py", line 1172, in run_one_example
compileflags, 1) in test.globs
File "<doctest __main__.example_0[32]>", line 1, in <module>
s = ZZ(subsage('initial_seed()'))###line 124:
: s = ZZ(subsage('initial_seed()'))
File "parent.pyx", line 288, in
sage.structure.parent.Parent.__call__ (sage/structure/parent.c:4320)
File "coerce_maps.pyx", line 155, in
sage.structure.coerce_maps.NamedConvertMap._call_ (sage/structure/
coerce_maps.c:4225)
File "/home/palmieri/Documents/sage-3.4.1.rc4-upgrade/local/lib/
python2.5/site-packages/sage/interfaces/expect.py", line 1648, in
_integer_
return sage.rings.all.Integer(repr(self))
File "integer.pyx", line 517, in
sage.rings.integer.Integer.__init__ (sage/rings/integer.c:6446)
TypeError: unable to convert x
(=---------------------------------------------------------------------------
AttributeError Traceback (most recent
call last)

/home/palmieri/.sage/temp/jpalmieri538/15614/
_home_palmieri__sage_init_sage_0.py in <module>()

/home/palmieri/Documents/sage-3.4.1.rc4-upgrade/local/lib/
python2.5/site-packages/sage/misc/functional.pyc in gen(x)
353 Return the generator of x.
354 """
--> 355 return x.gen()
356
357 def gens(x):

AttributeError: 'int' object has no attribute 'gen') to an integer
**********************************************************************
File "/home/palmieri/Documents/sage-3.4.1.rc4-upgrade/devel/sage/sage/
misc/randstate.pyx", line 131:
: r == ZZ.random_element(2^200)
Expected:
True
Got:
False
**********************************************************************
1 items had failures:
2 of 62 in __main__.example_0
***Test Failed*** 2 failures.


sage -t "devel/sage/sage/interfaces/sage0.py"
**********************************************************************
File "/home/palmieri/Documents/sage-3.4.1.rc4-upgrade/devel/sage/sage/
interfaces/sage0.py", line 55:
sage: a^3
Expected:
8
Got:
<BLANKLINE>
**********************************************************************
File "/home/palmieri/Documents/sage-3.4.1.rc4-upgrade/devel/sage/sage/
interfaces/sage0.py", line 62:
sage: V.gens()
Expected:
((1, 0, 0, 0), (0, 1, 0, 0), (0, 0, 1, 0), (0, 0, 0, 1))
Got:
<BLANKLINE>

(and this one goes on for a while longer).

Here's an excerpt from a sage session, showing some similar problems.

sage: subsage = Sage()
sage: subsage
(2)

sage: subsage
('2')
2
sage: a = subsage
('2')
sage:
a^3

sage:
a

sage: subsage('initial_seed
()')
2
sage: subsage('initial_seed
()')
112766853689368064777514174538283835612
sage: ZZ(subsage('initial_seed
()'))
---------------------------------------------------------------------------
TypeError Traceback (most recent call
last)

/home/palmieri/.sage/temp/jpalmieri538/10361/
_home_palmieri__sage_init_sage_0.py in <module>()

/usr/local/share/sage/local/lib/python2.5/site-packages/sage/structure/
parent.so in sage.structure.parent.Parent.__call__ (sage/structure/
parent.c:4320)()

/usr/local/share/sage/local/lib/python2.5/site-packages/sage/structure/
coerce_maps.so in sage.structure.coerce_maps.NamedConvertMap._call_
(sage/structure/coerce_maps.c:4225)()

/usr/local/share/sage/local/lib/python2.5/site-packages/sage/
interfaces/expect.pyc in _integer_(self, ZZ)
1646 """
1647 import sage.rings.all
-> 1648 return sage.rings.all.Integer(repr(self))
1649
1650 def _rational_(self):

/usr/local/share/sage/local/lib/python2.5/site-packages/sage/rings/
integer.so in sage.rings.integer.Integer.__init__ (sage/rings/
integer.c:6446)()

TypeError: unable to convert x
(=---------------------------------------------------------------------------
AttributeError Traceback (most recent call
last)

/home/palmieri/.sage/temp/jpalmieri538/10420/
_home_palmieri__sage_init_sage_0.py in <module>()

/usr/local/share/sage/local/lib/python2.5/site-packages/sage/misc/
functional.pyc in gen(x)
353 Return the generator of x.
354 """
--> 355 return x.gen()
356
357 def gens(x):

AttributeError: 'int' object has no attribute 'gen') to an integer

[mabshoff]

On Apr 20, 3:44 pm, John H Palmieri <jhpalmier...@gmail.com> wrote:
> On Apr 20, 12:17 am, mabshoff <mabsh...@googlemail.com> wrote:

<SNIP>

Hi John,

> I have the same problem I reported with 3.4.1.rc3: on an ubuntu box
> (perhaps ubuntu 8.04?), Sage() seems broken, leading to failures in
> randstate.pyx and sage0.py.
>
> $ uname -a
> Linux jpalmieri538 2.6.24-23-generic #1 SMP Wed Apr 1 21:47:28 UTC
> 2009 i686 GNU/Linux
>
> I'm appending logs from the failures, plus a sample sage session
> displaying some problems. What other information would help to track
> this down?
>
>   John

<SNIP>

Is this an upgrade (it seems to indicate that by the directory name).
After checking that there aren't any multiple heads I would recommend
to nuke devel/sage and force the rebuild of the sage-3.4.1.rc4.spkg.
Obviously this will delete any work you have been doing in the Sage
branch (just mentioning it if someone else reads this - I am sure you
are well aware of this :)).

Since no one else has reported the problem with Ubuntu 8.04 (which
seems to be common) I am not quite sure what to make of it. A failure
in randstate.pyx does worry me a lot more than Sage().

Cheers,

Michael

[Marshall Hampton]

All tests passed on my intel mac running 10.4.

-Marshall

[John H Palmieri]

On Apr 20, 3:53 pm, mabshoff <mabsh...@googlemail.com> wrote:
> On Apr 20, 3:44 pm, John H Palmieri <jhpalmier...@gmail.com> wrote:
>
> > On Apr 20, 12:17 am, mabshoff <mabsh...@googlemail.com> wrote:
>
> <SNIP>
>
> Hi John,
>
> > I have the same problem I reported with 3.4.1.rc3: on an ubuntu box
> > (perhaps ubuntu 8.04?), Sage() seems broken, leading to failures in
> > randstate.pyx and sage0.py.
>
> > $ uname -a
> > Linux jpalmieri538 2.6.24-23-generic #1 SMP Wed Apr 1 21:47:28 UTC
> > 2009 i686 GNU/Linux
>
> > I'm appending logs from the failures, plus a sample sage session
> > displaying some problems. What other information would help to track
> > this down?
>
> >   John
>
> <SNIP>
>
> Is this an upgrade (it seems to indicate that by the directory name).

It is an upgrade (based on an uncloned unmodified sage-main), but I
had the same problem with an upgrade and a fresh install of 3.4.1.rc3.

> After checking that there aren't any multiple heads I would recommend
> to nuke devel/sage and force the rebuild of the sage-3.4.1.rc4.spkg.
> Obviously this will delete any work you have been doing in the Sage
> branch (just mentioning it if someone else reads this - I am sure you
> are well aware of this :)).

When I left my office, it was still compiling from scratch, so I'll
also check that version.

> Since no one else has reported the problem with Ubuntu 8.04 (which
> seems to be common) I am not quite sure what to make of it. A failure
> in randstate.pyx does worry me a lot more than Sage().

It's the computer in my office at UW, so if it would help, you could
actually look at the computer...

Also, the failure in randstate.pyx is failing because Sage() is
failing: in the line "s = ZZ(subsage('initial_seed()'))", subsage is
defined to be Sage().

John

[Justin C. Walker]

On Apr 20, 2009, at 00:17 , mabshoff wrote:

>
> Hello folks,
>
> here goes rc4, only slightly later than planned :)

> As usual sources, the update bits and a sage.math binary can be found
> at
>
> http://sage.math.washington.edu/home/mabshoff/release-cycles-3.4.1/

Built as an upgrade to rc3 (upgraded from rc2, upgraded from rc1). No
problems in the build (Mac OS X, 10.5.6, Dual Quad Xeon). All tests
passed!

Justin

--
Justin C. Walker
Curmudgeon-at-large
Director
Institute for the Absorption of Federal Funds
----
186,000 Miles per Second
Not just a good idea:
it's the law!
----

[mabshoff]

Ok, the last patch awaiting review for 3.4.1 is at #5284. It finishes
the SSE2 only build mode and is a trivial change to $SAGE_LOCAL/bin/
sage-location. Once it is reviewed and merged I will cut 3.4.1.
Volunteers?

Cheers,

Michael

[mabshoff]

Thanks to Gonzalo and William the patch has been reviewed and merged.

I also tested cloning as well as nuking build and building from
scratch, so once doctest pass for that build I will cut the final
3.4.1 source tarball. It should be available for upgrades, etc, from
the sagemath.org website in the near future.

> Cheers,
>
> Michael

Cheers,

Michael