Update PARI to version 2.5.0

[jdemeyer]

We need to add bugfixes for

1. ​http://pari.math.u-bordeaux.fr/cgi-bin/bugreport.cgi?bug=1147 (#9334)
2. ​http://pari.math.u-bordeaux.fr/cgi-bin/bugreport.cgi?bug=1153 (#10195)
3. ​http://pari.math.u-bordeaux.fr/cgi-bin/bugreport.cgi?bug=1154 (#11604)
4. ​http://pari.math.u-bordeaux.fr/cgi-bin/bugreport.cgi?bug=1184 (related to #9937)
5. ​http://pari.math.u-bordeaux.fr/cgi-bin/bugreport.cgi?bug=1185 (PARI bug discovered by a Sage doctest)
6. ​http://pari.math.u-bordeaux.fr/cgi-bin/bugreport.cgi?bug=1186 (PARI performance regression discovered by a Sage doctest)
7. ​http://pari.math.u-bordeaux.fr/cgi-bin/bugreport.cgi?bug=1187 (PARI bug discovered by a Sage doctest)
8. ​http://pari.math.u-bordeaux.fr/cgi-bin/bugreport.cgi?bug=1188 (PARI bug discovered by a Sage doctest)
9. #10240 (pari-2.4.3.svn-12577.p9 incorrectly checks for the shared library on Cygwin). We simply use the spkg patch from that ticket.
10. ​http://pari.math.u-bordeaux.fr/cgi-bin/bugreport.cgi?bug=1192 (#10767)

We will do this by updating to PARI version 2.5.0, which is equal to svn revision 13228.

---

See also:

• #9343, #10430 (previous PARI upgrades)
• #10247 (Sage 4.6 has PARI problems on Cygwin)
• #10240 (pari-2.4.3.svn-12577.p9 incorrectly checks for the shared library on Cygwin), included in the 2.4.3.alpha.p7 spkg at #11605
• #11605 (Typos in PARI's spkg-install (2.4.3.alpha.p5)), included in the 2.4.3.alpha.p7 spkg at #11605

---

Apply:

1. spkg ​http://boxen.math.washington.edu/home/jdemeyer/spkg/pari-2.5.0.p0.spkg
2. spkg #11321 ​http://boxen.math.washington.edu/home/jdemeyer/spkg/lcalc-1.23.p7.spkg
3. 11130_sagelib.patch​ (jdemeyer)
4. trac_11130-doctest-poly.patch​ (cremona)
5. 11130_sagelib32.patch​ (cremona)
6. 11130-sagelib-simon.patch​ (cremona)
7. 11130_reviewer32.patch​ (jdemeyer)
8. extcode patch 11130-extcode-simon.patch​ (cremona)

[cremona]

I am currently testing this. To avoid duplication of effort, I'll fix things I find in the elliptic_curves directory only.

[cremona]

After (1) Building a fresh 4.7.alpha5 from scratch, (2) installing the spkg lined here with "sage -f", (3) applying the patch here to the sage library and (4) running "sage -b", I find that the Sage build will not start up properly:

ImportError                               Traceback (most recent call last)
...

/home/jec/sage-4.7.alpha5.11130/local/lib/python2.6/site-packages/sage/misc/functional.py in <module>()
     36 
     37 
---> 38 from sage.rings.complex_double import CDF
     39 from sage.rings.real_double import RDF, RealDoubleElement
     40 

/home/jec/sage-4.7.alpha5.11130/local/bin/gen.pxd in init sage.rings.complex_double (sage/rings/complex_double.c:15178)()

ImportError: /home/jec/sage-4.7.alpha5.11130/local/lib/python2.6/site-packages/sage/libs/pari/gen.so: undefined symbol: defaultOut
Error importing ipy_profile_sage - perhaps you should run %upgrade?
WARNING: Loading of ipy_profile_sage failed.

so I cannot test anything.

Did I do something wrong?

[jdemeyer]

Replying to cremona:

Did I do something wrong?

This ticket depends on #11230.

[cremona]

Replying to jdemeyer:

Replying to cremona:

Did I do something wrong?

This ticket depends on #11230.

I see! I'll have some time to spend on this tomorrow (Monday) so I'll have another go.

[jdemeyer]

Replying to cremona:

I am currently testing this. To avoid duplication of effort, I'll fix things I find in the elliptic_curves directory only.

Sounds good, I will look at everything else.

[cremona]

Applies after previous

[cremona]

I added a patch which fixes the doctest failures in sage/rings/polynomial/polynomial_quotient_ring.py . In all cases the new output was equivalent to the old.

There are now just some failures in sage/schemes/elliptic_curves/ell_rational_field.py (2 doctests failed) and sage/schemes/elliptic_curves/ell_number_field.py (1 doctests failed).

[cremona]

ell_rational_field.py: only one failure, looks completely trivial but will be left until #11005 to be fixed.

ell_number_field.py: one failure, even more trivial: the final output is exactly the same as it was but the verbose output is a little different, so this can be easily cleaned up at #11005.

As far as I am concerned this needs *no more work* on this ticket, but I'll delay marking it positive review until the same is possible at #11005. Still, it certainly gets "needs review" on that basis.

[jdemeyer]

This patch should also be tested on various systems first, PARI is known to produce different results on 32-bit and 64-bit systems.

[cremona]

Replying to jdemeyer:

This patch should also be tested on various systems first, PARI is known to produce different results on 32-bit and 64-bit systems.

Good point. I can test it on my 32-bit laptop.

[jdemeyer]

In sage/rings/number_field/number_field.py, there is a test which fails only when -long is not used.

[jdemeyer]

New patch fixes the long time issue (by setting a random seed explicitly). I will test on a Mac OS X 10.4 32-bit PPC system.

[cremona]

Testing now on a 32-bit ubuntu system.

[cremona]

Replying to cremona:

Testing now on a 32-bit ubuntu system.

... which gave several more failures:

	sage -t  devel/sage-main/sage/rings/number_field/number_field.py # 1 doctests failed
	sage -t  devel/sage-main/sage/schemes/elliptic_curves/ell_number_field.py # 2 doctests failed
	sage -t  devel/sage-main/sage/schemes/elliptic_curves/ell_rational_field.py # 1 doctests failed
	sage -t  devel/sage-main/sage/rings/number_field/number_field_element.pyx # 1 doctests failed
	sage -t  devel/sage-main/sage/rings/polynomial/polynomial_quotient_ring.py # 3 doctests failed
	sage -t  devel/sage-main/sage/rings/integer.pyx # 1 doctests failed

Details:

sage -t  "devel/sage-main/sage/rings/number_field/number_field.py"
**********************************************************************
File "/home/john/sage-4.7.alpha5/devel/sage-main/sage/rings/number_field/number_field.py", line 3616:
    sage: L.factor(a + 1)
Expected:
    (Fractional ideal (1/2*a*b + a + 1/2)) * (Fractional ideal (-1/2*b - 1/2*a + 1))
Got:
    (Fractional ideal (-1/2*a*b - a - 1/2)) * (Fractional ideal (1/2*b + 1/2*a - 1))

is trivial,

sage -t  "devel/sage-main/sage/rings/number_field/number_field_element.pyx"
**********************************************************************
File "/home/john/sage-4.7.alpha5/devel/sage-main/sage/rings/number_field/number_field_element.pyx", line 1142:
    sage: t = (2*a + b)._rnfisnorm(L); t[1]
Expected:
    (b - 2)*a + 2*b - 3
Got:
    (-4*b - 5)*a + 5*b + 6

needs looking at,

sage -t  "devel/sage-main/sage/rings/polynomial/polynomial_quotient_ring.py"

are just like the ones I fixed before on the other machine, and

sage -t  "devel/sage-main/sage/rings/integer.pyx"           
**********************************************************************
File "/home/john/sage-4.7.alpha5/devel/sage-main/sage/rings/integer.pyx", line 4389:
    sage: 7._bnfisnorm(CyclotomicField(7))
Expected:
    (-zeta7 + 1, 1)
Got:
    (-zeta7^5 + zeta7^4, 1)

is also trivial (multiplying by a power of zeta does not change the norm!).

That's all I have time for today, so I hope things look similar on the other 32-bit system being tested.

[cremona]

Apply after previous

[cremona]

I have added a new patch (which affects 4 files in sage/rings) after which all doctests pass on both 32- and 64-bit, apart from the simon-related ones.

That means that it is time to check #11005 on top of all this.

[jdemeyer]

lcalc fails to build with the new PARI:

Lcommandline.cc: In function 'int main(int, char**)':
Lcommandline.cc:476:54: error: 'allocatemoremem' was not declared in this scope
Lcommandline.cc:403:16: warning: unused variable 'C' [-Wunused-variable]
Lcommandline.cc:38:9: warning: unused variable 'i' [-Wunused-variable]
In file included from ../include/L.h:537:0,
                 from ../include/Lcommandline.h:36,
                 from Lcommandline.cc:31:
../include/Lvalue.h: In member function 'Complex L_function<ttype>::find_delta(Complex, Double) [with ttype = int, Complex = std::complex<double>, Double = double]':
Lcommandline.cc:463:50:   instantiated from here
../include/Lvalue.h:37:21: warning: unused variable 'f2' [-Wunused-variable]
make[1]: *** [Lcommandline.o] Error 1
make[1]: Leaving directory `/usr/local/src/sage-4.7.alpha5/spkg/build/lcalc-20100428-1.23.p6/src/src'
make: *** [all] Error 2
Error building lcalc 'make'

[cremona]

Replying to jdemeyer:

lcalc fails to build with the new PARI:

Mike Rubenstein needs to be made aware of this.

[fbissey]

What about genus2reduction? I am assuming John already made sure eclib is working.

[cremona]

Replying to fbissey:

What about genus2reduction? I am assuming John already made sure eclib is working.

A reasonable assumption, but...for a while now I have used Sage's Pari and NTL builds rather than building them myself independently, so I cannot yet confirm. (However, eclib's use of Pari is minimal, it's only for integer factorization.)

I am also preparing a new version of eclib, so I will combine these two tasks, though I don't have any time for this this week.

[jdemeyer]

Replying to cremona:

Replying to jdemeyer:

lcalc fails to build with the new PARI:

Mike Rubenstein needs to be made aware of this.

First I will see if I can fix the error and then send the patches to him.

[jdemeyer]

See #11321 for lcalc.

[jdemeyer]

I built Sage completely from scratch with the new PARI and lcalc packages, everything works. All tests pass except for the ones related to simon_two_descent.

[cremona]

Replying to jdemeyer:

I built Sage completely from scratch with the new PARI and lcalc packages, everything works. All tests pass except for the ones related to simon_two_descent.

So is the "Needs work" just because this ticket is dependent on #11005? I am planning to look now at the doctest failures relating to the Simon scripts and fix them, so that this ticket can then be closed, and the additional work needed on #11005 can depend on this.

[jdemeyer]

Replying to cremona:

I am planning to look now at the doctest failures relating to the Simon scripts and fix them, so that this ticket can then be closed, and the additional work needed on #11005 can depend on this.

That's precisely what I proposed.

[cremona]

Replying to jdemeyer:

Replying to cremona:

I am planning to look now at the doctest failures relating to the Simon scripts and fix them, so that this ticket can then be closed, and the additional work needed on #11005 can depend on this.

That's precisely what I proposed.

OK, so that's what I am working on doing. Patch up shortly. However, I ran into something awkward: the script ellQ.gp in data/extcode/pari/simon crashed randomly in the function ellredgen (using this new pari version). I saw that the offending lines had been changed in the newer ellQ.gp as found in #11005, so I made the same changes. This sorts the problem, but it means that for this ticket to be finished we need to also make a small patch to extcode. Any problems with that?

[cremona]

Apply to sage library after previous

[cremona]

Apply to extcode repository

[cremona]

Is the only thing stopping this going forward the latest reviewer patch?

[jdemeyer]

As far as I know, all patches and spkgs still need review. I can review your patches (but give me some time).

[cremona]

Replying to jdemeyer:

As far as I know, all patches and spkgs still need review. I can review your patches (but give me some time).

Well I considered that I had reviewed (positively) everything except my last patch fixing the Simon doctests so that's the only thing left needing a review (from you perhaps, especially as you made some extra fixes for 32/64 bit issues).

[jdemeyer]

Also lcalc (#11321) needs review.

[kcrisman]

The part of the ticket that fixes #10240 is okay, I think.

[kcrisman]

See #10240 for a request to merge that in 4.7.2 (or whatever the next version is) if this isn't getting merged quickly.

[leif]

See #11605 for a PARI 2.4.3.alpha.p7 spkg with minor but important fixes to spkg-install (and some corrections in SPKG.txt). I've meanwhile based this on Dima's p6 (which just adds a small, harmless change for Cygwin) from #10240.

(Haven't yet looked at this ticket / spkg here at all.)

[jdemeyer]

Needs to be rebased to sage-2.4.3.alpha7.spkg (#11605).