upgrade to flint 2.6.3 #29719

videlec · 2020-05-20T22:40:57Z

Flint 2.6.3 has been released

tarball: see checksums.ini [upstream_url]

Depends on #30805

Upstream: Reported upstream. Developers acknowledge bug.

CC: @timokau @kedlaya @jbalakrishnan @saraedum @isuruf @mkoeppe @kliem @videlec @w-bruns @slel

Component: packages: standard

Keywords: upgrade

Author: Dima Pasechnik, Matthias Koeppe

Branch/Commit: 7681b1a

Reviewer: Matthias Koeppe, Dima Pasechnik

Issue created by migration from https://trac.sagemath.org/ticket/29719

The text was updated successfully, but these errors were encountered:

dimpase · 2020-05-21T10:49:44Z

Branch: public/packages/flint260

dimpase · 2020-05-21T10:49:44Z

Commit: 3bb2c70

dimpase · 2020-05-21T10:49:44Z

comment:1

this is from the latest alpha2 (commit a960857c7d8e5ea7c4d4c2958e38ec52778d85d9)

Patches still need to be sorted out.

New commits:

`3bb2c70`	`update flint to 2.6.0 (alpha version)`

dimpase · 2020-05-21T10:49:44Z

Author: Dima Pasechnik

sagetrac-git · 2020-05-21T12:28:50Z

Changed commit from 3bb2c70 to 9b6e67c

sagetrac-git · 2020-05-21T12:28:50Z

Branch pushed to git repo; I updated commit sha1. This was a forced push. New commits:

`9b6e67c`	`update flint to 2.6.0 (alpha version), remove patches`

dimpase · 2020-05-21T12:31:00Z

comment:3

OK, can be tested now. All our patches got upstreamed, so they are gone now.

dimpase · 2020-05-21T13:00:00Z

comment:4

Neither arb 2.16 nor 2.17 work with this version of Flint.

One gets

gcc -fPIC -ansi -pedantic -Wall -O2 -funroll-loops -g -mpopcnt  -I/home/scratch2/dimpase/sage/sage/local/var/tmp/sage/build/arb-2.17.0/src -I/home/scratch2/dimpase/sage/sage/local/include -I/home/scratch2/dimpase/sage/sage/local/include -I/home/scratch2/dimpase/sage/sage/local/include -c mul_mpn.c -o ../build/fmpr/mul_mpn.lo -MMD -MP -MF "../build/fmpr/mul_mpn.d" -MT "../build/fmpr/mul_mpn.d" -MT "../build/fmpr/mul_mpn.lo"
In file included from ../fmpr.h:26,
                 from get_si.c:12:
../fmpz_extras.h:47:1: error: redefinition of 'fmpz_add_si'
   47 | fmpz_add_si(fmpz_t z, const fmpz_t x, slong y)
      | ^~~~~~~~~~~
In file included from ../fmpr.h:23,
                 from get_si.c:12:
../../../../../../../include/flint/fmpz.h:479:18: note: previous definition of 'fmpz_add_si' was here
  479 | FMPZ_INLINE void fmpz_add_si(fmpz_t f, const fmpz_t g, slong x)
      |                  ^~~~~~~~~~~
In file included from ../fmpr.h:26,
                 from get_si.c:12:
../fmpz_extras.h:56:1: error: redefinition of 'fmpz_sub_si'
   56 | fmpz_sub_si(fmpz_t z, const fmpz_t x, slong y)
      | ^~~~~~~~~~~
In file included from ../fmpr.h:23,
                 from get_si.c:12:
../../../../../../../include/flint/fmpz.h:487:18: note: previous definition of 'fmpz_sub_si' was here
  487 | FMPZ_INLINE void fmpz_sub_si(fmpz_t f, const fmpz_t g, slong x)
      |                  ^~~~~~~~~~~
make[5]: *** [../Makefile.subdirs:60: ../build/fmpr/get_si.lo] Error 1

dimpase · 2020-05-21T13:15:15Z

comment:5

One apparently may use arb patch: https://github.com/fredrik-johansson/arb/commit/d3d9983231e0f034e86a1e75761627eb8213b704.patch - trying this with arb 2.17.0 now.

fredrik-johansson · 2020-05-21T13:42:33Z

comment:6

Yes, there will be an immediate new Arb release. The current git master ought to work.

dimpase · 2020-05-21T19:50:04Z

comment:8

Replying to @fredrik-johansson:

Yes, there will be an immediate new Arb release. The current git master ought to work.

there are doctest errors (I made https://github.com/dimpase/arb/releases/tag/2.17.1, and removed all the arb patches)

sage -t --warn-long 59.4 src/sage/rings/complex_arb.pyx
**********************************************************************
File "src/sage/rings/complex_arb.pyx", line 4554, in sage.rings.complex_arb.ComplexBall.elliptic_pi
Failed example:
    CBF(2,3).elliptic_pi(CBF(1,1))
Expected:
    [0.27029997361983 +/- ...e-15] + [0.715676058329095 +/- ...e-16]*I
Got:
    [0.2702999736198 +/- 4.51e-14] + [0.7156760583291 +/- 1.78e-14]*I
**********************************************************************
File "src/sage/rings/complex_arb.pyx", line 4662, in sage.rings.complex_arb.ComplexBall.elliptic_pi_inc
Failed example:
    n.elliptic_pi_inc(CBF.pi()/2, m)
Expected:
    [0.8934793755173 +/- ...e-14] + [0.95707868710750 +/- ...e-15]*I
Got:
    nan + nan*I
**********************************************************************
File "src/sage/rings/complex_arb.pyx", line 4664, in sage.rings.complex_arb.ComplexBall.elliptic_pi_inc
Failed example:
    n.elliptic_pi(m)
Expected:
    [0.89347937551733 +/- ...e-15] + [0.95707868710750 +/- ...e-15]*I
Got:
    [0.8934793755173 +/- 4.27e-14] + [0.9570786871075 +/- 9.91e-15]*I
**********************************************************************
File "src/sage/rings/complex_arb.pyx", line 4669, in sage.rings.complex_arb.ComplexBall.elliptic_pi_inc
Failed example:
    n.elliptic_pi_inc(CBF.pi()/2, m)
Expected:
    [0.2969588746419 +/- ...e-14] + [1.3188795332738 +/- ...e-14]*I
Got:
    nan + nan*I
**********************************************************************
File "src/sage/rings/complex_arb.pyx", line 4671, in sage.rings.complex_arb.ComplexBall.elliptic_pi_inc
Failed example:
    n.elliptic_pi(m)
Expected:
    [0.29695887464189 +/- ...e-15] + [1.31887953327376 +/- ...e-15]*I
Got:
    [0.2969588746419 +/- 3.79e-14] + [1.3188795332738 +/- 7.19e-14]*I
**********************************************************************
File "src/sage/rings/complex_arb.pyx", line 4747, in sage.rings.complex_arb.ComplexBall.elliptic_rj
Failed example:
    CBF(0,1).elliptic_rj(CBF(-1/2,1), CBF(-1,-1), CBF(2))
Expected:
    [1.004386756285733 +/- ...e-16] + [-0.2451626834391645 +/- ...e-17]*I
Got:
    [1.00438675628573 +/- 6.85e-15] + [-0.24516268343916 +/- 8.11e-15]*I
**********************************************************************
3 items had failures:
   1 of   2 in sage.rings.complex_arb.ComplexBall.elliptic_pi
   4 of  10 in sage.rings.complex_arb.ComplexBall.elliptic_pi_inc
   1 of   2 in sage.rings.complex_arb.ComplexBall.elliptic_rj
    [639 tests, 6 failures, 8.14 s]

and

sage -t --warn-long 59.4 src/sage/rings/real_arb.pyx
**********************************************************************
File "src/sage/rings/real_arb.pyx", line 295, in sage.rings.real_arb.arb_to_mpfi
Failed example:
    RIF(RBF(2)**(2**100)) # indirect doctest
Expected:
    Traceback (most recent call last):
    ...
    ArithmeticError: Error converting arb to mpfi. Overflow?
Got:
    [5.8756537891115869e1388255822130839282 .. +infinity]
**********************************************************************
File "src/sage/rings/real_arb.pyx", line 1660, in sage.rings.real_arb.RealBall.mid
Failed example:
    b.mid()
Expected:
    Traceback (most recent call last):
    ...
    RuntimeError: unable to convert to MPFR (exponent out of range?)
Got:
    +infinity
**********************************************************************
2 items had failures:
   1 of   7 in sage.rings.real_arb.RealBall.mid
   1 of   2 in sage.rings.real_arb.arb_to_mpfi
    [542 tests, 2 failures, 0.64 s]

dimpase · 2020-05-22T09:55:30Z

comment:9

OK, I ended up using arb patch: https://github.com/fredrik-johansson/arb/commit/d3d9983231e0f034e86a1e75761627eb8213b704.patch
with arb 2.16.0 (the arb version in Sage now), and get one flint-related regression (a segfault)

sage: R.<x> = QQ['x']
sage: A,f = monsky_washnitzer.matrix_of_frobenius_hyperelliptic(x^5 - 2*x + 3, 5, 3)
-------------------------------------------------------------------------------------
/home/scratch2/dimpase/sage/sage/local/lib64/python3.7/site-packages/cysignals/signals.cpython-37m-x86_64-linux-gnu.so(+0x84a4)[0x7f98890224a4]
/home/scratch2/dimpase/sage/sage/local/lib64/python3.7/site-packages/cysignals/signals.cpython-37m-x86_64-linux-gnu.so(+0x8679)[0x7f9889022679]
/home/scratch2/dimpase/sage/sage/local/lib64/python3.7/site-packages/cysignals/signals.cpython-37m-x86_64-linux-gnu.so(+0xae41)[0x7f9889024e41]
/lib64/libc.so.6(+0x37ec0)[0x7f988a679ec0]
/lib64/libc.so.6(gsignal+0x145)[0x7f988a679e35]
/lib64/libc.so.6(abort+0x127)[0x7f988a664895]
/home/scratch2/dimpase/sage/sage/local/lib/libflint.so.14(+0x85dcd)[0x7f9880a64dcd]
/home/scratch2/dimpase/sage/sage/local/lib/libflint.so.14(flint_throw+0xe0)[0x7f9880a64eb0]
/home/scratch2/dimpase/sage/sage/local/lib/libflint.so.14(_nmod_poly_rem_q1+0xa1)[0x7f9880bd8bd1]
/home/scratch2/dimpase/sage/sage/local/lib/libflint.so.14(_nmod_poly_rem+0x195)[0x7f9880bc39f5]
/home/scratch2/dimpase/sage/sage/local/lib/libflint.so.14(_nmod_poly_gcd_euclidean+0x60)[0x7f9880babd50]
/home/scratch2/dimpase/sage/sage/local/lib/libflint.so.14(nmod_poly_gcd+0x95)[0x7f9880bb28b5]
/home/scratch2/dimpase/sage/sage/local/lib64/python3.7/site-packages/sage/rings/polynomial/polynomial_zmod_flint.cpython-37m-x86_64-linux-gnu.so(+0x1201c)[0x7f983d7b401c]
/lib64/libpython3.7m.so.1.0(_PyMethodDef_RawFastCallDict+0x33a)[0x7f988a402bea]
/lib64/libpython3.7m.so.1.0(+0x1ccd3f)[0x7f988a4c1d3f]
/home/scratch2/dimpase/sage/sage/local/lib64/python3.7/site-packages/sage/structure/element.cpython-37m-x86_64-linux-gnu.so(+0x134fc)[0x7f98897424fc]
/home/scratch2/dimpase/sage/sage/local/lib64/python3.7/site-packages/sage/structure/element.cpython-37m-x86_64-linux-gnu.so(+0x338a4)[0x7f98897628a4]
/lib64/libpython3.7m.so.1.0(_PyObject_FastCallKeywords+0x4bc)[0x7f988a433eec]
/lib64/libpython3.7m.so.1.0(+0x1404e9)[0x7f988a4354e9]
/lib64/libpython3.7m.so.1.0(_PyEval_EvalFrameDefault+0x55da)[0x7f988a46fdea]
/lib64/libpython3.7m.so.1.0(_PyEval_EvalCodeWithName+0x2f0)[0x7f988a4227e0]
/lib64/libpython3.7m.so.1.0(_PyFunction_FastCallKeywords+0x2a2)[0x7f988a423822]
/lib64/libpython3.7m.so.1.0(+0x14035f)[0x7f988a43535f]
...

sagetrac-git · 2020-05-22T09:58:13Z

Changed commit from 9b6e67c to d943e59

sagetrac-git · 2020-05-22T09:58:13Z

Branch pushed to git repo; I updated commit sha1. New commits:

`d943e59`	`backport flint compat patch from arb's trunk`

sagetrac-git · 2020-05-22T10:01:05Z

Branch pushed to git repo; I updated commit sha1. New commits:

`f80e315`	`url in checksum, for convenience (to be changed)`

sagetrac-git · 2020-05-22T10:01:05Z

Changed commit from d943e59 to f80e315

dimpase · 2020-05-22T10:20:29Z

comment:12

experiments tell that precision needs to be at least 25 for this example to run, i.e. this works:

sage: monsky_washnitzer.matrix_of_frobenius_hyperelliptic(x^5 - 2*x + 3, 5, 25)

dimpase · 2020-05-22T10:55:47Z

comment:13

But this works:

sage: R.<x> = QQ['x']
sage: C=HyperellipticCurve(x^5 - 2*x + 3)
sage: A,f=monsky_washnitzer.matrix_of_frobenius_hyperelliptic(C,5,3)
sage: A
[            4*5 + O(5^3)       5 + 2*5^2 + O(5^3) 2 + 3*5 + 2*5^2 + O(5^3)     2 + 5 + 5^2 + O(5^3)]
[      3*5 + 5^2 + O(5^3)             3*5 + O(5^3)             4*5 + O(5^3)         2 + 5^2 + O(5^3)]
[    4*5 + 4*5^2 + O(5^3)     3*5 + 2*5^2 + O(5^3)       5 + 3*5^2 + O(5^3)     2*5 + 2*5^2 + O(5^3)]
[            5^2 + O(5^3)       5 + 4*5^2 + O(5^3)     4*5 + 3*5^2 + O(5^3)             2*5 + O(5^3)]

So, apparently, some initialisation is missing, if C is created on the fly.

dimpase · 2020-05-22T12:31:46Z

comment:14

This is reproducible on the ticket branch, on Fedora 30 and on Debian 10.
This works:

sage: R.<x> = QQ['x']
sage: C=HyperellipticCurve(x^5 - 2*x + 3)
sage: A,f=monsky_washnitzer.matrix_of_frobenius_hyperelliptic(C,5,3)
sage: A

but

sage: R.<x> = QQ['x']
sage: A,f = monsky_washnitzer.matrix_of_frobenius_hyperelliptic(x^5 - 2*x + 3, 5, 3)

segfaults.

fredrik-johansson · 2020-05-22T12:42:41Z

comment:15

Dima, thanks for reporting the Arb doctest failures.

The slight regressions in accuracy for elliptic_pi, elliptic_pi_inc and elliptic_rj are due to using a different algorithm to compute the R_J function for certain complex parameters. The new algorithm is a bit slower and less accurate, but unlike the old algorithm always gives the right branch. These doctest results just need to be updated.

Unfortunately, the new algorithm doesn't work when phi is an inexact multiple of pi/2, leading to the NaN values. There is a workaround: acb_elliptic_pi_inc takes a pi flag to multiply the argument by pi exactly, so if you add a pi flag to the Sage wrapper and pass in phi=0.5 with pi=True in the doctest, it should give the expected result.

It's theoretically possible to fix these regressions, and I will open an Arb issue for it, but I'm not keen to spend time on it any time soon.

The other two examples look correct: converting an Arb number to an MPFR now rounds according to MPFR semantics (including rounding to infinity) instead of abort()ing when the exponents are out of range for MPFR.

dimpase · 2020-05-22T15:50:57Z

comment:16

This works too:

sage: sage: R.<x> = QQ['x']
....: sage: C=HyperellipticCurve(x^5 - 2*x + 7)
....: sage: A,f = monsky_washnitzer.matrix_of_frobenius_hyperelliptic(x^5-2*x+3, 5, 3)

That is, apparently, some kind of Flint initialisation needs to happen before
the latter function can be called.

sagetrac-git · 2020-10-20T08:34:11Z

Branch pushed to git repo; I updated commit sha1. This was a forced push. New commits:

`a75a4c4`	`update flint to 2.6.0 (alpha version), remove patches`
`e6da720`	`backport flint compat patch from arb's trunk`
`e47c42c`	`skip square-freeness test for polynomials non-fields`
`cba2cf9`	`fix and make robust related doctests`
`81e3c39`	`build/pkgs/flint: Add DESTDIR patch`
`de52816`	`build/pkgs/arb: Bump patch level`
`aff940d`	`build/pkgs/flint: Update to 2.6.1, drop upstreamed patch`
`333973d`	`flint 2.6.3`

sagetrac-git · 2020-10-20T08:34:11Z

Changed commit from fd5ff14 to 333973d

dimpase · 2020-10-20T08:35:14Z

comment:129

rebased over 9.2.rc3

mkoeppe · 2020-10-20T23:27:58Z

Work Issues: rebase on top of #30805

mkoeppe · 2020-10-20T23:27:58Z

Changed dependencies from #29826, #30262 to #30805

sagetrac-git · 2020-10-21T20:41:49Z

Branch pushed to git repo; I updated commit sha1. This was a forced push. New commits:

`14fd292`	`prevent segfaults with flint 2.6`
`6898cc6`	`update flint to 2.6.0 (alpha version), remove patches`
`436f15a`	`backport flint compat patch from arb's trunk`
`5de748d`	`fix and make robust related doctests`
`df7f4c2`	`build/pkgs/flint: Add DESTDIR patch`
`ee7b2bb`	`build/pkgs/arb: Bump patch level`
`1088acc`	`build/pkgs/flint: Update to 2.6.1, drop upstreamed patch`
`01271cb`	`flint 2.6.3`

sagetrac-git · 2020-10-21T20:41:49Z

Changed commit from 333973d to 01271cb

dimpase · 2020-10-21T20:43:06Z

comment:132

rebased over #30805

BrentBaccala · 2020-10-29T00:05:01Z

comment:133

To build the current version of this branch (commit 01271cb) on Ubuntu I had to apt install libgmp-dev.

I don't think that's listed as a build requirement.

mkoeppe · 2020-10-29T00:10:47Z

comment:134

Logs please

BrentBaccala · 2020-10-29T01:29:28Z

Attachment: flint-2.6.3.log

Build attempt on commit 01271cb

BrentBaccala · 2020-10-29T01:31:38Z

comment:135

I attached a log file.

There's really not much to see - a bunch of failed downloads because flint 2.6.3 isn't in any of the Sage mirrors yet, then a compile failure because it couldn't find "gmp.h", which I resolved with apt install libgmp-dev.

dimpase · 2020-10-29T19:26:46Z

comment:136

Replying to @BrentBaccala:

I attached a log file.

There's really not much to see - a bunch of failed downloads because flint 2.6.3 isn't in any of the Sage mirrors yet,

./configure has --enable-download-from-upstream-url option, which use would allow an automatic download from the url in checksums.iniof the package.

then a compile failure because it couldn't find "gmp.h", which I resolved with apt install libgmp-dev.

look at what ./configure tries to tell at the end of its run - there should be a list of system packages to install to make one's life easier.
On Debian like 90% of Sage's (non-python) libs, as well as Python itself, etc etc, are unvendored, see #27330

BrentBaccala · 2020-10-29T19:41:17Z

comment:137

Replying to @dimpase:

look at what ./configure tries to tell at the end of its run - there should be a list of system packages to install to make one's life easier.
On Debian like 90% of Sage's (non-python) libs, as well as Python itself, etc etc, are unvendored, see #27330

I had to re-run configure after installing libgmp-dev, and I didn't keep the old log, but I don't remember any glaring complaints. Furthermore, I found this in the (new) config.log:

configure:37965: result: gmp-6.1.2: using system package; SPKG will not be installed

I infer from this that a SPKG is available and should have been used by the original build.

I don't know enough about Sage packaging to know how a SPKG gmp should be used by flint.

dimpase · 2020-10-30T07:52:22Z

comment:138

Replying to @BrentBaccala:

To build the current version of this branch (commit 01271cb) on Ubuntu I had to apt install libgmp-dev.

I don't think that's listed as a build requirement.

How did you start the build?

I only can see this happening on an unconfigured tree if one does not start by
running ./configure, but rather by doing something like ./sage -p flint (which indeed does not check dependencies)

BrentBaccala · 2020-10-30T13:08:47Z

comment:139

Replying to @dimpase:

Replying to @BrentBaccala:

To build the current version of this branch (commit 01271cb) on Ubuntu I had to apt install libgmp-dev.

I don't think that's listed as a build requirement.

How did you start the build?

I only can see this happening on an unconfigured tree if one does not start by
running ./configure, but rather by doing something like ./sage -p flint (which indeed does not check dependencies)

After git checkout, I ran ./bootstrap, then ./configure, then MAKE="make -j8" make.

dimpase · 2020-10-30T14:03:48Z

comment:140

could be stale leftovers - how about make bootstrap-clean && make distclean ?
(for the former possibly #30795 is needed)

sagetrac-git · 2020-11-06T12:07:03Z

Changed commit from 01271cb to 7681b1a

sagetrac-git · 2020-11-06T12:07:03Z

Branch pushed to git repo; I updated commit sha1. This was a forced push. New commits:

`6b3a2ed`	`update flint to 2.6.0 (alpha version), remove patches`
`b53bf8e`	`fix and make robust related doctests`
`7731c60`	`build/pkgs/flint: Add DESTDIR patch`
`24ff512`	`build/pkgs/flint: Update to 2.6.1, drop upstreamed patch`
`7681b1a`	`flint 2.6.3`

dimpase · 2020-11-06T12:09:19Z

comment:142

rebased over 9.3.beta0, squashed few things. Let us get this in please!

In particular, here are patches that need to fix doctest on distros that ship flint 2.6.3 already, e.g. Homebrew, Ubuntu 20.10.

dimpase · 2020-11-06T20:03:56Z

Changed work issues from rebase on top of #30805 to none

vbraun · 2020-11-15T22:47:41Z

Changed branch from public/packages/flint260 to 7681b1a

videlec added this to the sage-9.2 milestone May 20, 2020

videlec added c: packages: standard labels May 20, 2020

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vbraun closed this as completed in 430c549 Nov 15, 2020

dimpase mentioned this issue May 31, 2020

port Sage to FreeBSD 12 #26249

Open

fredrik-johansson mentioned this issue Dec 13, 2020

Upgrade Arb to 2.18.1 #28623

Closed

slel mentioned this issue May 27, 2021

Upgrade: Flint 2.7.1 #31069

Closed

upgrade to flint 2.6.3 #29719

upgrade to flint 2.6.3 #29719

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vbraun commented Nov 15, 2020