Increase Precision in Failing Doctests #17238

strogdon · 2014-10-27T22:16:20Z

Certain doctests may now fail due to precision issues. This is apparently a consequence of #16858. For reference see

https://groups.google.com/forum/#!topic/sage-release/jdhuVBY7rLU

CC: @jpflori

Component: doctest coverage

Author: Steven Trogdon, Jean-Pierre Flori

Branch/Commit: ec64d52

Reviewer: Jeroen Demeyer

Issue created by migration from https://trac.sagemath.org/ticket/17238

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

strogdon · 2014-10-27T22:19:36Z

comment:1

With

uname -a
Linux ledaig 3.6.11-gentoo #6 SMP Mon Aug 25 17:39:25 CDT 2014 x86_64 Dual-Core AMD Opteron(tm) Processor 2218 AuthenticAMD GNU/Linux

and Sage-6.4.beta6 installed I have the following doctest failures

sage -t --long src/sage/rings/polynomial/polynomial_element.pyx
**********************************************************************
File "src/sage/rings/polynomial/polynomial_element.pyx", line 5360, in sage.rings.polynomial.polynomial_element.Polynomial.roots
Failed example:
    [f(z) for z in f.roots(multiplicities=False)]  # abs tol 1e-12
Expected:
    [1.3704315460216776e-15 + 3.3306690738754696e-15*I, 5.287107591627866e-16 + 1.9984014443252818e-15*I, 2.0616104309811867e-16 + 1.7763568394002505e-15*I]
Got:
    [1.1102230246251565e-16 - 8.881784197001252e-16*I,
     -8.728374398092689e-16,
     7.771561172376096e-16 + 6.661338147750939e-16*I]
**********************************************************************
sage -t --long src/sage/tests/french_book/mpoly.py
**********************************************************************
File "src/sage/tests/french_book/mpoly.py", line 364, in sage.tests.french_book.mpoly
Failed example:
    ys = CDF['y'](Jy.0).roots(); ys
Expected:
    [(-0.8000000000000002, 1), (0.0, 1), (0.8, 1)]
Got:
    [(-0.8, 1), (0.0, 1), (0.7999999999999997, 1)]
************************************************************************
sage -t --long src/sage/matrix/matrix_double_dense.pyx
File "src/sage/matrix/matrix_double_dense.pyx", line 1012, in sage.matrix.matrix_double_dense.Matrix_double_dense.singular_values
Failed example:
    A.singular_values(eps=None)  # abs tol 2e-16
Expected:
    [1.7953720595619975, 0.38027524595503703, 0.04473854875218107, 0.0037223122378911614, 0.0002330890890217751, 1.116335748323284e-05, 4.082376110397296e-07, 1.1228610675717613e
-08, 2.2519645713496478e-10, 3.1113486853814003e-12, 2.6500422260778388e-14, 9.87312834948426e-17]
Got:
    [1.795372059561997,
     0.3802752459550371,
     0.04473854875218108,
     0.0037223122378911614,
     0.00023308908902177134,
     1.1163357483233473e-05,
     4.0823761103887333e-07,
     1.1228610666951528e-08,
     2.2519645134867946e-10,
     3.1113495994353857e-12,
     2.649222799410179e-14,
     1.0793843611330301e-16]
Tolerance exceeded in 1 of 12:
    1.7953720595619975 vs 1.795372059561997, tolerance 5e-16 > 2e-16
**********************************************************************
File "src/sage/matrix/matrix_double_dense.pyx", line 1014, in sage.matrix.matrix_double_dense.Matrix_double_dense.singular_values
Failed example:
    A.singular_values(eps='auto')  # abs tol 2e-16
Expected:
    [1.7953720595619975, 0.38027524595503703, 0.04473854875218107, 0.0037223122378911614, 0.0002330890890217751, 1.116335748323284e-05, 4.082376110397296e-07, 1.1228610675717613e
-08, 2.2519645713496478e-10, 3.1113486853814003e-12, 2.6500422260778388e-14, 0.0]
Got:
    [1.795372059561997,
     0.3802752459550371,
     0.04473854875218108,
     0.0037223122378911614,
     0.00023308908902177134,
     1.1163357483233473e-05,
     4.0823761103887333e-07,
     1.1228610666951528e-08,
     2.2519645134867946e-10,
     3.1113495994353857e-12,
     2.649222799410179e-14,
     0.0]
Tolerance exceeded in 1 of 12:
    1.7953720595619975 vs 1.795372059561997, tolerance 5e-16 > 2e-16
**********************************************************************
File "src/sage/matrix/matrix_double_dense.pyx", line 1016, in sage.matrix.matrix_double_dense.Matrix_double_dense.singular_values
Failed example:
    A.singular_values(eps=1e-4)  # abs tol 2e-16
Expected:
    [1.7953720595619975, 0.38027524595503703, 0.04473854875218107, 0.0037223122378911614, 0.0002330890890217751, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]
Got:
    [1.795372059561997,
     0.3802752459550371,
     0.04473854875218108,
     0.0037223122378911614,
     0.00023308908902177134,
     0.0,
     0.0,
     0.0,
     0.0,
     0.0,
     0.0,
     0.0]
Tolerance exceeded in 1 of 12:
    1.7953720595619975 vs 1.795372059561997, tolerance 5e-16 > 2e-16
******************************************************************************************************************************************
sage -t --long src/doc/ru/tutorial/tour_linalg.rst
**********************************************************************
File "src/doc/ru/tutorial/tour_linalg.rst", line 109, in doc.ru.tutorial.tour_linalg
Failed example:
    ARDF.eigenvalues()
Expected:
    [-0.09317121994613098, 4.293171219946131]
Got:
    [-0.09317121994613091, 4.293171219946131]
**********************************************************************
File "src/doc/ru/tutorial/tour_linalg.rst", line 112, in doc.ru.tutorial.tour_linalg
Failed example:
    ACDF.eigenvectors_right()  # rel tol 1e-15
Expected:
    [(0.8818456983293743 - 0.8209140653434135*I, [(0.7505608183809549, -0.616145932704589 + 0.2387941530333261*I)], 1),
    (3.3181543016706256 + 0.8209140653434133*I, [(0.14559469829270957 + 0.3756690858502104*I, 0.9152458258662108)], 1)]
Got:
    [(0.8818456983293741 - 0.8209140653434133*I,
      [(0.7505608183809549, -0.6161459327045887 + 0.23879415303332602*I)],
      1),
     (3.3181543016706256 + 0.8209140653434132*I,
      [(0.14559469829270977 + 0.3756690858502104*I, 0.9152458258662107)],
      1)]
Tolerance exceeded in 1 of 12:
    0.14559469829270957 vs 0.14559469829270977, tolerance 1e-15 > 1e-15
**********************************************************************
sage -t --long src/doc/de/tutorial/tour_linalg.rst
**********************************************************************
File "src/doc/de/tutorial/tour_linalg.rst", line 117, in doc.de.tutorial.tour_linalg
Failed example:
    ARDF.eigenvalues()
Expected:
    [-0.09317121994613098, 4.293171219946131]
Got:
    [-0.09317121994613091, 4.293171219946131]
**********************************************************************
File "src/doc/de/tutorial/tour_linalg.rst", line 120, in doc.de.tutorial.tour_linalg
Failed example:
    ACDF.eigenvectors_right()  # rel tol 1e-15
Expected:
    [(0.8818456983293743 - 0.8209140653434135*I, [(0.7505608183809549, -0.616145932704589 + 0.2387941530333261*I)], 1),
    (3.3181543016706256 + 0.8209140653434133*I, [(0.14559469829270957 + 0.3756690858502104*I, 0.9152458258662108)], 1)]
Got:
    [(0.8818456983293741 - 0.8209140653434133*I,
      [(0.7505608183809549, -0.6161459327045887 + 0.23879415303332602*I)],
      1),
     (3.3181543016706256 + 0.8209140653434132*I,
      [(0.14559469829270977 + 0.3756690858502104*I, 0.9152458258662107)],
      1)]
Tolerance exceeded in 1 of 12:
    0.14559469829270957 vs 0.14559469829270977, tolerance 1e-15 > 1e-15
**********************************************************************
sage -t --long src/doc/fr/tutorial/tour_linalg.rst
**********************************************************************
File "src/doc/fr/tutorial/tour_linalg.rst", line 115, in doc.fr.tutorial.tour_linalg
Failed example:
    ARDF.eigenvalues()
Expected:
    [-0.09317121994613098, 4.293171219946131]
Got:
    [-0.09317121994613091, 4.293171219946131]
**********************************************************************
File "src/doc/fr/tutorial/tour_linalg.rst", line 118, in doc.fr.tutorial.tour_linalg
Failed example:
    ACDF.eigenvectors_right()  # rel tol 1e-15
Expected:
    [(0.8818456983293743 - 0.8209140653434135*I, [(0.7505608183809549, -0.616145932704589 + 0.2387941530333261*I)], 1),
    (3.3181543016706256 + 0.8209140653434133*I, [(0.14559469829270957 + 0.3756690858502104*I, 0.9152458258662108)], 1)]
Got:
    [(0.8818456983293741 - 0.8209140653434133*I,
      [(0.7505608183809549, -0.6161459327045887 + 0.23879415303332602*I)],
      1),
     (3.3181543016706256 + 0.8209140653434132*I,
      [(0.14559469829270977 + 0.3756690858502104*I, 0.9152458258662107)],
      1)]
Tolerance exceeded in 1 of 12:
    0.14559469829270957 vs 0.14559469829270977, tolerance 1e-15 > 1e-15
**********************************************************************
sage -t --long src/doc/en/tutorial/tour_linalg.rst
**********************************************************************
File "src/doc/en/tutorial/tour_linalg.rst", line 114, in doc.en.tutorial.tour_linalg
Failed example:
    ARDF.eigenvalues()
Expected:
    [-0.09317121994613098, 4.293171219946131]
Got:
    [-0.09317121994613091, 4.293171219946131]
**********************************************************************
File "src/doc/en/tutorial/tour_linalg.rst", line 117, in doc.en.tutorial.tour_linalg
Failed example:
    ACDF.eigenvectors_right()  # rel tol 1e-15
Expected:
    [(0.8818456983293743 - 0.8209140653434135*I, [(0.7505608183809549, -0.616145932704589 + 0.2387941530333261*I)], 1),
    (3.3181543016706256 + 0.8209140653434133*I, [(0.14559469829270957 + 0.3756690858502104*I, 0.9152458258662108)], 1)]
Got:
    [(0.8818456983293741 - 0.8209140653434133*I,
      [(0.7505608183809549, -0.6161459327045887 + 0.23879415303332602*I)],
      1),
     (3.3181543016706256 + 0.8209140653434132*I,
      [(0.14559469829270977 + 0.3756690858502104*I, 0.9152458258662107)],
      1)]
Tolerance exceeded in 1 of 12:
    0.14559469829270957 vs 0.14559469829270977, tolerance 1e-15 > 1e-15
**********************************************************************

which appear to be precision related.

strogdon · 2014-10-28T00:19:16Z

Branch: u/strogdon/increase_precision

strogdon · 2014-10-28T00:22:56Z

Commit: cad29f8

strogdon · 2014-10-28T00:22:56Z

comment:3

Here is a partial push that may not work for everyone. It does work here. I'm not quite sure how to handle the failure

sage -t --long src/sage/rings/polynomial/polynomial_element.pyx

New commits:

`01f8611`	`increase abs tol to prevent doctest failures in matrix_double_dense.pyx`
`57bb552`	`increase rel tol in ru/tutorial/tour_linalg.rst to prevent doctest failures`
`48e582e`	`increase rel tol in de/tutorial/tour_linalg.rst to prevent doctest failures`
`a772108`	`increase rel tol in fr/tutorial/tour_linalg.rst to prevent doctest failures`
`5110a8a`	`increase rel tol in en/tutorial/tour_linalg.rst to prevent doctest failures`
`cad29f8`	`increase abs tol in mpoly.py to prevent doctest failure`

jdemeyer · 2014-10-28T08:34:56Z

comment:6

Replying to @strogdon:

Here is a partial push that may not work for everyone. It does work here. I'm not quite sure how to handle the failure

sage -t --long src/sage/rings/polynomial/polynomial_element.pyx

Clearly, the intention of the test is to show that the zeros really are zeros. So I would replace it by

sage: [abs(f(z)) for z in f.roots(multiplicities=False)]  # abs tol 1e-12

Don't forget your Author name.

jpflori · 2014-10-28T12:18:35Z

comment:7

I need a little more fixes on ppc64.
I'll push them later.

sagetrac-git · 2014-10-28T15:01:59Z

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

`26eeff1`	`use abs to test for zeros`

sagetrac-git · 2014-10-28T15:01:59Z

Changed commit from cad29f8 to 26eeff1

strogdon · 2014-10-28T15:04:39Z

comment:9

Ahh! The nameless author(s).

New commits:

`26eeff1`	`use abs to test for zeros`

strogdon · 2014-10-28T15:04:39Z

Author: Steven Trogdon

jpflori · 2014-10-28T15:06:17Z

comment:10

Any idea why the test

[f(z) for z in f.roots(multiplicities=False)]

was failing before?

At first sight I see no reason...

strogdon · 2014-10-28T15:15:42Z

comment:11

The only thing that jumped out at me was that one of the zeros had no imaginary part. But I don't know why that would cause it to fail. No adjusting of the precision would allow it to pass unless I used abs(f(z)) Maybe something else is up?

jdemeyer · 2014-10-28T15:27:46Z

comment:12

Replying to @strogdon:

The only thing that jumped out at me was that one of the zeros had no imaginary part. But I don't know why that would cause it to fail.

Because

<floating point number>

doesn't match

<floating point number><floating point number>*I

no matter what the floating point numbers are.

jpflori · 2014-10-28T15:32:14Z

comment:13

Oh, I see...
That's tricky though and could lead to further problems (unless we change every test looking for zeros in CDF to compute norms of elements).

jdemeyer · 2014-10-28T15:35:06Z

comment:14

Same issue with polynomials:

x^3 + 1e-100

doesn't match

x^3

no matter the tolerance.

jpflori · 2014-10-28T15:36:10Z

Changed commit from 26eeff1 to 6566524

jpflori · 2014-10-28T15:36:10Z

comment:15

Here are a few others tweaks I need on ppc64.

New commits:

`9c30abb`	`Some doctests modifs to mitigate numerical noise.`
`6566524`	`Merge remote-tracking branch 'trac/u/strogdon/increase_precision' into ticket/17238`

jpflori · 2014-10-28T15:36:10Z

Changed branch from u/strogdon/increase_precision to u/jpflori/ticket/17238

strogdon · 2014-10-28T16:14:50Z

comment:16

For me there are now missing whitespaces in matrix2.pyx

sage -t --long src/sage/matrix/matrix2.pyx
**********************************************************************
File "src/sage/matrix/matrix2.pyx", line 4941, in sage.matrix.matrix2.Matrix.diagonal.eigenspaces_left
Failed example:
    eigenvalues = em[0]; eigenvalues.dense_matrix().zero_at(2e-15)
Expected:
    [13.348469228349...                0.0                 0.0]
    [               0.0 -1.348469228349...                 0.0]
    [               0.0                0.0                 0.0]
Got:
    [ 13.34846922834953                0.0                0.0]
    [               0.0 -1.348469228349535                0.0]
    [               0.0                0.0                0.0]
**********************************************************************
File "src/sage/matrix/matrix2.pyx", line 5600, in sage.matrix.matrix2.Matrix.diagonal.eigenmatrix_left
Failed example:
    evalues = em[0]; evalues.dense_matrix().zero_at(2e-15)
Expected:
    [13.348469228349...                0.0                 0.0]
    [               0.0 -1.348469228349...                 0.0]
    [               0.0                0.0                 0.0]
Got:
    [ 13.34846922834953                0.0                0.0]
    [               0.0 -1.348469228349535                0.0]
    [               0.0                0.0                0.0]
**********************************************************************

jpflori · 2014-10-28T16:31:18Z

comment:17

Oops, I indeed modified that one.
And actually need it for the test to pass.

sagetrac-git · 2014-10-28T17:24:42Z

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

`807b794`	`Let doctest with numerical noise in matrix2.pyx pass on different archs.`

strogdon · 2014-10-28T17:38:14Z

comment:20

This now works here.

jpflori · 2014-10-28T22:01:30Z

comment:21

Jeroen: would you mind having a final look at this? I basically agree with what Steven did and added minimal changes so that everything is fine on ppc64.

jdemeyer · 2014-10-29T10:04:01Z

comment:22

OK, I'm going to assume that it does indeed fix the problems you are having.

jdemeyer · 2014-10-29T10:06:46Z

comment:23

Please rebase this on top of #17126.

jdemeyer · 2014-10-29T10:06:46Z

Reviewer: Jeroen Demeyer

sagetrac-git · 2014-10-29T10:22:43Z

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

`1553f96`	`Additional failing doctest because of numerical noise.`
`f30a982`	`Fix numerical noise`
`7efdf3e`	`Merge remote-tracking branch 'trac/u/jdemeyer/ticket/17126' into ticket/17238`

sagetrac-git · 2014-10-29T10:22:43Z

Changed commit from 807b794 to 7efdf3e

jpflori · 2014-10-29T10:23:05Z

comment:25

Done.

Note that I also added a forgotten fix for ppc64 (in a separate commit)...

jpflori · 2014-10-29T10:23:38Z

comment:26

(As far as #17126 is concerned, the merge slightly increases the tolerance.)

jdemeyer · 2014-10-29T10:30:51Z

comment:27

Replying to @jpflori:

the merge slightly increases the tolerance.

Do we need such a large tolerance? Did you check that the tolerance of #17126 is not sufficient?

jpflori · 2014-10-29T10:31:52Z

comment:28

Sure, in fact for all the tolerances I used, I checked it was the minimal one needed on ppc64.

jpflori · 2014-10-29T10:34:14Z

comment:29

And it only goes from 1e-13 to 4e-13.

jdemeyer · 2014-10-29T10:35:09Z

comment:30

In the matrix2.pyx tests, can't you remove the zero_at() part?

jpflori · 2014-10-29T10:36:50Z

comment:31

Yes I think we can.

jpflori · 2014-10-29T10:39:15Z

comment:32

I'm changing the doctest now.

jpflori · 2014-10-29T10:40:49Z

comment:33

But I'll also have to use abs tol rather than rel tol as both zeros and non zeros values are to be checked.

sagetrac-git · 2014-10-29T11:21:56Z

Changed commit from 7efdf3e to ec64d52

sagetrac-git · 2014-10-29T11:21:56Z

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

`ec64d52`	`Use tolerance setting and matrix values from #17126.`

jpflori · 2014-10-29T11:22:28Z

comment:35

I've harmonized everything with #17126.
It still passes for me.

vbraun · 2014-10-30T09:45:49Z

Changed branch from u/jpflori/ticket/17238 to ec64d52

strogdon added this to the sage-6.4 milestone Oct 27, 2014

strogdon added t: tests labels Oct 27, 2014

strogdon added the s: needs info label Oct 28, 2014

jdemeyer added p: blocker / 1 and removed p: major / 3 labels Oct 28, 2014

strogdon added s: needs work and removed s: needs info labels Oct 28, 2014

jpflori added the s: needs review label Oct 28, 2014

jdemeyer added s: needs work and removed s: needs review labels Oct 29, 2014

jpflori added s: needs review and removed s: needs work labels Oct 29, 2014

jdemeyer added s: positive review and removed s: needs review labels Oct 29, 2014

vbraun removed the s: positive review label Oct 30, 2014

vbraun closed this as completed in 3f8b3d0 Oct 30, 2014

strogdon mentioned this issue Jun 26, 2015

Use abs() to test for accuracy of roots of complex-valued functions #18670

Closed

Increase Precision in Failing Doctests #17238

Increase Precision in Failing Doctests #17238

Comments

strogdon commented Oct 27, 2014

strogdon commented Oct 27, 2014

strogdon commented Oct 28, 2014

strogdon commented Oct 28, 2014

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jdemeyer commented Oct 28, 2014

jpflori commented Oct 28, 2014

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strogdon commented Oct 28, 2014

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vbraun commented Oct 30, 2014