Re: [sage-devel] Bug in modp sparse matrix multiply

[Daniel Roche]

Thanks, I submitted and fixed the bug here (in case anyone wants to review 
it):
https://trac.sagemath.org/ticket/23669

On Sunday, August 20, 2017 at 9:11:08 PM UTC-4, vdelecroix wrote:
>
> Dear Dan, 
>
> Thanks for the report! This is indeed a bug. If you want to go further 
> and fix the bug yourself, the procedure is described here 
>
> http://doc.sagemath.org/html/en/developer/ 
>
> Otherwise I will open the relevant ticket. 
>
> Vincent 
>
> On 20/08/2017 19:59, Daniel Roche wrote: 
> > Hi sagers, 
> > 
> > First let me say thanks for the great piece of software that is sage. 
> You 
> > all do a tremendous job and maybe don't get thanked enough. 
> > 
> > There appears to be a bug in sparse matrix multiplication over small 
> finite 
> > fields: 
> > 
> > sage: p = next_prime(2**15); p 
> > 32771 
> > sage: M = Matrix(GF(p), 1,3, lambda i,j: -1, sparse=True); M 
> > [32770 32770 32770] 
> > sage: M*M.transpose() 
> > [32738] # INCORRECT, should be 3 
> > sage: M*M.transpose() + 2**32 
> > [3] # it was off by 2^32, hmmm... 
> > 
> > Being off by 2^32 hints that there is an integer overflow or signedness 
> > issue, and indeed I believe the culprit is in the _matrix_times_matrix_ 
> > method on line 387 of matrix_modn_sparse.pyx 
> > <
> https://github.com/sagemath/sage/blob/master/src/sage/matrix/matrix_modn_sparse.pyx#L387>,
>  
>
> > where a cdef int s is added up without reducing modulo p. 
> > 
> > I am currently running release 8.0 on a 64-bit Debian machine. I had 
> some 
> > old versions of sage lying around and the bug seems to be present in 
> > versions going back at least to 5.6; it's not a recent change. 
> > 
> > Thanks for taking a look! 
> > 
> > -Dan 
> > 
>

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[sage-devel] Re: Size of Sage

[fidelbc]

Using some other definition of Change (ratio of 2017 sloc vs 2011 sloc, 
whenever defined).

*Directory   2011  2017   Change*
server  12093 1 0.000
gsl 3919  83 0.021
ext 7260  346   0.048
matrix  31540 19675 0.624
symbolic8389  5563   0.663
media   219   225   1.027
games   1608  1755   1.091
finance 1736  1904   1.097
interacts   971   1073   1.105
misc20517 23792 1.160
libs24475 29328 1.198
crypto  10686 13027 1.219
interfaces  18006 22776 1.265
modules 9920  12604 1.271
rings   88903 114242 1.285
logic   2074  2716   1.310
sandpiles   3879  5104   1.316
structure   7093  9620   1.356
sets3003  4073   1.356
graphs  39815 54461 1.368
quadratic_forms 4323  6037   1.396
plot11961 17403 1.455
top_dir 197   297   1.508
calculus3911  5908   1.511
tests   1435  2338   1.629
groups  11971 19508 1.630
schemes 47747 81663 1.710
monoids 1465  2530   1.727
modular 31019 61951 1.997
stats   1370  2837   2.071
databases   2647  5562   2.101
geometry17577 38966 2.217
functions   5670  13258 2.338
numerical   4798  11814 2.462
coding  6364  16132 2.535
lfunctions  906   2369   2.615
probability 275   720   2.618
categories  12775 35389 2.770
algebras8150  23008 2.823
homology5249  15111 2.879
combinat72913 224064 3.073
parallel308   2094   6.799
tensor  959   15348 16.004
docs0 92 
sat 0 799   
typeset 0 1211   
knots   0 2112   
quivers 0 2438   
data_structures 0 3246   
arith   0 3531   
doctest 0 3625   
game_theory 0 3781   
repl0 5295   
dynamics0 8550   
matroids0 14640 
manifolds   0 36399 


Happy 10^6 SageMath!
f

On Monday, August 21, 2017 at 5:46:53 PM UTC-4, David Roe wrote:
>
> Sage has recently passed 1,000,000 lines of code.
>
> I thought people might be interested in how Sage has changed in the last 
> six years.  The following compares Sage 4.8.alpha5 [1] with a late beta of 
> Sage 8.0.
>
> Directory   20112017Change
>
> server  12093   1   -12092
> matrix  31540   19675   -11865
> ext 7260346 -6914
> gsl 391983  -3836
> symbolic83895563-2826
> media   219 225 +6
> docs0   92  +92
> top_dir 197 297 +100
> interacts   971 1073+102
> games   16081755+147
> finance 17361904+168
> probability 275 720 +445
> logic   20742716+642
> sat 0   799 +799
> tests   14352338+903
> monoids 14652530+1065
> sets30034073+1070
> typeset 0   1211+1211
> sandpiles   38795104+1225
> lfunctions  906 2369+1463
> stats   13702837+1467
> quadratic_forms 43236037+1714
> parallel308 2094+1786
> calculus39115908+1997
> knots   0   2112+2112
> crypto  10686   13027   +2341
> quivers 0   2438+2438
> structure   70939620+2527
> modules 992012604   +2684
> databases   26475562+2915
> data_structures 0   3246+3246
> misc20517   23792   +3275
> arith   0   3531+3531
> doctest 0   3625+3625
> game_theory 0   3781+3781
> interfaces  18006   22776   +4770
> libs24475   29328   +4853
> repl0   5295+5295
> plot11961   17403   +5442
> numerical   479811814   +7016
> groups  11971   19508   +7537
> functions   567013258   +7588
> dynamics0   8550+8550
> coding  636416132   +9768
> homology

[sage-devel] Size of Sage

[David Roe]

Sage has recently passed 1,000,000 lines of code.

I thought people might be interested in how Sage has changed in the last
six years.  The following compares Sage 4.8.alpha5 [1] with a late beta of
Sage 8.0.

Directory   20112017Change

server  12093   1   -12092
matrix  31540   19675   -11865
ext 7260346 -6914
gsl 391983  -3836
symbolic83895563-2826
media   219 225 +6
docs0   92  +92
top_dir 197 297 +100
interacts   971 1073+102
games   16081755+147
finance 17361904+168
probability 275 720 +445
logic   20742716+642
sat 0   799 +799
tests   14352338+903
monoids 14652530+1065
sets30034073+1070
typeset 0   1211+1211
sandpiles   38795104+1225
lfunctions  906 2369+1463
stats   13702837+1467
quadratic_forms 43236037+1714
parallel308 2094+1786
calculus39115908+1997
knots   0   2112+2112
crypto  10686   13027   +2341
quivers 0   2438+2438
structure   70939620+2527
modules 992012604   +2684
databases   26475562+2915
data_structures 0   3246+3246
misc20517   23792   +3275
arith   0   3531+3531
doctest 0   3625+3625
game_theory 0   3781+3781
interfaces  18006   22776   +4770
libs24475   29328   +4853
repl0   5295+5295
plot11961   17403   +5442
numerical   479811814   +7016
groups  11971   19508   +7537
functions   567013258   +7588
dynamics0   8550+8550
coding  636416132   +9768
homology524915111   +9862
tensor  959 15348   +14389
matroids0   14640   +14640
graphs  39815   54461   +14646
algebras815023008   +14858
geometry17577   38966   +21389
categories  12775   35389   +22614
rings   88903   114242  +25339
modular 31019   61951   +30932
schemes 47747   81663   +33916
manifolds   0   36399   +36399
combinat72913   224064  +151151

python and cython:  1003911 (99.16%)
cpp:7004 (0.69%)
ansic:  1479 (0.15%)

Total Physical Source Lines of Code (SLOC)= 1,012,394
Development Effort Estimate, Person-Years (Person-Months) = 286.19
(3,434.22)
 (Basic COCOMO model, Person-Months = 2.4 * (KSLOC**1.05))
Schedule Estimate, Years (Months) = 4.60 (55.15)
 (Basic COCOMO model, Months = 2.5 * (person-months**0.38))
Estimated Average Number of Developers (Effort/Schedule)  = 62.27
Total Estimated Cost to Develop   = $ 38,659,716
 (average salary = $56,286/year, overhead = 2.40).

Keep up the good work!
David

[1] http://sagemath.blogspot.com/2011/12/how-big-is-core-sage-library.html

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Re: [sage-devel] Re: Sage 8.0 Build Error on MacOS, [mpir-3.0.0.p0] Error building MPIR.

[Dima Pasechnik]

On Monday, August 21, 2017 at 4:15:29 PM UTC+1, Michael Frey wrote:
>
> What is the best way to do this?  The file is extracted from the 
> mpir-3.0.0.tar.bz2 every time make is run.
>

the standard way would be to add the patch removing  this file (which one 
exactly, there are few files named so?)
build/pkgs/mpir/patches/



> On Wednesday, August 2, 2017 at 5:41:01 PM UTC-4, Bill Hart wrote:
>>
>> The only workaround I'm currently aware of is to remove the offending 
>> addmul_1.asm file. It is to do with our use of jump tables.
>>
>>


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Re: [sage-devel] Senseless leading_ methods introduced on all matrices

[Travis Scrimshaw]

On Sunday, August 20, 2017 at 12:02:32 PM UTC-5, John Cremona wrote:
>
>
> Don't get too carried away with thinking up ways in which users might 
> conceivably get confused!   The rings "matrices over polynomials over 
> F" and "polynomials over matrices over F" are isomorphic but not the 
> same. 
>

I think a really good example of this is the four 
isomorphic-but-not-identical:

ZZ['x']['y']
ZZ['y']['x']
ZZ['x,y']
ZZ['y,x']

Each will behave in slightly different ways with respect to the usual 
polynomial methods.

Best,
Travis

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Re: [sage-devel] Re: Sage 8.0 Build Error on MacOS, [mpir-3.0.0.p0] Error building MPIR.

[Michael Frey]

What is the best way to do this?  The file is extracted from the 
mpir-3.0.0.tar.bz2 every time make is run.

On Wednesday, August 2, 2017 at 5:41:01 PM UTC-4, Bill Hart wrote:
>
> The only workaround I'm currently aware of is to remove the offending 
> addmul_1.asm file. It is to do with our use of jump tables.
>
>
>>>

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Re: [sage-devel] Re: sage -docbuild useless

[Ralf Stephan]

No problem, I may have found a bug because of it.

On Monday, August 21, 2017 at 4:09:08 PM UTC+2, Daniel Krenn wrote:
>
> On 2017-08-21 15:08, Ralf Stephan wrote: 
> > Ah the citations need a make and  will not compile with a simple sage 
> > -docbuild. So it really is useless and should be disabled to not confuse 
> > people like me. 
>
> I am strongly against disabling "sage -docbuild": When developing and 
> only changing e.g. one file, then it takes ages for "make doc" to 
> complete, whereas "sage -docbuild ..." finishes within seconds. 
>
>

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Re: [sage-devel] Re: sage -docbuild useless

[Daniel Krenn]

On 2017-08-21 15:08, Ralf Stephan wrote:
> Ah the citations need a make and  will not compile with a simple sage
> -docbuild. So it really is useless and should be disabled to not confuse
> people like me.

I am strongly against disabling "sage -docbuild": When developing and
only changing e.g. one file, then it takes ages for "make doc" to
complete, whereas "sage -docbuild ..." finishes within seconds.

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[sage-devel] Re: sage -docbuild useless

[Ralf Stephan]

Ah the citations need a make and  will not compile with a simple sage 
-docbuild. So it really is useless and should be disabled to not confuse 
people like me.

Regards,

On Monday, August 21, 2017 at 3:05:14 PM UTC+2, Ralf Stephan wrote:
>
> This is peculiar. When I do 'make doc-clean; sage -docbuild reference' 
> then the abovementioned reference will not compile. But with 'make 
> doc-clean; make doc' in a plain develop branch, then add the reference, 
> finally 'sage -docbuild reference' can compile it. It appears a successful 
> 'make doc' sets something up that is necessary but is deleted with 'make 
> doc-clean'.
>

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[sage-devel] Re: sage -docbuild useless

[Ralf Stephan]

This is peculiar. When I do 'make doc-clean; sage -docbuild reference' then 
the abovementioned reference will not compile. But with 'make doc-clean; 
make doc' in a plain develop branch, then add the reference, finally 'sage 
-docbuild reference' can compile it. It appears a successful 'make doc' 
sets something up that is necessary but is deleted with 'make doc-clean'.

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Re: [sage-devel] Re: sage -docbuild useless

[François Bissey]

> On 21/08/2017, at 20:14, Dima Pasechnik  wrote:
> 
> 
> 
> On Monday, August 21, 2017 at 9:06:21 AM UTC+1, Ralf Stephan wrote:
> Hi,
> I just had made a rst document in reference that built nicely with sage 
> -docbuild. It fails with make doc. I consider it a serious bug because it 
> makes it impossible to refer to other refman documents. Am I missing 
> something?
> 
> Example: In reference/calculus/index.rst I can refer to :doc:`polynomial ring 
> elements ` and it works fine with sage -docbuild 
> reference. make doc fails.
> 
> does simply doing make work?
> 
> (there is no 'doc' target in the makefile, so I don't quite see what 'make 
> doc' is meant to do)
>  

Yes there is and it just depends on doc-html:
grep doc: build/make/*
build/make/Makefile:doc: doc-html
build/make/deps:doc: doc-html

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[sage-devel] Re: sage -docbuild useless

[Dima Pasechnik]

On Monday, August 21, 2017 at 9:06:21 AM UTC+1, Ralf Stephan wrote:
>
> Hi,
> I just had made a rst document in reference that built nicely with sage 
> -docbuild. It fails with make doc. I consider it a serious bug because it 
> makes it impossible to refer to other refman documents. Am I missing 
> something?
>
> Example: In reference/calculus/index.rst I can refer to :doc:`polynomial 
> ring elements ` and it works fine with sage 
> -docbuild reference. make doc fails.
>

does simply doing make work?

(there is no 'doc' target in the makefile, so I don't quite see what 'make 
doc' is meant to do)
 

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[sage-devel] sage -docbuild useless

[Ralf Stephan]

Hi,
I just had made a rst document in reference that built nicely with sage 
-docbuild. It fails with make doc. I consider it a serious bug because it 
makes it impossible to refer to other refman documents. Am I missing 
something?

Example: In reference/calculus/index.rst I can refer to :doc:`polynomial 
ring elements ` and it works fine with sage 
-docbuild reference. make doc fails.

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Re: [sage-devel] nbconvert new dependencies...

[François Bissey]

A maintainer removed pandoc from the dependencies of pandocfilters.
pandoc and all the haskell stuff has gone from my dependency tree
for nbconvert. There is still pandocfilters though.

> On 20/08/2017, at 20:26, Volker Braun  wrote:
> 
> Afaik nbconvert always dependend on pandoc for certain types of output (like 
> PDF). Just like LaTeX (which is also a dependency), users have to have 
> typesetting tools installed.
> 
> 
> 
> On Sunday, August 20, 2017 at 9:51:37 AM UTC+2, François Bissey wrote:
> Hi all, 
> 
> I am bit concerned by the new version of nbconvert released upstream (5.2.1). 
> Sage currently uses 4.2.0 as a standard package. 
> nbconvert now uses pandoc which is an haskell package. 
> That’s what my upgrade path for nbconvert, from zero haskell on the system, 
> looks like in Gentoo: 
> [ebuild  N~] dev-python/testpath-0.3.1::gentoo  USE="-doc {-test}" 
> PYTHON_TARGETS="python2_7 python3_4 python3_6 -python3_5" 90 KiB 
> [ebuild  N ] dev-python/bleach-1.5.0::gentoo  USE="{-test}" 
> PYTHON_TARGETS="python2_7 python3_4 python3_6 (-pypy) (-pypy3) (-python3_5)" 
> 36 KiB 
> [ebuild  N ] dev-lang/ghc-7.10.3:0/7.10.3::gentoo  USE="gmp -binary -doc 
> -ghcbootstrap -ghcmakebinary" 122,696 KiB 
> [ebuild  N ] app-admin/haskell-updater-1.2.10::gentoo  26 KiB 
> [ebuild  N ] dev-haskell/cabal-1.22.8.0:0/1.22.8.0::gentoo  USE="-profile 
> {-test}" 397 KiB 
> [ebuild  N ] dev-haskell/transformers-0.4.3.0:0/0.4.3.0::gentoo  
> USE="-doc -hscolour -profile" 0 KiB 
> [ebuild  N ] dev-haskell/data-default-class-0.0.1:0/0.0.1::gentoo  
> USE="-doc -hscolour -profile" 2 KiB 
> [ebuild  N ] dev-haskell/syb-0.4.4:0/0.4.4::gentoo  USE="-doc -hscolour 
> -profile {-test}" 39 KiB 
> [ebuild  N ] dev-haskell/old-locale-1.0.0.7:0/1.0.0.7::gentoo  USE="-doc 
> -hscolour -profile" 4 KiB 
> [ebuild  N ] dev-haskell/stm-2.4.2:0/2.4.2::gentoo  USE="-doc -hscolour 
> -profile" 10 KiB 
> [ebuild  N ] dev-haskell/binary-0.7.6.1:0/0.7.6.1::gentoo  USE="-doc 
> -hscolour -profile {-test}" 0 KiB 
> [ebuild  N ] dev-haskell/zlib-0.5.4.2:0/0.5.4.2::gentoo  USE="-doc 
> -hscolour -profile" 125 KiB 
> [ebuild  N ] dev-haskell/random-1.0.1.1-r1:0/1.0.1.1::gentoo  USE="-doc 
> -hscolour -profile" 9 KiB 
> [ebuild  N ] dev-haskell/primitive-0.5.1.0:0/0.5.1.0::gentoo  USE="-doc 
> -hscolour -profile" 11 KiB 
> [ebuild  N ] dev-haskell/dlist-0.7.1.2:0/0.7.1.2::gentoo  USE="-doc 
> -hscolour -profile {-test}" 7 KiB 
> [ebuild  N ] dev-haskell/extensible-exceptions-0.1.1.4:0/0.1.1.4::gentoo  
> USE="-doc -hscolour -profile" 9 KiB 
> [ebuild  N ] dev-haskell/base64-bytestring-1.0.0.1:0/1.0.0.1::gentoo  
> USE="-doc -hscolour -profile {-test}" 9 KiB 
> [ebuild  N ] dev-haskell/unix-compat-0.4.1.3:0/0.4.1.3::gentoo  USE="-doc 
> -hscolour -old-time -profile" 13 KiB 
> [ebuild  N ] dev-haskell/digest-0.0.1.2:0/0.0.1.2::gentoo  USE="-doc 
> -hscolour -profile" 4 KiB 
> [ebuild  N ] 
> dev-haskell/bytestring-builder-0.10.6.0.0:0/0.10.6.0.0::gentoo  
> USE="-profile" 44 KiB 
> [ebuild  N ] dev-haskell/utf8-string-0.3.8:0/0.3.8::gentoo  USE="-doc 
> -hscolour -profile" 9 KiB 
> [ebuild  N ] dev-haskell/deepseq-generics-0.1.1.2:0/0.1.1.2::gentoo  
> USE="-doc -hscolour -profile {-test}" 6 KiB 
> [ebuild  N ] dev-haskell/text-1.2.2.1:0/1.2.2.1::gentoo  USE="-doc 
> -hscolour -profile {-test}" 147 KiB 
> [ebuild  N ] dev-haskell/mtl-2.2.1-r1:0/2.2.1::gentoo  USE="-doc 
> -hscolour -profile" 16 KiB 
> [ebuild  N ] dev-haskell/vector-0.10.12.3:0/0.10.12.3::gentoo  
> USE="boundschecks -doc -hscolour -internalchecks -profile {-test} 
> -unsafechecks" 102 KiB 
> [ebuild  N ] dev-haskell/old-time-1.1.0.3-r1:0/1.1.0.3::gentoo  USE="-doc 
> -hscolour -profile" 73 KiB 
> [ebuild  N ] dev-haskell/sha-1.6.4.2:0/1.6.4.2::gentoo  USE="-doc -exe 
> -hscolour -profile {-test}" 2,652 KiB 
> [ebuild  N ] dev-haskell/haddock-library-1.2.1:0/1.2.1::gentoo  USE="-doc 
> -hscolour -profile {-test}" 38 KiB 
> [ebuild  N ] dev-haskell/async-2.0.1.4:0/2.0.1.4::gentoo  USE="-doc 
> -hscolour -profile {-test}" 9 KiB 
> [ebuild  N ] 
> dev-haskell/data-default-instances-base-0.0.1:0/0.0.1::gentoo  USE="-doc 
> -hscolour -profile" 2 KiB 
> [ebuild  N ] 
> dev-haskell/data-default-instances-dlist-0.0.1:0/0.0.1::gentoo  USE="-doc 
> -hscolour -profile" 2 KiB 
> [ebuild  N ] 
> dev-haskell/data-default-instances-containers-0.0.1:0/0.0.1::gentoo  
> USE="-doc -hscolour -profile" 2 KiB 
> [ebuild  N ] 
> dev-haskell/data-default-instances-old-locale-0.0.1:0/0.0.1::gentoo  
> USE="-doc -hscolour -profile" 2 KiB 
> [ebuild  N ] dev-haskell/tf-random-0.5:0/0.5::gentoo  USE="-profile" 19 
> KiB 
> [ebuild  N ] dev-haskell/parsec-3.1.9-r1:0/3.1.9::gentoo  USE="-doc 
> -hscolour -profile {-test}" 29 KiB 
> [ebuild  N ] dev-haskell/hashable-1.2.4.0:0/1.2.4.0::gentoo  USE="-doc 
> -hscolour -profile {-test}"