[sage-support] Re: trouble building 2.8.13 in Mac OS 10.5.1

[mabshoff]

On Nov 25, 4:04 am, "Justin C. Walker" <[EMAIL PROTECTED]> wrote:
> On Nov 24, 2007, at 17:07 , William Stein wrote:
>
>
>
>
>
> > On Nov 24, 2007 1:26 PM, Justin C. Walker <[EMAIL PROTECTED]> wrote:
>
> >> On Nov 24, 2007, at 12:58 , Neal wrote:
>
> >>> Hi All,
>
> >>> I had some trouble buidling the latest version of SAGE on my MacBook
> >>> Pro under 10.5.1.  Specifically, flint didn't install correctly.
> >>> Here's the relevant part of install.log:
>
> >> This has been discussed and, we hope, diagnosed and fixed.  Check
> >> Michael's message on [sage-devel] regarding 2.8.14.rc2.
>
> >> You can try the release candidate yourself:
> >><http://sage.math.washington.edu/home/mabshoff/
> >> sage-2.8.14.rc2.tar>
>
> > Try only the flint spkg in the release candidate.  The whole
> > release candidate
> > won't build for you, since building the cremona spkg in there is
> > currently
> > broken on OS X.
>
> Yep, it broke on both 10.4.11 and 10.5.1.  I assumed from Michael's
> message that it should work, and I didn't notice that the ".p1"
> version was much different than the original.

Oh well, cremona-20071124.p1 was a "safe" last minute merge back of
the original code by John with small cleanups to the makefiles on his
end. I tested it on sage.math, but as it turned out it got broken on
OSX because John and I only tested on Linux. So that is my bad, but
rc1 did build and test cleanly on 10.5.1.

William just fixed that and some small upgrade issues if earlier
versions of the libraries are still around. So 2.8.14 should be a
pleasure to build on OSX again :)

Cheers,

Michael

>
> I 'touched' the cremona package and continued.  'flint' built on both
> systems, and the build is proceeding.
>
> Justin
>
> --
> Justin C. Walker, Curmudgeon-At-Large
> Director
> Institute for the Enhancement of the Director's Income
> 
> "Weaseling out of things is what separates us from the animals.
>   Well, except the weasel."
>- Homer J Simpson
> 
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[sage-support] Re: trouble building 2.8.13 in Mac OS 10.5.1

[Justin C. Walker]

On Nov 24, 2007, at 17:07 , William Stein wrote:

>
> On Nov 24, 2007 1:26 PM, Justin C. Walker <[EMAIL PROTECTED]> wrote:
>>
>>
>> On Nov 24, 2007, at 12:58 , Neal wrote:
>>
>>>
>>> Hi All,
>>>
>>> I had some trouble buidling the latest version of SAGE on my MacBook
>>> Pro under 10.5.1.  Specifically, flint didn't install correctly.
>>> Here's the relevant part of install.log:
>>
>> This has been discussed and, we hope, diagnosed and fixed.  Check
>> Michael's message on [sage-devel] regarding 2.8.14.rc2.
>>
>> You can try the release candidate yourself:
>>> sage-2.8.14.rc2.tar>
>
> Try only the flint spkg in the release candidate.  The whole  
> release candidate
> won't build for you, since building the cremona spkg in there is  
> currently
> broken on OS X.

Yep, it broke on both 10.4.11 and 10.5.1.  I assumed from Michael's  
message that it should work, and I didn't notice that the ".p1"  
version was much different than the original.

I 'touched' the cremona package and continued.  'flint' built on both  
systems, and the build is proceeding.

Justin

--
Justin C. Walker, Curmudgeon-At-Large
Director
Institute for the Enhancement of the Director's Income

"Weaseling out of things is what separates us from the animals.
  Well, except the weasel."
   - Homer J Simpson




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[sage-support] Re: trouble building 2.8.13 in Mac OS 10.5.1

[William Stein]

On Nov 24, 2007 1:26 PM, Justin C. Walker <[EMAIL PROTECTED]> wrote:
>
>
> On Nov 24, 2007, at 12:58 , Neal wrote:
>
> >
> > Hi All,
> >
> > I had some trouble buidling the latest version of SAGE on my MacBook
> > Pro under 10.5.1.  Specifically, flint didn't install correctly.
> > Here's the relevant part of install.log:
>
> This has been discussed and, we hope, diagnosed and fixed.  Check
> Michael's message on [sage-devel] regarding 2.8.14.rc2.
>
> You can try the release candidate yourself:
>

Try only the flint spkg in the release candidate.  The whole release candidate
won't build for you, since building the cremona spkg in there is currently
broken on OS X.

William

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[sage-support] Re: using Singular's invariant_ring

[Simon King]

Dear David,

perhaps a better answer:

> Suppose a finite matrix group G generated by 3x3 matrices
> A1, A2, ..., Ar acts on the polynomial ring QQ[x,y,z].
> Singular has a command which computes a basis of
> invariants.

Are you actually interested in a Hironaka decomposition? Or are you
looking for a minimal set of generators for the invariant sub-algebra?

invariant_ring() first computes primary invariants and then
(irreducible) secondary invariants. But since Singular-3-0-3, there
are the two functions
 invariant_algebra_reynolds()
and
 invariant_algebra_perm()

These two functions _directly_ compute a minimal generating set in the
case of general finite matrix groups (..._reynolds) respectively of
permutation groups (..._perm), without to compute primary invariants.

They are MUCH faster than invariant_ring (which would yield a not
necessarily minimal generating set), and in my benchmarks it was
50-1000 times faster than the corresponding Magma function
FundamentalInvariants.

Moreover, the return is just a single matrix. Hence, the following
works:
sage: R = singular.ring(0, '(x,y,z)', 'dp')
sage: A = singular.matrix(3,3,'0,1,0,-1,0,0,0,0,-1')
sage: singular.LIB("finvar.lib")
sage: singular.eval('list L=group_reynolds(%s)'%(A.name()))
''   // note that L=A.group_reynolds() should work, but it doesn't
sage: REY=singular('L[1]')
sage: IR = REY.invariant_algebra_reynolds()
sage: IR
z^2,x^2+y^2,x^2*z-y^2*z,x*y*z,x^4+y^4,x^3*y-x*y^3

Hopefully this solves your problem.
 Cheers,
 Simon

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[sage-support] Re: using Singular's invariant_ring

[Simon King]

Dear David,

On Nov 24, 10:38 pm, "David Joyner" <[EMAIL PROTECTED]> wrote:

> sage: R = singular.ring(0, '(x,y,z)', 'dp')
> sage: A = singular.matrix(3,3,'0,1,0,-1,0,0,0,0,-1')
> sage: singular.eval('LIB "finvar.lib";')
>
> Now, I'm stuck. Everything I try returns an error.
> For example, I expected R.invariant_ring(A) to work.
> Are there any Singular experts here who can help with this?

Since i did the current version of finvar.lib, i think i'm supposed to
answer.

First, the argument of invariant_ring is a matrix, and not a ring and
a matrix. Hence, the syntax should be
 A.invariant_ring()

However, this does not work.

I guess the reason is that invariant_ring returns a tripel of matrices
(return(P,S,IS)) and that the Singular interface can not correctly
parse it.

In Singular, it is possible to say
 matrix P,S,IS = invariant_ring(A);
but in sage, the corresponding
 P,S,IS = A.invariant_ring()
does not work.

@Martin Albrecht:
- Is there a reasonable way to fix this in the interface?
- If not: What could we do on the side of Singular to make the return
of a tuple (like return(P,S,IS)) comprehensible for the interface? I
guess "return(list(P,S,IS))" would work, but i'm not sure if this
change of syntax wouldn't have nasty consequences for existing
applications.

There is a very clumsy way to pull the output of invariant_ring into
sage:
First, define A and R as above. Then say
  singular.eval('matrix P,S,IS=invariant_ring(%s)'%(A.name()))
  P=singular('P')
  S=singular('S')
  IS=singular('IS')

But definitely i do think the correct syntax should be
P,S,IS=A.invariant_ring()

Now, another question on the Singular interface:
In Singular, doing
 matrix P,S,IS = invariant_ring(A,1);
would make Singular to additionally print information about the
progress of computations (which, in big examples, might be nice to
have).

However, when i use the Singular interface, i can not see such
informations. Where are they gone?

Yours sincerely
Simon


Yours sincerely
  Simon

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[sage-support] Re: Possible bug in graph isomorphism search_tree function

[Dustin Pluta]

We didn't really have any expectations about the size of these
automorphism groups (this isn't the central part of the project), so
I'm not sure if this output is reasonable for the given graph.  But
here's what search_tree gives:

([[0, 6, 2, 3, 4, 5, 1, 7, 8, 14, 10, 11, 12, 13, 9, 15, 16, 17, 28,
29, 20, 21, 22, 23, 24, 25, 26, 27, 18, 19, 30, 31, 32, 33, 44, 45,
36, 37, 38, 39, 40, 41, 42, 43, 34, 35, 46, 47, 48, 49, 60, 61, 52,
53, 54, 55, 56, 57, 58, 59, 50, 51, 62, 63, 64, 65, 76, 77, 68, 69,
70, 71, 72, 73, 74, 75, 66, 67, 78, 79], [0, 7, 2, 3, 4, 5, 1, 6, 9,
14, 10, 11, 12, 13, 8, 15, 16, 17, 30, 31, 20, 21, 22, 23, 24, 25, 26,
27, 18, 19, 28, 29, 34, 35, 44, 45, 36, 37, 38, 39, 40, 41, 42, 43,
32, 33, 46, 47, 48, 49, 62, 63, 52, 53, 54, 55, 56, 57, 58, 59, 50,
51, 60, 61, 66, 67, 76, 77, 68, 69, 70, 71, 72, 73, 74, 75, 64, 65,
78, 79], [0, 1, 2, 3, 4, 8, 6, 10, 5, 9, 7, 11, 12, 13, 14, 15, 16,
17, 18, 19, 20, 21, 22, 23, 24, 25, 32, 33, 28, 29, 36, 37, 26, 27,
34, 35, 30, 31, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50,
51, 52, 53, 54, 55, 56, 57, 64, 65, 60, 61, 68, 69, 58, 59, 66, 67,
62, 63, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79], [0, 1, 2, 3, 5, 4, 6,
7, 8, 9, 11, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26,
27, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 36, 37, 40, 41,
42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 58, 59, 56,
57, 60, 61, 62, 63, 64, 65, 66, 67, 70, 71, 68, 69, 72, 73, 74, 75,
76, 77, 78, 79], [0, 1, 2, 4, 5, 3, 6, 7, 8, 9, 12, 10, 11, 13, 14,
15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 22, 23, 28, 29, 30, 31,
32, 33, 34, 35, 40, 41, 36, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48,
49, 50, 51, 52, 53, 56, 57, 58, 59, 54, 55, 60, 61, 62, 63, 64, 65,
66, 67, 72, 73, 68, 69, 70, 71, 74, 75, 76, 77, 78, 79], [0, 1, 3, 4,
5, 8, 6, 13, 2, 9, 7, 10, 11, 12, 14, 15, 16, 17, 18, 19, 22, 23, 24,
25, 26, 27, 32, 33, 28, 29, 42, 43, 20, 21, 34, 35, 30, 31, 36, 37,
38, 39, 40, 41, 44, 45, 46, 47, 48, 49, 50, 51, 54, 55, 56, 57, 58,
59, 64, 65, 60, 61, 74, 75, 52, 53, 66, 67, 62, 63, 68, 69, 70, 71,
72, 73, 76, 77, 78, 79]], Graph on 80 vertices)

And here's what the profiler had to say:

   ncalls  tottime  percall  cumtime  percall
filename:lineno(function)
1 19118.403 19118.403 19118.427 19118.427
{sage.graphs.graph_isom.search_tree}
4640.0110.0000.0120.000 xgraph.py:
293(edges_iter)
30.0070.0020.0070.002 graph.py:1059(relabel)
  2310.0020.0000.0040.000 xgraph.py:116(add_edge)
  2310.0010.0000.0010.000 xgraph.py:
233(has_neighbor)
10.0010.0010.0120.012 xgraph.py:439(copy)
  2310.0010.0000.0020.000 xgraph.py:198(has_edge)
  4630.0000.0000.0000.000 {method 'has_key' of
'dict' objects}
  2530.0000.0000.0000.000 {method 'iterkeys' of
'dict' objects}
  1600.0000.0000.0000.000 {method 'iteritems' of
'dict' objects}
  2330.0000.0000.0000.000 {len}
40.0000.0000.0000.000 graph.py:1022(vertices)
   800.0000.0000.0000.000 graph.py:205(add_node)
40.0000.0000.0000.000 {sorted}
10.0000.000 19118.427 19118.427 :1()
10.0000.0000.0000.000 graph.py:3173(__init__)
60.0000.0000.0000.000 graph.py:292(nodes_iter)
10.0000.0000.0120.012 graph.py:3365(copy)
40.0000.0000.0000.000 graph.py:
980(vertex_iterator)
20.0000.0000.0000.000 graph.py:713(order)
40.0000.0000.0000.000 graph.py:
129(prepare_nbunch)
20.0000.0000.0000.000 graph.py:316(order)
60.0000.0000.0000.000 {isinstance}
30.0000.0000.0000.000 {method 'keys' of 'dict'
objects}
10.0000.0000.0000.000 graph.py:
3688(edge_iterator)
10.0000.0000.0000.000 xgraph.py:100(__init__)
10.0000.0000.0000.000 graph.py:92(__iter__)
10.0000.0000.0000.000
{sage.structure.element.is_Matrix}
10.0000.0000.0000.000 {method 'disable' of
'_lsprof.Profiler' objects}

I'll post a similar graph later today hopefully, although I should
probably be careful when I say "similar".  I just mean graphs of the
same size or larger that I've arrived at in the same way (via
projection matrices coming from a class of matrices that I'm trying to
count).

Thanks,
-Dustin Pluta

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[sage-support] using Singular's invariant_ring

[David Joyner]

Hi:

Suppose a finite matrix group G generated by 3x3 matrices
A1, A2, ..., Ar acts on the polynomial ring QQ[x,y,z].
Singular has a command which computes a basis of
invariants. I'm stuck trying to run them in SAGE. The commands at
http://www.singular.uni-kl.de/Manual/latest/sing_1083.htm#SEC1142
are a good example to start. Using the SAGE interface to Singular,
it is easy to get started with

sage: R = singular.ring(0, '(x,y,z)', 'dp')
sage: A = singular.matrix(3,3,'0,1,0,-1,0,0,0,0,-1')
sage: singular.eval('LIB "finvar.lib";')

Now, I'm stuck. Everything I try returns an error.
For example, I expected R.invariant_ring(A) to work.
Are there any Singular experts here who can help with this?

- David

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[sage-support] Re: trouble building 2.8.13 in Mac OS 10.5.1

[Justin C. Walker]

On Nov 24, 2007, at 12:58 , Neal wrote:

>
> Hi All,
>
> I had some trouble buidling the latest version of SAGE on my MacBook
> Pro under 10.5.1.  Specifically, flint didn't install correctly.
> Here's the relevant part of install.log:

This has been discussed and, we hope, diagnosed and fixed.  Check  
Michael's message on [sage-devel] regarding 2.8.14.rc2.

You can try the release candidate yourself:
   

Justin

--
They said it couldn't be done, but sometimes,
it doesn't work out that way.
   - Casey Stengel
--




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[sage-support] trouble building 2.8.13 in Mac OS 10.5.1

[Neal]

Hi All,

I had some trouble buidling the latest version of SAGE on my MacBook
Pro under 10.5.1.  Specifically, flint didn't install correctly.
Here's the relevant part of install.log:

collect2: ld returned 1 exit status
make[2]: *** [fmpz_poly-test] Error 1
ls: qd: No such file or directory
gcc -std=c99 -I/Applications/sage-2.8.13/local/include/ -I/
Applications/sage-2.8.13/local/include -I/Applications/sage-2.8.13/
local/include  -funroll-loops -fexpensive-optimizations  -fPIC -
funroll-loops   -O3 -c mpn_extras-test.c -o mpn_extras-test.o
gcc -std=c99 -I/Applications/sage-2.8.13/local/include/ -I/
Applications/sage-2.8.13/local/include -I/Applications/sage-2.8.13/
local/include  -funroll-loops -fexpensive-optimizations  -fPIC -
funroll-loops   -O3 mpn_extras-test.o test-support.o -o mpn_extras-
test mpn_extras.o mpz_extras.o memory-manager.o ZmodF.o ZmodF_mul.o
ZmodF_mul-tuning.o fmpz.o fmpz_poly.o mpz_poly-tuning.o mpz_poly.o
ZmodF_poly.o long_extras.o -L/Applications/sage-2.8.13/local/lib/  -L/
Applications/sage-2.8.13/local/lib/ -L/Applications/sage-2.8.13/local/
include  -lgmp -lpthread -lm -lntl
ld: duplicate symbol ___gmpz_abs in test-support.o and mpn_extras-
test.o

collect2: ld returned 1 exit status
make[2]: *** [mpn_extras-test] Error 1
Failed to build FLINT dylib.


Also, I'm using gcc 4.0.1, and this was a fresh install.

Thanks!

Neal

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[sage-support] Re: bug in permutations?

[David Joyner]

Done. A patch was linked to on the trac ticket
http://sagetrac.org/sage_trac/ticket/1254

On Oct 28, 2007 1:20 PM, William Stein <[EMAIL PROTECTED]> wrote:
>
> On 10/28/07, Justin C. Walker <[EMAIL PROTECTED]> wrote:
> > Please: no printed "deprecated" warnings.  Anything would be better
> > than that.
>
> +2 -- I very strongly agree with this.  In fact, I think the best
> thing to do would be just get rid of entirely calling Gap via pexpect to
> create all permutations of an object.
>
> BIG NEWS FLASH: Using pseudo-tty's is slow and should be avoided when other
> options are available.  It allows us to very quickly get lots of
> functionality, whilst not reinventing the wheel.  But it's not
> panacea.
>
> -- William
>
>
> >
>

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[sage-support] Re: SAGE-2.8.13 released!

[mabshoff]

On Nov 24, 5:11 pm, Alexander Dreyer
<[EMAIL PROTECTED]> wrote:
> Hello William and Michael,
>
> > > > This looks like a 64 bit SuSE 10.1 box - am I correct?
> Yes.
> > > Also, do you have GMP installed system-wide?  It could be
> > > some broken weird GMP that confuses the mpfi build
> > > script.
>
> Yes, GMP ist installed systemwide.
>
> > Yep, I suspect something similar, but I have a couple more questions:
>
> > > It could also be some very weird error in sage the build system
> > > itself, where maybe it somehow tries to build mpfi but gmp didn't
> > > get installed correctly -- could you post your install.log online 
> > > somewhere
> > > and email us a link to it?
>
> > 1) Is this a virgin build or an upgrade?
>
> This is a complete virgin build.> 2) If an upgrade: What version did you 
> upgrade from? Was that a binary
> > or also build from source?
>
> > 3) Have previous versions build successfully on that particular box?
> > If so which ones?
>

Hello Alexander,

> I realized that 2.8.12 also do not compile. (Your servers were renewed
> recently, so this was a first attempt to build sage on it.)
> Meanwhile, I got sage compiled by changing the configure line in spkg-
> install of mpfi-1.3.4-rc3.p9 to
> ./configure --prefix="$SAGE_LOCAL" --with-mpfr-dir="$SAGE_LOCAL"
> CFLAGS="-fPIC"
>

Ok, if that does the trick I will merge the fix into 2.8.14 provided
it compiles locally on the test boxen (which it should). I looked at
the configure log in detail and it seems very weired that it fails
that late because it does find a gmp and gmp headers.

Oh well, Sage never builds out of the box for everybody. It is like
playing a whack a mole :)

Michael

> > gzipping the install.log and putting it up somewhere for us to
> > download would probably help a great bit.
>
> See here:http://polybori.sourceforge.net/tmp/installlog_sage.tar.bz2
>
> Best regards,
>Alexander Dreyer
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[sage-support] Re: SAGE-2.8.13 released!

[Alexander Dreyer]

Hello William and Michael,

> > > This looks like a 64 bit SuSE 10.1 box - am I correct?
Yes.
> > Also, do you have GMP installed system-wide?  It could be
> > some broken weird GMP that confuses the mpfi build
> > script.
Yes, GMP ist installed systemwide.

> Yep, I suspect something similar, but I have a couple more questions:
>
> > It could also be some very weird error in sage the build system
> > itself, where maybe it somehow tries to build mpfi but gmp didn't
> > get installed correctly -- could you post your install.log online somewhere
> > and email us a link to it?
>
> 1) Is this a virgin build or an upgrade?
This is a complete virgin build.
> 2) If an upgrade: What version did you upgrade from? Was that a binary
> or also build from source?
>
> 3) Have previous versions build successfully on that particular box?
> If so which ones?
I realized that 2.8.12 also do not compile. (Your servers were renewed
recently, so this was a first attempt to build sage on it.)
Meanwhile, I got sage compiled by changing the configure line in spkg-
install of mpfi-1.3.4-rc3.p9 to
./configure --prefix="$SAGE_LOCAL" --with-mpfr-dir="$SAGE_LOCAL"
CFLAGS="-fPIC"

> gzipping the install.log and putting it up somewhere for us to
> download would probably help a great bit.
See here:
http://polybori.sourceforge.net/tmp/installlog_sage.tar.bz2

Best regards,
   Alexander Dreyer

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[sage-support] Re: sage 2.8.13: g0n - cremona.spkg failed to build, 32bit linux, gcc-4.2.2

[Simon King]

> Ok, an updated spkg that merges John's changes is at
>
> http://sage.math.washington.edu/home/mabshoff/cremona-20071124.spkg
>
> I had some slight merge conflicts that I did resolve. It builds an
> passes doctests on sage.math. Please try this on systems with gcc
> 4.2.x and report back.

It works for me with gcc 4.2.1.
Thank you!

Yours
  Simon

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[sage-support] Re: sage 2.8.13: g0n - cremona.spkg failed to build, 32bit linux, gcc-4.2.2

[Andrzej Giniewicz]

Great work, that error is no longer here :)... I'm still compiling
other packages so if there will be any further problems I will report
back, but it is already after last time critical point...

sorry for long reply and no log, I was really busy with my tasks and
today checked list first time from posting...

best regards,
Andrzej.

On 24 Lis, 04:02, mabshoff <[EMAIL PROTECTED]
dortmund.de> wrote:
> On Nov 23, 9:15 pm, "John Cremona" <[EMAIL PROTECTED]> wrote:
>
> > I am currently making sure that my code compiles ok with gcc 4.2.1 and
> > will upload a patch so this will be fixed soon.
>
> > John Cremona
>
> Ok, an updated spkg that merges John's changes is at
>
> http://sage.math.washington.edu/home/mabshoff/cremona-20071124.spkg
>
> I had some slight merge conflicts that I did resolve. It builds an
> passes doctests on sage.math. Please try this on systems with gcc
> 4.2.x and report back.
>
> Cheers,
>
> Michael
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