Hello !!!
Do you have any suggestions ?
Could you please give us the output of sage -b right after you run this
touch command ? It looks like it the module is not compiled properly.
Nathann
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I already told Ed that I did not know if sub a thing was possible in Sage, but
thought of it a little bit since.. If we were to implement that, it would be
cool to have short notations for these sets, with set.tab thing.
Like :
sets.Circle(xo,xo,radius)
sets.Rectangle(xo,yo,x1,y1)
We could
Hello Peter !
Sorry for my late answer, I am away from everything at the moment, and I am
reduced to answer your message with a mobile phone :-)
I believe that this thing is slow because we did not inform the LP data
structure (which we do not encode ourselves in Sage) or the problem's size.
Hello everybody !
I just discovered this very nice feature :
sage: QQ(1.5)
3/2
It is quite cool to get the rational associated with a float ! LP solvers
often give such output.
This being said, the following is... Well... :-)
sage: QQ(0.3)
3/10
sage: QQ(0.33)
33/100
...
sage:
Hello !!!
Whoah. Some questions people might want to try answering which currently
have no answers:
What the hell ?
Come on guys, we have to do something...
We answer questions on
- Sage-devel
- Sage-support
- AskSage
And now there is stackexchange ? Hey, we have to do
Hello !
I'm doing calculations that involve DiGraphs, and I'd like to know whether
there's a path from one point to another.
Did you try computing D.distance(i,j) ? Or D.shortest_path(i,j) ?
I had been using
def Conn(G,i,j):
return(G.all_paths(i,j) != [])
But when the graphs got
The problem is not in the trace_faces() method, but in the is_planar()
calculation. The embedding of the second graph is not correct:
The is_planar method does not take the nodes_dict dictionary as an
input. Why do you say that its output is incorrect ?
Nathann
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March 2014 15:08, Nathann Cohen nathann.co...@gmail.com wrote:
Hello !
for a simple graph, trace_faces() gives the expected answer for the faces
of a planar graph
That's a good news :-D
the face that should exist between just nodes 3,4 and 5 is not found,
it's replaced
Hello !
for a simple graph, trace_faces() gives the expected answer for the faces
of a planar graph
That's a good news :-D
the face that should exist between just nodes 3,4 and 5 is not found, it's
replaced with a face around nodes 1,2,3,4,5. Any ideas what is wrong, or
Hell !!
Harald is looking for topics for Google Summer of Code, and I was
wondering
if you thought this some other issues w/MILP might be worth looking at.
Hmmm... Well, I always thought that it would be nice to have a way to
express constraints formally. I mean : it would be nice
And, as you point out, it isn't a problem to add a feature that works with
only one solver; we simply add an optional argument (or more), right?
Well, if it boils down to the addition of an optional argument
somewhere this would be a very easy way out :-)
Anyway, we have no reason to stop
For my purpose of learning Cython, this approach was more useful and
certainly faster.
As for this works usefulness for Sage: the numerical module is far more
than just a wrapper for GLPK (also, but not limited to, wrappers for CBC,
Gurobi, CPLEX, and a wrapper to unify them all). Such coverage
Yo !!!
I upgraded to Sage 6.0, and the output is still wrong. I then checked IBM,
and a new version of CPLEX was released in early December 2013. With CPLEX
12.6.0 and Sage 6.0, I now get the correct answers.
HMmmm O_o
So it seems that CPLEX 12.5.10 was the culprit.
Hellooo !!!
Something is indeed wrong, and I have experienced similar problems in the
past. What version of CPLEX and which version of Sage are you using? I am
using IBM ILOG CPLEX 12.5.1.0, and Sage 5.12 on Fedora Linux 19 and Sage
5.10 on Fedora 13.
What other information can I give
:30:27 PM UTC+1, Nathann Cohen wrote:
if i understand correctly, Nathann is implying that
if one works will multigraphs they shouldn't use sage
for this task.
Indeed. Or that they should attempt to code what they need, because right
now I wouldn't feel confortable myself computing stuff
Yoo !!
lol, thanks.
I liked your answers in this thread :)
Cool ! :-D
To be honest, I really believed that they had made you angry ^^;
Is .eulerian_circuit() expected to work on multigraphs?
Yes I believe so. The implementation of this function is really
elegant and calls
I am pretty sure sage has A LOT OF bugs,
Indeed.
why bother?
Because I use this thing and I need it to give correct answers :-P
Probably a lot of them never will be fixed,
never mind.
I am pretty sure that some bugs will never be fixed, but I won't allow a
bug to remain in the graph/ or
Yooo !!
Edge coloring multigraphs raises exception
Ahahaha. That's possible.
sage:
P=graphs.PetersenGraph();ep=P.edges(labels=0);P2=Graph(ep+ep,multiedges=1)
sage: graph_coloring.edge_coloring(P2,value_only=1)
7 # not sure this is correct
It most probably isn't.
Yooo !!
Why isn't are multigraphs (labelled graphs, graphs with loops etc)
implemented as a separate class(es) which inherit from a stripped down
version of graphs? This way graphs would not incur any speed penalty
because
of all of these extra checks that are needed for these more
if i understand correctly, Nathann is implying that
if one works will multigraphs they shouldn't use sage
for this task.
Indeed. Or that they should attempt to code what they need, because right
now I wouldn't feel confortable myself computing stuff on multigraphs.
agree with this and do so.
Hello !!!
It seems that Integer Programs solved with CPLEX sometimes have the wrong
bounds on binary variables. For instance,
Well, as you say CPLEX defined a binary type. And does not associate
bounds with such variables, because it knows it is binary. Anyway :
sage:
Helloo everybody !
This is what I spent the last hour finding :
sage: x = 1/2
sage: x
1/2
sage: x//2
1/4
I got some variable x as input, which was of rational type when I
expected it to be integer type (does not matter, this rational was
equal to an integer in my case). Unfortunately, x//2
I have opened http://trac.sagemath.org/ticket/15173 to track this.
http://trac.sagemath.org/ticket/15116http://trac.sagemath.org/ticket/15116#comment:1
Nathann
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Now waiting for a review !
http://trac.sagemath.org/ticket/14969
Nathann
On 17 July 2013 12:29, Nathann Cohen nathann.co...@gmail.com wrote:
Helloo everybody !!!
Is there a way to compute the longest common subsequence of two
(binary) words in Sage ? I can't find how, but it looks
Helloo everybody !!!
Is there a way to compute the longest common subsequence of two
(binary) words in Sage ? I can't find how, but it looks like something
Sage should be able to do :-)
Thaanks !
Nathann
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I seem to have missed this post ^^;
Well, if you need to fix it the patch has been available for a while, but
it will not get included into Sage unless somebody reviews it !
http://trac.sagemath.org/sage_trac/ticket/14522
Have fn !
Nathann
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Gloops ! You are right !
Gurobi is built if the two files exist, and the first of those is :
SAGE_INC + gurobi_c.h
Looks like the value of SAGE_INC changed and does not end with a '/'
anymore.
A patch fixes that. Very short patch, by the way :-)
http://trac.sagemath.org/sage_trac/ticket/14531
This is now http://trac.sagemath.org/14479 (needs review)
I love your style ! :-D
It says Welcome in the world of Sage, where no known bug makes it past the
day :-D
Nathann
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Hum... G is bipartite but its complement H is not...
Indeed. Right now .complement() preserves the layout.
If you want to plot the graph without using this information, you can also
do g.show(layout=spring ).
Nathann
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Helloo !!!
ok -- from here, what is the easiest way to add csts to p ?
Does this help ? It uses the fact that when you have any hashable object x
in Sage you can create an associated LP variable by writing p[x] :
sage: p = MixedIntegerLinearProgram()
sage: (x= 5).rhs()
5
sage:
Hi Nathan, it doesn't work if my constraint is say 2l + 3u - 8 = 0 ?
No... It just works for all kind of constraints that you have given so far
It seems I cant get around the hard work of 1) from the original cst,
figureout the variables (l,u) , then declare those variables with p
H... If you want to enumerate all partial permutations then you have
much better to do. If you have a n x m matrix with nm what you should do
it take all subsets of n elements of n, and enumerate all permutations
using those n columns among m. Even if I would LOVE to have a way to
I'm sure it's not fast, but in the file
devel/sage/sage/homology/examples.py, there is a function matching which
gets used in simplicial_complexes.ChessboardComplex(...).
Well, obviously there is a matching function in the Graph class. But
nothing to enumerate them.
Oh. Now that I think of
Hello !!!
Am I doing something wrong?
It's very hard to do something wrong with only two lines of code. I'll take
a look at that, but I would bet that the problem comes from a newer version
of Cython :-)
Nathann
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Hello !
It's very hard to do something wrong with only two lines of code. I'll
take
a look at that, but I would bet that the problem comes from a newer
version
of Cython :-)
It's fixed there : http://trac.sagemath.org/sage_trac/ticket/14310
Probably a Cython upgrade. Oh, and CBC
Hell !!!
The Gurobi and CPLEX backends for MixedIntegerLinearProgram() are extremely
convenient.
Glad to learn it :-)
Is there any prospect of solver_parameter() being implemented in the
Gurobi backend?
None from me ! I use CPLEX at the moment but I never mess
I have downloaded Sage 5.6 source-code at
http://www.sagemath.org/download-source.html in order to review the
Python code written to implement the graph theory module.
Why would you do that ? Code is never wrong unless you look at it too
closely. Then you will find a bug every third
Oh. I see. It's just that the default layout does not like disconnected
graphs at all. Your graph ha many connected components, and it would be
best to print them independently :-)
for cc in CG.connected_components_subgraphs():
cc.show()
Nathann
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Hell !!!
You problem may be solved by copying the graph's edges first :
dg2 = DiGraph()
dg2.add_edges(dg.edges())
dg2.show()
If it changes nothing there's not much that I can do unless you give us a
way to create your graph on our computers :-)
Nathann
On Sunday, January 13, 2013
It is a bug indeed ! Sage did not get that the graph was weighted, hence
thought that you had multiple edges in your graph, and hell followed. This
is fixed by this patch : http://trac.sagemath.org/sage_trac/ticket/13919
It will not be merged to Sage unless somebody reviews it, though. Thank
Thanks a lot :)
with t-design it was easy :)
result:
http://galvosukykla.lt/rodyk/thumbs.php?p=//stalo_zaidimai/73_cards/pngdim=150
My pleasure :-)
Happy new ye !!!
Nathann
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Helloo everybody !
Is it only me or is there something wrong with that ?
~/sage/sage$ sage -tp 5 .
...
Doctesting 0 files doing 0 jobs in parallel
Traceback (most recent call last):
File /home/ncohen/.Sage/local/bin/sage-ptest, line 445, in module
p =
Ahahahahah :-)
Beautiful problem ! Not really a graph problem, but a beautiful problem.
What do you think of this ?
http://www.sagemath.org/doc/reference/sage/combinat/designs/block_design.html#sage.combinat.designs.block_design.steiner_triple_system
Does it sound familiar ? But then it only
Hellooo !!!
Don't know if this is a bug, but sage numerically disagrees with
a paper about strong product of graphs.
I would trust Sage in that case :-D
I implemented |strong_product| and don't get the same products as sage
(C_4 bound passed, the Kneser one
The sage session i gave was on vanilla sage, didn't include results from
my implementation.
Good. There's been a patch on this function very recently :
http://trac.sagemath.org/sage_trac/ticket/13699
Is your version of Sage more recent than that ?
If so, as it looks like there's still a bug,
The bugfixes which are already written :-P
Nathann
On 5 December 2012 11:58, Georgi Guninski gunin...@guninski.com wrote:
On Wed, Dec 05, 2012 at 11:27:21AM +0100, Nathann Cohen wrote:
The sage session i gave was on vanilla sage, didn't include results
from
my implementation.
Good. There's
Welll... :-)
http://www.sagemath.org/doc/developer/index.html
Nathann
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http://trac.sagemath.org/sage_trac/ticket/10756
T_T
Of course I only did it for clique_maximum() T_T
Well, Georgi... Weren't you looking for an easy patch to write ? :-P
Nathann
On Monday, December 3, 2012 3:16:09 PM UTC+1, Jason Grout wrote:
On 12/1/12 8:30 AM, Georgi Guninski wrote:
On
Hello !!
So, I downloaded the most current version of the source code from
http://www.liafa.jussieu.fr/~fm/algos/dm.tar, compiled it and run the
exact
same code codifying the graph P. This time I got the right answer:
H O_O
So either Fabien modified it since I wrote to him
Hell !!
Indeed it worked!
Good !
Now I can report that the bug I have reported is solved.
Well.. It is solved on your (unique) version of Sage :-P
I haven't written the patch yet. I wait for an answer from the code's
author, and then it will be ready to be reviewed :-)
Thank you
The ticket is now waiting to be reviewed :-)
http://trac.sagemath.org/sage_trac/ticket/13744
Nathann
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Hello Paulo !
You did, and thank you for that !
The trouble is that the bug does not come from Sage, but rather from the
piece of code we call to solve the problem. In
sage/graph/modular_decomposition/src/ there is a dm.c file that contains
the smart code, and contains a line at the top of
Ahahaaha. Well, I wrote what I thought would be a good if hard to read
implementation, and it turns out to be... slower O_O
I still do not really understand why, except that copying the graph takes
time, too. For some reason.
The code is slower in interesting case, and faster in stupid cases :
May be you are right. Powers of the matrix appear easier to implement
IMHO. After some reading I don't think you can do better than
O(n^(3-epsilon)) because of odd cycles.
Ahahaahah. Well, implement the Matrix version and I will implement the
graph thing. We could be checking the results
Well, the documentation says
Computes the girth of the graph. For directed graphs, computes the
girth of the undirected graph.
So, that's what you are getting. :)
By the way, perhaps it is a bad idea to have this behaviour... What do you
think ??
Nathann
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Hello !!!
According to the doc, this seems to be a bug. Unfortunately, this behavior
produces wrong results. It took me some time to isolate the problem! Bugs
which just produce error messages are much friendlier ...
I totally agree. It has been reported before, and I definitely
Here's a trac ticket that -- at least -- prints a bug report.
http://trac.sagemath.org/sage_trac/ticket/13646
Nathann
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Hellooo !!
I'd say there are two bugs:
There are always too many.
1) p.new_variable() should raise an error if it doesn't understand the
argument, and not just silently do nothing.
Perfectly true. #13646 is meant to fix that :-)
2) the inequality operators should work both ways to
What is strange to me the SEGV is non-deterministic (different graphs
each time), which might be a sign of a deeper problem maybe not in your
code :)
Ahahaah. I do not doubt that the problem is in my code :-)
Nathann
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HM O_O;;
I wanted to rewrite it anyway :-D
No idea where it comes from. I will attempt to tell you today :-)
Nathann
On Saturday, October 13, 2012 9:15:06 AM UTC+2, Georgi Guninski wrote:
Package nauty is not needed, attached is gra2() |for g in graphs(k)|
On Sat, Oct 13, 2012 at
Helloo !!!
To consider the problem as linear program and use
MixedIntegerLinearProgram() with integer constrains works, but it is very
very slow for larger systems.
Well, your problem is *precisely* what Integer Linear Program solvers are
written for, so I guess that using
Since the OP's problem has no inequalities (such as requiring that all
integers in question are non-negative), it is solved by using Hermite
normal
form.
If A is an m by n integer matrix, the Hermite normal form of A is an upper
triangular integer matrix H (also m by n), along with an m by m
Hell !!
I have updated OO TSP page with link to the OpenOpt TSP class file:
Thank you ! It looks like you use the MTZ formulation, with some additional
simplifications when there are vertices of in/out degree 1 in the graph :-)
The formulation we have in Sage should be very
Honestly I don't think it's very constructive to tell users that they
should install a different operating system in order to use Sage, and
that is basically what this dual-booting suggestion amounts to -
dual-booting is unlikely to be a very convenient way for anyone to use
Sage unless
Hell !!
New free tool for TSP solving is available (for downloading as well) -
OpenOpt TSP class: TSP http://openopt.org/TSP (traveling salesman
problem).
Oh ! Nice ! Is it possible to read its implementation from a web page ?
(sorryyy, I do not have access to a real
Well, no it is not. We would need an interface with quadratic solvers to do
that, and all we have now are *linear* solvers. At least through the MILP
class.
Nathann
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Thanks. Can you recommend any good tool other than Sage (since it doesn't
have such interfaces yet) that would handle quadratic inequalities?
Well, that's a problem I would be very glad to be able to answer
myself But it highly depends on the characteristics of your
equations... CPLEX can
Helloo everybody
I just tried to install Sage on a notebook running Ubuntu 12 64bits, and I
fount out that Sage 5.0 is not available on this platform... Do you have
any idea whether it should be supported eventually, or would we need a new
computer for that ???
Thanks !!!
Hellooo !!
Why don't you build from source
Yeahyeah, I ended up doing just that but it was not my computer... Jo
(in Cc) is trying to use Sage for teaching in high school, and he
spent hours trying to get Sage to run without success. Turns out it
was because Wubi (a windows software
Can't you run 32bit SAGE on 64bit Ubuntu? I think there's an lzma file for
SAGE on 32bit Ubuntu 12.04.
Nop, we tried it and it failed immediately :-/
Nathann
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We currently don't have a buildbot running Ubuntu 12 64-bit.
Ok, the easiest explanation is often true :-)
Nathann
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One thing to watch out for is that the generators returned by
automorphism_group contain symbols that may not be the actual vertices. I
realised this once after several frustrating hours of bizarre results from
my program. I'm not sure if this is still the case in recent versions.
Yep. I
Hellooo Emil !!!
Well, I just tried something and it ended upi crashing Sage, so I can just
advise you to create all your variables in the first LP from the start,
*then* to copy the MixedIntegerLinearProgram object. Of course it is a bad
answer :-)
John Perry was the one who needed this
Well, you can call GAP, e.g. as follows:
sage: gap(Orbit(+str(ag._gap_())+,[1,2,7],OnSets);)
[ [ 1, 2, 7 ], [ 1, 2, 3 ], [ 1, 6, 9 ], [ 2, 3, 4 ], [ 3, 4, 10 ],
[ 1, 6, 8 ], [ 3, 4, 8 ], [ 4, 9, 10 ], [ 4, 7, 9 ], [ 5, 8, 10 ],
[ 2, 5, 7 ], [ 5, 6, 8 ], [ 3, 5, 8 ], [ 4, 6, 9 ], [ 5, 7,
Hellooo !!
Next issue is that the Gurobi backend doesn't support the copy:
Oops ^^;
Any idea how much work this would be to do?
Oh, it's usually quite straightforward to implement such things.
Usually the feature already exists in the solver's C api, and all the
work that needs to be
Hellooo everybody !!!
I would like to play with groups in Sage but I do not know how. I
actually get my groups from a graph in the following way :
sage: g = graphs.PetersenGraph()
sage: ag = g.automorphism_group()
sage: type(ag)
class
That's specifically the kind of questions that make me hate the scientific
spirit.
Prove it, or it does not exist, instead of It looks like it exists but I
don't get how.
I think that Sage is useless, and as the mathematics that made me work on
it are totally useless too I do not mind much.
I was going to suggest exactly the same thing in response to the same
personal email you sent me. It would be much better if you posted such
questions to sage-support, rather than emailing developers personally.
I received it too -_-
Nathann
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Hello !!!
Do you mean to say that you have complex numbers p_j and your inequalities
are of the form
|p_j-p_k|=C and |p_j-p_k|=D, and that you also have
some equations on Re(p_j) and Im(p_j) ?
Oh, well, if you have something like that it would of course solve my
problem too :-)
Hello everybody !!!
I would like to solve a set of equations with a very easy shape. My
equations are defined on variables p1_x, p1_y, p2_x, p2_y, ..., and I
would like to obtain values for them satisfying constraints like :
|p1 - p2| 1, i.e. (p1_x - p2_x)^2 + (p1_y - p2_y)^2 1
or something
Couldn't you use SCIP for this?
O probably !!
I will take a look at its documentation :-)
Nathann
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Hell Chris !!!
I found that when installing cbc I had to add #include cstdlib to
CbcEventHandler.cpp, otherwise I got compilation errors about NULL not
being defined.
Arg... Well, this interface is being rewritte anyway. I had a lot of
things to do during the previous week (job
Hello !!!
Thanks! I spent some time with the graph and milp support today, and it's
exactly what I was looking for.
Glad to hear it ! :-)
Do you have an idea of how the current
implementations scale with the size of the graph?
Oh. Well, I do not use LP to solve
Sage has a class name 'Mixed integer linear programming' for modeling
MIPs and class for LP Solver backends like Co-in, CPLEX, GLPK and Gurobi.
At the moment I haven't know any sage class only for vehicle routing
problem.
Yep ! There's a short tutorial about its use there
:
If I wanted to change the last constraint to be w[0]-w[1]-w[2]=1 can I do
this without resetting the whole p?
Not for the moment, but this can be added with a small patch. We just need
to expose the functions from the solver's API :-)
Nathann
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Yes, I checked local/include and local/lib. CPLEX runs fine also as a
64 bit standalone.
I recompiled everything with ./sage -ba, and now
MixedIntegerLinearProgram(solver=CPLEX) triggers a new error
message
I put the log below:
Hmmm... Well, I am sorry but I really have no idea what is
Heloo Yann !!!
Hmmm, like Karl said, what your error tells us is that something went wrong
when CPLEX was installed.
Sage detects that you want to install CPLEX by checking that there is a
file named libcplex.a in SAGE_ROOT/local/lib/ and a file cplex.h in
SAGE_ROOT/local/include/. It
Oh and by the way, I would be very glad to know what you are doing with
Sage and with LP ! Just being curious :-)
Nathann
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Helloo !!
New versions of CPLEX need one more symbolic link. See
http://trac.sagemath.org/sage_trac/ticket/11958 for the ticket from a couple
of months ago.
Arggg !! I had totally forgotten this ticket !
I just updated the patch :-)
Yann, could you add this link Jason mentionned, then
Unfortunately, I had already made the symbolic link to cpxconst.h
before requesting for help on this forum (I did found this ticket you
mentioned by googling) So the bug comes from elsewhere... I'm a
bit desperate :-(
Hello !!!
To be honest I have no idea what is going on. It
Hello !!!
I'll try to test it asap. Having some patch application issues. :-|
Just in case you're familiar with this, I'll throw it out there. But
this is probably a job for google:
Oh, not really. This problem comes from the fact that I am using a more
recent version of Sage than you
Hell !!!
and still much faster than the c_graph implementation.
Well... I spent *quite* some time over this problem, wrote a LOT of code
and documentation , to find out later that this could be solved in a *very
small* patch. I hope all the work I did could be used later on
Hell !
Thanks for looking into this. I believe that I stayed within Sage's
library when I wrote my test code.
You did ! My mistake ! But you actually call
strongly_connected_components_digraph instead of
strongly_connected_components, which mean the function is spending most of
its
Oh yes, and something else about your benchmark : try to avoid using rand
methods when you are doing one, especially when you test such low-level
methods, because often the rand() method represents an important part of
the time.
The best would be to compute all the random number you need in a
Hello Jesse !
Well, for a start it wouldn't be very fair to compare graph libraries if
you do not use our graph methods and recode your own ! You seem to have
rewritten your version of strongly connected components to test the
libraries, and such low-level methods are in Sage written in
Hello everybody !!!
Would anyone know if it is possible in a module's docstring to
interrupt the documentation ?
I would like to write something like that :
This module deals with []. Here is the first block of functions
def function():
rthe function's documentation
And here is the
Hello !!
Nonono, I want the docstring to be seen by sphinx, only it is not and I
would like it to be otherwise ! When I add this And here is the second
one in the middle of the document, it just does not appear in the HTML
documentation ! :-/
Nathann
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No, it's not possible since the second string doesn't get saved
anywhere. Sphinx doesn't parse the module, it just reads the Python
created docstrings, and only the first is saved under module.__doc__.
If you want more control over the resulting documentation, just create
a .rst file in the
Hello everybody !!!
I almost never use the sloane_find function, but it seems to be in a
very bad mood :
sage: sloane_find([1,1,2,3,5,8,13,21])
Searching Sloane's online database...
[]
Perhaps it is just tired of saying it's Fibonacci's sequence and you
should know it each time it is fed with
Hello !!
Thanks for fixing it! :) I forgot the issue so my reply is late.
Well, it took me a month to write it ;-)
I looked at the patch you produced.
I think it's fine except for that I would prefer the algorithm
keyword-argument to be placed at the end of the argument list for
backward
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