Re: [sage-devel] drop python2 compatibility in 9.1 ?
On Sun, 5 Jan 2020, Frédéric Chapoton wrote: > Do you agree that sage release 9.1 (and most of the 9.1.betas) will not be > kept compatible with Python 2 ? I agree. -- Jori Mäntysalo Tampereen yliopisto - Ihminen ratkaisee -- You received this message because you are subscribed to the Google Groups "sage-devel" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-devel+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/sage-devel/alpine.DEB.2.21..2001060825510.81373%40shell.sis.uta.fi.
Re: [sage-devel] Re: SageNB broken because of stmp???
On Sat, 23 Nov 2019, Frédéric Chapoton wrote: > The current stumbling point is that sagenb uses twisted and twisted is not > py3 compatible, despite pretending to be so. OK. I opened #28792 for better error message. Also I suppose we must change documentation. -- Jori Mäntysalo Tampereen yliopisto - Ihminen ratkaisee -- You received this message because you are subscribed to the Google Groups "sage-devel" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-devel+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/sage-devel/alpine.DEB.2.21..1911231939530.105900%40shell.sis.uta.fi.
[sage-devel] SageNB broken because of stmp???
I did a fresh install, i.e. start from git clone git://github.com/sagemath/sage.git and so on. Sage starts and I can start jupyter also. However ./sage --notebook=sagenb says DeprecationWarning: the imp module is deprecated in favour of importlib; see the module's documentation for alternative uses import imp Traceback (most recent call last): . . . from twisted.mail import smtp, relaymanager # problematic with python 3 ImportError: cannot import name 'smtp' from 'twisted.mail' (unknown location) So have we broken sagenb totally when moving to Python 3? -- Jori Mäntysalo Tampereen yliopisto - Ihminen ratkaisee -- You received this message because you are subscribed to the Google Groups "sage-devel" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-devel+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/sage-devel/alpine.DEB.2.21..1911231609500.101837%40shell.sis.uta.fi.
[sage-devel] Sphinx and links
I opened https://trac.sagemath.org/ticket/28569 thinking it is something easy. Is not for me. Someone understanding Sphinx should take a look. -- Jori Mäntysalo Tampereen yliopisto - Ihminen ratkaisee -- You received this message because you are subscribed to the Google Groups "sage-devel" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-devel+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/sage-devel/alpine.DEB.2.21..1910080818230.75723%40shell.sis.uta.fi.
[sage-devel] refering, recommented, registred and other typos
Might be of interest to someone painting a bikeshed. I played a little
with Levenshtein module.
$ egrep --no-filename -R -o -w '[a-z]{4,15}' src/sage > /tmp/all
$ cat /tmp/all | sort | uniq -c | fgrep -w 1 | colrm 1 8 > /tmp/singles
$ cat /tmp/all | sort | uniq -c | fgrep -v -w 1 | colrm 1 8 > /tmp/nonsingles
And now
#!/bin/python
from Levenshtein import distance
f = open('/tmp/singles', 'r')
singles = f.readlines()
f.close()
f = open('/tmp/nonsingles', 'r')
nonsingles = f.readlines()
f.close()
for s in singles:
for w in nonsingles:
if distance(s, w) == 1:
print(s+" "+w)
break
This can be used to spot at few typos.
--
Jori Mäntysalo
Tampereen yliopisto - Ihminen ratkaisee
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Re: [sage-devel] Re: how does the res/mod in "geng" work?
Btw, what is most simple way in SageMath to run parallel independent jobs without dependencies? For example, let G() be a generator outputting 1000 objects and let there be four cpu cores available. Now it would be nice if we could just fork four processes, each basically saying for example "Get an object o from G(), compute f(o), and if it is 42, save o to the list F." This needs an atomic way to call G(), and an atomic way to append a list. This seems so common form of computation that I suppose there is some nice way for this. -- Jori Mäntysalo Tampereen yliopisto - Ihminen ratkaisee -- You received this message because you are subscribed to the Google Groups "sage-devel" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-devel+unsubscr...@googlegroups.com. To post to this group, send email to sage-devel@googlegroups.com. Visit this group at https://groups.google.com/group/sage-devel. For more options, visit https://groups.google.com/d/optout.
Re: [sage-devel] Re: how does the res/mod in "geng" work?
On Sun, 24 Mar 2019, Nico Van Cleemput wrote: > If you use the normal splitting with geng, it might become more even if you > go to a higher number of > parts. However, it will never be completely even. We could also use geng to split output to for example 100 parts and then combine parts so that we get 10 almost equal sized part. But then, it may be that in following computation almost all time is used for only few graphs. As an example: take all posets on 10 elements and compute the dimension. Now exactly one poset, the standard example of 2 × 5 elements, will take very long time. Of course similar does not always occur, it depends on what we are computing. -- Jori Mäntysalo Tampereen yliopisto - Ihminen ratkaisee -- You received this message because you are subscribed to the Google Groups "sage-devel" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-devel+unsubscr...@googlegroups.com. To post to this group, send email to sage-devel@googlegroups.com. Visit this group at https://groups.google.com/group/sage-devel. For more options, visit https://groups.google.com/d/optout.
Re: [sage-devel] Re: Suggestion to speed up nauty_geng()?
On Fri, 22 Mar 2019, Ai Bo wrote: > With 12, I can't write to a file, it is at least 1500G. I can write to a > file up to around 300G at most. > That is why I am thinking how to divide the output of "geng 12". So > far, I don't have any idea. Any suggestion? You can (and should) use A/B -notation to geng: $ ./local/bin/geng 9 > /dev/null >A ./local/bin/geng -d0D8 n=9 e=0-36 >Z 274668 graphs generated in 0.15 sec $ ./local/bin/geng 9 0/10 > /dev/null >A ./local/bin/geng -X0x200d0D8 n=9 e=0-36 class=0/10 >Z 30682 graphs generated in 0.02 sec $ ./local/bin/geng 9 1/10 > /dev/null >A ./local/bin/geng -X0x200d0D8 n=9 e=0-36 class=1/10 >Z 26300 graphs generated in 0.02 sec and to verify this: ./local/bin/geng 9 | wc -l outputs 274668, just like for x in $(seq 0 9); do ./local/bin/geng 9 $x/10; done | wc -l (But I guess you must use splitting number bigger than 10, maybe ~100.) I think that you can run this in parallel and get you computation done in a day or two. But n=13 might need a supercomputer. -- Jori Mäntysalo Tampereen yliopisto - Ihminen ratkaisee -- You received this message because you are subscribed to the Google Groups "sage-devel" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-devel+unsubscr...@googlegroups.com. To post to this group, send email to sage-devel@googlegroups.com. Visit this group at https://groups.google.com/group/sage-devel. For more options, visit https://groups.google.com/d/optout.
Re: [sage-devel] Re: Suggestion to speed up nauty_geng()?
On Thu, 21 Mar 2019, Simon King wrote: > Does either of you plan to open a ticket and make the functionality > available, that according to Jori is present in nauty but according > to Ai isn't wrapped in Sage? At least I do not. -- Jori Mäntysalo Tampereen yliopisto - Ihminen ratkaisee -- You received this message because you are subscribed to the Google Groups "sage-devel" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-devel+unsubscr...@googlegroups.com. To post to this group, send email to sage-devel@googlegroups.com. Visit this group at https://groups.google.com/group/sage-devel. For more options, visit https://groups.google.com/d/optout.
Re: [sage-devel] Re: Suggestion to speed up nauty_geng()?
OK, more explanation.
* * *
First I compare time for generating graphs in Nauty and in Sage. As plain
graphs(n) uses nauty, I have test.sage containing
print(sum(1 for _ in graphs(9)))
It takes about 11½ seconds to run. I tested this with
time ./sage test.sage
Then,
./local/bin/geng 9 > /dev/null
says "274668 graphs generated in 0.12 sec". So, if we just want to sample
few graphs, we can get the speedup of ~50x. In other words, it is slow to
convert data to Python internal format.
OTOH number of many finite structures up to isomorphism grows very fast.
So you can for example test some hypothesis to n=10 on a mobile phone,
n=11 on a desktop computer and n=13 on a supercomputer. Same happens when
you optimize code.
* * *
Next, does geng use multiple cpu cores? No. There is no difference between
time taskset -c 1 ./local/bin/geng 9 > /dev/null
time taskset -c 1-4 ./local/bin/geng 9 > /dev/null
(You could also use "top" to see cpu usage.)
* * *
Now, how to use geng, make a sample, and then get them to Sage? First I
generated all graphs (here to n=9 for speed):
$ ./local/bin/geng 9 > g9
>A ./local/bin/geng -d0D8 n=9 e=0-36
>Z 274668 graphs generated in 0.12 sec
OK, now I have a big list of strings:
$ head -3 g9 ; tail -3 g9
H??
HA?
HB?
H]~
H^~
H~~
Every line is an encoded graph. I want to make a sample, lets say every
1000:th line. Every line is (HERE, not when n=12) 8 bytes long. So,
$ i=0; while [[ i -lt 274668 ]]; do dd if=g9 bs=8 skip=$i count=1 >> g9sample
2> /dev/null; i=$((i+1000)); done
will give you a file of 275 lines:
$ wc -l g9sample
275 g9sample
And now I did a test2.sage -file:
with open('g9sample', 'r') as fp:
c = 0
n = 0
for line in fp:
g = Graph(line, format='graph6')
n += 1
if g.is_connected():
c += 1
print("About %s percent are connected" % round(100.0*c/n))
and
$ ./sage test2.sage
About 95 percent are connected
Of course there are many other ways for this. For example you could read
the whole file with Python and just skip 99,9% of lines, or skip every
line with propability of 0.999 etc. Hopefully you get the idea from this.
--
Jori Mäntysalo
Tampereen yliopisto - Ihminen ratkaisee
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Re: [sage-devel] Suggestion to speed up nauty_geng()?
On Thu, 21 Mar 2019, Ai Bo wrote:
> Is there a way to "random access"? For example, access the nth element
> in the "generator", instead of one by one?
Kind of. As a most time is propably spent by creating Python data
structures for SageMath, you can use nautygen directly to generate huge
number of graphs.
As an example, it takes below 5 seconds to generate all biconnected graphs
on 10 vertices, and I took third last one:
$ nauty26r7/geng 10 -C | tail -3 | head -1
>A /home/jm58660/lat-koe/nauty26r7/geng -Cd2D9 n=10 e=10-45
>Z 9743542 graphs generated in 4.59 sec
I]~~w
and now
sage: g = Graph('I]~~w', format='graph6')
sage: g.is_biconnected()
True
--
Jori Mäntysalo
Tampereen yliopisto - Ihminen ratkaisee
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Re: [sage-devel] short python3 report (March of the last python2 year)
On Sun, 3 Mar 2019, Frédéric Chapoton wrote: > In sage 8.7.b6 built with python3, there are now 464 failing doctests, in a > total of 137 files. You forgot to say that this is great progress -- and we should thank you for a big part of this! It also seems that in py3 the testing framework does not initialize random seed -- i.e. I got errors randomly from a .random_element(). -- Jori Mäntysalo Tampereen yliopisto - Ihminen ratkaisee -- You received this message because you are subscribed to the Google Groups "sage-devel" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-devel+unsubscr...@googlegroups.com. To post to this group, send email to sage-devel@googlegroups.com. Visit this group at https://groups.google.com/group/sage-devel. For more options, visit https://groups.google.com/d/optout.
[sage-devel] Py2 vs. Py3 and random functions
Is this a known feature? ...~/sage$ ./sage -c 'set_random_seed(0); print(randint(1, 10^6))' 111440 ...~/sage3$ ./sage -c 'set_random_seed(0); print(randint(1, 10^6))' 116853 -- Jori Mäntysalo Tampereen yliopisto - Ihminen ratkaisee -- You received this message because you are subscribed to the Google Groups "sage-devel" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-devel+unsubscr...@googlegroups.com. To post to this group, send email to sage-devel@googlegroups.com. Visit this group at https://groups.google.com/group/sage-devel. For more options, visit https://groups.google.com/d/optout.
Re: [sage-devel] Re: Counting integer compositions with restrictions
On Tue, 19 Feb 2019, TB wrote: > There is the cardinality method of IntegerVectors. Note that the default for > min_part is 0. So this could be used for...? I do not know the area. I was just playing with numbers (original question was "In how many ways you can arrange a queue of 9 men and 7 women such that no two women are next to each other?"), and noticed that .cardinality() in sage/combinat/partition.py even has algorithm-parameter. So I think there might be existing code just waiting for interface. -- Jori Mäntysalo Tampereen yliopisto - Ihminen ratkaisee -- You received this message because you are subscribed to the Google Groups "sage-devel" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-devel+unsubscr...@googlegroups.com. To post to this group, send email to sage-devel@googlegroups.com. Visit this group at https://groups.google.com/group/sage-devel. For more options, visit https://groups.google.com/d/optout.
[sage-devel] Counting integer compositions with restrictions
Is there a fast way to compute for example Compositions(15, min_length=10, max_length=10).cardinality() in some package already integrated to SageMath? For Partitions(...) that seems to be the case, but Compositions(...) uses just brute enumeration. -- Jori Mäntysalo Tampereen yliopisto - Ihminen ratkaisee -- You received this message because you are subscribed to the Google Groups "sage-devel" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-devel+unsubscr...@googlegroups.com. To post to this group, send email to sage-devel@googlegroups.com. Visit this group at https://groups.google.com/group/sage-devel. For more options, visit https://groups.google.com/d/optout.
[sage-devel] SageNB and Firefox
(I know, I know... SageNB is deprecated.) In the newest firefox in Linux pressing backspace in an empty cell does not delete the input cell. It works in Chromium. Why that, any workaround on the server side? -- Jori Mäntysalo Tampereen yliopisto - Ihminen ratkaisee -- You received this message because you are subscribed to the Google Groups "sage-devel" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-devel+unsubscr...@googlegroups.com. To post to this group, send email to sage-devel@googlegroups.com. Visit this group at https://groups.google.com/group/sage-devel. For more options, visit https://groups.google.com/d/optout.
Re: [sage-devel] different graph canonical labels bliss vs Sage (was: doctest failures in databases/sql_db.py)
On Wed, 2 Jan 2019, Vincent Delecroix wrote: > I thought that the definition of the canonical labels was the > order on vertices that minimize the adjacency matrix in > lexicographic order... ?? Any function that translates isomorphism to equality is a canonical labeling. -- Jori Mäntysalo Tampereen korkeakoulut ovat yhdistyneet 1.1.2019 alkaen. Huomaa uusi, @tuni.fi -loppuinen sähköpostiosoitteeni. -- You received this message because you are subscribed to the Google Groups "sage-devel" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-devel+unsubscr...@googlegroups.com. To post to this group, send email to sage-devel@googlegroups.com. Visit this group at https://groups.google.com/group/sage-devel. For more options, visit https://groups.google.com/d/optout.
