[sage-devel] Error with Parallelism, case of nproc>1

[Richard_L]

Continuing with the example first discussed on ask.sagemath.org and 
graciously corrected/answered by Eric G, I now find that setting *nproc* to 
anything but *1* in the following will cause the last line to give 
incorrect results.

I am running sagemath version 8.5. According to trac, this should contain 
the last fix to parallelization on manifolds (ticket #26777), so it looks 
to me like a new bug.

sage: version()
'SageMath version 8.5, Release Date: 2018-12-22'
sage: ##
sage: ## If the following sets nproc>1, the last line in this script gives all 
zeroes, which is incorrect.
sage: ##
sage: Parallelism().set(nproc=1)
sage: #Patch to avoid maxima bug
sage: maxima_calculus.eval("domain:real;")
'real'
sage: M = Manifold(3,'R^3',field='real',start_index=1)
sage: c_C. = M.chart();
sage: c_C.add_restrictions(z>0)
sage: g = M.riemannian_metric('g');
sage: g[1,1],g[2,2],g[3,3] = 1,1,1; 
sage: g.display()
g = dx*dx + dy*dy + dz*dz
sage: c_S. = M.chart(r'r:(0,+oo) theta:(0,pi/2):\theta 
phi:(0,2*pi):\phi');
sage: ch_C_S = c_C.transition_map(c_S, (sqrt(x^2+y^2+z^2), 
arccos(z/(sqrt(x^2+y^2+z^2))), arctan2(y,x)))
sage: ch_C_S
Change of coordinates from Chart (R^3, (x, y, z)) to Chart (R^3, (r, theta, 
phi))
sage: ch_C_S.set_inverse(r*sin(theta)*cos(phi), r*sin(theta)*sin(phi), 
r*cos(theta))
sage: M.set_default_chart(c_S)# this saves a little typing later
sage: M.set_default_frame(c_S.frame())
sage: g.display()
g = dr*dr + r^2 dtheta*dtheta + r^2*sin(theta)^2 dphi*dphi
sage: chi_s = M.scalar_field({c_S:function('chi')(r,theta,phi)}, name='chi', 
latex_name=r'\chi')
sage: delChi = chi_s.laplacian(g)
sage: ddChi = delChi.expr()
sage: ddChi.collect_common_factors()
((r^2*diff(chi(r, theta, phi), r, r) + 2*r*diff(chi(r, theta, phi), r) + 
diff(chi(r, theta, phi), theta, theta))*sin(theta)^2 + 
cos(theta)*sin(theta)*diff(chi(r, theta, phi), theta) + diff(chi(r, theta, 
phi), phi, phi))/(r^2*sin(theta)^2)
sage: ddChi.coefficient(r,2)
diff(chi(r, theta, phi), r, r)/r^2
sage: for coord in [r, theta, phi]:
...   for order in [1, 2]:
...   der = diff(chi(r,theta,phi), coord, order)
...   print("{}:  {}".format(der, ddChi.coefficient(der, 1)))
diff(chi(r, theta, phi), r):  2/r
diff(chi(r, theta, phi), r, r):  1
diff(chi(r, theta, phi), theta):  cos(theta)/(r^2*sin(theta))
diff(chi(r, theta, phi), theta, theta):  r^(-2)
diff(chi(r, theta, phi), phi):  0
diff(chi(r, theta, phi), phi, phi):  1/(r^2*sin(theta)^2)

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Re: [sage-devel] Re: internet tests failing

[Dima Pasechnik]

On Thu, Mar 14, 2019 at 7:51 PM John H Palmieri  wrote:
>
> I'm seeing the same failure on a Mac running the most recent OS X. I have 
> openssl 1.1.1a installed on this machine, and I see the error in Sage. Then I 
> did './sage -i openssl' and './sage -f python2', and I still see the error. 
> The Python 2 log file does not list ssl among the modules which were not 
> built, so it looks like it was built with ssl support.
>
>
>
> On Thursday, March 14, 2019 at 11:19:37 AM UTC-7, Volker Braun wrote:
>>
>> I'm guessing you run this on an oldish mac, those have an outdated openssl 
>> that doesn't support TLS12. More and more sites are switching that on. 
>> Building Sage's openssl should fix that.
>>
>>
>>
>> On Thursday, March 14, 2019 at 7:09:50 PM UTC+1, kcrisman wrote:
>>>
>>> This could be just me.  But I am getting a lot of this when I try running 
>>> optional internet tests for e.g. src/sage/databases/oeis.py or 
>>> src/sage/symbolic/integration/external.py  Internet clearly works if you 
>>> can read this message, but apparently it doesn't work from within Sage, 
>>> because I get this message when I try it in the Sage command line as well 
>>> with e.g. this command.  Any ideas - do I need to rebuild Sage with 
>>> additional SSL support or something?  That should be mentioned somewhere.  
>>> Thanks!
>>>
>>> - kcrisman
>>>
>>> w = oeis(7540) ; w
>>>
>>>
>>> URLError: >> verify failed (_ssl.c:726)>
>
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on a Mac is much older than yours (8 years old :-)), running OSX 10.13,
I don't see this error with Sage 8.7.beta5 built under Homebrew (and
so it uses Homebrew's stable openssl, 1.0.2q).
(Rebuilding the latest beta now, but I don't expect a regression here).

Dima

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[sage-devel] Re: pretty print latex doctest error

[John H Palmieri]

On Thursday, March 14, 2019 at 1:46:38 PM UTC-7, kcrisman wrote:
>
> I just ran the following command, and amazingly got only one timeout and 
> one error.  The rest is fine.
>
> ./sage -tp 3 -T 600 --optional=sage,python2,latex src/sage
>
> **
>
> File "src/sage/repl/rich_output/pretty_print.py", line 217, in 
> sage.repl.rich_output.pretty_print.pretty_print
>
> Failed example:
>
> pretty_print(ZZ, 123, plt)# optional - latex 
>
> Expected:
>
>  type="math/tex">\newcommand{\Bold}[1]{\mathbf{#1}}\Bold{Z} 123 %% Creator: 
> Matplotlib, PGF backend...
>
> Got:
>
> doctest:warning
>
> 
>
>   File 
> "/Users/karl.crisman/Downloads/sage/local/lib/python2.7/site-packages/matplotlib/backends/backend_pgf.py",
>  
> line 50, in 
>
> warnings.warn('error getting fonts from fc-list', UserWarning)
>
> :
>
> UserWarning: error getting fonts from fc-list
>
> 

[sage-devel] pretty print latex doctest error

[kcrisman]

I just ran the following command, and amazingly got only one timeout and 
one error.  The rest is fine.

./sage -tp 3 -T 600 --optional=sage,python2,latex src/sage

**

File "src/sage/repl/rich_output/pretty_print.py", line 217, in 
sage.repl.rich_output.pretty_print.pretty_print

Failed example:

pretty_print(ZZ, 123, plt)# optional - latex 

Expected:

\newcommand{\Bold}[1]{\mathbf{#1}}\Bold{Z} 123 %% Creator: 
Matplotlib, PGF backend...

Got:

doctest:warning



  File 
"/Users/karl.crisman/Downloads/sage/local/lib/python2.7/site-packages/matplotlib/backends/backend_pgf.py",
 
line 50, in 

warnings.warn('error getting fonts from fc-list', UserWarning)

:

UserWarning: error getting fonts from fc-list

Re: [sage-devel] Re: internet tests failing

[kcrisman]

Perhaps it's some sort of certificate issue.
> If an up to date openssl has its certs improperly set up, it won't work, 
> IMHO.
>
>>
>>
Give the error message, this seems plausible.   Any ideas on where to go 
from here?  Is it user error for me to try to use the OEIS through Sage? 
 Volker is of course right that my Mac is nearly 4 years old.

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Re: [sage-devel] Re: internet tests failing

[Dima Pasechnik]

Perhaps it's some sort of certificate issue.
If an up to date openssl has its certs improperly set up, it won't work,
IMHO.

On Thu, 14 Mar 2019 19:51 John H Palmieri,  wrote:

> I'm seeing the same failure on a Mac running the most recent OS X. I have
> openssl 1.1.1a installed on this machine, and I see the error in Sage. Then
> I did './sage -i openssl' and './sage -f python2', and I still see the
> error. The Python 2 log file does not list ssl among the modules which were
> not built, so it looks like it was built with ssl support.
>
>
>
> On Thursday, March 14, 2019 at 11:19:37 AM UTC-7, Volker Braun wrote:
>>
>> I'm guessing you run this on an oldish mac, those have an outdated
>> openssl that doesn't support TLS12. More and more sites are switching that
>> on. Building Sage's openssl should fix that.
>>
>>
>>
>> On Thursday, March 14, 2019 at 7:09:50 PM UTC+1, kcrisman wrote:
>>>
>>> This could be just me.  But I am getting a lot of this when I try
>>> running optional internet tests for e.g. src/sage/databases/oeis.py or
>>> src/sage/symbolic/integration/external.py  Internet clearly works if you
>>> can read this message, but apparently it doesn't work from within Sage,
>>> because I get this message when I try it in the Sage command line as well
>>> with e.g. this command.  Any ideas - do I need to rebuild Sage with
>>> additional SSL support or something?  That should be mentioned somewhere.
>>> Thanks!
>>>
>>> - kcrisman
>>>
>>> w = oeis(7540) ; w
>>>
>>> URLError: >> certificate verify failed (_ssl.c:726)>
>>>
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[sage-devel] Re: internet tests failing

[John H Palmieri]

I'm seeing the same failure on a Mac running the most recent OS X. I have 
openssl 1.1.1a installed on this machine, and I see the error in Sage. Then 
I did './sage -i openssl' and './sage -f python2', and I still see the 
error. The Python 2 log file does not list ssl among the modules which were 
not built, so it looks like it was built with ssl support. 



On Thursday, March 14, 2019 at 11:19:37 AM UTC-7, Volker Braun wrote:
>
> I'm guessing you run this on an oldish mac, those have an outdated openssl 
> that doesn't support TLS12. More and more sites are switching that on. 
> Building Sage's openssl should fix that.
>
>
>
> On Thursday, March 14, 2019 at 7:09:50 PM UTC+1, kcrisman wrote:
>>
>> This could be just me.  But I am getting a lot of this when I try running 
>> optional internet tests for e.g. src/sage/databases/oeis.py or 
>> src/sage/symbolic/integration/external.py  Internet clearly works if you 
>> can read this message, but apparently it doesn't work from within Sage, 
>> because I get this message when I try it in the Sage command line as well 
>> with e.g. this command.  Any ideas - do I need to rebuild Sage with 
>> additional SSL support or something?  That should be mentioned somewhere. 
>>  Thanks!
>>
>> - kcrisman
>>
>> w = oeis(7540) ; w 
>>
>> URLError: > verify failed (_ssl.c:726)>
>>
>

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Re: [sage-devel] Something is wrong with my installed sage

[Dima Pasechnik]

On Thu, Mar 14, 2019 at 5:44 PM Ai Bo  wrote:
>
> I see. Thank you.
> As I don't know how and when the files will be cleaned on the local disk and 
> I don't know when my program, if launched at local disk, will be killed.

A typical HPC center policy with scratch disks is that files live a
certain amount of time, i.e. most probably 1 month since creation.
Surely local disks are not cleaned at random moments, otherwise what's
point of having them, they are basically useless.

>
> I downloaded the binary package. I am a little bit confused. Does the binary 
> package know where I already build ./sage?

I think you need to start from the beginning, again.

But I think it's much better idea to use the local disks, surely 30
days is long enough for a lot of work, and then you wipe your local
disk, copy there files from NFS, and may start again.


>
> On Thu, Mar 14, 2019 at 12:51 AM Dima Pasechnik  wrote:
>>
>> On Thu, Mar 14, 2019 at 7:24 AM Dima Pasechnik  wrote:
>> >
>> > On Thu, Mar 14, 2019 at 7:09 AM Dima Pasechnik  wrote:
>> > >
>> > > On Thu, Mar 14, 2019 at 3:39 AM Ai Bo  wrote:
>> > > >
>> > > > Sorry, it doesn't work if I build on local disk and then copy to /nfs.
>> > > > I got error:
>> > > > bash-4.3$ ./sage
>> >
>> > But did you try moving it back to the local disk, before starting it?
>> > Indeed, you just need to have a copy of your files on NFS, and copy it
>> > to the local disk for running.
>> (It's important that it's moved to the same place in the directory
>> tree where it was built).
>> >
>> > Sorry for confusion, again.
>> >
>> > > >
>> > > > ERROR:  The Sage installation tree has moved
>> > > >
>> > > > from /tmp/.../sage-8.6
>> > > >   to /nfs/.../Sage/sage-8.6
>> > > >
>> > > > This is not supported, and Sage will not work. To install Sage from a
>> > > > binary package:
>> > >
>> > > yes, you need to create a binary package in this case. It (not the
>> > > unpacked result, but the package itsel) can be
>> > > moved. Indeed, Sage binary installers have to come from somewhere, 
>> > > right? See
>> > >
>> > > https://github.com/sagemath/binary-pkg
>> > >
>> > > Sorry, I should have mentioned this earlier. It has to be built from
>> > > scratch, AFAIK.
>> > >
>> > >
>> > > >
>> > > > As I mentioned before, I can't save files on local disk more then 30 
>> > > > days. But it seems I can't copy the whole directory to /nfs either.
>> > > >
>> > > > Please advise.
>> > > >
>> > > > On Wed, Mar 13, 2019 at 11:21 AM Ai Bo  wrote:
>> > > >>
>> > > >> I see. Will try. Thank you.
>> > > >>
>> > > >> On Wed, Mar 13, 2019 at 11:04 AM Dima Pasechnik  
>> > > >> wrote:
>> > > >>>
>> > > >>> On Wed, Mar 13, 2019 at 5:57 PM Ai Bo  wrote:
>> > > >>> >
>> > > >>> > Sorry, I can't. All local disks are cleaned out every 30 days.
>> > > >>>
>> > > >>> but building does not take that long. :-)
>> > > >>> Besides, once you have a working build you can, with a bit of 
>> > > >>> effort, move it
>> > > >>> around.
>> > > >>>
>> > > >>> >
>> > > >>> > On Wed, Mar 13, 2019 at 9:43 AM Dima Pasechnik  
>> > > >>> > wrote:
>> > > >>> >>
>> > > >>> >> On Wed, Mar 13, 2019 at 4:18 PM Ai Bo  wrote:
>> > > >>> >> >
>> > > >>> >> > Yes. This is done on NFS.
>> > > >>> >> > I can't build on local disks as this is not on a particular 
>> > > >>> >> > machine. But I do own my own NFS disks.
>> > > >>> >>
>> > > >>> >> Normally multi-user systems have a "scratch" partition, a local 
>> > > >>> >> disk
>> > > >>> >> reserved for this kind of jobs, which is not backed up, but is 
>> > > >>> >> fast to
>> > > >>> >> access (as opposed to NFS).
>> > > >>> >> Ask your system admins for access to such a partition, it's a
>> > > >>> >> perfectly reasonable request.
>> > > >>> >>
>> > > >>> >> > Also, the reason I want to build on my machine as when I use 
>> > > >>> >> > the online version(server), a long running program will be 
>> > > >>> >> > paused from time to time. I want to run on some machines I have 
>> > > >>> >> > access to instead.
>> > > >>> >> >
>> > > >>> >> > If I can't build on NFS, this seems to be a dead end too.
>> > > >>> >> >
>> > > >>> >> > On Wed, Mar 13, 2019 at 9:03 AM E. Madison Bray 
>> > > >>> >> >  wrote:
>> > > >>> >> >>
>> > > >>> >> >> On Wed, Mar 13, 2019 at 4:58 PM Dima Pasechnik 
>> > > >>> >> >>  wrote:
>> > > >>> >> >> >
>> > > >>> >> >> > By looking at the output it looks as if the build it on an 
>> > > >>> >> >> > NFS, and this is known to be severely broken. Could you do 
>> > > >>> >> >> > the build on a local disk?
>> > > >>> >> >>
>> > > >>> >> >> Oh, nice catch.  Yes, many build tools can have problems on 
>> > > >>> >> >> NFS,
>> > > >>> >> >> especially on older kernels.  For example if timestamps are not
>> > > >>> >> >> fine-grained enough you can end up with screwy issues where 
>> > > >>> >> >> some
>> > > >>> >> >> dependencies don't get rebuilt properly and things like that.
>> > > >>> >> >>
>> > > >>> >> >> > On Wed, 13 Mar 2019 15:44 E. Madison Bray, 
>> > > >>> >> >> >  wr

[sage-devel] Re: internet tests failing

[Volker Braun]

I'm guessing you run this on an oldish mac, those have an outdated openssl 
that doesn't support TLS12. More and more sites are switching that on. 
Building Sage's openssl should fix that.



On Thursday, March 14, 2019 at 7:09:50 PM UTC+1, kcrisman wrote:
>
> This could be just me.  But I am getting a lot of this when I try running 
> optional internet tests for e.g. src/sage/databases/oeis.py or 
> src/sage/symbolic/integration/external.py  Internet clearly works if you 
> can read this message, but apparently it doesn't work from within Sage, 
> because I get this message when I try it in the Sage command line as well 
> with e.g. this command.  Any ideas - do I need to rebuild Sage with 
> additional SSL support or something?  That should be mentioned somewhere. 
>  Thanks!
>
> - kcrisman
>
> w = oeis(7540) ; w 
>
> URLError:  verify failed (_ssl.c:726)>
>

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[sage-devel] internet tests failing

[kcrisman]

This could be just me.  But I am getting a lot of this when I try running 
optional internet tests for e.g. src/sage/databases/oeis.py or 
src/sage/symbolic/integration/external.py  Internet clearly works if you 
can read this message, but apparently it doesn't work from within Sage, 
because I get this message when I try it in the Sage command line as well 
with e.g. this command.  Any ideas - do I need to rebuild Sage with 
additional SSL support or something?  That should be mentioned somewhere. 
 Thanks!

- kcrisman

w = oeis(7540) ; w 

URLError: 

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Re: [sage-devel] Something is wrong with my installed sage

[Ai Bo]

I see. Thank you.
As I don't know how and when the files will be cleaned on the local disk
and I don't know when my program, if launched at local disk, will be killed.

I downloaded the binary package. I am a little bit confused. Does the
binary package know where I already build ./sage?

On Thu, Mar 14, 2019 at 12:51 AM Dima Pasechnik  wrote:

> On Thu, Mar 14, 2019 at 7:24 AM Dima Pasechnik  wrote:
> >
> > On Thu, Mar 14, 2019 at 7:09 AM Dima Pasechnik 
> wrote:
> > >
> > > On Thu, Mar 14, 2019 at 3:39 AM Ai Bo  wrote:
> > > >
> > > > Sorry, it doesn't work if I build on local disk and then copy to
> /nfs.
> > > > I got error:
> > > > bash-4.3$ ./sage
> >
> > But did you try moving it back to the local disk, before starting it?
> > Indeed, you just need to have a copy of your files on NFS, and copy it
> > to the local disk for running.
> (It's important that it's moved to the same place in the directory
> tree where it was built).
> >
> > Sorry for confusion, again.
> >
> > > >
> > > > ERROR:  The Sage installation tree has moved
> > > >
> > > > from /tmp/.../sage-8.6
> > > >   to /nfs/.../Sage/sage-8.6
> > > >
> > > > This is not supported, and Sage will not work. To install Sage from a
> > > > binary package:
> > >
> > > yes, you need to create a binary package in this case. It (not the
> > > unpacked result, but the package itsel) can be
> > > moved. Indeed, Sage binary installers have to come from somewhere,
> right? See
> > >
> > > https://github.com/sagemath/binary-pkg
> > >
> > > Sorry, I should have mentioned this earlier. It has to be built from
> > > scratch, AFAIK.
> > >
> > >
> > > >
> > > > As I mentioned before, I can't save files on local disk more then 30
> days. But it seems I can't copy the whole directory to /nfs either.
> > > >
> > > > Please advise.
> > > >
> > > > On Wed, Mar 13, 2019 at 11:21 AM Ai Bo  wrote:
> > > >>
> > > >> I see. Will try. Thank you.
> > > >>
> > > >> On Wed, Mar 13, 2019 at 11:04 AM Dima Pasechnik 
> wrote:
> > > >>>
> > > >>> On Wed, Mar 13, 2019 at 5:57 PM Ai Bo  wrote:
> > > >>> >
> > > >>> > Sorry, I can't. All local disks are cleaned out every 30 days.
> > > >>>
> > > >>> but building does not take that long. :-)
> > > >>> Besides, once you have a working build you can, with a bit of
> effort, move it
> > > >>> around.
> > > >>>
> > > >>> >
> > > >>> > On Wed, Mar 13, 2019 at 9:43 AM Dima Pasechnik <
> dimp...@gmail.com> wrote:
> > > >>> >>
> > > >>> >> On Wed, Mar 13, 2019 at 4:18 PM Ai Bo 
> wrote:
> > > >>> >> >
> > > >>> >> > Yes. This is done on NFS.
> > > >>> >> > I can't build on local disks as this is not on a particular
> machine. But I do own my own NFS disks.
> > > >>> >>
> > > >>> >> Normally multi-user systems have a "scratch" partition, a local
> disk
> > > >>> >> reserved for this kind of jobs, which is not backed up, but is
> fast to
> > > >>> >> access (as opposed to NFS).
> > > >>> >> Ask your system admins for access to such a partition, it's a
> > > >>> >> perfectly reasonable request.
> > > >>> >>
> > > >>> >> > Also, the reason I want to build on my machine as when I use
> the online version(server), a long running program will be paused from time
> to time. I want to run on some machines I have access to instead.
> > > >>> >> >
> > > >>> >> > If I can't build on NFS, this seems to be a dead end too.
> > > >>> >> >
> > > >>> >> > On Wed, Mar 13, 2019 at 9:03 AM E. Madison Bray <
> erik.m.b...@gmail.com> wrote:
> > > >>> >> >>
> > > >>> >> >> On Wed, Mar 13, 2019 at 4:58 PM Dima Pasechnik <
> dimp...@gmail.com> wrote:
> > > >>> >> >> >
> > > >>> >> >> > By looking at the output it looks as if the build it on an
> NFS, and this is known to be severely broken. Could you do the build on a
> local disk?
> > > >>> >> >>
> > > >>> >> >> Oh, nice catch.  Yes, many build tools can have problems on
> NFS,
> > > >>> >> >> especially on older kernels.  For example if timestamps are
> not
> > > >>> >> >> fine-grained enough you can end up with screwy issues where
> some
> > > >>> >> >> dependencies don't get rebuilt properly and things like that.
> > > >>> >> >>
> > > >>> >> >> > On Wed, 13 Mar 2019 15:44 E. Madison Bray, <
> erik.m.b...@gmail.com> wrote:
> > > >>> >> >> >>
> > > >>> >> >> >> On Wed, Mar 13, 2019 at 4:40 AM Ai Bo <
> boaisp...@gmail.com> wrote:
> > > >>> >> >> >> >
> > > >>> >> >> >> > Just compiled sage from source code on Linux.
> > > >>> >> >> >> > When I launched ./sage, I can do simple math like 2+2
> which give correct
> > > >>> >> >> >> > But when I type:
> > > >>> >> >> >> > sage: import sage.graphs
> > > >>> >> >> >> >
> > > >>> >> >> >> > sage: print("%d" % len(list(graphs.nauty_geng("8"
> > > >>> >> >> >> >
> > > >>> >> >> >> > sage: print("%d" % len(list(graphs(8
> > > >>> >> >> >> >
> > > >>> >> >> >> > I got 0 for both which are not as expected. Something
> is wrong. Please help.
> > > >>> >> >> >>
> > > >>> >> >> >> I think that, considering the problems you've mentioned
> in other
> > > >>> >> >> >> thread

Re: [sage-devel] Re: schedule for 8.7 rc and final release

[Volker Braun]

Feel free to fix the Cygwin-related bugs, but some of these are 
longstanding issues that should be discussed with upstream first; 
Realistically thats not going to make it to the next Sage version.



On Thursday, March 14, 2019 at 2:36:29 PM UTC+1, E. Madison Bray wrote:
>
> Hi Volker, 
>
> I don't think there should be a release candidate at least until most 
> of the blocker issues [1] are resolved; in particular the four that 
> are already either positively reviewed or are in-progress. 
>
> Thanks 
>
>
> [1] 
> https://trac.sagemath.org/query?priority=blocker&status=needs_info&status=needs_review&status=needs_work&status=new&status=positive_review&milestone=sage-8.7&group=status&col=id&col=summary&col=priority&col=owner&col=type&col=component&col=time&order=priority
>  
>
> On Thu, Mar 14, 2019 at 2:25 PM Volker Braun  > wrote: 
> > 
> > Next develop release will be rc0 
> > 
> > IMHO changes to gmpy2 should wait until the next version to give it some 
> time to test out. 
> > 
> > -- 
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[sage-devel] Re: Sage 8.4 has broken Hilbert polynomials

[Simon King]

Hi John,

sorry, somehow I missed your posting.

 Le lundi 5 novembre 2018 18:55:25 UTC+1, john_perry_usm a écrit :
>
> This code works in Sage 8.3, but not in Sage 8.4.
>
> P. = PolynomialRing(QQ)
> I = Ideal([x^3, x*y^2, y^4, x^2*y*z, y^3*z, x^2*z^2, x*y*z^2, x*z^3])
> I.hilbert_polynomial()
>
> I haven't yet dug into the cause, but the error it reports is,
>
> AttributeError: 'sage.rings.rational.Rational' object has no 
> attribute 'leading_coefficient'

I am not sure how that has happened but apparently a rational number is
created where in fact a polynomial of degree zero should have been
created. I am confident that the issue can easily be fixed (see #27483).

Best regards,
Simon


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Re: [sage-devel] Re: Incorrect double integral result

[Christopher Subich]

On 3/14/19 8:54 AM, kcrisman wrote:


Following up, does this computation make any sense?  Presumably this 
is the core issue.


That computation makes sense, it's the second integration that breaks:

(x,y) = var('x y')
z = sqrt(1-x^2-y^2)
print(z)
assume(abs(x)<1)
assume(abs(y)<1)
zint_y = z.integrate(y)
print('Integrating in y:')
print('int(z dy) = %s' % zint_y)
print('Taylor expansions:')
print(zint_y.taylor((x,0),(y,0),5))
zp = z.taylor((x,0),(y,0),4)
zpint_y = zp.integrate(y)
print(zpint_y)

print('Integrating in x')
zint_xy = zint_y.integrate(x)
print('int(z dx dy) = %s' % zint_xy)
print('Taylor expansions:')
print(zint_xy.taylor((x,0),(y,0),6))
zpint_xy = zpint_y.integrate(x)
print(zpint_xy)

Prints:

sqrt(-x^2 - y^2 + 1)
Integrating in y:
int(z dy) = -1/2*x^2*arcsin(2*y/sqrt(-4*x^2 + 4)) + 1/2*sqrt(-x^2 - y^2 + 1)*y 
+ 1/2*arcsin(2*y/sqrt(-4*x^2 + 4))
Taylor expansions:
-1/8*x^4*y - 1/12*x^2*y^3 - 1/40*y^5 - 1/2*x^2*y - 1/6*y^3 + y
-1/8*x^4*y - 1/12*x^2*y^3 - 1/40*y^5 - 1/2*x^2*y - 1/6*y^3 + y
Integrating in x
int(z dx dy) = -1/4*(y^2*arcsin(2*x/sqrt(-4*y^2 + 4)) - sqrt(-x^2 - y^2 + 1)*x 
- arcsin(2*x/sqrt(-4*y^2 + 4)))*y
Taylor expansions:
-1/80*x^5*y - 1/24*x^3*y^3 - 1/16*x*y^5 - 1/12*x^3*y - 1/4*x*y^3 + 1/2*x*y
-1/40*x^5*y - 1/36*x^3*y^3 - 1/40*x*y^5 - 1/6*x^3*y - 1/6*x*y^3 + x*y

--
Christopher Subich

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Re: [sage-devel] another "cp: cannot overwrite non-directory '[..]./lib64' with directory"

[E. Madison Bray]

On Thu, Mar 14, 2019 at 4:50 PM E. Madison Bray  wrote:
>
> On Thu, Mar 14, 2019 at 4:37 PM E. Madison Bray  wrote:
> >
> > On Thu, Mar 14, 2019 at 4:23 PM Dima Pasechnik  wrote:
> > >
> > >
> > >
> > > On Thu, 14 Mar 2019 15:17 E. Madison Bray,  wrote:
> > >>
> > >> On Thu, Mar 14, 2019 at 12:06 AM Dima Pasechnik  
> > >> wrote:
> > >> >
> > >> > It's reproducible on my Linux machine, and I see that
> > >> > "non-directory '/opt/sage/local/./lib64'" is a symbolic link.
> > >> >
> > >> > removing it manually allows the install to complete.
> > >> > (whether it breaks anything I don't know, but should not be too hard 
> > >> > to fix...)
> > >>
> > >> At this point I like having it there essentially as a guard--the
> > >> package should not be trying to install anything into ${prefix}/lib64.
> > >> It should just use ${prefix}/lib.
> > >
> > >
> > > primecount uses cmake, which is so vastly superior to anything that 
> > > configuring by mere mortals is not allowed ;-)
> >
> > Yes, and apparently installing it also means building and installing
> > Sage's own cmake even though I already have cmake on my system.
> >
> > Additionally, on Ubuntu 14.04 it just worked--nothing tried to install
> > anything into lib64/
>
> Per share/cmake-3.11/Modules/GNUInstallDirs.cmake,
>
>   set(_LIBDIR_DEFAULT "lib")
>   # Override this default 'lib' with 'lib64' iff:
>   #  - we are on Linux system but NOT cross-compiling
>   #  - we are NOT on debian
>   #  - we are on a 64 bits system
>   # reason is: amd64 ABI: 
> https://github.com/hjl-tools/x86-psABI/wiki/X86-psABI
>   # For Debian with multiarch, use 'lib/${CMAKE_LIBRARY_ARCHITECTURE}' if
>   # CMAKE_LIBRARY_ARCHITECTURE is set (which contains e.g. "i386-linux-gnu"
>   # and CMAKE_INSTALL_PREFIX is "/usr"
>   # See http://wiki.debian.org/Multiarch
>
>
> Since I'm Ubuntu (Debian-based; CMake determines this by the presence
> of /etc/debian_version) and since CMAKE_INSTALL_PREFIX != /usr, it is
> keeping _LIBDIR_DEFAULT = "lib".
>
> Perhaps what we need is an "sdh_cmake" that forces 
> CMAKE_INSTALL_LIBDIR="lib/".

This is now https://trac.sagemath.org/ticket/27484 ; I will also make
a followup for primecount.

> > >> > On Wed, Mar 13, 2019 at 10:59 PM Dima Pasechnik  
> > >> > wrote:
> > >> > >
> > >> > > On Wed, Mar 13, 2019 at 8:07 PM Vincent Delecroix
> > >> > > <20100.delecr...@gmail.com> wrote:
> > >> > > >
> > >> > > > Dear all,
> > >> > > >
> > >> > > > I did try `sage -i primecount` to install the optional primecount
> > >> > > > package (archlinux with compiles SageMath 8.7.beta6). The 
> > >> > > > compilation
> > >> > > > went file but copying the files went wrong (see attached log).
> > >> > > >
> > >> > > > Any help on how to fix the problem is welcome.
> > >> > > looks very much like this: https://trac.sagemath.org/ticket/26996
> > >> > > >
> > >> > > > Best
> > >> > > > Vincent
> > >> > > >
> > >> > > > --
> > >> > > > You received this message because you are subscribed to the Google 
> > >> > > > Groups "sage-devel" group.
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> > >> > > > send an email to sage-devel+unsubscr...@googlegroups.com.
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> > >> >
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Re: [sage-devel] another "cp: cannot overwrite non-directory '[..]./lib64' with directory"

[E. Madison Bray]

On Thu, Mar 14, 2019 at 4:37 PM E. Madison Bray  wrote:
>
> On Thu, Mar 14, 2019 at 4:23 PM Dima Pasechnik  wrote:
> >
> >
> >
> > On Thu, 14 Mar 2019 15:17 E. Madison Bray,  wrote:
> >>
> >> On Thu, Mar 14, 2019 at 12:06 AM Dima Pasechnik  wrote:
> >> >
> >> > It's reproducible on my Linux machine, and I see that
> >> > "non-directory '/opt/sage/local/./lib64'" is a symbolic link.
> >> >
> >> > removing it manually allows the install to complete.
> >> > (whether it breaks anything I don't know, but should not be too hard to 
> >> > fix...)
> >>
> >> At this point I like having it there essentially as a guard--the
> >> package should not be trying to install anything into ${prefix}/lib64.
> >> It should just use ${prefix}/lib.
> >
> >
> > primecount uses cmake, which is so vastly superior to anything that 
> > configuring by mere mortals is not allowed ;-)
>
> Yes, and apparently installing it also means building and installing
> Sage's own cmake even though I already have cmake on my system.
>
> Additionally, on Ubuntu 14.04 it just worked--nothing tried to install
> anything into lib64/

Per share/cmake-3.11/Modules/GNUInstallDirs.cmake,

  set(_LIBDIR_DEFAULT "lib")
  # Override this default 'lib' with 'lib64' iff:
  #  - we are on Linux system but NOT cross-compiling
  #  - we are NOT on debian
  #  - we are on a 64 bits system
  # reason is: amd64 ABI: https://github.com/hjl-tools/x86-psABI/wiki/X86-psABI
  # For Debian with multiarch, use 'lib/${CMAKE_LIBRARY_ARCHITECTURE}' if
  # CMAKE_LIBRARY_ARCHITECTURE is set (which contains e.g. "i386-linux-gnu"
  # and CMAKE_INSTALL_PREFIX is "/usr"
  # See http://wiki.debian.org/Multiarch


Since I'm Ubuntu (Debian-based; CMake determines this by the presence
of /etc/debian_version) and since CMAKE_INSTALL_PREFIX != /usr, it is
keeping _LIBDIR_DEFAULT = "lib".

Perhaps what we need is an "sdh_cmake" that forces CMAKE_INSTALL_LIBDIR="lib/".



> >> > On Wed, Mar 13, 2019 at 10:59 PM Dima Pasechnik  
> >> > wrote:
> >> > >
> >> > > On Wed, Mar 13, 2019 at 8:07 PM Vincent Delecroix
> >> > > <20100.delecr...@gmail.com> wrote:
> >> > > >
> >> > > > Dear all,
> >> > > >
> >> > > > I did try `sage -i primecount` to install the optional primecount
> >> > > > package (archlinux with compiles SageMath 8.7.beta6). The compilation
> >> > > > went file but copying the files went wrong (see attached log).
> >> > > >
> >> > > > Any help on how to fix the problem is welcome.
> >> > > looks very much like this: https://trac.sagemath.org/ticket/26996
> >> > > >
> >> > > > Best
> >> > > > Vincent
> >> > > >
> >> > > > --
> >> > > > 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.
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> >> > > > Visit this group at https://groups.google.com/group/sage-devel.
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> >> >
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Re: [sage-devel] another "cp: cannot overwrite non-directory '[..]./lib64' with directory"

[Dima Pasechnik]

I just added cmake to our "spkg-configure-wanted" list

On Thu, 14 Mar 2019 15:37 E. Madison Bray,  wrote:

> On Thu, Mar 14, 2019 at 4:23 PM Dima Pasechnik  wrote:
> >
> >
> >
> > On Thu, 14 Mar 2019 15:17 E. Madison Bray, 
> wrote:
> >>
> >> On Thu, Mar 14, 2019 at 12:06 AM Dima Pasechnik 
> wrote:
> >> >
> >> > It's reproducible on my Linux machine, and I see that
> >> > "non-directory '/opt/sage/local/./lib64'" is a symbolic link.
> >> >
> >> > removing it manually allows the install to complete.
> >> > (whether it breaks anything I don't know, but should not be too hard
> to fix...)
> >>
> >> At this point I like having it there essentially as a guard--the
> >> package should not be trying to install anything into ${prefix}/lib64.
> >> It should just use ${prefix}/lib.
> >
> >
> > primecount uses cmake, which is so vastly superior to anything that
> configuring by mere mortals is not allowed ;-)
>
> Yes, and apparently installing it also means building and installing
> Sage's own cmake even though I already have cmake on my system.
>
> Additionally, on Ubuntu 14.04 it just worked--nothing tried to install
> anything into lib64/
>
>
> >> > On Wed, Mar 13, 2019 at 10:59 PM Dima Pasechnik 
> wrote:
> >> > >
> >> > > On Wed, Mar 13, 2019 at 8:07 PM Vincent Delecroix
> >> > > <20100.delecr...@gmail.com> wrote:
> >> > > >
> >> > > > Dear all,
> >> > > >
> >> > > > I did try `sage -i primecount` to install the optional primecount
> >> > > > package (archlinux with compiles SageMath 8.7.beta6). The
> compilation
> >> > > > went file but copying the files went wrong (see attached log).
> >> > > >
> >> > > > Any help on how to fix the problem is welcome.
> >> > > looks very much like this: https://trac.sagemath.org/ticket/26996
> >> > > >
> >> > > > Best
> >> > > > Vincent
> >> > > >
> >> > > > --
> >> > > > 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.
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> >> > > > Visit this group at https://groups.google.com/group/sage-devel.
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> >> >
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Re: [sage-devel] another "cp: cannot overwrite non-directory '[..]./lib64' with directory"

[E. Madison Bray]

On Thu, Mar 14, 2019 at 4:23 PM Dima Pasechnik  wrote:
>
>
>
> On Thu, 14 Mar 2019 15:17 E. Madison Bray,  wrote:
>>
>> On Thu, Mar 14, 2019 at 12:06 AM Dima Pasechnik  wrote:
>> >
>> > It's reproducible on my Linux machine, and I see that
>> > "non-directory '/opt/sage/local/./lib64'" is a symbolic link.
>> >
>> > removing it manually allows the install to complete.
>> > (whether it breaks anything I don't know, but should not be too hard to 
>> > fix...)
>>
>> At this point I like having it there essentially as a guard--the
>> package should not be trying to install anything into ${prefix}/lib64.
>> It should just use ${prefix}/lib.
>
>
> primecount uses cmake, which is so vastly superior to anything that 
> configuring by mere mortals is not allowed ;-)

Yes, and apparently installing it also means building and installing
Sage's own cmake even though I already have cmake on my system.

Additionally, on Ubuntu 14.04 it just worked--nothing tried to install
anything into lib64/


>> > On Wed, Mar 13, 2019 at 10:59 PM Dima Pasechnik  wrote:
>> > >
>> > > On Wed, Mar 13, 2019 at 8:07 PM Vincent Delecroix
>> > > <20100.delecr...@gmail.com> wrote:
>> > > >
>> > > > Dear all,
>> > > >
>> > > > I did try `sage -i primecount` to install the optional primecount
>> > > > package (archlinux with compiles SageMath 8.7.beta6). The compilation
>> > > > went file but copying the files went wrong (see attached log).
>> > > >
>> > > > Any help on how to fix the problem is welcome.
>> > > looks very much like this: https://trac.sagemath.org/ticket/26996
>> > > >
>> > > > Best
>> > > > Vincent
>> > > >
>> > > > --
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Re: [sage-devel] another "cp: cannot overwrite non-directory '[..]./lib64' with directory"

[Dima Pasechnik]

On Thu, 14 Mar 2019 15:17 E. Madison Bray,  wrote:

> On Thu, Mar 14, 2019 at 12:06 AM Dima Pasechnik  wrote:
> >
> > It's reproducible on my Linux machine, and I see that
> > "non-directory '/opt/sage/local/./lib64'" is a symbolic link.
> >
> > removing it manually allows the install to complete.
> > (whether it breaks anything I don't know, but should not be too hard to
> fix...)
>
> At this point I like having it there essentially as a guard--the
> package should not be trying to install anything into ${prefix}/lib64.
> It should just use ${prefix}/lib.
>

primecount uses cmake, which is so vastly superior to anything that
configuring by mere mortals is not allowed ;-)

>
>
> > On Wed, Mar 13, 2019 at 10:59 PM Dima Pasechnik 
> wrote:
> > >
> > > On Wed, Mar 13, 2019 at 8:07 PM Vincent Delecroix
> > > <20100.delecr...@gmail.com> wrote:
> > > >
> > > > Dear all,
> > > >
> > > > I did try `sage -i primecount` to install the optional primecount
> > > > package (archlinux with compiles SageMath 8.7.beta6). The compilation
> > > > went file but copying the files went wrong (see attached log).
> > > >
> > > > Any help on how to fix the problem is welcome.
> > > looks very much like this: https://trac.sagemath.org/ticket/26996
> > > >
> > > > Best
> > > > Vincent
> > > >
> > > > --
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Re: [sage-devel] another "cp: cannot overwrite non-directory '[..]./lib64' with directory"

[E. Madison Bray]

On Thu, Mar 14, 2019 at 12:06 AM Dima Pasechnik  wrote:
>
> It's reproducible on my Linux machine, and I see that
> "non-directory '/opt/sage/local/./lib64'" is a symbolic link.
>
> removing it manually allows the install to complete.
> (whether it breaks anything I don't know, but should not be too hard to 
> fix...)

As for whether it breaks anything, probably, because $SAGE_LOCAL/lib64
is not in the rpath.


> On Wed, Mar 13, 2019 at 10:59 PM Dima Pasechnik  wrote:
> >
> > On Wed, Mar 13, 2019 at 8:07 PM Vincent Delecroix
> > <20100.delecr...@gmail.com> wrote:
> > >
> > > Dear all,
> > >
> > > I did try `sage -i primecount` to install the optional primecount
> > > package (archlinux with compiles SageMath 8.7.beta6). The compilation
> > > went file but copying the files went wrong (see attached log).
> > >
> > > Any help on how to fix the problem is welcome.
> > looks very much like this: https://trac.sagemath.org/ticket/26996
> > >
> > > Best
> > > Vincent
> > >
> > > --
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Re: [sage-devel] another "cp: cannot overwrite non-directory '[..]./lib64' with directory"

[E. Madison Bray]

On Thu, Mar 14, 2019 at 12:06 AM Dima Pasechnik  wrote:
>
> It's reproducible on my Linux machine, and I see that
> "non-directory '/opt/sage/local/./lib64'" is a symbolic link.
>
> removing it manually allows the install to complete.
> (whether it breaks anything I don't know, but should not be too hard to 
> fix...)

At this point I like having it there essentially as a guard--the
package should not be trying to install anything into ${prefix}/lib64.
It should just use ${prefix}/lib.


> On Wed, Mar 13, 2019 at 10:59 PM Dima Pasechnik  wrote:
> >
> > On Wed, Mar 13, 2019 at 8:07 PM Vincent Delecroix
> > <20100.delecr...@gmail.com> wrote:
> > >
> > > Dear all,
> > >
> > > I did try `sage -i primecount` to install the optional primecount
> > > package (archlinux with compiles SageMath 8.7.beta6). The compilation
> > > went file but copying the files went wrong (see attached log).
> > >
> > > Any help on how to fix the problem is welcome.
> > looks very much like this: https://trac.sagemath.org/ticket/26996
> > >
> > > Best
> > > Vincent
> > >
> > > --
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[sage-devel] Re: Sage python3 doctests

[kcrisman]

> I wanted to run some doctests with my Python 3 Sage installation. 
> However, running "sage -t" results in 
>
> Using --optional=dochtml,memlimit,mpir,python2,sage 
>
> ie, python2 is in the list. Is that expected? How should I 
> run the tests? 
>


On a related note, I was attempting to test using the "external" flag (see 
http://doc.sagemath.org/html/en/developer/doctesting.html#run-optional-doctests)
 
and ran across a number of errors possibly related to how this was 
implemented.  Random file that failed below.  

(As some side notes, it didn't detect any external software for testing, 
which seems odd since I certainly have internet and latex, probably also 
imagemagick; also, the "optional - debug" command in this file crashed 
Sage, and apparently in that file there is the line P._random_uniform_rec(2, 
[1, 3, 4], (0,1), True, 2) which should be perhaps marked py3 since it 
fails.)

The main point is that it is running precisely two tests - the ones marked 
# py2 .  Note these are not marked "optional - py2", just py2.  I don't 
know what the right way to run these doctests is, but anyway it's not 
documented at http://doc.sagemath.org/html/en/developer/doctesting.html but 
probably should be.  I'm happy to open a ticket if someone can point me to 
what the actual behavior should be; unfortunately this was the 
closest-related message I could find on sage-devel.  For now I'll try using 
--optional=sage,python2,latex,internet as my arguments.  Thanks for any 
insight!
 
- kcrisman

$ ./sage -tp 3 --optional=external src/sage/rings/polynomial/pbori.pyx

too many failed tests, not using stored timings

Running doctests with ID 2019-03-14-09-49-33-56f7e373.

Git branch: develop

Using --optional=external

External software to be detected: 
cplex,ffmpeg,graphviz,gurobi,imagemagick,internet,latex,macaulay2,magma,maple,mathematica,matlab,octave,pandoc,scilab

Doctesting 1 file using 3 threads.

sage -t src/sage/rings/polynomial/pbori.pyx

**

File "src/sage/rings/polynomial/pbori.pyx", line 1250, in 
sage.rings.polynomial.pbori.BooleanPolynomialRing._random_uniform_rec

Failed example:

P._random_uniform_rec(2, [1, 3, 4], (0,1), True, 2)  # py2

Exception raised:

Traceback (most recent call last):

  File 
"/Users/karl.crisman/Downloads/sage/local/lib/python2.7/site-packages/sage/doctest/forker.py",
 
line 671, in _run

self.compile_and_execute(example, compiler, test.globs)

  File 
"/Users/karl.crisman/Downloads/sage/local/lib/python2.7/site-packages/sage/doctest/forker.py",
 
line 1095, in compile_and_execute

exec(compiled, globs)

  File "", 
line 1, in 

P._random_uniform_rec(Integer(2), [Integer(1), Integer(3), 
Integer(4)], (Integer(0),Integer(1)), True, Integer(2))  # py2

NameError: name 'P' is not defined

**

File "src/sage/rings/polynomial/pbori.pyx", line 1330, in 
sage.rings.polynomial.pbori.BooleanPolynomialRing._random_monomial_dfirst

Failed example:

[P._random_monomial_dfirst(3, (0,1,2)) for _ in range(10)]  # py2

Exception raised:

Traceback (most recent call last):

  File 
"/Users/karl.crisman/Downloads/sage/local/lib/python2.7/site-packages/sage/doctest/forker.py",
 
line 671, in _run

self.compile_and_execute(example, compiler, test.globs)

  File 
"/Users/karl.crisman/Downloads/sage/local/lib/python2.7/site-packages/sage/doctest/forker.py",
 
line 1095, in compile_and_execute

exec(compiled, globs)

  File "", 
line 1, in 

[P._random_monomial_dfirst(Integer(3), 
(Integer(0),Integer(1),Integer(2))) for _ in range(Integer(10))]  # py2

NameError: name 'P' is not defined

**

2 items had failures:

   1 of   2 in 
sage.rings.polynomial.pbori.BooleanPolynomialRing._random_monomial_dfirst

   1 of   2 in 
sage.rings.polynomial.pbori.BooleanPolynomialRing._random_uniform_rec

[2 tests, 2 failures, 0.08 s]

--

sage -t src/sage/rings/polynomial/pbori.pyx  # 2 doctests failed

--

Total time for all tests: 1.1 seconds

cpu time: 0.1 seconds

cumulative wall time: 0.1 seconds
External software detected for doctesting:  

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[sage-devel] Re: Sage 8.4 has broken Hilbert polynomials

[jplab]

This still does not work in Sage version 8.7.beta7.

I have created a ticket located at

https://trac.sagemath.org/ticket/27483

Best regards,


Le lundi 5 novembre 2018 18:55:25 UTC+1, john_perry_usm a écrit :
>
> This code works in Sage 8.3, but not in Sage 8.4.
>
> P. = PolynomialRing(QQ)
> I = Ideal([x^3, x*y^2, y^4, x^2*y*z, y^3*z, x^2*z^2, x*y*z^2, x*z^3])
> I.hilbert_polynomial()
>
> I haven't yet dug into the cause, but the error it reports is,
>
> AttributeError: 'sage.rings.rational.Rational' object has no 
> attribute 'leading_coefficient'
>
>
>

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Re: [sage-devel] Re: schedule for 8.7 rc and final release

[E. Madison Bray]

Hi Volker,

I don't think there should be a release candidate at least until most
of the blocker issues [1] are resolved; in particular the four that
are already either positively reviewed or are in-progress.

Thanks


[1] 
https://trac.sagemath.org/query?priority=blocker&status=needs_info&status=needs_review&status=needs_work&status=new&status=positive_review&milestone=sage-8.7&group=status&col=id&col=summary&col=priority&col=owner&col=type&col=component&col=time&order=priority

On Thu, Mar 14, 2019 at 2:25 PM Volker Braun  wrote:
>
> Next develop release will be rc0
>
> IMHO changes to gmpy2 should wait until the next version to give it some time 
> to test out.
>
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[sage-devel] Re: schedule for 8.7 rc and final release

[Volker Braun]

Next develop release will be rc0

IMHO changes to gmpy2 should wait until the next version to give it some 
time to test out.

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[sage-devel] schedule for 8.7 rc and final release

[Vincent Delecroix]

Dear Volker,

Do you have a rough schedule for the next Sage release?

I am interested because Vincent K is putting a lot of effort
towards having a new release of gmpy2 [1] that would be great
to have in 8.7.

 [1] https://github.com/aleaxit/gmpy/issues/199

Cheers
Vincent

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[sage-devel] Re: Incorrect double integral result

[kcrisman]

On Wednesday, March 13, 2019 at 7:11:02 PM UTC-4, Emmanuel Charpentier 
wrote:
>
> This integral turns out to be anything but trivial.
>
> Neither Sympy, Giac nor Fricas can solve it, in its original form nor in 
> polar coordinates. BTW, neither Mathematica nor Rubi running on Mathematica 
> can solve it in neither form.
>
> The analytic answer given (semi-)trivially by Maxima is probably false. 
> I'm unable to check it.
>

Following up, does this computation make any sense?  Presumably this is the 
core issue.

sage: maxima_console()



(%i1) z:sqrt(1-x^2-y^2);

  2 2

(%o1)sqrt((- y ) - x  + 1)

(%i2) display2d:false;


(%o2) false

(%i3) integrate(z,y);

Is (x-1)*(x+1) positive or negative?


n;

(%o3) (-(x^2*asin(y/sqrt(1-x^2)))/2)+asin(y/sqrt(1-x^2))/2+(y

   *sqrt(

(-y^2)-x^2+1))
   /2 

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[sage-devel] Re: polymake-3.1 build fails with std::__::numeric_limits<...>

[jplab]

Dear Harly Hallikas,

This error seems to be in polymake source code. You could report this 
compilation error to the polymake development team here:

https://forum.polymake.org/

to see if this fixed in the current version. The current version is 3.3 
available here:

https://polymake.org/doku.php/download/start

Which planned to be updated in the ticket:

https://trac.sagemath.org/ticket/24905

which should be ready soon (hopefully!).

Looking at the release page of polymake, it seems that they do not yet have 
a bundle for 10.14, so I do not know if it can work out of the box in this 
case.

As Dima said, this is an experimental package and any such report is very 
welcome to improve it!

Best,
Jean-Philippe



Le mercredi 13 mars 2019 12:52:01 UTC+1, Harly Hallikas a écrit :
>
> I'm not really C++ specialist, therefore, I'm not even trying to fix it 
> myself. 
>
> Looks like the numeric_types are already defined in stdlib.
>
> Attached the log file..
>
>
> Computer 2018 MacBookPro (Core i9), macOS Mojave Version 10.14.3 (18D109)
>

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[sage-devel] Failing doctest in src/sage/rings/integer.pyx

[jonathan.kliem via sage-devel]

I'm getting the same error as in #26002 
 in src/sage/rings/integer.pyx

In my patchbot run 
https://patchbot.sagemath.org/log/0/debian/9.8/x86_64/4.9.0-8-amd64/cofio/2019-03-13%2016:31:01
this just appeared as slow, but I don't see that this test should have this 
runtime:

sage -t --long --warn-long 46.7 src/sage/rings/integer.pyx
**
File "src/sage/rings/integer.pyx", line 3009, in sage.rings.integer.Integer.
divisors
Warning, slow doctest:
for i in range(20):  # long time
try:
alarm(RDF.random_element(1e-3, 0.5))
_ = n.divisors()
cancel_alarm()  # we never get here
except AlarmInterrupt:
pass
Test ran for 47.08 s
[1128 tests, 61.72 s]

Now it just keeps on failing:


sage -t --long --warn-long 48.7 src/sage/rings/integer.pyx
**
File "src/sage/rings/integer.pyx", line 3009, in sage.rings.integer.Integer.
divisors
Failed example:
for i in range(20):  # long time
try:
alarm(RDF.random_element(1e-3, 0.5))
_ = n.divisors()
cancel_alarm()  # we never get here
except AlarmInterrupt:
pass
Exception raised:
Traceback (most recent call last):
  File 
"/srv/public/kliem/patchbot-sage/sage/local/lib/python2.7/site-packages/sage/doctest/forker.py"
, line 671, in _run
self.compile_and_execute(example, compiler, test.globs)
  File 
"/srv/public/kliem/patchbot-sage/sage/local/lib/python2.7/site-packages/sage/doctest/forker.py"
, line 1095, in compile_and_execute
exec(compiled, globs)
  File "", line 4, in 

_ = n.divisors()
  File "sage/rings/integer.pyx", line 3079, in sage.rings.integer.
Integer.divisors (build/cythonized/sage/rings/integer.c:19782)
ptr = check_allocarray(divisor_count, 3 * sizeof(
unsigned long))
  File "memory.pxd", line 87, in cysignals.memory.check_allocarray (
build/cythonized/sage/rings/integer.c:47092)
MemoryError: failed to allocate 33554432 * 24 bytes
**
File "src/sage/rings/integer.pyx", line 3849, in sage.rings.integer.Integer
.?
Failed example:
n.factor(proof=True)
Exception raised:
Traceback (most recent call last):
  File 
"/srv/public/kliem/patchbot-sage/sage/local/lib/python2.7/site-packages/sage/doctest/forker.py"
, line 671, in _run
self.compile_and_execute(example, compiler, test.globs)
  File 
"/srv/public/kliem/patchbot-sage/sage/local/lib/python2.7/site-packages/sage/doctest/forker.py"
, line 1095, in compile_and_execute
exec(compiled, globs)
  File "", line 1, in 
n.factor(proof=True)
  File "sage/rings/integer.pyx", line 3931, in sage.rings.integer.
Integer.factor (build/cythonized/sage/rings/integer.c:24848)
F = factor_using_pari(n, int_=int_, debug_level=verbose, proof=proof
)
  File "sage/rings/factorint.pyx", line 352, in 
sage.rings.factorint.factor_using_pari 
(build/cythonized/sage/rings/factorint.c:6396)
p, e = n.__pari__().factor(proof=proof)
  File "cypari2/gen.pyx", line 4307, in cypari2.gen.Gen.factor
AlarmInterrupt
**

I'm on branch `patchbot/ticket_merged`, but this issue also appeared in a 
different install on branch
public/upgrade_polymake_to_version_3_2r4 


Btw, my patchbot was stopped due to https://trac.sagemath.org/ticket/27477. 
This is why I even noticed.

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Re: [sage-devel] Something is wrong with my installed sage

[Dima Pasechnik]

On Thu, Mar 14, 2019 at 7:24 AM Dima Pasechnik  wrote:
>
> On Thu, Mar 14, 2019 at 7:09 AM Dima Pasechnik  wrote:
> >
> > On Thu, Mar 14, 2019 at 3:39 AM Ai Bo  wrote:
> > >
> > > Sorry, it doesn't work if I build on local disk and then copy to /nfs.
> > > I got error:
> > > bash-4.3$ ./sage
>
> But did you try moving it back to the local disk, before starting it?
> Indeed, you just need to have a copy of your files on NFS, and copy it
> to the local disk for running.
(It's important that it's moved to the same place in the directory
tree where it was built).
>
> Sorry for confusion, again.
>
> > >
> > > ERROR:  The Sage installation tree has moved
> > >
> > > from /tmp/.../sage-8.6
> > >   to /nfs/.../Sage/sage-8.6
> > >
> > > This is not supported, and Sage will not work. To install Sage from a
> > > binary package:
> >
> > yes, you need to create a binary package in this case. It (not the
> > unpacked result, but the package itsel) can be
> > moved. Indeed, Sage binary installers have to come from somewhere, right? 
> > See
> >
> > https://github.com/sagemath/binary-pkg
> >
> > Sorry, I should have mentioned this earlier. It has to be built from
> > scratch, AFAIK.
> >
> >
> > >
> > > As I mentioned before, I can't save files on local disk more then 30 
> > > days. But it seems I can't copy the whole directory to /nfs either.
> > >
> > > Please advise.
> > >
> > > On Wed, Mar 13, 2019 at 11:21 AM Ai Bo  wrote:
> > >>
> > >> I see. Will try. Thank you.
> > >>
> > >> On Wed, Mar 13, 2019 at 11:04 AM Dima Pasechnik  
> > >> wrote:
> > >>>
> > >>> On Wed, Mar 13, 2019 at 5:57 PM Ai Bo  wrote:
> > >>> >
> > >>> > Sorry, I can't. All local disks are cleaned out every 30 days.
> > >>>
> > >>> but building does not take that long. :-)
> > >>> Besides, once you have a working build you can, with a bit of effort, 
> > >>> move it
> > >>> around.
> > >>>
> > >>> >
> > >>> > On Wed, Mar 13, 2019 at 9:43 AM Dima Pasechnik  
> > >>> > wrote:
> > >>> >>
> > >>> >> On Wed, Mar 13, 2019 at 4:18 PM Ai Bo  wrote:
> > >>> >> >
> > >>> >> > Yes. This is done on NFS.
> > >>> >> > I can't build on local disks as this is not on a particular 
> > >>> >> > machine. But I do own my own NFS disks.
> > >>> >>
> > >>> >> Normally multi-user systems have a "scratch" partition, a local disk
> > >>> >> reserved for this kind of jobs, which is not backed up, but is fast 
> > >>> >> to
> > >>> >> access (as opposed to NFS).
> > >>> >> Ask your system admins for access to such a partition, it's a
> > >>> >> perfectly reasonable request.
> > >>> >>
> > >>> >> > Also, the reason I want to build on my machine as when I use the 
> > >>> >> > online version(server), a long running program will be paused from 
> > >>> >> > time to time. I want to run on some machines I have access to 
> > >>> >> > instead.
> > >>> >> >
> > >>> >> > If I can't build on NFS, this seems to be a dead end too.
> > >>> >> >
> > >>> >> > On Wed, Mar 13, 2019 at 9:03 AM E. Madison Bray 
> > >>> >> >  wrote:
> > >>> >> >>
> > >>> >> >> On Wed, Mar 13, 2019 at 4:58 PM Dima Pasechnik 
> > >>> >> >>  wrote:
> > >>> >> >> >
> > >>> >> >> > By looking at the output it looks as if the build it on an NFS, 
> > >>> >> >> > and this is known to be severely broken. Could you do the build 
> > >>> >> >> > on a local disk?
> > >>> >> >>
> > >>> >> >> Oh, nice catch.  Yes, many build tools can have problems on NFS,
> > >>> >> >> especially on older kernels.  For example if timestamps are not
> > >>> >> >> fine-grained enough you can end up with screwy issues where some
> > >>> >> >> dependencies don't get rebuilt properly and things like that.
> > >>> >> >>
> > >>> >> >> > On Wed, 13 Mar 2019 15:44 E. Madison Bray, 
> > >>> >> >> >  wrote:
> > >>> >> >> >>
> > >>> >> >> >> On Wed, Mar 13, 2019 at 4:40 AM Ai Bo  
> > >>> >> >> >> wrote:
> > >>> >> >> >> >
> > >>> >> >> >> > Just compiled sage from source code on Linux.
> > >>> >> >> >> > When I launched ./sage, I can do simple math like 2+2 which 
> > >>> >> >> >> > give correct
> > >>> >> >> >> > But when I type:
> > >>> >> >> >> > sage: import sage.graphs
> > >>> >> >> >> >
> > >>> >> >> >> > sage: print("%d" % len(list(graphs.nauty_geng("8"
> > >>> >> >> >> >
> > >>> >> >> >> > sage: print("%d" % len(list(graphs(8
> > >>> >> >> >> >
> > >>> >> >> >> > I got 0 for both which are not as expected. Something is 
> > >>> >> >> >> > wrong. Please help.
> > >>> >> >> >>
> > >>> >> >> >> I think that, considering the problems you've mentioned in 
> > >>> >> >> >> other
> > >>> >> >> >> threads, you probably have a severely broken build.  Did you 
> > >>> >> >> >> take my
> > >>> >> >> >> previous advice of running
> > >>> >> >> >>
> > >>> >> >> >> $ make distclean
> > >>> >> >> >>
> > >>> >> >> >> and starting over again, making sure you can complete the full 
> > >>> >> >> >> build
> > >>> >> >> >> without errors?
> > >>> >> >> >>
> > >>> >> >> >> Also, is there a specific reason you need to build Sage 
> > >>> >> >> >> yours

Re: [sage-devel] Something is wrong with my installed sage

[Dima Pasechnik]

On Thu, Mar 14, 2019 at 7:09 AM Dima Pasechnik  wrote:
>
> On Thu, Mar 14, 2019 at 3:39 AM Ai Bo  wrote:
> >
> > Sorry, it doesn't work if I build on local disk and then copy to /nfs.
> > I got error:
> > bash-4.3$ ./sage

But did you try moving it back to the local disk, before starting it?
Indeed, you just need to have a copy of your files on NFS, and copy it
to the local disk for running.

Sorry for confusion, again.

> >
> > ERROR:  The Sage installation tree has moved
> >
> > from /tmp/.../sage-8.6
> >   to /nfs/.../Sage/sage-8.6
> >
> > This is not supported, and Sage will not work. To install Sage from a
> > binary package:
>
> yes, you need to create a binary package in this case. It (not the
> unpacked result, but the package itsel) can be
> moved. Indeed, Sage binary installers have to come from somewhere, right? See
>
> https://github.com/sagemath/binary-pkg
>
> Sorry, I should have mentioned this earlier. It has to be built from
> scratch, AFAIK.
>
>
> >
> > As I mentioned before, I can't save files on local disk more then 30 days. 
> > But it seems I can't copy the whole directory to /nfs either.
> >
> > Please advise.
> >
> > On Wed, Mar 13, 2019 at 11:21 AM Ai Bo  wrote:
> >>
> >> I see. Will try. Thank you.
> >>
> >> On Wed, Mar 13, 2019 at 11:04 AM Dima Pasechnik  wrote:
> >>>
> >>> On Wed, Mar 13, 2019 at 5:57 PM Ai Bo  wrote:
> >>> >
> >>> > Sorry, I can't. All local disks are cleaned out every 30 days.
> >>>
> >>> but building does not take that long. :-)
> >>> Besides, once you have a working build you can, with a bit of effort, 
> >>> move it
> >>> around.
> >>>
> >>> >
> >>> > On Wed, Mar 13, 2019 at 9:43 AM Dima Pasechnik  
> >>> > wrote:
> >>> >>
> >>> >> On Wed, Mar 13, 2019 at 4:18 PM Ai Bo  wrote:
> >>> >> >
> >>> >> > Yes. This is done on NFS.
> >>> >> > I can't build on local disks as this is not on a particular machine. 
> >>> >> > But I do own my own NFS disks.
> >>> >>
> >>> >> Normally multi-user systems have a "scratch" partition, a local disk
> >>> >> reserved for this kind of jobs, which is not backed up, but is fast to
> >>> >> access (as opposed to NFS).
> >>> >> Ask your system admins for access to such a partition, it's a
> >>> >> perfectly reasonable request.
> >>> >>
> >>> >> > Also, the reason I want to build on my machine as when I use the 
> >>> >> > online version(server), a long running program will be paused from 
> >>> >> > time to time. I want to run on some machines I have access to 
> >>> >> > instead.
> >>> >> >
> >>> >> > If I can't build on NFS, this seems to be a dead end too.
> >>> >> >
> >>> >> > On Wed, Mar 13, 2019 at 9:03 AM E. Madison Bray 
> >>> >> >  wrote:
> >>> >> >>
> >>> >> >> On Wed, Mar 13, 2019 at 4:58 PM Dima Pasechnik  
> >>> >> >> wrote:
> >>> >> >> >
> >>> >> >> > By looking at the output it looks as if the build it on an NFS, 
> >>> >> >> > and this is known to be severely broken. Could you do the build 
> >>> >> >> > on a local disk?
> >>> >> >>
> >>> >> >> Oh, nice catch.  Yes, many build tools can have problems on NFS,
> >>> >> >> especially on older kernels.  For example if timestamps are not
> >>> >> >> fine-grained enough you can end up with screwy issues where some
> >>> >> >> dependencies don't get rebuilt properly and things like that.
> >>> >> >>
> >>> >> >> > On Wed, 13 Mar 2019 15:44 E. Madison Bray, 
> >>> >> >> >  wrote:
> >>> >> >> >>
> >>> >> >> >> On Wed, Mar 13, 2019 at 4:40 AM Ai Bo  
> >>> >> >> >> wrote:
> >>> >> >> >> >
> >>> >> >> >> > Just compiled sage from source code on Linux.
> >>> >> >> >> > When I launched ./sage, I can do simple math like 2+2 which 
> >>> >> >> >> > give correct
> >>> >> >> >> > But when I type:
> >>> >> >> >> > sage: import sage.graphs
> >>> >> >> >> >
> >>> >> >> >> > sage: print("%d" % len(list(graphs.nauty_geng("8"
> >>> >> >> >> >
> >>> >> >> >> > sage: print("%d" % len(list(graphs(8
> >>> >> >> >> >
> >>> >> >> >> > I got 0 for both which are not as expected. Something is 
> >>> >> >> >> > wrong. Please help.
> >>> >> >> >>
> >>> >> >> >> I think that, considering the problems you've mentioned in other
> >>> >> >> >> threads, you probably have a severely broken build.  Did you 
> >>> >> >> >> take my
> >>> >> >> >> previous advice of running
> >>> >> >> >>
> >>> >> >> >> $ make distclean
> >>> >> >> >>
> >>> >> >> >> and starting over again, making sure you can complete the full 
> >>> >> >> >> build
> >>> >> >> >> without errors?
> >>> >> >> >>
> >>> >> >> >> Also, is there a specific reason you need to build Sage yourself 
> >>> >> >> >> on
> >>> >> >> >> this specific machine?  Not that I doubt it, nor that I wouldn't 
> >>> >> >> >> like
> >>> >> >> >> to try to help, but it seems like a lot of effort and 
> >>> >> >> >> frustration for
> >>> >> >> >> dubious benefit.
> >>> >> >> >>
> >>> >> >> >> Could you mention again exactly which Linux distribution this 
> >>> >> >> >> is, and
> >>> >> >> >> on what CPU architecture?  Perhaps I can start up a VM and try to

Re: [sage-devel] Something is wrong with my installed sage

[Dima Pasechnik]

On Thu, Mar 14, 2019 at 3:39 AM Ai Bo  wrote:
>
> Sorry, it doesn't work if I build on local disk and then copy to /nfs.
> I got error:
> bash-4.3$ ./sage
>
> ERROR:  The Sage installation tree has moved
>
> from /tmp/.../sage-8.6
>   to /nfs/.../Sage/sage-8.6
>
> This is not supported, and Sage will not work. To install Sage from a
> binary package:

yes, you need to create a binary package in this case. It (not the
unpacked result, but the package itsel) can be
moved. Indeed, Sage binary installers have to come from somewhere, right? See

https://github.com/sagemath/binary-pkg

Sorry, I should have mentioned this earlier. It has to be built from
scratch, AFAIK.


>
> As I mentioned before, I can't save files on local disk more then 30 days. 
> But it seems I can't copy the whole directory to /nfs either.
>
> Please advise.
>
> On Wed, Mar 13, 2019 at 11:21 AM Ai Bo  wrote:
>>
>> I see. Will try. Thank you.
>>
>> On Wed, Mar 13, 2019 at 11:04 AM Dima Pasechnik  wrote:
>>>
>>> On Wed, Mar 13, 2019 at 5:57 PM Ai Bo  wrote:
>>> >
>>> > Sorry, I can't. All local disks are cleaned out every 30 days.
>>>
>>> but building does not take that long. :-)
>>> Besides, once you have a working build you can, with a bit of effort, move 
>>> it
>>> around.
>>>
>>> >
>>> > On Wed, Mar 13, 2019 at 9:43 AM Dima Pasechnik  wrote:
>>> >>
>>> >> On Wed, Mar 13, 2019 at 4:18 PM Ai Bo  wrote:
>>> >> >
>>> >> > Yes. This is done on NFS.
>>> >> > I can't build on local disks as this is not on a particular machine. 
>>> >> > But I do own my own NFS disks.
>>> >>
>>> >> Normally multi-user systems have a "scratch" partition, a local disk
>>> >> reserved for this kind of jobs, which is not backed up, but is fast to
>>> >> access (as opposed to NFS).
>>> >> Ask your system admins for access to such a partition, it's a
>>> >> perfectly reasonable request.
>>> >>
>>> >> > Also, the reason I want to build on my machine as when I use the 
>>> >> > online version(server), a long running program will be paused from 
>>> >> > time to time. I want to run on some machines I have access to instead.
>>> >> >
>>> >> > If I can't build on NFS, this seems to be a dead end too.
>>> >> >
>>> >> > On Wed, Mar 13, 2019 at 9:03 AM E. Madison Bray 
>>> >> >  wrote:
>>> >> >>
>>> >> >> On Wed, Mar 13, 2019 at 4:58 PM Dima Pasechnik  
>>> >> >> wrote:
>>> >> >> >
>>> >> >> > By looking at the output it looks as if the build it on an NFS, and 
>>> >> >> > this is known to be severely broken. Could you do the build on a 
>>> >> >> > local disk?
>>> >> >>
>>> >> >> Oh, nice catch.  Yes, many build tools can have problems on NFS,
>>> >> >> especially on older kernels.  For example if timestamps are not
>>> >> >> fine-grained enough you can end up with screwy issues where some
>>> >> >> dependencies don't get rebuilt properly and things like that.
>>> >> >>
>>> >> >> > On Wed, 13 Mar 2019 15:44 E. Madison Bray,  
>>> >> >> > wrote:
>>> >> >> >>
>>> >> >> >> On Wed, Mar 13, 2019 at 4:40 AM Ai Bo  wrote:
>>> >> >> >> >
>>> >> >> >> > Just compiled sage from source code on Linux.
>>> >> >> >> > When I launched ./sage, I can do simple math like 2+2 which give 
>>> >> >> >> > correct
>>> >> >> >> > But when I type:
>>> >> >> >> > sage: import sage.graphs
>>> >> >> >> >
>>> >> >> >> > sage: print("%d" % len(list(graphs.nauty_geng("8"
>>> >> >> >> >
>>> >> >> >> > sage: print("%d" % len(list(graphs(8
>>> >> >> >> >
>>> >> >> >> > I got 0 for both which are not as expected. Something is wrong. 
>>> >> >> >> > Please help.
>>> >> >> >>
>>> >> >> >> I think that, considering the problems you've mentioned in other
>>> >> >> >> threads, you probably have a severely broken build.  Did you take 
>>> >> >> >> my
>>> >> >> >> previous advice of running
>>> >> >> >>
>>> >> >> >> $ make distclean
>>> >> >> >>
>>> >> >> >> and starting over again, making sure you can complete the full 
>>> >> >> >> build
>>> >> >> >> without errors?
>>> >> >> >>
>>> >> >> >> Also, is there a specific reason you need to build Sage yourself on
>>> >> >> >> this specific machine?  Not that I doubt it, nor that I wouldn't 
>>> >> >> >> like
>>> >> >> >> to try to help, but it seems like a lot of effort and frustration 
>>> >> >> >> for
>>> >> >> >> dubious benefit.
>>> >> >> >>
>>> >> >> >> Could you mention again exactly which Linux distribution this is, 
>>> >> >> >> and
>>> >> >> >> on what CPU architecture?  Perhaps I can start up a VM and try to
>>> >> >> >> build Sage myself to see if there are any specific problems I can
>>> >> >> >> identify.
>>> >> >> >>
>>> >> >> >> --
>>> >> >> >> 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/s