Re: [sage-devel] Re: Problems with 9.3.beta6 + OS X Big Sur

[Zachary Scherr]

I found something possibly relevant at

https://bugs.python.org/issue42691

although there the complaint was that Homebrew built python against system 
tcl and the suggestion was that Homebrew use its own tcl-tk.  It seems that 
Homebrew is correctly using its own tcl-tk
since the line

5   libtcl8.6.dylib 0x00032998c72e AtForkPrepare + 
38

says that python is using tcl 8.6 and system tcl is 8.5.  No idea what's 
going on, but it might be good to try to produce a minimal reproducible 
example to show to the python/tcl people.
On Wednesday, February 3, 2021 at 12:11:54 PM UTC-5 dim...@gmail.com wrote:

>
>
> On Wed, 3 Feb 2021, 17:03 John H Palmieri,  wrote:
>
>> Right, thank you. Python 3.9 builds successfully.
>>
>> On Monday, February 1, 2021 at 7:14:29 PM UTC-8 zsc...@gmail.com wrote:
>>
>>> For the --with-system-python3=no, I don't know what the problem is but I 
>>> think it was fixed by upgrading to python 3.9 in 
>>> https://trac.sagemath.org/ticket/30589
>>>
>>> On Monday, February 1, 2021 at 9:45:37 PM UTC-5 John H Palmieri wrote:
>>>
 On OS X Big Sur (intel), as of the most recent Xcode and homebrew, I am 
 currently unable to build Sage with either homebrew's Python or with 
 `./configure --with-system-python3=no`.

 - With homebrew's Python, actually Sage builds but the documentation 
 does not (similar problems on both Big Sur and Catalina), ending with
>>>
>>>
> yes, I see this too. (with latest Homebrew python 3.9.)
>
> What exactly is broken there?
>
>
>

 
 0   signals.cpython-39-darwin.so0x00010cd40542 
 print_backtrace + 66
 1   signals.cpython-39-darwin.so0x00010cd44167 sigdie + 39
 2   signals.cpython-39-darwin.so0x00010cd4406a 
 cysigs_signal_handler + 282
 3   libsystem_platform.dylib0x7fff203bcd7d _sigtramp + 
 29
 4   ??? 0x003f 0x0 + 63
 5   libtcl8.6.dylib 0x00032998c72e 
 AtForkPrepare + 38
 6   libsystem_pthread.dylib 0x7fff203781a3 
 _pthread_atfork_prepare_handlers + 90
 7   libSystem.B.dylib   0x7fff2a575934 
 libSystem_atfork_prepare + 11
 8   libsystem_c.dylib   0x7fff2025bb1b fork + 12
 9   _posixsubprocess.cpython-39-darwin. 0x00010b63db89 
 subprocess_fork_exec + 1573
 10  Python  0x00010af10904 
 cfunction_call + 127
 11  Python  0x00010aedffa3 
 _PyObject_MakeTpCall + 266
 12  Python  0x00010af88027 
 call_function + 455
 ...
 157 Python  0x00010afcf10f Py_BytesMain 
 + 42
 158 libdyld.dylib   0x7fff20393621 start + 1
 
 Unhandled SIGILL: An illegal instruction occurred.
 This probably occurred because a *compiled* module has a bug
 in it and is not properly wrapped with sig_on(), sig_off().
 Python will now terminate.
 
 ...
   File 
 "/Users/palmieri/Desktop/Sage/sage_builds/TESTING/sage-9.3.beta6/local/lib/python3.9/site-packages/sage_setup/docbuild/utils.py",
  
 line 221, in reap_workers
 w = bring_out_yer_dead(w, task, exitcode)
   File 
 "/Users/palmieri/Desktop/Sage/sage_builds/TESTING/sage-9.3.beta6/local/lib/python3.9/site-packages/sage_setup/docbuild/utils.py",
  
 line 157, in bring_out_yer_dead
 raise WorkerDiedException(
 sage_setup.docbuild.utils.WorkerDiedException: worker for 
 ('reference/misc', 'en', 'html', {}) died with non-zero exit code -4

 - With `./configure --with-system-python3=no`, Python fails to build 
 (on Big Sur only; it succeeds on Catalina), saying

 ModuleNotFoundError: No module named 'readline'

 and

 ModuleNotFoundError: No module named 'zlib'

 Any suggestions?

 -- 
 John


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>>  
>> 
>> .
>>
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[sage-devel] Re: [GSoC Mentors Announce] Now Accepting GSoC 2021 Mentoring Organization Applications until Feb 19

['Travis Scrimshaw' via sage-devel]

I am happy to mentor, but I am not sure I could take on being an admin this 
year (next year I could though).

Best,
Travis


On Tuesday, February 2, 2021 at 7:54:01 PM UTC+10 dim...@gmail.com wrote:

> Dear all,
>
> we are looking for projects and mentors for GSoC 2021.
>
> Myself, I'll pass this year, though.
> This means we need at least one more admin.
>
> Dima
>
> -- Forwarded message -
> From: 'Stephanie Taylor' via Google Summer of Code Mentors Announce
> List 
> Date: Tue, Feb 2, 2021 at 7:28 AM
> Subject: [GSoC Mentors Announce] Now Accepting GSoC 2021 Mentoring
> Organization Applications until Feb 19
> To: Google Summer of Code Mentors Announce List
> 
>
>
> Hi all,
>
> Org admins can submit their org's application to be a mentoring
> organization for GSoC 2021 at g.co/gsoc from today until Feb 19 at
> 1900UTC.
>
> Please remember for the 2021 GSoC program all projects students will
> be working on for the summer should be ~175 hr projects. Please adjust
> your Project Ideas as needed. Having a thorough and well thought out
> list of Project Ideas is the most important part of your application.
> Making sure you having enough mentors excited to mentor student
> projects and that are ready to commit to mentoring over the summer is
> very important.
>
> Please encourage other open source orgs to apply -- if you know of
> other open source projects that may be interested in applying to GSoC
> as a first time org please remind them to check out the available
> resources below and have them put your org (or you) down as a
> reference.
>
> Resources:
>
> Mentor Guide
>
> Timeline
>
> FAQs
>
> Roles and Responsibilities
>
> Marketing Materials (slide deck, flyers)
>
> Videos
>
> If you have any questions please email me at gsoc-s...@google.com
>
> Best,
>
> Stephanie Taylor
>
> GSoC Program Lead
>
> --
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> .
>

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[sage-devel] Introducing gappy

[E. Madison Bray]

Hi all,

I'm far enough along in its development that I'm happy to announce the
creation of gappy [1], a new Python interface to GAP with no
dependencies on Sage.

It is based on Sage's own sage.libs.gap package, but with a few
possible advantages:

* Having no heavy-weight Sage dependencies, it should make it easier
for users of GAP to integrate their GAP code with other Python
projects which do not otherwise require Sage.  This could also be
useful for projects such as a better GAP kernel for Jupyter.

* With just one or two minor exceptions (pending PRs to GAP) it no
longer depends on undocumented GAP internals, and instead sticks to
the semi-official "public" API for libgap that has been developed over
recent years, partly supported by the OpenDreamKit and OSCAR projects.

* Various minor performance improvements, mostly through more direct
use of the libgap API at the C level.

Additionally, there as is a ticket [2] in Sage to rework the
sage.lib.gap package as a thin wrapper around gappy.

I'd be very interested in any feedback, especially from anyone with
significant amounts of code depending on libgap or Sage permutation
groups.  In particular, while there are performance improvements
overall, I think there might be a performance regression in converting
Sage permutation groups to GAP*.

Thanks,
E

* Due to current lack of support for permutations in the libgap API.

[1] https://github.com/embray/gappy
[2] https://trac.sagemath.org/ticket/31297

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Re: [sage-devel] sage -b is broken

[dmo...@deductivepress.ca]

I believe this was fixed by gh-kliem in trac #31263.

On Wednesday, February 3, 2021 at 10:08:45 AM UTC-7 dim...@gmail.com wrote:

> finally :-) (not sure bug or feature)
>
> well,
>
> make build
>
> works
>
> On Wed, 3 Feb 2021, 17:05 John H Palmieri,  wrote:
>
>> I'm not sure when it happened, but with the latest beta, I see
>>
>> % ./sage -b
>> Makefile:25: *** This Makefile needs to be invoked by 
>> build/make/install.  Stop.
>>
>> -- 
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>> https://groups.google.com/d/msgid/sage-devel/8f906c06-3482-4ed7-ae28-dfedb09013a9n%40googlegroups.com
>>  
>> 
>> .
>>
>

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Re: [sage-devel] serious time loss in pari interface

[John Cremona]

As someone remarked on that ticket, the problem has gone away between 9.2 
and current beta, presumably due to an upgrade to cypari, so this can be 
ignored.

On Wednesday, February 3, 2021 at 5:13:36 PM UTC Dima Pasechnik wrote:

> we have a ticket to upgrade Pari to the latest version, 2.13, but it needs 
> work.
>
>
> On Wed, 3 Feb 2021, 14:11 John Cremona,  wrote:
>
>> I was looking again at https://trac.sagemath.org/ticket/25934 and now
>> think that the issue is more serious than first suggested.  The
>> immediate problem noticed was that after defining a sextic field and
>> creating the unit ideal, it took a very long time to display, and the
>> discussion side-tracked onto whether or not to call pari's bnfinit
>> function to properly initialise the number field structure, the
>> assumption being that that call was what was taking the time.  Well it
>> is, but it should not be!
>>
>> In fact, pari's bnfinit is very fast in this case, as you can tell
>> from switching to %gp:
>>
>> sage: %gp
>>   --> Switching to PARI/GP interpreter <--
>> pari: K = bnfinit(y^6 - y^5 - 5*y^4 + 4*y^3 + 6*y^2 - 3*y - 1);
>> pari: ##
>>   ***   last result computed in 24 ms.
>>
>> But doing the same in Sage:
>>
>> sage: y = polygen(QQ, 'y')
>> sage: f = pari(y^6 - y^5 - 5*y^4 + 4*y^3 + 6*y^2 - 3*y - 1)
>> sage: %time f.bnfinit()
>> CPU times: user 1min 9s, sys: 144 ms, total: 1min 9s
>> Wall time: 1min 9s
>>
>> The clincher is that if you run the previous lines (in a fresh
>> session) and interrupt the last line immediately, and then run it
>> again, it returns immediately.
>>
>> I don't know the libpari interface well enough to go further, but I
>> hope someone does.  (Jeroen, we miss you!)
>>
>> John
>>
>> -- 
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>> .
>>
>

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Re: [sage-devel] serious time loss in pari interface

[Dima Pasechnik]

we have a ticket to upgrade Pari to the latest version, 2.13, but it needs
work.


On Wed, 3 Feb 2021, 14:11 John Cremona,  wrote:

> I was looking again at https://trac.sagemath.org/ticket/25934 and now
> think that the issue is more serious than first suggested.  The
> immediate problem noticed was that after defining a sextic field and
> creating the unit ideal, it took a very long time to display, and the
> discussion side-tracked onto whether or not to call pari's bnfinit
> function to properly initialise the number field structure, the
> assumption being that that call was what was taking the time.  Well it
> is, but it should not be!
>
> In fact, pari's bnfinit is very fast in this case, as you can tell
> from switching to %gp:
>
> sage: %gp
>   --> Switching to PARI/GP interpreter <--
> pari: K = bnfinit(y^6 - y^5 - 5*y^4 + 4*y^3 + 6*y^2 - 3*y - 1);
> pari: ##
>   ***   last result computed in 24 ms.
>
> But doing the same in Sage:
>
> sage: y = polygen(QQ, 'y')
> sage: f = pari(y^6 - y^5 - 5*y^4 + 4*y^3 + 6*y^2 - 3*y - 1)
> sage: %time f.bnfinit()
> CPU times: user 1min 9s, sys: 144 ms, total: 1min 9s
> Wall time: 1min 9s
>
> The clincher is that if you run the previous lines (in a fresh
> session) and interrupt the last line immediately, and then run it
> again, it returns immediately.
>
> I don't know the libpari interface well enough to go further, but I
> hope someone does.  (Jeroen, we miss you!)
>
> John
>
> --
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> .
>

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Re: [sage-devel] Re: Problems with 9.3.beta6 + OS X Big Sur

[Dima Pasechnik]

On Wed, 3 Feb 2021, 17:03 John H Palmieri,  wrote:

> Right, thank you. Python 3.9 builds successfully.
>
> On Monday, February 1, 2021 at 7:14:29 PM UTC-8 zsc...@gmail.com wrote:
>
>> For the --with-system-python3=no, I don't know what the problem is but I
>> think it was fixed by upgrading to python 3.9 in
>> https://trac.sagemath.org/ticket/30589
>>
>> On Monday, February 1, 2021 at 9:45:37 PM UTC-5 John H Palmieri wrote:
>>
>>> On OS X Big Sur (intel), as of the most recent Xcode and homebrew, I am
>>> currently unable to build Sage with either homebrew's Python or with
>>> `./configure --with-system-python3=no`.
>>>
>>> - With homebrew's Python, actually Sage builds but the documentation
>>> does not (similar problems on both Big Sur and Catalina), ending with
>>
>>
yes, I see this too. (with latest Homebrew python 3.9.)

What exactly is broken there?



>>>
>>> 
>>> 0   signals.cpython-39-darwin.so0x00010cd40542
>>> print_backtrace + 66
>>> 1   signals.cpython-39-darwin.so0x00010cd44167 sigdie + 39
>>> 2   signals.cpython-39-darwin.so0x00010cd4406a
>>> cysigs_signal_handler + 282
>>> 3   libsystem_platform.dylib0x7fff203bcd7d _sigtramp + 29
>>> 4   ??? 0x003f 0x0 + 63
>>> 5   libtcl8.6.dylib 0x00032998c72e AtForkPrepare
>>> + 38
>>> 6   libsystem_pthread.dylib 0x7fff203781a3
>>> _pthread_atfork_prepare_handlers + 90
>>> 7   libSystem.B.dylib   0x7fff2a575934
>>> libSystem_atfork_prepare + 11
>>> 8   libsystem_c.dylib   0x7fff2025bb1b fork + 12
>>> 9   _posixsubprocess.cpython-39-darwin. 0x00010b63db89
>>> subprocess_fork_exec + 1573
>>> 10  Python  0x00010af10904
>>> cfunction_call + 127
>>> 11  Python  0x00010aedffa3
>>> _PyObject_MakeTpCall + 266
>>> 12  Python  0x00010af88027 call_function
>>> + 455
>>> ...
>>> 157 Python  0x00010afcf10f Py_BytesMain
>>> + 42
>>> 158 libdyld.dylib   0x7fff20393621 start + 1
>>> 
>>> Unhandled SIGILL: An illegal instruction occurred.
>>> This probably occurred because a *compiled* module has a bug
>>> in it and is not properly wrapped with sig_on(), sig_off().
>>> Python will now terminate.
>>> 
>>> ...
>>>   File
>>> "/Users/palmieri/Desktop/Sage/sage_builds/TESTING/sage-9.3.beta6/local/lib/python3.9/site-packages/sage_setup/docbuild/utils.py",
>>> line 221, in reap_workers
>>> w = bring_out_yer_dead(w, task, exitcode)
>>>   File
>>> "/Users/palmieri/Desktop/Sage/sage_builds/TESTING/sage-9.3.beta6/local/lib/python3.9/site-packages/sage_setup/docbuild/utils.py",
>>> line 157, in bring_out_yer_dead
>>> raise WorkerDiedException(
>>> sage_setup.docbuild.utils.WorkerDiedException: worker for
>>> ('reference/misc', 'en', 'html', {}) died with non-zero exit code -4
>>>
>>> - With `./configure --with-system-python3=no`, Python fails to build (on
>>> Big Sur only; it succeeds on Catalina), saying
>>>
>>> ModuleNotFoundError: No module named 'readline'
>>>
>>> and
>>>
>>> ModuleNotFoundError: No module named 'zlib'
>>>
>>> Any suggestions?
>>>
>>> --
>>> John
>>>
>>>
>>> --
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Re: [sage-devel] sage -b is broken

[Dima Pasechnik]

finally :-) (not sure bug or feature)

well,

make build

works

On Wed, 3 Feb 2021, 17:05 John H Palmieri,  wrote:

> I'm not sure when it happened, but with the latest beta, I see
>
> % ./sage -b
> Makefile:25: *** This Makefile needs to be invoked by build/make/install.
> Stop.
>
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> 
> .
>

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[sage-devel] sage -b is broken

[John H Palmieri]

I'm not sure when it happened, but with the latest beta, I see

% ./sage -b
Makefile:25: *** This Makefile needs to be invoked by build/make/install.  
Stop.

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[sage-devel] Re: Problems with 9.3.beta6 + OS X Big Sur

[John H Palmieri]

Right, thank you. Python 3.9 builds successfully.

On Monday, February 1, 2021 at 7:14:29 PM UTC-8 zsc...@gmail.com wrote:

> For the --with-system-python3=no, I don't know what the problem is but I 
> think it was fixed by upgrading to python 3.9 in 
> https://trac.sagemath.org/ticket/30589
>
> On Monday, February 1, 2021 at 9:45:37 PM UTC-5 John H Palmieri wrote:
>
>> On OS X Big Sur (intel), as of the most recent Xcode and homebrew, I am 
>> currently unable to build Sage with either homebrew's Python or with 
>> `./configure --with-system-python3=no`.
>>
>> - With homebrew's Python, actually Sage builds but the documentation does 
>> not (similar problems on both Big Sur and Catalina), ending with
>>
>> 
>> 0   signals.cpython-39-darwin.so0x00010cd40542 
>> print_backtrace + 66
>> 1   signals.cpython-39-darwin.so0x00010cd44167 sigdie + 39
>> 2   signals.cpython-39-darwin.so0x00010cd4406a 
>> cysigs_signal_handler + 282
>> 3   libsystem_platform.dylib0x7fff203bcd7d _sigtramp + 29
>> 4   ??? 0x003f 0x0 + 63
>> 5   libtcl8.6.dylib 0x00032998c72e AtForkPrepare 
>> + 38
>> 6   libsystem_pthread.dylib 0x7fff203781a3 
>> _pthread_atfork_prepare_handlers + 90
>> 7   libSystem.B.dylib   0x7fff2a575934 
>> libSystem_atfork_prepare + 11
>> 8   libsystem_c.dylib   0x7fff2025bb1b fork + 12
>> 9   _posixsubprocess.cpython-39-darwin. 0x00010b63db89 
>> subprocess_fork_exec + 1573
>> 10  Python  0x00010af10904 cfunction_call 
>> + 127
>> 11  Python  0x00010aedffa3 
>> _PyObject_MakeTpCall + 266
>> 12  Python  0x00010af88027 call_function 
>> + 455
>> ...
>> 157 Python  0x00010afcf10f Py_BytesMain + 
>> 42
>> 158 libdyld.dylib   0x7fff20393621 start + 1
>> 
>> Unhandled SIGILL: An illegal instruction occurred.
>> This probably occurred because a *compiled* module has a bug
>> in it and is not properly wrapped with sig_on(), sig_off().
>> Python will now terminate.
>> 
>> ...
>>   File 
>> "/Users/palmieri/Desktop/Sage/sage_builds/TESTING/sage-9.3.beta6/local/lib/python3.9/site-packages/sage_setup/docbuild/utils.py",
>>  
>> line 221, in reap_workers
>> w = bring_out_yer_dead(w, task, exitcode)
>>   File 
>> "/Users/palmieri/Desktop/Sage/sage_builds/TESTING/sage-9.3.beta6/local/lib/python3.9/site-packages/sage_setup/docbuild/utils.py",
>>  
>> line 157, in bring_out_yer_dead
>> raise WorkerDiedException(
>> sage_setup.docbuild.utils.WorkerDiedException: worker for 
>> ('reference/misc', 'en', 'html', {}) died with non-zero exit code -4
>>
>> - With `./configure --with-system-python3=no`, Python fails to build (on 
>> Big Sur only; it succeeds on Catalina), saying
>>
>> ModuleNotFoundError: No module named 'readline'
>>
>> and
>>
>> ModuleNotFoundError: No module named 'zlib'
>>
>> Any suggestions?
>>
>> -- 
>> John
>>
>>
>>

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[sage-devel] serious time loss in pari interface

[John Cremona]

I was looking again at https://trac.sagemath.org/ticket/25934 and now
think that the issue is more serious than first suggested.  The
immediate problem noticed was that after defining a sextic field and
creating the unit ideal, it took a very long time to display, and the
discussion side-tracked onto whether or not to call pari's bnfinit
function to properly initialise the number field structure, the
assumption being that that call was what was taking the time.  Well it
is, but it should not be!

In fact, pari's bnfinit is very fast in this case, as you can tell
from switching to %gp:

sage: %gp
  --> Switching to PARI/GP interpreter <--
pari: K = bnfinit(y^6 - y^5 - 5*y^4 + 4*y^3 + 6*y^2 - 3*y - 1);
pari: ##
  ***   last result computed in 24 ms.

But doing the same in Sage:

sage: y = polygen(QQ, 'y')
sage: f = pari(y^6 - y^5 - 5*y^4 + 4*y^3 + 6*y^2 - 3*y - 1)
sage: %time f.bnfinit()
CPU times: user 1min 9s, sys: 144 ms, total: 1min 9s
Wall time: 1min 9s

The clincher is that if you run the previous lines (in a fresh
session) and interrupt the last line immediately, and then run it
again, it returns immediately.

I don't know the libpari interface well enough to go further, but I
hope someone does.  (Jeroen, we miss you!)

John

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