Re: [sage-devel] error building pynormaliz with 8.8.beta6

[Sébastien Labbé]

On Wednesday, May 29, 2019 at 8:53:37 AM UTC+2, Samuel Lelievre wrote:
>
> Tue 2019-05-28 23:09:33 UTC+2, Sébastien Labbé:
>>
>>
>> On Tuesday, May 28, 2019 at 1:40:45 PM UTC+2, Michael Orlitzky wrote:
>>>
>>>
>>> First, can you find out where /bin/sh actually points? 
>>
>>
>> Sorry, I do not know how to answer this question. What command should I 
>> type?
>>
>  
> ls -halF /bin/sh
>

Here is what I get:

$ ls -halF /bin/sh
lrwxrwxrwx 1 root root 4 févr. 17  2016 /bin/sh -> dash*

 

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Re: [sage-devel] Re: sagenb failed to build on 8.8.beta3

[Dima Pasechnik]

On Wed, May 29, 2019 at 2:12 AM Colby Kelln  wrote:
>
> Hi,
>
> I'm receiving a similar error message. What exactly did you do to fix the 
> problem?

it depends - try starting sage, and post the error message (and
probably the relevant logs, too) here.

I wonder whether changing the way sagenb dependencies are dealt with
might make this error handling more robust.

>
> Thanks
>
> On Sunday, April 21, 2019 at 10:30:49 AM UTC-4, vdelecroix wrote:
>>
>> Indeed, sage did not start... After fixing it, sagenb installs.
>>
>> The error message is really confusing.
>>
>> Le 21/04/2019 à 16:25, Dima Pasechnik a écrit :
>> > this error is an indication of an earlier build error. Try starting sage.
>> >
>> > On Sun, 21 Apr 2019 15:13 Vincent Delecroix, <20100.d...@gmail.com>
>> > wrote:
>> >
>> >> Ignore the second e-mail: the error occurred again compiling
>> >> from scratch.
>> >>
>> >> Le 21/04/2019 à 14:24, Vincent Delecroix a écrit :
>> >>> It appears to be a problem with my setup.
>> >>>
>> >>> I had some Python libraries in my $HOME/.sage/local
>> >>> that made interference with the sage installation.
>> >>>
>> >>> Vincent
>> >>>
>> >>> Le 21/04/2019 à 13:22, Vincent Delecroix a écrit :
>>  Dear all,
>> 
>>  Starting from scratch, I failed to build sagenb. More precisely,
>>  it failed building its documentation with
>> 
>>  Running Sphinx v1.8.5
>>  making output directory...
>>  building [mo]: targets for 0 po files that are out of date
>>  building [html]: targets for 19 source files that are out of date
>>  updating environment: 19 added, 0 changed, 0 removed
>>  reading sources... [  5%] index
>>  reading sources... [ 10%] misc/introspect
>>  reading sources... [ 15%] misc/misc
>> 
>>  Exception occurred:
>>  File "sage/misc/lazy_import.pyx", line 218, in
>>  sage.misc.lazy_import.LazyImport._get_object
>>  (build/cythonized/sage/misc/lazy_import.c:2495)
>>    raise RuntimeError(f"resolving lazy import {self._name} during
>>  startup")
>>  RuntimeError: resolving lazy import dumps during startup
>> 
>>  See also the more complete log in attachment.
>> 
>>  Vincent
>> >>
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>
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Re: [sage-devel] error building pynormaliz with 8.8.beta6

[Dima Pasechnik]

dash is a bit of a problem. I am not sure whether currently it is
possible to build Sage with sh==dash
Perhaps modifying pynormaliz to actually use bash for building might
solve this.

On Wed, May 29, 2019 at 9:15 AM Sébastien Labbé  wrote:
>
>
>
> On Wednesday, May 29, 2019 at 8:53:37 AM UTC+2, Samuel Lelievre wrote:
>>
>> Tue 2019-05-28 23:09:33 UTC+2, Sébastien Labbé:
>>>
>>>
>>> On Tuesday, May 28, 2019 at 1:40:45 PM UTC+2, Michael Orlitzky wrote:


 First, can you find out where /bin/sh actually points?
>>>
>>>
>>> Sorry, I do not know how to answer this question. What command should I 
>>> type?
>>
>>
>> ls -halF /bin/sh
>
>
> Here is what I get:
>
> $ ls -halF /bin/sh
> lrwxrwxrwx 1 root root 4 févr. 17  2016 /bin/sh -> dash*
>
>
>
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Re: [sage-devel] Re: compiling error for 8.8.beta6 on Red Hat 6.10

[Dima Pasechnik]

assembly errors - means either broken toolchain (old `as` picked up ?), or
a failure to detect the correct architecture...

I guess sysadmins of this system see such errors every day, given how messy
that setup is.

On Wed, 29 May 2019 08:08 Christian Stump, 
wrote:

> Okay, thank you for checking -- I think that machine needs some upgrades!
>
> In case anyone else runs into this issue, here is a partial fix: I first
> compiled 8.6 from scratch and then upgraded to 8.8.beta6 and this worked.
>
> Unfortunately, my own code on top of 8.8.beta6 again does not build with
> the attached output.
>
> (Btw: the reason for me to be depending on that machine is that it has 100
> threads and 1tb memory.)
>
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Re: [sage-devel] error building pynormaliz with 8.8.beta6

[Dima Pasechnik]

On Wed, May 29, 2019 at 10:16 AM Dima Pasechnik  wrote:
>
> dash is a bit of a problem. I am not sure whether currently it is
> possible to build Sage with sh==dash

hmm, scratch this. it works at least on Debian stable.

> Perhaps modifying pynormaliz to actually use bash for building might
> solve this.
>
> On Wed, May 29, 2019 at 9:15 AM Sébastien Labbé  wrote:
> >
> >
> >
> > On Wednesday, May 29, 2019 at 8:53:37 AM UTC+2, Samuel Lelievre wrote:
> >>
> >> Tue 2019-05-28 23:09:33 UTC+2, Sébastien Labbé:
> >>>
> >>>
> >>> On Tuesday, May 28, 2019 at 1:40:45 PM UTC+2, Michael Orlitzky wrote:
> 
> 
>  First, can you find out where /bin/sh actually points?
> >>>
> >>>
> >>> Sorry, I do not know how to answer this question. What command should I 
> >>> type?
> >>
> >>
> >> ls -halF /bin/sh
> >
> >
> > Here is what I get:
> >
> > $ ls -halF /bin/sh
> > lrwxrwxrwx 1 root root 4 févr. 17  2016 /bin/sh -> dash*
> >
> >
> >
> > --
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[sage-devel] Re: direct sums, products and other categorical constructions

[Simon King]

Hi Simon,

On 2019-05-27, Simon Brandhorst  wrote:
> I would agree that I want unique representation with simple "ambient" 
> objects (usually constructed from an integer and maybe a ring). Then with 
> complicated objects I am not so sure anymore. Say subgroups of a group and 
> submodules of a module. There it might cause more trouble than benefit. 
> Plus it is quite common to create 
> (hundred) thousands of subgroups/submodules during a computation.

If you do not keep a reference chain to said hundred thousands of
different subgroups, then they would be automatically removed from the
"UniqueRepresentation" cache. If not, it's a bug (admittedly we had
instances of that bug quite often).

So, at least at first, one could think that equipping the result of a
universal construction with (co)projections wouldn't interfere with
UniqueRepresentation's weak cache. That's where my original suggestion
came from.

However, each map such as a projection or coprojection does involve 
references to domain or codomain. One of them can be weak (that's what we
do for coercion maps), but nonetheless adding the projections as attribute
to the constructed object X increases the likelyhood that X cannot be
garbage collected.

>From that point of view, keeping the (co)projections or deleting them
should be in the decision of the user, they shouldn't be automatically
stored as attribute of the object X.

Best regards,
Simon

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Re: [sage-devel] error building pynormaliz with 8.8.beta6

[Sébastien Labbé]

On Wednesday, May 29, 2019 at 10:17:08 AM UTC+2, Dima Pasechnik wrote:
>
> dash is a bit of a problem. I am not sure whether currently it is 
> possible to build Sage with sh==dash 
>

Well, I have been using this setup for more than 2 years now with no 
problem in compiling Sage hundreds of times.

Perhaps modifying pynormaliz to actually use bash for building might 
> solve this. 
>
>
The solution was found by Vincent earlier, it is to do "sh ./configure" 
instead of "sh configure" which in my case uses the wrong configure file. 
So, no need to use bash it seems.

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[sage-devel] Workshop Announcement

[Robert Jacobson]

I hope this is not too far off-topic, but it is something that is 
definitely relevant to the Sage development community.

The 12th Conference on Intelligent Computer Mathematics, CICM 2019, is July 
8-12, 2019 in Prague, Czech Republic. The conference will be located at the 
Czech Institute of Informatics, Robotics, and Cybernetics (CIIRC) of Czech 
Technical University in Prague (CTU). 

Of particular interest to this community is the workshop on Large 
Mathematics Libraries 
 (LML 
2019).

Large Mathematics Libraries (LML 2019)
>
> Large formal and semiformal mathematics libraries are needed to support 
> mathematics research, mathematics education, rigorous software development, 
> and formal proof development. This workshop will explore methods for 
> designing, constructing, and maintaining large mathematics libraries as 
> well as for finding, comparing, and applying the knowledge residing in 
> these libraries.
>
> Key topics of interest will include:
>
>- Methods for sharing knowledge between libraries.
>- Modular techniques for organizing the knowledge within libraries.
>- The translation of libraries to different languages and logics.
>- The construction of new libraries by integrating existing libraries.
>- Tools for exploring the contents of large libraries.
>- Observations about past results.
>
>
Best wishes,

Robert Jacobson 

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Re: [sage-devel] error building pynormaliz with 8.8.beta6

[Michael Orlitzky]

On 5/28/19 5:09 PM, Sébastien Labbé wrote:
> 
> $ cd /home/slabbe/GitBox/sage/local/var/tmp/sage/build/pynormaliz-2.5/src
> $ strace sh congiure
> ...
> 4000 lines in total including:
> ...
> faccessat(AT_FDCWD, "/home/slabbe/GitBox/sage/configure", R_OK) = 0
> stat("/home/slabbe/GitBox/sage/configure", {st_mode=S_IFREG|0775,
> st_size=398280, ...}) = 0
> ...
> 
> Therefore, it is using the configure from sage in fact. Indeed, the HOME
> directory of Sage is in my PATH.
> 

Aha, I suspect that "sh" is the problem and not "configure". You have a
lot of stuff in your PATH that probably shouldn't be there; or at least,
should be in a different order:

PATH: /home/slabbe/GitBox/sage/local/libexec/ccache
PATH: /home/slabbe/GitBox/sage/build/bin
PATH: /home/slabbe/GitBox/sage/src/bin
PATH: /home/slabbe/GitBox/sage/local/bin
PATH: /home/slabbe/GitBox/sage/build/bin
PATH: /home/slabbe/GitBox/sage/src/bin
PATH: /home/slabbe/GitBox/sage/local/bin
PATH: /home/slabbe/GitBox/sage
...
PATH: /bin

I'm guessing that when you run "sh configure", it runs some other "sh"
from one of those Sage directories, and not /bin/sh. In particular if
Sage's copy of "sh" changes the current working directory to
"/home/slabbe/GitBox/sage", then the subsequent execution of "configure"
would produce exactly the problem you're seeing.

First, please verify this by changing setup.py to run "/bin/sh" rather
than simply "sh". If my guess is right, two things should be done:

  * PyNormaliz should use "/bin/sh", to be on the safe side.

  * You should probably reorder PATH on your system so that things
in Sage's bin directories don't override the ones in /bin.

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Re: [sage-devel] error building pynormaliz with 8.8.beta6

[John H Palmieri]

On Wednesday, May 29, 2019 at 5:52:26 PM UTC-7, Michael Orlitzky wrote:
>
> On 5/28/19 5:09 PM, Sébastien Labbé wrote: 
> > 
> > $ cd 
> /home/slabbe/GitBox/sage/local/var/tmp/sage/build/pynormaliz-2.5/src 
> > $ strace sh congiure 
> > ... 
> > 4000 lines in total including: 
> > ... 
> > faccessat(AT_FDCWD, "/home/slabbe/GitBox/sage/configure", R_OK) = 0 
> > stat("/home/slabbe/GitBox/sage/configure", {st_mode=S_IFREG|0775, 
> > st_size=398280, ...}) = 0 
> > ... 
> > 
> > Therefore, it is using the configure from sage in fact. Indeed, the HOME 
> > directory of Sage is in my PATH. 
> > 
>
> Aha, I suspect that "sh" is the problem and not "configure". You have a 
> lot of stuff in your PATH that probably shouldn't be there; or at least, 
> should be in a different order: 
>
> PATH: /home/slabbe/GitBox/sage/local/libexec/ccache 
> PATH: /home/slabbe/GitBox/sage/build/bin 
> PATH: /home/slabbe/GitBox/sage/src/bin 
> PATH: /home/slabbe/GitBox/sage/local/bin 
> PATH: /home/slabbe/GitBox/sage/build/bin 
> PATH: /home/slabbe/GitBox/sage/src/bin 
> PATH: /home/slabbe/GitBox/sage/local/bin 
> PATH: /home/slabbe/GitBox/sage 
> ... 
> PATH: /bin 
>
> I'm guessing that when you run "sh configure", it runs some other "sh" 
> from one of those Sage directories, and not /bin/sh. 


Running "command -v sh" should tell you which "sh" is running, in case that 
helps.


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Re: [sage-devel] error building pynormaliz with 8.8.beta6

[Michael Orlitzky]

On 5/30/19 12:06 AM, John H Palmieri wrote:
> 
> I'm guessing that when you run "sh configure", it runs some other "sh"
> from one of those Sage directories, and not /bin/sh. 
> 
> Running "command -v sh" should tell you which "sh" is running, in case
> that helps.
> 

Yeah, nevermind... this is a real stinker. I can now reproduce the
problem. It only happens when all of the following are true:

  * The Sage root directory containing the wrong "configure" file
is in your $PATH.

  * Dash is what you get when you run "sh".

  * When Dash was compiled, the --disable-lineno option was passed to
its configure script.

Ironically, both Debian and Gentoo build Dash with that option to avoid
upstream build errors. Autoconf somehow detects the missing LINENO
support and re-execs itself with bash, and I guess that goes wrong
somehow in this case. Running "bash configure" will indeed search your
$PATH for a "configure" file if none is found in the current working
directory.

As yet unexplained is why manually running "bash configure" works, but
the autoconf bash re-exec does not. My own strace shows that running
"dash configure" will wind up running

  execve("/bin/bash", ["/bin/bash", "/home/mjo/src/sage-8.8.beta6
  /con"...], 0x55d1c04303f8 /* 68 vars */) = 0

instead of executing either "/bin/bash configure" in the CWD, or
"/bin/bash /path/to/pynormaliz's/configure".

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[sage-devel] Continuous benchmarking

[Samuel Lelièvre]

Dear sage-devel,

This blog post on continuous benchmarking looks interesting!

https://medium.com/@wolfv/building-an-open-source-continuous-benchmark-system-717839093962

There have been related discussions on this list in the past,
for example around airspeed velocity:

https://groups.google.com/forum/#!searchin/sage-devel/airspeed$20velocity%7Csort:date

Kind regards,
Samuel

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