Re: [sage-devel] Re: System upgrades breaking sage frequently

[Nils Bruin]

On Wednesday, 3 August 2022 at 23:41:02 UTC-7 isu...@gmail.com wrote:

> Can you try in a couple of hours and report back?
>

Yes, this time it looks like the instructions led to a successful build! 
Nice.
 

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Re: [sage-devel] Re: System upgrades breaking sage frequently

[Isuru Fernando]

Hi Nils,

We need to rebuild primecount for the latest primesieve version. That's why
an older primesieve version was used.
I've opened a PR at
https://github.com/conda-forge/primecount-feedstock/pull/7
Can you try in a couple of hours and report back?

Isuru

On Wed, Aug 3, 2022 at 11:44 PM Nils Bruin  wrote:

> Hi Isuru,
>
> I followed
> https://doc.sagemath.org/html/en/installation/conda.html#sec-installation-conda-develop
>
> except that for my bash,  the long compound "configure" invocation didn't
> work (is that even correct bash symtax? my shell is pretty vanilla, so I'd
> be surprised if my shell rejects syntax that others accept. I suspect the
> nested "$(...$(...)...)" made it fail ) so I broke it up as referenced in
> https://groups.google.com/g/sage-devel/c/Iz8ZsmQM3Pg/m/dgiXcfOhAQAJ :
>
> $ for pkg in $(./sage -package list :standard: \
>--has-file spkg-configure.m4  \
>--has-file distros/conda.txt); do  echo
> --with-system-$pkg=force; done > with
> $ ./configure --with-python=$CONDA_PREFIX/bin/python
> --prefix=$CONDA_PREFIX  `cat with`
>
> That then produced the two errors.
>
> On Wednesday, 3 August 2022 at 19:29:52 UTC-7 isu...@gmail.com wrote:
>
>> Hi Nils,
>>
>> Can you give me the commands that you did to get the primesive/conda
>> error? I'd like to fix that.
>>
>> Isuru
>>
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> 
> .
>

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Re: [sage-devel] Re: System upgrades breaking sage frequently

[Nils Bruin]

Hi Isuru,

I followed 
https://doc.sagemath.org/html/en/installation/conda.html#sec-installation-conda-develop

except that for my bash,  the long compound "configure" invocation didn't 
work (is that even correct bash symtax? my shell is pretty vanilla, so I'd 
be surprised if my shell rejects syntax that others accept. I suspect the 
nested "$(...$(...)...)" made it fail ) so I broke it up as referenced in 
https://groups.google.com/g/sage-devel/c/Iz8ZsmQM3Pg/m/dgiXcfOhAQAJ :

$ for pkg in $(./sage -package list :standard: \
   --has-file spkg-configure.m4  \
   --has-file distros/conda.txt); do  echo 
--with-system-$pkg=force; done > with
$ ./configure --with-python=$CONDA_PREFIX/bin/python --prefix=$CONDA_PREFIX 
 `cat with`

That then produced the two errors.

On Wednesday, 3 August 2022 at 19:29:52 UTC-7 isu...@gmail.com wrote:

> Hi Nils,
>
> Can you give me the commands that you did to get the primesive/conda 
> error? I'd like to fix that.
>
> Isuru
>
>

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Re: [sage-devel] Re: System upgrades breaking sage frequently

[Isuru Fernando]

Hi Nils,

Can you give me the commands that you did to get the primesive/conda error?
I'd like to fix that.

Isuru

On Wed, Jul 27, 2022 at 4:52 AM Samuel Lelièvre 
wrote:

> 2022-07-27 00:27 UTC, Matthias Koeppe:
> >
> > Only packages for which we have "spkg-configure.m4" scripts
> > can be taken from the system
>
> More and more packages have such scripts. Many thanks to
> people who authored and reviewed the corresponding tickets:
>
>
> https://trac.sagemath.org/query?order=id&desc=1&status=closed&max=200&summary=~spkg-configure&summary=~spkg_configure&col=id&col=summary&col=author&col=reviewer&col=milestone
>
> Remaining open tickets in that direction:
>
>
> https://trac.sagemath.org/query?order=id&desc=1&status=!closed&summary=~spkg-configure&summary=~spkg_configure
>
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> .
>

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Re: [sage-devel] Re: System upgrades breaking sage frequently

[Samuel Lelièvre]

2022-07-27 00:27 UTC, Matthias Koeppe:
>
> Only packages for which we have "spkg-configure.m4" scripts
> can be taken from the system

More and more packages have such scripts. Many thanks to
people who authored and reviewed the corresponding tickets:

https://trac.sagemath.org/query?order=id&desc=1&status=closed&max=200&summary=~spkg-configure&summary=~spkg_configure&col=id&col=summary&col=author&col=reviewer&col=milestone

Remaining open tickets in that direction:

https://trac.sagemath.org/query?order=id&desc=1&status=!closed&summary=~spkg-configure&summary=~spkg_configure

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Re: [sage-devel] Re: System upgrades breaking sage frequently

[Matthias Koeppe]

On Tuesday, July 26, 2022 at 5:34:07 PM UTC-7 Nils Bruin wrote:

> Things like not having to issue "sage -b" after making a little edit will 
> be nice to have eventually,
>

This feature (editable installs) is actually orthogonal to the decision on 
the conda install method.

You can activate it using "configure --enable-editable", and it is slated 
to become default in one of next betas (see 
https://trac.sagemath.org/ticket/32406).

 

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Re: [sage-devel] Re: System upgrades breaking sage frequently

[Nils Bruin]

On Tuesday, 26 July 2022 at 17:27:11 UTC-7 Matthias Koeppe wrote:

> Sort of. This is another way to build Sage with conda. It is described in 
> the 2nd of the 3 sections on the same page, 
> https://doc.sagemath.org/html/en/installation/conda.html#using-conda-to-provide-system-packages-for-the-sage-distribution,
>  
> "Using conda to provide system packages for the Sage distribution". This 
> works in the same way that it does on top of Fedora, or on top of any other 
> package distribution. You can control what packages are taken from the 
> system and what packages are built by the Sage distribution. And it has the 
> same restrictions as what the Sage distribution does on top of Fedora etc.: 
> Only packages for which we have "spkg-configure.m4" scripts can be taken 
> from the system -- and no Python packages can be taken from the system.


Ah, so that sounds like it's a lot closer to how most people have the 
build-environment organized. Things like not having to issue "sage -b" 
after making a little edit will be nice to have eventually, but it looks 
like that stuff is still too much in flux to be reliable at the moment. 
 

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Re: [sage-devel] Re: System upgrades breaking sage frequently

[Matthias Koeppe]

On Tuesday, July 26, 2022 at 5:12:47 PM UTC-7 Nils Bruin wrote:

> On Tuesday, 26 July 2022 at 15:58:18 UTC-7 Matthias Koeppe wrote:
>
>>
>> Whether the method described in section 
>> https://doc.sagemath.org/html/en/installation/conda.html#using-conda-to-provide-all-dependencies-for-the-sage-library-experimental
>>  
>> works always depends on the conda package maintainers providing packages 
>> that are up to date with respect to our requirements. It's not directly 
>> under control of our project. 
>>
>> Hm ... so I guess "configure"  with these 
> "--with-system-*=true/false/force" can then determine per-prerequisite 
> whether to try to get it from the system or build it by itself?
>
 

> And that the advantage of conda is that it can distribute binaries, that 
> are then hopefully built with approrpriate flags for your particular system?
>

The binaries are not any more tailored to your system than the binaries 
from the Fedora distribution are.
 

> And that the hope is that conda-provided prereqs are a better match than 
> what the OS may provide and/or are more stable (mainly because one can 
> afford to not update a conda env regularly).
>

... and you can use conda on machines where you are not root.
 

> Is it possible for prerequisites that conda fails at, such as primesieve 
> and primecount, to flick the "with-system" switches the other way, so that 
> sage builds that by itself? Is there a way to tell the system to get from 
> conda what it can and otherwise build it by itself? It seems like that's 
> what configure does normally (and with a WAY shorter configure command!), 
> so would it be able to do that within conda? 
>

Sort of. This is another way to build Sage with conda. It is described in 
the 2nd of the 3 sections on the same 
page, 
https://doc.sagemath.org/html/en/installation/conda.html#using-conda-to-provide-system-packages-for-the-sage-distribution,
 
"Using conda to provide system packages for the Sage distribution". This 
works in the same way that it does on top of Fedora, or on top of any other 
package distribution. You can control what packages are taken from the 
system and what packages are built by the Sage distribution. And it has the 
same restrictions as what the Sage distribution does on top of Fedora etc.: 
Only packages for which we have "spkg-configure.m4" scripts can be taken 
from the system -- and no Python packages can be taken from the system.




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Re: [sage-devel] Re: System upgrades breaking sage frequently

[Nils Bruin]

On Tuesday, 26 July 2022 at 15:58:18 UTC-7 Matthias Koeppe wrote:

>
> Whether the method described in section 
> https://doc.sagemath.org/html/en/installation/conda.html#using-conda-to-provide-all-dependencies-for-the-sage-library-experimental
>  
> works always depends on the conda package maintainers providing packages 
> that are up to date with respect to our requirements. It's not directly 
> under control of our project. 
>
> Hm ... so I guess "configure"  with these 
"--with-system-*=true/false/force" can then determine per-prerequisite 
whether to try to get it from the system or build it by itself? And that 
the advantage of conda is that it can distribute binaries, that are then 
hopefully built with approrpriate flags for your particular system? And 
that the hope is that conda-provided prereqs are a better match than what 
the OS may provide and/or are more stable (mainly because one can afford to 
not update a conda env regularly).

Is it possible for prerequisites that conda fails at, such as primesieve 
and primecount, to flick the "with-system" switches the other way, so that 
sage builds that by itself? Is there a way to tell the system to get from 
conda what it can and otherwise build it by itself? It seems like that's 
what configure does normally (and with a WAY shorter configure command!), 
so would it be able to do that within conda? It would seem that after:

$ conda env update --file environment.yml -n sage-build

(which is I think one of the commands where using mamba instead saves gobs 
of time!!!) conda has already exerted its best efforts to satisfy the 
prereqs, so anything that now fails should be built by sage itself ...




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Re: [sage-devel] Re: System upgrades breaking sage frequently

[Matthias Koeppe]

On Tuesday, July 26, 2022 at 2:08:32 PM UTC-7 Nils Bruin wrote:

>
> configure: error: 
>
> Given --with-system-primesieve=force, but no system package could be 
> used.
> That's an error.  Please install the indicated package to continue.
> (To override this error, use ./configure --without-system-primesieve)
> Given --with-system-primecount=force, but no system package could be 
> used.
> That's an error.  Please install the indicated package to continue.
> (To override this error, use ./configure --without-system-primecount)
>
> The documentation section about this is  marked "experimental", and I 
> think this shows it's indeed not ready for prime time yet.
>

Whether the method described in section 
https://doc.sagemath.org/html/en/installation/conda.html#using-conda-to-provide-all-dependencies-for-the-sage-library-experimental
 
works always depends on the conda package maintainers providing packages 
that are up to date with respect to our requirements. It's not directly 
under control of our project. 


 

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Re: [sage-devel] Re: System upgrades breaking sage frequently

[Nils Bruin]

Yup, rerunning "mamba env update -n sage-build -f src/environment.yml" 
installed eclib and now "./configure ..." produces one less error:

configure: error: 

Given --with-system-primesieve=force, but no system package could be 
used.
That's an error.  Please install the indicated package to continue.
(To override this error, use ./configure --without-system-primesieve)
Given --with-system-primecount=force, but no system package could be 
used.
That's an error.  Please install the indicated package to continue.
(To override this error, use ./configure --without-system-primecount)

The documentation section about this is  marked "experimental", and I think 
this shows it's indeed not ready for prime time yet.

It sounds like https://trac.sagemath.org/ticket/33345 would also solve the 
problem of depending on prone-to-change system libraries. Is that perhaps 
the route to go for development nowadays? Then there's no conda/mamba to 
worry about at all.
On Tuesday, 26 July 2022 at 06:12:52 UTC-7 Samuel Lelievre wrote:

> 2022-07-26 07:13:30 UTC, Dima Pasechnik:
>
> this says that conda is behind Sage in regard of versions of eclib 
> and primesieve/count 
>
> - eclib upgrade in Conda now done:
>   https://github.com/conda-forge/eclib-feedstock/pull/36
> - primesieve and primecount seem up to date
>

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Re: [sage-devel] Re: System upgrades breaking sage frequently

[Matthias Koeppe]

On Tuesday, July 26, 2022 at 6:47:47 AM UTC-7 wst...@gmail.com wrote:

> For CoCalc, [...] we run a 1-2 
> pages long "./configure ..." command before I even do "make". At the 
> top it starts with 
>
> --with-system-python3=no \ 
> --with-system-r=no \ 
> --with-system-primecount=no \ 
> --with-system-primesieve=no \ 
> --with-system-qhull=no \ 
> --with-system-cmake=no \ 
> [...]
>
> Could there be a single option to the Sage build system such as: 
> "--without-system" that disables all system libraries


That's https://trac.sagemath.org/ticket/33345
 

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Re: [sage-devel] Re: System upgrades breaking sage frequently

[William Stein]

For CoCalc, where we have a bunch of different specific versions of
Sage pre-installed that all stay stable over *years*, we run a 1-2
pages long "./configure ..." command before I even do "make". At the
top it starts with

--with-system-python3=no \
--with-system-r=no \
--with-system-primecount=no \
--with-system-primesieve=no \
--with-system-qhull=no \
--with-system-cmake=no  \
...
… so,that's why R, Python interpreter, and other stuff is independent. …

We should definitely check if there is more I could make independent.
I mean, technically it's not independent, because some underlying libs
are shared, but there are certainly less surprises and the dependency
graph is not a wide blinking christmas tree.  What we are not doing is
sharing Sage across linux editions. i.e. 20.04 will have a couple of
Sage installs and with 22.04 there will be a new 9.6 one. But that's
not the issue in the thread.

Could there be a single option to the Sage build system such as:
"--without-system" that disables all system libraries, and hence
behaves exactly like Sage used to?  Is there already such an option
that I don't know about?

William

On Mon, Jul 25, 2022 at 12:44 PM Nils Bruin  wrote:
>
> On Thursday, 21 July 2022 at 11:52:42 UTC-7 Nils Bruin wrote:
>>
>> On Thursday, 21 July 2022 at 11:31:35 UTC-7 Matthias Koeppe wrote:
>>>
>>>
>>> You really just need to stop your distribution from automatically 
>>> uninstalling the old shared library packages when you do upgrades. Both the 
>>> old version (needed for your from-source installation of Sage) and the new 
>>> version (needed as dependencies of upgraded system packages) can coexist in 
>>> your system.
>>>
>>
>> Right .. but that would require telling the system which libraries need to 
>> be preserved ... I guess one could collect the dependencies by a liberal ldd 
>> application, but then one would need to query the package manager which 
>> packages provide the requisite library files and then somehow register those 
>> packages *are* dependencies ... I guess that could be done by building a 
>> placeholder package (rpm or deb) that declares all the specific 
>> dependencies. And to "declare" these, one could install that package. Upon a 
>> reconfigure+rebuild, one could uninstall the old placeholder, recompute the 
>> new dependencies, and install a new placeholder ...
>
>
> Ouch ... and it looks like this wouldn't even work: if I try
>
> dnf whatprovides /usr/lib64/libflint.so.17
>
> I get:
>
> flint-2.9.0-1.fc36.x86_64
>
> and similarly
>
> dnf whatprovides /usr.lib64/libflint.so.16
> flint-2.8.4-2.fc36.x86_64
>
> Hence, if a compiled-from-source sagemath were to declare its dependencies to 
> the package manager it would have to do so by depending on a *specific 
> version* of flint, and hence "updating" flint should lead to a dependency 
> conflict. As long as fedora doesn't allow two different version of flint to 
> be installed at the same time (and the fact that flint-2.9 "upgrades" 
> flint-2.8 suggests that it won't), we'd need a version lock: just keeping an 
> unmanaged so-file hang around in space that's supposed to be managed by a 
> package manager would lead to a rather messy system state.
>
> So, based on that, I think build-from-source using these kinds of system 
> resources should actually *not* be a recommended install method: 
> build-from-source should have its less stable prerequisites satisfied by some 
> separate environment -- possibly/likely conda. Resources/libraries such as 
> libflint are clearly *only* managed and provided by the OS in a way that is 
> appropriate for other OS-managed/packaged software. Turns out there's still a 
> niche for sage-the-distribution; possibly replaced by 
> sage-in-conda-the-distribution. Can we get sage-on-conda modified so that it 
> works nicely with git-trac, so that a sage-conda container can be used for 
> development? I would be very interested in a guide to that.
>
>
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Re: [sage-devel] Re: System upgrades breaking sage frequently

[Samuel Lelievre]

2022-07-26 07:13:30 UTC, Dima Pasechnik:

this says that conda is behind Sage in regard of versions of eclib 
and primesieve/count 

- eclib upgrade in Conda now done:
  https://github.com/conda-forge/eclib-feedstock/pull/36
- primesieve and primecount seem up to date

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Re: [sage-devel] Re: System upgrades breaking sage frequently

[John Cremona]

On Tue, 26 Jul 2022 at 08:13, Dima Pasechnik  wrote:
>
> On Tue, Jul 26, 2022 at 8:24 AM Nils Bruin  wrote:
> >
> > On Monday, 25 July 2022 at 12:53:08 UTC-7 Matthias Koeppe wrote:
> >>
> >> Have you tried the existing instructions that I pointed you to?
> >
> >
> > I have now. I'm stuck on running configure.
> >
> >  * the ./configure command suggested doesn't work in my bash. I'm getting:
> >  bash: unexpected EOF while looking for matching `)'
> >
> > Instead I split it up a bit:
> > $ for pkg in $(./sage -package list :standard: \
> >--has-file spkg-configure.m4  \
> >--has-file distros/conda.txt); do
> >  echo --with-system-$pkg=force; done > with
> > $ ./configure --with-python=$CONDA_PREFIX/bin/python --prefix=$CONDA_PREFIX 
> >  `cat with`
> > That seemed to succeed in running configure, but resulted in an error:
> > configure: error:
> >
> > Given --with-system-eclib=force, but no system package could be used.
> > That's an error.  Please install the indicated package to continue.
> > (To override this error, use ./configure --without-system-eclib)
> > Given --with-system-primesieve=force, but no system package could be 
> > used.
> > That's an error.  Please install the indicated package to continue.
> > (To override this error, use ./configure --without-system-primesieve)
> > Given --with-system-primecount=force, but no system package could be 
> > used.
> > That's an error.  Please install the indicated package to continue.
> > (To override this error, use ./configure --without-system-primecount)
>
> this says that conda is behind Sage in regard of versions of  eclib

For what it's worth, Nils, Sage's eclib was recently updated: not
major but a bugfix.  See https://trac.sagemath.org/ticket/34029.

John

> and primesieve/count
>
> >
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Re: [sage-devel] Re: System upgrades breaking sage frequently

[Dima Pasechnik]

On Tue, Jul 26, 2022 at 8:24 AM Nils Bruin  wrote:
>
> On Monday, 25 July 2022 at 12:53:08 UTC-7 Matthias Koeppe wrote:
>>
>> Have you tried the existing instructions that I pointed you to?
>
>
> I have now. I'm stuck on running configure.
>
>  * the ./configure command suggested doesn't work in my bash. I'm getting:
>  bash: unexpected EOF while looking for matching `)'
>
> Instead I split it up a bit:
> $ for pkg in $(./sage -package list :standard: \
>--has-file spkg-configure.m4  \
>--has-file distros/conda.txt); do  
>echo --with-system-$pkg=force; done > with
> $ ./configure --with-python=$CONDA_PREFIX/bin/python --prefix=$CONDA_PREFIX  
> `cat with`
> That seemed to succeed in running configure, but resulted in an error:
> configure: error:
>
> Given --with-system-eclib=force, but no system package could be used.
> That's an error.  Please install the indicated package to continue.
> (To override this error, use ./configure --without-system-eclib)
> Given --with-system-primesieve=force, but no system package could be used.
> That's an error.  Please install the indicated package to continue.
> (To override this error, use ./configure --without-system-primesieve)
> Given --with-system-primecount=force, but no system package could be used.
> That's an error.  Please install the indicated package to continue.
> (To override this error, use ./configure --without-system-primecount)

this says that conda is behind Sage in regard of versions of  eclib
and primesieve/count

>
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[sage-devel] Re: System upgrades breaking sage frequently

[Nils Bruin]

On Monday, 25 July 2022 at 12:53:08 UTC-7 Matthias Koeppe wrote:

> Have you tried the existing instructions that I pointed you to?
>

I have now. I'm stuck on running configure.

 * the ./configure command suggested doesn't work in my bash. I'm getting:
 bash: unexpected EOF while looking for matching `)'

Instead I split it up a bit:
$ for pkg in $(./sage -package list :standard: \
   --has-file spkg-configure.m4  \
   --has-file distros/conda.txt); do   
  echo --with-system-$pkg=force; done > with
$ ./configure --with-python=$CONDA_PREFIX/bin/python --prefix=$CONDA_PREFIX 
 `cat with`
That seemed to succeed in running configure, but resulted in an error:
configure: error: 

Given --with-system-eclib=force, but no system package could be used.
That's an error.  Please install the indicated package to continue.
(To override this error, use ./configure --without-system-eclib)
Given --with-system-primesieve=force, but no system package could be 
used.
That's an error.  Please install the indicated package to continue.
(To override this error, use ./configure --without-system-primesieve)
Given --with-system-primecount=force, but no system package could be 
used.
That's an error.  Please install the indicated package to continue.
(To override this error, use ./configure --without-system-primecount)

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[sage-devel] Re: System upgrades breaking sage frequently

[Matthias Koeppe]

On Monday, July 25, 2022 at 7:09:00 PM UTC-7 Nils Bruin wrote:

> On Monday, 25 July 2022 at 18:55:54 UTC-7 Matthias Koeppe wrote:
>
>>
>> https://doc.sagemath.org/html/en/installation/conda.html#sec-installation-conda-develop
>> links to a different section, namely "Using conda to provide all 
>> dependencies for the Sage library (experimental)"
>> Read that
>>
>
> Ah, OK. so: pull sagemath source as usual, activate conda, then build in 
> some conda-specific way. It still requires conda, which dnf provides ... 
> but I guess if I pull it from there we'll have the same version problems if 
> fedora decides to upgrade conda? Or would "created" environments persist 
> from one conda version to the next?
>

I don't have experience with the Fedora-packaged conda package manager. I'm 
not sure if that is widely used.

At the top 
of 
https://doc.sagemath.org/html/en/installation/conda.html#install-from-conda-forge
 
we have instructions how to install conda as a user.

conda environments persist -- and normally have nothing to do with the 
system package manager's packages. All installed packages are coming from 
conda channels (our instructions have you use the conda-forge channel).

The trick with conda is that you can have many environments -- typically 
one per "project". When you update one, the others are not changed, so they 
will continue to work.
You can still break things by making unattended updates within an 
environment, of course.

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[sage-devel] Re: System upgrades breaking sage frequently

[Matthias Koeppe]

On Monday, July 25, 2022 at 6:39:35 PM UTC-7 Nils Bruin wrote:

> I've not been able to find the version-specific rpm's at all (if I do "dnf 
> search flint" these things do not show up). [...] as far as I can tell,  
> /usr/lib64/libflint.so.17 is really owned by flint-2.9.0-1.fc36.x86_64 and 
> nothing else.
>

You are right. I have to retract my claim regarding Fedora. I'll update 
https://trac.sagemath.org/ticket/34207 accordingly

# dnf install 'libflint.so.16()(64bit)' 'libflint.so.17()(64bit)'

Last metadata expiration check: 0:04:24 ago on Tue Jul 26 02:02:49 2022.
Error: 

 Problem: cannot install both flint-2.9.0-1.fc36.x86_64 and 
flint-2.8.4-2.fc36.x86_64

  - conflicting requests
 

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[sage-devel] Re: System upgrades breaking sage frequently

[Nils Bruin]

On Monday, 25 July 2022 at 18:55:54 UTC-7 Matthias Koeppe wrote:

>
> https://doc.sagemath.org/html/en/installation/conda.html#sec-installation-conda-develop
> links to a different section, namely "Using conda to provide all 
> dependencies for the Sage library (experimental)"
> Read that
>

Ah, OK. so: pull sagemath source as usual, activate conda, then build in 
some conda-specific way. It still requires conda, which dnf provides ... 
but I guess if I pull it from there we'll have the same version problems if 
fedora decides to upgrade conda? Or would "created" environments persist 
from one conda version to the next?

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[sage-devel] Re: System upgrades breaking sage frequently

[Matthias Koeppe]

https://doc.sagemath.org/html/en/installation/conda.html#sec-installation-conda-develop
links to a different section, namely "Using conda to provide all 
dependencies for the Sage library (experimental)"
Read that

On Monday, July 25, 2022 at 6:46:55 PM UTC-7 Nils Bruin wrote:

> On Monday, 25 July 2022 at 12:53:08 UTC-7 Matthias Koeppe wrote:
>
>> On Monday, July 25, 2022 at 12:44:20 PM UTC-7 Nils Bruin wrote:
>>
>>> Can we get sage-on-conda modified so that it works nicely with git-trac, 
>>> so that a sage-conda container can be used for development? I would be very 
>>> interested in a guide to that.
>>>
>>
>> Have you tried the existing instructions that I pointed you to?
>>
>
> Well, I looked at the instructions and found:
>
> "Installing all of SageMath from conda (not for development)"
>
> and not a corresponding section "Installing SageMath in/from conda for 
> development". That's the part that isn't addressed in the guide pointed to. 
> I'd expect sage to be pulled from a sagemath repository to be suitable for 
> git-trac workflows, not from conda.
>

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[sage-devel] Re: System upgrades breaking sage frequently

[Nils Bruin]

On Monday, 25 July 2022 at 12:53:08 UTC-7 Matthias Koeppe wrote:

> On Monday, July 25, 2022 at 12:44:20 PM UTC-7 Nils Bruin wrote:
>
>> Can we get sage-on-conda modified so that it works nicely with git-trac, 
>> so that a sage-conda container can be used for development? I would be very 
>> interested in a guide to that.
>>
>
> Have you tried the existing instructions that I pointed you to?
>

Well, I looked at the instructions and found:

"Installing all of SageMath from conda (not for development)"

and not a corresponding section "Installing SageMath in/from conda for 
development". That's the part that isn't addressed in the guide pointed to. 
I'd expect sage to be pulled from a sagemath repository to be suitable for 
git-trac workflows, not from conda.

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[sage-devel] Re: System upgrades breaking sage frequently

[Nils Bruin]

On Monday, 25 July 2022 at 12:57:06 UTC-7 Matthias Koeppe wrote:

> On Monday, July 25, 2022 at 12:44:20 PM UTC-7 Nils Bruin wrote:
>
>> As long as fedora doesn't allow two different version of flint to be 
>> installed at the same time
>>
>
> It does allow two different versions of the shared library package to be 
> installed. 
> Please see https://trac.sagemath.org/ticket/34207
>

OK, that at least helps a bit. But how do you query the package management 
system to report those specific packages as "owner" of the so file, i.e., 
how do you find the packages that need to be pinned? I thought "dnf 
whatprovides" would do that, but it reports the generic libflint package. 
In fact, I've not been able to find the version-specific rpm's at all (if I 
do "dnf search flint" these things do not show up). I was expecting that 
flint would have one of those version-specific packages as a dependency and 
that they simply changed the dependency to bump the version, but it looks 
like that's not how they do it: as far as I can tell,  
/usr/lib64/libflint.so.17 is really owned by flint-2.9.0-1.fc36.x86_64 and 
nothing else.

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[sage-devel] Re: System upgrades breaking sage frequently

[Matthias Koeppe]

On Monday, July 25, 2022 at 12:44:20 PM UTC-7 Nils Bruin wrote:

>  I think build-from-source using these kinds of system resources should 
> actually *not* be a recommended install method:
>

The installation guide 
(https://doc.sagemath.org/html/en/installation/index.html) only recommends 
it to people who want to do SageMath development. Take a look
 

>  
>

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[sage-devel] Re: System upgrades breaking sage frequently

[Matthias Koeppe]

On Monday, July 25, 2022 at 12:44:20 PM UTC-7 Nils Bruin wrote:

> As long as fedora doesn't allow two different version of flint to be 
> installed at the same time
>

It does allow two different versions of the shared library package to be 
installed. 
Please see https://trac.sagemath.org/ticket/34207

 

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[sage-devel] Re: System upgrades breaking sage frequently

[Matthias Koeppe]

On Monday, July 25, 2022 at 12:44:20 PM UTC-7 Nils Bruin wrote:

> Can we get sage-on-conda modified so that it works nicely with git-trac, 
> so that a sage-conda container can be used for development? I would be very 
> interested in a guide to that.
>

Have you tried the existing instructions that I pointed you to?

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[sage-devel] Re: System upgrades breaking sage frequently

[Nils Bruin]

On Thursday, 21 July 2022 at 11:52:42 UTC-7 Nils Bruin wrote:

> On Thursday, 21 July 2022 at 11:31:35 UTC-7 Matthias Koeppe wrote:
>
>>
>> You really just need to stop your distribution from automatically 
>> uninstalling the old shared library packages when you do upgrades. Both the 
>> old version (needed for your from-source installation of Sage) and the new 
>> version (needed as dependencies of upgraded system packages) can coexist in 
>> your system.
>>
>>
> Right .. but that would require telling the system which libraries need to 
> be preserved ... I guess one could collect the dependencies by a liberal 
> ldd application, but then one would need to query the package manager which 
> packages provide the requisite library files and then somehow register 
> those packages *are* dependencies ... I guess that could be done by 
> building a placeholder package (rpm or deb) that declares all the specific 
> dependencies. And to "declare" these, one could install that package. Upon 
> a reconfigure+rebuild, one could uninstall the old placeholder, recompute 
> the new dependencies, and install a new placeholder ...
>

Ouch ... and it looks like this wouldn't even work: if I try

dnf whatprovides /usr/lib64/libflint.so.17

I get:

flint-2.9.0-1.fc36.x86_64

and similarly

dnf whatprovides /usr.lib64/libflint.so.16
flint-2.8.4-2.fc36.x86_64

Hence, if a compiled-from-source sagemath were to declare its dependencies 
to the package manager it would have to do so by depending on a *specific 
version* of flint, and hence "updating" flint should lead to a dependency 
conflict. As long as fedora doesn't allow two different version of flint to 
be installed at the same time (and the fact that flint-2.9 "upgrades" 
flint-2.8 suggests that it won't), we'd need a version lock: just keeping 
an unmanaged so-file hang around in space that's supposed to be managed by 
a package manager would lead to a rather messy system state.

So, based on that, I think build-from-source using these kinds of system 
resources should actually *not* be a recommended install method: 
build-from-source should have its less stable prerequisites satisfied by 
some separate environment -- possibly/likely conda. Resources/libraries 
such as libflint are clearly *only* managed and provided by the OS in a way 
that is appropriate for other OS-managed/packaged software. Turns out 
there's still a niche for sage-the-distribution; possibly replaced by 
sage-in-conda-the-distribution. Can we get sage-on-conda modified so that 
it works nicely with git-trac, so that a sage-conda container can be used 
for development? I would be very interested in a guide to that.
 

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Re: [sage-devel] Re: System upgrades breaking sage frequently

[Dima Pasechnik]

On Sat, 23 Jul 2022, 20:31 Emmanuel Charpentier, <
emanuel.charpent...@gmail.com> wrote:

> FWIW, the very same mishap just happened to me
> 
> on Debian.testing.
>
> What I fail to understand is why Sake was linked to a *specific* version
> of libflint.so, rather than to the *generic* version…
>

Because the specific versions are not compatible with each other, and this
is the very reason to do the version bump dance.

​
> Le mercredi 20 juillet 2022 à 22:42:58 UTC+2, Nils Bruin a écrit :
>
>> I've noticed that after a modest upgrade (just "dnf update"), with some
>> regularity sage breaks. In the most recent edition, "libflint.so" couldn't
>> be found.
>>
>> I guess there is some prerequisite that sage was relying on to be
>> provided by the operating system was changed? Is sage relying on the system
>> python nowadays?
>>
>> The only way I have found to clean this up is by doing a "make
>> distclean", which makes for quite a heavy rebuild process! Is there a more
>> modest approach?
>>
>> It's nice that we're integrating better with OS-supplied prerequisites,
>> but it mixes very badly with building from source on an actual system one
>> works on:
>>
>> I can see the nightmare scenario where you've run a small system update
>> (as one should do to keep up-to-date with vulnerabilities) in the evening
>> (or perhaps your computer did it for you!) and the next morning you arrive
>> in front of the class with a demo where you now discover that sage is
>> broken and requires an hour's worth of build time to get up to snuff again.
>>
>> Is there a better/safer way of having both an up-to-date system and a
>> reliable sage install?
>>
>> [Is the problem perhaps that fedora bumps the default "python" to a newer
>> version for which sage doesn't have its libraries built/accessible? In that
>> case: fedora doesn't delete older versions. I can still run python3.9 or
>> python3.8. So in that case perhaps sage should be a little more careful
>> about what python interpreter it chooses and be a bit more explicit about
>> it (or at least have an option for that)?. I don't know if "python" is the
>> problem]
>>
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> .
>

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[sage-devel] Re: System upgrades breaking sage frequently

[Emmanuel Charpentier]

FWIW, the very same mishap just happened to me 
 on 
Debian.testing.

What I fail to understand is why Sake was linked to a *specific* version of 
libflint.so, rather than to the *generic* version…
​
Le mercredi 20 juillet 2022 à 22:42:58 UTC+2, Nils Bruin a écrit :

> I've noticed that after a modest upgrade (just "dnf update"), with some 
> regularity sage breaks. In the most recent edition, "libflint.so" couldn't 
> be found.
>
> I guess there is some prerequisite that sage was relying on to be provided 
> by the operating system was changed? Is sage relying on the system python 
> nowadays?
>
> The only way I have found to clean this up is by doing a "make distclean", 
> which makes for quite a heavy rebuild process! Is there a more modest 
> approach?
>
> It's nice that we're integrating better with OS-supplied prerequisites, 
> but it mixes very badly with building from source on an actual system one 
> works on:
>
> I can see the nightmare scenario where you've run a small system update 
> (as one should do to keep up-to-date with vulnerabilities) in the evening 
> (or perhaps your computer did it for you!) and the next morning you arrive 
> in front of the class with a demo where you now discover that sage is 
> broken and requires an hour's worth of build time to get up to snuff again.
>
> Is there a better/safer way of having both an up-to-date system and a 
> reliable sage install?
>
> [Is the problem perhaps that fedora bumps the default "python" to a newer 
> version for which sage doesn't have its libraries built/accessible? In that 
> case: fedora doesn't delete older versions. I can still run python3.9 or 
> python3.8. So in that case perhaps sage should be a little more careful 
> about what python interpreter it chooses and be a bit more explicit about 
> it (or at least have an option for that)?. I don't know if "python" is the 
> problem]
>

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Re: [sage-devel] Re: System upgrades breaking sage frequently

[Tomoaki Sato]

I have no idea what really happens in Fedora 36,
but I have had no problems with Sagemath 9.5 (installed from the source) on 
Fedora 35 for several months.
Of course, I have made "dnf update" a lot of times meanwhile.
(I have installed Fedora 35 on VMware workstation.)
Now, I use Fedora remix for WSL. This corresponds to Fedora 36, and I have 
installed Sagemath (9.6)
with "dnf install sagemath."
　
Tomoaki Sato (cxn00...@nifty.ne.jp)
> 
> From:   Matthias Koeppe 
> Reply-To: sage-devel@googlegroups.com
> To:    sage-devel 
> Subject:  [sage-devel] Re: System upgrades breaking sage frequently
>

> On Thursday, July 21, 2022 at 11:52:42 AM UTC-7 Nils Bruin wrote:
> > 
> > Conda looks like it has potential too,
> 
> 
> I'd say that's an understatement
>
> > 
> > It's presently unclear to me [...] whether a "production" conda build could 
> > co-exist with a "development" conda build: is "conda activate" something 
> > local or does it change the global state of conda (e.g., is it possible to 
> > have different conda environments activated in different concurrent 
> > processes)?
> 
> 
> Yes, "conda activate" only sets environment variables.
>
> 
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[sage-devel] Re: System upgrades breaking sage frequently

[Matthias Koeppe]

On Thursday, July 21, 2022 at 11:52:42 AM UTC-7 Nils Bruin wrote:

> Conda looks like it has potential too,
>

I'd say that's an understatement
 

> It's presently unclear to me [...] whether a "production" conda build 
> could co-exist with a "development" conda build: is "conda activate" 
> something local or does it change the global state of conda (e.g., is it 
> possible to have different conda environments activated in different 
> concurrent processes)?
>

Yes, "conda activate" only sets environment variables.
 

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[sage-devel] Re: System upgrades breaking sage frequently

[Matthias Koeppe]

On Thursday, July 21, 2022 at 11:52:42 AM UTC-7 Nils Bruin wrote:

> somehow register those packages *are* dependencies ... I guess that could 
> be done by building a placeholder package (rpm or deb) that declares all 
> the specific dependencies. And to "declare" these, one could install that 
> package. Upon a reconfigure+rebuild, one could uninstall the old 
> placeholder, recompute the new dependencies, and install a new placeholder 
> ...
>

Basically you are entering downstream territory. You maintain a private 
version of the Fedora sagemath package based on your current branch.

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[sage-devel] Re: System upgrades breaking sage frequently

[Matthias Koeppe]

I have opened https://trac.sagemath.org/ticket/34207 with the goal of 
adding documentation on best practices. Help welcome


On Thursday, July 21, 2022 at 11:31:35 AM UTC-7 Matthias Koeppe wrote:

> On Thursday, July 21, 2022 at 11:14:13 AM UTC-7 Nils Bruin wrote:
>
>> On Wednesday, 20 July 2022 at 23:33:09 UTC-7 Antonio Rojas wrote:
>>
>>>
>>> They are not, that's exactly the point of library soversions. The 
>>> soversion, if correctly used, is bumped when a release contains some ABI 
>>> incompatible change that requires a rebuild of consumers. So you can't just 
>>> link to the .so symlink, that would just defeat the point. 
>>>
>>
>> Ah boy, that explains why packaging binary software for linux 
>> distributions is such a complicated task. For binary distributions,  even 
>> FC36 isn't a stable target! Is that a Fedora-specific disease or do other 
>> distribution just push ABI-incompatible changes within a release as well? A 
>> binary distribution really does need to include all libraries.
>>
>
> You really just need to stop your distribution from automatically 
> uninstalling the old shared library packages when you do upgrades. Both the 
> old version (needed for your from-source installation of Sage) and the new 
> version (needed as dependencies of upgraded system packages) can coexist in 
> your system.
>
> development requires to have two installs: one "production" version, 
>> possibly the OS-packaged one [that might as well be binary] and one 
>> built-from-source one that should either be properly sandboxed in an 
>> environment where the prerequisites are ensured to be stable or where one 
>> accepts that arbitrary rebuilds (including a distclean build) may be 
>> necessary.
>>
>
> Definitely. Basically, don't bring a random development build to the 
> classroom.
>
>
>  
>

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[sage-devel] Re: System upgrades breaking sage frequently

[Nils Bruin]

On Thursday, 21 July 2022 at 11:31:35 UTC-7 Matthias Koeppe wrote:

>
> You really just need to stop your distribution from automatically 
> uninstalling the old shared library packages when you do upgrades. Both the 
> old version (needed for your from-source installation of Sage) and the new 
> version (needed as dependencies of upgraded system packages) can coexist in 
> your system.
>
>
Right .. but that would require telling the system which libraries need to 
be preserved ... I guess one could collect the dependencies by a liberal 
ldd application, but then one would need to query the package manager which 
packages provide the requisite library files and then somehow register 
those packages *are* dependencies ... I guess that could be done by 
building a placeholder package (rpm or deb) that declares all the specific 
dependencies. And to "declare" these, one could install that package. Upon 
a reconfigure+rebuild, one could uninstall the old placeholder, recompute 
the new dependencies, and install a new placeholder ...

Conda looks like it has potential too, provided the " pip install 
--no-build-isolation -v -v --editable src" can somehow be overlaid with the 
git-managed repository and have git-trac configuration with it? Then that 
could make for a reasonable development environment. It's presently unclear 
to me (but that's probably just inexperience) whether a "production" conda 
build could co-exist with a "development" conda build: is "conda activate" 
something local or does it change the global state of conda (e.g., is it 
possible to have different conda environments activated in different 
concurrent processes)? 


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[sage-devel] Re: System upgrades breaking sage frequently

[Matthias Koeppe]

On Thursday, July 21, 2022 at 11:14:13 AM UTC-7 Nils Bruin wrote:

> On Wednesday, 20 July 2022 at 23:33:09 UTC-7 Antonio Rojas wrote:
>
>>
>> They are not, that's exactly the point of library soversions. The 
>> soversion, if correctly used, is bumped when a release contains some ABI 
>> incompatible change that requires a rebuild of consumers. So you can't just 
>> link to the .so symlink, that would just defeat the point. 
>>
>
> Ah boy, that explains why packaging binary software for linux 
> distributions is such a complicated task. For binary distributions,  even 
> FC36 isn't a stable target! Is that a Fedora-specific disease or do other 
> distribution just push ABI-incompatible changes within a release as well? A 
> binary distribution really does need to include all libraries.
>

You really just need to stop your distribution from automatically 
uninstalling the old shared library packages when you do upgrades. Both the 
old version (needed for your from-source installation of Sage) and the new 
version (needed as dependencies of upgraded system packages) can coexist in 
your system.

development requires to have two installs: one "production" version, 
> possibly the OS-packaged one [that might as well be binary] and one 
> built-from-source one that should either be properly sandboxed in an 
> environment where the prerequisites are ensured to be stable or where one 
> accepts that arbitrary rebuilds (including a distclean build) may be 
> necessary.
>

Definitely. Basically, don't bring a random development build to the 
classroom.


 

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[sage-devel] Re: System upgrades breaking sage frequently

[Nils Bruin]

On Wednesday, 20 July 2022 at 23:33:09 UTC-7 Antonio Rojas wrote:

>
> They are not, that's exactly the point of library soversions. The 
> soversion, if correctly used, is bumped when a release contains some ABI 
> incompatible change that requires a rebuild of consumers. So you can't just 
> link to the .so symlink, that would just defeat the point. 
>

Ah boy, that explains why packaging binary software for linux distributions 
is such a complicated task. For binary distributions,  even FC36 isn't a 
stable target! Is that a Fedora-specific disease or do other distribution 
just push ABI-incompatible changes within a release as well? A binary 
distribution really does need to include all libraries.

It sounds like Conda is the next "distribution within a distribution" that 
can isolate sagemath from the shifting ABI foundations the OS offers (in 
cases where using a distribution-offered sagemath isn't tracking close 
enough). 

It also sounds like sagemath has now matured to the point where development 
requires to have two installs: one "production" version, possibly the 
OS-packaged one [that might as well be binary] and one built-from-source 
one that should either be properly sandboxed in an environment where the 
prerequisites are ensured to be stable or where one accepts that arbitrary 
rebuilds (including a distclean build) may be necessary. It's unfortunate 
that the plain "pull from git and build from source" days of sage are over 
... and that it's basically unreliable for *any* software out there.


 

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[sage-devel] Re: System upgrades breaking sage frequently

[Antonio Rojas]

El jueves, 21 de julio de 2022 a las 7:32:59 UTC+2, Nils Bruin escribió:

> In that case, shouldn't sagemath be linking to libflint.so instead of 
> libflint.so.16 then? That's the thing that seems to be available between 
> the different versions. Are they not ABI compatible? (or at least in one 
> direction)?
>

They are not, that's exactly the point of library soversions. The 
soversion, if correctly used, is bumped when a release contains some ABI 
incompatible change that requires a rebuild of consumers. So you can't just 
link to the .so symlink, that would just defeat the point. 

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[sage-devel] Re: System upgrades breaking sage frequently

[Nils Bruin]

On Wednesday, 20 July 2022 at 15:09:56 UTC-7 Matthias Koeppe wrote:

> On Wednesday, July 20, 2022 at 3:05:44 PM UTC-7 Nils Bruin wrote:
>
>> I'm pretty sure that if a package has been "dnf install"-ed, then it's 
>> considered desired, and not just there as a prerequisite.
>>
>
> Yes, but you likely did "dnf install libflint-devel". The shared library 
> package, in some version, is merely a dependency.
>
> https://fedora.pkgs.org/36/fedora-updates-aarch64/flint-devel-2.9.0-1.fc36.aarch64.rpm.html
> Current is the package "libflint.so.17". On an update of your system, dnf 
> replaced the previous package,  likely libflint.so.16.
>

In that case, shouldn't sagemath be linking to libflint.so instead of 
libflint.so.16 then? That's the thing that seems to be available between 
the different versions. Are they not ABI compatible? (or at least in one 
direction)?

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[sage-devel] Re: System upgrades breaking sage frequently

[Matthias Koeppe]

On Wednesday, July 20, 2022 at 3:05:44 PM UTC-7 Nils Bruin wrote:

> I'm pretty sure that if a package has been "dnf install"-ed, then it's 
> considered desired, and not just there as a prerequisite.
>

Yes, but you likely did "dnf install libflint-devel". The shared library 
package, in some version, is merely a dependency.
https://fedora.pkgs.org/36/fedora-updates-aarch64/flint-devel-2.9.0-1.fc36.aarch64.rpm.html
Current is the package "libflint.so.17". On an update of your system, dnf 
replaced the previous package,  likely libflint.so.16.

 

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[sage-devel] Re: System upgrades breaking sage frequently

[Nils Bruin]

I'm pretty sure that if a package has been "dnf install"-ed, then it's 
considered desired, and not just there as a prerequisite. So preventing 
libraries from being removed should be as simple as including the requisite 
package in the recommended "dnf install ..." as written at:

https://doc.sagemath.org/html/en/installation/source.html#linux-recommended-installation

(it's probably good if that gets updated with "dnf" instead of "yum" -- 
that change happened around 2015!)

On Wednesday, 20 July 2022 at 13:59:07 UTC-7 Matthias Koeppe wrote:

> On Wednesday, July 20, 2022 at 1:55:52 PM UTC-7 Matthias Koeppe wrote:
>
>> On Wednesday, July 20, 2022 at 1:42:58 PM UTC-7 Nils Bruin wrote:
>>
>>> I've noticed that after a modest upgrade (just "dnf update"), with some 
>>> regularity sage breaks. In the most recent edition, "libflint.so" couldn't 
>>> be found.
>>>
>>> I guess there is some prerequisite that sage was relying on to be 
>>> provided by the operating system was changed?
>>>
>>
>> When system packages no longer need a specific old version of a shared 
>> library, then the system package manager may remove that version.
>> It does not know about user-built programs that link to system libraries. 
>> That's not Sage-specific.
>>
>> Perhaps there is a way to stop dnf or other package managers from 
>> removing unused library packages?
>> That would be worth investigating.
>>
>
>
> https://www.reddit.com/r/Fedora/comments/3pqrv9/dnf_remove_package_keep_dependencies/
>
>

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[sage-devel] Re: System upgrades breaking sage frequently

[Matthias Koeppe]

On Wednesday, July 20, 2022 at 1:55:52 PM UTC-7 Matthias Koeppe wrote:

> On Wednesday, July 20, 2022 at 1:42:58 PM UTC-7 Nils Bruin wrote:
>
>> I've noticed that after a modest upgrade (just "dnf update"), with some 
>> regularity sage breaks. In the most recent edition, "libflint.so" couldn't 
>> be found.
>>
>> I guess there is some prerequisite that sage was relying on to be 
>> provided by the operating system was changed?
>>
>
> When system packages no longer need a specific old version of a shared 
> library, then the system package manager may remove that version.
> It does not know about user-built programs that link to system libraries. 
> That's not Sage-specific.
>
> Perhaps there is a way to stop dnf or other package managers from removing 
> unused library packages?
> That would be worth investigating.
>

https://www.reddit.com/r/Fedora/comments/3pqrv9/dnf_remove_package_keep_dependencies/

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[sage-devel] Re: System upgrades breaking sage frequently

[Matthias Koeppe]

On Wednesday, July 20, 2022 at 1:42:58 PM UTC-7 Nils Bruin wrote:

> I've noticed that after a modest upgrade (just "dnf update"), with some 
> regularity sage breaks. In the most recent edition, "libflint.so" couldn't 
> be found.
>
> I guess there is some prerequisite that sage was relying on to be provided 
> by the operating system was changed?
>

When system packages no longer need a specific old version of a shared 
library, then the system package manager may remove that version.
It does not know about user-built programs that link to system libraries. 
That's not Sage-specific.

Perhaps there is a way to stop dnf or other package managers from removing 
unused library packages?
That would be worth investigating.

Is sage relying on the system python nowadays?
>

Yes.

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