Re: [sage-devel] Re: conda sage

[Isuru Fernando]

Hi William,

Let me know if you have any questions regarding conda installation of sage.
It'd be great to have more visibility towards conda installation to attract
more
users and developers in particular who can help out.

Thanks,
Isuru

On Sun, Mar 10, 2024 at 7:37 PM William Stein  wrote:

> Minor correction -- they say "Given its wide usage, there are no plans to
> deprecate Mambaforge."  So Mambaforge isn't deprecated as I incorrectly
> wrote.  It's just "discouraged".
>
> I'm sorry for the noise, but the *conda* packaging ecosystem makes me
> dizzy...
>
> On Sun, Mar 10, 2024 at 5:31 PM William Stein  wrote:
>
>> I was just carefully reading the page about Mambaforge linked to from
>> Sage, i.e., this page
>>
>> https://github.com/conda-forge/miniforge
>>
>> and it says that Mambaforge is deprecated and no longer recommended, and
>> instead people should install Miniforge, i.e., "(Discouraged as of
>> September 2023)".  We should update the instructions at
>>
>>
>> https://deploy-livedoc--sagemath.netlify.app/html/en/installation/conda#install-from-conda-forge
>>
>> since they recommend the now discouraged Mambaforge.
>>
>> The page https://github.com/conda-forge/miniforge suggests that
>> Mambaforge is somehow "just as good", but when I tried doing clean
>> installs, then installing Sage, I had the best experience (i.e., completely
>> perfect!) with Miniforge, which is what they recommend.  Basically, we
>> should instead recommend:
>>
>> curl -L -O
>> https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname
>> -m).sh
>>
>> sh Miniforge3-$(uname)-$(uname -m).sh -b -u -p /conda
>>
>> -- William
>>
>> On Sun, Mar 10, 2024 at 4:05 PM William Stein  wrote:
>>
>>> Hi,
>>>
>>> So I was using MicroMamba, whereas that page says Sage only
>>> supports Mambaforge, Miniforge, Miniconda or Anaconda.I tried with
>>> Mambaforge (as recommended there) and everything works perfectly, with
>>> sage-10.2 being available, and nicely integrated with the conda ecosystem,
>>> and also it's easy to switch Python versions.  So I'll switch from using
>>> MicroMamba to Mambaforge.  Problem solved.
>>>
>>> William
>>>
>>> On Sun, Mar 10, 2024 at 1:47 PM William Stein  wrote:
>>>


 On Sun, Mar 10, 2024 at 1:39 PM Matthias Koeppe <
 matthiaskoe...@gmail.com> wrote:

> William, do the instructions in our Installation Guide work for you?
>
> https://deploy-livedoc--sagemath.netlify.app/html/en/installation/conda#install-from-conda-forge
>
>

> Note in particular this step: "Change channel priority to strict:
> conda config --set channel_priority strict"
>

 I'm using micromamba, which is supposed to be a drop in replacement for
 conda, but it just gives an error for the above, so maybe it is missing
 critical features needed to install sage:

 ---

 (compute-server-1540) ~/anaconda$ micromamba config --set
 channel_priority strict
 The following arguments were not expected: strict channel_priority --set
 Run with --help for more information.

 ---

 I'll revisit whether I need to switch to another conda...

 That said micromamba has strict by default:
 https://github.com/mamba-org/provision-with-micromamba/issues/33

 (compute-server-1540) ~/anaconda$ micromamba config --set
 channel_priority strict --help
 Configuration of micromamba
 Usage: /usr/local/bin/micromamba config [OPTIONS] [SUBCOMMAND]

 Options:
   -h,--help   Print this help message and exit


 Configuration options:
   --rc-file TEXT ...  Paths to the configuration files to use
   --no-rc Disable the use of configuration files
   --no-envDisable the use of environment variables


 Global options:
   -v,--verboseSet verbosity (higher verbosity with
 multiple -v, e.g. -vvv)
   --log-level ENUM:value in
 {critical->5,debug->1,error->4,info->2,off->6,trace->0,warning->3} OR
 {5,1,4,2,6,0,3}
   Set the log level
   -q,--quiet  Set quiet mode (print less output)
   -y,--yesAutomatically answer yes on prompted
 questions
   --json  Report all output as json
   --offline   Force use cached repodata
   --dry-run   Only display what would have been done
   --download-only Only download and extract packages, do
 not link them into environment.
   --experimental  Enable experimental features


 Prefix options:
   -r,--root-prefix TEXT   Path to the root prefix
   -p,--prefix TEXTPath to the target prefix
   --relocate-prefix TEXT  Path to the relocation prefix
   -n,--name TEXT  Name of the target prefix

Re: [sage-devel] Unable to `load` or `import/cimport` Cython files into Sage while developing

[Isuru Fernando]

With conda, you can use sage on macOS 10.13. We supply our own linker built
from Apple's sources.

Isuru

On Mon, Jan 1, 2024 at 5:08 AM Dima Pasechnik  wrote:

>
>
> On 31 December 2023 23:20:28 WET, Jing Guo  wrote:
> >It’s fine, I’m not building Sage on Mac anyway.
>
> You're doing a complicated enough thing to put you into "building Sage"
> ballpark.
>
> >
> >I used homebrew in the past but it doesn’t support old macOS versions any
> more. Also I find MacPorts to be easier to manage and keep the versions
> consistent.
>
> Oops, sorry, only now I realised how old macOS 10.13 actually is (it's
> well past EOL). I think you are seriously out of luck here,  due to
> outdated Apple's tools for this platform.
>
>
> >
> >Jing
> >2024年1月1日 +0100 00:16 Dima Pasechnik ，写道：
> >>
> >>
> >> On 31 December 2023 23:05:42 WET, Jing Guo  wrote:
> >> > Thank you for all your helps. I asked in that GitHub repo and here is
> the
> >> > issue: https://github.com/3-manifolds/Sage_macOS/issues/62
> >> >
> >> > The reason it does not work is probably caused by my macOS being too
> old
> >> > (10.13.6), so `ld` does not recognize `-platform_version` flag.
> MacPorts
> >> > does not seem to support `ld` as well. I guess I will try to find
> other
> >> > workarounds.
> >>
> >> Building Sage with Homebrew is well-supported.
> >> With MacPorts, no, noone I think managed to build Sage from source
> using a nontrivial number of MacPorts packages.
> >> So it's probably a MacPorts problem too.
> >>
> >>
> >>
> >>
> >>
> >> >
> >> > 在2023年12月28日星期四 UTC+1 08:32:34 写道：
> >> >
> >> > > Dear Jing,
> >> > >
> >> > > Not being able to use Cython from this sage app is indeed
> problematic.
> >> > > However as Dima said this is more a problem of the app rather than a
> >> > > problem with sage itself. You would better open an issue at
> >> > > https://github.com/3-manifolds/Sage_macOS. If you do, please post
> the
> >> > > link of the issue in this thread.
> >> > >
> >> > > Best
> >> > > Vincent
> >> > >
> >> > > On Wed, 27 Dec 2023 at 13:43, Dima Pasechnik 
> wrote:
> >> > > >
> >> > > > On Wed, Dec 27, 2023 at 12:23 PM Jing Guo 
> wrote:
> >> > > > >
> >> > > > > I just did. The following is the new error.
> >> > > > >
> >> > > > > ➜ local-hom-count git:(main) ✗ sage
> >> > > > >
> ┌┐
> >> > > > > │ SageMath version 10.2, Release Date: 2023-12-03 │
> >> > > > > │ Using Python 3.11.1. Type "help()" for help. │
> >> > > > >
> └┘
> >> > > > > sage: load("helper_functions.pyx")
> >> > > > > Compiling ./helper_functions.pyx...
> >> > > > >
> >> > >
> ---
> >> > > > > DistutilsExecError Traceback (most recent call last)
> >> > > > > File
> >> > >
> /private/var/tmp/sage-10.2-current/local/var/lib/sage/venv-python3.11.1/lib/python3.11/site-packages/setuptools/_distutils/unixccompiler.py:266,
> >> > > in UnixCCompiler.link(self, target_desc, objects, output_filename,
> >> > > output_dir, libraries, library_dirs, runtime_library_dirs,
> export_symbols,
> >> > > debug, extra_preargs, extra_postargs, build_temp, target_lang)
> >> > > > > 264 linker = compiler_fixup(linker, ld_args)
> >> > > > > --> 266 self.spawn(linker + ld_args)
> >> > > > > 267 except DistutilsExecError as msg:
> >> > > > >
> >> > > > > File
> >> > >
> /private/var/tmp/sage-10.2-current/local/var/lib/sage/venv-python3.11.1/lib/python3.11/site-packages/setuptools/_distutils/ccompiler.py:1041,
> >> > > in CCompiler.spawn(self, cmd, **kwargs)
> >> > > > > 1040 def spawn(self, cmd, **kwargs):
> >> > > > > -> 1041 spawn(cmd, dry_run=self.dry_run, **kwargs)
> >> > > > >
> >> > > > > File
> >> > >
> /private/var/tmp/sage-10.2-current/local/var/lib/sage/venv-python3.11.1/lib/python3.11/site-packages/setuptools/_distutils/spawn.py:70,
> >> > > in spawn(cmd, search_path, verbose, dry_run, env)
> >> > > > > 69 cmd = cmd[0]
> >> > > > > ---> 70 raise DistutilsExecError(
> >> > > > > 71 "command {!r} failed with exit code {}".format(cmd, exitcode)
> >> > > > > 72 )
> >> > > > >
> >> > > > > DistutilsExecError: command '/usr/bin/gcc' failed with exit
> code 1
> >> > > >
> >> > > > Please check
> >> > > https://doc.sagemath.org/html/en/installation/index.html#macos
> >> > > > and note that you re doing development. I.e.
> >> > > > you are trying to do Sage development in an unsupported
> environment.
> >> > > > The app you are using does not come with all the tools needed to
> >> > > > create Python extensions from Cython (this needs Apple software,
> which
> >> > > > one cannot just bundle for copyright reasons).
> >> > > >
> >> > > > Having said that, your errors probably indicate that you have an
> >> > > > outdated XCode/command line tools installed. But I don't know
> whether
> >> > > > this can be made to work at all, or you really need a different
> >> > > > install of Sage for your 

Re: [sage-devel] Re: What was/is/will be the purpose of maintaining the Sage distribution?

[Isuru Fernando]

On Thu, Apr 27, 2023 at 1:00 PM Michael Orlitzky 
wrote:

> On Thu, 2023-04-27 at 05:49 -0700, William Stein wrote:
> > Hi,
> >
> > To what extent does or could Conda with a little more work solve most
> > of these problems?   There are some notes below from me poking around,
> > and I'm very optimistic.
>
> This isn't the first time the idea has come up. Burcin got pretty far
> with it using Gentoo Prefix in place of Conda:
>
>   https://groups.google.com/g/sage-devel/c/XFJn3jGVBG8
>
> Nix could also work. All three serve roughly the same purpose.
>

True. Guix and spack could also work.

I guess there are several requirements we need

1. Support for all major OS/architecture combinations
2. Easy to build for rare OS/architecture combinations
3. Possible to install as a non-root user
4. Binaries are available for non-root

AFAIK, there's no package manager that has all 4 above and we will have to
pick which
requirements are more important than others.

Isuru


>
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Re: [sage-devel] Re: What was/is/will be the purpose of maintaining the Sage distribution?

[Isuru Fernando]

> it fails with "└─ sage   is uninstallable because there are no viable
options"

We don't have a python 3.11 version of sage in conda yet. I started a PR
manually as the automatic update
failed for some reason.

> What is it doing that first time, and why is it silent?  It's very
unnerving.

macOS 10.15+ does some shady things when users request to run "untrusted"
applications. For eg:

% clang hello.c
% time ./a.out
Hello world!
./a.out  0.00s user 0.00s system 0% cpu 0.380 total
% time ./a.out
Hello world!
./a.out  0.00s user 0.00s system 62% cpu 0.006 total

See https://lapcatsoftware.com/articles/catalina-executables.html for a
possible explanation.
Sage loads hundreds of dynamic libraries not all at the same time, so macOS
sends multiple requests
to Apple servers.

> and took 5.8GB disk instead of the 3GB disk of the Sage mac app).

Yes, conda packages usually come with batteries included which means
packages come with their
optional build time dependencies installed. That's usually not a big deal
for other packages, but
Sage is special in that it has tons of dependencies.

As usual, the biggest hurdle to making things work more seamlessly is
manpower.
Most of the niche packages that sage depends on are maintained by me and
Julian and improvements
to supporting conda in the sage build system are mostly Matthias and Tobias.

Isuru



On Thu, Apr 27, 2023 at 7:49 AM William Stein  wrote:

> Hi,
>
> To what extent does or could Conda with a little more work solve most
> of these problems?   There are some notes below from me poking around,
> and I'm very optimistic.
>
> I looked at
>
> https://doc.sagemath.org/html/en/installation/conda.html
>
> and I would love some further discussion of that and whether with
> enough help it could be viable.
> For example, on my M1 mac I just tried what seems to me to be the most
> obvious first thing to do
> based on the instructions:
>
> (base) wstein@max ~ % mamba create -n sage sage python=3.11
>
> and it fails with "└─ sage   is uninstallable because there are no
> viable options"
> Obviously I'm going to nex try "mamba create -n sage sage", which works,
> but
> that's not what our docs say to do.  Incidentally, it took about a
> minute to download
> and install everything (and took 5.8GB disk instead of the 3GB disk of
> the Sage mac app).
> Then a few minutes of me being confused if I should do
> "mamba activate sage" or "conda activate sage", and finally I typed "sage"
> and
> strangely it just shows nothing at all while it mysteriously takes
> about a minute
> for sage to start the first time (on my M1 max laptop with SSD).  Sage then
> starts and works fine. Subsequent sage startups are very fast (e.g., 1
> second).
> What is it doing that first time, and why is it silent?  It's very
> unnerving.
>
> I also think this section
>
> https://doc.sagemath.org/html/en/installation/conda.html#using-conda-to-provide-all-dependencies-for-the-sage-library-experimental
> called "Using conda to provide all dependencies for the Sage library
> (experimental)" is pretty exciting!
>
> For many years when I gave talks about Sage, I had a slide: "What is
> Sage", with two points:
>
> 1. A distribution of open source math software
> 2. A new library tying everything together
>
> I definitely only started 1 out of necessity because nothing existed
> at the time.  My hope is that
> at this point in time conda is good enough that maybe it could totally
> solve 1, and we can focus on 2?
>
> In any case, I think that migrating from "Sage the distribution" to
> solving a lot of the misc environment issues
> via conda would be very analogous to switching to Github, instead of
> maintaining our own issue tracker.
> I.e., if you want the latest version of sage on Ubuntu 22.04 (say),
> then our recommendation is "use conda",
> and we put effort into making Sage-via-conda extremely good.  If you
> want some random version of sage,
> then you can use system packages.
>
> For CoCalc.com, the key thing we need is a way to have self-contained
> stable installations of sage-9.1, 9.2, 9.3, 9.4, 9.5, 9.6, 9.7, 9.8,
> 10.0, etc. all on the same Ubuntu system, all at once, and have them
> not get screwed up when we do normal system updates. Doing major
> Ubuntu version updates (e.g., 20.04 --> 22.04) doesn't have to be
> supported.
> My impression is that conda potentially solves this problem at least
> as well as sage-the-distribution does right now.
>
>  -- William
>
> PS Thanks again to the people who put so much work into packaging sage
> and its dependencies for conda!
>
> On Thu, Apr 27, 2023 at 5:12 AM kcrisman  wrote:
> >
> >
> > As of today, it is plausible that such situations still exist.
> >
> >
> > I am wondering about such situations existing in less-resourced areas
> globally (which would include less-resourced parts of developed
> countries).  One big advantage of Sage-the-distribution historically was
> the ability to make USB drives that had the complete thing (maybe also a
> 

Re: [sage-devel] Re: MIgration to GitHub: Heads-up on org invitations

[Isuru Fernando]

Just wanted to mention that the invitation can be found at
https://github.com/orgs/sagemath/invitation if you didn't
get an email.

Isuru

On Wed, Feb 1, 2023 at 8:37 PM Matthias Koeppe 
wrote:

> All invitations have now been sent out.
>
> Right now we have 180 members and 590 outstanding invitations.
>
> If you aren't already an org member (check
> https://github.com/orgs/sagemath/people) and haven't received an
> invitation, please check that the email address that you have on file with
> GitHub.com is current. This is also a good opportunity to check that the
> email addresses that you use / have used for git commits are known to
> GitHub as secondary email addresses. Then your commits will be counted in
> the repository contribution statistics.
>
>
> On Wednesday, February 1, 2023 at 6:23:16 PM UTC-8 Kwankyu Lee wrote:
>
>> I received the invitation an hour ago. It worked great!
>
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Re: [sage-devel] Re: building from develop branch fails / openssl / MacOS 10.13.6

[Isuru Fernando]

Or use conda which supports all the way back to MacOS 10.9

Isuru

On Mon, Jan 30, 2023 at 2:49 PM Matthias Koeppe 
wrote:

> I think your best bet to continue using this machine is to install Linux
> on it, replacing this old macOS version unsupported by Apple.
>
> On Monday, January 30, 2023 at 12:34:21 PM UTC-8 la...@math.luc.edu wrote:
>
>> I'm trying to catch up to the current develop branch. (It's been over a
>> year since I did this.)
>>
>> Running Mac OSX 10.13.6 (High Sierra)
>> with XCode 10.0
>>
>> Asking Google, I run across an old comment about XCode being part of the
>> problem, and some version variables not getting parsed correctly.  [so I
>> upgraded from 9 or whatever I had.]
>>
>> I cannot upgrade my OS (machine is too old), and can only barely upgrade
>> my XCode (I e.g., I don't think i can get to XCode 10.3).
>>
>> openssl-3.0.5.log file attached.
>>
>> [openssl-3.0.5] crypto/bn/rsaz-avx512.s:860:2: error: instruction
>> requires: AVX-512 ISA AVX-512 VL ISA
>>
>> [openssl-3.0.5]  vmovdqu64 %ymm4,128(%rdi)
>>
>> [openssl-3.0.5]  ^
>>
>> any advice?
>>
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Re: [sage-devel] gap, gap_packages, binder and conda

[Isuru Fernando]

Have you tried installing the `gap` conda package which has all the gap
packages including nq?

Isuru

On Wed, Aug 17, 2022 at 5:18 PM enriqu...@gmail.com 
wrote:

> Hi everyone,
> I would like to know why there are some gap packages included in the
> standard package gap, some other ones included in gap_packages and other
> ones nowhere. I think someone said sometime ago that some of them could
> interfere with other sage packages but I am not sure which ones.
> These days I have been using binder with an image created with conda-forge
> (thanks to the team of sage-binder-env). It works great (the last docker
> images stopped working some time ago, even cocalc images which worked a
> little bit longer).
> I find binder is a useful tool for teaching and it also gives the
> possibility of verification purposes for people not having access to
> sagemath.
> For this purposes, there is a problem when one uses optional packages;
> very recently, it is possible to build images working with some optional
> packages (bliss or sirocco, thanks to Fernando Isuru and also to Julian
> Rüth). It would be useful to construct such images also for several
> packages at the same time.
> Maybe some packages of gap could be include in the core packages. Is it
> worth to open tickets for these questions?
> Best, Enrique.
>
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>

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Re: [sage-devel] Re: Proposal: downgrade some packages to experimental

[Isuru Fernando]

I haven't seen any reports about symengine.py failing to build. Can you
open an issue?

Isuru

On Sat, Aug 6, 2022 at 1:55 PM John H Palmieri 
wrote:

> Also, the various sage_numerical_backend_* packages fail to build, with
> errors like
>
>
>   Error compiling Cython file:
>   
>   ...
>   from sage.numerical.backends.generic_backend cimport GenericBackend
>   ^
>   
>
>   check_add_col_untyped_args.pyx:1:0:
> 'sage/numerical/backends/generic_backend.pxd' not found
>
>
> Also downgrade? Is there a ticket for this?
>
> On Friday, August 5, 2022 at 11:07:51 PM UTC-7 Matthias Koeppe wrote:
>
>> On Friday, August 5, 2022 at 9:49:21 PM UTC-7 John H Palmieri wrote:
>>
>>> The following packages do not build for me on OS X 12.5 (Monterrey),
>>> Intel chip:
>>>
>>>- polylib (#33758)
>>>- symengine_py (#34141)
>>>- p_group_cohomology (#30787)
>>>- r_jupyter
>>>- rubiks
>>>
>>> I propose that these be downgraded from optional to experimental until
>>> the issues are fixed. What do people think?
>>>
>>>
>> Also on various Linux platforms (
>> https://github.com/sagemath/sage/actions/runs/204587) I see failures
>> for
>> symengine_py,
>> p_group_cohomology,
>> r_jupyter
>>
>> So these 3 definitely need to be changed to "experimental".
>>
>>
>>
>>
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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

[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=1=closed=200=~spkg-configure=~spkg_configure=id=summary=author=reviewer=milestone
>
> Remaining open tickets in that direction:
>
>
> https://trac.sagemath.org/query?order=id=1=!closed=~spkg-configure=~spkg_configure
>
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> .
>

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Re: [sage-devel] Install SageMath in Red Hat Enterprise Linux Server

[Isuru Fernando]

See https://doc.sagemath.org/html/en/installation/conda.html

Isuru

On Thu, Feb 3, 2022 at 11:55 AM SAMANTA  wrote:

> Hi all,
> I want to use SageMath on my Red Hat Enterprise Linux Server (version
> 7.9). The mentioned binaries (in 
> http://ftp.riken.jp/sagemath/linux/64bit/index.html
> ) are for Ubuntu and Debian, but there is no such option for Red Hat.
> Could you suggest which distribution and packages I should install for
> SageMath in my server? Or is there any need for the installation of some
> additional packages?
> The details of my server, along with its gcc version, are written in the
> attached file.
>
> Thanks
>
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> 
> .
>

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Re: [sage-devel] Re: pari-jupyter is back

[Isuru Fernando]

You can do `conda install pari_jupyter -c conda-forge` to install
pari_jupyter and pari in a conda environment.

Isuru

On Fri, Dec 10, 2021 at 10:10 AM Murray Eisenberg 
wrote:

> Under macOS Big Sur (11.6.1), I run jupyter under Anaconda's conda
> environment (conda 4.10.3 and python 3.8.12) . There, I executed "pip
> install pari-jupyter" but got a build failure with error message including:
>   'PARIKernel/kernel.c:618:10: fatal error: pari/pari.h: No such file or
> directory 618 | #include "pari/pari.h"'.
>
> I do have the latest macOS binary PariGP.app installed (version 2.13.3).
>
> How do I make the needed file(s) available for building pari-jupyter?
>
> On Thursday, December 9, 2021 at 11:11:17 AM UTC-5 Samuel Lelievre wrote:
>
>> Thank you!   --Samuel
>
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Re: [sage-devel] Re: pip-21.1.2 compile fails on MacOS

[Isuru Fernando]

I suggest running `conda activate sage-build` and then doing a `make
dist-clean`.

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Re: [sage-devel] Re: pip-21.1.2 compile fails on MacOS

[Isuru Fernando]

It's not good to have two conda environments. I'm not sure how you got them
both involved in the build.

`mamba install pari -n sage-build` will install sage in `sage-build` env.

Isuru

On Thu, Nov 11, 2021 at 5:15 PM Dima Pasechnik  wrote:

> Conda's pari packages are a bit broken (they are per env, but not
> quite), and this test fails:
>
> configure:21400: result: libpari's datadir does not match GP's datadir.
> Not good
> configure:21449: no suitable system package found for SPKG pari
>
> namely, GP's datadir is
> /Users/dima/opt/miniconda3/envs/sage-build/share/pari
> but libpari's datadir is
> /Users/dima/opt/miniconda3/envs/sage/share/pari
>
> and if I try "mamba install pari" I just get
>
> All requested packages already installed.
>
> I suppose I don't understand conda's environments well - how does one tell
> conda to install pari (and libpari) into sage-build?
>
>
>
> On Thu, Nov 11, 2021 at 9:56 PM Isuru Fernando  wrote:
> >
> > > Can one install Sage on macOS 12 using (mini)Conda at all ?
> >
> > Sure. It should work fine. Bug reports are welcome.
> >
> > Isuru
> >
> > On Thu, Nov 11, 2021 at 3:38 PM Dima Pasechnik 
> wrote:
> >>
> >> Hi Harald,
> >>
> >> We don't have Sage ported to macos 12 yet, I am afraid.
> >> We have been fighting macos 11 until April, see
> >> https://trac.sagemath.org/ticket/30651
> >>
> >> I've just opened https://trac.sagemath.org/ticket/32855
> >>
> >> Binaries built on macOS 10 or 11 might run on 12, but building is
> another story.
> >>
> >> Can one install Sage on macOS 12 using (mini)Conda at all ?
> >>
> >> I think building might be easier with Homebrew rather than Conda, too.
> >>
> >> Cheers,
> >> Dima
> >>
> >>
> >> On Thursday, November 11, 2021 at 7:00:06 PM UTC harald@gmail.com
> wrote:
> >>>
> >>> Hi,
> >>>
> >>> I'm trying to build Sagemath from source (within miniconda) on an
> Intel-based Mac Mini running MacOS Monterrey. I get:
> >>>
> >>> [pip-21.1.2] Error building a wheel for pip-21.1.2
> >>> ...
> >>>
> >>> [pip-21.1.2] Error installing package pip-21.1.2
> >>>
> >>> See the log files.
> >>>
> >>> Best
> >>>
> >>> Harald
> >>
> >> --
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> .
> >
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Re: [sage-devel] Re: pip-21.1.2 compile fails on MacOS

[Isuru Fernando]

> Am I right that it's possible to change Sage's Cython files in such an
installation, and  update Sage this way?

No, it's binary only. See https://wiki.sagemath.org/Conda section "Conda
for sage developers" if you want to do that.
(Btw, that hasn't been updated in a while and might not work due to a
recent restructure of sage build system)

Isuru

On Thu, Nov 11, 2021 at 4:04 PM Dima Pasechnik  wrote:

>
>
> On Thu, Nov 11, 2021 at 9:56 PM Isuru Fernando  wrote:
>
>> > Can one install Sage on macOS 12 using (mini)Conda at all ?
>>
>> Sure. It should work fine. Bug reports are welcome.
>>
>> Am I right that it's possible to change Sage's Cython files in such an
> installation, and  update Sage this way?
>
> Isuru
>>
>> On Thu, Nov 11, 2021 at 3:38 PM Dima Pasechnik  wrote:
>>
>>> Hi Harald,
>>>
>>> We don't have Sage ported to macos 12 yet, I am afraid.
>>> We have been fighting macos 11 until April, see
>>> https://trac.sagemath.org/ticket/30651
>>>
>>> I've just opened https://trac.sagemath.org/ticket/32855
>>>
>>> Binaries built on macOS 10 or 11 might run on 12, but building is
>>> another story.
>>>
>>> Can one install Sage on macOS 12 using (mini)Conda at all ?
>>>
>>> I think building might be easier with Homebrew rather than Conda, too.
>>>
>>> Cheers,
>>> Dima
>>>
>>>
>>> On Thursday, November 11, 2021 at 7:00:06 PM UTC harald@gmail.com
>>> wrote:
>>>
>>>> Hi,
>>>>
>>>> I'm trying to build Sagemath from source (within miniconda) on an
>>>> Intel-based Mac Mini running MacOS Monterrey. I get:
>>>>
>>>> [pip-21.1.2] Error building a wheel for pip-21.1.2
>>>> ...
>>>>
>>>> [pip-21.1.2] Error installing package pip-21.1.2
>>>>
>>>> See the log files.
>>>>
>>>> Best
>>>>
>>>> Harald
>>>>
>>> --
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>>> .
>>>
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Re: [sage-devel] Re: pip-21.1.2 compile fails on MacOS

[Isuru Fernando]

For this issue, you need setuptools 58 or higher.
Or remove the line
https://github.com/sagemath/sage/blob/f5efe4883f348e01ca3069ed82bf517a4de337f6/build/bin/sage-build-env#L174

Isuru

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Re: [sage-devel] Re: pip-21.1.2 compile fails on MacOS

[Isuru Fernando]

> Can one install Sage on macOS 12 using (mini)Conda at all ?

Sure. It should work fine. Bug reports are welcome.

Isuru

On Thu, Nov 11, 2021 at 3:38 PM Dima Pasechnik  wrote:

> Hi Harald,
>
> We don't have Sage ported to macos 12 yet, I am afraid.
> We have been fighting macos 11 until April, see
> https://trac.sagemath.org/ticket/30651
>
> I've just opened https://trac.sagemath.org/ticket/32855
>
> Binaries built on macOS 10 or 11 might run on 12, but building is another
> story.
>
> Can one install Sage on macOS 12 using (mini)Conda at all ?
>
> I think building might be easier with Homebrew rather than Conda, too.
>
> Cheers,
> Dima
>
>
> On Thursday, November 11, 2021 at 7:00:06 PM UTC harald@gmail.com
> wrote:
>
>> Hi,
>>
>> I'm trying to build Sagemath from source (within miniconda) on an
>> Intel-based Mac Mini running MacOS Monterrey. I get:
>>
>> [pip-21.1.2] Error building a wheel for pip-21.1.2
>> ...
>>
>> [pip-21.1.2] Error installing package pip-21.1.2
>>
>> See the log files.
>>
>> Best
>>
>> Harald
>>
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> 
> .
>

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Re: [sage-devel] Remove nose package?

[Isuru Fernando]

> It looks to be required to run tests for networkx, cvxopt and symengine.
Will tests for those packages just need to be run after installing nose
manually?

At least for symengine, we can change to pytest. I suppose other packages
can too.

Isuru

On Wed, Sep 29, 2021 at 4:49 PM David Roe  wrote:

> I don't have a strong opinion on whether to drop nose or not, but I was
> curious how it was used in Sage.  It looks to be required to run tests for
> networkx, cvxopt and symengine.  Will tests for those packages just need to
> be run after installing nose manually?
> David
>
> On Wed, Sep 29, 2021 at 5:35 PM Isuru Fernando  wrote:
>
>> Building the nose package requires 'use_2to3' in setuptools, but the
>> latest setuptools version
>> has dropped support for 'use_2to3'. We can either run 2to3 manually or
>> drop the nose
>> package. Since nose hasn't had an update since 2016 and is unmaintained,
>> I think it's time
>> to drop it.
>>
>> Isuru
>>
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>>
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[sage-devel] Remove nose package?

[Isuru Fernando]

Building the nose package requires 'use_2to3' in setuptools, but the latest
setuptools version
has dropped support for 'use_2to3'. We can either run 2to3 manually or drop
the nose
package. Since nose hasn't had an update since 2016 and is unmaintained, I
think it's time
to drop it.

Isuru

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Re: [sage-devel] alternative approach to distributing sage -- jupyterlab_app

[Isuru Fernando]

> Maybe the conda or JupyterLab community has tools for this, but Marc
Culler's experience with [1] is that getting the Apple Developer
subscription solves at most 10% of the problem.  If one is building an
application with Xcode, then signing is trivial, but for apps built with
other tools it's a tedious trial-and-error process as Apple's documentation
on what is allowed in a code-signed bundle is very poor.  You sign the
code, upload to Apple, have it rejected, study the error message, and
repeat.

We already have tools in conda to create a dmg. I just haven't tried it.
For eg:
https://repo.anaconda.com/miniconda/Miniconda3-py39_4.10.3-MacOSX-x86_64.pkg
is built using open source tools. We can do the same for sage and build an
image.

Isuru


On Fri, Sep 24, 2021 at 9:42 AM Dima Pasechnik  wrote:

>
>
> On Fri, Sep 24, 2021 at 2:18 PM Nathan Dunfield 
> wrote:
>
>> > Signing is a bit tricky to set up.

 Is that mainly due to paying the Apple Developer subscription fee?

>>>
>>> Yes, and the fact that I don't have a macOS machine with a GUI to try
>>> things out.
>>> I only have access to a macOS machine through SSH.
>>>
>>
>> Maybe the conda or JupyterLab community has tools for this, but Marc
>> Culler's experience with [1] is that getting the Apple Developer
>> subscription solves at most 10% of the problem.  If one is building an
>> application with Xcode, then signing is trivial, but for apps built with
>> other tools it's a tedious trial-and-error process as Apple's documentation
>> on what is allowed in a code-signed bundle is very poor.  You sign the
>> code, upload to Apple, have it rejected, study the error message, and
>> repeat.
>>
>> Best,
>>
>> Nathan
>>
>> [1] https://github.com/3-manifolds/sage_macOS
>>
>
> https://github.com/3-manifolds/Sage_macOS/blob/main/SETUP
>
> looks pretty informative as far as notarization is concerned.
>
>>
>>
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>> 
>> .
>>
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> .
>

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Re: [sage-devel] alternative approach to distributing sage -- jupyterlab_app

[Isuru Fernando]

On Wed, Sep 22, 2021 at 2:49 PM William Stein  wrote:

> Thanks -- that was certainly an *extremely easy command line
> experience* regarding installing Sage on my Macbook M1!   It does seem
> to fully work as well.
>
> On finish it says: "If you'd prefer that conda's base environment not
> be activated on startup,  set the auto_activate_base parameter to
> false:   conda config --set auto_activate_base false"
>
> which I have to do because with it auto activated, every time I open
> any terminal I have to wait to a count of maybe 7 while a bunch of
> stuff happens before I get the shell prompt.   So I'm going to disable
> this by default, but of course just typing "conda activate" works to
> get the sage env again.
>

Sure, that works. I'm not sure which command is taking that long, but we
should fix that if possible.


> Anyway, what you've just done is vastly better than anything anybody
> else has done regarding making it possible to run Sage natively on an
> M1 macbook during the last 10 months.   You should make a little page
> with these instructions, and there should be a link to your page from
> (e.g.,)
>
> https://mirror.csclub.uwaterloo.ca/sage/osx/index.html
>
> which currently has zero support for M1 macbooks after all this time.
>
> > Signing is a bit tricky to set up.
>
> Is that mainly due to paying the Apple Developer subscription fee?
>

Yes, and the fact that I don't have a macOS machine with a GUI to try
things out.
I only have access to a macOS machine through SSH.


> William
>
>
>
> On Wed, Sep 22, 2021 at 11:50 AM Isuru Fernando  wrote:
> >
> > This should be easy to set up.
> >
> > I have a small POC that works for x86_64-apple-darwin (intel macs),
> arm64-apple-darwin (Apple silicon), x86_64-linux-gnu, aarch64-linux-gnu.
> > Signing is a bit tricky to set up.
> >
> > curl -L -O
> https://github.com/isuruf/sagemath-forge/releases/latest/download/sagemath-forge-$(uname)-$(uname
> -m).sh
> > bash sagemath-forge-$(uname)-$(uname -m).sh
> >
> > --
> > You received this message because you are subscribed to the Google
> Groups "sage-devel" group.
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> an email to sage-devel+unsubscr...@googlegroups.com.
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> .
>
>
>
> --
> William (http://wstein.org)
>
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> .
>

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Re: [sage-devel] alternative approach to distributing sage -- jupyterlab_app

[Isuru Fernando]

This should be easy to set up.

I have a small POC that works for x86_64-apple-darwin (intel macs),
arm64-apple-darwin (Apple silicon), x86_64-linux-gnu, aarch64-linux-gnu.
Signing is a bit tricky to set up.

curl -L -O
https://github.com/isuruf/sagemath-forge/releases/latest/download/sagemath-forge-$(uname)-$(uname
-m).sh
bash sagemath-forge-$(uname)-$(uname -m).sh

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Re: [sage-devel] Refactoring/modularization work on the Symbolic Ring

[Isuru Fernando]

Here's the correct benchmark script,
https://gist.github.com/isuruf/857e2236d2443ebd9085273b3e6ada3b

Isuru

On Fri, Aug 27, 2021 at 2:14 PM Isuru Fernando  wrote:

> Hi,
>
> On Fri, Aug 27, 2021 at 1:23 PM William Stein  wrote:
>
>> Hello Isuru -- thanks for popping in to comment!
>>
>> On Fri, Aug 27, 2021 at 10:56 AM Isuru Fernando  wrote:
>> >
>> > Hi,
>> >
>> > A SymEngine maintainer here.
>> >
>> > > Pynac has a lot of I think nontrivial efficient hooks back into Sage
>> > for working with various data types, and doing things like equality
>> > testing, fast evaluation of expression (fast_float, etc.),
>> >
>> > With SymEngine, we do have fast evaluation of expressions with
>> > several backends. One backend is LLVM, where we compile the function
>> > using LLVM and generate a callable C function using that.
>>
>> Wow, that's very cool.  Do you know how it compares to Sage's
>> fast_float and fast_callable "compilers" in terms of speed?   Sage's
>> don't actually depend on having LLVM installed (they aren't compiling
>> to machine code), so I assume might be significantly slower, except
>> that the people (=Robert Bradshaw) who wrote them are very clever, so
>> you never know.  It's probably also interesting to benchmark the
>> compile time itself.
>>
>
> I've attached a small script that I put together just now. Note how we can
> pass sage expressions in symbolic ring to symengine functions.
>
> Timings are below. First one is sage and the second is symengine.
>
> one element
> 625 loops, best of 3: 68 μs per loop
> 625 loops, best of 3: 12.9 μs per loop
>
> create an output numpy array of 1000 elements
> 5 loops, best of 3: 175 ms per loop
> 625 loops, best of 3: 18.1 μs per loop
>
> compile time
> 625 loops, best of 3: 478 μs per loop
> 125 loops, best of 3: 2.69 ms per loop
>
> SymEngine LLVM backend has optimization levels (0, 1, 2, 3). 3 is the
> default.
> By setting to optimization level 0, compile time is half with a
> performance penalty
> of around 10%.
>
> Isuru
>

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Re: [sage-devel] Refactoring/modularization work on the Symbolic Ring

[Isuru Fernando]

Hi,

On Fri, Aug 27, 2021 at 1:23 PM William Stein  wrote:

> Hello Isuru -- thanks for popping in to comment!
>
> On Fri, Aug 27, 2021 at 10:56 AM Isuru Fernando  wrote:
> >
> > Hi,
> >
> > A SymEngine maintainer here.
> >
> > > Pynac has a lot of I think nontrivial efficient hooks back into Sage
> > for working with various data types, and doing things like equality
> > testing, fast evaluation of expression (fast_float, etc.),
> >
> > With SymEngine, we do have fast evaluation of expressions with
> > several backends. One backend is LLVM, where we compile the function
> > using LLVM and generate a callable C function using that.
>
> Wow, that's very cool.  Do you know how it compares to Sage's
> fast_float and fast_callable "compilers" in terms of speed?   Sage's
> don't actually depend on having LLVM installed (they aren't compiling
> to machine code), so I assume might be significantly slower, except
> that the people (=Robert Bradshaw) who wrote them are very clever, so
> you never know.  It's probably also interesting to benchmark the
> compile time itself.
>

I've attached a small script that I put together just now. Note how we can
pass sage expressions in symbolic ring to symengine functions.

Timings are below. First one is sage and the second is symengine.

one element
625 loops, best of 3: 68 μs per loop
625 loops, best of 3: 12.9 μs per loop

create an output numpy array of 1000 elements
5 loops, best of 3: 175 ms per loop
625 loops, best of 3: 18.1 μs per loop

compile time
625 loops, best of 3: 478 μs per loop
125 loops, best of 3: 2.69 ms per loop

SymEngine LLVM backend has optimization levels (0, 1, 2, 3). 3 is the
default.
By setting to optimization level 0, compile time is half with a performance
penalty
of around 10%.

Isuru

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wilk = prod((x-i) for i in [1 .. 20]);
fc_wilk = fast_callable(wilk, vars=[x])
import numpy as np
N = 1000
arr = np.random.rand(N)
def run():
arr2 = np.empty_like(arr)
for i in range(N):
arr2[i] = fc_wilk(arr[i])
return arr2

import symengine
fc_wilk_se = symengine.Lambdify([x], [wilk_se], backend="llvm")
def run_se():
return fc_wilk_se(arr).reshape(N)

assert np.allclose(run(), run_se())

print('one element')
timeit('fc_wilk(0.0)')
timeit('fc_wilk_se(0.0)')

print('create an output numpy array of 1000 elements')
timeit('run()')
timeit('run_se()')

print('compile time')
timeit('fc_wilk = fast_callable(wilk, vars=[x])')
timeit('fc_wilk_se = symengine.Lambdify([x], [wilk_se], backend="llvm")')

Re: [sage-devel] Refactoring/modularization work on the Symbolic Ring

[Isuru Fernando]

Hi,

A SymEngine maintainer here.

> Pynac has a lot of I think nontrivial efficient hooks back into Sage
for working with various data types, and doing things like equality
testing, fast evaluation of expression (fast_float, etc.),

With SymEngine, we do have fast evaluation of expressions with
several backends. One backend is LLVM, where we compile the function
using LLVM and generate a callable C function using that.

As part of my GSoC project 5 years ago, I added a lot of functionality
that was missing in SymEngine like MPFR types, MPC types, etc.
We also have sage interoperability where we can use an arbitrary
pynac/sympy function object and pass it around in C++ and evaluate when
necessary.

I think the biggest obstacle would be the quirks of different CASs
instead of the functionality needed.
Some design decisions would impact a lot of downstreams.
For eg: SymEngine doesn't expand 2*a - (b + a) automatically
unless specifically asked to, while SymPy does.

If there's specific functionality you are looking for, please let us know
and
we'll probably be able to find someone to do it through GSoC.

Isuru Fernando

On Fri, Aug 27, 2021 at 12:45 PM William Stein  wrote:

> On Fri, Aug 27, 2021 at 2:21 AM Dima Pasechnik  wrote:
> > How are these integrals above computed by Sage? Via Maxima, or in some
> > other way?
>
> When I implemented this, they were all computed in Maxima by default,
> unless otherwise requested.  Thus symbolic integration may be
> orthogonal to the pynac vs symengine discussion.  You can browse  some
> of the beautiful decades(!) old Maxima lisp code for integration
> starting here:
> https://github.com/andrejv/maxima/blob/master/src/defint.lisp
> I'm cc'ing RJF in case he has some perspective to add.
>
> Pynac has a lot of I think nontrivial efficient hooks back into Sage
> for working with various data types, and doing things like equality
> testing, fast evaluation of expression (fast_float, etc.), so it'll be
> quite a lot of work to switch away from.   I created pynac as a fork
> of ginac only because there was a very talented student trying for a
> year to do something similar more from scratch in Cython, and I got
> impatient.   It's too bad pynac is unmaintained now; I think the basic
> idea wasn't so bad, and the performance was pretty good.
>
> -- William
>
> > > and sympy.integrate(*map(sympify, (dgamma(x, a, b), (x, 0,
> 1.simplify()._sage_() never returns. Res ipsa loquitur…
> > >
> > > BTW : many Sympy integrations result in Sympy’s Piecewise expressions
> (correctly transcripted as Sage’s cases) involving logical expressions
> using Sympy’s symbolic logical functions/operators And, Or and Not, which
> have currently no equivalent in Sage (but see Trac#31911…)
> > >
> > > --
> > > You received this message because you are subscribed to the Google
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> an email to sage-devel+unsubscr...@googlegroups.com.
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> .
> >
> > --
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> .
>
>
>
> --
> William (http://wstein.org)
>
> --
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> .
>

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Re: [sage-devel] 9.4.rc2, dochtml failed if configured with CC=clang and CXX=clang++ (gcc was used sometimes?)

[Isuru Fernando]

Ah, you are using the system python that was built with gcc, but you want
to build sage with clang/clang++.

In python, setting CC will override the compiler used for building
extension modules, but
it will not override the linker used for building an extension module.

What happens here is a file is compiled with `-fopenmp` with clang (meaning
it needs to be linked with libomp from LLVM),
but linked with `-fopenmp` with gcc (meaning it links to libgomp from GNU).

To fix this, you'll have to set env variable LDSHARED="clang -pthread
-shared"

Isuru Fernando

On Tue, Aug 17, 2021 at 1:52 PM Kazuyoshi Furutaka <
furutaka.kazuyo...@gmail.com> wrote:

>
>
> 2021年8月17日(火) 17:05 Isuru Fernando :
>
>> Did you rebuild python? You might have to do "make distclean".
>>
>> Isuru
>>
>>
> I believe I didn't.
>
> excerpt from the config.log...
>
>>
>>4360 ##  ##
>>4361 ## Checking whether SageMath should install SPKG python3... ##
>>4362 ##  ##
>>4363 configure:33651: checking whether any of bzip2 xz libffi is
>> installed as or will be installed as SPKG
>>4364 configure:33660: result: no
>>4365 configure:33664: checking for python3 >= 3.7.0, < 3.10.0 with
>> modules sqlite3, ctypes, math, hashlib, crypt, socket, zlib, distutils.core
>>4366 configure:34331: result:
>>4367 configure:34355: checking ... whether /usr/bin/python3 is good
>>4368 CC=clang CXX=clang++ -std=gnu++11 conftest_venv/bin/python3
>> conftest.py --verbose build --build-base=conftest.dir
>>4369 running build
>>4370 running build_ext
>>4371 building 'config_check_distutils' extension
>>4372 creating conftest.dir
>>4373 creating conftest.dir/temp.linux-x86_64-3.9
>>4374 clang -Wno-unused-result -Wsign-compare
>> -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g
>> -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOU
>>4374 RCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64
>> -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection
>> -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O
>>4374 2 -fexceptions -g -grecord-gcc-switches -pipe -Wall
>> -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS
>> -fstack-protector-strong -m64 -mtune=generic -fasyn
>>4374 chronous-unwind-tables -fstack-clash-protection -fcf-protection
>> -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe
>> -Wall -Werror=format-security -Wp,-D_
>>4374 FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS
>> -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables
>> -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC
>>4374  -fwrapv -Dlinux -I/usr/include -fPIC
>> -I/home/furutaka/work/sage/sage-9.4.rc2-git-clang2/conftest_venv/include
>> -I/usr/include/python3.9 -c conftest.c -o conftest.dir/temp.linux-
>>4374 x86_64-3.9/conftest.o
>>4375 creating conftest.dir/lib.linux-x86_64-3.9
>>4376 gcc -pthread -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -g
>> -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -g -Dlinux -I/usr/include
>> conftest.dir/temp.linux-x86_64-3.9/conftest.o -
>>4376 L/usr/lib64 -o conftest.dir/lib.linux-x86_64-3.9/
>> config_check_distutils.cpython-39-x86_64-linux-gnu.so
>>4377 CC=clang CXX=clang++ -std=gnu++11 conftest_venv/bin/python3
>> conftest.py --verbose build --build-base=conftest.dir
>>4378 running build
>>4379 running build_ext
>>4380 building 'config_check_distutils_cxx' extension
>>4381 creating conftest.dir
>>4382 creating conftest.dir/temp.linux-x86_64-3.9
>>4383 clang -Wno-unused-result -Wsign-compare
>> -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g
>> -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOU
>>4383 RCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64
>> -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection
>> -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O
>>4383 2 -fexceptions -g -grecord-gcc-switches -pipe -Wall
>> -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS
>> -fstack-protector-strong -m64 -mtune=generic -fasyn
>>4383 chronous-unwind-tables -fstack-clash-protection -fcf-protection
>> -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe
>> -Wall -Werror=format-security -Wp,-D_
>>4383 FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX

Re: [sage-devel] 9.4.rc2, dochtml failed if configured with CC=clang and CXX=clang++ (gcc was used sometimes?)

[Isuru Fernando]

Did you rebuild python? You might have to do "make distclean".

Isuru

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Re: [sage-devel] linbox does not build with clang (sage 9.4.bet4)

[Isuru Fernando]

You can replace `-fabi-version=6` with `-D__GXX_ABI_VERSION=1006`.

Isuru

On Fri, Jul 9, 2021 at 4:51 AM Vincent Delecroix <20100.delecr...@gmail.com>
wrote:

> Dear all,
>
> I tried to build sage 9.4.beta4 using clang 12.0.0. It failed for
> linbox with
>
> /usr/bin/bash ../../libtool  --tag=CXX   --mode=compile clang++
> -std=gnu++11 -DHAVE_CONFIG_H -I. -I../..  -I../.. -fopenmp
> -DFFLAS_COMPILED -DFFPACK_COMPILED -fabi-version=6 -fabi-version=6
> -O2   -Wall -g -DNDEBUG -U_LB_DEBUG -DDISABLE_COMMENTATOR  -O2 -g
> -march=native  -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx
> -mavx2 -mfma -c -o error.lo error.C
> libtool: compile:  clang++ -std=gnu++11 -DHAVE_CONFIG_H -I. -I../..
> -I../.. -fopenmp -DFFLAS_COMPILED -DFFPACK_COMPILED -fabi-version=6
> -fabi-version=6 -O2 -Wall -g -DNDEBUG -U_LB_DEBUG -DDISABLE_COMMENTATOR
> -O2 -g -march=native -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx
> -mavx2 -mfma -c error.C  -fPIC -DPIC -o .libs/error.o
> clang-12: error: unknown argument: '-fabi-version=6'
> clang-12: error: unknown argument: '-fabi-version=6'
>
> Does someone know a way around?
>
> Best
> Vincent
>
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Re: [sage-devel] conda pari refused by spkg-configure.m4

[Isuru Fernando]

Thanks. I've updated pari to 2.13 and rebuilt all downstreams. Please try
updating your pari version in conda.

Isuru

On Mon, Jun 28, 2021 at 5:31 PM Dima Pasechnik  wrote:

> there is a check for pari version; your pari has version 133892, but
> Sage wants 2.13.1 (i.e. 134401)
>
> git blame build/pkgs/pari/spkg-configure.m4
>
> says that it's your change:
>
> 558b5e820c1 (Vincent Delecroix 2021-04-21 20:12:59 +0200   3)
> m4_pushdef([SAGE_PARI_MINVER],["134401"])
>
> On Mon, Jun 28, 2021 at 11:01 PM Vincent Delecroix
> <20100.delecr...@gmail.com> wrote:
> >
> > Dear all,
> >
> > I am trying to build sage 9.4.beta3 in a conda environment. I noticed
> > something fishy with the pari detection. My environment includes
> > a recent enough pari with the necessary optional packages as can be
> > seen with
> >
> > $ which gp
> > /home/vincent/miniconda3/envs/sage-build/bin/gp
> > $ gp --version
> >
> >   GP/PARI CALCULATOR Version 2.11.4 (released)
> > amd64 running linux (x86-64/GMP-6.2.1 kernel) 64-bit version
> > compiled: Jun  9 2021, gcc version 9.3.0 (crosstool-NG
> > 1.24.0.133_b0863d8_dirty)
> >
> > threading engine: single
> > (readline v8.1 disabled, extended
> > help enabled)
> >
> > $ gp -q
> > ? ellinit("11a1")
> > %1 = [0, -1, 1, -10, -20, -4, -20, -79, -21, 496, 20008, -161051,
> > -122023936/161051, Vecsmall([1]), [Vecsmall([128, -1])], [0, 0, 0, 0, 0,
> > 0, 0, 0]]
> > ? En effet, le 8-9 ça sera le dernier exposé.~^C  ***   user interrupt
> > after 2 ms
> > ? galoisgetpol(8)
> > %2 = 5
> > ? galoisgetname(12,1)
> > %3 = "C3 : C4"
> > ? ellmodulareqn(11)
> > %4 = [x^12 + (-y + 744)*x^11 + 196680*x^10 + (187*y + 21354080)*x^9 +
> > (506*y + 830467440)*x^8 + (-11440*y + 16875327744)*x^7 + (-57442*y +
> > 208564958976)*x^6 + (184184*y + 1678582287360)*x^5 + (1675784*y +
> > 9031525113600)*x^4 + (1867712*y + 32349979904000)*x^3 + (-8252640*y +
> > 7424681088)*x^2 + (-19849600*y + 9899773440)*x + (y^2 -
> > 872*y + 5841107200), 1]
> > ? polgalois(x^8-2)
> > %5 = [16, -1, 8, "2D_8(8)=[D(4)]2"]
> >
> > However, the configure scripts refuses it because it claims
> > that "matpermanent" is not available in the library
> >
> > configure:19515: checking for library containing matpermanent
> > configure:19546:
> > /home/vincent/miniconda3/envs/sage-build/bin/x86_64-conda-linux-gnu-c++
> > -std=gnu++11 -o conftest -fvisibility-inlines-hidden -std=c++17
> > -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC
> > -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem
> > /home/vincent/miniconda3/envs/sage-build/include
> > -I/home/vincent/miniconda3/envs/sage-build/include -DNDEBUG
> > -D_FORTIFY_SOURCE=2 -O2 -isystem
> > /home/vincent/miniconda3/envs/sage-build/include -Dlinux
> > -I/home/vincent/miniconda3/envs/sage-build/include -march=nocona
> > -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og
> > -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe
> > -isystem /home/vincent/miniconda3/envs/sage-build/include
> >
> -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/ecl_1622575242000/work=/usr/local/src/conda/ecl-21.2.1
> >
> -fdebug-prefix-map=/home/vincent/miniconda3/envs/sage-build=/usr/local/src/conda-prefix
> > -I/home/vincent/miniconda3/envs/sage-build/include -Wl,-O2
> > -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now
> > -Wl,--disable-new-dtags -Wl,--gc-sections
> > -Wl,-rpath,/home/vincent/miniconda3/envs/sage-build/lib
> > -Wl,-rpath-link,/home/vincent/miniconda3/envs/sage-build/lib
> > -L/home/vincent/miniconda3/envs/sage-build/lib conftest.cpp
> > -L/home/vincent/miniconda3/envs/sage-build/lib -lcurl -lcliquer -lcddgmp
> > -lbz2 -larb -lflint -lmpfr -lgmp -lm  -lntl >&5
> >
> /home/vincent/miniconda3/envs/sage-build/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld:
> > /tmp/ccN4zFHb.o: in function `main':
> > /opt/sage/conftest.cpp:79: undefined reference to `matpermanent'
> >
> > But matpermanent is available in gp
> >
> > $ gp -q
> > ? matpermanent([1,2;3,4])
> > %1 = 10
> >
> > And nm confirms it is there in the library.
> >
> > $ nm -gD /home/vincent/miniconda3/envs/sage-build/lib/libpari.so | grep
> > matpermanent
> > 004ae880 T matpermanent
> >
> >
> > Is that a bug somewhere in the script? Is it normal that the above
> > compilation command does not include a -lpari?
> >
> > Vincent
> >
> > --
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> Groups "sage-devel" group.
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> an email to sage-devel+unsubscr...@googlegroups.com.
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Re: [sage-devel] conda pari refused by spkg-configure.m4

[Isuru Fernando]

That's normal. It first checks without any libs and then with -lpari. See
configure lines below.

Isuru


for ac_lib in '' pari; do
 if test -z "$ac_lib"; then
   ac_res="none required"
 else
   ac_res=-l$ac_lib
   LIBS="-l$ac_lib  $ac_func_search_save_LIBS"
 fi
 if ac_fn_cxx_try_link "$LINENO"; then :
 ac_cv_search_matpermanent=$ac_res
fi

On Mon, Jun 28, 2021 at 5:01 PM Vincent Delecroix <20100.delecr...@gmail.com>
wrote:

> Dear all,
>
> I am trying to build sage 9.4.beta3 in a conda environment. I noticed
> something fishy with the pari detection. My environment includes
> a recent enough pari with the necessary optional packages as can be
> seen with
>
> $ which gp
> /home/vincent/miniconda3/envs/sage-build/bin/gp
> $ gp --version
>
>   GP/PARI CALCULATOR Version 2.11.4 (released)
> amd64 running linux (x86-64/GMP-6.2.1 kernel) 64-bit version
> compiled: Jun  9 2021, gcc version 9.3.0 (crosstool-NG
> 1.24.0.133_b0863d8_dirty)
>
> threading engine: single
> (readline v8.1 disabled, extended
> help enabled)
>
> $ gp -q
> ? ellinit("11a1")
> %1 = [0, -1, 1, -10, -20, -4, -20, -79, -21, 496, 20008, -161051,
> -122023936/161051, Vecsmall([1]), [Vecsmall([128, -1])], [0, 0, 0, 0, 0,
> 0, 0, 0]]
> ? En effet, le 8-9 ça sera le dernier exposé.~^C  ***   user interrupt
> after 2 ms
> ? galoisgetpol(8)
> %2 = 5
> ? galoisgetname(12,1)
> %3 = "C3 : C4"
> ? ellmodulareqn(11)
> %4 = [x^12 + (-y + 744)*x^11 + 196680*x^10 + (187*y + 21354080)*x^9 +
> (506*y + 830467440)*x^8 + (-11440*y + 16875327744)*x^7 + (-57442*y +
> 208564958976)*x^6 + (184184*y + 1678582287360)*x^5 + (1675784*y +
> 9031525113600)*x^4 + (1867712*y + 32349979904000)*x^3 + (-8252640*y +
> 7424681088)*x^2 + (-19849600*y + 9899773440)*x + (y^2 -
> 872*y + 5841107200), 1]
> ? polgalois(x^8-2)
> %5 = [16, -1, 8, "2D_8(8)=[D(4)]2"]
>
> However, the configure scripts refuses it because it claims
> that "matpermanent" is not available in the library
>
> configure:19515: checking for library containing matpermanent
> configure:19546:
> /home/vincent/miniconda3/envs/sage-build/bin/x86_64-conda-linux-gnu-c++
> -std=gnu++11 -o conftest -fvisibility-inlines-hidden -std=c++17
> -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC
> -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem
> /home/vincent/miniconda3/envs/sage-build/include
> -I/home/vincent/miniconda3/envs/sage-build/include -DNDEBUG
> -D_FORTIFY_SOURCE=2 -O2 -isystem
> /home/vincent/miniconda3/envs/sage-build/include -Dlinux
> -I/home/vincent/miniconda3/envs/sage-build/include -march=nocona
> -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og
> -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe
> -isystem /home/vincent/miniconda3/envs/sage-build/include
> -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/ecl_1622575242000/work=/usr/local/src/conda/ecl-21.2.1
>
> -fdebug-prefix-map=/home/vincent/miniconda3/envs/sage-build=/usr/local/src/conda-prefix
>
> -I/home/vincent/miniconda3/envs/sage-build/include -Wl,-O2
> -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now
> -Wl,--disable-new-dtags -Wl,--gc-sections
> -Wl,-rpath,/home/vincent/miniconda3/envs/sage-build/lib
> -Wl,-rpath-link,/home/vincent/miniconda3/envs/sage-build/lib
> -L/home/vincent/miniconda3/envs/sage-build/lib conftest.cpp
> -L/home/vincent/miniconda3/envs/sage-build/lib -lcurl -lcliquer -lcddgmp
> -lbz2 -larb -lflint -lmpfr -lgmp -lm  -lntl >&5
> /home/vincent/miniconda3/envs/sage-build/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld:
>
> /tmp/ccN4zFHb.o: in function `main':
> /opt/sage/conftest.cpp:79: undefined reference to `matpermanent'
>
> But matpermanent is available in gp
>
> $ gp -q
> ? matpermanent([1,2;3,4])
> %1 = 10
>
> And nm confirms it is there in the library.
>
> $ nm -gD /home/vincent/miniconda3/envs/sage-build/lib/libpari.so | grep
> matpermanent
> 004ae880 T matpermanent
>
>
> Is that a bug somewhere in the script? Is it normal that the above
> compilation command does not include a -lpari?
>
> Vincent
>
> --
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> .
>

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Re: [sage-devel] conda python3 and system python3

[Isuru Fernando]

Looks like the check for misconfigured python is a little bit too extreme.
If sysconfig's CFLAGS includes any path in the environment's CFLAGS,
then it shouldn't be considered misconfigured.

Isuru

On Mon, Jun 28, 2021 at 4:35 PM Vincent Delecroix <20100.delecr...@gmail.com>
wrote:

> Hello,
>
> I am trying to build sage in a conda environment. I did install a lot
> of things in it (including Python 3.9). However, the configure
> scripts does choose a strange solution
>
> configure:34331: result: no, this is a misconfigured Python whose
> sysconfig compiler/linker flags contain -I or -L options, which may
> cause wrong versions of libraries to leak into the build
> of Python packages - see https://trac.sagemath.org/ticket/31132; to use
> it anyway, use ./configure
> --with-python=/home/vincent/miniconda3/envs/sage-build/bin/python3
> configure:33784: checking ... whether /usr/bin/python3 is good
>
> Instead of using the conda Python3 it succeeds in using the system
> one. Which would better be avoided here.
>
> Vincent
>
> --
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>

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[sage-devel] Re: sage 9.3 now available on Apple silicon through conda

[Isuru Fernando]

rything went
> > perfectly,
> >
> > (2) Sage starts up fine and all the random "old favorite" commands I
> > tried worked fine.
> >
> > (3) It's fast for the first thing I tried!  Here's a little benchmark:
> >
> > sage: a = random_matrix(GF(7),1)
> > sage: %time b=a*a
> > CPU times: user 1min 2s, sys: 3.99 s, total: 1min 6s
> > Wall time: 10.9 s
> >
> > vs my random remote intel server:
> >
> > sage: a = random_matrix(GF(7),1)
> > sage: %time b=a*a
> > :
> > CPU times: user 18.8 s, sys: 543 ms, total: 19.3 s
> > Wall time: 22 s
> >
> > But then strangely the next thing I tried it was WAY slower than my
> > remote Intel server:
> >
> > # M1
> > sage: %time ModularSymbols(2*997, sign=1).fcp(3)
> > Wall time: 12.5 s
> >
> > # Intel server
> > sage: %time ModularSymbols(2*997, sign=1).fcp(3)
> > Wall time: 753 ms
> >
> > Wow, the M1 gets killed by an order of magnitude..
> > Both benchmarks involve linear algebra -- though different libraries
> > -- so I wonder if cross compilation messes that up.
> >
> > Other things like 2d plots pop up just fine.
> >
> > In any case, excellent work and many, many thanks!
> >
> > I'll run the full test suite and report back.
> >
> >
> > On Sun, Jun 20, 2021 at 6:30 PM Isuru Fernando  wrote:
> > >
> > > Is there anyone with a M1 Mac who can test this out? It'd be great to
> see how much of sage works.
> > >
> > > Isuru
> >
> >
> >
> > --
> >
> > Best Regards,
> > William Stein
> >
> > CEO, SageMath, Inc.
> > https://cocalc.com
>
>
>
> --
>
> Best Regards,
> William Stein
>
> CEO, SageMath, Inc.
> https://cocalc.com
>

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[sage-devel] Re: sage 9.3 now available on Apple silicon through conda

[Isuru Fernando]

Is there anyone with a M1 Mac who can test this out? It'd be great to see
how much of sage works.

Isuru

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Re: [sage-devel] python3-3.9.2 failed to build while running 'sage -i pynormaliz' (ModuleNotFoundError: No module named 'binascii')

[Isuru Fernando]

conda doesn't have pynormaliz yet. You can install normaliz through conda
and pynormaliz through pip

conda create -n sage sage=9.3 python=3.9
conda activate sage
conda install normaliz
export NORMALIZ_LOCAL_DIR=$CONDA_PREFIX
pip install pynormaliz


Isuru


On Sun, Jun 20, 2021 at 12:05 PM Dima Pasechnik  wrote:

> Conda's package is called normaliz, as far as I know it includes python
> interface
>
> On Sun, 20 Jun 2021, 17:06 Max Alekseyev,  wrote:
>
>> I've tried to use Conda distribution, but it says
>> "FeatureNotPresentError: PyNormaliz is not available."
>> So, I'm stuck -- I cannot install Normaliz within the binary distribution
>> of Sage 9.3, and I cannot compile Sage 9.3 with Normaliz from the sources,
>> getting all kinds of errors here and there. It's very frustrating ;(
>> I was able to install Normaliz from the binary distribution of Sage 9.2
>> without an issue.
>> Max
>>
>>
>>
>> On Saturday, June 19, 2021 at 8:29:28 AM UTC-4 dim...@gmail.com wrote:
>>
>>> On Sat, Jun 19, 2021 at 12:41 PM Max Alekseyev 
>>> wrote:
>>> >
>>> > A source distribution has many more points to break (I'll send my
>>> issues in a new thread), and it takes ages to compile.
>>> > For now, it's still unresolved why 'configure' in the binary
>>> distribution fails to detect python3 in the system.
>>>
>>> A binary distribution normally speaking is not something that has or
>>> needs configure.
>>>
>>> By the way, conda distribution might be something you'd prefer, this
>>> is a configurable binary distribution
>>> as you might know.
>>> https://wiki.sagemath.org/Conda
>>> They have normaliz, as far as I know.
>>>
>>> >
>>> > Regards,
>>> > Max
>>> >
>>> > On Friday, June 18, 2021 at 7:18:00 PM UTC-4 dim...@gmail.com wrote:
>>> >>
>>> >> On Fri, Jun 18, 2021 at 11:02 PM Max Alekseyev 
>>> wrote:
>>> >> >
>>> >> > I'll try the source distribution, but I'd like to mention that
>>> building optional packages from a binary distribution worked well in
>>> earlier Sage versions (e.g., 9.1 and 9.2)
>>> >>
>>> >> please bear with us. We aim at
>>> >>
>>> >> pip install sagemath -u
>>> >>
>>> >> to be the normal, Pythonic way to deal with Sage...
>>> >>
>>> >>
>>> >> > Regards,
>>> >> > Max
>>> >> >
>>> >> >
>>> >> > On Friday, June 18, 2021 at 5:50:20 PM UTC-4 dim...@gmail.com
>>> wrote:
>>> >> >>
>>> >> >> On Fri, Jun 18, 2021 at 10:37 PM Max Alekseyev 
>>> wrote:
>>> >> >> >
>>> >> >> > I installed Sage from sage-9.3-Ubuntu_20.04-x86_64.tar.bz2
>>> >> >>
>>> >> >> this is a binary distribution. It doesn't really allow for
>>> building
>>> >> >> optional packages.
>>> >> >> Please get the source distribution instead.
>>> >> >>
>>> >> >>
>>> >> >> >
>>> >> >> > I've just run
>>> >> >> >
>>> >> >> > make python3-clean
>>> >> >> > ./bootstrap
>>> >> >> > ./configure
>>> >> >> >
>>> >> >> > but it still complaints that python3 is not installed in the
>>> system.
>>> >> >> > Why?
>>> >> >> >
>>> >> >> > Regards,
>>> >> >> > Max
>>> >> >> >
>>> >> >> >
>>> >> >> > On Friday, June 18, 2021 at 5:32:56 PM UTC-4 dim...@gmail.com
>>> wrote:
>>> >> >> >>
>>> >> >> >> On Fri, Jun 18, 2021 at 10:20 PM Max Alekseyev <
>>> max...@gmail.com> wrote:
>>> >> >> >> >
>>> >> >> >> > Please find config.log attached. The system has Python 3.8.5
>>> installed.
>>> >> >> >>
>>> >> >> >> ## Checking whether SageMath should install SPKG python3... ##
>>> >> >> >> ##  ##
>>> >> >> >> configure:32260: python3 has already been installed by SageMath
>>> >> >> >>
>>> >> >> >> here is why it does not use system python3 - because you
>>> already had
>>> >> >> >> python3 built by Sage from source.
>>> >> >> >>
>>> >> >> >> (and the same for the host of other packages.)
>>> >> >> >>
>>> >> >> >> You can uninstall packages by doing
>>> >> >> >>
>>> >> >> >> make -clean
>>> >> >> >>
>>> >> >> >> e.g.
>>> >> >> >>
>>> >> >> >> make python3-clean
>>> >> >> >>
>>> >> >> >> if you don't want to build from scratch.
>>> >> >> >>
>>> >> >> >>
>>> >> >> >>
>>> >> >> >>
>>> >> >> >>
>>> >> >> >>
>>> >> >> >>
>>> >> >> >> > Max
>>> >> >> >> >
>>> >> >> >> > On Friday, June 18, 2021 at 4:49:16 PM UTC-4 dim...@gmail.com
>>> wrote:
>>> >> >> >> >>
>>> >> >> >> >> please post top-level config.log
>>> >> >> >> >>
>>> >> >> >> >> Do you have python3 excecutable, version 3.7 or newer?
>>> >> >> >> >>
>>> >> >> >> >>
>>> >> >> >> >> On Fri, Jun 18, 2021 at 9:46 PM Max Alekseyev <
>>> max...@gmail.com> wrote:
>>> >> >> >> >> >
>>> >> >> >> >> > I'd be happy to, but Sage somehow decides that it needs to
>>> build its own Python from scratch.
>>> >> >> >> >> > I simply sun 'sage -i pynormaliz' and get a broken sage as
>>> a result.
>>> >> >> >> >> > What's wrong?
>>> >> >> >> >> >
>>> >> >> >> >> > Regards,
>>> >> >> >> >> > Max
>>> >> >> >> >> >
>>> >> >> >> >> > On Friday, June 18, 2021 at 4:42:00 PM UTC-4
>>> dim...@gmail.com wrote:
>>> >> >> >> >> >>
>>> >> >> >> >> >> don't build Python, use one from the system.
>>> >> >> 

[sage-devel] sage 9.3 now available on Apple silicon through conda

[Isuru Fernando]

To get a native conda on Apple silicon, run the following

curl -L -O
https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-$(uname)-$(uname
-m).sh
bash Mambaforge-$(uname)-$(uname -m).sh

Start a new session and then you can create a new environment with sage,

mamba create -n sage sage python=3.9

This is largely untested as all the dependencies were cross compiled from
macos-x86_64 to macos-arm64
except for NTL and pari which had to be compiled natively.

Let me know how it goes. You can run the tests by doing,

mamba install conda-build -n base
conda build -t ~/mambaforge/pkgs/

Isuru

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Re: [sage-devel] lcalc upstream

[Isuru Fernando]

https://gitlab.com/sagemath/lcalc

Isuru

On Tue, May 4, 2021 at 6:26 PM François Bissey  wrote:

> Hi all,
>
> Do we have a fork and repo for lcalc to add our changes?
> Some lcalc headers are currently preventing sage to compile with gcc-11
> and rather than just adding some more patch to lcalc I was wondering
> if we had made headways in using a forked repo for it since its upstream
> development is pretty much abandoned.
>
> Cheers,
> François
>
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> .
>

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Re: [sage-devel] [ARM] Problem on M1 Mac through a Docker Ubunt image

[Isuru Fernando]

Hi,

You can use conda packages on aarch64 to provide all the dependencies for a
sage development build. (Or sage itself if you are not developing on that
machine)

Isuru

On Mon, Feb 15, 2021 at 1:34 PM William Stein  wrote:

>
>
> On Mon, Feb 15, 2021 at 9:24 AM Gonçalo Almeida 
> wrote:
>
>> I've tried everything and since there ins't a proper version for M1 Macs
>> natively (at least public yet), I got a Docker image for an Ubuntu terminal
>> and tried to install Sage there, but it failed to build.
>>
>
> I tried exactly this approach about a month ago with my M1 Mac and it does
> work and is by far the easiest/most efficient way to get Sage running on
> M1.   One critical surprise was that I had to be careful to increase the
> amount of RAM that the Docker hypervisor has **significantly above the
> default** (at least 4GB of RAM, maybe more).  Make sure to do that.
> Otherwise, various aspects of the build will fail in confusing ways due to
> running out of memory.
>
> For what it's worth, here's a paste of some notes I kept for myself:
>
> Goal -- SageMath on M1
> 
>
> I think the best hope for efficient Sage on M1 Mac is via Docker but without
> QEMU.  I.e., use ARM64 Linux via Docker, which runs via a hypervisor, so
> will be very fast/performant.
>
> https://news.ycombinator.com/item?id=25447153
>
> docker run -td --name=sage-arm  -v ~/sage-arm:/sage-arm ubuntu
>
> According to
>
> root@79ac2b56798b:/# uname -a
> Linux 79ac2b56798b 4.19.104-linuxkit #1 SMP PREEMPT Sat Feb 15 00:49:47 UTC 
> 2020 aarch64 aarch64 aarch64 GNU/Linux
>
> this is ARM linux, so should be fast.
>
> apt update
> apt install tmux dpkg-dev git python m4
> git clone https://github.com/sagemath/sage.git
> cd sage
> make configure
> ./configure --enable-build-as-root
>
> apt-get install  texlive-latex-extra texlive-xetex latexmk pandoc dvipng 
> default-jdk ffmpeg libavdevice-dev libflint-arb-dev libboost-dev libboost-dev 
> libbrial-dev libbrial-groebner-dev libbz2-dev bzip2 coinor-cbc 
> coinor-libcbc-dev libcdd-dev libcdd-tools cliquer libcliquer-dev cmake curl 
> libcurl4-openssl-dev libec-dev eclib-tools gmp-ecm libecm-dev fflas-ffpack 
> libflint-dev flintqs libfreetype6-dev libgc-dev libgf2x-dev gfan gfortran 
> libgiac-dev xcas libgivaro-dev glpk-utils libglpk-dev libgmp-dev pari-gp2c 
> libgsl-dev libigraph-dev libiml-dev libisl-dev lcalc liblfunction-dev 
> libatomic-ops-dev libbraiding-dev libffi-dev libgd-dev libhomfly-dev 
> libnauty-dev libxml2-dev liblrcalc-dev libm4rie-dev libmpc-dev libmpfi-dev 
> libmpfr-dev nauty libncurses5-dev ninja-build libntl-dev libopenblas-dev 
> openssl libssl-dev palp pandoc pari-gp2c libpari-dev pari-doc pari-elldata 
> pari-galdata pari-galpol pari-seadata libpcre3-dev libxml-libxslt-perl 
> libxml-writer-perl libxml2-dev libperl-dev libfile-slurp-perl libjson-perl 
> libsvg-perl libterm-readkey-perl libterm-readline-gnu-perl libmongodb-perl 
> libterm-readline-gnu-perl pkg-config libplanarity-dev planarity libppl-dev 
> ppl-dev python3 libpython3-dev python3-distutils r-base-dev r-cran-lattice 
> libreadline-dev librw-dev libsqlite3-dev sqlite3 libsuitesparse-dev 
> libsymmetrica2-dev sympow tachyon tox xz-utils liblzma-dev libzmq3-dev 
> libz-dev libzn-poly-dev
>
> ./config.status --recheck && ./config.status
> export MAKE="make -j8"
> make
>
> First try -- I think it failed building sagelib due to not enough RAM, so
> trying again with 8 cpu and 4GB RAM.  It can be very resource intensive.
> This worked for me.
>
>
>  -- William
>
> --
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> 
> .
>

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Re: [sage-devel] Re: incremental migration to github? [prompted by FUNDING issues!!!]

[Isuru Fernando]

It should be sagemath.zulipchat.com right? (Instead of .org)

Isuru

On Thu, Jan 7, 2021 at 2:47 PM David Roe  wrote:

>
>
> On Thu, Jan 7, 2021 at 3:30 PM Harald Schilly  wrote:
>
>> On Thu, Jan 7, 2021 at 9:23 PM Dima Pasechnik  wrote:
>> > Harald - can you take care of this?
>> >
>>
>> Uhm, what's happening? Could someone please summarize this for me?
>>
>
> zulip.sagemath.org used to point to a google virtual machine.  We'd like
> it to redirect to sagemath.zulipchat.org so that people looking for the
> Zulip server are sent to the right place.
> David
>
>
>>
>> --
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>> .
>>
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> 
> .
>

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Re: [sage-devel] Apple M1 Chip

[Isuru Fernando]

At conda-forge, we are using a gfortran fork (
https://github.com/iains/gcc-darwin-arm64) and it works great so far.
scipy, numpy test suites pass.

Isuru

On Tue, Nov 24, 2020 at 12:49 PM François Bissey 
wrote:

> That would be a new fortran compiler. I did builds in the past with
> the intel fortran compiler and the PG compiler but not NAG.
> You’ll be in totally uncharted territory.
>
> Fraçois
>
> > On 25/11/2020, at 5:36 AM, Dima Pasechnik  wrote:
> >
> > Anyhow, there is
> > https://www.nag.com/news/first-fortran-compiler-apple-silicon-macs
> > (and we have insiders in NAG, perhaps we can get these for free...)
> >
> >>
> >> On Tuesday, November 24, 2020 at 10:47:42 AM UTC-5 kcrisman wrote:
> >>>
> >>> Hi sage-devel,
> >>>
> >>> The only references I could find to this so far are
> >>> https://ask.sagemath.org/question/54220/apple-silicon-m1-chip/
> >>> and
> >>> https://groups.google.com/g/sage-devel/c/5yY3VmkT4kE/m/P21QdaMUBgAJ
> >>> where I asked more generally about ARM.
> >>>
> >>> I am likely to be assigned such a laptop in the near future, but it
> would be nice not to be a total guinea pig (since I rely on having Sage for
> a number of different purposes in my teaching).  Though I am willing to be
> a partial guinea pig if I get the computer early enough in our semester
> break!
> >>>
> >>> Anyway, in the intervening weeks since those posts, has anyone
> happened to hear more about this (either for Sage or for dependencies like
> BLAS/Numpy/MPIR)?  This will be the default for a lot of people pretty soon.
> >>>
> >>> Thanks,
> >>> kcrisman
> >>
> >> --
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> .
> >
>
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Re: [sage-devel] Re: Apple M1 Chip

[Isuru Fernando]

See https://conda-forge.org/blog/posts/2020-10-29-macos-arm64/
I added sage to the build of macos-arm64 packages and the progress can be
seen at
https://raw.githubusercontent.com/regro/cf-graph-countyfair/master/status/armosxaddition.svg?sanitize=true

Isuru

On Tue, Nov 24, 2020 at 9:51 AM Zachary Scherr  wrote:

> You may want to take a look at with
> https://github.com/Homebrew/brew/issues/7857.  I think the biggest thing
> at the moment is that gfortran won't be available for the M1 for some time.
>
> On Tuesday, November 24, 2020 at 10:47:42 AM UTC-5 kcrisman wrote:
>
>> Hi sage-devel,
>>
>> The only references I could find to this so far are
>> https://ask.sagemath.org/question/54220/apple-silicon-m1-chip/
>> and
>> https://groups.google.com/g/sage-devel/c/5yY3VmkT4kE/m/P21QdaMUBgAJ
>> where I asked more generally about ARM.
>>
>> I am likely to be assigned such a laptop in the near future, but it would
>> be nice not to be a total guinea pig (since I rely on having Sage for a
>> number of different purposes in my teaching).  Though I am willing to be a
>> partial guinea pig if I get the computer early enough in our semester break!
>>
>> Anyway, in the intervening weeks since those posts, has anyone happened
>> to hear more about this (either for Sage or for dependencies like
>> BLAS/Numpy/MPIR)?  This will be the default for a lot of people pretty soon.
>>
>> Thanks,
>> kcrisman
>>
> --
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>

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Re: [sage-devel] Ubuntu 20.10 build of 9.3beta1 failing on fplll

[Isuru Fernando]

Sage should probably add --without-qd to
https://github.com/sagemath/sage/blob/9.3.beta1/build/pkgs/fplll/spkg-install.in#L30

Isuru

On Thu, Nov 12, 2020 at 3:43 PM Dima Pasechnik  wrote:

> On Thu, Nov 12, 2020 at 9:40 PM Kiran Kedlaya  wrote:
> >
> > I'm trying to build Sage 9.3beta1 on my Ubuntu 20.10 laptop, and the
> build is failing in fplll-5.3.3. The relevant lines seem to be
> >
> > [fplll-5.3.3] /usr/bin/ld: /usr/local/lib/libqd.a(dd_const.o): warning:
> relocation against `_ZN7dd_real4_pi4E' in read-only section `.text.startup'
> > [fplll-5.3.3] /usr/bin/ld: /usr/local/lib/libqd.a(dd_real.o): relocation
> R_X86_64_PC32 against symbol `_ZSt4cerr@@GLIBCXX_3.4' can not be used
> when making a shared object; recompile with -fPIC
> >
> > I can include a more detailed log if needed, but let's see if this is
> already enough to generate some suggestions...
>
> perhaps you have some stale libraries in /usr/local/lib/ ?
> On Ubuntu one should be able to use libqd from the system.
>
> >
> > Kiran
> >
> > --
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Re: [sage-devel] How do I report a bug in Sage 9.2 (app version) for macOS?

[Isuru Fernando]

Is your firewall blocking
https://conda.anaconda.org/conda-forge/noarch/_r-mutex-1.0.1-anacondar_1.tar.bz2
?

Isuru

On Tue, Nov 10, 2020 at 1:09 PM Murray Eisenberg 
wrote:

> I get an unexpected error doing that (with conda/anaconda already
> installed):
>
> # >> ERROR REPORT <<
>
> Traceback (most recent call last):
>   File
> "/opt/anaconda3/lib/python3.8/site-packages/conda/exceptions.py", line
> 1079, in __call__
> return func(*args, **kwargs)
>   File "/opt/anaconda3/lib/python3.8/site-packages/mamba/mamba.py",
> line 900, in exception_converter
> raise e
>   File "/opt/anaconda3/lib/python3.8/site-packages/mamba/mamba.py",
> line 894, in exception_converter
> exit_code = _wrapped_main(*args, **kwargs)
>   File "/opt/anaconda3/lib/python3.8/site-packages/mamba/mamba.py",
> line 853, in _wrapped_main
> result = do_call(args, p)
>   File "/opt/anaconda3/lib/python3.8/site-packages/mamba/mamba.py",
> line 741, in do_call
> exit_code = create(args, parser)
>   File "/opt/anaconda3/lib/python3.8/site-packages/mamba/mamba.py",
> line 620, in create
> return install(args, parser, "create")
>   File "/opt/anaconda3/lib/python3.8/site-packages/mamba/mamba.py",
> line 570, in install
> downloaded =
> transaction.prompt(PackageCacheData.first_writable().pkgs_dir, repos)
> RuntimeError: Download error (6) Couldn't resolve host name [
> https://conda.anaconda.org/conda-forge/noarch/_r-mutex-1.0.1-anacondar_1.tar.bz2
> ]
>
> `$ /opt/anaconda3/bin/mamba create -n sage sage -c conda-forge`
>
>   environment variables:
>  CIO_TEST=
> CLASSPATH=:/Library/Java/Extensions/mysql-connector-java-
>   bin.jar:/Users/murray/Library/texmf/texhyphj
>CONDA_ROOT=/opt/anaconda3
>CURL_CA_BUNDLE=
>
> EVOLVERPATH=/Users/Shared/ApplicationDocs/Math/Evolver/fe:/Users/Shared/Applicatio
>   nDocs/Math/Evolver/doc
>  INFOPATH=/Applications/Macaulay2/Macaulay2-1.13/share/info
>   LD_LIBRARY_PATH=/Applications/Macaulay2/Macaulay2-1.13/lib
>
> MANPATH=/opt/local/share/man::/Applications/Macaulay2/Macaulay2-1.13/share/man
>
> PATH=/Users/murray/.local/bin:/Users/murray/.elan/bin:/opt/anaconda3/bin:/o
>
> pt/local/lib/mysql8/bin:/Library/TeX/texbin:/opt/local/bin:/opt/local/
>
> sbin:/opt/local/apache2/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sb
>
> in:/Library/TeX/texbin:/usr/local/share/dotnet:/opt/local/bin:/opt/X11
>
> /bin:~/.dotnet/tools:/Library/Apple/usr/bin:/Library/Frameworks/Mono.f
>
> ramework/Versions/Current/Commands:/usr/local/sbin:/opt/local/Library/
>
> Frameworks/Python.framework/Versions/3.8/lib:/Library/Frameworks/Pytho
>
> n.framework/Versions/3.7/bin:/Library/Frameworks/Python.framework/Vers
>
> ions/3.6/bin:/Library/Frameworks/Python.framework/Versions/2.7/bin:/Ap
>
> plications/Postgres.app/Contents/Versions/latest/bin:/Users/murray/Lib
>   rary/Application
> Support/GoodSync:/Users/murray/bin:/Users/murray/bin/
>
> shell:/Users/murray/bin/python:/Applications/Julia-1.5.app/Contents/Re
>
> sources/julia/bin:/Applications/Math/Singular/Contents/bin:/Applicatio
>
> ns/Math/Singular/Contents/bin/lib:/Library/PostgreSQL/12/bin:/Applicat
>   ions/Macaulay2/Macaulay2-1.13/bin
>REQUESTS_CA_BUNDLE=
> SSL_CERT_FILE=
>
>  active environment : None
>user config file : /Users/murray/.condarc
>  populated config files :
>   conda version : 4.9.1
> conda-build version : 3.18.11
>  python version : 3.8.3.final.0
>virtual packages : __osx=10.15.7=0
>   __unix=0=0
>   __archspec=1=x86_64
>base environment : /opt/anaconda3  (writable)
>channel URLs : https://conda.anaconda.org/conda-forge/osx-64
>   https://conda.anaconda.org/conda-forge/noarch
>   https://repo.anaconda.com/pkgs/main/osx-64
>   https://repo.anaconda.com/pkgs/main/noarch
>   https://repo.anaconda.com/pkgs/r/osx-64
>   https://repo.anaconda.com/pkgs/r/noarch
>   package cache : /opt/anaconda3/pkgs
>   /Users/murray/.conda/pkgs
>envs directories : /opt/anaconda3/envs
>   /Users/murray/.conda/envs
>platform : osx-64
>  user-agent : conda/4.9.1 requests/2.24.0 CPython/3.8.3
> Darwin/19.6.0 OSX/10.15.7
> UID:GID : 501:20
>  netrc file : None
>offline mode : False
>
>
> An unexpected error has occurred. Conda has prepared the above report.
>
> On 10 Nov2020, at 12:13 PM, Dima Pasechnik  wrote:
>
> I can only lament about the sorry state of macOS binaries support for
> 9.2 on macOS 10.15.7.
> I 

Re: [sage-devel] Re: Apple on ARM

[Isuru Fernando]

conda-forge provides sage=9.2 binaries on linux-aarch64. Installers are at
https://github.com/conda-forge/miniforge#download
To install sage, follow the directions at
https://doc.sagemath.org/html/en/installation/conda.html

We have started initial support for osx-arm64 platform as well, but it's
only a small set of packages for now.

Isuru

On Wed, Jun 24, 2020 at 11:35 AM Samuel Lelievre 
wrote:

> And I missed this Sage Trac ticket:
>
> - Build failure of fplll-5.3.2 on Raspbian Buster (ARM)
>   https://trac.sagemath.org/ticket/29091
>
> where the fplll issue is discussed.
>
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> 
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Re: [sage-devel] Numpy crashing on sage 9.2.RC0

[Isuru Fernando]

Hi Zachary,

You might be hitting https://github.com/xianyi/OpenBLAS/issues/2728 which
is fixed in https://github.com/xianyi/OpenBLAS/pull/2729 but not in 0.3.10.

Isuru

On Mon, Oct 12, 2020 at 10:01 PM Zachary Scherr  wrote:

> Hi Isuru,
>
>I've been trying to fix homebrew's openblas, and I'm running into an
> issue that I was hoping you might know something about.  If I build
> openBLAS with TARGET=HASWELL then I don't have any issues with numpy.
> However, if I build it with TARGET=NEHALEM, which is what they want for
> homebrew, then I still run into the same numpy error.  I see that
> Conda-forge uses TARGET=PRESCOTT, but if I try that I also run into the
> same numpy problem.  Do you have any insight into why this might be the
> case?
>
> Thanks,
> Zach
>
> On Monday, October 12, 2020 at 4:14:28 PM UTC-4 Zachary Scherr wrote:
>
>> Ah, thank you.  I'll post the issue and see if I can get homebrew to
>> resolve it!
>>
>> On Monday, October 12, 2020 at 2:29:10 PM UTC-4 isu...@gmail.com wrote:
>>
>>> You don't need different TARGETs. `DYNAMIC_ARCH=1` means that it will
>>> detect at runtime what the CPU is and will use the kernel matching the CPU
>>> at runtime. `TARGET` gives the oldest CPU that this code will run on so
>>> that the common code is compiled to target this.
>>>
>>> Isuru
>>>
>>> On Mon, Oct 12, 2020 at 1:24 PM Zachary Scherr  wrote:
>>>
>>>> I posted about it on their discussion page, but I'm not sure there will
>>>> be anything they can do.  They build their libraries on several different
>>>> versions of MacOS, but I'm not sure they build with several different
>>>> TARGETS.  I can try to pursue this, but the easy fix for now is that if
>>>> people want to install openblas via homebrew they should install from
>>>> source.
>>>>
>>>> On Monday, October 12, 2020 at 2:09:28 PM UTC-4 dim...@gmail.com wrote:
>>>>
>>>>> On Mon, Oct 12, 2020 at 6:17 PM Isuru Fernando 
>>>>> wrote:
>>>>> >
>>>>> > I looked at the openblas formula in homebrew and they are not
>>>>> passing the TARGET option. When using DYNAMIC_ARCH=1, a target should be
>>>>> specified.
>>>>>
>>>>> care to open an issue with them on
>>>>> https://github.com/Homebrew/homebrew-core ?
>>>>>
>>>>> >
>>>>> > Isuru
>>>>> >
>>>>> > On Mon, Oct 12, 2020 at 11:34 AM Zachary Scherr 
>>>>> wrote:
>>>>> >>
>>>>> >> In case anyone is curious, I've tracked the problem down to
>>>>> homebrew's openBLAS and so it has nothing to do with sage. If I build 
>>>>> numpy
>>>>> from source through homebrew then I get exactly the same error using my
>>>>> system python3. I'm wondering if maybe this has something to do with the
>>>>> fact that openBLAS is bottled with a different processor type than the one
>>>>> that is on my system. In any case I'll ask over there and see if I can get
>>>>> some help.
>>>>> >>
>>>>> >> On Sunday, October 11, 2020 at 10:17:43 PM UTC-4 Zachary Scherr
>>>>> wrote:
>>>>> >>>
>>>>> >>> Hi Dima,
>>>>> >>>
>>>>> >>> My system-wide numpy is installed via pip. I was just remarking
>>>>> that I didn't build my system-wide numpy from source so it's not a fair
>>>>> comparison. It's possible that the issues aren't sage related but are
>>>>> related to building sage's numpy against some homebrew libraries.
>>>>> >>>
>>>>> >>> On Sunday, October 11, 2020 at 8:11:13 PM UTC-4 dim...@gmail.com
>>>>> wrote:
>>>>> >>>>
>>>>> >>>> On Mon, Oct 12, 2020 at 1:00 AM Zachary Scherr 
>>>>> wrote:
>>>>> >>>> >
>>>>> >>>> > That also crashes with: 86622 segmentation fault ./sage
>>>>> --python
>>>>> >>>> >
>>>>> >>>> > I tested this both with building sage against homebrew python
>>>>> 3.8.6 and against sage's default python 3.8.5 and the same error occurred
>>>>> in both cases. I don't have this problem using my system-wide numpy so 
>>>>> it's
>>>>> possible th

Re: [sage-devel] Numpy crashing on sage 9.2.RC0

[Isuru Fernando]

You don't need different TARGETs. `DYNAMIC_ARCH=1` means that it will
detect at runtime what the CPU is and will use the kernel matching the CPU
at runtime. `TARGET` gives the oldest CPU that this code will run on so
that the common code is compiled to target this.

Isuru

On Mon, Oct 12, 2020 at 1:24 PM Zachary Scherr  wrote:

> I posted about it on their discussion page, but I'm not sure there will be
> anything they can do.  They build their libraries on several different
> versions of MacOS, but I'm not sure they build with several different
> TARGETS.  I can try to pursue this, but the easy fix for now is that if
> people want to install openblas via homebrew they should install from
> source.
>
> On Monday, October 12, 2020 at 2:09:28 PM UTC-4 dim...@gmail.com wrote:
>
>> On Mon, Oct 12, 2020 at 6:17 PM Isuru Fernando  wrote:
>> >
>> > I looked at the openblas formula in homebrew and they are not passing
>> the TARGET option. When using DYNAMIC_ARCH=1, a target should be specified.
>>
>> care to open an issue with them on
>> https://github.com/Homebrew/homebrew-core ?
>>
>> >
>> > Isuru
>> >
>> > On Mon, Oct 12, 2020 at 11:34 AM Zachary Scherr 
>> wrote:
>> >>
>> >> In case anyone is curious, I've tracked the problem down to homebrew's
>> openBLAS and so it has nothing to do with sage. If I build numpy from
>> source through homebrew then I get exactly the same error using my system
>> python3. I'm wondering if maybe this has something to do with the fact that
>> openBLAS is bottled with a different processor type than the one that is on
>> my system. In any case I'll ask over there and see if I can get some help.
>> >>
>> >> On Sunday, October 11, 2020 at 10:17:43 PM UTC-4 Zachary Scherr wrote:
>> >>>
>> >>> Hi Dima,
>> >>>
>> >>> My system-wide numpy is installed via pip. I was just remarking that
>> I didn't build my system-wide numpy from source so it's not a fair
>> comparison. It's possible that the issues aren't sage related but are
>> related to building sage's numpy against some homebrew libraries.
>> >>>
>> >>> On Sunday, October 11, 2020 at 8:11:13 PM UTC-4 dim...@gmail.com
>> wrote:
>> >>>>
>> >>>> On Mon, Oct 12, 2020 at 1:00 AM Zachary Scherr 
>> wrote:
>> >>>> >
>> >>>> > That also crashes with: 86622 segmentation fault ./sage --python
>> >>>> >
>> >>>> > I tested this both with building sage against homebrew python
>> 3.8.6 and against sage's default python 3.8.5 and the same error occurred
>> in both cases. I don't have this problem using my system-wide numpy so it's
>> possible that because sage numpy is built from source that maybe one of my
>> homebrew libraries is causing issues. I found
>> https://github.com/numpy/numpy/issues/11551 which could be relevant and
>> might indicate that it's not a sage problem.
>> >>>>
>> >>>> If you are talking about Homebrew's numpy, it should be more or less
>> >>>> identical with Sage's numpy (assuming you use Homebrew's openblas in
>> >>>> Sage)
>> >>>> cf.
>> https://github.com/Homebrew/homebrew-core/blob/master/Formula/numpy.rb
>> >>>>
>> >>>> >
>> >>>> > I should also add that if I lower the dimension of x to 10
>> then it works without problem.
>> >>>> >
>> >>>> > On Sunday, October 11, 2020 at 3:26:11 PM UTC-4 dim...@gmail.com
>> wrote:
>> >>>> >>
>> >>>> >> On Sun, Oct 11, 2020 at 8:14 PM Zachary Scherr 
>> wrote:
>> >>>> >> >
>> >>>> >> > Hi All,
>> >>>> >> >
>> >>>> >> > I was doing some bug hunting and noticed that scipy's pytests
>> crashed pretty early. I tracked down exactly what was causing the problem
>> and noticed it can be reproduced by the following sequence of commands:
>> >>>> >> >
>> >>>> >> > sage: import numpy as np
>> >>>> >> > sage: x = np.random.randn(100,2)
>> >>>> >> > sage: y = np.random.randn(2,2)
>> >>>> >> > sage: x.dot(y)
>> >>>> >>
>> >>>> >> please test this in "plain" Sage python, i.e. does
>

Re: [sage-devel] Numpy crashing on sage 9.2.RC0

[Isuru Fernando]

I looked at the openblas formula in homebrew and they are not passing the
TARGET option. When using DYNAMIC_ARCH=1, a target should be specified.

Isuru

On Mon, Oct 12, 2020 at 11:34 AM Zachary Scherr  wrote:

> In case anyone is curious, I've tracked the problem down to homebrew's
> openBLAS and so it has nothing to do with sage.  If I build numpy from
> source through homebrew then I get exactly the same error using my system
> python3.  I'm wondering if maybe this has something to do with the fact
> that openBLAS is bottled with a different processor type than the one that
> is on my system.  In any case I'll ask over there and see if I can get some
> help.
>
> On Sunday, October 11, 2020 at 10:17:43 PM UTC-4 Zachary Scherr wrote:
>
>> Hi Dima,
>>
>>My system-wide numpy is installed via pip.  I was just remarking that
>> I didn't build my system-wide numpy from source so it's not a fair
>> comparison.  It's possible that the issues aren't sage related but are
>> related to building sage's numpy against some homebrew libraries.
>>
>> On Sunday, October 11, 2020 at 8:11:13 PM UTC-4 dim...@gmail.com wrote:
>>
>>> On Mon, Oct 12, 2020 at 1:00 AM Zachary Scherr 
>>> wrote:
>>> >
>>> > That also crashes with: 86622 segmentation fault ./sage --python
>>> >
>>> > I tested this both with building sage against homebrew python 3.8.6
>>> and against sage's default python 3.8.5 and the same error occurred in both
>>> cases. I don't have this problem using my system-wide numpy so it's
>>> possible that because sage numpy is built from source that maybe one of my
>>> homebrew libraries is causing issues. I found
>>> https://github.com/numpy/numpy/issues/11551 which could be relevant and
>>> might indicate that it's not a sage problem.
>>>
>>> If you are talking about Homebrew's numpy, it should be more or less
>>> identical with Sage's numpy (assuming you use Homebrew's openblas in
>>> Sage)
>>> cf.
>>> https://github.com/Homebrew/homebrew-core/blob/master/Formula/numpy.rb
>>>
>>> >
>>> > I should also add that if I lower the dimension of x to 10 then it
>>> works without problem.
>>> >
>>> > On Sunday, October 11, 2020 at 3:26:11 PM UTC-4 dim...@gmail.com
>>> wrote:
>>> >>
>>> >> On Sun, Oct 11, 2020 at 8:14 PM Zachary Scherr 
>>> wrote:
>>> >> >
>>> >> > Hi All,
>>> >> >
>>> >> > I was doing some bug hunting and noticed that scipy's pytests
>>> crashed pretty early. I tracked down exactly what was causing the problem
>>> and noticed it can be reproduced by the following sequence of commands:
>>> >> >
>>> >> > sage: import numpy as np
>>> >> > sage: x = np.random.randn(100,2)
>>> >> > sage: y = np.random.randn(2,2)
>>> >> > sage: x.dot(y)
>>> >>
>>> >> please test this in "plain" Sage python, i.e. does
>>> >>
>>> >> ./sage --python
>>> >>
>>> >> >>> import numpy as np
>>> >> >>> x = np.random.randn(100,2)
>>> >> >>> y = np.random.randn(2,2)
>>> >> >>> x.dot(y)
>>> >>
>>> >> reproduce the crash?
>>> >>
>>> >>
>>> >>
>>> >> >
>>> >> > produces:
>>> >> >
>>> >> >
>>> 
>>> >> > 0 signals.cpython-38-darwin.so 0x0001088bc62a print_backtrace
>>> + 58
>>> >> > 1 signals.cpython-38-darwin.so 0x0001088c0277 sigdie + 39
>>> >> > 2 signals.cpython-38-darwin.so 0x0001088c0212 sigdie_for_sig +
>>> 290
>>> >> > 3 libsystem_platform.dylib 0x7fff6c88e5fd _sigtramp + 29
>>> >> >
>>> 
>>> >> > Unhandled SIGBUS: A bus error 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.
>>> >> >
>>> 
>>> >> > /Users/zscherr/sage/src/bin/sage-python: line 2: 78812 Bus error:
>>> 10 sage -python "$@"
>>> >> >
>>> >> > I haven't tested on any other platforms, but for what it's worth I
>>> have Catalina 10.15.7 with Xcode 12.
>>> >> >
>>> >> > Thanks,
>>> >> > Zach
>>> >> >
>>> >> > --
>>> >> > 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+...@googlegroups.com.
>>> >> > To view this discussion on the web visit
>>> https://groups.google.com/d/msgid/sage-devel/28f58136-d3c7-40b7-9a46-36fc347acc2en%40googlegroups.com.
>>>
>>> >
>>> > --
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>>>
>>>
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Re: [sage-devel] gsl build failure on Centos 6

[Isuru Fernando]

This is an issue with the openblas build. You might need
https://github.com/conda-forge/openblas-feedstock/blob/master/recipe/0002-Fix-gfortran-detection-for-ctng-based-cross-compilers.patch
(That patch was not sent upstream because it breaks other gcc builds. Need
to figure out a patch that works for all)

Also, I'm curious to hear more about the illegal instructions. We can fix
that if you report them. I'm a conda-forge maintainer.

We also have Normaliz packaged in conda-forge.

Isuru

On Fri, Jul 24, 2020 at 10:43 AM Dima Pasechnik  wrote:

> Can you use gsl provided by Conda?
>
> If you run can Sage's ./configure with conda active then it will list
> "system" packages to install.
>
>
>
> On Fri, 24 Jul 2020, 16:36 Nathan Dunfield,  wrote:
>
>> I am trying to build Sage 9.1 from source on Scientific Linux 6.10
>> (=Centos 6) using gcc 7.5 provided by Conda, and am having problems getting
>> gsl to build:
>>
>> [gsl-2.5]
>> /data/keeling/a/nmd/miniconda3/envs/sage_base_lite4/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.5.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld:
>> /data/keeling/a/nmd/pkgs/sage-9.1/local/lib/libopenblas.so: undefined
>> reference to `_gfortran_concat_string'
>>
>> Attached are the logs for gsl, openblas, and config.  The config command
>> was:
>>
>> ./configure --with-system-gmp=no --with-system-openblas=no
>> --with-system-gfan=no --with-system-iconv=no --with-system-libffi=no
>> --with-system-sqlite=no
>>
>> Thanks,
>>
>> Nathan
>>
>> P.S. In case you are wondering why I don't just use Sage via Conda, the
>> answer is (a) some nodes on this cluster are old enough the Sage-on-conda
>> binaries occasionally generate exceptions from missing instructions and (b)
>> I need to install certain Sage optional packages, specifically Normaliz.
>>
>>
>> --
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Re: [sage-devel] Re: Porting sagemath to Raspberry Pi OS

[Isuru Fernando]

You can track the progress here,
https://github.com/conda-forge/sagelib-feedstock/pull/100

Gap and rpy2 are now available. Need to build rw 0.7 now. Is there a reason
for not going to rw 0.8 in sage? I couldn't find a trac ticket for it.

Isuru

On Thu, Jul 9, 2020 at 11:14 AM Dima Pasechnik  wrote:

>
>
> On Thu, 9 Jul 2020, 17:07 Isuru Fernando,  wrote:
>
>> Hi,
>>
>> In conda-forge, we have all the dependencies of sage for aarch64 already
>> built except for gap and rpy2.
>> If those two are done, we can build sage the library and you can use
>> conda-forge to install a binary version of sage.
>> Any help is appreciated.
>>
>
> Could you point out concrete issues?
>
>
>> Isuru
>>
>> On Thu, Jul 9, 2020 at 9:09 AM Jaap Spies  wrote:
>>
>>> Done.
>>>
>>> On Thursday, July 9, 2020 at 3:58:20 PM UTC+2, Matthias Koeppe wrote:
>>>>
>>>> On Thursday, July 9, 2020 at 5:31:52 AM UTC-7, Jaap Spies wrote:
>>>>>
>>>>> ... Raspberry Pi ...
>>>>>
>>>>
>>>> https://trac.sagemath.org/ticket/29091, which adds test infrastructure
>>>> for raspbian-buster, still needs review.
>>>>
>>>>
>>>> --
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>>> .
>>>
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>>
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Re: [sage-devel] Re: Porting sagemath to Raspberry Pi OS

[Isuru Fernando]

Hi,

In conda-forge, we have all the dependencies of sage for aarch64 already
built except for gap and rpy2.
If those two are done, we can build sage the library and you can use
conda-forge to install a binary version of sage.
Any help is appreciated.

Isuru

On Thu, Jul 9, 2020 at 9:09 AM Jaap Spies  wrote:

> Done.
>
> On Thursday, July 9, 2020 at 3:58:20 PM UTC+2, Matthias Koeppe wrote:
>>
>> On Thursday, July 9, 2020 at 5:31:52 AM UTC-7, Jaap Spies wrote:
>>>
>>> ... Raspberry Pi ...
>>>
>>
>> https://trac.sagemath.org/ticket/29091, which adds test infrastructure
>> for raspbian-buster, still needs review.
>>
>>
>> --
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> 
> .
>

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Re: [sage-devel] CentOS binary (via binary-pkg)

[Isuru Fernando]

That document seems to be written by a person who only had a cursory look
at conda without realizing that there are options that you could use to
avoid these issues.

As Dima said, if they want you to install from source, they should provide
a compiler and other tools that you can use to compile sage.

I've added some responses below.

Isuru


> Anaconda very often installs software (compilers, scientific libraries
etc.) which already exist on Compute Canada clusters as modules, with a
configuration that is not optimal.

Given that they allow singularity, this is moot. binary-pkg, python wheels
does the same thing.

> It installs binaries which are not optimized for the processor
architecture on our clusters.

Sure. But if you are going to use binary-pkg, you'll get the same issue.
Python wheels have the same issue.

> It makes incorrect assumptions about the location of various system
libraries.

I don't know what this is referring to.

> Anaconda uses the $HOME directory for its installation, where it writes
an enormous number of files.
> A single Anaconda installation can easily absorb almost half of your
quota for the number of files in your home directory.

Same issue with singularity and binary-pkg. You can install conda to some
other place.

> Anaconda is slower than the installation of packages via Python wheels.

Okay. I don't know why this is a huge problem. Most of your time is spent
on calculations anyway. Installation time is a tiny fraction.

> Anaconda modifies the $HOME/.bashrc file, which can easily cause
conflicts.

You are asked about this in the command line and can opt out.

> A conda recipe forces the installation of R. This installation does not
perform nearly as well as the version we provide as a module (which uses
Intel MKL). This same R does not work well, and jobs launched with it may
die and waste both computing resources as well as your time.

You can use R with MKL from conda-forge. You can even use Sage with MKL on
conda-forge. (You can't use MKL with python wheels or binary-pkg)

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Re: [sage-devel] CentOS binary (via binary-pkg)

[Isuru Fernando]

Hi,

You can install conda on your local machine, make a new sage environment
using conda and then pack up that environment using `conda-pack` and then
distribute the sage environment to the cluster. This way, you will only
have sage distributed and no conda-pack. This is similar to what you would
do with binary-pkg.

Btw, do you know what the issue is with using conda?

Isuru

On Mon, Jun 22, 2020 at 2:09 PM Franco Saliola  wrote:

>
> Hi Isuru,
>
> Thank you for the suggestion. I looked into this, and although it looks
> intriguing, there seems to be a site policy of avoiding conda on the
> cluster I am trying to use.
>
> I think I will post the question about binary-pkg to the github issues
> page for that project.
>
> Best,
> Franco
>
> On Sat, Jun 20, 2020 at 2:54 PM Isuru Fernando  wrote:
>
>> Have you looked at installing sage from conda? It's a package manager
>> that can be installed without root privileges and you don't have to compile
>> sage because it's already compiled.
>>
>> https://doc.sagemath.org/html/en/installation/conda.html
>>
>> Isuru
>>
>> On Sat, Jun 20, 2020 at 1:44 PM Franco Saliola  wrote:
>>
>>>
>>> Hello,
>>>
>>> I am trying to create a binary for CentOS 7. I have not been able to
>>> find a guide on how to create binaries, so I've been piecing together the
>>> procedure from various sources and so I have a few questions.
>>>
>>> First of all, my goal is to use sage on a cluster running CentOS 7. I
>>> can't install the dependencies to compile sage, so I thought of creating a
>>> CentOS binary on a virtual machine and transferring the resulting binary to
>>> the cluster. Any ideas or pointers on how to get sage running in this
>>> situation would be most welcome!
>>>
>>> As for creating the binary, here is what I have done so far:
>>>
>>> - I created a VM with a *minimal* CentOS 7 installation and installed
>>> the dependencies listed in the SageMath installation guide
>>> <https://doc.sagemath.org/html/en/installation/source.html#linux-recommended-installation>
>>> .
>>> - I cloned sagemath/binary-pkg <https://github.com/sagemath/binary-pkg>.
>>> - I changed the branch in sage.yaml from *develop* to *master.*
>>> *- *I executed: make bdist-sage-linux
>>>
>>> Eventually, it failed with a "No space left on device" error. Is it
>>> expected that this process would take more than 20GB of disk space? If so,
>>> then how much disk space do I need?
>>>
>>> Best,
>>> Franco
>>>
>>> --
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>>> Groups "sage-devel" group.
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>>> an email to sage-devel+unsubscr...@googlegroups.com.
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>>> https://groups.google.com/d/msgid/sage-devel/7792aae0-c0f8-4bc5-bf90-612f9bf91d89o%40googlegroups.com
>>> <https://groups.google.com/d/msgid/sage-devel/7792aae0-c0f8-4bc5-bf90-612f9bf91d89o%40googlegroups.com?utm_medium=email_source=footer>
>>> .
>>>
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Re: [sage-devel] CentOS binary (via binary-pkg)

[Isuru Fernando]

Have you looked at installing sage from conda? It's a package manager that
can be installed without root privileges and you don't have to compile sage
because it's already compiled.

https://doc.sagemath.org/html/en/installation/conda.html

Isuru

On Sat, Jun 20, 2020 at 1:44 PM Franco Saliola  wrote:

>
> Hello,
>
> I am trying to create a binary for CentOS 7. I have not been able to find
> a guide on how to create binaries, so I've been piecing together the
> procedure from various sources and so I have a few questions.
>
> First of all, my goal is to use sage on a cluster running CentOS 7. I
> can't install the dependencies to compile sage, so I thought of creating a
> CentOS binary on a virtual machine and transferring the resulting binary to
> the cluster. Any ideas or pointers on how to get sage running in this
> situation would be most welcome!
>
> As for creating the binary, here is what I have done so far:
>
> - I created a VM with a *minimal* CentOS 7 installation and installed the
> dependencies listed in the SageMath installation guide
> 
> .
> - I cloned sagemath/binary-pkg .
> - I changed the branch in sage.yaml from *develop* to *master.*
> *- *I executed: make bdist-sage-linux
>
> Eventually, it failed with a "No space left on device" error. Is it
> expected that this process would take more than 20GB of disk space? If so,
> then how much disk space do I need?
>
> Best,
> Franco
>
> --
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> 
> .
>

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Re: [sage-devel] Crash Report - please help

[Isuru Fernando]

Hi,

Can you send the output of running,

conda list -n sage

Isuru

On Thu, Jun 18, 2020 at 3:42 PM Nujcharee Haswell 
wrote:

> Download Sage from coda forge today and also from
> http://www.mirrorservice.org/sites/www.sagemath.org/osx/index.html
> Want to SageMath on Jupyter notebook. I am on Mac but I got this crash
> report
>
> ImportError: 
> dlopen(/Users/nhaswell/anaconda3/envs/sage/lib/python3.7/site-packages/sage/matrix/matrix_mod2_dense.cpython-37m-darwin.so,
>  2): Library not loaded: @rpath/libwebp.7.dylib
>   Referenced from: /Users/nhaswell/anaconda3/envs/sage/lib/libgd.3.dylib
>   Reason: image not found
>
>
> Please help
>
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> 
> .
>

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Re: [sage-devel] Re: AttributeError: type object 'sage.misc.lazy_import.LazyImport' has no attribute '__div__'

[Isuru Fernando]

Here's the traceback.

Isuru

$sage -c 1+1
SageMath version 9.1, Release Date: 2020-05-20
Traceback (most recent call last):
  File
"/home/conda/feedstock_root/build_artifacts/sagelib_1592119926566/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/bin/sage-eval",
line 4, in 
from sage.all import *
  File
"/home/conda/feedstock_root/build_artifacts/sagelib_1592119926566/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/lib/python3.6/site-packages/sage/all.py",
line 117, in 
import sage.misc.lazy_import
  File "sage/misc/lazy_import.pyx", line 1, in init sage.misc.lazy_import
(build/cythonized/sage/misc/lazy_import.c:10174)
AttributeError: type object 'sage.misc.lazy_import.LazyImport' has no
attribute '__div__'

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[sage-devel] AttributeError: type object 'sage.misc.lazy_import.LazyImport' has no attribute '__div__'

[Isuru Fernando]

I'm trying to package sage 9.1 for conda and I get this error with latest
Cython 0.29.20

If I downgrade to Cython 0.29.12, the error goes away. Any ideas?

Isuru

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Re: [sage-devel] Linking to libstdc++

[Isuru Fernando]

Yes, it was probably NTL related.
https://github.com/sagemath/sage/commit/bc333c78b0369377657452e340cb6b3f27c5cee0

I think distutils now knows to link with the C++ compiler even though it
compiles C++ sources with a C compiler. OSX build works fine without
`libc++` being linked in explicitly, so that must mean that we are using
clang++ on OSX at the correct place, right?

Isuru

On Sat, Jun 13, 2020 at 11:10 PM François Bissey 
wrote:

> That far back? It was probably something like ntl or singular (or
> something that has since then
> been removed) that didn’t link properly.
> More seriously, it may have been because the linker used was gcc instead
> of g++ even when linking
> C++ code. We know there is/was that issue about C/C++ compiler in
> distutils (I haven’t been keeping
> track, are we still patching python for that in distros?).
>
> > On 14/06/2020, at 4:03 PM, Isuru Fernando  wrote:
> >
> > Hi,
> >
> > Anybody know why sage is linking to libstdc++?
> >
> >
> https://github.com/sagemath/sage/blob/cdb4c0b073efce77b08de4aa24df6583cdb74fa3/src/setup.py#L371-L374
> >
> > In OSX, we don't need libstdc++, because we are using libc++. Git
> history says it was added 13 years ago by William Stein.
> >
> > Isuru
> >
> > --
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> .
>
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[sage-devel] Linking to libstdc++

[Isuru Fernando]

Hi,

Anybody know why sage is linking to libstdc++?

https://github.com/sagemath/sage/blob/cdb4c0b073efce77b08de4aa24df6583cdb74fa3/src/setup.py#L371-L374

In OSX, we don't need libstdc++, because we are using libc++. Git history
says it was added 13 years ago by William Stein.

Isuru

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Re: [sage-devel] Error installing package openblas-0.3.6.p0 on mac

[Isuru Fernando]

That looks like a bug in Xcode 7.3, can you update your Xcode version?

Isuru

On Mon, May 18, 2020 at 8:06 PM Valentin Buciumas <
valentin.buciu...@gmail.com> wrote:

> Hello,
>
> I tried installing Sage 9.0 from the source code on my mac (operating
> system macOS Catalina 10.15.4) and got an error while installing the
> openblas package. The log file is here:
> https://drive.google.com/open?id=11Pfdffpd1oEBV0nkEqekYchRplK3Dwmn (it is
> too large to attach). I am wondering if anyone came across this problem and
> has a fix for it?
>
> Thanks,
> Valentin
>
>
> [openblas-0.3.6.p0] collect2: error: ld returned 1 exit status
>
> [openblas-0.3.6.p0] make[3]: *** [libopenblas_atomp-r0.3.6.dylib] Error 1
>
> [openblas-0.3.6.p0] make[2]: *** [shared] Error 2
>
> [openblas-0.3.6.p0]
> 
>
> [openblas-0.3.6.p0] Error building openblas-0.3.6.p0
>
> [openblas-0.3.6.p0]
> 
>
> [openblas-0.3.6.p0]
>
> [openblas-0.3.6.p0] real 8m18.239s
>
> [openblas-0.3.6.p0] user 45m45.392s
>
> [openblas-0.3.6.p0] sys 9m42.448s
>
> [openblas-0.3.6.p0]
> 
>
> [openblas-0.3.6.p0] Error installing package openblas-0.3.6.p0
>
> [openblas-0.3.6.p0]
> 
>
> [openblas-0.3.6.p0] Please email sage-devel (
> http://groups.google.com/group/sage-devel)
>
> [openblas-0.3.6.p0] explaining the problem and including the log file
>
> [openblas-0.3.6.p0]
> /Users/valentinbuciumas/workspace/sage/sage-9.0/logs/pkgs/openblas-0.3.6.p0.log
>
> [openblas-0.3.6.p0] Describe your computer, operating system, etc.
>
> [openblas-0.3.6.p0] If you want to try to fix the problem yourself,
> *don't* just cd to
>
> [openblas-0.3.6.p0]
> /Users/valentinbuciumas/workspace/sage/sage-9.0/local/var/tmp/sage/build/openblas-0.3.6.p0
> and type 'make' or whatever is appropriate.
>
> [openblas-0.3.6.p0] Instead, the following commands setup all environment
> variables
>
> [openblas-0.3.6.p0] correctly and load a subshell for you to debug the
> error:
>
> [openblas-0.3.6.p0]   (cd
> '/Users/valentinbuciumas/workspace/sage/sage-9.0/local/var/tmp/sage/build/openblas-0.3.6.p0'
> && '/Users/valentinbuciumas/workspace/sage/sage-9.0/sage' --sh)
>
> [openblas-0.3.6.p0] When you are done debugging, you can type "exit" to
> leave the subshell.
>
> [openblas-0.3.6.p0]
> 
>
> make[1]: ***
> [/Users/valentinbuciumas/workspace/sage/sage-9.0/local/var/lib/sage/installed/openblas-0.3.6.p0]
> Error 1
>
>
> real 8m25.741s
>
> user 45m48.679s
>
> sys 9m47.707s
>
> ***
>
> Error building Sage.
>
>
> The following package(s) may have failed to build (not necessarily
>
> during this run of 'make openblas'):
>
>
> * package: openblas-0.3.6.p0
>
>   log file:
> /Users/valentinbuciumas/workspace/sage/sage-9.0/logs/pkgs/openblas-0.3.6.p0.log
>
>   build directory:
> /Users/valentinbuciumas/workspace/sage/sage-9.0/local/var/tmp/sage/build/openblas-0.3.6.p0
>
>
> The build directory may contain configuration files and other potentially
>
> helpful information. WARNING: if you now run 'make' again, the build
>
> directory will, by default, be deleted. Set the environment variable
>
> SAGE_KEEP_BUILT_SPKGS to 'yes' to prevent this.
>
>
> make: *** [openblas] Error 1
>
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>

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Re: [sage-devel] Packaging Sage?

[Isuru Fernando]

At conda, we don't use system packages at all and use `python setup.py` to
build the sage python package.

https://github.com/conda-forge/sagelib-feedstock/blob/master/recipe/build.sh#L25-L42

Isuru

On Sun, May 10, 2020 at 10:19 AM Thierry Thomas 
wrote:

> Le dim. 10 mai 20 à 16:02:51 +0200, Julien Puydt 
>  écrivait :
>
> > > TL;TR: Packagers, how do you deal with Sage to package it for your
> > > Linux distribution (or *BSD system)?
> >
> >
> > For Debian, we use our packages as much as possible ; the repository
> > can be seen here:
> >
> > https://salsa.debian.org/science-team/sagemath
>
> Thanks Julien and Dima! I did not find the group sage-packaging, and
> I´ll check the Debian pages.
> --
> Th. Thomas.
>
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Re: [sage-devel] Re: https://wiki.sagemath.org/ReleaseTours/sage-9.1

[Isuru Fernando]

I've added the changes from 9.0 to standard packages which is of interest
to packagers of sage.

Isuru

On Thu, Apr 16, 2020 at 7:36 AM Eric Gourgoulhon 
wrote:

> Le mardi 14 avril 2020 20:36:38 UTC+2, Matthias Koeppe a écrit :
>>
>> Let's prepare https://wiki.sagemath.org/ReleaseTours/sage-9.1
>> by collaborative editing.
>>
>
>
> Thanks a lot! I've added a threejs entry and will add a manifold one later
> on.
> Btw, shouldn't there be a link from https://www.sagemath.org/ to that
> page?
>
> Eric.
>
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> 
> .
>

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Re: [sage-devel] Re: Poll: make giacpy_sage a standard package

[Isuru Fernando]

How is making this standard affect the plans for making sage pip
installable?

This would be the first package in a while that depends on sage-the-library
that is also standard in sage-the-distribution.

Isuru

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Re: [sage-devel] Error building Sage 9.0 on CentOS 7.5

[Isuru Fernando]

> " WARNING: 'aclocal-1.15' is missing on your system." Which seems
unimportant since it's followed with the text "You only need it if..." with
reasons that don't pertain to me.

One possible reason is that somehow the timestamps for the files got messed
up. Easiest solution would be to install automake 1.15. You can also do a
make clean and try again.

Isuru

On Thu, Jan 30, 2020 at 9:00 PM Josh Bevan  wrote:

> Hello,
>
> I'm trying to build Sage 9.0 from source on CentOS 7.5.1804 and it fails
> with:
> "Error installing package sqlite-329"
> Here is the ".../sage-9.0/logs/pkgs/sqlite-329.log" log file that the
> error message says to include:
> https://pastebin.com/SCy98UXK
>
> The two main messages that jump out to me are:
> "configure: WARNING: unrecognized options: --disable-maintainer-mode" I
> had seen that option listed in a post from a decade ago as a solution to a
> Sage Sqlite build error, although I doubt that is still relevant
> and
> " WARNING: 'aclocal-1.15' is missing on your system." Which seems
> unimportant since it's followed with the text "You only need it if..." with
> reasons that don't pertain to me.
>
> For some additional context:
> This is being built on a cluster with SGE (Sun Grid Engine) and uses Lmod
> for a module system. I have gcc 8.3.0, python 3.6.9, and blis 0.6.0
> (OpenBLAS alternative with better performance) modules loaded, any other
> dependencies (e.g. Perl) I've left as the system defaults and they have not
> been overridden by the module system. I unpacked the zip and simply ran
> "make" with no additional messing with config or modifications.
>
> If there is any additional info I should supply that would prove helpful
> feel free to let me know.
>
> Thanks!
> Josh
>
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> 
> .
>

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Re: [sage-devel] fail to build fflas_ffpack on 9.1. beta1

[Isuru Fernando]

Permission issue is a different issue. This happens when configure is run
the second time.

For example, the following fails

touch foo.pc
chmod -w foo.pc
cp foo.pc bar.pc
cp foo.pc bar.pc

Isuru


On Fri, Jan 24, 2020 at 5:27 AM Dima Pasechnik  wrote:

> On Wed, Jan 22, 2020 at 2:20 PM Vincent Delecroix
> <20100.delecr...@gmail.com> wrote:
> >
> > The reason for the error seems to be that the pkgconfig
> > are pointing to my system pkgconfig (which are of not writable)
>
>
> I fail to understand how this can happen, unless you modified what we
> do with pkg-config.
> Since https://trac.sagemath.org/ticket/27827 (already in Sage 8.9)
> we prepend SAGE_PKG_CONFIG_PATH, set to SAGE_LOCAL/lib/pkgconfig/ if
> if system pkg-config is detected ,
> to PKG_CONFIG_PATH and that's where *blas.pc should be installed if
> you install OpenBLAS in Sage.
>
> By the way, I hope the problem that you reported is fixed by
> https://trac.sagemath.org/ticket/29071
> - please test this branch on Arch if you can.
>
> Dima
> >
> >
> > $ ls -l /opt/sage/local/lib/pkgconfig/
> > total 52
> > lrwxrwxrwx 1 vincent vincent  30 22 janv. 15:59 blas.pc ->
> > /usr/lib/pkgconfig/openblas.pc
> > lrwxrwxrwx 1 vincent vincent  30 22 janv. 15:59 cblas.pc ->
> > /usr/lib/pkgconfig/openblas.pc
> > lrwxrwxrwx 1 vincent vincent  30 22 janv. 15:59 lapack.pc ->
> > /usr/lib/pkgconfig/openblas.pc
> > -rw-r--r-- 1 vincent vincent 517 22 janv. 16:07 openblas.pc
> > lrwxrwxrwx 1 vincent vincent  13 22 janv. 16:02 python-3.7m.pc ->
> > python-3.7.pc
> > lrwxrwxrwx 1 vincent vincent  13 22 janv. 16:02 python3.pc ->
> python-3.7.pc
> >
> > Le 22/01/2020 à 16:17, Vincent Delecroix a écrit :
> > > This was not the error (just a warning). Problem is
> > >
> > > cp: cannot create regular file
> > > '/opt/sage/local/./lib/pkgconfig/blas.pc': Permission denied
> > > cp: cannot create regular file
> > > '/opt/sage/local/./lib/pkgconfig/cblas.pc': Permission denied
> > > cp: cannot create regular file
> > > '/opt/sage/local/./lib/pkgconfig/lapack.pc': Permission denied
> > >
> > >
> > > Le 22/01/2020 à 16:16, Vincent Delecroix a écrit :
> > >> With the option --without-system-openblas, the compilation fails at
> > >> openblas with
> > >>
> > >> getarch.c:96: warning: "NO_AVX512" redefined
> > >> 96 | #define NO_AVX512
> > >>
> > >> (see also attachment)
> > >>
> > >> Vincent
> > >>
> > >> Le 22/01/2020 à 13:46, Dima Pasechnik a écrit :
> > >>> there was a thread
> > >>> https://groups.google.com/d/msg/sage-devel/pIOnFyFJMtM/_FbzM2OxCQAJ
> > >>> just on this 10 days ago.
> > >>>
> > >>> the system's openblas on Arch is broken, so you'd need to build with
> > >>> ---without-system-openblas
> > >>>
> > >>> and also it might be related to
> > >>> https://trac.sagemath.org/ticket/27444#comment:34
> > >>>
> > >>> On Wed, Jan 22, 2020 at 12:27 PM Vincent Delecroix
> > >>> <20100.delecr...@gmail.com> wrote:
> > 
> >  Dear all,
> > 
> >  I am experiencing trouble compiling fflas_ffpack (in the sage
> >  compilation process). It is the same error appearing multiple
> >  times related to openblas_set_num_threads being not declared.
> > 
> >  Note that I am running archlinux.
> > 
> >  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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> > 
> https://groups.google.com/d/msgid/sage-devel/6d203341-930b-c660-ca0e-c743cda11a56%40gmail.com
> .
> > 
> > >>>
> >
> > --
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Re: [sage-devel] 9.1.beta0 build failure on Arch

[Isuru Fernando]

It depends on the fortran name mangling. For gfortran, one symbol would be
dgeqrf_.

Isuru

On Thu, Jan 23, 2020 at 12:05 PM Dima Pasechnik  wrote:

> On Thu, Jan 23, 2020 at 5:36 PM Antonio Rojas  wrote:
> >
> >
> >
> > El jueves, 23 de enero de 2020, 18:11:51 (UTC+1), Dima Pasechnik
> escribió:
> >>
> >> On Wed, Jan 22, 2020 at 5:20 PM Isuru Fernando 
> wrote:
> >> >
> >> > [root@50586643ff22 /]# pkg-config --modversion blas
> >> > 0.3.7
> >> > [root@50586643ff22 /]# pkg-config --modversion cblas
> >> > 3.9.0
> >> > [root@50586643ff22 /]# pkg-config --modversion lapack
> >> > 3.9.0
> >> > [root@50586643ff22 /]# pkg-config --modversion openblas
> >> > 0.3.7
> >>
> >> To make it robust, I'd only allow cblas.pc to be used if it really is
> >> based on openblas
> >> and the same for lapack.pc
> >>
> >> One way to do this is to  test openblas for a symbol that is on Arch
> >> in cblas, not in openblas,
> >> and the same for lapack.
> >>
> >> Could someone figure out these symbols, or give me access to an Arch
> box?
> >>
> >
> > fflas-fflack configure tests need cblas_dgemm, so you should check for
> that function.
>
> Thanks, but how about lapack? What is a symbol in liblapack to check for?
>
> >
> >
> > --
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Re: [sage-devel] 9.1.beta0 build failure on Arch

[Isuru Fernando]

> One way to do this is to  test openblas for a symbol that is on Arch
in cblas, not in openblas,

I'm not sure I understand. Are you asking for a symbol in libcblas.so that
is not in an libopenblas.so compiled with CBLAS?

> Could someone figure out these symbols, or give me access to an Arch box?

Sorry, I'm using docker for this.

Isuru

On Thu, Jan 23, 2020 at 11:11 AM Dima Pasechnik  wrote:

> On Wed, Jan 22, 2020 at 5:20 PM Isuru Fernando  wrote:
> >
> > [root@50586643ff22 /]# pkg-config --modversion blas
> > 0.3.7
> > [root@50586643ff22 /]# pkg-config --modversion cblas
> > 3.9.0
> > [root@50586643ff22 /]# pkg-config --modversion lapack
> > 3.9.0
> > [root@50586643ff22 /]# pkg-config --modversion openblas
> > 0.3.7
>
> To make it robust, I'd only allow cblas.pc to be used if it really is
> based on openblas
> and the same for lapack.pc
>
> One way to do this is to  test openblas for a symbol that is on Arch
> in cblas, not in openblas,
> and the same for lapack.
>
> Could someone figure out these symbols, or give me access to an Arch box?
>
> >
> > On Wed, Jan 22, 2020 at 11:18 AM Dima Pasechnik 
> wrote:
> >>
> >> On Wed, Jan 22, 2020 at 5:03 PM Isuru Fernando 
> wrote:
> >> >
> >> > > On Arch, does cblas.pc exist?
> >> >
> >> > Yes.
> >>
> >> Thanks. I wonder what on Arch is the output of
> >>
> >> pkg-config --modversion X
> >>
> >> for X in [cblas,blas,lapack,openblas]
> >>
> >>
> >> >
> >> > > this is system-dependent.
> >> >
> >> > Yes, that's why we need to have fallbacks.
> >> >
> >> > Isuru
> >> >
> >> > On Wed, Jan 22, 2020 at 11:00 AM Dima Pasechnik 
> wrote:
> >> >>
> >> >> On Wed, Jan 22, 2020 at 4:17 PM Isuru Fernando 
> wrote:
> >> >> >
> >> >> > > maybe they split openblas.so into separate sections for an
> unclear to me reason, but most applications I know uses cblas, blas and
> lapack, so they need to link them all anyway.
> >> >> >
> >> >> > True, but in sage you are copying `openblas.pc` to `cblas.pc` and
> `lapack.pc` which is wrong. `openblas.pc` should only be expected to
> provide blas.
> >> >>
> >> >> this is system-dependent. Debian and Fedora have no libcblas  and no
> >> >> cblas.pc, cblas  is provided by openblas.
> >> >> Some *BSD systems have libcblas conflcting with libopenblas.
> >> >>
> >> >> On Arch, does cblas.pc exist?
> >> >>
> >> >>
> >> >> >
> >> >> > A solution would be to check that `blas.pc`, `cblas.pc`,
> `lapack.pc` are already on the system and if not copy `openblas.pc` to the
> three names.
> >> >> >
> >> >> > Isuru
> >> >> >
> >> >> > On Wed, Jan 22, 2020 at 10:14 AM Isuru Fernando 
> wrote:
> >> >> >>
> >> >> >> > errors we see here, regarding absence of certain openmp
> functions in cblas, seem to indicate that cblas on Arch does not come from
> openblas. perhaps what we see are reference cblas and blas from openblas
> installed at the same time, in error.
> >> >> >>
> >> >> >> Can you please explain more? As I said earlier, it doesn't matter
> where CBLAS is coming from. I checked in Arch linux and cblas is linked to
> openblas.
> >> >> >>
> >> >> >> [root@50586643ff22 /]# ldd /usr/lib/libcblas.so.3
> >> >> >> linux-vdso.so.1 (0x7ffd2f7bb000)
> >> >> >> libblas.so.3 => /usr/lib/libblas.so.3 (0x7f848f079000)
> >> >> >> libc.so.6 => /usr/lib/libc.so.6 (0x7f848eeb2000)
> >> >> >> libm.so.6 => /usr/lib/libm.so.6 (0x7f848ed6c000)
> >> >> >> libpthread.so.0 => /usr/lib/libpthread.so.0
> (0x7f848ed4a000)
> >> >> >> libgomp.so.1 => /usr/lib/libgomp.so.1 (0x7f848ed11000)
> >> >> >> /usr/lib64/ld-linux-x86-64.so.2 (0x7f84902dc000)
> >> >> >> libdl.so.2 => /usr/lib/libdl.so.2 (0x7f848ed0c000)
> >> >> >>
> >> >> >> [root@50586643ff22 /]# ls -al /usr/lib/libblas.so.3
> >> >> >> lrwxrwxrwx 1 root root 22 Aug 20 10:35 /usr/lib/libblas.so.3 ->
> libopenblasp-r0.3.7.so
>

Re: [sage-devel] 9.1.beta0 build failure on Arch

[Isuru Fernando]

[root@50586643ff22 /]# pkg-config --modversion blas
0.3.7
[root@50586643ff22 /]# pkg-config --modversion cblas
3.9.0
[root@50586643ff22 /]# pkg-config --modversion lapack
3.9.0
[root@50586643ff22 /]# pkg-config --modversion openblas
0.3.7

On Wed, Jan 22, 2020 at 11:18 AM Dima Pasechnik  wrote:

> On Wed, Jan 22, 2020 at 5:03 PM Isuru Fernando  wrote:
> >
> > > On Arch, does cblas.pc exist?
> >
> > Yes.
>
> Thanks. I wonder what on Arch is the output of
>
> pkg-config --modversion X
>
> for X in [cblas,blas,lapack,openblas]
>
>
> >
> > > this is system-dependent.
> >
> > Yes, that's why we need to have fallbacks.
> >
> > Isuru
> >
> > On Wed, Jan 22, 2020 at 11:00 AM Dima Pasechnik 
> wrote:
> >>
> >> On Wed, Jan 22, 2020 at 4:17 PM Isuru Fernando 
> wrote:
> >> >
> >> > > maybe they split openblas.so into separate sections for an unclear
> to me reason, but most applications I know uses cblas, blas and lapack, so
> they need to link them all anyway.
> >> >
> >> > True, but in sage you are copying `openblas.pc` to `cblas.pc` and
> `lapack.pc` which is wrong. `openblas.pc` should only be expected to
> provide blas.
> >>
> >> this is system-dependent. Debian and Fedora have no libcblas  and no
> >> cblas.pc, cblas  is provided by openblas.
> >> Some *BSD systems have libcblas conflcting with libopenblas.
> >>
> >> On Arch, does cblas.pc exist?
> >>
> >>
> >> >
> >> > A solution would be to check that `blas.pc`, `cblas.pc`, `lapack.pc`
> are already on the system and if not copy `openblas.pc` to the three names.
> >> >
> >> > Isuru
> >> >
> >> > On Wed, Jan 22, 2020 at 10:14 AM Isuru Fernando 
> wrote:
> >> >>
> >> >> > errors we see here, regarding absence of certain openmp functions
> in cblas, seem to indicate that cblas on Arch does not come from openblas.
> perhaps what we see are reference cblas and blas from openblas installed at
> the same time, in error.
> >> >>
> >> >> Can you please explain more? As I said earlier, it doesn't matter
> where CBLAS is coming from. I checked in Arch linux and cblas is linked to
> openblas.
> >> >>
> >> >> [root@50586643ff22 /]# ldd /usr/lib/libcblas.so.3
> >> >> linux-vdso.so.1 (0x7ffd2f7bb000)
> >> >> libblas.so.3 => /usr/lib/libblas.so.3 (0x7f848f079000)
> >> >> libc.so.6 => /usr/lib/libc.so.6 (0x7f848eeb2000)
> >> >> libm.so.6 => /usr/lib/libm.so.6 (0x7f848ed6c000)
> >> >> libpthread.so.0 => /usr/lib/libpthread.so.0
> (0x7f848ed4a000)
> >> >> libgomp.so.1 => /usr/lib/libgomp.so.1 (0x7f848ed11000)
> >> >> /usr/lib64/ld-linux-x86-64.so.2 (0x7f84902dc000)
> >> >> libdl.so.2 => /usr/lib/libdl.so.2 (0x7f848ed0c000)
> >> >>
> >> >> [root@50586643ff22 /]# ls -al /usr/lib/libblas.so.3
> >> >> lrwxrwxrwx 1 root root 22 Aug 20 10:35 /usr/lib/libblas.so.3 ->
> libopenblasp-r0.3.7.so
> >> >>
> >> >>
> >> >> Isuru
> >> >>
> >> >> On Wed, Jan 22, 2020 at 10:09 AM Dima Pasechnik 
> wrote:
> >> >>>
> >> >>>
> >> >>>
> >> >>> On Wed, 22 Jan 2020, 15:59 Isuru Fernando, 
> wrote:
> >> >>>>
> >> >>>> > But Arch does not do this, it instead provides dog-slow CBLAS and
> >> >>>> LAPACK, built
> >> >>>> from another (reference, i.e. no assembler, no optimisation)
> implementation.
> >> >>>>
> >> >>>> This is simply not true. CBLAS's performance does not depend on
> which implementation it comes from. CBLAS's performance depends on the
> underlying BLAS implementation and on ArchLinux, when OpenBLAS is
> installed, CBLAS uses OpenBLAS as the underlying BLAS implementation. In
> fact, OpenBLAS uses the CBLAS code from Netlib's reference implementation.
> >> >>>
> >> >>>
> >> >>> errors we see here, regarding absence of certain openmp functions
> in cblas, seem to indicate that cblas on Arch does not come from openblas.
> perhaps what we see are reference cblas and blas from openblas installed at
> the same time, in error.
> >> >>>
> >> >>> maybe they split openblas.so into

Re: [sage-devel] 9.1.beta0 build failure on Arch

[Isuru Fernando]

> On Arch, does cblas.pc exist?

Yes.

> this is system-dependent.

Yes, that's why we need to have fallbacks.

Isuru

On Wed, Jan 22, 2020 at 11:00 AM Dima Pasechnik  wrote:

> On Wed, Jan 22, 2020 at 4:17 PM Isuru Fernando  wrote:
> >
> > > maybe they split openblas.so into separate sections for an unclear to
> me reason, but most applications I know uses cblas, blas and lapack, so
> they need to link them all anyway.
> >
> > True, but in sage you are copying `openblas.pc` to `cblas.pc` and
> `lapack.pc` which is wrong. `openblas.pc` should only be expected to
> provide blas.
>
> this is system-dependent. Debian and Fedora have no libcblas  and no
> cblas.pc, cblas  is provided by openblas.
> Some *BSD systems have libcblas conflcting with libopenblas.
>
> On Arch, does cblas.pc exist?
>
>
> >
> > A solution would be to check that `blas.pc`, `cblas.pc`, `lapack.pc` are
> already on the system and if not copy `openblas.pc` to the three names.
> >
> > Isuru
> >
> > On Wed, Jan 22, 2020 at 10:14 AM Isuru Fernando 
> wrote:
> >>
> >> > errors we see here, regarding absence of certain openmp functions in
> cblas, seem to indicate that cblas on Arch does not come from openblas.
> perhaps what we see are reference cblas and blas from openblas installed at
> the same time, in error.
> >>
> >> Can you please explain more? As I said earlier, it doesn't matter where
> CBLAS is coming from. I checked in Arch linux and cblas is linked to
> openblas.
> >>
> >> [root@50586643ff22 /]# ldd /usr/lib/libcblas.so.3
> >> linux-vdso.so.1 (0x7ffd2f7bb000)
> >> libblas.so.3 => /usr/lib/libblas.so.3 (0x7f848f079000)
> >> libc.so.6 => /usr/lib/libc.so.6 (0x7f848eeb2000)
> >> libm.so.6 => /usr/lib/libm.so.6 (0x7f848ed6c000)
> >> libpthread.so.0 => /usr/lib/libpthread.so.0 (0x7f848ed4a000)
> >> libgomp.so.1 => /usr/lib/libgomp.so.1 (0x7f848ed11000)
> >> /usr/lib64/ld-linux-x86-64.so.2 (0x7f84902dc000)
> >> libdl.so.2 => /usr/lib/libdl.so.2 (0x7f848ed0c000)
> >>
> >> [root@50586643ff22 /]# ls -al /usr/lib/libblas.so.3
> >> lrwxrwxrwx 1 root root 22 Aug 20 10:35 /usr/lib/libblas.so.3 ->
> libopenblasp-r0.3.7.so
> >>
> >>
> >> Isuru
> >>
> >> On Wed, Jan 22, 2020 at 10:09 AM Dima Pasechnik 
> wrote:
> >>>
> >>>
> >>>
> >>> On Wed, 22 Jan 2020, 15:59 Isuru Fernando,  wrote:
> >>>>
> >>>> > But Arch does not do this, it instead provides dog-slow CBLAS and
> >>>> LAPACK, built
> >>>> from another (reference, i.e. no assembler, no optimisation)
> implementation.
> >>>>
> >>>> This is simply not true. CBLAS's performance does not depend on which
> implementation it comes from. CBLAS's performance depends on the underlying
> BLAS implementation and on ArchLinux, when OpenBLAS is installed, CBLAS
> uses OpenBLAS as the underlying BLAS implementation. In fact, OpenBLAS uses
> the CBLAS code from Netlib's reference implementation.
> >>>
> >>>
> >>> errors we see here, regarding absence of certain openmp functions in
> cblas, seem to indicate that cblas on Arch does not come from openblas.
> perhaps what we see are reference cblas and blas from openblas installed at
> the same time, in error.
> >>>
> >>> maybe they split openblas.so into separate sections for an unclear to
> me reason, but most applications I know uses cblas, blas and lapack, so
> they need to link them all anyway.
> >>>
> >>>
> >>>>
> >>>> As for LAPACK, in OpenBLAS, they have implemented a handful of
> functions to use OpenBLAS internals to make it parallel, but most of the
> LAPACK functions are from Netlib's Reference implementation. So, when
> ArchLinux is using LAPACK from netlib, they are losing out on only a few
> LAPACK functions.
> >>>>
> >>>> Isuru
> >>>>
> >>>> On Wed, Jan 22, 2020 at 9:27 AM Dima Pasechnik 
> wrote:
> >>>>>
> >>>>>
> >>>>>
> >>>>> On Wed, 22 Jan 2020, 15:12 Vincent Delecroix, <
> 20100.delecr...@gmail.com> wrote:
> >>>>>>
> >>>>>> Le 22/01/2020 à 15:41, Dima Pasechnik a écrit :
> >>>>>> > On Wed, Jan 22, 2020 at 2:31 PM Vincent Delecroix
> >>>>>> > <20100.delecr...@gmail.

Re: [sage-devel] 9.1.beta0 build failure on Arch

[Isuru Fernando]

> maybe they split openblas.so into separate sections for an unclear to me
reason, but most applications I know uses cblas, blas and lapack, so they
need to link them all anyway.

True, but in sage you are copying `openblas.pc` to `cblas.pc` and
`lapack.pc` which is wrong. `openblas.pc` should only be expected to
provide blas.

A solution would be to check that `blas.pc`, `cblas.pc`, `lapack.pc` are
already on the system and if not copy `openblas.pc` to the three names.

Isuru

On Wed, Jan 22, 2020 at 10:14 AM Isuru Fernando  wrote:

> > errors we see here, regarding absence of certain openmp functions in
> cblas, seem to indicate that cblas on Arch does not come from openblas.
> perhaps what we see are reference cblas and blas from openblas installed at
> the same time, in error.
>
> Can you please explain more? As I said earlier, it doesn't matter where
> CBLAS is coming from. I checked in Arch linux and cblas is linked to
> openblas.
>
> [root@50586643ff22 /]# ldd /usr/lib/libcblas.so.3
> linux-vdso.so.1 (0x7ffd2f7bb000)
> libblas.so.3 => /usr/lib/libblas.so.3 (0x7f848f079000)
> libc.so.6 => /usr/lib/libc.so.6 (0x7f848eeb2000)
> libm.so.6 => /usr/lib/libm.so.6 (0x7f848ed6c000)
> libpthread.so.0 => /usr/lib/libpthread.so.0 (0x7f848ed4a000)
> libgomp.so.1 => /usr/lib/libgomp.so.1 (0x7f848ed11000)
> /usr/lib64/ld-linux-x86-64.so.2 (0x7f84902dc000)
> libdl.so.2 => /usr/lib/libdl.so.2 (0x7f848ed0c000)
>
> [root@50586643ff22 /]# ls -al /usr/lib/libblas.so.3
> lrwxrwxrwx 1 root root 22 Aug 20 10:35 /usr/lib/libblas.so.3 ->
> libopenblasp-r0.3.7.so
>
>
> Isuru
>
> On Wed, Jan 22, 2020 at 10:09 AM Dima Pasechnik  wrote:
>
>>
>>
>> On Wed, 22 Jan 2020, 15:59 Isuru Fernando,  wrote:
>>
>>> > But Arch does not do this, it instead provides dog-slow CBLAS and
>>> LAPACK, built
>>> from another (reference, i.e. no assembler, no optimisation)
>>> implementation.
>>>
>>> This is simply not true. CBLAS's performance does not depend on which
>>> implementation it comes from. CBLAS's performance depends on the underlying
>>> BLAS implementation and on ArchLinux, when OpenBLAS is installed, CBLAS
>>> uses OpenBLAS as the underlying BLAS implementation. In fact, OpenBLAS uses
>>> the CBLAS code from Netlib's reference implementation.
>>>
>>
>> errors we see here, regarding absence of certain openmp functions in
>> cblas, seem to indicate that cblas on Arch does not come from openblas.
>> perhaps what we see are reference cblas and blas from openblas installed at
>> the same time, in error.
>>
>> maybe they split openblas.so into separate sections for an unclear to me
>> reason, but most applications I know uses cblas, blas and lapack, so they
>> need to link them all anyway.
>>
>>
>>
>>> As for LAPACK, in OpenBLAS, they have implemented a handful of functions
>>> to use OpenBLAS internals to make it parallel, but most of the LAPACK
>>> functions are from Netlib's Reference implementation. So, when ArchLinux is
>>> using LAPACK from netlib, they are losing out on only a few LAPACK
>>> functions.
>>>
>>> Isuru
>>>
>>> On Wed, Jan 22, 2020 at 9:27 AM Dima Pasechnik 
>>> wrote:
>>>
>>>>
>>>>
>>>> On Wed, 22 Jan 2020, 15:12 Vincent Delecroix, <
>>>> 20100.delecr...@gmail.com> wrote:
>>>>
>>>>> Le 22/01/2020 à 15:41, Dima Pasechnik a écrit :
>>>>> > On Wed, Jan 22, 2020 at 2:31 PM Vincent Delecroix
>>>>> > <20100.delecr...@gmail.com> wrote:
>>>>> >>
>>>>> >> I had the same annoying trouble... Is it really a bug in arch? I
>>>>> don't
>>>>> >> find anywhere where libopenblas is supposed to provide the LAPACK
>>>>> >> interface. To me it is just true for SageMath and false for
>>>>> Archlinux.
>>>>> >
>>>>> > well, a "bug", in the sense that their openblas configuration just
>>>>> > does not make any sense,
>>>>> > because if you install a highly optimised BLAS implementation, which
>>>>> can also
>>>>> > provided a highly optimised CBLAS and LAPACK, in a sane world you'd
>>>>> install them
>>>>> > too. But Arch does not do this, it instead provides dog-slow CBLAS
>>>>> and
>>>>> > LAPACK, built
>>>>> > from 

Re: [sage-devel] 9.1.beta0 build failure on Arch

[Isuru Fernando]

> errors we see here, regarding absence of certain openmp functions in
cblas, seem to indicate that cblas on Arch does not come from openblas.
perhaps what we see are reference cblas and blas from openblas installed at
the same time, in error.

Can you please explain more? As I said earlier, it doesn't matter where
CBLAS is coming from. I checked in Arch linux and cblas is linked to
openblas.

[root@50586643ff22 /]# ldd /usr/lib/libcblas.so.3
linux-vdso.so.1 (0x7ffd2f7bb000)
libblas.so.3 => /usr/lib/libblas.so.3 (0x7f848f079000)
libc.so.6 => /usr/lib/libc.so.6 (0x7f848eeb2000)
libm.so.6 => /usr/lib/libm.so.6 (0x7f848ed6c000)
libpthread.so.0 => /usr/lib/libpthread.so.0 (0x7f848ed4a000)
libgomp.so.1 => /usr/lib/libgomp.so.1 (0x7f848ed11000)
/usr/lib64/ld-linux-x86-64.so.2 (0x7f84902dc000)
libdl.so.2 => /usr/lib/libdl.so.2 (0x7f848ed0c000)

[root@50586643ff22 /]# ls -al /usr/lib/libblas.so.3
lrwxrwxrwx 1 root root 22 Aug 20 10:35 /usr/lib/libblas.so.3 ->
libopenblasp-r0.3.7.so


Isuru

On Wed, Jan 22, 2020 at 10:09 AM Dima Pasechnik  wrote:

>
>
> On Wed, 22 Jan 2020, 15:59 Isuru Fernando,  wrote:
>
>> > But Arch does not do this, it instead provides dog-slow CBLAS and
>> LAPACK, built
>> from another (reference, i.e. no assembler, no optimisation)
>> implementation.
>>
>> This is simply not true. CBLAS's performance does not depend on which
>> implementation it comes from. CBLAS's performance depends on the underlying
>> BLAS implementation and on ArchLinux, when OpenBLAS is installed, CBLAS
>> uses OpenBLAS as the underlying BLAS implementation. In fact, OpenBLAS uses
>> the CBLAS code from Netlib's reference implementation.
>>
>
> errors we see here, regarding absence of certain openmp functions in
> cblas, seem to indicate that cblas on Arch does not come from openblas.
> perhaps what we see are reference cblas and blas from openblas installed at
> the same time, in error.
>
> maybe they split openblas.so into separate sections for an unclear to me
> reason, but most applications I know uses cblas, blas and lapack, so they
> need to link them all anyway.
>
>
>
>> As for LAPACK, in OpenBLAS, they have implemented a handful of functions
>> to use OpenBLAS internals to make it parallel, but most of the LAPACK
>> functions are from Netlib's Reference implementation. So, when ArchLinux is
>> using LAPACK from netlib, they are losing out on only a few LAPACK
>> functions.
>>
>> Isuru
>>
>> On Wed, Jan 22, 2020 at 9:27 AM Dima Pasechnik  wrote:
>>
>>>
>>>
>>> On Wed, 22 Jan 2020, 15:12 Vincent Delecroix, <20100.delecr...@gmail.com>
>>> wrote:
>>>
>>>> Le 22/01/2020 à 15:41, Dima Pasechnik a écrit :
>>>> > On Wed, Jan 22, 2020 at 2:31 PM Vincent Delecroix
>>>> > <20100.delecr...@gmail.com> wrote:
>>>> >>
>>>> >> I had the same annoying trouble... Is it really a bug in arch? I
>>>> don't
>>>> >> find anywhere where libopenblas is supposed to provide the LAPACK
>>>> >> interface. To me it is just true for SageMath and false for
>>>> Archlinux.
>>>> >
>>>> > well, a "bug", in the sense that their openblas configuration just
>>>> > does not make any sense,
>>>> > because if you install a highly optimised BLAS implementation, which
>>>> can also
>>>> > provided a highly optimised CBLAS and LAPACK, in a sane world you'd
>>>> install them
>>>> > too. But Arch does not do this, it instead provides dog-slow CBLAS and
>>>> > LAPACK, built
>>>> > from another (reference, i.e. no assembler, no optimisation)
>>>> implementation.
>>>> > This causes Sage's logic, which expects that openblas will also
>>>> > provide CBLAS and LAPACK, to fail.
>>>> >
>>>> > Yes, it is possible to make tests to detect this silly setup, but I
>>>> > think that everyone's time
>>>> > is much better spent if Arch provided a full build of openblas, with
>>>> > CBLAS and LAPACK,
>>>> > instead.
>>>>
>>>> Hence there are two bugs
>>>>
>>>> * a "logical" bug in archlinux that provides a slow lapack for
>>>>(apparently) no good reason
>>>>
>>>> * a structural bug in SageMath that assumes that openblas does
>>>>install the LAPACK interface
>>>>
>>>>
>>

Re: [sage-devel] 9.1.beta0 build failure on Arch

[Isuru Fernando]

There's also a 3rd bug which is in fflas-ffpack which assumes that if
there's no cblas, then it's not openblas. This can be fixed by copying the
lines
https://github.com/linbox-team/fflas-ffpack/blob/2d3af1a5bec51983b5a896fae12e60914d9bdc4d/fflas-ffpack/config-blas.h#L315-L317
to Line 311 above the #else

Isuru

On Wed, Jan 22, 2020 at 9:13 AM Vincent Delecroix <20100.delecr...@gmail.com>
wrote:

> Le 22/01/2020 à 15:41, Dima Pasechnik a écrit :
> > On Wed, Jan 22, 2020 at 2:31 PM Vincent Delecroix
> > <20100.delecr...@gmail.com> wrote:
> >>
> >> I had the same annoying trouble... Is it really a bug in arch? I don't
> >> find anywhere where libopenblas is supposed to provide the LAPACK
> >> interface. To me it is just true for SageMath and false for Archlinux.
> >
> > well, a "bug", in the sense that their openblas configuration just
> > does not make any sense,
> > because if you install a highly optimised BLAS implementation, which can
> also
> > provided a highly optimised CBLAS and LAPACK, in a sane world you'd
> install them
> > too. But Arch does not do this, it instead provides dog-slow CBLAS and
> > LAPACK, built
> > from another (reference, i.e. no assembler, no optimisation)
> implementation.
> > This causes Sage's logic, which expects that openblas will also
> > provide CBLAS and LAPACK, to fail.
> >
> > Yes, it is possible to make tests to detect this silly setup, but I
> > think that everyone's time
> > is much better spent if Arch provided a full build of openblas, with
> > CBLAS and LAPACK,
> > instead.
>
> Hence there are two bugs
>
> * a "logical" bug in archlinux that provides a slow lapack for
>(apparently) no good reason
>
> * a structural bug in SageMath that assumes that openblas does
>install the LAPACK interface
>
> I tend to agree that the resolution of any of these two would solve
> the compilation. But in an ideal world we would just solve the two.
>
> >>
> >> Le 13/01/2020 à 11:44, Dima Pasechnik a écrit :
> >>> On Sat, Jan 11, 2020 at 11:35 AM arojas  wrote:
> 
>  El sábado, 11 de enero de 2020, 11:23:32 (UTC+1), Dima Pasechnik
> escribió:
> >
> >
> >
> > On Sat, 11 Jan 2020, 10:19 arojas,  wrote:
> >>
> >> I suspect this may be due to our openblas package only providing
> libblas.so (not libcblas.so or liblapack.so, which in our case come from
> the netlib blas).
> >
> >
> > Are you saying that your libopenblas.so does not provide everything
> that is in openblas by default?
> >
> > This is largely defeating its purpose.
> > Sage's openblas does provide the cblas and lapack capabilities.
> 
> 
> In that case, openblas' spkg-configure should check whether cblas
> symbols are provided by the system openblas, and if not it should compile
> sage's one. It shouldn't unconditionally assume that that's always the case.
> >>>
> >>> I maintain that it's a bug in Arch, that libopenblas cannot be used as
> >>> a replacement of cblas and lapack, for it defeats its purpose.
> >>> Most uses of BLAS routines are either via LAPACK, or from C/C++, via
> cblas.
> >>>
> >>>
> >>>
> 
>  --
>  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,
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> .
> >>>
> >>
> >> --
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> >
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> .
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Re: [sage-devel] 9.1.beta0 build failure on Arch

[Isuru Fernando]

> But Arch does not do this, it instead provides dog-slow CBLAS and
LAPACK, built
from another (reference, i.e. no assembler, no optimisation) implementation.

This is simply not true. CBLAS's performance does not depend on which
implementation it comes from. CBLAS's performance depends on the underlying
BLAS implementation and on ArchLinux, when OpenBLAS is installed, CBLAS
uses OpenBLAS as the underlying BLAS implementation. In fact, OpenBLAS uses
the CBLAS code from Netlib's reference implementation.

As for LAPACK, in OpenBLAS, they have implemented a handful of functions to
use OpenBLAS internals to make it parallel, but most of the LAPACK
functions are from Netlib's Reference implementation. So, when ArchLinux is
using LAPACK from netlib, they are losing out on only a few LAPACK
functions.

Isuru

On Wed, Jan 22, 2020 at 9:27 AM Dima Pasechnik  wrote:

>
>
> On Wed, 22 Jan 2020, 15:12 Vincent Delecroix, <20100.delecr...@gmail.com>
> wrote:
>
>> Le 22/01/2020 à 15:41, Dima Pasechnik a écrit :
>> > On Wed, Jan 22, 2020 at 2:31 PM Vincent Delecroix
>> > <20100.delecr...@gmail.com> wrote:
>> >>
>> >> I had the same annoying trouble... Is it really a bug in arch? I don't
>> >> find anywhere where libopenblas is supposed to provide the LAPACK
>> >> interface. To me it is just true for SageMath and false for Archlinux.
>> >
>> > well, a "bug", in the sense that their openblas configuration just
>> > does not make any sense,
>> > because if you install a highly optimised BLAS implementation, which
>> can also
>> > provided a highly optimised CBLAS and LAPACK, in a sane world you'd
>> install them
>> > too. But Arch does not do this, it instead provides dog-slow CBLAS and
>> > LAPACK, built
>> > from another (reference, i.e. no assembler, no optimisation)
>> implementation.
>> > This causes Sage's logic, which expects that openblas will also
>> > provide CBLAS and LAPACK, to fail.
>> >
>> > Yes, it is possible to make tests to detect this silly setup, but I
>> > think that everyone's time
>> > is much better spent if Arch provided a full build of openblas, with
>> > CBLAS and LAPACK,
>> > instead.
>>
>> Hence there are two bugs
>>
>> * a "logical" bug in archlinux that provides a slow lapack for
>>(apparently) no good reason
>>
>> * a structural bug in SageMath that assumes that openblas does
>>install the LAPACK interface
>>
>>
>> I tend to agree that the resolution of any of these two would solve
>> the compilation. But in an ideal world we would just solve the two.
>>
>
> a meaningful resolution of this would be to test openblas for lapack and
> cblas capacities.
>
> this is relatively easy, and would result in openblas on Arch being built
> by Sage.
>
> as far as expanding this to other implementations of blas/lapack,
> it is harder.
>
>>
>>
>> >>
>> >> Le 13/01/2020 à 11:44, Dima Pasechnik a écrit :
>> >>> On Sat, Jan 11, 2020 at 11:35 AM arojas  wrote:
>> 
>>  El sábado, 11 de enero de 2020, 11:23:32 (UTC+1), Dima Pasechnik
>> escribió:
>> >
>> >
>> >
>> > On Sat, 11 Jan 2020, 10:19 arojas,  wrote:
>> >>
>> >> I suspect this may be due to our openblas package only providing
>> libblas.so (not libcblas.so or liblapack.so, which in our case come from
>> the netlib blas).
>> >
>> >
>> > Are you saying that your libopenblas.so does not provide everything
>> that is in openblas by default?
>> >
>> > This is largely defeating its purpose.
>> > Sage's openblas does provide the cblas and lapack capabilities.
>> 
>> 
>> In that case, openblas' spkg-configure should check whether cblas
>> symbols are provided by the system openblas, and if not it should compile
>> sage's one. It shouldn't unconditionally assume that that's always the case.
>> >>>
>> >>> I maintain that it's a bug in Arch, that libopenblas cannot be used as
>> >>> a replacement of cblas and lapack, for it defeats its purpose.
>> >>> Most uses of BLAS routines are either via LAPACK, or from C/C++, via
>> cblas.
>> >>>
>> >>>
>> >>>
>> 
>>  --
>>  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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>> https://groups.google.com/d/msgid/sage-devel/a1516e56-ab25-410e-be0f-75a7a6713466%40googlegroups.com
>> .
>> >>>
>> >>
>> >> --
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>> .
>> >
>>
>> --
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>> To unsubscribe 

Re: [sage-devel] Re: drop python2 compatibility in 9.1 ?

[Isuru Fernando]

On Fri, Jan 10, 2020 at 3:53 PM E. Madison Bray 
wrote:

> On Fri, Jan 10, 2020 at 10:41 AM Timo Kaufmann 
> wrote:
> >
> > I have said this before, but I feel like the point was dropped out of
> the discussion so I'll stress it again. The major issue here is *not* the
> compatibility of sage's own codebase. A few "from __future__ import"'s are
> not so bad.
> >
> > The issue is that python2 compatibility forces us to use outdated
> versions of a lot of libraries, since many libraries have dropped python2
> support a while ago. This is a big headache especially for packagers. Those
> outdated libraries are generally not available on distros. At the same time
> sage is usually not compatible with the newer versions. Sage is already
> difficult to package, and that makes it a lot more difficult.
>
> Can you be more specific about this?  What is it about Sage's upstream
> codebase maintaining backwards-compatibility for Python 2 that
> prevents you from packaging it for Python 3 only, given that it does
> support Python 3?  No one is saying that just because upstream support
> is maintained for Python 2 for one or two (at the most) more releases,
> any downstream packagers have to package it for Python 2.
>

I'll give an example. sage has rpy2 2.8.2.
rpy2 latest is 3.2.4 but 3.x series is python 3 only and sage requires
breaking changes to support rpy2 3.x. See
https://trac.sagemath.org/ticket/28494#comment:6
While python2 support for rpy2 is required, sage codebase can't be updated
to 3.x (unless someone adds code to detect rpy2 version and support both
2.8.2 and 3.2.4)

Isuru


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[sage-devel] Re: Bad CEq in Find_Equations

[Isuru Fernando]

Fixed it. It was a bad build of PALP built with -DNDEBUG.

Isuru

On Wed, Jan 1, 2020 at 5:34 AM Isuru Fernando  wrote:

> I get thousands of test failures in 9.0.rc1 due to an error from palp. Any
> ideas?
>
> Isuru
>
> sage: toric_varieties.dP6()
>  Bad CEq in Find_Equations
> ---
> ValueErrorTraceback (most recent call last)
>  in ()
> > 1 toric_varieties.dP6()
>
> /projects/66d93023-00f0-4c12-8a25-5d6d4e486740/miniconda3/envs/sage90/lib/python2.7/site-packages/sage/schemes/toric/library.pyc
> in dP6(self, names, base_ring)
> 313 (x, u, y, v, z, w)
> 314 """
> --> 315 return self._make_CPRFanoToricVariety('dP6', names,
> base_ring)
> 316
> 317 def dP7(self, names='x u y v z', base_ring=QQ):
>
> /projects/66d93023-00f0-4c12-8a25-5d6d4e486740/miniconda3/envs/sage90/lib/python2.7/site-packages/sage/schemes/toric/library.pyc
> in _make_CPRFanoToricVariety(self, name, coordinate_names, base_ring)
> 265 if dict_key not in self.__dict__:
> 266 polytope = LatticePolytope(rays,
> lattice=ToricLattice(len(rays[0])))
> --> 267 points = [tuple(_) for _ in polytope.points()]
> 268 ray2point = [points.index(r) for r in rays]
> 269 charts = [ [ray2point[i] for i in c] for c in cones ]
>
> /projects/66d93023-00f0-4c12-8a25-5d6d4e486740/miniconda3/envs/sage90/lib/python2.7/site-packages/sage/geometry/lattice_polytope.pyc
> in points(self, *args, **kwds)
>3746 if self.dim() == self.lattice_dim():
>3747 print(type(result), result)
> -> 3748 points =
> read_palp_point_collection(StringIO(result), M)
>3749 else:
>3750 m = self._embed(read_palp_matrix(result))
>
> /projects/66d93023-00f0-4c12-8a25-5d6d4e486740/miniconda3/envs/sage90/lib/python2.7/site-packages/sage/geometry/point_collection.pyx
> in sage.geometry.point_collection.read_palp_point_collection
> (build/cythonized/sage/geometry/point_collection.c:8111)()
> 998 return None
> 999 first_line = first_line.split()
> -> 1000 m = int(first_line[0])
>1001 n = int(first_line[1])
>1002 if m >= n:
>
> ValueError: invalid literal for int() with base 10: 'Bad'
>

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[sage-devel] Bad CEq in Find_Equations

[Isuru Fernando]

I get thousands of test failures in 9.0.rc1 due to an error from palp. Any
ideas?

Isuru

sage: toric_varieties.dP6()
 Bad CEq in Find_Equations
---
ValueErrorTraceback (most recent call last)
 in ()
> 1 toric_varieties.dP6()

/projects/66d93023-00f0-4c12-8a25-5d6d4e486740/miniconda3/envs/sage90/lib/python2.7/site-packages/sage/schemes/toric/library.pyc
in dP6(self, names, base_ring)
313 (x, u, y, v, z, w)
314 """
--> 315 return self._make_CPRFanoToricVariety('dP6', names,
base_ring)
316
317 def dP7(self, names='x u y v z', base_ring=QQ):

/projects/66d93023-00f0-4c12-8a25-5d6d4e486740/miniconda3/envs/sage90/lib/python2.7/site-packages/sage/schemes/toric/library.pyc
in _make_CPRFanoToricVariety(self, name, coordinate_names, base_ring)
265 if dict_key not in self.__dict__:
266 polytope = LatticePolytope(rays,
lattice=ToricLattice(len(rays[0])))
--> 267 points = [tuple(_) for _ in polytope.points()]
268 ray2point = [points.index(r) for r in rays]
269 charts = [ [ray2point[i] for i in c] for c in cones ]

/projects/66d93023-00f0-4c12-8a25-5d6d4e486740/miniconda3/envs/sage90/lib/python2.7/site-packages/sage/geometry/lattice_polytope.pyc
in points(self, *args, **kwds)
   3746 if self.dim() == self.lattice_dim():
   3747 print(type(result), result)
-> 3748 points =
read_palp_point_collection(StringIO(result), M)
   3749 else:
   3750 m = self._embed(read_palp_matrix(result))

/projects/66d93023-00f0-4c12-8a25-5d6d4e486740/miniconda3/envs/sage90/lib/python2.7/site-packages/sage/geometry/point_collection.pyx
in sage.geometry.point_collection.read_palp_point_collection
(build/cythonized/sage/geometry/point_collection.c:8111)()
998 return None
999 first_line = first_line.split()
-> 1000 m = int(first_line[0])
   1001 n = int(first_line[1])
   1002 if m >= n:

ValueError: invalid literal for int() with base 10: 'Bad'

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Re: [sage-devel] Re: sage-system-python use in runtime

[Isuru Fernando]

Thanks for the reply.

`sage` script calls `sage-location` and `sage-env` which in turn calls
`sage-num-threads.py`.  So, only `sage-location` and `sage-num-threads.py`
causes problems.

> Most of these are for development work and/or with package maintenance
(for example sage-pkg or sage-unzip), and since they are also used in
various command line options ("./sage -pkg ..."), they should be in src/bin

If that is the case, then shouldn't `sage-system-python` also be in src/bin?

Isuru

On Tue, Dec 31, 2019 at 9:27 PM John H Palmieri 
wrote:

>
>
> On Monday, December 30, 2019 at 9:57:25 PM UTC-8, Isuru Fernando wrote:
>>
>> I'm trying to build sage 9.0.rc1 for conda. For conda what I do is I run,
>> 1. Run configure
>> 2. cp src/bin/* to /bin
>> 3. cp src/ext/* to /share/sage/ext
>> 4. run `python setup.py install` in src
>>
>> This has worked fine until 8.9
>>
>> In 9.0 some scripts in `src/bin/` use `sage-system-python` which is in
>> `build/bin/`. Shouldn't scripts like `sage-system-python` be used only in
>> scripts under `build`?
>>
>> Isuru
>>
>
> These scripts use sage-system-python:
>
> sage-coverage
> sage-coverageall
> sage-location
> sage-num-threads.py
> sage-pkg
> sage-pypkg-location
> sage-unzip
>
> Most of these are for development work and/or with package maintenance
> (for example sage-pkg or sage-unzip), and since they are also used in
> various command line options ("./sage -pkg ..."), they should be in
> src/bin. Also, scripts which are supposed to run even if Sage has not been
> built should use sage-system-python, and some of these fit into that
> category (e.g. the packaging scripts, sage-coverage, maybe
> sage-num-threads). Which scripts are causing problems for you?
>
> --
> John
>
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[sage-devel] sage-system-python use in runtime

[Isuru Fernando]

I'm trying to build sage 9.0.rc1 for conda. For conda what I do is I run,
1. Run configure
2. cp src/bin/* to /bin
3. cp src/ext/* to /share/sage/ext
4. run `python setup.py install` in src

This has worked fine until 8.9

In 9.0 some scripts in `src/bin/` use `sage-system-python` which is in
`build/bin/`. Shouldn't scripts like `sage-system-python` be used only in
scripts under `build`?

Isuru

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Re: [sage-devel] Sage 8.9 build fails on macOS Catalina

[Isuru Fernando]

You can install gfortran from conda (conda install fortran-compiler) or
homebrew (brew install gcc) and sage would pick it up.

Isuru

On Sat, Dec 21, 2019 at 11:26 AM Dima Pasechnik  wrote:

> On Sun, Dec 22, 2019 at 12:34 AM Clayton Cafiero 
> wrote:
> >
> > I'd like to be able to build packages for Sage (e.g., Conjecturing) and
> this doesn't work when installing with conda.
>
> one can build Sage in conda environment, as described in
>
> https://git.sagemath.org/sage.git/diff?id=a596dec9240295b25cd1b48c4092d7eef4d60aed
> on https://trac.sagemath.org/ticket/28745 (which is, admittedly, work
> in progress).
>
> Then one should able to build packages etc.
>
>
> > I may try the beta, that's a good suggestion. Thanks.
> >
> > On Saturday, December 21, 2019 at 11:22:40 AM UTC-5, Dima Pasechnik
> wrote:
> >>
> >> Probably the easiest would be to install Sage from conda:
> >> http://doc.sagemath.org/html/en/installation/conda.html
> >> (provided they already have it for MacOS 10.15 - they do for 10.14,
> >> not sure about 10.15)
> >>
> >> To build from source, you might be on your own, as Sage 8.9 did not
> >> support 10.15  - after all it was released before MacOS 10.15 was
> >> released.
> >> You may have better luck with the latest beta, Sage 9.0.beta9.
> >> In this case you might like to minimise the trouble by using tools
> >> from Homebrew or a similar "missing package manager" - e.g.
> >> then you'd already have gfortran available, you won't need to build it
> yourself.
> >>
> >> HTH,
> >> Dmitrii
> >>
> >>
> >>
> >>
> >>
> >> On Sat, Dec 21, 2019 at 11:40 PM Clayton Cafiero 
> wrote:
> >> >
> >> > macOS Catalina 10.15.2 (19C57)
> >> >
> >> > Tried downloading and installing binary
> (sage-8.9-OSX_10.14.6-x86_64.dmg) but when run macOS complained bitterly
> about every file Sage tried to load when starting with
> >> >
> >> > “python2.7” cannot be opened because the developer cannot be
> verified."
> >> >
> >> >
> >> > If I use System Preferences > Security & Privacy to allow python2.7,
> then another warning appears:
> >> >
> >> >
> >> > “libpython2.7.dylib” cannot be opened because the developer cannot be
> verified."
> >> >
> >> >
> >> > ...I had patience for about the first 100 files (_locale.so, zlib.so,
> _collections.so, blah, blah, blah), then I threw in the towel and tried to
> build.
> >> >
> >> >
> >> > % xcodebuild -version
> >> > Xcode 11.2
> >> > Build version 11B52
> >> >
> >> > Downloaded Sage 8.9 source from mirror. Followed instructions in
> README.md, specifically
> >> >
> >> > * __OS X:__
> >> >* Make sure you have installed the most recent version
> >> >of Xcode which you can install for free from the App Store.
> >> >* You also need to install the "command line tools". When
> >> >using OS X Mavericks, after installing Xcode, run
> >> >`xcode-select --install` from a terminal window:
> >> >Then click "Install" in the pop-up window.
> >> >When using OS X Mountain Lion or earlier, you need to install
> the
> >> >command line tools from Xcode: run Xcode; then from the File
> >> >menu, choose "Preferences", then the "Downloads" tab, and then
> >> >"Install" the Command Line Tools. You might also have Homebrew
> or
> >> >a similar "Apple's missing package manager" system installed,
> with
> >> >and libraries such gfortran, gmp, etc installed. (However, this
> >> >is still experimental as of May 2019).
> >> >
> >> > ...
> >> >
> >> > Extract the tarball
> >> >
> >> >tar zxvf sage-*.tar.gz
> >> >
> >> > cd into the Sage directory and type make
> >> >
> >> >cd sage-*/
> >> >make
> >> >
> >> > This ran for quite a while and then failed, informing me to check
> /Users/myname/Downloads/sage-8.9/logs/pkgs/gfortran-7.4.0.log for more
> information. This file has over 500k lines and ends with
> >> >
> >> > ../../../src/libssp/gets-chk.c:59:13: error: storage class specified
> for parameter '__chk_fail'
> >> >  extern void __chk_fail (void) __attribute__((__noreturn__));
> >> >  ^~
> >> > ../../../src/libssp/gets-chk.c:63:1: error: expected '=', ',', ';',
> 'asm' or '__attribute__' before '{' token
> >> >  {
> >> >  ^
> >> > In file included from
> /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/sys/wait.h:110:0,
> >> >  from
> /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/stdlib.h:66,
> >> >  from ../../../src/libssp/gets-chk.c:39:
> >> >
> /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/sys/resource.h:447:9:
> error: old-style parameter declarations in prototyped function definition
> >> >  int getiopolicy_np(int, int)
> __OSX_AVAILABLE_STARTING(__MAC_10_5, __IPHONE_2_0);
> >> >  ^~
> >> >
> 

Re: [sage-devel] Static libraries

[Isuru Fernando]

On Thu, Dec 19, 2019 at 9:43 PM Dima Pasechnik  wrote:

> On Mon, Dec 16, 2019 at 7:32 PM E. Madison Bray 
> wrote:
> >
> > On Thu, Oct 10, 2019 at 9:24 PM Dima Pasechnik 
> wrote:
> > >
> > > On Debian gp (from pari/gp) links statically to  libpari, for
> performance reasons.
> >
> > Okay, but that's no reason Sage needs to install static libs in
> > $SAGE_LOCAL/lib.  It should only ever be necessary if one package
> > needs to statically link a library from another package at build time
> > for some reason...
>
> a further size saving might be achieved by letting GSL use OpenBLAS
> rather than built its own BLAS.
> While OpenBLAS is listed as GSL's dependency, it's actually not used
> in Sage (so it's puzzling to me
> why $(BLAS) is even a dependency of GSL, perhaps some historical reasons)
>

It is linked. See
https://github.com/sagemath/sage/blob/f0ae571d17e685258c1de89c2a29953f4d8fb302/build/pkgs/gsl/spkg-install#L11


> Alternatively one, I suppose, may use GSL's BLAS in the whole of Sage,
> and do not build OpenBLAS
> (this is certainly a loss in efficiency, but a win in ease of building etc)
>

No, GSL's gslcblas provides only CBLAS API and doesn't provide BLAS or
LAPACK APIs.

Isuru

>
> Dima
>
>
> >
> > > On Thu, Oct 10, 2019 at 2:19 PM François Bissey 
> wrote:
> > >>
> > >>
> > >>
> > >> > On 11/10/2019, at 4:53 AM, Dima Pasechnik 
> wrote:
> > >> >
> > >> > (IIRC there are few places that need static libs)
> > >>
> > >> There are a few places where people claim they want the static
> libraries
> > >> for performance reasons. I live perfectly well without static
> libraries
> > >> in sage-on-gentoo and I would think most other distros would too.
> > >>
> > >> François
> > >>
> > >> --
> > >> 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] CentOS installation problems

[Isuru Fernando]

On Tue, Nov 12, 2019 at 11:21 AM Mike Zabrocki 
wrote:

> So make freetype-clean
> returns:
>
> make build/make/Makefile --stop
>
> make[1]: Entering directory `/usr/local/sage-8.9'
>
> make[1]: `build/make/Makefile' is up to date.
>
> make[1]: Leaving directory `/usr/local/sage-8.9'
>
> build/bin/sage-logger \
>
> "cd build/make && ./install 'freetype-clean'" logs/install.log
>
> make[1]: Entering directory `/usr/local/sage-8.9/build/make'
>
> make[1]: Leaving directory `/usr/local/sage-8.9/build/make'
>
> *** ALL ENVIRONMENT VARIABLES BEFORE BUILD: ***
>
> }
>
> BASH_FUNC_module()=() {  eval `/usr/bin/modulecmd bash $*`
>
> _=/bin/env
>
> CONFIGURED_CC=gcc
>
> CONFIGURED_CXX=g++
>
> CONFIGURED_FC=gfortran
>
> CONFIGURED_OBJC=gcc
>
> CONFIGURED_OBJCXX=g++
>
> CVS_RSH=ssh
>
> G_BROKEN_FILENAMES=1
>
> HISTCONTROL=ignoredups
>
> HISTSIZE=1000
>
> ...
>
> ***
>
> make[1]: Entering directory `/usr/local/sage-8.9/build/make'
>
> sage-spkg-uninstall  freetype '/usr/local/sage-8.9/local'
>
> Package 'freetype' is currently not installed
>
> No legacy uninstaller found for 'freetype'; nothing to do
>
> make[1]: Leaving directory `/usr/local/sage-8.9/build/make'
>
>
> real 0m0.080s
>
> user 0m0.060s
>
> sys 0m0.018s
>
> Sage build/upgrade complete!
>
> The version is "CentOS release 6.10"
> If the problem is that is too old, then I'll start by upgrading the OS.
>

It's not. We build conda binary packages for Sage on CentOS 6.10 and they
work fine.

Isuru


> -Mike
>
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> 
> .
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Re: [sage-devel] Linux install fails

[Isuru Fernando]

What does

ldd /home/tengely/software/sage-8.9/local/lib/liblinbox.so.0

give you? Looks like libgomp used at runtime is older than what is at build
time.

Isuru

On Thu, Nov 7, 2019 at 4:07 PM Dima Pasechnik  wrote:

> sagenb build error is a red herring here.
>
> the problem is that Sage, needed to build sagenb, does not start.
>
>
> On Thu, 7 Nov 2019, 21:51 Sz Tengely,  wrote:
>
>> install.log contains the following:
>>
>> [sagenb-1.1.2] Exception occurred:
>> [sagenb-1.1.2]   File "sage/misc/lazy_import.pyx", line 218, in
>> sage.misc.lazy_i
>> mport.LazyImport._get_object
>> (build/cythonized/sage/misc/lazy_import.c:2502)
>> [sagenb-1.1.2] raise RuntimeError(f"resolving lazy import
>> {self._name} durin
>> g startup")
>> [sagenb-1.1.2] RuntimeError: resolving lazy import dumps during startup
>> [sagenb-1.1.2] The full traceback has been saved in
>> /tmp/sphinx-err-F4trNY.log,
>> if you want to report the issue to the developers.
>> [sagenb-1.1.2] Please also report this if it was a user error, so that a
>> better
>> error message can be provided next time.
>> [sagenb-1.1.2] A bug report can be filed in the tracker at <
>> https://github.com/s
>> phinx-doc/sphinx/issues>. Thanks!
>> [sagenb-1.1.2] make[4]: *** [Makefile:20: html] Error 2
>> [sagenb-1.1.2] make[4]: Leaving directory
>> '/home/tengely/software/sage-8.9/local
>> /var/tmp/sage/build/sagenb-1.1.2/src/doc'
>> [sagenb-1.1.2]
>> *
>> ***
>> [sagenb-1.1.2] Error building the documentation
>>
>>
>>
>>
>> On Thursday, November 7, 2019 at 10:41:45 PM UTC+1, Sz Tengely wrote:
>>>
>>> The log file is attached.
>>>
>>>
>>> On Thursday, November 7, 2019 at 10:08:51 PM UTC+1, Dima Pasechnik wrote:

 ImportError: /home/tengely/software/sage-8.9/local/lib/liblinbox.so.0: 
 undefined symbol: GOMP_loop_ull_maybe_nonmonotonic_runtime_next


 something went wrong with installing linbox.


 please post the relevant log.


 On Thu, 7 Nov 2019, 21:01 Sz Tengely,  wrote:

> Hi,
>
> I tried to install SageMath 8.9 from source and there was an error
> message at the end related to sagenb-1.1.2 (attached the log file). Google
> search directed me to the post
> https://groups.google.com/forum/#!topic/sage-devel/icbegwpf_3I where Dima
> Pasechnik wrote that one should try to run ./sage, so I did so and the
> appropriate crash report is attached as well.
>
> Operating system: 64 bit Linux, Manjaro 18.1.2
>
> Sage was installed: source, version 8.9, with export MAKE="make -j4"
>
> Reproduce the crash: I followed the README.md file, extracted the
> tarball, export MAKE="make -j4" and make.
>
> Thank you for your help in advance.
>
> With kind regards,
>  Szabolcs
>
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> .
>
 --
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Re: [sage-devel] MacOS 10.15.1: gfortran does not compile in sage-8.9

[Isuru Fernando]

Can you do `source
/Volumes/Transcend/wooster/computer-algebra/anaconda3/bin/activate -p
/Volumes/Transcend/wooster/computer-algebra/anaconda3/envs/mac1015-env` ?

On Fri, Nov 1, 2019 at 1:39 PM David Joyner  wrote:

>
>
> On Fri, Nov 1, 2019 at 1:25 PM Isuru Fernando  wrote:
>
>> You need to activate the sage environment which would set SAGE_ROOT.
>>
>> `conda activate mac1015-env`
>>
>>
> This gives me an error with the zsh shell not being initialized, while
>
> conda init zsh
>
> lists things like
>
> no change /Users/wdj/.zshrc
> No action taken.
>
> I also tried switching to the bash shell, but that did not work
> either.
>
>
>
>> Isuru
>>
>> On Fri, Nov 1, 2019 at 6:07 AM David Joyner  wrote:
>>
>>>
>>>
>>> On Thu, Oct 31, 2019 at 9:58 PM Isuru Fernando  wrote:
>>>
>>>> Try installing sage to a new environment instead of an existing one.
>>>>
>>>>
>>> This seemed to work, at least it installed the sage scripts in
>>>
>>> /Volumes/Transcend/wooster/computer-algebra/anaconda3/envs/mac1015-env/bin
>>> (the environment is called mac1015-env). The sage script doesn't run
>>> since I don't know where to set SAGE_ROOT. I don't see any binaries.
>>> I think I managed to activate the new environment since it modified the
>>> .zshrc file but adding that directory to the PATH.
>>>
>>>
>>>> On Thu, Oct 31, 2019 at 5:31 PM David Joyner 
>>>> wrote:
>>>>
>>>>>
>>>>>
>>>>> On Wed, Oct 30, 2019 at 6:04 PM Dima Pasechnik 
>>>>> wrote:
>>>>>
>>>>>> I think at the moment most people who tried cannot build Sage on MacOS
>>>>>> 10.15 with Xcode 11.1 (the latest one).
>>>>>> Regarding gfortran, perhaps one can try installing Homebrew and use
>>>>>> gfortram from there.
>>>>>>
>>>>>> If you just need a working Sage, your best bet on MacOS 10.15 might be
>>>>>> the one from conda-forge.
>>>>>> https://anaconda.org/conda-forge/sage
>>>>>>
>>>>>>
>>>>> This doesn't seem to work for me either.
>>>>> anaconda installed but
>>>>> conda install -c conda-forge sage
>>>>> (and friends) returned lots of "Solving environment: failed ..."
>>>>> lines.
>>>>>
>>>>>
>>>>>
>>>>>>
>>>>>>
>>>>>> On Wed, Oct 30, 2019 at 10:57 PM Rob Gross <
>>>>>> robert.gross.1...@gmail.com> wrote:
>>>>>> >
>>>>>> > Hi,
>>>>>> >
>>>>>> > I tried both upgrading to sage-8.9 and compiling from scratch, and
>>>>>> both times gfortran would not compile.  I cannot attach the entire log 
>>>>>> file
>>>>>> without an error.  I attach the first few lines and the last few lines, 
>>>>>> and
>>>>>> of course I can e-mail anyone with as much information as needed.
>>>>>> >
>>>>>> > Here is the first error message in the log file:
>>>>>> >
>>>>>> > libtool: compile:
>>>>>> /Users/gross/sage-8.9/local/var/tmp/sage/build/gfortran-7.4.0/gcc-build/./gcc/xgcc
>>>>>> -B/Users/gross/sage-8.9/local/var/tmp/sage/build/gfortran-7.4.0/gcc-build/./gcc/
>>>>>> -B/Users/gross/sage-8.9/local/x86_64-apple-darwin19.0.0/bin/
>>>>>> -B/Users/gross/sage-8.9/local/x86_64-apple-darwin19.0.0/lib/ -isystem
>>>>>> /Users/gross/sage-8.9/local/x86_64-apple-darwin19.0.0/include -isystem
>>>>>> /Users/gross/sage-8.9/local/x86_64-apple-darwin19.0.0/sys-include
>>>>>> -DHAVE_CONFIG_H -I. -I../../../src/libssp -Wall -g -O2 -MT gets-chk.lo 
>>>>>> -MD
>>>>>> -MP -MF .deps/gets-chk.Tpo -c ../../../src/libssp/gets-chk.c  -fno-common
>>>>>> -DPIC -o .libs/gets-chk.o
>>>>>> > In file included from
>>>>>> /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/sys/wait.h:110:0,
>>>>>> >  from
>>>>>> /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/stdlib.h:66,
>>>>>> >  from ../../../src/l

Re: [sage-devel] MacOS 10.15.1: gfortran does not compile in sage-8.9

[Isuru Fernando]

You need to activate the sage environment which would set SAGE_ROOT.

`conda activate mac1015-env`

Isuru

On Fri, Nov 1, 2019 at 6:07 AM David Joyner  wrote:

>
>
> On Thu, Oct 31, 2019 at 9:58 PM Isuru Fernando  wrote:
>
>> Try installing sage to a new environment instead of an existing one.
>>
>>
> This seemed to work, at least it installed the sage scripts in
> /Volumes/Transcend/wooster/computer-algebra/anaconda3/envs/mac1015-env/bin
> (the environment is called mac1015-env). The sage script doesn't run
> since I don't know where to set SAGE_ROOT. I don't see any binaries.
> I think I managed to activate the new environment since it modified the
> .zshrc file but adding that directory to the PATH.
>
>
>> On Thu, Oct 31, 2019 at 5:31 PM David Joyner  wrote:
>>
>>>
>>>
>>> On Wed, Oct 30, 2019 at 6:04 PM Dima Pasechnik 
>>> wrote:
>>>
>>>> I think at the moment most people who tried cannot build Sage on MacOS
>>>> 10.15 with Xcode 11.1 (the latest one).
>>>> Regarding gfortran, perhaps one can try installing Homebrew and use
>>>> gfortram from there.
>>>>
>>>> If you just need a working Sage, your best bet on MacOS 10.15 might be
>>>> the one from conda-forge.
>>>> https://anaconda.org/conda-forge/sage
>>>>
>>>>
>>> This doesn't seem to work for me either.
>>> anaconda installed but
>>> conda install -c conda-forge sage
>>> (and friends) returned lots of "Solving environment: failed ..."
>>> lines.
>>>
>>>
>>>
>>>>
>>>>
>>>> On Wed, Oct 30, 2019 at 10:57 PM Rob Gross 
>>>> wrote:
>>>> >
>>>> > Hi,
>>>> >
>>>> > I tried both upgrading to sage-8.9 and compiling from scratch, and
>>>> both times gfortran would not compile.  I cannot attach the entire log file
>>>> without an error.  I attach the first few lines and the last few lines, and
>>>> of course I can e-mail anyone with as much information as needed.
>>>> >
>>>> > Here is the first error message in the log file:
>>>> >
>>>> > libtool: compile:
>>>> /Users/gross/sage-8.9/local/var/tmp/sage/build/gfortran-7.4.0/gcc-build/./gcc/xgcc
>>>> -B/Users/gross/sage-8.9/local/var/tmp/sage/build/gfortran-7.4.0/gcc-build/./gcc/
>>>> -B/Users/gross/sage-8.9/local/x86_64-apple-darwin19.0.0/bin/
>>>> -B/Users/gross/sage-8.9/local/x86_64-apple-darwin19.0.0/lib/ -isystem
>>>> /Users/gross/sage-8.9/local/x86_64-apple-darwin19.0.0/include -isystem
>>>> /Users/gross/sage-8.9/local/x86_64-apple-darwin19.0.0/sys-include
>>>> -DHAVE_CONFIG_H -I. -I../../../src/libssp -Wall -g -O2 -MT gets-chk.lo -MD
>>>> -MP -MF .deps/gets-chk.Tpo -c ../../../src/libssp/gets-chk.c  -fno-common
>>>> -DPIC -o .libs/gets-chk.o
>>>> > In file included from
>>>> /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/sys/wait.h:110:0,
>>>> >  from
>>>> /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/stdlib.h:66,
>>>> >  from ../../../src/libssp/gets-chk.c:39:
>>>> >
>>>> /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/sys/resource.h:
>>>> In function 'getiopolicy_np':
>>>> >
>>>> /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/sys/resource.h:443:34:
>>>> error: expected declaration specifiers before '__OSX_AVAILABLE_STARTING'
>>>> >  int getiopolicy_np(int, int)
>>>> __OSX_AVAILABLE_STARTING(__MAC_10_5, __IPHONE_2_0);
>>>> >   ^~~~
>>>> >
>>>> /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/sys/resource.h:449:39:
>>>> error: expected '=', ',', ';', 'asm' or '__attribute__' before
>>>> '__OSX_AVAILABLE_STARTING'
>>>> >  int setiopolicy_np(int, int, int)
>>>> __OSX_AVAILABLE_STARTING(__MAC_10_5, __IPHONE_2_0);
>>>> >
>>>> > Any ideas?
>>>> >
>>>> > Thanks.--Rob
>>>> >
>>>> > --
>>>> > You received this message because you are subscribed t

Re: [sage-devel] MacOS 10.15.1: gfortran does not compile in sage-8.9

[Isuru Fernando]

Try installing sage to a new environment instead of an existing one.

On Thu, Oct 31, 2019 at 5:31 PM David Joyner  wrote:

>
>
> On Wed, Oct 30, 2019 at 6:04 PM Dima Pasechnik  wrote:
>
>> I think at the moment most people who tried cannot build Sage on MacOS
>> 10.15 with Xcode 11.1 (the latest one).
>> Regarding gfortran, perhaps one can try installing Homebrew and use
>> gfortram from there.
>>
>> If you just need a working Sage, your best bet on MacOS 10.15 might be
>> the one from conda-forge.
>> https://anaconda.org/conda-forge/sage
>>
>>
> This doesn't seem to work for me either.
> anaconda installed but
> conda install -c conda-forge sage
> (and friends) returned lots of "Solving environment: failed ..."
> lines.
>
>
>
>>
>>
>> On Wed, Oct 30, 2019 at 10:57 PM Rob Gross 
>> wrote:
>> >
>> > Hi,
>> >
>> > I tried both upgrading to sage-8.9 and compiling from scratch, and both
>> times gfortran would not compile.  I cannot attach the entire log file
>> without an error.  I attach the first few lines and the last few lines, and
>> of course I can e-mail anyone with as much information as needed.
>> >
>> > Here is the first error message in the log file:
>> >
>> > libtool: compile:
>> /Users/gross/sage-8.9/local/var/tmp/sage/build/gfortran-7.4.0/gcc-build/./gcc/xgcc
>> -B/Users/gross/sage-8.9/local/var/tmp/sage/build/gfortran-7.4.0/gcc-build/./gcc/
>> -B/Users/gross/sage-8.9/local/x86_64-apple-darwin19.0.0/bin/
>> -B/Users/gross/sage-8.9/local/x86_64-apple-darwin19.0.0/lib/ -isystem
>> /Users/gross/sage-8.9/local/x86_64-apple-darwin19.0.0/include -isystem
>> /Users/gross/sage-8.9/local/x86_64-apple-darwin19.0.0/sys-include
>> -DHAVE_CONFIG_H -I. -I../../../src/libssp -Wall -g -O2 -MT gets-chk.lo -MD
>> -MP -MF .deps/gets-chk.Tpo -c ../../../src/libssp/gets-chk.c  -fno-common
>> -DPIC -o .libs/gets-chk.o
>> > In file included from
>> /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/sys/wait.h:110:0,
>> >  from
>> /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/stdlib.h:66,
>> >  from ../../../src/libssp/gets-chk.c:39:
>> >
>> /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/sys/resource.h:
>> In function 'getiopolicy_np':
>> >
>> /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/sys/resource.h:443:34:
>> error: expected declaration specifiers before '__OSX_AVAILABLE_STARTING'
>> >  int getiopolicy_np(int, int) __OSX_AVAILABLE_STARTING(__MAC_10_5,
>> __IPHONE_2_0);
>> >   ^~~~
>> >
>> /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/sys/resource.h:449:39:
>> error: expected '=', ',', ';', 'asm' or '__attribute__' before
>> '__OSX_AVAILABLE_STARTING'
>> >  int setiopolicy_np(int, int, int)
>> __OSX_AVAILABLE_STARTING(__MAC_10_5, __IPHONE_2_0);
>> >
>> > Any ideas?
>> >
>> > Thanks.--Rob
>> >
>> > --
>> > 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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>> https://groups.google.com/d/msgid/sage-devel/b557aad7-51f6-469b-9dac-bac679275400%40googlegroups.com
>> .
>>
>> --
>> You received this message because you are subscribed to the Google Groups
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>> To unsubscribe from this group and stop receiving emails from it, send an
>> email to sage-devel+unsubscr...@googlegroups.com.
>> To view this discussion on the web visit
>> https://groups.google.com/d/msgid/sage-devel/CAAWYfq3LG%2Bj6eWxrYtJ7K%3Dc__PTtC%3DkNyWX9J8ywNY-u%3DPeugA%40mail.gmail.com
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>>
> --
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> .
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Re: [sage-devel] sagemath 8.9 is not complied on macOS Catalina with python3

[Isuru Fernando]

Yes, sage on conda-forge supports python 2.7, 3.6 and 3.7 on linux (glibc
x86_64) and osx-64.

Isuru

On Fri, Oct 18, 2019 at 11:07 AM Dima Pasechnik  wrote:

> It's hit and miss for Sage to build on Catalina, I think the latest
> Xcode cannot not build it.
> Otherwise there is an option to use Conda, which allows you to select
> Python3, as far as I know
> (Isuru will correct me if I'm wrong...)
>
> On Fri, Oct 18, 2019 at 4:07 PM Junwei Wang  wrote:
> >
> > Besides, could the SAGE team officially release binary with Python 3
> (although it is not stable), since we are force to use python3 in many
> cases and it is painful to compile by user themselves?
> >
> > --
> > 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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> https://groups.google.com/d/msgid/sage-devel/819fdf68-241e-4b1f-98e7-07306733a5da%40googlegroups.com
> .
>

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Re: [sage-devel] Error installing scipy-1.2.0 when compiling sage math 9.0.beta1

[Isuru Fernando]

You have the same issue as https://github.com/sagemath/binary-pkg/issues/19

Can you try downloading 10.14 SDK from
https://github.com/phracker/MacOSX-SDKs/releases/download/10.14-beta4/MacOSX10.14.sdk.tar.xz
extracting it inside
`/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk`

Isuru

On Sun, Oct 13, 2019 at 10:27 AM David Coudert 
wrote:

> No, but MacOSX10.15.sdk
>
> confetti:lib dcoudert$ ll
> /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
> ls:
> /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk:
> No such file or directory
> confetti:lib dcoudert$ ll
> /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/
> total 0
> drwxr-xr-x  4 root  wheel  128 12 sep 05:13 DriverKit19.0.sdk
> drwxr-xr-x  8 root  wheel  256 12 sep 05:13 MacOSX.sdk
> lrwxr-xr-x  1 root  wheel   10  8 oct 15:28 MacOSX10.15.sdk -> MacOSX.sdk
>
>
> Le 13 oct. 2019 à 17:16, Isuru Fernando  a écrit :
>
> Hi,
>
> Do you have the folder 
> /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
> ?
>
> Isuru
>
> On Sun, Oct 13, 2019 at 10:14 AM David Coudert 
> wrote:
>
>> here it is.
>>
>> confetti:lib dcoudert$  /Users/dcoudert/sage3/sage/local/bin/gfortran
>> -print-prog-name=ld
>> ld
>> confetti:lib dcoudert$  /Users/dcoudert/sage3/sage/local/bin/gfortran -v
>> Using built-in specs.
>> COLLECT_GCC=/Users/dcoudert/sage3/sage/local/bin/gfortran
>>
>> COLLECT_LTO_WRAPPER=/Users/dcoudert/sage3/sage/local/libexec/gcc/x86_64-apple-darwin18.6.0/7.4.0/lto-wrapper
>> Target: x86_64-apple-darwin18.6.0
>> Configured with: ../src/configure
>> --prefix=/Users/dcoudert/sage3/sage/local
>> --with-local-prefix=/Users/dcoudert/sage3/sage/local
>> --with-gmp=/Users/dcoudert/sage3/sage/local
>> --with-mpfr=/Users/dcoudert/sage3/sage/local
>> --with-mpc=/Users/dcoudert/sage3/sage/local --with-system-zlib
>> --without-isl --disable-multilib --disable-nls --disable-libitm
>> --with-build-config=bootstrap-debug --without-isl --without-cloog
>> --with-sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
>> --disable-bootstrap --enable-languages=fortran
>> Thread model: posix
>> gcc version 7.4.0 (GCC)
>>
>>
>> Le 13 oct. 2019 à 16:47, Isuru Fernando  a écrit :
>>
>> Hi,
>>
>> This is a problem with gfortran using an incorrect linker.
>>
>> Can you post the output of,
>>
>>  /Users/dcoudert/sage3/sage/local/bin/gfortran -print-prog-name=ld
>>
>>  /Users/dcoudert/sage3/sage/local/bin/gfortran -v
>>
>> Isuru
>>
>>
>> On Sun, Oct 13, 2019 at 8:21 AM David Coudert 
>> wrote:
>>
>>> confetti:lib dcoudert$ otool -L libfflas.dylib
>>> libfflas.dylib:
>>> /Users/dcoudert/sage3/sage/local/lib/libfflas.1.dylib (compatibility
>>> version 2.0.0, current version 2.0.0)
>>> /Users/dcoudert/sage3/sage/local/lib/libgivaro.9.dylib (compatibility
>>> version 11.0.0, current version 11.1.0)
>>> /Users/dcoudert/sage3/sage/local/lib/libgmp.23.dylib (compatibility
>>> version 24.0.0, current version 24.3.0)
>>> /Users/dcoudert/sage3/sage/local/lib/libgmpxx.8.dylib (compatibility
>>> version 13.0.0, current version 13.3.0)
>>> /Users/dcoudert/sage3/sage/local/lib/libopenblas_haswellp-r0.3.6.dylib
>>> (compatibility version 0.0.0, current version 0.0.0)
>>> /usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version
>>> 400.9.4)
>>> /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version
>>> 1252.250.1)
>>>
>>>
>>> Le 13 oct. 2019 à 15:19, Dima Pasechnik  a écrit :
>>>
>>> oops sorry, your gfortran is ok.
>>> how about fflas* package, it is probably broken...
>>>
>>> On Sun, 13 Oct 2019, 14:17 Dima Pasechnik,  wrote:
>>>
>>>> are you building gfortran in Sage, or using a prebuilt one?
>>>>
>>>> it might be that its libgfortran got broken
>>>>
>>>> On Sun, 13 Oct 2019, 13:01 David Coudert, 
>>>> wrote:
>>>>
>>>>>
>>>>>
>>>>> confetti:lib dcoudert$ pwd
>>>>>
>>>>> /Users/dcoudert/sage3/sage/local/lib
>>>>>
>>>>> confetti:lib dcoudert$ otool -L libgfortran.dylib
>>>>>
>>>>> libgfortran.d

Re: [sage-devel] Error installing scipy-1.2.0 when compiling sage math 9.0.beta1

[Isuru Fernando]

Hi,

Do you have the folder
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
?

Isuru

On Sun, Oct 13, 2019 at 10:14 AM David Coudert 
wrote:

> here it is.
>
> confetti:lib dcoudert$  /Users/dcoudert/sage3/sage/local/bin/gfortran
> -print-prog-name=ld
> ld
> confetti:lib dcoudert$  /Users/dcoudert/sage3/sage/local/bin/gfortran -v
> Using built-in specs.
> COLLECT_GCC=/Users/dcoudert/sage3/sage/local/bin/gfortran
>
> COLLECT_LTO_WRAPPER=/Users/dcoudert/sage3/sage/local/libexec/gcc/x86_64-apple-darwin18.6.0/7.4.0/lto-wrapper
> Target: x86_64-apple-darwin18.6.0
> Configured with: ../src/configure
> --prefix=/Users/dcoudert/sage3/sage/local
> --with-local-prefix=/Users/dcoudert/sage3/sage/local
> --with-gmp=/Users/dcoudert/sage3/sage/local
> --with-mpfr=/Users/dcoudert/sage3/sage/local
> --with-mpc=/Users/dcoudert/sage3/sage/local --with-system-zlib
> --without-isl --disable-multilib --disable-nls --disable-libitm
> --with-build-config=bootstrap-debug --without-isl --without-cloog
> --with-sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
> --disable-bootstrap --enable-languages=fortran
> Thread model: posix
> gcc version 7.4.0 (GCC)
>
>
> Le 13 oct. 2019 à 16:47, Isuru Fernando  a écrit :
>
> Hi,
>
> This is a problem with gfortran using an incorrect linker.
>
> Can you post the output of,
>
>  /Users/dcoudert/sage3/sage/local/bin/gfortran -print-prog-name=ld
>
>  /Users/dcoudert/sage3/sage/local/bin/gfortran -v
>
> Isuru
>
>
> On Sun, Oct 13, 2019 at 8:21 AM David Coudert 
> wrote:
>
>> confetti:lib dcoudert$ otool -L libfflas.dylib
>> libfflas.dylib:
>> /Users/dcoudert/sage3/sage/local/lib/libfflas.1.dylib (compatibility
>> version 2.0.0, current version 2.0.0)
>> /Users/dcoudert/sage3/sage/local/lib/libgivaro.9.dylib (compatibility
>> version 11.0.0, current version 11.1.0)
>> /Users/dcoudert/sage3/sage/local/lib/libgmp.23.dylib (compatibility
>> version 24.0.0, current version 24.3.0)
>> /Users/dcoudert/sage3/sage/local/lib/libgmpxx.8.dylib (compatibility
>> version 13.0.0, current version 13.3.0)
>> /Users/dcoudert/sage3/sage/local/lib/libopenblas_haswellp-r0.3.6.dylib
>> (compatibility version 0.0.0, current version 0.0.0)
>> /usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version
>> 400.9.4)
>> /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version
>> 1252.250.1)
>>
>>
>> Le 13 oct. 2019 à 15:19, Dima Pasechnik  a écrit :
>>
>> oops sorry, your gfortran is ok.
>> how about fflas* package, it is probably broken...
>>
>> On Sun, 13 Oct 2019, 14:17 Dima Pasechnik,  wrote:
>>
>>> are you building gfortran in Sage, or using a prebuilt one?
>>>
>>> it might be that its libgfortran got broken
>>>
>>> On Sun, 13 Oct 2019, 13:01 David Coudert, 
>>> wrote:
>>>
>>>>
>>>>
>>>> confetti:lib dcoudert$ pwd
>>>>
>>>> /Users/dcoudert/sage3/sage/local/lib
>>>>
>>>> confetti:lib dcoudert$ otool -L libgfortran.dylib
>>>>
>>>> libgfortran.dylib:
>>>>
>>>> /Users/dcoudert/sage3/sage/local/lib/libgfortran.4.dylib (compatibility
>>>> version 5.0.0, current version 5.0.0)
>>>>
>>>> /Users/dcoudert/sage3/sage/local/lib/libquadmath.0.dylib (compatibility
>>>> version 1.0.0, current version 1.0.0)
>>>>
>>>> /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current
>>>> version 1252.250.1)
>>>>
>>>> /Users/dcoudert/sage3/sage/local/lib/libgcc_s.1.dylib (compatibility
>>>> version 1.0.0, current version 1.0.0)
>>>>
>>>>
>>>> but I don't have the 2 others
>>>>
>>>> confetti:sage dcoudert$ ls -lR | grep ftpack | grep dylib
>>>>
>>>> confetti:sage dcoudert$ pwd
>>>>
>>>> /Users/dcoudert/sage3/sage
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> Le dimanche 13 octobre 2019 13:48:55 UTC+2, Dima Pasechnik a écrit :
>>>>>
>>>>> I gather that the error comes from one of  -ldfftpack -lfftpack
>>>>> -lgfortran
>>>>> being incorrectly linked/broken.
>>>>>
>>>>> please locate the relevant lib*.dylib files (in SAGE_LOCAL?) and run
>>>>> "otool -L" on each of them
>>>>> to see if they are OK.
>>>>>
>>>&

Re: [sage-devel] Error installing scipy-1.2.0 when compiling sage math 9.0.beta1

[Isuru Fernando]

Hi,

This is a problem with gfortran using an incorrect linker.

Can you post the output of,

 /Users/dcoudert/sage3/sage/local/bin/gfortran -print-prog-name=ld

 /Users/dcoudert/sage3/sage/local/bin/gfortran -v

Isuru


On Sun, Oct 13, 2019 at 8:21 AM David Coudert 
wrote:

> confetti:lib dcoudert$ otool -L libfflas.dylib
> libfflas.dylib:
> /Users/dcoudert/sage3/sage/local/lib/libfflas.1.dylib (compatibility
> version 2.0.0, current version 2.0.0)
> /Users/dcoudert/sage3/sage/local/lib/libgivaro.9.dylib (compatibility
> version 11.0.0, current version 11.1.0)
> /Users/dcoudert/sage3/sage/local/lib/libgmp.23.dylib (compatibility
> version 24.0.0, current version 24.3.0)
> /Users/dcoudert/sage3/sage/local/lib/libgmpxx.8.dylib (compatibility
> version 13.0.0, current version 13.3.0)
> /Users/dcoudert/sage3/sage/local/lib/libopenblas_haswellp-r0.3.6.dylib
> (compatibility version 0.0.0, current version 0.0.0)
> /usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version
> 400.9.4)
> /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version
> 1252.250.1)
>
>
> Le 13 oct. 2019 à 15:19, Dima Pasechnik  a écrit :
>
> oops sorry, your gfortran is ok.
> how about fflas* package, it is probably broken...
>
> On Sun, 13 Oct 2019, 14:17 Dima Pasechnik,  wrote:
>
>> are you building gfortran in Sage, or using a prebuilt one?
>>
>> it might be that its libgfortran got broken
>>
>> On Sun, 13 Oct 2019, 13:01 David Coudert,  wrote:
>>
>>>
>>>
>>> confetti:lib dcoudert$ pwd
>>>
>>> /Users/dcoudert/sage3/sage/local/lib
>>>
>>> confetti:lib dcoudert$ otool -L libgfortran.dylib
>>>
>>> libgfortran.dylib:
>>>
>>> /Users/dcoudert/sage3/sage/local/lib/libgfortran.4.dylib (compatibility
>>> version 5.0.0, current version 5.0.0)
>>>
>>> /Users/dcoudert/sage3/sage/local/lib/libquadmath.0.dylib (compatibility
>>> version 1.0.0, current version 1.0.0)
>>>
>>> /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version
>>> 1252.250.1)
>>>
>>> /Users/dcoudert/sage3/sage/local/lib/libgcc_s.1.dylib (compatibility
>>> version 1.0.0, current version 1.0.0)
>>>
>>>
>>> but I don't have the 2 others
>>>
>>> confetti:sage dcoudert$ ls -lR | grep ftpack | grep dylib
>>>
>>> confetti:sage dcoudert$ pwd
>>>
>>> /Users/dcoudert/sage3/sage
>>>
>>>
>>>
>>>
>>>
>>> Le dimanche 13 octobre 2019 13:48:55 UTC+2, Dima Pasechnik a écrit :

 I gather that the error comes from one of  -ldfftpack -lfftpack
 -lgfortran
 being incorrectly linked/broken.

 please locate the relevant lib*.dylib files (in SAGE_LOCAL?) and run
 "otool -L" on each of them
 to see if they are OK.


 On Sun, Oct 13, 2019 at 12:43 PM David Coudert 
 wrote:
 >
 > it's an incremental build from 9.0.beta0.
 > I upgraded my OS in July after a system crash. So I had to reinstall
 everything from scratch.
 >
 > In case, I have Xcode Version 11.1 (11A1027).
 >
 > Le dimanche 13 octobre 2019 13:29:21 UTC+2, Dima Pasechnik a écrit :
 >>
 >> Is this a build from scratch?
 >> (after an OS upgrade, incremental builds may break)
 >>
 >>
 >> On Sun, Oct 13, 2019 at 12:19 PM David Coudert 
 wrote:
 >> >
 >> >
 >> >
 >> > Le dimanche 13 octobre 2019 12:53:02 UTC+2, Dima Pasechnik a écrit
 :
 >> >>
 >> >> We have already seen that puzzling
 >> >>
 >> >> ld: library not found for -lSystem
 >> >>
 >> >> error message.
 >> >>
 >> >> Is there a /usr/lib/libSystem.dylib present?
 >> >
 >> >
 >> > Yes:
 >> >
 >> >
 >> > confetti:sage dcoudert$ ll /usr/lib/libSystem.dylib
 >> >
 >> > lrwxr-xr-x  1 root  wheel  17 19 jul 08:15
 /usr/lib/libSystem.dylib -> libSystem.B.dylib
 >> >
 >> >
 >> >
 >> >>
 >> >> If yes, then I guess this means a broken dependency of scipy, more

 >> >> specifically, a broken dylib, built
 >> >> along the way.
 >> >> or Xcode that needs to be reinstalled...
 >> >>
 >> >> Can you do
 >> >> ./sage --python
 >> >> >> import numpy
 >> >>
 >> >> without an error?
 >> >
 >> >
 >> > yes too:
 >> >
 >> > confetti:sage dcoudert$ ./sage --python
 >> >
 >> > Python 3.7.3 (default, Oct 13 2019, 02:06:13)
 >> >
 >> > [Clang 11.0.0 (clang-1100.0.33.8)] on darwin
 >> >
 >> > Type "help", "copyright", "credits" or "license" for more
 information.
 >> >
 >> > >>> import numpy
 >> >
 >> > >>>
 >> >
 >> >
 >> >
 >> >
 >> > --
 >> > 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-...@googlegroups.com.
 >> > To view this discussion on the web visit
 https://groups.google.com/d/msgid/sage-devel/848357f8-1c79-481a-abb3-e87331775d8a%40googlegroups.com
 .
 >
 > 

Re: [sage-devel] NTL error with conda sage

[Isuru Fernando]

Yes, that's the expected output, but for me sage crashes with,

sage: matrix(ZZ,3,[1..9]).hermite_form(algorithm='ntl') ## line 1883 ##

halt 2

**

On Fri, Sep 27, 2019 at 6:59 PM François Bissey 
wrote:

> Is this what you expect to happen but doesn’t?
> fbissey@moonloop ~ $ sage
> ┌┐
> │ SageMath version 8.9.rc0, Release Date: 2019-09-11 │
> │ Using Python 2.7.15. Type "help()" for help.   │
> └┘
> ┏┓
> ┃ Warning: this is a prerelease version, and it may be unstable. ┃
> ┗┛
> sage: matrix(ZZ,3,[1..9]).hermite_form(algorithm='ntl')
> ---
> ValueErrorTraceback (most recent call last)
>  in ()
> > 1
> matrix(ZZ,Integer(3),(ellipsis_range(Integer(1),Ellipsis,Integer(9.hermite_form(algorithm='ntl')
>
> /usr/lib64/python2.7/site-packages/sage/matrix/matrix_integer_dense.pyx in
> sage.matrix.matrix_integer_dense.Matrix_integer_dense.echelon_form
> (/dev/shm/portage/sci-mathematics/sage-/work/sage-/src-python2_7/build/cythonized/sage/matrix/matrix_integer_dense.c:17896)()
>2033 w1 = v.HNF(D=D)
>2034 except RuntimeError: # HNF may fail if a nxm matrix
> has rank < m
> -> 2035 raise ValueError("ntl only computes HNF for square
> matrices of full rank.")
>2036
>2037 if include_zero_rows:
>
> ValueError: ntl only computes HNF for square matrices of full rank.
>
> > On 28/09/2019, at 11:26 AM, Isuru Fernando  wrote:
> >
> > Hi,
> >
> > Running
> >
> > matrix(ZZ,3,[1..9]).hermite_form(algorithm='ntl')
> >
> > in sage from conda results in the process exiting with "halt 2" as
> opposed to catching the NTL LogicError (child class of std::runtime_error)
> and raising a python exception.
> >
> > Any ideas on why this is?
> >
> > Isuru
> >
> > --
> > You received this message because you are subscribed to the Google
> Groups "sage-devel" group.
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> an email to sage-devel+unsubscr...@googlegroups.com.
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> .
>
> --
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> .
>

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[sage-devel] NTL error with conda sage

[Isuru Fernando]

Hi,

Running

matrix(ZZ,3,[1..9]).hermite_form(algorithm='ntl')

in sage from conda results in the process exiting with "halt 2" as opposed
to catching the NTL LogicError (child class of std::runtime_error) and
raising a python exception.

Any ideas on why this is?

Isuru

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Re: [sage-devel] NTL 11.3.4

[Isuru Fernando]

On Sun, Sep 8, 2019 at 4:19 AM Victor Shoup  wrote:

> Wow! That is great!!
>
> Since I have to support this going forward, I'd like to understand it
> better before adopting it.
> For example, where does "mach_desch.h" get built?
>

Thanks for trying it out. I added generating "mach_desc.h". I somehow
missed it and also didn't get an error because of a system install of NTL.


> As far as the Wizard goes, we can discuss if there are any issues there
> that need special attention.
> Maybe a "make tune" that is run afterwords would be easier.
>

It's a bit more coding to do, so that's why I asked for comments on the
rest before doing that.

Isuru


> On Saturday, September 7, 2019 at 11:23:14 PM UTC-4, Isuru Fernando wrote:
>>
>> I spent a few hours today adding a CMake build system as you mentioned
>> that you are open to having a cmake build system. My work is at
>> https://github.com/isuruf/ntl
>>
>> The CMake build system has all of the options in the perl script except
>> for the wizard.
>>
>> You can try it by doing,
>>
>> cmake -DNATIVE=1 -DBUILD_SHARED_LIBS=yes -DBUILD_TESTING=yes ..
>> make -j8
>> ctest
>>
>> Let me know what you think. If you want to use this as the build system
>> for ntl going forward, then I can add support for the wizard as well.
>>
>> Isuru
>>
>>
>> On Sat, Sep 7, 2019 at 10:56 AM Victor Shoup  wrote:
>>
>>> I just posted NTL 11.3.4.
>>>
>>> Details here [ https://www.shoup.net/ntl/ ].
>>>
>>> This (I hope) fixes the "-lpthread underlinking issue" reported here [
>>> https://trac.sagemath.org/ticket/28406 ] and discussed at excessive
>>> length (mostly due to my own obstinance) here [
>>> https://groups.google.com/forum/#!topic/sage-devel/Xjc5BZ9QUFs ].
>>>
>>> My solution was to simply have NTL's makefile pass -lpthread to libtool
>>> when building the library (but only if the library is shared and
>>> multithreaded).  There is also a way to explicitly override this behavior,
>>> if that is necessary (but I hope it's not).
>>>
>>> If this does not fix the issue, please let me know.
>>>
>>> Thanks to everyone for their help in sorting out the problem and for
>>> putting up with my foot dragging on the issue.
>>>
>>> Some day, I have to make NTL's build system more "standard".  Some day,
>>> I have to put NTL on GitHub. Some day, I have to do a lot of things...
>>>
>>> --
>>> 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-...@googlegroups.com.
>>> To view this discussion on the web visit
>>> https://groups.google.com/d/msgid/sage-devel/7495bf0a-c2ad-4c8d-a22f-4813c1ed6683%40googlegroups.com
>>> <https://groups.google.com/d/msgid/sage-devel/7495bf0a-c2ad-4c8d-a22f-4813c1ed6683%40googlegroups.com?utm_medium=email_source=footer>
>>> .
>>>
>> --
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Re: [sage-devel] NTL 11.3.4

[Isuru Fernando]

I spent a few hours today adding a CMake build system as you mentioned that
you are open to having a cmake build system. My work is at
https://github.com/isuruf/ntl

The CMake build system has all of the options in the perl script except for
the wizard.

You can try it by doing,

cmake -DNATIVE=1 -DBUILD_SHARED_LIBS=yes -DBUILD_TESTING=yes ..
make -j8
ctest

Let me know what you think. If you want to use this as the build system for
ntl going forward, then I can add support for the wizard as well.

Isuru


On Sat, Sep 7, 2019 at 10:56 AM Victor Shoup  wrote:

> I just posted NTL 11.3.4.
>
> Details here [ https://www.shoup.net/ntl/ ].
>
> This (I hope) fixes the "-lpthread underlinking issue" reported here [
> https://trac.sagemath.org/ticket/28406 ] and discussed at excessive
> length (mostly due to my own obstinance) here [
> https://groups.google.com/forum/#!topic/sage-devel/Xjc5BZ9QUFs ].
>
> My solution was to simply have NTL's makefile pass -lpthread to libtool
> when building the library (but only if the library is shared and
> multithreaded).  There is also a way to explicitly override this behavior,
> if that is necessary (but I hope it's not).
>
> If this does not fix the issue, please let me know.
>
> Thanks to everyone for their help in sorting out the problem and for
> putting up with my foot dragging on the issue.
>
> Some day, I have to make NTL's build system more "standard".  Some day, I
> have to put NTL on GitHub. Some day, I have to do a lot of things...
>
> --
> You received this message because you are subscribed to the Google Groups
> "sage-devel" group.
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> email to sage-devel+unsubscr...@googlegroups.com.
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> https://groups.google.com/d/msgid/sage-devel/7495bf0a-c2ad-4c8d-a22f-4813c1ed6683%40googlegroups.com
> 
> .
>

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Re: [sage-devel] Re: Binary sage-8.7-OSX_10.11.6-x86_64.tar.bz2 doesn't work on my Mac

[Isuru Fernando]

You can try the conda package.
https://github.com/sagemath/sage/blob/develop/src/doc/en/installation/conda.rst

Isuru

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[sage-devel] How do you close a trac ticket?

[Isuru Fernando]

If there's another ticket for the same issue, how do you close the
duplicate one?

Isuru

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Re: [sage-devel] Building sage-8.8 from source fails due to flint

[Isuru Fernando]

Issue is that your system copy of ntl is a static library compiled without
PIC. Try doing `./configure --without-system-ntl` which would build ntl and
ignore the system copy.

Isuru

On Mon, Jul 8, 2019 at 12:27 PM E Poen  wrote:

> I'm using Ubuntu 18.04 with gcc 7.4.0, and I wanted to build sage-8.8 from
> source however it fails. I had successfully build the earlier versions
> before,
> so this was a bit suspicious to me. Please note that I have installed the
> dependencies specified here:
> https://doc.sagemath.org/html/en/installation/source.html
>
> And all I did was:
> ./configure
> make -j8
>
> And this is the error that I get about flint:
>
> make[7]: Entering directory
> '/home/myuser/app/sage-8.8/local/var/tmp/sage/build/flint-2.5.2.p4/src'
> g++ -std=gnu++11 -fPIC -pedantic -Wall -O2 -funroll-loops -g -mpopcnt
> -I/home/myuser/app/sage-8.8/local/var/tmp/sage/build/flint-2.5.2.p4/src
> -I/usr/local/include -I/usr/local/include -I/usr/local/include -c
> interfaces/NTL-interface.cpp -o build/interfaces/NTL-interface.lo
> make[7]: Leaving directory
> '/home/myuser/app/sage-8.8/local/var/tmp/sage/build/flint-2.5.2.p4/src'
> /usr/bin/ld: /usr/local/lib/libntl.a(ZZX.o): relocation R_X86_64_TPOFF32
> against
> `_ZZN3NTL8PlainSqrEPNS_2ZZEPKS0_lE36_ntl_hidden_variable_tls_local_ptr_t'
> can not be used when making a shared object; recompile with -fPIC
> /usr/bin/ld: /usr/local/lib/libntl.a(ZZ_p.o): relocation R_X86_64_TPOFF32
> against symbol `_ZN3NTL8ZZ_pInfoE' can not be used when making a shared
> object; recompile with -fPIC
> /usr/bin/ld: /usr/local/lib/libntl.a(ZZ_pE.o): relocation R_X86_64_TPOFF32
> against symbol `_ZN3NTL9ZZ_pEInfoE' can not be used when making a shared
> object; recompile with -fPIC
> /usr/bin/ld: /usr/local/lib/libntl.a(ZZ_pEX.o): relocation
> R_X86_64_TPOFF32 against
> `_ZZN3NTLeqERKNS_6ZZ_pEXElE37_ntl_hidden_variable_tls_local_ptr_bb' can not
> be used when making a shared object; recompile with -fPIC
> /usr/bin/ld: /usr/local/lib/libntl.a(ZZ_pX.o): relocation R_X86_64_TPOFF32
> against `_ZZN3NTLeqERKNS_5ZZ_pXElE37_ntl_hidden_variable_tls_local_ptr_bb'
> can not be used when making a shared object; recompile with -fPIC
> /usr/bin/ld: /usr/local/lib/libntl.a(ZZ_pX1.o): relocation
> R_X86_64_TPOFF32 against
> `_ZZZN3NTL12InnerProductERNS_5ZZ_pXERKNS_3VecINS_4ZZ_pEEEllRKNS2_IS0_EElRNS_5ZZVecEENKUlllE_clEllE36_ntl_hidden_variable_tls_local_ptr_s'
> can not be used when making a shared object; recompile with -fPIC
> /usr/bin/ld: /usr/local/lib/libntl.a(lip.o): relocation R_X86_64_TPOFF32
> against
> `_ZZ15_ntl_gaorsmul_1P17_ntl_gbigint_bodyllPS0_E38_ntl_hidden_variable_tls_local_ptr_tmp'
> can not be used when making a shared object; recompile with -fPIC
> /usr/bin/ld: /usr/local/lib/libntl.a(lzz_p.o): relocation R_X86_64_TPOFF32
> against
> `_ZZN3NTLL44_ntl_hidden_function_tls_access_zz_pInfo_stgEvE47_ntl_hidden_variable_tls_local_ptr_zz_pInfo_stg'
> can not be used when making a shared object; recompile with -fPIC
> /usr/bin/ld: /usr/local/lib/libntl.a(lzz_pE.o): relocation
> R_X86_64_TPOFF32 against symbol `_ZN3NTL9zz_pEInfoE' can not be used when
> making a shared object; recompile with -fPIC
> /usr/bin/ld: /usr/local/lib/libntl.a(lzz_pEX.o): relocation
> R_X86_64_TPOFF32 against symbol `_ZN3NTL14zz_pEXArgBoundE' can not be used
> when making a shared object; recompile with -fPIC
> /usr/bin/ld: /usr/local/lib/libntl.a(lzz_pX1.o): relocation
> R_X86_64_TPOFF32 against symbol `_ZN3NTL13zz_pXArgBoundE' can not be used
> when making a shared object; recompile with -fPIC
> /usr/bin/ld: /usr/local/lib/libntl.a(mat_ZZ_p.o): relocation
> R_X86_64_TPOFF32 against
> `_ZZN3NTL3mulERNS_3MatINS_4ZZ_pEEERKS2_RKS1_E36_ntl_hidden_variable_tls_local_ptr_b'
> can not be used when making a shared object; recompile with -fPIC
> /usr/bin/ld: /usr/local/lib/libntl.a(mat_lzz_p.o): relocation
> R_X86_64_TPOFF32 against
> `_ZZN3NTL3mulERNS_3VecINS_4zz_pEEERKS2_RKNS_3MatIS1_EEE46_ntl_hidden_variable_tls_local_ptr_mul_aux_vec'
> can not be used when making a shared object; recompile with -fPIC
> /usr/bin/ld: /usr/local/lib/libntl.a(tools.o): relocation R_X86_64_TPOFF32
> against symbol `_ZN3NTL16ErrorMsgCallbackE' can not be used when making a
> shared object; recompile with -fPIC
> /usr/bin/ld: /usr/local/lib/libntl.a(vec_ZZ_p.o): relocation
> R_X86_64_TPOFF32 against
> `_ZZN3NTL12InnerProductERNS_4ZZ_pERKNS_3VecIS0_EES5_lE40_ntl_hidden_variable_tls_local_ptr_accum'
> can not be used when making a shared object; recompile with -fPIC
> /usr/bin/ld: /usr/local/lib/libntl.a(vec_ZZ_pE.o): relocation
> R_X86_64_TPOFF32 against
> `_ZZN3NTL3mulERNS_3VecINS_5ZZ_pRKS2_RKNS_4ZZ_pEE36_ntl_hidden_variable_tls_local_ptr_b'
> can not be used when making a shared object; recompile with -fPIC
> /usr/bin/ld: /usr/local/lib/libntl.a(BasicThreadPool.o): relocation
> R_X86_64_TPOFF32 against
> `_ZZN3NTLL49_ntl_hidden_function_tls_access_NTLThreadPool_stgEvE52_ntl_hidden_variable_tls_local_ptr_NTLThreadPool_stg'
> can 

Re: [sage-devel] Sage 8.8 on conda-forge

[Isuru Fernando]

On Mon, Jul 1, 2019 at 4:15 PM Vincent Delecroix <20100.delecr...@gmail.com>
wrote:

> Many thanks Isuru for your hard work on this! It will be very helpful
> for continuous integration testing (among other things).
>
> I strongly hope that later versions of Sage will also be available
> in conda-forge. Do you have an idea to handle the upgrades smoothly?
>
Is there something that we could do on the "Sage side" to make
> it easier.
>

Recently, I've seen more and more patches being sent upstream and getting
merged which makes the packaging much easier. So, keep up the good work of
upstreaming patches and also keeping dependencies up-to-date. conda-forge
has recent versions and when sage lags behind, it makes it harder. For eg:
sage is not ready for Singular 4.1.2 (https://trac.sagemath.org/ticket/25993)
and I had to build 4.1.1 and dependencies like pynac with it. On this note,
a review of https://trac.sagemath.org/ticket/26932 would be appreciated as
well)

Another way to ease packaging is to set up a patchbot that would test on a
sage installation without the sources (i.e. on sage the library instead of
sage the distribution) and make the tests pass.

Isuru


>
> Vincent
>
> Le 01/07/2019 à 21:43, Isuru Fernando a écrit :
> > sage 8.8 is on conda-forge now. Packages are built for linux-64 and
> osx-64
> > for python 2.7, 3.6 and 3.7
> >
> > You can do,
> >
> > conda create -n sage sage python=3.7 -c conda-forge
> >
> > to install sage.
> >
> > There were 7 patches to build sage. (trac tickets 25786, 26932, 28007,
> > 28014, 28038, 28083, 28086).
> > With the 7 patches above, on linux-64 python 2.7, there were 27 doctest
> > failures. Any help in fixing them (and also with 25786) is appreciated.
> >
> > Full doctest log:
> >
> https://k8s.sagemath.org/projects/3ae7bec7-0b36-47fd-9e01-c1fda619cf35/files/conda-sagelib-tests/sagemath/doctest.txt
> >
> > Thanks to Erik, James, Julian, Luca, Nicolas, Philip, Samuel, Sebastian
> and
> > Vincent for creating PRs and issues to conda-forge and for all the
> helpful
> > discussions during Sage Days 101.
> >
> > Isuru
> >
>
> --
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[sage-devel] Sage 8.8 on conda-forge

[Isuru Fernando]

sage 8.8 is on conda-forge now. Packages are built for linux-64 and osx-64
for python 2.7, 3.6 and 3.7

You can do,

conda create -n sage sage python=3.7 -c conda-forge

to install sage.

There were 7 patches to build sage. (trac tickets 25786, 26932, 28007,
28014, 28038, 28083, 28086).
With the 7 patches above, on linux-64 python 2.7, there were 27 doctest
failures. Any help in fixing them (and also with 25786) is appreciated.

Full doctest log:
https://k8s.sagemath.org/projects/3ae7bec7-0b36-47fd-9e01-c1fda619cf35/files/conda-sagelib-tests/sagemath/doctest.txt

Thanks to Erik, James, Julian, Luca, Nicolas, Philip, Samuel, Sebastian and
Vincent for creating PRs and issues to conda-forge and for all the helpful
discussions during Sage Days 101.

Isuru

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Re: [sage-devel] Re: Gap pexpect error when most Gap packages are installed

[Isuru Fernando]

On Sun, Jun 23, 2019 at 6:24 PM Antonio Rojas  wrote:

> I just noticed this yesterday after updating GAP to 4.10.2 in Arch.
> SymmetricGroup(n).conjugacy_classes_subgroups() works fine for n<=4, and
> fails for n>=5. Same as you, it works after removing all additional GAP
> packages.
>
> Additionally, after the update (and with all GAP packages installed) some
> tests started failing due to using more memory than the default 330
> maximum. Running them with -m0 makes them pass. Again, no issue if I remove
> the additional packages.
>

I did see this issue, but it somehow got fixed and I can't reproduce it
anymore.

Isuru


> El domingo, 23 de junio de 2019, 16:25:45 (UTC+2), Isuru Fernando escribió:
>>
>> In the conda package for gap, we packaged almost all of the gap packages
>> (136 of 145) and sage pexpect gives an error for the following,
>>
>> sage: SymmetricGroup(7).conjugacy_classes_subgroups()
>>
>> saying,
>> RuntimeError: Gap produced error output
>> Error, sorry, the GAP Tables Of Marks Library is not installed
>>
>> I checked gap separately and tomlib imports fine and also running the
>> equivalent command on gap runs fine. When I run the command in gap with the
>> sage created workspace I get the same issue.
>>
>> I removed all gap packages except for the 18 packages that sage installs,
>> cleared the cache and it works. So, this is clearly an issue with a package
>> that sage doesn't install.
>>
>> Has anyone seen such an error before?
>>
>> Isuru
>>
>>
>> --
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Re: [sage-devel] Gap pexpect error when most Gap packages are installed

[Isuru Fernando]

Hi,

Thanks for trying out sage conda package.
sage on conda comes only with "gap-core" which is just gap + those 4
packages.
You need to install "gap" to get all the other packages.

Isuru

On Sun, Jun 23, 2019 at 5:48 PM Vincent Delecroix <20100.delecr...@gmail.com>
wrote:

> Isuru, I installed successfully Sage in conda yesterday and my
> version *does* work
>
> $ conda activate sage
> $ conda list|grep sage
> sage   8.8.rc1   py36hcb32578_0   conda-forge
>
> and then in the Sage console I obtain
>
> sage: SymmetricGroup(7).conjugacy_classes_subgroups()
> [Subgroup generated by [()] of
>(Symmetric group of order 7! as a permutation group),
> ...
>   Subgroup generated by [(1,2), (1,2,3,4,5,6,7)] of
>(Symmetric group of order 7! as a permutatio
>
> However, launching gap I see a lot of warnings about missing packages
> such as
>
> #I  autpgrp package is not available. Check that the name is correct
> #I  and it is present in one of the GAP root directories (see
> '??RootPaths')
>
> and then gap informs me that only the following are available
>
> Packages:   GAPDoc 1.6.2, PrimGrp 3.3.2, SmallGrp 1.3, TransGrp 2.0.4
>
> It is clear that we don't have the same setup! What did i miss in the
> installation?
>
> Vincent
>
> Le 23/06/2019 à 16:44, Isuru Fernando a écrit :
> > Yes, gap.load_package("tomlib") works and running the
> > "SymmetricGroup(7).conjugacy_classes_subgroups()" command doesn't work
> even
> > tomlib is imported. I cleared the gap workspace and it doesn't help
> either.
> >
> > Isuru
> >
> > On Sun, Jun 23, 2019 at 4:39 PM Dima Pasechnik 
> wrote:
> >
> >> does
> >>
> >> sage: gap.load_package("tomlib")
> >>
> >> work?
> >>
> >> if it does, do you get the same error message if you run your command
> >> after this one?
> >>
> >> On Sun, 23 Jun 2019 15:25 Isuru Fernando,  wrote:
> >>
> >>> In the conda package for gap, we packaged almost all of the gap
> packages
> >>> (136 of 145) and sage pexpect gives an error for the following,
> >>>
> >>> sage: SymmetricGroup(7).conjugacy_classes_subgroups()
> >>>
> >>> saying,
> >>> RuntimeError: Gap produced error output
> >>> Error, sorry, the GAP Tables Of Marks Library is not installed
> >>>
> >>> I checked gap separately and tomlib imports fine and also running the
> >>> equivalent command on gap runs fine. When I run the command in gap
> with the
> >>> sage created workspace I get the same issue.
> >>>
> >>> I removed all gap packages except for the 18 packages that sage
> installs,
> >>> cleared the cache and it works. So, this is clearly an issue with a
> package
> >>> that sage doesn't install.
> >>>
> >>> Has anyone seen such an error before?
> >>>
> >>> Isuru
> >>>
> >>>
> >>>
> >>>
> >>>
> ---
> >>> RuntimeError  Traceback (most recent call
> >>> last)
> >>>  in ()
> >>> > 1 SymmetricGroup(Integer(7)).conjugacy_classes_subgroups()
> >>>
> >>>
> /projects/3ae7bec7-0b36-47fd-9e01-c1fda619cf35/conda-sagelib-tests/sagemath/local/lib/python2.7/site-packages/sage/groups/perm_gps/permgroup.pyc
> >>> in conjugacy_classes_subgroups(self)
> >>> 3372 - David Joyner (2006-10)
> >>> 3373 """
> >>> -> 3374 cl = self._gap_().ConjugacyClassesSubgroups()
> >>> 3375 return [self.subgroup(gap_group=sub.Representative())
> for
> >>> sub in cl]
> >>> 3376
> >>>
> >>>
> /projects/3ae7bec7-0b36-47fd-9e01-c1fda619cf35/conda-sagelib-tests/sagemath/local/lib/python2.7/site-packages/sage/interfaces/interface.pyc
> >>> in __call__(self, *args, **kwds)
> >>>
> >>>
> >>>  661
> >>>  662 def __call__(self, *args, **kwds):
> >>> --> 663 return self._obj.parent().function_call(self._name,
> >>> [self._obj] + list(args), kwds)
> >>>  664
> >>>  665 def help(self):
> >>>
> >>>
> /projects/3ae7bec7-0b36-47fd-9e01-c1fda619cf35/conda-sagelib-tests/sagemath/local/lib/python2.7/site-packages/sage/interfaces/gap.pyc
> >>>

Re: [sage-devel] Gap pexpect error when most Gap packages are installed

[Isuru Fernando]

Yes, gap.load_package("tomlib") works and running the
"SymmetricGroup(7).conjugacy_classes_subgroups()" command doesn't work even
tomlib is imported. I cleared the gap workspace and it doesn't help either.

Isuru

On Sun, Jun 23, 2019 at 4:39 PM Dima Pasechnik  wrote:

> does
>
> sage: gap.load_package("tomlib")
>
> work?
>
> if it does, do you get the same error message if you run your command
> after this one?
>
> On Sun, 23 Jun 2019 15:25 Isuru Fernando,  wrote:
>
>> In the conda package for gap, we packaged almost all of the gap packages
>> (136 of 145) and sage pexpect gives an error for the following,
>>
>> sage: SymmetricGroup(7).conjugacy_classes_subgroups()
>>
>> saying,
>> RuntimeError: Gap produced error output
>> Error, sorry, the GAP Tables Of Marks Library is not installed
>>
>> I checked gap separately and tomlib imports fine and also running the
>> equivalent command on gap runs fine. When I run the command in gap with the
>> sage created workspace I get the same issue.
>>
>> I removed all gap packages except for the 18 packages that sage installs,
>> cleared the cache and it works. So, this is clearly an issue with a package
>> that sage doesn't install.
>>
>> Has anyone seen such an error before?
>>
>> Isuru
>>
>>
>>
>>
>> ---
>> RuntimeError  Traceback (most recent call
>> last)
>>  in ()
>> > 1 SymmetricGroup(Integer(7)).conjugacy_classes_subgroups()
>>
>> /projects/3ae7bec7-0b36-47fd-9e01-c1fda619cf35/conda-sagelib-tests/sagemath/local/lib/python2.7/site-packages/sage/groups/perm_gps/permgroup.pyc
>> in conjugacy_classes_subgroups(self)
>>3372 - David Joyner (2006-10)
>>3373 """
>> -> 3374 cl = self._gap_().ConjugacyClassesSubgroups()
>>3375 return [self.subgroup(gap_group=sub.Representative()) for
>> sub in cl]
>>3376
>>
>> /projects/3ae7bec7-0b36-47fd-9e01-c1fda619cf35/conda-sagelib-tests/sagemath/local/lib/python2.7/site-packages/sage/interfaces/interface.pyc
>> in __call__(self, *args, **kwds)
>>
>>
>> 661
>> 662 def __call__(self, *args, **kwds):
>> --> 663 return self._obj.parent().function_call(self._name,
>> [self._obj] + list(args), kwds)
>> 664
>> 665 def help(self):
>>
>> /projects/3ae7bec7-0b36-47fd-9e01-c1fda619cf35/conda-sagelib-tests/sagemath/local/lib/python2.7/site-packages/sage/interfaces/gap.pyc
>> in function_call(self, function, args, kwds)
>>
>>
>> 937 # We combine the two commands so we only run eval()
>> once and the
>> 938 #   only output would be from the second command
>> --> 939 res = self.eval(marker+cmd)
>> 940 else:
>> 941 self.eval(marker)
>>
>> /projects/3ae7bec7-0b36-47fd-9e01-c1fda619cf35/conda-sagelib-tests/sagemath/local/lib/python2.7/site-packages/sage/interfaces/gap.pyc
>> in eval(self, x, newlines, strip, split_lines, **kwds)
>>
>>
>> 581 if not input_line.endswith(';'):
>> 582 input_line += ';'
>> --> 583 result = Expect.eval(self, input_line, **kwds)
>> 584 if not newlines:
>> 585 result = result.replace("\\\n","")
>>
>> /projects/3ae7bec7-0b36-47fd-9e01-c1fda619cf35/conda-sagelib-tests/sagemath/local/lib/python2.7/site-packages/sage/interfaces/expect.pyc
>> in eval(self, code, strip, synchronize, locals, allow_use_file,
>> split_lines, **kwds)
>>
>>1350 elif split_lines:
>>1351 return '\n'.join([self._eval_line(L,
>> allow_use_file=allow_use_file, **kwds)
>> -> 1352 for L in code.split('\n')
>> if L != ''])
>>1353 else:
>>1354 return self._eval_line(code,
>> allow_use_file=allow_use_file, **kwds)
>>
>> /projects/3ae7bec7-0b36-47fd-9e01-c1fda619cf35/conda-sagelib-tests/sagemath/local/lib/python2.7/site-packages/sage/interfaces/gap.pyc
>> in _eval_line(self, line, allow_use_file, wait_for_prompt,
>> restart_if_needed)
>>
>> 788 return ''
>> 789 else:
>> --> 790 raise RuntimeError(message)
>> 791
>> 792 except KeyboardInterrupt:
>>
>> RuntimeError: Ga

[sage-devel] Gap pexpect error when most Gap packages are installed

[Isuru Fernando]

In the conda package for gap, we packaged almost all of the gap packages
(136 of 145) and sage pexpect gives an error for the following,

sage: SymmetricGroup(7).conjugacy_classes_subgroups()

saying,
RuntimeError: Gap produced error output
Error, sorry, the GAP Tables Of Marks Library is not installed

I checked gap separately and tomlib imports fine and also running the
equivalent command on gap runs fine. When I run the command in gap with the
sage created workspace I get the same issue.

I removed all gap packages except for the 18 packages that sage installs,
cleared the cache and it works. So, this is clearly an issue with a package
that sage doesn't install.

Has anyone seen such an error before?

Isuru



---
RuntimeError  Traceback (most recent call last)
 in ()
> 1 SymmetricGroup(Integer(7)).conjugacy_classes_subgroups()

/projects/3ae7bec7-0b36-47fd-9e01-c1fda619cf35/conda-sagelib-tests/sagemath/local/lib/python2.7/site-packages/sage/groups/perm_gps/permgroup.pyc
in conjugacy_classes_subgroups(self)
   3372 - David Joyner (2006-10)
   3373 """
-> 3374 cl = self._gap_().ConjugacyClassesSubgroups()
   3375 return [self.subgroup(gap_group=sub.Representative()) for
sub in cl]
   3376

/projects/3ae7bec7-0b36-47fd-9e01-c1fda619cf35/conda-sagelib-tests/sagemath/local/lib/python2.7/site-packages/sage/interfaces/interface.pyc
in __call__(self, *args, **kwds)


661
662 def __call__(self, *args, **kwds):
--> 663 return self._obj.parent().function_call(self._name,
[self._obj] + list(args), kwds)
664
665 def help(self):

/projects/3ae7bec7-0b36-47fd-9e01-c1fda619cf35/conda-sagelib-tests/sagemath/local/lib/python2.7/site-packages/sage/interfaces/gap.pyc
in function_call(self, function, args, kwds)


937 # We combine the two commands so we only run eval()
once and the
938 #   only output would be from the second command
--> 939 res = self.eval(marker+cmd)
940 else:
941 self.eval(marker)

/projects/3ae7bec7-0b36-47fd-9e01-c1fda619cf35/conda-sagelib-tests/sagemath/local/lib/python2.7/site-packages/sage/interfaces/gap.pyc
in eval(self, x, newlines, strip, split_lines, **kwds)


581 if not input_line.endswith(';'):
582 input_line += ';'
--> 583 result = Expect.eval(self, input_line, **kwds)
584 if not newlines:
585 result = result.replace("\\\n","")

/projects/3ae7bec7-0b36-47fd-9e01-c1fda619cf35/conda-sagelib-tests/sagemath/local/lib/python2.7/site-packages/sage/interfaces/expect.pyc
in eval(self, code, strip, synchronize, locals, allow_use_file,
split_lines, **kwds)

   1350 elif split_lines:
   1351 return '\n'.join([self._eval_line(L,
allow_use_file=allow_use_file, **kwds)
-> 1352 for L in code.split('\n')
if L != ''])
   1353 else:
   1354 return self._eval_line(code,
allow_use_file=allow_use_file, **kwds)

/projects/3ae7bec7-0b36-47fd-9e01-c1fda619cf35/conda-sagelib-tests/sagemath/local/lib/python2.7/site-packages/sage/interfaces/gap.pyc
in _eval_line(self, line, allow_use_file, wait_for_prompt,
restart_if_needed)

788 return ''
789 else:
--> 790 raise RuntimeError(message)
791
792 except KeyboardInterrupt:

RuntimeError: Gap produced error output
Error, sorry, the GAP Tables Of Marks Library is not installed

   executing
__SAGE_LAST__:="__SAGE_LAST__";;ConjugacyClassesSubgroups(\$sage1);;

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