Upgrade polymake to version 3.4

[mkoeppe]

https://polymake.org/doku.php/download/start#get_latest_stable_release33

To build it for Sage do:

(cd upstream && wget https://polymake.org/lib/exe/fetch.php/download/polymake-3.4-minimal.tar.bz2)

pull this ticket and build sage

make build

Then
Read (and follow) the installation instructions regarding Perl prereqs on your platform:

./sage -info polymake

Finally:

./sage -i polymake

Upstream: Reported upstream. No feedback yet.

CC: @simon-king-jena @jplab @videlec @slel @sophiasage paffenholz@mathematik.tu-darmstadt.de kastner@math.tu-berlin.de

Component: packages: optional

Keywords: IMA-PolyGeom, thursdaysbdx

Author: Matthias Koeppe, Jean-Philippe Labbé, Dima Pasechnik

Branch/Commit: public/upgrade_polymake_to_version_3_2r4 @ 2eda6e1

Reviewer: Matthias Koeppe, Jean-Philippe Labbé, Dima Pasechnik

Issue created by migration from https://trac.sagemath.org/ticket/24905

[mkoeppe]

Dependencies: #24921

[mkoeppe]

Branch: u/mkoeppe/upgrade_polymake_to_version_3_2r2

[sagetrac-git]

Branch pushed to git repo; I updated commit sha1. New commits:

ca75153

polymake: Add ninja_build as dependency

[sagetrac-git]

Commit: ca75153

[mkoeppe]

Author: Matthias Koeppe

[jdemeyer]

comment:5

ninja_build should be an order-only dependency (after the | symbol)

[jdemeyer]

comment:6

All other packages have $(MP_LIBRARY) in their dependencies instead of $(INST)/$(SAGE_MP_LIBRARY). I guess this should be changed.

[jdemeyer]

comment:7

Unfortunately, I cannot test this because perl_term_readline_gnu fails to install:

[perl_term_readline_gnu-1.34] Could not find neither libtermcap.a, libncurses.a, or libcurses.

Indeed, there is no libncurses.a installed (but libncurses.so is).

[mkoeppe]

comment:8

Replying to @jdemeyer:

Unfortunately, I cannot test this because perl_term_readline_gnu fails to install:

[perl_term_readline_gnu-1.34] Could not find neither libtermcap.a, libncurses.a, or libcurses.

Indeed, there is no libncurses.a installed (but libncurses.so is).

Could you create a separate ticket for this (and include more log detail)?

[sagetrac-git]

Branch pushed to git repo; I updated commit sha1. New commits:

4fc26ff	ninja_build: Add python dependency
3d6ae67	ninja_build: Make Python an order-only dependency
acc3026	Merge remote-tracking branch 'trac/u/mkoeppe/add_optional_package__ninja_build___build_system_for_polymake_' into t/24905/upgrade_polymake_to_version_3_2r2
196eb49	polymake dependencies: Use current format for MP_LIBRARY, make ninja_build order-only

[sagetrac-git]

Changed commit from ca75153 to 196eb49

[mkoeppe]

Work Issues: Failures in test suite

[mkoeppe]

comment:12

This upgrade seems to break the whole polymake interface. Next step: Compare what's happening on the wire (pexpect log) between the two polymake versions.

[mkoeppe]

comment:13

Replying to @mkoeppe:

Replying to @jdemeyer:

Unfortunately, I cannot test this because perl_term_readline_gnu fails to install:

[perl_term_readline_gnu-1.34] Could not find neither libtermcap.a, libncurses.a, or libcurses.

Indeed, there is no libncurses.a installed (but libncurses.so is).

Could you create a separate ticket for this (and include more log detail)?

We have reproduced this problem on another linux box. Fix is in #25112.

[mkoeppe]

Changed dependencies from #24921 to #24921, #25112

[sagetrac-git]

Branch pushed to git repo; I updated commit sha1. New commits:

3ffafdf	Update perl_term_readline_gnu to 1.35
672a3a2	perl_term_readline_gnu: Find ncurses
0b818c3	Merge remote-tracking branch 'trac/u/mkoeppe/perl_term_readline_gnu__upgrade_to_1_35_and_patch_away_ncurses_problem' into t/24905/upgrade_polymake_to_version_3_2r2

[sagetrac-git]

Changed commit from 196eb49 to 0b818c3

[sagetrac-git]

Branch pushed to git repo; I updated commit sha1. New commits:

b613e57

Mention libterm-readline-gnu-perl

[sagetrac-git]

Branch pushed to git repo; I updated commit sha1. New commits:

e5c3249	polymake: Mention MOngoDB for polydb
b89376a	polymake: Update info on macOS

[sagetrac-git]

Changed commit from b613e57 to b89376a

[dimpase]

comment:151

Let's get this done and open another ticket for promotion to optional.
IMHO it is not quite ready, e.g. it does not run on all supported platforms.
And the installation procedure isn't nice. I don't think we have a optional package where to install it one needs to install many things by hand in an ad hoc way.

---

New commits:

e5c3249	polymake: Mention MOngoDB for polydb
b89376a	polymake: Update info on macOS

[sagetrac-git]

Branch pushed to git repo; I updated commit sha1. New commits:

0c1b044

polymake: update MongoDB information for linux distros

[sagetrac-git]

Changed commit from b89376a to 0c1b044

[mkoeppe]

comment:153

Replying to @dimpase:

Let's get this done and open another ticket for promotion to optional.
IMHO it is not quite ready, e.g. it does not run on all supported platforms.
And the installation procedure isn't nice. I don't think we have a optional package where to install it one needs to install many things by hand in an ad hoc way.

OK, I agree, good point.

[mkoeppe]

comment:154

I added one more perl package. Could you check this on Linux?
After adding it, the following should work:

polytope > $A = db_query( { "_id"=>"F.4D.0047" }, db=>"LatticePolytopes", collection=>"SmoothReflexive" );
polymake: used package polyDB
   Access to the polymake polytope database.
   (c) 2013-2018 Silke Horn, Andreas Paffenholz
   http://solros.de
   http://www.mathematik.tu-darmstadt.de/~paffenholz


polymake:  ERROR: #
# *** DEPRECATION WARNING ***
# ...

(The deprecation warning is normal.}

[dimpase]

comment:155

Building 72 more Perl packages now :-) Why is polymake itself not on CPAN?

[dimpase]

comment:156

this is what I got (after installing moar perl and rebuilding polymake)

 $ ./sage --polymake
Welcome to polymake version 3.4
Copyright (c) 1997-2019
Ewgenij Gawrilow, Michael Joswig (TU Berlin)
https://polymake.org

This is free software licensed under GPL; see the source for copying conditions.
There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

Press F1 or enter 'help;' for basic instructions.

Application polytope currently uses following contributed and third-party software packages:
SVG, bliss, cdd, graphviz, latte, libnormaliz, lrs, permlib, polyDB, povray, ppl, qhull, singular, sketch, sympol, threejs, tikz, tosimplex
For more details:  show_credits;
polytope > $A = db_query( { "_id"=>"F.4D.0047" }, db=>"LatticePolytopes", collection=>"SmoothReflexive" );
polymake: used package polyDB
   Access to the polymake polytope database.
   (c) 2013-2018 Silke Horn, Andreas Paffenholz
   http://solros.de
   http://www.mathematik.tu-darmstadt.de/~paffenholz


polytope > 

perhaps you could add a meaningful doctest, tagged internet, for this?

[mkoeppe]

comment:157

When MongoDB is not available, the function db_query is not even present.
Not sure if/why we want to doctest that.

Let's postpone doctesting the db_query function in Sage to #27802, which adds support for the dictionary that appears in the argument list.

[dimpase]

comment:158

OK then.

[dimpase]

comment:159

one last nitpick yum install perl-Term-ReadLine-Gnu should be added to Fedora instructions

[mkoeppe]

comment:160

Thank you!

[sagetrac-git]

Branch pushed to git repo; I updated commit sha1 and set ticket back to needs_review. New commits:

2eda6e1

polymake: add to fedora instructions

[sagetrac-git]

Changed commit from 0c1b044 to 2eda6e1

[dimpase]

comment:163

Fedora's 26 perl is however not good.

[polymake-3.4] FAILED: /home/scratch2/dimpase/sage/sage/local/var/tmp/sage/build/polymake-3.4/src/build/perlx/5.24.4/x86_64-linux-thread-multi/Customize.cc
[polymake-3.4] /usr/bin/perl /usr/share/perl5/ExtUtils/xsubpp -typemap /usr/share/perl5/ExtUtils/typemap  --output /home/scratch2/dimpase/sage/sage/local/var/tmp/sage/build/polymake-3.4/src/build/perlx/5.24.4/x86_64-linux-thread-multi/Customize.cc /home/scratch2/dimpase/sage/sage/local/var/tmp/sage/build/polymake-3.4/src/lib/core/src/perl/Customize.xxs
[polymake-3.4] Can't open perl script "/usr/share/perl5/ExtUtils/xsubpp": No such file or directory

This seems to be a known problem - not sure it's worthwhile to try to fix it though.

And, by the way, on stable Debian I get a problem building with (the standard) gcc 6.3.

[mkoeppe]

comment:164

Replying to @dimpase:

Fedora's 26 perl is however not good.

[polymake-3.4] FAILED: /home/scratch2/dimpase/sage/sage/local/var/tmp/sage/build/polymake-3.4/src/build/perlx/5.24.4/x86_64-linux-thread-multi/Customize.cc
[polymake-3.4] /usr/bin/perl /usr/share/perl5/ExtUtils/xsubpp -typemap /usr/share/perl5/ExtUtils/typemap  --output /home/scratch2/dimpase/sage/sage/local/var/tmp/sage/build/polymake-3.4/src/build/perlx/5.24.4/x86_64-linux-thread-multi/Customize.cc /home/scratch2/dimpase/sage/sage/local/var/tmp/sage/build/polymake-3.4/src/lib/core/src/perl/Customize.xxs
[polymake-3.4] Can't open perl script "/usr/share/perl5/ExtUtils/xsubpp": No such file or directory

This seems to be a known problem - not sure it's worthwhile to try to fix it though.

Known to who?

[mkoeppe]

comment:165

Follow-up ticket: Fix polymake 3.4 lrslib detection (#27803).

[dimpase]

comment:166

It's known to the internet that !Fedora/Centos perform a surgery on its Perl installation resulting in breakages like in comment:163 (missing /usr/share/perl5/ExtUtils/xsubpp; of course xsubpp is present, it's only not in this locaton, hardcoded somewhere...)

[vbraun]

comment:169

Too late, a previous version was released in 8.8.beta5. Move any new code to a separate ticket

[mkoeppe]

comment:170

Replying to @vbraun:

Too late, a previous version was released in 8.8.beta5. Move any new code to a separate ticket

No problem, the missing commit is on the branch of #27803