polymake

README.md

polymake, bistellar

env

• https://polymake.org/doku.php/start
• https://metacpan.org/dist/App-perlbrew/view/script/perlbrew

# it is obv. not necessary to install bliss or nauty system-wide (compiling polymake against them didn't work in my tests)
emerge -av dev-libs/stb dev-perl/App-perlbrew sci-libs/{cddlib,lrslib,soplex} sci-mathematics/{flint,normaliz,singular}

additional references:

• https://matsguru.com/?p=222
• https://arxiv.org/abs/1302.6856
• https://api-depositonce.tu-berlin.de/server/api/core/bitstreams/bc34a078-25f4-4aab-948e-b5e94baec197/content#cite.Ranicki

problems encountered so far

• OOM (not enough RAM + swap). A single bistellar.* invocation can easily allocate up to 80GiB.
• segmentation faults (the backtrace wasn't really helpful and I currently can't find it)
• stack overflows during AVL; FaceMap tree destroy. (during face_map::tree_traits::destroy_node <-> AVL::tree::destroy_nodes recursion)
• ASAN appears to prohibit tail-call elimination and massively increases memory usage while decreasing performance.
• It appears to make sense to compile polymake with LTO and debug symbols (e.g. -ggdb3). ASAN is probably not worth it (unless one encounters a very specific symptom that can't be pinned to some introduction chain)

bistellar.pl

#!/home/fogti/.local/bin/polymake --script

# Simplify simplicial complex using edge contractions and bistellar flips

use application "topaz";
use strict;
use warnings;

#require "./lib.pl"; # load common functions

my $obname = shift @ARGV;
#my $obname="AK_I_015";

my $outpath="$obname.d";

if (! -d $outpath ) {
    mkdir $outpath;
}

my $regdesc="_";

STDOUT->autoflush(1);

print(STDOUT "$obname: starting to load data\n");

my $q=load_data("$obname.poly");

#$q=edge_contraction($q);

print(STDOUT "$obname: loaded data\n");

$q=barycentric_subdivision($q);

print(STDOUT "$obname: triangulated data\n");

$q=bistellar_simplification($q);

print(STDOUT "$obname: simplified data\n");

my $vert = @{$q->F_VECTOR}[0];

if (! -d "$outpath/$vert") {
    mkdir "$outpath/$vert";
}

print(STDOUT "$obname: saving data\n");
save($q, "$outpath/$vert/$regdesc.poly");
print(STDOUT "$obname: saved data\n");

bistellar.sh

#!/usr/bin/zsh

. /etc/profile
. "$HOME/perl5/perlbrew/etc/bashrc"
export PATH="$HOME/.local/bin:$PATH"

if ! [ -n "$1" ]; then
  echo "ERROR: no instance specified." 1>&2
  exit 1
fi

cd /home/fogti/Uni/poly-stuff
perlbrew use pmperl
time ASAN_OPTIONS=detect_odr_violation=0 LD_PRELOAD=/usr/lib/gcc/x86_64-pc-linux-gnu/13/libasan.so.8 ./bistellar.pl "$1" 2>&1 | tee "$1".log

invoke-configure.sh

# NOTE: nauty stuff won't compile as-is
#   apply the debian + gentoo patches (see also https://packages.gentoo.org/packages/sci-mathematics/nauty + linked ebuilds)
#   and remove the entry mentioning rng.c from polymake-4.*/bundled/nauty/apps/graph/src/build_flags.pl
#   also, some headers need to be symlinked into the nauty2_8_6/nauty folder so the can be found (yes this is cursed, some of these headers are generated inside of the polymake build tree)
./configure --prefix="$HOME/.local" --without-bliss --with-nauty-src=~/src/nauty2_8_6 --with-cdd=/usr --with-flint=/usr --with-libnormaliz=/usr --with-lrs-include=/usr/include/lrslib --with-singular=/usr --with-soplex=/usr CFLAGS="-O2 -pipe -march=znver4 -flto -ggdb3" CXXFLAGS="-O2 -pipe -march=znver4 -flto -ggdb3" LDFLAGS="-flto"

ls src~nauty2_8_6~nauty

total 20
 4 drwxr-sr-x 2 fogti fogti 4096 Oct  7 21:44 .
12 drwxr-sr-x 4 fogti fogti 8192 Oct  6 16:09 ..
 4 -rw-r--r-- 1 fogti fogti  672 Oct  6 16:09 Makefile.am
 0 lrwxrwxrwx 1 fogti fogti   50 Oct  7 21:44 gtools.h -> ../../polymake-4.10/build/staticlib/nauty/gtools.h
 0 lrwxrwxrwx 1 fogti fogti   11 Oct  7 21:41 gutils.h -> ../gutils.h
 0 lrwxrwxrwx 1 fogti fogti   13 Oct  7 21:41 naugroup.h -> ../naugroup.h
 0 lrwxrwxrwx 1 fogti fogti   11 Oct  7 21:41 naurng.h -> ../naurng.h
 0 lrwxrwxrwx 1 fogti fogti   14 Oct  7 21:41 nausparse.h -> ../nausparse.h
 0 lrwxrwxrwx 1 fogti fogti   12 Oct  7 21:41 nautinv.h -> ../nautinv.h
 0 lrwxrwxrwx 1 fogti fogti   52 Oct  7 21:44 naututil.h -> ../../polymake-4.10/build/staticlib/nauty/naututil.h
 0 lrwxrwxrwx 1 fogti fogti   49 Oct  7 21:44 nauty.h -> ../../polymake-4.10/build/staticlib/nauty/nauty.h
 0 lrwxrwxrwx 1 fogti fogti   13 Oct  7 21:41 schreier.h -> ../schreier.h
 0 lrwxrwxrwx 1 fogti fogti   11 Oct  7 21:41 traces.h -> ../traces.h

Luckily, most of this is no longer relevant, as polymake is packaged again in gentoo.