Add interface for PALP polytope databases #12553

vbraun · 2012-02-21T07:16:03Z

This ticket implements an interface to read databases of reflexive polytopes:

Add databases in PALP format to the polytopes_db.spkg.
A class PALPreader that can read the palp output and yield it in various Sage representations.
Finally, this ticket contains a specialized PPL lattice polytope that is fast enough to construct to go through the 500 million 4-d reflexive polytopes and compute integral points.

The updated polytopes spkg is here:
http://boxen.math.washington.edu/home/vbraun/spkg/polytopes_db-20120220.spkg

Apply:

Depends on #11763
Depends on #11634
Depends on #12544
Depends on #14467

CC: @novoselt @jdemeyer

Component: packages: huge

Keywords: PALP reflexive polytopes

Author: Volker Braun

Reviewer: Dmitrii Pasechnik

Merged: sage-5.10.beta2

Issue created by migration from https://trac.sagemath.org/ticket/12553

The text was updated successfully, but these errors were encountered:

vbraun · 2012-02-21T07:27:23Z

Dependencies: #11763, #11634

vbraun · 2012-06-03T22:28:17Z

comment:4

I've updated the patches with various minor improvements.

SnarkBoojum · 2012-06-11T15:46:39Z

comment:5

I had a look and have some remarks to do:

now spkg-install checks for SAGE_DATA before using SAGE_DATA (the one in sage 5.0 checks SAGE_ROOT before using SAGE_DATA...), which is good!
the sources aren't in a directory src/ but in reflexive_polytopes/ -- isn't it against the conventions?
both build.sh scripts lack a shebang ;
is it normal that the installation is dumping everything in SAGE_DATA/reflexive_polytopes/ ? Shouldn't the spkg (1) depend on palp (2) in the build phase, use it to create the database (3) in the install phase, only install the resulting database?

vbraun · 2012-06-11T16:20:52Z

comment:6

I've added the shebang to the build.sh scripts, even though we are entering deep into bikeshedding territory here as these are not executed but only show how the database can be built.

I've also renamed the directory to src/, thats just something I inherited from the previous version.

All databases in Sage just copy their content. Usually they require non-trivial computer resources to build, so you specifically don't want to recompute them when you are installing Sage. In this case its actually computationally easy, but just wait until we add the 4-d case ;-)

SnarkBoojum · 2012-06-11T16:53:09Z

comment:7

Copying the contents is ok -- what bothers me is that you copy the scripts too.

You says that "these are not executed but only show how the database can be built" -- does that mean you don't guarantee they effectively work?

vbraun · 2012-06-11T17:01:18Z

comment:8

Well you have my word that the scripts work :-P I think having the scripts is better than not having them. Who cares if they end up in the database directory or not.

SnarkBoojum · 2012-06-11T18:13:48Z

comment:9

I see two reasons to care:

sage is big enough ;
if it's not data, it doesn't belong to SAGE_DATA.

vbraun · 2012-06-11T18:27:12Z

comment:10

Lets call it documentation, then, shall we?

SnarkBoojum · 2012-06-11T19:15:36Z

comment:11

If it's documentation, it belongs into SAGE_DOC ; installing things in correct places isn't as frivolous as you seem to think...

vbraun · 2012-06-12T17:56:23Z

comment:12

$SAGE_DOC contains docs like the developer manual. You want me to typeset the script in sphinx and include it in the developer manual? That doesn't sound reasonable to me.

SnarkBoojum · 2012-06-12T18:16:56Z

comment:13

Why not just cp the right files into $SAGE_DATA?

vbraun · 2012-06-12T19:05:53Z

comment:14

I've deleted the build.sh scripts. Updated spkg at the same location.

vbraun · 2012-07-01T16:27:13Z

comment:15

Updating the database patch for the new PointCollection output introduced in #12544, which is one of the possible output formats.

vbraun · 2012-07-01T16:27:13Z

Changed dependencies from #11763, #11634 to #11763, #11634, #12544

vbraun · 2012-07-01T16:27:26Z

Updated patch

vbraun · 2012-07-02T20:20:56Z

Attachment: trac_12553_palp_database.patch.gz

Rediffed patch

dimpase · 2012-07-09T13:43:17Z

comment:16

Attachment: trac_12553_ppl_count_points.patch.gz

can this ticket be rebased so that it does not depend upon anything that is in sage-pending, such as #11310 ?

vbraun · 2012-07-09T14:54:49Z

comment:17

I think Jeroen just used sage-pending in #11310 since we didn't have a sage-5.3 milestone at that time and sage-5.2 is supposed to be just a new sagenb + trivial tickets. But maybe Jeroen had some other reason?

jdemeyer · 2012-07-09T14:59:03Z

comment:18

It's mainly because of #13109. The current plan is to merge #13109 in sage-5.2 but all follow-ups (including #11310) in sage-5.3. It's certainly not meant to be a long-term sage-pending.

novoselt · 2012-07-25T18:58:58Z

comment:19

Hi Volker, do you actually have the package for 4d polytopes which is mentioned in the patch documentation?

(By the way, maybe polytopes_reflexive_4d_db would be a better name for it?)

vbraun · 2012-08-04T15:09:39Z

comment:20

Sorry forgot to reply.. I haven't packaged the 4d database... 10 GB spkg? ;-) But the updated spkg contains the 2d and 3d analogues in PALP's binary database format.

dimpase · 2013-04-17T16:11:09Z

comment:21

somewhere down in the first patch you have

The database is very large and not installed by default. You can 
install it with the command ``install_package('polytopes_db_4d')``.

but this does not work. Was it meant to be added later?

vbraun · 2013-04-17T17:27:05Z

comment:22

Yes. Though there is also the question whether we want to host a 4+gb database (and I don't have a firm opinion either way)

vbraun · 2013-04-17T18:26:02Z

comment:23

For fun: http://boxen.math.washington.edu/home/vbraun/www/polytopes_db_4d-1.0.spkg

Still takes a day or so to upload...

dimpase · 2013-04-18T08:54:44Z

comment:24

Replying to @vbraun:

Yes. Though there is also the question whether we want to host a 4+gb database (and I don't have a firm opinion either way)

IMHO, if it is hosted elsewhere, we might rather want to host an interface only.
Anyhow that comment in the source about install_package('polytopes_db_4d') is misleading, and should be rectified.

vbraun · 2013-04-20T15:15:19Z

comment:25

Updated polytopes_db-20120220.spkg to merge in the changes that others have done in the year+ that it has been lingering here.

vbraun · 2013-04-20T15:29:06Z

Changed dependencies from #11763, #11634, #12544 to #11763, #11634, #12544, #14467

vbraun · 2013-04-20T15:29:06Z

comment:26

I made a ticket for the 4-d database at #14467.

dimpase · 2013-04-22T06:16:16Z

comment:27

Replying to @vbraun:

Updated polytopes_db-20120220.spkg to merge in the changes that others have done in the year+ that it has been lingering here.

This spkg can only be found on http://www.stp.dias.ie/~vbraun/Sage/spkg/.
Is this how this is meant to be?

vbraun · 2013-04-22T08:44:00Z

comment:28

I'm leaving Ireland and my DIAS account will be closed in the coming weeks. I uploaded the spkg to boxen, and this is where it should be. The link in the ticket description works for me.

dimpase · 2013-04-25T06:04:22Z

comment:29

Replying to @vbraun:

I'm leaving Ireland and my DIAS account will be closed in the coming weeks. I uploaded the spkg to boxen, and this is where it should be. The link in the ticket description works for me.

Wohin, Volker?

vbraun · 2013-05-05T15:41:07Z

Attachment: trac_12553_ppl_lattice_polytope.patch.gz

Updated patch

jdemeyer · 2013-05-07T10:07:48Z

Reviewer: Dmitrii Pasechnik

jdemeyer · 2013-05-08T07:44:01Z

Merged: sage-5.10.beta2

vbraun added this to the sage-5.10 milestone Feb 21, 2012

vbraun added c: packages: optional labels Feb 21, 2012

vbraun assigned williamstein Feb 21, 2012

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dimpase added s: positive review and removed s: needs review labels Apr 25, 2013

jdemeyer removed this from the sage-5.10 milestone Apr 29, 2013

jdemeyer added the pending label Apr 29, 2013

jdemeyer added this to the sage-5.10 milestone May 7, 2013

jdemeyer removed the pending label May 7, 2013

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jdemeyer closed this as completed May 8, 2013

bobmoretti mannequin mentioned this issue Oct 28, 2013

Weierstrass form and Jacobian for cubics and certain other genus-one curves #3416

Closed

This was referenced Jun 19, 2013

Weierstrass form for toric elliptic curves #13084

Closed

Database of 4-d reflexive polytopes #14467

Closed

Add interface for PALP polytope databases #12553

Add interface for PALP polytope databases #12553

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