Opened 10 years ago
Closed 9 years ago
#12553 closed enhancement (fixed)
Add interface for PALP polytope databases
Reported by: | vbraun | Owned by: | was |
---|---|---|---|
Priority: | major | Milestone: | sage-5.10 |
Component: | packages: huge | Keywords: | PALP reflexive polytopes |
Cc: | novoselt, jdemeyer | Merged in: | sage-5.10.beta2 |
Authors: | Volker Braun | Reviewers: | Dmitrii Pasechnik |
Report Upstream: | N/A | Work issues: | |
Branch: | Commit: | ||
Dependencies: | #11763, #11634, #12544, #14467 | Stopgaps: |
Description (last modified by )
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
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Attachments (3)
Change History (36)
comment:1 Changed 10 years ago by
- Description modified (diff)
- Status changed from new to needs_review
comment:2 Changed 10 years ago by
- Cc novoselt added
- Description modified (diff)
comment:3 Changed 10 years ago by
- Dependencies set to #11763, #11634
comment:4 Changed 10 years ago by
comment:5 Changed 10 years ago by
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?
comment:6 Changed 10 years ago by
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 ;-)
comment:7 Changed 10 years ago by
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?
comment:8 Changed 10 years ago by
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.
comment:9 Changed 10 years ago by
I see two reasons to care:
- sage is big enough ;
- if it's not data, it doesn't belong to SAGE_DATA.
comment:10 Changed 10 years ago by
Lets call it documentation, then, shall we?
comment:11 Changed 10 years ago by
If it's documentation, it belongs into SAGE_DOC ; installing things in correct places isn't as frivolous as you seem to think...
comment:12 Changed 10 years ago by
$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.
comment:13 Changed 10 years ago by
Why not just cp the right files into $SAGE_DATA?
comment:14 Changed 10 years ago by
I've deleted the build.sh scripts. Updated spkg at the same location.
comment:15 Changed 10 years ago by
- Dependencies changed from #11763, #11634 to #11763, #11634, #12544
Updating the database patch for the new PointCollection
output introduced in #12544, which is one of the possible output formats.
comment:16 Changed 10 years ago by
can this ticket be rebased so that it does not depend upon anything that is in sage-pending
, such as #11310 ?
comment:17 Changed 10 years ago by
- Cc jdemeyer added
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?
comment:18 Changed 10 years ago by
comment:19 Changed 10 years ago by
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?)
comment:20 Changed 10 years ago by
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.
comment:21 Changed 9 years ago by
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?
comment:22 follow-up: ↓ 24 Changed 9 years ago by
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)
comment:23 Changed 9 years ago by
For fun: http://boxen.math.washington.edu/home/vbraun/www/polytopes_db_4d-1.0.spkg
Still takes a day or so to upload...
comment:24 in reply to: ↑ 22 Changed 9 years ago by
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.
comment:25 follow-up: ↓ 27 Changed 9 years ago by
- Description modified (diff)
Updated polytopes_db-20120220.spkg
to merge in the changes that others have done in the year+ that it has been lingering here.
comment:26 Changed 9 years ago by
- Dependencies changed from #11763, #11634, #12544 to #11763, #11634, #12544, #14467
I made a ticket for the 4-d database at #14467.
comment:27 in reply to: ↑ 25 Changed 9 years ago by
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?
comment:28 follow-up: ↓ 29 Changed 9 years ago by
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.
comment:29 in reply to: ↑ 28 Changed 9 years ago by
- Status changed from needs_review to positive_review
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?
comment:30 Changed 9 years ago by
- Milestone changed from sage-5.10 to sage-pending
comment:31 Changed 9 years ago by
- Reviewers set to Dmitrii Pasechnik
comment:32 Changed 9 years ago by
- Milestone changed from sage-pending to sage-5.10
comment:33 Changed 9 years ago by
- Merged in set to sage-5.10.beta2
- Resolution set to fixed
- Status changed from positive_review to closed
I've updated the patches with various minor improvements.