Opened 3 years ago
Closed 15 months ago
#26029 closed defect (fixed)
polytopes_db_4d converted to new style package
Reported by:  embray  Owned by:  

Priority:  major  Milestone:  sage9.2 
Component:  packages: huge  Keywords:  
Cc:  mkoeppe, vbraun  Merged in:  
Authors:  Dima Pasechnik  Reviewers:  Travis Scrimshaw 
Report Upstream:  N/A  Work issues:  
Branch:  b49f89a (Commits, GitHub, GitLab)  Commit:  b49f89a5c8429619d576a5c998b890dcf09f7b86 
Dependencies:  Stopgaps: 
Description (last modified by )
This spkg is mentioned in #14467 and was apparently "huge" (and hence optional). But it is no longer listed under build/pkgs
nor does it appear to be available on the download mirrors.
Here is a branch to convert it to a new style experimental (but, maybe optional?) package.
the tarball is the old *.spkg file, but as it's a tar file, it works
tarball url (see in checksum.ini), but it's the same as one gets
via ./sage p polytopes_db_4d
(which still works with old style pkfs)
A few options:
1) If someone has a copy of this package we can convert it to a newstyle SPKG (we will probably need to upload the tarball somewhere with enough space to host it).
Done.
Change History (20)
comment:1 Changed 3 years ago by
comment:2 Changed 3 years ago by
The package is listed at:
comment:3 Changed 3 years ago by
And it's available from each of the SageMath download mirrors. E.g.
 LIP6 Paris: http://wwwftp.lip6.fr/pub/math/sagemath/spkg/huge/
 Riken Japan: ftp://ftp.riken.jp/sagemath/spkg/huge/index.html
etc.
The problems encountered with this huge package might instead have to do with
comment:4 Changed 3 years ago by
As I wrote on sagedevel, we could keep supporting this package if it were repackaged as a .tar.<whatever compression method works best>
, and we added an appropriate build/pkgs/polytopes_db_4d
for it. We would then want to move it to a standard location on the mirrors, not under "spkg/huge". That, or leave it under "spkg/huge" (if there is some advantage to that) but modify sagedownloadfile
to be able to find tarballs under that path on the mirrors.
comment:5 Changed 3 years ago by
 Milestone changed from sage8.4 to sage8.5
comment:6 Changed 3 years ago by
The following shows sage can find packages in "huge":
$ sage info polytopes_db_4d Attempting to get online info for package polytopes_db_4d >>> Checking online list of optional packages. >>> Checking online list of experimental packages. >>> Checking online list of huge packages. >>> Found polytopes_db_4d1.0 ...
The package cannot be installed with sage i
because it is an "oldstyle SPKG"
$ sage i polytopes_db_4d ... Error: package 'polytopes_db_4d' not found Note: if it is an oldstyle package, use p instead of i to install it
but sage p
can install "oldstyle spkg" packages that still work, including this one.
$ sage p polytopes_db_4d Attempting to download package polytopes_db_4d >>> Checking online list of optional packages. >>> Checking online list of experimental packages. >>> Checking online list of huge packages. >>> Found polytopes_db_4d1.0 ================================== NOTE ================================== You are about to download and install an oldstyle package. While this might still work fine, oldstyle packages are unmaintained and deprecated. This package will be removed in future versions of SageMath. If you care about this package, you should make a proper newstyle package instead. For more information about making Sage packages, see http://doc.sagemath.org/html/en/developer/packaging.html ========================================================================== Are you sure (automatically continuing in 30 seconds) [Y/n]?
Once this is done and after restarting Sage, one can follow the SageMath documentation on using the palp_database of reflexive Hodge 4polytopes. I tried it in Sage 8.4 as installed on the "k8s" CoCalc server for development, which currently runs Ubuntu 17.04.
sage: version() 'SageMath version 8.4, Release Date: 20181017'
sage: from sage.geometry.polyhedron.palp_database import Reflexive4dHodge sage: ref = Reflexive4dHodge(1, 101) sage: next(iter(ref)).Vrepresentation() (A vertex at (1, 1, 1, 1), A vertex at (0, 0, 0, 1), A vertex at (0, 0, 1, 0), A vertex at (0, 1, 0, 0), A vertex at (1, 0, 0, 0))
comment:7 Changed 3 years ago by
 Milestone changed from sage8.5 to sage8.7
Retargeting some of my tickets (somewhat optimistically for now).
comment:8 Changed 2 years ago by
 Milestone changed from sage8.7 to sagepending
Removing most of the rest of my open tickets out of the 8.7 milestone, which should be closed.
comment:9 Changed 2 years ago by
According to Andrey Novoseltev:
Data originates from http://hep.itp.tuwien.ac.at/~kreuzer/CY/
The whole list can be generated using PALP (a standard package in Sage), but when they have done it first, it took about a year on multiple computers, so there is sense in just downloading these polytopes. Sage package contains precomputed data for Hodge numbers as well, allowing quick search for particular cases. Volker knows more about exact details, I was just happily using the result.
While we are at it: it would be awesome if installation of this package after upgrade was faster. "Installation" just means unpacking files and copying them somewhere, but it takes something like 45 minutes. Some time ago I asked to use parallel decompressor if it is available in the system, which helped a lot, but then it stopped again.
As I wrote on sagedevel, perhaps it would make sense to host this data (as well as the 3D polytopes; why not?) on an online database somewhere that can be easily queried (including by the code in Sage which uses this data)? This way it is possible to use asneeded without downloading the entire, very large database (though perhaps with the possibility of predownloading/caching all or parts of it as needed).
It would be very easy to write a simple web service, and perhaps the data and service could be hosted on sagemath.org. This might also be a good opportunity for some MitM synergy. There is a workshop later this year on mathematical data, and frameworks and services for accessing them, so that might be a good opportunity to work on such a project (I would be happy to help, especially if someone can help me with the math end of things as I have no idea what a reflexive Hodge polytope is much less how it would be represented in a MitM framework): https://opendreamkit.org/2019/08/17/WorkshopOnDataInMathematics/
comment:10 Changed 2 years ago by
A reflexive polytope is a fulldimensional lattice polytope (i.e. the vertices have integer coordinates), containing the origin in the interior, so that its dual is also a lattice polytope. All this is readily available in Sage.
comment:11 Changed 2 years ago by
3D polytopes take so little space, that there is no sense at all removing them from Sage in their current form. As for 4D, there are probably very few people who are using them and so there is a lack of effort to do something about them. On the other hand, since there are papers referring to the use of this package in Sage, it would be nice to support repeating those computations in some way, even if installation is "nonstandard".
comment:12 Changed 15 months ago by
 Branch set to u/dimpase/packages/refpoly4d
 Cc mkoeppe vbraun added
 Commit set to 2ed5a53f8f3805f54962a0ce908ba23f2cc375b6
 Description modified (diff)
 Milestone changed from sagepending to sage9.2
 Status changed from new to needs_review
 Summary changed from Missing spkg: polytopes_db_4d to polytopes_db_4d converted to new style package
New commits:
2ed5a53  converting polytopes_db_4d into a new style package

comment:13 Changed 15 months ago by
Do we want this to be experimental or optional? I feel like optional would be the better option for this.
comment:14 Changed 15 months ago by
I also think it should be "optional"
comment:15 Changed 15 months ago by
 Commit changed from 2ed5a53f8f3805f54962a0ce908ba23f2cc375b6 to b49f89a5c8429619d576a5c998b890dcf09f7b86
Branch pushed to git repo; I updated commit sha1. New commits:
b49f89a  make it optional

comment:16 Changed 15 months ago by
OK, done
comment:17 Changed 15 months ago by
 Reviewers set to Travis Scrimshaw
Thanks. I am ready to set a positive review. Any objections?
comment:18 Changed 15 months ago by
No objection; I haven't tried it though because downloading was taking too long.
comment:19 Changed 15 months ago by
 Status changed from needs_review to positive_review
It built for me without any problems, so I am setting it to positive.
comment:20 Changed 15 months ago by
 Branch changed from u/dimpase/packages/refpoly4d to b49f89a5c8429619d576a5c998b890dcf09f7b86
 Resolution set to fixed
 Status changed from positive_review to closed
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