On Sun, Jun 11, 2017 at 3:20 PM, John H Palmieri <jhpalmier...@gmail.com> wrote: > On Sunday, June 11, 2017 at 10:13:52 AM UTC-7, David Joyner wrote: >> >> On Sun, Jun 11, 2017 at 11:30 AM, John H Palmieri >> <jhpalm...@gmail.com> wrote: >> > >> > >> > On Saturday, June 10, 2017 at 7:05:49 PM UTC-7, David Joyner wrote: >> >> >> >> On Thu, Jun 8, 2017 at 10:49 PM, John H Palmieri <jhpalm...@gmail.com> >> >> wrote: >> >> > >> >> > >> >> > On Thursday, June 8, 2017 at 5:16:15 PM UTC-7, David Joyner wrote: >> >> >> >> >> >> Hi all: >> >> >> >> >> >> This is kind of a newbie question, as I'm not an expert on >> >> >> simplicial >> >> >> complexes. It's also a minor technical issue on the documentation, >> >> >> not >> >> >> the code. >> >> >> >> >> >> I'm trying to debug some code of mine and, on reading the >> >> >> documentation for chain_complex on >> >> >> >> >> >> >> >> >> >> >> >> http://doc.sagemath.org/html/en/reference/homology/sage/homology/simplicial_complex.html, >> >> >> found this: "The rows and columns of the boundary matrices are >> >> >> indexed >> >> >> by the lists given by the n_cells() method, which by default are >> >> >> sorted." On the other hand, the documentation for n_cells has this >> >> >> statement: "Sort the list if the argument sort is True. If sort is >> >> >> None (the default), then sort depending on the value of the >> >> >> sort_facets parameter (from the initialization of the simplicial >> >> >> complex)." However, the sort_facets parameter (unless I'm mistaken) >> >> >> does not sort the individual faces but rather sorts the vertices in >> >> >> each facet. >> >> > >> >> > >> >> > The documentation means that if "sort_facets" was True originally, >> >> > then >> >> > n_cells will also sort its result before returning it. ("then sort >> >> > depending >> >> > on the value of the sort_facets parameter": so if sort_facets was >> >> > True, >> >> > then >> >> > n_cells should also sort. It doesn't mean "sort using the effect of >> >> > the >> >> > sort_facets parameter", but sort depending on its value, which is >> >> > True >> >> > or >> >> > False. This could be made clearer, I guess.) >> >> > >> >> >> >> >> >> To be clear, I am getting different computations using the same sage >> >> computations on different machines. One (recent, but used, linux) >> >> machine consistently gives ones result, the other gives (randomly?) >> >> several others. The "other" (a 8 yr old, a mac with possibly memory >> >> issues) machine gives different results. I'm not saying your methods >> >> are machine dependent, just that *for me* they seem to be. >> >> >> >> To be clear, these "inconsistent" computations take at least one day. >> >> The "toy" (consistent) examples are okay. >> > >> > >> > That's strange. Are you just getting different orders when you sort, or >> > different answers for homology? Are the answers consistent on each >> > machine? >> > What type of object are the vertices? >> > >> >> The example which gives strange output is the bipyramid complex: >> >> S = SimplicialComplex(maximal_faces=[(1,2,3), (1,2,4),\ >> (1,2,5), (1,3,4),(1,3,5),(2,3,4),(2,3,5)]) >> >> which has 9 1-faces. I'm computing the list of all stable configurations, >> namely vectors c in ZZ^9 having non-negative components which cannot >> fire (in the sense of chip-firing - see Duval, Klivans, Martin >> https://arxiv.org/pdf/1101.3981.pdf) with respect to the 1-dimls >> simplicial >> spanning tree given by the 1-faces (1, 4), (1,5), (2,5), (3,4). On an old >> mac running OS 10.11.6 and sage 7.2.b0, the output is usually 268125, >> after about a day, but once I also got 137500. On a linux machine running >> ubuntu and sage 7.3, I always get 395625. These computations use >> the S.chain_complex.differential method to compute the 1-diml >> combinatorial up Laplacian, Q, then does a time-consuming search. >> (Basically, I check that no column vector q of Q, except possibly one >> corresponding to a face in the spanning tree, has the property that >> all components of c-q remain non-negative, except possibly those >> corresponding to a face in the spanning tree.) >> >> A similar computation using the 3-simplex is relatively quick and >> always produces >> 2500 stable configurations for both machines. > > > The sorting was introduced after 7.2, so it's not surprising if that version > gives different results. The sorting certainly affects the chain complex,
I'm relieved to hear this. > and it is possible in older versions that the ordering used for the > simplices to define the matrices for the chain complex is somewhat > arbitrary, and not necessarily consistent with other methods for simplicial > complexes. I would trust Sage 7.3 over 7.2 because of this sorting. I don't > think any relevant changes have been made since 7.3, but it would be > interesting to see if you get different results with 7.6 or 8.0. > Yesterday, I deleted 7.2 and installed 7.6. After a long computation, it too produces 395625. Thank you! > John > > >> >> >> >> >> >> >> >> >> >> >> > I don't know if there is ever a good reason to specify >> >> > sort_facets=False. >> >> > Maybe we should deprecate it? >> >> > >> >> >> >> >> >> In my code, I expected the faces of a fixed dimension to >> >> >> be returned as a deterministic sorted list not a set whose ordering >> >> >> could be random. Now, it *does* seem as though the faces are sorted. >> >> >> It's just that, to me, the documentation of n_cells doesn't make >> >> >> that >> >> >> clear. >> >> >> >> >> >> I'm asking if I'm mis-understanding something here or not. >> >> >> >> >> >> - David Joyner >> >> > >> >> > >> >> > -- >> >> > John >> >> > >> >> > >> >> > -- >> >> > You received this message because you are subscribed to the Google >> >> > Groups >> >> > "sage-support" group. >> >> > To unsubscribe from this group and stop receiving emails from it, >> >> > send >> >> > an >> >> > email to sage-support...@googlegroups.com. >> >> > To post to this group, send email to sage-s...@googlegroups.com. >> >> > Visit this group at https://groups.google.com/group/sage-support. >> >> > For more options, visit https://groups.google.com/d/optout. >> > >> > -- >> > You received this message because you are subscribed to the Google >> > Groups >> > "sage-support" group. >> > To unsubscribe from this group and stop receiving emails from it, send >> > an >> > email to sage-support...@googlegroups.com. >> > To post to this group, send email to sage-s...@googlegroups.com. >> > Visit this group at https://groups.google.com/group/sage-support. >> > For more options, visit https://groups.google.com/d/optout. > > -- > You received this message because you are subscribed to the Google Groups > "sage-support" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to sage-support+unsubscr...@googlegroups.com. > To post to this group, send email to sage-support@googlegroups.com. > Visit this group at https://groups.google.com/group/sage-support. > For more options, visit https://groups.google.com/d/optout. -- You received this message because you are subscribed to the Google Groups "sage-support" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-support+unsubscr...@googlegroups.com. To post to this group, send email to sage-support@googlegroups.com. Visit this group at https://groups.google.com/group/sage-support. For more options, visit https://groups.google.com/d/optout.
