[sage-combinat-devel] trouble install sage-combinat with sage-5.10.rc0
Hello! Has something changed with installing sage-combinat with respect to sage-5.10.rc0. I get the following error message: ... [reference] dumping object inventory... done [reference] build succeeded. Build finished. The built documents can be found in /Applications/sage-5.10.rc0/devel/sage/doc/output/html/en/reference *** WARNING *** If you are cloning a previous revision or have uncommitted changes to cython files do sage -ba Otherwise Sage might build using the wrong .c files !! real23m14.785s user57m0.047s sys 3m5.823s Done Switching to sage combinat root directory: /Applications/sage-5.10.rc0/devel/sage-combinat Uploading sage-combinat patches into .hg/patches: cd .hg/; hg --config 'extensions.hgext.mq=' --config 'ui.username=sage-combinat script' clone http://combinat.sagemath.org/patches/ patches abort: error: nodename nor servname provided, or not known Abort My other installations work fine and I can still pull from the server from those. Best, Anne -- You received this message because you are subscribed to the Google Groups sage-combinat-devel group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-combinat-devel+unsubscr...@googlegroups.com. To post to this group, send email to sage-combinat-devel@googlegroups.com. Visit this group at http://groups.google.com/group/sage-combinat-devel?hl=en. For more options, visit https://groups.google.com/groups/opt_out.
Re: [sage-combinat-devel] trouble install sage-combinat with sage-5.10.rc0
On Sun, Jun 02, 2013 at 09:53:54AM -0700, Anne Schilling wrote: Has something changed with installing sage-combinat with respect to sage-5.10.rc0. Hmm, not that I know of. I get the following error message: Switching to sage combinat root directory: /Applications/sage-5.10.rc0/devel/sage-combinat Uploading sage-combinat patches into .hg/patches: cd .hg/; hg --config 'extensions.hgext.mq=' --config 'ui.username=sage-combinat script' clone http://combinat.sagemath.org/patches/ patches abort: error: nodename nor servname provided, or not known I think it's the first time I see this error. Anyone else having this problem? Could it be just a temporary network issue? I guess you can try doing the clone by hand after removing the previous .hg/patches directory. Cheers, Nicolas -- Nicolas M. Thiéry Isil nthi...@users.sf.net http://Nicolas.Thiery.name/ -- You received this message because you are subscribed to the Google Groups sage-combinat-devel group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-combinat-devel+unsubscr...@googlegroups.com. To post to this group, send email to sage-combinat-devel@googlegroups.com. Visit this group at http://groups.google.com/group/sage-combinat-devel?hl=en. For more options, visit https://groups.google.com/groups/opt_out.
Re: [sage-combinat-devel] trouble install sage-combinat with sage-5.10.rc0
On 6/2/13 10:30 AM, Nicolas M. Thiery wrote: On Sun, Jun 02, 2013 at 09:53:54AM -0700, Anne Schilling wrote: Has something changed with installing sage-combinat with respect to sage-5.10.rc0. Hmm, not that I know of. I get the following error message: Switching to sage combinat root directory: /Applications/sage-5.10.rc0/devel/sage-combinat Uploading sage-combinat patches into .hg/patches: cd .hg/; hg --config 'extensions.hgext.mq=' --config 'ui.username=sage-combinat script' clone http://combinat.sagemath.org/patches/ patches abort: error: nodename nor servname provided, or not known I think it's the first time I see this error. Anyone else having this problem? Could it be just a temporary network issue? I guess you can try doing the clone by hand after removing the previous .hg/patches directory. Thanks. I reinstalled from scratch and it worked this time. Sorry for the noise. Best, Anne -- You received this message because you are subscribed to the Google Groups sage-combinat-devel group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-combinat-devel+unsubscr...@googlegroups.com. To post to this group, send email to sage-combinat-devel@googlegroups.com. Visit this group at http://groups.google.com/group/sage-combinat-devel?hl=en. For more options, visit https://groups.google.com/groups/opt_out.
[sage-devel] Re: LELA for matrices?
On 2013-06-01, Volker Braun vbraun.n...@gmail.com wrote: [...] On a related note, sparse matrices in Sage suck (dictionary of keys). Sparse matrices in LELA only suck slightly less (list of lists). For fast computation one should implement compressed sparse row/column, I think. IMHO one needs to create a framework where one can choose a backend for sparse matrices, rather than aim for a complete from scratch implementation. E.g. there is a kind of standard, in numerics world, implementation of sparse matrices, which comes with a lot of extra goodies (including such important things like sparse Cholesky factorization, etc): http://www.cise.ufl.edu/research/sparse/SuiteSparse/ A part of it, complete with a Python interface, is already in Sage, in CVXOPT. (sucking of sparse matrices seems to be a common CAS illness, e.g. GAP has it too :-)) -- You received this message because you are subscribed to the Google Groups sage-devel group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-devel+unsubscr...@googlegroups.com. To post to this group, send email to sage-devel@googlegroups.com. Visit this group at http://groups.google.com/group/sage-devel?hl=en. For more options, visit https://groups.google.com/groups/opt_out.
Re: [sage-devel] LELA for matrices?
On Jun 2, 2013, at 9:20 AM, Dima Pasechnik wrote: On 2013-06-01, Volker Braun vbraun.n...@gmail.com wrote: [...] On a related note, sparse matrices in Sage suck (dictionary of keys). Sparse matrices in LELA only suck slightly less (list of lists). For fast computation one should implement compressed sparse row/column, I think. IMHO one needs to create a framework where one can choose a backend for sparse matrices, rather than aim for a complete from scratch implementation. I don't know what kind of interface do these package exhibit to access/modify/compute with a sparse matrix (eg. Linbox VS numerical-stuff) There is a presumably standard sparse-blas API : http://math.nist.gov/spblas/ E.g. there is a kind of standard, in numerics world, implementation of sparse matrices, which comes with a lot of extra goodies (including such important things like sparse Cholesky factorization, etc): http://www.cise.ufl.edu/research/sparse/SuiteSparse/ A part of it, complete with a Python interface, is already in Sage, in CVXOPT. And part of this is accessible already through SciPy (for floating-point matrices) : http://docs.scipy.org/doc/scipy/reference/sparse.linalg.html#module-scipy.sparse.linalg http://docs.scipy.org/doc/scipy/reference/sparse.linalg.html --- Charles -- You received this message because you are subscribed to the Google Groups sage-devel group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-devel+unsubscr...@googlegroups.com. To post to this group, send email to sage-devel@googlegroups.com. Visit this group at http://groups.google.com/group/sage-devel?hl=en. For more options, visit https://groups.google.com/groups/opt_out.
[sage-devel] Re: GSoC New decoding error-correcting codes algorithm for Sage
@Veronica: Hello and welcome. I look forward to your contributions! On Sunday, June 2, 2013 6:19:13 AM UTC+8, mmarco wrote: Welcome on board, Veronica. Please keep us up to date to your progress. I am your mentor, but i am sure the rest of the sage community would like to have you involved. Just a little clarification: Veronica has been selected under the umbrella of lmonade, even thoigh her work will be focused on sage. @mmarco: Perhaps you can add her blog's feed to Planet Sage? Then everyone will automatically get any updates she posts on the blog. -- You received this message because you are subscribed to the Google Groups sage-devel group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-devel+unsubscr...@googlegroups.com. To post to this group, send email to sage-devel@googlegroups.com. Visit this group at http://groups.google.com/group/sage-devel?hl=en. For more options, visit https://groups.google.com/groups/opt_out.
[sage-devel] Re: GSoC New decoding error-correcting codes algorithm for Sage
I have emailed Harald about it. -- You received this message because you are subscribed to the Google Groups sage-devel group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-devel+unsubscr...@googlegroups.com. To post to this group, send email to sage-devel@googlegroups.com. Visit this group at http://groups.google.com/group/sage-devel?hl=en. For more options, visit https://groups.google.com/groups/opt_out.
[sage-devel] Re: recompilation with sage -clone and after sage -sync-build
leif wrote: leif wrote: 4) Minimally adapt sage-sync-build.py to reflect the (hard-coded) change by #14570. [May be easy as well, but potentially unsafe.] Even that turns out to be non-trivial, AFAICS, i.e., the whole strategy would have to get changed, as opposed to just some file / directory names in a few places. Just for the record: I've meanwhile managed to hack sage-sync-build.py such that it /seems/^TM to work with a Cython build_dir (below $SAGE_SRC/build/) as well, but the patch would need clean-up and thorough testing. And as mentioned, the script needs further, not directly related, fixes anyway, so I'd prefer to postpone changes to sage-sync-build to 5.11. -leif -- () The ASCII Ribbon Campaign /\ Help Cure HTML E-Mail -- You received this message because you are subscribed to the Google Groups sage-devel group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-devel+unsubscr...@googlegroups.com. To post to this group, send email to sage-devel@googlegroups.com. Visit this group at http://groups.google.com/group/sage-devel?hl=en. For more options, visit https://groups.google.com/groups/opt_out.
[sage-devel] Re: recompilation with sage -clone and after sage -sync-build
Hey, Could we at least get the hacked sage-sync-build into 5.10? The combinat queue has a few patch which create new cython files that replace python files (i.e. cythonizes them) which requires the sync-build to be run when people are moving ahead of those patches. Rebuilding all cython files in sage seems like a high price to me for something we can put a quick patch (no pun intended) over. Thanks, Travis On Sunday, June 2, 2013 3:32:12 AM UTC-7, leif wrote: leif wrote: leif wrote: 4) Minimally adapt sage-sync-build.py to reflect the (hard-coded) change by #14570. [May be easy as well, but potentially unsafe.] Even that turns out to be non-trivial, AFAICS, i.e., the whole strategy would have to get changed, as opposed to just some file / directory names in a few places. Just for the record: I've meanwhile managed to hack sage-sync-build.py such that it /seems/^TM to work with a Cython build_dir (below $SAGE_SRC/build/) as well, but the patch would need clean-up and thorough testing. And as mentioned, the script needs further, not directly related, fixes anyway, so I'd prefer to postpone changes to sage-sync-build to 5.11. -leif -- () The ASCII Ribbon Campaign /\ Help Cure HTML E-Mail -- You received this message because you are subscribed to the Google Groups sage-devel group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-devel+unsubscr...@googlegroups.com. To post to this group, send email to sage-devel@googlegroups.com. Visit this group at http://groups.google.com/group/sage-devel?hl=en. For more options, visit https://groups.google.com/groups/opt_out.
Re: [sage-devel] LELA for matrices?
On Sunday, June 2, 2013 10:01:01 AM UTC+2, Charles Bouillaguet wrote: http://docs.scipy.org/doc/scipy/reference/sparse.linalg.html yes, i just wanted to point to that. this is the list of implementations, i.e. CSC/CSR (compressed sparse columns or rows) is already there. http://docs.scipy.org/doc/scipy/reference/sparse.html#sparse-matrix-classes h -- You received this message because you are subscribed to the Google Groups sage-devel group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-devel+unsubscr...@googlegroups.com. To post to this group, send email to sage-devel@googlegroups.com. Visit this group at http://groups.google.com/group/sage-devel?hl=en. For more options, visit https://groups.google.com/groups/opt_out.
Re: [sage-devel] LELA for matrices?
On Sunday, June 2, 2013 9:01:01 AM UTC+1, Charles Bouillaguet wrote: There is a presumably standard sparse-blas API : http://math.nist.gov/spblas/ Yes, though it doesn't seem to mandate any matrix storage format. So apparently you can't let it run on a given chunk of memory but you need to trust its internal (implementation-dependent) storage. Does anybody have any opinion on the performance of sparse blas and the reference implementation? -- You received this message because you are subscribed to the Google Groups sage-devel group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-devel+unsubscr...@googlegroups.com. To post to this group, send email to sage-devel@googlegroups.com. Visit this group at http://groups.google.com/group/sage-devel?hl=en. For more options, visit https://groups.google.com/groups/opt_out.
Re: [sage-devel] LELA for matrices?
Le 02/06/2013 19:28, Volker Braun a écrit : On Sunday, June 2, 2013 9:01:01 AM UTC+1, Charles Bouillaguet wrote: There is a presumably standard sparse-blas API : http://math.nist.gov/spblas/ Yes, though it doesn't seem to mandate any matrix storage format. So apparently you can't let it run on a given chunk of memory but you need to trust its internal (implementation-dependent) storage. Does anybody have any opinion on the performance of sparse blas and the reference implementation? Sparse Matrices are a big problem for people like me working in the field of numerical solution of PDEs (elliptic and parabolic ones); and nowadays, there are some interesting researches. - Whatever the data structure you use (and CSR or CSR like structures are used by everybody), the main problem is that the algorithms show a poor numerical intensity; let me explain: linear solvers are generally iterative krylov type methods (- evaluate a polynomial of the matrix times a vector): the arithmetic intensity is the ratio: q=bytes transfered between ram and cache /number of floating points performed q is very low with sparse matrices and the performances are typically bounded by memory bandwidth to much less than 1 gigaflop. To improve this, the best is to modify the algorithms (a bit too long to explain here!) to try to make more operations by byte transfered: I think nobody knows a miraculous data structure, and so we keep the CSR. - Ok, this is the scientific computing perspective, where you want to solve say Poisson equation in 3d with 10^9 unknowns. But I am not sure it is what we want to do in Sage, at least nowadays; you can solve moderate size systems with sparse matrices (say a 2d Poisson equation -- there are 5 non zero terms by line-- with 10^6 unknowns using SuperLU which is a *direct* method (LU adapted to sparse matrices), which uses CSR structures, and it will work very well. - In that case, I recall that the main problem will be actually to *create* the CSR structure: you want to enter non zero coefficients (i,j)- a_ij in any order. The mechanism used by by scipy (and thus sage) is very very slow much too slow (may be it changed... this must be tested). - Making CSR structures for other sets of coefficients is not difficult (at least in C++), if the coefficients have the same sizeof. t.d. -- You received this message because you are subscribed to the Google Groups sage-devel group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-devel+unsubscr...@googlegroups.com. To post to this group, send email to sage-devel@googlegroups.com. Visit this group at http://groups.google.com/group/sage-devel?hl=en. For more options, visit https://groups.google.com/groups/opt_out. attachment: tdumont.vcf
Re: [sage-devel] LELA for matrices?
On Sunday, June 2, 2013 7:58:05 PM UTC+1, tdumont wrote: - In that case, I recall that the main problem will be actually to *create* the CSR structure: you want to enter non zero coefficients (i,j)- a_ij in any order. The mechanism used by by scipy (and thus sage) is very very slow I don't think you can eat the cake and have it, too... Setting entries in CSR is to be avoided. Though I thought that you'd just switch (to dictionary-of-keys, say) to generate the matrix and then compress it in one step. Or maintain a lazy-write cache as dictionary of keys. Is that still not fast enough? -- You received this message because you are subscribed to the Google Groups sage-devel group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-devel+unsubscr...@googlegroups.com. To post to this group, send email to sage-devel@googlegroups.com. Visit this group at http://groups.google.com/group/sage-devel?hl=en. For more options, visit https://groups.google.com/groups/opt_out.
