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*From*: Alexis Tantet <alexis dot tantet at gmail dot com>*To*: Patrick Alken <alken at colorado dot edu>*Cc*: "gsl-discuss at sourceware dot org" <gsl-discuss at sourceware dot org>*Date*: Sun, 14 Feb 2016 12:06:04 +0100*Subject*: Re: Sparse matrix extension*Authentication-results*: sourceware.org; auth=none*References*: <CAMWWPT3uJj4Vrn7ut6+F18gY===zd6+1r1UJhz0hcCj--zwtdg at mail dot gmail dot com> <CAMWWPT3Y=x-vYphaV+2gHPb9WZqEfYdDxs4T0KqBq987VjvDQA at mail dot gmail dot com> <569E6C33 dot 1090505 at colorado dot edu> <CAMWWPT2kMe=R0qUz4P6n_xzG+oW-8pOFwCtBuaritZ5MF6jzAg at mail dot gmail dot com> <569EA1A9 dot 2080101 at colorado dot edu> <CAMWWPT2d=PnK1cexcZ+OLQAYJudRk9QLGac-Wcn33OaES5UjJA at mail dot gmail dot com> <56B689B1 dot 5090005 at colorado dot edu> <CAMWWPT1mog0HrviL1tMo=f-rrSc2PhamWDGg7ZYLrVnnqkY3ng at mail dot gmail dot com> <56B77E13 dot 1000306 at colorado dot edu> <CAMWWPT2KTLjufNdwW=y-xaJ1dKkxDNQwgat4DB4ZwKDrK_fZSA at mail dot gmail dot com> <56B7A59D dot 5040707 at colorado dot edu> <CAMWWPT0CX+ti2j6QM8YmHqv+n8yg7sK69dtSdzKOQMFx3pXeBA at mail dot gmail dot com> <56B7B85C dot 10508 at colorado dot edu> <CAMWWPT1ELN9_BFLG=KUQ=Z6rC6ytYGTm0_K-=4-urJ6HGxfFJQ at mail dot gmail dot com> <CAMWWPT0qUccM6cNkX6fWezmj09SdcgYqYzGE3eoqetpuyZW6Vg at mail dot gmail dot com> <56BB5D84 dot 20804 at colorado dot edu> <CAMWWPT0a77RXNkg=a=Y8fJoxbYKpz-7tgvsXGPQNd4X_e=pNag at mail dot gmail dot com> <56BF86FC dot 8010509 at colorado dot edu>

Great! I've just figured that the printf/scanf need a modification. I had the indices starting from 0 as in C, while the MatrixMarket standard starts from 1. It is just a matter of adding one to the indices in printf and removing one for scanf. Could you take care of it? On Sat, Feb 13, 2016 at 8:41 PM, Patrick Alken <alken@colorado.edu> wrote: > Ok I've added the MatrixMarket stuff to fprintf/fscanf. I also merged > all the new sparse matrix stuff into the master branch on git. > > I've added almost your whole patch, except for all the stuff in > spmanip.c and also the gt_elements() routines in spprop.c. I'm not sure > these routines belong in a general purpose matrix library....although I > can possibly see a need for the row/col multiplication stuff, since we > can't easily make vector views of rows/columns of sparse matrices.. > > I'll need to think some more about this. > > Also I haven't yet modified dgemm, because I'm hesitant to use the > dynamic allocation method in your patch. Also I found a sparse blas > document on netlib which tries to outline a standard and I realize our > sparse blas routines don't adhere to this standard...so I may try to > redesign everything to follow that document. > > Anyway thanks a lot for all your work on this. > > Patrick > > On 02/12/2016 03:42 AM, Alexis Tantet wrote: >> I corrected _fscanf. There was an error when reading the comment header. >> >> On Wed, Feb 10, 2016 at 4:55 PM, Patrick Alken <alken@colorado.edu> wrote: >>> I'm in favor of simplicity and easy-parsing, so matrix market sounds good to >>> me. I'll take a look at your latest code in the next few days. >>> >>> Patrick >>> >>> >>> On 02/10/2016 06:16 AM, Alexis Tantet wrote: >>>> Hi Patrick, >>>> >>>> Regarding the file format for sparse matrices, the one I have coded >>>> actually happen to be the coordinate format implemented by Matrix >>>> Market (the platform to share test data such as sparse matrices), with >>>> the addition of a matrix type header: >>>> http://math.nist.gov/MatrixMarket/formats.html >>>> >>>> It is also written that "Harwell-Boeing" is the most commonly used >>>> sparse matrix format, but that: >>>> "Unfortunately the HB specification is somewhat complex difficult to >>>> parse from languages other than Fortran, biased in favor of compressed >>>> column representation and not easily extensible. Some of these factors >>>> may have impeded the more widespread use of the HB format" >>>> >>>> It seems to me that complying to the Matrix Market coordinate format >>>> would be the right choice, in terms of ease of implementation, >>>> compliance to other packages and user-friendliness. I could update the >>>> print/scan functions accordingly (mostly handling the header). What do >>>> you think? >>>> >>>> Best, >>>> Alexis >>>> >>>> >>>> >>>> >>>> On Mon, Feb 8, 2016 at 1:59 AM, Alexis Tantet <alexis.tantet@gmail.com> >>>> wrote: >>>>> Ok, my mistake, now I see where I got confused. >>>>> I had in mind to add all the elements first to the triplets and only >>>>> while converting to compressed sum up the duplicates. >>>>> While, indeed, if there's a way you can sum up the duplicates directly >>>>> while adding them to the triplet matrix (thanks to _ptr), this is more >>>>> handy and efficient. >>>>> >>>>> Thanks for the clarification, >>>>> Alexis >>>>> >>>>> On Sun, Feb 7, 2016 at 10:34 PM, Patrick Alken <alken@colorado.edu> >>>>> wrote: >>>>>> By design, gsl_spmatrix_set won't allow you to do this. >>>>>> >>>>>> If you add element (i, j, x) and then later to try add element (i, j, >>>>>> y), gsl_spmatrix_set will detect that there exists an element in the (i, >>>>>> j) spot and it will simply change x to y - the value of x will be >>>>>> overwritten by y. This is the same behavior as gsl_matrix_set. >>>>>> >>>>>> So no duplicates are allowed by design. If you have such an application >>>>>> where you want to keep track of duplicates, you could do the following: >>>>>> >>>>>> double *ptr = gsl_spmatrix_ptr(m, i, j); >>>>>> if (ptr) >>>>>> *ptr += x; /* sum duplicate values */ >>>>>> else >>>>>> gsl_spmatrix_set(m, i, j, x); /* initalize to x */ >>>>>> >>>>>> On 02/07/2016 01:31 PM, Alexis Tantet wrote: >>>>>>> I'm not sure I got your last point. I have the following situation in >>>>>>> mind: >>>>>>> >>>>>>> Start to construct a transition matrix in triplet format, adding one >>>>>>> element after another. >>>>>>> In this particular example, each element is one count of a transition >>>>>>> from (state, box, etc.) i to j, >>>>>>> so I add elements (i, j, 1) to the triplet object, with possibly >>>>>>> duplicates. >>>>>>> What happen to these duplicates in the binary tree? >>>>>>> >>>>>>> Eventually, when I compress to CRS or CCS, I would like the duplicates >>>>>>> to be summed up, so that element (i, j) counts transitions from i to j >>>>>>> (and no duplicates exist after compression). >>>>>>> >>>>>>> Is this more clear? >>>>>>> >>>>>>> On Sun, Feb 7, 2016 at 9:14 PM, Patrick Alken <alken@colorado.edu> >>>>>>> wrote: >>>>>>>> Hi Alexis, >>>>>>>> >>>>>>>>>> I'm not sure what you mean. I've added a new function >>>>>>>>>> gsl_spmatrix_ptr >>>>>>>>>> to the git, which as far as I can tell does exactly what your >>>>>>>>>> sum_duplicate flag does. It searches the matrix for an (i,j) >>>>>>>>>> element, >>>>>>>>>> and if found returns a pointer. If not found a null pointer is >>>>>>>>>> returned. >>>>>>>>>> This makes it easy for the user to modify A(i,j) after it has been >>>>>>>>>> added >>>>>>>>>> to the matrix. Are you thinking of something else? Can you point me >>>>>>>>>> to >>>>>>>>>> the Eigen routine? >>>>>>>>>> >>>>>>>>> What I meant is to have the equivalent of gsl_spmatrix_compress, >>>>>>>>> with the difference that gsl_spmatrix_ptr is used instead of >>>>>>>>> gsl_spmatrix_set, >>>>>>>>> so has to build the compressed matrix from triplets, summing the >>>>>>>>> duplicates, instead of replacing them. >>>>>>>>> This is what is done here : >>>>>>>>> The >>>>>>>>> http://eigen.tuxfamily.org/dox/classEigen_1_1SparseMatrix.html#a5bcf3187e372ff7cea1e8f61152ae49b >>>>>>>>> >>>>>>>>> Best, >>>>>>>>> Alexis >>>>>>>> I'm not sure why a user would ever need to do this. The whole point of >>>>>>>> the binary tree structure in the triplet storage is to efficiently >>>>>>>> find >>>>>>>> duplicate entries, so that if a user tries to call gsl_spmatrix_set on >>>>>>>> an element which is already been previously set, it can find that >>>>>>>> element with a binary search (rather than linearly searching the >>>>>>>> arrays) >>>>>>>> and change the value of that element. >>>>>>>> >>>>>>>> Therefore, the way the triplet storage is designed, there is will >>>>>>>> never >>>>>>>> be a duplicate element in the triplet arrays. All of the (i[n],j[n]) >>>>>>>> will be unique for each n <= nz. >>>>>>>> >>>>>>>> Am I missing something? >>>>>>>> >>>>>>>> Patrick >>>>>>> >>>>> >>>>> -- >>>>> Alexis Tantet >>>> >>>> >> >> > -- Alexis Tantet

**Follow-Ups**:**Re: Sparse matrix extension***From:*Patrick Alken

**References**:**Re: Sparse matrix extension***From:*Alexis Tantet

**Re: Sparse matrix extension***From:*Patrick Alken

**Re: Sparse matrix extension***From:*Alexis Tantet

**Re: Sparse matrix extension***From:*Patrick Alken

**Re: Sparse matrix extension***From:*Alexis Tantet

**Re: Sparse matrix extension***From:*Patrick Alken

**Re: Sparse matrix extension***From:*Alexis Tantet

**Re: Sparse matrix extension***From:*Patrick Alken

**Re: Sparse matrix extension***From:*Alexis Tantet

**Re: Sparse matrix extension***From:*Patrick Alken

**Re: Sparse matrix extension***From:*Alexis Tantet

**Re: Sparse matrix extension***From:*Patrick Alken

**Re: Sparse matrix extension***From:*Alexis Tantet

**Re: Sparse matrix extension***From:*Alexis Tantet

**Re: Sparse matrix extension***From:*Patrick Alken

**Re: Sparse matrix extension***From:*Alexis Tantet

**Re: Sparse matrix extension***From:*Patrick Alken

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