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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*: Fri, 12 Feb 2016 11:42:58 +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>

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

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