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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*: Wed, 10 Feb 2016 14:48:05 +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>

I actually just had to add the one line header to _fprintf and _fscanf did not need to be modified (sum_duplicate should eventually be removed though). I have pushed the change to my clone on branch dev. Also, in spmanip.c, there are some function returning a pointer to a gsl_vector. It may be better to let them return an exit status instead and put the vector as an output argument. Alexis On Wed, Feb 10, 2016 at 2:16 PM, Alexis Tantet <alexis.tantet@gmail.com> 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 -- Alexis Tantet

**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

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