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Re: Sparse matrix extension


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 <> 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 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 <> 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:
>>>> 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 <>
>>>> 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 <>
>>>>> 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 <>
>>>>>>> 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
>>>>>>>>> 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

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