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Re: Sparse matrix extension

Ok fixed

On 02/14/2016 04:06 AM, Alexis Tantet wrote:
> 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 <> 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

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