Re: Sparse matrix extension

[Patrick Alken <alken@colorado.edu>]

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
>
>