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From: Alexis Tantet <alexis.tantet@gmail.com>
To: Patrick Alken <alken@colorado.edu>
Cc: "gsl-discuss@sourceware.org" <gsl-discuss@sourceware.org>
Subject: Re: Sparse matrix extension
Date: Wed, 10 Feb 2016 13:16:00 -0000	[thread overview]
Message-ID: <CAMWWPT0qUccM6cNkX6fWezmj09SdcgYqYzGE3eoqetpuyZW6Vg@mail.gmail.com> (raw)
In-Reply-To: <CAMWWPT1ELN9_BFLG=KUQ=Z6rC6ytYGTm0_K-=4-urJ6HGxfFJQ@mail.gmail.com>

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

  reply	other threads:[~2016-02-10 13:16 UTC|newest]

Thread overview: 25+ messages / expand[flat|nested]  mbox.gz  Atom feed  top
     [not found] <CAMWWPT3uJj4Vrn7ut6+F18gY===zd6+1r1UJhz0hcCj--zwtdg@mail.gmail.com>
2016-01-19 16:43 ` Alexis Tantet
2016-01-19 17:02   ` Patrick Alken
2016-01-19 19:55     ` Alexis Tantet
2016-01-19 20:50       ` Patrick Alken
2016-01-20 18:31         ` Alexis Tantet
2016-02-07  0:03           ` Patrick Alken
2016-02-07  1:03             ` Alexis Tantet
2016-02-07 17:25               ` Patrick Alken
2016-02-07 19:32                 ` Alexis Tantet
2016-02-07 20:14                   ` Patrick Alken
2016-02-07 20:31                     ` Alexis Tantet
2016-02-07 21:34                       ` Patrick Alken
2016-02-08  0:59                         ` Alexis Tantet
2016-02-10 13:16                           ` Alexis Tantet [this message]
2016-02-10 13:48                             ` Alexis Tantet
2016-02-10 15:56                             ` Patrick Alken
2016-02-12 10:43                               ` Alexis Tantet
2016-02-13 19:42                                 ` Patrick Alken
2016-02-14 11:06                                   ` Alexis Tantet
2016-02-14 18:11                                     ` Patrick Alken
2016-02-14 18:25                                       ` Brian Gladman
2016-02-15  5:10                                         ` Patrick Alken
2016-02-15 11:09                                           ` Brian Gladman
     [not found]                                             ` <CAMWWPT0J9ENRZjJHLO=cxot4DGdSLer+n2HkBVnhFnO0oiVV8g@mail.gmail.com>
2016-02-15 13:56                                               ` Alexis Tantet
2016-02-15 17:17                                                 ` Patrick Alken

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