From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: (qmail 123265 invoked by alias); 10 Feb 2016 13:48:10 -0000 Mailing-List: contact gsl-discuss-help@sourceware.org; run by ezmlm Precedence: bulk List-Id: List-Subscribe: List-Archive: List-Post: List-Help: , Sender: gsl-discuss-owner@sourceware.org Received: (qmail 123254 invoked by uid 89); 10 Feb 2016 13:48:09 -0000 Authentication-Results: sourceware.org; auth=none X-Virus-Found: No X-Spam-SWARE-Status: No, score=-1.8 required=5.0 tests=AWL,BAYES_00,FREEMAIL_FROM,RCVD_IN_DNSWL_LOW,SPF_PASS autolearn=ham version=3.3.2 spammy=market X-HELO: mail-ig0-f172.google.com Received: from mail-ig0-f172.google.com (HELO mail-ig0-f172.google.com) (209.85.213.172) by sourceware.org (qpsmtpd/0.93/v0.84-503-g423c35a) with (AES128-GCM-SHA256 encrypted) ESMTPS; Wed, 10 Feb 2016 13:48:07 +0000 Received: by mail-ig0-f172.google.com with SMTP id mw1so14206217igb.1 for ; Wed, 10 Feb 2016 05:48:07 -0800 (PST) X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20130820; h=x-gm-message-state:mime-version:in-reply-to:references:date :message-id:subject:from:to:cc:content-type; bh=VHP8/89OvWDZfr6ZaV753SyPiCjrF6o9ryb9wM3Fo7g=; b=jDbIBCSjDYcYwlZELE4bLB/tetWj7Np1rUYXnMQzz8OtWkPmbIRPM3/4j85dhYUwqL eG1MaJ54xkwV/08u/c/3YZxB61ZxZSqagmyAK70W0tZ7ICmrZScK5iDOelmriX+gHcgH ESMGTZ3hlcWLIQskORlDHARFyk7wmJflvvOScNK6rFCj+a7WoW9mw3G/dcrdTRpnSBbT xt7FdWTy2jALlwxhsD8LPYawYGeOl1cBDUOK8MjC6tGEYSbhTXOTBYteIBm9/owP1phV S+kiT4p7fv0GrJstX+UY9k6KehLb3VIR6q7yrOQ2RZHQq3C8YDiyeveDtCgubCUl30fq Qj8Q== X-Gm-Message-State: AG10YOSsSislyankEgsuDaq6ECbnFk6yOwVJqGgsy7SGrduxSrlNbJF9FUJfI3xlQap/wsLtcuQP9BLOX48tIw== MIME-Version: 1.0 X-Received: by 10.50.134.129 with SMTP id pk1mr10383506igb.11.1455112085823; Wed, 10 Feb 2016 05:48:05 -0800 (PST) Received: by 10.79.118.141 with HTTP; Wed, 10 Feb 2016 05:48:05 -0800 (PST) In-Reply-To: References: <569E6C33.1090505@colorado.edu> <569EA1A9.2080101@colorado.edu> <56B689B1.5090005@colorado.edu> <56B77E13.1000306@colorado.edu> <56B7A59D.5040707@colorado.edu> <56B7B85C.10508@colorado.edu> Date: Wed, 10 Feb 2016 13:48:00 -0000 Message-ID: Subject: Re: Sparse matrix extension From: Alexis Tantet To: Patrick Alken Cc: "gsl-discuss@sourceware.org" Content-Type: text/plain; charset=UTF-8 X-SW-Source: 2016-q1/txt/msg00014.txt.bz2 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 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 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 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