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*From*: Alexis Tantet <alexis dot tantet at gmail dot com>*To*: Patrick Alken <alken at colorado dot edu>*Cc*: gsl-discuss at sourceware dot org*Date*: Tue, 19 Jan 2016 20:55:05 +0100*Subject*: Re: Sparse matrix extension*Authentication-results*: sourceware.org; auth=none*References*: <CAMWWPT3uJj4Vrn7ut6+F18gY===zd6+1r1UJhz0hcCj--zwtdg at mail dot gmail dot com> <CAMWWPT3Y=x-vYphaV+2gHPb9WZqEfYdDxs4T0KqBq987VjvDQA at mail dot gmail dot com> <569E6C33 dot 1090505 at colorado dot edu>

Hi Patrick, Thanks for the quick reply! I wanted to be sure that this contribution is useful before to spend time on the merging with the latest version. I will create the gsl.git repository and work on it during the week. I had already had a look at the documentation but did not know about the iterative solvers (a link between each modules would be useful). My contribution indeed fits in the sparse matrix module + the update of the dgemm and dgemv functions to support CRS (an update may also be needed for the solvers). I have also developed a simple C++ object allowing to use gsl_spmatrix as a user-defined matrix in ARPACK++ (a maintained fork of ARPACK++ can be found at https://github.com/m-reuter/arpackpp), allowing to avoid having to use other libraries such as superLU. It could be useful to others, maybe as an extension. Now that I think about it, the iterative solvers could also be used to support the shift and invert modes (see ARPACK++ documentation). What do you think (I could work on it)? If you have major comments, the sooner the better, so that I can work on them while merging. Thank you for your interest, Alexis On Tue, Jan 19, 2016 at 6:02 PM, Patrick Alken <alken@colorado.edu> wrote: > Hi Alexis, > > This looks like very good work! Adding compressed row storage has been on > my todo list for a while. The 'gslsp' extension is unfortunately very out of > date, and the current git contains newer code (including a GMRES iterative > linear solver). I removed the gslsp extension from the web page a while back > to reflect this. You can browse the latest manual to see the current sparse > matrix capabilities (http://www.gnu.org/software/gsl/manual/gsl-ref.pdf) - > there are 3 chapters: sparse matrices, sparse blas and sparse linear algebra > - it looks like your contributions will fit into the sparse matrices > chapter. > > Would you be able to verify that your changes are compatible with the > current gsl.git repository? This will make it much easier for me to merge > everything into the git when ready. It would be best if you made a new > branch of gsl.git, and add your changes so I can then pull them from github > or somewhere. I will try to find some time in the next few days to look over > your code. > > Thanks again, > Patrick > > > On 01/19/2016 09:43 AM, Alexis Tantet wrote: >> >> Dear GSLers, >> >> As a scientist rather than a developer, I have developed an extension >> of the sparse matrix module (CRS, I/O, manipulation, see below), which >> I have tested. These modifications conserve the structure of the >> original module and be useful for a large number of sparse matrices >> users. >> >> I'm not familiar with the contributing process here. My repository can >> be found there: >> https://github.com/atantet/gslsp >> Unfortunately, I did not know of the gsl.git repository and I forked it >> froml: >> https://github.com/drjerry/gslsp , >> which seems to be a bit older than gsl.git. >> >> How can I push/merge to gsl.git ? Should it be as an update or another >> extension? Is it necessary to adapt to the newest version of the code >> ? >> >> Best regards, >> Alexis Tantet >> >> CHANGES.md: >> >> Extension of the sparse matrix module of GSL >> >> =================================== >> >> Introduction >> ------------ >> >> Usages of sparse matrices are numerous in scientific computing. >> When numerical linear algebra problems become large, sparse >> matrices become necessary to avoid memory overload and unnecessary >> computations, at the cost of element access and matrix construction. >> As a result, most large scale linear solvers or eigen solvers perform >> on sparse matrices. >> >> Fortunately, a very useful sparse matrix module has recently been >> introduced to GSL. >> However, important features are still lacking, such has >> Compressed Row Storage (CRS) matrices, input/output functions and >> other matrix properties and manipulation functions. >> This new version attempts to address this, conserving the original >> structure of the module and conventions. >> >> Major changes >> ------------- >> >> * Add CRS format and update functions manipulating compressed matrices : >> - additional flag GSL_SPMATRIX_CRS and macro GSLSP_ISMATRIX ( >> gsl_spmatrix.h ) >> - additional members innerSize and outerSize used to iterate >> matrix elements ( gsl_spmatrix.h ) >> - rename some variables for coherence ( gsl_spmatrix.h , *.c ) >> - update all functions on compressed matrices ( *.c ) >> * Allow to sum duplicate elements when compressing ( spcompress.c ) : >> - modify gsl_spmatrix_compress >> - add gsl_spmatrix_sum_duplicate >> * CCS <-> CRS and fast transpose inplace in spswap.c : >> - add gsl_spmatrix_switch_major >> - add gsl_spmatrix_transpose >> * Add printing and scanning functions in spio.c : >> - add gsl_spmatrix_fprintf >> - add gsl_spmatrix_fscanf >> * Add manipulation functions in spmanip.c (particularly useful for >> Markov chain transition matrices) : >> - add gsl_spmatrix_get_rowsum : get vector of sum over row elements >> - add gsl_spmatrix_get_colsum : get vector of sum over column >> elements >> - add gsl_spmatrix_div_rows : divide all elements of each row >> by a vector element >> - add gsl_spmatrix_div_cols : divide all elements of each >> column by a vector element >> * Add test functions in atprop.c : >> - add gsl_spmatrix_gt_elements : greater than test for each matrix >> element >> - add gsl_spmatrix_ge_elements : greater or equal than test for >> each matrix element >> - add gsl_spmatrix_lt_elements : lower than test for each matrix >> element >> - add gsl_spmatrix_le_elements : lower or equal than test for >> each matrix element >> - add gsl_spmatrix_any : test if any non-zero element in >> matrix >> >> Other minor changes have been made, such as error tests. >> test.c has also been updated to test new features. > > -- Alexis Tantet

**Follow-Ups**:**Re: Sparse matrix extension***From:*Patrick Alken

**References**:**Re: Sparse matrix extension***From:*Alexis Tantet

**Re: Sparse matrix extension***From:*Patrick Alken

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