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Re: Sparse matrix extension
- From: Patrick Alken <alken at colorado dot edu>
- To: <gsl-discuss at sourceware dot org>
- Date: Tue, 19 Jan 2016 10:02:43 -0700
- Subject: Re: Sparse matrix extension
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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very out of date, and the current git contains newer code (including a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.
On 01/19/2016 09:43 AM, Alexis Tantet wrote:
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
I'm not familiar with the contributing process here. My repository can
be found there:
Unfortunately, I did not know of the gsl.git repository and I forked it froml:
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
Extension of the sparse matrix module of GSL
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.
* Add CRS format and update functions manipulating compressed matrices :
- additional flag GSL_SPMATRIX_CRS and macro GSLSP_ISMATRIX (
- 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.