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Re: [Help-gsl] finite element assembly and calling UMFPACK for linear sy

From: Patrick Alken
Subject: Re: [Help-gsl] finite element assembly and calling UMFPACK for linear system solution
Date: Wed, 19 Jun 2019 19:45:49 +0000
User-agent: Mozilla/5.0 (X11; Linux x86_64; rv:60.0) Gecko/20100101 Thunderbird/60.6.1

A new feature on the git is the ability to parallelize the assembly of the 
sparse matrix. This feature is not yet documented, but I can give you more 
details if interested.

Essentially you do a first assembly (non-parallized) so GSL can learn the 
non-zero pattern of the matrix. Then, if you want to change the matrix entries 
later (without changing the non-zero pattern), you can essentially "lock" the 
binary tree structure so that no new nodes will be inserted. Then you can 
change existing matrix entries from multiple threads without worrying.

This is useful if you need to build many sparse matrices quickly which all 
share the same non-zero pattern. Let me know if you want more details.


On 6/19/19 1:40 PM, Brijesh Upadhaya wrote:
Thank Patrick for your prompt response.

I saw lots of new update in git.gsl. And yes now I assemble the entire matrix 
and add boundary conditions before compressing it. For now I'll just clone and 
compile the newer version.


On Wed, Jun 19, 2019 at 7:41 PM Patrick Alken 
<address@hidden<mailto:address@hidden>> wrote:

On 6/19/19 9:15 AM, Brijesh Upadhaya wrote:
> Hi everyone,
> I am working on a finite element problem and wanted to ask if anyone of you
> have tried using UMFPACK for the linear algebra. I have following findings
> when using sparse matrix module from gsl-2.5.
> 1. In CCS the row indices are not sorted so UMFPACK gives error (see
> attached example)
Its on my todo list to add a "sorted CSC" and "sorted CSR" spmatrix
type. Hopefully it will get done for the next release.
> 2. Adding boundary conditions were also difficult once compressed, so I
> couldn't utilize gsl_spmatrix_add() to add mass matrix with stiffness
> matrix. Instead I had to do it with triplet and calling the get/set
> routines. Could only add boundary condition at triplet level and compressed
> at the end and passed the pointers to UMFPACK routines.
Yes the triplet (COO) format is designed for easy set/get operations,
using a binary tree for fast lookup and insertion. Once you compress the
matrix, the binary tree disappears, and you can only modify existing
matrix entries - you cannot add new ones. Can't you assemble the entire
matrix, including boundary conditions, before compressing it?
> 3. Another thing (not related to gsl) was that UMFPACK don't use (size_t
> *), instead it has (int *) and (long *) for column pointers and row
> indices. I tried to cast (size_t *) to (long *) to utilize the pointers of
> gsl_spmatrix object.
I have decided to change the size_t pointers to int in gsl_spmatrix, for
the reason you cite. Many external libraries use integer arrays instead
of size_t. This has already been done on the git repository (you can
just clone the gsl git).
> I am bit curious to know if anyone have a better experience. I wanted to
> use direct solver instead of iterative solver.
I would also like to include a direct solver in GSL itself, though I
don't know when I'll have time to implement it.
> King Regards,
> Brijesh

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