assembly

[Hong Zhang]

On Sat, 2 Feb 2008, Thomas Geenen wrote:

> Dear Petsc users,
>
> I would like to understand what is slowing down the assembly phase of my matrix.
> I create a matrix with MatCreateMPIAIJ i make a rough guess of the
> number of off diagonal entries and then use a conservative value to
> make sure I do not need extra mallocs. (the number of diagonal entries
> is exact)
> next i call MatSetValues and MatAssemblyBegin, MatAssemblyEnd.
> The first time i call MatSetValues and MatAssemblyBegin,
> MatAssemblyEnd it takes about 170 seconds
> the second time 0.3 seconds.
> I run it on 6 cpu's and I do fill quit a number of row-entries on the
> "wrong" cpu. However thats also the case the second run. I checked
> that there are no additional mallocs
> MatGetInfo info.mallocs=0 both after MatSetValues and after
> MatAssemblyBegin, MatAssemblyEnd.

Run your code with the option '-log_summary' and check which function
call dominates the execution time.

> I run it on 6 cpu's and I do fill quit a number of row-entries on the
> "wrong" cpu.

Likely, the communication that sending the entries to the
corrected cpu consume the time. Can you fill the entries in the
correct cpu?

Hong
>
> cheers
> Thomas
>
>