[petsc-dev] Slowness of PetscSortIntWithArrayPair in MatAssembly

[Fande Kong]

YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault: 11
(signal 11)

Segmentation fault :-)


As Jed said, it might be a good idea to rewrite the code using the hashing
table.


Fande,


On Tue, Jul 2, 2019 at 1:27 PM Zhang, Junchao <jczhang at mcs.anl.gov> wrote:

> Try this to see if it helps:
>
> diff --git a/src/sys/utils/sorti.c b/src/sys/utils/sorti.c
> index 1b07205a..90779891 100644
> --- a/src/sys/utils/sorti.c
> +++ b/src/sys/utils/sorti.c
> @@ -294,7 +294,8 @@ static PetscErrorCode
> PetscSortIntWithArrayPair_Private(PetscInt *L,PetscInt *J,
>      }
>      PetscFunctionReturn(0);
>    }
> -  SWAP3(L[0],L[right/2],J[0],J[right/2],K[0],K[right/2],tmp);
> +  i = MEDIAN(L,right);
> +  SWAP3(L[0],L[i],J[0],J[i],K[0],K[i],tmp);
>    vl   = L[0];
>    last = 0;
>    for (i=1; i<=right; i++) {
>
>
> On Tue, Jul 2, 2019 at 12:14 PM Fande Kong via petsc-dev <
> petsc-dev at mcs.anl.gov> wrote:
>
>> BTW,
>>
>> PetscSortIntWithArrayPair is used in MatStashSortCompress_Private.
>>
>> Any way to avoid to use PetscSortIntWithArrayPair in
>> MatStashSortCompress_Private?
>>
>> Fande,
>>
>> On Tue, Jul 2, 2019 at 11:09 AM Fande Kong <fdkong.jd at gmail.com> wrote:
>>
>>> Hi Developers,
>>>
>>> John just noticed that the matrix assembly was slow when having
>>> sufficient amount of off-diagonal entries. It was not a MPI issue since I
>>> was  able to reproduce the issue using two cores on my desktop, that is,
>>> "mpirun -n 2".
>>>
>>> I turned  on a profiling, and 99.99% of the time was spent
>>> on PetscSortIntWithArrayPair (recursively calling).   It took THREE MINUTES
>>>  to get the assembly done. And then changed to use the option
>>> "-matstash_legacy" to restore
>>> the code to the old assembly routine, and the same code took ONE SECOND
>>> to get the matrix assembly done.
>>>
>>> Should write any better sorting algorithms?
>>>
>>>
>>> Fande,
>>>
>>
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