[mpich-discuss] MPI_Alltoall problem

[Jie Chen]

Rhys: thank you for the heads up. Actually my question stems from using fftw. I do not feel fftw fast enough, considering that I need to do the transforms millions, even billions times.  I timed its routine and found that it was actually the transpose of the data that killed me. I know that when creating the plan, fftw would test different options, including the mpi_alltoall way, and choose the fastest option to do transpose. I just hope that someone here might have a smarter solution that what fftw provides...

Jie



On Oct 8, 2011, at 4:52 AM, Rhys Ulerich <rhys.ulerich at gmail.com> wrote:

>> Hi, I am working on some application that heavily uses MPI_Alltoall---matrix transpose.
>> ... So the performance of MPI_Alltoall becomes very critical. Does anyone know an
>> alternative to directly calling the MPI_Alltoall routine and reduce the run time?
> 
> One possibility would be trying FFTW 3.3's MPI transpose capabilities
> [1].  You pay a
> one-time planning cost while FFTW figures out what the fastest way is
> to perform your
> transpose (Alltoall, pairwise sendrecv, etc) and then you can
> repeatedly execute the
> optimum choice.
> 
> If this looks like a good option, be sure to read the entire FFTW MPI chapter as
> many of the useful tidbits are buried within it (e.g. [2]).  Lastly,
> if you structure your
> computation so that you perform an MPI transpose of your matrix A and in the
> "transposed" logic you compute with data strided like A^T, you may find that
> FFTW_MPI_TRANSPOSED_OUT [3] will improve your runtime.
> 
> Hope that helps,
> Rhys
> 
> [1] http://www.fftw.org/fftw3_doc/FFTW-MPI-Transposes.html#FFTW-MPI-Transposes
> [2] http://www.fftw.org/fftw3_doc/FFTW-MPI-Performance-Tips.html#FFTW-MPI-Performance-Tips
> [3] http://www.fftw.org/fftw3_doc/Transposed-distributions.html#Transposed-distributions
> _______________________________________________
> mpich-discuss mailing list     mpich-discuss at mcs.anl.gov
> To manage subscription options or unsubscribe:
> https://lists.mcs.anl.gov/mailman/listinfo/mpich-discuss