question about Maker-MPI

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question about Maker-MPI

Xabier Vázquez Campos
Hi Carson,
We finally got Maker working with MPI (mpich, openmpi was a dead end...) and I have a question about how Maker distributes the computation load.
I know, correct me if I'm wrong, that with MPI, Maker runs blast in parallel (1 instance per thread) for protein2genome and est2genome. This indeed improves enormously the speed for the initial run.
But, does it take advance of this at the time of running the gene predictors? I think there is no benefit on multiple cpus in non-MPI mode but I have no idea in MPI.
Thank you in advance,
Xabi

--
Xabier Vázquez-Campos, PhD
Research Associate
NSW Systems Biology Initiative
School of Biotechnology and Biomolecular Sciences
The University of New South Wales
Sydney NSW 2052 AUSTRALIA

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Re: question about Maker-MPI

Carson Holt-2
MAKER parallelizes at multiple levels. For the ab initio predictors, it will run multiple contigs simultaneously (so each one will get their own ab initio predictor running). For large contigs it will further divide it into 10Mb chunks, and each will run simultaneously.

—Carson




On Sep 26, 2017, at 1:23 AM, Xabier Vázquez-Campos <[hidden email]> wrote:

Hi Carson,
We finally got Maker working with MPI (mpich, openmpi was a dead end...) and I have a question about how Maker distributes the computation load.
I know, correct me if I'm wrong, that with MPI, Maker runs blast in parallel (1 instance per thread) for protein2genome and est2genome. This indeed improves enormously the speed for the initial run.
But, does it take advance of this at the time of running the gene predictors? I think there is no benefit on multiple cpus in non-MPI mode but I have no idea in MPI.
Thank you in advance,
Xabi

--
Xabier Vázquez-Campos, PhD
Research Associate
NSW Systems Biology Initiative
School of Biotechnology and Biomolecular Sciences
The University of New South Wales
Sydney NSW 2052 AUSTRALIA


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maker-devel mailing list
[hidden email]
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