Re: [AMBER] MPI+threads in Amber

From: Daniel Roe <>
Date: Tue, 31 Mar 2020 13:35:49 -0400


Cpptraj can be compiled with MPI+OpenMP (also with CUDA, in any
combination). Note that the different types of parallelization
(processes vs threads) are orthogonal; trajectory reading/writing is
parallelized with MPI, while certain CPU-intensive actions are
parallelized with OpenMP (or CUDA in certain cases). A more complete
description can be found in the following publication:

Hope this helps - feel free to ask more questions as needed!


On Mon, Mar 30, 2020 at 1:01 PM Rohit Zambre <> wrote:
> Hi,
> I am a Ph.D. candidate at UC Irvine. I learned about Amber as an
> application that was used for research related to the ongoing COVID-19
> problem.
> My research has been on the MPI+threads programming model (e.g.
> MPI+OpenMP). In particular, I am working on optimizing the MPI library
> (MPICH) to improve the communication performance of MPI+threads.
> Does Amber contain programs that use the MPI+threads programming model? In
> particular, I am interested in programs that already use
> On the Intel Support website, there's some description of MPI+OpenMP
> support. Is there a separate codebase for the MPI+OpenMP codes?
> Thank you,
> Rohit Zambre
> Ph.D. Candidate, Computer Engineering
> University of California, Irvine
> *rohitzambre dot com*
> _______________________________________________
> AMBER mailing list

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Received on Tue Mar 31 2020 - 11:00:02 PDT
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