[gmx-developers] Infusing GROMACS with an implementation of Newton's method.

Carl Christian K. Mikkelsen spock at cs.umu.se
Fri Feb 18 12:53:45 CET 2022


I represent a group of researchers who are working towards infusing the 
SHAKE algorithm in GROMACS with a parallel implementation of Newton's 
We have the necessary expertise to write the required kernels from 
scratch without the overhead associated with using a general purpose 
library for solving sparse linear systems.

An obstacle remains. We need the ability to redistribute the coordinates 
and velocities of the atoms of a large molecule as described below.

Consider a GROMACS simulation that includes of a large molecule with 
bond constraints.
*Given an arbitrary coloring of the vertices of the molecular graph, is 
there in GROMACS a mechanism that will allow us to collect the data of 
all atoms with the same color on the same MPI rank?*
If the answer is yes, then how can this be done?

We make no assumptions on the number of atoms, bonds, ranks or colors.
The ideal mechanism will work regardless of how GROMACS has distributed 
the data at the current time.
The ideal mechanism will allow us to use a subcommunicator of the MPI 
communicator used by GROMACS.

Kind regards

Carl Christian.

Carl Christian Kjelgaard Mikkelsen, Ph.D
Department of Computing Science and HPC2N
Umeå University
90187 Sweden

Telephone: +46(0)90-786 5759
Email:spock at cs.umu.se  /carl.c.kjelgaard.mikkelsen at umu.se

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