[gmx-users] Domain decomposition error, is mdrun_mpi now obsolete?

[Justin Lemkul]

On 9/22/12 6:05 PM, Ladasky wrote:
> Hello again everyone,
>
> I'm currently running GROMACS 4.5.4 on Ubuntu Linux 11.10.  I'm trying to
> clean up my simulation conditions.  Many of my MDP files are hold-overs from
> earlier versions of GROMACS, as far back as v. 3.3.  I have written some
> shell scripts which should handle this work automatically -- that is, as
> long as I get no errors.
>
> I have a six-core CPU, and my scripts invoke mdrun_mpi to take advantage of
> the parallel processors.
>
> While doing my cleanup work, I just got my first domain decomposition error
> message:
>
> http://www.gromacs.org/Documentation/Errors#There_is_no_domain_decomposition_for_n_nodes_that_is_compatible_with_the_given_box_and_a_minimum_cell_size_of_x_nm
>
> Of course, I'll need to work on fixing that error -- though why GROMACS
> would complain about having too many CPUs at its disposal, rather than just
> running with fewer CPUs, is a bit of a mystery to me.
>

One cannot decompose a system across any arbitrary number of processors.  Rule 
of thumb is at least several hundred atoms per processor.  There are algorithmic 
constraints and performance reasons for this.

> Reading through the comments at that link, I surmise that I may no longer
> need to download and build a separate MPI package, that multiprocessing is
> the default behavior of mdrun.  Is that correct?
>

There are two methods for parallelization, threading and MPI.  Depending on the 
setup of the system, one or the other can be used, but they are mutually 
exclusive.  For a multi-core workstation, threading is straightforward and does 
not require external MPI libraries, but one can certainly compile and 
MPI-enabled mdrun if desired.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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