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

[Ladasky]

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.

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?




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