[gmx-users] Domain decomposition error, is mdrun_mpi now obsolete?
blind.watchmaker at yahoo.com
Sun Sep 23 00:05:23 CEST 2012
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
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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