[gmx-users] Parallel installation core2 quad -mpi?

Mark Abraham Mark.Abraham at anu.edu.au
Wed May 13 09:56:09 CEST 2009

Peyman Yamin wrote:
> Hello everyone,
> I'm coming back to Gromacs. Before installing gromacs on our new SC I want to 
> do it on my desktop running SuSe 11.1 on an Intel Core2 Quad Q6700 @2.66GHz 
> CPU-arch.
> Gromacs version 4.0.3
> gmxtests version 4.0.4 
> 1. Are these compatible? I could find neither a testset for 4.0.3 nor a 
> version 4.0.4 of gromacs!

Sort of. There are some problems with Buckingham LJ in 4.0.x such that 
quite a few tests seem to fail. 4.0.5 exists but there seems not to have 
been a formal announcement yet. See 
http://www.gromacs.org/content/view/79/98/ or the front page

gmxtest.pl also needs updating to work "out of the box". We've seen so 
many confused-new-user posts that were I in charge, I'd be tempted to 
take it down until it's been updated and proven to work correctly with 
the most recent release. :-) A test set is a good idea, but not if it 
doesn't succeed at its objective in the hands of a newbie!

> 2. The parallel installation (with --enable-mpi) leads to failure in all 
> tests. Can I run MPI-parallel runs with lam on my cpu at all? lamboot is 
> scared to be run by root and tests get some permission denied message for 
> grompp when run otherwise. How is the whole OpenMP(I) story going on?

You need a functional MPI installation. Pretty much any flavour should 
interact fine with GROMACS 4.x, I understand.

> 3. normal installation (without --enable-mpi) leads to failure in (complex 
> only) "field", "tip4p" and "water". concerning pdb2gmx:
> Error not all 45 pdb2gmx tests have been done successfully
> Only 44 energies in the log file

There's a known bug going on here that was fixed sometime since 4.0.3

> however, -np 2 or 4 leads to a faster finishing  with everything t he same 
> other than "only 0 energies in the log file"!

These flags will have no effect on a non-MPI GROMACS.

> I'm wondering how does it all go parallel with no mpi?

It doesn't.


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