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.
Mark
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