Corina Stratan a écrit :
Hi,
I would like to thank you and David for the answers. By "multiple
programs", I meant batch scripts that contain other
preprocessing/postprocessing programs besides mdrun (like grompp,
pdb2gmx,...) - so this would be a case in which the processing is done
in multiple steps. I asked this because we're especially interested in
multi-step processes (workflows); and in the Gromacs tutorials most of
the examples are like this (some other programs are invoked before and
after mdrun).
Thanks again!
Corina
Your mileage may depend on your cpu availability, for instance, you can
do in one batch job either:
- grompp+mdrun
- grompp+mdrun(em1), grompp+mdrun(em2), grompp+mdrun(pr1), ...
Ideally, one would do (in order to share ressources:
- 1 batch file containing all the "setup" steps (those are quite "rapid"
usually), namely energy minimisation and positional restraints
- this batch job launches the next step (after some verification if you
need to) automatically, thus *chaining* them
- 1 batch file for the "production" (the one you'll use for your
analyses/statistics), which can itself be splitted.
That would be:
batch-setup --
|
->batch-production1 (--
|
->batch-production2...n).
The more you chain, the more you'll need to validate your steps :-)
For the benchmark in itself, you can easily generate a *big* box of
water but you'll not really benchmark the system even with such a big
system if your interconnection is not fast enough (i.e. you have fast
network *and* low latency, gigabit for instance is not very efficient
for a good scaling).
Cheers,
Stéphane
--
Stéphane Téletchéa, PhD. http://www.steletch.org
Unité Mathématique Informatique et Génome http://migale.jouy.inra.fr/mig
INRA, Domaine de Vilvert Tél : (33) 134 652 891
78352 Jouy-en-Josas cedex, France Fax : (33) 134 652 901
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